title: Blood of newborn infant, s186

description: Sample name: s186

source_name: newborn whole blood, maternal age 21yr


title: Blood of newborn infant, s192

status: Public on Jun 08 2016

type: genomic

city: Research Triangle Park

first: Zongli

last: Xu

address: 111 tw alexander Dr.

country: USA

institute: NIH/NIEHS

description: Sample name: s192

hyb_protocol: Bisulphite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting.

data_processing: BeadStudio software v3.2.

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: newborn whole blood, maternal age 23yr

label_protocol: Standard Illumina Protocol.

extract_protocol: Genomic DNA was extracted and purified using the automated Autopure LS system (Gentra, Minneapolis, MN). Extracted DNA was quantified using Quant-iTTM PicoGreen dsDNA reagents (Invitrogen, Grand Island, NY) and stored at -20C. One microgram of DNA was bisulfite converted using the EZ DNA Methylation kit (Zymo Research, Irvine, CA) following the manufacturer's protocol.

tag: tissue

value: whole blood

tag: age

value: newborn

tag: gender

value: female

tag: maternalage


title: Blood of newborn infant, s190

description: Sample name: s190

source_name: newborn whole blood, maternal age 32yr

value: male


title: Blood of newborn infant, s200

description: Sample name: s200

source_name: newborn whole blood, maternal age 24yr


title: Blood of newborn infant, s188

description: Sample name: s188

source_name: newborn whole blood, maternal age 29yr


title: Blood of newborn infant, s182

description: Sample name: s182


title: Blood of newborn infant, s184

description: Sample name: s184

source_name: newborn whole blood, maternal age 27yr


title: Blood of newborn infant, s171

description: Sample name: s171

source_name: newborn whole blood, maternal age 25yr


title: Blood of newborn infant, s178

description: Sample name: s178

source_name: newborn whole blood, maternal age 34yr


title: Blood of newborn infant, s175

description: Sample name: s175

source_name: newborn whole blood, maternal age 35yr


title: Blood of newborn infant, s177

description: Sample name: s177


title: Blood of newborn infant, s173

description: Sample name: s173


title: Blood of newborn infant, s187

description: Sample name: s187


title: Blood of newborn infant, s181

description: Sample name: s181

source_name: newborn whole blood, maternal age 28yr


title: Blood of newborn infant, s169

description: Sample name: s169


title: Blood of newborn infant, s174

description: Sample name: s174


title: Blood of newborn infant, s176

description: Sample name: s176


title: Blood of newborn infant, s170

description: Sample name: s170

source_name: newborn whole blood, maternal age 31yr


title: Blood of newborn infant, s185

description: Sample name: s185


title: Blood of newborn infant, s183

description: Sample name: s183


title: Blood of newborn infant, s179

description: Sample name: s179


title: Blood of newborn infant, s180

description: Sample name: s180

source_name: newborn whole blood, maternal age 26yr


title: Blood of newborn infant, s166

description: Sample name: s166

source_name: newborn whole blood, maternal age 19yr


title: Blood of newborn infant, s161

description: Sample name: s161


title: Blood of newborn infant, s172

description: Sample name: s172


title: Blood of newborn infant, s167

description: Sample name: s167


title: Blood of newborn infant, s168

description: Sample name: s168


title: Blood of newborn infant, s159

description: Sample name: s159


title: Cord Tissue_Late Passage 3

type: RNA

city: Royal Oak

first: Bryan

last: Thibodeau

state: MI

address: 3811 West 13 Mile Road

department: BioBank

institute: Beaumont Research Institute

description: Gene expression data from late passage in vitro cell culture originating from cord tissue

hyb_protocol: The amplified cDNA was quantified, fragmented, and labeled in preparation for hybridization to GeneChip™ Human Transcriptome 2.0 Arrays (Affymetrix, Santa Clara, CA) using 5.5μg of ss-cDNA product following protocols outlined in the aforementioned user manual.

scan_protocol: Washing, staining (GeneChip® Fluidics Station 450, Affymetrix) and scanning (GeneChip® Scanner 3000, Affymetrix) were performed following protocols outlined in the GeneChip™ Expression Wash, Stain, and Scan User Manual for Cartridge Arrays.

data_processing:
Analysis was conducted in Affymetrix Transcriptome Analysis Console (version 1.0.0.234). Differential gene expression was determined by One-Way Between-Subject ANOVA (Unpaired), with p-value < 0.05 and a 2-fold cutoff.
HTA-2_0

label: biotin

molecule: total RNA

source_name: Cord tissue

label_protocol: RNA was then amplified and labeled using the GeneChip™ WT PLUS Reagent Kit (Affymetrix, Santa Clara, CA) which enables amplification and target preparation for whole transcriptome expression analysis. Amplification was performed with 500ng of total RNA input following procedures described in the WT PLUS Reagent Kit user manual.

growth_protocol:
The cells were cultured in medium including DMEM with 4500 mg/mL glucose and 2 mM L-glutamine (Invitrogen, Carlsbad, CA, USA), supplemented with 10% FBS (Aleken Biologicals, Nash, TX, USA).  The culture flask medium was changed every 2 days until the cells reached to approximately 70% confluency, they were dissociated using TrypLE Select (Invitrogen, Carlsbad, CA, USA) and further passaged at a concentration of 10,000  cells/cm2 for amplification.
Early passage cells are defined as cells that are below P5. Late passage cells are defined as cells passaged higher than P15.

extract_protocol: RNA was isolated from frozen cell pellets using the E.Z.N.A. Total RNA Kit I (Omega, Norcross, GA).  Following the manufacturer’s protocol, RNA was purified using spin cartridge technology, quantified (Nanodrop 8000, Thermo Scientific), and then stored at -80°C.

value: Cord tissue

tag: passage

value: Late


title: Blood of newborn infant, s165

description: Sample name: s165


title: Wharton's jelly_Late Passage 2

description: Gene expression data from late passage in vitro cell culture originating from Wharton's jelly

source_name: Wharton's jelly

value: Wharton's jelly


title: Wharton's jelly_Late Passage 1


title: Blood of newborn infant, s158

description: Sample name: s158


title: Blood of newborn infant, s160

description: Sample name: s160


title: Blood of newborn infant, s162

description: Sample name: s162


title: Blood of newborn infant, s157

description: Sample name: s157


title: Blood of newborn infant, s163

description: Sample name: s163


title: Blood of newborn infant, s152

description: Sample name: s152


title: Blood of newborn infant, s154

description: Sample name: s154

source_name: newborn whole blood, maternal age 37yr


title: Cord-placenta junction_Late Passage 2

source_name: Cord-placenta junction

value: Cord-placenta junction


title: Cord Tissue_Late Passage 2


title: Blood of newborn infant, s143

description: Sample name: s143


title: Cord-placenta junction_Late Passage 3


title: Blood of newborn infant, s144

description: Sample name: s144

source_name: newborn whole blood, maternal age 21yr


title: Blood of newborn infant, s153

description: Sample name: s153


title: Cord-placenta junction_Late Passage 1


title: Blood of newborn infant, s156

description: Sample name: s156

source_name: newborn whole blood, maternal age 33yr


title: Wharton's jelly_Early Passage 2

description: Gene expression data from early passage in vitro cell culture originating from Wharton's jelly

value: Early


title: Blood of newborn infant, s148

description: Sample name: s148


title: Blood of newborn infant, s149

description: Sample name: s149

source_name: newborn whole blood, maternal age 38yr


title: Wharton's jelly_Early Passage 1


title: Blood of newborn infant, s146

description: Sample name: s146


title: Blood of newborn infant, s145

description: Sample name: s145

source_name: newborn whole blood, maternal age 24yr


title: Blood of newborn infant, s151

description: Sample name: s151


title: Cord-placenta junction_Early Passage 1

description: Gene expression data from early passage in vitro cell culture originating from cord-placenta junction


title: Blood of newborn infant, s150

description: Sample name: s150


title: Cord Tissue_Early Passage 3

description: Gene expression data from early passage in vitro cell culture originating from cord tissue


title: Wharton's jelly_Patient G

description:
#10_1.15.14_(HTA-2_0).CEL
Gene expression data from in vitro cell culture originating from Wharton's jelly

data_processing: Analysis was conducted in Affymetrix Transcriptome Analysis Console (version 1.0.0.234). Differential gene expression was determined by One-Way Between-Subject ANOVA (Unpaired), with p-value < 0.05 and a 2-fold cutoff.

growth_protocol: The cells were cultured in medium including DMEM with 4500 mg/mL glucose and 2 mM L-glutamine (Invitrogen, Carlsbad, CA, USA), supplemented with 10% FBS (Aleken Biologicals, Nash, TX, USA).  The culture flask medium was changed every 2 days until the cells reached to approximately 70% confluency, they were dissociated using TrypLE Select (Invitrogen, Carlsbad, CA, USA) and further passaged at a concentration of 10,000  cells/cm2 for amplification.

tag: patient id

value: Patient G

value: Wharton's jelly (WJ)

tag: cell type

value: mesenchymal stem cells (MSCs)


title: Wharton's jelly_Patient E

description:
#9_1.15.14_(HTA-2_0).CEL
Gene expression data from in vitro cell culture originating from Wharton's jelly

value: Patient E


title: Cord Tissue_Patient F

description:
#6_1.15.14_(HTA-2_0).CEL
Gene expression data from in vitro cell culture originating from cord tissue

value: Patient F

value: Cord tissue (CT)


title: Cord-placenta junction_Early Passage 2


title: Cord Tissue_Early Passage 1


title: Cord-placenta junction_Patient E

description:
#7_1.15.14_(HTA-2_0).CEL
Gene expression data from in vitro cell culture originating from cord-placenta junction

value: Cord-placenta junction (CPJ)


title: Cord Tissue_Patient E

description:
#5_1.15.14_(HTA-2_0).CEL
Gene expression data from in vitro cell culture originating from cord tissue


title: Cord Tissue_Early Passage 2


title: Cord-placenta junction_Patient G

description:
#8_1.15.14_(HTA-2_0).CEL
Gene expression data from in vitro cell culture originating from cord-placenta junction


title: Wharton's jelly_Late Passage 3


title: Blood of newborn infant, s142

description: Sample name: s142


title: Blood of newborn infant, s140

description: Sample name: s140

source_name: newborn whole blood, maternal age 22yr


title: Cord Tissue_Patient D

description:
#4_1.15.14_(HTA-2_0).CEL
Gene expression data from in vitro cell culture originating from cord tissue

value: Patient D


title: Blood of newborn infant, s138

description: Sample name: s138

value: whole blood


title: Blood of newborn infant, s141

description: Sample name: s141

source_name: newborn whole blood, maternal age 27yr

value: newborn


title: PeripheralBlood_RNA_AppenDX_Project discovery  154

city: Washington

first: Ian

middle: V

last: Toma

state: DC

address: 2300 Eye Str., NW, Ross Hall, Rm. 443D

department: Medicine

institute: The George Washington University

hyb_protocol: For each sample, 750 ng of cRNA was hybridized to a Human-HT-12v4 BeadChip array for 16 hours folllowed by washing, blocking and streptavidin-Cy3 staining according to the Whole-Genome Gene Expression Direct Hybridization protocol (Illumina, Inc., San Diego, CA).

scan_protocol: Samples were scanned using an Illumina HiScanSQ System

data_processing:
Image files were analyzed by GenomeStudio™ Gene Expression module (Illumina)
The non-norm matrix contains raw non-normalized data from Illumina GenomeStudio™ Gene Expression software exported to Partek dataset. All samples were split in Discovery and Validation sets. Final analysis was done in Genespring GS 12.5 version of software.
The norm matrix contains normalized data from GeneSpring GX 12.5 software imported from Partek dataset with normalization to the 75-percentile  of expression, but without baseline transformation. The values are represented in log2 expression values

source_name: peripheral blood RNA

label_protocol: Biotin labeling of cRNA according to TotalPrep-96 RNA Amplification Kit (Ambion, Austin TX)

growth_protocol: samples were prepared for gene expression using the Illumina TotalPrep-96 RNA Amplification kit (Ambion, Austin TX)

extract_protocol: peripheral blood RNA extracted from Tempus tubes according to MFR protocol and treated with TurboDNAse to remove the remnant DNA molecules

treatment_protocol: 200 ng of total RNA for each sample underwent 1st and 2nd strand cDNA synthesis followed by an in vitro transcription (IVT) amplification that generates biotinylated, antisense RNA copies of each mRNA, referred to as cRNA

tag: category

value: Appendicitis

value: Male

tag: race

value: White

tag: final dx

value: Acute appendicitis


title: PeripheralBlood_RNA_AppenDX_Project discovery  148


title: PeripheralBlood_RNA_AppenDX_Project discovery  149


title: PeripheralBlood_RNA_AppenDX_Project discovery  153

value: Female


title: Blood of newborn infant, s137

description: Sample name: s137

source_name: newborn whole blood, maternal age 42yr

value: male


title: PeripheralBlood_RNA_AppenDX_Project discovery  147


title: Blood of newborn infant, s136

description: Sample name: s136


title: PeripheralBlood_RNA_AppenDX_Project discovery  141


title: Blood of newborn infant, s139

description: Sample name: s139


title: Blood of newborn infant, s135

description: Sample name: s135

source_name: newborn whole blood, maternal age 35yr


title: PeripheralBlood_RNA_AppenDX_Project discovery  140


title: Blood of newborn infant, s134

description: Sample name: s134

value: female


title: Blood of newborn infant, s132

description: Sample name: s132

source_name: newborn whole blood, maternal age 23yr


title: PeripheralBlood_RNA_AppenDX_Project discovery  137


title: PeripheralBlood_RNA_AppenDX_Project discovery  139

value: Acute gangrenous appendicitis, nonperforated


title: Blood of newborn infant, s133

description: Sample name: s133

source_name: newborn whole blood, maternal age 29yr


title: Blood of newborn infant, s128

description: Sample name: s128


title: Blood of newborn infant, s122

description: Sample name: s122


title: Cord Tissue_Late Passage 1

value: Cord tissue

value: Late


title: Blood of newborn infant, s129

description: Sample name: s129

source_name: newborn whole blood, maternal age 30yr


title: PeripheralBlood_RNA_AppenDX_Project discovery  118

value: Perforated gangrenous appendicitus


title: PeripheralBlood_RNA_AppenDX_Project discovery  117

value: Abdominal Pain

value: Diverticulitis of colon without mention of hemorrhage


title: Blood of newborn infant, s164

description: Sample name: s164

source_name: newborn whole blood, maternal age 28yr


title: Blood of newborn infant, s126

description: Sample name: s126


title: Blood of newborn infant, s131

description: Sample name: s131

source_name: newborn whole blood, maternal age 25yr


title: Blood of newborn infant, s120

description: Sample name: s120

source_name: newborn whole blood, maternal age 36yr


title: Blood of newborn infant, s123

description: Sample name: s123


title: Blood of newborn infant, s124

description: Sample name: s124


title: Blood of newborn infant, s125

description: Sample name: s125


title: Blood of newborn infant, s121

description: Sample name: s121

source_name: newborn whole blood, maternal age 26yr


title: Blood of newborn infant, s127

description: Sample name: s127


title: Blood of newborn infant, s130

description: Sample name: s130


title: Blood of newborn infant, s119

description: Sample name: s119


title: PeripheralBlood_RNA_AppenDX_Project discovery  114

value: Black

value: Diarrhea


title: Blood of newborn infant, s117

description: Sample name: s117

value: whole blood


title: PeripheralBlood_RNA_AppenDX_Project discovery  138


title: Blood of newborn infant, s118

description: Sample name: s118

value: newborn


title: Blood of newborn infant, s115

description: Sample name: s115

source_name: newborn whole blood, maternal age 31yr


title: Blood of newborn infant, s155

description: Sample name: s155


title: PeripheralBlood_RNA_AppenDX_Project discovery  111

value: Epigastric pain, acute pancreatitis


title: PeripheralBlood_RNA_AppenDX_Project discovery  110

value: Abdominal pain


title: PeripheralBlood_RNA_AppenDX_Project discovery  115

value: GI Bleed


title: PeripheralBlood_RNA_AppenDX_Project validation 102

value: Appendicitis

value: White

value: Acute gangrenous appendicitis


title: PeripheralBlood_RNA_AppenDX_Project validation 100

value: Female

value: Acute Appendicitis


title: PeripheralBlood_RNA_AppenDX_Project discovery  112

value: Abdominal pain, epigastric


title: Blood of newborn infant, s114

description: Sample name: s114

source_name: newborn whole blood, maternal age 21yr

value: male


title: PeripheralBlood_RNA_AppenDX_Project discovery  113

value: Male

value: Diverticulitis with diverticulosis, abdominal pain, epigastric pain


title: PeripheralBlood_RNA_AppenDX_Project validation 096


title: PeripheralBlood_RNA_AppenDX_Project discovery  116

value: Abdominal Pain

value: Ureterolothiasis, abdominal pain


title: Blood of newborn infant, s113

description: Sample name: s113

source_name: newborn whole blood, maternal age 34yr


title: Blood of newborn infant, s116

description: Sample name: s116


title: Blood of newborn infant, s111

description: Sample name: s111


title: PeripheralBlood_RNA_AppenDX_Project discovery  109

value: Small bowel obstruction


title: Blood of newborn infant, s108

description: Sample name: s108

source_name: newborn whole blood, maternal age 38yr

value: whole blood


title: PeripheralBlood_RNA_AppenDX_Project validation 103


title: PeripheralBlood_RNA_AppenDX_Project validation 089

value: Hernia

value: Inguinal hernia repair, right


title: PeripheralBlood_RNA_AppenDX_Project validation 084


title: PeripheralBlood_RNA_AppenDX_Project validation 086


title: PeripheralBlood_RNA_AppenDX_Project validation 091


title: PeripheralBlood_RNA_AppenDX_Project validation 085


title: PeripheralBlood_RNA_AppenDX_Project validation 090

value: Black


title: PeripheralBlood_RNA_AppenDX_Project validation 094

value: Umbilical hernia and inguinal hernia repair, left


title: PeripheralBlood_RNA_AppenDX_Project validation 088

value: Inguinal hernia repair, left


title: Blood of newborn infant, s112

description: Sample name: s112

value: newborn

value: female


title: PeripheralBlood_RNA_AppenDX_Project validation 082

value: Pneumonia

value: Female

value: White

value: Pneumonia respitaory failure and Anemia aplastic NOS


title: Blood of newborn infant, s110

description: Sample name: s110


title: PeripheralBlood_RNA_AppenDX_Project validation 080

value: Unknown


title: PeripheralBlood_RNA_AppenDX_Project validation 081

value: Appendicitis

value: Acute Appendicitis


title: PeripheralBlood_RNA_AppenDX_Project validation 083

value: Male

value: Cardiac Arrest,  Aspirational pneumonia and Acute respitatory failure


title: Blood of newborn infant, s147

description: Sample name: s147

source_name: newborn whole blood, maternal age 39yr

value: whole blood

value: male


title: PeripheralBlood_RNA_AppenDX_Project validation 093


title: Blood of newborn infant, s100

description: Sample name: s100


title: Blood of newborn infant, s109

description: Sample name: s109


title: PeripheralBlood_RNA_AppenDX_Project validation 076

value: Acute Appendicitis, gangrenous


title: PeripheralBlood_RNA_AppenDX_Project validation 074


title: Blood of newborn infant, s107

description: Sample name: s107


title: Blood of newborn infant, s106

description: Sample name: s106


title: Blood of newborn infant, s98

description: Sample name: s98

source_name: newborn whole blood, maternal age 16yr


title: Blood of newborn infant, s103

description: Sample name: s103

source_name: newborn whole blood, maternal age 19yr


title: Blood of newborn infant, s96

description: Sample name: s96

source_name: newborn whole blood, maternal age 24yr


title: Blood of newborn infant, s87

description: Sample name: s87

source_name: newborn whole blood, maternal age 17yr


title: Blood of newborn infant, s88

description: Sample name: s88


title: PeripheralBlood_RNA_AppenDX_Project validation 073

source_name: peripheral blood RNA

value: Black

value: Pneumonia and Pulmonary embolism


title: Blood of newborn infant, s93

description: Sample name: s93


title: Blood of newborn infant, s105

description: Sample name: s105


title: Blood of newborn infant, s101

description: Sample name: s101


title: Blood of newborn infant, s95

description: Sample name: s95

source_name: newborn whole blood, maternal age 20yr


title: Blood of newborn infant, s91

description: Sample name: s91

source_name: newborn whole blood, maternal age 33yr


title: Blood of newborn infant, s86

description: Sample name: s86

source_name: newborn whole blood, maternal age 32yr


title: Blood of newborn infant, s94

description: Sample name: s94


title: Blood of newborn infant, s102

description: Sample name: s102


title: Blood of newborn infant, s89

description: Sample name: s89


title: Blood of newborn infant, s90

description: Sample name: s90


title: Blood of newborn infant, s85

description: Sample name: s85


title: Blood of newborn infant, s104

description: Sample name: s104


title: Blood of newborn infant, s97

description: Sample name: s97


title: Blood of newborn infant, s84

description: Sample name: s84


title: Blood of newborn infant, s92

description: Sample name: s92

source_name: newborn whole blood, maternal age 27yr


title: Blood of newborn infant, s78

description: Sample name: s78


title: Blood of newborn infant, s80

description: Sample name: s80


title: Blood of newborn infant, s82

description: Sample name: s82


title: Blood of newborn infant, s81

description: Sample name: s81


title: Blood of newborn infant, s83

description: Sample name: s83


title: Blood of newborn infant, s77

description: Sample name: s77

source_name: newborn whole blood, maternal age 30yr


title: Blood of newborn infant, s73

description: Sample name: s73


title: Male hippocampus Biol. Rep. 2

city: Magdalenka

first: Adrian

middle: Mateusz

last: Stankiewicz

state: Mazovia

address: Jastrzebiec, ul. Postepu 36A

department: Animal Behaviour

country: Poland

institute: Institute of Genetics and Animal Breeding of the Polish Academy of Sciences

hyb_protocol: cRNA was hybridized using Gene Expression Hybridization Kit (Agilent). Hybridized microarrays were washed using standard Washing Buffer kit (Agilent). All procedures were performed according to manufacturer's protocol

scan_protocol: Data were extracted using G2565CA Microarray Scanner (Agilent, USA) and Agilent Feature Extraction Software (Agilent, USA) on default settings (GE2_1010_Sep10).

data_processing: Background correction method normexp with an offset set to 50 was used and followed by loess method for within-array normalization and between-array normalization carried out with the Aquantile method. Median values of channels' intensities and backgrounds' signals were taken as an input for all calculations.

organism: Mus musculus

label_protocol: RNA was labeled using Two-Color Low Input Quick Amp Labeling Kits (Agilent) according to manufacturer's protocol

growth_protocol: All mice were housed in 30 × 13 × 11 cm cages, under controlled light and temperature, and were given ad libitum access to water and food. Breeding pairs were established using an cohort of females, aged 15-18M (AMA) or 3M (YMA), which were paired with 3M virgin males. Male offscpring was sacrificed at P120.

extract_protocol: RNA was extracted using column-based Universal RNA Purification Kit (Eurx, Gdansk, Poland) according to manufacturer protocol

treatment_protocol: Mice were rapidly sacrificed by cervical dislocation

tag: group

value: advanced maternal age (AMA)

value: hippocampus

tag: Sex

value: young maternal age (Control)


title: Blood of newborn infant, s76

description: Sample name: s76

value: newborn

value: female


title: Th2 cells 10 µM Flavopiridol treatment 6 hrs reactivated

city: London

first: Richard

last: Jenner

address: 72 Huntley Street

department: Cancer Biology

country: United Kingdom

institute: UCL Cancer Institute

hyb_protocol: 300 ng of sample cRNA was mixed with 300 ng of reference cRNA and hybridised to SurePrint G3 Mouse GE 8x60K microarrays. Hybridisation and washing of the array slides was done following the specifications in the Agilent Low Input Quick Amp Labeling protocol.

scan_protocol: Arrays were scanned on an Agilent High Resolution C scanner and images were quantified using Agilent Feature Extraction Software (version 10.7)

data_processing: Raw intensity values were background corrected with normexp using an offset of 50 and log2 transformed expression ratios (Cy3 channel vs trimmed mean of Cy5 channel across all arrays) were loess normalised.

source_name: In vitro differentiated Th2 cells, treated with 10 µM Flavopiridol for 6 hrs, reactivated

label_protocol: 200 ng total RNA was labelled with the two colour Low Input Quick Amp Labeling Kit according to the manufacturers instructions. Sample cRNA was mixed with spike A mix and labelled with Cy3. Reference RNA was mixed with spike B mix and labelled with Cy5

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

value: In vitro differentiated Th2 cells

tag: treatment

value: treated with 10 µM Flavopiridol

tag: time

value: 6 hrs

tag: strain

source_name: Naïve CD4+CD62L+CD25-CD44lo T cells isolated from lymph nodes and spleens


title: Blood of newborn infant, s72

description: Sample name: s72

source_name: newborn whole blood, maternal age 28yr


title: Male hippocampus Biol. Rep. 3


title: Th2 cells 10 µM Flavopiridol treatment 6 hrs unstimulated

source_name: In vitro differentiated Th2 cells, treated with 10 µM Flavopiridol for 6 hrs, unstimulated


title: Blood of newborn infant, s68

description: Sample name: s68


title: Blood of newborn infant, s61

description: Sample name: s61


title: Th2 cells 1 µM Flavopiridol treatment 6 hrs unstimulated

source_name: In vitro differentiated Th2 cells, treated with 1 µM Flavopiridol for 6 hrs, unstimulated

value: treated with 1 µM Flavopiridol


title: Th2 cells 1 µM Flavopiridol treatment 6 hrs reactivated

source_name: In vitro differentiated Th2 cells, treated with 1 µM Flavopiridol for 6 hrs, reactivated


title: Blood of newborn infant, s69

description: Sample name: s69

source_name: newborn whole blood, maternal age 23yr


title: Blood of newborn infant, s75

description: Sample name: s75


title: Blood of newborn infant, s70

description: Sample name: s70

source_name: newborn whole blood, maternal age 26yr


title: Blood of newborn infant, s71

description: Sample name: s71

source_name: newborn whole blood, maternal age 31yr


title: Blood of newborn infant, s66

description: Sample name: s66


title: Blood of newborn infant, s65

description: Sample name: s65

source_name: newborn whole blood, maternal age 25yr


title: Blood of newborn infant, s67

description: Sample name: s67

source_name: newborn whole blood, maternal age 42yr


title: Th1 cells 10 µM Flavopiridol treatment 6 hrs reactivated

source_name: In vitro differentiated Th1 cells, treated with 10 µM Flavopiridol for 6 hrs, reactivated

value: In vitro differentiated Th1 cells


title: Blood of newborn infant, s58

description: Sample name: s58

source_name: newborn whole blood, maternal age 29yr


title: Blood of newborn infant, s60

description: Sample name: s60

source_name: newborn whole blood, maternal age 21yr


title: Blood of newborn infant, s62

description: Sample name: s62


title: Blood of newborn infant, s57

description: Sample name: s57


title: Blood of newborn infant, s79

description: Sample name: s79

source_name: newborn whole blood, maternal age 37yr


title: Th1 cells 1 µM Flavopiridol treatment 6 hrs unstimulated

source_name: In vitro differentiated Th1 cells, treated with 1 µM Flavopiridol for 6 hrs, unstimulated


title: Th2 cells 500 nM JQ1 treatment 6 hrs reactivated

source_name: In vitro differentiated Th2 cells, treated with 500 nM JQ1 for 6 hrs, reactivated

value: treated with 500 nM JQ1


title: Blood of newborn infant, s56

description: Sample name: s56

source_name: newborn whole blood, maternal age 34yr


title: Blood of newborn infant, s74

description: Sample name: s74

source_name: newborn whole blood, maternal age 24yr


title: Th1 cells 1 µM Flavopiridol treatment 6 hrs reactivated

source_name: In vitro differentiated Th1 cells, treated with 1 µM Flavopiridol for 6 hrs, reactivated

source_name: Naïve CD4+CD62L+CD25-CD44lo T cells isolated from lymph nodes and spleens


title: Th2 cells 500 nM JQ1 treatment 6 hrs unstimulated

source_name: In vitro differentiated Th2 cells, treated with 500 nM JQ1 for 6 hrs, unstimulated


title: Blood of newborn infant, s55

description: Sample name: s55


title: Blood of newborn infant, s63

description: Sample name: s63

source_name: newborn whole blood, maternal age 32yr


title: Blood of newborn infant, s99

description: Sample name: s99


title: Male hippocampus Biol. Rep. 1

value: Male


title: Blood of newborn infant, s64

description: Sample name: s64

source_name: newborn whole blood, maternal age 30yr

value: whole blood


title: Th2 cells 50 nM JQ1 treatment 6 hrs reactivated

source_name: In vitro differentiated Th2 cells, treated with 50 nM JQ1 for 6 hrs, reactivated

value: treated with 50 nM JQ1


title: Th1 cells 500 nM JQ1 treatment 6 hrs unstimulated

source_name: In vitro differentiated Th1 cells, treated with 500 nM JQ1 for 6 hrs, unstimulated


title: Th1 cells 500 nM JQ1 treatment 24 hrs unstimulated

source_name: In vitro differentiated Th1 cells, treated with 500 nM JQ1 for 24 hrs, unstimulated

value: 24 hrs


title: Th1 cells 50 nM JQ1 treatment 6 hrs reactivated

source_name: In vitro differentiated Th1 cells, treated with 50 nM JQ1 for 6 hrs, reactivated


title: Th1 cells 500 nM JQ1 treatment 6 hrs reactivated

source_name: In vitro differentiated Th1 cells, treated with 500 nM JQ1 for 6 hrs, reactivated


title: Th1 cells 50 nM JQ1 treatment 6 hrs unstimulated

source_name: In vitro differentiated Th1 cells, treated with 50 nM JQ1 for 6 hrs, unstimulated


title: Blood of newborn infant, s59

description: Sample name: s59

source_name: newborn whole blood, maternal age 25yr


title: Th1 cells 500 nM JQ1 treatment 24 hrs reactivated

source_name: In vitro differentiated Th1 cells, treated with 500 nM JQ1 for 24 hrs, reactivated


title: Blood of newborn infant, s54

description: Sample name: s54

source_name: newborn whole blood, maternal age 41yr


title: Th2 cells DMSO control 24 hrs reactivated

source_name: In vitro differentiated Th2 cells, DMSO control 6 hrs, reactivated

value: DMSO control


title: Th1 cells DMSO control 24 hrs reactivated

source_name: In vitro differentiated Th1 cells, DMSO control 24 hrs, reactivated


title: Th1 cells 10 µM Flavopiridol treatment 6 hrs unstimulated

source_name: In vitro differentiated Th1 cells, treated with 10 µM Flavopiridol for 6 hrs, unstimulated


title: Blood of newborn infant, s52

description: Sample name: s52

source_name: newborn whole blood, maternal age 29yr


title: Blood of newborn infant, s53

description: Sample name: s53

source_name: newborn whole blood, maternal age 27yr

value: male


title: Th1 cells DMSO control 6 hrs reactivated

source_name: In vitro differentiated Th1 cells, DMSO control 6 hrs, reactivated

source_name: Naïve CD4+CD62L+CD25-CD44lo T cells isolated from lymph nodes and spleens


title: Th1 cells DMSO control 24 hrs unstimulated

source_name: In vitro differentiated Th1 cells, DMSO control 24 hrs, unstimulated


title: Th2 cells DMSO control 24 hrs unstimulated

source_name: In vitro differentiated Th2 cells, DMSO control 6 hrs, unstimulated


title: Blood of newborn infant, s51

description: Sample name: s51

source_name: newborn whole blood, maternal age 26yr


title: Th1 cells DMSO control 6 hrs unstimulated

source_name: In vitro differentiated Th1 cells, DMSO control 6 hrs, unstimulated


title: Blood of newborn infant, s50

description: Sample name: s50


title: Blood of newborn infant, s49

description: Sample name: s49

source_name: newborn whole blood, maternal age 33yr


title: Th2 cells 50 nM JQ1 treatment 6 hrs unstimulated

source_name: In vitro differentiated Th2 cells, treated with 50 nM JQ1 for 6 hrs, unstimulated


title: Blood of newborn infant, s45

description: Sample name: s45

source_name: newborn whole blood, maternal age 21yr


title: Blood of newborn infant, s47

description: Sample name: s47


title: Blood of newborn infant, s44

description: Sample name: s44


title: Blood of newborn infant, s46

description: Sample name: s46


title: Blood of newborn infant, s42

description: Sample name: s42

source_name: newborn whole blood, maternal age 25yr


title: crestin (-) scale 3 [exon-level]

city: Boston

first: Leonard

last: Zon

state: MA

address: 1 Blackfan Circle

department: Oncology/Hematology

institute: Boston Children's Hospital

description:
G-III.071813_(ZebGene-1_0-st).CEL
RMA expression value derived from Expression Console software

hyb_protocol: Samples were hybridized to Zebarfish Gene 1.0 ST Arrays (Affymetrix) and scanned at the Microarray Core Facility at the IDDRC of Boston Children's Hospital and Harvard Medical School.

scan_protocol: Scanning was done per manufacturer's instructions.

data_processing: Raw data were processed using the Affymetrix Command Console Software to determine RMA-normalized expression values (log2) and used to identify differences in gene expression between GFP (+) and (-) samples.

organism: Danio rerio

label_protocol: Amplification and library preparation was performed using the Ovation Pico WTA System V2 and Encore Biotin Module labeling.

growth_protocol: Adult zebrafish grown under standard husbandry conditions in pH-monitored, fish water at 28.5 C fed with Artemia per institutional and IACUC protocols.

extract_protocol: Transgenic p53/BRAF/Na/MiniCoopR/crestin:EGFP melanoma-prone zebrafish adults were viewed under the fluorescent dissecting scope for the presence of crestin:EGFP (+) scales.  Single EGFP (+) and adjacent (-) scales were plucked and immediately placed into Trizol, vortexed for 2 minutes, and then purified per manufacturer's instructions with the use of Sigma LPA polymer during precipitation.  RNA was run on a Bioanalyzer to ensure high quality.

tag: scale

value: crestin:EGFP (-)


title: crestin (-) scale 1 [exon-level]

description:
G-I.071813_(ZebGene-1_0-st).CEL
RMA expression value derived from Expression Console software


title: crestin (-) scale 2 [exon-level]

description:
G-II.071813_(ZebGene-1_0-st).CEL
RMA expression value derived from Expression Console software


title: crestin (+) scale 3 [exon-level]

description:
G+III.071813_(ZebGene-1_0-st).CEL
RMA expression value derived from Expression Console software

value: crestin:EGFP (+)


title: Blood of newborn infant, s38

description: Sample name: s38

source_name: newborn whole blood, maternal age 30yr


title: Blood of newborn infant, s30

description: Sample name: s30


title: Blood of newborn infant, s32

description: Sample name: s32


title: Blood of newborn infant, s33

description: Sample name: s33


title: Blood of newborn infant, s31

description: Sample name: s31

source_name: newborn whole blood, maternal age 28yr


title: Blood of newborn infant, s35

description: Sample name: s35

source_name: newborn whole blood, maternal age 22yr


title: Blood of newborn infant, s40

description: Sample name: s40


title: Blood of newborn infant, s43

description: Sample name: s43


title: Blood of newborn infant, s41

description: Sample name: s41


title: Blood of newborn infant, s37

description: Sample name: s37

source_name: newborn whole blood, maternal age 23yr


title: Blood of newborn infant, s36

description: Sample name: s36


title: crestin (+) scale 1 [exon-level]

description:
G+I.071813_(ZebGene-1_0-st).CEL
RMA expression value derived from Expression Console software


title: Blood of newborn infant, s39

description: Sample name: s39


title: Blood of newborn infant, s27

description: Sample name: s27


title: Blood of newborn infant, s29

description: Sample name: s29


title: crestin (+) scale 2 [exon-level]

description:
G+II.071813_(ZebGene-1_0-st).CEL
RMA expression value derived from Expression Console software


title: Blood of newborn infant, s25

description: Sample name: s25

source_name: newborn whole blood, maternal age 31yr


title: Blood of newborn infant, s26

description: Sample name: s26

source_name: newborn whole blood, maternal age 35yr


title: Donor3 Naïve

hyb_protocol: Sample cRNA was mixed with reference cRNA and hybridised to SurePrint G3 Human Gene Expression 8x60K microarrays . Hybridisation and washing of the array slides was done following the specifications in the Agilent Low Input Quick Amp Labeling protocol.

data_processing:
Fluorescence intensities were converted into log base 10 expression ratio of Cy5 to Cy3 using Feature Extraction software
Data was converted into log base 2 expression ratios of Cy3 (sample) to Cy5 (reference) signal.

source_name: Naïve CD4+ T cells

label_protocol: Sample RNA  was mixed with spike-in control (Agilent, # 5188-5279) A and labelled with Cy3-CTP. Reference RNA (Stratagene Universal Human Reference RNA, Agilent) was mixed with spike-in control B and labelled with Cy5-CTP.

value: Naïve CD4+ T cells

tag: activation

value: naïve

tag: sample type


title: Blood of newborn infant, s22

description: Sample name: s22

tag: tissue

tag: age

value: newborn


title: Blood of newborn infant, s28

description: Sample name: s28

tag: gender

value: female

tag: maternalage


title: Blood of newborn infant, s34

description: Sample name: s34


title: Donor1 Naïve

source_name: Stratagene Universal Human Reference RNA


title: Donor2 Naïve

value: Stratagene Universal Human Reference RNA


title: Blood of newborn infant, s24

description: Sample name: s24


title: Donor3 day 13 Th2 activated

value: Donor3 day 13 Th2 activated


title: Blood of newborn infant, s48

description: Sample name: s48


title: Blood of newborn infant, s15

description: Sample name: s15

source_name: newborn whole blood, maternal age 24yr


title: MCF7_tacc3_none_rep3 [miRNA]

city: Duesseldorf

first: Antje

last: Lindecke

address: Universitaetsstr. 1

department: BMFZ

country: Germany

institute: Universitaet Duesseldorf

description: no dox treatment , tacc3 not depleted

hyb_protocol: The Cy3 labeled miRNA were hybridised on Human miRNA Microarray version 2 8x15K (Agilent #G4470B) according to the manufactures protocol.

scan_protocol: Scannning of the arrays were performed by the Agilent High-Resolution Microarray Scanner

data_processing:
The fluorescence intensities were calculated with the Feature Extraction Software. For further data analysis the FE files were imported to GeneSpring GX.
raw data were normalized in GeneSpring using the shift to 75% percentile algorithm

source_name: MCF7_tacc3 shRNA_untreated

label_protocol: 100 ng of total RNA were labeled using the miRNA Complete Labeling and Hyb Kit (Agilent p/n 5190-0456)

growth_protocol: MCF-7 breast carcinoma cells were cultured in Dulbecco’s Modified Eagle’s Medium (4.5 g/l glucose) supplemented with 10% FCS (Invitrogen, Karlsruhe, Germany), 100 U/ml penicillin and 100 μg/ml of streptomycin.

extract_protocol: The total RNA containing miRNAs was isolated using the RNeasy Plus Mini Kit (Qiagen) following the Qiagen Supplementary Protocol: Purification of miRNAs from animal cells using the RNeasy Plus Mini Kit and RNeasy MinElute Cleanup Kit, Protocol 1: Purification of total RNA containing miRNA from animal cells using the RNeasy Plus Mini Kit. Cell lysates were homogenized using Qiashredder spin columns (Qiagen).

treatment_protocol: Lentiviral transduction of MCF7 breast carcinoma cells with an inducible shRNA system and subsequent induction of shRNA expression using doxycycline.MCF-7 breast carcinoma cells were transduced with retro- and lentiviruses essentially as described (Leurs et al.,2003).Cells were plated one day prior to doxycycline treatment at a density of 3x103/cm2. Expression of control shRNA and TACC3 shRNA was induced by adding doxycycline (5 μg/ml) to the culture medium four 4 days.

tag: cell line

value: breast carcinoma cells

tag: transduced with

value: tacc3 shRNA

tag: treated with

value: none (untreated)


title: Blood of newborn infant, s17

description: Sample name: s17

source_name: newborn whole blood, maternal age 34yr


title: Blood of newborn infant, s23

description: Sample name: s23


title: Blood of newborn infant, s20

description: Sample name: s20

source_name: newborn whole blood, maternal age 36yr


title: Blood of newborn infant, s19

description: Sample name: s19


title: Donor3 day 7 Th2 unactivated

tag: cell type

value: Donor3 day 7 Th2 unactivated


title: MCF7_tacc3_none_rep1 [miRNA]

description: no dox treatment , tacc3 not depleted


title: Donor3 day7 Th2 activated

value: Donor3 day7 Th2 activated


title: MCF7_tacc3_none_rep2 [miRNA]

description: no dox treatment , tacc3 not depleted


title: Blood of newborn infant, s16

description: Sample name: s16

value: whole blood


title: Donor2 day 13 Th2 activated

value: Donor2 day 13 Th2 activated


title: MCF7_tacc3_Dox_rep3 [miRNA]

description: dox treatment , tacc3 depleted

source_name: MCF7_tacc3 shRNA_Dox treatment

value: doxycycline (5 μg/ml) for 4 days


title: Donor2 day 13 Th2 unactivated

value: Donor2 day 13 Th2 unactivated


title: Blood of newborn infant, s14

description: Sample name: s14


title: MCF7_tacc3_Dox_rep2 [miRNA]

description: dox treatment , tacc3 depleted


title: Donor2 day 7 Th2

value: Donor2 day 7 Th2


title: Blood of newborn infant, s18

description: Sample name: s18

source_name: newborn whole blood, maternal age 42yr


title: Blood of newborn infant, s9

description: Sample name: s9


title: Blood of newborn infant, s5

description: Sample name: s5

source_name: newborn whole blood, maternal age 29yr

value: male


title: Donor1 day 13 Th2 unactivated

value: Donor1 day 13 Th2 unactivated


title: Blood of newborn infant, s10

description: Sample name: s10


title: Donor3 day 7 Th1 activated

value: Donor3 day 7 Th1 activated


title: Donor1 day 7 Th2

value: Donor1 day 7 Th2


title: Blood of newborn infant, s7

description: Sample name: s7

value: newborn

value: female


title: Donor3 day 13 Th1 activated

value: Donor3 day 13 Th1 activated

value: Stratagene Universal Human Reference RNA


title: Blood of newborn infant, s12

description: Sample name: s12

source_name: newborn whole blood, maternal age 20yr


title: Donor3 day 13 Th1 unactivated

value: Donor3 day 13 Th1 unactivated


title: Donor2 day 13 Th1 activated

value: Donor2 day 13 Th1 activated


title: Blood of newborn infant, s8

description: Sample name: s8


title: Donor2 day 7 Th1

value: Donor2 day 7 Th1


title: Donor3 day 7 Th1 unactivated

value: Donor3 day 7 Th1 unactivated


title: Donor2 day 13 Th1 unactivated

value: Donor2 day 13 Th1 unactivated


title: Blood of newborn infant, s1

description: Sample name: s1

source_name: newborn whole blood, maternal age 33yr

value: whole blood


title: Blood of newborn infant, s4

description: Sample name: s4


title: Blood of newborn infant, s21

description: Sample name: s21

source_name: newborn whole blood, maternal age 21yr


title: Donor1 day 13 Th1 activated

value: Donor1 day 13 Th1 activated


title: Blood of newborn infant, s2

description: Sample name: s2

source_name: newborn whole blood, maternal age 30yr


title: Blood of newborn infant, s3

description: Sample name: s3


title: Blood of newborn infant, s13

description: Sample name: s13


title: MCF7_control_Dox_rep1 [miRNA]

description: dox treatment , tacc3 not depleted

source_name: MCF7_control shRNA_Dox treatment

value: breast carcinoma cells

value: control shRNA

value: doxycycline (5 μg/ml) for 4 days


title: Donor1 day 13 Th1 unactivated

value: Donor1 day 13 Th1 unactivated


title: Donor3 day 13 Th2 unactivated

value: Donor3 day 13 Th2 unactivated


title: MCF7_gamma_6d_rep1

description: SAMPLE 6

hyb_protocol: The Cy3 labeled cRNA were hybridised on Whole Human Genome 4x44K Arrays (Agilent) according to the manufactures protocol.

data_processing:
The fluorescence intensities were calculated with the Feature Extraction Software. For further data analysis the FE files were imported to GeneSpring GX.
All values in the matrix table are normalized using the  Shift to 75 percentile function of GeneSpring GX  and were baseline transformed to the median of all samples.

source_name: MCF7_6 days_20 Gy gamma irradiation

label_protocol: 500 ng of total RNA were reverse transcribed, linear amplified and labeled using the Quick Amp Labeling Kit (one-color) from Agilent.

extract_protocol: The total RNA (> 200 bp) was extracted using the RNeasy Plus Mini Kit (Qiagen) following the standard protocol. Cell lysates were homogenized using Qiashredder spin columns (Qiagen).

treatment_protocol: Trypsinized MCF7 breast carcinoma cells were exposed to gamma IR (20 Gy) using a Gammacell 1000 Elite irradiator (Nordion International, Inc., Fleurus, Belgium). After irradiation, cells were plated at a density of 3x10^3/cm2 (control) and 6x10^3/cm2 (20 Gy) and cultured for 4 and 6 days

tag: cultured for

value: 20 Gy gamma irradiation

tag: exposed to

value: 6 days


title: MCF7_gamma_6d_rep3

description: SAMPLE 8


title: MCF7_gamma_6d_rep2

description: SAMPLE 7


title: Blood of newborn infant, s6

description: Sample name: s6

value: newborn

value: male


title: MCF7_control_rep1

description: SAMPLE 1

source_name: MCF7_control_no gamma irradiation

value: none (control)


title: MCF7_control_rep2

description: SAMPLE 2


title: Donor1 day 7 Th1

value: Donor1 day 7 Th1

value: Stratagene Universal Human Reference RNA


title: MCF7_tacc3_Dox_rep1 [miRNA]

description: dox treatment , tacc3 depleted

value: tacc3 shRNA


title: 07PB5883

city: Berlin

first: Lars

last: Bullinger

address: Augustenburger Platz 1

department: Hematology, Oncology and Tumorimmunology

institute: Charité

description:
MYC mutant AML
SAMPLE 46

hyb_protocol: Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.

scan_protocol: Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.

data_processing: The data were analyzed with BRB ArrayTools using RMA. Intensity values were log2 transformed

label: Biotin

source_name: mononuclear cells from peripheral blood or bone marrow

label_protocol: For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using the 3' IVT Express Kit from Affymetrix according to the manufacturer's recommendations.

extract_protocol: The total RNA was purified with a TRIzol-based protocol.

treatment_protocol: Primary AML samples were enriched for mononuclear cells (myeloid blasts) by Ficoll density gradient centrifugation.

tag: diagnosis

value: Acute myeloid leukemia

value: peripheral blood or bone marrow

value: mononuclear cells

tag: myc mutation

value: Yes


title: MCF7_gamma_4d_rep3

description: SAMPLE 5

source_name: MCF7_4 days_20 Gy gamma irradiation

value: breast carcinoma cells

value: 4 days


title: 01KM975

description:
MYC mutant AML
SAMPLE 44


title: MCF7_gamma_4d_rep2

description: SAMPLE 4


title: 04PB336

description:
MYC mutant AML
SAMPLE 45


title: MCF7_tacc3_Dox_rep4

description:
tacc3 depleted
SAMPLE 12

source_name: MCF7 cells_tacc3 shRNA_Dox treatment

treatment_protocol: Lentiviral transduction of MCF7 breast carcinoma cells with an inducible shRNA system and subsequent induction of shRNA expression using doxycycline. MCF-7 breast carcinoma cells were transduced with retro- and lentiviruses essentially as described (Leurs et al.,2003). Cells were plated one day prior to doxycycline treatment at a density of 3x10^3/cm2. Expression of control shRNA and TACC3 shRNA was induced by adding doxycycline (5 μg/ml) to the culture medium for 4 days.

value: doxycycline (5 μg/ml) for 4 days


title: 08KM5032

description:
MYC mutant AML
SAMPLE 42


title: MCF7_tacc3_Dox_rep2

description:
tacc3 depleted
SAMPLE 10


title: 08KM7132

description:
MYC mutant AML
SAMPLE 43


title: 04PB477

description:
MYC mutant AML
SAMPLE 40


title: MCF7_tacc3_Dox_rep3

description:
tacc3 depleted
SAMPLE 11


title: 03PB264

description:
MYC mutant AML
SAMPLE 39


title: Blood of newborn infant, s11

description: Sample name: s11

value: whole blood

value: female


title: 02PPB1453

description:
MYC mutant AML
SAMPLE 38


title: MCF7_tacc3_none_rep4

description:
tacc3 not depleted
SAMPLE 8

source_name: MCF7 cells_tacc3 shRNA_untreated

value: none (untreated)


title: 06KM2068

description:
MYC mutant AML
SAMPLE 41


title: MCF7_tacc3_none_rep3

description:
tacc3 not depleted
SAMPLE 7


title: Donor1 day 13 Th2 activated

value: Donor1 day 13 Th2 activated

source_name: Stratagene Universal Human Reference RNA


title: 02PB3311

description:
MYC mutant AML
SAMPLE 37


title: MCF7_tacc3_Dox_rep1

description:
tacc3 depleted
SAMPLE 9


title: MCF7_tacc3_none_rep2

description:
tacc3 not depleted
SAMPLE 6


title: MCF7_control_Dox_rep4

description:
tacc3 not depleted
SAMPLE 4

source_name: MCF7 cells_control shRNA_Dox treatment

value: control shRNA


title: MCF7_control_Dox_rep1

description:
tacc3 not depleted
SAMPLE 1


title: 02PB1332

description:
MYC mutant AML
SAMPLE 36


title: 01PB580

description:
MYC mutant AML
SAMPLE 35


title: MCF7_tacc3_none_rep1

description:
tacc3 not depleted
SAMPLE 5


title: MCF7_control_Dox_rep2

description:
tacc3 not depleted
SAMPLE 2


title: 08PB3963

description:
MYC mutant AML
SAMPLE 33


title: Het GFP+(2)

city: dallas

first: Jonathan

middle: m

last: graff

state: tx

address: 6000 harry hines blvd

institute: ut southwestern medical center

description: replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

source_name: adipose tissue

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

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: genotype

value: PPARG het

value: flow-sorted GFP+

value: Black 6

value: 2 months

value: adipose tissue


title: Null GFP+(3)

description: replicate 3

value: PPARG null

tag: strain


title: 00PB1111

description:
MYC mutant AML
SAMPLE 34

value: Acute myeloid leukemia

value: peripheral blood or bone marrow


title: MCF7_control_Dox_rep3

description:
tacc3 not depleted
SAMPLE 3


title: Monocytes__meningitis_plasma_immunodepleted for IL-10_3hours_patient3

city: Oslo

first: Unni

last: Gopinathan

address: Kirkeveien 166

department: Department of Medical Biochemistry

country: Norway

institute: Oslo University Hospital

hyb_protocol: Fragmented and labeled sense strand DNA was hybridized to the GeneChip Human Gene 1.0 ST Array (Affymetrix, Santa Clara, CA). The arrays were washed and stained using FS-450 fluidics station (Affymetrix.

scan_protocol: Fluorescent images were scanned by Hewlett Packard Gene Array Scanner 3000 7G (Hewlett Packard, Palo Alto, CA).The scanned images were then analyzed using Affymetrix GeneChip Command Console

data_processing: The CEL files were imported into Partek Genomics Suite software (Partek, Inc., St. Louis, MO). Robust microarray analysis (RMA) was applied for normalization. Exon array data were filtered to include only those probe sets derived from the core meta-probe list.

source_name: Monocytes, stimulated in meningitis plasma with low LPS levels after immunodepletion of IL-10, 3 hours

label_protocol: Total RNA (100 ng) from each sample was prepared using the Ambion WT Expression Kit (Ambion Inc., Austin, Texas, USA) according to manufacturer’s instructions.

growth_protocol: Human monocytes from consenting, healthy donors were purified by elutriation, and crypreserved until use for this experiment.

extract_protocol: RNA from human monocytes were extracted by use of miRNeasy minikit from Qiagen, according to the manufacturer's instructions.

treatment_protocol: Human monocytes (from one consenting donor) was stimulated for three hours with plasma samples (n=3) from patients with with meningococcal sepsis, before and after immunodepletion of IL-10, and with plasma samples (n=3) from patients with mild meningococal disease or meningitisis, before and after immunodepletion of IL-10. In parrallel to the patient plasma samples, human monocytes from the same donor were stimulated with wild-type N. meningitidis, recombinant IL-10, wild-type N. meningitidis and IL-10, and vehicle.

value: Monocytes

tag: disease state

value: meningitis


title: Null GFP-(3)

description: replicate 3

value: flow-sorted GFP-


title: 07KM5653

description:
MYC mutant AML
SAMPLE 31

value: mononuclear cells

value: Yes


title: Null GFP+(1)

description: replicate 3


title: Monocytes__mild_meningococcemia_plasma_immunodepleted for IL-10_3hours_patient2

source_name: Monocytes, stimulated with mild meningococcemia plasma with low LPS levels after immunodepletion of IL-10, 3 hours


title: 08KM2644

description:
MYC mutant AML
SAMPLE 32


title: 05PB5344

description:
MYC mutant AML
SAMPLE 30


title: 08KM1085

description:
wild-type MYC AML
SAMPLE 28

value: No


title: 07KM3322

description:
MYC mutant AML
SAMPLE 29


title: 07KM2846

description:
wild-type MYC AML
SAMPLE 26


title: 98KM1551

description:
wild-type MYC AML
SAMPLE 27


title: 03KM85

description:
wild-type MYC AML
SAMPLE 24


title: Monocytes__mild_meningococcemia_plasma_3hours_patient2

source_name: Monocytes, stimulated in mild meningococcemia plasma with low LPS levels, 3 hours


title: Monocytes__meningitis_plasma_3hours_patient3

source_name: Monocytes, stimulated in meningitis plasma with low LPS levels, 3 hours


title: Monocytes__mild_meningococcemia_plasma_immunodepleted for IL-10_3hours_patient1


title: 05KM971

description:
wild-type MYC AML
SAMPLE 25


title: Monocytes__meningococcal_sepsis_plasma_immunodepleted_for_IL-10_3hours_patient1

source_name: Monocytes, stimulated in meningococcal sepsis plasma after immunodepletion of IL-10, 3 hours

value: meningococcal sepsis


title: Monocytes__meningococcal_sepsis_plasma_3hours_patient3

source_name: Monocytes, stimulated in meningococcal sepsis plasma , 3 hours


title: Monocytes__meningococcal_sepsis_plasma_3hours_patient2


title: Monocytes__mild_meningococcemia_plasma_3hours_patient1


title: Monocytes__meningococcal_sepsis_plasma_immunodepleted_for_IL-10_3hours_patient3


title: 07KM4610

description:
wild-type MYC AML
SAMPLE 19


title: 01KM1863

description:
wild-type MYC AML
SAMPLE 21


title: 01KM327

description:
wild-type MYC AML
SAMPLE 22


title: Monocytes__meningococcal_sepsis_plasma_immunodepleted_for_IL-10_3hours_patient2


title: 06KM7226

description:
wild-type MYC AML
SAMPLE 14


title: 06PB6357

description:
wild-type MYC AML
SAMPLE 17


title: 03KM249

description:
wild-type MYC AML
SAMPLE 23


title: Monocytes__meningococcal_sepsis_plasma_3hours_patient1


title: Monocytes_Nm+IL-10_3hours_rep5

source_name: Monocytes, stimulated with Nm and IL-10 in pooled normal plasma, 3 hours

treatment_protocol: Human monocytes (from five different consenting donors) were stimulated for three hours with N. meningitidis, IL-10, N. meningitidis and IL-10, and vehicle.


title: Monocytes_Nm_3hours_rep5

source_name: Monocytes, stimulated with Nm in pooled normal plasma, 3 hours


title: 07KM3429

description:
wild-type MYC AML
SAMPLE 18


title: 07PB3681

description:
wild-type MYC AML
SAMPLE 20


title: 06PB4879

description:
wild-type MYC AML
SAMPLE 15


title: Monocytes_IL-10_3hours_rep5

source_name: Monocytes, stimulated with IL-10 in pooled normal plasma, 3 hours


title: Monocytes_unstimulated_3hours_rep5

source_name: Monocytes, unstimulated in pooled normal plasma, 3 hours


title: 06PB5090

description:
wild-type MYC AML
SAMPLE 16

source_name: mononuclear cells from peripheral blood or bone marrow


title: HSC alone; rep 3

first: Aurore

last: Saudemont

address: Royal Free Campus, Pond Street

department: Anthony Nolan Research Institute

institute: University College London

hyb_protocol: Standard protocol used UCL genomics facilities following Affymetrix reccomendations.

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

source_name: HSC were cultured in the absence of Tregs from day 9 until day 12, then HSC were re-isolated using a MoFlow cell sorter

growth_protocol: UCB HSC were cultured alone or in the presence of resting or activated Tregs from day 9 until day 12, then HSC were re-isolated using a MoFlow cell sorter.

extract_protocol: RNA extraction was performed using the Rneasy mini kit (Qiagen) following manufacturer's recommendations. RNA concentration was measured using the NanoDrop 1000 Spectrophotometer (Thermo Scientific, USA).

treatment_protocol: Resting or activated umbilical cord blood Tregs were added at day 9 of culture. Resting Tregs were added freshly isolated whereas activated Tregs were pre-activated for 24 h with plate bound CD3, soluble CD28 and IL-2 and washed before being added to HSC cultures.

value: umbilical cord blood

value: HSC

tag: treatment


title: Monocytes_Nm+IL-10_3hours_rep4


title: Monocytes_Nm_3hours_rep4


title: HSC alone; rep 2

scan_protocol: Standard protocol used UCL genomics facilities following Affymetrix reccomendations.

value: HSC were cultured in the absence of Tregs from day 9 until day 12, then HSC were re-isolated using a MoFlow cell sorter


title: 06KM6457

description:
wild-type MYC AML
SAMPLE 12


title: 06KM4234

description:
wild-type MYC AML
SAMPLE 10


title: Monocytes_Nm_3hours_rep3


title: 06KM5070

description:
wild-type MYC AML
SAMPLE 11


title: Monocytes_IL-10_3hours_rep4


title: MCF7_gamma_4d_rep1

description: SAMPLE 3

source_name: MCF7_4 days_20 Gy gamma irradiation

value: breast carcinoma cells

value: 20 Gy gamma irradiation

value: 4 days


title: 06KM6585

description:
wild-type MYC AML
SAMPLE 13


title: 06PB0656

description:
wild-type MYC AML
SAMPLE 7


title: Monocytes_unstimulated_3hours_rep3


title: Monocytes_unstimulated_3hours_rep4


title: HSC alone; rep 1

label_protocol: Standard protocol used UCL genomics facilities following Affymetrix reccomendations.


title: HSC after culture with activated Tregs; rep 2

source_name: HSC were cultured in the presence of activated Tregs from day 9 until day 12, then HSC were re-isolated using a MoFlow cell sorter

growth_protocol: UCB HSC were cultured in the presence of resting or activated Tregs from day 9 until day 12, then HSC were re-isolated using a MoFlow cell sorter.


title: 06PB3720

description:
wild-type MYC AML
SAMPLE 8


title: Monocytes_IL-10_3hours_rep3


title: HSC after culture with resting Tregs; rep 3

source_name: HSC were cultured in the presence of resting Tregs from day 9 until day 12, then HSC were re-isolated using a MoFlow cell sorter


title: Monocytes_Nm_3hours_rep2


title: 07KM0942

description:
wild-type MYC AML
SAMPLE 9


title: Monocytes_Nm+IL-10_3hours_rep3


title: 06KM2168

description:
wild-type MYC AML
SAMPLE 5


title: HSC after culture with activated Tregs; rep 1

value: HSC were cultured in the presence of activated Tregs from day 9 until day 12, then HSC were re-isolated using a MoFlow cell sorter


title: Monocytes_Nm+IL-10_3hours_rep2


title: Monocytes_IL-10_3hours_rep2


title: HSC after culture with activated Tregs; rep 3


title: Ex vivo expanded day 28 CD19-specific CAR+ T cells_P459

city: houston

first: sourindra

last: maiti

state: texas

address: 7455 Fannin Street

department: Pediatrics

institute: M.D. Anderson Cancer Center

description:
donor-2
P459-D28

hyb_protocol: nCounter hybridization protocol

scan_protocol: nCounter scanning protocol

data_processing: The data were normalised according to nCounter guidelines using positive control and House-keeping genes.

label_protocol: nCounter technology

extract_protocol: Total RNA from quiescent CD3+ T cells or ex vivo expanded CD19-specific CAR+ T cells were isolated by by Allprep DNA/RNA Micro Kit (Qiagen). Integrity of RNA was validated by Bioanalyzer (2100 Expert, Agilent). Gene expression analysis was undertaken using the in house proprietary Lymphocyte specific gene code-set.

tag: patient id

value: Patient 459

value: hematopoietic stem cells


title: HSC after culture with resting Tregs; rep 2

tag: tissue

value: HSC were cultured in the presence of resting Tregs from day 9 until day 12, then HSC were re-isolated using a MoFlow cell sorter


title: HSC after culture with resting Tregs; rep 1


title: CD3+ quiescent unmanipulated T cells_P459

description:
donor-1
P459-D0

source_name: CD3+ quiescent unmanipulated T cells


title: 06KM3121

description:
wild-type MYC AML
SAMPLE 6

value: Acute myeloid leukemia

value: peripheral blood or bone marrow


title: Monocytes_unstimulated_3hours_rep2

value: Monocytes


title: 05KM531

description:
wild-type MYC AML
SAMPLE 3

value: mononuclear cells


title: 05KM2304

description:
wild-type MYC AML
SAMPLE 2


title: Ex vivo expanded day 28 CD19-specific CAR+ T cells_P396

description:
donor-1
P396-D28

value: Patient 396


title: CD3+ quiescent unmanipulated T cells_P458

description:
donor-1
P458-D0

value: Patient 458


title: 05PB3897

description:
wild-type MYC AML
SAMPLE 4

value: No


title: CD3+ quiescent unmanipulated T cells_P396

description:
donor-1
P396-D0


title: Ex vivo expanded day 28 CD19-specific CAR+ T cells_P458

description:
donor-1
P458-D28


title: Monocytes_Nm_3hours_rep1


title: 05KM1764

description:
wild-type MYC AML
SAMPLE 1


title: Monocytes_IL-10_3hours_rep1


title: Monocytes_Nm+IL-10_3hours_rep1


title: BCR_480min_III

status: Public on Jun 07 2016

city: Regensburg

first: Christian

middle: W

last: Kohler

state: Bavaria

address: Am BioPark 9

department: Institute of Functional Genomics

institute: University of Regensburg

scan_protocol: not provided

data_processing: Probe level normalization was done using the calibration and variance stabilization method by Huber et al. (Bioinformatics 2002, PMID: 12169536). Probe-set summarization was performed using the median polish method on the normalised data (Irizarry et al. Nucleic Acids Research 2003, PMID: 12582260). Expression values of multiple probeIDs targeting the same gene where summarized into a single representative value by fitting a standard additive model using Tukey’s median polish procedure.

label_protocol: cDNA was synthesized using 1 μg corresponding RNA and including Poly-A RNA controls with the help of the Affymetrix GeneChip® Poly-A RNA control Kit. Secondly, cRNA synthesis and cleanup was carried out using the Affymetrix GeneChip® IVT Labelling Kit. Subsequently, fragmentation and labeling for microarray hybridization was accomplished with the corresponding kits according to manufacturer’s instructions.

growth_protocol: Burkitt Lymphoma cell lines were cultured in RPMI-1640, 10 % (v/v) FCS, 200 U/ml Penicilin, 200 μg/ml Streptomycin, 20 nM BCS, 50 μM α-Thioglycerol, 1 mM Sodium pyruvate. Cells were cultured at 37°C, 5 % CO2 and split daily depending on the observed cell proliferation (cell density: 0.3x10^6 cells/ml - 1x10^6 cells/ml). The day before the experiment 0.3x10^6 cells/ml were seeded.

extract_protocol: Cells were harvested (10 min, 300 x g, 4°C) and washed with PBS containing 100 mM sodium orthovanadate. Samples were frozen at -80°C. RNA was isolated with the RNeasy Kit (Qiagen) for microarray analyses or with the NucleoSpin® RNA II Kit (Macherey-Nagel, Düren Germany)

treatment_protocol: In order to stimulate the cells, they were counted, centrifuged at 250 x g, 7 min and resuspended in fresh corresponding medium supplied with 10 mM Hepes (1x106 cells/ml) and supplemented with sCD40L (200 ng/ml) or anti human IgM F(ab)2 fragment (13 μg/ml). Cells were incubated at 37°C, 5 % CO2 for 15 min, 30 min, 60 min, 90 min, 120 min, 150 min, 180 min, 210 min, 240 min, 360 min, 480 min and 24 hours for microarray analyses.

value: Burkitt Lymphoma

tag: experiment

value: BCR

tag: timepoint


title: BCR_360min_III

hyb_protocol: microarray hybridization was accomplished with the corresponding kits according to manufacturer’s instructions


title: BCR_480min_IIN


title: BCR_480min_I


title: BCR_180min_II


title: DMSO A

city: Columbia

first: Jing

last: Fang

state: SC

address: 715 Sumter Street

department: Drug Discovery and Biomedical Sciences

institute: University of South Carolina

hyb_protocol: Hybridize about 10 μg of biotinylated shRNA target with Human Genome U133 Plus 2.0 GeneChip arrays (Affymetrix; #900470), using the manufacturer’s standard protocols and recommended reagents. Use Affymetrix Hybridization buffer with DMSO and hybridize at 45°C overnight.

scan_protocol: Arrays were scanned using the Affymetrix GeneChip® Scanner 3000 7G. All files including .dat, .cel, and .chp files were created by the scanning and analysis software, the Genechip Operating Software (Affymetrix).

data_processing: GeneNet Library Data Analysis Software (System Biosciences) was used to generate expression values for individual shRNAs by comparing the background-corrected and normalized signal values for each shRNA in LEN-treated and control samples. The list of enriched shRNAs was calculated based on the absolute mean difference of expression values of shRNAs in LEN- versus control-treated replicate samples. Only shRNAs with >1.5-fold enrichment were further considered. P values were calculated based on the biological replicates of individual shRNA clones using the Student’s t-test. To further narrow the list of hits for adjusted P values, a false discovery rate (FDR) correction was applied.

source_name: DMSO A

label_protocol: Lentiviral constructs integrated into genomic DNA produce an alternative transcript from the CMV promoter that is a fusion of the marker gene (copGFP or Puro) with the shRNA  sequence. This alternative transcript is used as a template to amplify the shRNA insert. Amplification of the inserts from total RNA requires two rounds of PCR. During the  second round of PCR with two nested primers (one primer has biotin residues at the 5’-end and another a 5’-phospate group), the amplified shRNA targets are labeled with biotin, sense strands removed by lambda exonuclease, and biotin-labeled antisense strands are used as hybridization targets for Affymetrix GeneChip® Arrays using standard protocols.

growth_protocol: Loss of function screen was performed with GeneNetTM Lentiviral shRNA Libraries (System Biosciences, S12XXB-1) and analyzed by GeneNet Library Data Analysis Software (System Biosciences) according to the manufacturer. Briefly, VSV-G pseudotyped lentiviral particles targeting ~47,000 transcripts in the human genome according to the NCBI RefSeq database (GRCh38.p6) were transduced into 2 x 10^6 MDSL cells with MOI at 0.5–1. Within this range, each cell that has been successfully transduced is expected to contain only one copy of a given shRNA construct.

extract_protocol: 5 x 10^6 viable MDSL cells were then isolated for RNA extraction. Total RNA was extracted using TRIzol Reagent (Invitrogen, #15596-026). Measurement of RNA concentration and examination of RNA integrity was with BioAnalyzer (Agilent Technologies).

treatment_protocol: Three days post transduction, GFP+ transduced MDSL cells were purified for drug selection with DMSO or 10 μM LEN for seven days.

value: MDSL cells

value: transduced with lentivirus targeting transcripts of whole human genome were treated with DMSO for 7 days.


title: LEN C

source_name: LEN C

value: transduced with lentivirus targeting transcripts of whole human genome were treated with LEN for 7 days.


title: LEN D

source_name: LEN D


title: BCR_210min_I


title: DMSO B

source_name: DMSO B


title: BCR_360min_IIN


title: BCR_210min_II


title: BCR_240min_I


title: BCR_240min_IIIN


title: BCR_120min_IIN


title: BCR_240min_II


title: BCR_210min_III


title: Monocytes_unstimulated_3hours_rep1


title: BCR_120min_III


title: BCR_120min_I


title: BCR_90min_III


title: BCR_60min_III


title: BCR_180min_III


title: BCR_90min_I


title: BCR_60min_I


title: BCR_180min_I


title: BCR_360min_I


title: BCR_60min_II


title: BCR_15min_III


title: BCR_30min_II


title: BCR_30min_III


title: BCR_90min_II


title: BCR_15min_I


title: 0min_neg_I

value: control


title: 0min_neg_III


title: BCR_30min_I


title: KO_HDF_AGED_4

city: New Haven

first: Hailong

last: Meng

state: CT

address: 300 George Str

institute: Yale University

description: LDLr-/- KO mice

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

source_name: Aorta

label_protocol: Preparation of cDNA, cRNA, and labeling were carried out by the Yale Center for Genomic Analysis using the standard Illumina protocols.   Hybridization buffer from the BeadChip kit (Illumina) was mixed with 1500 ng of biotin-labeled cRNA, heated to 65°C for 5 minutes, and then loaded onto the BeadChip.  The BeadChips were sealed in a hybridization chamber and placed in an oven at 58°C with a rocker for 16-20 hours.  After the hybridization, the BeadChips were washed and stained in a series of washes and stains as outlined in the Illumina protocol.  The BeadChips were scanned on the Illumina Iscan.

extract_protocol: Total RNA samples was extracted using the RNeasy mini kit (Qiagen, CA)

value: aorta

value: LDLr-/- KO mice

tag: developmental stage

value: AGED

tag: age (months)

tag: diet

value: HDF

tag: type

value: KO


title: KO_HDF_AGED_1

description: LDLr-/- KO mice


title: KO_HDF_AGED_3

description: LDLr-/- KO mice


title: BCR_15min_II

tag: cell type


title: 0min_neg_II


title: KO_HDF_YOUNG_4

description: LDLr-/- KO mice

value: YOUNG


title: KO_HDF_AGED_2

description: LDLr-/- KO mice


title: KO_HDF_YOUNG_1

description: LDLr-/- KO mice


title: KO_HDF_YOUNG_3

description: LDLr-/- KO mice


title: KO_HDF_YOUNG_2

description: LDLr-/- KO mice


title: KO_CHOW_AGED_3

description: LDLr-/- KO mice

value: CHOW


title: KO_CHOW_AGED_4

description: LDLr-/- KO mice


title: KO_CHOW_AGED_1

description: LDLr-/- KO mice


title: KO_CHOW_AGED_2

description: LDLr-/- KO mice


title: KO_CHOW_YOUNG_4

description: LDLr-/- KO mice


title: KO_CHOW_YOUNG_2

description: LDLr-/- KO mice


title: WT_CHOW_AGED_4

description: Wild type

value: Wild type

value: WT


title: KO_CHOW_YOUNG_3

description: LDLr-/- KO mice


title: WT_CHOW_AGED_3

description: Wild type


title: KO_CHOW_YOUNG_1

description: LDLr-/- KO mice


title: WT_CHOW_AGED_2

description: Wild type


title: Tumor transduced with p19Arf_3

city: SAO PAULO

first: João Paulo

middle: PORTELA

last: CATANI

state: SAO PAULO

address: 251 AV DR ARNALDO

department: CTO

country: Brazil

institute: ICESP

description:
Gene expression data from tumors treated by intratumoral applications of adenovector carrying p19Arf gene.
P19Arf_T5

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on mouse 1.0 st Array, according to manufacturer's instructions

scan_protocol: GeneChips were scanned using the Affimetrix GeneChip® Scanner 3000

data_processing:
affymetrix-algorithm-name = rma-gene-default
affymetrix-algorithm-version = 1.0
affymetrix-array-type = MoGene-1_0-st-v1
program-name = Expression Console
The data were analyzed with Affymetrics GeneChip Operating (GCOS) and TM4-MeV

source_name: Tumor transduced with p19Arf

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

treatment_protocol:
[adenovirus production] Adenovirus were produced on 293-A cells
[adenovirus purification] Purification was done by iodixanol method, followed by desalinization on sephadex collunm
[adenovirus titration] Titration was performed using  Adeno-X™ Rapid Titer Ki (cat  632250) clontech
[intratumoral gene transfer] Mice were submitted to intratumoral injection of 25ul of PBS solution containing a viral load of 10^8. Applications were done each 48h, five times.

tag: strain of host

value: implanted LLC-1 tumor

value: Tumor transduced with p19Arf


title: WT_CHOW_YOUNG_3

description: Wild type


title: WT_CHOW_YOUNG_1

description: Wild type


title: WT_CHOW_AGED_1

description: Wild type


title: Tumor transduced with p19Arf_5

description:
Gene expression data from tumors treated by intratumoral applications of adenovector carrying p19Arf gene.
P19Arf_T12


title: WT_CHOW_YOUNG_4

description: Wild type


title: WT_CHOW_YOUNG_2

description: Wild type


title: Tumor transduced with p19Arf_4

description:
Gene expression data from tumors treated by intratumoral applications of adenovector carrying p19Arf gene.
P19Arf_T8


title: Tumor transduced with AdIFNBeta and p19Arf_3

description:
Gene expression data from tumors treated by intratumoral applications of adenovector carrying IFNBeta gene and p19Arf genes.
P19Arf_and_IFNbeta_T7


title: Tumor transduced with AdIFNBeta_4

description:
Gene expression data from tumors treated by intratumoral applications of adenovector carrying IFNBeta gene.
IFNBeta_T8

source_name: Tumor transduced with AdIFNBeta

value: Tumor transduced with AdIFNBeta


title: Tumor transduced with AdIFNBeta and p19Arf_4

description:
Gene expression data from tumors treated by intratumoral applications of adenovector carrying IFNBeta gene and p19Arf genes.
P19Arf_and_IFNbeta_T9


title: Tumor transduced with AdIFNBeta and p19Arf_1

description:
Gene expression data from tumors treated by intratumoral applications of adenovector carrying IFNBeta gene and p19Arf genes.
P19Arf_and_IFNbeta_T1


title: Tumor transduced with p19Arf_1

description:
Gene expression data from tumors treated by intratumoral applications of adenovector carrying p19Arf gene.
P19Arf_T2


title: Tumor transduced with AdIFNBeta_3

description:
Gene expression data from tumors treated by intratumoral applications of adenovector carrying IFNBeta gene.
IFNBeta_T5


title: Tumor transduced with AdIFNBeta and p19Arf_5

description:
Gene expression data from tumors treated by intratumoral applications of adenovector carrying IFNBeta gene and p19Arf genes.
P19Arf_and_IFNbeta_T11


title: Tumor transduced with AdIFNBeta_5

description:
Gene expression data from tumors treated by intratumoral applications of adenovector carrying IFNBeta gene.
IFNBeta_T9


title: Tumor transduced with p19Arf_2

description:
Gene expression data from tumors treated by intratumoral applications of adenovector carrying p19Arf gene.
P19Arf_T4


title: Tumor transduced with AdIFNBeta_2

description:
Gene expression data from tumors treated by intratumoral applications of adenovector carrying IFNBeta gene.
IFNBeta_T4


title: Tumor transduced with AdIFNBeta and p19Arf_2

description:
Gene expression data from tumors treated by intratumoral applications of adenovector carrying IFNBeta gene and p19Arf genes.
P19Arf_and_IFNbeta_T3


title: Tumor transduced with AdIFNBeta_1

description:
Gene expression data from tumors treated by intratumoral applications of adenovector carrying IFNBeta gene.
IFNBeta_T1


title: Tumor transduced with AdeGFP_3

description:
Gene expression data from tumors treated by intratumoral applications of adenovector carrying eGFP gene.
eGFP_T9

source_name: Tumor transduced with AdeGFP

value: Tumor transduced with AdeGFP


title: Tumor transduced with AdeGFP_5

description:
Gene expression data from tumors treated by intratumoral applications of adenovector carrying eGFP gene.
eGFP_T11


title: Tumor transduced with AdeGFP_1

description:
Gene expression data from tumors treated by intratumoral applications of adenovector carrying eGFP gene.
eGFP_T1


title: Tumor transduced with AdeGFP_4

description:
Gene expression data from tumors treated by intratumoral applications of adenovector carrying eGFP gene.
eGFP_T10


title: AL_T_a5_5dpi_rep1

city: Murcia

first: Cristina

middle: Gómez

last: Aix

address: Campus universitario de Espinardo

country: Spain

institute: CEBAS

description: Asymptomatic systemic leaf (cv. Tendral) after 15 days post inoculation of MNSV-Ma5 in cotyledons

hyb_protocol: Hybridizations were done by NimbleGen’s microarray hybridization service (IRB Functional Genomics Core, BaldiriReizac, 10-12, 08028, Barcelona, Spain).

scan_protocol: Scanning were done by NimbleGen’s microarray hybridization service (IRB Functional Genomics Core, BaldiriReizac, 10-12, 08028, Barcelona, Spain).

data_processing: Data were normalized and transformed to a log2 scale using the RMA (Robust Multi-array Average) algorithm found in the oligo package (Carvalho and Irizarry, 2010) from Bioconductor (http://www.bioconductor.org).

organism: Cucumis melo

label_protocol: Labeling were done by NimbleGen’s microarray hybridization service (IRB Functional Genomics Core, BaldiriReizac, 10-12, 08028, Barcelona, Spain).

extract_protocol: All the samples were independently harvested and frozen in liquid N2 and stored at -80 ºC. The RNA extractions were performed with Tri-Reagent (Sigma-Aldrich, St. Louis), according to the manufacturer's instructions. After the extraction, the RNA was analyzed by dot-blot to check for the presence of virus in the infected samples. To eliminate traces of genomic DNA, total RNA was incubated with DNAse I (New England Biolabs, London) for 10 min at 37 °C. The reaction volume was adjusted to 100 µl, and the aqueous phase was extracted with phenol/chloroform/isoamyl alcohol (25:24:1). Lastly, the RNA was precipitated with 10% (v/v) NaOAc (3M) and 2.5 volumes of absolute alcohol by centrifugation (12,000 x g, 20 min at 4 °C). The quality and quantity of RNA was verified with a ND-1000 spectrometer (Nano Drop Technologies, Wilmington, DE, USA) and a Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA).

value: Leaf

tag: cultivar

value: Tendral

tag: virus

value: Asymptomatic

tag: Stage


title: AL_T_a5_5dpi_rep2


title: Tumor transduced with AdeGFP_2

description:
Gene expression data from tumors treated by intratumoral applications of adenovector carrying eGFP gene.
eGFP_T2


title: SL_T_a5_5dpi_rep3

description: Systemically-infected leaf (cv. Tendral) after 15 days post inoculation of MNSV-Ma5 in cotyledons


title: SL_T_a5_5dpi_rep4


title: AL_T_a5_5dpi_rep3


title: SL_T_a5_5dpi_rep1


title: SL_T_a5_5dpi_rep2


title: Dil_T_mock_3dpi_rep2

description: mock inoculated leaf (cv. Tendral) at 5 days post inoculation

value: Mock


title: Dil_T_Ma5/3´264_3dpi_rep1

description: MNSV-Ma5/3´264 directly inoculated leaf (cv. Tendral) at 5 days post inoculation


title: Dil_PJ_Ma5/3´264_3dpi_rep3

description: MNSV-Ma5/3´264 directly inoculated leaf (cv. PJ) at 5 days post inoculation

value: Planters Jumbo


title: Dil_T_a5_3dpi_rep2

description: MNSV-Ma5 directly inoculated leaf (cv. Tendral) at 5 days post inoculation


title: Dil_PJ_mock_3dpi_rep3

description: mock inoculated leaf (cv. PJ) at 5 days post inoculation


title: Dil_PJ_Ma5/3´264_3dpi_rep2


title: Dil_T_a5_3dpi_rep3


title: Dil_PJ_mock_3dpi_rep2


title: T_Ma5/3´264_5dpi_rep2

description: melo cotyledons (cv. Tendral) infected with MNSV-Ma5/3´264 at 5 days post inoculation

extract_protocol: All the samples were independently harvested and frozen in liquid N2 and stored at -80 °C. The RNA extractions were performed with Tri-Reagent (Sigma-Aldrich, St. Louis), according to the manufacturer's instructions. After the extraction, the RNA was analyzed by dot-blot to check for the presence of virus in the infected samples. To eliminate traces of genomic DNA, total RNA was incubated with DNAse I (New England Biolabs, London) for 10 min at 37 °C. The reaction volume was adjusted to 100 Âµl, and the aqueous phase was extracted with phenol/chloroform/isoamyl alcohol (25:24:1). Lastly, the RNA was precipitated with 10% (v/v) NaOAc (3M) and 2.5 volumes of absolute alcohol by centrifugation (12,000 x g, 20 min at 4 °C). The quality and quantity of RNA was verified with a ND-1000 spectrometer (Nano Drop Technologies, Wilmington, DE, USA) and a Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA).

value: Cotyledon


title: T_Ma5/3´264_5dpi_rep1


title: Dil_T_Ma5/3´264_3dpi_rep2


title: T_Ma5/3´264_5dpi_rep3


title: Dil_T_mock_3dpi_rep3


title: Dil_PJ_mock_3dpi_rep1


title: Dil_T_mock_3dpi_rep1


title: PJ_Ma5/3´264_5dpi_rep1

description: melo cotyledons (cv. PJ) infected with MNSV-Ma5/3´264 at 5 days post inoculation

source_name: Planters Jumbo_MNSV-Ma5/3´264_5dpi


title: PJ_mock_5dpi_rep1

description: melo cotyledons (cv. PJ) mock inoculated at 5 days post inoculation

source_name: Planters Jumbo_mock_5dpi


title: PJ_mock_5dpi_rep3


title: Dil_T_a5_3dpi_rep1


title: PJ_mock_5dpi_rep2


title: T_a5_5dpi_rep3

description: melo cotyledons (cv. Tendral) infected with MNSV-Ma5 at 5 days post inoculation


title: PJ_Ma5/3´264_5dpi_rep3


title: Dil_T_Ma5/3´264_3dpi_rep3


title: T_a5_5dpi_rep2


title: Dil_PJ_Ma5/3´264_3dpi_rep1


title: PJ_Ma5/3´264_5dpi_rep2


title: T_mock_5dpi_rep3

description: melo cotyledons (cv. Tendral) mock inoculated at 5 days post inoculation


title: T_mock_5dpi_rep2


title: T_Ma5/3´264_3dpi_rep3

description: melo cotyledons (cv. Tendral) infected with MNSV-Ma5/3´264 at 3 days post inoculation


title: T_mock_5dpi_rep1


title: T_Ma5/3´264_3dpi_rep1


title: T_Ma5/3´264_3dpi_rep2


title: ANAC069 overexpression plants_200 mM NaCl for 3 h_rep2

city: Harbin

first: Lin

last: He

address: 26 Hexing Road

country: China

institute: Northeast Forestry University

description: Identification of the target genes regulated by ANAC069

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

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

organism: Arabidopsis thaliana

source_name: Four-week-old  ANAC069 overexpression plants,  treated with 200 mM NaCl, 3 h.

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

growth_protocol: Plants were grown in a controlled environment at 22°C and 16/8 h light/dark cycles with a light intensity of 100 μmol photons m-2 s-1.

treatment_protocol: Four-week-old ANAC069 overexpression plants and  ANAC069 knockout  plants were treated with 200 mM NaCl for 3 h.

tag: genotype/variation

value: ANAC069 overexpression plants


title: PJ_Ma5/3´264_3dpi_rep2

description: melo cotyledons (cv. PJ) infected with MNSV-Ma5/3´264 at 3 days post inoculation

source_name: Planters Jumbo_MNSV-Ma5/3´264_3dpi


title: PJ_Ma5/3´264_3dpi_rep3


title: ANAC069 overexpression plants_200 mM NaCl for 3 h_rep1


title: T_a5_5dpi_rep1


title: PJ_mock_3dpi_rep2

description: melo cotyledons (cv. PJ) mock inoculated at 3 days post inoculation

source_name: Planters Jumbo_mock_3dpi


title: ANAC069 overexpression plants_200 mM NaCl for 3 h_rep3


title: PJ_Ma5/3´264_3dpi_rep1


title: ANAC069 knockout plants_200 mM NaCl for 3 h_rep1

source_name: Four-week-old  ANAC069 knockout plants,  treated with 200 mM NaCl, 3 h.

value: ANAC069 knockout plants


title: PJ_mock_3dpi_rep1


title: ANAC069 knockout plants_200 mM NaCl for 3 h_rep2


title: T_mock_3dpi_rep2

description: melo cotyledons (cv. Tendral) mock inoculated at 3 days post inoculation


title: T_mock_3dpi_rep3


title: PGC-1a4 2

city: Huddinge

first: Karin

last: Dahlman-Wright

address: Blickagången 16

department: Department of Biosciences and Nutrition

country: Sweden

institute: Karolinska Institutet

hyb_protocol: According to Affymetrix protocol

scan_protocol: According to Affymetrix protocol

data_processing: Data were processed through Qlucore and Partek.

source_name: PGC-1a isoform 1

label_protocol: Total RNA was converted to sense strand cDNA using Ambion WT Expression kit. For fragmentation and labeling WT GeneChip WT target Labeling kit was used.

growth_protocol: During the growth phase, mouse primary myoblasts were plated in collagen-coated plates and maintained in Ham´s F-10 Nutrient Mixture (Gibco), 20% FBS (Sigma), 1% Penicillin/Streptomycin (Gibco) and 2.5 ng/ml basic Fibroblast Growth Factor (Gibco). After achieving 90% confluence, cells were changed to Differentiation Media consisting of DMEM (Gibco), 5% Horse Serum (Gibco), and 1% Penicillin/Streptomycin.

extract_protocol: Approximately 60 hours post-transduction, cells were harvested in Isol-RNA lysis reagent (5PRIME) and purified with Nucleospin RNA II columns (Macherey-Nagel) according to manufacturer’s instructions to achieve optimal purity levels

treatment_protocol: Upon myotube formation (48h after induction of differentiation) we expressed GFP alone or GFP and one of the four PGC-1α isoforms via adenoviral vectors at an MOI of 100. GFP and PGC-1α isoforms are expressed from independent promoters. Adenoviruses expressing the different mouse PGC1α isoforms or GFP have been previously described (3). Twelve hours after transduction, media was replaced with fresh Differentiation Media. Approximately 60 hours post-transduction, cells were harvested in Isol-RNA lysis reagent.

value: Mouse primary myoblasts


title: T_mock_3dpi_rep1


title: PJ_mock_3dpi_rep3


title: PGC-1a4 3


title: PGC-1a3 1

source_name: PGC-1a isoform 3


title: PGC-1a4 1


title: PGC-1a3 3


title: PGC-1a3 2


title: T_a5_3dpi_rep2

description: melo cotyledons (cv. Tendral) infected with MNSV-Ma5 at 3 days post inoculation


title: T_a5_3dpi_rep3


title: SKOV3-TR, Aldefluor High replicate 3

city: Baltimore

middle: J

last: Jones

state: MD

address: 1650 Orleans St.

institute: Johns Hopkins University School of Medicine

description: SKOV3-TR ALDH High 3

hyb_protocol: 750 ng biotin-labeled cRNA was hybridized and stained with streptavidin-Cy3.

scan_protocol: Arrays were scanned with the iScan System.

data_processing: Data were extracted with the Gene Expression Module in GenomeStudio Software (GSGX Version 1.9.0).

source_name: Taxol-Resistant SKOV3_Aldefluor High

label_protocol: RNA was amplified and labeled using the Illumina Total Prep RNA Amplification Kit.

growth_protocol: Aldefluor low cells were cultured in standard medium containing 10% FBS.  Aldefluor high samples were cultured in KnockOut medium.

extract_protocol: Cells were stained with Aldefluor, then sorted by flow cytometry into RNAprotect.  Total RNA was isolated with the RNeasy Mini Kit with QIAshredder columns.

tag: cell line

value: human ovarian cancer cells

tag: sorted population

value: High


title: T_a5_3dpi_rep1


title: PGC-1a1 2


title: PGC-1a2 3

source_name: PGC-1a isoform 2


title: SKOV3-TR, Aldefluor High replicate 2

description: SKOV3-TR ALDH High 2


title: PGC-1a2 2


title: PGC-1a1 3


title: SKOV3, Aldefluor Low, replicate 2

description: SKOV3 ALDH Low 2

source_name: SKOV3_Aldefluor Low

value: Aldefluor Low


title: PGC-1a2 1


title: SKOV3-TR, Aldefluor High replicate 1

description: SKOV3-TR ALDH High 1

value: Aldefluor High


title: SKOV3, Aldefluor Low, replicate 3

description: SKOV3 ALDH Low 3


title: PGC-1a1 1


title: GFP 2

source_name: GFP control


title: MDA_tRNA-Glu-OE_9h_r1

city: San Francisco

first: Hani

last: Goodarzi

state: CA

department: Biochemistry and Biophysics

institute: UCSF

description: replicate 1

hyb_protocol: Per manufacturer's instruction

scan_protocol: Per manufacturer's instruction

data_processing: Data were quantile-normalized and processed using the Lumi package. Non-normalized values indicate the average probe hybrydization signal. Further processed data representing logFC of samples relative to control are linked to the Series record.

label_protocol: Samples were biotin-labeled using the TargetAmp-Nano Labeling Kit for Ilumina Expression BeadChip

growth_protocol: Cells were grown in DMEM-based media supplemented with 10% FBS, 1% L-glutamine, 1% Sodium Pyruvate, and 1% Pen/Strep

extract_protocol: Total RNA was extracted and on-column Dnase treated using Norgen Biotek total RNA extraction kit (per manufacturer instructions).

treatment_protocol: Cells were treated with a-amanitin (10ug/mL) for 0 or 9 hours prior to RNA extraction.

tag: overexpression

value: tRNA-Glu

tag: time point


title: GFP 3


title: MDA_Ctrl_9h_r2

description: replicate 2

value: mock


title: SKOV3, Aldefluor Low, replicate 1

description: SKOV3 ALDH Low 1


title: MDA_tRNA-Arg-OE_9h_r1

description: replicate 1

value: tRNA-Arg


title: MDA_tRNA-Arg-OE_9h_r2

description: replicate 2


title: MDA_tRNA-Glu-OE_0h_r2

description: replicate 2


title: MDA_tRNA-Glu-OE_9h_r2

description: replicate 2


title: MDA_tRNA-Glu-OE_0h_r1

description: replicate 1


title: GFP 1


title: Blood-Stress-rep3

city: Indianapolis

first: Leni

last: Moldovan

state: IN

address: 980 W Walnut St., Rm. C422

department: Ophthalmology

institute: Indiana University

hyb_protocol: Chips were hybridized for 18 hrs, at 45°C, 60 rpm, with 3.75 μg cDNA, and stained using protocol EukGE-WS2v5, with Fluidics station FS400.

scan_protocol: Scanning was done with the GeneChip Scanner 3000 (Affymetrix).  Data acquisition and preliminary analysis were done with the GeneChip® Operating Software (GCOS) v1.4.0.036 (Affymetrix).

data_processing: .CEL files were analyzed in Affymetrix Expression Console 1.2.0.20, using algorithm 3' espression arrays - RMA. Data analysis was done with Partek Genomic Suite and Ingenuity Pathway Analysis.

source_name: Blood, Stress

label_protocol: 30 ng RNA were processed and labeled using Ovation™RNA Amplification System and FL-Ovation™cDNA Biotin Module V2 (NuGEN Technologies, Inc., San Carlos, CA).

extract_protocol: mRNA was extracted from whole blood of RST and control mice sacrificed on Day 7 using a Mouse RiboPure RNA Isolation Kit (Invitrogen, Carlsbad, CA) according to manufacturer’s instructions

treatment_protocol: Female mice (age 6-8 weekes) were subjected to seven days of daily restraint stress (6 hours).Following an acclimation period of 7-10 days, each mouse receiving restraint stress was placed in an individual well-ventilated 50 mL polystyrene tube at 0900h and returned to its respective cage in a horizontal resting position. At 1500h RST animals were removed from restraint tubes and allowed to freely move until the next restraint exposure. Control animals were denied access to food and water during the RST period (0900-1500h) and were otherwise not disturbed.

tag: gender

value: female

tag: age

value: 6-8 weekes

tag: group

value: Stress subject 3


title: Blood-Stress-rep1

value: Stress subject 1


title: Blood-Stress-rep4

value: Stress subject 4


title: Blood-Stress-rep2

value: Stress subject 2


title: MDA_Ctrl_9h_r1

description: replicate 1


title: ANAC069 knockout plants_200 mM NaCl for 3 h_rep3


title: MDA_tRNA-Arg-OE_0h_r1

description: replicate 1


title: MDA_tRNA-Arg-OE_0h_r2

description: replicate 2


title: Blood-NoStress-rep4

source_name: Blood, no stress

value: Control subject 4


title: MDA_Ctrl_0h_r2

description: replicate 2


title: Blood-NoStress-rep1

value: Control subject 1


title: MDA_Ctrl_r2

description: replicate 2

data_processing: Data were quantile-normalized and processed using the Lumi package.  Non-normalized values indicate the average probe hybrydization signal. Further processed data representing logFC of samples relative to control are linked to the Series record.

value: control


title: Blood-NoStress-rep2

value: Control subject 2


title: Blood-NoStress-rep3

value: Control subject 3


title: MDA_Ctrl_r1

description: replicate 1


title: MDA_tRNA-Glu-OE_r2

description: replicate 2

value: chr1.trna5 (Glu-TTC)


title: MDA_tRNA-Arg-OE_r2

description: replicate 2

value: chr16.trna1 (Arg-CCG)


title: MDA_tRNA-Arg-OE_r1

description: replicate 1


title: MDA_tRNA-Glu-OE_r1

description: replicate 1


title: MDA_Ctrl_0h_r1

description: replicate 1


title: ctrl_T105_Probe13

growth_protocol: 1x10^6 fresh CD10+ B cells were resuspended in RPMI 1640 (GIBCO, Paisley UK), 100 U/ml penicillin, 100 μg/ml streptomycin (Sigma-Aldrich, Dorset UK), 10 μg/ml ciprofloxacin (Bayer, Newbury UK) + 10% (v/v) FBS (Sigma-Aldrich, Dorset UK)

treatment_protocol: In order to stimulate the cells, they were counted, centrifuged at 250 x g, 7 min and resuspended in fresh corresponding medium supplied with 10 mM Hepes (1x106 cells/ml) and supplemented with sCD40L (200ng/ml), anti human IgM/IgG F(ab)2 (13μg/ml), rhIL21 (100ng/ml), rhBAFF (100ng/ml and 200ng/ml) or LPS (1μM). Cells were incubated at 37°C, 5% CO2 for 3hrs for microarray analyses.

tag: experiment

value: CD10+ B cells

tag: tissue

value: faucial tonsil


title: ctrl_T97_Probe24


title: WT H14 antibody replicate 1

city: Kansas City

first: Madelaine

last: Gogol

state: MO

address: 1000 E. 50th Street

department: Computational Biology Core

institute: Stowers Institute

description:
wt_h14_rep1
wt_h14_2

hyb_protocol: A mass of 5ug cy labeled samples with specific activity of greater than 15 pmol/ug were combined for each channel and hybridized according to the “Agilent Yeast ChIP-on-chip Analysis protocol Version 9.2, Mat 2007”.  Hybridization occurred in an Agilent Rotisserie Hybridization Oven set to 20RPM at 65C for 40 hours.

scan_protocol: Scanning was performed on the Agilent DNA Microarray Scanner (Agilent Technologies, Model#G2505B)

data_processing: Agilent Feature Extraction Software (v 10.5.1.1) was used to quantify images. Data was read into R and normalized using median normalization.

organism: Saccharomyces cerevisiae

source_name: yeast, wt, H14 ip, rep1

label_protocol: Input was labeled with Cy3 dye, while immunoprecipitated samples were labeled with Cy5 dye.

growth_protocol: Cells were grown to an OD600 of 0.8-1 in YPD at 30 degrees.

extract_protocol: Immune complexes were eluted at 65C for 30min with 1% SDS in TE supplemented with 250mM NaCl.  Samples were treated with RNaseA followed by Proteinase K and crosslinks were reversed overnight at 65C.  DNA was recovered by phenol chloroform isoamyl alcohol extraction followed by ethanol precipitation.

treatment_protocol: Immunoprecipitation was performed with 5 uL of H14 antisera (Covance)

tag: genotype

value: wt

tag: ip antibody

value: H14 antisera (5uL)

source_name: yeast, wt, H14 input, rep1

value: none (input)


title: ctrl_T102_Probe48

tag: cell type


title: ctrl_T99_Probe34


title: WT H14 antibody replicate 2

description:
wt_h14_rep2
wt_ser5

source_name: yeast, wt, H14 ip, rep2

source_name: yeast, wt, H14 input, rep2


title: ctrl_T103_Probe1


title: rtr1 H14 antibody replicate 1

description:
rtr1_h14_rep1
rtr1_h14_2

source_name: yeast, rtr1, H14 ip, rep1

source_name: yeast, rtr1, H14 input, rep1


title: ctrl_T98_Probe29


title: ctrl_T96_Probe19


title: BCR_T97_Probe25

value: BCR


title: BCR_T98_Probe30


title: rtr1 H14 antibody replicate 2

description:
rtr1_h14_rep2
rtr1_ser5

source_name: yeast, rtr1, H14 ip, rep2

source_name: yeast, rtr1, H14 input, rep2


title: ctrl_T104_Probe7


title: BCR_T103_Probe2


title: BCR_T104_Probe8


title: BCR_T102_Probe49


title: ctrl_T100_Probe39


title: BCR_T101_Probe44


title: BCR_T105_Probe14


title: BCR_T100_Probe40


title: BCR_T96_Probe20


title: O-7111524 (prim)

city: Madrid

first: Silvana

last: Mouron

state: Madrid

address: Calle Melchor Fdez Almagro

department: Clinical Research

institute: CNIO

hyb_protocol: According to protocol, CGH arrays where hybrizdized 24 hours, at 65ºC and 20 rpm

scan_protocol: Agilent G2565CA scanner was used to scan slides at 3um resolution for both Cy5 and Cy3 channels

data_processing: Microarray data were extracted and visualized using Feature Extraction software v10.7 and Agilent Genomic Workbench v5.0 (Agilent Technologies). CNA regions were detected using the ADM-2 (set as 6) statistic provided by DNA Analytics, with a minimum number of 10 consecutive probes. The segmentation process was carried out using the dnacopy Bioconductor package. Bioconductor´s CGHcall package was employed for determining the step, and CGHregions and CGHtest packages were used to estimate genomic regions and false discovery rate, respectively.

source_name: Epithelial tissue (breast cancer)

label_protocol: Labeling protocol was done according to the Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis, ULS labeling for FFPE sections v3.2 (G4410-90020)

extract_protocol: 10um tissue sections were deparaffined using heated Xylol and rehidratation was conducted with subsequent lowered EtOH (00%,80%, 50%, H20). Tissue was then treated with sodium thiocyanate. DNA then was extracted with DNA was extracted a tissue protocol from Qiagen Dneasy blood and tissue kit, using EtOH 80% instead of Wash Buffer 2 (according to ULS protocols)

tag: disease state

value: HRPBC

tag: tumor pair

value: O

tag: tumor state

value: Primary Tumor

tag: Sex

value: Female

source_name: reference

tag: reference

value: PROMEGA CONTROL DNA

value: Male


title: ctrl_T101_Probe43

value: control