title: control rep1

description:
SAMPLE 1
Replicate 1
shRNA knock down


title: NPC KT001_167

status: Public on Apr 24 2014

type: RNA

city: Kyoto

first: Kazutoshi

last: Takahashi

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

department: Center for iPS Cell Research and Application

country: Japan

institute: Kyoto University

description: Neural projenitor cells

hyb_protocol: standard Agilent protocol

scan_protocol: Slides were scanned on the G2565CA Microarray Scanner System (Agilent).

data_processing: GeneSpring GX. Signals were normalized to percentile.

molecule: total RNA

organism: Homo sapiens

source_name: Neural projenitor cells

label_protocol: standard Agilent protocol

growth_protocol: Manufacturer’s recommended condition.

extract_protocol: RNA was prepared using the miRNeasy Purification kit (Qiagen) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).

tag: cell type

value: Neural projenitor cells

tag: sample group

value: Tissue-derived cells


title: wt-tl006-a

city: Utrecht

first: Patrick

last: Kemmeren

state: Utrecht

address: Universiteitsweg 100

department: Department of Molecular Cancer Research

country: Netherlands

institute: UMC Utrecht

hyb_protocol: Hybridization protocol v2.2

scan_protocol: scanning of slides using Agilent G256BA Imagene feature extraction

data_processing: genes, no bg corr, dye corr

organism: Saccharomyces cerevisiae

source_name: refpool

label_protocol: aminoallyl labeling v2.1.1

growth_protocol: yeast-deleteome[grow]

extract_protocol: yeast RNA isolation for robotic amplification v1.0

tag: strainorline

value: refpool

source_name: wt

value: wt


title: Thyroid KT001_162

description: Thyroid

source_name: Thyroid

tag: tissue

value: Thyroid

value: Human tissue


title: Tonsil KT001_163

description: Tonsil

source_name: Tonsil

value: Tonsil


title: wt-thm008-b

hyb_protocol: Tecan HS4800 hybridization

label_protocol: robot amplification and labeling v1.0


title: control rep2

city: Cambridge

first: Felicia

last: Ng

address: Wellcome Trust/MRC Building, Addenbrooke's Hospital, Hills Road

country: United Kingdom

institute: Cambridge Institute for Medical Research

description:
SAMPLE 2
Replicate 2
shRNA knock down

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw data was processed in R by applying a variance stabilizing transformation method from the lumi package.  Probes with detection call ≥ 0.01 in all samples were removed and then the data was quantile normalized.

label: biotin

organism: Mus musculus

source_name: control_bone marrow

label_protocol: RNA samples were amplified using TotalPrep 96-RNA amplification kit (Applied Biosystems/Ambion, Warrington, UK)

growth_protocol: Mast cells were derived from bone marrow cells collected from tibias and femurs of 3- to 5- month old adult mice. Cells were cultured in Iscove’s modified Dulbecco’s medium (IMDM) supplemented with 10% fetal bovine serum (Sigma), 1% penicillin/streptomycin (Sigma), 150 micromolar MTG (Sigma), 10% stem cell factor conditional media from BHK/MKL cells and 10ng/ml of recombinant mIL-3 (Peprotech). Cells were frequently transferred to new flasks to remove adherent cells and experiments were performed after 3 weeks, when cultures were homogenous. Homogeneity of culture was confirmed by presence of FcERI by FACS and toluidine blue staining of cytospins.

extract_protocol: Total RNA was isolated using Tri-Reagent (Sigma-Aldrich, Dorset, UK) according to the manufacturer's instructions. Contaminating genomic DNA was removed by DNAseI treatment with Turbo DNA free (Applied Biosystems/Ambion, Warrington, UK).

value: primary mast cell

tag: genotype/variation

value: control


title: wt-thm004-b


title: shGata2 rep1

description:
SAMPLE 4
Replicate 1
shRNA knock down

source_name: shGata2_bone marrow


title: Smooth muscle KT001_157

description: Smooth muscle

source_name: Smooth muscle

value: Smooth muscle


title: wt-thm002-a


title: wt-thm005-a


title: Trachea KT001_164

description: Trachea

source_name: Trachea

value: Trachea


title: Uterus KT001_165

description: Uterus

source_name: Uterus

value: Uterus


title: PBMC KT001_166

description: Peripheral blood mononuclear cells

source_name: Peripheral blood mononuclear cells

value: Peripheral blood mononuclear cells


title: wt-tl007-b


title: Thymus KT001_161

description: Thymus

source_name: Thymus

value: Thymus


title: wt-sv026-b


title: Stomach KT001_159

description: Stomach

source_name: Stomach

value: Stomach


title: wt-sv021-b


title: Testis  KT001_160

description: Testis

source_name: Testis

value: Testis


title: wt-sv026-a


title: Small intestine KT001_156

description: Small intestine

source_name: Small intestine

value: Small intestine


title: wt-thm002-b


title: Spleen KT001_158

description: Spleen

source_name: Spleen

value: Spleen


title: wt-sv085-a


title: wt-sv021-a


title: Prostate KT001_153

description: Prostate

source_name: Prostate

value: Prostate


title: wt-nbr035-b

value: refpool


title: wt-nbr035-a

value: wt


title: Salivary gland KT001_154

description: Salivary gland

source_name: Salivary gland

value: Salivary gland


title: Skeletal muscle KT001_155

description: Skeletal muscle

source_name: Skeletal muscle

value: Skeletal muscle

value: Human tissue


title: Placenta KT001_152

description: Placenta

source_name: Placenta

value: Placenta


title: wt-nbr032-b

source_name: wt

source_name: refpool


title: wt-nbr032-a


title: Lung  KT001_149

description: Lung

source_name: Lung

value: Lung


title: wt-nbr025-b


title: wt-nbr021-b


title: wt-nbr024-a


title: Liver KT001_148

description: Liver

source_name: Liver

value: Liver


title: wt-nbr020-a


title: Ovary KT001_150

description: Ovary

source_name: Ovary

value: Ovary


title: wt-nbr024-b


title: Pancreas KT001_151

description: Pancreas

source_name: Pancreas

value: Pancreas


title: wt-nbr020-b


title: Fetal liver KT001_144

description: Fetal liver

source_name: Fetal liver

value: Fetal liver


title: Fetal kidney KT001_143

description: Fetal kidney

source_name: Fetal kidney

value: Fetal kidney


title: Fetal spleen KT001_145

description: Fetal spleen

source_name: Fetal spleen

value: Fetal spleen


title: Fetal heart KT001_142

description: Fetal heart

source_name: Fetal heart

value: Fetal heart


title: Kidney KT001_147

description: Kidney

source_name: Kidney

value: Kidney


title: wt-nbr017-b

extract_protocol: yeast mRNA extraction v1.3


title: Heart KT001_146

description: Heart

source_name: Heart

value: Heart


title: wt-nbr018-a


title: Colon KT001_140

description: Colon

source_name: Colon

value: Colon


title: Brain KT001_139

description: Brain

source_name: Brain

value: Brain


title: Bone marrow KT001_138

description: Bone marrow

source_name: Bone marrow

value: Bone marrow


title: Fetal brain KT001_141

description: Fetal brain

source_name: Fetal brain

value: Fetal brain


title: wt-thm010-a

value: refpool

value: wt


title: wt-nbr016-b


title: wt-nbr017-a


title: wt-nbr018-b


title: wt-nbr013-a


title: Adrenal gland KT001_137

description: Adrenal gland

source_name: Adrenal gland

value: Adrenal gland

value: Human tissue


title: wt-nbr007-a

source_name: wt


title: EDM_2 KT001_135

description: Normal human epidermal keratinocyte

source_name: Normal human epidermal keratinocyte, sample 2

value: Normal human epidermal keratinocytes

value: Tissue-derived cells


title: wt-nbr011-b

source_name: refpool


title: wt-nbr006-b


title: wt-nbr007-b


title: EDM_1 KT001_134

description: Normal human epidermal keratinocyte

source_name: Normal human epidermal keratinocyte, sample 1


title: wt-nbr004-a_2


title: EDM_3 KT001_136

description: Normal human epidermal keratinocyte

source_name: Normal human epidermal keratinocyte, sample 3


title: wt-mmk032-b


title: PrEC_OSKM_d15_2 KT001_126

description: Nascent reprogrammed cells derived from human prostate epithelial cells on day 15

source_name: Nascent reprogrammed cells derived from PrEC, day 15, sample 2

growth_protocol: Primate ESC medium (ReproCELL) supplemented with 4 ng/ml bFGF at 37ºC in a humidified incubator with 5% CO2.

treatment_protocol: Human somatic cells were transduced with OCT3/4, SOX2, KLF4 and c-MYC using retrovirus. Then, we collected TRA-1-60 positive cells as nascent reprogrammed cells.

value: Nascent reprogrammed cells


title: ESC_GLIS1_2 KT001_132

description: Human embryonic stem cells transfected with GLIS1

source_name: ESC transduced GLIS1, sample 2

growth_protocol: TeSR1 medium (Veritas) on Matrigel-coated plates (BD Biosciences) at 37ºC in a humidified incubator with 5% CO2.

treatment_protocol: Human ESCs were transduced with PB/CAG-GLIS1-IP vector, and selected with 1 μg/ml puromycin.

value: Transgenic ESC line


title: ESC_Mock_1 KT001_128

description: Human embryonic stem cells transfected with Mock

source_name: ESC transduced empty vector (Mock), sample 1

treatment_protocol: Human ESCs were transduced with PB/CAG-IP vector, and selected with 1 μg/ml puromycin.


title: wt-nbr011-a


title: wt-nbr004-b_2


title: wt-nbr006-a


title: wt-nbr016-a


title: ESC_Mock_3 KT001_130

source_name: ESC transduced empty vector (Mock), sample 3

treatment_protocol: Human ESCs were transduced with PB/CAG-IB vector, and selected with 10 μg/ml blasticidin S.

value: Human embryonic stem cells transfected with Mock


title: ESC_GLIS1_3 KT001_133

source_name: ESC transduced GLIS1, sample 3

treatment_protocol: Human ESCs were transduced with PB/CAG-GLIS1--IB vector, and selected with 10 μg/ml blasticidin S.

value: Human embryonic stem cells transfected with GLIS1


title: PrEC_OSKM_d28 KT001_127

description: Nascent reprogrammed cells derived from human prostate epithelial cells on day 28

source_name: Nascent reprogrammed cells derived from PrEC, day 28


title: wt-mmk032-a


title: wt-nbr002-a


title: PrEC_OSKM_d11_3 KT001_124

source_name: Nascent reprogrammed cells derived from PrEC, day 11, sample 3

value: Nascent reprogrammed cells derived from human prostate epithelial cells


title: ESC_GLIS1_1 KT001_131

source_name: ESC transduced GLIS1, sample 1


title: PrEC_OSKM_d11_2 KT001_123

description: Nascent reprogrammed cells derived from human prostate epithelial cells on day 11

source_name: Nascent reprogrammed cells derived from PrEC, day 11, sample 2


title: wt-nbr002-b


title: wt-mmk031-b


title: PrEC_OSKM_d15_1 KT001_125

source_name: Nascent reprogrammed cells derived from PrEC, day 15, sample 1


title: wt-mmk028-b


title: wt-mmk028-a


title: ESC_Mock_2 KT001_129

source_name: ESC transduced empty vector (Mock), sample 2


title: wt-mmk027-a


title: PrEC_OSKM_d7_2 KT001_120

description: Nascent reprogrammed cells derived from human prostate epithelial cells on day 7

source_name: Nascent reprogrammed cells derived from PrEC, day 7, sample 2


title: PrEC_OSKM_d7_3 KT001_121

source_name: Nascent reprogrammed cells derived from PrEC, day 7, sample 3


title: wt-mmk026-a

source_name: wt


title: PrEC_OSKM_d7_1 KT001_119

source_name: Nascent reprogrammed cells derived from PrEC, day 7, sample 1


title: PrEC_1 KT001_113

description: Human prostate epithelial cells

source_name: Human prostate epithelial cell line 1

value: Human prostate epithelial cells


title: PrEC_OSKM_d3_2 KT001_117

description: Nascent reprogrammed cells derived from human prostate epithelial cells on day 3

source_name: Nascent reprogrammed cells derived from PrEC, day 3, sample 2

treatment_protocol: Human somatic cells were transduced with OCT3/4, SOX2 (IRES-EGFP), KLF4 and c-MYC using retrovirus. Then, we collected EGFP positive cells as nascent reprogrammed cells.


title: PrEC_OSKM_d11_1 KT001_122

source_name: Nascent reprogrammed cells derived from PrEC, day 11, sample 1


title: PrEC_OSKM_d3_3 KT001_118

source_name: Nascent reprogrammed cells derived from PrEC, day 3, sample 3


title: NHBE_OSKM_d28_3 KT001_112

description: Nascent reprogrammed cells derived from human bronchial epithelium on day 28

source_name: Nascent reprogrammed cells derived from NHBE, day 28, sample 3


title: wt-mmk022-b

source_name: refpool


title: PrEC_3 KT001_115

description: Human prostate epithelial cells

source_name: Human prostate epithelial cell line 3


title: wt-mmk027-b


title: wt-mmk019-a


title: wt-mmk021-a


title: PrEC_2 KT001_114

description: Human prostate epithelial cells

source_name: Human prostate epithelial cell line 2


title: wt-mmk017-b


title: wt-mmk016-b


title: wt-mmk030-a


title: wt-mmk023-a


title: PrEC_OSKM_d3_1 KT001_116

source_name: Nascent reprogrammed cells derived from PrEC, day 3, sample 1


title: wt-mmk025-a


title: NHBE_OSKM_d28_2 KT001_111

source_name: Nascent reprogrammed cells derived from NHBE, day 28, sample 2

value: Nascent reprogrammed cells derived from human bronchial epithelium


title: NHBE_OSKM_d15_3 KT001_109

description: Nascent reprogrammed cells derived from human bronchial epithelium on day 15

source_name: Nascent reprogrammed cells derived from NHBE, day 15, sample 3


title: wt-mmk016-a


title: NHBE_OSKM_d28_1 KT001_110

source_name: Nascent reprogrammed cells derived from NHBE, day 28, sample 1


title: NHBE_OSKM_d15_2 KT001_108

source_name: Nascent reprogrammed cells derived from NHBE, day 15, sample 2


title: NHBE_OSKM_d15_1 KT001_107

source_name: Nascent reprogrammed cells derived from NHBE, day 15, sample 1


title: wt-mmk018-a


title: wt-mmk012-a


title: wt-mmk015-a


title: NHBE_OSKM_d11_2 KT001_105

description: Nascent reprogrammed cells derived from human bronchial epithelium on day 11

source_name: Nascent reprogrammed cells derived from NHBE, day 11, sample 2


title: wt-mmk010-b

source_name: wt


title: wt-mmk014-a


title: wt-mmk010-a


title: NHBE_OSKM_d11_3 KT001_106

source_name: Nascent reprogrammed cells derived from NHBE, day 11, sample 3


title: NHBE_OSKM_d7_4 KT001_103

description: Nascent reprogrammed cells derived from human bronchial epithelium on day 7

source_name: Nascent reprogrammed cells derived from NHBE, day 7, sample 4


title: NHBE_OSKM_d11_1 KT001_104

source_name: Nascent reprogrammed cells derived from NHBE, day 11, sample 1


title: wt-mmk008-b


title: NHBE_OSKM_d7_3 KT001_102

source_name: Nascent reprogrammed cells derived from NHBE, day 7, sample 3


title: wt-mmk009-a


title: NHBE_OSKM_d7_1 KT001_100

source_name: Nascent reprogrammed cells derived from NHBE, day 7, sample 1


title: wt-mmk006-b


title: NHBE_OSKM_d3_3 KT001_099

description: Nascent reprogrammed cells derived from human bronchial epithelium on day 3

source_name: Nascent reprogrammed cells derived from NHBE, day 3, sample 3


title: wt-mmk013-b

source_name: refpool


title: wt-mmk008-a


title: Neuroectoderm derived from mouse embryonic stem cells

description: sample name: KT001_m15

data_processing: GeneSpring GX. Signals were normalized to percentile (75th percentile).

treatment_protocol: Mouse ESCs were differentiated into neuroectoderm.

value: Neuroectoderm derived from moouse embryonic stem cells

value: mouse cells


title: wt-mmk005-b


title: NHBE_OSKM_d7_2 KT001_101

source_name: Nascent reprogrammed cells derived from NHBE, day 7, sample 2


title: NHBE_OSKM_d3_1 KT001_097

source_name: Nascent reprogrammed cells derived from NHBE, day 3, sample 1


title: NHBE_3 KT001_096

description: Human bronchial epithelium

source_name: Normal human bronchial epithelium line 3

value: Human bronchial epithelium


title: NHBE_OSKM_d3_2 KT001_098

source_name: Nascent reprogrammed cells derived from NHBE, day 3, sample 2


title: HA_OSKM_d42_3 KT001_093

description: Nascent reprogrammed cells derived from human astrocytes on day 42

source_name: Nascent reprogrammed cells derived from HA, day 42, sample 3


title: NHBE_2 KT001_095

description: Human bronchial epithelium

source_name: Normal human bronchial epithelium line 2


title: NHBE_1 KT001_094

description: Human bronchial epithelium

source_name: Normal human bronchial epithelium line 1


title: wt-mmk005-a


title: Endoderm derived from mouse embryonic stem cells

description: sample name: KT001_m14

treatment_protocol: Mouse ESCs were differentiated into endoderm.

value: Endoderm derived from moouse embryonic stem cells


title: HA_OSKM_d42_2 KT001_092

source_name: Nascent reprogrammed cells derived from HA, day 42, sample 2

value: Nascent reprogrammed cells derived from human astrocytes


title: wt-nbr013-b

value: wt

value: refpool


title: HA_OSKM_d42_1 KT001_091

source_name: Nascent reprogrammed cells derived from HA, day 42, sample 1


title: wt-mmk004-b

source_name: wt


title: Mesoderm derived from mouse embryonic stem cells

description: sample name: KT001_m13

treatment_protocol: Mouse ESCs were differentiated into mesoderm.

value: Mesoderm derived from moouse embryonic stem cells


title: HA_OSKM_d35_3 KT001_090

description: Nascent reprogrammed cells derived from human astrocytes on day 35

source_name: Nascent reprogrammed cells derived from HA, day 35, sample 3


title: HA_OSKM_d28_3 KT001_087

description: Nascent reprogrammed cells derived from human astrocytes on day 28

source_name: Nascent reprogrammed cells derived from HA, day 28, sample 3


title: HA_OSKM_d35_2 KT001_089

source_name: Nascent reprogrammed cells derived from HA, day 35, sample 2


title: wt-mmk004-a


title: wt-mmk003-a


title: Mouse Embryonic Stem cell line (1B4)

description: sample name: KT001_m11

source_name: Mouse Embryonic Stem cell line (1B4)

growth_protocol: Knockout DMEM (Life Technologies) containing 15% Knockout serum replacement (Life Technologies), 1% Glutamax (Life Technologies), 1% NEAA (Life Technologies), 100 nM 2-ME (Life Technologies), 0.5% Pen/Strep (Life Technologies) and 1000 units/ml LIF (Millipore) on gelatinized plates at 37ºC in a humidified incubator with 5% CO2.

value: Mouse Embryonic Stem cell line (1B4)


title: Primitive streak-like mesendoderm derived from mouse embryonic stem cells

description: sample name: KT001_m12

treatment_protocol: Mouse ESCs were differentiated into primitive streak-like mesendoderm.

value: Primitive streak-like mesendoderm derived from moouse embryonic stem cells


title: wt-mmk003-b


title: HA_OSKM_d35_1 KT001_088

source_name: Nascent reprogrammed cells derived from HA, day 35, sample 1

value: Nascent reprogrammed cells


title: wt-mmk001-b


title: HA_OSKM_d28_1 KT001_085

source_name: Nascent reprogrammed cells derived from HA, day 28, sample 1


title: HA_OSKM_d28_2 KT001_086

source_name: Nascent reprogrammed cells derived from HA, day 28, sample 2


title: SSEA-1 (+)/Nanog-GFP (+) cells on day 20

description: sample name: KT001_m8

treatment_protocol: MEFs were transduced with OCT3/4, SOX2, KLF4, c-MYC and GLIS1 using retrovirus. Then, we collected SSEA-1 and/or Nanog-GFP positive cells as nascent reprogrammed cells.


title: Mouse induced Pluripotent Stem cell line (20D17)

description: sample name: KT001_m10


title: wt-mmk001-a

source_name: refpool


title: HA_OSKM_d20_3 KT001_084

description: Nascent reprogrammed cells derived from human astrocytes on day 20

source_name: Nascent reprogrammed cells derived from HA, day 20, sample 3


title: HA_OSKM_d20_1 KT001_082

source_name: Nascent reprogrammed cells derived from HA, day 20, sample 1


title: HA_OSKM_d15_3 KT001_081

description: Nascent reprogrammed cells derived from human astrocytes on day 15

source_name: Nascent reprogrammed cells derived from HA, day 15, sample 3


title: HA_OSKM_d20_2 KT001_083

source_name: Nascent reprogrammed cells derived from HA, day 20, sample 2


title: HA_OSKM_d11_3 KT001_078

description: Nascent reprogrammed cells derived from human astrocytes on day 11

source_name: Nascent reprogrammed cells derived from HA, day 11, sample 3


title: SSEA-1 (+)/Nanog-GFP (+) cells on day 11

description: sample name: KT001_m6


title: SSEA-1 (+)/Nanog-GFP (+) cells on day 24

description: sample name: KT001_m9


title: wt-matA-nbr015-a

source_name: wt-matA

value: wt-matA


title: HA_OSKM_d15_1 KT001_079

source_name: Nascent reprogrammed cells derived from HA, day 15, sample 1


title: SSEA-1 (+)/Nanog-GFP (+) cells on day 15

description: sample name: KT001_m7


title: HA_OSKM_d15_2 KT001_080

source_name: Nascent reprogrammed cells derived from HA, day 15, sample 2


title: wt-matA-nbr014-b


title: wt-matA-nbr014-a


title: HA_OSKM_d7_4 KT001_075

description: Nascent reprogrammed cells derived from human astrocytes on day 7

source_name: Nascent reprogrammed cells derived from HA, day 7, sample 4


title: HA_OSKM_d7_3 KT001_074

source_name: Nascent reprogrammed cells derived from HA, day 7, sample 3


title: HA_OSKM_d7_1 KT001_072

source_name: Nascent reprogrammed cells derived from HA, day 7, sample 1


title: SSEA-1 (+)/Nanog-GFP (-) cells on day 11

description: sample name: KT001_m5


title: wt-matA-lpa005-b


title: HA_OSKM_d11_1 KT001_076

source_name: Nascent reprogrammed cells derived from HA, day 11, sample 1


title: SSEA-1 (+)/Nanog-GFP (+) cells on day 7

description: sample name: KT001_m4

source_name: SSEA-1 (+)/Nanog-GFP (+) cells on day 7

value: SSEA-1 (+)/Nanog-GFP (+) cells on day 7


title: Mouse embryonic fibroblast transfected OSKMG on day 3

description: sample name: KT001_m2

treatment_protocol: MEFs were transduced with OCT3/4, SOX2, KLF4, c-MYC and GLIS1 using retrovirus.


title: HA_OSKM_d3_2 KT001_070

description: Nascent reprogrammed cells derived from human astrocytes on day 3

source_name: Nascent reprogrammed cells derived from HA, day 3, sample 2


title: wt-matA-lpa003-b


title: HA_OSKM_d3_1 KT001_069

source_name: Nascent reprogrammed cells derived from HA, day 3, sample 1


title: wt-matA-lpa005-a


title: HA_OSKM_d7_2 KT001_073

source_name: Nascent reprogrammed cells derived from HA, day 7, sample 2


title: wt-matA-lpa003-a

source_name: refpool


title: HA_3 KT001_068

description: Human astrocytes

source_name: Human astrocyte line 3

value: Human astrocytes

value: Tissue-derived cells


title: Mouse embryonic fibroblast

description: sample name: KT001_m1

source_name: Mouse embryonic fibroblast

growth_protocol: DMEM (Nacalai tesque) containing 10% fetal bovine serum and 0.5% Pen/Strep (Life Technologies) at 37ºC in a humidified incubator with 5% CO2.

value: Mouse embryonic fibroblast


title: wt-matA-nbr015-b


title: HA_2 KT001_067

description: Human astrocytes

source_name: Human astrocyte line 2


title: HA_OSKM_d3_3 KT001_071

source_name: Nascent reprogrammed cells derived from HA, day 3, sample 3


title: HA_1 KT001_066

description: Human astrocytes

source_name: Human astrocyte line 1


title: ASC_OSKM_d28_2 KT001_064

description: Nascent reprogrammed cells derived from human adipose-derived stem cells on day 28

source_name: Nascent reprogrammed cells derived from ASC, day 28, sample 2


title: wt-lpa013-a

source_name: wt


title: SSEA-1 (+)/Nanog-GFP (-) cells on day 7

description: sample name: KT001_m3

source_name: SSEA-1 (+)/Nanog-GFP (-) cells on day 7

value: SSEA-1 (+)/Nanog-GFP (-) cells on day 7


title: ASC_OSKM_d28_3 KT001_065

source_name: Nascent reprogrammed cells derived from ASC, day 28, sample 3

value: Nascent reprogrammed cells derived from human adipose-derived stem cells


title: wt-lpa011-b


title: ASC_OSKM_d20 KT001_062

description: Nascent reprogrammed cells derived from human adipose-derived stem cells on day 20

source_name: Nascent reprogrammed cells derived from ASC, day 20


title: ASC_OSKM_d11_3 KT001_061

description: Nascent reprogrammed cells derived from human adipose-derived stem cells on day 11

source_name: Nascent reprogrammed cells derived from ASC, day 11, sample 3


title: ASC_OSKM_d28_1 KT001_063

source_name: Nascent reprogrammed cells derived from ASC, day 28, sample 1


title: wt-lpa011-a


title: wt-lpa009_1-a


title: ASC_OSKM_d7_3 KT001_058

description: Nascent reprogrammed cells derived from human adipose-derived stem cells on day 7

source_name: Nascent reprogrammed cells derived from ASC, day 7, sample 3


title: wt-lpa003-a


title: ASC_OSKM_d11_1 KT001_059

source_name: Nascent reprogrammed cells derived from ASC, day 11, sample 1


title: wt-lpa009_1-b


title: wt-lpa002-b_2


title: ASC_3 KT001_052

description: Human adipose-derived stem cells

source_name: Adipose derived stem cell line, sample 3

value: Human adipose-derived stem cells


title: ASC_OSKM_d3_2 KT001_054

description: Nascent reprogrammed cells derived from human adipose-derived stem cells on day 3

source_name: Nascent reprogrammed cells derived from ASC, day 3, sample 2


title: ASC_OSKM_d7_2 KT001_057

source_name: Nascent reprogrammed cells derived from ASC, day 7, sample 2


title: ASC_1 KT001_050

description: Human adipose-derived stem cells

source_name: Adipose derived stem cell line, sample 1


title: HDF_OSKM_d49_3 KT001_049

description: Nascent reprogrammed cells derived from human dermal fibroblast on day 49

source_name: Nascent reprogrammed cells derived from HDF, day 49, sample 3

value: Nascent reprogrammed cells derived from human dermal fibroblasts


title: Snail1 KO ECs

city: Ann Arbor

first: Zhaoqiu

last: Wu

state: MI

address: 210 Washtenaw Ave

department: Life Sciences Institute

country: USA

institute: University of Michigan

description: Gene expression data from E10.5 embryos

hyb_protocol: Following fragmentation, 16 ug of aRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix 3000 7G GeneChip Scanner with Autoloader.

data_processing: Data was analyzed using the affy Bioconductor package implemented in the R-statistical environment(Version 2.12). RMA was used to normalize the data and fit log2 transformed expression values.

label: Biotin

source_name: Cultured embryonic ECs

label_protocol: Biotinylated aRNA were prepared according to the Ambion Premier kit protocol from 250 ng total RNA (MessageAmp Premier RNA Amplification Kit Instruction Manual, 2008, Ambion).

growth_protocol: Primary embryonic ECs were cultured in DMEM culture medium supplemented with 20% fetal bovine serum (FBS) and EC growth factor cocktail.

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

treatment_protocol: embryonic ECS were infected with Adeno-βGal or -Cre and recovered for several days.

tag: strain

tag: developmental stage

value: embyros at E10.5

value: endothelial


title: wt-lpa002-b

value: wt

source_name: refpool


title: ASC_OSKM_d3_1 KT001_053

source_name: Nascent reprogrammed cells derived from ASC, day 3, sample 1


title: ASC_2 KT001_051

description: Human adipose-derived stem cells

source_name: Adipose derived stem cell line, sample 2


title: ASC_OSKM_d3_3 KT001_055

source_name: Nascent reprogrammed cells derived from ASC, day 3, sample 3


title: WT ECs

description: Gene expression data from E10.5 embryos


title: ASC_OSKM_d11_2 KT001_060

source_name: Nascent reprogrammed cells derived from ASC, day 11, sample 2


title: wt-lpa002-a_2

value: refpool

source_name: wt


title: ASC_OSKM_d7_1 KT001_056

source_name: Nascent reprogrammed cells derived from ASC, day 7, sample 1


title: wt-lpa003-b


title: HDF_OSKM_d42_3 KT001_046

description: Nascent reprogrammed cells derived from human dermal fibroblast on day 42

source_name: Nascent reprogrammed cells derived from HDF, day 42, sample 3


title: HDF_OSKM_d49_2 KT001_048

source_name: Nascent reprogrammed cells derived from HDF, day 49, sample 2


title: HDF_OSKM_d49_1 KT001_047

source_name: Nascent reprogrammed cells derived from HDF, day 49, sample 1


title: HDF_OSKM_d42_2 KT001_045

source_name: Nascent reprogrammed cells derived from HDF, day 42, sample 2


title: wt-lpa002-a


title: HDF_OSKM_d35_3 KT001_043

description: Nascent reprogrammed cells derived from human dermal fibroblast on day 35

source_name: Nascent reprogrammed cells derived from HDF, day 35, sample 3


title: HDF_OSKM_d35_2 KT001_042

source_name: Nascent reprogrammed cells derived from HDF, day 35, sample 2


title: wt-lpa001-b


title: wt-lpa001-a


title: HDF_OSKM_d35_1 KT001_041

source_name: Nascent reprogrammed cells derived from HDF, day 35, sample 1


title: HDF_OSKM_d42_1 KT001_044

source_name: Nascent reprogrammed cells derived from HDF, day 42, sample 1


title: HDF_OSKM_d28_3 KT001_040

description: Nascent reprogrammed cells derived from human dermal fibroblast on day 28

source_name: Nascent reprogrammed cells derived from HDF, day 28, sample 3


title: HA_OSKM_d11_2 KT001_077

source_name: Nascent reprogrammed cells derived from HA, day 11, sample 2

value: Nascent reprogrammed cells derived from human astrocytes


title: HDF_OSKM_d20_1 KT001_035

description: Nascent reprogrammed cells derived from human dermal fibroblast on day 20

source_name: Nascent reprogrammed cells derived from HDF, day 20, sample 1


title: wt-ic021-a

source_name: refpool


title: HDF_OSKM_d20_2 KT001_036

source_name: Nascent reprogrammed cells derived from HDF, day 20, sample 2


title: HDF_OSKM_d20_3 KT001_037

source_name: Nascent reprogrammed cells derived from HDF, day 20, sample 3


title: wt-htp87-b

growth_protocol: Yeast growth for expression profiling in Tecan platereader v1.0

extract_protocol: yeast HTP RNA isolation for robot v2.0


title: wt-htp97-a


title: HDF_OSKM_d15_2 KT001_033

description: Nascent reprogrammed cells derived from human dermal fibroblast on day 15

source_name: Nascent reprogrammed cells derived from HDF, day 15, sample 2


title: HDF_OSKM_d11_2 KT001_030

description: Nascent reprogrammed cells derived from human dermal fibroblast on day 11

source_name: Nascent reprogrammed cells derived from HDF, day 11, sample 2


title: HDF_OSKM_d28_2 KT001_039

source_name: Nascent reprogrammed cells derived from HDF, day 28, sample 2


title: HDF_OSKM_d28_1 KT001_038

source_name: Nascent reprogrammed cells derived from HDF, day 28, sample 1


title: wt-htp80-b

source_name: wt


title: HDF_OSKM_d7_3 KT001_028

description: Nascent reprogrammed cells derived from human dermal fibroblast on day 7

source_name: Nascent reprogrammed cells derived from HDF, day 7, sample 3


title: HDF_OSKM_d11_3 KT001_031

source_name: Nascent reprogrammed cells derived from HDF, day 11, sample 3


title: HDF_OSKM_d15_3 KT001_034

source_name: Nascent reprogrammed cells derived from HDF, day 15, sample 3


title: HDF_OSKM_d15_1 KT001_032

source_name: Nascent reprogrammed cells derived from HDF, day 15, sample 1


title: wt-htp83-a


title: HDF_OSKM_d11_1 KT001_029

source_name: Nascent reprogrammed cells derived from HDF, day 11, sample 1


title: wt-htp78-a


title: wt-htp78-b


title: HDF_OSKM_d3_3 KT001_025

description: Nascent reprogrammed cells derived from human dermal fibroblast on day 3

source_name: Nascent reprogrammed cells derived from HDF, day 3, sample 3

growth_protocol: DMEM (Nacalai Tesque) containing 10% fetal bovine serum and 0.5% Pen/Strep (Life Technologies) at 37ºC in a humidified incubator with 5% CO2.


title: HDF_OSKM_d7_2 KT001_027

source_name: Nascent reprogrammed cells derived from HDF, day 7, sample 2


title: PELP1 ChIP-chip (replicate B)

type: genomic

city: Dallas

first: W. Lee

last: Kraus

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

hyb_protocol: see NimbleGen website

scan_protocol: see NimbleGen website

data_processing: Genomic data analysis was performed using the statistical programming language R (R Development Core Team, version 2.6.1). All data processing scripts are available upon request. The log2 ratio data from each of the arrays was subjected to lowess normalization.

molecule: genomic DNA

source_name: input

label_protocol: see NimbleGen website

extract_protocol: IMR90 breast cancer cells were grown to ~80 to 90% confluence, cross-linked with 1% paraformaldehyde in PBS for 10 min. at 37°C, and quenched in 125 mM glycine in PBS for 5 min at 4°C. The cells were collected by centrifugation and sonicated in lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris•HCl, pH 7.9, 1x protease inhibitor cocktail) to generate chromatin fragments of ~500 bp in length. The material was clarified by centrifugation, diluted 10-fold in dilution buffer (0.5% Triton X-100, 2 mM EDTA, 150 mM NaCl, 20 mM Tris•HCl, pH 7.9, 1x protease inhibitor cocktail), and pre-cleared with protein A-agarose beads. The pre-cleared, chromatin-containing supernatant was used in immunoprecipitation reactions with antibodies against PELP1 (Bethyl). The immunoprecipitated genomic DNA and a sample of input material were cleared of protein and residual RNA by digestion with proteinase K and RNase H, respectively. The DNA was then extracted with phenol:chloroform:isoamyl alcohol and precipitated with ethanol. The material was then amplified with LM-PCR.

tag: cell line

tag: antibody

source_name: IP

value: PELP1 (Bethyl Laboratories, Cat #A300-180A, Lot #A300-180A-1)


title: HDF_OSKM_d7_1 KT001_026

source_name: Nascent reprogrammed cells derived from HDF, day 7, sample 1


title: PELP1 ChIP-chip (replicate A)


title: HDF3 KT001_022

description: Human dermal fibroblast line 3

source_name: Human dermal fibroblast line 3

value: Human dermal fibroblasts


title: HDF_OSKM_d3_1 KT001_023

source_name: Nascent reprogrammed cells derived from HDF, day 3, sample 1

value: Nascent reprogrammed cells


title: HDF1 KT001_020

description: Human dermal fibroblast line 1

source_name: Human dermal fibroblast line 1


title: wt-htp77-a

source_name: refpool


title: wt-htp73-b


title: ME3 KT001_016

description: Mesodermal cells differentiated from human induced pluripotent stem cells

source_name: Mesoderm derived from iPSC

treatment_protocol: The single cell suspensions of human pluripotent stem cells were plated onto Collagen I-coated plates (BD biosciences) in DMEM/F12 containing 2% B27, 100 ng/ml Activin A, 3 µM CHIR99021 and 0.5% Pen/Strep. Forty-eight hours later, the medium was replaced with DMEM/F12 supplemented with 2% B27, 25 ng/ml BMP4, and 0.5% Pen/Strep. The medium was changed every other day until day 8.

value: Differentiated cells from human induced Pluripotent Stem cells

value: Differentiated cells


title: HDF_OSKM_d3_2 KT001_024

source_name: Nascent reprogrammed cells derived from HDF, day 3, sample 2


title: ME2 KT001_015


title: wt-htp73-a

source_name: wt


title: HDF2 KT001_021

description: Human dermal fibroblast line 2

source_name: Human dermal fibroblast line 2


title: NE3 KT001_019

description: Neuroectoderm differentiated from human induced pluripotent stem cells

source_name: Neuroectoderm derived from iPSC

treatment_protocol: The single cell suspensions of pluripotent stem cells were transferred to Lipidure-coated low binding 96-well plates (NOF corporation) in DMEM/F12 containing 5% KSR, 1% NEAA, 1% Glutamax, 100 nM 2-ME, 2 µM Dorsomorphin (Stemgent) and 10 µM SB431542 (Stemgent). The medium was changed on days 5, 8 and 11. The total differentiation period was 14 days.


title: wt-htp69-b


title: wt-htp70-a


title: EN2 KT001_012

description: Endodermal cells differentiated from human induced pluripotent stem cells

source_name: Endoderm derived from iPSC

treatment_protocol: The single cell suspensions of human pluripotent stem cells were plated onto Matrigel-coated plates in RPMI1640 (Life Technologies) containing 2% B27, 100 ng/ml Activin A, 3 µM CHIR99021 and 0.5% Pen/Strep. We added 0.5 mM sodium butyrate (Sigma) on days 1 to 3, and then carried out sodium butyrate-free culture until day 7.

value: Differentiated cells from human induced Pluripotent stem cells


title: wt-htp69-a


title: NE1 KT001_017

description: Neuroectoderm differentiated from humanembryonic stem cells

source_name: Neuroectoderm derived from ESC

value: Differentiated cells from human embryonic stem cells


title: ME1 KT001_014

description: Mesodermal cells differentiated from human embryonic stem cells

source_name: Mesoderm derived from ESC


title: PrS4 KT001_010

description: Primitive streak differentiated from human induced pluripotent stem cells 2

source_name: Primitive streak derived from iPSC

treatment_protocol: Single cell suspensions of human ESCs/iPSCs were plated onto fibronectin-coated plates (BD biosciences) in DMEM/F12 supplemented with 1% Insulin-Transferrin-Selenite (ITS, Life Technologies), 1% Glutamax, 1% NEAA, 2% B27 (Life Technologies), 100 nM 2-ME and 0.5% Pen/Strep. We added 3 µM CHIR99021 (Stemgent) and 50 ng/ml Activin A (Peprotech) on day 1, 3 µM CHIR99021, 25 ng/ml Activin A and 20 ng/ml bFGF on day 2 and 3 µM CHIR99021, 10 ng/ml Activin A, 20 ng/ml bFGF and 40 ng/ml BMP4 (R&D systems) on day 3.


title: wt-htp71-a


title: wt-htp71-b


title: EN3 KT001_013


title: NE2 KT001_018


title: PrS2 KT001_008

description: Primitive streak differentiated from human embryonic stem cells 2

source_name: Primitive streak derived from ESC


title: EN1 KT001_011

description: Endodermal cells differentiated from human embryonic stem cells

source_name: Endoderm derived from ESC


title: wt-ic021-b


title: wt-htp68-b


title: iPSC2 KT001_005

description: Human induced pluripotent stem cell line 2

source_name: Human induced pluripotent stem cell line 1 (253G1)

treatment_protocol: TRA-1-60 positive cells were sorted by flow cytometry.

value: Human undifferentiated induced Pluripotent Stem cells

value: Undifferentiated pluripotent stem cells


title: PrS3 KT001_009

description: Primitive streak differentiated from human induced pluripotent stem cells 1


title: Small RNAs from Petunia leaves

type: SRA

city: Udine

first: Emanuele

last: De Paoli

state: UDINE

address: via delle Scienze 206

department: Agricultural, Food, Environmental and Animal Sciences

country: Italy

institute: University of Udine

description: Total RNA was submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. Low molecular weight RNA was gel-sized in the ~18-33 nt range. The small RNA library was sequenced with the Sequencing-by-synthesis (SBS) technology by Illumina.

library_source: transcriptomic

data_processing: A custom script was designed to trim 3' adapters from native illumina short reads as well as detect and remove 5' or 3' adapter artefacts.

organism: Petunia x hybrida

source_name: Leaves

extract_protocol:
Total RNA was extracted with the Plant RNA Purification Reagent (Invitrogen).  Low molecular weight RNA was gel-sized in the ~18-33 nt range.  Quality of total RNA was evaluated by agarose gel electrophoresis, micro-electrophoresis (Agilent 2100 Bioanalyzer, Ambion) and O.D. measurements (Nanodrop ND-1000).
Small RNA libraries were constructed at Illumina using approaches described in (Lu et al., 2007) with minor modifications. The small RNA libraries were sequenced with the Sequencing-By-Synthesis (SBS) technology by Illumina.

value: Leaves


title: PrS1 KT001_007

description: Primitive streak differentiated from human embryonic stem cells 1


title: wt-htp48-a


title: ESC3 KT001_003

description: Human embryonic stem cell line 3

source_name: Human embryonic stem cell line 1 (KhES3)

value: Human undifferentiated embryonic stem cells


title: wt-htp64-a


title: wt-htp68-a


title: wt-htp63-a


title: ESC2 KT001_002

description: Human embryonic stem cell line 2

source_name: Human embryonic stem cell line 1 (KhES1)


title: wt-htp36-a


title: wt-htp64-b


title: wt-htp48-b


title: wt-htp45-a


title: iPSC3 KT001_006

description: Human induced pluripotent stem cell line 3

source_name: Human induced pluripotent stem cell line 1 (TIG120-4F1)


title: wt-htp46-a

source_name: refpool


title: wt-htp61-b


title: wt-htp47-1-a


title: wt-htp61-a


title: iPSC1 KT001_004

source_name: Human induced pluripotent stem cell line 1 (201B7)


title: ESC1 KT001_001

description: Human embryonic stem cell line 1

source_name: Human embryonic stem cell line 1 (H1)

value: Human undifferentiated  embryonic stem cells


title: wt-htp63-b

source_name: wt


title: wt-htp59-a


title: wt-htp46-b


title: wt-htp45-b


title: wt-htp47-b


title: wt-htp45-d


title: Braindead Best PEEP rep  14

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 5, from SAS. Gene expression profiling was performed using arrays of  RaGene10stv1-type from Affymetrix. A Custom CDF Version 14 with entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization.

organism: Rattus norvegicus

source_name: Lung biopsy of a braindead rat ventilated with Best PEEP method

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

extract_protocol: Total RNA of right lung tissue was extracted using Trizol® Reagent (Invitrogen GmbH, Karslruhe, Germany). DNase treatment was carried out, using DNA Free Kit (Ambion / Life Technologies GmbH, Darmstadt). RNA yield, quality, and integrity were assessed by agarose gel electrophoresis and spectrophotometry. RNA concentration was assessed by 260/280 measurements using the Infinite® 200 PRO NanoQuant (Tecan Group Ltd., CH), and RNA integrity was measured by Agilent Bioanalyzer 2100 System (Agilent, Böblingen, Germany).  1 µg RNA was transcribed to cDNA according to the protocol provided with the High Capacity cDNA Reverse Transcription kit (Life Technologies GmbH, Darmstadt, Germany). Recombinant ribonuclease inhibitor was added to prevent RNase-mediated degradation.

tag: stain

value: Wistar

tag: gender

value: male

tag: age

value: adult

tag: brain status

value: brain damage (BD)

tag: ventilation type

value: best PEEP ventilation


title: Braindead Best PEEP rep  7


title: Braindead Best PEEP rep  9


title: wt-htp162-b

value: wt

value: refpool


title: wt-htp36


title: Braindead Best PEEP rep  18


title: Braindead Best PEEP rep  16


title: Braindead HT_rep 22

source_name: Lung biopsy of a braindead rat ventilated with HT method

value: high tidal volume ventilation (HT)


title: Liver_fed_vanin1_KO_rep3

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Mouse Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument (Affymetrix, Santa Clara, CA) according to the manufacturer's recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.24.2).

source_name: liver_vanin-1 knockout_fed state

label_protocol: One hundred nanogram of RNA was used for whole transcript cDNA synthesis with the Ambion WT expression kit [catalog number 4411974] (Applied Biosystems/Life Technologies, Nieuwekerk a/d IJssel, The Netherlands).

growth_protocol: Male wild type (C57Bl/6J) and vanin-1 null mice  were individually housed in a light- and temperature-controlled facility (lights on 21:00 to 09:00, 21 °C). Mice were fed a standard laboratory chow, and had free access to drinking water.

extract_protocol: Total RNA was isolated using RNeasy micro kit from Qiagen. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: At the age of 14-16 weeks, mice were fasted for 24h (09.00-09.00h). Mice were then anaesthetized with isoflurane and livers were removed, snap frozen  on dry-ice  and stored at -80°C.

tag: strain background

value: vanin-1 knockout

tag: time point

value: after 24h of normal feeding

value: liver


title: wt-htp150-b


title: wt-htp141-a


title: wt-htp16-c


title: Liver_fed_vanin1_KO_rep1


title: Braindead HT_rep 26


title: wt-htp134-a


title: wt-htp134-b


title: Liver_fed_WT_rep1

source_name: liver_wild type_fed state

value: wild type


title: Braindead HT_rep 11


title: Liver_fed_WT_rep3


title: Braindead HT_rep 24


title: Braindead HT_rep 28


title: Liver_fed_vanin1_KO_rep4


title: Liver_fed_vanin1_KO_rep2


title: Liver_fed_WT_rep2


title: Liver_fed_WT_rep4


title: wt-htp150-a


title: wt-htp141-b


title: wt-htp132-b


title: Braindead HT_rep 37


title: Braindead Best PEEP rep  20


title: Liver_24h_fasted_vanin1_KO_rep4

source_name: liver_vanin-1 knockout_after 24h fasting

value: after 24h of fasting


title: wt-htp162-a


title: Non-Braindead Best PEEP rep  5

source_name: Lung biopsy of a non-braindead rat ventilated with Best PEEP method

value: no brain damage (NBD)


title: Non-Braindead Best PEEP rep  6


title: wt-htp13-b


title: Liver_24h_fasted_vanin1_KO_rep3


title: Non-Braindead Best PEEP rep  23


title: Liver_24h_fasted_vanin1_KO_rep1


title: Liver_24h_fasted_WT_rep4

source_name: liver_wild type_after 24h fasting


title: Non-Braindead Best PEEP rep  29


title: Non-Braindead HT_rep 19

source_name: Lung biopsy of a non-braindead rat ventilated with HT method


title: wt-htp132-a


title: Non-Braindead Best PEEP rep  30


title: wt-htp121-a


title: Non-Braindead Best PEEP rep  27


title: wt-htp126-a


title: Liver_24h_fasted_vanin1_KO_rep2


title: Rosette_HD+High CO2_36 DAS_rep4

city: Antwerp

first: Han

last: Asard

state: Antwerpen

address: Groenenborgerlaan 171

department: Department of Biology

country: Belgium

institute: University of Antwerp

description:
raw data file: Array_2.3.gpr
Sample_16_HD+CO2_Array_2.3.gpr_Cy5
4rth biological replicate of plants stressed by the combination of heat and drought stress under high CO2. Whole rosette was harvested after 36 DAS.

hyb_protocol: Hybridizations and washing steps were performed using the Gene Expression Hybridization Kit and Gene Expression Wash Buffer Kit (Agilent, USA) and following the manufacturer’s instructions.

scan_protocol: Microarrays were scanned using a Genepix Personal 4100A confocal scanner (Axon Instruments), at a resolution of 5 µm and excitation wavelengths of 635 nm and 532 nm. All spots were identified and quantified by GenePix Pro 6.0 software (Axon Instruments)

data_processing: In the dataset, spots for which the criterion FG < BG + 2SD (FG: foreground, BG: background, SD: standard deviation of the local background of the entire array; Sclep et al., 2007) was true for all arrays were excluded from analysis. Background correction was carried out using a normal-exponential convolution model (Ritchie et al., 2007) as implemented by the Limma R package (Smyth, 2005). Within-array adjustment was done by loess normalization (Smyth, 2005),

organism: Arabidopsis thaliana

source_name: Rosette, Heat&Drought + High CO2 at 36 DAS

label_protocol: Samples were labelled using the Quick Amp Labelling Kit (Two Color, Agilent), which generates amplified fluorescent cRNA starting from total RNA. The labelled samples were purified (by RNeasy Mini Kit), and cRNA yield and relative amount of incorporated labelled dCTPs were determined on a NanoDrop ND-1000 UV-VIS Spectrophotometer (Thermo Scientific, USA).

growth_protocol: Five seeds of Arabidopsis thaliana L. (Columbia) were evenly sown per pot and stratified in potting mix (Tref EGO substrates, Moerdijk, The Netherlands, 5×5 cm pots), and transferred to walk-in climate chambers (WeissTechnik, Belgium), at ambient (380 ppm) and elevated CO2 (730 ppm). Plants were watered daily to keep the soil at 70 % soil relative water content (RWC), the optimal water requirement. Soil RWC was adjusted by weighing the pots daily, and watering them to the desired RWC. Thirty-two days after sowing (DAS), plants were subjected to a realistic climate extreme event, simultaneously generating heat and drought stress, by a step-wise increase of the day/night temperature to 26/22 ºC on 32 DAS, 32/26 ºC on 33 DAS and 38/30 ºC on 34 DAS, and withholding water supply until soil RWC reached to a target value of 45%. Stress was maintained until 40 DAS, after which plants were re-watered back to 70 % and temperature was reset to the level of the control treatment (21/18 ºC).

extract_protocol: RNA was extracted using the RNeasy Plant Mini Kit (Qiagen, Netherlands). RNA was quantified using NanoDrop ND-1000 UV-VIS Spectrophotometer (Thermo Scientific, USA) and quality was assessed by using a gel cartridge on a QIAxcel platform (Qiagen, Hilden, Germany).

treatment_protocol: Our experimental set-up comprised four treatments: 1) ambient CO2  (control, C); 2) elevated CO2 (CO2); 3) heat wave combined with water deficit under ambient CO2 (HD), and, 4) heat wave combined with water deficit under elevated CO2 (HD+CO2). At the same time of the day (10:00-12:00 h), before (31 days after sowing, DAS), during (36, 40 DAS) and after (45 DAS) of heat and drought exposure, whole rosettes from each treatment were harvested and weighed (g fresh weight, g FW). At each sampling date, eight independent samples, each composed of twelve rosettes, were pooled per treatment, frozen in liquid nitrogen and stored at -80 ºC for further biochemical and microarray analysis. Microarray analysis was performed at  36 DAS.

tag: ecotype

value: Columbia

tag: stress

value: Heat&Drought + High CO2

value: Rosette

tag: time

value: 36 DAS


title: Liver_24h_fasted_WT_rep2

value: male


title: Liver_24h_fasted_WT_rep3


title: Liver_24h_fasted_WT_rep1


title: wt-htp70-b

tag: strainorline


title: Non-Braindead HT_rep 10

value: Wistar

value: adult


title: Non-Braindead HT_rep 13


title: wt-htp119-b


title: Rosette_HD+High CO2_36 DAS_rep3

description:
raw data file: Array_2.2.gpr
Sample_15_HD+CO2_Array_2.2.gpr_Cy3
3rd biological replicate of plants stressed by the combination of heat and drought stress under high CO2. Whole rosette was harvested after 36 DAS.

tag: tissue


title: wt-htp125-b


title: Rosette_HD+High CO2_36 DAS_rep2

description:
raw data file: Array_1.3.gpr
Sample_14_HD+CO2_Array_1.3.gpr_Cy5
2nd biological replicate of plants stressed by the combination of heat and drought stress under high CO2. Whole rosette was harvested after 36 DAS.


title: wt-htp121-b


title: wt-htp126-b


title: Non-Braindead HT_rep 33


title: wt-htp125-a


title: Rosette_High CO2_36 DAS_rep4

description:
raw data file: Array_2.4.gpr
Sample_12_CO2_Array_2.4.gpr_Cy5
4rth biological replicate of plants grown under high CO2

source_name: Rosette, High CO2 at 36 DAS

value: High CO2


title: wt-htp119-a

value: wt


title: Rosette_HD+High CO2_36 DAS_rep1

description:
raw data file: Array_1.2.gpr
Sample_13_HD+CO2_Array_1.2.gpr_Cy3
1st biological replicate of plants stressed by the combination of heat and drought stress under high CO2. Whole rosette was harvested after 36 DAS.


title: Rosette_High CO2_36 DAS_rep3

description:
raw data file: Array_1.2.gpr
Sample_11_CO2_Array_1.2.gpr_Cy5
3rd biological replicate of plants grown under high CO2


title: Non-Braindead HT_rep 12


title: Rosette_High CO2_36 DAS_rep2

description:
raw data file: Array_2.3.gpr
Sample_10_CO2_Array_2.3.gpr_Cy3
2nd biological replicate of plants grown under high CO2


title: wt-htp105-b

value: refpool


title: wt-htp118-matA-b

source_name: wt-matA

value: wt-matA


title: wt-htp118-b


title: wt-htp102-b


title: wt-htp116-a


title: Rosette_Heat&Drought_36 DAS_rep2

description:
raw data file: Array_2.1.gpr
Sample_6_HD_Array_2.1.gpr_Cy3
2nd  biological replicate of plants stressed by the combination of heat and drought stress. Whole rosette was harvested after 36 DAS.

source_name: Rosette, Heat & Drought stress at 36 DAS

value: Heat&Drought


title: Rosette_Control_36 DAS_rep4

description:
raw data file: Array_2.1.gpr
Sample_4_C_Array_2.1.gpr_Cy5
4rth biological replicate of Control plants. Whole rosette was harvested after 36 DAS.

source_name: Rosette, Control at 36 DAS

value: Control


title: Rosette_Heat&Drought_36 DAS_rep1

description:
raw data file: Array_1.3.gpr
Sample_5_HD_Array_1.3.gpr_Cy3
1st biological replicate of plants stressed by the combination of heat and drought stress. Whole rosette was harvested after 36 DAS.


title: Rosette_Heat&Drought_36 DAS_rep3

description:
raw data file: Array_1.4.gpr
Sample_7_HD_Array_1.4.gpr_Cy5
3rd biological replicate of plants stressed by the combination of heat and drought stress. Whole rosette was harvested after 36 DAS.


title: BCR-ABL1 transformed murine ALL-like cells, Grp78 deletion, replicate 3

city: San Francisco

first: Huimin

last: Geng

state: CA

address: 513 Parnassus Ave., MSB HSW 1201

department: Department of Laboratory Medicine

institute: UCSF

hyb_protocol: Standard Affymetrix protocols (Affymetrix GeneChip Expression Analysis Technical Manual)

data_processing: RMA

source_name: mouse Grp78fl/fl cells transduced with p190 (BCR-ABL1) and CRE, Grp78 deletion

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual)

extract_protocol: Extraction Method: Qiagen RNeasy Kit

tag: cell type

tag: genetic background

tag: genotype

value: Grp78 deletion


title: Non-Braindead HT_rep 34

value: high tidal volume ventilation (HT)


title: wt-htp102-a

source_name: refpool


title: wt-htp117-a


title: wt-htp118-a


title: wt-htp-04-a


title: Rosette_High CO2_36 DAS_rep1

description:
raw data file: Array_1.1.gpr
Sample_9_CO2_Array_1.1.gpr_Cy3
1st biological replicate of plants grown under high CO2. Whole rosette was harvested after 36 DAS.


title: Rosette_Heat&Drought_36 DAS_rep4

description:
raw data file: Array_2.2.gpr
Sample_8_HD_Array_2.2.gpr_Cy5
4rth  biological replicate of plants stressed by the combination of heat and drought stress. Whole rosette was harvested after 36 DAS.


title: wt-htp-04-b


title: BCR-ABL1 transformed murine ALL-like cells, Grp78 wild type, replicate 3

scan_protocol: Standard Affymetrix protocols (Affymetrix GeneChip Expression Analysis Technical Manual)

source_name: mouse Grp78fl/fl cells transduced with p190 (BCR-ABL1) and an empty vector (EV), Grp78 wild type

value: Grp78 wild type


title: BCR-ABL1 transformed murine ALL-like cells, Grp78 deletion, replicate 2


title: wt-htp101-b

source_name: wt


title: BCR-ABL1 transformed murine ALL-like cells, Grp78 deletion, replicate 1


title: Rosette_Control_36 DAS_rep3

description:
raw data file: Array_2.4.gpr
Sample_3_C_Array_2.4.gpr_Cy3
3rd biological replicate of Control plants. Whole rosette was harvested after 36 DAS.


title: Rosette_Control_36 DAS_rep2

description:
raw data file: Array_1.1.gpr
Sample_2_C_Array_1.1.gpr_Cy5
2nd biological replicate of Control plants. Whole rosette was harvested after 36 DAS.


title: BCR-ABL1 transformed murine ALL-like cells, Grp78 wild type, replicate 1


title: BCR-ABL1 transformed murine ALL-like cells, Grp78 wild type, replicate 2


title: wt-htp-03-a


title: wt-gam006-a


title: wt-gam006-b


title: breast_primary_MGH674

city: Boston

first: Ben

middle: S.

last: Wittner

state: MA

address: 149 13th Street

department: Center for Cancer Research

institute: Massachusetts General Hospital

scan_protocol: According to manufacturer's instructions (Affymetrix, Santa Clara, CA, USA). The scanner model used to scan the arrays was an Affymetrix GeneChip Scanner 3000-7G.

data_processing: MAS5.0 as implemented by Bioconductor package simpleaffy, version 2.14.05.

source_name: primary breast tumor

growth_protocol: Not applicable.

extract_protocol: 4,000–5,000 malignant epithelial cells were procured by laser capture microdissection using a PixCell IIe system (Molecular Devices, Mountain View, CA, USA) as described in PubMed ID: 19187537. Total RNA was isolated from captured cells using the PicoPure RNA isolation kit (Molecular Devices), then amplified by T7 RNA amplification (RiboAmp; Molecular Devices).

treatment_protocol: The 19 HER2+ breast cancer brain metastatic specimens were fresh-frozen biopsies obtained from the M.D. Anderson Cancer Center between 1998 and 2001. The HER2+ primary breast cancer specimens were fresh-frozen biopsies obtained from the Massachusetts General Hospital in 2006.

tag: disease state

value: nonmetastatic breast cancer

value: primary breast tumor

tag: er status

value: ER-

tag: her2 status

value: 53 yr


title: breast_primary_MGH1102

hyb_protocol: According to manufacturer's instructions (Affymetrix, Santa Clara, CA, USA).

value: ER+

value: 51 yr


title: wt-gam004-a


title: breast_primary_MGH1084

label_protocol: According to manufacturer's instructions (Affymetrix, Santa Clara, CA, USA).

value: 57 yr


title: wt-gam004-b


title: wt-ea033-1-a


title: Rosette_Control_36 DAS_rep1

description:
raw data file: Array_1.4.gpr
Sample_1_C_Array_1.4.gpr_Cy3
1st biological replicate of Control plants. Whole rosette was harvested after 36 DAS.

value: Columbia

value: Rosette

value: 36 DAS


title: wt-erlenmeyer-b

value: wt

value: refpool


title: wt-erlenmeyer-a


title: Knockdown from late leukemic vs matched wildtype 6

city: Heidelberg

first: Miriam

last: Sonnet

address: Im Neuenheimer Feld 280

institute: German Cancer Research Center

description: Biological replicate 6 of 7

hyb_protocol: Differentially labeled DNA samples from age and gender matched animals were pooled and hybridized with the Agilent aCGH Hybridization Kit to Agilent mouse CpG island tiling arrays according to the manufacturer´s instructions

scan_protocol: Scanned on an Agilent G2565CA scanner. Agilent Feature Extraction Software (v 8.5.1.1)

data_processing: Data from arrays were extracted with the Agilent Feature extraction software, background-corrected with the NormExp method (offset 50) and within-array-normalised with a rank-invariant loess regression method.

source_name: Bone marrow from wildtype animal

label_protocol: Enriched highly methylated DNA (approx. 30 ng) was labeled in a 50 µl reaction mix (Invitrogen, BioPrime Total Genomic Labeling System) with either Alexa 5 (PU.1 knockdown animals) or Alexa 3 (wildtype animals) and subsequently purified using the BioPrime Purification Module

growth_protocol: Heterozygous mice were bred to obtain homozygous wildtype and knockdown littermates

extract_protocol: DNA was extracted using the Qiagen AllPrep kit following the manufacturer´s instructions. Highly methylated DNA was enriched using methyl-CpG immunoprecipitation according to Gebhard et al., Cancer Res. 2006.

value: wild type

value: 22 weeks

value: Balb/c

value: bone marrow

value: control

source_name: Bone marrow from knockdown animal late leukemic

tag: type

value: PU.1 knockdown

value: late leukemic


title: Knockdown from late leukemic vs matched wildtype 5

description: Biological replicate 5 of 7

tag: age

value: 27 weeks


title: breast_primary_MGH455

value: nonmetastatic breast cancer

value: primary breast tumor

value: ER-

value: 61 yr


title: Knockdown from late leukemic vs matched wildtype 2

description: Biological replicate 2 of 7

value: 12 weeks


title: breast_primary_MGH1057

value: 47 yr


title: Knockdown from late leukemic vs matched wildtype 3

description: Biological replicate 3 of 7

value: 21 weeks


title: Knockdown from late leukemic vs matched wildtype 4

description: Biological replicate 4 of 7

value: 28 weeks


title: breast_primary_MGH963

value: 41 yr


title: breast_primary_MGH482

value: 66 yr


title: breast_primary_MGH421

value: 71 yr


title: wt-ea018-1-b

value: wt

value: refpool


title: breast_primary_MGH1038

value: 50 yr


title: Knockdown from late leukemic vs matched wildtype 1

description: Biological replicate 1 of 7

value: wild type

value: Balb/c

value: bone marrow

value: control

value: PU.1 knockdown


title: wt-ea030-1-a


title: breast_primary_MGH450

value: nonmetastatic breast cancer

value: primary breast tumor

value: ER-

value: 60 yr


title: wt-ea012-1-b


title: Knockdown from early leukemic vs matched wildtype 4

description: Biological replicate 4 of 5

value: 8 weeks

source_name: Bone marrow from knockdown animal early leukemic

value: intermediate leukemia


title: Knockdown from early leukemic vs matched wildtype 5

description: Biological replicate 5 of 5

value: 12 weeks


title: Knockdown from late leukemic vs matched wildtype 7

description: Biological replicate 7 of 7

value: 24 weeks

value: late leukemic


title: wt-ea018-1-a

value: wt


title: breast_primary_MGH434

value: 51 yr


title: wt-ea012-1-a

value: refpool


title: breast_primary_MGH574

value: 73 yr


title: breast_primary_MGH1104

value: 32 yr


title: Knockdown from preleukemic stage vs matched wildtype 7

description: Biological replicate 7 of 7

value: wild type

value: 4 weeks

value: Balb/c

value: bone marrow

source_name: Bone marrow from knockdown animal preleukemic stage

value: pre-leukemia


title: Knockdown from preleukemic stage vs matched wildtype 6

description: Biological replicate 6 of 7

value: 13 weeks

value: control

value: PU.1 knockdown


title: Knockdown from early leukemic vs matched wildtype 2

description: Biological replicate 2 of 5

value: 9 weeks

value: intermediate leukemia


title: breast_primary_MGH133

value: nonmetastatic breast cancer

value: primary breast tumor

value: ER-

value: 44 yr


title: wt-ea004-1-a

value: refpool

value: wt


title: breast_primary_MGH351

value: ER+

value: 54 yr


title: wt-dl003-a


title: wt-SEL007-b-2


title: wt-LPA022-a


title: wt-SEL007-b


title: Knockdown from early leukemic vs matched wildtype 1

description: Biological replicate 1 of 5

value: wild type

value: 4 weeks


title: wt-SEL007-a-2


title: Knockdown from preleukemic stage vs matched wildtype 3

description: Biological replicate 3 of 7

value: 12 weeks

value: Balb/c

value: bone marrow


title: breast_primary_MGH153

value: 46 yr


title: Knockdown from preleukemic stage vs matched wildtype 2

description: Biological replicate 2 of 7

value: control

value: PU.1 knockdown

value: pre-leukemia


title: breast_primary_MGH46

value: nonmetastatic breast cancer

value: 56 yr


title: breast_primary_MGH42

value: primary breast tumor

value: 50 yr


title: breast_primary_MGH16

value: ER-

value: 51 yr


title: Knockdown from preleukemic stage vs matched wildtype 4

description: Biological replicate 4 of 7

value: 18 weeks


title: Knockdown from preleukemic stage vs matched wildtype 5

description: Biological replicate 5 of 7

value: 8 weeks


title: wt-LPA020-b

value: wt

value: refpool


title: wt-JG2-b


title: wt-JG2-a


title: brain_met_J10

source_name: brain metastasis

value: brain metastatic breast cancer

value: brain metastasis


title: wt-LPA019-a


title: I_hospitalis_coculture_S2_Rep2

city: Knoxville

first: Louie

last: Wurch

state: TN

address: M313 Walters Life Sciences

institute: University of Tennessee

description: This is the second replicate of Ignicoccus hospitalis grown in co-culture with Nanoarchaeum equitans at late stationary phase.

hyb_protocol: A high density gene expression microarray (1plex, 385k) containing 60mer oligonucleotide probes (up to 20 different probe per gene) for the protein encoding genes of I. hospitalis was designed and manufactured by Nimblegen (Roche NimbleGen, IN). Hybridization of the cDNAs to the arrays and washing were performed according to manufacturer’s instructions

scan_protocol: Scanning was performed with a Surescan HR DNA Microarray Scanner (Agilent, CA).

data_processing: Images were quantified using NimbleScan 2.6 (Roche NimbleGen, IN). Individual array raw data was log2 transformed and imported into and analyzed by the statistical analysis software JMP Genomics 3.0 (SAS Institute, Cary, NC).

organism: Ignicoccus hospitalis KIN4/I

source_name: Ignicoccus hospitalis KIN4/I (DSM 18386) + Nanoarchaeum equitans

label_protocol: For each sample 10 μg RNA were converted to cDNA with the ds-cDNA synthesis kit (Invitrogen, CA) and labeled with the One Color DNA labeling kit (Roche NimbleGen IN).

growth_protocol: Ignicoccus hospitalis KIN4/I (DSM 18386) was cultured either singly or in co-culture with Nanoarchaeum equitans at 90°C in a 300 liter fermenter at the University of Regensburg Archaea Center using 0.5xSME medium, elemental sulfur and H2/CO2 gas phase, as previously described (Huber et al 2002, Jahn et al 2008).

extract_protocol: Cell pellets were homogenized in Trizol (Invitrogen, CA) and total RNA was purified in triplicate from each sample using the PureLinkRNA kit (Invitrogen, CA) with on-column removal of contaminating DNA. RNA quality and concentration were determined with an Agilent Bioanalyzer (Agilent, CA).

treatment_protocol: The cultures were sampled at various time-points along the ~24-hr growth course, covering the transition from relatively mid log to stationary phase.

tag: treatment

value: co-culture with Nanoarchaeum equitans

tag: growth phase

value: Late stationary (S2)


title: I_hospitalis_coculture_S1_Rep1

description: This is the first replicate of Ignicoccus hospitalis grown in co-culture with Nanoarchaeum equitans at early stationary phase.

value: Early stationary (S1)


title: I_hospitalis_coculture_S1_Rep2

description: This is the second replicate of Ignicoccus hospitalis grown in co-culture with Nanoarchaeum equitans at early stationary phase.


title: wt-HTP160-b


title: brain_met_BT40

value: ER+


title: brain_met_J11


title: brain_met_J7


title: wt-JG1-b


title: wt-JG1-a


title: brain_met_BT31


title: I_hospitalis_coculture_L2_Rep2

description: This is the second replicate of Ignicoccus hospitalis grown in co-culture with Nanoarchaeum equitans at late log phase.

value: Late log (L2)


title: Knockdown from preleukemic stage vs matched wildtype 1

description: Biological replicate 1 of 7

value: wild type

value: 5 weeks

value: Balb/c

value: bone marrow

value: control

value: PU.1 knockdown

value: 4 weeks

value: pre-leukemia


title: brain_met_BT51

value: ER-


title: Knockdown from early leukemic vs matched wildtype 3

description: Biological replicate 3 of 5

value: 9 weeks

value: intermediate leukemia


title: wt-HTP160-a

value: refpool

value: wt


title: brain_met_J5

value: brain metastatic breast cancer

value: brain metastasis


title: wt-HTP158-b


title: brain_met_BT57

value: 66 yr


title: I_hospitalis_coculture_L2_Rep1

description: This is the first replicate of Ignicoccus hospitalis grown in co-culture with Nanoarchaeum equitans at late log phase.

value: co-culture with Nanoarchaeum equitans

value: Late log (L2)


title: I_hospitalis_coculture_L1_Rep2

description: This is the second replicate of Ignicoccus hospitalis grown in co-culture with Nanoarchaeum equitans at mid log phase.

value: Mid log (L1)


title: I_hospitalis_pure_S2_Rep2

description: This is the second replicate of Ignicoccus hospitalis grown in pure culture at late stationary phase.

source_name: Ignicoccus hospitalis KIN4/I (DSM 18386)

value: pure culture

value: Late stationary (S2)


title: I_hospitalis_pure_S2_Rep1

description: This is the first replicate of Ignicoccus hospitalis grown in pure culture at late stationary phase.


title: I_hospitalis_coculture_L1_Rep1

description: This is the first replicate of Ignicoccus hospitalis grown in co-culture with Nanoarchaeum equitans at mid log phase.


title: wt-HTP144-b


title: wt-HTP158-a


title: brain_met_J4


title: brain_met_BT30


title: I_hospitalis_pure_S1_Rep1

description: This is the first replicate of Ignicoccus hospitalis grown in pure culture at early stationary phase.

value: Early stationary (S1)


title: I_hospitalis_pure_L2_Rep2

description: This is the second replicate of Ignicoccus hospitalis grown in pure culture at late log phase.


title: wt-HTP144-a


title: I_hospitalis_pure_L2_Rep1

description: This is the first replicate of Ignicoccus hospitalis grown in pure culture at late log phase.


title: brain_met_J2


title: wt-HTP133-b


title: wt-FR002-b


title: brain_met_J1


title: wt-HTP140-a


title: brain_met_BT16


title: brain_met_BT34

value: ER+


title: I_hospitalis_pure_L1_Rep2

description: This is the second replicate of Ignicoccus hospitalis grown in pure culture at mid log phase.


title: wt-HTP140-b


title: I_hospitalis_pure_L1_Rep1

description: This is the first replicate of Ignicoccus hospitalis grown in pure culture at mid log phase.


title: I_hospitalis_pure_S1_Rep2

description: This is the second replicate of Ignicoccus hospitalis grown in pure culture at early stationary phase.


title: wt-HTP133-a


title: brain_met_BT11


title: wt-FR001-b


title: wt-FR002-a


title: brain_met_J12


title: brain_met_J8


title: wt-FR001-a


title: Sample 40 mg #3

status: Public on Apr 23 2014

city: Porto Alegre

first: Ricardo

middle: F

last: Savaris

state: Rs

address: Rua Ramro Barcelos 2350/1124

department: Ginecologia e Obstetrícia

country: Brazil

institute: Universidade Federal do Rio Grande do Sul

data_processing:
The data were normalised to log scale for parametric statistical analysis wiiht GeneSpring 12.0
supplementary file of normalized data generated by baseline normalization (transcript id)

source_name: human endometrium

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.

treatment_protocol: subjects received treatment with leuprolide acetate (1 mg, s.c. daily; TAP Pharmaceuticals, Lake Forest, IL, USA), beginning in the midluteal phase of a natural cycle (as documented by serum P > 3.0 ng/mL) and continuing throughout the duration of the study.  After effective down-regulation of the hypothalamic-pituitary-ovarian axis was confirmed (serum estradiol < 40 pg/mL, no ovarian follicle > 10 mm in mean diameter), subjects received treatment with transdermal estradiol 0.2 mg/day (Vivelle Dot, Novartis, East Hanover, NJ), for a total of 20 days. After 10 days of estradiol treatment, subjects were randomly allocated to receive treatment with one of four doses (2.5 mg, 5.0 mg, 10.0 mg, or 40.0 mg i.m. daily) of progesterone in oil (Pfizer, New York, NY) for 10 days.

value: mid-secretory endometrium

value: 40 mg progesterone


title: Sample 5 mg #3

value: 5 mg progesterone


title: sample 40 mg #2


title: Sample 2.5 mg #2

value: 2.5 mg progesterone


title: brain_met_J3

value: ER-

value: 51 yr


title: brain_met_BT25


title: Sample 2.5 mg #4


title: Control #5

value: Control


title: Sample 10 mg #4

value: 10 mg progesterone


title: Sample 10 mg #2


title: Control #3


title: Control #6


title: Control #7


title: Sample 40 mg#1


title: Sample 10 mg #3


title: Sample 40 mg #4


title: Control #9


title: Sample 40 mg #5


title: Sample 5 mg #4


title: Control #8


title: Sample 2.5 mg #3 replicate


title: Control #10


title: Control #4


title: Sample 10mg #5

value: 10mg progesterone


title: Sample 10mg #1


title: Control #2


title: I_hospitalis_coculture_S2_Rep1

description: This is the first replicate of Ignicoccus hospitalis grown in co-culture with Nanoarchaeum equitans at late stationary phase.


title: Sample 2.5 mg #3


title: Sample 5 mg #1


title: stage10_rep4

first: Enrico

last: Ferrero

address: Downing Street

department: Genetics

institute: University of Cambridge

description:
S109870
biological replicate 4 of 4 stage 10

hyb_protocol: Add 140 µl of Ocimum hybridisation buffer to the labelled mixture and heat at 100 °C for 2 minutes on a hot-block. Centrifuge for 3 minutes at 13,000 rpm. Load 140 µl of the labelled sample to the microarray, and hybridise for 16 hours at 51 °C. Perform post-hybridisation washes as per PowerMatrix slides protocol (FMB). Pre-heat wash solution 1 (0.2 x SSC; 0.2% SDS) and wash solution 2 (0.2 x SSC) to 55 °C using a water bath. Incubate slides in a slide staining dish with pre-heated wash solution 1 on an orbital shaker at 50 rpm for 20 minutes. Transfer the slides to a staining trough containing pre-heated wash solution 2. Gently dip the slides up and down for 1 minute in wash solution 2. Repeat step in fresh wash solution 2 twice. Rinse the slides 3 times with fresh deionized water at room temperature (dip the rack in MilliQ water for 3 seconds). Transfer the slides to a clean microscope slide box with tissue at the base and centrifuge at 1000 rpm for 5 minutes. The slides are now ready to be scanned.

scan_protocol: Arrays are scanned at 5 µm resolution with a GenePix 4000B (Axon) dual laser scanner at 100% Power, with Lines to average = 1 and Focus position = 0 at their respective optimal PMT gains selected by the Auto-PMT function (0.005% saturation tolerance). Images are saved as Single-image TIFF.

data_processing: Images are processed and spot quantified by the Dapple software (v.0.88, http://www.cs.wustl.edu/~jbuhler/research/dapple/). Raw data are then loaded into limma (Bioconductor) and normalised with the vsn package using the limma package (R. 2.15 and Bioconductor v. 2.11). The resulting ratios are log2 ratio of sample/control (where SoxN heterozygous embryos are the controls, while SoxN homozygous embryos are considered the samples).

organism: Drosophila melanogaster

label_protocol: To 3 to 5 µg of total RNA, add 1 µl 500 ng/ µl of Oligo(dT)23 anchored primer (Sigma) and adjust volume to 5 µl with DEPC- water. Incubate at 65 °C for 10 min, then snap cool on ice. Add 4 µl 5x First Strand Buffer (Invitrogen), 2 µl 0.1M DTT (Invitrogen), 1 µl 10 mM dNTP mix, 0.25 µl 40 U/µl RNasin (Promega) and 0.75 µl 200 U/µl Superscript III (Invitrogen). Incubate at 46 °C for 2 hours, then at 65 °C for 15 minutes, snap cool on ice. For second strand synthesis: Add 7.5 µl Second Strand Buffer (Invitrogen), 0.75 µl 10 mM dNTP mix, 2 µl 10 U/µl DNA Polymerase I (Invitrogen), 0.1 µl 5 U/µl RnaseH (Promega), 0.5 µl 10 U/µl E. coli Ligase (NEB) adjust volume to 40 µl with DEPC-water. Incubate at 16 °C for 2 hours, then purification using QIAquick PCR Purification Kit. In PCR tubes take 1 µg double stranded DNA, add 40 diluted Cy3 or Cy5-Random Nonamers (Nimblegen Dual Colour Kit) and make up to a volume of 80 µl with Nuclease-free Water (Nimblegen Dual Colour Kit). Heat-denature samples in a thermocycler at 98°C for 10 minutes. Quickchill on ice for 10 minutes. Add 10 µl 10mM dNTP Mix (Nimblegen Dual Colour Kit), 8 Nuclease-free Water (Nimblegen Dual Colour Kit) and 2 µl 50U/μl Klenow Fragment (3’->5’ exo-) (Nimblegen Dual Colour Kit), mix gently by pipetting. Incubate at 37°C for 3 hours in thermocycler. Stop the reaction by adding 21.5 µl Stop Solution (Nimblegen Dual Colour Kit). Transfer samples to 1.5 ml tubes and add 110 µl Isopropanol, mix and incubate for 10 minutes at room temperature in the dark. Centrifuge at 13,000rpm for 10 minutes and discard supernatant. Add 500 µl ice-cold 80% ethanol and centrifuge at 13,000rpm for 2 minutes. Discard supernatant and dry pellet for 5 minutes in the dark. Resuspend labeled DNA in 50 µl Nuclease-free Water (Nimblegen) and measure the concentration on the Nanodrop. Combine 34 µg of sample with 34 µg control and dry samples in a speed vac with medium heat.

growth_protocol: Grow flies at 25°C; collect and age embryos on grape agar juice plates supplemented with yeast paste, at 25°C

extract_protocol: Homogenise tissue in 300 µl TRIzol (Invitrogen) in a 1.5 ml tube using an RNAase-free polypropylene pellet pestle. Centrifuge at 13,000 rpm in a microcentriuge for 10 minutes 4 °C to pellet debris and transfer supernatant to a fresh 1.5 ml tube. Add 0.2 volumes chloroform, vortex for 60 seconds. Centrifuge at 13,000 rpm for 15 minutes. Remove upper phase to a new RNase-free tube, being careful not to touch the interface. Add 0.4 µl GeneElute Linear Polyacrylamide (Sigma) (25 µg / µl stock diluted 1:10 in DEPC MilliQ water) and 0.8 volumes of isopropanol, invert and then incubate for 1 hour at -20°C. Pellet the RNA by centrifugation at 13,000 rpm for 30 minutes. Discard the supernatant and wash the RNA pellet with 500 µl 70% ethanol/DEPC MilliQ water. Air-dry the pellet. Resuspend in an appropriate volume of DEPC MilliQ water, e.g. 5 µl. Verify quality of RNA on a 0.8 % agarose gel stained with SYBR-gold (Molecular Probes).

tag: strain

value: SoxN[null]

value: whole embryos

tag: developmental stage

value: stage 10

value: SoxN[null] / CyO, twi-Gal4, UAS-EGFP


title: stage12-13_rep3

description:
S109730
biological replicate 3 of 4 stage 12-13

value: stage 12-13


title: stage12-13_rep1

description:
S109728
biological replicate 1 of 4 stage 12-13


title: stage7-8_rep4

description:
S109814
biological replicate 4 of 4 stage 7-8

label_protocol: Adjust RNA volume to 3 µL with DEPC-water and add 1 µL 3'-SMART CDS Primer IIA (10 µM) and 1 µL SMART IIA chimeric oligo (10 µM). Incubate at 70 °C for 5 minutes, then snap cool on ice. Add 2 µl 5x First Strand Buffer (Invitrogen), 0.5 µL 0.1M DTT (Invitrogen), 0.5 µL 10 mM dNTP mix and 1 µl 200 U/µL Superscript III (Invitrogen). Incubate at 46 °C for 1.5 hours, then cool on ice (store samples at 4 °C or -20 °C). To determine the optimal number of cycles required for generating products in exponential phase, 2 µL of the PCR products from a parallel run are visualised at every second cycle from cycle 18 to 26 on 1% agarose gel using one reaction of each sample type. To 5 µL of the first-strand reaction (include negative and positive controls) add 5 µL 10x Advantage II PCR buffer (Clontech), 1 µL 10 mM dNTP mix, 2 µL 20 µM 5' PCR Primer II, 1 µL 50x Advantage II Polymerase Mix (Clontech) and adjust volume to 50 µL with DEPC-water. Run PCR program: step 1: 95 °C - 1 min, step 2: 95 °C - 5 sec, step 3: 65 °C - 5 sec, step 4: 68 °C - 6 min, cycle from step 2 for 27 more times. Run PCR aliquots on 1% agarose gel and select cycle number below saturation. Then perform amplification using the optimal number of XX cycles on the remaining 5 µL of the first-strand reaction. Purify PCR products using QIAquick PCR Purification Kit. To label take up to 1 µg double stranded DNA and make up to a total volume of 25 µl with DEPC-water. Add 20 µl 2.5x Random Primer Reaction Buffer (Invitrogen – BioPrime DNA Labelling Kit). Incubate at 100 °C for 5 minutes, snap cool on ice. Add 1 µl 10 X low-C dNTP mix (5mM dATP,dGTP,dTTP, 2 mM dCTP), 2 µl 1 mM Cy3 or Cy5 dCTP (GE Healthcare) and 1 µl 40U/µl Klenow (Invitrogen – BioPrime DNA Labelling Kit). Incubate at 37°C for 2 to 3 hours. Stop the reaction by adding 5 µl Stop Buffer (Invitrogen – BioPrime DNA Labelling Kit). Resuspend the resin in the AutoSeq G-50 column (GE Healthcare) by vortexing gently. Loosen the cap a quarter turn and snap off the bottom closure. Place the column in a collection tube. Pre-spin column at 5,000 rpm for 1 minute to remove the buffer. Remove the top cap and place column in a new 1.5 ml tube. Pipette half of the sample onto the centre of the angled surface of the compacted resin bed being careful not to disturb the resin. Spin for 1 minute at 5,000 rpm. Discard the column. Place a second column into the same 1.5 ml microfuge tube and then add the second half of the sample. Spin for 1 minute and 5,000 rmp. Reduce volume of probe to between 2 to 5 µl by placing in a speed vac with medium heat. Add 2 µl of 10 mg / ml sonicated salmon sperm DNA (Invitrogen). SMART II A chimeric primer: 5'-AAG-CAG-TGG-TAT-CAA-CGC-AGA-GTA-CGC-888-3'  (8 = riboG). 3' SMART CDS Primer IIA: 5'-AAG-CAG-TGG-TAT-CAA-CGC-AGA-GTA-CTT-TTT-TTT-TTT-TTT-TTT-TTT-TTT-TTT-TTT-VN-3' (V = G+A+C, N = A+C+G+T). 5' PCR Primer II: 5'-AAG-CAG-TGG-TAT-CAA-CGC-AGA-GT-3'. In PCR tubes take 1 µg double stranded DNA, add 40 diluted Cy3 or Cy5-Random Nonamers (Nimblegen Dual Colour Kit) and make up to a volume of 80 µl with Nuclease-free Water (Nimblegen Dual Colour Kit). Heat-denature samples in a thermocycler at 98°C for 10 minutes. Quickchill on ice for 10 minutes. Add 10 µl 10mM dNTP Mix (Nimblegen Dual Colour Kit), 8 Nuclease-free Water (Nimblegen Dual Colour Kit) and 2 µl 50U/μl Klenow Fragment (3’->5’ exo-) (Nimblegen Dual Colour Kit), mix gently by pipetting. Incubate at 37°C for 3 hours in thermocycler. Stop the reaction by adding 21.5 µl Stop Solution (Nimblegen Dual Colour Kit). Transfer samples to 1.5 ml tubes and add 110 µl Isopropanol, mix and incubate for 10 minutes at room temperature in the dark. Centrifuge at 13,000rpm for 10 minutes and discard supernatant. Add 500 µl ice-cold 80% ethanol and centrifuge at 13,000rpm for 2 minutes. Discard supernatant and dry pellet for 5 minutes in the dark. Resuspend labeled DNA in 50 µl Nuclease-free Water (Nimblegen) and measure the concentration on the Nanodrop. Combine 34 µg of sample with 34 µg control and dry samples in a speed vac with medium heat.

value: stage 7-8


title: stage12-13_rep2

description:
S109729
biological replicate 2 of 4 stage 12-13


title: stage11_rep4

description:
S109874
biological replicate 4 of 4 stage 11

value: stage 11


title: stage11_rep3

description:
S109873
biological replicate 3 of 4 stage 11


title: stage11_rep2

description:
S109872
biological replicate 2 of 4 stage 11


title: Sample 2.5 mg #1


title: stage11_rep1

description:
S109871
biological replicate 1 of 4 stage 11


title: stage9_rep2

description:
S109816
biological replicate 2 of 4 stage 9

value: stage 9


title: stage10_rep3

description:
S109869
biological replicate 3 of 4 stage 10


title: stage12-13_rep4

description:
S109731
biological replicate 4 of 4 stage 12-13


title: stage7-8_rep2

description:
S109812
biological replicate 2 of 4 stage 7-8


title: KK10-specific CD8+ T cells No Pept Pt 553064

first: Gaurav

middle: Das

last: Gaiha

address: 400 Technolology Square

department: Ragon Institute

description:
HIV-specific CD8+ T cells No Pept
2904 - 553064 Hi.AVG_Signal

hyb_protocol: Per Washington University Microarray Core Laboratory Illumina BeadArray Protocol

data_processing: Quantile Normalized  & Background Subtracted

label: Nugen Pico Amplification/Labeling

growth_protocol: RPMI-1640, with 10% FBS

extract_protocol: Ambion RNAqueous micro kit, catalogue number AM1931

treatment_protocol: 10 ng/mL of KK10 peptide

value: KK10-specific CD8+ T cells

tag: treatment protocol

value: No Peptide


title: stage9_rep4

description:
S109818
biological replicate 4 of 4 stage 9


title: stage9_rep3

description:
S109817
biological replicate 3 of 4 stage 9


title: stage7-8_rep3

description:
S109813
biological replicate 3 of 4 stage 7-8


title: stage10_rep1

description:
S109867
biological replicate 1 of 4 stage 10


title: stage7-8_rep1

description:
S109811
biological replicate 1 of 4 stage 7-8


title: stage10_rep2

description:
S109868
biological replicate 2 of 4 stage 10


title: stage9_rep1

description:
S109815
biological replicate 1 of 4 stage 9


title: KK10-specific CD8+ T cells No Pept Pt 828656

description:
HIV-specific CD8+ T cells No Pept
2907 - 828656 Hi.AVG_Signal

scan_protocol: Per Washington University Microarray Core Laboratory Illumina BeadArray Protocol


title: KK10-specific CD8+ T cells +Pept Pt 311360

description:
HIV-specific CD8+ T cells +Pept
2912 - 311360 Lo.AVG_Signal

label_protocol: Per Washington University Microarray Core Laboratory Illumina BeadArray Protocol

value: Peptide


title: Bulk CD8 T cells Pt 763012

description:
Bulk CD8+ T cells
2908 - 763012 Bulk.AVG_Signal

value: Bulk CD8 T cells

value: Bulk


title: Bulk CD8 T cells Pt 311360

description:
Bulk CD8+ T cells
2911 - 311360 Bulk.AVG_Signal


title: KK10-specific CD8+ T cells +Pept Pt 828656

description:
HIV-specific CD8+ T cells +Pept
2906 - 828656 Lo.AVG_Signal


title: KK10-specific CD8+ T cells No Pept Pt 311360

description:
HIV-specific CD8+ T cells No Pept
2913 - 311360 Hi.AVG_Signal


title: Bulk CD8 T cells Pt 553064

description:
Bulk CD8+ T cells
2902 - 553064 Bulk.AVG_Signal


title: KK10-specific CD8+ T cells No Pept Pt 763012

description:
HIV-specific CD8+ T cells No Pept
2910 - 763012 Hi.AVG_Signal


title: KK10-specific CD8+ T cells +Pept Pt 763012

description:
HIV-specific CD8+ T cells +Pept
2909 - 763012 Lo.AVG_Signal


title: KK10-specific CD8+ T cells +Pept Pt 553064

description:
HIV-specific CD8+ T cells +Pept
2903 - 553064 Lo.AVG_Signal


title: Bulk CD8 T cells Pt 828656

description:
Bulk CD8+ T cells
2905 - 828656 Bulk.AVG_Signal


title: HUVEC_Control_6 hours _rep4

city: Suita

first: Takashi

last: Nojiri

state: Osaka

address: 5-7-1, Fujishirodai

department: Biochemistry

institute: National Cerebral and Cardiovascular Center Research Institute

description: Gene expression data from untreated HUVEC for 6 hours

hyb_protocol: 1.65ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55ul containing 25x Agilent GE fragmentation buffer and 10x AgilentGE  blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55ul of 2x Agilent GE hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan resolution 5µm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Intensities were extracted with Agilent Feature Extraction software ver.10.7.3.1. Data analyses were conducted with Agilent GeneSpring GX software ver.12.5.

source_name: HUVEC, Control, 6 hours, replicate 4

label_protocol: Cy3 labeled cRNA was prepared from 200 ng RNA using the Agilent Low Input Quick Amp Labeling Kit according to the manufacturer's instructions, followed by Qiagen RNAeasy column purification.  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: HUVEC was purchased from Lonza (Walkersville, MD, USA), then maintained in EGM-2 according to the manufacturer's instructions at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: RNA are extracted from HUVEC using the Qiagen RNeasy Mini Kit.

treatment_protocol: HUVECs are incubated with 0.1μM ANP or vehicle for 0, 1 and 6 hours.

value: Human Umbilical Vein Endothelial Cells (HUVEC)

value: vehicle

tag: time point

value: 6 hours


title: Sample 5 mg #2

value: mid-secretory endometrium

value: 5 mg progesterone


title: HUVEC_Control_1 hour_rep4

description: Gene expression data from untreated HUVEC for 1 hour

source_name: HUVEC, Control, 1 hour, replicate 4

value: 1 hour


title: HUVEC_ANP_6 hours _rep4

description: Gene expression data from HUVEC treated with ANP for 6 hours

source_name: HUVEC, ANP, 6 hours, replicate 4

value: 0.1uM ANP


title: HUVEC_ANP_0 hour _rep4

description: Gene expression data from HUVEC treated with ANP for 0 hour

source_name: HUVEC, ANP, 0 hours, replicate 4

value: 0 hour


title: HUVEC_Control_0 hour_rep4

description: Gene expression data from untreated HUVEC for 0 hour

source_name: HUVEC, Control, 0 hour, replicate 4


title: HUVEC_ANP_6 hours _rep3

source_name: HUVEC, ANP, 6 hours, replicate 3


title: HUVEC_Control_6 hours _rep3

source_name: HUVEC, Control, 6 hours, replicate 3


title: HUVEC_ANP_1 hour_rep4

description: Gene expression data from HUVEC treated with ANP for 1 hour

source_name: HUVEC, ANP, 1 hour, replicate 4


title: HUVEC_Control_1 hour_rep3

source_name: HUVEC, Control, 1 hour, replicate 3


title: HUVEC_ANP_1 hour_rep3

source_name: HUVEC, ANP, 1 hour, replicate 3


title: HUVEC_Control_0 hour_rep3

source_name: HUVEC, Control, 0 hour, replicate 3


title: HUVEC_ANP_0 hour _rep3

source_name: HUVEC, ANP, 0 hour, replicate 3


title: Holoclone_H460/2E1_vs_H460

first: David

middle: J.

last: Waxman

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

description:
Total RNA was prepared from each set of tumors, either parental H460-derived or H460 holoclone (tumor stem-like cell)-derived, as indicated.
Dye-swap design (POOL A, POOL B)
POOL A:
H460 parental (Alexa 555)_vs_H460 Holoclone 2E1 (Alexa 647)
Raw file = 02172012_252665214386_S01_GE2_107_Sep09_1_1.txt
POOL B:
H460 Holoclone 2E1 (Alexa 555)_vs_H460 parental (Alexa 647)
Raw file = 02172012_252665214387_S01_GE2_107_Sep09_1_1.txt

hyb_protocol: Hybridization was performed using 0.825 µg of Alexa 555-labeled aRNA and 0.825 µg of Alexa 647-labeled aRNA. Agilent’s SureHyb hybridization chambers were used in a hybridization oven and rotation rack for 17 hr at 65° C at 10 rpm. After hybridization, the slides were washed per Agilent’s SSPE wash protocol.

scan_protocol: Slides were scanned using an Agilent dual laser scanner using the extended dynamic range option, which utilizes two 5 um scans of each slide at settings of PMT 100% and PMT 10% to increase signal dynamic range and avoid feature saturation. TIFF images were analyzed using Agilent’s feature extraction software.

data_processing: Linear and LOWESS normalization and analysis using Rosetta Resolver pipeline (version 5.1). Rosetta Resolver combines the pair of dye swap arrays into a single dataset.

label: Alexa 555, Alexa 647

source_name: H460 parental (pool A)

label_protocol: RNA samples were amplified as antisense-RNA (aRNA) while incorporating aminoallyl modified bases using the TargetAMP 1-Round Aminoallyl-aRNA Amplification Kit 101 per the vendor’s protocol (Epicentre, Madison, WI).  Five µg of each aminoallyl-aRNA sample was fluorescent labeled using Alexa 555 or Alexa 647 by incubating with an amine-reactive dye conjugate for 1 hr at room temperature.  Unincorporated dye was removed using an RNeasy column (Qiagen, Valencia, CA).  Dye incorporation efficiency was determined using a Nanodrop spectrophotometer.

extract_protocol: Trizol extraction of total RNA. Total RNA was prepared from individual tumors, and then pooled (n=3-5 independent tmor RNA samples for pool A, and the same for pool B, with each tumor RNA pool corresponding to a biological replicate). RNA pools were prepared by combining equal amounts of RNA from each tumor included in the pool to minimize the effects of inter-tumor variability

tag: tumor line

value: H460 parental tumor

tag: colony morphology

value: Mixed

source_name: H460 Holoclone 2E1 (pool A)

tag: cell line

value: H460/2E1 tumor

value: Holoclone


title: Holoclone_H460/3F1_vs_H460

description:
Total RNA was prepared from each set of tumors, either parental H460-derived or H460 holoclone (tumor stem-like cell)-derived, as indicated.
Dye-swap design (POOL A, POOL B)
POOL A:
H460 parental (Alexa 555)_vs_H460 Holoclone 3F1 (Alexa 647)
Raw file = 02172012_252665214386_S01_GE2_107_Sep09_1_3.txt
POOL B:
H460 Holoclone 3F1 (Alexa 555)_vs_H460 parental (Alexa 647)
Raw file = 02172012_252665214387_S01_GE2_107_Sep09_1_3.txt

source_name: H460 Holoclone 3F1 (pool A)

value: H460/3F1 tumor


title: HUVEC_Control_6 hours _rep2

source_name: HUVEC, Control, 6 hours, replicate 2

tag: cell type


title: Holoclone_H460/2H3_vs_H460

description:
Total RNA was prepared from each set of tumors, either parental H460-derived or H460 holoclone (tumor stem-like cell)-derived, as indicated.
Dye-swap design (POOL A, POOL B)
POOL A:
H460 parental (Alexa 555)_vs_H460 Holoclone 2H3 (Alexa 647)
Raw file = 02172012_252665214386_S01_GE2_107_Sep09_1_2.txt
POOL B:
H460 Holoclone 2H3 (Alexa 555)_vs_H460 parental (Alexa 647)
Raw file = 02172012_252665214387_S01_GE2_107_Sep09_1_2.txt

source_name: H460 Holoclone 2H3 (pool A)

value: H460/2H3 tumor


title: Holoclone_H460/2E7_vs_H460

description:
Total RNA was prepared from each set of tumors, either parental H460-derived or H460 holoclone (tumor stem-like cell)-derived, as indicated.
Dye-swap design (POOL A, POOL B)
POOL A:
H460 parental (Alexa 555)_vs_H460 Holoclone 2E7 (Alexa 647)
Raw file = 02172012_252665214386_S01_GE2_107_Sep09_1_4.txt
POOL B:
H460 Holoclone 2E7 (Alexa 555)_vs_H460 parental (Alexa 647)
Raw file = 02172012_252665214387_S01_GE2_107_Sep09_1_4.txt

source_name: H460 Holoclone 2E7 (pool A)

value: H460/2E7 tumor


title: HUVEC_ANP_6 hours _rep2

source_name: HUVEC, ANP, 6 hours, replicate 2


title: Chuvash polycythemia Cohort, VHL wildtype_CP68

city: Chicago

first: Xu

last: Zhang

state: Illinois

address: 820 South Wood St

institute: University of Illinois at Chicago

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix GeneChip Expression Wash, Stain and Scan protocol

data_processing:
Raw probe intensity was log2 transformed, background corrected, quantile normalized, subtracted by probe mean across samples, and summarized as mean probe intensity of transcript cluster. Signals were read by affxparser, other processing/normalization procedures were carried out custom R codes.
HuEx-1_0-st-v2.r2.pgf, HuEx-1_0-st-v2.r2.clf, HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

label_protocol: Affymetrix GeneChip Whole Transcript Sense Target Labeling Assay

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

value: Peripheral blood mononuclear cells

tag: gender

value: male


title: HUVEC_Control_1 hour_rep2

source_name: HUVEC, Control, 1 hour, replicate 2

value: Human Umbilical Vein Endothelial Cells (HUVEC)


title: Chuvash polycythemia Cohort, VHL wildtype_CP66


title: Chuvash polycythemia Cohort, VHL wildtype_CP65


title: Chuvash polycythemia Cohort, VHL wildtype_CP64

value: female


title: Chuvash polycythemia Cohort, VHL wildtype_CP67_2


title: HUVEC_ANP_1 hour_rep2

source_name: HUVEC, ANP, 1 hour, replicate 2


title: SoxNPA179 Late vs βgal rep2

description:
Sample 14
Biological replicate 2 of 3, SoxNPA179 Late

hyb_protocol: Resuspend samples in 12.3 µl water.  For each hybridisation, combine 29.5µl 2X Hybridization Buffer, 11.8µl Hybridization Component A and 1.2µl Alignment Oligo (NimbleGen Hybridization Kit) and add 31.7µl to each hybridisation sample. Incubate samples at 95°C for 5 minutes, 42°C for 5 minutes and load 41 µl onto the array. The hybridisation is performed to NimbleGen D. melanogaster ChIP-chip 2.1M Whole-Genome Tiling Arrays in the Nimbelegen hybridisation station at 42°C (mix mode B) for 16 hours. Perform post hybridisation washes according to the NimbleGen Wash Buffer Kit instructions.

scan_protocol: Arrays are scanned at 5 µm resolution with a GenePix 4000B (Axon) dual laser scanner at 100% Power, with Lines to average = 1 and Focus position = 0 at their respective optimal PMT gains. Signal for Cy3 and Cy5 channels are balanced using the histogram view in the GenePix software. Images are saved as Single-image TIFF.

data_processing:
Images are processed with NimbleScan software (v.2.6, Roche-Nimblegen) as per manufacturer instructions. Raw data files (*.pair) are created for each channel. Perform Nimblescan loess spatial correction and quantile normalise the raw data.
Supplemetary processed data *quant-all.sgr file description: the first field is the chromosome ("chr"), the second field is the starting nucleotide position of the oligo on the array ("nt"), and the third is a score representing the log2 ratio of sample intensity over control intensity for that oligo, aka M-value ("score"). "quant-all" refers to the fact that scores/M-values/log2 ratios have been quantile normalised.

source_name: SoxNPA179 Late

label_protocol: In PCR tubes take 1 µg double stranded DNA, add 40 diluted Cy3 or Cy5-Random Nonamers (Nimblegen Dual Colour Kit) and make up to a volume of 80 µl with Nuclease-free Water (Nimblegen Dual Colour Kit). Heat-denature samples in a thermocycler at 98°C for 10 minutes. Quickchill on ice for 10 minutes. Add 10 µl 10mM dNTP Mix (Nimblegen Dual Colour Kit), 8 Nuclease-free Water (Nimblegen Dual Colour Kit) and 2 µl 50U/μl Klenow Fragment (3’->5’ exo-) (Nimblegen Dual Colour Kit), mix gently by pipetting. Incubate at 37°C for 3 hours in thermocycler. Stop the reaction by adding 21.5 µl Stop Solution (Nimblegen Dual Colour Kit). Transfer samples to 1.5 ml tubes and add 110 µl Isopropanol, mix and incubate for 10 minutes at room temperature in the dark. Centrifuge at 13,000rpm for 10 minutes and discard supernatant. Add 500 µl ice-cold 80% ethanol and centrifuge at 13,000rpm for 2 minutes. Discard supernatant and dry pellet for 5 minutes in the dark. Resuspend labeled DNA in 50 µl Nuclease-free Water (Nimblegen) and measure the concentration on the Nanodrop. Combine 34 µg of sample with 34 µg control and dry samples in a speed vac with medium heat.

extract_protocol: Crosslink dechorionated embryos with formaldehyde, isolate and lyse nuclei to extract protein-DNA complexes. Incubate chromatin overnight poth protein A agarose beads / salmon sperm DNA and anti-βgal or anti-SoxN antibodies. After extensive washes, reverse crosslinking by incubating at 65°C for 6 hours and purify DNA trough phenol-chloroform extraction. Amplify DNA with two rounds of ligation-mediated PCR. See Sandmann et al., 2007 for a detailed protocol.

value: Oregon R

tag: tissue

value: whole embryos

value: stage 11-13

source_name: βgal


title: Chuvash polycythemia Cohort, VHL wildtype_CP63


title: Chuvash polycythemia Cohort, VHL wildtype_CP62


title: SoxNPA179 Early vs βgal rep3

description:
Sample 12
Biological replicate 3 of 3, SoxNPA179 Early

value: stage 7-10

source_name: SoxNPA179 Early


title: HUVEC_Control_0 hour_rep2

source_name: HUVEC, Control, 0 hour, replicate 2

value: vehicle


title: SoxNPA179 Late vs βgal rep1

description:
Sample 13
Biological replicate 1 of 3, SoxNPA179 Late


title: Chuvash polycythemia Cohort, VHL wildtype_CP61


title: SoxNPA179 Early vs βgal rep2

description:
Sample 11
Biological replicate 2 of 3, SoxNPA179 Early


title: SoxND2 vs βgal rep2

description:
Sample 8
Biological replicate 2 of 3, SoxND2

value: stage 8-11


title: HUVEC_ANP_0 hour _rep2

source_name: HUVEC, ANP, 0 hour, replicate 2

value: 0.1uM ANP

value: 0 hour


title: HUVEC_Control_6 hours _rep1

source_name: HUVEC, Control, 6 hours, replicate 1

value: 6 hours


title: Chuvash polycythemia Cohort, VHL wildtype_CP59


title: SoxND1 vs βgal rep2

description:
Sample 5
Biological replicate 2 of 3, SoxND1


title: Chuvash polycythemia Cohort, VHL wildtype_CP58


title: Chuvash polycythemia Cohort, VHL wildtype_CP56


title: SoxND1 vs βgal rep1

description:
Sample 4
Biological replicate 1 of 3, SoxND1