title: Adult male, whole-body 67, rep 2

description: Sample 142

source_name: adult male, whole-body

value: line

value: whole-body


title: Adult female, ovaries, rep 1

status: Public on Nov 05 2013

type: RNA

city: St Lucia

first: Stephen

last: Chenoweth

state: QLD

address: The School of Biological Sciences, The University of Queensland

department: Biological Sciences

country: Australia

institute: The University of Queensland, Australia

description: Sample 151

hyb_protocol: Hybridization was performed by The Centre for Genomics and Bioinformatics, Bloomington, IN USA, following the standard NimbleGen operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by The Centre for Genomics and Bioinformatics, Bloomington, IN USA, following the standard NimbleGen operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was normalised via a log (base 2) transformation. Summarisation was performed by first taking the mean of replicated probes followed by the median of a probe set.

molecule: total RNA

organism: Drosophila serrata

source_name: adult female, ovaries

label_protocol: Labeling was performed by The Centre for Genomics and Bioinformatics, Bloomington, IN USA, following the standard NimbleGen operating protocol. See www.nimblegen.com.

growth_protocol: A panel of 43 wild-derived inbred lines of D. serrata were used for the whole-body samples and a laboratory stock was used to obtain samples. All flies were reared in 10ml vials of a standard yeast medium and maintained at 25°C with a 12 hour day/night cycle. One generation before the collection of flies for RNA extraction, we used a density controlling procedure to minimise possible effects of developmental environment on gene expression. Each line was propagated with a uniform number of parents (5 virgin females with 3 virgin males) that were allowed to mate and lay eggs for 24 hours. Offspring were randomly collected as virgins from three replicate developmental vials per whole-body sample line and 50 replicate developmental vials for the tissue sample laboratory stock and aged for three days in same-sex groups of 5 flies. Two replicate pools of 30 flies per line per sex and four replicate pools of 100 flies were collected without the use of CO2 anaesthesia and snap frozen in liquid nitrogen for the whole-body and tissue samples, respectively.

extract_protocol: Each whole-body pool was homogenised in Trizol® and immediately stored at -80 degrees Celcius. During tissue disection, flies were suspended in RNALater® to inhibit RNA degradation, pools of 100 tissue disects were stored at -80 degrees Celsius. RNA extraction of the whole-body samples was performed by using the Trizol® procedure followed by RNA isolation using RNeasy minikits®. RNA extraction of the tissue samples was identical to that of the whole-body samples except that the Trizol® was added to 10µl of RNA Later®.

tag: line/stock

value: stock

tag: Sex

value: female

tag: tissue

value: ovaries


title: Adult male, thorax, rep 2

description: Sample 146

source_name: adult male, thorax

value: male

value: thorax


title: Adult female, whole-body 37, rep 2

description: Sample 140

source_name: adult female, whole-body


title: Adult female, head, rep 1

description: Sample 145

source_name: adult female, head

value: head


title: Adult female, head, rep 2

description: Sample 150


title: Adherent osteosarcoma cells, biological rep4

city: Edinburgh

first: Lisa

last: Pang

address: Easter Bush Estate

country: United Kingdom

institute: Roslin Institute

description:
ADH_04
Gene expression data from osteosarcoma adherent cells.

hyb_protocol: 5 μg of cRNA was hybridised for 16 hr at 45oC to the Affymetrix GeneChip® Canine Genome 2.0 Array by ARK-Genomics (Edinburgh).

scan_protocol: GeneChips were scanned using the Affymetrix™ GeneTitan (ARK-Genomics (Edinburgh)).

data_processing: GC-RMA data was generated by Partek® Genomics Suite™. The data was analysed with Partek® Genomics Suite™ (ARK-Genomics (Edinburgh)).

label: Biotin

organism: Canis lupus familiaris

source_name: Canine adherent osteosarcoma cells, a primary cell line KTOSA5

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetix IVT express protocol (revision 1 of the manual, 2008) by ARK-Genomics (Edinburgh).

growth_protocol: The KTOSA5 cell line was derived from an osteosarcoma affecting the right hind leg of an 8-year-old, chemotherapy naive, female, entire Rottweiler. The cells were grown in DMEM at 5% CO2 at 37 oC. Canine mesenchymal stem cells (MSC) were derived from the bone marrow of 21 recently euthanised dogs of mixed breeds. All samples were taken with the owners consent and approval of the Local Institutional Animal Care and Ethics Committee. MSCs were grown in DMEM containing Glutamax-I at 5% CO2 at 37 oC.

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

treatment_protocol: Osteosarcoma stem cells were derived from the KTOSA5 cell line by plating as single cells in serum-free conditional medium which contained William's E Medium with GlutaMAX supplemented with putrescine (100 μM), sodium selenite (30 nM), transferring (25 μg/ml), insulin (20 μg/ml), human recombinant bFGF (10 ng/ml) and EGF (10 ng/ml).

tag: breed

value: Rottweiler

tag: cell line

tag: cell type

value: adherent osteosarcoma cells

tag: disease state

value: cancerous


title: Adherent osteosarcoma cells, biological rep2

description:
ADH_02
Gene expression data from osteosarcoma adherent cells.


title: Osteosarcoma stem cells, biological rep3

description:
CSC_03
Gene expression data from osteosarcoma stem cells.

source_name: Canine osteosarcoma stem cells isolated from the primary tumour cell line KTOSA5

value: osteosarcoma stem cells


title: Mesenchymal stem cells, biological rep3

description:
MSC_03
Gene expression data from mesenchymal stem cells.

source_name: Canine mesenchymal stem cells

value: mixed

value: mesenchymal stem cells

value: normal


title: Adult male, whole-body 44, rep 2

description: Sample 138


title: Mesenchymal stem cells, biological rep4

description:
MSC_04
Gene expression data from mesenchymal stem cells.


title: Osteosarcoma stem cells, biological rep1

description:
CSC_01
Gene expression data from osteosarcoma stem cells.


title: Adult male, thorax, rep 1

description: Sample 143


title: Mesenchymal stem cells, biological rep2

description:
MSC_02
Gene expression data from mesenchymal stem cells.


title: Adult male, whole-body 54, rep 2

description: Sample 136


title: BoneMarrow_NormalControl_Untreated expression

city: Little Rock

first: Jason

middle: Eli

last: Farrar

state: AR

address: 1 Children's Way, #512-10

department: Pediatrics/Hematology-Oncology

country: USA

institute: University of Arkansas for Medical Sciences

description: Normal bone marrow

hyb_protocol: cDNA was hybridized to HG-U133A_2 microarrays following standard Affymetrix procedures

scan_protocol: standard Affymetrix protocol

data_processing: Raw expression values were normalized using Robust Multi-array Averaging (RMA)

label: biotin

organism: Homo sapiens

source_name: Unfractionated bone marrow

label_protocol: Linear amplification of 20 ng of total RNA was performed using the Ovation Biotin RNA Amplification and Labeling System (Nugen)

extract_protocol: RNA was purified from bone marrow mononuclear cells using Trizol (Invitrogen)

value: Unfractionated bone marrow

tag: treatment

value: control

tag: relationship to proband


title: Osteosarcoma stem cells, biological rep2

description:
CSC_02
Gene expression data from osteosarcoma stem cells.


title: PeripheralBlood_DBA_Proband_0673_Untreated

type: genomic

description:
Genomic DNA extracted from whole peripheral blood was genotyped using Infinium HumanOmni1_Quad Genotyping BeadChips (Illumina).
Unfractionated DNA is extracted from WBC pelleted from peripheral blood  after RBC lysis in 0.15M NH4Cl.  WBC are lysed overnight at 55 °C in WBC lysis solution (Qiagen), and protein precipitated and spun at 4 °C in protein precipitation solution (Qiagen).  DNA is preciptated in ethanol, pelleted and resuspended in 10mM Tris EDTA.

hyb_protocol: Standard Illumina Infinium HD protocol

scan_protocol: Standard Illumina scanning protocol on S101 or N0345 scanner

data_processing: Intensity data were extracted in Genome Studio (v2011.1); SNPs with GenTrain score <0.15 were not called.

label: C-Bio; A-DNP

molecule: genomic DNA

source_name: Unfractionated peripheral blood

label_protocol: Standard Illumina Infinium HD protocol

tag: gender

value: Female

tag: tissue source

value: Peripheral Blood

tag: tissue separation

value: Unfractionated Peripheral Blood DNA

tag: lenolidamide treatment

value: Untreated

value: Proband


title: Adherent osteosarcoma cells, biological rep1

description:
ADH_01
Gene expression data from osteosarcoma adherent cells.


title: PeripheralBlood_DBA_Father_0673_Untreated

extract_protocol: Unfractionated DNA is extracted from WBC pelleted from peripheral blood  after RBC lysis in 0.15M NH4Cl.  WBC are lysed overnight at 55 °C in WBC lysis solution (Qiagen), and protein precipitated and spun at 4 °C in protein precipitation solution (Qiagen).  DNA is preciptated in ethanol, pelleted and resuspended in 10mM Tris EDTA.

value: Male

value: Unaffected Parent


title: Adult male, whole-body 59, rep 2

description: Sample 139

value: line

value: male

value: whole-body


title: PeripheralBloodLymphoid_DBA_Proband_0673_Untreated

description:
Genomic DNA extracted from peripheral blood cells retained on CD3/CD10 magnetic beads was genotyped using Infinium HumanOmni1_Quad Genotyping BeadChips (Illumina).
Fractionated cell DNA was prepared using Qiagen Blood DNA isolation kit according to the manufacturer's instructions

source_name: Lymphoid-enriched peripheral blood

value: Lymphoid Peripheral Blood DNA


title: PeripheralBlood_DBA_Mother_0673_Untreated


title: PeripheralBloodMyeloid_DBA_Proband_0673_Untreated

description:
Genomic DNA extracted from peripheral blood cells NOT retained on CD3/CD10 magnetic beads was genotyped using Infinium HumanOmni1_Quad Genotyping BeadChips (Illumina).
Fractionated cell DNA was prepared using Qiagen Blood DNA isolation kit according to the manufacturer's instructions

source_name: Myeloid enriched peripheral blood

value: Myeloid Peripheral Blood DNA


title: Adult male, whole-body 61, rep 2

description: Sample 137


title: Adult male, whole-body 61, rep 1

description: Sample 134


title: Mesenchymal stem cells, biological rep1

description:
MSC_01
Gene expression data from mesenchymal stem cells.

value: mixed


title: Adult female, whole-body 41, rep 2

description: Sample 135

value: female


title: Adult female, whole-body 35, rep 2

description: Sample 132


title: BoneMarrow_DBA_Proband_0673_Untreated expression

description: Patient bone marrow sample obtained prior to initiation of lenalidomide therapy

value: baseline

value: 5q- Myelodysplastic Syndrome Masquerading as Diamond Blackfan Anemia

value: proband


title: Adult female, whole-body 11, rep 2

description: Sample 133


title: Adult male, whole-body 47, rep 2

description: Sample 130


title: BoneMarrow_DBA_Proband_0673_Treated expression

description: Patient bone marrow sample obtained during lenalidomide therapy

value: Unfractionated bone marrow

value: lenalidomide therapy


title: control group

city: Haidian District

first: Zhongquan

last: Dai

state: Beijing

address: No. 26 Beiqing Road

country: China

institute: Astronaut Research and training Center

description: Gene expression data from rat soleus muscle

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rattus Norvegicus Genome Array with Hybridization Oven 640: Affymetrix, 800139. GeneChips were washed and stained in the Wash and Stain Kit of Affymetrix, P/N 900720.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner Scanner 3000: Affymetrix, P/N 00-00212.

data_processing: The data were analyzed with GCOS1.4 using Affymetrix default analysis settings and global scaling as normalization method.

organism: Rattus norvegicus

source_name: Soleus muscle at 7 days of control group

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

growth_protocol: All animal procedures were carried out in accordance with the Guidelines for Animal Care and Experimentation of the Astronaut Research and Training Center.Feed rats normally.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.Then, purification with QIAGEN RNeasy Kit.

treatment_protocol: Briefly, the rats were suspended at an approximately 30° angle by taping the tail to mimic unloading condition.

value: control

tag: time

value: soleus muscle

tag: genotype

value: white and Sprague-Dawley rats

tag: age

value: 8 weeks of age


title: BS3-LLL (MA2)

city: Singapore

first: Vivek

last: Tanavde

state: Singapore

address: 30 Biopolis Street, #07-01, Matrix

department: Genome and Gene Expression Data Analysis Division

country: Singapore

institute: Bioinformatics Institute, A*STAR, Singapore

description:
7963862018 F
Microarray 2 (MA2)

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data was normalized (quantile normalization) and background substracted using Genome Studio

source_name: iPSC Clone

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

growth_protocol: ESC and iPSC were cultured on iMEF feeders in KSR-based media or feeder-free in StemPro SFM media on Geltrex-coated dishes

extract_protocol: RNA was extracted with Trizol reagent and treated with DNase I treatment using DNAfree (Ambion, Life Technologies), as per manufacturer's recommendations. RNA was quantified using Nanodrop and Quality control performed on Agilent Bioanalyser.

treatment_protocol: BJ Fibroblasts were reprogrammed using CytoTune Reprogramming Kit as per Manufacturer's recommendations.

value: BJ_Sendai-set3-iPSCclone LLL - StemPro SFM on Geltrex

tag: passage number

tag: cell state

value: Pluripotent


title: HS at 7 days

source_name: Soleus muscle at 7 days of HS

value: hind limb suspension


title: Adult female, whole-body 39, rep 2

description: Sample 131

tag: line/stock

value: line

tag: Sex

value: whole-body


title: Adult female, whole-body 34, rep 2

description: Sample 141

tag: tissue


title: Adult male, whole-body 82, rep 2

description: Sample 129

value: male


title: BS3-C (MA2)

description:
7963862018 D
Microarray 2 (MA2)
replicate 2

tag: cell line

value: BJ_Sendai-set3-iPSCclone C - on iMEF feeders


title: BS3-III (MA2)

description:
7963862018 E
Microarray 2 (MA2)

value: BJ_Sendai-set3-iPSCclone III - StemPro SFM on Geltrex


title: H9 ESC (MA2)

description:
7963862018 B
Microarray 2 (MA2)
replicate 2

source_name: Embryonic Stem Cell

value: H9 ESC on iMEF feeders


title: HS at 14 days


title: Adult female, whole-body 26, rep 2

description: Sample 124

value: female


title: ff H9 ESC (MA2)

description:
7963862018 C
Microarray 2 (MA2)
replicate 2

value: Feeder-free H9 ESC in StemPro SFM on Geltrex


title: Adult male, whole-body 64, rep 2

description: Sample 126


title: Adult female, whole-body 28, rep 2

description: Sample 127


title: BJ (MA2)

description:
7963862018 A
Microarray 2 (MA2)
replicate 2

source_name: Fibroblast

value: Parental human BJ Fibroblasts

value: Non Pluripotent


title: Adult female, whole-body 4, rep 2

description: Sample 123


title: Adult female, whole-body 33, rep 2

description: Sample 125


title: Adult female, whole-body 20, rep 2

description: Sample 128


title: Adult male, whole-body 76, rep 2

description: Sample 120

source_name: adult male, whole-body


title: BS3-III (MA1)

description:
6334175133 K
Microarray 1 (MA1)

value: BJ_Sendai3-iPSCclone III - StemPro SFM on Geltrex


title: BS3-LLL (MA1)

description:
6334175133 L
Microarray 1 (MA1)

value: BJ_Sendai3-iPSCclone LLL - StemPro SFM on Geltrex


title: Adult male, whole-body 79, rep 2

description: Sample 121


title: Adult male, whole-body 43, rep 2

description: Sample 122


title: ff H9 (MA1)

description:
6334175133 C
Microarray 1 (MA1)
replicate 1


title: BS1-L (MA1)

description:
6334175133 G
Microarray 1 (MA1)

value: BJ_Sendai1-iPSCclone L - on iMEF feeders


title: Adult female, whole-body 40, rep 2

description: Sample 116


title: Adult female, whole-body 42, rep 2

description: Sample 119


title: Adult female, whole-body 13, rep 2

description: Sample 118


title: BS1-D (MA1)

description:
6334175133 E
Microarray 1 (MA1)

value: BJ_Sendai1-iPSCclone D - on iMEF feeders


title: BS3-C (MA1)

description:
6334175133 H
Microarray 1 (MA1)
replicate 1

value: BJ_Sendai3-iPSCclone C - on iMEF feeders


title: WA09_HESC_SHP63_Diff_Diff_d6___87.2348.1.1

city: La Jolla

first: Mana

last: Parast

state: California

address: 9500 Gilman drive #0695

department: Pathology

institute: University of California San Diego

description: SAMPLE 124

data_processing: The data were filtered for detection pValue > 0.01 and normalised using Robust Spline Normalisation with lumi in R

growth_protocol: Most hESC and hiPSC were grown in feeder-free conditions according to the WiCell protocol in mTESR (Stem Cell Technologies). Samples marked with * were grown in StemPro (Invitrogen) with 12ng/mL bFGF.

extract_protocol: Total RNA was purified using the MirVana RNA extraction kit (Ambion) excluding sample 55 (**) where TRIzol (Life Technologies) was used. Total RNA was quantified using the Ribogreen reagent (Lifetech, Inc.), and quality-controlled on a Bioanalyzer (Agilent). Two hundred nanograms of input total RNA was amplified and labeled using the TotalPrep kit (Ambion). The labeled product was then hybridized to Illumina HT12 arrays and scanned on a BeadArray Reader (Illumina, Inc.) according to the manufacturer’s instructions.

treatment_protocol: For trophoblast differentiation WA09_HESC cells were treated with 10ng/mL of BMP4 (R&D Systems) in feeder-conditioned media containing 20% Knock-out Serum Replacement, 1mM L-Glutamine, 1% non-essential aminoacids and 0.1mM 2-mercaptoethanol in Knock-out DMEM. Before differentiation these cells were previously maintained in StemPro media (Invitrogen) with 12ng/mL bFGF.

tag: origin

value: SHP63 d6

tag: cell type

value: pluripotent stem cell

tag: pipeline sample id


title: BS1-F (MA1)

description:
6334175133 F
Microarray 1 (MA1)

value: BJ_Sendai1-iPSCclone F - on iMEF feeders

value: Pluripotent


title: WA09_HESC_SHP63_Diff_Undiff_d0___87.2345.1.1

description: SAMPLE 126

value: SHP63 d0

tag: treatment


title: Adult male, whole-body 48, rep 1

description: Sample 117

value: line

value: male

value: whole-body


title: Adult female, whole-body 7, rep 2

description: Sample 115

value: female


title: Adult male, whole-body 67, rep 1

description: Sample 112


title: WA09_HESC_SCRAM_Diff_Undiff_d0___87.2340.1.1

description: SAMPLE 121

value: SCRAMBLE d0


title: WA09_HESC_SHP63_Diff_Diff_d4___87.2347.1.1

description: SAMPLE 123

value: SHP63 d4


title: Adult male, whole-body 83, rep 2

description: Sample 113


title: WA09_HESC_SHP63_Diff_Diff_d8___87.2349.1.1

description: SAMPLE 125

value: SHP63 d8


title: BJ (MA1)

description:
6334175133 A
Microarray 1 (MA1)
replicate 1

value: Parental human BJ Fibroblasts

value: Non Pluripotent


title: Ep iPSC (MA1)

description:
6334175133 D
Microarray 1 (MA1)

source_name: Induced Pluripotent Stem Cell (iPSC)

value: Gibco® Episomal iPSC on iMEF feeders


title: WA09_HESC _Undiff_d0___87.2134.2.1

description: SAMPLE 115

value: FCM-BMP4 d0


title: WA09_HESC_SCRAM_Diff_Diff_d6___87.2343.1.1

description: SAMPLE 119

value: SCRAMBLE d6


title: Adult male, whole-body 73, rep 2

description: Sample 111


title: WA09_HESC _Undiff_d0___87.2134.3.1

description: SAMPLE 116


title: WA09_HESC_SCRAM_Diff_Diff_d8___87.2344.1.1

description: SAMPLE 120

value: SCRAMBLE d8


title: H9 ESC (MA1)

description:
6334175133 B
Microarray 1 (MA1)
replicate 1

value: H9 ESC on iMEF feeders


title: WA09_HESC_SHP63_Diff_Diff_d2___87.2346.1.1

description: SAMPLE 122

value: SHP63 d2

value: pluripotent stem cell


title: WA09_HESC_SCRAM_Diff_Diff_d4___87.2342.1.1

description: SAMPLE 118

value: SCRAMBLE d4


title: Adult female, whole-body 12, rep 2

description: Sample 110

value: line


title: WA09_HESC _Diff_d4 _NormO2_-bFGF__87.1945.3.1

description: SAMPLE 110

value: FCM-BMP4 d4


title: WA09_HESC _Diff_d6 _NormO2_-bFGF__87.2127.1.1

description: SAMPLE 111

value: FCM-BMP4 d6


title: WA09_HESC_SCRAM_Diff_Diff_d2___87.2341.1.1

description: SAMPLE 117

value: SCRAMBLE d2


title: WA09_HESC _Diff_d6 _NormO2_-bFGF__87.2127.2.1

description: SAMPLE 112


title: WA09_HESC _Diff_d6 _NormO2_-bFGF__87.2127.3.1

description: SAMPLE 113


title: Adult female, whole-body 14, rep 2

description: Sample 114

value: female

value: whole-body


title: Adult female, whole-body 36, rep 2

description: Sample 108


title: Adult male, whole-body 47, rep 1

description: Sample 109

value: male


title: Adult male, whole-body 63, rep 2

description: Sample 107


title: Adult female, whole-body 35, rep 1

description: Sample 105


title: WA09_HESC _Undiff_d0___87.2134.1.1

description: SAMPLE 114


title: WA09_HESC _Diff_d4 _NormO2_-bFGF__87.1945.1.1

description: SAMPLE 108


title: WA09_HESC _Diff_d4 _NormO2_-bFGF__87.1945.2.1

description: SAMPLE 109


title: Adult female, whole-body 6, rep 1

description: Sample 106


title: WA09_HESC ____87.521.5.8

description: SAMPLE 101

value: PSC


title: WA09_HESC ____87.521.5.11

description: SAMPLE 98


title: Adult male, whole-body 56, rep 2

description: Sample 101


title: WA09_HESC _Diff_d2 _NormO2_-bFGF__87.1929.1.1

description: SAMPLE 105

value: FCM-BMP4 d2


title: WA09_HESC ____87.521.5.9

description: SAMPLE 102


title: WA09_HESC _Diff_d2 _NormO2_-bFGF__87.1929.3.1

description: SAMPLE 107


title: Adult female, whole-body 33, rep 1

description: Sample 100


title: WA09_HESC ____87.663.2.3

description: SAMPLE 104


title: Adult male, whole-body 81, rep 2

description: Sample 102


title: Ovary-Tumor7

city: Atlanta

first: Christopher

middle: G

last: Hill

state: GA

address: 315 Ferst Dr

department: Biology

institute: Georgia Institute of Technology

description:
CEPI551
Gene expression from ovarian adenocarcinoma

hyb_protocol: as per manufacturer's protocol

scan_protocol: as per manufacturer's protocol

data_processing: GCRMA at arrayanalysis.org for signals and FDR using SAM ( http://www-stat.stanford.edu/~tibs/SAM/ ) and MAS5 from Affymetrix Expression Console for present/absent calls. Probe_sets lacking a gene symbol annotation and x_at probes are ignored.

source_name: ovarian-primary-tumor

label_protocol: Affymetrix IVT Labeling Kit

extract_protocol: RNA was isolated with Trizol (Invitrogen) and purified with PicoPure RNA Isolation Kit (Arcturus). RNA quality was verified on the Bioanalyzer RNA Pico Chip (Agilent Technologies).

treatment_protocol: Normal ovarian surface epithelial (OSE) cells were collected from ovaries at time of surgery using a Cytobrush ® Plus (Medscand) and immediately stabilized in RNAlater (Ambion) and stored at –20 degrees C.

value: ovarian-primary-tumor

tag: Stage

value: IIIc/IV


title: Adult female, whole-body 20, rep 1

description: Sample 103

source_name: adult female, whole-body


title: WA09_HESC ____87.521.5.10

description: SAMPLE 97


title: WA09_HESC ____87.521.5.7

description: SAMPLE 100


title: Adult female, whole-body 16, rep 1

description: Sample 104


title: WA09_HESC ____87.1139.3.2

description: SAMPLE 94*


title: Ovary-Tumor9

description:
CEPI606
Gene expression from ovarian adenocarcinoma

value: IIIa


title: WA09_HESC ____87.1653.1.1

description: SAMPLE 95


title: Ovary-Tumor10

description:
CEPI620
Gene expression from ovarian adenocarcinoma

value: III/IV


title: WA09_HESC ____87.521.6.2

description: SAMPLE 103


title: WA09_HESC ____87.521.5.6

description: SAMPLE 99


title: Adult male, whole-body 80, rep 2

description: Sample 99


title: Ovary-Tumor8

description:
CEPI588
Gene expression from ovarian adenocarcinoma

value: IIIc


title: WA09_HESC _Diff_d2 _NormO2_-bFGF__87.1929.2.1

description: SAMPLE 106


title: WA09_HESC ____87.521.4.2

description: SAMPLE 96


title: WA09_HESC ____87.1138.3.2

description: SAMPLE 93*


title: Adult female, whole-body 34, rep 1

description: Sample 97


title: WA07_HESC____47.1300.1.1

description: SAMPLE 92


title: Ovary-Tumor5

description:
CEPI537
Gene expression from ovarian adenocarcinoma


title: UC06_HESC____39.4.1.1

description: SAMPLE 91


title: Ovary-Tumor3

description:
CEPI369
Gene expression from ovarian adenocarcinoma


title: Stroma__Wk7.1_Tr1_P721_778.2436.1.2

description: SAMPLE 90

value: P-Stroma

value: stroma


title: Stroma__Wk6.4_Tr1_P722_778.2437.1.2

description: SAMPLE 88


title: Adult male, whole-body 68, rep 2

description: Sample 98


title: Ovary-Tumor4

description:
CEPI528
Gene expression from ovarian adenocarcinoma


title: Stroma__Wk6.4_Tr1_P722_778.2437.1.1

description: SAMPLE 87


title: Ovary-Tumor2

description:
CEPI336
Gene expression from ovarian adenocarcinoma

value: Ic


title: SIVF043_HESC____284.754.1.1

description: SAMPLE 86

value: pluripotent stem cell


title: Adult male, whole-body 52, rep 2

description: Sample 95

value: line


title: Ovary-Tumor6

description:
CEPI542
Gene expression from ovarian adenocarcinoma

value: IV


title: Adult male, whole-body 78, rep 2

description: Sample 96


title: Adult female, whole-body 2, rep 2

description: Sample 94


title: SIVF029_HESC____277.747.1.1

description: SAMPLE 85


title: SIVF025_HESC____296.775.1.3

description: SAMPLE 83


title: SIVF027_HESC____297.777.1.2

description: SAMPLE 84


title: Stroma__Wk7.1_Tr1_P721_778.2436.1.1

description: SAMPLE 89


title: Ovary-Tumor1

description:
CEPI183
Gene expression from ovarian adenocarcinoma

value: III


title: Adult female, whole-body 5, rep 2

description: Sample 93

value: female


title: SIVF015_HESC____274.744.1.1

description: SAMPLE 80


title: SIVF022_HESC____121.768.1.1

description: SAMPLE 82


title: Ovary-Normal10

description:
OSE567
Gene expression from normal ovarian surface epithelia

source_name: ovarian-epithelial-cells-normal

value: ovarian-epithelial-cells-normal

value: wnl


title: Ovary-Normal9

description:
OSE563
Gene expression from normal ovarian surface epithelia


title: Adult male, whole-body 74, rep 2

description: Sample 90

value: male

value: whole-body


title: Ovary-Normal8

description:
OSE552
Gene expression from normal ovarian surface epithelia


title: PLACENTA_Wk4_Tr1___108.1592.1.1

description: SAMPLE 78

value: Placenta

value: placenta


title: Adult female, whole-body 21, rep 2

description: Sample 92


title: Adult male, whole-body 79, rep 1

description: Sample 91


title: Ovary-Normal6

description:
OSE475
Gene expression from normal ovarian surface epithelia


title: Ovary-Normal7

description:
OSE541
Gene expression from normal ovarian surface epithelia


title: SIVF002_HESC____290.763.1.1

description: SAMPLE 79

value: PSC


title: MEL1_HESC____35.125.2.1

description: SAMPLE 75


title: SIVF019_HESC____118.761.1.1

description: SAMPLE 81


title: Ovary-Normal3

description:
OSE440
Gene expression from normal ovarian surface epithelia


title: Adult female, whole-body 2, rep 1

description: Sample 86


title: HDF51IPS9_HIPSC____160.473.1.2

description: SAMPLE 72


title: HES3_HESC____33.112.2.1

description: SAMPLE 74


title: PLACENTA_Wk4_Tr1___108.1589.1.1

description: SAMPLE 76


title: Adult male, whole-body 57, rep 2

description: Sample 89


title: HDF51IPS9_HIPSC____160.649.1.1

description: SAMPLE 73


title: PLACENTA_Wk4_Tr1___108.1590.1.1

description: SAMPLE 77


title: Adult male, whole-body 75, rep 1

description: Sample 85


title: HDF51IPS7_HIPSC____158.648.1.2

description: SAMPLE 71


title: Adult female, whole-body 12, rep 1

description: Sample 87


title: Ovary-Normal5

description:
OSE470
Gene expression from normal ovarian surface epithelia


title: Adult male, whole-body 59, rep 1

description: Sample 84


title: Adult male, whole-body 62, rep 2

description: Sample 83


title: HDF51IPS2_HIPSC____154.644.1.1

description: SAMPLE 65


title: HDF51IPS5_HIPSC____156.646.1.2

description: SAMPLE 69


title: Ovary-Normal4

description:
OSE452
Gene expression from normal ovarian surface epithelia


title: HDF51IPS5_HIPSC____156.440.1.2

description: SAMPLE 68


title: HDF51IPS14_HIPSC____165.472.1.2

description: SAMPLE 62


title: Ovary-Normal2

description:
OSE437
Gene expression from normal ovarian surface epithelia


title: HDF51IPS7_HIPSC____158.442.1.2

description: SAMPLE 70


title: Adult female, whole-body 39, rep 1

description: Sample 82


title: HDF51IPS3_HIPSC____155.645.1.1

description: SAMPLE 67


title: Ovary-Normal1

description:
OSE434
Gene expression from normal ovarian surface epithelia


title: HDF51IPS2_HIPSC____154.438.1.1

description: SAMPLE 63


title: HDF51IPS14_HIPSC____165.1029.1.1

description: SAMPLE 61


title: 10A.Parental

city: Houston

first: Jia

last: Xu

state: TX

address: 1515 Holcombe Blvd.

department: Molecular & Cellular Oncology

institute: UT-M.D. Anderson Cancer Center

description: Gene expression data from 10A.Parental cells

hyb_protocol: Following fragmentation, 10 ug of cDNA were hybridized for 16 hr at 45C on Affymatrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

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

source_name: MCF-10A cells without any modification

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

growth_protocol: cells were cultured and metained in MCF-10A special 3D culture medium

value: mammary epithelial


title: HDF51IPS2_HIPSC____154.489.1.1

description: SAMPLE 64


title: 10A.ζ

description: Gene expression data from 10A.ζ cells normalized to 10A.Parental cells

source_name: MCF-10A cells stably expressed 14-3-3ζ


title: Adult female, whole-body 8, rep 2

description: Sample 81


title: 10A.Vec

description: Gene expression data from 10A.Vec cells normalized to 10A.Parental cells

source_name: MCF-10A cells stably expressed vector control


title: HDF51IPS12_HIPSC____163.651.1.1

description: SAMPLE 58


title: HDF51IPS12_HIPSC____163.447.1.2

description: SAMPLE 57


title: HDF51IPS13_HIPSC____164.652.1.3

description: SAMPLE 60


title: HDF51IPS13_HIPSC____164.471.1.1

description: SAMPLE 59


title: Adult female, whole-body 30, rep 2

description: Sample 80


title: Adult female, whole-body 31, rep 2

description: Sample 79


title: HDF51IPS10_HIPSC____161.900.1.3

description: SAMPLE 54


title: T04_3ML29_s25

city: Baltimore

first: Maria

last: Salvato

state: MD

address: 725 W Lombard Street

department: Institute of Human Virology

institute: University of Maryland School of Medicine

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on Human Genome U133 Plus 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scanning was carried out by using the GeneArray scanner (Hewlett-Packard).

data_processing: The data were analyzed using the R Bioconductor package using the gcRma algorithm. Probeset which marked as absent in all of samples were removed.

source_name: Mop/Las virus_4 hours_Donor 3

label_protocol: Staining with R-phycoerythrin-streptavidin (Molecular Probes) was followed by antibody amplification with a biotinylated streptavidin antibody (Vector Laboratories).

extract_protocol: PBMC were isolated from blood using density centrifugation. RNA was extracted using Trizol (Gibco-BRL) followed by a Qiagen Rneasy kit to clean the RNA.

value: peripheral blood mononuclear cells (PBMC)


title: HDF51IPS3_HIPSC____155.439.1.2

description: SAMPLE 66


title: HDF51IPS11_HIPSC____162.650.1.2

description: SAMPLE 56


title: HDF51IPS1_HIPSC____153.894.1.1

description: SAMPLE 52


title: Adult male, whole-body 55, rep 2

description: Sample 77


title: HDF51IPS11_HIPSC____162.475.1.1

description: SAMPLE 55


title: HDF51IPS1_HIPSC____153.2149.1.1

description: SAMPLE 49*


title: T08_3ML29_s26

source_name: Mop/Las virus_8 hours_Donor 3


title: T24_3ML29_s27

source_name: Mop/Las virus_24 hours_Donor 3


title: HDF51IPS1_HIPSC____153.437.2.1

description: SAMPLE 51


title: Adult male, whole-body 66, rep 2

description: Sample 78


title: HDF51IPS10_HIPSC____161.445.1.2

description: SAMPLE 53


title: Adult male, whole-body 52, rep 1

description: Sample 74


title: T04_3LASV_s22

source_name: Lassa Virus_4 hours_Donor 3


title: FETAL_THYMUS____551.1440.1.2

description: SAMPLE 47

value: F-Thymus

value: fetal Thymus


title: FETAL_STOMACH____101.414.1.2

description: SAMPLE 46

value: F-Stomach

value: fetal Stomach


title: Adult female, whole-body 24, rep 2

description: Sample 75

value: line


title: T24_3Uninf_s21

source_name: Uninfected_24 hours_Donor 3


title: T08_3LASV_s23

source_name: Lassa Virus_8 hours_Donor 3


title: FETAL_THYMUS____551.1442.1.2

description: SAMPLE 48


title: HDF51IPS1_HIPSC____153.2149.2.1

description: SAMPLE 50*

value: pluripotent stem cell


title: FETAL_STOMACH____101.407.1.1

description: SAMPLE 44


title: FETAL_SPLEEN____91.1441.1.2

description: SAMPLE 43

value: F-Spleen

value: fetal Spleen


title: T08_3Uninf_s20

source_name: Uninfected_8 hours_Donor 3


title: T24_3LASV_s24

source_name: Lassa Virus_24 hours_Donor 3


title: Adult male, whole-body 54, rep 1

description: Sample 73


title: T04_3Uninf_s19

source_name: Uninfected_4 hours_Donor 3


title: FETAL_STOMACH____101.412.1.2

description: SAMPLE 45


title: Adult female, whole-body 5, rep 1

description: Sample 88

value: female


title: Adult female, whole-body 11, rep 1

description: Sample 70


title: T04_2ML29_s16

source_name: Mop/Las virus_4 hours_Donor 2


title: T08_2ML29_s17

source_name: Mop/Las virus_8 hours_Donor 2


title: FETAL_SKIN____103.1855.1.4

description: SAMPLE 37

value: F-Skin

value: fetal Skin


title: Adult male, whole-body 57, rep 1

description: Sample 71

source_name: adult male, whole-body

value: male

value: whole-body


title: FETAL_SMALLINTESTINE____146.1836.1.3

description: SAMPLE 40

value: F-Small Int

value: fetal Small Int


title: Adult female, whole-body 17, rep 1

description: Sample 68

source_name: adult female, whole-body


title: T24_2ML29_s18

source_name: Mop/Las virus_24 hours_Donor 2


title: Adult male, whole-body 82, rep 1

description: Sample 72


title: FETAL_SMALLINTESTINE____146.412.1.2

description: SAMPLE 41


title: FETAL_SMALLINTESTINE____146.1442.1.2

description: SAMPLE 39


title: Adult male, whole-body 64, rep 1

description: Sample 69


title: T08_2LASV_s14

source_name: Lassa Virus_8 hours_Donor 2


title: FETAL_LUNG____94.1440.1.2

description: SAMPLE 31

value: F-Lung

value: fetal Lung


title: FETAL_LUNG____94.1441.1.2

description: SAMPLE 32


title: FETAL_PANCREAS____220.1841.1.1

description: SAMPLE 34

value: F-Pancreas

value: fetal Pancreas


title: FETAL_SKIN____103.1846.1.3

description: SAMPLE 36


title: FETAL_SKIN____103.1860.1.2

description: SAMPLE 38


title: FETAL_LUNG____94.1442.1.2

description: SAMPLE 33


title: T04_2LASV_s13

source_name: Lassa Virus_4 hours_Donor 2

value: peripheral blood mononuclear cells (PBMC)


title: FETAL_LIVER____147.1441.1.2

description: SAMPLE 29

value: F-Liver

value: fetal Liver


title: FETAL_LIVER____147.1442.1.2

description: SAMPLE 30


title: FETAL_PANCREAS____220.1850.1.1

description: SAMPLE 35


title: FETAL_LIVER____147.1440.1.2

description: SAMPLE 28


title: Adult male, whole-body 60, rep 2

description: Sample 65

value: line


title: FETAL_KIDNEY____143.1442.1.3

description: SAMPLE 27

value: F-Kidney

value: fetal Kidney


title: T24_2LASV_s15

source_name: Lassa Virus_24 hours_Donor 2


title: Adult female, whole-body 24, rep 1

description: Sample 66

value: female


title: Adult male, whole-body 53, rep 2

description: Sample 64


title: FETAL_KIDNEY____143.1441.1.2

description: SAMPLE 26


title: Adult male, whole-body 49, rep 1

description: Sample 67


title: FETAL_HEART____111.1441.1.2

description: SAMPLE 23

value: F-Heart

value: fetal Heart


title: Adult female, whole-body 36, rep 1

description: Sample 63


title: FETAL_HEART____111.1442.1.2

description: SAMPLE 24


title: Adult male, whole-body 69, rep 1

description: Sample 62

value: male


title: Adult female, whole-body 3, rep 1

description: Sample 61

value: whole-body


title: Adult male, whole-body 53, rep 1

description: Sample 59


title: Adult female, whole-body 27, rep 1

description: Sample 76


title: Adult female, whole-body 4, rep 1

description: Sample 60


title: FETAL_SPLEEN____91.1440.1.2

description: SAMPLE 42

value: F-Spleen

value: fetal Spleen


title: FETAL_KIDNEY____143.1440.1.2

description: SAMPLE 25


title: T24_2Uninf_s12

source_name: Uninfected_24 hours_Donor 2


title: FETAL_ADRENAL____95.412.1.3

description: SAMPLE 18

value: F-Adrenal

value: fetal Adrenal


title: T08_2Uninf_s11

source_name: Uninfected_8 hours_Donor 2


title: FETAL_HEART____111.1440.1.2

description: SAMPLE 22


title: FETAL_BRAIN____21.1442.1.2

description: SAMPLE 21

value: F-Brain

value: fetal Brain


title: T24_1ML29_s9

source_name: Mop/Las virus_24 hours_Donor 1

value: peripheral blood mononuclear cells (PBMC)


title: FETAL_ADRENAL____95.414.1.2

description: SAMPLE 19


title: Adult male, whole-body 81, rep 1

description: Sample 58


title: T08_1ML29_s8

source_name: Mop/Las virus_8 hours_Donor 1


title: T08_1LASV_s5

source_name: Lassa Virus_8 hours_Donor 1


title: CTB_EGFR+ _Wk8_Tr1_P720_581.2435.1.1

description: SAMPLE 16

value: CTB

value: cytotrophoblast


title: T24_1LASV_s6

source_name: Lassa Virus_24 hours_Donor 1


title: CTB__Wk8.6_Tr1__581.1925.1.1

description: SAMPLE 11


title: CTB_EGFR+ _Wk7.2_Tr1_P723_581.2438.1.1

description: SAMPLE 15


title: FETAL_ADRENAL____95.1440.1.2

description: SAMPLE 17


title: CTB_EGFR+ _Wk6.4_Tr1_P722_581.2437.1.1

description: SAMPLE 14


title: T04_1Lassa_s4

source_name: Lassa Virus_4 hours_Donor 1


title: CTB_EGFR+ _Wk6.3_Tr1_P718_581.2433.1.1

description: SAMPLE 13


title: FETAL_BRAIN____21.1440.1.2

description: SAMPLE 20


title: T04_1ML29_s7

source_name: Mop/Las virus_4 hours_Donor 1


title: CTB__Wk8_Tr1__581.1924.1.1

description: SAMPLE 12


title: Adult male, whole-body 62, rep 1

description: Sample 57

value: line


title: T04_2Uninf_s10

source_name: Uninfected_4 hours_Donor 2


title: CTB__Wk39_Tr3__581.1587.1.1

description: SAMPLE 9


title: CTB__Wk12_Tr1__581.1585.1.1

description: SAMPLE 8


title: Adult female, whole-body 19, rep 1

description: Sample 56


title: T08_1Uninf_s2

source_name: Uninfected_8 hours_Donor 1


title: Adult female, whole-body 25, rep 2

description: Sample 53


title: CTB__Wk12_Tr1__581.1584.1.1

description: SAMPLE 7


title: CTB__Wk39_Tr3__581.1588.1.1

description: SAMPLE 10


title: Adult female, whole-body 42, rep 1

description: Sample 55


title: Adult male, whole-body 77, rep 2

description: Sample 54


title: CTB__Wk10_Tr1__581.1586.1.1

description: SAMPLE 5


title: Amnion__Wk39_Tr3_P724_777.2439.3.1

description: SAMPLE 2

value: P-Amnion

value: amnion


title: BG02_HESC____54.215.1.3

description: SAMPLE 3*,**

value: PSC

value: pluripotent stem cell


title: T04_1Uninf_s1

source_name: Uninfected_4 hours_Donor 1


title: pediatric T-ALL TLX3 ES_00116 class prediction

city: Padova

first: Andrea

last: Zangrando

address: Via Giustiniani, 3

department: Woman and Child's Health

country: Italy

institute: University of Padova

description: Gene expression data from pediatric T-ALL samples

hyb_protocol: Following fragmentation, 11 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450DX.

scan_protocol: GeneChips were scanned using the Scan GCS3000Dx.

data_processing: Expression data were analyzed using R software [www.r-ptoject.org] with BioConductor package [www.bioconductor.org].

source_name: human white blood cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Lysis of the mononuclear cells followed by lysate homonogenization using a biopolymer shredding system in a microcentrifuge spin-column format followed by total RNA purification using selective binding columns

treatment_protocol: White blood cells were isolated by density gradient centrifugation (Biocoll separating solution, Biochrome AG, Berlin, Germany).

tag: disease state

value: pediatric T-ALL

tag: genetic category ci-fish

value: white blood cells


title: Adult male, whole-body 63, rep 1

description: Sample 52

source_name: adult male, whole-body

value: male

value: whole-body


title: T24_1Uninf_s3

source_name: Uninfected_24 hours_Donor 1


title: Adult female, whole-body 10, rep 1

description: Sample 51

source_name: adult female, whole-body

value: female


title: CM7_HESC____243.621.2.2

description: SAMPLE 4


title: Amnion__Wk39_Tr3_P724_777.2439.2.1

description: SAMPLE 1


title: CTB__Wk10_Tr1__581.1921.1.1

description: SAMPLE 6


title: pediatric T-ALL TLX3 ES_00126 class prediction


title: pediatric T-ALL TLX3 ES_00121 class prediction


title: Adult male, whole-body 72, rep 2

description: Sample 49


title: U2Os GR3KR_dex_6h_rep2

city: Kuopio

first: Ville

last: Paakinaho

address: Yliopistonranta 8

department: School of Medicine

country: Finland

institute: University of Eastern Finland

description: stably expressing GR3KR

hyb_protocol: Standart Illumina hybridization protocol

scan_protocol: Standart Illumina scanning protocol

data_processing: Obtained data was normalized using VST transformation and RSN normalization  used as standard approach for Illumina arrays with the R/lumi package

source_name: U2Os Cells, dex treated, 6 h

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

growth_protocol: U2Os cells were grown in Dulbecco's Modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum, 1 mM Na-puryvate, 25 U/ml penicillin and 25 µg/ml streptomycin, and 400 µg geneticin, and kept at 37 °C in a humidified 95% air/ 5% CO2

extract_protocol: Total RNA was extracted using TriPure (Roche Diagnostics GmbH, Mannheim, Germany) according to manufacture's instructions

treatment_protocol: 2.5x105x of U2Os cells were seeded at 6-well plates and allowed to grow in steroid-depleted medium (2.5 %  charcoal stripped FBS in DMEM) 36 h and the cells were subsequently treated with 100 nM of dexamethasone for 6 h prior extraction of RNA

value: U2 Osteosarcoma (U2Os) Cells

value: 100 nM of dexamethasone

value: 6 h


title: Adult male, whole-body 71, rep 2

description: Sample 50


title: pediatric T-ALL TLX3 ES_00129 class prediction


title: U2Os GR3KR_vehicle_6h_rep2

description: stably expressing GR3KR

source_name: U2Os Cells, vehicle treated, 6 h

value: vehicle


title: U2Os GR3KR_vehicle_6h_rep3

description: stably expressing GR3KR


title: U2Os GR3KR_dex_6h_rep3

description: stably expressing GR3KR


title: U2Os GR3KR_dex_6h_rep1

description: stably expressing GR3KR


title: Adult female, whole-body 31, rep 1

description: Sample 48


title: U2Os wtGR_vehicle_6h_rep3

description: stably expressing wtGR


title: U2Os wtGR_dex_6h_rep3

description: stably expressing wtGR


title: U2Os wtGR_dex_6h_rep1

description: stably expressing wtGR


title: U2Os GR3KR_vehicle_6h_rep1

description: stably expressing GR3KR


title: U2Os wtGR_dex_6h_rep2

description: stably expressing wtGR


title: Adult female, whole-body 7, rep 1

description: Sample 47


title: Adult female, whole-body 21, rep 1

description: Sample 46


title: pediatric T-ALL TLX3 PAD_00459 class prediction


title: pediatric T-ALL TLX3 PAD_00131 class prediction


title: pediatric T-ALL TLX3 PAD_00165 class prediction


title: U2Os wtGR_vehicle_6h_rep1

description: stably expressing wtGR


title: pediatric T-ALL HOXA ES_00119 class prediction

value: HOXA


title: pediatric T-ALL HOXA ES_00115 class prediction


title: GR3KR_dex_6h_rep1

description:
stably expressing GR3KR
3KR_10

source_name: Isogenic HEK293 Cells, dex treated, 6 h

growth_protocol: Isogenic HEK293 cells were grown in Dulbecco's Modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum, 25 U/ml penicillin and 25 µg/ml streptomycin, and 100 µg hygromycin-B,  and kept at 37 °C in a humidified 95% air/ 5% CO2

treatment_protocol: 3x105x of Isogenic HEK293 cells were seeded at 6-well plates and allowed to grow in steroid-depleted medium (2.5 %  charcoal stripped FBS in DMEM) 36 h and the cells were subsequently treated with 100 nM of dexamethasone for 6 h prior extraction of RNA

value: Isogenic Human Embryonal Kidney (HEK293) Cells


title: GR3KR_dex_6h_rep2

description:
stably expressing GR3KR
3KR_11


title: Adult male, whole-body 56, rep 1

description: Sample 45


title: GR3KR_dex_6h_rep3

description:
stably expressing GR3KR
3KR_12


title: U2Os wtGR_vehicle_6h_rep2

description: stably expressing wtGR


title: Adult female, whole-body 1, rep 2

description: Sample 42


title: Adult male, whole-body 74, rep 1

description: Sample 43


title: HS at 7 days

description: Gene expression data from rat soleus muscle

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rattus Norvegicus Genome Array. GeneChips were washed and stained in the Wash and Stain Kit of Affymetrix, P/N 900720.

data_processing:
Use the free miRNA QC Tool software for data summarization, normalization, and quality control.
miRNA QC Tool software

source_name: Soleus muscle at 7 days of HS

value: hind limb suspension

value: soleus muscle

value: white and Sprague-Dawley rats

value: 8 weeks of age


title: Adult male, whole-body 83, rep 1

description: Sample 41

value: line


title: HS at 14 days

source_name: Soleus muscle at 14 days of HS


title: wtGR_dex_6h_rep3

description:
stably expressing wtGR
GR_6


title: wtGR_vehicle_6h_rep2

description:
stably expressing wtGR
GR_2

source_name: Isogenic HEK293 Cells, vehicle treated, 6 h


title: pediatric T-ALL HOXA PAD_00115 class prediction


title: GR3KR_vehicle_6h_rep2

description:
stably expressing GR3KR
3KR_8


title: wtGR_dex_6h_rep2

description:
stably expressing wtGR
GR_5


title: pediatric T-ALL HOXA ES_00132 class prediction


title: GR3KR_vehicle_6h_rep3

description:
stably expressing GR3KR
3KR_9


title: wtGR_vehicle_6h_rep3

description:
stably expressing wtGR
GR_3


title: wtGR_vehicle_6h_rep1

description:
stably expressing wtGR
GR_1


title: wtGR_dex_6h_rep1

description:
stably expressing wtGR
GR_4


title: Adult female, whole-body 25, rep 1

description: Sample 44


title: pediatric T-ALL HOXA PAD_00427 class prediction


title: pediatric T-ALL HOXA PAD_00402 class prediction


title: pediatric T-ALL HOXA PAD_00257 class prediction


title: GR3KR_vehicle_6h_rep1

description:
stably expressing GR3KR
3KR_7


title: pediatric T-ALL HOXA PAD_00387 class prediction


title: Adult female, whole-body 18, rep 1

description: Sample 40


title: Adult female, whole-body 23, rep 2

description: Sample 39


title: Adult male, whole-body 72, rep 1

description: Sample 37


title: WT3

city: Columbus

first: Sukhinder

last: Sandhu

state: OH

address: 460 W 12th Ave

institute: The Ohio State University Wexner Medical Center

description: Total RNA from wild type (WT) mice B-cells, replicate #3

hyb_protocol: Hybridization of labeled RNA to DNA chip, 3D-GeneTM for 16 hrs, 37℃, 250 rpm.

scan_protocol: Scanning DNA chips by Toray 3D-GeneTM Scanner

data_processing: Data was quantile normalized

organism: Mus musculus

source_name: Spleen B-cells

label_protocol: aRNA was synthesized from 1 micro_g total RNA with Ambion Amino Allyl MessageAmpTM II aRNA Amplification kit & Labeled 10 micro_g of aRNA with Cy5 Mono-ReactiveDyePack

extract_protocol: Spleen B-cells were isolated using MACs (Miltenyi) and total RNA isolated using Trizol

treatment_protocol: miR-17~92 was overexpressed under emu enhancer, IgH promoter for B-cell specificity

value: Wild Type

value: Spleen B-cells


title: WT2

description: Total RNA from wild type (WT) mice B-cells, replicate #2


title: Adult male, whole-body 50, rep 1

description: Sample 38


title: pediatric T-ALL TALLMO ES_00117 class prediction

value: pediatric T-ALL

value: TALLMO

value: white blood cells


title: pediatric T-ALL HOXA PAD_00117 class prediction


title: WT1

description: Total RNA from wild type (WT) mice B-cells, replicate #1


title: Tg79-3

description: Total RNA from miR-17~92 transgenic mice B-cells, Founder #79, replicate #3

value: miR-17~92 Transgenic


title: Tg79-2

description: Total RNA from miR-17~92 transgenic mice B-cells, Founder #79, replicate #2


title: Tg79-1

description: Total RNA from miR-17~92 transgenic mice B-cells, Founder #79, replicate #1


title: Tg9-2

description: Total RNA from miR-17~92 transgenic mice B-cells, Founder #9, replicate #2


title: Adult male, whole-body 71, rep 1

description: Sample 34

value: male

value: whole-body


title: Adult female, whole-body 8, rep 1

description: Sample 35

value: female


title: Adult male, whole-body 73, rep 1

description: Sample 36


title: Tg9-1

description: Total RNA from miR-17~92 transgenic mice B-cells, Founder #9, replicate #1


title: Adult female, whole-body 41, rep 1

description: Sample 33


title: Tg9-3

description: Total RNA from miR-17~92 transgenic mice B-cells, Founder #9, replicate #3


title: Healthy control subject 12 after exercise training

city: Nijmegen

first: Gerwen

last: Lammers

address: PO Box 9101

country: Netherlands

institute: Radboud University Nijmegen Medical Centre

hyb_protocol: According to the Affymetrix GeneChip whole transcript sense target labelling assay

scan_protocol: According to the Affymetrix GeneChip Expression Wash, Stain and Scan User Manual

data_processing: The Affymetrix CEL files were imported into Genomic Suite software (Version 6.4, Partek, St. Louis, MO, USA). Probe sets were normalised using the Robust Multiarray Analysis (RMA) algorithm including background correction for probe GC content. Transcript summaries were calculated using the mean intensities of the corresponding probe sets, representing the quantitative gene expression levels.

source_name: vastus lateralis muscle, healthy subject, 6 months exercise training

growth_protocol: not applicable

extract_protocol: Frozen muscle biopsy samples were ground using a mortar and pestle, placed in RNA-Bee, which contains phenol and guanidine thiocyanate (Tel-test, Friendswood, TX, USA), and homogenised using an T25 ultra-turrax dispenser (IKA, Staufen, Germany). RNA was isolated using phenol/chloroform extraction, and purified according to the RNeasy mini kit clean-up protocol including an on-column DNase digestion (Qiagen, Hilden, Germany). The RNA concentration and purity were measured with a Nanodrop spectrophotometer (Thermo Scientific, Waltham, MA, USA) and RNA integrity was analysed on an Agilent Bioanalyser (Santa Clara, CA, USA).

treatment_protocol: Local aneasthesia with 2% (w/v) lidocaine, incision of the skin and fascia, ~100 mg mucle tissue needle biopsy ~15 cm above the knee according to the Bergström technique, immediately frozen in liquid nitrogen and stored at -80°C

tag: individual

value: subject 12

value: Healthy subject

value: Exercise training

value: 6 months

value: vastus lateralis muscle

tag: gender


title: pediatric T-ALL TALLMO ES_00141 class prediction


title: Healthy control subject 12 before exercise training

source_name: vastus lateralis muscle, healthy subject, baseline

label_protocol: According to the Affymetrix GeneChip whole transcript sense target labelling assay

tag: time

value: baseline


title: pediatric T-ALL TALLMO ES_00135 class prediction


title: pediatric T-ALL TALLMO ES_00127 class prediction


title: pediatric T-ALL TALLMO PAD_00101 class prediction


title: Healthy control subject 11 after exercise training

value: subject 11


title: Healthy control subject 11 before exercise training


title: Healthy control subject 10 after exercise training

value: subject 10


title: Adult female, whole-body 9, rep 2

description: Sample 32

value: line


title: pediatric T-ALL TALLMO ES_00111 class prediction


title: Healthy control subject 8 after exercise training

value: subject 8


title: Healthy control subject 8 before exercise training


title: Healthy control subject 9 after exercise training

value: subject 9


title: Healthy control subject 10 before exercise training


title: Healthy control subject 9 before exercise training


title: pediatric T-ALL TALLMO PAD_00082 class prediction

value: pediatric T-ALL

value: TALLMO


title: Healthy control subject 7 after exercise training

value: subject 7


title: Adult male, whole-body 77, rep 1

description: Sample 31

value: male


title: pediatric T-ALL TALLMO PAD_00281 class prediction

value: white blood cells


title: pediatric T-ALL TALLMO ES_00139 class prediction


title: Metabolic syndrome subject 6 after exercise training

source_name: vastus lateralis muscle, metabolic syndrome, 6 months exercise training

value: subject 6

value: Metabolic syndrome

value: female


title: Healthy control subject 7 before exercise training

value: Healthy subject

value: Exercise training


title: Adult female, whole-body 1, rep 1

description: Sample 30

value: whole-body


title: Adult male, whole-body 43, rep 1

description: Sample 29


title: Adult male, whole-body 60, rep 1

description: Sample 28


title: pediatric T-ALL TALLMO PAD_00508 class prediction


title: Adult male, whole-body 45, rep 2

description: Sample 25


title: pediatric T-ALL TALLMO PAD_00154 class prediction


title: pediatric T-ALL TALLMO PAD_00086 class prediction


title: Metabolic syndrome subject 4 after exercise training

value: subject 4

value: 6 months

value: vastus lateralis muscle


title: Metabolic syndrome subject 5 after exercise training

value: subject 5


title: Adult male, whole-body 45, rep 1

description: Sample 24

value: line


title: Metabolic syndrome subject 6 before exercise training

source_name: vastus lateralis muscle, metabolic syndrome, baseline

value: baseline


title: Metabolic syndrome subject 4 before exercise training


title: Metabolic syndrome subject 2 after exercise training

value: subject 2


title: Metabolic syndrome subject 5 before exercise training


title: Metabolic syndrome subject 2 before exercise training


title: Adult male, whole-body 55, rep 1

description: Sample 23


title: Adult female, whole-body 9, rep 1

description: Sample 27


title: Metabolic syndrome subject 1 after exercise training

value: subject 1


title: pediatric T-ALL TALLMO ES_00128 class prediction

value: pediatric T-ALL

value: TALLMO


title: pediatric T-ALL TALLMO PAD_00063 class prediction

value: white blood cells


title: Metabolic syndrome subject 3 before exercise training

value: subject 3


title: Adult male, whole-body 46, rep 1

description: Sample 22

value: male


title: Metabolic syndrome subject 1 before exercise training

value: Metabolic syndrome

value: female


title: kidney_anti-miR-214_3

city: Glasgow

first: Laura

last: Denby

address: 126 University Place

department: BHF GCRC

institute: University of Glasgow

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

source_name: kidney, UUO + 7 days

label_protocol: Biotinylated cRNA was prepared using Illumina® TotalPrep™ RNA Amplification Kit

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

tag: developmental stage

value: adult

tag: strain

value: kidney


title: Adult male, whole-body 65, rep 2

description: Sample 20

value: whole-body


title: pediatric T-ALL TALLMO PAD_00108 class prediction


title: pediatric T-ALL TALLMO PAD_00156 class prediction


title: Metabolic syndrome subject 3 after exercise training

value: Exercise training

value: 6 months


title: pediatric T-ALL OTHERS ES_00138

value: other


title: Adult female, whole-body 22, rep 2

description: Sample 21

value: line


title: kidney_anti-miR-214_1


title: Adult female, whole-body 23, rep 1

description: Sample 19


title: kidney_anti-miR-214_2


title: pediatric T-ALL OTHERS PAD_00073


title: kidney_anti-miR-214_4


title: kidney_control antimiR_3

value: control antimiR


title: kidney_control antimiR_4


title: pediatric T-ALL OTHERS PAD_00385


title: Adult male, whole-body 66, rep 1

description: Sample 18


title: pediatric T-ALL OTHERS PAD_00151


title: Kidney_saline_5

city: Indianapolis

first: Michael

middle: Thomas

last: Eadon

state: IN

address: 950 W. Walnut St R2 202

department: Medicine

institute: Indiana University

data_processing:
The raw probe intensities were background subtracted and quartile normalized to adjust for variation that arose from microarray technology and not from biological differences. The normalized probe signals were then summarized into gene-level, during which signals of multiple probes that represent the same gene will be averaged to obtain gene expression level in GenomeStudio™ and exported as a tab-delimited txt file, which was imported into Partek, minimum value shifted to 1.0, and log2 transformed [*gene_level.txt]. Genes that were not expressed in any sample (Non-expressed genes, NEGs, identified by detection P value >= 0.05) were removed from further studies removed to improve the sensitivity of differential gene expression detection
If a gene is expressed in at least one of the 12 samples, the gene was kept for final output; if a gene is not expressed in any sample, it was excluded from subsequent analysis. After this pre-filtering step, 16,410 out of 30,854 genes (53.2%) were kept for DEG detection in Partek.

label_protocol: Standard Illumina protocol

growth_protocol: Mice were purchased at 7-8 weeks of age from Charles River laboratory

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 protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: age

value: 10 weeks

tag: treated with

value: 0.1% saline twice daily

tag: sentrix id

tag: sentrix position

value: C

tag: experimental sample name


title: pediatric T-ALL OTHERS PAD_00144

value: pediatric T-ALL


title: Kidney_colistin_3

value: colistin at 16 mg/kg/day in 2 divided doses

tag: tissue

value: F


title: Adult female, whole-body 22, rep 1

description: Sample 17

data_processing: The raw data (.pair file) was normalised via a log (base 2) transformation. Summarisation was performed by first taking the mean of replicated probes followed by the median of a probe set.

tag: line/stock

tag: Sex


title: Kidney_saline_6

value: male

value: E


title: pediatric T-ALL OTHERS PAD_00098

tag: cell type

value: white blood cells


title: kidney_control antimiR_1

value: adult

tag: treatment


title: Adult female, whole-body 30, rep 1

description: Sample 16

value: female


title: Kidney_colistin_2

value: kidney

value: D


title: pediatric T-ALL OTHERS PAD_00128

tag: disease state


title: pediatric T-ALL OTHERS ES_00130

tag: genetic category ci-fish


title: Kidney_colistin_1

value: B


title: Adult male, whole-body 70, rep 1

description: Sample 15

value: whole-body


title: kidney_control antimiR_2


title: Kidney_saline_4

value: A


title: Adult female, whole-body 40, rep 1

description: Sample 26

value: line


title: Adult female, whole-body 37, rep 1

description: Sample 14


title: Adult female, whole-body 14, rep 1

description: Sample 12


title: lin-54;mes-4_3

city: Santa Cruz

first: Susan

last: Strome

state: CA

address: 1156 High St

department: MCD Biology

institute: UC Santa Cruz

description: lin-54 (n3423); mes-4 (ok2326) dissected germline 3

hyb_protocol: aRNA probes of three replicates were hybridized to GeneChip C. elegans genome arrays (Affymetrix). Probe-preparation, hybridization, and scanning of microarray were performed at the Genomics Core facility at University of Massachusetts Medical School.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Statistical analyses were performed using custom scripts and packages in R (http://www.r-project. org) and Bioconductor (Gentleman et al., 2004). The affy package was used to quantile normalize the data across replicates and the Robust Multichip Average (RMA) algorithm was used to obtain probe-set expression values (Irizarry et al.,2003). Log2 transformed data were used in subsequent analysis and plotting. Statistical analysis for misexpression was performed using the moderated t-test from the Bioconductor package limma (Smyth. 2004). Statistical significance of mis-expression (False Discovery Rate) was obtained with the qvalue package (Storey et at., 2003).

organism: Caenorhabditis elegans

source_name: lin-54(n3423); mes-4(ok2326) double mutant C.elegans germline

label_protocol: aRNA was labeled with biotinylated UTP using the MessageAmp II aRNA Amplification Kit (Ambion).

growth_protocol: Strains for  germline were cultured at 20C, using standard methods.

extract_protocol: Germline RNA was isolated as described in Chi and Reinke (2006), and linearly amplified once using MessageAmp II aRNA Amplification Kit (Ambion).

treatment_protocol: Germlines were dissected in 1X egg buffer to excise the germline including mitotic tip through meiotic late pachytene 24 hours after L4 stage.

tag: genotype/variation

value: hermaphrodite


title: Adult male, whole-body 65, rep 1

description: Sample 10


title: pediatric T-ALL TLX3 ES_00116

source_name: human white blood cells


title: pediatric T-ALL TLX3 ES_00126


title: lin-54;mes-4_1

description: lin-54 (n3423); mes-4 (ok2326) dissected germline 1

value: lin-54(n3423); mes-4(ok2326) double mutant

tag: gender


title: Adult male, whole-body 68, rep 1

description: Sample 9

source_name: adult male, whole-body


title: Adult female, whole-body 28, rep 1

description: Sample 11


title: mes-4_3

description: mes-4(ok2326) dissected germline 3

source_name: mes-4(ok2326) C.elegans germline


title: Kidney_saline_3

value: 10 weeks

value: 0.1% saline twice daily


title: mes-4_2

description: mes-4(ok2326) dissected germline 2


title: Adult female, whole-body 15, rep 1

description: Sample 13

source_name: adult female, whole-body


title: Kidney_colistin_5

value: colistin at 16 mg/kg/day in 2 divided doses


title: lin-54;mes-4_2

description: lin-54 (n3423); mes-4 (ok2326) dissected germline 2


title: pediatric T-ALL TLX3 PAD_00131

value: pediatric T-ALL


title: mes-4_1

description: mes-4(ok2326) dissected germline 1


title: pediatric T-ALL TLX3 PAD_00459


title: pediatric T-ALL TLX3 ES_00129


title: Kidney_saline_2

value: male

value: C


title: Adult female, whole-body 13, rep 1

description: Sample 8


title: lin-54_3

description: lin-54(n3423) dissected germline 3

source_name: lin-54(n3423) C.elegans germline


title: Kidney_colistin_6

value: F


title: pediatric T-ALL TLX3 PAD_00165

value: white blood cells


title: Kidney_saline_1


title: Adult male, whole-body 58, rep 1

description: Sample 7


title: Adult female, whole-body 29, rep 1

description: Sample 6

value: female


title: Adult male, whole-body 78, rep 1

description: Sample 3


title: wildtype_3

description: wild-type N2 dissected germline 3

source_name: wild type C.elegans germline

value: wild type


title: pediatric T-ALL HOXA ES_00119

value: HOXA


title: Adult male, whole-body 80, rep 1

description: Sample 5


title: pediatric T-ALL HOXA PAD_00427


title: lin-54_1

description: lin-54(n3423) dissected germline 1


title: pediatric T-ALL HOXA ES_00115


title: pediatric T-ALL HOXA ES_00132


title: wildtype_1

description: wild-type N2 dissected germline 1


title: PUGKO mice uterus at DOPP3.5, biological rep2

city: Columbia

first: Thomas

last: Spencer

state: MO

address: 920 East Campus Drive

department: Animal Sciences

institute: University of Missouri

description: Gene expression data from whole uterus on day of pseudopregnancy 3.5

hyb_protocol: Following fragmentation, 5.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 and GeneChip Command Console software (Affymetrix).

data_processing: The data was analyzed with RMA Limma package in Bioconductor (cut-off, p value<0.05, FDR 5% and -1.5> fold change <1.5).

source_name: day of pseudopregnancy 3.5 female mouse

label_protocol: Biotinylated cRNA were prepared using GeneChip WT Terminal Labeling kitaccording to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. cRNA was generated from a 150 ng of total RNA using Ambion WT Expression Kit according to manufactures recommendations.

treatment_protocol: Progesterone induced uterine gland knockout mice (or PUGKO) were generated by progesterone treatment from postnatal day 2 to 10. Six week old control and PUGKO female mice were bred to wild type vasectomized male. Day of the vaginal plug detection was designated as day of pseudopregnancy (DOPP) 0.5. Mice (n=4/treatment) were sacrificed on DOPP 3.5 and whole uteri snap frozen in liquid nitrogen.

value: whole uterus

tag: genotype

value: PUGKO


title: PUGKO mice uterus at DOPP3.5, biological rep3


title: PUGKO mice uterus at DOPP3.5, biological rep4


title: PUGKO mice uterus at DOPP3.5, biological rep1


title: wildtype_2

description: wild-type N2 dissected germline 2


title: Adult female, whole-body 38, rep 1

city: St Lucia

first: Stephen

last: Chenoweth

address: The School of Biological Sciences, The University of Queensland

institute: The University of Queensland, Australia

description: Sample 4

label_protocol: Labeling was performed by The Centre for Genomics and Bioinformatics, Bloomington, IN USA, following the standard NimbleGen operating protocol. See www.nimblegen.com.

extract_protocol: Each whole-body pool was homogenised in Trizol® and immediately stored at -80 degrees Celcius. During tissue disection, flies were suspended in RNALater® to inhibit RNA degradation, pools of 100 tissue disects were stored at -80 degrees Celsius. RNA extraction of the whole-body samples was performed by using the Trizol® procedure followed by RNA isolation using RNeasy minikits®. RNA extraction of the tissue samples was identical to that of the whole-body samples except that the Trizol® was added to 10µl of RNA Later®.

value: whole-body


title: pediatric T-ALL TLX3 ES_00121


title: Kidney_colistin_4

value: kidney

value: B


title: pediatric T-ALL HOXA PAD_00402


title: Adult female, whole-body 32, rep 1

description: Sample 2

value: line


title: Non-Habits associated tongue tumor_YTO98N

city: Trivandrum

first: Ramkumar

last: Hariharan

state: Kerala

address: Poojapura, Thycaud PO

department: Cancer Research Program

country: India

institute: Rajiv Gandhi Center for Biotechnology

data_processing: Preliminary data analysis and normalization done with Bead Studio software and other tools written in R.Processed data contains background subtracted, normalized data. Only data for 18374 REF_ID's was available for processing.This was because outliers with 3 median absolute deviations (3 MADs) above the mean are removed by default by Bead Studio software before raw data is produced.

source_name: non-habits associated tongue tumor

label_protocol: cRNA was generated by adding in vitro transcription reagents (buffer, DTT, RNase Inhibitor, T7 RNA Polymerase) containing biotin-labeled ribonucleotides from the kit. IVT was carried out at 37C for 14 hours (overnight incubation). The incorporated biotin was used to bind a fluorescent dye conjugated to streptavidin.

extract_protocol: RNA extraction using All DNA- RNA prep kit from Qiagen. Pleasee manufacturers protocols for details.

value: carcinoma of anterior tongue

tag: tumor type

value: non-habits associated tongue tumor

tag: tumor grade

value: Well differentiated


title: lin-54_2

description: lin-54(n3423) dissected germline 2

value: hermaphrodite


title: pediatric T-ALL HOXA PAD_00387

value: pediatric T-ALL


title: Adult male, whole-body 51, rep 1

description: Sample 1

value: male


title: wild type uterus at DOPP3.5, biological rep2

treatment_protocol: Control (Pgr+/+Foxa2+/+) and conditional Foxa2 (PgrCre/+Foxa2flox/flox) mutant female mice were bred to wild type vasectomized male. Day of the vaginal plug detection was designated as day of pseudopregnancy (DOPP) 0.5. Mice (n=4/genotype) were sacrificed on DOPP 3.5 and whole uteri snap frozen in liquid nitrogen.

value: Pgr+/+ Foxa2+/+


title: wild type uterus at DOPP3.5, biological rep3


title: Habits associated tongue tumor_YTO65T

source_name: habits associated tongue tumor

tag: age

value: habits associated tongue tumor

value: Moderately differentiated


title: Non-Habits associated tongue tumor_YTO98T

value: female


title: wild type uterus at DOPP3.5, biological rep1


title: Non-Habits associated tongue tumor_YTY91N


title: pediatric T-ALL HOXA PAD_00117

value: HOXA

value: white blood cells


title: Habits associated tongue tumor_YTO78T


title: glandular epithelial cells from day of pseudopregnancy 3.5 mouse uterus, biological rep1

hyb_protocol: Following fragmentation, biotin-labeled cRNA was hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

data_processing: GeneSpring 7.0 software was used for analysis of microarray data.  Array output was normalized via the robust multiarray method, and probe sets were filtered based on expression calls. Differentially expressed genes were identified using ANOVA (P=0.05) with a Benjamini and Hochberg false discovery rate multiple test correction (FDR 5%).

source_name: glandular epithelium from day of pseudopregnancy 3.5 mouse uterus

label_protocol: Purified cRNA (5 ug) was then fragmented and labeled with biotin using the Encore Biotin Module (Nugen), according to the manufacturer's instructions.

extract_protocol: Total RNA was extracted using Qiagen RNeasy MinElute kit  (Qiagen) according to the manufacturer's instructions.   Total RNA (0.6-3.5 ng) of  was amplified using Ovation Pico WTA System V2 (Nugen) according to the manufacturer's instructions.

treatment_protocol: Uterine samples were cryosectioned, mounted on RNAse-free polyethylene napthalate (PEN)-coated slides (Carl Zeiss) and stained with 1% cresyl violet. Luminal epithelial (LE) or glandular epithelial (GE) cells were dissected using laser capture microdissection was performed using PALM MicroBeam LCM microscope (Carl Zeis).

value: glandular epithelial cells

value: day of pseudopregnancy 3.5


title: pediatric T-ALL TALLMO ES_00117

value: TALLMO


title: Non-Habits associated tongue tumor_YTO89T


title: glandular epithelial cells from day of pseudopregnancy 3.5 mouse uterus, biological rep2


title: pediatric T-ALL TALLMO PAD_00101


title: pediatric T-ALL TALLMO ES_00135


title: pediatric T-ALL HOXA PAD_00257


title: Habits associated tongue tumor_YTO71T


title: PeripheralBloodLymphoid_DBA_Proband_0673_Treated

city: Little Rock

first: Jason

last: Farrar

address: 1 Children's Way, #512-10

institute: University of Arkansas for Medical Sciences

description:
Genomic DNA extracted from peripheral blood cells retained on CD3/CD10 magnetic beads was genotyped using Infinium HumanOmni1_Quad Genotyping BeadChips (Illumina).
Fractionated cell DNA was prepared using Qiagen Blood DNA isolation kit according to the manufacturer's instructions

data_processing: Intensity data were extracted in Genome Studio (v2011.1); SNPs with GenTrain score <0.15 were not called.

source_name: Lymphoid-enriched peripheral blood while on lenolidamide treatment

label_protocol: Standard Illumina Infinium HD protocol

value: Female

tag: tissue source

value: Peripheral Blood

tag: tissue separation

value: Lymphoid Peripheral Blood DNA

tag: lenolidamide treatment

value: Treated

tag: relationship to proband

value: Proband


title: ZHBTc4-Oct4-EGFP vs Nr5a2-EGFP

city: Mapo

first: kyeng

middle: won

last: choi

state: Seoul

address: Sinsu

department: Lifescience

country: South Korea

institute: Sogang

description: Stable Oct4-EGFP or Nr5a2-EGFP gene transfected ZHBTc4 ES cells, Monoclonal cell line, Doxycyclin treatment before harvest

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: Agilent Feature Extraction Software (v 9.3.2.1) was used for background subtraction and LOWESS normalization.

source_name: ZHBTc4-Oct4-EGFP clone #9

label_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label

growth_protocol: ES cells were cultured in the absence of feeder cells in Dulbecco's modified Eagles's medium(Gibco-BRL) supplied with 15% heat-inactivated fetal bovine serum(Sigma aldrich), 1mM sodium pyruvate(Sigma Aldrich), 10^-4M 2-mercaptoethanol, 1X nonessential amino acids(Sigma Aldrich), and  1000 IU/ml leukemia inhibitory factor (LIF; Millipore) on gelatin(0.2%) coated dishes.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions.

treatment_protocol: Doxycylin treated stable cells were harvest and extracted total RNA

tag: cell line

value: ZHBTc4 ES cell

tag: transfection

source_name: ZHBTc4-Nr5a2-EGFP clone #26


title: PeripheralBloodMyeloid_DBA_Proband_0673_Treated

description:
Genomic DNA extracted from peripheral blood cells NOT retained on CD3/CD10 magnetic beads was genotyped using Infinium HumanOmni1_Quad Genotyping BeadChips (Illumina).
Fractionated cell DNA was prepared using Qiagen Blood DNA isolation kit according to the manufacturer's instructions

source_name: Myeloid enriched peripheral blood while on lenolidamide treatment

value: Myeloid Peripheral Blood DNA


title: M. smegmatis-Acid-NO treated

city: Amherst

last: Cossu

state: MA

address: 102 Holdsworth way

department: Department of Food Science

institute: University of Massachusetts, Amherst

description: Technical (spot) replicates 1 to 3. Mycobacterium smegmatis, Acid-NO treated.

hyb_protocol: Hybridization was performed following the Recommended Sample Preparation and Hybridization Protocol drawn-up by the MYcroarrays® Company (Biodiscovery LLC) with some modifications. 220µl of hybridization solution (66µl of 20X SSPE (3M NaCl, 20mM EDTA, 118.2mM NaH2PO4, 81.8mM Na2HPO4), 10% formamide, 0.01mg/ml BSA, 0.01% Tween-20, 1mM DTT, 1% manufacturer control oligos, 10µg of each target coupled-aRNA, RNAse-free water to final volume) was prepared and pre-warmed at 56°C. Hybridizations were carried out in a water bath at 55°C for 18h with OneArray Sealed Hybridization Chambers (PhalanxBio Inc., Palo Alto, CA, USA). After incubation, slides were washed twice with SSPE 1X- 0.1mM DTT for 2 min followed by a 30 sec final wash with 0.25 X SSPE – 0.1mM DTT, dried with air-spray and immediately scanned.

scan_protocol: Scans were carried out with the GenePix AXON 4200A instrument (Axon Instruments) at 5-um resolution with full dynamic range of signal intensities at 1 – 65.000 in two-colour red/green mode (635nm and 532 nm filters).

data_processing:
The intensities of the two dyes for each spot were quantified using the GenePix 6.0 Software and calculated as the mean of median intensity of each replicate spot for each gene. Total array intensity was used to normalize spot signal intensities with the ratio-mean based algorithm option. Subtraction of local feature background median was achieved as default. Negative corrected intensities were set to 10.
A change of 2-fold in the intensities with a p-value < 0.05 was considered significant for a differential gene expression. Data were transformed in normalized log2 ratio (Alexa Fluor dye 555/647) representing MSMEG-exp/MSMEGk-.

label: Alexa Fluor 555

organism: Mycolicibacterium smegmatis MC2 155

source_name: M. smegmatis acid-NO treated

label_protocol: Forty µg samples of amplified RNA (aRNA) were labelled with either Alexa Fluor dye 647 or 555  purchased from Invitrogen, USA, following the manufacturer's protocol. Purification of coupled aRNA was performed by the RNeasy purification system (Qiagen) and incorporation of dye was evaluated using the Nanodrop spectrophotometer. Before hybridization, coupled aRNA was fragmented using the RNA fragmentation reagents (Ambion, Inc) following the manufacturer's protocol.

growth_protocol: MSMEG MC2155 (ATCC 700084) was cultured in Middlebrook 7H9 medium (Sigma-Aldrich, MO, USA) supplemented with  0.2% glycerol (Sigma-Aldrich, MO, USA), 0.05% Tween 80 (Sigma-Aldrich, MO, USA) and 10% v/v albumin dextrose catalase (ADC, Sigma-Aldrich, MO, USA) in 25 cm2 vented tissue culture flasks (T25) positioned up-right at 37°C before stress treatment.

extract_protocol: Total RNA extracted with the RiboPure-Bacteria Kit (Ambion, Inc). Mycobacterial cells were re-suspended in 350µl of RNAwiz solution and transferred to a 0.5ml RNAse-free skirted screw-cap microcentrifuge tube containing 250µl of 0.1mm ice-cold Zirconia Beads. Tubes were immediately processed in the RiboLyser RNA Lysing Machine (RiboLyser FP120-HY-230, Hybaid) for 2 cycles (30s at speed 6.5 with 1 min of cooling interval between each bead beating step). Remaining steps were performed according to the manufacturer’s instructions. All RNA samples were treated with Dnase I (Ambion, Inc)  and  purified by RNeasy column (Qiagen). RNA yield and purity was evaluated with the Nanodrop spectrophotometer (NanoDrop1000, Thermo Scientific) and RNA quality was examined by Denaturing Gel Electrophoresis. We carried out three independent experiments on three different flasks. Good quality RNA samples obtained from each pellet were then pooled together and used for microarray experiments to get an average of three separate experiments. mRNA was obtained by using the MICROBExpress Bacterial mRNA Purification Kit (Ambion) and was lineary amplified bu using the MessageAmp II Bacterial Kit (Ambion, Inc).

treatment_protocol: Mid-log-phase cells were treated with a 7H9/ADC/Tw80 buffered pH 5.3 medium with a final concentration of 5 mM of sodium nitrite (NaNO2) (Sigma) and exposed to the stress for 3 hours at 37°C. Cells were harvested by centrifugation at 5800 x g for 15min at 4°C and re-suspended in RNAlater solution (Sigma). Pellets were then incubated overnight at 4°C and stored at -80°C until RNA extraction.

tag: strain

value: acid-nitrosative multi-stress

label: Alexa Fluor 647

source_name: M. smegmatis control untreated

growth_protocol: MSMEG MC2155 (ATCC 700084) was cultured in Middlebrook 7H9 medium (Sigma-Aldrich, MO, USA) supplemented with  0.2% glycerol (Sigma-Aldrich, MO, USA), 0.05% Tween 80 (Sigma-Aldrich, MO, USA) and 10% v/v albumin dextrose catalase (ADC, Sigma-Aldrich, MO, USA) in 25 cm2 vented tissue culture flasks (T25) positioned up-right at 37°C until mid-log phase.

treatment_protocol: Mid-log-phase cells were grown in 7H9/ADC/Tw80 medium for 3h at 37°C. Cells were harvested by centrifugation at 5800 x g for 15min at 4°C and re-suspended in RNAlater solution (Sigma). Pellets were then incubated overnight at 4°C and stored at -80°C until RNA extraction.


title: luminal epithelial cells from from day of pseudopregnancy 3.5 mouse uterus, biological rep2

source_name: luminal epithelium from day of pseudopregnancy 3.5 mouse uterus

tag: cell type

value: luminal epithelial cells


title: luminal epithelial cells from from day of pseudopregnancy 3.5 mouse uterus, biological rep1


title: luminal epithelial cells from from day of pseudopregnancy 2.5 mouse uterus, biological rep2

source_name: luminal epithelium from day of pseudopregnancy 2.5 mouse uterus

value: day of pseudopregnancy 2.5


title: PeripheralBlood_DBA_Proband_139-3_Untreated

description:
Genomic DNA extracted from whole peripheral blood was genotyped using Infinium HumanOmniExpress Genotyping BeadChips (Illumina).
Unfractionated DNA is extracted from WBC pelleted from peripheral blood  after RBC lysis in 0.15M NH4Cl.  WBC are lysed overnight at 55 °C in WBC lysis solution (Qiagen), and protein precipitated and spun at 4 °C in protein precipitation solution (Qiagen).  DNA is preciptated in ethanol, pelleted and resuspended in 10mM Tris EDTA.

source_name: Unfractionated peripheral blood

value: Unfractionated Peripheral Blood DNA

value: Untreated


title: pediatric T-ALL TALLMO ES_00111

description: Gene expression data from pediatric T-ALL samples

source_name: human white blood cells

value: pediatric T-ALL


title: glandular epithelial cells from day of pseudopregnancy 2.5 mouse uterus, biological rep1

source_name: glandular epithelium from day of pseudopregnancy 2.5 mouse uterus


title: Habits associated tongue tumor_YTY81T

value: male

tag: tissue

value: carcinoma of anterior tongue

value: habits associated tongue tumor

value: Well differentiated


title: pediatric T-ALL TALLMO ES_00141

tag: disease state

value: TALLMO

value: white blood cells


title: Habits associated tongue tumor_YTY94T


title: ZHBTc4-EGFP vs Nr5a2-EGFP

description: Stable EGFP or Nr5a2-EGFP gene transfected ZHBTc4 ES cells, Monoclonal cell line, Doxycyclin treatment before harvest

source_name: ZHBTc4-EGFP clone #2-5

value: pCAG-IP/EGFP


title: Habits associated tongue tumor_YTY115T

value: Moderately differentiated


title: pediatric T-ALL HOXA PAD_00115

tag: genetic category ci-fish

value: HOXA


title: Non-Habits associated tongue tumor_YTY91T

value: female

value: non-habits associated tongue tumor


title: glandular epithelial cells from day of pseudopregnancy 2.5 mouse uterus, biological rep2

value: glandular epithelial cells


title: pediatric T-ALL TALLMO PAD_00508


title: pediatric T-ALL TALLMO PAD_00154


title: Habits associated tongue tumor_YTY96T


title: pediatric T-ALL TALLMO PAD_00086


title: wild type uterus at DOPP3.5, biological rep4

value: whole uterus

value: Pgr+/+ Foxa2+/+


title: pediatric T-ALL TALLMO PAD_00281


title: pediatric T-ALL TALLMO PAD_00082


title: pediatric T-ALL TALLMO ES_00128


title: Non-Habits associated tongue tumor_YTY121T


title: Non-Habits associated tongue tumor_YTO92T


title: pediatric T-ALL TALLMO ES_00127


title: Animal RQ7280_GFPneg

city: Bethesda

first: Yanqin

last: Yang

state: Maryland

address: 10 Center Dr.

institute: NIH

hyb_protocol: Hybridization was performed at 45ºC overnight, followed by washing and staining using FS450 fluidics station. Hybridization, washing and laser scanning of microarrays were performed according to the manufacturer’s protocol

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Data were processed using Affymetrix expression console software. Global background correction were applied to probe intensities, gene level expression were summarized from the corrected intensities and then quantile normalized.

organism: Macaca mulatta

source_name: GFP-

label_protocol: Biotin Labeled sense targets were prepared with total RNA using the Affymetrix Whole-Transcript (WT) Sense Target Labeling Protocol without rRNA reduction following the manufacturer’s directions (Affymetix, Santa Clara, CA).

growth_protocol: Rhesus macaques 3-9 years following autologous hematopoietic stem and progenitor cell transplantation with lentivirally-transduced CD34+ cells

extract_protocol: CD34+ GFP + and GFP- cells obtained by flow cytometry were immediately processed for RNA using the Qiagen RNeasy Micro Kit

treatment_protocol: CD34+ cells were enriched using a biotinylated anti-CD34 clone 12.8 antibody via the Miltenyi Biotec MACS cell separation system, and then sorted on a FACS AriaII instrument for expression of the vector-encoded GFP marker gene

tag: time post transplant

value: 3 years

value: bone marrow

value: CD34+ cells


title: Non-Habits associated tongue tumor_YTO70T

tag: gender


title: Non-Habits associated tongue tumor_YTY95T


title: Habits associated tongue tumor_YTO68T

value: male


title: Animal RQ7280_GFPpos

source_name: GFP+


title: pediatric T-ALL TALLMO ES_00139

value: pediatric T-ALL


title: pediatric T-ALL TALLMO PAD_00108


title: pediatric T-ALL TALLMO PAD_00156


title: Non-Habits associated tongue tumor_YTY88T

source_name: non-habits associated tongue tumor

value: carcinoma of anterior tongue


title: Control, biological rep2

city: Milwaukee

first: Yan

last: Lu

state: WI

address: 8701 Watertown Plank Rd

department: Physiology

institute: Medical College of Wisconsin

hyb_protocol: Hybridization was performed using 5 micrograms of biotinylated target, which was incubated with the GeneChip® Rat Exon 1.0 ST array (Affymetrix) at 45oC for 16 h. After hybridization, non-specifically bound material was removed by washing and specifically bound target was detected using the GeneChip Hybridization, Wash and Stain kit, and the GeneChip Fluidics Station 450 (Affymetrix).

scan_protocol: Arrays were scanned using the GeneChip Scanner 3000 7G (Affymetrix) and .CEL intensity files were produced using GeneChip Operating Software version 1.4 (Affymetrix).

data_processing:
Data were processed using Expression Console software v1.1.1 from Affymetrix Inc. MAT background correction were applied to probe intensities, gene level expression were summarized using IterPLIER algorithm.
probe group file: RaEx-1_0-st-v1.r2.pgf
meta-probeset file: RaEx-1_0-st-v1.r2.dt1.rn4..full.mps

label_protocol: Biotin-labeled targets for the microarray experiment were prepared using 1µg of total RNA. Ribosomal RNA was removed with the RiboMinus Human/Mouse Transcriptome Isolation kit (Invitrogen), and cDNA was synthesized using the GeneChip® WT (Whole Transcript) Sense Target Labeling and Control Reagents kit as described by the manufacturer (Affymetrix, Santa Clara, CA, USA).

growth_protocol: All rats were housed individually, given free access to water and food, and maintained under controlled conditions of temperature (21±1°C) and humidity (50±10%), under a 12 hr light/dark cycle.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. RNA was further purified by Dnase treatment and Rneasy Mini kit (Qiagen, UK).

treatment_protocol: rats administered naproxen (400 mg/kg), NO-naproxen (550 mg/kg) or control diet for 7 days

value: Sprague Dawley

tag: treated with

value: none (control diet) for 7 days

value: liver


title: Habits associated tongue tumor_YTY82T

source_name: habits associated tongue tumor

tag: tumor type

value: habits associated tongue tumor


title: Control, biological rep3


title: Habits associated tongue tumor_YTY84T

tag: tumor grade

value: Moderately differentiated


title: Control, biological rep1


title: Naproxen, biological rep2

value: Naproxen (400mg/kg diet) for 7 days


title: Naproxen, biological rep3


title: Animal RQ6897_GFPpos

value: 4 years


title: pediatric T-ALL TALLMO PAD_00063

data_processing: Expression data were analyzed using R software [www.r-ptoject.org] with BioConductor package [www.bioconductor.org].

value: TALLMO

value: white blood cells


title: Naproxen, biological rep4


title: Non-Habits associated tongue tumor_YTO67T

value: female

tag: age

value: non-habits associated tongue tumor


title: Non-Habits associated tongue tumor_YTY78T


title: Naproxen, biological rep1


title: Animal RQ6897_GFPneg


title: Animal RQ7387_GFPneg

value: 3.5 years


title: Control, biological rep4


title: Animal RQ2617_GFPpos

value: 9 years

value: bone marrow


title: WT2

description: Total RNA from wild type (WT) mice B-cells, replicate #2

source_name: Spleen B-cells

tag: genotype

value: Wild Type

value: Spleen B-cells


title: WT3

description: Total RNA from wild type (WT) mice B-cells, replicate #3


title: Tg79-2

description: Total RNA from miR-17~92 transgenic mice B-cells, Founder #79, replicate #2

value: miR-17~92 Transgenic


title: Tg79-1

description: Total RNA from miR-17~92 transgenic mice B-cells, Founder #79, replicate #1


title: Animal RQ2617_GFPneg

value: CD34+ cells


title: Tg79-3

description: Total RNA from miR-17~92 transgenic mice B-cells, Founder #79, replicate #3


title: WT1

description: Total RNA from wild type (WT) mice B-cells, replicate #1


title: Animal RQ7387_GFPpos


title: Tg9-3

description: Total RNA from miR-17~92 transgenic mice B-cells, Founder #9, replicate #3


title: Tg9-2

description: Total RNA from miR-17~92 transgenic mice B-cells, Founder #9, replicate #2


title: Tg9-1

description: Total RNA from miR-17~92 transgenic mice B-cells, Founder #9, replicate #1


title: BoneMarrowMyeloid_DBA_Proband_0673_Treated

description: Genomic DNA extracted from bone marrow cells NOT retained on CD3/CD10 magnetic beads was genotyped using Infinium HumanOmniExpressExome Genotyping BeadChips (Illumina).

hyb_protocol: Standard Illumina Infinium HD protocol

source_name: Myeloid-enriched bone marrow while on lenolidamide treatment

extract_protocol: Fractionated cell DNA was prepared using Qiagen Blood DNA isolation kit according to the manufacturer's instructions

value: Female

tag: tissue separation

value: Bone Marrow

value: Myeloid Bone Marrow DNA

value: Treated

value: Proband


title: NO-naproxen, biological rep4

value: Sprague Dawley

value: NO-naproxen (550mg/kg diet) for 7 days

value: liver


title: luminal epithelial cells from from day of pseudopregnancy 2.5 mouse uterus, biological rep1

value: luminal epithelial cells

value: day of pseudopregnancy 2.5


title: NO-naproxen, biological rep1


title: NO-naproxen, biological rep3


title: 448116A03_2012-09-07

status: Public on Nov 04 2013

city: Rochester

first: Elena

last: Rustchenko

state: NY

address: 601 Elmwood Ave., Box 712

department: Biochemistry & Biophysics

institute: University of Rochester

description: Mixture of DNA from RO20G1-Cy5 and Sor343-Cy3 Hyb. to aCGH

hyb_protocol: A total of 31 µg of each labelled DNA samples were combined and hybridized with each array ar 42° C for 72 hours in the Nimblegen  Hybridization System.

scan_protocol: NimbleGen MS 200 Microarray scanner was used at a resolution of 2 µm (49 pixels/13 µm feature) per manufacturers protocol (http://www.nimblegen.com/products/lit/scanner_ms200_manual_v1p0.pdf.)

data_processing:
Arrays were processed using Nimblegen's standard protocol from Nimblescan 2.5 CGH data analysis.
Scaled log 2 ratio (parental/mutant)

organism: Candida albicans

source_name: DNA from RO20G1

label_protocol: Labeling was performed, as two separate 2 µg of DNA reactions for each strain using either Cy3 or Cy5 conjugated random nanomers for 2 hours at 37° C. as per manufaturers protocol (http://www.nimblegen.com/products/lit/kits_labeling_dual_color_2009_04_22.pdf)

extract_protocol: Genomic DNA isolation according to Sambrook et al. 1989. Moelcular cloning.  A laboratory manual.  Cold Spring Harbor Laboratory  Press:  Cold Spring, NY.

source_name: DNA from Sor343


title: 448116A02_2012-09-07


title: 448116A01_2012-09-07

description: Mixture of DNA from RO29R4-Cy5 and Sor322-Cy3 Hyb. to aCGH

source_name: DNA from RO29R4

source_name: DNA from Sor322


title: BoneMarrow_DBA_Proband_0673_Treated

state: AR

department: Pediatrics/Hematology-Oncology

description: Genomic DNA extracted from unfractionated bone marrow cells was genotyped using Infinium HumanOmniOmniExpressExome Genotyping BeadChips (Illumina).

scan_protocol: Standard Illumina scanning protocol on S101 or N0345 scanner

source_name: Bone marrow while on lenolidamide treatment

value: Unfractionated Bone Marrow DNA

tag: lenolidamide treatment


title: NO-naproxen, biological rep2


title: BoneMarrowLymphoid_DBA_Proband_0673_Treated

description: Genomic DNA extracted from bone marrow cells retained on CD3/CD10 magnetic beads was genotyped using Infinium HumanOmniExpressExome Genotyping BeadChips (Illumina).

source_name: Lymphoid-enriched bone marrow while on lenolidamide treatment

value: Lymphoid Bone Marrow DNA

tag: relationship to proband


title: 446709A03_2012-09-07

description: Mixture of DNA from RO29R4-Cy5 and Sor321-Cy3 Hyb. to aCGH

source_name: DNA from Sor321


title: 446709A02_2012-09-07


title: 446709A01_2012-09-07

description: Mixture of DNA from JRCT1-Cy5 and Sor91-Cy3 Hyb. to aCGH

source_name: DNA from JRCT1

source_name: DNA from Sor91


title: 5B4 Replicate 2 Batch 4 ; Immunogen= 2007-08 ; Survive = No

type: protein

city: Tempe

first: Joseph

middle: Barten

last: Legutki

state: Arizona

address: 1001 S. McAllister Ave

department: Center for Innovations in Medicine

institute: The Biodesign Institute at Arizona State University

hyb_protocol: No hybridization was done, but antibodies were incubated with the peptide microarrays for 1 hour at room temperature according to Stafford et al. (Stafford, Halperin, Legutki, Magee, Galgiani, Johnston, Physical characterization of the Immunosignaturing Effect, MCP 11(4), 2012).

scan_protocol: Scanning was done on an Agilent C type scanner at 10um resolution, high laser power, 100% PMT, autofocus ON, 635nm.

data_processing:
Median normalization per array was done, and any negative values were adjusted to 0.01. ComBat normalization was used to remove batch effects with the Immunogen as the covariate.  Replicates were averaged.
GeneSpring 7.3.1 was used to load and median-normalize raw gpr files.  Matrix of values was copied directly from GeneSpring into Excel as double-precision values.

label: biotinylated anti-mouse IgG & streptavidin-Alexaflour647

molecule: protein

source_name: ASU

label_protocol: Alexafluor 647-labeled Streptavidin was used to detect biotinylated anti-mouse secondary antibody.

tag: source

value: serum

tag: immunogen

tag: survival

value: No


title: genomic DNA from differentiated, NLRP7 knockdown H9 hESC, replicate C

city: Houston

first: Sangeetha

middle: Kaveri

last: Mahadevan

state: Texas

address: 1250 Moursund St, Room 1025

department: Obsterics and Gynecology

institute: Baylor College of Medicine

description:
samples were hybridized on to 2 different arrays, this sample was done on array 2
H9-6C

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

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

data_processing:
non_normalized_array*.txt contains unmethylated and methylated signal intensities
Illumina Genome Studio Methylation data were imported into the Illumina Genome Studio software and converted to a Partek Project File (.ppj) with the Partek Methylation Module
GenomeStudio Data Analysis Software’s Gene Expression Module (GSGX) Version 1.1.0

label: Cy5 and Cy3

source_name: differentiated_NLRP7 knockdown H9 hESC

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from cultured cells using Gentra Puregene DNA extraction Kit according to standard instructions

tag: cell line

tag: cell type

value: Cultured hESC

tag: genotype/variation

value: NLRP7 knockdown


title: 5B4 Replicate 1 Batch 2 ; Immunogen= 2007-08 ; Survive = No


title: 5B3 Replicate 1 Batch 2 ; Immunogen= 2007-08 ; Survive = Yes

value: Yes


title: genomic DNA from undifferentiated, untransduced H9 hESC, replicate C

description:
samples were hybridized on to 2 different arrays, this sample was done on array 2
H9-1C

source_name: undifferentiated_untransduced H9 hESC

value: untransduced control


title: 5B3 Replicate 2 Batch 3 ; Immunogen= 2007-08 ; Survive = Yes


title: genomic DNA from differentiated, untransduced H9 hESC, replicate A

description:
samples were hybridized on to 2 different arrays, this sample was done on array 1
H9-4A

source_name: differentiated_untransduced H9 hESC


title: genomic DNA from undifferentiated, untransduced H9 hESC, replicate A

description:
samples were hybridized on to 2 different arrays, this sample was done on array 1
H9-1A


title: genomic DNA from differentiated, NLRP7 knockdown H9 hESC, replicate B

description:
samples were hybridized on to 2 different arrays, this sample was done on array 2
H9-6B


title: 5B2 Replicate 1 Batch 1 ; Immunogen= 2007-08 ; Survive = No


title: genomic DNA from undifferentiated, NLRP7 knockdown H9 hESC, replicate A

description:
samples were hybridized on to 2 different arrays, this sample was done on array 1
H9-3A

source_name: undifferentiated_NLRP7 knockdown H9 hESC


title: genomic DNA from differentiated, scrambled H9 hESC, replicate C

description:
samples were hybridized on to 2 different arrays, this sample was done on array 2
H9-5C

source_name: differentiated_scrambled H9 hESC

value: scrambled control