title: gcn5 mutant exposed to Congo Red 3 h_3

city: Madrid

first: Javier

last: Arroyo

state: Madrid

address: Plaza Ramón y Cajal, S/N

department: Facultad de Farmacia, Departamento de Microbiologia II

country: Spain

institute: Universidad Complutense de Madrid

description: All the procedure for microarrays experiments was carried out following the instructions of affymetrix for each of the steps

hyb_protocol: Following Affymetrix hybridation instructions

scan_protocol: Following Affymetrix scanning instructions

data_processing: CEL files from scaner were analyzed using GCRMA algorithm from Bioconductor software

organism: Saccharomyces cerevisiae

source_name: yeast

label_protocol: Following Affymetrix labelling instructions

growth_protocol: Cells were grown overnight in liquid media YPD. The culture was  refreshed to 0.2 (A600) in YPD, grown for an additional 2 h 30 min and then divided into two parts. One part continued growing under the same conditions (non-treated culture), while the other one was supplemented with Congo Red (CR) (30 µg/ml; Merck, Darmstadt, Germany), during 3 hours.

extract_protocol: Total RNA was isolated from exponentially growing cells by the “mechanical disruption protocol” using the RNeasy kit (Qiagen, Hilden, Germany), following the instructions of the manufacturer. RNA concentrations were determined by measuring absorbance at 260 nm. RNA purity and integrity were assessed using RNA Nano Labchips in an Agilent 2100B Bioanalyzer (Agilent Technologies, Palo Alto, CA) following the manufacturer’s instructions.

tag: genetic background

value: gcn5 mutant


title: wild type exposed to Congo Red 3 h_2

status: Public on Oct 01 2015

type: RNA

label: biotin

molecule: total RNA

treatment_protocol: Cells were grown overnight in liquid media YPD. The culture was  refreshed to 0.2 (A600) in YPD, grown for an additional 2 h 30 min and then divided into two parts. One part continued growing under the same conditions (non-treated culture), while the other one was supplemented with Congo Red (CR) (30 µg/ml; Merck, Darmstadt, Germany), during 3 hours.

tag: genotype/variation

value: wild type


title: wild type exposed to Congo Red 3 h_3


title: wild type exposed to Congo Red 3 h_1


title: gcn5 3 h_2


title: Fetal liver, p130 KO, rep1

city: New York

first: Paul

middle: A

last: Ney

state: NY

address: 310 E 67th St

country: USA

institute: New York Blood Center

description: p130 KO-1

hyb_protocol: Biotin-labeled cRNA (15ug) was hybridized overnight at 45C to the Mouse Genome 430 2.0 GeneChip array

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

data_processing: Expression values were summarized using the MAS5 algorithm as implemented in the GCOS v1.4 software. Signals were normalized for each array by scaling to a 2% trimmed mean of 500.

organism: Mus musculus

source_name: Freshly isolated, unfractionated fetal liver, p130 KO

label_protocol: Total RNA (1-10ug) was processed in the Hartwell Center microarray core according to the Affymetrix eukaryote one-cycle target labeling protocol (P/N 701025 Rev.6).

growth_protocol: Freshly isolated fetal liver cells.

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

treatment_protocol: The samples were untreated.

tag: tissue

value: liver

tag: developmental stage

value: E14.5 fetal

tag: genotype

value: p130 KO


title: Fetal liver, p107;p130 DKO, rep1

description: p107;p130 DKO-1

source_name: Freshly isolated, unfractionated fetal liver, p107;p130 DKO


title: gcn5 3 h_3


title: Spc1K49R-OP-biological replicate -2

city: Kolkata

first: Geetanjali

last: Sundaram

address: 35 Ballugunje circular road

department: Biochemistry

country: India

institute: University of Calcutta

hyb_protocol: GeneChip® Hybridization, Wash, and Stain Kit

scan_protocol: Affymetrix Scanner G 300 7G

data_processing: GeneSpring GX12.6

organism: Schizosaccharomyces pombe

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

extract_protocol: total RNA extraction using Epicentre yeast RNA extraction kit

tag: transfection


title: gcn5 3 h_1


title: control (empty vector OP)-biological replicate -1

value: empty vector


title: gcn5 mutant exposed to Congo Red 3 h_1


title: wild type 3 h_2


title: wild type 3 h_3


title: Fetal liver, p130 KO, rep2

description: p130 KO-2


title: gcn5 mutant exposed to Congo Red 3 h_2


title: wild type 3 h_1


title: wild-type

city: Suita

first: Junko

last: Kanoh

state: Osaka

address: 3-1 Yamadaoka

department: Institute for Protein Research

country: Japan

institute: Osaka University

description: Gene expression data of exponentially growing cells

hyb_protocol: After the fragmentation of the biotynylated cRNA, 5 microg of the cRNA were hybridized for 16 hours at 45C on GeneChip® Yeast Genome 2.0 Array (Affymetrix). The GeneChips were washed and stained using Mini_euk2v3 protocol in the Affymetrix Fluidics Station 400 (Affymetrix).

scan_protocol: The GeneChips were scanned with a GeneChip® Scanner 3000 G7 (Affymetrix).

data_processing: Data analyses were performed with GeneChip® Operating Software (GCOS 1.4) using default settings and scaling as mormalization method with s_pombe.msk file (Affymetrix) to mask S. cerevisiae probe sets.

molecule: polyA RNA

source_name: S. pombe exponentially growing cells

label_protocol: cDNA synthesis and biotinylated cRNA preparation were performed with GeneChip® One-Cycle Target Labeling and Control Reagents (Affymetrix) using 0.3 microg of polyA RNA.

growth_protocol: Cells were grown in YES liquid medium at 32˚C.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. And then mRNA was purified by oligo dT column.

treatment_protocol: 4×10^8 cells were used for RNA extraction. Cells were collected by centrifugation, washed by H2O once, and then freezed by liquid nitrogen.

tag: strain

tag: Stage

value: Exponentially growing cells

value: wild-type (h-)


title: WT_Propyl_Pyrazole_Triol_24h, rep2

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description:
251486831871_1_2
Gene expression in WT ovariectomized PPT 24 hour treated uterus.

hyb_protocol: For each sample, 1.65ug of Cy3-labeled cRNAs were fragmented and hybridized for 17 hours in a rotating hybridization oven.

scan_protocol: Slides were washed and then scanned with an Agilent Scanner.

data_processing: Data was obtained using the Agilent Feature Extraction software (v9.5), using the 1-color defaults for all parameters.

source_name: WT uterus, PPT treated 24 hours

label_protocol: Starting with 500ng of total RNA, Cy3-labeled cRNA was produced according to manufacturer’s protocol.

growth_protocol: WT mice were ovariectomized and rested for 10-14 days to clear endogenous ovarian hormones.

extract_protocol: Frozen uterine tissue was pulverized and each uterus was homogenized in 800 ul of Trizol (Invitrogen) with 250 ug/ml glycogen. Extraction proceeded as described in manufacturer's protocol. Following resuspension of RNA pellet, a second precipitation was done. RNA was DNase treated and cleaned up using RNeasy kits.

treatment_protocol: Mice were injected with 100 ul saline, E2, DES or PPT and uteri were collected 2 or 24 hours later and snap frozen in liquid nitrogen.

tag: strain/background

value: WT

tag: age

value: adult (10+ weeks)

tag: gender

value: ovariectomized female

value: uterus

tag: treatment

value: propyl pyrazole triol (PPT)

tag: time point

value: 24 hours


title: Fetal liver, p107;p130 DKO, rep5

description: p107;p130 DKO-5


title: sgo2-deletion

value: Sgo2-deleted (h-)


title: WT_diethystilbestrol_24h, rep2

description:
251486831473_1_2
Gene expression in WT ovariectomized DES 24 hour treated uterus.

source_name: WT uterus, DES treated 24 hours

value: diethylstilbestrol (DES)


title: WT_Propyl_Pyrazole_Triol_24h, rep1

description:
251486831870_1_2
Gene expression in WT ovariectomized PPT 24 hour treated uterus.


title: WT_Propyl_Pyrazole_Triol_2h, rep2

description:
251486831472_1_2
Gene expression in WT ovariectomized PPT 2 hour treated uterus.

source_name: WT uterus, PPT treated 2 hours

value: 2 hours


title: WT_Propyl_Pyrazole_Triol_2h, rep1

description:
251486831871_1_1
Gene expression in WT ovariectomized PPT 2 hour treated uterus.


title: WT_diethystilbestrol_2h, rep1

description:
251486831473_1_1
Gene expression in WT ovariectomized DES 2 hour treated uterus.

source_name: WT uterus, DES treated 2 hours


title: WT_diethystilbestrol_2h, rep2

description:
251486831573_1_1
Gene expression in WT ovariectomized DES 2 hour treated uterus.


title: WT_estradiol_2h, rep1

description:
251486831574_1_2
Gene expression in WT ovariectomized E2 2 hour treated uterus.

source_name: WT uterus, E2 treated 2 hours

value: estradiol (E2)


title: WT_estradiol_2h, rep2

description:
251486831869_1_1
Gene expression in WT ovariectomized E2 2 hour treated uterus.


title: WT_Saline_24h, rep1

description:
251486831572_1_4
Gene expression in WT ovariectomized saline vehicle treated uterus.

source_name: WT uterus, saline control

value: saline control


title: BMP4.3

city: Chicago

first: Chian-Yu

last: Peng

state: IL

address: 303 E. Chicago, Ave.

department: Neurology

institute: Northwestern University

description: SAMPLE 11

hyb_protocol: Performed using standard Illumina protocol on Illumina Mouse6 v1.1 bead arrays by Northwestern University Genomics Core facility

scan_protocol: Arrays were scanned with an Illumina BeadArray Reader confocal scanner (BeadStation 500GXDW) according to the manufacturer's instructions.

data_processing: Array data was processed on Illumina BeadStudio software v.3 and were normalised using the default quantile normalisation with R/bioconductor package lumi version 2.15.1.

label: Biotin

source_name: Astrocytes generated from neural stem cells differentiated for 7 days with BMP4

label_protocol: The resulting cDNA was biotin labeled using the Illumina biotinylation kit.

growth_protocol: Dissected and chopped subventricular tissue from postnatal day 1 mouse brain was incubated with 0.05% trypsin for 5min, quenched with trypsin inhibitor, and then titerated to dissociate into single cells. Cells were filtered through 70 micrometer filter and resuspended at 50 cells per microliter concentration in neurosphere growth media containing DMEM/F12, N2/B27 supplements, and 20ng/ml EGF for 3 days before passaging. Cells are infected after passage 1 with GFAP-GFP (LIF.NOG and BMP4 groups) or control GFP (Neurosphere group) retroviruses and grow 3 more days before isolating for GFP-expressing cells by FACS for differentiation.

extract_protocol: Total RNA was extracted using RNAqeous for PCR kit (Ambion/Life technology) following manufacturer's instructions.

treatment_protocol: Total RNA was harvested from FACS sorted neurospheres for the neurosphere group. For astrocyte groups, sorted cells were plated at 20 cells per microliter in differentiation media (neurosphere growth media with 1ng/ml EGF) with either recombinant human BMP4 (20ng/ml, R&D) or LIF (20ng/ml, R&D) plus noggin (250ng/ml, R&D). Cytokines were replenished 3 days after plating at half concentration and cells were harvested on day 7 for total RNA extraction.

tag: strain background

value: Postnatal Day 1

tag: tissue source

value: brain; subventricular tissue

tag: cell type

value: neural stem cells (NSCs)

tag: transfected with

value: GFAP-GFP retrovirus

tag: cell subtype

value: Astrocytes generated from NSCs differentiated for 7 days with BMP4


title: WT_Saline_24h, rep2

description:
251486831574_1_1
Gene expression in WT ovariectomized saline vehicle treated uterus.

tag: genotype/variation


title: WT_estradiol_24h, rep1

description:
251486831573_1_2
Gene expression in WT ovariectomized E2 24 hour treated uterus.

source_name: WT uterus, E2 treated 24 hours

tag: tissue


title: BMP4.4

description: SAMPLE 12


title: Neurosphere.4

description: SAMPLE 4

source_name: Neural stem cells from postnatal day 1 mouse subventricular zone

value: control GFP retrovirus


title: BMP4.1

description: SAMPLE 9


title: LIF.NOG.3

description: SAMPLE 7

source_name: Astrocytes generated from neural stem cells differentiated for 7 days with LIF and noggin

value: Astrocytes generated from NSCs differentiated for 7 days with LIF and noggin


title: LIF.NOG.1

description: SAMPLE 5


title: Neurosphere.3

description: SAMPLE 3


title: Control 2

city: rennes

first: Chunxiang

last: HAO

address: 263, ave du Général Leclerc

country: France

institute: Université de Rennes 1

description: The gene expression data from control testis tissue

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US) in Hybridization Oven 645 (Cat#00‐0331‐220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00‐0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00‐00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Obtained raw data (.CEL intensity files) were processed with Affymetrix Expression Console where RMA was applied yielding normalized, log2 transformed signal intensities.

source_name: whole testis from 10 weeks adult control mice

label_protocol: Total RNA were amplified, labeled and purified by using Affymetrix WT Terminal Labeling Kit (Cat#900671)

extract_protocol: Total RNA from testi  was extracted by using TRIzol reagent (Life Technologies)

treatment_protocol: Mice were treated 3 weeks with atrazine at a concentration of 100 mg/l in drinking water nearly corresponding to 25mg/kg/days. Treatment was stopped two weeks after to observe the effect of atrazine on a complete round of spermatogenesis from moment of treatment.

value: Testis


title: BMP4.2

description: SAMPLE 10


title: LIF.NOG.4

description: SAMPLE 8


title: Control 3


title: Neurosphere.1

description: SAMPLE 1


title: WT_diethystilbestrol_24h, rep1

description:
251486831472_1_1
Gene expression in WT ovariectomized DES 24 hour treated uterus.

value: WT

value: adult (10+ weeks)

value: ovariectomized female


title: Atrazine_treated 3

description: The gene expression data from ATZ treated testis tissue

source_name: whole testis from 10 weeks adult mice treated with ATZ


title: Neurosphere.2

description: SAMPLE 2


title: Atrazine_treated 2


title: WT_estradiol_24h, rep2

description:
251486831870_1_1
Gene expression in WT ovariectomized E2 24 hour treated uterus.

value: uterus

value: 24 hours


title: LIF.NOG.2

description: SAMPLE 6


title: HMD-GATA1_3

city: Cambridge

first: Vijay

middle: G

last: Sankaran

state: MA

address: 7 Cambridge Center

institute: Broad Institute

hyb_protocol: Standard Affymetrix Human Gene ST 2.0 arrays were hybridized with purified RNA samples.

scan_protocol: Signal amplication on Affymetrix Fluidics station 400

data_processing: Microarrays (GeneChip® Human Gene 2.0 ST Arrays, Affymetrix) were performed 48 hours after infection. Raw files were processed and normalized using the RMA algorithm from the oligo package in R 3.2 (Carvalho and Irizarry, 2010). Differential expression analyses were conducted using limma (Ritchie et al., 2015). Gene set enrichment analysis (GSEA) was performed comparing GATA1 overexpression to control with gene set permutation (Subramanian et al., 2005). The erythroid differentiation signature gene set was derived by identifying the top 200 genes that were expressed significantly higher in intermediate erythroblasts (CD71+/ CD235a+) compared to colony forming unit erythroid cells (CD71+/ CD235a-) (Merryweather-Clarke et al., 2011). The GATA1 target gene set has been previously described (Ludwig et al., 2014).

organism: Homo sapiens

label_protocol: Standard Affymetrix label protocol

growth_protocol: The erythroleukemia K562 cell line was cultured in RPMI medium with 10% FBS, Penicillin/ Streptomycin, and Glutamine.

extract_protocol: Qiagen RNA purification

treatment_protocol: For HMD-GATA1, we infected 500,000 K562 cells per well of a 6-well plate with 1.9ml of viral supernatant in the presence of polybrene (8ug/ml). Cells were spun at 2,500 rpm for 90 min at 22 °C and incubated overnight in the viral supernatant. Media was replaced 24 hours after infection, and 3 days later the cells were checked for GFP expression by flow cytometry to assess for infectivity, which was typically around 90%.

tag: cell line


title: Fibroblast_Serum_Challenged_60min_Patient#2

city: Berlin

first: Markus

last: Schuelke

state: Berlin

address: Augustenburger Platz 1

department: Neuropediatrics

country: Germany

institute: Charite

hyb_protocol: According to the Affymetrix protocol for the GeneChip® Human Gene 2.0 ST Array in a certified laboratory.

scan_protocol: 428 scanner (Affymetrix), according to the Affymetrix protocol for GeneChip® Human Gene 2.0 ST Array in a certified laboratory

data_processing:
RMA for Affymetrix data; generation of CEL files using the original Affymetrix software.
Normalization on the GenePattern platform using PreprocessDatset with the following parameters: threshold filter: yes; floor: 20; ceiling: 20000; min fold change: 1.5; min delta: 100, row normalization: yes; log2 transform: no

growth_protocol: Growth of fibroblasts in DMEM + 15% FBS + Pen/Strep until semiconfluency

extract_protocol: TRIzol method according to the manufacturers instructions

treatment_protocol: Serum challenge (after starvation) with DMEM + 15% FBS + Penicillin/Streptomycin for 60 minutes

tag: affected

value: affected

tag: genotype

value: Cultured skin fibroblasts (passage 3)


title: Fibroblast_Serum_Challenged_30min_Patient#2

label_protocol: According to the Affymetrix protocol for the GeneChip® Human Gene 2.0 ST Array in a certified laboratory.

treatment_protocol: Serum challenge (after starvation) with DMEM + 15% FBS + Penicillin/Streptomycin for 30 minutes


title: Fibroblast_Serum_Starved_Patient#2

treatment_protocol: Serum starvation für 24 h by growth in DMEM + 0.5% FBS + Penicillin/Streptomycin


title: HMD_2


title: Fibroblast_Serum_Challenged_60min_Patient#1


title: HMD-GATA1_1


title: GATA5-KD cells rep3

city: Ottawa

first: Smail

last: Messaoudi

state: Ontario

address: 451 smyth road

department: BMI

country: Canada

institute: University of Ottawa

description: Gene expression data from Human dermal microvascular endothelial cells infected with lentivirus containing anti-Gata5 shRNA replicate 3

hyb_protocol: Biotin-labeled cDNA probes were hybridized for 17 hr at 45C to the Human Gene 2.0 ST Array.  Genechips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Arrays were scanned with the Affymetrix Genechip scanner 7G

data_processing: RMA expression values were generated the Affymetrix Expression Console v1.4.1.46 . All fold change analysis was performed using the R package limma, p-values were BH adjusted. HuGene chip annotations are based on the HuGene-2_0-st-v1.na35.hg19.transcript.csv annotations downloaded from Affymetrix; the first gene identifier associated with a given probeset (transcript cluster identifier) was chosen as the symbol representing it.

label_protocol: cDNA were prepared from 300 ng of Total RNA using the Ambion WT Expression Kit (PN4411974).  Fragmentation and labeling of cDNA was performed using the Affymetrix GeneChip® WT Terminal Labeling Kit (PN 901524).

growth_protocol: Gata5 MISSION® TRC2 pLKO.shRNA (TRCN0000431556) and MISSION® TRC2 pLKO-puro Non-Mammalian shRNA Control (SHC202) plasmids were purchased from Sigma-Aldrich (ref xxx). Viral particles were generated by co-transfection of phoenix cells with the lentiviral vector (Gata5 TRC2 shRNA or the shRNA control plasmids), the packaging vector psPAX2 and the envelope vector pMD2G. Co-transfection was performed using the Qiagen’s Effectene transfection reagent (301425). Twenty-four hours after transfection, medium was discarded and replaced by Endothelial Growth Medium 2 (Promocell, C-22021). Forty-eight hours later, the medium (EGM2) was collected, filtered, and used for infection of Human Dermal Microvascular Endothelial Cells (HDMEC; Promocell, C-14016). Infected cells were selected with addition of puromycin (Sigma-Aldrich, P8833) to culture medium at the concentration of 2.5 μg/ml for 15 days. Control (pLKO) and Gata5-KD cells were then grown and maintained in EGM2 containing puromycine at the concentration of 0.25 μg/ml.

extract_protocol: Total RNA extraction was performed using Qiagen RNEASY minikit following the manufacturer recommendations


title: Fibroblast_Serum_Challenged_30min_Patient#1


title: Fibroblast_Serum_Starved_Patient#1


title: HMD_1


title: GATA5-KD cells rep1

description: Gene expression data from Human dermal microvascular endothelial cells infected with lentivirus containing anti-Gata5 shRNA replicate 1


title: Fibroblast_Serum_Challenged_60min_Control#4

value: healthy

value: wildtype


title: Fibroblast_Serum_Challenged_30min_Control#3


title: Fibroblast_Serum_Challenged_60min_Control#3


title: Fibroblast_Serum_Challenged_30min_Control#2


title: Fibroblast_Serum_Starved_Control#4


title: Fibroblast_Serum_Starved_Control#3


title: Ctrl cells rep3

description: Gene expression data from Human dermal microvascular endothelial cells infected with lentivirus containing empty vector replicate 3


title: Fibroblast_Serum_Starved_Control#2


title: GATA5-KD cells rep2

description: Gene expression data from Human dermal microvascular endothelial cells infected with lentivirus containing anti-Gata5 shRNA replicate 2


title: HMD-GATA1_2


title: Ctrl cells rep2

description: Gene expression data from Human dermal microvascular endothelial cells infected with lentivirus containing empty vector replicate 2


title: HMD_3


title: Ctrl cells rep1

description: Gene expression data from Human dermal microvascular endothelial cells infected with lentivirus containing empty vector replicate 1


title: Fibroblast_Serum_Challenged_30min_Control#4


title: Fibroblast_Serum_Challenged_30min_Control#1


title: Control 1

tag: strain


title: Fibroblast_Serum_Challenged_60min_Control#1


title: TNF-α treated U6A cells+S734>A-STAT2, rep1

city: Philadelphia

first: Ana

middle: Maria

last: Gamero

state: PA

address: 3440 N. Broad St.

institute: Temple University

description: U6A cells+S734- STAT2

hyb_protocol: RNA samples were labeled and hybridized to the Affymetrix mouse Gene 2.0 ST Array according to the manufacturer's instructions.

data_processing: Affymetrix data were RMA-normalized using Affymetrix Expression Console Software, version 1.3.1

source_name: U6A cells+S734- STAT2

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

growth_protocol: Tumor cells were maintained in complete DMEM medium containing 10% fetal calf serum and antibiotics at 37oC.

extract_protocol: Total RNA was isolated using TRIzol reagent (Invitrogen, Carlsbad, CA) and further purified by RNeasy kit (Qiagen, Valencia, CA).  The quality of total RNA was assessed using an Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA).

treatment_protocol: Tumor cells were seeded on 100mm dishes and left to adhere overnight. The next day cells were left untreated or treated with IFN-α (1000U/mL) or TNF-α (10ng/mL) for 4 hours at 37oC.

value: TNF

value: U6A (STAT2 null 2fTGH)


title: Fibroblast_Serum_Challenged_60min_Control#2


title: TNF-α treated U6A cells+S734>A-STAT2, rep3

description: U6A cells+S734- STAT2


title: TNF-α treated U6A cells+S734>A-STAT2, rep2

description: U6A cells+S734- STAT2


title: IFN-α treated U6A cells+STAT2, rep3

description: U6A cells+WT STAT2

source_name: U6A cells+WT STAT2

value: IFN


title: Fibroblast_Serum_Starved_Control#1


title: 43hpi Unlabeled

city: University Park

first: Heather

middle: J

last: Painter

state: Pennsylvania

address: Millennium Science Center

department: Molecular Biology & Biochemistry

institute: Penn State University

description: Sample name: 43 hpi U

hyb_protocol: Painter, H. J., Altenhofen, L. M., Kafsack, B. F. C. & Llinás, M. Whole-genome analysis of Plasmodium spp. Utilizing a new agilent technologies DNA microarray platform. Methods Mol. Biol. 923, 213–219 (2013).

scan_protocol: Agilent G2505B Microarray Scanner. Images were quantified using Agilent Feature Extraction Software (version 9.5.3.1).

data_processing: Agilent Feature Extraction Software (v 9.5.3.1) was used for background subtraction and dye bias correction.  Princeton University Microarray Database (https://puma.princeton.edu/) was utilized for log2 ratio calculation. Data normalization is based upon a novel methodology as follows: 1) filter out probes that are AGILENT_CONTROL, *rRNA*, NOT_UNIQUE, and NO_HIT 2) Determine log2 ratio (normalized based on intensity and background subtraction) on a set of 47 expression profiles for each sample type (Total, Unlabeled, and Label).  3) smooth 48 time-course profiles of each probe. 4) set negative values to a small positive value. 5) fit non-negative least squares (NNLS) for each probe to estimate how much of the unlabeled and labeled gene expression cntribute to the total gene expression. 6) compute fitted values for Total sample by adding estimated unlabeled and estimated labeled expression.

organism: Plasmodium falciparum

source_name: 43 hpi 3D7attb::yFCU

growth_protocol: P. falciparum strain 3D7 was highly synchronized parasites were grown under standard culturing conditions

extract_protocol: Starting at 0 hours post invasion, samples were harvested in Trizol for total RNA extraction every hour for 48 hours.

treatment_protocol: 50ml of standard culture was pulsed with 40uM 4-TU for 10 min prior to Trizol RNA extraction.  This was repeated every hour for 48 hours of intraerythrocytic development

tag: time (hours post invasion)

value: 43 hpi

tag: sample type

value: Unlabeled RNA

source_name: 3D7 Mixed Stage Reference Pool

tag: stages

value: Mixed stages


title: 42hpi Unlabeled

description: Sample name: 42 hpi U

source_name: 42 hpi 3D7attb::yFCU

label_protocol: Painter, H. J., Altenhofen, L. M., Kafsack, B. F. C. & Llinás, M. Whole-genome analysis of Plasmodium spp. Utilizing a new agilent technologies DNA microarray platform. Methods Mol. Biol. 923, 213–219 (2013).

value: 42 hpi


title: untreated U6A cells+S734>A-STAT2, rep3

description: U6A cells+S734- STAT2


title: TNF-α treated U6A cells+STAT2, rep3

description: U6A cells+WT STAT2


title: untreated U6A cells+STAT2, rep2

description: U6A cells+WT STAT2


title: IFN-α treated U6A cells+S734>A-STAT2, rep2

description: U6A cells+S734- STAT2


title: 44hpi Unlabeled

description: Sample name: 44 hpi U

source_name: 44 hpi 3D7attb::yFCU

value: 44 hpi


title: 46hpi Unlabeled

description: Sample name: 46 hpi U

source_name: 46 hpi 3D7attb::yFCU

value: 46 hpi


title: 47hpi Unlabeled

description: Sample name: 47 hpi U

source_name: 47 hpi 3D7attb::yFCU

value: 47 hpi


title: untreated U6A cells+S734>A-STAT2, rep2

description: U6A cells+S734- STAT2


title: IFN-α treated U6A cells+STAT2, rep2

description: U6A cells+WT STAT2

value: WT


title: untreated U6A cells+S734>A-STAT2, rep1

description: U6A cells+S734- STAT2


title: IFN-α treated U6A cells+S734>A-STAT2, rep1

description: U6A cells+S734- STAT2


title: IFN-α treated U6A cells+STAT2, rep1

description: U6A cells+WT STAT2


title: TNF-α treated U6A cells+STAT2, rep1

description: U6A cells+WT STAT2


title: 45hpi Unlabeled

description: Sample name: 45 hpi U

source_name: 45 hpi 3D7attb::yFCU

value: 45 hpi


title: untreated U6A cells+STAT2, rep3

description: U6A cells+WT STAT2


title: untreated U6A cells+STAT2, rep1

description: U6A cells+WT STAT2


title: 41hpi Unlabeled

description: Sample name: 41 hpi U

source_name: 41 hpi 3D7attb::yFCU

value: 41 hpi


title: TNF-α treated U6A cells+STAT2, rep2

description: U6A cells+WT STAT2


title: 40hpi Unlabeled-2

description: Sample name: 40 hpi U

source_name: 40 hpi 3D7attb::yFCU

value: 40 hpi


title: 36hpi Unlabeled

description: Sample name: 36 hpi U

source_name: 36 hpi 3D7attb::yFCU

value: 36 hpi


title: 39hpi Unlabeled

description: Sample name: 39 hpi U

source_name: 39 hpi 3D7attb::yFCU

value: 39 hpi


title: 38hpi Unlabeled-2

description: Sample name: 38 hpi U

source_name: 38 hpi 3D7attb::yFCU

value: 38 hpi


title: 37hpi Unlabeled

description: Sample name: 37 hpi U

source_name: 37 hpi 3D7attb::yFCU

value: 37 hpi


title: 34hpi Unlabeled

description: Sample name: 34 hpi U

source_name: 34 hpi 3D7attb::yFCU

value: 34 hpi


title: 35hpi Unlabeled

description: Sample name: 35 hpi U

source_name: 35 hpi 3D7attb::yFCU

value: 35 hpi


title: 29hpi Unlabeled

description: Sample name: 29 hpi U

source_name: 29 hpi 3D7attb::yFCU

value: 29 hpi


title: 23hpi Unlabeled

description: Sample name: 23 hpi U

source_name: 23 hpi 3D7attb::yFCU

value: 23 hpi

value: Unlabeled RNA


title: 28hpi Unlabeled

description: Sample name: 28 hpi U

source_name: 28 hpi 3D7attb::yFCU

value: 28 hpi

value: Mixed stages


title: 26hpi Unlabeled

description: Sample name: 26 hpi U

source_name: 26 hpi 3D7attb::yFCU

value: 26 hpi

source_name: 3D7 Mixed Stage Reference Pool


title: 27hpi Unlabeled

description: Sample name: 27 hpi U

source_name: 27 hpi 3D7attb::yFCU

value: 27 hpi


title: 32hpi Unlabeled

description: Sample name: 32 hpi U

source_name: 32 hpi 3D7attb::yFCU

value: 32 hpi


title: 24hpi Unlabeled

description: Sample name: 24 hpi U

source_name: 24 hpi 3D7attb::yFCU

value: 24 hpi


title: 17hpi Unlabeled

description: Sample name: 17 hpi U

source_name: 17 hpi 3D7attb::yFCU

value: 17 hpi


title: 30hpi Unlabeled

description: Sample name: 30 hpi U

source_name: 30 hpi 3D7attb::yFCU

value: 30 hpi


title: 20hpi Unlabeled-2

description: Sample name: 20 hpi U

source_name: 20 hpi 3D7attb::yFCU

value: 20 hpi


title: 16hpi Unlabeled

description: Sample name: 16 hpi U

source_name: 16 hpi 3D7attb::yFCU

value: 16 hpi


title: 18hpi Unlabeled-2

description: Sample name: 18 hpi U

source_name: 18 hpi 3D7attb::yFCU

value: 18 hpi


title: 31hpi Unlabeled

description: Sample name: 31 hpi U

source_name: 31 hpi 3D7attb::yFCU

value: 31 hpi


title: 33hpi Unlabeled

description: Sample name: 33 hpi U

source_name: 33 hpi 3D7attb::yFCU

value: 33 hpi


title: 19hpi Unlabeled-2

description: Sample name: 19 hpi U

source_name: 19 hpi 3D7attb::yFCU

value: 19 hpi


title: Atrazine_treated 1

source_name: whole testis from 10 weeks adult mice treated with ATZ

value: Testis


title: 22hpi Unlabeled-2

description: Sample name: 22 hpi U

source_name: 22 hpi 3D7attb::yFCU

value: 22 hpi


title: 15hpi Unlabeled-2

description: Sample name: 15 hpi U

source_name: 15 hpi 3D7attb::yFCU

value: 15 hpi

value: Unlabeled RNA


title: 25hpi Unlabeled

description: Sample name: 25 hpi U

source_name: 25 hpi 3D7attb::yFCU

value: 25 hpi

value: Mixed stages


title: 21hpi Unlabeled-2

description: Sample name: 21 hpi U

source_name: 21 hpi 3D7attb::yFCU

value: 21 hpi


title: 9hpi Unlabeled

description: Sample name: 9 hpi U

source_name: 9 hpi 3D7attb::yFCU

value: 9 hpi

source_name: 3D7 Mixed Stage Reference Pool


title: 8hpi Unlabeled

description: Sample name: 8 hpi U

source_name: 8 hpi 3D7attb::yFCU

value: 8 hpi


title: 14hpi Unlabeled

description: Sample name: 14 hpi U

source_name: 14 hpi 3D7attb::yFCU

value: 14 hpi


title: 10hpi Unlabeled

description: Sample name: 10 hpi U

source_name: 10 hpi 3D7attb::yFCU

value: 10 hpi


title: 12hpi Unlabeled

description: Sample name: 12 hpi U

source_name: 12 hpi 3D7attb::yFCU

value: 12 hpi


title: 11hpi Unlabeled

description: Sample name: 11 hpi U

source_name: 11 hpi 3D7attb::yFCU

value: 11 hpi


title: 5hpi Unlabeled

description: Sample name: 5 hpi U

source_name: 5 hpi 3D7attb::yFCU

value: 5 hpi


title: 7hpi Unlabeled-2

description: Sample name: 7 hpi U

source_name: 7 hpi 3D7attb::yFCU

value: 7 hpi


title: 6hpi Unlabeled

description: Sample name: 6 hpi U

source_name: 6 hpi 3D7attb::yFCU

value: 6 hpi


title: 45hpi Labeled

description: Sample name: 45 hpi L

source_name: 45 hpi 3D7attb::yFCU

value: 45 hpi

value: 4-TU Labeled RNA


title: 2hpi Unlabeled

description: Sample name: 2 hpi U

source_name: 2 hpi 3D7attb::yFCU

value: 2 hpi


title: 3hpi Unlabeled

description: Sample name: 3 hpi U

source_name: 3 hpi 3D7attb::yFCU

value: 3 hpi


title: 46hpi Labeled

description: Sample name: 46 hpi L

source_name: 46 hpi 3D7attb::yFCU

value: 46 hpi


title: 38hpi Labeled

description: Sample name: 38 hpi L

source_name: 38 hpi 3D7attb::yFCU

value: 38 hpi


title: 47hpi Labeled

description: Sample name: 47 hpi L

source_name: 47 hpi 3D7attb::yFCU

value: 47 hpi

value: Mixed stages


title: 39hpi Labeled-2

description: Sample name: 39 hpi L

source_name: 39 hpi 3D7attb::yFCU

value: 39 hpi


title: 44hpi Labeled

description: Sample name: 44 hpi L

source_name: 44 hpi 3D7attb::yFCU

value: 44 hpi


title: 0hpi Unlabeled

description: Sample name: 0 hpi U

source_name: 0 hpi 3D7attb::yFCU

value: 0 hpi

value: Unlabeled RNA

source_name: 3D7 Mixed Stage Reference Pool


title: 36hpi Labeled

description: Sample name: 36 hpi L

source_name: 36 hpi 3D7attb::yFCU

value: 36 hpi


title: 13hpi Unlabeled-2

description: Sample name: 13 hpi U

source_name: 13 hpi 3D7attb::yFCU

value: 13 hpi


title: 1hpi Unlabeled

description: Sample name: 1 hpi U

source_name: 1 hpi 3D7attb::yFCU

value: 1 hpi


title: 43hpi Labeled

description: Sample name: 43 hpi L

source_name: 43 hpi 3D7attb::yFCU

value: 43 hpi


title: 40hpi Labeled

description: Sample name: 40 hpi L

source_name: 40 hpi 3D7attb::yFCU

value: 40 hpi


title: 42hpi Labeled

description: Sample name: 42 hpi L

source_name: 42 hpi 3D7attb::yFCU

value: 42 hpi


title: 35hpi Labeled

description: Sample name: 35 hpi L

source_name: 35 hpi 3D7attb::yFCU

value: 35 hpi

value: 4-TU Labeled RNA


title: 4hpi Unlabeled

description: Sample name: 4 hpi U

source_name: 4 hpi 3D7attb::yFCU

value: 4 hpi


title: 33hpi Labeled

description: Sample name: 33 hpi L

source_name: 33 hpi 3D7attb::yFCU

value: 33 hpi


title: 41hpi Labeled

description: Sample name: 41 hpi L

source_name: 41 hpi 3D7attb::yFCU

value: 41 hpi


title: 32hpi Labeled

description: Sample name: 32 hpi L

source_name: 32 hpi 3D7attb::yFCU

value: 32 hpi


title: 34hpi Labeled

description: Sample name: 34 hpi L

source_name: 34 hpi 3D7attb::yFCU

value: 34 hpi

value: Mixed stages


title: 37hpi Labeled-2

description: Sample name: 37 hpi L

source_name: 37 hpi 3D7attb::yFCU

value: 37 hpi


title: 31hpi Labeled

description: Sample name: 31 hpi L

source_name: 31 hpi 3D7attb::yFCU

value: 31 hpi


title: 29hpi Labeled

description: Sample name: 29 hpi L

source_name: 29 hpi 3D7attb::yFCU

value: 29 hpi


title: 28hpi Labeled

description: Sample name: 28 hpi L

source_name: 28 hpi 3D7attb::yFCU

value: 28 hpi


title: 30hpi Labeled

description: Sample name: 30 hpi L

source_name: 30 hpi 3D7attb::yFCU

value: 30 hpi

source_name: 3D7 Mixed Stage Reference Pool


title: 27hpi Labeled

description: Sample name: 27 hpi L

source_name: 27 hpi 3D7attb::yFCU

value: 27 hpi


title: 25hpi Labeled

description: Sample name: 25 hpi L

source_name: 25 hpi 3D7attb::yFCU

value: 25 hpi


title: 24hpi Labeled

description: Sample name: 24 hpi L

source_name: 24 hpi 3D7attb::yFCU

value: 24 hpi


title: 26hpi Labeled

description: Sample name: 26 hpi L

source_name: 26 hpi 3D7attb::yFCU

value: 26 hpi


title: 22hpi Labeled

description: Sample name: 22 hpi L

source_name: 22 hpi 3D7attb::yFCU

value: 22 hpi


title: 21hpi Labeled

description: Sample name: 21 hpi L

source_name: 21 hpi 3D7attb::yFCU

value: 21 hpi

value: 4-TU Labeled RNA


title: 20hpi Labeled

description: Sample name: 20 hpi L

source_name: 20 hpi 3D7attb::yFCU

value: 20 hpi


title: 23hpi Labeled

description: Sample name: 23 hpi L

source_name: 23 hpi 3D7attb::yFCU

value: 23 hpi


title: 19hpi Labeled

description: Sample name: 19 hpi L

source_name: 19 hpi 3D7attb::yFCU

value: 19 hpi


title: 12hpi Labeled

description: Sample name: 12 hpi L

source_name: 12 hpi 3D7attb::yFCU

value: 12 hpi


title: 17hpi Labeled

description: Sample name: 17 hpi L

source_name: 17 hpi 3D7attb::yFCU

value: 17 hpi

value: Mixed stages


title: 16hpi Labeled

description: Sample name: 16 hpi L

source_name: 16 hpi 3D7attb::yFCU

value: 16 hpi


title: 13hpi Labeled

description: Sample name: 13 hpi L

source_name: 13 hpi 3D7attb::yFCU

value: 13 hpi


title: 10hpi Labeled

description: Sample name: 10 hpi L

source_name: 10 hpi 3D7attb::yFCU

value: 10 hpi


title: 15hpi Labeled-2

description: Sample name: 15 hpi L

source_name: 15 hpi 3D7attb::yFCU

value: 15 hpi


title: 11hpi Labeled

description: Sample name: 11 hpi L

source_name: 11 hpi 3D7attb::yFCU

value: 11 hpi


title: 18hpi Labeled

description: Sample name: 18 hpi L

source_name: 18 hpi 3D7attb::yFCU

value: 18 hpi

source_name: 3D7 Mixed Stage Reference Pool


title: 9hpi Labeled

description: Sample name: 9 hpi L

source_name: 9 hpi 3D7attb::yFCU

value: 9 hpi


title: 14hpi Labeled

description: Sample name: 14 hpi L

source_name: 14 hpi 3D7attb::yFCU

value: 14 hpi


title: 4hpi Labeled

description: Sample name: 4 hpi L

source_name: 4 hpi 3D7attb::yFCU

value: 4 hpi


title: 3hpi Labeled

description: Sample name: 3 hpi L

source_name: 3 hpi 3D7attb::yFCU

value: 3 hpi


title: 6hpi Labeled

description: Sample name: 6 hpi L

source_name: 6 hpi 3D7attb::yFCU

value: 6 hpi

value: 4-TU Labeled RNA


title: 8hpi Labeled

description: Sample name: 8 hpi L

source_name: 8 hpi 3D7attb::yFCU

value: 8 hpi


title: 7hpi Labeled

description: Sample name: 7 hpi L

source_name: 7 hpi 3D7attb::yFCU

value: 7 hpi


title: 2hpi Labeled

description: Sample name: 2 hpi L

source_name: 2 hpi 3D7attb::yFCU

value: 2 hpi


title: 5hpi Labeled

description: Sample name: 5 hpi L

source_name: 5 hpi 3D7attb::yFCU

value: 5 hpi


title: 1hpi Labeled

description: Sample name: 1 hpi L

source_name: 1 hpi 3D7attb::yFCU

value: 1 hpi

value: Mixed stages


title: 46hpi Total

description: Sample name: 46 hpi T

source_name: 46 hpi 3D7attb::yFCU

value: 46 hpi

value: Total RNA


title: 47hpi Total

description: Sample name: 47 hpi T

source_name: 47 hpi 3D7attb::yFCU

value: 47 hpi


title: 39hpi Total

description: Sample name: 39 hpi T

source_name: 39 hpi 3D7attb::yFCU

value: 39 hpi


title: 38hpi Total-2

description: Sample name: 38 hpi T

source_name: 38 hpi 3D7attb::yFCU

value: 38 hpi


title: 44hpi Total

description: Sample name: 44 hpi T

source_name: 44 hpi 3D7attb::yFCU

value: 44 hpi


title: 42hpi Total

description: Sample name: 42 hpi T

source_name: 42 hpi 3D7attb::yFCU

value: 42 hpi


title: 43hpi Total

description: Sample name: 43 hpi T

source_name: 43 hpi 3D7attb::yFCU

value: 43 hpi

source_name: 3D7 Mixed Stage Reference Pool


title: 31hpi Total

description: Sample name: 31 hpi T

source_name: 31 hpi 3D7attb::yFCU

value: 31 hpi


title: 35hpi Total

description: Sample name: 35 hpi T

source_name: 35 hpi 3D7attb::yFCU

value: 35 hpi


title: 0hpi Labeled

description: Sample name: 0 hpi L

source_name: 0 hpi 3D7attb::yFCU

value: 0 hpi

value: 4-TU Labeled RNA


title: 37hpi Total-2

description: Sample name: 37 hpi T

source_name: 37 hpi 3D7attb::yFCU

value: 37 hpi


title: 40hpi Total

description: Sample name: 40 hpi T

source_name: 40 hpi 3D7attb::yFCU

value: 40 hpi


title: 30hpi Total

description: Sample name: 30 hpi T

source_name: 30 hpi 3D7attb::yFCU

value: 30 hpi


title: 36hpi Total

description: Sample name: 36 hpi T

source_name: 36 hpi 3D7attb::yFCU

value: 36 hpi


title: 34hpi Total

description: Sample name: 34 hpi T

source_name: 34 hpi 3D7attb::yFCU

value: 34 hpi

value: Mixed stages


title: 28hpi Total

description: Sample name: 28 hpi T

source_name: 28 hpi 3D7attb::yFCU

value: 28 hpi

value: Total RNA


title: 41hpi Total

description: Sample name: 41 hpi T

source_name: 41 hpi 3D7attb::yFCU

value: 41 hpi


title: 45hpi Total

description: Sample name: 45 hpi T

source_name: 45 hpi 3D7attb::yFCU

value: 45 hpi


title: 29hpi Total

description: Sample name: 29 hpi T

source_name: 29 hpi 3D7attb::yFCU

value: 29 hpi


title: 25hpi Total

description: Sample name: 25 hpi T

source_name: 25 hpi 3D7attb::yFCU

value: 25 hpi


title: 26hpi Total

description: Sample name: 26 hpi T

source_name: 26 hpi 3D7attb::yFCU

value: 26 hpi


title: 32hpi Total

description: Sample name: 32 hpi T

source_name: 32 hpi 3D7attb::yFCU

value: 32 hpi


title: 33hpi Total

description: Sample name: 33 hpi T

source_name: 33 hpi 3D7attb::yFCU

value: 33 hpi


title: 24hpi Total

description: Sample name: 24 hpi T

source_name: 24 hpi 3D7attb::yFCU

value: 24 hpi

source_name: 3D7 Mixed Stage Reference Pool


title: 23hpi Total

description: Sample name: 23 hpi T

source_name: 23 hpi 3D7attb::yFCU

value: 23 hpi


title: 22hpi Total

description: Sample name: 22 hpi T

source_name: 22 hpi 3D7attb::yFCU

value: 22 hpi


title: 21hpi Total

description: Sample name: 21 hpi T

source_name: 21 hpi 3D7attb::yFCU

value: 21 hpi


title: 19hpi Total

description: Sample name: 19 hpi T

source_name: 19 hpi 3D7attb::yFCU

value: 19 hpi


title: IFN-α treated U6A cells+S734>A-STAT2, rep3

description: U6A cells+S734- STAT2

source_name: U6A cells+S734- STAT2

value: IFN

value: U6A (STAT2 null 2fTGH)


title: 27hpi Total

description: Sample name: 27 hpi T

source_name: 27 hpi 3D7attb::yFCU

value: 27 hpi

value: Mixed stages


title: 18hpi Total

description: Sample name: 18 hpi T

source_name: 18 hpi 3D7attb::yFCU

value: 18 hpi

value: Total RNA


title: 16hpi Total

description: Sample name: 16 hpi T

source_name: 16 hpi 3D7attb::yFCU

value: 16 hpi


title: 17hpi Total

description: Sample name: 17 hpi T

source_name: 17 hpi 3D7attb::yFCU

value: 17 hpi


title: 20hpi Total

description: Sample name: 20 hpi T

source_name: 20 hpi 3D7attb::yFCU

value: 20 hpi


title: 15hpi Total

description: Sample name: 15 hpi T

source_name: 15 hpi 3D7attb::yFCU

value: 15 hpi


title: 12hpi Total

description: Sample name: 12 hpi T

source_name: 12 hpi 3D7attb::yFCU

value: 12 hpi


title: 7hpi Total

description: Sample name: 7 hpi T

source_name: 7 hpi 3D7attb::yFCU

value: 7 hpi


title: 9hpi Total

description: Sample name: 9 hpi T

source_name: 9 hpi 3D7attb::yFCU

value: 9 hpi


title: 13hpi Total

description: Sample name: 13 hpi T

source_name: 13 hpi 3D7attb::yFCU

value: 13 hpi


title: 3hpi Total

description: Sample name: 3 hpi T

source_name: 3 hpi 3D7attb::yFCU

value: 3 hpi


title: MEFs-2

city: Minneapolis

first: Nobuaki Kikyo

email: kikyo001@umn.edu, hiraih@umich.edu

state: MN

address: 2001 6th St SE

department: Genetics, Cell Biology and Development

institute: University of Minnesota

description: Sample name: M7

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a microcirculation pump (Atactic Technologies).

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

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

source_name: Cell Line

label_protocol: Two micrograms of total RNA was extended at the 3′ terminus with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent dye staining.

growth_protocol: ESCs and iPSCs-LIF(+) were cultured on irradiated MEF feeder cells in iPSC medium (DMEM, 20% FBS or KnockOut Serum Replacement [Life Technologies], 100 µM MEM non-essential amino acids, 100 µM 2-mercaptoethanol, and 2 mM L-glutamine with or without 1,000 U/ml LIF)

extract_protocol: Total RNA was prepared from each cell type with a mirVana miRNA Isolation Kit (Life Technologies).

treatment_protocol: LIF was omitted during establishment and maintenance of M3O-lenti-iPSCs-LIF(–).

value: embryonic fibroblasts


title: ESCs (CGR8)

description: Sample name: M8

value: ESCs


title: O-retro-iPSCs-LIF(+) B

description: Sample name: M9

value: iPSCs

tag: leukemia inhibitory factor (lif) treatment


title: O-lenti-iPSCs-LIF(+) B

description: Sample name: M10


title: 4hpi Total

description: Sample name: 4 hpi T

source_name: 4 hpi 3D7attb::yFCU

value: 4 hpi

source_name: 3D7 Mixed Stage Reference Pool


title: 10hpi Total

description: Sample name: 10 hpi T

source_name: 10 hpi 3D7attb::yFCU

value: 10 hpi


title: M3O-lenti-iPSCs-LIF(-) B

description: Sample name: M12


title: M3O-lenti-iPSCs-LIF(+) B

description: Sample name: M11


title: M3O-lenti-iPSCs-LIF(-) A

description: Sample name: M6


title: 2hpi Total

description: Sample name: 2 hpi T

source_name: 2 hpi 3D7attb::yFCU

value: 2 hpi

value: Mixed stages


title: 5hpi Total

description: Sample name: 5 hpi T

source_name: 5 hpi 3D7attb::yFCU

value: 5 hpi

value: Total RNA


title: 1hpi Total

description: Sample name: 1 hpi T

source_name: 1 hpi 3D7attb::yFCU

value: 1 hpi


title: 11hpi Total

description: Sample name: 11 hpi T

source_name: 11 hpi 3D7attb::yFCU

value: 11 hpi


title: 6hpi Total

description: Sample name: 6 hpi T

source_name: 6 hpi 3D7attb::yFCU

value: 6 hpi


title: 0hpi Total

description: Sample name: 0 hpi T

source_name: 0 hpi 3D7attb::yFCU

value: 0 hpi


title: M3O-lenti-iPSCs-LIF(+) A

description: Sample name: M5


title: O-retro-iPSCs-LIF(+) A

description: Sample name: M3


title: 8hpi Total

description: Sample name: 8 hpi T

source_name: 8 hpi 3D7attb::yFCU

value: 8 hpi


title: MEFs-1

description: Sample name: M1


title: ESCs (CJ7)

description: Sample name: M2


title: O-lenti-iPSCs-LIF(+) A

description: Sample name: M4


title: TEB-rep3

city: Sydney

first: Daniel

last: Roden

state: NSW

address: 384 Victoria Street

country: Australia

institute: Garvan Institute

description: microRNA expression of TEBs

hyb_protocol: 10x GE blocking buffer and 2x Hi-RPM hybridization buffer was added to Cy3-pCp labelled total RNA to a final volume of 45uL, before being incubated at 100°C for 5 minutes and later transferred to the ice water bath for 5 minutes according to the manufacturer's instructions. Following that the labelled miRNA samples were hybridized to the Agilent mouse microRNA microarray (G4472A)  in the Agilent Surehyb chamber (G2530-60029) for 20 hours at 55°C. After hybridization, the microarray was washed with GE wash buffer 1 (Agilent) for 5 minutes at room temperature, followed by GE wash buffer 2 (Agilent) for 5 minutes at 37°C. Prepare the hybridization chamber disassembly according to the manufacturers instructions.

scan_protocol: Microarray slides were scanned on the microarray scanner (G2565BA) utilising a color scan setting for 8x15k array slides (Scan area 61x21.6mm, Scan resolution 5um, Select eXtended Dynamic range, Dye channel is set to Green and Green PMT Is set to XDR Hi 100% and XDR lo 5%).

data_processing: The scanned images were analysed with Agilent  Feature Extraction Software version 9.5.3 or higher specifying the default miRNA protocol in the FE Grid Template properties. To set the FE Project properties, use default settings as suggested by manufacturer in the input section, in the Other section, select the miRNA_QCM_Apr07 from the QC Metric Set drop-down list. Select miRNA-v1_95_May07 as the selected protocol for miRNA microarrays. GeneView miRNA data files were collated, and gTotalGeneSignal and gIsDetected columns were extracted for each miRNA. Due to the presence of many slightly negative expression values (ie in the range -8 to 0), data were transformed by adding an offset of 8.0 to all values, thresholding all remaining values < 1.0 to 1.0, and then transformed by log-base-2. Data were quantile normalised, and restricted to human only miRNA’s, that were expressed in at least one sample, derived form the gIsDetected value, where 1 means detected, 0 means not detected on the microarray.

source_name: TEBs

label_protocol: 100ng total RNA was dephosphorylated using calf intesinal phosphatase for 30 mins at 37°C, denatured at 100°C between 5 to 10 minutes, followed by being ligated to Cy3-pCp using T4 RNA ligase.

extract_protocol: RNA was extracted using Trizol reagent (Invitrogen) using the manufacturers protocol and further ethanol precipitated to remove salt contaminants. The RNA was quantified using the Nanodrop 1000 spectrophotometre and the integrity of the RNA was determined using the Agilent  2100 bioanalyser. (Agilent Technologies, Santa Clara, CA)

treatment_protocol: TEBs, mature ducts and distal stroma regions of mammary glands 2-5 were microdissected from anesthetised 5-week-old beta actin-GFP reportert mice using the Leica MZFLIII fluorescence microscope

tag: gender

value: Female

tag: age

value: 5 weeks

value: mammary gland

tag: region

value: TEBs


title: STROMA-rep1

description: microRNA expression of stroma regions

source_name: Stroma

value: stroma regions


title: TEB-rep2

description: microRNA expression of TEBs


title: STROMA-rep2

description: microRNA expression of stroma regions


title: DUCT-rep1

description: microRNA expression of mature ducts

source_name: Mature ducts

value: mature ducts


title: DUCT-rep2

description: microRNA expression of mature ducts


title: STROMA-rep3

description: microRNA expression of stroma regions


title: TEB-rep1

description: microRNA expression of TEBs


title: 14hpi Total

description: Sample name: 14 hpi T

source_name: 14 hpi 3D7attb::yFCU

value: 14 hpi


title: TGF-β3_1

city: Salt Lake City

first: Aik Choon

last: Tan

state: UT

address: 2000 Circle of Hope

department: Oncological Sciences

institute: Huntsman Cancer Institute

description:
Affymetrix Mouse Gene 1.1 ST Array Strips
Sample 3

hyb_protocol: Following fragmentation, hybridization was performed for 20 hr at 48C on Affymetrix Mouse Gene 1.1 ST Array Strips using the Gene Atlas Hybridization Station. Following hybridization, washing and staing washing and staining was performed using the GeneAtlas Fluidics Station.

scan_protocol: Array strips were scanned using GeneAtlas Instrument Control software.

data_processing: RMA normalization using Affymetrix Power Tools

source_name: EpH4 cells

label_protocol: Labeling was performed using the GeneChip WT Terminal Labeling Kit per manufacturer's instructions.

growth_protocol: Prior to treatment, EpH4 cells were cultured in confluent conditions for 7 days to form a monolayer with established tight junctions. Tight junction integrity was monitored by measuring the transepithelial electrical resistance daily.

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

treatment_protocol: 1 ng/ml TGF-β3 or vehicle in serum-free media for 24 hours.

value: EpH4 mammary epithelial cells

tag: agent


title: WT brain 2

city: Cincinnati

first: Nupur

last: dasgupta

state: OH

address: 3333, Burnet Avenue

department: human Genetics

institute: CCHMC

description: 42-45 days old Gene expression data from WT mouse brain

hyb_protocol: Create a hybridization cocktail for a single probe array that contains biotin-labeled low molecular RNA molecules, 20X Eukaryotic Hybridization Controls (1.5 pM bioB, 5 pM bioC, 25 pM bioD, 100 pM cre) (Affymetrix), 10% DMSO, 4% Formamide, 50 pM Control Oligo B2, and 1X Hybridization Mix.  Heat hybridization cocktail to 99°C for 5 minutes, to 45°C for 5 minutes, and spin at maximum speed in a microcentrifuge. Fill probe array with 100 mL of the hybridization cocktail. Incubate at 48°C for 16 -18 hrs in the GeneChip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm.

scan_protocol: Affymetrix GeneChip Scanner 3000 7G scanner  and Genechip Operating Software 1v4 (Affymetrix) was usedfor scanning

data_processing: Data analyses were performed using Gene Spring Software (Agilent Technologies, Inc., Santa Clara, CA). Normalization was performed using the RMA (robust multiarray average) algorithm [42]. Post normalization unpaired T Test (Asymptotic) was performed. The false discovery rate (FDR) was calculated according to the Benjamini and Hochberg algorithm

source_name: 42-45 days old WTmouse brain

label_protocol: The FlashTag™ Biotin HSR RNA Labeling Kit is used to biotin label low molecular weight RNA molecules. The labeled samples are hybridized to GeneChip® miRNA 2.0 Arrays.

growth_protocol: Genotype of 4L;C* mice have combined V394L/V394L Gba1 (4L) and saposin C-/- (C*). The strain background of 4L;C* mice was C57BL/6J/129SvEV. The strain- and age-matched WT mice were used as control. All mice were housed under pathogen-free conditions in the barrier animal facility and according to IACUC approved protocol at Cincinnati Children’s Hospital Research Foundation

extract_protocol: Isolated whole brain  were immediately immersed in RNA Later. RNAs (mRNA and miRNA) were extracted using the Ambion mirVana™ miRNA Isolation Kit (Ambion, AM1560) following manufacture instruction

treatment_protocol: The 4L;C* mice were treated with a pharmacological chaperone, isofagamine tartrate (IFG), at 60 mg/kg/d by drinking water as described . The pregnant dames were given drinking water containing IFG staring 3 to 5 days prior to birth and during the weaning period. After weaning, the pups were continued on 60 mg/kg/d IFG in drinking water for entire course .

value: Brain

value: WT


title: WT brain 1


title: 4LC brain 2

description: 42-45 days old Gene expression data from4L;C* mouse brain

source_name: 42-45 days old  4L;C* mouse brain


title: WT brain 4


title: 4LC brain 1


title: 4LC brain 4


title: BoneMarrowMacrophages_WGP6h_2

city: Louisville

first: Sabrin

middle: H

last: Albeituni

state: KY

address: 505 S Hancock St

department: Microbiology and Immunulogy

institute: University of Louisville

hyb_protocol: Cy3-labelled cRNA  was fragmented at 60°C for 30 minutes in 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: BMDM_6h WGP

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from RNA using the Agilent's Low Input Quick Amp WT labeling Kit according to the manufacturer's instructions, followed by RNA  purification using Qiagen's RNeasy mini spin column's kit .  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 UV-VIS Spectrophotometer.

extract_protocol: RNA was extracted from bone-marrow derived macrophages using Qiagen kit according to manufacturer's protocol

treatment_protocol: M2 Bone-marrow derived macrophages were incubed for 6 hours with complete DMEM with or without WGP

tag: mouse age

value: 6-8 weeks

tag: cell type

value: Polarized M2 bone-marrow derived macrophages

tag: incubated in

value: complete DMEM with WGP for 6hrs


title: 4LC brain 3


title: BoneMarrowMacrophages_medium_2

source_name: BMDM_6h media

value: complete DMEM (without WGP) for 6hrs


title: WT brain 3


title: BoneMarrowMacrophages_WGP6h_3


title: Vehicle_2

description:
Affymetrix Mouse Gene 1.1 ST Array Strips
Sample 5

value: Vehicle


title: TGF-β3_2

description:
Affymetrix Mouse Gene 1.1 ST Array Strips
Sample 7


title: Vehicle_3

description:
Affymetrix Mouse Gene 1.1 ST Array Strips
Sample 9


title: TGF-β3_3

description:
Affymetrix Mouse Gene 1.1 ST Array Strips
Sample 11


title: Vehicle_1

description:
Affymetrix Mouse Gene 1.1 ST Array Strips
Sample 1


title: BoneMarrowMacrophages_medium_3


title: MCF-10Acells_untreated_2_cy3

type: genomic

city: Hamilton

first: Caitlin

last: Mills

address: 1280 Main St West

institute: McMaster University

hyb_protocol: Hybridization was according to the Perkin Elmer protocol. Slides were incubated for 16 hours in Corning

scan_protocol: The slides were scanned on a GenePix 4200A microarray scanner at a resolution of 5 um.

data_processing: Data were analyzed using oneClickCGH software. The following analysis parameters were selected: Background correction: local; Normalization: LOWESS, pin-wise, X&Y adjusted, var stab, Detection algorithm: CBS v2, P-value: 0.01, Gain:0.25, Loss: -0.25, Minimum clones: 1.

molecule: genomic DNA

source_name: Mammary epithelium

label_protocol: Dye swap labelling of 2ug of test and reference DNA was preformed according to directions supplied by Perkin Elmer for the Constitutional Chip 4.0.

growth_protocol: MCF-10A cells were cultured in a 1:1 mix of DMEM:F-12 media supplemented with 5% horse serum, 1% pen/strep, 10 ug/ml insulin, 0.5 ug/ml hydrocortisone, 20 ng/ml EGF, and 100 ng/ml cholera toxin. Cells were incubated at 37oC, and 5% CO2.

extract_protocol: DNA was purified using a Qiagen Gentra Puregene Cell kit.

treatment_protocol: Cells were untreated.

source_name: Reference

tag: reference

value: Pooled reference DNA


title: BoneMarrowMacrophages_medium_1


title: BoneMarrowMacrophages_WGP6h_1


title: MCF-10Acells_untreated_2_cy5


title: MCF-10Acells_untreated_1_cy3


title: scramble+doxy+ins 2 poly

city: Milan

first: Daniela

last: Brina

address: Via Sforza 35

country: Italy

institute: INGM

description: Gene expression after 1 hr insulin 100 nM

hyb_protocol: For microarray on AML12, polysomal and subpolysomal RNAs were hybridized on the Agilent SurePrint G3 Mouse GE 8x60K Microarray G4852A following the manifacturer’s protocol. The experiment was performed in biological quadruplicate.

scan_protocol: Hybridized microarray slides were scanned with an Agilent DNA Microarray Scanner G2505C at 3μm resolution with the manufacturer’s software (Agilent Scan Control 8.1.3).

data_processing: The scanned TIFF images were analyzed numerically and the background was corrected using the Agilent Feature Extraction Software version 10.7.7.1 according to the Agilent standard protocol GE1_107_Sep09. The output of Feature Extraction was analyzed with the R software environment for statistical computing (http://www.r-project.org/) and the Bioconductor library of biostatistical packages (http://www.bioconductor.org/). Low signal Agilent features, distinguished by a repeated “undetected” flag across the majority of the arrays in every condition, were filtered out from the analysis, leaving 18905 features corresponding to 14108 MGI genes. Signal intensities across arrays were normalized with the quantile method.

source_name: AML12 scramble+doxy+ins 2 poly

growth_protocol: AML12 hepatocytes were grown in DMEM-F12 plus 1% glutamine-penycillin-streptomycin (Gibco),10% heat-inactivated FBS, ITS 1X reagent (Life technologies) and dexamethasone 40 ug/ul. The cultures were incubated at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: RNA was extracted using the Phenol:Chloroform acid reagent (Sigma), following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: AML12 were treated with 100 mM insulin (Life technologies), diluited in DMEM-F12. The cultures were incubated for 1 hour at 37 ºC in a humidified incubator with 5% CO2.

tag: cells

value: AML12 hepatocytes

value: male

tag: treatment

value: scramble+doxy+ins


title: shrna+doxy+ins 2 sub

source_name: AML12 shrna+doxy+ins 2 sub

value: shrna+doxy+ins


title: shrna+doxy+ins 2 poly

source_name: AML12 shrna+doxy+ins 2 poly


title: MCF-10Acells_untreated_1_cy5

tag: cell line


title: scramble+doxy+ins 1 poly

source_name: AML12 scramble+doxy+ins 1 poly


title: shrna+doxy+ins 4 sub

source_name: AML12 shrna+doxy+ins 4 sub


title: shrna+doxy+ins 1 sub

source_name: AML12 shrna+doxy+ins 1 sub


title: shrna+doxy+ins 1 poly

source_name: AML12 shrna+doxy+ins 1 poly


title: scramble+doxy+ins 2 sub

source_name: AML12 scramble+doxy+ins 2 sub


title: shrna+doxy+ins 3 poly

source_name: AML12 shrna+doxy+ins 3 poly


title: scramble+doxy+ins 3 poly

source_name: AML12 scramble+doxy+ins 3 poly


title: scramble+doxy+ins 3 sub

source_name: AML12 scramble+doxy+ins 3 sub


title: shrna+doxy+ins 3 sub

source_name: AML12 shrna+doxy+ins 3 sub


title: shrna+doxy+ins 4 poly

source_name: AML12 shrna+doxy+ins 4 poly


title: scramble+doxy+ins 4 sub

source_name: AML12 scramble+doxy+ins 4 sub


title: scramble+doxy+ins 4 poly

source_name: AML12 scramble+doxy+ins 4 poly


title: Placenta [14S1003047]

city: Hong Kong

first: Zirui

last: DONG

address: Shatin, N.T.

department: Dept. of Obstetrics and Gynaecology

country: China

institute: The Chinese University of Hong Kong

hyb_protocol: After clean up and QC check, Cy3 and Cy5 labeled DNA samples were mixed together with Cot-1 DNA, blocking agent and hybridization buffer using Agilent Oligo aCGH/ChIP-on-Chip Hybridization kit according to manufacturer's protocol. Samples were hybridized on array for 24 hours at 65oC. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2505C scanner.

data_processing:
Agilent Feature Extraction Software (v 11.5.1.1) was used for background subtraction
Dye was normalized automatically according to the dye norm list in eArray generating the normalized log10 ratio (Cy5/Cy3), representing test/reference

source_name: Induced abortion_Placental tissue

label_protocol: Three costumized aCGH approach have different procedure for DNA fragmentation and labelling; Agilent-022023:1 µg of Genomic DNA samples were fragmented. The fragmented DNA sample were labeled with Cy5 and the corresponding fragmented reference controls were labeled Cy3 using Agilent SureTag DNA Labeling Kit.  Agilent-068656:300 ng of Genomic DNA samples were heat fragmented. The fragmented DNA samples were labeled with Cy5 and the corresponding fragmented reference controls were labeled Cy3 using Agilent SureTag DNA Labeling Kit. Agilent-035130:300 ng of Genomic DNA samples were enzyme digested. The digested DNA samples were labeled with Cy5 and the corresponding fragmented reference controls were labeled Cy3 using Agilent SureTag DNA Labeling Kit.

growth_protocol: Uncultured samples of chorionic villus sampling, amniotic fluid,  placental tissue and blood were used for direct DNA extraction

extract_protocol: Genomic DNA extraction done by Qiagen DNeasy® Blood & Tissue Kit following manufacturer's instructions

treatment_protocol: Samples were untreated

tag: sample origin

value: Induced abortion

tag: clinical indication

value: Ultrasound abnormality:ureteral obstruction; transposition of right kidney in pelvic cavity

tag: tissue

value: Placental tissue

value: Healthy Chinese adult control

value: blood


title: Emb_MO-Tbx5a_24hpf_rep2

city: Pisa

first: Romina

last: D'Aurizio

state: PI

address: via Moruzzi 1

department: IIT

institute: CNR

description: Gene expression after Mo-Tbx5a injection

hyb_protocol: Microarray hybridizations were carried out in Agilent’s SureHyb Hybridization Chambers containing 1650 ng of Cyanine 3-labelled cRNA per hybridization. The hybridization reactions were performed at  65°C for 17 hours using Agilent’s Gene Expression Hybridization Kit with the 4x44K whole Danio rerio genome chip (grid ID 026437, G2519F chip). After hybridization, slides were washed with Agilent Gene Expression Wash Buffer 1, Gene Expression Wash Buffer 2 and Acetonitrile for one minute at room temperature.

scan_protocol: Chips were scanned on an Agilent G2505C scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version 10.7) and the GE1_107_Sep09 extraction protocol.

organism: Danio rerio

source_name: Embryos, MO-Tbx5a, 24hpf, replicate2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using LowInput QuickAmp Labeling Kit One-Color (Agilent Technologies) according to the manufacturer's instructions, followed by RNAeasy column purification.

growth_protocol: Zebrafish was raised and maintained under standard laboratory conditions (Westerfileld M zebrafish book) in Zebrafish Housing Systems (Tecniplast, Varese, Italy).

extract_protocol: Total RNA was extracted using miRNeasy Mini kit (Qiagen) following the manufacturer's recommendations.   RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: 1-cell stage zebrafish embryos were microinjected with 1,5 ng of morpholino against dre-Tbx5a (MO-Tbx5a) or with 1,5 ng of control morpholino

value: embryo

tag: strain

value: AB

value: Mo-Tbx5a injection

tag: developmental stage


title: scramble+doxy+ins 1 sub

source_name: AML12 scramble+doxy+ins 1 sub


title: Normoxia_Replicate 4

city: GAINESVILLE

first: Charles

middle: Evans

last: Wood

state: Florida

address: 1345 Center Drive/Room M552

department: Physiology and Functional Genomics

institute: University of Florida

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity: 10.2 to 12.8 pmol Cy3/μg RNA) was fragmented and hybridized to Agilent Sheep Oligo Microarrays (G4813A) design 019921 by the ICBR facility at the University of Florida according to Agilent's methodology.

scan_protocol: Slides were scanned on the Agilent DNA Microarray Scanner (G2505B) using one color (green) scan setting for 8x15k array slides, by the ICBR facility at University of Florida.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.1.1.1 (Agilent) using default parameters (protocol GE1-v5_10 and Grid: 019921_D_F_20100112)  background detrended Processed Signal. The limma package was employed to import the raw data into R (http://www.r-project.org), perform background correction and normalize the data by the quantile normalization method. Control probes and low expressed probes were filtered out, retaining for further analysis the probes that were at least 10% brighter than the negative controls on at least four arrays.

organism: Ovis aries

source_name: Fetal Pituitary, Normoxia

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 500 ng RNA using the One-Color Quick Amp Labeling Kit (Agilent, Newcastle DE) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was extracted from fetal hyothalamus with Trizol (Life Technologies, Carlsbad, CA), and purified through Qiagen RNeasy+ kits with on-column DNase digestion (QIAGEN, Valencia, CA) according to manufacturers' protocols.Total RNA concentration was measured by Nanodrop ND-1000 and RNA quality was monitored by Agilent Bioanalyzer.

treatment_protocol: Chronically catheterized late gestation fetal sheep were subjected to 30 min hypoxia (n=4) or normoxia (n=4). Fetuses were euthanized 60 min after the onset of hypoxia or normoxia and pituitaries removed for microarray analysis.  Gene expression was measured using Agilent 15k ovine microarrays.

value: Fetal Pituitary

tag: developmental age

tag: Sex

value: normoxia


title: Normoxia_Replicate 3

value: female


title: Emb_MO-Tbx5a_24hpf_rep3

source_name: Embryos, MO-Tbx5a, 24hpf, replicate3


title: Emb_MO-Ct_24hpf_rep2

description: Gene expression after Mo-Ct injection

source_name: Embryos, MO-Ct, 24hpf, replicate2

value: Mo-Ct injection


title: Emb_MO-Tbx5a_mir19_24hpf_rep1

description: Gene expression after Mo-Tbx5a and MO-19a injections

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Embryos, MO-Tbx5a, MO-19a, 24hpf, replicate1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Wild-type zebrafish strain AB were raised and maintained under standard laboratory conditions (Westerfileld M zebrafish book) in Zebrafish Housing Systems (Tecniplast, Varese, Italy)

extract_protocol: Total RNA was extracted using the miRNeasy Mini kit (Qiagen) and quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: AB zebrafish embryos were injected at 1-cell stage into the yolk with the indicated mix of morpholinos and miRNA mimics

value: Mo-Tbx5a and MO-19a injections


title: Emb_MO-Ct_24hpf_rep1

description: Gene expression after Mo-Ct injection

source_name: Embryos, MO-Ct, 24hpf, replicate1


title: Emb_MO-Tbx5a_mir19_24hpf_rep3

source_name: Embryos, MO-Tbx5a, MO-19a, 24hpf, replicate3


title: Emb_MO-Tbx5a_mir19_24hpf_rep2

source_name: Embryos, MO-Tbx5a, MO-19a, 24hpf, replicate2


title: CVS [14S0593155]

value: Miscarriage

value: Chorionic villus sampling (CVS)


title: Hypoxia_Replicate 3

source_name: Fetal Pituitary, Hypoxia

value: male

value: hypoxia


title: Hypoxia_Replicate 1


title: Hypoxia_Replicate 4


title: Hypoxia_Replicate 2


title: Small intestine HF-Q replicate 11

city: Wageningen

first: Evert

middle: M.

last: van Schothorst

address: De Elst 1

country: Netherlands

institute: Wageningen University

description: Cy3 samples were pooled on a equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.

hyb_protocol: Individual Cy5-labelled samples were hybridized against the Cy3-labelled reference pool according to the manufacturers' procedure using Agilent Gene Expression Hybridization Kit. Samples were applied to microarrays enclosed in Agilent SureHyb hybridization chambers and hybridized at 65C for 17 hours at 10rpm rotation. After hybridization, slides were washed sequential following Agilents' recommendations.

scan_protocol: Scanned with an Agilent Technologies Scanner G2505B with 10 and 100% laser-power intensities.

data_processing: Images were quantified using Agilent Feature Extraction Software (10.7.3.1) to obtain raw median signal and background values for both Cy5 and Cy3. Spots with a mean signal higher than twice the background value over all arrays were considered to be expressed. Data was normalized according to Pellis et al., (Physiol Genomics 2003; 16:99-106) based on the Cy3-reference pool, and log2 transformation.

source_name: small intestinal scraping, high fat diet_with_quercetin

label_protocol: 200 ng of purified individual total RNA was used for cDNA synthesis, splitted in two equal fractions and used for subsequent cRNA labeling and synthesis using Cy5 and Cy3 dyes and the Agilent low RNA input fluorescent lineair amplification protocol, as described previously by van Schothorst et al., (Anal Biochem 2007;363:315-7).

extract_protocol: Total RNA was isolated from liver tissue using RNeasy Mini columns (Qiagen) according to the manufacturer’s instruction, quantified using Nanodrop (IsoGen Life Science) and qualified using Experion Automated Electrophoresis System (BioRad).

treatment_protocol: All mice started with a three week adaptation phase, in which they were fed a normal-fat diet. During the intervention the mice received a high-fat diet without (HF) or with supplementation of 0.33% (w/w) quercetin (HF-Q) for 12 weeks. Animals were fasted for 2-4 hr prior anaestetization and sacrifice.

tag: gender

value: adult

value: small intestine

source_name: small intestine, reference pool of all samples


title: Small intestine HF-Q replicate 02


title: Small intestine HF-Q replicate 05


title: Small intestine HF-Q replicate 07


title: Small intestine HF replicate 12

source_name: small intestinal scraping, high fat diet


title: Small intestine HF-Q replicate 01


title: Small intestine HF-Q replicate 06


title: Small intestine HF replicate 05


title: Small intestine HF replicate 04


title: Small intestine HF replicate 06


title: Small intestine HF replicate 08


title: Small intestine HF-Q replicate 03


title: Small intestine HF-Q replicate 09


title: Small intestine HF-Q replicate 10


title: Normoxia_Replicate 1


title: Normoxia_Replicate 2


title: Small intestine HF-Q replicate 08


title: Small intestine HF-Q replicate 04


title: Small intestine HF replicate 07


title: Small intestine HF replicate 10


title: Emb_MO-Tbx5a_24hpf_rep1

source_name: Embryos, MO-Tbx5a, 24hpf, replicate1


title: Small intestine HF replicate 09


title: Small intestine HF replicate 02


title: KK151-UM-IU1_1408

city: Uppsala

first: Chiara

last: Rasi

state: Sweden

address: Husargatan 3

department: Department of Immunology, Genetics and Pathology

country: Sweden

institute: Uppsala University

description:
uninvolved margin of breast carcinoma
KK151-UM-IU1

hyb_protocol: starndard protocol

scan_protocol: The majority of genotyping experiments were conducted at the SNP&SEQ Technology Platform in Uppsala by using four similar in SNP-density Illumina platforms (Human 660W-Quad, Human1M-Duo, HumanOmniExpress and HumanOmniExpressExome beadchips), according to the recommendations of the manufacturer.

data_processing:
The genotyping data was normalized and analyzed using Nexus Copy Number 7 (Biodiscovery). Copy number and allelic imbalances calls were made by using the SNP-FASST segmentation algorithm with the following settings: Significance Threshold: 5.0E-9; Max Contiguous Probe Spacing 500-1000; Min. number of probes per segment: 10; Homozygous Frequency Threshold: 0.85; Homozygous Value Threshold: 0.95; and Heterozygous Imbalance Threshold: 0.46. All the other parameters were left default. Data included in this GEO project was generated using the utility  “convert .ivg to .txt” from Nexus 7.
Log R Ratio and B Allele frequency values are reported for each probe from the four different platforms used in the study.

source_name: breast tissue from mastectomy, taken outside the site of primary tumor(s)

label_protocol: starndard protocol

extract_protocol: The tissues were stored at -70 degrees C prior to DNA extraction. The solid tissues were homogenized with a Tissuerupter (Qiagen). Proteinase K and Sarcosine was then added and the sample was incubated at 50oC over-night. The samples were transferred to PhaseLock Gel tubes and the DNA was purified with phenol/chloroform extraction. Due to very rich content of fat in UMs, phenol/chloroform extraction was repeated 6 times for all UMs, and 3 times for PTs and control samples from skin. The purified DNA was precipitated with sodium acetate, pH 5.4 and 95% ethanol. The DNA precipitate was dried before dissolving in water. Control samples of blood were extracted with QIAmp DNA Blood Maxi Kit (Qiagen).

tag: age at cancer diagnosis (yrs)

tag: tumor grade

value: Luminal B, HER2+

tag: tumor focality

value: unifocal


title: KK151-UM-IU_1407

description:
uninvolved margin of breast carcinoma
KK151-UM-IU


title: KK151-UM-EU2_1405

description:
uninvolved margin of breast carcinoma
KK151-UM-EU2


title: KK151-UM-IU2_1409

description:
uninvolved margin of breast carcinoma
KK151-UM-IU2


title: KK151-VB1-M_1410

description:
uninvolved margin in the immediate vicinity of the mammilla
KK151-VB1-M


title: KK151-VB2-M_1411

description:
uninvolved margin in the immediate vicinity of the mammilla
KK151-VB2-M


title: KK151-UM-EL_1400

description:
uninvolved margin of breast carcinoma
KK151-UM-EL


title: JW167-VB2-M_1397

description:
uninvolved margin in the immediate vicinity of the mammilla
JW167-VB2-M


title: JW167-UM-IU_1395

description:
uninvolved margin of breast carcinoma
JW167-UM-IU


title: JW167-VB1-M_1396

description:
uninvolved margin in the immediate vicinity of the mammilla
JW167-VB1-M


title: JW167-UM-IL1_1393

description:
uninvolved margin of breast carcinoma
JW167-UM-IL1


title: KK151-UM-EL2_1402

description:
uninvolved margin of breast carcinoma
KK151-UM-EL2


title: KK151-UM-EU_1403

description:
uninvolved margin of breast carcinoma
KK151-UM-EU


title: JW167-UM-IL2_1394

description:
uninvolved margin of breast carcinoma
JW167-UM-IL2


title: KK151-UM-EL1_1401

description:
uninvolved margin of breast carcinoma
KK151-UM-EL1


title: KK151-UM-EU1_1404

description:
uninvolved margin of breast carcinoma
KK151-UM-EU1


title: JW167-UM-EU_1390

description:
uninvolved margin of breast carcinoma
JW167-UM-EU


title: Small intestine HF replicate 01

description: Cy3 samples were pooled on a equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: Small intestine HF replicate 11


title: Small intestine HF replicate 03


title: JW167-UM-EU1_1391

description:
uninvolved margin of breast carcinoma
JW167-UM-EU1


title: Global gene expression signatures in fibrous root of I. carnea grown at ambient temperature

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

institute: Genotypic Technology

description: Global gene expression in fibrous root of I. cornea grown at ambient temperature (day  30oC; night  23oC)

hyb_protocol: 600ng of labeled cRNA were hybridized on the array using the Gene Expression Hybridization kit (Part Number 5190-0404; Agilent) in Sure hybridization Chambers (Agilent) at 65º C for 16 hours. Hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5242).

scan_protocol: Slides were then scanned on a G2505C scanner (Agilent Technologies)

data_processing: Images were quantified using Agilent Feature Extraction Software  and Analyis perfomed using  background subtracted and spatially detrended Processed Signal intensities and Percentile Shift Normalization

organism: Ipomoea carnea

source_name: Fibrous roots from I. cornea grown at ambient temperature

label_protocol: The samples were labeled using Agilent Quick Amp Kit (Part number: 5190-0442). 500ng of total RNA was reverse transcribed using oligodT primer tagged to T7 promoter sequence. cDNA thus obtained was converted to double stranded cDNA in the same reaction. Further the cDNA was converted to cRNA in the in-vitro transcription step using T7 RNA polymerase enzyme and Cy3 dye was added into the reaction mix. During cRNA synthesis Cy3 dye was incorporated into the newly synthesized strands. cRNA obtained was cleaned up using Qiagen RNeasy columns(Qiagen, Cat No: 74106). Concentration and amount of dye incorporated was determined using Nanodrop.

growth_protocol: Sweet potato plants of variety Sree Arun were grown in earthen pots of 7 kg soil holding capacity and irrigated daily. Nitrogen (0.6 g urea), phosphorous (0.3 g P2O5) and potassium (0.6 g K2O ) fertilizers were added one week after planting. Plants were illuminated for 12 hours per day under 700 µ mol m2 h-1.

extract_protocol: Total RNA was extracted from the leaf, fibrous root and tuberous root by the method as described by Chomczynski, P. and Sacchi, N. 1987. Anal. Biochem 162:156. Total intact high quality RNA were extracted from young newly emerging tender leaves, fibrous roots and tuber forming roots harvested from 30 days old sweet potato plants grown in ambient temperature and from plants subjected to high temperature stress.

treatment_protocol: One set of 30 plants were kept in ambient conditions and another set of 30 plants were used as control. Ambient temperature conditions were 30oC ± 2oC during day time and 23oC ± 1oC during night time. Another set of 21 days old 30 plants were subjected to high temperature stress for 7 hours daily at 40oC ±2oC during day time and 23 oC ± 1oC during night time for 7 days.

value: ambient temperature

value: Fibrous roots

tag: age

value: 30 days old


title: Global gene expression signatures in sweet potato fibrous root grown at ambient temperature

description: Global gene expression sweet potato fibrous root grown at ambient temperature (day 30oC; night 23oC)

organism: Ipomoea batatas

source_name: Fibrous roots from sweet potato plants grown at ambient temperature


title: Global gene expression signatures in sweet potato tuberous root grown at ambient temperature

description: Global gene expression in sweet potato tuberous root grown at ambient temperature (day  30oC; night  23oC)

source_name: Tuberous root from sweet potato plants grown at ambient temperature

value: Tuberous roots


title: Global gene expression signatures in high temperature stressed sweet potato tuberous root as

description: Global gene expression in sweet potato tuberous root after 7 hours high temperature stress (40oC) treatment for 7 days

source_name: Tuberous root from high temperature stressed sweet potato plants

value: high temperature stressed


title: Global gene expression signatures in sweet potato leaf grown at at ambient temperature

description: Global gene expression in sweet potato leaf grown at ambient temperature (day  30oC; night  23oC)

source_name: Leaves from sweet potato plants grown at ambient temperature

value: Leaf


title: Global gene expression signatures in high temperature stressed sweet potato fibrous root

description: Global gene expression fibrous root after 7 hours high tempersture (day 40oC; night 23oC) treatment for 7 days

source_name: Fibrous roots from high temperature stressed sweet potato plants


title: Global gene expression signatures in high temperature stressed sweet potato leaf

description: Global gene expression in sweet potato leaf after 7 hours high temperature (day 40oC; night 23oC) treatment for 7 days

source_name: Leaves from high temperature stressed sweet potato plants


title: JP149-UM-IU1_1384

description:
uninvolved margin of breast carcinoma
JP149-UM-IU1

value: female

value: Triple negative


title: JP149-UM-IU2_1385

description:
uninvolved margin of breast carcinoma
JP149-UM-IU2


title: JP149-UM-IL_1382

description:
uninvolved margin of breast carcinoma
JP149-UM-IL


title: KK151-UM-IL_1406

description:
uninvolved margin of breast carcinoma
KK151-UM-IL


title: JP149-UM-EU_1379

description:
uninvolved margin of breast carcinoma
JP149-UM-EU


title: JP149-UM-EU2_1381

description:
uninvolved margin of breast carcinoma
JP149-UM-EU2


title: JM154-VB2-M_1373

description:
uninvolved margin in the immediate vicinity of the mammilla
JM154-VB2-M

value: Luminal B, HER2-


title: JP149-VB1_1386

description:
uninvolved margin in the immediate vicinity of the mammilla
JP149-VB1


title: JP149-UM-EL2_1378

description:
uninvolved margin of breast carcinoma
JP149-UM-EL2


title: JW167-UM-IL_1392

description:
uninvolved margin of breast carcinoma
JW167-UM-IL


title: JM154-UM-EU2_1369

description:
uninvolved margin of breast carcinoma
JM154-UM-EU2


title: JM154-UM-EL1_1366

description:
uninvolved margin of breast carcinoma
JM154-UM-EL1


title: JP149-UM-EL_1376

description:
uninvolved margin of breast carcinoma
JP149-UM-EL


title: JP149-UM-EU1_1380

description:
uninvolved margin of breast carcinoma
JP149-UM-EU1


title: JE009-UM99_1363

description:
uninvolved margin of breast carcinoma
JE009-UM99


title: JP149-UM-EL1_1377

description:
uninvolved margin of breast carcinoma
JP149-UM-EL1


title: JM154-UM-EU1_1368

description:
uninvolved margin of breast carcinoma
JM154-UM-EU1


title: JE009-UM1_1362

description:
uninvolved margin of breast carcinoma
JE009-UM1


title: JM154-UM-EL2_1367

description:
uninvolved margin of breast carcinoma
JM154-UM-EL2


title: ILS024-UM98_1356

description:
uninvolved margin of breast carcinoma
ILS024-UM98

value: Luminal A

value: multifocal


title: ILS024-UM99_1357

description:
uninvolved margin of breast carcinoma
ILS024-UM99


title: ILS024-UM3_1355

description:
uninvolved margin of breast carcinoma
ILS024-UM3


title: ILS024-UM2_1354

description:
uninvolved margin of breast carcinoma
ILS024-UM2


title: ILN025-UM99_1348

description:
uninvolved margin of breast carcinoma
ILN025-UM99


title: JP149-VB2_1387

description:
uninvolved margin in the immediate vicinity of the mammilla
JP149-VB2


title: JP149-UM-IU_1383

description:
uninvolved margin of breast carcinoma
JP149-UM-IU


title: JM154-UM-IU2_1371

description:
uninvolved margin of breast carcinoma
JM154-UM-IU2


title: JM154-UM-IU1_1370

description:
uninvolved margin of breast carcinoma
JM154-UM-IU1


title: ILN025-UM2_1347

description:
uninvolved margin of breast carcinoma
ILN025-UM2


title: JM154-VB1-M_1372

description:
uninvolved margin in the immediate vicinity of the mammilla
JM154-VB1-M


title: HZK162-VB2-M_1341

description:
uninvolved margin in the immediate vicinity of the mammilla
HZK162-VB2-M


title: HZK162-UM-IU1_1721

description:
uninvolved margin of breast carcinoma
HZK162-UM-IU1


title: ILN025-UM1_1346

description:
uninvolved margin of breast carcinoma
ILN025-UM1


title: HZK162-UM-IL_1338

description:
uninvolved margin of breast carcinoma
HZK162-UM-IL


title: HZK162-UM-EU2_1337

description:
uninvolved margin of breast carcinoma
HZK162-UM-EU2


title: HZK162-UM-IU2_1339

description:
uninvolved margin of breast carcinoma
HZK162-UM-IU2


title: HZK162-UM-EU1_1336

description:
uninvolved margin of breast carcinoma
HZK162-UM-EU1


title: HZK162-UM-EL1_1334

description:
uninvolved margin of breast carcinoma
HZK162-UM-EL1


title: HL057-UM99_1330

description:
uninvolved margin of breast carcinoma
HL057-UM99


title: HL057-UM98_1329

description:
uninvolved margin of breast carcinoma
HL057-UM98


title: HL057-UM4_1328

description:
uninvolved margin of breast carcinoma
HL057-UM4


title: HL057-UM3_1327

description:
uninvolved margin of breast carcinoma
HL057-UM3


title: HL057-UM2_1326

description:
uninvolved margin of breast carcinoma
HL057-UM2


title: HL057-UM1_1325

description:
uninvolved margin of breast carcinoma
HL057-UM1


title: HZK162-VB1-M_1340

description:
uninvolved margin in the immediate vicinity of the mammilla
HZK162-VB1-M


title: HB054-UM4_1318

description:
uninvolved margin of breast carcinoma
HB054-UM4


title: NM48A2_4

description:
TUMORS1: 4_primaryTumors_GPL18636.txt
Genotyping on DNA extracted from a primary tumor

hyb_protocol: standard protocol

data_processing:
The genotyping data was normalized and analyzed using Nexus Copy Number 7 (Biodiscovery). Copy number and allelic imbalances calls were made by using the SNP-FASST segmentation algorithm with the following settings: Significance Threshold: 5.0E-9; Max Contiguous Probe Spacing 500-1000; Min. number of probes per segment: 10; Homozygous Frequency Threshold: 0.85; Homozygous Value Threshold: 0.95; and Heterozygous Imbalance Threshold: 0.46. All the other parameters were left default. Data included in this GEO project was generated using the utility “convert .ivg to .txt” from Nexus 7.
Log R Ratio and B Allele frequency values are reported for each probe from the four different platforms used in the study.

source_name: DNA extracted from primary tumor

label_protocol: standard protocol

tag: age at cancer diagnosis

value: primary tumor


title: HB054-UM99_1320

description:
uninvolved margin of breast carcinoma
HB054-UM99


title: HB054-UM2_1316

description:
uninvolved margin of breast carcinoma
HB054-UM2


title: NM48A1_3


title: HZK162-UM-EL2_1335

description:
uninvolved margin of breast carcinoma
HZK162-UM-EL2


title: HB054-UM3_1317

description:
uninvolved margin of breast carcinoma
HB054-UM3


title: HB054-UM1_1315

description:
uninvolved margin of breast carcinoma
HB054-UM1


title: ML36A3_2


title: HB054-UM98_1319

description:
uninvolved margin of breast carcinoma
HB054-UM98


title: GS166-VB2-M_1310

description:
uninvolved margin in the immediate vicinity of the mammilla
GS166-VB2-M


title: ML36A2_1


title: OH113K_5

description:
CONTROLS1: 5_controls_GPL18636.txt
Control experiment, DNA genotyping on DNA extracted from whole blood

source_name: DNA extracted from whole blood

value: whole blood


title: Knockdown Control#1 vs Knockdown SNGH1#a rep3-1

city: Beijing

first: Guifeng

last: Wei

state: Beijing

address: 15 Datun Road

institute: Institute of Biophysics, Chinese Academy of Sciences

description:
Sample3.Cy3
raw data file:
US10313827_255290910133_S01_GE2_107_Sep09_1_1.txt.gz

hyb_protocol: (1) Reverse transcribed into first strand cDNA with the T7-oligo(dT) primer and T7-random primer. (2) systhesis of the second cDNA (3) in vitro transcribed into cRNA with T7 Enzyme mix (4) cRNA purification (5) reverse transcription using the cRNA as template with random primers (6) labelling the cDNA with Klenow Fragment Enzyme, as well as the Cy3 or Cy5-labelled dNTPs.

scan_protocol: Arrays were scanned with the Agilent DNA Microarray Scanner and processed with the Agilent Feature Extraction v10.7

data_processing: The microarray data were quantile normalized using the R limma package. The fold change and two-tailed Student’s t test were applied for statistical analysis of differentially expressed genes. Heatmap and Scatterplot were drawn with the functions in R.

source_name: HCT116-Control a

label_protocol: 500 ng RNAs were used to generate fluorescence-labelled cDNA for hybridization according to the Agilent standard workflow

growth_protocol: HCT116 cells were cultured in Mccoy’s 5A medium supplemented with 10% FBS.

extract_protocol: Total RNA was isolated using the Trizol following the manufacturer’s instructions and RNA integrity assessed on a Nanodrop 2000.

treatment_protocol: siRNAs targeting the SNHG1 sequence or control were transfected into HCT116 using Lipofectamine 2000.

tag: cell type

value: human colorectal carcinoma

tag: genotype/variation

value: control


title: Knockdown Control#2 vs Knockdown SNGH1#b rep1-2

description:
Sample4.Cy5
raw data file:
US10313827_255290910153_S01_GE2_107_Sep09_1_2.txt.gz

value: SNHG1 knockdown


title: Knockdown Control#2 vs Knockdown SNGH1#b rep2-1

description:
Sample5.Cy3
raw data file:
US10313827_255290910153_S01_GE2_107_Sep09_1_4.txt.gz

source_name: HCT116-Control b


title: Knockdown Control#1 vs Knockdown SNGH1#a rep2-2

description:
Sample2.Cy5
raw data file:
US10313827_255290910153_S01_GE2_107_Sep09_1_3.txt.gz


title: NM48K_4

value: Luminal B, HER2+

value: unifocal


title: GS166-UM-IU2_1308

description:
uninvolved margin of breast carcinoma
GS166-UM-IU2


title: ML36K_3


title: Knockdown Control#1 vs Knockdown SNGH1#a rep1-1

description:
Sample1.Cy3
raw data file:
US10313827_255290910153_S01_GE2_107_Sep09_1_1.txt.gz


title: Knockdown Control#2 vs Knockdown SNGH1#b rep1-1

description:
Sample4.Cy3
raw data file:
US10313827_255290910153_S01_GE2_107_Sep09_1_2.txt.gz


title: GS166-UM-IU1_1307

description:
uninvolved margin of breast carcinoma
GS166-UM-IU1


title: Knockdown Control#1 vs Knockdown SNGH1#a rep3-2

description:
Sample3.Cy5
raw data file:
US10313827_255290910133_S01_GE2_107_Sep09_1_1.txt.gz


title: Knockdown Control#2 vs Knockdown SNGH1#b rep2-2

description:
Sample5.Cy5
raw data file:
US10313827_255290910153_S01_GE2_107_Sep09_1_4.txt.gz


title: JD67K_2


title: Knockdown Control#2 vs Knockdown SNGH1#b rep3-2

description:
Sample6.Cy5
raw data file:
US10313827_255290910133_S01_GE2_107_Sep09_1_2.txt.gz


title: GS166-UM-IL1_1305

description:
uninvolved margin of breast carcinoma
GS166-UM-IL1


title: Knockdown Control#1 vs Knockdown SNGH1#a rep1-2

description:
Sample1.Cy5
raw data file:
US10313827_255290910153_S01_GE2_107_Sep09_1_1.txt.gz


title: GS166-UM-EU2_1304

description:
uninvolved margin of breast carcinoma
GS166-UM-EU2


title: GS166-UM-IL2_1306

description:
uninvolved margin of breast carcinoma
GS166-UM-IL2


title: BK9K_1


title: GS166-UM-EU1_1303

description:
uninvolved margin of breast carcinoma
GS166-UM-EU1


title: SK58B_595

description:
uninvolved margin of breast carcinoma
SK58B


title: PK6B_569

description:
uninvolved margin of breast carcinoma
PK6B


title: Knockdown Control#2 vs Knockdown SNGH1#b rep3-1

description:
Sample6.Cy3
raw data file:
US10313827_255290910133_S01_GE2_107_Sep09_1_2.txt.gz


title: PE129B_551

description:
uninvolved margin of breast carcinoma
PE129B


title: GS166-VB1-M_1309

description:
uninvolved margin in the immediate vicinity of the mammilla
GS166-VB1-M


title: PF27B_556

description:
uninvolved margin of breast carcinoma
PF27B


title: GI004-UM2_1295

description:
uninvolved margin of breast carcinoma
GI004-UM2


title: Knockdown Control#1 vs Knockdown SNGH1#a rep2-1

description:
Sample2.Cy3
raw data file:
US10313827_255290910153_S01_GE2_107_Sep09_1_3.txt.gz


title: OH113B_546

description:
uninvolved margin of breast carcinoma
OH113B


title: NM48B_540

description:
uninvolved margin of breast carcinoma
NM48B


title: NA71B_533

description:
uninvolved margin of breast carcinoma
NA71B


title: GI004-UM1_1294

description:
uninvolved margin of breast carcinoma
GI004-UM1


title: RA35B_574

description:
uninvolved margin of breast carcinoma
RA35B


title: GGB040-UM99_1291

description:
uninvolved margin of breast carcinoma
GGB040-UM99


title: ML36B_518

description:
uninvolved margin of breast carcinoma
ML36B


title: GS166-UM-EL2_1302

description:
uninvolved margin of breast carcinoma
GS166-UM-EL2


title: KJ42B_439

description:
uninvolved margin of breast carcinoma
KJ42B


title: KU25B_461

description:
uninvolved margin of breast carcinoma
KU25B


title: GGB040-UM2_1287

description:
uninvolved margin of breast carcinoma
GGB040-UM2


title: GS166-UM-EL1_1301

description:
uninvolved margin of breast carcinoma
GS166-UM-EL1


title: GGB040-UM98_1290

description:
uninvolved margin of breast carcinoma
GGB040-UM98


title: JM43B_413

description:
uninvolved margin of breast carcinoma
JM43B


title: GGB040-UM1_1286

description:
uninvolved margin of breast carcinoma
GGB040-UM1


title: GC147-VB2_1278

description:
uninvolved margin in the immediate vicinity of the mammilla
GC147-VB2


title: GGB040-UM4_1289

description:
uninvolved margin of breast carcinoma
GGB040-UM4


title: KH95B_435

description:
uninvolved margin of breast carcinoma
KH95B


title: GGB040-UM3_1288

description:
uninvolved margin of breast carcinoma
GGB040-UM3


title: KG13B_433

description:
uninvolved margin of breast carcinoma
KG13B


title: JD67B_408

description:
uninvolved margin of breast carcinoma
JD67B


title: GI004-UM98_1296

description:
uninvolved margin of breast carcinoma
GI004-UM98


title: GC147-VB1_1277

description:
uninvolved margin in the immediate vicinity of the mammilla
GC147-VB1


title: GW55B_391

description:
uninvolved margin of breast carcinoma
GW55B


title: GC147-UM-IU1_1275

description:
uninvolved margin of breast carcinoma
GC147-UM-IU1


title: GC147-UM-IU2_1276

description:
uninvolved margin of breast carcinoma
GC147-UM-IU2


title: FK12B_381

description:
uninvolved margin of breast carcinoma
FK12B


title: GC147-UM-IU_1274

description:
uninvolved margin of breast carcinoma
GC147-UM-IU


title: GC147-UM-IL_1273

description:
uninvolved margin of breast carcinoma
GC147-UM-IL


title: BK9B_325

description:
uninvolved margin of breast carcinoma
BK9B


title: DE22B_369

description:
uninvolved margin of breast carcinoma
DE22B


title: GC147-UM-EU_1272

description:
uninvolved margin of breast carcinoma
GC147-UM-EU


title: BE89B_316

description:
uninvolved margin of breast carcinoma
BE89B


title: MV4-11 Control_scrambled shRNA_3

city: Jacksonville

first: Catherine

last: Dumur

state: FL

address: 5008 Mustang Rd

department: Anatomic Pathology

institute: Sonic Healthcare USA

description:
GG31
Replicate 3 of 3.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HG-U133A 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GC3000 scanner.

data_processing: After scanning, the raw intensities for every probe were stored in electronic files (in .DAT and .CEL formats) by the Affymetrix GeneChip Operating Software (GCOSv1.4). Background correction, normalization, and estimation of probe set expression summaries were performed using the log-scale Robust Multiarray Analysis (RMA) method.

source_name: Human MV4-11 AML cells transfected with scrambled shRNA

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500 ng total RNA (GeneChip® Expression Analysis Technical Manual, Affymetrix).

growth_protocol: The human AML cell lines, U937 and MV4-11, were maintained in RPMI supplemented with 10% Fetal Bovine Serum, and 2% penicillin/streptomycin.

treatment_protocol: Lentiviral constructs (pRRL.H1.shRNA) expressing GFP were used as vectors that either contained non-silencing, scramble, short hairpin RNA (shRNA) or shRNAs against CDH4.

value: AML cell line

tag: shRNA

value: scrambled


title: GK1B_383

description:
uninvolved margin of breast carcinoma
GK1B


title: MV4-11 CDH4_shRNA_3

description:
GG32
Replicate 3 of 3.

source_name: Human MV4-11 AML cells transfected with CDH4 shRNA

tag: cell line


title: GC147-UM-EL1_1270

description:
uninvolved margin of breast carcinoma
GC147-UM-EL1


title: MV4-11 CDH4_shRNA_2

description:
GG30
Replicate 2 of 3.