title: AcutePancreatitis003

status: Public on Mar 31 2014

type: RNA

city: Auckland

first: Cherie

last: Blenkiron

address: Private bag 92019

department: Surgery

country: New Zealand

institute: University of Auckland

description: miRNA expression data from acute pancreatitis lymph

hyb_protocol: biotinylated RNA was hybridised to GeneChip miRNA V1.0 arrays at 480C, 60rpm for 16 hours. GeneChips were washed and stained in the Affy Fluidics station 450.

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

data_processing: Affymetrix .CEL files were analysed using the statistical programming language R using the Bioconductor packages affy, affyPLM and limma. The data was preprocessed using RMA.

label: biotin

molecule: total RNA

organism: Rattus norvegicus

source_name: Mesenteric lymph, taurocholate induced pancreatitis animals

label_protocol: 8ul RNA was direct labelled using the Flashtag HSR kit as standard

extract_protocol: RNA was extracted from 250ul mesenteric lymph using trizol and a Purelink microRNA kit (Life Technologies) and eluted in a volume of 30ul water

tag: strain

value: Wistar

tag: weight

tag: age

value: 70-110 days old

tag: Sex

value: male

tag: rna

value: enriched small RNA

tag: tissue

value: mestenteric lymph


title: ResuscitatedAcutePancreatitis005

description: miRNA expression data from resuscitated acute pancreatitis lymph

source_name: Mesenteric lymph, taurocholate induced pancreatitis animals which also received fluid resuscitation


title: ResuscitatedAcutePancreatitis003


title: ResuscitatedAcutePancreatitis004


title: Sham003

description: miRNA expression data from control rat lymph

source_name: Mesenteric lymph, control animals


title: AcutePancreatitis004


title: Sham001


title: AcutePancreatitis005


title: AcutePancreatitis002


title: ResuscitatedAcutePancreatitis001


title: Sham002


title: Sham005


title: ResuscitatedAcutePancreatitis002


title: Sham004


title: AcutePancreatitis001


title: hippocampus_CA3_no-febrile seizure NFS12

city: Sao Paulo

first: Carlos

middle: Alberto

last: Moreira-Filho

state: SP

address: Av. Dr. Eneas Carvalho de Aguiar 647

department: Departments of Pediatrics

country: Brazil

institute: Faculdade de Medicina da Universidade de Sao Paulo

description: Gene expression from CA3 explant

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 and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven.

scan_protocol: Slides were scanned immediately after washing on the Agilent Bundle using one color scan setting for 1x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software version 9.5.3.1 (Agilent) using default parameters (protocol GE1-v5_95 and Grid: 014850_D__F_20060807) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Homo sapiens

source_name: hippocampus, CA3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Microarray-Based Gene Expression Analysis - Quick Amp Labeling (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (Qiagen). RNA concentration and purity was determined by reading the absorbance at 260 and 280 nm on a spectrophotometer (NanoVue, GE Health Care, USA).

extract_protocol: Brain tissue explants from GD (3-4 mm3) were homogenized with TissueRupter (Qiagen) and total RNA was extracted from the homogenates using the RNeasy Lipid Tissue Kit (Qiagen)

treatment_protocol: Fresh ex-vivo explants of patients were obtained at the surgery room and immediately preserved with 600 uL of RNAlater (Qiagen).

tag: gender

value: Female

tag: febrile seizure

value: no

tag: age of ipi (yr/mo)

tag: age of epilepsy onset (yr)

tag: age of epilepsy duration (yr)

tag: age at surgery

tag: side

value: left


title: hippocampus_CA3_no-febrile seizure NFS15

description: Gene expression from CA3 explant

value: Male


title: hippocampus_CA3_no-febrile seizure NFS19

description: Gene expression from CA3 explant

value: right


title: hippocampus_CA3_no-febrile seizure NFS22

description: Gene expression from CA3 explant


title: hippocampus_CA3_no-febrile seizure NFS18

description: Gene expression from CA3 explant


title: hippocampus_CA3_no-febrile seizure NFS23

description: Gene expression from CA3 explant


title: hippocampus_CA3_no-febrile seizure NFS11

description: Gene expression from CA3 explant


title: hippocampus_CA3_no-febrile seizure NFS9

description: Gene expression from CA3 explant


title: hippocampus_CA3_no-febrile seizure NFS20

description: Gene expression from CA3 explant


title: hippocampus_CA3_no-febrile seizure NFS17

description: Gene expression from CA3 explant


title: hippocampus_CA3_no-febrile seizure NFS10

description: Gene expression from CA3 explant


title: hippocampus_CA3_febrile seizure FS6

description: Gene expression from CA3 explant

value: yes


title: hippocampus_CA3_no-febrile seizure NFS16

description: Gene expression from CA3 explant


title: hippocampus_CA3_febrile seizure FS5

description: Gene expression from CA3 explant


title: hippocampus_CA3_febrile seizure FS7

description: Gene expression from CA3 explant


title: GS-2_IFNb300_24h_rep1

city: Duesseldorf

first: Karl

last: Koehrer

address: Universitaetsstr. 1

department: BMFZ

country: Germany

institute: University of Duesseldorf

hyb_protocol: Samples were hybridized for 16h at 45°C using Hybridization Kit materials (PN 900720, Affymetrix) according to the GeneChip® 3’ IVT Express Kit Protocol (PN 702646 Rev. 6, Affymetrix)

scan_protocol: Affymetrix Gene Chip Scanner 3000 7G; AGCC

data_processing: Quantile normalization / RMA summarization (GeneSpring 12.1, Agilent)

label: Biotin

label_protocol: Sample preparation was done with 100 ng total-RNA using the GeneChip® 3´ IVT Express Kit (PN 901229) from Affymetrix (Santa Clara, USA) according to the instructions of the Affymetrix GeneChip® 3´ IVT Express Technical Manual (PN 702646). 10 µg of the fragmented cRNA were hybridized on the Gene Chip® Human Genome U133A 2.0 Arrays (Affymetrix, PN 900469)

growth_protocol: LNT-229 cells were grown in DMEM with 10% FCS and glutamine; GS-cells were grown in Neurobasal medium supplemented with growth factors and B27.

extract_protocol: RNA was extracted with the miRNeasy Mini Kit (Qiagen, Hilden, Germany, Cat. No. 217004); RNA qualitiy was checked with the 2100 BioAnalyzer (Agilent, Santa Clara, USA)

treatment_protocol: IFN-beta was dissolved in ddH2O. Cells were exposed to either IFN 300 IU/ml or ddH2O for either 6 h or 24 h before assembly of the cell pellets.

value: glioma

tag: cell line


title: hippocampus_CA3_febrile seizure FS1

description: Gene expression from CA3 explant


title: hippocampus_CA3_febrile seizure FS2

description: Gene expression from CA3 explant


title: hippocampus_CA3_febrile seizure FS4

description: Gene expression from CA3 explant


title: GS-2_Ctrl_24h_rep1


title: GS-9_Ctrl_6h_rep1


title: GS-9_IFNb300_24h_rep1


title: GS-2_IFNb300_6h_rep1


title: GS-9_IFNb300_6h_rep1


title: LNT-229_Ctrl_24h_rep1


title: LNT-229_IFNb300_24h_rep1


title: LNT-229_IFNb300_6h_rep1


title: GS-9_Ctrl_24h_rep1


title: GS-2_Ctrl_6h_rep1


title: MDCK-3DHGF+UO-01

city: Philadelphia

first: Maria

middle: Fernanda

last: Chacon-Heszele

state: Pennsylvania

address: 415 Curie Blvd - 411 CRB

country: USA

institute: University of Pennsylvania

description: Sample name: HGF_3D_UO_C1

hyb_protocol: Fragmentation to 200 nt or less; incubation at 99C for 5 minutes; hybridization at 45C for 16hrs to GeneChip Canine Genome 2.0 array; low & high stringency washes; stain with streptavidin-phycoetrythrin; amplification with byotinylated anti-streptavidin and additional streptavidin-phycoetrythrin stain.

scan_protocol: Agilent 2100 Bioanalyzer (G2938A, Firmware Version A.01.16) Confocal scanner at Upenn microarray core facility used to collect signal at 3nm resolution after excitation at 570 nm.

data_processing: Absent, Marginal and Present flags were calculated with MAS5 in Affymetrix Expression Console v1.1 and GCRMA log2-intensities were calculated with Partek Genomics Suite v6.6

organism: Canis lupus familiaris

source_name: 3D MDCK+HGF+U0126

label_protocol: biotynilated CTP and UTP

extract_protocol: total RNA isolation (Qiagen RNEasy), first strand cDNA synthesis and in vitro transcription

value: MDCK

tag: culture

value: 3D (collagen)

tag: hgf treatment

value: Yes

tag: mapk-inhibitor


title: Expression data from E18.5 Igf1+/+ (normal wild type control) mouse lungs - Sample 2

city: Salamanca

first: Javier

last: De Las Rivas

address: Campus Miguel de Unamuno

department: CSIC and University of Salamanca

country: Spain

institute: Cancer Research Center (CiC-IBMCC)

description: Lungs from E18.5 were isolated from both Igf1+/+ wild type and Igf1-/- null mice and pooled to obtain RNA. Heterozygous male and female with a genetic background C57BL/6J were mated to obtain embryos at embrionic (E) stage 18.5 days post coitum (E18.5).

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse MOE430A Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned at 3-mm density with a GeneChip® Scanner 3000 7G 4C (Affymetrix).

data_processing: To normalize and calculate gene expression signals, the RMA algorithm was used. To detect the probe-sets with differential expression, the SAM algorithm was applied, and the data was normalized using the FDR value (False discovery rate or proportion of false negatives). The final list corresponds to the 640 differentially expressed genes with a FDR<0,20 (p<0,001; 640 probe sets; 566 genes).

organism: Mus musculus

source_name: Lungs from embryos at embrionic (E) stage 18.5 days post coitum (E18.5)

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

extract_protocol: RNA was isolated by using the Trizol (Invitrogen) method following manufacturer’s instructions. Trizol-purified RNA was then treated with RNase-free DNase I (Roche) and mRNA purified with RNeasy spin columns (Qiagen). RNA quantity and quality was assessed with an Agilent Bioanalyzer 2100 (Agilent Technologies).

tag: genotype

value: Igf1+/+ (normal wild type control)

value: lung


title: MDCK-2DHGF+UO-01

description: Sample name: HGF_2D_UO_W1

source_name: 2D MDCK+HGF+U0126

value: 2D (transwell)


title: MDCK-2DHGF+UO-03

description: Sample name: HGF_2D_UO_W4


title: MDCK-2DHGF+UO-02

description: Sample name: HGF_2D_UO_W3


title: LNT-229_Ctrl_6h_rep1


title: MDCK-2DHGF+PD-03

description: Sample name: HGF_2D_PD_X3

source_name: 2D MDCK+HGF+PD-98059


title: MDCK-3DHGF+UO-03

description: Sample name: HGF_3D_UO_C3


title: MDCK-3DHGF+UO-02

description: Sample name: HGF_3D_UO_C2


title: MDCK-2DHGF+PD-01

description: Sample name: HGF_2D_PD_X1


title: Expression data from E18.5 Igf1-/- (homozygous mutant) mouse lungs - Sample 3

value: Igf1-/- (homozygous mutant)


title: MDCK-3DHGF+PD-03

description: Sample name: HGF_3D_PD_D3

source_name: 3D MDCK+HGF+PD-98059


title: MDCK-2DHGF+PD-04

description: Sample name: HGF_2D_PD_X4


title: MDCK-2DHGF+PD-02

description: Sample name: HGF_2D_PD_X2


title: MDCK-3DHGF+PD-02

description: Sample name: HGF_3D_PD_D2


title: MDCK-3DHGF+PD-01

description: Sample name: HGF_3D_PD_D1


title: Expression data from E18.5 Igf1+/+ (normal wild type control) mouse lungs - Sample 3


title: MDCK-2DHGF-02

description: Sample name: HGF_2D_V2

source_name: 2D MDCK+HGF


title: Expression data from E18.5 Igf1+/+ (normal wild type control) mouse lungs - Sample 1


title: MDCK-2DControl-03

description: Sample name: control_2D_T3

source_name: 2D MDCK

value: No


title: MDCK-2DHGF-03

description: Sample name: HGF_2D_V3


title: MDCK-2DHGF-01

description: Sample name: HGF_2D_V1


title: MDCK-2DControl-04

description: Sample name: control_2D_T4


title: MDCK-3DHGF-01

description: Sample name: HGF_3D_B1

source_name: 3D MDCK+HGF


title: MDCK-3DHGF-03

description: Sample name: HGF_3D_B3


title: MDCK-3DHGF-04

description: Sample name: HGF_3D_B4


title: MDCK-2DControl-02

description: Sample name: control_2D_T2


title: MDCK-3DHGF-02

description: Sample name: HGF_3D_B2


title: MDCK-3DControl-04

description: Sample name: control_3D_A5

source_name: 3D MDCK


title: MDCK-2DHGF-04

description: Sample name: HGF_2D_V4


title: MDCK-3DControl-02

description: Sample name: control_3D_A2


title: MDCK-2DControl-01

description: Sample name: control_2D_T1


title: MDCK-3DControl-01

description: Sample name: control_3D_A1


title: MDCK-3DControl-03

description: Sample name: control_3D_A4


title: Expression data from E18.5 Igf1-/- (homozygous mutant) mouse lungs - Sample 2


title: Low-2-4014328

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

country: Italy

institute: University of Padova

description:
Tissue was extracted from three different pig (12 month old) and small RNA was pooled.
Retrotranscribed small RNA
RAKE technology. Extended primer (hybridized miRNA) incorporate dATP biotinilated than labelled with Cy3-streptavidin
RNA-primed Array-based Klenow Extension (RAKE) is based on the ability of a RNA molecule to function as a primer for Klenow polymerase extension when fully base-paired with a microarray probe. As the exact 3’ end of the miRNA should be known for successful extension, and computational predictions are not optimal for predicting the correct start and end of the mature miRNA, we designed a tiling path of 16 probes complementary to the predicted pre-miRNAs responding for the presence of a 3’ end of the miRNA (see Figure).

hyb_protocol: Microarrays were probed with 1 ug of the retrotranscribed small RNA pool for 20 hours at 37° C in a static hybridization oven (SSPE 6X; BSA 8 mg/ml; 1 ug of small RNAs and spike-in). First, microarrays were pre-hybridized for 2 hours at 37° C with the following pre-hybridization water solution: SSPE 6X and BSA 8 mg/ml. After the retrotranscribed small RNAs hybridization, microarrays were washed with the following stringent washing solutions: 1 minute at room temperature with 6x SSPET (SSPE added with 0.05% of Tween-20); 1 minute at room temperature with 3x SSPET; 1 minute at room temperature with PBS 2X; 1 minute at room temperature with Buffer 2, 1X (the buffer for the klenow enzyme). After the washing step it was performed the RAKE reaction at 36.5° C incubating the microarray for 1 hour and 30 minutes with the following solution: Buffer 2 1X; Biotin-14-dATP (Invitrogen) 16 μM; Klenow Fragment (3´→5´ exo–) (NEB) 0.25 U/μl. Than microarray was washed two times with Buffer 2 1X and than incubated with the biotin blocking solution (PBS 2X; Tween-20 0.1% and BSA 10 mg/ml) for one hour at room temperature. Extended miRNAs (primers) were labeled incubating the microarray with the Dye labeling solution (PBS 2X; Tween-20 0.1% ; BSA 10 mg/ml and 1.6 ng of Cy3-streptavidin; Amersham) for one hour at room temperature. Microarray was rinsed with PBST (PBS 2X added with Tween-20 0.1%) for one minute at room temperature and with PBS 2X for one minute at room temperature (see Figure).

scan_protocol: Microarrays were scanned with the VersArray scanner (Biorad) (3 μm resolution).

data_processing:
The RAKE experimental setup associates fluorescence levels to 16 tailed probes corresponding to the 3' ends of each retrotranscribed miRNA (see Figure).  To identify the most probable endpoints, we then need to analyze these values looking for spots with a fluorescence level significantly higher from the rest of the group. We implemented this search with a bootstrap approach. Given a group of 16 measures, we extract in turn one of them and we build ten thousand simulated groups by sampling the remaining 15 values with replacement. The number of samples with an average fluorescence level lower than the value of the observed group, divided by ten thousand, is taken as an estimate of the probability of having picked a true endpoint for the miRNA. For the rest of the analysis, we keep only the results with a probability higher than 0.65 and for a minor group . 5’ end had a probability higher than 0.58.
Data for the identification of the 3' end of the miRNAs (in this case 3' end of the retrotranscribed miRNA correspond to the 5' end of the mature miRNA) did not need to be normalized because we did not compared different experiments, but we extracted from each experiments peaks corresponding to miRNA end.

organism: Sus scrofa

source_name: Pool of same quantity of small RNA from tissues listed in 'characteristics'

label_protocol: The small RNA was not labelled when it was used to probe microarray. RNA-primed Array-based Klenow Extension (RAKE) is based on the ability of a RNA molecule to function as a primer for Klenow polymerase extension when fully base-paired with a microarray probe. As the exact 3’ end of the miRNA should be known for successful extension, and computational predictions are not optimal for predicting the correct start and end of the mature miRNA, we designed a tiling path of 16 probes complementary to the predicted pre-miRNAs responsive for the 3’ end of the miRNA. The protocol for the identification of the 5’ end of miRNAs was the same used for the identification of the 3’ end, but the 12K microarray was probed with the retrotranscribed miRNAs (see Figure). A poly(A) tail was added to small RNAs from the same pool used for the identification of the 3’ end of miRNAs. 1 μg of small RNAs was added to the polyadenilation mix (E-PAP Buffer 1X; MnCl2 2.5 mM; ATP 1mM; E-Polyadenylase Polymerase Invitrogen 0.08 U/μl in 100 μl of reaction) incubated for 1 hour at 37° C than precipitated using Na-Acetate and 4 volumes of ethanol. Tailed small RNAs were retrotranscribed with Superscript III (Invitrogen) enzyme that does not have terminal-transferase activity. Retrotranscription was performed incubating the mix (First strand Buffer 1X; DTT 1 mM; dNTPs 0.5 mM; Superscript III enzyme Invitrogen 8 U/μl in 50 μl of  volume reaction) for 1 hour at 42° C.

growth_protocol: Pigs were maintained at normal food regime

extract_protocol: Total RNA and miRNAs were extracted independently from each tissue sample by TRIzol reagent (Invitrogen) in association with PureLink miRNA isolation kit (Invitrogen). Briefly, approximately 200 mg of tissue was homogenized in 3.5 ml of TRIzol reagent (Invitrogen) using a tissue homogenizer (IKA Werke). After chloroform addition and centrifugation colorless upper aqueous phase containing RNAs was added with 96-100% ethanol to obtain a final concentration of 35% of ethanol and charged to PureLink membrane (Invitrogen) to separate total RNA and small RNAs from the same sample following the manufacturer manual. Total RNA and small RNAs were quantized using Nanodrop ND 1000 spectrophotometer (Thermo Fisher Scientific). Samples derived from the same tissues were pooled adding the same quantity from the three pigs used. “Pool tissues” were performed with 700 ng of small RNAs from each pool sample. Quality of small RNA of pooled samples was tested on Agilent Bioanalizer 2100 using the RNA small LabChip.

treatment_protocol: After the sedation, pigs were sacrificed and portions of the described organs were took and maintained in the RNALater solution (Ambion), excluding blood that was collected in the BD Vacutainer CPT cell preparation tubes, and processed according to manufacturer's directions to recover white blood cells.

value: superior vena cava, adipose tissue, lung, spleen, stomach, liver, intestine, kidney, descending aorta, left atrium, left ventricle, skeletal muscle, pulmonary aorta, skin, tongue, ascending aorta, arterial white cells blood, venal white cells blood, coronary valve, lymph node

value: 12 month old

tag: breed

value: vietnamite


title: Med-3-4014328

tag: age


title: High-1-4014328


title: Med-2-4014328


title: Med-1-4014328


title: Low-3-4014328


title: High-3-4014328


title: Low-1-4014328


title: High-2-4014328


title: MSC_SGA_Sample1_60mins rep 2

city: Singapore

first: Dennis

last: Wang

address: 30 Medical Drive

country: Singapore

institute: Singapore Institute for Clinical Sciences

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Background subtraction was performed in GenomeStudio then data was exported. Probes were filtered for detection p-value <0.05 and NBEADS>3 in R. Data was then loaded into Arraystudio version 6 (Omicsoft). All expression values were log2 transformed. Data were normalised amongst samples using quantile normalization.

source_name: MSC SGA at 60 Minutes

label_protocol: Biotinylated cRNA were prepared with the Illumina® TotalPrep™-96 RNA Amplification Kit (Ambion®)

growth_protocol: Cells were grown in DMEM media supplemented with 20%Fetal Bovine Serum, BetaMercaptoEthanol, Antibacterial-Antifungal, bFGF, and Insulin-Transferin-Selenium

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

treatment_protocol: Cells were treated with 100nM Insulin at 10, 30, 60, 360, and 1440 mins

tag: group

value: Small for Gestational Age (SGA)

tag: cell type

value: umbilical cord derived mesenchymal stem cells (UC-MSC)

tag: treated with

value: 100nM insulin for 60 Minutes


title: MSC_Control_Sample1_0min rep 2

source_name: MSC Control at 0 Minute

value: Control


title: MSC_Control_Sample1_360mins rep 1

source_name: MSC Control at 360 Minutes

value: 100nM insulin for 360 Minutes


title: MSC_Control_Sample1_10mins rep 1

source_name: MSC Control at 10 Minutes

value: 100nM insulin for 10 Minutes


title: MSC_Control_Sample1_30mins rep 2

source_name: MSC Control at 30 Minutes

value: 100nM insulin for 30 Minutes


title: MSC_SGA_Sample1_30mins rep 2

source_name: MSC SGA at 30 Minutes


title: MSC_SGA_Sample1_0min rep 2

source_name: MSC SGA at 0 Minute


title: MSC_Control_Sample1_1440mins rep 2

source_name: MSC Control at 1440 Minutes

value: 100nM insulin for 1440 Minutes


title: MSC_SGA_Sample1_10mins rep 2

source_name: MSC SGA at 10 Minutes


title: MSC_Control_Sample1_30mins rep 1


title: MSC_Control_Sample1_0min rep 1


title: MSC_SGA_Sample1_360mins rep 2

source_name: MSC SGA at 360 Minutes


title: MSC_SGA_Sample1_1440mins rep 1

source_name: MSC SGA at 1440 Minutes


title: MSC_SGA_Sample1_0min rep 1


title: MSC_SGA_Sample1_1440mins rep 2


title: MSC_Control_Sample1_10mins rep 2


title: MSC_Control_Sample1_360mins rep 2


title: MSC_SGA_Sample1_60mins rep 1


title: MSC_SGA_Sample1_30mins rep 1


title: MSC_Control_Sample1_60mins rep 2

source_name: MSC Control at 60 Minutes


title: MSC_Control_Sample1_60mins rep 1


title: MSC_SGA_Sample1_360mins rep 1


title: MSC_Control_Sample1_1440mins rep 1


title: MSC_SGA_Sample4_1440mins rep2

value: 100nM Insulin for 1440min


title: MSC_SGA_Sample1_10mins rep 1


title: MSC_Control_Sample2_0min rep2


title: MSC_Control_Sample2_30mins rep2

value: 100nM Insulin for 30min


title: MSC_SGA_Sample4_10mins rep2

value: 100nM Insulin for 10min


title: MSC_SGA_Sample4_60mins rep2

value: 100nM Insulin for 60min


title: MSC_Control_Sample2_360mins rep2

value: 100nM Insulin for 360min


title: MSC_SGA_Sample4_30mins rep2


title: MSC_SGA_Sample4_0min rep2


title: Rec8_4h_input

type: genomic

city: Suita

first: Masaru

last: Ito

state: Osaka

address: Yamadaoka 3-2

country: Japan

institute: Osaka University

hyb_protocol: 16 h at 45C using a hybridization oven 640 (affymetrix) as described in the Affymetrix Chromatin Immunoprecipitation Assay Protocol (P/N 702238 Rev. 3)

scan_protocol: Fluidics station 400 protocol Midi-euk2.v3 (affymetrix) was performed to wash and stain arrays. The arrays were scanned on GeneChip Scanner 3000 7G (affymetrix).

data_processing: Quantile normalization and calculation of MA statistics (bar file) were performed with CisGenome v2 (Ji et al., 2008).

molecule: genomic DNA

organism: Schizosaccharomyces pombe

source_name: WCE at 4h after meiotic induction (REC8-HA cells)

label_protocol: Immunoprecipitated DNA and input DNA were amplified and end-labeled with the IVT (in vitro transcription). The amplification method is as described elsewhere (Katou et al., 2006).

growth_protocol: For the synchronous induction of meiosis, the pat1-114 mutant strain was cultured in EMM medium containing nitrogen (0.5% NH4Cl) at 25ºC. This culture was washed and re-suspended in EMM medium without nitrogen and starved for 20 h at 25ºC to arrest the cell cycle in G1. The cells were then released into EMM containing nitrogen (0.05% NH4Cl) at 34ºC to allow for synchronous progression into meiosis.

extract_protocol: The cells were disrupted using Multi-Beads Shocker (YASUI KIKAI, Osaka) with 0.5-mm zirconia beads. Cell lysates were sonicated to obtain average 500 bp of genomic DNA fragments. Whole cell extracts (WCEs) were subjected to immunoprecipitation with anti-HA antibody 16B12 (Covance) coupled to Dynabeads protein A (Invitrogen). A small amount of WCEs was used as input sample. The chromatin immunoprecipitated sample and input sample were incubated overnight at 75ºC, incubated for 3 hours at 55ºC with proteinase K, and DNA was purified using QIAquick Spin Purification Kit (QIAGEN).

treatment_protocol: The cells were fixed in 1% formaldehyde for 15 min at room temperature and then incubated on ice for 45 min. The cells were washed with ice-cold PBS twice, freezed with liquid nitrogen, and stored at -80ºC.

tag: strain

value: wild type (pat1-114)

value: 4h after transfer to EMM containing nitrogen (0.05% NH4Cl) at 34ºC


title: Rec8_4h_IP

source_name: Rec8-HA ChIP at 4h after meiotic induction


title: MSC_Control_Sample2_1440mins rep2


title: MSC_Control_Sample2_60mins rep2


title: MSC_SGA_Sample4_360mins rep2


title: MSC_Control_Sample2_10mins rep2


title: Expression data from E18.5 Igf1-/- (homozygous mutant) mouse lungs - Sample 1 (of 3 biological replicates)

source_name: Lungs from embryos at embrionic (E) stage 18.5 days post coitum (E18.5)

value: Igf1-/- (homozygous mutant)

tag: tissue

value: lung


title: MSC_SGA_Sample4_1440mins rep1

value: Small for Gestational Age (SGA)


title: MSC_Control_Sample2_1440mins rep1

value: umbilical cord derived mesenchymal stem cells (UC-MSC)


title: MSC_SGA_Sample4_10mins rep1


title: MSC_SGA_Sample4_60mins rep1


title: MSC_Control_Sample2_60mins rep1


title: MSC_Control_Sample2_10mins rep1


title: MSC_SGA_Sample4_30mins rep1


title: PC3 DMSO vehicle at 24 hrs, Biological rep2

city: London

first: Matteo

last: Righi

state: London

address: The MediaWorks, 191 Wood Ln

country: United Kingdom

institute: Autolus Therapeutics

description: Gene expression data from PC3 DMSO vehicle at 24 hrs

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

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

source_name: PC3 DMSO vehicle at 24 hrs

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

extract_protocol: PolyA mRNA was extracted according to the manufacturer's instructions.

treatment_protocol: Prostate cell lines were treated with DMSO or BET inhibitor GSK525762A (0.5 or 10 uM) at 24 hours

value: Human cancer cell line, PC3

tag: dose

value: vehicle

tag: time

value: 24 hrs


title: LNCAP GSK525762A 10uM at 24 hrs, Biological rep2

description: Gene expression data from LNCAP GSK525762A 10uM at 24 hrs

source_name: LNCAP GSK525762A 10uM at 24 hrs

value: Human cancer cell line, LNCAP


title: LNCAP GSK525762A .5uM at 24 hrs, Biological rep1

description: Gene expression data from LNCAP GSK525762A .5uM at 24 hrs

source_name: LNCAP GSK525762A .5uM at 24 hrs


title: LNCAP GSK525762A 10uM at 24 hrs, Biological rep1


title: PC3 GSK525762A .5uM at 24 hrs, Biological rep1

description: Gene expression data from PC3 GSK525762A .5uM at 24 hrs

source_name: PC3 GSK525762A .5uM at 24 hrs


title: PC3 GSK525762A .5uM at 24 hrs, Biological rep2


title: MSC_SGA_Sample4_360mins rep1


title: LNCAP GSK525762A .5uM at 24 hrs, Biological rep2


title: PC3 GSK525762A 10uM at 24 hrs, Biological rep2

description: Gene expression data from PC3 GSK525762A 10uM at 24 hrs

source_name: PC3 GSK525762A 10uM at 24 hrs


title: LNCAP DMSO vehicle at 24 hrs, Biological rep1

description: Gene expression data from LNCAP DMSO vehicle at 24 hrs

source_name: LNCAP DMSO vehicle at 24 hrs


title: PC3 GSK525762A 10uM at 24 hrs, Biological rep1


title: PC3 DMSO vehicle at 24 hrs, Biological rep1


title: VCAP GSK525762A 10uM at 24 hrs, Biological rep2

description: Gene expression data from VCAP GSK525762A 10uM at 24 hrs

source_name: VCAP GSK525762A 10uM at 24 hrs

value: Human cancer cell line, VCAP


title: LNCAP DMSO vehicle at 24 hrs, Biological rep2


title: VCAP GSK525762A .5uM at 24 hrs, Biological rep2

description: Gene expression data from VCAP GSK525762A .5uM at 24 hrs

source_name: VCAP GSK525762A .5uM at 24 hrs


title: SIRT1 KD 1 1

city: Newcastle

first: Simon

last: Cockell

address: Framlington Place

institute: Newcastle University

description:
60098402
Methylation profile of DNA from Caco-2 cells after transfection with SIRT1 siRNA.

hyb_protocol: Hybridisation was performed using the NimbleGen Hybridisation System as per the manufacturer's instructions. The hybridised arrays were then washed with the NimbleGen Wash Buffer Kit, and dried with the NimbleGen Microarray Drier as per the manufacturer's instructions.

scan_protocol: Signal peak intensities for each probe were measured with the NimbleGen MS 200 Microarray Scanner as per manufacturer's instructions.

data_processing: These data were used to detect peaks through manual inspection in Excel (Microsoft), accepting positive enrichment being where at least 2 of 3 biological replicates of each sample analysed (SIRT1 overexpressed by transfection with pCMV6-ENTRY-SIRT1, corresponding vector control, each of the siRNAs that target SIRT1 and control siRNA) met a >2 p-value minimum cut off.

source_name: INPUT DNA from Caco-2 cells expressing SIRT1 siRNA construct 1

label_protocol: Input and methylation-enriched samples were labelled with Cy3 and Cy5, respectively, using the NimbleGen Dual-Colour DNA Labelling Kit.

growth_protocol: Caco-2 cells (passage 30) were seeded into 25-cm2 flasks at a density of approximately one million cells per flask and maintained at 37 °C in a humidified atmosphere of 5% CO2 in air in Dulbecco's Modified Eagle's Medium (with 4.5 g/liter glucose) supplemented with 10% (v/v) fetal calf serum, 60 μg/ml gentamycin, 2 mm l-glutamine, and 1% (v/v) nonessential amino acids.

extract_protocol:
DNA was extracted from Caco-2 cells using the QIAamp® DNA Mini Kit (Qiagen).
Caco-2 DNA was fragmented by sonication and purified from agarose gels to produce DNA fragments ranging from 200-1000 bp in length. Purified fragmented DNA was then spiked with unmethylated and methylated internal controls generated from Lambda phage genomic DNA. An aliquot of each PCR product was then methylated in vitro using SssI DNA methylase (New England Biolabs). The methylation status of the unmethylated and methylated controls was confirmed by digestion with the methylation-sensitive restriction enzyme AciI (Fermentas). Spiked DNA samples were denatured at 95C, then incubated for 4 h at 4oC with anti-5-methylcytidine (5mC) antibody (Eurogentec, cat no.: BI-MECY-0100, lot#: 90120) (12 ul per 4.5 ug DNA) in 10 mM Na-Phosphate pH 7.0, 140 mM NaCl, 0.05 % Triton X-100. DNA was then captured using sheep anti-mouse IgG Dynabeads (Invitrogen), following the manufacturer's instructions. Dynabeads were then incubated with Proteinase K (Roche) at 50C for 2 h with shaking and beads were then removed using a magnetic rack. DNA was then purified using the DNA Clean and Concentrator 5 kit (Zymo Research). Whole genome amplification of input or immunoprecipitated DNA was then performed using the GenomePlex Complete Whole Genome Amplification kit (Sigma), and retention of fragment size was confirmed by agarose gel electrophoresis.

treatment_protocol: Cells transfected with SIRT1 Validated Stealth RNAi™ siRNAs (Invitrogen).

value: intestinal cell line

tag: construct

value: SIRT1 siRNA 1

tag: chip antibody

source_name: MEDIP DNA from Caco-2 cells expressing SIRT1 siRNA construct 1


title: Control 1

description:
60098502
Methylation profile of DNA from Caco-2 cells.

source_name: INPUT DNA from Caco-2 cells

treatment_protocol: Cells transfected with vector control.

value: vector

source_name: MEDIP DNA from Caco-2 cells


title: VCAP DMSO vehicle at 24 hrs, Biological rep1

description: Gene expression data from VCAP DMSO vehicle at 24 hrs

source_name: VCAP DMSO vehicle at 24 hrs


title: Med-4-9003467

description:
Tissue was extracted from three different pig (12 month old) and small RNA was pooled.
RAKE technology. Extended primer (hybridized miRNA) incorporate dATP biotinilated than labelled with Cy3-streptavidin
RNA-primed Array-based Klenow Extension (RAKE) is based on the ability of a RNA molecule to function as a primer for Klenow polymerase extension when fully base-paired with a microarray probe. As the exact 3’ end of the miRNA should be known for successful extension, and computational predictions are not optimal for predicting the correct start and end of the mature miRNA, we designed a tiling path of 22 probes complementary to the predicted pre-miRNAs to detect the exact 3’ end of the miRNA

hyb_protocol: Microarrays were probed with 1 ug of the small RNA pool for 20 hours at 37° C in a static hybridization oven (SSPE 6X; BSA 8 mg/ml; 1 ug of small RNAs and spike-in). First, microarrays were pre-hybridized for 2 hours at 37° C with the following pre-hybridization water solution: SSPE 6X and BSA 8 mg/ml. After the small RNAs hybridization microarrays were washed with the following stringent washing solutions: 1 minute at room temperature with 6x SSPET (SSPE added with 0.05% of Tween-20); 1 minute at room temperature with 3x SSPET; 1 minute at room temperature with PBS 2X; 1 minute at room temperature with Buffer 2, 1X (the buffer for the klenow enzyme). After the washing step it was performed the RAKE reaction at 36.5° C incubating the microarray for 1 hour and 30 minutes with the following solution: Buffer 2 1X; Biotin-14-dATP (Invitrogen) 16 μM; Klenow Fragment (3´→5´ exo–) (NEB) 0.25 U/μl. Than microarray was washed two times with Buffer 2 1X and than incubated with the biotin blocking solution (PBS 2X; Tween-20 0.1% and BSA 10 mg/ml) for one hour at room temperature. Extended miRNAs (primers) were labeled incubating the microarray with the Dye labeling solution (PBS 2X; Tween-20 0.1% ; BSA 10 mg/ml and 1.6 ng of Cy3-streptavidin; Amersham) for one hour at room temperature. Microarray was rinsed with PBST (PBS 2X added with Tween-20 0.1%) for one minute at room temperature and with PBS 2X for one minute at room temperature.

data_processing:
The RAKE experimental setup associates fluorescence levels to 22 tailed probes corrponding to the 3' ends of each predicted pre-miRNA. Tailing probes were constructed in each pre-miRNA arm. To identify the most probable endpoints, we then need to analyze these values looking for spots with a fluorescence level significantly higher from the rest of the group. We implemented this search with a bootstrap approach. Given a group of 22 measures, we extract in turn one of them and we build ten thousand simulated groups by sampling the remaining 21 values with replacement. The number of samples with an average fluorescence level lower than the value of the observed group, divided by ten thousand, is taken as an estimate of the probability of having picked a true endpoint for the miRNA. For the rest of the analysis, we keep only the results with a probability higher than 0.75.
Data for the identification of the 3' end of the miRNAs did not need to be normalized because we did not compared different experiments, but we extracted from each experiments peaks corresponding to miRNA end.

source_name: Pool of same quantity of small RNA from tissues listed in 'characteristics'

label_protocol: The small RNA was not labelled when it was used to probe microarray. RNA-primed Array-based Klenow Extension (RAKE) is based on the ability of a RNA molecule to function as a primer for Klenow polymerase extension when fully base-paired with a microarray probe. As the exact 3’ end of the miRNA should be known for successful extension, and computational predictions are not optimal for predicting the correct start and end of the mature miRNA, we designed a tiling path of 22 probes complementary to the predicted pre-miRNAs to detect the exact 3’ end of the miRNA

value: superior vena cava, adipose tissue, lung, spleen, stomach, liver, intestine, kidney, descending aorta, left atrium, left ventricle, skeletal muscle, pulmonary aorta, skin, tongue, ascending aorta, arterial white cells blood, venal white cells blood, coronary valve, lymph node

value: 12 month old

value: vietnamite


title: NCIH660 GSK525762A .5uM at 24 hrs, Biological rep1

description: Gene expression data from NCIH660 GSK525762A .5uM at 24 hrs

source_name: NCIH660 GSK525762A .5uM at 24 hrs

value: Human cancer cell line, NCIH660


title: Control 2

description:
59984502
Methylation profile of DNA from Caco-2 cells.


title: Med-1-9003467


title: VCAP DMSO vehicle at 24 hrs, Biological rep2


title: SIRT1 KD 2 1

description:
60058102
Methylation profile of DNA from Caco-2 cells after transfection with SIRT1 siRNA.

source_name: INPUT DNA from Caco-2 cells expressing SIRT1 siRNA construct 2

value: SIRT1 siRNA 2

source_name: MEDIP DNA from Caco-2 cells expressing SIRT1 siRNA construct 2


title: MSC_SGA_Sample4_10mins_rep2

source_name: SGA_UC-MSC_insulin 10min

treatment_protocol: Cells were treated with 100nM Insulin for 10 or 60min

value: 100nM Insulin for 10min


title: NCIH660 DMSO vehicle at 24 hrs, Biological rep2

description: Gene expression data from NCIH660 DMSO vehicle at 24 hrs

source_name: NCIH660 DMSO vehicle at 24 hrs


title: Low-4-9003467


title: Control siRNA 1

description:
59984402
Methylation profile of DNA from Caco-2 cells after transfection with negative control siRNA.

source_name: INPUT DNA from Caco-2 cells expressing siRNA control construct

treatment_protocol: Cells transfected with Stealth RNAi™ siRNA negative control LO GC.

value: control siRNA

source_name: MEDIP DNA from Caco-2 cells expressing siRNA control construct


title: Med-3-9003467


title: SIRT1 KD 2 2

description:
60098302
Methylation profile of DNA from Caco-2 cells after transfection with SIRT1 siRNA.


title: NCIH660 GSK525762A 10uM at 24 hrs, Biological rep2

description: Gene expression data from NCIH660 GSK525762A 10uM at 24 hrs

source_name: NCIH660 GSK525762A 10uM at 24 hrs


title: SIRT1 OE 2

description:
60058002
Methylation profile of DNA from Caco-2 cells after over-expression of SIRT1.

source_name: INPUT DNA from SIRT1 over-expression in Caco-2 cells

treatment_protocol: Overexpression of SIRT1 in Caco-2 cells was by transient transfection with the plasmid pCMV6-ENTRY-SIRT1 (Origene).

source_name: MEDIP DNA from SIRT1 over-expression in Caco-2 cells


title: MSC_Control_Sample2_30mins rep1

source_name: MSC Control at 30 Minutes

value: Control

value: 100nM Insulin for 30min


title: Med-2-9003467


title: NCIH660 GSK525762A 10uM at 24 hrs, Biological rep1


title: MSC_Control_Sample2_0min rep1

source_name: MSC Control at 0 Minute

value: umbilical cord derived mesenchymal stem cells (UC-MSC)


title: MSC_SGA_Sample4_0min rep1

source_name: MSC SGA at 0 Minute

value: Small for Gestational Age (SGA)


title: MSC_Control_Sample2_360mins rep1

source_name: MSC Control at 360 Minutes

value: 100nM Insulin for 360min


title: VCAP GSK525762A 10uM at 24 hrs, Biological rep1

source_name: VCAP GSK525762A 10uM at 24 hrs

value: 24 hrs


title: NCIH660 GSK525762A .5uM at 24 hrs, Biological rep2


title: VCAP GSK525762A .5uM at 24 hrs, Biological rep1

source_name: VCAP GSK525762A .5uM at 24 hrs

value: Human cancer cell line, VCAP


title: Control siRNA 2

description:
60058202
Methylation profile of DNA from Caco-2 cells after transfection with negative control siRNA.

value: intestinal cell line


title: MSC_SGA_Sample4_60mins_rep2

source_name: SGA_UC-MSC_insulin 60min

value: 100nM Insulin for 60min


title: NCIH660 DMSO vehicle at 24 hrs, Biological rep1

value: vehicle


title: MSC_SGA_Sample4_0min_rep2


title: MSC_SGA_Sample4_10mins_rep1


title: MSC_SGA_Sample4_60mins_rep1


title: Psoriasis treatment_1803

city: New York

first: Mayte

last: Suarez-Farinas

state: NY

address: 1425 Madison Ave, L2-70C, Box 1077,

institute: Mount SinaiSchool of Medicine

hyb_protocol: Affymetrix protocol

scan_protocol: Hewlett-Packard GeneArray Scanner G25Time: 0Time: 0A.

data_processing: GCRMA (using gcrma package from R/Bioconductor)

source_name: whole blood_Psoriasis treatment

label_protocol: Affymetrix single amplification protocol

extract_protocol: QIAGEN Rneasy Kit

tag: subject id

tag: sample group

value: Psoriasis treatment

tag: subject condition

value: psoriasis patients

tag: time point

value: week 2, after ixekizumab 150mg subcutaneous treatment

value: whole blood


title: SIRT1 OE 1

description:
59984302
Methylation profile of DNA from Caco-2 cells after over-expression of SIRT1.

tag: cell line


title: Psoriasis treatment_1710


title: Low-3-9003467

source_name: Pool of same quantity of small RNA from tissues listed in 'characteristics'

value: superior vena cava, adipose tissue, lung, spleen, stomach, liver, intestine, kidney, descending aorta, left atrium, left ventricle, skeletal muscle, pulmonary aorta, skin, tongue, ascending aorta, arterial white cells blood, venal white cells blood, coronary valve, lymph node

value: 12 month old

value: vietnamite


title: Psoriasis treatment_1611


title: Low-2-9003467


title: MSC_SGA_Sample4_0min_rep1


title: Psoriasis treatment_1615


title: Low-1-9003467


title: High-4-9003467


title: Psoriasis treatment_1209


title: Psoriasis Baseline_1611

source_name: whole blood_Psoriasis Baseline

value: Psoriasis Baseline

value: baseline; before treatment


title: MSC_Control_Sample2_60mins_rep2

source_name: control_UC-MSC_insulin 60min

value: Control

value: umbilical cord derived mesenchymal stem cells (UC-MSC)


title: MSC_Control_Sample2_10mins_rep2

source_name: control_UC-MSC_insulin 10min

value: 100nM Insulin for 10min


title: Psoriasis Baseline_1209


title: Psoriasis Baseline_1615


title: High-1-9003467


title: MSC_Control_Sample2_0min_rep2


title: Psoriasis Baseline_1610


title: Psoriasis Baseline_1710


title: Psoriasis Baseline_1208


title: High-3-9003467


title: High-2-9003467


title: Psoriasis treatment_1208


title: MSC_Control_Sample2_60mins_rep1


title: Psoriasis Baseline_1706


title: Psoriasis Baseline_1207


title: Psoriasis Baseline_1803


title: Psoriasis Baseline_1902


title: MSC_Control_Sample2_10mins_rep1


title: atsf1-2 mutant seedling, biological rep 3

city: Seoul

first: Jeong-Kook

last: Kim

address: 5-1, Anam-Dong, Seongbuk-Gu

department: Life Sciences

country: South Korea

institute: Korea University

description: AtSF1 is required for pre-mRNA splicing in Arabidopsis.

hyb_protocol: Following fragmentation, fragmented cDNA were hybridized for 16 hr at 45C on Affymetrix GeneChip® Arabidopsis Genome Array. The GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The Microarray Suite version 5.0 (MAS 5.0) algorithm implemented in Affymetrix Expression Console software (version1.2) was used to normalize the raw data. To reduce noise for the significance analysis, probe sets that were called "Present" by the MAS5 detection call in 100% of the samples were selected.  Highly expressed genes that showed over 2-fold difference between the signal values of control and test samples were selected for further study.

organism: Arabidopsis thaliana

source_name: atsf1-2 mutant seedling

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 300  ng total RNA (GeneChip® 3’ IVT Express Kit User Manual P/N 702646 Rev. 1, Affymetrix).

growth_protocol: The Col-0 and atsf1-2 mutant seeds were plated on MS agar plates.  Seedlings were grown at 23 C with 16-h light and 8-h dark cycles for 9 days before being harvested.

extract_protocol: Rneasy Plant Mini kit, Qiagen

treatment_protocol: No treatment

tag: ecotype

value: seedlings

tag: genotype/variation

value: atsf1-2 mutant


title: MSC SGA Sample 4

data_processing: Background subtraction was performed in GenomeStudio then data was exported.  Probes were filtered for detection p-value <0.05 and NBEADS>3 in R.  Data was then loaded into Arraystudio version 6 (Omicsoft). All expression values were log2 transformed. Data were normalised amongst samples using quantile normalization.

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

value: Small for Gestational Age (SGA)


title: atsf1-2 mutant seedling, biological rep 2


title: Psoriasis Baseline_1707


title: Psoriasis Baseline_1612


title: MSC_Control_Sample2_0min_rep1


title: MSC Control Sample 4


title: Psoriasis Baseline_1609


title: atsf1-2 mutant seedling, biological rep 1


title: Psoriasis Baseline_1801


title: Psoriasis Baseline_1607


title: Psoriasis Baseline_1109


title: Psoriasis Baseline_1606


title: MSC Control Sample 3


title: Col-0 seedling, biological rep 2

source_name: Col-0 seedling

value: wild-type


title: Col-0 seedling, biological rep 3


title: Psoriasis Baseline_1608


title: HIV- blood donor 6, replicate 2 (dye flip)

first: Suman

last: Laal

address: 423 Esat 23rd Street, 18N

department: Pathology

institute: VA/NYU

description:
Sample name: p16cy3 rvcy5
total RNA (amplified)

hyb_protocol: For hybridization, labeled cDNA probes generated from aRNA obtained from M. tb grown in each blood sample was mixed with the labeled reference cDNA probe prior to purification with Microcon YM10 filter (Millipore). For each M. tb-infected blood sample, the M. tb arrays were hybridized over night with the mixed labeled cDNA probes in duplicate including a Cy3/Cy5 dye swap (Fontan et al, 2008)

scan_protocol: The microarrays were scanned and processed with an Axon 4000B scanner and GenePix Pro 6.1 software, respectively.

data_processing: Normalized by the print-tip Lowess method; intensity ratio data obtained used to perform Significance Analysis of Microarrays (SAM) with Multiarray Viewer Software on the TMEV website for determination of differentially expressed genes; ≥ 2 fold change at a false discovery rate of < 2% were considered significantly differentially expressed.

organism: Mycobacterium tuberculosis H37Rv

source_name: M. tb in HIV- blood (donor P16)

label_protocol: The synthesis and fluorescent labeling of cDNA with Cy3 or Cy5 from aRNA was accomplished by first performing reverse transcriptase (RT) reaction with Superscript II RT followed by labeling with Klenow fragment using Bioprime Kit (Invitrogen) following a published method (Schlingemann 2005).

growth_protocol: Fresh human whole blood from 6 HIV- and 6 HIV+ was diluted with equal volumes RPMI-1640 supplemented with L-glutamine and heparin and infected with M. tb H37Rv (10^6 CFU/ml) and incubated at 37°C shaking at 20 rpm for 96 hr. Fot reference, M. tb H37Rv was grown in Middlebrook 7H9 broth to log phase.

extract_protocol: Blood cells lysed with 0.1% triton X 100 with 6M urea and bacteria and cells pelleted. Pellets imediately resuspended in GTC solution for lysis of remainig cells. After washing with GTC, bacterial pellets suspended in TRI reagent with polyacrylamide carrier and disrupted in bead beater using sterile 0.1 mm zirconia. Total RNA was extracted accordig to published protocol (Dunau E. e al. 2002). An RNA amplification strategy was used (MessageAmp II-bacteria RNA amplification kit- Ambion) (Schlingemann etal., 2005; Garton et al., 2008)

tag: donor

tag: hiv status

value: HIV-

tag: growth protocol

value: M. tb in HIV- blood

source_name: 7H9 broth-grown M. tb (reference)

value: 7H9 broth-grown


title: Psoriasis Baseline_1402

value: psoriasis patients


title: MSC SGA Sample 3

tag: group

tag: cell type


title: MSC Control Sample 2


title: Psoriasis Baseline_1404

tag: tissue

value: whole blood


title: MSC SGA Sample 2


title: Psoriasis Baseline_1403


title: Psoriasis Baseline_1410


title: HIV- blood donor 5, replicate 1

description:
Sample name: p15cy5rvcy3
total RNA (amplified)

source_name: M. tb in HIV- blood (donor P15)


title: HIV- blood donor 5, replicate 2 (dye flip)

description:
Sample name: p15cy3rvcy5
total RNA (amplified)


title: Col-0 seedling, biological rep 1


title: HIV- blood donor 4, replicate 1

description:
Sample name: p14cy5 rvcy3
total RNA (amplified)

source_name: M. tb in HIV- blood (donor P14)


title: HIV- blood donor 4, replicate 2 (dye flip)

description:
Sample name: P14cy3 7H9 Cy5
total RNA (amplified)


title: Psoriasis Baseline_1504


title: HIV- blood donor 3, replicate 2 (dye flip)

description:
Sample name: p13cy3rvcy5
total RNA (amplified)

source_name: M. tb in HIV- blood (donor P13)


title: Psoriasis Baseline_1605


title: MSC Control Sample 1


title: Psoriasis Baseline_1502


title: MSC SGA Sample 1


title: Psoriasis Baseline_1303


title: Psoriasis Baseline_1401


title: Psoriasis Baseline_1104


title: Psoriasis Baseline_1604


title: Psoriasis Baseline_1602


title: Psoriasis Baseline_1102


title: Psoriasis Baseline_1301


title: HIV- blood donor 6, replicate 1

description:
Sample name: p16cy5 rvcy3
total RNA (amplified)


title: Psoriasis Baseline_1603


title: HIV- blood donor 3, replicate 1

description:
Sample name: p13cy5rvcy3
total RNA (amplified)


title: HIV- blood donor 2, replicate 1

description:
Sample name: p7cy5 rvcy3
total RNA (amplified)

source_name: M. tb in HIV- blood (donor P7)


title: HIV- blood donor 2, replicate 2 (dye flip)

description:
Sample name: p7cy3 rvcy5
total RNA (amplified)


title: HIV- blood donor 1, replicate 2 (dye flip)

description:
Sample name: p3cy3rvcy5
total RNA (amplified)

source_name: M. tb in HIV- blood (donor P3)


title: Psoriasis Baseline_1601


title: Psoriasis treatment_1207

value: Psoriasis treatment

value: week 2, after ixekizumab 150mg subcutaneous treatment


title: HIV- blood donor 1, replicate 1

description:
Sample name: p3cy5rvcy3
total RNA (amplified)


title: Psoriasis Baseline_1613


title: HIV+ blood donor 6, replicate 2 (dye flip)

description:
Sample name: h34cy3 rvcy5
total RNA (amplified)

source_name: M. tb in HIV+ blood (donor H34)

value: HIV+

value: M. tb in HIV+ blood


title: Psoriasis Baseline_1614

value: Psoriasis Baseline

value: baseline; before treatment


title: Psoriasis Baseline_1507


title: Psoriasis Baseline_1205


title: Psoriasis Baseline_1304


title: HIV+ blood donor 6, replicate 1

description:
Sample name: h34cy5 rvcy3
total RNA (amplified)


title: HIV+ blood donor 5, replicate 2 (dye flip)

description:
Sample name: H30 Cy3 7H9 Cy5
total RNA (amplified)

source_name: M. tb in HIV+ blood (donor H30)


title: Psoriasis Baseline_1108


title: HIV+ blood donor 5, replicate 1

description:
Sample name: h30 cy5 rv cy3
total RNA (amplified)


title: Psoriasis Baseline_1405


title: Psoriasis Baseline_1503


title: Healthy Control_11855

source_name: whole blood_Healthy Control

value: Healthy Control

value: healthy volunteer


title: Healthy Control_11854


title: Psoriasis Baseline_1702


title: Healthy Control_11851


title: HIV+ blood donor 4, replicate 2 (dye flip)

description:
Sample name: h28cy3RVcy5
total RNA (amplified)

source_name: M. tb in HIV+ blood (donor H28)


title: Healthy Control_11852


title: Healthy Control_11850


title: HIV+ blood donor 3, replicate 2 (dye flip)

description:
Sample name: h24cy3 rvcy5
total RNA (amplified)

source_name: M. tb in HIV+ blood (donor H24)


title: HIV+ blood donor 4, replicate 1

description:
Sample name: h28cy5RVcy3
total RNA (amplified)


title: Healthy Control_11853


title: Healthy Control_11849


title: HIV+ blood donor 2, replicate 1

description:
Sample name: 7H9(cy3) vs H20(cy5)
total RNA (amplified)

source_name: M. tb in HIV+ blood (donor H20)


title: B. subtilis_presence of 1.2M NaCl, 1mM GB_rep3

city: Greifswald

first: Ulrike

last: Mäder

address: F.-L.-Jahn-Str. 15A

department: Functional Genomics

institute: University Medicine Greifswald

hyb_protocol: 600 ng of Cy5-labeled cDNA and 600 ng of Cy3-labeled cDNA were hybridized to the microarray following Agilent’s hybridization, washing and scanning protocol (Two-Color Microarray-based Gene Expression Analysis, version 5.5).

scan_protocol: The microarray was scanned using an Agilent Microarray Scanner G2565CA (Agilent Technologies).

data_processing:
Data were extracted using the Agilent Feature Extraction software (version 10.5, Agilent Technologies).  The normalization/ dye bias correction method is: Linear and Lowess.
The normalization/ dye bias correction method as defined by the Agilent Feature Extraction protocol for 2 color gene expression arrays (protocol GE2_105_Dec08) is: Linear and Lowess.  The normalization/ dye bias correction method is: Linear and Lowess.

organism: Bacillus subtilis

source_name: pooled RNA (equal amounts of RNA from all samples)

label_protocol: For cDNA synthesis, 10 µg of total RNA were mixed with random primers (Promega) and spike-ins (Two-Color RNA Spike-In Kit, Agilent Technologies). The RNA/primer mixture was incubated at 70 °C for 10 min followed by 5 min incubation on ice. Then, the following reagents were added: 10 µl of 5x First Strand Buffer (Invitrogen), 5 µl of 0.1 M DTT (Invitrogen), 0.5 µl of a dNTP mix (10 mM dATP, dGTP, and dTTP, 2.5 mM dCTP), 1.25 µl of Cy3-dCTP or Cy5-dCTP (GE Healthcare) and 2µl of SuperScript II reverse transcriptase (Invitrogen). The reaction mixture was incubated at 42 °C for 60 min and then heated to 70 °C for 10 min. After 5 min on ice, the RNA was degraded by incubation with 2 units of RNaseH (Invitrogen) at room temperature for 30 min. Labeled cDNA was then purified using the CyScribe GFX Purification Kit (GE Healthcare).

growth_protocol: B. subtilis BSB1 was grown in minimal M9 medium with 1 g/l glucose as sole carbon source. Continuous cultivation was performed at 0.1 h-1 in a parallelized 1 l bioreactor system with a working volume of 300 ml, kept at an aeration rate of 9 l/h.

extract_protocol: Cells were harvested and total RNA was isolated by the mechanical cell disruption/ acid phenol method (Eymann et al., 2002).

treatment_protocol: The medium was supplemented with 70.13 g/l NaCl (1.2 M) with or without 117.15 mg/l glycine betaine (1 mM) to mimic osmotic stress and osmoprotection of B. subtilis cells by an externally provided compatible solute. Cultivations were performed until metabolic steady state was reached, i.e. for five volume changes.

tag: strain

value: BSB1 (Trp+ derivative of strain 168)

source_name: B. subtilis wild type_glucose lim. chemostat+1.2M NaCl+1mM GB


title: Healthy Control_11847


title: HIV+ blood donor 2, replicate 2 (dye flip)

description:
Sample name: 7H9(cy5) vs H20(cy3)
total RNA (amplified)


title: Healthy Control_11824


title: Healthy Control_11848


title: B. subtilis_presence of 1.2M NaCl, 1mM GB_rep2


title: Healthy Control_11823


title: Healthy Control_11846


title: HIV+ blood donor 1, replicate 1

description:
Sample name: 7H9(cy3) vs H16(cy5)
total RNA (amplified)

source_name: M. tb in HIV+ blood (donor H16)


title: HIV+ blood donor 3, replicate 1

description:
Sample name: h24cy5 rvcy3
total RNA (amplified)


title: B. subtilis_presence of 1.2M NaCl, 1mM GB_rep1


title: Healthy Control_11821


title: HIV+ blood donor 1, replicate 2 (dye flip)

description:
Sample name: 7H9(cy5) vs H16(cy3)
total RNA (amplified)


title: Healthy Control_11819


title: B. subtilis_presence of 1.2M NaCl_rep1

source_name: B. subtilis wild type_glucose lim. chemostat+1.2M NaCl


title: Psoriasis Baseline_1505

source_name: whole blood_Psoriasis Baseline


title: B. subtilis_presence of 1.2M NaCl_rep3


title: B. subtilis_presence of 1.2M NaCl_rep2


title: Healthy Control_11822


title: B. subtilis_glucose limitation_rep3

source_name: B. subtilis wild type_glucose lim. chemostat


title: Healthy Control_11820


title: Healthy Control_11816


title: RN Reacclimated 2d 2st biological pool

city: Jerusalem

first: Michal

last: Horowitz

address: Hadassah Med Center

country: Israel

institute: The Hebrew University

description: Gene expression

hyb_protocol: Following fragmentation, 5.5 ug of cDNA were hybridized for 16 hr at 45C on GeneChip Rat Gene 1.0 ST Array (Platform GPL6247). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G

data_processing: The data were analyzed with GeneChip Command Console Software (AGCC) using Affymetrix default analysis settings

source_name: RN Reacclimated 2d 2st biological pool

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from  total RNA (~100-200ng/ul, Expression Analysis Technical Manual,  Affymetrix).

growth_protocol: Rattus norvegicus, albino, sabra strain, 3 weeks old at the onset of the experiments were used.

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

treatment_protocol: Experimental paradigm included heat acclimation at 34°C for 2d (AC2d) or 30d (AC30), deacclimation (DeAC, 24°C, 30d) and reacclimation (ReAC, 34°C, 2d) . Untreated rats were served as controls  ( C ). Rats were euthanized using Ketamin/xylasin and hearts were extirpated. For gene expression analyses, the left ventricle of the heart, two pools of 5 animals each, for each experimental phase were used.

value: cardiac left ventricle

value: Sabra strain

tag: age


title: RN 30d acclimated 2nd biological pool

description: Gene expression

source_name: RN 30d acclimated 2nd biological pool


title: RN 30d deacclimated 2nd biological pool

description: Gene expression

source_name: RN 30d deacclimated 2nd biological pool


title: Healthy Control_11815


title: RN Reacclimated 2d 1st biological pool

description: Gene expression

source_name: RN Reacclimated 2d 1st biological pool


title: B. subtilis_glucose limitation_rep1


title: Healthy Control_11698


title: RN 2d acclimated 1st biological pool

description: Gene expression

source_name: RN 2d acclimated 1st biological pool


title: B. subtilis_glucose limitation_rep2


title: RN 30d deacclimated 1st biological pool

description: Gene expression

source_name: RN 30d deacclimated 1st biological pool


title: Healthy Control_11697


title: Healthy Control_11818


title: Ankrd2-KO myotubes+Ad-GFP I

description:
SAMPLE 31
Gene expression after 20h Ad-GFP infection in Ankrd2-null differentiated myoblasts, 96h from differentiation induction

hyb_protocol: 600 ng of Cy3-labeled, linearly amplified cRNA was mixed with 5 µl of 10X Blocking Agent, 1 µl of 25X Fragmentation Buffer, and water of Agilent Hybridization Kit (catalogue number 5188-5242) to a final volume of 25 µl. Reaction was incubated at 60°C for exactly 30 min to fragment cRNA. 40 µl of hybridization mix, composed by equal volumes of fragmented cRNA and 2X GEx Hybridization Buffer HI-RPM, was dispensed onto one of the 8 arrays of the Agilent SurePrint G3 Mouse GE 8x60K Microarrays (catalogue number G4852A). The full microarray slide was loaded into an Agilent SureHyb chamber and hybridization was performed in a hybridization oven at 65°C for 17 h. Rotation was set at 10 rpm. At the end of hybridization, slides were washed for 1 min at 22C in Wash Solution 1 (catalogue number 5188-5325) and 1 min in Wash Solution 2, pre-warmed to 37 C (catalogue number 5188-5326).

scan_protocol: Microarrays were scanned using the Agilent Technologies Scanner G2505C US22502723 (ChipScan software version A.8.5.1), scan region 61 X 21.6 mm, scan resolution 3 micron single pass, Green PTM 100%, no extended dynamic range (NO XDR).

data_processing: Data was extracted from the scanned image using the Agilent Feature Extraction Software version 10.7.3.1 (protocol GE1_107_Sep09). Quantile inter-arrays normalization was performed with the Expander software (Bioinformatics 2003; 19:1787-99) on the gProcessedSignal column of the result table and normalized data is reported in the VALUE column. Only characterized lincRNAs (with the “accession string” field of platform defined with a symbol) was used in the normalization process. The other lincRNAs (with the 'accession string' field of platform defined with the chromosomal location) was not used in the normalization process and marked as “null”. Probes with gIsPosAndSignif value of zero were disregarded and labeled as 'null'. Mean values were calculated for multiple probes with the same Agilent Probe ID.

source_name: Primary myoblasts derived from Ankrd2-KO mice, induced to differentiate 96h and infected by AdGFP

label_protocol: 50 ng RNA was amplified and labeled using the Agilent’s Low Input Quick Amp WT Labeling Kit, one-color, (catalogue number 5190-2943), following the Manufacturer’s instructions. 2.3 µl of RNA sample was mixed to 1 µl WT Primer, 2 µl Agilent One-Color RNA Spike-In (1:20,000 dilution, catalogue number 5188-5282) and denatured for 10 min at 65 ºC. First Strand Buffer, DTT, dNTP mix, and AffinityScript RNaseBlock mix were added and cDNA synthesis was carried out for 2 h at 40 ºC. After 15 min at 70 ºC to inactivate the enzymes, complementary RNA (cRNA) was generated using T7 RNA polymerase, which simultaneously amplifies target material and incorporates Cy3-labeled CTP. Run-off in vitro transcription reactions proceeded for 2 h at 40 °C. RNeasy Mini spin columns (Qiagen) were used to further purify the labeled-amplified cRNA samples.

growth_protocol: The pups of both Ankrd2-KO and WT mice were sacrificed at day 2-3. The limbs were dissected by removing the skin and pulling the arms and legs out of their sockets.  The tissues were minced by cutting into small pieces and were digested by 5-6 rounds of trypsin incubation/centrifugation.The surnatants containing mostly blood cells were discarded. The cell mixtures were triturated and the fat cells from the higher phase were removed. The remaining cells, myoblasts, were filtered and plated.

extract_protocol: Total RNA was isolated with TRIzol reagent (Invitrogen) following the standard protocol. The Nanodrop ND-1000 was used for RNA quantification and RNA 6000 Nano LabChip kit (Agilent Technologies) was used for RNA quality control in conjunction with an Agilent Bioanalyzer 2001.(Agilent Technologies) was used for RNA quality control in conjunction with an Agilent Bioanalyzer 2001.

treatment_protocol: Growing myoblasts were infected with adenoviruses expressing Ankrd2 (Ad-Ankrd2) or GFP (Ad-GFP) 20h  before collection (Stage1: proliferating myoblasts). When the confluence went above 80%, the differentiation medium was added to the proliferating myoblasts (normally day 2 in the morning) for 24h (Stage2: Fusing myoblasts) or 96h (Stage3: Differentiated myoblasts). For both stage 2 and stage 3 samples Ad-Ankrd2 or Ad-GFP were added 20h before collection. Two kind’s of media were used: 1) Proliferation medium: 20% FBS,1% Penicillin-Streptomycin,1% Glutamine,DMEM with 4500 g/l glucose. 2) Differentiation medium: 2% Horse Serum, 1% Penicillin-Streptomycin,1% Glutamine,DMEM with 4500 g/l glucose. Cultures were incubated at 37 ºC in a humidified incubator with 5% CO2.

tag: strain background

value: mixed between SvJ/129 and Black Swiss (Taconic)

value: Ankrd2-knockout (KO)

value: 2-3 days, pups

value: Skeletal muscle

tag: developmental stages

value: Differentiated primary myoblasts

tag: infected with

value: adenovirus expressing control GFP


title: Ankrd2-KO myotubes+Ad-GFP II

description:
SAMPLE 32
Gene expression after 20h Ad-GFP infection in Ankrd2-null differentiated myoblasts, 96h from differentiation induction


title: RN 30d acclimated 1st biological pool

description: Gene expression

source_name: RN 30d acclimated 1st biological pool


title: WT myotubes+Ad-Ankrd2 III

description:
SAMPLE 30
Gene expression after 20h Ad-Ankrd2 infection in WT differentiated myoblasts, 96h from differentiation induction

source_name: Primary myoblasts derived from WT mice, induced to differentiate 96h  and infected by AdAnkrd2

value: wild type (WT)

value: adenovirus expressing Ankrd2 or control GFP


title: WT myotubes+Ad-GFP I

description:
SAMPLE 34
Gene expression after 96h Ad-GFP infection in WT differentiated myoblasts, 96h from differentiation induction

source_name: Primary myoblasts derived from WT mice, induced to differentiate 96h  and infected by AdGFP


title: WT myotubes+Ad-GFP II

description:
SAMPLE 35
Gene expression after 96h Ad-GFP infection in WT differentiated myoblasts, 96h from differentiation induction


title: Ankrd2-KO myotubes+Ad-GFP III

description:
SAMPLE 33
Gene expression after 20h Ad-GFP infection in Ankrd2-null differentiated myoblasts, 96h from differentiation induction


title: Healthy Control_11695

source_name: whole blood_Healthy Control

tag: subject id

tag: sample group

value: whole blood


title: RN Control 1st biological pool

description: Gene expression

source_name: RN Control 1st biological pool


title: RN Control 2nd biological pool

description: Gene expression

source_name: RN Control 2nd biological pool


title: Healthy Control_11696

tag: subject condition


title: RN 2d acclimated 2nd biological pool

description: Gene expression

source_name: RN 2d acclimated 2nd biological pool


title: Healthy Control_11817


title: WT myotubes+Ad-Ankrd2 II

description:
SAMPLE 29
Gene expression after 20h Ad-Ankrd2 infection in WT differentiated myoblasts, 96h from differentiation induction


title: Healthy Control_11694


title: Healthy Control_11693


title: Ankrd2-KO myotubes+Ad-Ankrd2 III

description:
SAMPLE 27
Gene expression after 20h Ad-Ankrd2 infection in Ankrd2-null differentiated myoblasts, 96h from differentiation induction

source_name: Primary myoblasts derived from Ankrd2-KO mice, induced to differentiate 96h and infected by AdAnkrd2


title: EpiSCs-3

city: San Francisco

first: Ron

last: Parchem

address: 35 Medical Center Way

institute: UCSF

description:
replicate 3
Sample48.AVG_Signal

data_processing: The data were preprocessed using Combat and quantile normalized in R

source_name: mouse epiblast stem cells

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

tag: plate

value: PSCs


title: EpiSCs-2

description:
replicate 2
Sample47.AVG_Signal


title: ESCs-diff-dB-day7-3

description:
replicate 3
Sample45.AVG_Signal

source_name: mouse es cells


title: Healthy Control_11692


title: WT fusing myoblasts+Ad-GFP III

description:
SAMPLE 24
Gene expression after 20h Ad-GFP infection in WT fusing myoblasts, after 24h differentiation induction

source_name: Primary myoblasts derived from WT mice, induced to differentiate 24h  and infected by AdGFP

value: Fusing primary myoblasts


title: EpiSCs-1

description:
replicate 1
Sample46.AVG_Signal


title: Healthy Control_11691


title: WT fusing myoblasts+Ad-GFP II

description:
SAMPLE 23
Gene expression after 20h Ad-GFP infection in WT fusing myoblasts, after 24h differentiation induction


title: WT fusing myoblasts+Ad-GFP I

description:
SAMPLE 22
Gene expression after 20h Ad-GFP infection in WT fusing myoblasts, after 24h differentiation induction


title: V_lesional_pre-dose

city: Seattle

first: Jeannette

last: Bigler

state: WA

address: 3200 NE 92nd Street

institute: BJ Group, LLC

hyb_protocol: Procedure used standard Affymetrix protocol.

data_processing: Scans were imported into Rosetta Resolver and pre-processed using the 'Resolver Affymetrix Rosetta Intensity Profile Builder (saves reporters)' pipeline.

source_name: Lesional skin biopsy from psoriasis patient, pre-treatment

label_protocol: Total RNA was reverse-transcribed and amplified using the NuGen Ovation™ RNA amplification system V2 with Ovation™WB reagent. Amplified RNA was fragmented and labeled using the NuGen FL-Ovation™ cDNA Biotin Module V2. Amplification and labeling were performed on a Beckman-Coulter ArrayPlex.

extract_protocol: The frozen biopsy was homogenized using a TissueRuptor, and RNA was extracted using the mirVana™ kit with on-column DNase treatment.

tag: disease state

value: psoriasis

value: lesional skin

tag: time

value: pre-dose

tag: patient

value: V


title: ESCs-diff-dG-day7-2

description:
replicate 2
Sample41.AVG_Signal


title: Ankrd2-KO myotubes+Ad-Ankrd2 I

description:
SAMPLE 25
Gene expression after 20h Ad-Ankrd2 infection in Ankrd2-null differentiated myoblasts, 96h from differentiation induction

tag: genotype/variation


title: Ankrd2-KO myotubes+Ad-Ankrd2 II

description:
SAMPLE 26
Gene expression after 20h Ad-Ankrd2 infection in Ankrd2-null differentiated myoblasts, 96h from differentiation induction


title: V_non-lesional_pre-dose

scan_protocol: Procedure used standard Affymetrix protocol.

source_name: Non-lesional skin biopsy from psoriasis patient, pre-treatment

value: non-lesional skin


title: ESCs-diff-dB-day7-1

description:
replicate 1
Sample43.AVG_Signal


title: P_non-lesional_pre-dose

value: P


title: WT myotubes+Ad-Ankrd2 I

description:
SAMPLE 28
Gene expression after 20h Ad-Ankrd2 infection in WT differentiated myoblasts, 96h from differentiation induction

value: mixed between SvJ/129 and Black Swiss (Taconic)


title: Healthy Control_11690

value: Healthy Control

value: healthy volunteer


title: ESCs-diff-dB-day7-2

description:
replicate 2
Sample44.AVG_Signal


title: B_lesional_pre-dose

value: B


title: B_non-lesional_pre-dose


title: ESCs-diff-dG-day7-3

description:
replicate 3
Sample42.AVG_Signal


title: ESCs-diff-dG-day7-1

description:
replicate 1
Sample40.AVG_Signal


title: Ankrd2-KO fusing myoblasts+Ad-GFP III

description:
SAMPLE 21
Gene expression after 20h Ad-GFP infection in Ankrd2-null fusing myoblasts, after 24h differentiation induction

source_name: Primary myoblasts derived from Ankrd2-KO mice, induced to differentiate 24h and infected by AdGFP

value: Ankrd2-knockout (KO)

value: 2-3 days, pups

value: Skeletal muscle


title: ESCs-diff-dY-day4-3

description:
replicate 3
Sample39.AVG_Signal


title: Ankrd2-KO fusing myoblasts+Ad-GFP I

description:
SAMPLE 19
Gene expression after 20h Ad-GFP infection in Ankrd2-null fusing myoblasts, after 24h differentiation induction

value: adenovirus expressing control GFP


title: WT fusing myoblasts+Ad-Ankrd2 III

description:
SAMPLE 18
Gene expression after 20h Ad-Ankrd2 infection in WT fusing myoblasts, after 24h differentiation induction

source_name: Primary myoblasts derived from WT mice, induced to differentiate 24h  and infected by AdAnkrd2

value: wild type (WT)

value: adenovirus expressing Ankrd2 or control GFP


title: Ankrd2-KO fusing myoblasts+Ad-GFP II

description:
SAMPLE 20
Gene expression after 20h Ad-GFP infection in Ankrd2-null fusing myoblasts, after 24h differentiation induction

value: Fusing primary myoblasts


title: Y_non-lesional_pre-dose

value: psoriasis

value: Y


title: ESCs-diff-dR-day1-3

description:
replicate 3
Sample36.AVG_Signal

value: PSCs


title: P_lesional_pre-dose

value: lesional skin

value: pre-dose


title: WT fusing myoblasts+Ad-Ankrd2 I

description:
SAMPLE 16
Gene expression after 20h Ad-Ankrd2 infection in WT fusing myoblasts, after 24h differentiation induction


title: ESCs-diff-dY-day4-2

description:
replicate 2
Sample38.AVG_Signal


title: ESCs-diff-dR-day1-1

description:
replicate 1
Sample34.AVG_Signal


title: Q_lesional_pre-dose

value: Q


title: Q_non-lesional_pre-dose

value: non-lesional skin


title: ESCs-diff-dR-day1-2

description:
replicate 2
Sample35.AVG_Signal


title: WT fusing myoblasts+Ad-Ankrd2 II

description:
SAMPLE 17
Gene expression after 20h Ad-Ankrd2 infection in WT fusing myoblasts, after 24h differentiation induction

value: mixed between SvJ/129 and Black Swiss (Taconic)


title: Ankrd2-KO fusing myoblasts+Ad-Ankrd2 III

description:
SAMPLE 15
Gene expression after 20h Ad-Ankrd2 infection in Ankrd2-null fusing myoblasts, after 24h differentiation induction

source_name: Primary myoblasts derived from Ankrd2-KO mice, induced to differentiate 24h and infected by AdAnkrd2


title: L_lesional_pre-dose

value: L


title: ESCs-Lif2i-3

description:
replicate 3
Sample33.AVG_Signal


title: ESCs-diff-dY-day4-1

description:
replicate 1
Sample37.AVG_Signal


title: WT myoblasts+Ad-GFP III

description:
SAMPLE 12
Gene expression after 20h Ad-GFP infection in WT proliferating myoblasts

source_name: Primary myoblasts derived from WT mice, infected by control AdGFP

value: Proliferating primary myoblasts


title: H_non-lesional_pre-dose

value: H


title: H_lesional_pre-dose


title: ESCs-Lif2i-2

description:
replicate 2
Sample32.AVG_Signal


title: L_non-lesional_pre-dose


title: WT myoblasts+Ad-GFP II

description:
SAMPLE 11
Gene expression after 20h Ad-GFP infection in WT proliferating myoblasts

value: 2-3 days, pups


title: ESCs-Lif2i-1

description:
replicate 1
Sample31.AVG_Signal


title: Healthy Control_11699

value: Healthy Control

value: healthy volunteer

value: whole blood


title: Ankrd2-KO fusing myoblasts+Ad-Ankrd2 I

description:
SAMPLE 13
Gene expression after 20h Ad-Ankrd2 infection in Ankrd2-null fusing myoblasts, after 24h differentiation induction

value: Ankrd2-knockout (KO)

value: Skeletal muscle

value: adenovirus expressing Ankrd2 or control GFP


title: Ankrd2-KO fusing myoblasts+Ad-Ankrd2 II

description:
SAMPLE 14
Gene expression after 20h Ad-Ankrd2 infection in Ankrd2-null fusing myoblasts, after 24h differentiation induction

value: Fusing primary myoblasts


title: WT myoblasts+Ad-GFP I

description:
SAMPLE 10
Gene expression after 20h Ad-GFP infection in WT proliferating myoblasts

value: wild type (WT)

value: adenovirus expressing control GFP


title: Sall4+OSK-iPSCs-2

description:
replicate 2
Sample29.AVG_Signal

source_name: mouse iPS cells

tag: transfection

value: Sall 4 + OSK

value: iPSCs


title: Ankrd2-KO myoblasts+Ad-GFP II

description:
SAMPLE 8
Gene expression after 20h Ad-GFP infection in Ankrd2-null proliferating myoblasts

source_name: Primary myoblasts derived from Ankrd2-KO mice, infected by control AdGFP


title: WT myotubes+Ad-GFP III

description:
SAMPLE 36
Gene expression after 96h Ad-GFP infection in WT differentiated myoblasts, 96h from differentiation induction

source_name: Primary myoblasts derived from WT mice, induced to differentiate 96h  and infected by AdGFP

value: Differentiated primary myoblasts


title: Sall4+OSK-green-3

description:
replicate 3
Sample27.AVG_Signal

source_name: mouse reprogramming cells

value: embryonic fibroblasts


title: Ankrd2-KO myoblasts+Ad-GFP I

description:
SAMPLE 7
Gene expression after 20h Ad-GFP infection in Ankrd2-null proliferating myoblasts

value: mixed between SvJ/129 and Black Swiss (Taconic)


title: Sall4+OSK-iPSCs-3

description:
replicate 3
Sample30.AVG_Signal


title: S_non-lesional_pre-dose

value: psoriasis

value: non-lesional skin

value: pre-dose

value: S


title: G_lesional_pre-dose

value: lesional skin

value: G


title: WT myoblasts+Ad-Ankrd2 III

description:
SAMPLE 6
Gene expression after 20h Ad-Ankrd2 infection in WT proliferating myoblasts

source_name: Primary myoblasts derived from WT mice, infected by AdAnkrd2

value: 2-3 days, pups

value: Proliferating primary myoblasts


title: Sall4+OSK-green-2

description:
replicate 2
Sample26.AVG_Signal


title: WT myoblasts+Ad-Ankrd2 II

description:
SAMPLE 5
Gene expression after 20h Ad-Ankrd2 infection in WT proliferating myoblasts

value: Skeletal muscle

value: adenovirus expressing Ankrd2 or control GFP


title: E_lesional_pre-dose

value: E


title: G_non-lesional_pre-dose


title: U_non-lesional_pre-dose

value: U


title: Ankrd2-KO myoblasts+Ad-GFP III

description:
SAMPLE 9
Gene expression after 20h Ad-GFP infection in Ankrd2-null proliferating myoblasts

value: Ankrd2-knockout (KO)

value: adenovirus expressing control GFP


title: Sall4+OSK-yellow-3

description:
replicate 3
Sample24.AVG_Signal

value: Sall 4 + OSK


title: WT myoblasts+Ad-Ankrd2 I

description:
SAMPLE 4
Gene expression after 20h Ad-Ankrd2 infection in WT proliferating myoblasts

value: wild type (WT)


title: S_lesional_pre-dose


title: Sall4+OSK-iPSCs-1

description:
replicate 1
Sample28.AVG_Signal

value: iPSCs


title: Sall4+OSK-yellow-2

description:
replicate 2
Sample23.AVG_Signal

value: embryonic fibroblasts


title: E_non-lesional_pre-dose

value: psoriasis

value: non-lesional skin


title: M_non-lesional_pre-dose

value: pre-dose

value: M


title: Sall4+OSK-green-1

description:
replicate 1
Sample25.AVG_Signal


title: U_lesional_pre-dose

value: lesional skin


title: Sall4+OSK-yellow-1

description:
replicate 1
Sample22.AVG_Signal


title: Sall4+OSK-red-3

description:
replicate 3
Sample21.AVG_Signal


title: Ankrd2-KO myoblasts+Ad-Ankrd2 III

description:
SAMPLE 3
Gene expression after 20h Ad-Ankrd2 infection in Ankrd2-null proliferating myoblasts

source_name: Primary myoblasts derived from Ankrd2-KO mice, infected by AdAnkrd2

value: mixed between SvJ/129 and Black Swiss (Taconic)

value: 2-3 days, pups


title: M_lesional_pre-dose


title: Ankrd2-KO myoblasts+Ad-Ankrd2 I

description:
SAMPLE 1
Gene expression after 20h Ad-Ankrd2 infection in Ankrd2-null proliferating myoblasts

value: Skeletal muscle

value: Proliferating primary myoblasts


title: Ankrd2-KO myoblasts+Ad-Ankrd2 II

description:
SAMPLE 2
Gene expression after 20h Ad-Ankrd2 infection in Ankrd2-null proliferating myoblasts

value: adenovirus expressing Ankrd2 or control GFP


title: T_lesional_pre-dose

value: T


title: R_non-lesional_pre-dose

value: R


title: Sall4+OSK-black-2

description:
replicate 2
Sample17.AVG_Signal


title: Sall4+OSK-black-3

description:
replicate 3
Sample18.AVG_Signal


title: A_non-lesional_pre-dose

value: A


title: Sall4+OSK-red-2

description:
replicate 2
Sample20.AVG_Signal

value: Sall 4 + OSK


title: R_lesional_pre-dose


title: Sall4+OSK-red-1

description:
replicate 1
Sample19.AVG_Signal


title: OSK-iPSCs-1

description:
replicate 1
Sample13.AVG_Signal

value: OSK


title: A_lesional_pre-dose


title: D_lesional_pre-dose

value: D


title: Sall4+OSK-black-1

description:
replicate 1
Sample16.AVG_Signal

value: embryonic fibroblasts


title: OSK-iPSCs-2

description:
replicate 2
Sample14.AVG_Signal

value: iPSCs


title: Y_lesional_pre-dose

value: psoriasis

value: Y


title: OSK-iPSCs-3

description:
replicate 3
Sample15.AVG_Signal


title: J_lesional_pre-dose

value: pre-dose

value: J


title: BC5

city: Bellaterra

first: Jordi

last: Corominas Galbany

state: Barcelona

address: UAB Campus

department: Animal genetics

institute: CRAG

hyb_protocol: Approximately 10μg of fragmented cRNA was hybridzed per array using the Affymetrix hybridization kit. Arrays were hybridized for 16 hours at 45° at 60rpm using an Affymetrix hybridization oven.

scan_protocol: Arrays were scanned on an Affymetrix Scanner 3000 7G

data_processing: RMA algorithm was used to normalize the arrays and summarized the probes.

source_name: Backfat

label_protocol: Samples (12μg of cRNA with biotin-conjugated nucleotide) were chemically fragmented and labeled using the Fragmentation Buffer included in the IVT Express kit (Affymetrix)

extract_protocol: From the 5 selected animals, total RNA was isolated from liver using the RiboPureTM Isolation of High Quality Total RNA (Ambion®, Austin, TX) following the manufacturer’s recommendations. RNA was quantified using the NanoDrop ND-1000 spectrophotometer (NanoDrop products, Wilmington, USA) and checked for purity and integrity in a Bioanalyzer-2100 (Agilent Technologies, Inc., Santa Clara CA, USA).

value: backfat

tag: Sex

value: Female


title: Mouse_embryonic_tetraploid_cell_clone2

city: osaka

first: Hisakatsu

last: Nawata

department: Medicine

institute: Kyoto University

description:
Gene expression in p56-/- mouse embryonic tetraploid cells
Sample name: RRI2-4

hyb_protocol: 500ng of Cy3 labelled aRNA were hybridized competitively for 17 hrs in a 65 C hybridization oven set to 10 rpm in a final concentration of 1X GEx Hybridization Buffer HI-RPM, according to the manufacturer's recommnded protocol (One-Color Microarray-Based Gene Expression Analysis, Agilent). Arrays were washed according to the manufacturer's recommended protocol including the Stabilization and Drying Solution step (One-Color Microarray-Based Gene Expression Analysis, Agilent)

scan_protocol: Arrays were scanned at 3um resolution on an Agilent DNA Microarray Scanner (G2565CA) using the default settings for 8x60K format one-color arrays.

data_processing: Data was analyzed with Agilent Feature Extraction and GeneSpring GX v11.5 softwares. Data was normalized to RRI2.

source_name: Mouse embryonic tetraploid cell, clone2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using Quick Amp Labeling 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: Mouse embryonic cells were cultured in Eagle’s Minimum Essential Medium (MEM) supplemented with 10% fetal bovine serum at 37℃ with 5% CO2 in a humidified environment.

extract_protocol: RNA was prepared using the RNeasy Mini Kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: Cells were not treated prior to RNA extraction.

tag: cell type

value: embryonic cells

tag: ploidy

value: tetraploid


title: BC6

tag: tissue


title: W_lesional_pre-dose

value: lesional skin

value: W


title: O_non-lesional_pre-dose

value: non-lesional skin

value: O


title: J_non-lesional_pre-dose


title: Mouse_embryonic_triploid_cell_clone3

description:
Gene expression in p59-/- mouse embryonic triploid cells
Sample name: RRI2-15

source_name: Mouse embryonic triploid cell, clone3

value: triploid


title: Mouse_embryonic_triploid_cell_clone2

description:
Gene expression in p58-/- mouse embryonic triploid cells
Sample name: RRI2-12

source_name: Mouse embryonic triploid cell, clone2


title: Mouse_embryonic_diploid_cell_clone2

description:
Gene expression in p54-/- mouse embryonic diploid cells
Sample name: RRI15

source_name: Mouse embryonic diploid cell, clone2

value: diploid


title: OSK-green-3

description:
replicate 3
Sample12.AVG_Signal

tag: strain

value: OSK


title: Mouse_embryonic_tetraploid_cell_clone1

description:
Gene expression in p55-/- mouse embryonic tetraploid cells
Sample name: RRI2-2

source_name: Mouse embryonic tetraploid cell, clone1


title: W_non-lesional_pre-dose

source_name: Non-lesional skin biopsy from psoriasis patient, pre-treatment


title: Mouse_embryonic_triploid_cell_clone1

description:
Gene expression in p57-/- mouse embryonic triploid cells
Sample name: RRI2-5

source_name: Mouse embryonic triploid cell, clone1


title: OSK-green-2

description:
replicate 2
Sample11.AVG_Signal

value: embryonic fibroblasts


title: Mouse_embryonic_tetraploid_cell_clone3

description:
Gene expression in p57-/- mouse embryonic tetraploid cells
Sample name: RRI2-6

source_name: Mouse embryonic tetraploid cell, clone3


title: OSK-green-1

description:
replicate 1
Sample10.AVG_Signal


title: Mouse_embryonic_diploid_cell_clone3

description:
Gene expression in p55-/- mouse embryonic diploid cells
Sample name: RRI2-1

source_name: Mouse embryonic diploid cell, clone3


title: Mouse_embryonic_diploid_cell_clone1

description:
Gene expression in p53-/- mouse embryonic diploid cells.
Sample name: RRI2
RRI2 used for normalization during data processing.

source_name: Mouse embryonic diploid cell, clone1


title: BC4


title: D_non-lesional_pre-dose

value: D


title: OSK-red-3

description:
replicate 3
Sample06.AVG_Signal


title: W303 1B, biological rep. 3

city: Seville

first: Andrés

last: Aguilera

address: Av. Américo Vespucio 24

department: Genome BIology

institute: CABIMER, Universidad de Sevilla

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Yeast Genome 2.0 Array. GeneChips were washed and stained in the GeneChip® Fluidics Station 450 according to GeneChip® Expression AnalysisTechnical Manual, Affymetrix, 2004.

scan_protocol: Microarrays were scanned using GeneChip® Scanner 3000 7G

data_processing: The .DAT image files for each array were converted into .CEL files using Affimetrix GCOS software. These .CEL files were normalized using Robust Microarray Average (RMA) method by Irrizarry et al. Statistical analysis was performed using the limma package  (affyImGUI interface) of R/Bioconductor project. Genes showing at least 2-fold expression change compared to wild type, false discovery rate-adjusted p-value<0.01, B-statistic value>2, and average log2 intensity A>7 were considered as significantly altered.

organism: Saccharomyces cerevisiae

source_name: Wild type W303 1B

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA One-Cycle Target Labeling Assays (GeneChip® Expression AnalysisTechnical Manual, Affymetrix, 2004).

growth_protocol: Each strain was grown to mid-log phase in liquid YPAD medium at 30°C

extract_protocol: Total RNA were isolated with the RNeasy Midi kit (QIAGEN)

tag: genotype


title: OSK-yellow-2

description:
replicate 2
Sample08.AVG_Signal


title: Z_non-lesional_pre-dose

value: psoriasis

value: Z


title: Z_lesional_pre-dose

source_name: Lesional skin biopsy from psoriasis patient, pre-treatment

value: pre-dose


title: OSK-red-2

description:
replicate 2
Sample05.AVG_Signal


title: OSK-yellow-3

description:
replicate 3
Sample09.AVG_Signal


title: O_lesional_pre-dose


title: OSK-yellow-1

description:
replicate 1
Sample07.AVG_Signal


title: OSK-black-3

description:
replicate 3
Sample03.AVG_Signal


title: W303 1B, biological rep. 4


title: W303 1B, biological rep. 1


title: rna15-1, biological rep. 3

source_name: Mutant rna15-1

value: rna15-1 W


title: OSK-red-1

description:
replicate 1
Sample04.AVG_Signal

source_name: mouse reprogramming cells


title: BC2

value: backfat


title: X_non-lesional_pre-dose

value: X


title: OSK-black-2

description:
replicate 2
Sample02.AVG_Signal


title: W303 1B, biological rep. 5


title: rna15-1, biological rep. 2


title: I_non-lesional_pre-dose

value: I


title: W303 1B, biological rep. 2


title: rna15-1, biological rep. 1


title: I_lesional_pre-dose


title: OSK-black-1

description:
replicate 1
Sample01.AVG_Signal


title: F_lesional_pre-dose

value: F


title: X_lesional_pre-dose

value: lesional skin


title: F_non-lesional_pre-dose


title: C_non-lesional_pre-dose

value: C


title: rna14-1, biological rep. 3

source_name: Mutant rna14-1

value: rna14-1 W


title: B_lesional_day8

source_name: Lesional skin biopsy from psoriasis patient, 350mg brodalumab treated, day 8

tag: treatment

value: 350mg brodalumab

value: day 8

value: B


title: K_lesional_pre-dose

value: K


title: C_lesional_pre-dose


title: V_lesional_day8

source_name: Lesional skin biopsy from psoriasis patient, placebo treated, day 8

value: placebo

value: V


title: rna14-1, biological rep. 1


title: K_non-lesional_pre-dose

value: psoriasis

value: non-lesional skin


title: Tissue_NCR_rep5

city: Cluj-Napoca

first: Ovidiu

last: Balacescu

state: Cluj

address: 34-36 Republicii

department: Functional Genomics, Proteomics and Experimental Pathology

country: Romania

institute: The Oncology Institute I. Chiricuta

description:
Gene expression in cervical primary biopsy of patient with not complete response at 6 month
TT_17

hyb_protocol: After fragmentation to an average size of 60 – 100 nucleotides, each cRNA was hybridized to whole-human-genome 4x44K microarray slides (product G4112F; Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven, following the manufacturer’s protocol (Agilent Technologies).

scan_protocol: After hybridization, microarray slides were washed as follow: 1 minute at room temperature with GE Wash Buffer 1 (Agilent), 1 minute at 37°C with GE Wash Buffer 2 (Agilent), 10 seconds with Acetonitrile at rome temperature and 30 seconds with Stabilization and Drying solution at room temperature. The slides were scanned with an Agilent G2505B US45102867 microarray scanner, and gridding was performed with Feature Extraction Software v.10.5.1.1

data_processing: The scanned images were analyzed with Feature Extraction Software version 10.5.1.1 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid:014850_D_20070820) to obtain Median Signal intensities. Quantile method was used for normalization.  Features flagged in Feature Extraction as Saturated and Feature Non-uniform outliers were excluded.

source_name: Cervical tumor tissue, non-complete response, replicate 5

label_protocol: Microarray probes (cRNA-Cy3) were synthesized from 200 ng of total RNA in two reaction steps using a one-color Agilent Low Input Quick Amp Labeling Kit according to the manufacturer’s instructions. All labeled cRNAs (Cy3) were purified using an RNeasy Mini kit (Qiagen) and were evaluated for quality control using a Nanodrop ND-1000 spectrophotometer. All cRNAs had a minimum yields of 1.65 µg and specific activities of 6 pmol/µl Cy3 per μg cRNA and were selected for further analysis.

growth_protocol: Twenty-one patients with locally advanced squamous cell carcinoma (FIGO stage IIB-IIIB) were enrolled in the genomics study. A tissue fragment from a primary biopsy specimen was harvested from each patient prior to the therapy. Tissue samples were stored in liquid nitrogen until use for RNA extraction.

extract_protocol: Tumor sections with a minimum of 70% tumor cells were harvested by macrodissection from primary biopsies of cervical cancers. Total RNA was extracted with TriReagent (Sigma-Aldrich) and purified using an RNeasy Mini kit (Qiagen) according to the manufacturer’s protocols.Extracted RNA was assessed for quality with a Lab-on-a-chip Bioanalyzer 2100 (Agilent Technologies). The RNA Integrity Number (RIN) and rRNA 28S/18S ratio were used to define the quality of the total RNA. The RNAs with RINs >7.5 and rRNA 28S/18S ratios >1.8 were used for further analysis. RNA was quantified using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies).

treatment_protocol: The patients were treated with concomitant chemoradiotherapy (CRT). The radiotherapy protocol includes external beam radiotherapy (EBRT) to the pelvis delivered by a linear accelerator at 15MV for a dose of 46Gy/23 fractions and a cervical boost given by intracavitary high-dose-rate (HDR) brachytherapy (BT) in a dose of 10 Gy/2 fractions. Cisplatin was administered concomitant with the radiotherapy as a radiosensitizer. The tumor response was clinically evaluated at 6 months after the end of the CRT treatment and was defined as complete response (CR) or non-complete response (NCR) (partial response and stable disease).

value: cervical primary biopsy

tag: clinical response (6 months after chemoradiotherapy treatment)

value: non-complete response


title: Tissue_NCR_rep8

description:
Gene expression in cervical primary biopsy of patient with not complete response at 6 month
TT_20

source_name: Cervical tumor tissue, non-complete response, replicate 8


title: Tissue_NCR_rep4

description:
Gene expression in cervical primary biopsy of patient with not complete response at 6 month
TT_16

source_name: Cervical tumor tissue, non-complete response, replicate 4


title: Y_lesional_day8

value: Y


title: Tissue_NCR_rep6

description:
Gene expression in cervical primary biopsy of patient with not complete response at 6 month
TT_18

source_name: Cervical tumor tissue, non-complete response, replicate 6


title: Tissue_NCR_rep9

description:
Gene expression in cervical primary biopsy of patient with not complete response at 6 month
TT_21

source_name: Cervical tumor tissue, non-complete response, replicate 9


title: Tissue_NCR_rep3

description:
Gene expression in cervical primary biopsy of patient with not complete response at 6 month
TT_15

source_name: Cervical tumor tissue, non-complete response, replicate 3


title: P_lesional_day8

value: P


title: Tissue_NCR_rep7

description:
Gene expression in cervical primary biopsy of patient with not complete response at 6 month
TT_19

source_name: Cervical tumor tissue, non-complete response, replicate 7


title: Q_lesional_day43

source_name: Lesional skin biopsy from psoriasis patient, 350mg brodalumab treated, day 43

value: day 43

value: Q


title: L_lesional_day8

value: lesional skin

value: L


title: H_lesional_day43

value: H


title: G_lesional_day43

source_name: Lesional skin biopsy from psoriasis patient, 140mg brodalumab treated, day 43

value: 140mg brodalumab

value: G


title: Normal brain tissue 10 - Normal-HT-12

city: Toronto

first: Pawel

last: Buczkowicz

state: Ontario

address: 686 Bay Street

department: Paediatric Laboratory Medicine

country: Canada

institute: Hospital for Sick Children

description:
Dx: diagnosis, OS: overral survival
Hybridized to HT-12

hyb_protocol: RNA was hybridized to each array according to the manufacturer's standard hybridization protocol.

scan_protocol: The arrays were scanned using standard Illumina scanning protocol

data_processing: The data was normalized using per-probe median centered quantile normalzation in Partek Genomic Suite v6.6

source_name: Normal brain tissue 10 - Normal

label_protocol: As per manufacturer (Illumina)

extract_protocol: Total RNA was extracted from formalin fixed parrafin embedded (FFPE) biopsy and autopsy samples from DIPG patients using the TRIzol extraction method. RNA quality and quantity was assessed using a Nanodrop Spectrophotometer and Bioanalyzer 2100.

value: normal brain

tag: gender

tag: age at dx (years)

tag: os (years)


title: BC3

source_name: Backfat

value: backfat

value: Female


title: Normal brain tissue 16 - Normal-HT-12

source_name: Normal brain tissue 16 - Normal


title: Normal brain tissue 15 - Normal-HT-12

source_name: Normal brain tissue 15 - Normal


title: E_lesional_day43

value: 350mg brodalumab

value: E


title: Tissue_NCR_rep2

description:
Gene expression in cervical primary biopsy of patient with not complete response at 6 month
TT_14

source_name: Cervical tumor tissue, non-complete response, replicate 2


title: Normal brain tissue 4 - Normal-HT-12

source_name: Normal brain tissue 4 - Normal


title: Normal brain tissue 8 - Normal-HT-12

source_name: Normal brain tissue 8 - Normal


title: U_lesional_day43

value: psoriasis

value: U


title: Normal brain tissue 3 - Normal-HT-12

source_name: Normal brain tissue 3 - Normal


title: S_lesional_day43

source_name: Lesional skin biopsy from psoriasis patient, placebo treated, day 43

value: placebo

value: S


title: M_lesional_day43

value: M


title: Tissue_CR_rep10

description:
Gene expression in cervical primary biopsy of patient with 6-month complete response.
TT_10

source_name: Cervical tumor tissue, complete response, replicate 10

value: cervical primary biopsy

value: complete response


title: Tissue_CR_rep11

description:
Gene expression in cervical primary biopsy of patient with 6-month complete response.
TT_11

source_name: Cervical tumor tissue, complete response, replicate 11


title: Tissue_CR_rep9

description:
Gene expression in cervical primary biopsy of patient with 6-month complete response.
TT_09

source_name: Cervical tumor tissue, complete response, replicate 9


title: Tissue_CR_rep12

description:
Gene expression in cervical primary biopsy of patient with 6-month complete response.
TT_12

source_name: Cervical tumor tissue, complete response, replicate 12


title: Normal brain tissue 5 - Normal-HT-12

source_name: Normal brain tissue 5 - Normal


title: Normal brain tissue 9 - Normal-HT-12

source_name: Normal brain tissue 9 - Normal


title: Normal brain tissue 2 - Normal-HT-12

source_name: Normal brain tissue 2 - Normal


title: T_lesional_day43

value: lesional skin

value: day 43

value: T


title: Tissue_NCR_rep1

description:
Gene expression in cervical primary biopsy of patient with not complete response at 6 month
TT_13

source_name: Cervical tumor tissue, non-complete response, replicate 1

value: non-complete response


title: R_lesional_day43

source_name: Lesional skin biopsy from psoriasis patient, 140mg brodalumab treated, day 43

value: 140mg brodalumab

value: R