title: PHH_Chlorpromazine_7d_2


title: cervix after delivery after PTL_318

status: Public on May 22 2017

type: RNA

city: Stockholm

first: Aurelija

last: Dubicke

address: Karolinska University Hospital Solna

department: Department of Women's and Children's Health

country: Sweden

institute: Karolinska Institutet

description: human cervical tissues after delivery at PTL, 27 full gestational weeks

hyb_protocol: Hybridization coctail was prepared according to the standard protocol. Samples were hybridizedin arrays for 16 hours, at 45C in Affymetrics Gene Chip Hybridization Oven 640

scan_protocol: GeneChips were scanned using the Affymetrics Gene Chip Scanner 30

data_processing: The data was analyzed in the Plier using ANOVA and  false discovery rate

label: biotin

molecule: total RNA

organism: Homo sapiens

label_protocol: Biotinylated cRNA were prepared according to the Gene Chip  Whole Transcript (WT)  Sense Target Labeling Assay Manual, 100 ng RNA was used as input

growth_protocol: Cervical biopsies were obtained from women immediately postpartum (within 30 minutes). The biopsies were taken transvaginally with scissors and tweezers at twelve o'clock position.

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

treatment_protocol: The samples for mRNA analysis were immediately immersed in RNAlater® (Ambion Inc, Austin, TX, USA), kept at 4o C for 24 hours and thereafter frozen and stored at -70o.

tag: maternal age

tag: delivery

value: preterm delivery (PTL)

tag: gestation time

value: 27 full gestational weeks

tag: tissue

value: cervix


title: cervix after delivery after TL_202

description: human cervical tissues after delivery at TL, 41 full gestational weeks

value: term delivery (TL)

value: 41 full gestational weeks


title: cervix after delivery after PPROM_102

description: human cervical tissues after delivery at PPROM, 36 full gestational weeks

value: delivery after preterm premature rupture of membranes (PPROM)

value: 36 full gestational weeks


title: cervix after delivery after PPROM_301

description: human cervical tissues after delivery at PPROM, 35 full gestational weeks

value: 35 full gestational weeks


title: PHH_Aflatoxin_7d_2

first: Magnus

last: Ingelman-Sundberg

address: Nanna Svartz väg 2

description: Gene expression after 7 day treatment (3 re-dosings) with 0.002uM aflatoxin B1 (0.4% DMSO), PHH 3D spheroid

hyb_protocol: Agilent 8x60K Whole Human Genome Oligo Microarray slides (G4851B) were hybridised, washed and then scanned on an Agilent Microarray Scanner

data_processing: Images from the Agilent scanner were processed using Agilent Feature Extraction Software v10.7.3.1.

source_name: Primary human hepatocyte 3D spheroid

label_protocol: Total RNA samples (45ng) were labelled with Cy3 using the Low Input Quick Amp Labeling Kit–One Colour (Agilent# 5190-2305)

growth_protocol: Primary human hepatocytes were seeded in ultra-low attachment plates at  1500 cells/well in 100ul Williams E basal medium supplemented with 10% FBS and centrifuged at 100g for 2 minutes. From day 4 onwards daily medium changes with FBS-free medium were performed. Treatments were initiated on day 7.

extract_protocol: RNA was extracted with the AllPrep DNA/RNA Mini Kit (Qiagen) according to the manufacturer’s instructions. RNA concentration and quality was assessed using the Agilent Bioanalyzer

treatment_protocol: Medium supplemented with 0.4% DMSO was changed every 2-3 days. For PHH spheroids cells were also treated with either aflatoxin B1 (0.002uM), amiodarone (4uM) or chlorpromazine (6uM).

tag: cell type

value: Primary human hepatocyte (PHH)

tag: treatment time

tag: treatment

value: Aflatoxin B1


title: cervix after delivery after PPROM_321

source_name: human cervical tissues after delivery at PPROM, 35 full gestational weeks


title: UmiR-194-5p SAHA 24h vs UmiR-194-5p replicate 1

city: Naples

first: carmela

last: dell'aversana

address: Pietro Castellino 111

country: Italy

institute: IGB - Institute of Genetics and Biophysics - CNR

description: Biological replicate 1 of 2.UmiR-194-5p SAHA 24h vs UmiR-194-5p

hyb_protocol: Two color microarray based gene expression analysis with tecan hs pro protocol. Gene expression hybridization Kit (Agilent p/n 5188-5242)

scan_protocol: Agilent Microarray Scanner G2565BA Images were quantified using Agilent Feature Extraction Software (version A.10.5.1.1)

data_processing: Agilent Feature Extraction Software (v 10.5.1.1) was used for background subtraction and LOWESS and Quantile normalizations.

source_name: UmiR-194-5p treated with SAHA 24h

label_protocol: Two color microarray based gene expression analysis with tecan hs pro protocol. RNA Spike-in Kit two color (Agilent p/n 5188-5279) and Quick Amp Labeling Kit, Two color (Agilentp/n 5190-0444)

growth_protocol: U937 (Human leukemic monocyte lymphoma cell line) miR-194-5p were cultured in RPMI 1640, containing 10% decomplemented FBS plus G418 0,5 µg/µl

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

treatment_protocol: SAHA treatment at 5 µM concentration for 6 and 24 hours

tag: cell line

value: leukemic monocyte lymphoma cell line

tag: transfection

value: miR-194-5p vector

value: SAHA 24h

source_name: UmiR-194-5p (U937 transfected with miR-194-5p vector)


title: PHH_Amiodarone_7d_3

description: Gene expression after 7 day treatment (3 re-dosings) with 4uM amiodarone (0.4% DMSO), PHH 3D spheroid

scan_protocol: Agilent 8x60K Whole Human Genome Oligo Microarray slides (G4851B) were hybridised, washed and then scanned on an Agilent Microarray Scanner

value: Amiodarone


title: UmiR-194-5p SAHA 24h vs UmiR-194-5p replicate 2

description: Biological replicate 2 of 2.UmiR-194-5p SAHA 24h vs UmiR-194-5p


title: UmiR-194-5p MS275 24h vs UmiR-194-5p replicate 2

description: Biological replicate 2 of 2. UmiR-194-5p MS275 24h vs UmiR-194-5p

source_name: UmiR-194-5p treated with MS-275 24h

treatment_protocol: MS-275 at 5uM concetration for 24 hours


title: ∆modcl1_a

type: SRA

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

country: USA

institute: Donald Danforth Plant Science Center

description: Mycelial tissues from targeted deletion mutant of M. oryzae Dicer-like protein1 (MGG_01541.6), replicate 1

library_source: transcriptomic

data_processing:
For data processing, the adapter sequences were trimmed from raw sequence reads. The small RNA sequences were further trimmed to the lengths between 18 and 34 nucleotides. RNA-seq sequences were maintained at the length after adapter trimming.
Sequence data processing was conducted using in-house Perl scripts developed by Meyers lab in University of Delaware
Genome_build: Magnaporthe oryzae genome assembly 8 from Broad Institute
Supplementary_files_format_and_content: tag count file

organism: Pyricularia oryzae

source_name: Mycelium

extract_protocol:
Mycelial tissues were collected and flash frozen in liquid nitrogen. Total RNA was extracted by TRIzol Reagent (Ambion by Life Technologies) according to manufacturer's protocol.
Small RNA libraries were constructed from 1 microgram of  total RNA using Illumina Truseq small RNA sample preparation kit (RS-930-1012). RNA-seq libraries were constructed using the Illumina TruSeq RNA sample preparation kit (RS-930-2001).

value: Mycelium grown in complete media for 5 days

tag: genotype/variation


title: Wt7015_d

description: Mycelial tissues from wild type, Magnaporthe oryzae strain 70-15, replicate 4


title: PHH_Amiodarone_7d_2


title: PHH_Aflatoxin_7d_1


title: UmiR-194-5p MS275 24h vs UmiR-194-5p replicate 1

description: Biological replicate 1 of 2. UmiR-194-5p MS275 24h vs UmiR-194-5p


title: Wt7015_c

description: Mycelial tissues from wild type, Magnaporthe oryzae strain 70-15, replicate 3


title: PHH_Amiodarone_7d_1


title: PHH_DMSO_7d_3

description: Gene expression after 7 day treatment (3 re-dosings) with 0.4% DMSO, PHH 3D spheroid

value: DMSO


title: PHH_Chlorpromazine_48h_3

description: Gene expression after 48h treatment with 2uM chlorpromazine (0.4% DMSO), PHH 3D spheroid

value: Chlorpromazine


title: PHH_Aflatoxin_48h_3

description: Gene expression after 48h treatment with 0.002uM aflatoxin B1 (0.4% DMSO), PHH 3D spheroid


title: TPO_4h_rep1

city: Cambridge

first: Anthony

last: Green

state: Cambridgeshire

address: Hills Road

department: Department of heamatology

country: United Kingdom

institute: University of Cambridge

description:
SAMPLE 10
Replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Illumina iScan array scanner

data_processing:
Raw data was extracted with the lumi R package
Data was normalized with the function lumiExpresso from the lumi R package

molecule: polyA RNA

organism: Mus musculus

source_name: TPO treated for 4 hours

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

growth_protocol: HPC7 cells were grown in Iscove's Modified Dulbecco's Medium (IMDM, Gibco-Life technologies) supplemented with 10% FCS, 10% SCF conditioned media and 74.8 mM MTG (Sigma).

extract_protocol: Total RNA was extracted using a RNeasy Kit (Qiagen) according to the manufacturer's recommendations.

treatment_protocol: Cells were serum-starved and stimulated with Tpo for 30 minutes, 1 hour and 4 hours.

value: TPO

tag: time


title: TPO_4h_rep3

description:
SAMPLE 12
Replicate 3


title: PHH_Chlorpromazine_48h_1


title: PHH_DMSO_7d_1


title: TPO_1h_rep2

description:
SAMPLE 8
Replicate 2

source_name: TPO treated for 1 hour


title: TPO_4h_rep2

description:
SAMPLE 11
Replicate 2


title: UmiR-194-5p vs Usc replicate 1

description: Biological replicate 1 of 2.UmiR-194-5p (U937 transfected with miR-194-5p vector) vs Usc (U937 transfected with empty vector)

growth_protocol: U937 (Human leukemic monocyte lymphoma cell line) scramble and miR-194-5p were cultured in RPMI 1640, containing 10% decomplemented FBS plus G418 0,5 µg/µl

value: empty vector


title: PHH_DMSO_7d_2


title: TPO_30m_rep3

description:
SAMPLE 6
Replicate 3

source_name: TPO treated for 30 minutes


title: PHH_Aflatoxin_48h_2


title: PHH_Aflatoxin_48h_1


title: TPO_1h_rep3

description:
SAMPLE 9
Replicate 3


title: PHH_Chlorpromazine_48h_2


title: TPO_30m_rep2

description:
SAMPLE 5
Replicate 2


title: TPO_30m_rep1

description:
SAMPLE 4
Replicate 1


title: TPO_1h_rep1

description:
SAMPLE 7
Replicate 1


title: TPO_0h_rep3

description:
SAMPLE 3
Replicate 3

source_name: Serum starved

value: control


title: TPO_0h_rep2

description:
SAMPLE 2
Replicate 2


title: PHH_Amiodarone_48h_2

description: Gene expression after 48h treatment with 4uM amiodarone (0.4% DMSO), PHH 3D spheroid


title: PHH_Amiodarone_48h_3


title: PHH_DMSO_48h_1

description: Gene expression after 48h treatment with 0.4% DMSO, PHH 3D spheroid


title: PHH_Amiodarone_48h_1


title: PHH_DMSO_48h_2


title: TPO_0h_rep1

description:
SAMPLE 1
Replicate 1


title: PHH_DMSO_48h_3


title: HepaRG_DMSO_14d_2

description: Gene expression after 14 day treatment (6 re-dosings) with 0.4% DMSO, HepaRG 2D

source_name: HepaRG 2D

growth_protocol: HepaRG cells (Biopredic International) were cultured and maintained in culture medium (William’s E Basal Medium + GlutaMAX containing phenol red; Invitrogen) with Additive 710 (Biopredic International). For differentiation, cells were cultured in culture medium with Additive 720 (Biopredic International). Cells were maintained in growth medium for 2 weeks followed by 2 weeks of differentiation medium. Medium was changed to culture medium without phenol red and DMSO one day prior to the initiation of treatment

value: HepaRG cells


title: HepaRG_DMSO_7d_2

description: Gene expression after 7 day treatment (3 re-dosings) with 0.4% DMSO, HepaRG 2D


title: HepaRG_DMSO_48h_2

description: Gene expression after 48h treatment with 0.4% DMSO, HepaRG 2D


title: HepaRG_DMSO_48h_3


title: BAY1436032 replicate 3

city: Hannover

first: Anuhar

last: Chaturvedi

address: Cral Neuberg Strasse-1

department: Hematology, Hemostasis, Oncology and Stem Cell Transplantation

country: Germany

institute: Hannover Medical School

description: Gene expression data from IDH1mut PDX mice treated with BAY1436032.

hyb_protocol: 7.5 µg of biotinylated cRNA were fragmented and placed in a hybridization cocktail containing four biotinylated hybridization controls (BioB, BioC, BioD, and Cre) as recommended by the manufacturer. Samples were hybridized to an identical lot of Affymetrix GeneChip HG-U133 2.0 for 16 hours at 45°C. Steps for washing and SA-PE staining were processed on the Fluidics Station 450 using the recommended FS450 protocol (Affymetrix; Santa Clara, CA).

scan_protocol: Image analysis was performed on GCS3000 Scanner and GCOS1.2 Software Suite (Affymetrix; Santa Clara, CA).

data_processing: Analysis of microarray data was performed using GeneSpring 11.5.1 software suite (Agilent Technologies, CA, USA). Signal intensities (raw data) were background corrected, normalized and summarized using RMA. Gene expression values per condition are given as log2 relative expression to mean expression value calculated from log2 intensities of all conditions (mean centralization, normalized data). Significance of differential gene expression was calculated by GeneSpring software using error corrected unpaired T-Test.

source_name: sorted human CD45+ cells from bone marrow of PDX mouse treated with BAY1436032

label_protocol: 500 ng of total RNA were used for biotin labelling according to the 3' IVT Express Kit (Affymetrix; Santa Clara, CA).

growth_protocol: in vivo from NSG mice.

extract_protocol: Qiagen RNeasy Plus Mini Kit according to manufacturer's instructions.

treatment_protocol: Human IDH1mut AML patient cells were transplanted in NSG mice. Mice were treated with either vehicle or 150mg/kg/day of BAY1436032. Four weeks post treatment, bone marrow was isolated and human CD45+ positive cells were sorted for RNA preparation.

tag: pdx mouse

value: NSG mouse transplanted with human IDH1mut AML patient cells


title: HepaRG_DMSO_7d_1


title: C24 developing seeds, 8-9 days after flower opening, biological replicate 2 [re-analysis]

status: Public on May 21 2017

city: Stadt Seeland

first: Renate

middle: Hanna

last: Schmidt

state: Sachsen-Anhalt

address: Corrensstrasse 3

department: Breeding Research

institute: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)

hyb_protocol: Hybridisation was performed by ATLAS Biolabs GmbH, Berlin Germany (Affymetrix authorised service provider)

scan_protocol: Scanning was performed by ATLAS Biolabs GmbH, Berlin Germany (Affymetrix authorised service provider)

data_processing: Array elements had to pass the following four criteria in order to be selected for a restricted set of probes (R selection). (1) The oligonucleotides had to show unique best matches that corresponded to perfect sequence alignments when compared to the Col-0 as well as the C24 nuclear genomes. (2) Probes had to reveal perfect sequence alignments with TAIR10 representative gene models, any additional matches had to span less than 22 consecutive bp of perfectly aligned sequences. (3) Selected probes that belonged to a particular probe set were required to map to the same representative gene model. (4) Probe sets had to consist of three or more probes which passed criteria (1) to (3). Only probes belonging to the R selection were considered and processed (Custom probe grouping). The raw hybridisation intensity data files (‘CEL’ files) were corrected by using Bioconductor packages in the open-source statistical R environment and a custom C++ script. The corrected ‘CEL’ files and the identities of the probe sets that were to be kept in the data set were used to modify the CDF file corresponding to the GeneChip® Arabidopsis ATH1 Genome Array by using the Convert function of the RMAExpress 1.0.5 program. After imposing these restrictions, background correction, quantile normalisation and transformation to log2 values were performed with the RMAExpress 1.0.5 program.

label: Biotin

organism: Arabidopsis thaliana

source_name: C24 developing seeds_8-9 days after flower opening

label_protocol: Labeling was performed by ATLAS Biolabs GmbH, Berlin Germany (Affymetrix authorised service provider)

growth_protocol: Arabidopsis thaliana seeds of accessions Col-0 and C24 were sown in pots with substrate 1 (Klasmann‐Deilmann GmbH, Geeste, Germany) and grown after stratification for 3 days at 4°C in long‐day conditions (16 h light at 20°C and 70% relative humidity/8 h dark at 16°C and 60% relative humidity). Light intensity during the light phase amounted to approximately 250 µE m−2 s−1. In each of two experiments six plants per accession were grown.

extract_protocol: RNA was isolated from 200 mg samples of seeds. After grinding for 45 s at 27 Hz with Mixer Mill MM400 (Retsch GmbH, Haan, Germany) the samples were mixed with 0.7 ml extraction buffer (1 M Tris-HCl (pH 9.0), 1% (v/v) SDS, 10 mM EDTA (pH 8.0), 0.5% (v/v) β-mercaptoethanol in DEPC-H2O (0.1% (v/v)) and subsequently with 0.7 ml of phenol/chloroform/isoamyl alcohol (25:24:1). After centrifugation for 10 min, the aqueous phases were extracted once more with phenol/chloroform/isoamyl alcohol and then with chloroform. After adding 0.1 volume of 3 M sodium acetate (pH 5.4) and 2.5 volumes of 96% ethanol the samples were kept for 45 min at -80°C and then centrifuged for 5 min. The resulting RNA pellets were dissolved in 0.4-0.5 ml of DEPC-H2O (0.1% (v/v) and after centrifugation the supernatants were mixed with 1 volume of 4 M LiCl. After an overnight incubation on ice, RNA pellets were collected by centrifugation, washed in 1 ml each of 2 M LiCl, 96% and 70% ethanol, dried and dissolved in ribonuclase-free water. All centrifugation steps were carried out at 14,000 rpm and 4°C. Purification of RNA samples was achieved with RNeasy columns (Qiagen) and the peqGOLD OptiPure reagent (Peqlab Biotechnologie GmbH, Erlangen, Germany) according to manufacturer’s instructions.

treatment_protocol: Individual flowers were tagged with coloured threads on the day of flower opening and every second day siliques of defined age were collected. Siliques of Col-0 and C24 plants were harvested eight or nine days, ten or eleven days as well as twelve or thirteen days after flower opening and immediately frozen in liquid nitrogen. Eight siliques each from six different plants of a certain developmental stage were pooled per accession; in all cases siliques from plants grown in the two different experiments were included. The siliques were dissected and only the seeds were used for RNA extraction. For each of the two parental accessions three replicates consisting of seeds from 48 siliques were prepared for each of the three harvest time points.

tag: genotype/accession

tag: Stage

value: 8-9 days after flower opening

value: developing seeds


title: HepaRG_DMSO_48h_1


title: C24 developing seeds, 12-13 days after flower opening, biological replicate 1 [re-analysis]

source_name: C24 developing seeds_12-13 days after flower opening

value: 12-13 days after flower opening


title: C24 developing seeds, 10-11 days after flower opening, biological replicate 2 [re-analysis]

source_name: C24 developing seeds_10-11 days after flower opening

value: 10-11 days after flower opening


title: BAY1436032 replicate 1

value: sorted human CD45+ cells from bone marrow of PDX mouse


title: HepaRG_DMSO_14d_3


title: BAY1436032 replicate 2


title: HepaRG_DMSO_7d_3


title: HepaRG_DMSO_14d_1


title: C24 developing seeds, 8-9 days after flower opening, biological replicate 3 [re-analysis]


title: C24 developing seeds, 10-11 days after flower opening, biological replicate 3 [re-analysis]


title: Col-0 developing seeds, 12-13 days after flower opening, biological replicate 2 [re-analysis]

source_name: Col-0 developing seeds_12-13 days after flower opening


title: Vehicle replicate 2

description: Gene expression data from IDH1mut PDX mice treated with Vehicle.

source_name: sorted human CD45+ cells from bone marrow of PDX mouse treated with vehicle

value: vehicle


title: C24 developing seeds, 12-13 days after flower opening, biological replicate 2 [re-analysis]


title: C24 developing seeds, 10-11 days after flower opening, biological replicate 1 [re-analysis]


title: UmiR-194-5p vs Usc replicate 2

description: Biological replicate 2 of 2.UmiR-194-5p (U937 transfected with miR-194-5p vector) vs Usc (U937 transfected with empty vector)

value: leukemic monocyte lymphoma cell line

value: miR-194-5p vector


title: Vehicle replicate 3


title: C24 developing seeds, 12-13 days after flower opening, biological replicate 3 [re-analysis]


title: C24 developing seeds, 8-9 days after flower opening, biological replicate 1 [re-analysis]


title: Col-0 developing seeds, 12-13 days after flower opening, biological replicate 1 [re-analysis]


title: Vehicle replicate 1


title: Col-0 developing seeds, 12-13 days after flower opening, biological replicate 3 [re-analysis]


title: Col-0 developing seeds, 10-11 days after flower opening, biological replicate 1 [re-analysis]

source_name: Col-0 developing seeds_10-11 days after flower opening


title: PHH_Amiodarone_14d_3

description: Gene expression after 14 day treatment (6 re-dosings) with 4uM amiodarone (0.4% DMSO), PHH 3D spheroid

source_name: Primary human hepatocyte 3D spheroid

value: Primary human hepatocyte (PHH)

value: Amiodarone


title: Col-0 developing seeds, 10-11 days after flower opening, biological replicate 2 [re-analysis]


title: C24 developing seeds, 12-13 days after flower opening, biological replicate 3

data_processing: The raw hybridisation intensity data files (‘CEL’ files) were directly imported into the RMAExpress 1.0.5 program (Irizarry et al. 2003) in order to carry out background correction, quantile normalisation and the transformation to log2 values with the normalisation approach robust multi-array average.

source_name: Col-0 developing seeds, 12-13 days after flower opening

growth_protocol: A. thaliana seeds of accessions Col-0 and C24 were sown in pots with substrate 1 (Klasmann‐Deilmann GmbH, Geeste, Germany) and grown after stratification for 3 days at 4°C in long‐day conditions (16 h light at 20°C and 70% relative humidity/8 h dark at 16°C and 60% relative humidity). Light intensity during the light phase amounted to approximately 250 µE m−2 s−1. In each of two experiments six plants per accession were grown.


title: C24 developing seeds, 8-9 days after flower opening, biological replicate 3

source_name: Col-0 developing seeds, 8-9 days after flower opening


title: Col-0 developing seeds, 8-9 days after flower opening, biological replicate 3 [re-analysis]

source_name: Col-0 developing seeds_8-9 days after flower opening


title: C24 developing seeds, 10-11 days after flower opening, biological replicate 3

source_name: Col-0 developing seeds, 10-11 days after flower opening


title: C24 developing seeds, 8-9 days after flower opening, biological replicate 2


title: C24 developing seeds, 12-13 days after flower opening, biological replicate 1


title: Col-0 developing seeds, 10-11 days after flower opening, biological replicate 3 [re-analysis]


title: C24 developing seeds, 10-11 days after flower opening, biological replicate 2


title: wtIDH1  sample2

city: Seattle

first: Sonali

last: Arora

state: WA

address: 1100 Fairview Ave N,

institute: FHCRC

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using R/Bioconductor package limma

source_name: gliomas

label_protocol: wtIDH1 is the control group and muIDH1 is the experimental group.

growth_protocol: Ntva_Ink4a/Arf-/- mice were used to generate mouse gliomas. The genetic backgrounds of tva mice are FVB/N, C57BL6, BALB/C, and 129. To generate wtIDH1- and muIDH1-expressing mouse gliomas, we used the RCAS/tva system as described previously. PDGFa-expressing DF1 cells were mixed with either wtIDH1-shp53- or muIDH1-shp53-expressing DF1 cells. These mixed DF1 cells were injected into Ntva_ Ink4a/Arf-/- mice. Mice were monitored daily until they developed signs of illness, such as lethargy, poor grooming, weight loss, dehydration, macrocephaly, seizure, jumping, and/or paralysis. Whole tumor tissue was used for RNA extraction. Total RNA was extracted from tumor tissues using RNeasy Mini kits (QIAGEN).

extract_protocol: Total RNA was extracted from tumor tissues using RNeasy Mini kit (QIAGEN) using the manufacturer’s protocol.

treatment_protocol: No treatment

tag: tumor type

tag: genotype/variatoin

tag: background mouse strain

value: FVB/N, C57BL6, BALB/C, and 129


title: Col-0 developing seeds, 8-9 days after flower opening, biological replicate 1 [re-analysis]


title: C24 developing seeds, 10-11 days after flower opening, biological replicate 1


title: Col-0 developing seeds, 8-9 days after flower opening, biological replicate 2 [re-analysis]


title: Col-0 developing seeds, 12-13 days after flower opening, biological replicate 3

source_name: C24 developing seeds, 12-13 days after flower opening


title: wtIDH1  sample1


title: Col-0 developing seeds, 12-13 days after flower opening, biological replicate 2


title: C24 developing seeds, 12-13 days after flower opening, biological replicate 2


title: C24 developing seeds, 8-9 days after flower opening, biological replicate 1


title: mutIDH1  sample3


title: Col-0 developing seeds, 12-13 days after flower opening, biological replicate 1


title: mutIDH1  sample1


title: KI testis, biological rep3

city: Adelaide

first: Fatwa

last: Adikusuma

state: South Australia

address: MLS building Gate 8 Victoria Drive

department: Molecular & Cellular Biology

country: Australia

institute: University of Adelaide

hyb_protocol: Fragmented, biotin-labelled cRNA samples (5.5ug) were hybridised to GeneChips for 17hr at 45C

scan_protocol: GeneChips were scanned using the Affymetrix Scanner 3000 7G and Affymetrix GeneChip Command Console.

data_processing:
CHP files were generated using Expression Console, and further analysis was performed using Partek Genomics Suite V6.6. CEL files were imported using the RMA method for normalisation and probeset summarisation. ANOVA was performed to determine differentially expressed probesets between experimental groups.
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.3.1.187
program-company = Affymetrix

source_name: 2 weeks whole testis of KI mice

label_protocol: RNA samples (500ng) were processed using the Affymetrix WT PLUS Reagent Kit as per the manufacturer’s instructions.

growth_protocol: mice were maintained in standard condition

extract_protocol: RNA was extracted using Trizol (Invitrogen), purified using RNeasy mini kit (Qiagen) after  DNAse treatment on column using RNase-Free DNase Set (Qiagen).

tag: strain background

tag: age

value: 2 weeks

value: whole testis


title: Col-0 developing seeds, 10-11 days after flower opening, biological replicate 3

source_name: C24 developing seeds, 10-11 days after flower opening


title: KI testis, biological rep2


title: Col-0 developing seeds, 10-11 days after flower opening, biological replicate 2


title: blood_pre.cDC2_1

city: Singapore

first: Kaibo

last: Duan

address: 8A Biomedical Grove, Immunos Building, Level 4

country: Singapore

institute: Singapore Immunology Network

description: pre.cDC2 isolated from PBMC of healthy donor 1

hyb_protocol: Hybridization of cRNA was performed on Illumina Human-HT12 Version 4 chips.

data_processing: Probe level expression data were exported from Illlumina GenomeStudio software without background subtraction. These raw data were log (base 2) transformed and quantile normalized in R using Bioconductor lumi package.

label_protocol: Biotinylated cRNA was prepared according to the protocol by Epicentre TargetAmpTM 2-Round Biotin-aRNA Amplification Kit 3.0 using 500pg of total RNA.

extract_protocol: Total RNA was isolated from FACS-sorted blood pre-DC and DC subsets with the Qiagen Rneasy Micro Kit (Qiagen) according to the manufacturer's protocol. Total RNA integrity was assessed using Agilent Bioanalyzer.

tag: subject id

value: donor 1

tag: subject status

value: healthy

value: Peripheral Blood Mononuclear Cells (PBMCs)

tag: cell subtype


title: Col-0 developing seeds, 10-11 days after flower opening, biological replicate 1

tag: tissue


title: mutIDH1  sample2


title: KI testis, biological rep1


title: blood_pre.cDC2_2

description: pre.cDC2 isolated from PBMC of healthy donor 2

value: donor 2

tag: cell type


title: blood_pre.cDC1_3

description: pre.cDC1 isolated from PBMC of healthy donor 3

value: donor 3


title: blood_pre.cDC2_3

description: pre.cDC2 isolated from PBMC of healthy donor 3


title: Col-0 developing seeds, 8-9 days after flower opening, biological replicate 1

source_name: C24 developing seeds, 8-9 days after flower opening

value: 8-9 days after flower opening

value: developing seeds


title: Col-0 developing seeds, 8-9 days after flower opening, biological replicate 3


title: Col-0 developing seeds, 8-9 days after flower opening, biological replicate 2


title: blood_pre.cDC1_2

description: pre.cDC1 isolated from PBMC of healthy donor 2


title: KO testis, biological rep2

source_name: 2 weeks whole testis of KO mice


title: blood_pDC_3

description: pDC isolated from PBMC of healthy donor 3

value: pDC


title: blood_pre.cDC1_1

description: pre.cDC1 isolated from PBMC of healthy donor 1


title: blood_pDC_1

description: pDC isolated from PBMC of healthy donor 1


title: KO testis, biological rep1


title: WT testis, biological rep6

source_name: 2 weeks whole testis of WT mice (KO littermate)

value: wild type (KO littermate)


title: KO testis, biological rep3


title: WT testis, biological rep2

source_name: 2 weeks whole testis of WT mice (KI littermate)

value: wild type (KI littermate)


title: WT testis, biological rep3


title: blood_early.pre.DC_3

description: early.pre.DC isolated from PBMC of healthy donor 3


title: WT testis, biological rep1


title: blood_pDC_2

description: pDC isolated from PBMC of healthy donor 2


title: blood_early.pre.DC_2

description: early.pre.DC isolated from PBMC of healthy donor 2


title: blood_cDC2_3

description: cDC2 isolated from PBMC of healthy donor 3


title: WT testis, biological rep5


title: WT testis, biological rep4


title: saliva derived genomic DNA [SA040]_SNP_genotype

status: Public on May 20 2017

type: genomic

city: Stony Brook

first: Shyamalika

last: Gopalan

address: 100 Nicolls Road

institute: Stony Brook University

description: saliva sample

hyb_protocol: genomic DNA was amplified, fragmented and hybridised to Illumina OmniExpress, OmniExpress Plus, and HumanHap550 arrays using standard Illumina protocol

scan_protocol: chips were scanned using an Illumina iScan and recommended settings

data_processing:
genotypes were oriented to the hg19 build, filtered for quality and missingness, and merged with other datasets to yield a final set of 298346 SNPs which were used for all analyses in the study. PLINK software was used for analysis.
The .bim file contains positional information about each SNP. It has 6 columns: chromosome, rsID or other identifier, genetic distance in morgans, physical distance in base pairs, and two columns with the alleles.
The .fam file contains information about the individuals. It has 6 columns: family ID, individual ID, paternal ID, maternal ID, sex, and phenotype. The parental IDs are unknown for these individuals, so these columns are set to 0 for all. There is also no relevant phenotype for these individuals, so  this column is set to -9 for all.
The .bed.data file contains the information about each SNP for each individual encoded in binary format.
The .map file contains the same data as the .bim file except that it does not contain last two columns with the specific alleles.
The .ped file is the same as the .fam file except it contains additional columns, two for every SNP position, which contain the genotypes.

molecule: genomic DNA

source_name: Oragene saliva

label_protocol: standard Illumina protocol

extract_protocol: genomic DNA was extracted from saliva sampled using Oragene kits by DNA Genotek using PrepIT reagent and a standard protocol

tag: gender

value: female


title: saliva derived genomic DNA [SA045]_SNP_genotype

description: saliva sample


title: saliva derived genomic DNA [SA004]_SNP_genotype

description: saliva sample

value: male


title: saliva derived genomic DNA [SA032]_SNP_genotype

description: saliva sample


title: saliva derived genomic DNA [SA019]_SNP_genotype

description: saliva sample


title: saliva derived genomic DNA [SA053]_SNP_genotype

description: saliva sample


title: blood_early.pre.DC_1

description: early.pre.DC isolated from PBMC of healthy donor 1


title: saliva derived genomic DNA [SA049]_SNP_genotype

description: saliva sample


title: saliva derived genomic DNA [SA030]_SNP_genotype

description: saliva sample


title: blood_cDC1_3

description: cDC1 isolated from PBMC of healthy donor 3


title: saliva derived genomic DNA [SA028]_SNP_genotype

description: saliva sample


title: saliva derived genomic DNA [SA036]_SNP_genotype

description: saliva sample


title: blood_cDC2_2

description: cDC2 isolated from PBMC of healthy donor 2


title: blood_cDC2_1

description: cDC2 isolated from PBMC of healthy donor 1


title: saliva derived genomic DNA [SA048]_SNP_genotype

description: saliva sample


title: blood_cDC1_2

description: cDC1 isolated from PBMC of healthy donor 2


title: saliva derived genomic DNA [SA009]_SNP_genotype

description: saliva sample


title: saliva derived genomic DNA [SA061]_SNP_genotype

description: saliva sample


title: saliva derived genomic DNA [SA037]_SNP_genotype

description: saliva sample


title: saliva derived genomic DNA [SA039]_SNP_genotype

description: saliva sample


title: saliva derived genomic DNA [SA072]_SNP_genotype

description: saliva sample


title: saliva derived genomic DNA [SA1000]_SNP_genotype

description: saliva sample


title: saliva derived genomic DNA [SA029]_SNP_genotype

description: saliva sample


title: saliva derived genomic DNA [SA1022]_SNP_genotype

description: saliva sample


title: saliva derived genomic DNA [SA1010]_SNP_genotype

description: saliva sample


title: saliva derived genomic DNA [SA1009]_SNP_genotype

description: saliva sample


title: saliva derived genomic DNA [SA003]_SNP_genotype

description: saliva sample


title: saliva derived genomic DNA [SA050]_SNP_genotype

description: saliva sample


title: saliva derived genomic DNA [SA1006]_SNP_genotype

description: saliva sample


title: blood_cDC1_1

description: cDC1 isolated from PBMC of healthy donor 1


title: saliva derived genomic DNA [SA1011]_SNP_genotype

description: saliva sample


title: saliva derived genomic DNA [SA095]_SNP_genotype

description: saliva sample


title: saliva derived genomic DNA [SA086]_SNP_genotype

description: saliva sample


title: saliva derived genomic DNA [SA1028]_SNP_genotype

description: saliva sample


title: saliva derived genomic DNA [SA1030]_SNP_genotype

description: saliva sample


title: saliva derived genomic DNA [SA1025]_SNP_genotype

description: saliva sample


title: saliva derived genomic DNA [SA1015]_SNP_genotype

description: saliva sample


title: saliva derived genomic DNA [SA1039]_SNP_genotype

description: saliva sample


title: saliva derived genomic DNA [SA069]_SNP_genotype

description: saliva sample


title: saliva derived genomic DNA [SA1023]_SNP_genotype

description: saliva sample


title: saliva derived genomic DNA [SA068]_SNP_genotype

description: saliva sample


title: saliva derived genomic DNA [SA080]_SNP_genotype

description: saliva sample


title: saliva derived genomic DNA [SA074]_SNP_genotype

description: saliva sample


title: saliva derived genomic DNA [SA1001]_SNP_genotype

description: saliva sample


title: saliva derived genomic DNA [SA1029]_SNP_genotype

description: saliva sample


title: saliva derived genomic DNA [SA064]_SNP_genotype

description: saliva sample


title: saliva derived genomic DNA [SA1041]_SNP_genotype

description: saliva sample


title: saliva derived genomic DNA [SA017]_SNP_genotype

description: saliva sample


title: saliva derived genomic DNA [SA057]_SNP_genotype

description: saliva sample


title: saliva derived genomic DNA [SA046]_SNP_genotype

description: saliva sample


title: saliva derived genomic DNA [SA022]_SNP_genotype

description: saliva sample


title: saliva derived genomic DNA [SA020]_SNP_genotype

description: saliva sample


title: saliva derived genomic DNA [SA043]_SNP_genotype

description: saliva sample


title: saliva derived genomic DNA [SA063]_SNP_genotype

description: saliva sample


title: TIE2- monocytes miRNA_rep3

status: Public on May 19 2017

city: Shanghai

first: Xinjing

last: Wang

address: 536 Changle Road

country: China

institute: Shanghai First Maternity and Infant Hospital Corporation

description: miRNA expression in TEMs

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25ul containing 25x Agilent fragmentation buffer and 10x Agient blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 25ul of 2x GEx Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent-046065 Mouse miRNA Microarray V19.0 8x60K(Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 12.0(Agilent). Probe that at least 100.0 percent of samples in any 1 condition out of 2 conditions have flags in Detected were maintained.

source_name: TIE2- monocytes,replicate 3

label_protocol: 0.1ug total RNA were dephosphorylated, denaturated and then labeled with Cyanine-3-CTP（Cy3）using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions,then followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 UV-VIS Spectrophotometer  version 3.2.1.

extract_protocol: total RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/n AM1556 ) following the manufacturer's instructions

treatment_protocol: PBMCs were isolated from freshly peripheral blood donated by healthy volunteers and then cultured in RPMI 1640 medium supplemented with 10%  fetal bovine serum at 37 ºC in a humidified incubator with 5% CO2. Then TEMs and their paired TIE2-Monoytes were isolated by positive immunomagnetic selection and FACS-sorting following the manufacturer's instructions.

value: whole blood

tag: cell markers


title: TIE2 expressing monocytes miRNA_rep1

description: miRNA expression in TEMs

source_name: TIE2 expressing monocytes,replicate 1


title: TIE2- monocytes miRNA_rep2

description: miRNA expression in TEMs

source_name: TIE2- monocytes,replicate 2


title: TIE2- monocytes miRNA_rep1

description: miRNA expression in TEMs

source_name: TIE2- monocytes,replicate 1


title: TIE2 expressing monocytes miRNA_rep3

description: miRNA expression in TEMs

source_name: TIE2 expressing monocytes,replicate 3


title: TIE2 expressing monocytes miRNA_rep2

description: miRNA expression in TEMs

source_name: TIE2 expressing monocytes,replicate 2


title: 691-MES-prrx1-shrna_647-prrx1-6d+IPTG

city: Amsterdam

first: Richard

last: Volckmann

state: Noord-Holland

address: van der Boechorststraat 6a

department: Laboratory of Experimental Oncology and Radiobiology

country: Netherlands

institute: msterdam UMC and University of Amsterdam

hyb_protocol: 10 µg of labeled cRNA was hybridized to Affymetrix Human genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).

scan_protocol: Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protoco

data_processing: Expression data (cel files) were normalized with the MAS5.0 algorithm (target signal = 100) using GCOS software (Affymetrix)

label_protocol: RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.

growth_protocol: sknas and gimen cells were cultured in DMEM (Invitrogen) containing 10% fetal calf serum. 691-MES cells were cultured in neural stem cell medium.

extract_protocol: Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer’s protocol,

treatment_protocol: IPTG was used to silence PRRX1 in 691-MES-prrx1-shrna_647

value: Neuroblastoma TIC line 691-MES with inducible shRNA against PRRX1


title: 691-MES-prrx1-shrna_647-prrx1-6d-IPTG


title: crispr-cas-prrx1-3_1

source_name: gimen

value: Neuroblastoma cell line gimen clone with crispr/CAS expression of PRRX1 knock-out


title: 691-MES-prrx1-shrna_647-prrx1-3d-IPTG


title: 691-MES-prrx1-shrna_647-prrx1-3d+IPTG


title: crispr-cas-prrx1-3_6


title: crispr-cas-control-84_1 nb1983


title: crispr-cas-prrx1-2_4


title: crispr-cas-control-86_3 nb1984


title: crispr-cas-prrx1-3_5

source_name: sknas

value: Neuroblastoma cell line sknas clone with crispr/CAS expression of PRRX1 knock-out


title: central memory CD4 T-cells from pSS pSS_K7734_CD4TCM

city: Fujisawa

first: Shinya

last: Tasaki

state: Kanagawa

address: 26-1, Muraoka-Higashi 2-chome

country: Japan

institute: Takeda Pharmaceutical Company Limited

description: central memory CD4 T-cells from pSS

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized for 18 hr at 45℃ on Human Genome U133 Plus2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with the frozen robust multiarray analysis (fRMA) using Biocunductor with default settings and absence/presence calls were estimated by Microarray Suite version 5.0 (MAS 5.0).

source_name: central memory CD4 T-cells from pSS

label_protocol: Biotinylated cDNA were prepared using NuGEN Encore Biotin Module from 5ug of amplified cDNA.

growth_protocol: Purifined CD4 T-cells from pSS patients and human healthy volunteers

extract_protocol: Total RNA from sorted cells were extracted using miRCURY RNA Isolation Kit (Exiqon), purified by RNeasy MinElute Cleanup Kit (Qiagen), and amplified with Ovation Pico WTA System V2 (NuGEN Technologies).

treatment_protocol: Peripheral mononuclear cells were isolated by density gradient centrifugation, and CD4+ T cell were purified from them using CD4+ T Cell Isolation Kit. Cells were sorted by FACS Aria Ⅲ. Tn, Tscm, Tcm, and Tem cells were defined as CD45RO-CCR7+CD95-, CD45RO-CCR7+CD95+, CD45RO+CCR7+, and CD45RO-CCR7-, respectively.

tag: disease

value: pSS

tag: celltype

value: central memory CD4

tag: patient

value: Female


title: effector memory CD4 T-cells from pSS pSS_K7734_CD4TEM

description: effector memory CD4 T-cells from pSS

source_name: effector memory CD4 T-cells from pSS

value: effector memory CD4


title: naive CD4 T-cells from pSS pSS_K3775_CD4TN

description: naive CD4 T-cells from pSS

source_name: naive CD4 T-cells from pSS

value: naive CD4


title: crispr-cas-prrx1-2_2


title: naive CD4 T-cells from pSS pSS_K7734_CD4TN

description: naive CD4 T-cells from pSS


title: effector memory CD4 T-cells from pSS pSS_K3775_CD4TEM

description: effector memory CD4 T-cells from pSS


title: naive CD4 T-cells from pSS pSS_K9008_CD4TN

description: naive CD4 T-cells from pSS


title: crispr-cas-control-86_3 nb1978


title: genomic DNA from SNU719

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

institute: Chiba University

description: cell line derived from EBV+ gastric cancer

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

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

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from cell lines or clinical samples using QIAquick DNA mini kit according to standard instructions

value: Male

tag: sample type

value: cell line

tag: disease state

value: gastric cancer


title: central memory CD4 T-cells from pSS pSS_K9008_CD4TCM

description: central memory CD4 T-cells from pSS


title: central memory CD4 T-cells from pSS pSS_K3775_CD4TCM

description: central memory CD4 T-cells from pSS


title: effector memory CD4 T-cells from pSS pSS_K9008_CD4TEM

description: effector memory CD4 T-cells from pSS


title: genomic DNA from KT

description: xenograft derived from EBV+ gastric cancer

source_name: KT

value: xenograft


title: crispr-cas-control-84_1 nb1977


title: central memory CD4 T-cells from pSS pSS_K1017_CD4TCM

description: central memory CD4 T-cells from pSS


title: effector memory CD4 T-cells from pSS pSS_K3797_CD4TEM

description: effector memory CD4 T-cells from pSS


title: effector memory CD4 T-cells from pSS pSS_K1017_CD4TEM

description: effector memory CD4 T-cells from pSS


title: central memory CD4 T-cells from pSS pSS_K3797_CD4TCM

description: central memory CD4 T-cells from pSS


title: naive CD4 T-cells from pSS pSS_K1017_CD4TN

description: naive CD4 T-cells from pSS


title: naive CD4 T-cells from pSS pSS_K3797_CD4TN

description: naive CD4 T-cells from pSS


title: naive CD4 T-cells from pSS pSS_K9576_CD4TN

description: naive CD4 T-cells from pSS


title: central memory CD4 T-cells from HC HC_N_CD4TCM

description: central memory CD4 T-cells from HC

source_name: central memory CD4 T-cells from HC

value: HC

value: HC-N


title: central memory CD4 T-cells from pSS pSS_K9576_CD4TCM

description: central memory CD4 T-cells from pSS


title: effector memory CD4 T-cells from HC HC_N_CD4TEM

description: effector memory CD4 T-cells from HC

source_name: effector memory CD4 T-cells from HC


title: naive CD4 T-cells from HC HC_N_CD4TN

description: naive CD4 T-cells from HC

source_name: naive CD4 T-cells from HC


title: naive CD4 T-cells from HC HC_M_CD4TN

description: naive CD4 T-cells from HC

value: HC-M


title: central memory CD4 T-cells from HC HC_M_CD4TCM

description: central memory CD4 T-cells from HC


title: central memory CD4 T-cells from HC HC_K_CD4TCM

description: central memory CD4 T-cells from HC

value: HC-K


title: effector memory CD4 T-cells from HC HC_K_CD4TEM

description: effector memory CD4 T-cells from HC


title: effector memory CD4 T-cells from HC HC_M_CD4TEM

description: effector memory CD4 T-cells from HC


title: effector memory CD4 T-cells from HC HC_J_CD4TEM

description: effector memory CD4 T-cells from HC

value: HC-J


title: naive CD4 T-cells from HC HC_K_CD4TN

description: naive CD4 T-cells from HC


title: central memory CD4 T-cells from HC HC_J_CD4TCM

description: central memory CD4 T-cells from HC


title: naive CD4 T-cells from HC HC_31_CD4TN

description: naive CD4 T-cells from HC


title: naive CD4 T-cells from HC HC_J_CD4TN

description: naive CD4 T-cells from HC


title: central memory CD4 T-cells from HC HC_31_CD4TCM

description: central memory CD4 T-cells from HC


title: central memory CD4 T-cells from HC HC_26_CD4TCM

description: central memory CD4 T-cells from HC


title: effector memory CD4 T-cells from HC HC_26_CD4TEM

description: effector memory CD4 T-cells from HC


title: effector memory CD4 T-cells from HC HC_31_CD4TEM

description: effector memory CD4 T-cells from HC


title: naive CD4 T-cells from HC HC_26_CD4TN

description: naive CD4 T-cells from HC


title: central memory CD8 T-cells from pSS (pSS_K7734_TCM)

description:
central memory CD8 T-cells from pSS
pSS_K7734_TCM

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized for 18 hr at 45℃ on Human Genome U133 Plus2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

data_processing: The data were analyzed with the frozen robust multiarray analysis (fRMA) using Bioconductor.

source_name: central memory CD8 T-cells from pSS

growth_protocol: Purifined CD8 T-cells from pSS patients and human healthy volunteers

extract_protocol: Total RNA was isolated with miRCURY RNA Isolation kit (EXIQON), and then concentrated with RNeasy MinElute Cleanup.

treatment_protocol: Peripheral CD8 T-cell magnetically were purified with CD8 T-cell isolation kit (Myltenyi Biotech.).  After staining with CD45RO APC-Cy7 (Clone UCHL1, BioLegend) and CCR7 Alexa647 (Clone TG8, BioLegend), each subset was isolated with FACS Aria III (BD Biosciences)

value: central memory CD8

value: patient K7734


title: effector memory CD8 T-cells from pSS (pSS_K7734_TEM)

description:
effector memory CD8 T-cells from pSS
pSS_K7734_TEM

source_name: effector memory CD8 T-cells from pSS

value: effector memory CD8


title: CD45RO- memory CD8 T-cells from pSS (pSS_K9370_TEMRA)

description:
CD45RO- memory CD8 T-cells from pSS
pSS_K9370_TEMRA

source_name: CD45RO- memory CD8 T-cells from pSS

value: pSS

value: CD45RO- memory CD8

value: patient K9370


title: CD45RO- memory CD8 T-cells from pSS (pSS_K7734_TEMRA)

description:
CD45RO- memory CD8 T-cells from pSS
pSS_K7734_TEMRA

value: Female


title: effector memory CD4 T-cells from pSS pSS_K9576_CD4TEM

description: effector memory CD4 T-cells from pSS

value: effector memory CD4


title: effector memory CD8 T-cells from pSS (pSS_K9370_TEM)

description:
effector memory CD8 T-cells from pSS
pSS_K9370_TEM


title: naive CD8 T-cells from pSS (pSS_K7734_TN)

description:
naive CD8 T-cells from pSS
pSS_K7734_TN

source_name: naive CD8 T-cells from pSS

value: naive CD8


title: central memory CD8 T-cells from pSS (pSS_K9370_TCM)

description:
central memory CD8 T-cells from pSS
pSS_K9370_TCM


title: effector memory CD8 T-cells from pSS (pSS_K3657_TEM)

description:
effector memory CD8 T-cells from pSS
pSS_K3657_TEM

value: patient K3657


title: naive CD8 T-cells from pSS (pSS_K9370_TN)

description:
naive CD8 T-cells from pSS
pSS_K9370_TN


title: CD45RO- memory CD8 T-cells from pSS (pSS_K3657_TEMRA)

description:
CD45RO- memory CD8 T-cells from pSS
pSS_K3657_TEMRA


title: central memory CD8 T-cells from pSS (pSS_K3657_TCM)

description:
central memory CD8 T-cells from pSS
pSS_K3657_TCM


title: naive CD8 T-cells from pSS (pSS_K3657_TN)

description:
naive CD8 T-cells from pSS
pSS_K3657_TN


title: CD45RO- memory CD8 T-cells from pSS (pSS_K3797_TEMRA)

description:
CD45RO- memory CD8 T-cells from pSS
pSS_K3797_TEMRA

value: patient K3797


title: effector memory CD8 T-cells from pSS (pSS_K3797_TEM)

description:
effector memory CD8 T-cells from pSS
pSS_K3797_TEM


title: naive CD8 T-cells from pSS (pSS_K3797_TN)

description:
naive CD8 T-cells from pSS
pSS_K3797_TN


title: CD45RO- memory CD8 T-cells from HC (HC_M_TEMRA)

description:
CD45RO- memory CD8 T-cells from HC
HC_M_TEMRA

source_name: CD45RO- memory CD8 T-cells from HC

value: patient HC-M


title: naive CD8 T-cells from pSS (pSS_K9120_TN)

description:
naive CD8 T-cells from pSS
pSS_K9120_TN

value: patient K9120


title: central memory CD8 T-cells from pSS (pSS_K4674_TCM)

description:
central memory CD8 T-cells from pSS
pSS_K4674_TCM

value: patient K4674


title: central memory CD8 T-cells from pSS (pSS_K3797_TCM)

description:
central memory CD8 T-cells from pSS
pSS_K3797_TCM


title: effector memory CD8 T-cells from HC (HC_L_TEM)

description:
effector memory CD8 T-cells from HC
HC_L_TEM

source_name: effector memory CD8 T-cells from HC

value: HC

value: patient HC-L


title: effector memory CD8 T-cells from HC (HC_M_TEM)

description:
effector memory CD8 T-cells from HC
HC_M_TEM


title: CD45RO- memory CD8 T-cells from pSS (pSS_K9120_TEMRA)

description:
CD45RO- memory CD8 T-cells from pSS
pSS_K9120_TEMRA


title: effector memory CD8 T-cells from pSS (pSS_K4674_TEM)

description:
effector memory CD8 T-cells from pSS
pSS_K4674_TEM


title: central memory CD8 T-cells from pSS (pSS_K9120_TCM)

description:
central memory CD8 T-cells from pSS
pSS_K9120_TCM


title: central memory CD8 T-cells from HC (HC_M_TCM)

description:
central memory CD8 T-cells from HC
HC_M_TCM

source_name: central memory CD8 T-cells from HC


title: naive CD8 T-cells from pSS (pSS_K4674_TN)

description:
naive CD8 T-cells from pSS
pSS_K4674_TN


title: CD45RO- memory CD8 T-cells from HC (HC_K_TEMRA)

description:
CD45RO- memory CD8 T-cells from HC
HC_K_TEMRA

value: patient HC-K


title: central memory CD8 T-cells from HC (HC_L_TCM)

description:
central memory CD8 T-cells from HC
HC_L_TCM

value: central memory CD8


title: naive CD8 T-cells from HC (HC_K_TN)

description:
naive CD8 T-cells from HC
HC_K_TN

source_name: naive CD8 T-cells from HC


title: effector memory CD8 T-cells from HC (HC_K_TEM)

description:
effector memory CD8 T-cells from HC
HC_K_TEM


title: CD45RO- memory CD8 T-cells from pSS (pSS_K4674_TEMRA)

description:
CD45RO- memory CD8 T-cells from pSS
pSS_K4674_TEMRA


title: CD45RO- memory CD8 T-cells from HC (HC_L_TEMRA)

description:
CD45RO- memory CD8 T-cells from HC
HC_L_TEMRA


title: naive CD8 T-cells from HC (HC_L_TN)

description:
naive CD8 T-cells from HC
HC_L_TN


title: central memory CD8 T-cells from HC (HC_K_TCM)

description:
central memory CD8 T-cells from HC
HC_K_TCM


title: naive CD8 T-cells from HC (HC_33_TN)

description:
naive CD8 T-cells from HC
HC_33_TN

value: patient HC-033


title: CD45RO- memory CD8 T-cells from HC (HC_31_TEMRA)

description:
CD45RO- memory CD8 T-cells from HC
HC_31_TEMRA

value: patient HC-031


title: CD45RO- memory CD8 T-cells from HC (HC_33_TEMRA)

description:
CD45RO- memory CD8 T-cells from HC
HC_33_TEMRA


title: effector memory CD8 T-cells from HC (HC_33_TEM)

description:
effector memory CD8 T-cells from HC
HC_33_TEM

value: effector memory CD8


title: naive CD8 T-cells from HC (HC_M_TN)

description:
naive CD8 T-cells from HC
HC_M_TN


title: effector memory CD8 T-cells from pSS (pSS_K9120_TEM)

description:
effector memory CD8 T-cells from pSS
pSS_K9120_TEM

value: pSS


title: central memory CD8 T-cells from HC (HC_33_TCM)

description:
central memory CD8 T-cells from HC
HC_33_TCM


title: effector memory CD8 T-cells from HC (HC_31_TEM)

description:
effector memory CD8 T-cells from HC
HC_31_TEM


title: naive CD8 T-cells from HC (HC_31_TN)

description:
naive CD8 T-cells from HC
HC_31_TN


title: effector memory CD8 T-cells from HC (HC_26_TEM)

description:
effector memory CD8 T-cells from HC
HC_26_TEM

value: patient HC-026


title: CD45RO- memory CD8 T-cells from HC (HC_26_TEMRA)

description:
CD45RO- memory CD8 T-cells from HC
HC_26_TEMRA

value: CD45RO- memory CD8

value: Female


title: central memory CD8 T-cells from HC (HC_31_TCM)

description:
central memory CD8 T-cells from HC
HC_31_TCM


title: non-induced control, T=144 hrs

data_processing: Expression data (cel files) were normalized with the MAS5.0 algorithm (target signal = 100) using GCOS software (Affymetrix),

source_name: SK-N-BE(2C)_PRRX1_non-induced control

growth_protocol: SK-N-BE(2C) cells were cultured in DMEM (Invitrogen) containing 10% fetal calf serum at 37 degrees Celsius.

treatment_protocol: SK-N-BE(2C) cells were transduced with pInducer virus particles with doxycycline-inducible expression of PRRX1

tag: cell line

value: adrenergic-type neuroblastoma cells

tag: transfected with

value: lentiviral vector pInducer containing a doxycycline-inducible promoter driving PRRX1A

tag: genotype/variation

value: non-induced control for PRRX1 time-course

tag: time point

value: 144 hrs


title: non-induced control, T= 0 hrs

value: 0 hrs


title: non-induced control, T= 216hrs


title: PRRX1, T=504 hrs

value: doxycycline-inducible expression of PRRX1

value: 504 hrs after induction


title: central memory CD8 T-cells from HC (HC_26_TCM)

description:
central memory CD8 T-cells from HC
HC_26_TCM

value: HC


title: naive CD8 T-cells from HC (HC_26_TN)

description:
naive CD8 T-cells from HC
HC_26_TN

value: naive CD8


title: non-induced control, T= 168hrs


title: PRRX1, T=672 hrs

value: 672 hrs after induction


title: non-induced control, T= 672hrs


title: PRRX1, T=216 hrs

value: 216 hrs after induction


title: 717T-MES, mesenchymal-type

growth_protocol: SH-EP2 and SH-SY5Y cells were cultured in DMEM (Invitrogen) containing 10% fetal calf serum . 691T, 700B and 717T cells were cultured in neural stem cell medium.

value: Neuroblastoma cell line with mesenchymal phenotype


title: PRRX1, T=336 hrs

value: 336 hrs after induction


title: PRRX1, T=72 hrs

value: 72 hrs after induction


title: non-induced control, T= 72 hrs

value: 72 hrs


title: 691B, adrenergic-type

value: Neuroblastoma cell line with adrenergic phenotype


title: PRRX1, T=144 hrs

value: 144 hrs after induction


title: SH-SY5Y, adrenergic-type

description:
GSE28019;GSM692874
itcc0396


title: PRRX1, T=48 hrs

value: adrenergic-type neuroblastoma cells

value: 48 hrs after induction


title: PRRX1, T=8 hrs

value: lentiviral vector pInducer containing a doxycycline-inducible promoter driving PRRX1A

value: 8 hrs after induction


title: 717T, adrenergic-type


title: 700B CD133+, mesenchymal-type

source_name: 700B sorted CD133positive cells

value: 700B sorted CD133positive cells


title: PRRX1, T=168 hrs

value: doxycycline-inducible expression of PRRX1

value: 168 hrs after induction


title: 691T, mesenchymal-type


title: 700B CD133-, adrenergic-type

source_name: 700B sorted CD133negative cells

value: 700B sorted CD133negative cells


title: SH-EP2, mesenchymal-type

description:
GSE28019;GSM692875
itcc0401


title: PRRX1, T=24 hrs

value: 24 hrs after induction


title: pSS029

description: Whole blood transcriptome of primary Sjogren's syndrome 029

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized for 18 hr at 45C on Human Genome U133 Plus2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

source_name: Whole blood of primary Sjogren's syndrome 029

growth_protocol: Human healthy volunteer

extract_protocol: Total  RNA was isolated with  the  PAXgeneTM  Blood  RNA Kit  (Qiagen,  Valencia,   CA,  USA) after  freezing and  storage. The  Ambion  GLOBINclearTM  (Ambion,  Austin  TX, USA) was applied to  total  RNA samples to remove globin transcripts.

treatment_protocol: Blood  samples were collected from healthy  and  pSS  human  donors in  PAXGene tubes.

value: primary Sjogren's syndrome

tag: rin

tag: age

value: Female

tag: rf

tag: ana

tag: igg

tag: iga

tag: igm

tag: essdai

value: whole blood


title: pSS028

description: Whole blood transcriptome of primary Sjogren's syndrome 028

source_name: Whole blood of primary Sjogren's syndrome 028

tag: disease

tag: gender

tag: tissue


title: pSS027

description: Whole blood transcriptome of primary Sjogren's syndrome 027

source_name: Whole blood of primary Sjogren's syndrome 027


title: pSS021

description: Whole blood transcriptome of primary Sjogren's syndrome 021

source_name: Whole blood of primary Sjogren's syndrome 021


title: pSS024

description: Whole blood transcriptome of primary Sjogren's syndrome 024

source_name: Whole blood of primary Sjogren's syndrome 024


title: pSS022

description: Whole blood transcriptome of primary Sjogren's syndrome 022

source_name: Whole blood of primary Sjogren's syndrome 022


title: pSS019

description: Whole blood transcriptome of primary Sjogren's syndrome 019

source_name: Whole blood of primary Sjogren's syndrome 019


title: pSS026

description: Whole blood transcriptome of primary Sjogren's syndrome 026

source_name: Whole blood of primary Sjogren's syndrome 026


title: pSS030

description: Whole blood transcriptome of primary Sjogren's syndrome 030

source_name: Whole blood of primary Sjogren's syndrome 030


title: pSS025

description: Whole blood transcriptome of primary Sjogren's syndrome 025

source_name: Whole blood of primary Sjogren's syndrome 025


title: pSS016

description: Whole blood transcriptome of primary Sjogren's syndrome 016

source_name: Whole blood of primary Sjogren's syndrome 016


title: pSS012

description: Whole blood transcriptome of primary Sjogren's syndrome 012

source_name: Whole blood of primary Sjogren's syndrome 012


title: pSS013

description: Whole blood transcriptome of primary Sjogren's syndrome 013

source_name: Whole blood of primary Sjogren's syndrome 013


title: pSS023

description: Whole blood transcriptome of primary Sjogren's syndrome 023

source_name: Whole blood of primary Sjogren's syndrome 023


title: pSS018

description: Whole blood transcriptome of primary Sjogren's syndrome 018

source_name: Whole blood of primary Sjogren's syndrome 018


title: pSS011

description: Whole blood transcriptome of primary Sjogren's syndrome 011

source_name: Whole blood of primary Sjogren's syndrome 011


title: pSS010

description: Whole blood transcriptome of primary Sjogren's syndrome 010

source_name: Whole blood of primary Sjogren's syndrome 010


title: pSS017

description: Whole blood transcriptome of primary Sjogren's syndrome 017

source_name: Whole blood of primary Sjogren's syndrome 017

value: Male


title: pSS014

description: Whole blood transcriptome of primary Sjogren's syndrome 014

source_name: Whole blood of primary Sjogren's syndrome 014


title: pSS009

description: Whole blood transcriptome of primary Sjogren's syndrome 009

source_name: Whole blood of primary Sjogren's syndrome 009


title: pSS006

description: Whole blood transcriptome of primary Sjogren's syndrome 006

source_name: Whole blood of primary Sjogren's syndrome 006


title: pSS002

description: Whole blood transcriptome of primary Sjogren's syndrome 002

source_name: Whole blood of primary Sjogren's syndrome 002


title: pSS005

description: Whole blood transcriptome of primary Sjogren's syndrome 005

source_name: Whole blood of primary Sjogren's syndrome 005


title: pSS003

description: Whole blood transcriptome of primary Sjogren's syndrome 003

source_name: Whole blood of primary Sjogren's syndrome 003


title: pSS020

description: Whole blood transcriptome of primary Sjogren's syndrome 020

source_name: Whole blood of primary Sjogren's syndrome 020


title: non-induced control, T= 336hrs

source_name: SK-N-BE(2C)_PRRX1_non-induced control

tag: cell type

value: non-induced control for PRRX1 time-course


title: pSS001

description: Whole blood transcriptome of primary Sjogren's syndrome 001

source_name: Whole blood of primary Sjogren's syndrome 001


title: pSS015

description: Whole blood transcriptome of primary Sjogren's syndrome 015

source_name: Whole blood of primary Sjogren's syndrome 015


title: pSS008

description: Whole blood transcriptome of primary Sjogren's syndrome 008

source_name: Whole blood of primary Sjogren's syndrome 008


title: pSS004

description: Whole blood transcriptome of primary Sjogren's syndrome 004

source_name: Whole blood of primary Sjogren's syndrome 004


title: HC030

description: Whole blood transcriptome of Healthy control 030

source_name: Whole blood of Healthy control 030

value: Healthy control


title: pSS007

description: Whole blood transcriptome of primary Sjogren's syndrome 007

source_name: Whole blood of primary Sjogren's syndrome 007


title: HC028

description: Whole blood transcriptome of Healthy control 028

source_name: Whole blood of Healthy control 028


title: HC026

description: Whole blood transcriptome of Healthy control 026

source_name: Whole blood of Healthy control 026


title: HC029

description: Whole blood transcriptome of Healthy control 029

source_name: Whole blood of Healthy control 029


title: HC024

description: Whole blood transcriptome of Healthy control 024

source_name: Whole blood of Healthy control 024


title: HC022

description: Whole blood transcriptome of Healthy control 022

source_name: Whole blood of Healthy control 022


title: HC025

description: Whole blood transcriptome of Healthy control 025

source_name: Whole blood of Healthy control 025


title: HC017

description: Whole blood transcriptome of Healthy control 017

source_name: Whole blood of Healthy control 017


title: HC023

description: Whole blood transcriptome of Healthy control 023

source_name: Whole blood of Healthy control 023


title: HC021

description: Whole blood transcriptome of Healthy control 021

source_name: Whole blood of Healthy control 021


title: HC019

description: Whole blood transcriptome of Healthy control 019

source_name: Whole blood of Healthy control 019


title: HC016

description: Whole blood transcriptome of Healthy control 016

source_name: Whole blood of Healthy control 016


title: SPCHPPP DMSO rep2

city: Toledo

first: Alberto

last: de Marcos Serrano

state: Toledo

address: Av carlos III s/n, Edificio Sabatini Lab 0.8 F.V

country: Spain

institute: Universidad de Castilla-La Mancha

description:
gene expression of SPCHPPP seedlings after 3-days growth on mock medium
PD2

hyb_protocol: Preparation of probes and hybridization were performed as described (One-Color Microarray-Based Gene Expression Analysis, Agilent Technologies). Briefly, for each hybridization 600 ng of Cy3-cRNA were added to 5 µl of 10x Blocking Agent, 1 µl of 25x Fragmentation Buffer in a 25 µl reaction and incubated at 60ºC for 30 minutes to fragment RNA, and stopped with 25 µl 2xHybridization Buffer. The samples were placed on ice and quickly loaded onto arrays, hybridized at 65ºC for 17 hours and then washed once in GE wash buffer 1 at room temperature (1 minute) and once in GE Wash Buffer 2 at 37ºC (1 minute). Arrays were drained by centrifugation at 2000 rpm for 2 minutes.

scan_protocol: Images for the Cy3 channel were captured with an Agilent DNA Microarray Scanner at a resolution of 2 µm, and spots quantified using Agilent Feature Extraction Software.

data_processing: Background correction and quantile normalization of expression data were performed using LIMMA (Smyth and Speed, 2003; Smyth, 2004).  Linear model methods were used for determining differentially expressed genes. Each probe was tested for changes in expression over replicates by using an empirical Bayes moderated t-statistic (Smyth, 2004).

source_name: 3 days, SPCHPPP, DMSO, rep2

label_protocol: Total RNA (500 ng each) was amplified and Cyanine 3- (Cy3-) labeled using One-Color Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer´s instructions. Briefly, total RNA was converted into double stranded cDNA using oligo-dT-T7 primer and AffinityScript Reverse Transcriptase. cDNA was then used as template for in vitro transcription reaction with T7 RNA polymerase and incorporated Cy3-CTP. Cy3-labelled cRNA was purified with RNeasy columns (Qiagen) and RNA yield and Cy3 incorporation measured in a Nanodrop spectrophotometer (Nanodrop Technologies)

growth_protocol: Seeds were surface-sterilized using overnight exposure to chlorine gas (Clough and Bent, 1998) and sowed in MS medium supplemented with 1% sucrose. After a 2 days stratification period at 4ºC in the dark, plates were placed at 21ºC and 16-h light photoperiod with 70 µmol m-2 s-1 of photosynthetically active radiation (PAR) for three days.

extract_protocol: RNA was obtained from 50 seedlings collected 3 days after sowing. Samples from 3 independent biological replicates were frozen in liquid nitrogen and RNA was extracted with Trizol® (Invitrogen), followed by column purification using High Pure RNA extraction kit (Roche Diagnostics). RNA quality was determined with electrophoresis analysis with an Agilent 2100 Bioanalyzer.

treatment_protocol: 50 nM Brassinolide (E1641 , Sigma) or an equivalent volume of DMSO (D8418, Sigma)

value: seedling

value: 3 days-old

tag: genotype

value: SPCHPPP


title: HC020

description: Whole blood transcriptome of Healthy control 020

source_name: Whole blood of Healthy control 020


title: SPCHPPP DMSO rep1

description:
gene expression of SPCHPPP seedlings after 3-days growth on mock medium
PD1

source_name: 3 days, SPCHPPP, DMSO, rep1


title: HC012

description: Whole blood transcriptome of Healthy control 012

source_name: Whole blood of Healthy control 012


title: HC014

description: Whole blood transcriptome of Healthy control 014

source_name: Whole blood of Healthy control 014


title: spch-5 BL rep3

description:
gene expression of spch-5 seedlings after 3-days growth on BL medium
5B3

source_name: 3 days, spch-5, BL, rep3


title: SPCHPPP BL rep1

description:
gene expression of SPCHPPP seedlings after 3-days growth on BL medium
PB1

source_name: 3 days, SPCHPPP, BL, rep1


title: SPCHPPP BL rep2

description:
gene expression of SPCHPPP seedlings after 3-days growth on mock medium
PB2

source_name: 3 days, SPCHPPP, BL, rep2


title: HC010

description: Whole blood transcriptome of Healthy control 010

source_name: Whole blood of Healthy control 010


title: HC013

description: Whole blood transcriptome of Healthy control 013

source_name: Whole blood of Healthy control 013


title: HC027

description: Whole blood transcriptome of Healthy control 027

source_name: Whole blood of Healthy control 027


title: HC015

description: Whole blood transcriptome of Healthy control 015

source_name: Whole blood of Healthy control 015


title: HC011

description: Whole blood transcriptome of Healthy control 011

source_name: Whole blood of Healthy control 011


title: HC018

description: Whole blood transcriptome of Healthy control 018

source_name: Whole blood of Healthy control 018


title: HC009

description: Whole blood transcriptome of Healthy control 009

source_name: Whole blood of Healthy control 009


title: Tumor_mtCK1dP66TR69K_rep3

city: Ulm

first: Uwe

last: Knippschild

address: Albert-Einstein-Allee 23

department: General and Visceral Surgery

institute: University Hospital Ulm

description:
mtCK1dP66TR69K_3
Gene expression data from tumors induced by HT29 expressing mtCK1dP66TR69K.

hyb_protocol: Affymetrix Human Gene 1.0 ST Arrays according to Whole Transcript (WT) Sense Target Labeling Assay.

scan_protocol: According to Affymetrix protocols using a GeneChip 3000 Scanner.

data_processing: Affymetrix® Expression Console™ Software for normalization, BRB Array Tools for statistical analysis.

source_name: Tumor induced by HT29 expressing mtCK1dP66TR69K

label_protocol: Affymetrix Whole Transcript (WT) Sense Target Labeling Assay.

growth_protocol: Mice were kept under barrier conditions with a 12 h light/dark cycle and access to food and water ad libitum for 27 days.

extract_protocol: Total RNA was isolated from frozen tumor tissue using the RNeasy Mini Kit (Qiagen, Hilden, Germany) protocol as described by the manufacturer.

treatment_protocol: 5x10^6 cells of HT29 cells stably expressing vector alone or different CK1δ point mutations were resuspended in 200 µl of DPBS and injected subcutaneously into the dorsolateral site of 6- to 8-week-old BALB/C athymic mice. Animals were regularly monitored for tumor formation and were sacrificed by asphyxiation with CO2 27 days after injection. Tumors were excised, measured, weighed, and fixed in formalin or shock frozen. Tumor volume was calculated according to the formula for a rotational ellipsoid (length x height x width x 0.5236).

tag: cell line

value: stably expressing mtCK1dP66TR69K

tag: strain/background of injected mice

value: athymic BALB/c Nude-Foxn1nu

value: tumor induced by xenograft


title: Tumor_ctrl_rep3

description:
empty vector_ctrl_3
Gene expression data from tumors induced by HT29 expressing empty vector.

source_name: Tumor induced by HT29 expressing empty vector

tag: genotype/variation

value: stably expressing empty vector


title: Tumor_ctrl_rep2

description:
empty vector_ctrl_2
Gene expression data from tumors induced by HT29 expressing empty vector.


title: spch-5 DMSO rep3

description:
gene expression of spch-5 seedlings after 3-days growth on mock medium
5D3

source_name: 3 days, spch-5, DMSO, rep3


title: spch-5 BL rep2

description:
gene expression of spch-5 seedlings after 3-days growth on BL medium
5B2

source_name: 3 days, spch-5, BL, rep2


title: spch-5 BL rep1

description:
gene expression of spch-5 seedlings after 3-days growth on BL medium
5B1

source_name: 3 days, spch-5, BL, rep1


title: Tumor_ctrl_rep1

description:
empty vector_ctrl_1
Gene expression data from tumors induced by HT29 expressing empty vector.


title: Tumor_mtCK1dP66TR69K_rep2

description:
mtCK1dP66TR69K_2
Gene expression data from tumors induced by HT29 expressing mtCK1dP66TR69K.


title: Col-0 BL rep3

description:
gene expression of Col-0 seedlings after 3-days growth on BL medium
CB3

source_name: 3 days, Col-0, BL, rep2


title: HC006

description: Whole blood transcriptome of Healthy control 006

source_name: Whole blood of Healthy control 006


title: spch-5 DMSO rep1

description:
gene expression of spch-5 seedlings after 3-days growth on mock medium
5D1

source_name: 3 days, spch-5, DMSO, rep1


title: HC008

description: Whole blood transcriptome of Healthy control 008

source_name: Whole blood of Healthy control 008


title: HC007

description: Whole blood transcriptome of Healthy control 007

source_name: Whole blood of Healthy control 007


title: Tumor_mtCK1dT67S_rep3

description:
mtCK1dT67S_3
Gene expression data from tumors induced by HT29 expressing mtCK1dT67S.

source_name: Tumor induced by HT29 expressing mtCK1dT67S

value: stably expressing mtCK1dT67S


title: HC002

description: Whole blood transcriptome of Healthy control 002

source_name: Whole blood of Healthy control 002


title: Col-0 DMSO rep1

description:
gene expression of Col-0 seedlings after 3-days growth on mock medium
CD1

source_name: 3 days, Col-0, DMSO, rep1


title: Tumor_mtCK1dP66TR69K_rep1

description:
mtCK1dP66TR69K_1
Gene expression data from tumors induced by HT29 expressing mtCK1dP66TR69K.


title: Col-0 BL rep1

description:
gene expression of Col-0 seedlings after 3-days growth on BL medium
CB1

source_name: 3 days, Col-0, BL, rep1


title: Tumor_mtCK1dI68N_rep2

description:
mtCK1dI68N_2
Gene expression data from tumors induced by HT29 expressing mtCK1dI68N.

source_name: Tumor induced by HT29 expressing mtCK1dI68N

value: stably expressing mtCK1dI68N


title: Tumor_mtCK1dT67S_rep1

description:
mtCK1dT67S_1
Gene expression data from tumors induced by HT29 expressing mtCK1dT67S.


title: Col-0 BL rep2

description:
gene expression of Col-0 seedlings after 3-days growth on BL medium
CB2


title: Col-0 DMSO rep2

description:
gene expression of Col-0 seedlings after 3-days growth on mock medium
CD2

source_name: 3 days, Col-0, DMSO, rep2


title: Tumor_mtCK1dT67S_rep2

description:
mtCK1dT67S_2
Gene expression data from tumors induced by HT29 expressing mtCK1dT67S.


title: Tumor_mtCK1dI68N_rep3

description:
mtCK1dI68N_3
Gene expression data from tumors induced by HT29 expressing mtCK1dI68N.


title: HC001

description: Whole blood transcriptome of Healthy control 001

source_name: Whole blood of Healthy control 001


title: HC005

description: Whole blood transcriptome of Healthy control 005

source_name: Whole blood of Healthy control 005


title: HC003

description: Whole blood transcriptome of Healthy control 003

source_name: Whole blood of Healthy control 003


title: Col-0 DMSO rep3

description:
gene expression of Col-0 seedlings after 3-days growth on mock medium
CD3


title: HC004

description: Whole blood transcriptome of Healthy control 004

source_name: Whole blood of Healthy control 004


title: Tumor_mtCK1dI68N_rep1

description:
mtCK1dI68N_1
Gene expression data from tumors induced by HT29 expressing mtCK1dI68N.


title: Huvec RS Single Donor

status: Public on May 18 2017

city: Barcelona

first: Francesco

last: Prattichizzo

address: Carrer del Rossellò 149

institute: IDIBAPS

description:
Test
SAMPLE 7

data_processing: For the normalization we used the average of two housekeeping genes: HPRT1 and RPL0. Fold Change file reports test/control (HG/NG and RS/NG) ratios.

label: SYBR Green

growth_protocol: Human umbilical vein endothelial primary cells (HUVECs) were cultured with EGM™-2 Bulletkit™, adding supplemental growth factors: Epidermal Growth Factor (hEGF), Hydrocortisone, human recombinant Fibroblast Growth Factor-Beta (hFGF-b), Heparin, 2% Fetal Bovine Serum (FBS), and Gentamicin/Amphotericin-B (GA), provided with the media, at 37ºC in a humidified atmosphere with 5% CO2.

extract_protocol: Total RNA was purified from HUVECs using Norgen Biotek RNA purification kit according to the manufacturer’s instructions.

treatment_protocol: HUVECs were treated with high glucose (25 mM) condition for one week or sub-cultured until replicative exhaustion

value: Umbilical vein endothelial primary cells

tag: treatment

value: Normal glucose

tag: cpd


title: Huvec RS Pool 1

description:
Test
SAMPLE 8

source_name: Human umbilical vein endothelial primary cells


title: Huvec HG Pool 2

description:
Test
SAMPLE 6

value: High glucose


title: Huvec HG Pool 1

description:
Test
SAMPLE 5


title: Huvec RS Pool 2

description:
Test
SAMPLE 9


title: Huvec NG Pool 2

description:
Control
SAMPLE 3


title: Huvec NG Pool 1

description:
Control
SAMPLE 2


title: Huvec NG Single donor

description:
Control
SAMPLE 1


title: Huvec HG Single Donor

description:
Test
SAMPLE 4


title: Zur_MT_rep2

city: Seoul

first: Kanglok

last: Lee

address: 1 Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

description: Chip-chip M145 Zur

hyb_protocol: 4 ug of labelled DNA were hybridized on 385K NimbleGen custom arrays according to NimbleGen's protocol.

scan_protocol: Arrays were scanned on an Axon 4000B scanner according to the manufacturer's protocol.

data_processing:
Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction. The signal from the zur mutant ChIP was subtracted from the signals from the wild-type ChIP after normalization to remove non-specific signal.
Normalized log2 ratio of Zur ChIP signal over genomic DNA control

organism: Streptomyces coelicolor

source_name: Input DNA from M145

label_protocol: Before labelling, the ChIP DNA was amplified using ligation mediated PCR. 1 ug of DNA was labelled using the NimbleGen Dual-color DNA labelling Kit (05223547001) according to the manufacturer's protoco

growth_protocol: S. coelicolor cells were grown to exponential phase (OD~0.3)

extract_protocol: Cells were fixed with 1% formaldehyde in culture medium for 4 minutes at 30°C followed by quenching with 0.125 M clycine for 30 minutes on ice. The cells were washed twice with ice cold PBS, frozen in dry/ethanol bath and stored at -80°C. Cells were resuspended in 500uL IP buffer (100 mM Tris pH 8, 300 mM NaCl, 2% TritinX-100), and sonicated for 20 seconds 8 times to shear the DNA to fragments of 1 kbp in average. 50 units of micrococcal DNase and 0.5ug of RNaseA were added to the lysate and incubated for 1 hour at 4°C to reduce fragment size to 500 bp in avergage and degrade RNA. To stop the nucleases EDTA was added to 10mM final concentration. The lysate was cenrtrifuged to remove cell debris and 100 uL was saved for Input DNA. The lysate was was incubated without any antibodies at 4°C over night as a mock immuno-precipitation step to obtain the control DNA. Then, ProteinA coated sepharose beads were added to the lysate, which was incubated for another 3 hours. Beads were centrifuged from the sample and discarded. The remaining DNA in solution was cleaned using QIAGen DNA purification kit.

value: M145 delta  zur

tag: strain

tag: chip antibody

value: None; Input DNA

value: Zur


title: Zur_WT_rep2

description: Chip-chip M145 Zur


title: Zur_MT_rep3

description: Chip-chip M145 Zur


title: Muscle of trout fasted for 30 days and then refed for 36 days, sample 1

city: Rennes

first: Aurelie

last: LE CAM

address: Campus de Beaulieu

department: PHASE

country: France

institute: INRA

hyb_protocol: 600ng of labelled cRNA was then fragmented in the appropriate buffer (Agilent) for 30 min at 60°C before dilution (v/v) in hybridization buffer. Hybridizations were performed in a microarray hybridization oven (Agilent) overnight at 65°C, using three high-density oligonucleotide microarray slides.  Following hybridization, the slides were rinsed in gene expression wash buffers 1 and 2 (Agilent)

scan_protocol: Microarrays were scanned with an Agilent Scanner (Agilent DNA Microarray Scanner, Agilent Technologies, Massy, France) using the standard parameters for a gene expression 8x60K oligoarray (3µm and 20bits)

data_processing: Data were then obtained with the Agilent Feature Extraction software (10.7.3.1) according to the appropriate GE protocol (GE1_107_Sep09). Normalization and statistical analysis were performed using GeneSpring software (Agilent).

organism: Oncorhynchus mykiss

label_protocol: 150ng of total RNA was labelled with Cy3 according to the manufacturer’s instructions (Agilent). Briefly, RNA was first reverse transcribed, using a polydTT7 primer, Cy3 was incorporated by a T7 polymerase mediated transcription and excess dye was removed using an RNeasy kit (Quiagen). The level of dye incorporation was evaluated using a spectrophotometer (Nanodrop ND1000, LabTech).

extract_protocol: A transverse slice of fast muscle situated just beneath the dorsal fin was taken for RNA extraction.

treatment_protocol: At the beginning of the experiment fish weighing 132 grams ± 6.0  were randomly distributed in two groups: a fasted group that was composed of trout that were deprived of food for and a control group that was composed of trout that were normally fed to satiation (n=10). Refed groups were composed of fasted trout collected after a 30 days fasting period and refed at a rate three time higher than the normal ration. Sampling included (i) trout of the fasted group sacrificed 30 days after the beginning of the experiment (termed F0), (ii) trout of the normally fed (control) group also sacrificed 30 days after the beginning of the experiment (termed C0) and (iii) refed trout sacrificed sequentially at 4, 11 and 36 days post-refeeding (termed RF4, RF11 and RF36 respectively)

tag: time-course


title: Muscle of trout fasted for 30 days and then refed for 11 days, sample 4


title: Zur_WT_rep3

description: Chip-chip M145 Zur


title: deltaZur_chip_rep1

description: Chip-chip M145 Zur


title: Muscle of trout fasted for 30 days and then refed for 4 days, sample 5


title: Muscle of control trout normally fed, sample 2

source_name: Muscle of control trout normally fed


title: Muscle of trout fasted for 30 days and then refed for 4 days, sample 3


title: Muscle of control trout normally fed, sample 4


title: WT_Zur_chip_rep1

description: Chip-chip M145 Zur


title: Muscle of trout fasted for 30 days and then refed for 11 days, sample 6


title: Muscle of trout fasted for 30 days and then refed for 36 days, sample 2


title: Muscle of control trout normally fed, sample 3


title: Muscle of trout fasted for 30 days and then refed for 11 days, sample 5


title: Muscle of control trout normally fed, sample 1


title: Muscle of trout fasted for 30 days and then refed for 11 days, sample 1


title: Muscle of trout fasted for 30 days and then refed for 36 days, sample 3


title: Muscle of trout fasted for 30 days and then refed for 4 days, sample 7


title: Muscle of trout fasted for 30 days and then refed for 11 days, sample 2


title: Muscle of trout fasted for 30 days and then refed for 4 days, sample 2


title: Muscle of trout fasted for 30 days, sample 7

source_name: Muscle of trout fasted for 30 days


title: Muscle of trout fasted for 30 days, sample 5


title: Muscle of trout fasted for 30 days, sample 4


title: Muscle of trout fasted for 30 days and then refed for 4 days, sample 4


title: Muscle of trout fasted for 30 days, sample 3


title: Muscle of trout fasted for 30 days and then refed for 36 days, sample 4


title: 12 month-564 Igi-rep4

first: Chong-Su

last: Kim

address: Gwanak-ro 1, Gwanak-gu

department: Food and nutrition

institute: Seoul national university

hyb_protocol: Chips were prehybridized in a sealed chamber immersed in a 42°C waterbath using established procedures.Chips were then washed twice for 2 min with agitation, first in ultra-pure water, then in isopropyl alcohol. After the last isopropyl alcohol wash, samples were quickly placed in a room-temperature centrifuge and spun dry (3000 rmp, 5 min). The chips were hybridized overnight in a sealed humidified slide chamber immersed in a light-protected 42°C waterbath, then washed, dried, and stored in the dark until scanned.

scan_protocol: Chips were scanned using an Axon 4000B scanner and GenePix 4.0 software. Photomultiplier tube voltage settings were adjusted to allow 1% saturation of signal in both channels.

data_processing: Image data were extracted, and extracted data were normalized with lowess smoothing function.

source_name: 12 month-564 Igi

label_protocol: Labeling RNA,(one for Cy3 and one for Cy5) using dUTP-Cy3 OR dUTP Cy5 by incubating reverse transcription reaction mixture at 42°C for 90 min, followed by degrading RNA and cleaning up labeled cDNA.

growth_protocol: 564+/- and C57BL/6J (B6) control mice were bred and maintained at the National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH).

extract_protocol: Isolate RNA using Trizol Reagent and clean up RNAs with Qiagen Rnase kit

treatment_protocol: 564+/- mice were crossed to generate mice homozygous for the knockins at both loci (here termed 564+/+ mice) that were used for all studies of this strain. A part of the 564+/+ mouse colony was bred and maintained on water supplemented with Ampicillin (1mg/ml; Sigma), Metronidazole (1mg/ml; Sigma), Neomycin (1mg/ml; Sigma) and Vancomycin (500mg/ml; Hospira). All mice used in this study were maintained under specific pathogen free conditions.

tag: strain background

value: female

tag: age

value: 12 months

value: spleen

source_name: Reference RNA

tag: sample type

value: Universal reference RNA


title: 12 month-564 Igi-rep3


title: spch-5 DMSO rep2

description:
gene expression of spch-5 seedlings after 3-days growth on mock medium
5D2

source_name: 3 days, spch-5, DMSO, rep2

value: seedling

value: 3 days-old


title: 12 month-564 Igi-rep2


title: 4 month-564 Igi-rep2

source_name: 4 month-564 Igi

value: 4 months


title: 4 month-564 Igi-rep3


title: AdultTestes hs-Bam; ;bam[1]/bam[delta86], 48 hours post heat shock

city: Ithaca

first: Jongmin

middle: J

state: NY

address: 930 Campus Road

department: Biomedical Sciences

institute: Cornell University

description: Adult testes from  hs-Bam; ;bam[1]/bam[delta86] flies after 48 hours from applying a pulse of 30 minutes, 37C heat shock. Representing spermatocytes progressing into terminal differentiation and started to express hundreds of testis-specific differentiation transcripts.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Data were background adjusted and normalized using R program (v3.0.2) with the BioConductor package GCRMA.

organism: Drosophila melanogaster

source_name: adult testes without accessory glands

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from ~250ng total RNA (GeneChip 3' IVT expression kit)

growth_protocol: Crosses and experimental flies were grown on cornmeal and molasses media at 25 °C except the lines having bam-gal4 transgene, which were grown at 30 °C

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

treatment_protocol: Testes with or without heat shock treatment were dissected in PBS and immediately frozen in liquid nitrogen before transferred to -80°C for longer stroage. Total RNA was extracted using TRIzol (Invitrogen).  RNA quality was assessed by checking rRNA integrity using Bioanalyzer. ~250ngs of total RNA was processed for each replicate.

value: testes


title: 4 month-564 Igi-rep1


title: AdultTestes hs-Bam; ;bam[1]/bam[delta86], 24 hours post heat shock, rep1

growth_protocol: Crosses and experimental flies were grown on cornmeal and molasses media at 25 °C

value: Adult testes

value: hs-Bam; ;bam[1]/bam[delta86] flies after 24 hours from applying a pulse of 30 minutes, 37C heat shock. Representing your spermatocytes initiating terminal differentiation.


title: AdultTestes hs-Bam; ;bam[1]/bam[delta86], no heat shock, rep1

value: hs-Bam; ;bam[1]/bam[delta86] flies without heat shock. Representing proliferating spermatogonia.


title: Muscle of trout fasted for 30 days, sample 2


title: 4 month-C57BL/6-rep1

source_name: 4 month-C57BL/6

value: wild type control


title: 4 month-C57BL/6-rep2


title: AdultTestes hs-Bam; ;bam[1]/bam[delta86], no heat shock, rep2


title: 12 month-564 Igi-rep1


title: 8 month-564 Igi-rep2

source_name: 8 month-564 Igi

value: 8 months


title: AdultTestes w; ;bam[1]/bam[delta86], no heat shock

value: w; ;bam[1]/bam[delta86] flies without heat shock.  This sample is a negative control to exclude gene expression changes based on just heat shock response.


title: AdultTestes w; ;bam[1]/bam[delta86], 24 hours pos heat shock

value: w; ;bam[1]/bam[delta86] flies after 24 hours from applying a pulse of 30 minutes, 37C heat shock. This samples is a negative control to exclude gene expression changes based on just heat shock response.


title: 8 month-564 Igi-rep3


title: AdultTestes hs-Bam; ;bam[1]/bam[delta86], 24 hours post heat shock, rep2


title: AdultTestes_UAS-RNAi-dMi-2 (VDRC# 107204); TM6b_rep1

data_processing: Data were background adjusted and normalized using R program (v3.0.2) with the BioConductor package GCRMA. Samples in the following data were normalized together with bam-/-, aly-/-, sa-/-, wild-type data from GSE28728. All values are log2 transformed.

source_name: adult testes without seminal vesicles and accessory glands

growth_protocol: Crosses and experimental flies were grown on cornmeal and molasses media at 30 °C

treatment_protocol: kmg ctrl, kmg KD, kmg KD; aly-/-; dMi-2 ctrl, and dMi-2 KD testes without seminal vesicle and accessory glands were dissected in PBS for 30 minutes and immediately frozen in liquid nitrogen before transferred to -80°C. Total RNA was extracted using TRIzol (Invitrogen).  RNA quality was assessed by checking rRNA integrity using Bioanalyzer. ~250ngs of total RNA was processed for each replicate.

value: adult testes

value: UAS-RNAi-dMi-2 (VDRC# 107204); TM6b flies 0~1 day post eclosion


title: AdultTestes_UAS-RNAi-dMi-2 (VDRC# 107204); bam-gal4, UAS-dicer2_rep2

value: UAS-RNAi-dMi-2 (VDRC# 107204); bam-gal4, UAS-dicer2 flies 0~1 day post eclosion


title: AdultTestes_UAS-RNAi-kmg(VDRC# 107395); bam-gal4, aly[2]/aly[5p]_rep1

value: UAS-RNAi-kmg(VDRC# 107395); bam-gal4, aly[2]/aly[5p] flies 0~1 day post eclosion


title: AdultTestes_UAS-RNAi-kmg (VDRC# 107395); TM6b_rep1

value: UAS-RNAi-kmg (VDRC# 107395); TM6b flies 0~1 day post eclosion


title: AdultTestes_UAS-RNAi-kmg(VDRC# 107395); bam-gal4, aly[2]/aly[5p]_rep2


title: AdultTestes_UAS-RNAi-dMi-2 (VDRC# 107204); bam-gal4, UAS-dicer2_rep1


title: AdultTestes_UAS-RNAi-dMi-2 (VDRC# 107204); TM6b_rep2


title: AdultTestes_UAS-RNAi-kmg (VDRC# 107395); bam-gal4, UAS-dicer2_rep1

value: UAS-RNAi-kmg (VDRC# 107395); bam-gal4, UAS-dicer2 flies 0~1 day post eclosion


title: AdultTestes_UAS-RNAi-kmg (VDRC# 107395); bam-gal4, UAS-dicer2_rep2


title: AdultTestes_UAS-RNAi-kmg (VDRC# 107395); TM6b_rep2


title: 8 month-564 Igi-rep1

value: female

value: spleen

value: Universal reference RNA


title: Case5_CGH

city: San Francisco

first: Iwei

last: Yeh

state: California

address: 1701 Divisadero St. Ste 280

department: Dermatology

institute: UCSF

hyb_protocol: After the labelling process the refernce and the sample DNA are cleaned to remove unused primers and unincorporated dyes. Then the sample and the reference DNA are combined together and incubated in a hybridization mix containing Cot-1 and bolcking agents. This mixture is hybridized onto an Agilent catalog 4X180K array (Agilent Technologies). The array is hybridized in a hybridization oven for 40hrs at 65°C.  After the hybridization, the array is washed and scanned according to the manufacturer’s protocol.

scan_protocol: The arrays are scanned at 3µ using the DNA Microarray Scanner with SureScan - High Resolution Technology (Agilent Technologies). The tiff image generated is processed thru feature extraction software 12.0.0.7 (Agilent Technologies) to generate raw data. .

data_processing: The raw data is analyzed using NEXUS (Biodiscovery ) and Cytogenomics (Agilent Technologies) software. The log2ratio is calculated with Cy5 (tumor) as the numerator and Cy3 (normal) as the denominator

label_protocol: 1ug of reference and sample DNA was labeled with CY3/CY5 dyes respectively using the Bioprime Total FFPE genomic labeling system (Life Technologies) according to manufacturer's protocol.

extract_protocol: Manual micro-dissection of the tumor bearing region was performed on 5-10-µm paraffin sections using a stereo-microscope to avoid significant normal cell contamination. DNA was extracted using phenol-chloroform extraction method.

tag: diagnosis

value: probable Spitz nevus

tag: age (yrs)

value: male

tag: ntrk3 fusion

tag: tumor stage

value: primary

source_name: reference DNA

tag: source

value: Male DNA from Promega (Cat # G1471)


title: Case8_CGH

value: atypical Spitz tumor

tag: gender


title: Case7_CGH


title: Case6_CGH


title: Case4_CGH


title: Case3_CGH


title: Case2_CGH


title: saliva derived genomic DNA [SA1022]

description: saliva sample

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation450 BeadChip using standard Illumina protocol

data_processing: Illumina GenomeStudio 2011.1 software

source_name: Oragene saliva

tag: batch

tag: european ancestry

tag: bantu ancestry


title: saliva derived genomic DNA [SA1039]

description: saliva sample


title: saliva derived genomic DNA [SA004rep]

description: saliva sample


title: Case1_CGH

value: Spitz nevus with unusual features


title: saliva derived genomic DNA [SA064]

description: saliva sample


title: Parsi2

city: Tartu

first: Tuuli

last: Reisberg

address: Riia 23

country: Estonia

institute: University of Tartu

description: Genomic DNA extracted from blood was genotyped using Human660W-Quad v1.0 Genotyping BeadChip (Illumina).

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48°C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining, BeadChip arrays were coated with XC4/ethanol, dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing: Image data was analyzed using GenomeStudio v2011.1 with GT module 1.9.4 (Illumina).

label: Cy3, Cy5

source_name: Blood

label_protocol: 200ng of genomic DNA was whole-genome amplified in an overnight reaction at 37°C using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation, the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

extract_protocol: Extraction of genomic DNA from blood was performed using standard extraction protocols.

tag: tissue

value: Blood

tag: population

value: Parsi

tag: region

value: India


title: Parsi34


title: Parsi26


title: Parsi8


title: Parsi24


title: Parsi11


title: saliva derived genomic DNA [SA1023]

description: saliva sample


title: saliva derived genomic DNA [SA1015]

description: saliva sample


title: Parsi4


title: saliva derived genomic DNA [SA1028]

description: saliva sample


title: saliva derived genomic DNA [SA1010]

description: saliva sample


title: Parsi7


title: saliva derived genomic DNA [SA095]

description: saliva sample


title: ParsiZ178


title: ParsiZ183


title: Parsi13


title: ParsiZ185


title: saliva derived genomic DNA [SA1027]

description: saliva sample


title: ParsiZ181


title: saliva derived genomic DNA [SA086]

description: saliva sample


title: Parsi10


title: ParsiZ177


title: ParsiZ180


title: saliva derived genomic DNA [SA1025]

description: saliva sample


title: ParsiZ179


title: saliva derived genomic DNA [SA1030]

description: saliva sample


title: ParsiZ186


title: ParsiZ182


title: saliva derived genomic DNA [SA022]

description: saliva sample


title: saliva derived genomic DNA [SA072]

description: saliva sample


title: saliva derived genomic DNA [SA1009]

description: saliva sample


title: saliva derived genomic DNA [SA1000]

description: saliva sample


title: saliva derived genomic DNA [SA068]

description: saliva sample


title: saliva derived genomic DNA [SA1006]

description: saliva sample


title: saliva derived genomic DNA [SA080]

description: saliva sample


title: saliva derived genomic DNA [SA069]

description: saliva sample


title: saliva derived genomic DNA [SA1041]

description: saliva sample


title: saliva derived genomic DNA [SA074]

description: saliva sample


title: saliva derived genomic DNA [SA1029]

description: saliva sample


title: saliva derived genomic DNA [SA032]

description: saliva sample


title: saliva derived genomic DNA [SA063]

description: saliva sample


title: saliva derived genomic DNA [SA1011]

description: saliva sample


title: saliva derived genomic DNA [SA1019]

description: saliva sample


title: saliva derived genomic DNA [SA085]

description: saliva sample


title: saliva derived genomic DNA [SA019]

description: saliva sample


title: saliva derived genomic DNA [SA1013]

description: saliva sample


title: saliva derived genomic DNA [SA004]

description: saliva sample