title: haploid parthenogenetic blastocysts_ES2_cnv

city: shanghai

first: cuiqing

last: zhong

address: yueyang road 320

institute: institute of biochemistry and cell biology

description: haploid parthenogenetic blastocysts_ES2

hyb_protocol: Prepare hybridization buffers and perform array hybridization at 50℃ in Hybridization Over (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US). After 16 hours hybridization, arrays were washed in Fluidics Station (Cat#00-0079, Affymetrix, Santa Clara, CA, US) according to Affymetrix CytoScan™ Assay User Manual (Cat#703038 Rev. 3, Affymetrix, Santa Clara, CA, US).

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

data_processing: Raw data passed quality control were further analyzed by Affymetrix® Chromosome Analysis Suite (Affymetrix, Santa Clara, CA, US) .

source_name: ESCs from haploid parthenogenetic blastocysts

label_protocol: Sample DNA was digested by restriction enzymes NspI, adaptors were ligated to the fragment DNA to perform a PCR amplification. Amplified DNA was labeled and further fragmented using Affymetrix Cytoscan HD array kit and reagent kit bundle, (Cat#901835, Affymetrix, Santa Clara, CA,US) followed the manufacturer’s instruction Affymetrix CytoScan™ Assay User Manual (Cat#703038 Rev. 3, Affymetrix, Santa Clara, CA, US) to obtain biotin labeled DNA.

growth_protocol: human ESCs were cultured on feeder in human ES medium supplemented with 10μM Y-27635

extract_protocol: Sample DNA was extracted using DNeasy Blood &Tissue Kit (Cat#69506, QIAGEN, GmBH, Germany), following the manufacturer’s instructions. We use Nano Drop (Cat#ND-1000, Thermo Fisher, Waltham, MA, US) and run a 1% agarose gel electrophoresis to check the quantity and quality of purified DNA.

treatment_protocol: ESCs were washed with DPBS and trypsinizd with Accutase and collected by centrifugation.


title: human_embryonic_stem_cells_rep3

status: Public on Jul 13 2016

type: RNA

city: San Diego

first: Laurence

middle: M.

last: Brill

state: CA

address: 10420 Wateridge Circle

country: USA

institute: Intertek Pharmaceutical Services

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation in GenomeStudio (v.2010.2.0.25786).

molecule: total RNA

organism: Homo sapiens

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

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

tag: cell type

value: Pluripotent WA-09 cells


title: haploid parthenogenetic blastocysts_ES1_cnv

type: genomic

country: China

description: haploid parthenogenetic blastocysts_ES1

label: Biotin

molecule: genomic DNA

tag: gender

value: female


title: Irs-1+/+ mice

city: Changsha

first: Hou-De

last: Zhou

state: Hunan

address: Renmin middle road 139

department: Department of Metabolism & Endocrinology

institute: The Second Xiangya Hospital, Central South University

hyb_protocol: The Hy3TM-labeled samples were hybridized on the miRCURYTM LNA Array (Exiqon) according to array manual.

scan_protocol: The slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing: Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities >=50 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, differentially expressed miRNAs with statistical significance were identified through Volcano Plot filtering.

organism: Mus musculus

source_name: skeletal stem cells, Irs-1+/+

label_protocol: The miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer's guideline for miRNA labelling.

growth_protocol:
Experimental animals were male and commercially available C57BL/6 mice (SLAC, Shanghai, China).
All mice were raised in pathogen-free room and the room was maintained at a constant temperature of 23±1℃ with a 12 h light/dark cycle. Food and water were available ad libitum in the home cages.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer's instructions, which efficiently recovered all RNA species, including miRNAs. RNA quality and quantity were measured by using Nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis.

treatment_protocol: Mice were deeply anesthetized with pentobarbital sodium and then femurs were rapidly dissected from the body. Each end of the bone was cut off, and the bone marrow was expelled by spraying a jet of PBS from a syringe. The liquid containing the skeletal stem cells was collected in polypropylene tubes and centrifuged for 10 min. The supernatant was discarded, and the cells were washed twice with PBS, transferred into 60-mm dishes, and cultured at 37°C for 14 days.

tag: strain/background

tag: genotype/variation

value: skeletal stem cells

tag: age

value: 8 weeks

tag: Sex

value: male


title: Caco-2 ZG16p rep2

city: Bunkyo-ku

first: Kyoko

last: Kojima-Aikawa

state: Tokyo

address: 2-1-1 Otsuka

department: Faculty of Core Research, Natural Science Division

country: Japan

institute: Ochanomizu University

description: Test

data_processing:
All the data analyses were performed according to the manufacturers' instructions using their web-based software package: http://pcrdataanalysis.sabiosciences.com/pcr/arrayanalysis.php
For the normalization, the average of five housekeeping genes, ACTB, B2M, GAPDH, HPRT1 and RPLP0, was used. Target gene signals were normalized to housekeeping genes; 2^-ΔCt, where ΔCt = (Ct_Target - Ct_HKG).
The web-based software package automatically performed all ΔΔCt based fold-change calculations and statistical analysis from the uploaded raw threshold cycle data. Fold change worksheet reports test/control (i.e., ZG16p/PBS) ratio.

label: SYBR Green

label_protocol: PCR assays were performed using the Human Cell Cycle RT2 Profiler PCR Array (SABiosciences) following the manufacturer's instructions. Reverse transcription was performed from 1 μg total RNA using the RT2 First Strand Kit (SABiosciences). Quantitative real-time PCR were performed (StepOnePlus, Applied Biosystems) with a 10-min heat activation of the enzyme at 95 °C, followed by 40 cycles at 95 °C for 15 seconds and 60 °C for 60 seconds.

growth_protocol: Caco-2 cells were grown in DMEM (high glucose) supplemented with 20% FBS and 1% NEAA in a fully humidified incubator with 5% CO2 at 37 °C.

extract_protocol: Total RNA was isolated from Caco-2 cells using illustra RNAspin Mini RNA Isolation Kit (GE Healthcare) following the manufacturer's instructions.

treatment_protocol: Caco-2 cells (8.0 × 10^5 cells/dish) were cultured in 10 cm dishes for 24 h. After washing with the serum-free medium ASF104 supplemented with penicillin and streptomycin, the cells were cultured in ASF104 containing 70 μg/mL Strep-tagII-ZG16p for 72 h. For the control group, the same volume of PBS was added to the medium instead of Strep-tagII-ZG16p solution.

value: colon adenocarcinoma

tag: cell line

tag: passage


title: Caco-2 ZG16p rep1

description: Test


title: Irs-1+/smla mice

source_name: skeletal stem cells, Irs-1+/smla


title: Caco-2 PBS rep1

description: Control


title: Caco-2 PBS rep3

description: Control


title: Irs-1smla/smla mice

description: RNA

source_name: skeletal stem cells, Irs-1smla/smla


title: Caco-2 PBS rep2

description: Control


title: 9422492148_R01C02

city: Cincinnati

first: Scott

middle: M

last: Langevin

state: OH

address: 160 Panzeca Way, ML0056

department: Department of Environmental Health

institute: University of Cincinnati College of Medicine

description:
Packyrs: smoking pack-years = (average packs per day)*(total years of smoking)
Alcohol_consumption: Alcohol consumption in a typical week. 0 = non-drinker; 1 = >0 and < 14 drinks per day; 2 = > 14 drinks per week

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

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

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

source_name: genomic DNA from oral rinse

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted DNeasy blood and tissue kit according to standard instructions

tag: site

value: Oral Rinse

tag: group

value: OPSCC Case

tag: age at diagnosis (years)

tag: packyrs


title: 9422493075_R04C02


title: 9422493041_R06C01


title: SvGRP-transformant_150mM_rep2

status: Public on Jul 12 2016

city: Hachioji

first: Yuichi

last: Tada

address: 1404-1 Katakura

institute: Tokyo University of Technology

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-021169 Arabidopsis 4 Oligo Microarray (V4)  over night at 65°C in a rotating 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 (G2505B) using one color scan setting for 4x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 8 (Agilent) using default parameter to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Arabidopsis thaliana

source_name: SvGRP-seedlings on 150 mM NaCl agar plate

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions.

growth_protocol: Steriled seeds were germinated on 1/2 MS medium for 5 days.

extract_protocol: Total RNA was extracted using Rneasy Plant RNA extraction Kit (Qiagen).

treatment_protocol: Seedlings were transplanted on to 0 or 150 mM NaCl medium and incubated for 24 h.

tag: tissue

value: whole plant


title: SvGRP-transformant_150mM_rep3


title: SvGRP-transformant_150mM_rep1


title: 9422493042_R03C01


title: 9422493067_R06C01


title: 9422493067_R05C02


title: 7507875106_R01C02


title: 9422491028_R04C01


title: 7507875123_R04C01


title: 7507875107_R03C02


title: SvGRP-transformant_0mM_rep2

source_name: SvGRP-seedlings on 0 mM NaCl agar plate


title: 9422493008_R01C02


title: 9422491125_R05C01


title: 9422493042_R03C02


title: WT_150mM_rep2

source_name: WT seedlings on 150 mM NaCl agar plate


title: 7507875123_R05C01


title: WT_0mM_rep3

source_name: WT seedlings on 0 mM NaCl agar plate


title: 7507875106_R03C01


title: 7507875086_R06C02


title: 7507875073_R04C02


title: 7507875133_R04C01


title: 7507875133_R06C02


title: WT_0mM_rep2


title: 7507875115_R02C01


title: WT_0mM_rep1


title: ADI-PEG20 resistant Ju77 cell line rep3

city: London

first: Ai

last: Nagano

state: --- Select a state ---

address: John Vane Science Centre, Charterhouse Square

department: Centre for Molecular Oncology

country: United Kingdom

institute: Barts Cancer Institute

description:
Ju77R_m3
replicate 3

data_processing: The data were normalized with LUMI in R

label: biotin

source_name: malignant mesothelioma cells from human lung

growth_protocol: described by Locke et al 2015 manuscript

extract_protocol: RNA was extracted using the RNeasy kit (Qiagen). Quantification and quality control of RNA was performed on a Nanodrop spectrophotometer (Thermo) and Agilent Bioanalyser (Agilent Technologies), respectively.

tag: resistance

value: ADI-PEG20 resistant


title: SvGRP-transformant_0mM_rep1


title: Parental Ju77 cell line  rep2

description:
Ju77S_m2
replicate 2

treatment_protocol: described by Locke et al 2015 manuscript

value: Parental


title: 9422493042_R04C02


title: Parental Ju77 cell line  rep1

description:
Ju77S_m1
replicate 1


title: 7507875115_R03C02


title: JEG3 placental cell line exposed to Cadmium for 48 hrs 1

city: Chapel Hill

first: Rebecca

middle: Catherine

last: Fry

address: 1213 MHRC

department: Environmental Sciences and Engineering

institute: UNC-Chapel Hill

description:
25uM Cd JEG3 48hr 1
Placental cell line miRNA

hyb_protocol: Following fragmentation, cRNA was hybridized on Agilent Human miRNA Microarray, v16.0

scan_protocol: Microarrays were scanned using Agilent Microarray Scanner

data_processing: The green meidan signal was extracted. Probes that expressed values of 1 deviation from the mean of the negative controls in more than 50% of the samples were removed and data were quantile normalized using Partek Genomic Suite 6.4

source_name: JEG3_Cadmium for 48 hours

label_protocol: Human placental tissues and JEG3 cell extractslabeled cRNA were prepared with Cyanine 3-Cytidine bisphosphate (pCp) reagent according to the standard Agilent protocol

growth_protocol: No growth protocol was used for human placental tissue. For JEG3 placental cell ines cells were gorwn in Dulbecco's Eagle Minimum Essential Media with 10% FBS, sodium pyruvate and penicillin/streptomycin

extract_protocol: For human placental tissue a 0.2 g subsession was cut and miRNAs were extracted using the all prep DNA/RNA/miRNA Universal Kit. For JEG3 placental cell ines  miRNAs were extracted using the all prep DNA/RNA/miRNA Universal Kit.

treatment_protocol: No treatment protocol was used for human placental tissue. For JEG3 placental cell ines CdCl2 was dissolved into the mediua by vortex for a final concentration of 1 uM.

value: placental cell line

tag: exposed to

value: Cadmium for 48 hours

tag: molecule subtype

value: miRNA


title: Placental Tissue_Preeclamptic_subejct_9

description:
Q9
Placental tissue miRNA expression after delivery

source_name: Placental Tissue_Preeclamptic

tag: race

value: African American

tag: subject status

value: Preeclamptic subject

tag: maternal age (yrs)

tag: gestational age (wks)

value: Placental Tissue


title: JEG3 placental cell line exposed to Cadmium for 48 hrs 3

description:
25uM Cd JEG3 48hr 3
Placental cell line miRNA

tag: cell type


title: JEG3 placental cell line unexposed for 48 hrs 1

description:
JEG3 48hr Control 1
Placental cell line miRNA

source_name: JEG3_unexposed for 48 hours

value: none for 48 hrs


title: JEG3 placental cell line unexposed for 48 hrs 2

description:
JEG3 48hr Control 2
Placental cell line miRNA


title: JEG3 placental cell line exposed to Cadmium for 48 hrs 2

description:
25uM Cd JEG3 48hr 2
Placental cell line miRNA


title: JEG3 placental cell line unexposed for 48 hrs 3

description:
JEG3 48hr Control 3
Placental cell line miRNA


title: ADI-PEG20 resistant Ju77 cell line rep2

description:
Ju77R_m2
replicate 2


title: Parental Ju77 cell line  rep3

description:
Ju77S_m3
replicate 3


title: 7507875073_R05C02

value: female


title: Placental Tissue_Preeclamptic_subejct_8

description:
Q8
Placental tissue miRNA expression after delivery

value: Caucasian


title: Placental Tissue_Preeclamptic_subejct_4

description:
Q4
Placental tissue miRNA expression after delivery


title: Placental Tissue_Preeclamptic_subejct_14

description:
Q14
Placental tissue miRNA expression after delivery


title: Placental Tissue_Preeclamptic_subejct_15

description:
Q15
Placental tissue miRNA expression after delivery


title: ADI-PEG20 resistant Ju77 cell line rep1

description:
Ju77R_m1
replicate 1


title: SvGRP-transformant_0mM_rep3

tag: age


title: Placental Tissue_Preeclamptic_subejct_19

description:
Q19
Placental tissue miRNA expression after delivery

value: Other


title: Placental Tissue_Preeclamptic_subejct_13

description:
Q13
Placental tissue miRNA expression after delivery


title: Placental Tissue_Preeclamptic_subejct_6

description:
Q6
Placental tissue miRNA expression after delivery


title: Placental Tissue_Preeclamptic_subejct_18

description:
Q18
Placental tissue miRNA expression after delivery


title: Placental Tissue_Preeclamptic_subejct_11

description:
Q11
Placental tissue miRNA expression after delivery

value: Hispanic


title: WT_150mM_rep3


title: Placental Tissue_Normotensive_Subject_20

description:
P20
Placental tissue miRNA expression after delivery

source_name: Placental Tissue_Normotensive

value: Normotensive subject


title: Placental Tissue_Normotensive_Subject_6

description:
P6
Placental tissue miRNA expression after delivery


title: Placental Tissue_Normotensive_Subject_17

description:
P17
Placental tissue miRNA expression after delivery


title: WT_150mM_rep1


title: Placental Tissue_Preeclamptic_subejct_12

description:
Q12
Placental tissue miRNA expression after delivery


title: Placental Tissue_Preeclamptic_subejct_5

description:
Q5
Placental tissue miRNA expression after delivery


title: Placental Tissue_Preeclamptic_subejct_1

description:
Q1
Placental tissue miRNA expression after delivery


title: Placental Tissue_Normotensive_Subject_15

description:
P15
Placental tissue miRNA expression after delivery


title: Placental Tissue_Preeclamptic_subejct_17

description:
Q17
Placental tissue miRNA expression after delivery


title: Placental Tissue_Normotensive_Subject_1

description:
P1
Placental tissue miRNA expression after delivery


title: Placental Tissue_Normotensive_Subject_7

description:
P7
Placental tissue miRNA expression after delivery


title: Placental Tissue_Normotensive_Subject_16

description:
P16
Placental tissue miRNA expression after delivery


title: Placental Tissue_Normotensive_Subject_2

description:
P2
Placental tissue miRNA expression after delivery


title: Placental Tissue_Normotensive_Subject_4

description:
P4
Placental tissue miRNA expression after delivery


title: Placental Tissue_Normotensive_Subject_10

description:
P10
Placental tissue miRNA expression after delivery


title: Placental Tissue_Normotensive_Subject_12

description:
P12
Placental tissue miRNA expression after delivery


title: Placental Tissue_Normotensive_Subject_13

description:
P13
Placental tissue miRNA expression after delivery


title: Placental Tissue_Preeclamptic_subejct_7

description:
Q7
Placental tissue miRNA expression after delivery


title: Placental Tissue_Normotensive_Subject_11

description:
P11
Placental tissue miRNA expression after delivery


title: Placental Tissue_Preeclamptic_subejct_10

description:
Q10
Placental tissue miRNA expression after delivery


title: Placental Tissue_Normotensive_Subject_19

description:
P19
Placental tissue miRNA expression after delivery


title: Placental Tissue_Normotensive_Subject_5

description:
P5
Placental tissue miRNA expression after delivery


title: Placental Tissue_Normotensive_Subject_18

description:
P18
Placental tissue miRNA expression after delivery


title: C4

city: Barcelona

first: Ivon

last: Cuscó

address: C/Dr Aiguader, 88

department: Departament de Ciències Experimentals i de la Salut

country: Spain

institute: Universitat Pompeu Fabra

description: DNA sample hybridized to Infinium 450K

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to  Illumina Infinium 450K array using standard Illumina protocol

data_processing:
BeadStudio software v3.2
Average Beta and Pval obtained after Subset-quantile Within Array Normalization (SWAN) using minfi tool.

source_name: Control, peripheral blood

extract_protocol: Genomic DNA was extracted and purified from Peripheral blood samples using Qiagen Dneasy Blood and Tissue Kit according to standard instructions

tag: status

value: Control

tag: gender

value: Male

value: Peripheral Blood


title: C10

description: DNA sample hybridized to Infinium 450K


title: C8

description: DNA sample hybridized to Infinium 450K


title: ASD_48

description: DNA sample hybridized to Infinium 450K

source_name: ASD, peripheral blood

value: Case


title: ASD_50

description: DNA sample hybridized to Infinium 450K


title: C3

description: DNA sample hybridized to Infinium 450K


title: C5

description: DNA sample hybridized to Infinium 450K


title: ASD_53

description: DNA sample hybridized to Infinium 450K


title: C6

description: DNA sample hybridized to Infinium 450K


title: ASD_41

description: DNA sample hybridized to Infinium 450K


title: ASD_44

description: DNA sample hybridized to Infinium 450K


title: C9

description: DNA sample hybridized to Infinium 450K


title: ASD_52

description: DNA sample hybridized to Infinium 450K


title: ASD_35

description: DNA sample hybridized to Infinium 450K


title: Primary AML patient 75

city: Padova

first: Matteo

last: Zampini

state: PD

address: corso stati uniti 4

country: Italy

institute: Istituto di Ricerca Pediatrica (IRP)  Città della Speranza

description: Gene expression data from pediatric AML patient harboring FLT3-ITD mutation (gene-level)

hyb_protocol: Labeled single-stranded DNA in the sense orientation was hybridized for 16 hours at 45 °C on Affymetrix HTA 2.0 microarrays. The microarrays were washed and stained with a streptavidin-phycoerythrin conjugate in an Affymetrix Fluidics Station 450. Signal amplification with antibodies was applied following the instructions provided by Affymetrix.

scan_protocol: The Genechips were scanned with an Affymetrix 7G scanner according to manifacturer guidelines.

data_processing: The CEL files generated were analyzed through Affymetrix Expression Console Software (version 1.3) which normalizes array signals using a robust multiarray averaging (RMA) algorithm. Normalized data were analyzed using Transcriptome Analysis Console (TAC) 3.0 Software (Affymetrix). An unpaired t-test was applied to identify differentially expressed transcript genes between sample pairs and probes with P-values less than 0.01 and fold-change >2 were declared significant.

source_name: FLT3-ITD AML BM

label_protocol: According to the Affymetrix Whole Transcript (WT) manual, cRNA was prepared from 100 ng total RNA. The cRNA was then used to generate single-stranded DNA, which was fragmented and biotinylated.

extract_protocol: Total bone marrow RNA was extracted using TRIzol reagent (Invitrogen) according to manufacturer guidelines, quantified using UV spectroscopy (Nanodrop Technologies), and qualitatively assessed using an Agilent2100 Bioanalyzer (Agilent Technologies).

tag: fab

tag: c/ebpsigma quartile

value: Bone Marrow

tag: mutation

tag: diagnosis

value: acute myeloid leukemia

tag: karyotypic aberration


title: ASD_38

description: DNA sample hybridized to Infinium 450K

tag: tissue


title: ASD_40

description: DNA sample hybridized to Infinium 450K


title: ASD_39

description: DNA sample hybridized to Infinium 450K


title: ASD_47

description: DNA sample hybridized to Infinium 450K


title: ASD_42

description: DNA sample hybridized to Infinium 450K


title: ASD_49

description: DNA sample hybridized to Infinium 450K


title: C7

description: DNA sample hybridized to Infinium 450K


title: ASD_43

description: DNA sample hybridized to Infinium 450K


title: ASD_45

description: DNA sample hybridized to Infinium 450K


title: C1

description: DNA sample hybridized to Infinium 450K


title: Primary AML patient 58

value: NEG


title: Primary AML patient 81


title: ASD_34

description: DNA sample hybridized to Infinium 450K


title: ASD_46

description: DNA sample hybridized to Infinium 450K


title: ASD_36

description: DNA sample hybridized to Infinium 450K


title: Primary AML patient 57


title: Primary AML patient 74


title: C2

description: DNA sample hybridized to Infinium 450K


title: Primary AML patient 38


title: Primary AML patient 53


title: Primary AML patient 54


title: Primary AML patient 50


title: Primary AML patient 37


title: ASD_37

description: DNA sample hybridized to Infinium 450K


title: ASD_33

description: DNA sample hybridized to Infinium 450K


title: ASD_51

description: DNA sample hybridized to Infinium 450K


title: Primary AML patient 30


title: Primary AML patient 51


title: Primary AML patient 25


title: Primary AML patient 56


title: Mouse blastema, biological replicate 3

city: Toronto

first: Freda

last: Miller

state: ON

address: 686 Bay St

country: Canada

institute: Hospital for Sick Children

description: Gene expression of mouse blastema 2 weeks post-injury

hyb_protocol: Affymetrix Mouse Gene 2.0 ST arrays were washed, stained and scanned according to the Fluidics Protocol FS450_0002 using 5.5 ug of cDNA

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: The data were analyzed using the oligo package of Bioconductor in R. The data were background corrected, normalized with quantile normalization, transformed into the log2 scale, and summarized into probesets using the Robust Multichip Analysis (RMA) method.

source_name: Regenerating mouse digit 2 weeks post-injury

label_protocol: cDNA was prepared using the Ambion WT Expression Kit using 400 ng of total RNA

growth_protocol: Uninjured digits were harvested from C57Bl/6 mice

extract_protocol: RNA was extracted using the Qiagen Rneasy kit according to the manufacturer's instructions

treatment_protocol: Blastemas were harvested 2 week post amputation from C57Bl/6 mice

tag: strain

tag: treatment group

value: 2 weeks post-injury digit


title: Mouse blastema, biological replicate 2


title: ASD_32

description: DNA sample hybridized to Infinium 450K


title: Mouse control digit, biological replicate 4

description: Gene expression of uninjured mouse digit

source_name: Uninjured mouse digit

value: Uninjured digit


title: Mouse control digit, biological replicate 2


title: AORTAE LDLR -/- HFSC, replicate 2

city: Vienna

first: Thomas

last: Stulnig

address: Waehringer Guertel 18-20

department: Christian Doppler Laboratory for Cardio-Metabolic Immunotherapy and Clinical Division of Endocrinology and Metabolism, Department of Medicine III

country: Austria

institute: Medical University of Vienna

description:
AORTAE Gene expression data from a LDLR KO mouse placed at 9 weeks of age for up to 20 weeks on HFSC
SAMPLE 17

hyb_protocol: Affymetrix GeneChip® Mouse Gene 2.0 ST arrays were washed, stained and scanned according to the protocol described in GeneChip® WT Terminal Labeling and Hybridization User Manual (Fluidics Protocol FS450_0002)

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 3000 7G, software AGCC 3.1.1

data_processing: RMA (Robust Multiarray average) Signal extraction using Affymetrix Expression Console Version 1.1

source_name: AORTAE_LDLR -/- mouse placed at 9 weeks of age for up to 20 weeks on HFSC

label_protocol: 200ng of total RNA were amplified and labeled using the GeneChip® WT PLUS Reagent Kit (Catalog Number 902281, Affymetrix, Santa Clara, CA)

growth_protocol: At 9 weeks of age WT were placed on HFD  and Ldlr-/- mice were placed on HFSC, both for up to 20 weeks. Their respective controls were kept on NC for up to 20 weeks.

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

treatment_protocol: Described above (growth protocol)

tag: strain background

tag: genotype/variation

value: LDLR-/-; LDLR KO

tag: diet

value: Sucrose enriched high fat diet (HFSC)

value: whole aortae


title: Mouse control digit, biological replicate 3


title: Mouse control digit, biological replicate 1


title: ASD_31

description: DNA sample hybridized to Infinium 450K


title: AORTAE LDLR -/- HFSC, replicate 3

description:
AORTAE Gene expression data from a LDLR KO mouse placed at 9 weeks of age for up to 20 weeks on HFSC
SAMPLE 18


title: Mouse blastema, biological replicate 1


title: ASD_29

description: DNA sample hybridized to Infinium 450K


title: AORTAE LDLR -/- HFSC, replicate 1

description:
AORTAE Gene expression data from a LDLR KO mouse placed at 9 weeks of age for up to 20 weeks on HFSC
SAMPLE 16


title: AORTAE LDLR -/- NC, replicate 1

description:
AORTAE Gene expression data from a LDLR KO mouse placed for up to 20 weeks on NC
SAMPLE 13

source_name: AORTAE_LDLR -/- mouse placed for up to 20 weeks on NC

value: Normal chow (NC)


title: AORTAE LDLR -/- NC, replicate 2

description:
AORTAE Gene expression data from a LDLR KO mouse placed for up to 20 weeks on NC
SAMPLE 14


title: GWAT WT HFD, replicate 5

description:
GWAT Gene expression data from a WT mouse placed at 9 weeks of age for up to 20 weeks on HFD
SAMPLE 11

source_name: GWAT_WT mouse placed at 9 weeks of age for up to 20 weeks on HFD

value: wild type (WT)

value: High fat diet (HFD)

value: gonadal white adipose tissue (GWAT)


title: ASD_30

description: DNA sample hybridized to Infinium 450K


title: ASD_25

description: DNA sample hybridized to Infinium 450K


title: ASD_28

description: DNA sample hybridized to Infinium 450K


title: ASD_24

description: DNA sample hybridized to Infinium 450K


title: ASD_20

description: DNA sample hybridized to Infinium 450K


title: AORTAE LDLR -/- NC, replicate 3

description:
AORTAE Gene expression data from a LDLR KO mouse placed for up to 20 weeks on NC
SAMPLE 15


title: GWAT WT HFD, replicate 4

description:
GWAT Gene expression data from a WT mouse placed at 9 weeks of age for up to 20 weeks on HFD
SAMPLE 10


title: GWAT WT HFD, replicate 3

description:
GWAT Gene expression data from a WT mouse placed at 9 weeks of age for up to 20 weeks on HFD
SAMPLE 9


title: ASD_27

description: DNA sample hybridized to Infinium 450K


title: ASD_23

description: DNA sample hybridized to Infinium 450K


title: GWAT WT HFD, replicate 2

description:
GWAT Gene expression data from a WT mouse placed at 9 weeks of age for up to 20 weeks on HFD
SAMPLE 8


title: ASD_18

description: DNA sample hybridized to Infinium 450K


title: GWAT WT NC, replicate 6

description:
GWAT Gene expression data from a WT mouse placed for up to 20 weeks on NC
SAMPLE 6

source_name: GWAT_WT mouse placed for up to 20 weeks on NC


title: GWAT WT HFD, replicate 1

description:
GWAT Gene expression data from a WT mouse placed at 9 weeks of age for up to 20 weeks on HFD
SAMPLE 7


title: GWAT WT NC, replicate 1

description:
GWAT Gene expression data from a WT mouse placed for up to 20 weeks on NC
SAMPLE 1


title: GWAT WT NC, replicate 2

description:
GWAT Gene expression data from a WT mouse placed for up to 20 weeks on NC
SAMPLE 2


title: GWAT WT NC, replicate 5

description:
GWAT Gene expression data from a WT mouse placed for up to 20 weeks on NC
SAMPLE 5


title: GWAT WT NC, replicate 3

description:
GWAT Gene expression data from a WT mouse placed for up to 20 weeks on NC
SAMPLE 3


title: GWAT WT NC, replicate 4

description:
GWAT Gene expression data from a WT mouse placed for up to 20 weeks on NC
SAMPLE 4


title: ASD_19

description: DNA sample hybridized to Infinium 450K


title: DRG_ob/ob_ 5

city: Grand Forks

first: Junguk

last: Hur

state: ND

address: 1301 N. Columbia Rd. Stop 9037

department: Biomedical Sciences

institute: University of North Dakota

description: gene expression data

hyb_protocol: Following Labeling, 4 ug of cDNA were hybridized for 16 hr at 45C on GeneChip Mouse 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The Affymetrix CEL files were initially analyzed using a local version of the GenePattern genomic analysis platform from the Broad Institute.  The samples were Robust Multi-array Average (RMA) normalized using the BrainArray Custom CDF 16 Entrez.

source_name: dorsal root ganglia, female, 26 week, diabetic

label_protocol: Biotinylated cDNA were prepared according to the Nugen Ovation V2 kit protocol from 75 ng total RNA (Ovation RNA Amplification System V2 Manual, 2007, NuGEN).

extract_protocol: Total RNA was isolated from dorsal root ganglia and sciatic nerve biopsies using a commercially available kit (RNeasy Mini Kit; QIAGEN, Inc., Valencia, CA), including an on-column deoxyribonuclease digestion and following the manufacturer’s protocol. RNA quality and quantity were assessed by microfluid electrophoresis using an RNA 6000 Pico LabChip on a 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA).

value: female

value: ob/ob

value: dorsal root ganglia


title: DRG_ob/ob_ 4

description: gene expression data


title: ASD_13

description: DNA sample hybridized to Infinium 450K

value: Male

value: Peripheral Blood


title: ASD_16

description: DNA sample hybridized to Infinium 450K

value: Case


title: ASD_26

description: DNA sample hybridized to Infinium 450K


title: ASD_12

description: DNA sample hybridized to Infinium 450K


title: DRG_ob/ob_ 2

description: gene expression data


title: GWAT WT HFD, replicate 6

description:
GWAT Gene expression data from a WT mouse placed at 9 weeks of age for up to 20 weeks on HFD
SAMPLE 12


title: DRG_ob/ob_ 3

description: gene expression data


title: ASD_11

description: DNA sample hybridized to Infinium 450K


title: DRG_ob/ob_ 1

description: gene expression data


title: DRG_ob/+_ 4

description: gene expression data

source_name: dorsal root ganglia, female, 26 week, control

value: ob/+


title: DRG_ob/+_ 5

description: gene expression data


title: DRG_ob/+_ 3

description: gene expression data


title: ASD_10

description: DNA sample hybridized to Infinium 450K


title: ASD_21

description: DNA sample hybridized to Infinium 450K


title: ASD_15

description: DNA sample hybridized to Infinium 450K


title: ASD_14

description: DNA sample hybridized to Infinium 450K


title: Neonatal rat NSCPs, biological replicate 3

description: Gene expression of neonatal rat NSCPs

hyb_protocol: Affymetrix Rat Gene 2.0 ST arrays were washed, stained and scanned according to the Fluidics Protocol FS450_0002 using 5.5 ug of cDNA

organism: Rattus norvegicus

source_name: Neonatal Rat NSCPs

growth_protocol: Cells were cultured at 50,000 cells/ml in SKPs basal growth medium (DMEM-F12, 3:1 and 40 ng/ml FGF2, 20 ng/ml EGF, NSCP were cultured in growth medium containing 1% P/S, 2% N2 supplement , 25 ng/ml neuregulin-1β, and 5 μM forskolin on coated plates (4 μg/ml laminin, 30 μg/ml poly-D-lysine hydrobromide)  2% B27, and 1 μg/ml fungizone) and allowed to form spheres

treatment_protocol: Secondary SKPs spheres were dissociated and cultured at 50,000 cells/ml in SKPs basal growth medium (DMEM-F12, 3:1 and 40 ng/ml FGF2, 20 ng/ml EGF, NSCP were cultured in growth medium containing 1% P/S, 2% N2 supplement , 25 ng/ml neuregulin-1β, and 5 μM forskolin on coated plates (4 μg/ml laminin, 30 μg/ml poly-D-lysine hydrobromide)

value: NSCPs

value: Sprague-Dawley wild-type rats


title: Neonatal rat NSCPs, biological replicate 2

description: Gene expression of neonatal rat NSCPs


title: ASD_17

description: DNA sample hybridized to Infinium 450K


title: SCN_ob/ob_ 5

description: gene expression data

source_name: sciatic nerve, female, 26 week, diabetic

value: sciatic nerve


title: Neonatal rat NSCPs, biological replicate 1

description: Gene expression of neonatal rat NSCPs


title: SCN_ob/ob_ 4

description: gene expression data


title: ASD_22

description: DNA sample hybridized to Infinium 450K


title: SCN_ob/ob_ 2

description: gene expression data


title: DRG_ob/+_ 1

description: gene expression data


title: DRG_ob/+_ 2

description: gene expression data


title: Neonatal rat SKPs, biological replicate 3

description: Gene expression of neonatal rat SKPs

source_name: Neonatal Rat SKPs

value: SKPs


title: ASD_9

description: DNA sample hybridized to Infinium 450K


title: SCN_ob/+_ 5

description: gene expression data

source_name: sciatic nerve, female, 26 week, control


title: SCN_ob/+_1

description: gene expression data


title: SCN_ob/+_ 4

description: gene expression data


title: Neonatal rat SKPs, biological replicate 2

description: Gene expression of neonatal rat SKPs


title: SCN_ob/+_ 3

description: gene expression data


title: ASD_4

description: DNA sample hybridized to Infinium 450K


title: ASD_6

description: DNA sample hybridized to Infinium 450K


title: ASD_3

description: DNA sample hybridized to Infinium 450K


title: SCN_ob/ob_ 3

description: gene expression data


title: Neonatal rat SKPs, biological replicate 1

description: Gene expression of neonatal rat SKPs


title: preSC 3

city: Tampa

first: Youngchul

last: Kim

address: 12902 Magnolia Dr

institute: H. Lee Moffitt Cancer Center

description: The cells were isolated from the lungs of Rb/p53/p130 conditional mice infected with Adeno-Cre virus.

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

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

data_processing: The data were acquired using Affymetrix GeneChip Command Concole and analyzed with RMA with quantile normalization method using Affy package in R v3.0.1.

molecule: polyA RNA

source_name: preSC (preneoplastic lung neuroendocrine cells)

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

growth_protocol: The cells were grown in RPMI1640 supplemented with 10% bovine growth serum and penicillin-streptomycin. The culture conditions include 37 celcius degress and 5% CO2.

value: mixed; C57BL/6 and 129/Sv

value: lung

tag: stroma

value: no


title: SCN_ob/ob_ 1

description: gene expression data


title: preSC 2

value: preSC (preneoplastic lung neuroendocrine cells)


title: L-Myc-preSC 1

description: The cells were infected with retroviral L-Myc vector and underwent transformation.

source_name: preSC transduced with retro-L-Myc virus

tag: transduced with

value: retro-L-Myc virus


title: C-Myc-preSC 2

source_name: preSC tranaduced with retro-C-Myc virus

treatment_protocol: No treatment

tag: cell type

value: retro-C-Myc virus


title: ProB_Ctrl2

city: Los Angeles

first: Wenyuan

last: Wang

state: cA

address: 651 Charles E Young Drive

institute: UCLA

description: Gene expression analysis of Mef2c deficient B cell progenitors

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: R package Limma provided through Bioconductor for assessing differential expression. Robust Multiarray Averaging (RMA) method for background adjustment, quantile normalization and probe level. Affymetrix Mouse Genome 430 2.0 Array GeneChip plateform for analysis. Bioconductor annotation database mouse4302.db for official gene symbols.

source_name: BM pro-B cells

label_protocol: standard Affymetrix protocol

extract_protocol: Fresh bone marrow cells were sorted by FACS based on surface marker expression. RNA was isolated from sorted cells with QIAshredder and RNEasy Micro kit.

tag: genotype

value: control

tag: age

value: 9 months old

value: bone marrow pro-B cells


title: C-Myc-preSC 1


title: ProB_Ctrl3


title: N-Myc-preSC 1

source_name: preSC tranaduced with retro-N-Myc virus

value: retro-N-Myc virus


title: ProB_Mut1

value: Vav-Cre Mef2cfl/fl


title: N-Myc-preSC 2


title: ASD_8

description: DNA sample hybridized to Infinium 450K

source_name: ASD, peripheral blood

tag: status

value: Case

tag: gender

value: Male

value: Peripheral Blood


title: ProB_Mut2


title: L-Myc-preSC 2


title: SCN_ob/+_ 2

description: gene expression data

value: female

value: ob/+


title: preSC 1


title: ASD_5

description: DNA sample hybridized to Infinium 450K


title: Hepa 4wk-2

city: Guangzhou

first: Chong

last: Wu

address: 135 Xin Gang Xi Road

institute: Sun Yat-sen University

description:
Test
SAMPLE 6

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: http://sabiosciences.com/pcrarraydataanalysis.php
Fold Change file reports test/control ratios.

source_name: Spleen

label_protocol: Aliquots containing 2 μg total RNA were used to generate complimentary DNA (cDNA) using the SuperScript. III Reverse Transcriptase (invitrogen).PCR assays were performed using the RT² Profiler PCR array-mouse chemokines & receptors assay pannel (SABioscience) following the Manufacturer’s instructions. Quantitative real-time PCR were performed (Light Cycler 480, Roche) with 40 cycles at 95℃ for 15 seconds and 60℃ for 60 seconds.

growth_protocol: All mice were maintained under specific pathogen-free conditions in the animal facilities of Sun Yat-sen University Cancer Center (Guangzhou, China)

extract_protocol: A total of 50-100 mg mouse spleens from control or Hepa1-6 orthotopic hepatoma-bearing mice were grinded with a mortar and pestle in liquid nitrogen, and homogenized in TRIzol Reagent (Ambion). Total RNA was extracted according to the manufacturer’s instructions and quantified with a Nanodrop Instrument (Thermo Scientific).

treatment_protocol: Orthotopic hepatic tumor was established by a subcapsular intrahepatic injection of 7.5 × 105 Hepa1-6 tumor cells suspended in 25 μl of 50% Basement Membrane Extract (Trevigen) into the left lobe of livers of anesthetized B6 mice.

value: spleen

tag: tumor status

value: Four weeks


title: PreB_Mut1

source_name: BM pre-B cells

value: bone marrow pre-B cells


title: ASD_1

description: DNA sample hybridized to Infinium 450K


title: ASD_7

description: DNA sample hybridized to Infinium 450K


title: PreB_Mut2


title: ProB_Ctrl1


title: Hepa 4wk-1

description:
Test
SAMPLE 5


title: ASD_2

description: DNA sample hybridized to Infinium 450K


title: Hepa 4wk-1

description:
Test
SAMPLE 5

label_protocol: Aliquots containing 2 μg total RNA were used to generate complimentary DNA (cDNA) using the SuperScript. III Reverse Transcriptase (invitrogen).PCR assays were performed using the RT² Profiler PCR array-mouse common cytokines assay pannel (SABioscience) following the Manufacturer’s instructions. Quantitative real-time PCR were performed (Light Cycler 480, Roche) with 40 cycles at 95℃ for 15 seconds and 60℃ for 60 seconds.


title: Hepa 2wk-2

description:
Test
SAMPLE 4

value: Two weeks


title: EtOH Vehicle Control

city: Dublin

first: Paul

middle: Joseph

last: McKiernan

address: Beaumont Hospital - ERC

department: Medicine

country: Ireland

institute: RCSI

description: EtOH

data_processing:
Prior to calculating relative expression values, mean normalisation was carried out by subtracting the mean sample CT from the individual miRNA CT values. The threshold line is the level of detection or the point at which a reaction reaches a fluorescent intensity above background. The threshold line is set in the exponential phase of the amplification for the most accurate reading. All miRNA with CT values greater than 35 were considered ‘non-amplified’ or ‘not expressed’ and excluded from analysis. Relative quantification of microRNA expression was determined using the comparative cycle threshold method 2(−ΔΔCT).
Matrix normalized worksheet reports normalized signal (against housekeeping genes).
Fold Change worksheet reports test/control (i.e., Estradiol/Ethanol vehicle control) ratios.

label: FAM

source_name: THP-1 cells

label_protocol: Prior to miRNA expression profiling, RNA from triplicates treatments were pooled and miRNA expression profiling was performed by a stem-loop real-time PCR-based miRNA expression profiling method using the TaqMan MicroRNA Arrays v3.0 (4444913) from  Applied Biosystems (Austin, TX). RNA (30 ng)  was reverse transcribed with the Megaplex primer pool allowing simultaneous reverse transcription of 754 miRNA and 4 endogenous controls across 2 RT pools on a Thermal cycler. A pre-amplification step was performed on the Megaplex™ RT  product (5 μl) using TaqMan® PreAmp Master Mix (2×) and PreAmp Primer Mix (10×) in a 25 μl reaction on the 7900HT fast real time PCR system The PreAmp primer pool contained forward primers specific for each miRNA, and a universal reverse primer. Specific Megaplex™ primer pools and PreAmp Primer Mix were used for A and B cards. PCR for TLDA was carried out with a sample specific cDNA pool, made up to 100 μl (25 μl of PreAmp reaction and 75 μl of H20) and combined with TaqMan® 2× Universal PCR Master Mix. One hundred μl of each sample was added to the 8 fill ports on each card to populate individual wells. The cards were sealed, centrifuged and then run on the 7900HT.

extract_protocol: Total RNA was extracted from cells using TRI-Reagent as per manufacturers instructions

tag: agent

value: EtOH Vehicle Control


title: Estradiol

value: Estradiol


title: Hepa 2wk-1

description:
Test
SAMPLE 3


title: Hepa 4wk-2

description:
Test
SAMPLE 6


title: Hepa 2wk-2

description:
Test
SAMPLE 4


title: Control-2

description:
Control
SAMPLE 2


title: CTR12

status: Public on Jul 11 2016

city: Milan

first: Fabio

last: Martelli

address: via morandi 30

institute: IRCCS-Policlinico San Donato

description: SAMPLE 25

data_processing:
Target gene signals of each samples were normalized to the median of each samples; deltaCt, where deltaCt = (Ct_Target − Ct_median)
Gene normalized data of HF and controls were compared to each other using the deltadeltaCt = (deltaCt_HF − mean deltaCt_control)
The fold_change.txt reports relative RNA expression calculated with 2^-deltadeltaCt, where deltadeltaCt = (deltaCt_HF -mean of deltaCt_control)

label: SYBR-GREEN

source_name: heart_left ventricle biopsies_control

label_protocol: 1 µg total RNA was retro-transcribed using the SuperScript III Reverse Transcriptase kit (Life Technologies, Thermo Fisher Scientific Inc.) according to the manufacturer’s instructions. cDNAs were analyzed using the SYBR-GREEN qPCR method (Life Technologies, Thermo Fisher Scientific Inc.) according to the manufacturer’s instructions.

extract_protocol: Trizol (Life Technologies, Thermo Fisher Scientific Inc.)

tag: subject status

value: male

value: Left ventricle


title: PreB_Mut3

value: 9 months old


title: Control-1

description:
Control
SAMPLE 1


title: Control-2

description:
Control
SAMPLE 2


title: PreB_Ctrl1

value: control


title: CTR10

description: SAMPLE 23


title: PreB_Ctrl2


title: Thymic stromal cells from E14.5 mice

first: Ryo

last: Motosugi

address: 7-3-1 Hongo

department: Graduate School of Pharmaceutical Sciences

institute: The University of Tokyo

description: Thymic stromal cells were harvested at 72 hours after culture following 8 days Fetal thymus organ culture

hyb_protocol: 1.65 µg of Cy3-labeled cRNA was fragmented and hybridized to Agilent Whole Mouse Genome Oligo Microarray  (G4846A) using the Agilent Gene Expression Hybridization Kit. Hybridizations were performed for 17 hours at 65ºC at 10 rpm in a rotating hybridization oven.

scan_protocol: Slides were scanned with SureScan Microarray Scanner (Agilent Technologies) using a scan resolution of 5µm and dye channel of Green with PMT set to 100%.

data_processing: Data was obtained using the Agilent Feature Extraction software (v11.5.1.1) with set to default for all parameters.

source_name: E14.5 fetal thymus_2D culture

label_protocol: 200 ng of total RNA was amplified and labeled using the Agilent Low Input Quick Amp Labeling Kit according to the manufacturer's protocol.

growth_protocol: Fetal thymus lobes, treated with 1.35 mM deoxyguanosine, were enzymatically dispersed, and grown on 35-mm culture dish for 2D culture. Or dispersed cells were resuspended and placed on Nucleopore Track-Etch membrane (Whatman) for RTOC.

extract_protocol: RNA was prepared using the TRIzol  (Life technologies, Carlsbad CA ) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

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

tag: developmental stage

value: fetal thymus

value: thymic stromal cells

tag: culture type

value: 2D culture

source_name: E14.5 fetal thymus_RTOC

value: RTOC


title: PreB_Ctrl3


title: CTR11

description: SAMPLE 24

tag: tissue


title: CTR9

description: SAMPLE 22


title: Thymic stromal cells from E15.5 mice

description: Thymic stromal cells were harvested at 72 hours after culture following 9 days Fetal thymus organ culture

source_name: E15.5 fetal thymus_2D culture

tag: strain

source_name: E15.5 fetal thymus_RTOC


title: Hepa 2wk-1

description:
Test
SAMPLE 3


title: Control-1

description:
Control
SAMPLE 1


title: CTR7

description: SAMPLE 20


title: CTR8

description: SAMPLE 21


title: CTR6

description: SAMPLE 19


title: CTR4

description: SAMPLE 17


title: CTR5

description: SAMPLE 18


title: HF6

description: SAMPLE 6

source_name: heart_non-ischemic left ventricle biopsy_HF patient

value: patients affected by non-end-stage dilated hypokinetic ischemic cardiomyopathy (HF)

value: Non-ischemic left ventricle


title: HF8

description: SAMPLE 8


title: CTR1

description: SAMPLE 14


title: HF13

description: SAMPLE 13


title: HF7

description: SAMPLE 7


title: CTR2

description: SAMPLE 15


title: HF12

description: SAMPLE 12


title: HF4

description: SAMPLE 4


title: HF3

description: SAMPLE 3


title: HF11

description: SAMPLE 11


title: HF1

description: SAMPLE 1


title: HF10

description: SAMPLE 10


title: HF9

description: SAMPLE 9


title: HF2

description: SAMPLE 2


title: CTR3

description: SAMPLE 16


title: HF5

description: SAMPLE 5


title: A_lyrata_RNAseq

type: SRA

city: Athens

first: Robert

middle: J

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

description: Reanalyzed data of A. lyrata (MN47) RNAseq (data from Seymour et al, 2014) http://www.ebi.ac.uk/ena/data/view/ERR575736

library_source: transcriptomic

data_processing:
For MethylC-seq data: Reads were trimmed, aligned, and methylation called using the methylpy pipeline (Schultz et al. 2015). The genome is converted into a forward strand reference (all Cs to Ts) and a reverse strand reference (all Gs to As). Cutadapt (Martin et al. 2011) is used to trim adaptor sequences and then bowtie (Langmead et al. 2009) aligns reads to the two converted reference genomes. Only uniquely aligned reads are retained and the non-conversion rate calculated from unmethylated reads aligned to the chloroplast genome or spiked in unmethylated lambda DNA.
For RNA-seq data: Raw FASTQ reads were trimmed for adapters, preprocessed to remove low quality reads using Trimmomatic v0.32 (Bolger et al. 2014). Reads were aligned using Tophat v2.0.13 (Trapnell et al. 2010) supplied with a reference GFF file and the following arguments: -I 50000 --b2-very-sensitive --b2-D 50. Transcripts were then quantified using Cufflinks v2.2.1 (Trapnell et al. 2012) supplied with a reference GFF file.
For CHIP-seq data: Raw ChIP reads were trimmed for adapters and low-quality bases using Trimmomatic version 0.32 (Bolger et al. 2014). Reads were trimmed for TruSeq version 3 single-end adapters with maximum of two seed mismatches, palindrome clip threshold of 30 and simple clip threshold of 10. Additionally, leading and trailing bases with quality less than 10 were removed; reads shorter than 50 bp were discarded. Trimmed reads were mapped to the TAIR10 genome using bowtie2 version 2.2.3 (Langmead et al. 2012) with default options. Mapped reads were sorted using samtools verison 1.2 (Li et al. 2009) then clonal duplicates were removed using samtools version 0.1.9 (Li et al. 2009). BAM files were then converted to BED files using bedtools v2.21.1 (Quinlan and Hall 2010).
Genome_build: A. thaliana = TAIR10; A. lyrata = v1.0; B. rapa = FPsc v1.3 (http://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_BrapaFPsc);  B. oleracea = TO1000 v1.0 (GCF_000695525.1); C. rubella = v1.0 (GCF_000375325.1);  E. salsugineum = v1.0 (GCF_000478725.1)
Supplementary_files_format_and_content: MethylC-seq data (marked as “allc_total.tsv”) column 1 = chr = chromosome; column 2 = pos = coordinate for the cytosine position on the chromosome; column 3 = strand = + or - strand; column 4 = mc_class = context of the cytosine and the two following bases from the same strand; column 5 = mc_count = number of reads supporting a methylated cytosine; column 6 = total = total number of reads at that position; column 7 = methylated = cytosine is considered methylated if there is a 1 or unmethylated if there is a 0
Supplementary_files_format_and_content: RNAseq data column 1 = gene_ID = gene identifier; column 2 = FPKM = gene expression in fragments per kilobase per million (FPKM)
Supplementary_files_format_and_content: BED file of H2A.Z CHIP-Seq data

organism: Arabidopsis lyrata

growth_protocol: All plants with the exception of met1/sdg7/sdg8 mutants and their controls were sown onto soil and grown in growth chamber under 18 hr light, 6 hr dark at 23-25C. met1/sdg7/sdg8 mutants and their wild-type controls were sown and germinated on MS media.

extract_protocol:
Tissue was flash frozen in liquid nitrogen for all experiments including ChIP-seq, RNA-seq and MethylC-seq. DNA was isolated using a Qiagen Plant DNeasy kit (Qiagen, Valencia, CA) following the manufacturer’s recommendations. RNA was isolated using TRIzol (Thermo Scientific, Waltham, MA) following the manufacturer’s instructions
MethylC-seq libraries were constructed using the MethylC-seq protocol (Urich et al. 2015).
RNA-seq: RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 µg, and all volumes were reduced to a third of the described quantity.
CHIP-seq: Immunoprecipitated DNA was end repaired using the End-It DNA Repair Kit (Epicentre, Madison, WI) according to the manufacturer’s instructions. DNA was purified using Sera-Mag (Thermo Scientific, Waltham, MA) at a 1:1 DNA to beads ratio. The reaction was then incubated for 10 minutes at room temperature, placed on a magnet to immobilize the beads, and the supernatant was removed. The samples were washed two times with 500µL of 80% ethanol, air dried at 37C and then resuspended in 50ul of 10 mM Tris-Cl pH8.0. Finally, the samples were incubated at room temperature for 10 minutes, placed on the magnet, and the supernatant was transferred to a new tube, which contained reagents for “A-tailing.” A-tailing reactions were performed at 37C according to the manufacturers instructions (New England Biolabs, Ipswich, MA). The samples were cleaned using Sera-Mag beads as previously described. Next, adapter ligation was performed using Illumina Truseq Universal Y-adapters and T4 DNA ligase (New England Biolabs, Ipswich, MA) overnight at 16C. A double clean-up using the Sera-Mag beads was performed to remove any adapter-adapter dimers and the elution was used for 15 rounds of PCR. Lastly, samples were cleaned up one final time using the procedures described above.

tag: accession

value: shoot


title: fibroblastic reticular cells of tumour draining lymph node day 11_1

city: Cambridge

first: Angela

last: Riedel

address: Hutchison/MRC Research Centre, Box 197, Cambridge Biomedical Campus

department: MRC Cancer Unit

institute: University of Cambridge

data_processing: lumi package; details provided in the 'data_processing_details.txt'

source_name: FRCs of tumour draining lymph node day 11

label_protocol: biotinIL kit (NuGEN)

extract_protocol: RNA was extracted with QIAGEN Rneasy plus micro Kit, whole transriptome amplification was performed with Ovation PicoSL WTA V2 Kit (NuGEN). Quality control was performed with Agilent Bioanalyser.

value: female

value: lymph node

value: fibroblastic reticular cells (FRCs)


title: fibroblastic reticular cells of tumour draining lymph node day 11_3


title: fibroblastic reticular cells of tumour draining lymph node day 11_2


title: fibroblastic reticular cells of tumour draining lymph node day 4_2

source_name: FRCs of tumour draining lymph node day 4


title: fibroblastic reticular cells of PBS draining lymph node_3

source_name: FRCs of PBS draining lymph node


title: fibroblastic reticular cells of PBS draining lymph node_1


title: siCtrl treated cells 0h rep 2 (TOP1 reanalysis)

city: New York

first: Ivan

last: Marazzi

address: 1468 Madison Avenue

department: Department of Microbiology

institute: Icahn School of Medicine at Mount Sinai

description: Replicate 2

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol

data_processing: Data was analysed using Genespring GX12.5 . To analyze gene expression changes during stimulation, raw data were subject to quantile normalization and baseline transformation was performed to the median of all 9 samples

source_name: A549 cells

label_protocol: Biotin-labeled RNA was prepared with MessageAmp™ Premier RNA Amplification Kit (Applied Biosystems)

growth_protocol: Standard culture techniques

extract_protocol: QIAGEN Rneasy mini kit

treatment_protocol: A549 cells were transfected with either control siRNA (D-001810-10-05, Dharmacon) or TOP1 siRNA (L-005278-00-0005, Dharmacon) pools using the Lipofectamine™ RNAiMAX Transfection Reagent (Invitrogen). Transfections were performed according to the manufacturer’s instructions and cells were used for further experiments 48 hours post intransfection.RNA and protein levels of SETX were quantified to determine knockdown efficiency.

tag: treatment

value: Control siRNA

tag: infection

value: no infection

tag: cell line


title: siCtrl treated cells 12h rep 1 (TOP1)

description: Replicate 1

data_processing: Data was analysed using Genespring GX12.5 . To analyze gene expression changes during stimulation, raw data were subject to quantile normalization and baseline transformation was performed to the median of unstimulated samples of the corresponding siRNA treatment.

treatment_protocol: A549 cells were transfected with either control siRNA (D-001810-10-05, Dharmacon) or TOP1 siRNA (L-005278-00-0005, Dharmacon) pools using the Lipofectamine™ RNAiMAX Transfection Reagent (Invitrogen). Transfections were performed according to the manufacturer’s instructions. 48 hours post transfection, the cells were infected with the Influenza A/Puerto Rico/8/34(ΔNS1) strain at an multiplicity of infection of 3. Wells of uninfected cells were used as controls for infection. Cells were collected for further processing 12 hours post infection. RNA and protein levels of SETX were quantified to determine knockdown efficiency.

value: A/PR/8/34(ΔNS1) Infection


title: Untransfected cells 12h rep 2 (TOP1)

description: Replicate 2

value: no siRNA


title: Untransfected cells 0h rep 3 (TOP1 reanalysis)

description: Replicate 3


title: fibroblastic reticular cells of tumour draining lymph node day 4_3


title: siTop1 treated cells 0h rep 2 (TOP1 reanalysis)

description: Replicate 2

value: Top1 siRNA


title: siCtrl treated cells 12h rep 2 (TOP1)

description: Replicate 2


title: Untransfected cells 12h rep 3 (TOP1)

description: Replicate 3


title: Untransfected cells 0h rep 2 (TOP1 reanalysis)

description: Replicate 2


title: siTop1 treated cells 0h rep 3 (TOP1)

description: Replicate 3


title: fibroblastic reticular cells of PBS draining lymph node_2


title: Untransfected cells 0h rep 1 (TOP1 reanalysis)

description: Replicate 1


title: siTop1 treated cells 0h rep 1 (TOP1)

description: Replicate 1


title: fibroblastic reticular cells of tumour draining lymph node day 4_1


title: siCtrl treated cells 12h rep 3 (TOP1)

description: Replicate 3


title: siCtrl treated cells 0h rep 1 (TOP1)

description: Replicate 1


title: siTop1 treated cells 0h rep 3 (TOP1 reanalysis)

description: Replicate 3


title: siTop1 treated cells 12h rep 3 (TOP1)

description: Replicate 3


title: siTop1 treated cells 0h rep 1 (TOP1 reanalysis)

description: Replicate 1


title: Untransfected cells 12h rep 1 (TOP1)

description: Replicate 1


title: siCtrl treated cells 0h rep 3 (TOP1)

description: Replicate 3


title: siCtrl treated cells 0h rep 1 (TOP1 reanalysis)

description: Replicate 1


title: siTop1 treated cells 12h rep 2 (TOP1)

description: Replicate 2


title: siTop1 treated cells 0h rep 2 (TOP1)

description: Replicate 2


title: siCtrl treated cells 0h rep 2 (TOP1)

description: Replicate 2


title: siTop1 treated cells 12h rep 1 (TOP1)

description: Replicate 1


title: C_rubella_MethylC-seq

description: Reanalyzed data of C. rubella (MTE) Whole Genome Bisulphite Sequencing (data from Seymour et al, 2014) http://www.ebi.ac.uk/ena/data/view/ERR575719

library_source: genomic

organism: Capsella rubella

value: MTE


title: Untransfected cells 0h rep 3 (TOP1)

description: Replicate 3


title: C_rubella_RNAseq

description: Reanalyzed data of C. rubella (MTE) RNAseq (data from Seymour et al, 2014)  http://www.ebi.ac.uk/ena/data/view/ERR575748

value: MT


title: A_thaliana_MethylC-seq

description: Reanalyzed data of A. thaliana (Col-0) Whole Genome Bisulphite Sequencing (data from Schmitz et al, 2011) http://www.ncbi.nlm.nih.gov/sra/?term=SRR342382

value: leaf


title: met1_MethylC-seq

description: Reanalyzed data of A. thaliana met1 (data from Stroud et. al (2013) http://www.ncbi.nlm.nih.gov/sra/?term=SRR534239


title: cmt3_MethylC-seq

description: Reanalyzed data of A. thaliana cmt3 (data from Stroud et. al (2013) http://www.ncbi.nlm.nih.gov/sra/?term=SRR534209


title: A_lyrata_MethylC-seq

description: Reanalyzed data of A. lyrata (MN47) Whole Genome Bisulphite Sequencing (data from Seymour et al, 2014) http://www.ebi.ac.uk/ena/data/view/ERR575712


title: Untransfected cells 0h rep 2 (TOP1)

description: Replicate 2


title: wk2 P.acnes P6 2 vs wk2 uninfected 2

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

country: Germany

institute: Max-Planck-Institute for Infection Biology

hyb_protocol: Whole human genome 44k microarrays were done according to the supplier’s protocol (Agilent Technologies) using the SSC wash protocol

scan_protocol: Scanning of microarrays was performed with 5 µm resolution using a DNA microarray laser scanner (Agilent Technologies)

data_processing: Raw microarray image data were analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.11.5.1.1, Agilent). The extracted MAGE-ML files were analyzed with the Rosetta Resolver Biosoftware (Rosetta Biosoftware)

source_name: wk2  P.agnes P6 2

label_protocol: RNA labeling was performed with the Quick Amp Labeling Kit (Agilent Technologies) according supplier's instructions.

growth_protocol: Human primary prostate epithelial cells (PrEC) from prostate resections were checked for expression of the epithelial cell markers EpCAM and E-cadherin, confirming that the primary culture did not contain any contaminating mesenchymal cells.

extract_protocol: Total RNA was isolated by the Trizol (Invitrogen) method following the manufacturer´s protocol.

treatment_protocol: PrEC cells were infected with a clinical P. acnes prostate isolate (strain P6) for different time points. Unifected cells were used as reference.

tag: sample

value: PrEC cells sample 2

value: P.acnes P6 infected

tag: time

value: 2 weeks

source_name: wk2 uninfected 2

value: uninfected


title: 24h P.acnes P6 1 vs 24h uninfected 4

source_name: 24h P.agnes P6 1

value: PrEC cells sample 1

source_name: 24h uninfected 4

value: PrEC cells sample 4


title: 24h uninfected 4 vs 24h P.acnes P6 1

source_name: 24h P.acnes P6 1


title: wk2 uninfected 1 vs wk2 P.acnes P6 1

source_name: wk2 uninfected 1

source_name: wk2 P.acnes P6 1


title: 48h P.acnes P6 6 vs 48h uninfected 9

source_name: 48h P.agnes P6 6

value: PrEC cells sample 6

source_name: 48h uninfected 9

value: PrEC cells sample 9


title: siCtrl treated cells 0h rep 3 (TOP1 reanalysis)

description: Replicate 3


title: CLP YNG 2 hr  r3

status: Public on Jul 10 2016

city: Gainesville

first: M Cecilia

last: Lopez

state: FL

address: 1376 Mowry Road

department: Molecular Genetics and Microbiology

institute: University of Florida

hyb_protocol: Equal amounts of RNA from samples were labeled and hybridized on a mouse GeneChip following the protocol described in the GeneChip Expression Analysis Technical manual (Affymetrix, Santa Clara, CA).

scan_protocol: The GeneChip arrays were stained and scanned in an Affymetrix GCS 3000 7G Scanner.

data_processing: The data was normalized  using RMA. Analyzed using BRB array tools

source_name: CLP YNG 2hr r3

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

growth_protocol: Mus musculus 6 to 12 weeks

extract_protocol: Extraction of total RNA was performed with QIAGEN Rneasy mini kit according to the manufacturer's instructions.

treatment_protocol: Used the Cecal Ligation and Puncture (CLP), and Polytrauma (PT), and Polytrauma plus Pseudomonas Infections (PT + Pp) models

value: white blood cells

value: 6-12 weeks

value: Cecal Ligation and Puncture (CLP)


title: vehicle,biological replicate 3

city: Boston

first: Peter

middle: Geon

state: MA

address: 360 Longwood Ave, Lc8202

department: Hematology/Oncology

institute: Dana Farber Cancer Institute

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

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

data_processing:
The data were Robust Multi-array Average-summarized, quantile normalized, ComBat normalized for batch effects using covariates for treatment and tissue type using R/Bioconductor;
nsFilter in the R package to obtain 20881 unique probe to gene name correlations,
ComBat with covariates for treatment and tissue type to correct for batch effects as samples are RNA amplified using NuGen.

source_name: VE+CD45+ cells from the AGM region_vehicle

label_protocol: NuGen amplified, biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA.

growth_protocol: E11.5 aorta-gonad-mesonephros region was microdissected, dissociated using DNase I, Collagenase IV and Hyaluronidase, then sorted for VE+CD45+ cells using 100um nozzle on FACSAria. Cells were cultured in 10%FBS/IMDM.

extract_protocol: RNA was extracted with RNeasy Micro Kit (Qiagen)

treatment_protocol: Cells were treated with IFNa (0.5ng/ml) for 4 hours.

value: E11.5 embryo

value: aorta-gonad-mesonephros (AGM) region

tag: cell type

value: hematopoietic stem cell (HSCs); VE+CD45+ cells

tag: treated with

value: vehicle for 4hrs


title: CLP YNG Day 1 r4

source_name: CLP YNG Day1 r4

tag: age


title: IFNa,biological replicate 3

source_name: VE+CD45+ cells from the AGM region_IFNa

value: IFNa (0.5ng/ml) for 4 hrs


title: 48h uninfected 9 vs 48h P.acnes P6 6

source_name: 48h P.acnes P6  6


title: vehicle,biological replicate 2


title: CLP YNG Day 1 r1

source_name: CLP YNG Day1 r1


title: Untransfected cells 0h rep 1 (TOP1)

description: Replicate 1

value: no siRNA

value: no infection


title: CLP YNG 2 hr  r4

source_name: CLP YNG 2hr r4


title: CLP YNG Day 1 r2

source_name: CLP YNG Day1 r2


title: CLP YNG Day 3 r1

source_name: CLP YNG Day3 r1


title: CLP YNG 2 hr  r2

source_name: CLP YNG 2hr r2


title: CLP YNG Day 3 r4

source_name: CLP YNG Day3 r4


title: PT YNG Pp r2

source_name: PT YNG Pp r2

value: Polytrauma (PT)


title: CLP YNG Day 3 r2

source_name: CLP YNG Day3 r2


title: CLP YNG 2 hr  r1

source_name: CLP YNG 2hr r1


title: CLP YNG Day 1 r3

source_name: CLP YNG Day1 r3


title: PT YNG Pp r3

source_name: PT YNG Pp r3


title: IFNa,biological replicate 2


title: CLP YNG Day 3 r3

source_name: CLP YNG Day3 r3


title: PT YNG Pp r1

source_name: PT YNG Pp r1


title: IFNa,biological replicate 1


title: Glucocorticoid Receptor ChIP-Seq_H-300 Ab_300ug/kg corticosterone treatment

status: Public on Jul 09 2016

first: Richard

middle: G.

last: Hunter

state: Massachusetts

address: 100 William Morrissey Blvd.

department: Psychology

institute: University of Massachusetts Bo

data_processing:
We used the Burrows-Wheeler Aligner to align 35-bp reads to the rat genome (rn4), controlling for unique tags, mismatch, and DNA gaps. Using BEDtools, we generated BED files that were used for model-based analysis of ChIP-Seq (MACS) and wiggle files which could be used to visualize the reads on the UCSC genome browser (http://genome.ucsc.edu).  GR-binding sites (GBS) in the DNA relative to the nonspecific binding of the corresponding IgG ChIP-Seq sample were identified with the MACS peak caller (34). For peak calling, a P value cutoff of 1.00 × 10−5, a model fold of 30 and a λ set of 1000/5000/10 000 were used to determine significant bound DNA regions. Per peak, a false discovery rate (FDR) was calculated by MACS.  Using Galaxy (http://main.g2.bx.psu.edu/), Refseq genes near the GBS were determined. As a reference genome, Rattus norvegicus 4 (rn4) was used. Data were visualized by uploading wiggle files containing the raw ChIP-Seq data on the UCSC genome browser.
Genome_build: rn4
Supplementary_files_format_and_content: bed files with read alignments used for peak calling in MACS and wig files

source_name: Glucocorticoid Receptor ChIP-Seq data, Santa Cruz H-300 Ab, Hippocampus, 300ug/kg corticosterone treatment.

extract_protocol:
Because in vivo ChIP-Seq on brain tissue requires a minimum amount of chromatin as input, more than could be obtained from a single animal, 6 hippocampal hemispheres of 1 experimental group were pooled after shearing by sonication and divided in 2 equal portions, so that 2 ChIP procedures on identical samples (technical replicates) could be performed. This was done for both hemispheres, resulting in 4 ChIP samples that were stored at −80°C until further processing.  The ChIP procedure was performed as described before (31). A detailed description of the ChIP procedure is available in Supplemental Document 1. Briefly, the samples were separately precleared by incubating them with Sepharose A beads. After preclearing, an input aliquot was taken of each sample to control for the amount of DNA used as input for the ChIP procedure. To reduce technical and biological variation, each sample was divided in 3 portions and incubated overnight at 4°C under continuous rotation with 6 μg of either a GR, MR, or normal rabbit IgG antibody (Santa Cruz Biotechnology, Santa Cruz, California). Subsequently, the antibody-bound DNA fragments were isolated by incubating the samples with blocked protein A beads, after which the beads were washed and incubated with elution buffer to isolate the DNA-protein complexes. Finally, the DNA fragments were isolated by reverse cross-linking the samples, followed by ribonuclease treatment and purification on Nucleospin columns (Macherey-Nagel, Düren, Germany) (31). The immunoprecipitated samples were eluted in 50 μl elution buffer.
For sequencing, IgG and GR ChIP samples of rats that received 3000 μg/kg CORT were prepared according to the protocol supplied with the Illumina Genome Analyzer GA1 (Illumina, San Diego, California). In brief, the DNA fragments were blunted and ligated to sequencing adapters after which the DNA was amplified for 18 rounds of PCR. The DNA was electrophoresed on a 2% agarose gel, of which a region containing DNA fragments 100 to 500 base pairs (bp) in length was excised and the DNA extracted with the QIAGEN Gel Extraction Kit (QIAGEN, Hilden, Germany). DNA quality was checked on the Agilent Bioanalyzer (Waldbronn, Germany). Single end sequencing of the first 35 bp of the resulting DNA library was performed on the Illumina Genome Analyzer (Leiden Genome Technology Center, Leiden University Medical Center, Leiden University).

treatment_protocol: For ChIP analysis, 8-week-old male Sprague Dawley rats (Harlan, Venray, The Netherlands) were housed in groups of 4 with food and water available ad libitum in a temperature (21°C) and humidity (55%) controlled room with a 12-hour light, 12-hour dark cycle (lights on at 7:30 am). All experiments were conducted during the light phase. The rats were adrenalectomized as described before to completely deplete endogenous CORT levels and ensure there were no GR bound to the DNA. Three days after adrenalectomy (ADX), 2 groups of animals received an ip injection with 300, or 3000 μg/kg CORT-hydroxypropyl-cyclodextrin complex while 1 group was left undisturbed (n = 6 per group). All animals were decapitated after 1 hour for ChIP, and their hippocampi were isolated and processed for ChIP.

value: Sprague-Dawley

value: Brain

tag: brain region

value: hippocampus


title: Glucocorticoid Receptor ChIP-_IgG control_3000ug/kg corticosterone treatment

source_name: Glucocorticoid Receptor ChIP-Seq data, IgG control , Hippocampus, 3000ug/kg corticosterone treatment.


title: Glucocorticoid Receptor ChIP-Seq_IgG control_300ug/kg corticosterone treatment

source_name: Glucocorticoid Receptor ChIP-Seq data, IgG control, Hippocampus, 300ug/kg corticosterone treatment.


title: GC-2 + diethylstilbestrol

status: Public on Jul 08 2016

city: ChongqingPR China

first: Li

last: Yin

address: 69 Hongguang Road Huaxi Street, Banan District

department: College of Pharmacy and Biological Engineering

institute: Chongqing University of Technology

description: DNA methylation proﬁling in GC-2 cells following 2×10-5M diethylstilbestrol exposure

hyb_protocol: Affymetrix Chromatin Immunoprecipitation Assay Protocol

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

data_processing: Affymetrix GCOS processed image files to generate CEL files. The Affymetrix CEL files were analyzed  by  R package Starr to obtain enrichment peaks() and annotated the result with Ensembl(mm10).

source_name: mouse spermatocyte-derived GC-2 cell line, 2×10-5M diethylstilbestrol exposure for 72h

growth_protocol: GC-2 cells were cultured in high-glucose DMEM containing 10% fetal bovine serum at 37°C in a 5% CO2 humidified atmosphere.

extract_protocol: Sonicate sample to lyse cells and shear DNA to 100-1000 bp fragments.

treatment_protocol: GC-2 cells were exposed to 2×10-5M diethylstilbestrol exposure for 72h


title: Yellow_Onion_Digest_2

city: Wageningen

last: Hendriksen

address: Akkermaalsbos 2

department: RIKILT

country: Netherlands

institute: Wageningen University & Research

hyb_protocol: RNAs  of each independent rat intestine experiment (n=3 per treatment) were hybridized to Affymetrix Rat 1.1 ST arrays according to standard Affymetrix protocols. Quality control of the datasets was performed using Bioconductor packages [PMID: 15461798] integrated in an on-line pipeline. Array data were normalized using the Robust Multiarray Average (RMA) M-estimator method, probe sets were defined according to Dai et al. 2005 (PMID: 16284200).

scan_protocol: Scanning was performed according to standard Affymetrix equipment.

data_processing: Array data were normalized using the Robust Multiarray Average (RMA) M-estimator method (PMID: 12538238).  Probe sets were defined according to Dai et al. PMID: 16284200. To exclude interference of non- or very lowly expressed genes, genes were floored to an intensity by which 40% of the lowly expressed genes obtained  this flooring value. To identify differential gene expression induced by WOd and YOd, paired-wise comparison analyses were performed (WOd/Sd and YOd/Sd) and genes with a LIMMA raw p-value <0.05 and fold change (FC) >1.5 or <-1.5 were selected for further data analyses.

source_name: rat small intestine slices cultured for 6 h in the presence of yellow onion digest

label_protocol: Labeling was performed according to standard Affymetrix protocols.

extract_protocol: For the rat intestine, the mRNA was extracted using the QIAshredder and RNeasy Mini kits (Qiagen, Venlo, The Netherlands) according to the manufacturers’ protocols with minor modifications. In short, the frozen slices were transferred to tubes containing 10 beads and 600 µL RLT buffer with 1% β-mercaptoethanol, shortly vortexed and placed in a homogenizer (Bertin Technologies) for 2 times 15 s at 6500 x g. The samples were centrifuged in an Eppendorf centrifuge at maximal speed and the supernatant was transferred to a clean tube. From this point, the procedure continues according the manufacturer’s protocol and the quality and amount of RNA was evaluated by UV spectrometry on a Nanodrop spectrophotometer.

treatment_protocol:
onion extracts were obtained by incubating mashed white onions to 1) pepsin in 0.1 M HCl, and thereafter 2) pancreatin
Approximately 8 weeks old male Sprague-Dawley rats were sacrificed and the small intestine was taken out as quickly as possible and directly put in ice cold Krebs-Henseleit buffer (KHB) previously flushed with carbogen gas (5% CO2 and 95% oxygen). Adhering fatty tissue was removed and the jejunum was cut in segments of approximately 3 cm which were flushed with ice cold oxygenated KHB. The segments were tightened at one end with surgical thread and filled with 3% agarose in 0.9% NaCl of 37°C until the intestine segments reached their normal diameter of approximately 5 mm. The segments were closed using forceps and immediately transferred into ice cold oxygenated KHB, turning the agarose into a flexible gel. Segments were cut into two halves with a surgical blade and each segment half was transferred to a precooled cylindrical mold-plunger assembly of the tissue-embedding unit (Krumdieck, Alabama Research and Development, Munford, AL). The mold was filled with 3% agarose of 37°C which was allowed to solidify into a gel. The plunger was removed and the jejunum embedded in agarose was placed in a Krumdieck slicer previously conditioned with ice cold oxygenated KHB. Slices of ~335 µm thickness were cut and collected in a beaker with ice cold oxygenated KHB. The slices were transferred into a beaker containing Williams’ Medium E of 37°C (WME) supplemented with glucose (25 mM), gentamicin (50 μg/mL), amphotericin B (2.5 µg/mL) and 5% FCS. Three slices were added to each well of 6-well plates that contained 2.0 mL supplemented WME and 0.4 mL sample extract (6 times diluted sample extracts). These 6-well plates were pre-incubated for at least 1 h at 5% CO2, 80% O2 at 37°C. The plates were immediately placed back in the oxygenated incubator equipped with a reciprocal shaker and incubated for 6 h at 5% CO2, 80% O2, 37°C and 35 cycles per min. Each sample was tested in six-fold while the non-digested 140 mmol L−1 NaCl / 5 mmol L−1 KCl control (physiologic salt control=Sal) was tested in twelve-fold. After exposure, the individual intestinal slices were dried by slightly touching a piece of Whatman paper, frozen in liquid nitrogen and stored at -80°C until mRNA isolation and ATP measurements.

value: 8 weeks

tag: gender

value: male

value: small intestine slices

tag: cultured with

value: yellow onion digest (yOd)


title: Yellow_Onion_Digest_1


title: Saline_Digest_2

source_name: rat small intestine slices cultured for 6 h in the presence of Saline_Digest

value: saline digest


title: Saline_Digest_1


title: White_Onion_Digest_2

source_name: rat small intestine slices cultured for 6 h in the presence of white onion digest

value: white onion digest (wOd)


title: DMSO_3

source_name: rat small intestine slices cultured for 6 h without treatment

value: DMSO (no treatment control)


title: PT YNG Pp r4

source_name: PT YNG Pp r4

value: white blood cells

value: 6-12 weeks


title: White_Onion_Digest_3


title: GC-2 + DMSO

description: DNA methylation proﬁling in GC-2 cells

source_name: mouse spermatocyte-derived GC-2 cell line, DMSO

label_protocol: Affymetrix  Chromatin  Immunoprecipitation  Assay Protocol


title: White_Onion_Digest_1


title: Glucocorticoid Receptor ChIP-Seq_H-300 Ab_3000ug/kg corticosterone treatment

source_name: Glucocorticoid Receptor ChIP-Seq data, Santa Cruz H-300 Ab, Hippocampus, 3000ug/kg corticosterone treatment.


title: Yellow_Onion_Digest_3


title: DMSO_2


title: Saline_Digest_3


title: 5. Rb E2F4

city: Madrid

first: Monica

last: Martinez-Fernandez

address: Avda Complutense 40

institute: CIEMAT

hyb_protocol: Following fragmentation, 2.3 ug of DNAs were hybridized for 16 hr at 45C in the Affymetrix Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 7G.

data_processing: The data were analyzed with RMA using RMAExpress.

source_name: skin tissue, Rbf/f;K14creERTM;E2F4-/-, tamoxifen treated

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200 ngs total RNA (GeneChip Whole Transcript WT Expression Arrays, Affymetrix).

extract_protocol: Extraction of total RNA was performed with RNeasy Qiagen Kit according to the manufacturer's instructions.

treatment_protocol: Tamoxifen treatment was topically administered in the shaved backskin of animals (2x2 cm) at 20 mg/per day dissolved in DMSO/acetone for 5 consecutive days.

tag: genetic background

value: FVB/N

tag: genotype/variation

value: skin


title: DMSO_1


title: 3. Rb E2F4


title: 8. E2F4

source_name: skin tissue, Rbf/f, E2F4-/-, tamoxifen treated


title: 6. E2F4


title: 1. Rb

source_name: skin tissue, Rbf/f;K14creERTM, tamoxifen treated


title: 4. Rb E2F4


title: 2. Rb E2F1

source_name: skin tissue, Rbf/f;K14creERTM;E2F1-/-, tamoxifen treated


title: 7. E2F4


city: BUSAN

first: Bum-Joon

last: Park

address: Busandaehak-ro 63

department: Molecular Biology

country: South Korea

institute: Pusan National University

description: Gene expression data from JH4-treated HGPS cell

hyb_protocol: Following fragmentation, fragmented cDNA were hybridized for 16 hr at 45C on Affymetrix GeneChip® Human Gene 1.0 ST Array. The GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The Robust Multiarray Average (RMA) algorithm implemented in Affymetrix Expression Console software (version1.3.1) was used to normalize the raw data. Highly expressed genes that showed over 2-fold difference between the signal values of control and test samples were selected for further study.  Fold-change and gene ontology data are available in the archive fold-change_data.tar on the series record.

source_name: Human fibroblast cells from HGPS patients_JH4 3μM_7 days

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 300  ng total RNA (GeneChip® WT Terminal Labeling and Controls Kit P/N 901525 1, Affymetrix).

growth_protocol: Human fibroblast cells from HGPS patients and controls were maintained in EMEM, containing 15% FBS, 2 mM glutamine or HEMEM with 26 mM HEPES without antibiotics.

extract_protocol: 500 ng of total RNA extracted using the RNAeasy kit (Qiagen).

treatment_protocol: HGPS were treated with JH4 or vehicle for 7days and normal fibroblasts (9-yr, 81-yr) were not treated

value: fibroblast

value: female

tag: diagnosis

value: Hutchinson-Gilford progeria syndrome (HGPS)


title: mHPC_50ngIL-4_1

city: Bethesda

middle: Lee

last: Gieseck

state: MD

address: 4 Memorial Drive

department: NIAID

institute: NIH

description:
Mmib-9986350002-E
replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol with Illumina HiScan-SQ

data_processing: Signal data was extracted from the image files with the Gene Expression module (v. 1.9.0) of the GenomeStudio software (v. 2011.1) from Illumina, Inc. Samples were normalized to 500 based on median and then coverted to log2 scale using NIH mAdb platform. Subsequent statistical analyses were performed in TM4 Mev Suite.

label_protocol: Illumina TotalPrep RNA Amplification Kit (Ambion)

growth_protocol: Cells were cultured in William's E Media with 10% FBS, 17.6 mM NaHCO3, 20mM HEPES pH 7.5, 10 mM Nicotinamide, 1mM Sodium Pyruvate, 1X ITS, 100nM Dexamethasone, 0.2 mM Ascorbic Acid, 14mM glucose, 10ng/mL IL-6, 10ng/mL HGF, 10ng/mL EGF

extract_protocol: The RNA was extracted using Trizol reagent and cleaned up using a Qiagen Rneasy miniprep kit.

treatment_protocol: Cells were serum starved for 24 hours and then treated with 0.1% BSA vehicle, 50ng/mL recombinant IL-4, or 50ng/mL recombinant IL-13.

value: DAPI-CD45-CD31-TER119-EpCAM+CD24+CD133+ hepatic progenitor cells


title: mHPC_50ngIL-13_3

description:
Mmib-9986350005-C
replicate 3


title: mHPC_Control_4

description:
Mmib-9986350005-B
replicate 4

value: control


title: mHPC_50ngIL-4_3

description:
Mmib-9986350005-E
replicate 3


title: mHPC_50ngIL-13_4

description:
Mmib-9986350005-D
replicate 4


title: mHPC_50ngIL-13_2

description:
Mmib-9986350002-D
replicate 2


title: mHPC_50ngIL-13_1

description:
Mmib-9986350002-C
replicate 1


title: mHPC_50ngIL-4_2

description:
Mmib-9986350002-F
replicate 2


title: mHPC_Control_1

description:
Mmib-9986350002-A
replicate 1


title: mHPC_Control_2

description:
Mmib-9986350002-B
replicate 2


title: Human fibroblast cells from HGPS patients_DMSO

description: Gene expression data from untreated HGPS cell

tag: tissue


title: Hypothalamus of mice treated with Withaferin A, biological rep4

city: Daegu

first: Jaemin

last: Lee

state: Select One

address: 333 Techno Jungang Daero, Hyeonpung-Myeon, Dalseong-Gun

department: New Biology

institute: DGIST

description: Gene expression data from the hypothalamus of obese mice after Celastrol or withaferin A treatment

hyb_protocol: Per manufacturer's protocol (Affymetrix GeneChip Hybridization, Stain and Wash kit)

scan_protocol: Scanned on GeneChip Scanner 3000 7G

data_processing: Data were analyzed with Affymetrix software to normalize and background correct using RMA

source_name: Mouse hypothalamus

label_protocol: Per manufacturer's protocol (Affymetrix Ambion WT Expression kit and GeneChip WT Terminal labeling kit)

growth_protocol: 3-week-old C57BL/6J male mice were fed with 45% high fat diet for 20 weeks

extract_protocol: Trizol extraction and subsequent purification of total RNA using QIAgen RNeasy MinElute Cleanup kit were performed according to the manufacturer's instructions.

treatment_protocol: Mice were intraperitoneally injected with DMSO for 4 days and then daily received either DMSO, Celastrol (100 ug/kg) or Withaferin A (2 mg/kg) for additional 4 days by intraperitoneal injection

value: Hypothalamus

tag: strain

value: 23 weeks old

value: Withaferin A


title: mHPC_50ngIL-4_4

description:
Mmib-9986350005-F
replicate 4


title: Hypothalamus of mice treated with Celastrol, biological rep3

value: male

value: Celastrol


title: Hypothalamus of mice treated with Celastrol, biological rep2


title: Hypothalamus of mice treated with DMSO, biological rep4

value: DMSO


title: Hypothalamus of mice treated with Withaferin A, biological rep1


title: Hypothalamus of mice treated with Celastrol, biological rep1


title: Human nomal fibroblast_untreated_9 yr

description: Gene expression data from normal young cell

source_name: Human nomal fibroblast_untreated_9 yr

tag: donor age

value: 9 years

value: healthy


title: Hypothalamus of mice treated with Withaferin A, biological rep3

tag: treatment


title: Hypothalamus of mice treated with DMSO, biological rep3


title: mHPC_Control_3

description:
Mmib-9986350005-A
replicate 3


title: Hypothalamus of mice treated with DMSO, biological rep2


title: Cells treated with doxy and Tm for 12 h rep3

city: Rehovot

first: Rina

last: Wassermann Dozorets

address: Herzl St 234

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

hyb_protocol: 2ug ss cDNA in 80 ul were hybridized to a Mouse Gene 1.0 ST array and hybridized for 17 hours at 45° at 60rpm using GeneChip Hybridization, Wash and Stain Kit materials (Affymetrix, PN 900720). Post-hyb washes were done with Affymetrix wash solutions on the FS450 station using FS450_0002 protocol.

scan_protocol: Arrays were scanned on the Affymetrix GeneChip Scanner 3000 7G.

data_processing: The data was analyzed with Partek Genomic Suite version 6.6 , (Partek Inc., St. Louis, Missouri 63141, http://www.partek.com), using RMA.

source_name: C/EBPβ LIP overexpression 12h tunicamycin

label_protocol: Synthesis of cDNA was performed using the Ambion WT Expression Kit (PN 4411974). A starting amount of 250 ng total RNA was used for each sample. Fragmentation and Labeling was performed using the Affymetrix GeneChip WT Terminal Labeling Kit (PN 900671).

growth_protocol: Murine B16 F10.9-4 cells were cultured in DMEM containing 10% FBS, 2 mM L-glutamine solution, 50 U/ml penicillin and 0.1 mg/ml steptomycin in humidified 8% CO2 incubator at 37°C.

extract_protocol: Total RNA was isolated using PerfectPure RNA Cultured Cell Kit (5 Prime, #2900319) according to the manufacturer’s protocol.

treatment_protocol: Mouse B16 F10.9-4 cells were pretreated with doxycycline (to induce LIP overexpression) followed by tunicamycin. After 0, 5, and 12 h the cells were harvested and total RNA was purified.


title: Hypothalamus of mice treated with Withaferin A, biological rep2


title: Hypothalamus of mice treated with Celastrol, biological rep4


title: Cells treated with Tm for 12 h rep3

source_name: tunicamycin 12h


title: Hypothalamus of mice treated with DMSO, biological rep1


title: Cells treated with Tm for 5 h rep3

source_name: tunicamycin 5h


title: Cells treated with doxy and Tm for 12 h rep2


title: Cells treated with doxy and Tm for 5 h rep2

source_name: C/EBPβ LIP overexpression 5h tunicamycin


title: Cells treated with doxy rep2

source_name: C/EBPβ LIP overexpression 0h tunicamycin


title: Cells treated with doxy and Tm for 12 h rep1


title: Cells treated with doxy and Tm for 5 h rep3


title: Cells treated with Tm for 12 h rep2


title: Cells treated with vehicle rep3

source_name: vehicle


title: Cells treated with Tm for 5 h rep2


title: Cells treated with Tm for 12 h rep1


title: Cells treated with doxy rep3


title: Cells treated with vehicle rep2


title: MEFs treated with DMSO

description: Gene expression data from MEFs after Celastrol treatment

source_name: mouse embryonic fibroblasts (MEFs)

treatment_protocol: Mouse embryonic fibroblasts infected with adenovirus expressing LacZ were treated with DMSO or Celastrol (250 nM) for 7h in DMEM media with 1% FBS

value: mouse embryonic fibroblasts


title: Cells treated with doxy and Tm for 5 h rep1


title: Cells treated with Tm for 5 h rep1


title: MEFs treated with Celastrol


title: lactoferrin-sophorolipids-assembly treatment_1

city: Davis

first: Rulan

last: Jiang

address: One Shields Ave.

institute: University of California, Davis

description:
Replicate 1
Sample name: Sample 10

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R. The normalized data in the data table and the non-normalized data available in a text file on the series record were filtered to include only those probes with Detection Pval < 0.05.

source_name: HDFn

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

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up with QIAGEN RNeasy mini kit following the manufacturer's instructions. Quality control was performed with Agilent Bioanalyser.

value: dermal fibroblasts


title: lactoferrin treatment_2

description:
Replicate 2
Sample name: Sample 5


title: Control_2

description:
Replicate 2
Sample name: Sample 2


title: lactoferrin-sophorolipids-assembly treatment_2

description:
Replicate 2
Sample name: Sample 11


title: lactoferrin treatment_3

description:
Replicate 3
Sample name: Sample 6


title: Control_3

description:
Replicate 3
Sample name: Sample 3


title: lactoferrin treatment_1

description:
Replicate 1
Sample name: Sample 4


title: lactoferrin-sophorolipids-assembly treatment_3

description:
Replicate 3
Sample name: Sample 12


title: Cells treated with vehicle rep1


title: sophorolipids treatment_3

description:
Replicate 3
Sample name: Sample 9


title: sophorolipids treatment_2

description:
Replicate 2
Sample name: Sample 8


title: ST-00080362_S-001045386_5988071007_E

city: New Haven

first: Jen-hwa

last: Chu

state: CT

department: Pulmonary, Critical Care and Sleep Medicine

institute: Yale University School of Medicine

hyb_protocol: standard as recommended by illumina

scan_protocol: standard as recommended by illumina

data_processing: VSN normalized, background corrected

source_name: Whole blood sample from human subject

label_protocol: standard as recommended by illumina

extract_protocol: standard as recommended by illumina

tag: occupation

value: Pick-up and Delivery Driver


title: ST-00080362_S-001045330_5988071007_D


title: Control_1

description:
Replicate 1
Sample name: Sample 1


title: ST-00080362_S-001045388_5988071007_F


title: ST-01000521_S-001045384_5988071007_I


title: ST-01000521_S-001045367_5988071007_H


title: Human nomal fibroblas_untreated_81 yr

description: Gene expression data from normal aged cell

source_name: Human nomal fibroblas_untreated_81 yr

value: skin

value: 81 years


title: sophorolipids treatment_1

description:
Replicate 1
Sample name: Sample 7


title: ST-00080356_S-001045396_5988071018_D

value: Dockworker


title: ST-00008300_S-001045582_5988071013_A

value: Officeworker


title: ST-00007371_S-001045522_5988071007_C


title: ST-00008300_S-001045585_5988071013_B


title: ST-00080360_S-001045349_5988071018_F


title: ST-00080360_S-001045321_5988071018_E


title: ST-00040453_S-001045517_5988071013_E


title: ST-01000521_S-001045352_5988071007_G


title: ST-00073499_S-001045297_5988071013_F


title: ST-00040453_S-001045293_5988071013_C


title: ST-00073499_S-001045424_5988071013_G


title: ST-01000605_S-001045370_5988071005_I


title: ST-00073499_S-001045426_5988071013_H


title: ST-00040453_S-001045423_5988071013_D


title: ST-00008298_S-001045523_5988071005_D


title: ST-00080356_S-001045395_5988071018_C


title: ST-00007368_S-001045593_5988071007_A


title: ST-00080356_S-001045313_5988071018_B


title: ST-00080360_S-001045392_5988071018_G


title: ST-01000526_S-001045358_5988071006_J


title: ST-01000526_S-001045379_5988071006_K


title: ST-01000605_S-001045381_5988071005_J


title: ST-00007371_S-001045413_5988071007_B


title: ST-01000526_S-001045341_5988071006_I


title: ST-00037457_S-001045540_5988071006_D


title: Cells treated with doxy rep1

tag: cell line


title: ST-01000522_S-001045363_5988071006_H


title: ST-00073500_S-001045425_5988071025_K


title: ST-00008304_S-001045554_5988071006_A


title: ST-00037457_S-001045542_5988071006_E


title: ST-00073500_S-001045298_5988071025_J


title: ST-01000522_S-001045357_5988071006_G


title: ST-00037457_S-001045535_5988071006_C


title: ST-00008304_S-001045568_5988071006_B


title: ST-00073500_S-001045282_5988071025_I


title: ST-00073498_S-001045427_5988071025_G


title: ST-00050565_S-001045586_5988071025_E


title: ST-00073498_S-001045520_5988071025_H


title: ST-00073501_S-001048870_5988071017_L


title: ST-00049608_S-001045529_5988071017_I


title: ST-00045241_S-001045541_5988071025_A


title: ST-00080354_S-001045371_5988071021_G


title: ST-00039434_S-001045537_5988071017_A


title: ST-00039434_S-001045564_5988071017_B


title: ST-00080358_S-001045350_5988071020_I


title: ST-00039001_S-001045534_5988071020_C


title: ST-00073498_S-001045285_5988071025_F


title: ST-00046315_S-001045515_5988071017_F


title: ST-00080358_S-001045320_5988071020_H


title: ST-00045241_S-001045547_5988071025_B


title: ST-00043035_S-001045526_5988071021_E


title: ST-00039001_S-001045551_5988071020_D


title: ST-01000516_S-001045383_5988071021_K


title: ST-00080358_S-001045391_5988071020_J


title: ST-00039001_S-001045597_5988071020_E


title: ST-01000516_S-001045307_5988071021_I


title: ST-00080354_S-001045394_5988071021_H


title: ST-00050565_S-001045405_5988071025_C


title: ST-00050565_S-001045571_5988071025_D


title: ST-00080354_S-001045331_5988071021_F


title: ST-01000516_S-001045339_5988071021_J


title: ST-00037790_S-001045416_5988071021_A


title: ST-00037790_S-001045590_5988071021_C


title: ST-01000522_S-001045353_5988071006_F


title: ST-01000509_S-001045334_5988071011_I


title: ST-00037790_S-001045418_5988071021_B


title: ST-00073501_S-001048873_5988071011_L


title: ST-00046315_S-001045521_5988071017_G


title: ST-01000509_S-001045314_5988071011_H


title: ST-00043035_S-001045345_5988071021_D


title: ST-00080361_S-001045374_5988071011_F


title: ST-00080361_S-001045373_5988071011_E


title: ST-01000511_S-001045375_5988071023_K


title: ST-01000511_S-001045316_5988071023_I


title: ST-00080361_S-001045329_5988071011_D


title: ST-00007369_S-001045414_5988071011_A


title: ST-01000511_S-001045335_5988071023_J


title: ST-00039098_S-001045592_5988071023_H


title: ST-01000604_S-001045355_5988071014_I


title: ST-01000604_S-001045385_5988071014_K


title: ST-00007366_S-001045532_5988071023_B


title: ST-01000604_S-001045380_5988071014_J


title: ST-00038515_S-001045421_5988071023_E


title: ST-01000528_S-001045365_5988071001_I


title: ST-00007369_S-001045565_5988071011_B


title: ST-01000509_S-001045300_5988071011_G


title: ST-00044533_S-001045573_5988071001_F


title: ST-00044533_S-001045575_5988071001_G


title: ST-00038515_S-001045291_5988071023_C


title: ST-00045078_S-001045406_5988071015_K


title: ST-00039098_S-001045347_5988071023_F


title: ST-00008301_S-001045584_5988071001_D


title: ST-00007369_S-001045594_5988071011_C


title: ST-00038515_S-001045387_5988071023_D


title: ST-00039098_S-001045417_5988071023_G


title: ST-01000528_S-001045311_5988071001_H


title: ST-00046315_S-001045528_5988071017_H


title: ST-00007366_S-001045412_5988071023_A


title: ST-00045078_S-001045397_5988071015_J


title: ST-00038545_S-001045288_5988071015_H


title: ST-00007370_S-001045407_5988071015_D


title: ST-00007187_S-001045578_5988071015_C


title: ST-00038545_S-001045319_5988071015_I


title: ST-00044533_S-001045550_5988071001_E


title: ST-00038545_S-001045278_5988071015_G


title: ST-00007187_S-001045408_5988071015_A