title: BrdU IP in wild-type

hyb_protocol: Equal amounts of Cy5- and Cy3-labeled DNA were mixed and combined with human Cot1 DNA, Agilent Blocking Agent and Agilent Hybridization buffer, and hybridized to high-density microarrays in Agilent SureHyb hybridization chamber for 24 hours at 65˚C, 10 rpm. After hybridization, slides were washed according to Agilent protocol.

source_name: cdc10-v50, BrdU IP DNA

label_protocol: Immunoprecipitated and whole-cell extract DNA were amplified by random-primed PCR and conjugated with Cy5 (IP DNA) or Cy3 (whole-cell extract DNA).

growth_protocol: Cdc10-v50 cells carrying thymidine kinase expression module Pnmt1-TK and nucleoside transport module Padh1-hENT were grown at 26˚C and arrested by raising temperature to 35˚C for 4h. Cells were released from block by reducing temperature to 26˚C, and cultures were supplemented at this time by 10mM hydroxyurea and 200μΜ 5-bromo-2'-deoxyuridine.

extract_protocol: The DNA was phenol-extracted from fixed cells by bead-beating with glass beads, sheared by sonication and immunoprecipitated with anti-BrdU antibody (BD Pharmigen) immobilized to Dynal anti-mouse magnetic beads (Invitrogen).

treatment_protocol: Cells were fixed with 0.1% sodium azide.

tag: molecule subtype

value: immunoprecipitated DNA

tag: ip antibody

value: anti-BrdU (BD Pharmingen #B5002)

source_name: cdc10-v50, whole-cell extract

value: Whole-cell extract DNA


title: BrdU IP in sap1-1

status: Public on Aug 22 2017

type: genomic

city: Bethesda

first: Shiv

last: Grewal

state: MD

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

country: USA

institute: NCI

scan_protocol: Scanned on an Agilent G2600D scanner.

data_processing: Data were extracted using Agilent Feature Extraction Software. Signal was normalized by combined rank consistency filtering with LOWES intensity normalization.

molecule: genomic DNA

organism: Schizosaccharomyces pombe

source_name: cdc10-v50 sap1-1, BrdU IP DNA

tag: strain/background

tag: genotype/variation

source_name: cdc10-v50 sap1-1, whole-cell extract


title: Placenta_Hypoxia_Saline_02_rep3

type: RNA

city: Cardiff

first: Hannah

last: Scott

address: Hadyn Ellis Building, Maindy Road

department: UK Dementia Research Institute

country: United Kingdom

institute: Cardiff University

description: Placenta_NS21_v_HS02.txt; Placenta_HS02_v_HM02.txt

hyb_protocol: Samples were hybridised using the NanoString nCounter rat miRNA Expression Assay kit. See nCounter miRNA Expression Assay User Manual for protocol.

scan_protocol: Samples were analysed using the NanoString nCounter Analysis System (Gen2). See Gen2 Prep Station User Manual.

data_processing:
Raw output files were converted into lists of counts. To compare two groups, the respective raw counts were passed into RUVSeq for normalisation and removal of unwanted variation. Adjusted counts were then analysed for differential expression analysis using edgeR.
Normalised counts can be found in attached text files, instead of in the matrix table, as specified in the 'Description' column under the 'Samples' heading. Values are Reporter Probe signal intensities captured with the nCounter Analysis System and normalised using RUVSeq.

label: biotin

molecule: total RNA

organism: Rattus norvegicus

source_name: placenta conditioned medium, maternal hypoxia, maternal saline injection, exposure to 2% oxygen in vitro

label_protocol: Samples were labelled using the NanoString nCounter rat miRNA Expression Assay kit. See nCounter miRNA Expression Assay User Manual for protocol.

growth_protocol: Three-month-old female Sprague-Dawley rats were maintained on ad libitum standard rat chow and tap water in a 10:14-h light-dark cycle and acclimatised before breeding. All protocols were approved by the University of Alberta Health Sciences Animal Policy and Welfare Committee, in accordance with the Canadian Council on Animal Care guidelines.

extract_protocol: Foetal blood was collected into EDTA-containing tubes, pooled per litter, and plasma was extracted. Placentae were isolated, placed into cell culture medium and incubated at 2, 8 or 21% oxygen for 24 h. Total RNA was extracted from 100 μl foetal plasma using the Qiagen miRNeasy Serum/Plasma Kit or from 200 μl conditioned media using the Qiagen miRNeasy Mini Kit.

treatment_protocol: On gestational day 15 of pregnancy the rats were injected ntravenously with saline or 125 μM MitoQ-nanoparticles and exposed for the next 6 days to 21% or 11% oxygen.

tag: foetal age

tag: tissue

value: Pacenta

tag: maternal oxygen status

value: Hypoxia

tag: maternal injections

value: Saline

tag: in vitro oxygen condition


title: microRNA profile of case 747N

city: Guangzhou

first: Heng-Ying

last: Pu

address: 651, Dongfeng East Road

country: China

institute: Cancer Centre, Sun Yat-sen University

hyb_protocol: The labeled RNAs from NSCLC and NC were hybridized to the array with a 1×hybridization solution (5× Denhart’s solution, 0.5% SDS, 5× SSC) in a Hybridization Chamber (Corning Inc, Corning, NY, USA) at 46°C for 12 to 16 hours.

scan_protocol: Scanned in a LuxScanTM -10K Scanner (capitalBio Inc.,Beijing, China).

data_processing: Quantile normalization across multiple arrays, log 2 transformation of expression levels, BRB ArrayTools v.3.8.0 was used.

organism: Homo sapiens

source_name: Matched noncancerous lung tissue of NSCLC

label_protocol: 2.5 μg of total RNA was employed with 100 nmol/L of pCp-DY547 (Dharmacon, Lafayette, CO, USA) and 15 Units of T4 RNA ligase (USB, Cleveland, Oh, USA) in a total reaction volume of 20 µL at 16°C overnight

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

tag: survival


title: CGH_Revertant_2

hyb_protocol: Equal amounts of Cy5-labeled DNA and Cy3-labeled DNA were mixed and combined with human Cot1 DNA, Agilent Blocking Agent and Agilent Hybridization buffer, and hybridized to high-density microarrays in Agilent SureHyb hybridization chamber for 24 hours at 65˚C, 10 rpm. After hybridization, slides were washed according to Agilent protocol.

data_processing:
Data were extracted using Agilent Feature Extraction Software. Signal was normalized by combined rank consistency filtering with LOWES intensity normalization.
Relative copy number values were calculated as a log 2 ratio of Cy5 processed signal/ Cy3 processed signal.

source_name: sap1-1 revertant

label_protocol: Genomic DNA from wild type or sap1-1 revertant was digested with AluI and RsaI. Digested DNA was used as template for a genomic DNA labelling reaction using the BioPrime® Array CGH Genomic Labeling kit (Invitrogen) according to the manufacturer's protocol.

extract_protocol: Grow 20 ml cells to OD595 of 1.0. After cell wall digestion using Zymolyase 100T, cells were resuspended in 0.55 ml TE, 1% SDS, 100ug of proteinase K and incubated at 65°C for 30 min. Add 175 µl 5M potassium acetate. Keep on ice for 5 minutes. Lysate was centrifuged for 15 min at maximum speed for removing the cell debris. Genomic DNA was precipitated with isopropanol. After RNaseA treatment, genomic DNA was purified by phenol/chloroform/isoamyl alcohol (PCI) extraction twice and precipitated with ethanol.

source_name: wild-type

value: wild-type


title: microRNA profile of case 739N


title: Placenta_Hypoxia_Saline_02_rep2


title: microRNA profile of case 741N


title: microRNA profile of case 738N


title: microRNA profile of case 736N


title: microRNA profile of case 734N


title: microRNA profile of case 735N


title: Placenta_Hypoxia_Saline_21_rep3

description: Placenta_NS21_v_HS21.txt; Placenta_HS21_v_HM21.txt

source_name: placenta conditioned medium, maternal hypoxia, maternal saline injection, exposure to 21% oxygen in vitro


title: microRNA profile of case 733N


title: TGRL+LpL, biological rep1

city: Davis

first: Hnin

middle: H

last: Aung

state: CA

address: 451 E Health Science Dr., GBSF 5404

department: Internal Medicine

institute: University of California, Davis

description: Gene expression data from TGRL lipolysis products (TL).

hyb_protocol: The fragmentation of labeled aRNA samples were hybridized to Human Genome U133A 2.0 Array high-density oligonucleotide arrays. The hybridization, washing, labeling, and scanning of the GeneChips were performed as described in the Affymetrix protocols by the Microarray Core Facility in the UC Davis Genome and Biomedical Sciences Facility.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner.

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

source_name: Human Astrocytes

label_protocol: Microarray experiments were performed with pooled RNA isolates from each treatment group. A 200 ng aliquot of total RNA from each pooled sample was reverse-transcribed, followed by aRNA Amplification, reverse transcription to synthesize first-strand cDNA, second-strand cDNA Synthesis, in vitro transcription to synthesize labeled aRNA, purification and fragmentation of aRNA as described in the Affymetrix 3´ IVT Express Kit protocol (Affymetrix).

growth_protocol: Normal Human Astrocytes  (NHA) were cultured in ABM Complete Medium which includes ABM basal media (CC-3187) supplemented with AGM SingleQuot kit suppl. & growth factors (CC-4123) (Lonza, Walkersville MD) under an atmosphere of 5 % CO2: 95% air at 37°C.

extract_protocol: total RNA was performed RNeasy Mini Kit (Qiagen) including the DNA digestion step as according to the manufacturer's instructions.

treatment_protocol: NHA were exposed for 3 hr to the following conditions, media, TGRL (150 mg/dL =1.5 mg/mL), lipoprotein lipase (LpL) (2 U/mL), and TGRL lipolysis product (TGRL (150 mg/dL) + LpL (2 U/mL)).

value: brain

tag: treatment

value: triglyceride-rich lipoprotein lipolysis products treated


title: Placenta_Hypoxia_Saline_21_rep1


title: microRNA profile of case 732N


title: Placenta_Normoxia_Saline_21_rep4

description: Placenta_NS21_v_HM02.txt; Placenta_NS21_v_HM21.txt; Placenta_NS21_v_HS02.txt; Placenta_NS21_v_HS21.txt;Placenta_NS21_v_NM21

source_name: placenta conditioned medium, maternal normoxia, maternal saline injection, exposure to 21% oxygen in vitro

value: Normoxia


title: Media, biological rep1

description: Gene expression data from media (M).

value: media treated


title: TGRL, biological rep1

description: Gene expression data from triglyceride-rich lipoprotein (T).

value: triglyceride-rich lipoprotein treated


title: Placenta_Hypoxia_Saline_02_rep1


title: microRNA profile of case 729N


title: Placenta_Normoxia_Saline_21_rep1


title: Placenta_Normoxia_Saline_21_rep3


title: Plasma_Hypoxia_MitoQNP_rep4

source_name: foetal plasma at E20, maternal hypoxia, maternal MitoQ-nanoparticle injection

value: Plasma

value: MitoQ-nanoparticles


title: Placenta_Normoxia_Saline_21_rep2


title: microRNA profile of case 749N


title: microRNA profile of case 728N


title: microRNA profile of case 726N


title: microRNA profile of case 725N


title: microRNA profile of case 722N


title: Plasma_Hypoxia_MitoQNP_rep3


title: microRNA profile of case 724N


title: microRNA profile of case 721N


title: Placenta_Hypoxia_Saline_21_rep2


title: LpL, biological rep1

description: Gene expression data from lipoprotein lipase (L).

value: lipoprotein lipase treated


title: microRNA profile of case 718N


title: microRNA profile of case 717N


title: Plasma_Hypoxia_MitoQNP_rep1


title: Plasma_Normoxia_MitoQNP_rep4

source_name: foetal plasma at E20, maternal normoxia, maternal MitoQ-nanoparticle injection


title: Plasma_Normoxia_MitoQNP_rep3


title: microRNA profile of case 714N


title: microRNA profile of case 711N


title: Plasma_Normoxia_MitoQNP_rep1


title: Plasma_Normoxia_MitoQNP_rep2


title: Plasma_Hypoxia_Saline_rep3

description: Plasma_NS_v_HS.txt; Plasma_HS_v_HM.txt

source_name: foetal plasma at E20, maternal hypoxia, maternal saline injection


title: microRNA profile of case 710N


title: Plasma_Hypoxia_MitoQNP_rep2


title: microRNA profile of case 709N


title: Plasma_Hypoxia_Saline_rep1

description: Plasma_NS_v_HS.txt; Plasma_HS_v_HM.txt


title: Plasma_Hypoxia_Saline_rep2

description: Plasma_NS_v_HS.txt; Plasma_HS_v_HM.txt


title: microRNA profile of case 706N


title: microRNA profile of case 705N


title: Plasma_Normoxia_Saline_rep4

description: Plasma_NS_v_HS.txt; Plasma_NS_v_NM.txt

source_name: foetal plasma at E20, maternal normoxia, maternal saline injection


title: gat2 SPLEEN male 7months

city: Chicago

first: John

last: Crispino

state: IL

address: 303 E Superior

department: Medicine-Hematology/Oncology

institute: Northwestern University

hyb_protocol: The hybridization, washing and staining of the arrays was performed according to Illumina provided protocols.

scan_protocol: The arrays were scanned using the Illumina HiScan or BeadArray Reader (Cleveland)

data_processing: The data were processed and normalised using Illumina GenomeStudio

organism: Mus musculus

source_name: spleen

label_protocol: Biotinylated, amplified RNA for hybridization with the Illumina HT12v4 arrays was prepared using the Illumina® TotalPrep™ RNA Amplification Kit (Ambion, Cat. no: AMIL1791)

growth_protocol:
These are primary spleen cells from mice matched for sex and age. Cells were obtained by flashing spleen tissue through progressively smaller neddles (19g to 21g)
with IMDM supplemented with 100 U /ml penicillin/streptomycin, 2 mM l-glutamine, 76nM α-monothioglycerol, 1.5% BSA, 20 μg/ml lipids, insulin transferrin selenium and 10ng/mL of recombinant human thrombopoietin.
Cells were then cryopreserved in DMSO and stored in liquid nitrogen until the time of analysis.

extract_protocol: Total RNA were extracted using RNeasy Micro Kit (Qiagen) according to manufacturer's instructions. The quantity and quality of the isolated RNAs was determined using ND-1000 Spectrophotometer.

treatment_protocol: The cells were not treated in any way

tag: Sex

value: male

value: gat


title: microRNA profile of case 145T

source_name: non-small-cell lung cancer


title: gat3 SPLEEN male 7months


title: gat1 SPLEEN male 1month old


title: microRNA profile of case 704N


title: cd2 SPLEEN female 7months

value: female

value: wild type


title: microRNA profile of case 703N


title: Plasma_Normoxia_Saline_rep3

description: Plasma_NS_v_HS.txt; Plasma_NS_v_NM.txt


title: microRNA profile of case 701N


title: Plasma_Normoxia_Saline_rep2

description: Plasma_NS_v_HS.txt; Plasma_NS_v_NM.txt


title: microRNA profile of case 217T


title: gat3 BM male 7months

source_name: primary bone marrow cells

growth_protocol:
These are primary bone marrow cells from mice matched for sex and age. Cells were obtained by flashing bone marrow tissue through progressively smaller neddles (19g to 21g)
with IMDM supplemented with 100 U /ml penicillin/streptomycin, 2 mM l-glutamine, 76nM α-monothioglycerol, 1.5% BSA, 20 μg/ml lipids, insulin transferrin selenium and 10ng/mL of recombinant human thrombopoietin.
Cells were then cryopreserved in DMSO and stored in liquid nitrogen until the time of analysis.


title: gat1 BM male 1month old


title: cd3 SPLEEN female 7months


title: microRNA profile of case 700N


title: microRNA profile of case 153T


title: microRNA profile of case 699N


title: gat2 BM male 7months


title: Plasma_Normoxia_Saline_rep1

description: Plasma_NS_v_HS.txt; Plasma_NS_v_NM.txt


title: cd1 SPLEEN male 7months


title: cd2 BM female 7months


title: microRNA profile of case 696N


title: microRNA profile of case 659N


title: microRNA profile of case 660N


title: microRNA profile of case 692N


title: cd1 BM male 7months


title: microRNA profile of case 698N


title: microRNA profile of case 697N


title: Placenta_Hypoxia_Saline_21_rep4


title: microRNA profile of case 653N


title: microRNA profile of case 657N


title: microRNA profile of case 652N


title: microRNA profile of case 655N


title: microRNA profile of case 694N


title: cd3 BM female 7months


title: microRNA profile of case 646N


title: microRNA profile of case 641N


title: DaxxB MEFs-2

city: philadelphia

first: Xianxin

last: Hua

state: PA

address: 421 Curie BLVD

department: Department of Cancer Biology

institute: University of Pennsylvania Perelman School of Medicine

description: Gene expression data from Daxx knockout Mouse embryonic fibroblasts complemented with Daxx

hyb_protocol: Five and a half micrograms of labeled cDNA were added to Affymetrix hybridization cocktails, heated at 99ºC for 5 min and hybridized for 16 h at 45ºC to Mouse Gene 1.0 ST GeneChips (Affymetrix Inc., Santa Clara CA) using the GeneChip Hybridization oven 645.

scan_protocol: The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain. A GeneChip 3000 7G scanner was used to collect fluorescence signal.

data_processing: Affymetrix Command Console and Expression Console were used to quantitate expression levels for targeted genes; default values provided by Affymetrix were applied to all analysis parameters. Probes for each targeted gene were averaged and inter-array normalization performed using the RMA algorithm

label_protocol: 250 ng of total RNA was converted to first-strand cDNA using reverse transcriptase primed by poly(T) and random oligomers that incorporated the T7 promoter sequence. Second-strand cDNA synthesis was followed by in vitro transcription with T7 RNA polymerase for linear amplification of each transcript, and the resulting cRNA was converted to cDNA, fragmented, assessed by Bioanalyzer, and biotinylated by terminal transferase end labeling.

growth_protocol: Cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% FBS and 1% Pen/Strep at 37C

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

treatment_protocol: Seeded cells into 10 cm2 plate at 70% density. After 24 hours incubation at 37C, detached the cells with 0.25% Tripsin and harvested the cells.

tag: strain

value: FVB/N background

tag: genotype

value: Daxx knockout

value: Mouse embryonic fibroblasts


title: Daxx-/- MEFs-4

description: Gene expression data from Daxx knockout Mouse embryonic fibroblasts complemented with vector


title: Daxx-/- MEFs-3

source_name: Daxx knockout Mouse embryonic fibroblasts complemented with vector


title: DaxxA MEFs-2

source_name: Daxx knockout Mouse embryonic fibroblasts complemented with Daxx


title: DaxxB MEFs-1


title: Daxx-/- MEFs-2


title: microRNA profile of case 627N


title: microRNA profile of case 640N


title: microRNA profile of case 626N


title: Daxx-/- MEFs-1


title: DaxxA MEFs-1


title: Panc1_Ctrl_unstim_#1-90410

city: Kiel

first: Robert

last: Haesler

address: Schittenhelmstr. 12

department: IKMB / 1st Dept. of Medicine

country: Germany

institute: University Clinic of Schleswig Holstein

description: mRNA expression profiles from primary tissue

hyb_protocol: according to the manufacturers guidelines (Affymetrix)

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: Sample data was processed using AGCC (Affymetrix default settings) and normalized using RMA

source_name: Panc1 cells, unstimulated

growth_protocol: Panc1 cells were cultured in RPMI 1640 medium supplemented with 10 % FCS, 1% L-glutamine and 1% sodium pyruvate. The cells were incubated at 37°C with 5% CO2 at 85% humidity.

extract_protocol: RNA extracted using miRVana (Ambion) according to the manufacturers guidelines

treatment_protocol: samples origin from human cell culture

tag: cell type

value: unstimulated


title: Panc1_RelA_Trail5h_#9-90410

source_name: Panc1 cells, stimulated with TRAIL, 5h, RelA si-RNA

label_protocol: according to the manufacturers guidelines (Affymetrix)

value: stimulated with TRAIL, 5h, RelA si-RNA


title: Panc1_RelA_Trail5h_#15-10410


title: microRNA profile of case 642N

source_name: Matched noncancerous lung tissue of NSCLC


title: Panc1_RelA_Trail5h_#9-110310


title: microRNA profile of case 611N


title: Panc1_Ctrl_Trail5h_#7-110310

source_name: Panc1 cells, stimulated with TRAIL, 5h

value: stimulated with TRAIL, 5h


title: Panc1_Ctrl_unstim_#1-110310


title: microRNA profile of case 625N


title: Panc1_Ctrl_Trail5h_#13-10410


title: microRNA profile of case 608N


title: microRNA profile of case 545N


title: microRNA profile of case 547N


title: microRNA profile of case 597N


title: microRNA profile of case 594N


title: microRNA profile of case 543N


title: microRNA profile of case 541N


title: microRNA profile of case 542N


title: Panc1_Ctrl_unstim_#1-10410


title: Panc1_Ctrl_Trail5h_#7-90410


title: microRNA profile of case 534N


title: microRNA profile of case 539N


title: microRNA profile of case 523N


title: microRNA profile of case 513N


title: microRNA profile of case 516N


title: microRNA profile of case 535N


title: microRNA profile of case 517N


title: microRNA profile of case 510N


title: microRNA profile of case 511N


title: microRNA profile of case 508N


title: microRNA profile of case 509N


title: microRNA profile of case 512N


title: microRNA profile of case 503N


title: microRNA profile of case 504N


title: microRNA profile of case 505N


title: Patient No 97

city: Sendai

first: Yoichi

last: Kakuta

state: Miyagi

address: 1-1 Seiryo Aoba

country: Japan

institute: Tohoku University

hyb_protocol: As per manufacturer (Affymetrix)

scan_protocol: As per manufacturer (Affymetrix)

data_processing:
The genotype calling was performed using the Genotyping Console 4.0 with default parameters.
Genotype Call (Allele1/Allele2 or --- ), Confidence

label: Biotin

source_name: peripheral blood

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: genomic DNA was obtained from peripheral blood leukocytes by standard phenol–chloroform extraction precipitation or by utilizing NA1000 Automated Nucleic Acid Extraction Machine (Kurabo, Osaka, Japan) or PAXgene DNA Kit (BD, New Jersey, USA).

value: peripheral blood

tag: disease

value: Crohn's disease

tag: percentage of normal paneth cells

tag: ethnicity

value: Japanese


title: microRNA profile of case 498N


title: Patient No 96


title: microRNA profile of case 502N


title: microRNA profile of case 501N


title: microRNA profile of case 460N


title: microRNA profile of case 459N


title: microRNA profile of case 458N


title: microRNA profile of case 456N


title: microRNA profile of case 506N


title: microRNA profile of case 457N


title: Patient No 92


title: Patient No 94


title: Patient No 91


title: Patient No 98


title: Patient No 95


title: Patient No 86


title: microRNA profile of case 454N


title: microRNA profile of case 455N


title: Patient No 85


title: Patient No 89


title: Patient No 88


title: Patient No 84


title: Patient No 83


title: microRNA profile of case 452N


title: microRNA profile of case 451N


title: Patient No 90


title: microRNA profile of case 445N


title: microRNA profile of case 449N


title: microRNA profile of case 447N


title: microRNA profile of case 446N


title: Patient No 87


title: microRNA profile of case 441N


title: Patient No 81


title: Patient No 82


title: microRNA profile of case 453N


title: microRNA profile of case 439N


title: Patient No 80


title: Patient No 78


title: microRNA profile of case 436N


title: Patient No 73


title: Patient No 75


title: Patient No 72


title: Patient No 74


title: microRNA profile of case 429N


title: microRNA profile of case 431N


title: microRNA profile of case 434N


title: microRNA profile of case 430N


title: Patient No 71


title: microRNA profile of case 426N


title: Patient No 70


title: microRNA profile of case 433N


title: microRNA profile of case 423N


title: microRNA profile of case 427N


title: microRNA profile of case 424N


title: Patient No 93


title: Patient No 69


title: Patient No 77


title: Patient No 68


title: microRNA profile of case 422N


title: Patient No 67


title: Patient No 66


title: Patient No 64


title: Patient No 63


title: Patient No 65


title: microRNA profile of case 428N


title: Patient No 62


title: microRNA profile of case 417N


title: microRNA profile of case 419N


title: microRNA profile of case 416N


title: microRNA profile of case 421N


title: microRNA profile of case 418N


title: microRNA profile of case 420N


title: Patient No 61


title: microRNA profile of case 415N


title: microRNA profile of case 413N


title: Patient No 59


title: Patient No 79


title: microRNA profile of case 411N


title: Patient No 60


title: Patient No 76


title: Patient No 57


title: microRNA profile of case 410N


title: Patient No 56


title: siMed23B

type: SRA

city: Shanghai

first: Min

last: Xia

address: 320 YueYang Road

institute: SIBCB

library_source: transcriptomic

data_processing:
Basecalls performed using CASAVA version 1.4
Clean reads were aligned to the mm9 genome assembly using Tophat with default settings.
RPKM was calculated using Cufflinks,
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: Melanoma cell line

growth_protocol: Cells are culturing in DMEM with 10% FBS and 1% P/S.

extract_protocol:
Total RNAs was extracted using Trizol reagent (Invitrogen), purified by QIAGEN RNAesasy kit, and 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Med23 knockdown-2

value: total RNA


title: siMed23A

value: Med23 knockdown-1


title: siCtrl


title: Patient No 58


title: Patient No 54


title: Patient No 53


title: Patient No 55


title: ISX n2

city: Indianapolis

first: Michael

middle: A

last: Kalwat

state: IN

address: 1210 Waterway Blvd Suite 2000

department: Lilly Diabetes Center of Excellence

institute: Indiana Biosciences Research Institute

description: CHP file generated for Alternative Splicing Analysis from the Expression Console software and then analyzed in the Transcriptome Analysis Console v2.0 for log2 expression values.

hyb_protocol: Samples were hybridized with GeneChip Human HTA Arrays (Affymetrix)

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

data_processing: Raw data were processed with the Expression Console (Affymetrix) for RMA summarization and Quantile normalization.

source_name: Long-term cultured Human Pancreatic Islet cells

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT Plus cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Human pacreatic islets were cultured for 8-14 months in RPMI-1640 with 10% FBS and Pen/Strep prior to treatment.

extract_protocol: Total RNA was isolated using the PureLink RNA Mini Kit (Life Technologies) per manufacturers instructions. On-column DNAse treatment was performed during the purification to eliminate trace genomic DNA.

treatment_protocol: Long-term cultured human pancreatic islet cells were treated with ISX (20uM) or DMSO (0.1%) for 7d with drug/media replacement at day 4.

value: Pancreatic Islet cells, long-term culture


title: DMSO n1


title: microRNA profile of case 425N


title: Patient No 51


title: pcDNA3.1(+)_Cdg7_FLc_0990 full-length_3

city: Omaha

first: Xianming

last: Chen

state: NE

address: 2500 california plaza

institute: creighton university

description: Sample name: CP-D3

hyb_protocol: The labeled cRNAs were hybridized onto the microarray. The Agilent SurePrint G3 Mouse Gene Expression Microarray (G4851B) was used for the analysis, which provides full coverage of genes and transcripts with the most up-to-date content, including mRNAs and lincRNAs (http://www.chem.agilent.com/store/en_US/Prod-G4851B/G4851B

scan_protocol: A total of 2 µg RNA from each sample was then labeled with the Agilent Gene Expression Hybridization Kit (Agilent p/n 5188-5242). After hybridization, the slides were scanned with the Agilent Microarray Scanner (Agilent p/n G2505C),

data_processing: Quantified signals were extracted and analyzed by using the Agilent Feature Extraction Software, in accordance with MIAME guidelines

source_name: pcDNA3.1(+)_Cdg7_FLc_0990 full-length

label_protocol: The sample labeling, microarray hybridization and washing were performed based on the manufacturer’s standard protocols. Briefly, total RNA were transcribed to double strand cDNA, then synthesized into cRNA and labeled with Cyanine-3-CTP.

growth_protocol: The FHs 74 Int human small intestine epithelial cells were obtained from ATCC and cultured in Hybri-Care Medium ATCC 46-X supplemented with 30 ng/ml epidermal growth factor (EGF), 10% fetal bovine serum and antibiotics (100 IU/ml of penicillin and 100 µg/ml of streptomycin). Atmosphere: air, 95%; carbon dioxide (CO2), 5% ; Temperature: 37°C

extract_protocol: Total RNAs were prepared with the RNeasy Mini kit (Qiagen) according to the manufacturer’s instruction.

treatment_protocol: The FHs 74 Int  were grown to 80% confluence for four groups:  control (Group 00-C), C. parvum infection (Group 00-D, cells treated with C. parvum), pcDNA3.1(+) empty vector (Group CP-A, cells transfected with pcDNA3.1(+) empty vector), and pcDNA3.1(+)_Cdg7_FLc_0990 full-length (Group CP-D, cells transfected with pcDNA3.1(+)_Cdg7_FLc_0990 full-length ). 48h later, total RNAs were prepared with the RNeasy Mini kit (Qiagen) according to the manufacturer’s instruction.

value: Small intestine epithelial cell

tag: cell line

value: FHs 74 Int


title: pcDNA3.1(+)_Cdg7_FLc_0990 full-length_1

description: Sample name: CP-D1


title: pcDNA3.1(+)_Cdg7_FLc_0990 full-length_2

description: Sample name: CP-D2


title: pcDNA3.1(+) empty vector_2

description: Sample name: CP-A2

source_name: pcDNA3.1(+) empty vector


title: ISX n1


title: PSPI 3month 4

city: Stanford

first: Joseph

last: Wu

state: Carlifornia

address: Stanford University School of Medicine

institute: Stanford University School of Medicine

description: Sample name: SAMPLE 24

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

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for mGE8x60k array slides (Dye channel is set to Green).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (GE1_107 and Grid: 028005_D_F_20110614) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Right Ventricle

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

extract_protocol: RNA was extracted by QIAGEN RNeasy kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Thermofisher Nanodrop.

treatment_protocol: Sham operated vs surgery to create right ventricular (RV) pressure and volume overload (PSPI)

value: heart

tag: tissue compartment

value: right ventricle


title: PSPI 3month 2

description: Sample name: SAMPLE 22


title: DMSO n2


title: Patient No 49


title: pcDNA3.1(+) empty vector_3

description: Sample name: CP-A3


title: PSPI 3month 1

description: Sample name: SAMPLE 21


title: DMSO n3


title: Patient No 52


title: PSPI 3month 3

description: Sample name: SAMPLE 23


title: C. parvum infection_3

description: Sample name: 00-D3

source_name: C. parvum infection


title: swr1∆ 30°C replicate1

city: San Francisco

first: Kelly

last: Nissen

address: 600 16th Street

department: Biochemistry and Biophysics

institute: UCSF

hyb_protocol: Labelled cDNA was hybridized according to (Inada, M & Pleiss, JA. 2010, PMID 20946806)

scan_protocol: Arrays were scanned on GenePix 4000B scanner and images were quantified GenePic Pro 6.1 software

data_processing: Background subtraction and lowess normalization was applied according to (Inada, M & Pleiss, JA. 2010, PMID 20946806)

label_protocol: Total RNA was reverse transcribed and labelled according to (Inada, M & Pleiss, JA. 2010, PMID 20946806)

growth_protocol: Strains were grown in YES5 overnight at 30°C and then diluted to 0.1 OD600 the next morning to allow for growth to mid log-phase. Cultures were harvested by centrifugation between 0.5–0.8 OD600. Pellets were washed once in water and then flash-frozen in liquid nitrogen and stored at -80°C.

extract_protocol: RNA was isolated using hot acid phenol followed by isopropanol precipitation as previously described (Bergkessel et al. 2011, PMID: 21697354).

treatment_protocol: Temperature shifts, where indicated, occurred when strains had reached 0.3-0.5 OD600. 37°C shifts took place for 2 hours and 16°C shifts for 9 hours.

tag: temperature shift

value: none, grown exclusively at 30 C

source_name: WT


title: PSPI 2month 5

description: Sample name: SAMPLE 20


title: C. parvum infection_2

description: Sample name: 00-D2


title: swr1∆ 30°C replicate2


title: pcDNA3.1(+) empty vector_1

description: Sample name: CP-A1


title: Patient No 48


title: swr1∆ prp16DAmP 37°C replicate3

source_name: swr1-delta prp16DAmP

value: shifted to 37 C for 2 hours


title: swr1∆ 30°C replicate3


title: PSPI 2month 4

description: Sample name: SAMPLE 19


title: C. parvum infection_1

description: Sample name: 00-D1


title: Patient No 47


title: ISX n3


title: Patient No 45


title: Patient No 44


title: swr1∆ prp16DAmP 37°C replicate2


title: PSPI 2month 2

description: Sample name: SAMPLE 17


title: PSPI 2month 1

description: Sample name: SAMPLE 16


title: PSPI 1month 4

description: Sample name: SAMPLE 14


title: Ctrl_3

description: Sample name: 00-C3

source_name: Ctrl


title: prp16DAmP 37°C replicate2


title: Ctrl_1

description: Sample name: 00-C1


title: PSPI 1month 5

description: Sample name: SAMPLE 15


title: Patient No 46


title: swr1∆ prp16DAmP 37°C replicate1


title: Patient No 43


title: Ctrl_2

description: Sample name: 00-C2


title: prp16DAmP 37°C replicate1


title: LAP+/OC.2- E19 fetal hepatocytes bio rep 2

city: Providence

first: Jennifer

middle: Ann

last: Sanders

state: RI

address: 593 Eddy Street

department: Pediatric Endocrinology

institute: Rhode Island Hospital

description:
OC2- 2
OC.2-  2

hyb_protocol: ~ 2.3 ug/array, 17 h, 45 C, 60 rpm, Fluidics protocol FS450_0001

scan_protocol: Arrays were scanned using an Affymetrix GeneScanner 3000 7G

data_processing: Partek Genomics Suite, version 6.6, RMA ANOVA with contrast, 0.05 % FDR correction

source_name: LAP+/OC.2- E19 fetal hepatocytes

label_protocol: Affymetrix WT amplification protocol was performed according to manufacturer's instructions.  150 ng total RNA input at start of RT rx, fragmentation: 5.5ug dUTP labeled sscDNA/rx, labeling: ~5.15 ug/rx

growth_protocol: All animals were housed under standard conditions with access to food and water ad libitum.  See sample columns for treatment protocols related to the different experimental groups.

extract_protocol: RNA was extracted using the Mirvana kit according to the manufacturer's directions.

treatment_protocol: RNA was extracted from freshly isolated cells.  The methodology for immunopurification of cells is described in Sanders JA. Late gestation fetal hepatocytes for repopulation in the rat.  Methods Mol Biol. 2017;1506:45-60

tag: age

value: Embryonic Day 19

value: Liver

value: LAP+/OC.2- E19 fetal hepatocytes

tag: cell isolation

value: Collagenase digestion, Immunopurification with monoclonal antibodies against leucine amino peptidase and OC.2.  AutoMacs purified with double positive selection program


title: PSPI 1month 3

description: Sample name: SAMPLE 13

tag: tissue


title: Patient No 42

value: peripheral blood


title: LAP+/OC.2- E19 fetal hepatocytes bio rep 3

description:
OC2- 3
OC.2- 3


title: LAP+/OC.2- E19 fetal hepatocytes bio rep 1

description:
OC2- 1
OC.2- 1


title: Patient No 41

value: Crohn's disease


title: swr1∆ 37°C replicate2


title: LAP+/OC.2+ E19 fetal hepatocytes bio rep 3

description:
LAP-OC2+ 3
LAP-OC.2+  3

source_name: LAP+/OC.2+ E19 fetal hepatocytes

value: LAP+/OC.2+ E19 fetal hepatocytes


title: PSPI 1month 2

description: Sample name: SAMPLE 12


title: prp16DAmP 37°C replicate3


title: swr1∆ 37°C replicate3


title: LAP+/OC.2+ E19 fetal hepatocytes bio rep 2

description:
LAP-OC2+ 2
LAP-OC.2+ 2


title: swr1∆ 37°C replicate1


title: PSPI 1month 1

description: Sample name: SAMPLE 11


title: Sham 10

description: Sample name: SAMPLE 10


title: Patient No 40

value: Japanese


title: Patient No 39


title: Patient No 38


title: LAP+/OC.2+ E19 fetal hepatocytes bio rep 1

description:
LAP-OC2+ 1
LAP-OC.2+ 1


title: Patient No 37


title: Patient No 35


title: Adult Hepatocytes, bio rep 3

description:
Adult 3
Adult Heaptocytes Rep 3

source_name: Adult Hepatocytes

value: 5-6 weeks

value: Adult Hepatocytes

value: Perfusion with 2-step collagenase digestion


title: pht1∆ prp16DAmP 16°C replicate2

source_name: pht1-delta prp16DAmP

value: shifted to 16 C for 9 hours


title: Patient No 34


title: Men1-/- MEFs-2

description: Gene expression data from Men1 knockout Mouse embryonic fibroblasts complemented with vector

hyb_protocol: 15 ug labeled cDNA were added to Affymetrix hybridization cocktails, heated at 99ºC for 5 min and hybridized for 16 h at 45ºC to Affymetrix Murine Genome U74Av2 GeneChips using the GeneChip Hybridization oven 640.

data_processing: Affymetrix Command Console and Expression Console were used to quantitate expression levels for targeted genes using MAS 5.0

label_protocol: Total RNA was converted to first-strand cDNA using reverse transcriptase primed by poly(T) and random oligomers that incorporated the T7 promoter sequence. Second-strand cDNA synthesis was followed by in vitro transcription with T7 RNA polymerase for linear amplification of each transcript, and the resulting cRNA was converted to cDNA, fragmented, assessed by Bioanalyzer, and biotinylated by terminal transferase end labeling.

value: mixed FVB;129Sv background

value: Men1 knockout

value: Mouse embryonic fibroblasts


title: Adult Hepatocytes, bio rep 2

description:
Adult 2
Adult Heaptocytes Rep 2


title: Men1 MEFs-2

description: Gene expression data from Men1 knockout Mouse embryonic fibroblasts complemented with Men1


title: pht1∆ prp16DAmP 16°C replicate3


title: pht1∆ prp16DAmP 16°C replicate1


title: Sham 9

description: Sample name: SAMPLE 9

value: heart

value: right ventricle


title: prp16DAmP 16°C replicate3


title: Adult Hepatocytes, bio rep 1

description:
Adult 1
Adult Hepatocytes Rep 1


title: Sham 6

description: Sample name: SAMPLE 6


title: Sham 7

description: Sample name: SAMPLE 7


title: Men1-/- MEFs-1

source_name: Men1 knockout Mouse embryonic fibroblasts complemented with vector


title: Sham 8

description: Sample name: SAMPLE 8


title: Sham 5

description: Sample name: SAMPLE 5


title: Patient No 36


title: pht1∆ 16°C replicate3


title: Patient No 33


title: Patient No 32


title: PSPI 2month 3

description: Sample name: SAMPLE 18


title: prp16DAmP 16°C replicate1


title: prp16DAmP 16°C replicate2


title: Patient No 31


title: Patient No 30


title: Men1 MEFs-1

source_name: Men1 knockout Mouse embryonic fibroblasts complemented with Men1


title: Patient No 29


title: Patient No 28


title: pht1∆ 16°C replicate2


title: Sham 3

description: Sample name: SAMPLE 3


title: Patient No 27


title: Sham 4

description: Sample name: SAMPLE 4


title: Patient No 26


title: Patient No 50


title: Patient No 24


title: pht1∆ usp107DAmP 30°C replicate2

source_name: pht1-delta usp107DAmP

value: none, grown exclusively at 30 C


title: pht1∆ usp107DAmP 30°C replicate3


title: Sham 1

description: Sample name: SAMPLE 1


title: usp107DAmP 30°C replicate1


title: pht1∆ 16°C replicate1


title: pht1∆ usp107DAmP 30°C replicate1


title: Patient No 25

source_name: peripheral blood


title: Sham 2

description: Sample name: SAMPLE 2


title: usp107DAmP 30°C replicate2


title: usp107DAmP 30°C replicate3


title: Patient No 23


title: pht1∆ 30°C replicate3


title: Patient No 21


title: Patient No 22


title: Patient No 19


title: Patient No 18


title: pht1∆ 30°C replicate2


title: Patient No 17


title: Patient No 20


title: pht1∆ 30°C replicate1


title: Patient No 14


title: Patient No 16


title: Patient No 12


title: Patient No 15


title: Patient No 13


title: Patient No 11


title: Patient No 9


title: Case 3 Nodule 6

city: Rochester

first: Keith

middle: D

last: Robertson

state: Minnesota

address: 200 1st St SW

department: Molecular Pharmacology & Experimental Therapeutics

institute: Mayo Clinic

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

scan_protocol: Arrays were imaged using Illumina iScan using standard recommended Illumina scanner setting

data_processing: Subset-quantile Within Array Normalization (SWAN) via R Bioconductor package minfi.

label: Cy5 and Cy3

source_name: Liver

label_protocol: Standard Illumina Infinium HD Methylation assay protocol

extract_protocol: DNA was extracted from FFPE tissue using the WaxFree DNA Extraction Kit (TrimGen). DNA was quantified using the Quant-iT PicoGreen dsDNA Assay Kit (ThermoFisher) and checked for quality using a custom TaqMan probe

tag: disease state

value: HCV-infection

tag: individual

value: patient 3

tag: gender

value: Male

value: Liver

tag: tissue region

value: cirrhotic nodule


title: Case 3 Nodule 8


title: Patient No 8

value: peripheral blood

value: Crohn's disease


title: Case 3 Nodule 5


title: Case 3 Tumor 1

value: tumor


title: Case 3 Nodule 9


title: Patient No 10

value: Japanese


title: Patient No 6


title: Patient No 7


title: Patient No 5


title: Case 3 Nodule 10


title: Case 3 Nodule 7


title: Patient No 3


title: Patient No 4


title: Case 2 Nodule 7

value: patient 2


title: Case 3 Nodule 1


title: Patient No 2


title: Patient No 1


title: Case 2 Nodule 5


title: Case 3 Nodule 4


title: Case 2 Nodule 1


title: Case 3 Nodule 2


title: Case 3 Nodule 3


title: Case 1 Nodule 9

value: patient 1


title: Case 2 Nodule 8


title: Case 1 Nodule 8


title: Case 2 Nodule 9


title: Case 2 Nodule 4


title: Case 1 Nodule 7


title: NILDOG6 AR Imb (AR_DOG6.2)

status: Public on Aug 21 2017

city: Wageningen

first: Leónie

last: Bentsink

address: Droevendaalsesteeg 1

country: Netherlands

institute: Wageningen University

hyb_protocol: The GeneChip (#900720) HWS kit was used for hybridisation, washing and staining of the cartridges.

scan_protocol: Scanning of the arrays was performed using the Affymetrix 3000G scanner.

data_processing: The GeneChip data were analyzed using the R statistical programming environment and Bioconductor packages. The data were normalized using the RMA algorithm using a custom chip definition file (.cdf) from the CustomCDF project (Ath1121501_At_TAIRG.cdf v18.0.0, released 23rd January 2014 obtained via http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/).

organism: Arabidopsis thaliana

source_name: Imbibed seeds, DELAY OF GERMINATION 6 NIL, after-ripened

label_protocol: RNA was processed and cRNA synthesized according to the 3' GeneChips OneCycle kit.

growth_protocol: For the transcriptome analyses of Ler and the NILs, plants were grown in a randomized complete block design with three replicates. Each replicate consisted of a bulk of eight plants. The precise growth conditions used were described by (El-Lithy et al., Genetics, 2006).

extract_protocol: Total RNA was prepared from dry seeds using RNAqueous columns with Plant RNA isolation aid (Ambion) according to the manufacturer's protocol. The RNA was further purified through precipitations with isopropanol and a high-salt precipitation solution containing 0.24 M sodium citrate and 0.16 M sodium chloride and subsequently with 2 M lithium chloride. RNA was qualitatively assessed and quantified using an Agilent 2100 Bioanalyzer with the RNA 6000 Nano LabChip kit (Agilent) and NanoDrop1000 spectrometry (NanoDrop Technologies).

treatment_protocol: RNA was extracted from whole seeds that were imbibed for 24h in water.

tag: ecotype/background

value: Landsberg erecta

tag: genotype/variation

value: DELAY OF GERMINATION 6

value: Whole seeds

tag: plant stage

value: After-ripened

tag: protocol

value: After-ripened seeds imbibed in water for 24h


title: Case 2 Nodule 3


title: NILDOG3 AR Imb (AR_DOG3.3)

source_name: Imbibed seeds, DELAY OF GERMINATION 3 NIL, after-ripened

value: DELAY OF GERMINATION 3


title: NILDOG6 AR Imb (AR_DOG6.1)


title: Case 2 Nodule 2

value: HCV-infection


title: Case 2 Nodule 10


title: NILDOG2 AR Imb (AR_DOG2.3)

source_name: Imbibed seeds, DELAY OF GERMINATION 2 NIL, after-ripened

value: DELAY OF GERMINATION 2


title: NILDOG2 AR Imb (AR_DOG2.1)


title: Case 2 Nodule 6

value: Male


title: NILDOG1 AR Imb (AR_DOG1.2)

source_name: Imbibed seeds, DELAY OF GERMINATION 1 NIL, after-ripened

value: DELAY OF GERMINATION 1


title: NILDOG1 AR Imb (AR_DOG1.3)


title: NILDOG6 AR Imb (AR_DOG6.3)


title: Case 1 Nodule 4

value: Liver

value: cirrhotic nodule


title: Case 1 Nodule 10


title: NILDOG2 AR Imb (AR_DOG2.2)


title: Case 1 Nodule 5


title: Case 1 Nodule 3


title: Ler AR Imb (AR_Ler.1)

source_name: Imbibed seeds, wild-type Landsberg erecta, after-ripened

value: Wild-type


title: Ler AR Imb (AR_Ler.3)


title: NILDOG3 AR Imb (AR_DOG3.2)


title: NILDOG6 D Imb (FR_DOG6.2)

source_name: Imbibed seeds, DELAY OF GERMINATION 6 NIL, dormant

value: Dormant

value: Dormant seeds imbibed in water for 24h


title: NILDOG3 D Imb (FR_DOG3.2)

source_name: Imbibed seeds, DELAY OF GERMINATION 3 NIL, dormant


title: NILDOG3 D Imb (FR_DOG3.3)


title: Case 1 Nodule 1


title: Case 1 Nodule 6


title: Case 1 Nodule 2


title: NILDOG1 AR Imb (AR_DOG1.1)


title: NILDOG1 D Imb (FR_DOG1.4)

source_name: Imbibed seeds, DELAY OF GERMINATION 1 NIL, dormant


title: NILDOG1 D Imb (FR_DOG1.5)


title: NILDOG2 D Imb (FR_DOG2.1)

source_name: Imbibed seeds, DELAY OF GERMINATION 2 NIL, dormant


title: NILDOG6 D Imb (FR_DOG6.1)


title: NILDOG1 D Imb (FR_DOG1.1)


title: NILDOG1 D Imb (FR_DOG1.2)


title: NILDOG1 D Imb (FR_DOG1.3)


title: Ler D Imb (FR_Ler.4)

source_name: Imbibed seeds, wild-type Landsberg erecta, dormant


title: Ler AR Imb (AR_Ler.2)


title: NILDOG3 AR Imb (AR_DOG3.1)


title: NILDOG2 D Imb (FR_DOG2.3)


title: NILDOG6 D Imb (FR_DOG6.3)


title: Ler D Imb (FR_Ler.2)


title: US22502698_251521010066

city: la jolla

first: Wolfgang

last: Busch

state: CALIFORNIA

address: Salk institute, 10010 n torrey pines rd

institute: Salk Institute for Biological Studies

hyb_protocol: Hybridization was performed according to the Agilent ChIP-chip protocol

scan_protocol: Images were obtained using an Agilent microarray scanner (model G2565BA) at a resolution of 5 μm. Signal extraction and initial data processing were done using the Agilent feature extraction software

data_processing: For ChIP-chip analysis, to assess genome-wide binding the processed signal ratios of each experiment were randomly sampled 10,000 times and an empirical P-value was estimated for each ratio [like in like described in Busch W, Miotk A, Ariel FD, Zhao Z, Forner J, Daum G, Suzaki T, Schuster C, Schultheiss SJ, Leibfried A, Haubeiss S, Ha N, Chan RL, Lohmann JU. (2010) Transcriptional control of a plant stem cell niche. Dev. Cell 18:849-61]. The empirical P-values for each probe of the independent ChIP-chip experiments were multiplied.

source_name: roots of Col-0 plants

label_protocol: After labelling with Cy3 and Cy5, respectively, following an amino-allyl-dye coupling protocol (http://camd.bio.indiana.edu/files/amino-allyl-protocol.pdf), DNA was cleaned up using the PCR purification kit (Qiagen) and 3 μg from the ChIP and from the mock samples were taken and mixed for hybridization to a custom long oligonucleotide (~60 bases) Arabidopsis promoter microarray.

growth_protocol: Roots were used of of 5-day-old seedlings expressing ARR1 genomic sequence under the control of its own promoter, fused to GFP (pARR1::ARR1:GFP plants)

extract_protocol: Chip was performed like described in Busch W, Miotk A, Ariel FD, Zhao Z, Forner J, Daum G, Suzaki T, Schuster C, Schultheiss SJ, Leibfried A, Haubeiss S, Ha N, Chan RL, Lohmann JU. (2010) Transcriptional control of a plant stem cell niche. Dev. Cell 18:849-61. except that DNA-free protein A agarose beads (Invitrogen) were used. Immunoprecipitation was performed using a rabbit polyclonal antibody against GFP (ab290, Abcam). DNA from the ChIP and mock experiments was amplified using a random-primer-based genome amplification method described in http://cat.ucsf.edu/pdfs/22_Round_A_B_C_protocol.pdf, with minor modifications.

value: root

tag: strain

source_name: roots of pARR1::ARR1:GFP plants


title: Ler D Imb (FR_Ler.3)


title: US22502698_251521010069


title: NILDOG2 D Imb (FR_DOG2.2)


title: Ler D Imb (FR_Ler.1)


title: Hippocampus, Stroke at 7d

city: Berkeley

first: Soo Young

last: Kim

department: IB

institute: UC Berkeley

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized according to the manufacturer's protocol.

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

data_processing: Using Expression Console (Affymetrix), the data were normalized using the RMA algorithm. Ratios of normalized probeset intensity values were calculated for each sample pair and then averaged among the three replicate pairs.

source_name: Hippocampus, stroke, 7d

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA.

growth_protocol: Animals were maintained, provided with food and water ad libitum.

treatment_protocol: Brain regions (isolated cortices or hippocampi) were extracted and fresh frozen.

tag: strain/background

value: Wistar

value: Dissected brain (hippocampus)

value: male

value: adult

tag: treatment

value: stroke

tag: time point


title: Cortex, Undercut at 24h, biological rep2

source_name: Neocortex, undercut, 24h

value: Sprague-Dawley

value: Dissected brain (neocortex)

value: undercut


title: US22502698_251521010068


title: Hippocampus, Sham (Stroke) at 12h

source_name: Hippocampus, sham for stroke, 12h

value: sham for stroke


title: Hippocampus, Sham (Stroke) at 7d

source_name: Hippocampus, sham for stroke, 7d


title: Ler D Imb (FR_Ler.5)

value: Landsberg erecta

value: Whole seeds


title: Hippocampus, Sham (Stroke) at 24h

source_name: Hippocampus, sham for stroke, 24h


title: US22502698_251521010067


title: NILDOG3 D Imb (FR_DOG3.1)

value: DELAY OF GERMINATION 3


title: Cortex, Undercut at 24h, biological rep1


title: Cortex, Sham (UC) at 24h, biological rep1

source_name: Neocortex, sham for undercut, 24h

value: sham for undercut


title: Cortex, Sham (UC) at 24h, biological rep3


title: Cortex, Sham (UC) at 24h, biological rep2


title: Hippocampus, Stroke at 12h

source_name: Hippocampus, stroke, 12h


title: Hippocampus, Stroke at 24h

source_name: Hippocampus, stroke, 24h


title: CD8a+DC biological rep3

city: Illkirch

first: Doulaye

last: Dembele

address: 1 rue Laurent Fries

department: Biopuces

country: France

institute: IGBMC

description: Gene expression data from lymph node Cd8a+DC

hyb_protocol: Following fragmentation and end-labelling, 2.07 μg of cDNAs were hybridized for 16 hours at 45oC on GeneChip® Mouse Gene 1.0 ST arrays (Affymetrix) interrogating 28.853 genes represented by approximately 27 probes spread across the full length of the gene.

scan_protocol: The chips were washed and stained in the GeneChip® Fluidics Station 450 (Affymetrix) and scanned with the GeneChip® Scanner 3000 7G (Affymetrix) at a resolution of 0,7 µm.

data_processing: Raw data (.CEL Intensity files) were extracted from the scanned images using the Affymetrix GeneChip® Command Console (AGCC) version 4.0. CEL files were further processed with Affymetrix Expression Console software version 1.3.1 to calculate probe set signal intensities using Robust Multi-array Average (RMA) algorithms with default settings.

source_name: mouse lymph node

label_protocol: Enriched cells were labelled with various fluorescent antibodies and sorted as follows: LN TZM (GFPhi, MertK+ CD169- CD11b+); brain macrophages (GFPhi, CD11b+ CD45+); splenic CD8 DC (CD64- CD11chi MHCIIhi CD8+).

extract_protocol: Scissor minced lymph nodes (LN), brain and spleen from CX3CR1gfp+/- mice were incubated for 45 min at 37 °C in RPMI medium containing 0.1 mg/ml Dnase I (Sigma), 400U/ml collagenase I (Invitrogen). Single-cell suspension underwent positive enrichment for CD11b+ cells (TZM and brain macrophages) and CD11c+ cells (CD8 DC) through the use of CD11c microbeads (Miltenyi Biotec).

tag: genotype

value: CX3CR1 gfp+/-

value: lymph node

tag: cell type


title: Control rep2

city: Yangling

first: Haibo

address: 3rd, Taicheng Road

institute: Northwest A&F University

data_processing:
Clean reads were obtained from the raw reads by removing the adaptor sequences, reads with >5% ambiguous bases (noted as N) and low-quality reads containing more than 20 percent of bases with qualities of <13. The clean reads were then aligned to mouse genome (version: mm10) using the MapSplice program (v2.1.6). In alignment, preliminary experiments were performed to optimize the alignment parameters (-s 22 -p 15 --ins 6 --del 6 --non-canonical).
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.We applied DEseq algorithm to filter the differentially expressed genes, after the significant analysis and FDR analysis under the following criteria: i) Fold Change>2 or <0.5; ii) FDR<0.05.
Pathway analysis was used to find out the significant pathway of the differential genes according to KEGG database. We turn to the Fisher’s exact test to select the significant pathway, and the threshold of significance was defined by P-value and FDR.
Gene ontology (GO) analysis was performed to facilitate elucidating the biological implications of unique genes in the significant or representative profiles of the differentially expressed gene in the experiment. We downloaded the GO annotations from NCBI (http://www.ncbi.nlm.nih.gov/), UniProt (http://www.uniprot.org/) and the Gene Ontology (http://www.geneontology.org/). Fisher’s exact test was applied to identify the significant GO categories and FDR was used to correct the p-values.
We present Gene co-expression Networks to find the relations among genes. Gene co-expression Networks were built according to the normalized expression values of genes selected from genes in significant GO-terms. For each pair of genes, we calculate the Pearson Correlation and choose the significant correlation pairs (FDR<0.05) to constructed the network.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample …

source_name: J1 ES cells

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
RNA libraries were prepared for sequencing using IonProton,The cDNA libraries were then processed for the Proton Sequencing process according to the commercially available protocols.

tag: cell line

value: embryonic stem cell

value: wild type


title: Control rep1


title: Control rep3


title: TZM biological rep1

description: Gene expression data from lymph node T cell zone macrophages (TZM)

value: T cell zone macrophages (TZM)


title: microglia biological rep2

description: Gene expression data from brain macrophages (microglia)

source_name: mouse brain

value: brain

value: macrophages (microglia)


title: microglia biological rep3


title: CD8a+DC biological rep2


title: TZM biological rep3


title: CD8a+DC biological rep1


title: TZM biological rep2


title: microglia biological rep1


title: +NAM early, cl.14

city: Marseille

first: Julien

last: Maurizio

address: Centre d’Immunologie de Marseille-Luminy

institute: INSERM

description: Maf-DKO + NAM early_14

hyb_protocol: Following fragmentation and end-labeling, 1.9 µg of CDNAs were hybridized for 16 hours at 45°C on GeneChip® Mouse Gene 1.0 ST arrays (Affymetrix) interrogating 28.853 genes represented by approximately 27 probes spread across the full length of the gene. The chips were washed and stained in the GeneChip® Fluidics Station 450 (Affymetrix).

scan_protocol: The chips were scanned with the GeneChip® Scanner 3000 7G (Affymetrix) at a resolution of 0.7 µm.

data_processing: Raw data (.CEL Intensity files) were extracted from the scanned images using the Affymetrix GeneChip® Command Console (AGCC) version 3.2. CEL files were further processed with affy Bioconductor package (release 2.9) to calculate normalized probe set signal intensities using Robust Multi-array Average (RMA) algorithm with default settings.

source_name: murine macrophage_NAM for 1h

label_protocol: Biotinylated single strand cDNA targets were prepared, starting from 200 ng of total RNA, using the Ambion WT Expression Kit (Cat # 4411974) and the Affymetrix GeneChip® WT Terminal Labeling Kit (Cat # 900671) according to Affymetrix recommendations.

growth_protocol: Maf-DKO macrophages were seeded in 6-well plate and cultured overnight in M-CSF conditioned medium at a densitity of 2x105 cells/well. Thee independent clones for each sample were used as biological replicates.

extract_protocol: Total RNA of Maf-DKO cells (n=3 biological replicates for each sample/treatment) was extracted using Qiagen RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions. The quality of RNA was assessed using Agilent 2100 Bioanalyzer using Eukaryote Total RNA Nano Chip platform (Agilent Technologies). The extracted RNAs had a RIN > 8.9.

treatment_protocol: The next day, cells were stimulated with fresh M-CSF conditioned medium supplied (or not) with 10 mM Nicotinamide for 1h or 10h prior to RNA isolation.

value: double deficiency for MafB and c-Maf (Maf-DKO)

value: murine primary macrophage

tag: clone id

value: clone 14

tag: treated with

value: 10 mM Nicotinamide (NAM) for 1h


title: Patient17_EGC

city: Beijing

first: li

middle: cheng

last: Zhang

state: Beijing

address: No. 17 Panjiayuan Nanli, Chaoyang District

institute: National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College

description: Gene expression after gastroscopic biopsy

hyb_protocol: 600 ng 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 25 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions.  On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE  8x60K Microarray (G4851B) for 17 hours at 65 °C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37 °C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on Agilent SureScan Microarray Scanner (G2600D) using default settings for 8x60k array slides.

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (protocol: GE1_105_Dec08 and Grid: 039494_D_F_20120628) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
Normalized signal intensity using  GeneSpring GX v12.6.1 (Silicon Genetics, CA, USA) by its default settings.

source_name: gastroscopic biopsy, patient17, EGC

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (Qiagen, MD, United States).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was extracted using an RNeasy Mini Kit (Qiagen, MD, United States) following the manufacturers instructions. RNA concentration and integrity were determined using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, USA) and an Agilent 2100 Bioanalyser (Agilent, CA, United States), respectively.

value: Patient 17

tag: tissue

value: gastroscopic biopsy

tag: age

value: Female

tag: pathological stage

value: early gastric carcinoma (EGC)


title: no NAM, cl.14

description: Maf-DKO no NAM_14

source_name: murine macrophage_untreated

value: untreated (proliferating)


title: +NAM late, cl.11

description: Maf-DKO + NAM late_11

source_name: murine macrophage_NAM for 10h

value: clone 11

value: 10 mM Nicotinamide (NAM) for 10h


title: Patient18_EGC

source_name: gastroscopic biopsy, patient18, EGC

tag: individual

value: Patient 18

tag: gender

value: Male


title: Cortex, Undercut at 24h, biological rep3

value: Sprague-Dawley

value: Dissected brain (neocortex)

value: male

value: adult

value: undercut


title: Patient15_EGC

source_name: gastroscopic biopsy, patient15, EGC

value: Patient 15


title: +NAM late, cl.14

description: Maf-DKO + NAM late_14

tag: genotype/variation

value: double deficiency for MafB and c-Maf (Maf-DKO)

value: murine primary macrophage

value: clone 14


title: Patient16_EGC

source_name: gastroscopic biopsy, patient16, EGC

value: Patient 16

value: gastroscopic biopsy


title: Patient19_EGC

source_name: gastroscopic biopsy, patient19, EGC

value: Patient 19

value: early gastric carcinoma (EGC)


title: +NAM early, cl.11

description: Maf-DKO + NAM early_11

value: clone 11

value: 10 mM Nicotinamide (NAM) for 1h


title: Patient14_EGC

source_name: gastroscopic biopsy, patient14, EGC

value: Patient 14

value: Female


title: +NAM late, cl.01

description: Maf-DKO + NAM late_01

value: clone 01

value: 10 mM Nicotinamide (NAM) for 10h


title: no NAM, cl.11

description: Maf-DKO no NAM_11

value: untreated (proliferating)


title: +NAM early, cl.01

description: Maf-DKO + NAM early_01


title: Patient13_HGIN

source_name: gastroscopic biopsy, patient13, HGIN

value: Patient 13

value: Male

value: high-grade intraepithelial neoplasia (HGIN)


title: Patient12_HGIN

source_name: gastroscopic biopsy, patient12, HGIN

value: Patient 12


title: Patient11_HGIN

source_name: gastroscopic biopsy, patient11, HGIN

value: Patient 11


title: Patient7_LGIN

source_name: gastroscopic biopsy, patient7, LGIN

value: Patient 7

value: low-grade intraepithelial neoplasia (LGIN)


title: Patient10_HGIN

source_name: gastroscopic biopsy, patient10, HGIN

value: Patient 10

value: gastroscopic biopsy


title: Patient3_HGIN

source_name: gastroscopic biopsy, patient3, HGIN

value: Patient 3


title: Patient3_LGIN

source_name: gastroscopic biopsy, patient3, LGIN


title: Patient6_LGIN

source_name: gastroscopic biopsy, patient6, LGIN

value: Patient 6


title: Patient2_HGIN

source_name: gastroscopic biopsy, patient2, HGIN

value: Patient 2


title: Patient4_LGIN

source_name: gastroscopic biopsy, patient4, LGIN

value: Patient 4


title: Patient9_HGIN

source_name: gastroscopic biopsy, patient9, HGIN

value: Patient 9

value: Female


title: Patient2_LGIN

source_name: gastroscopic biopsy, patient2, LGIN


title: Patient8_HGIN

source_name: gastroscopic biopsy, patient8, HGIN

value: Patient 8


title: Patient1_HGIN

source_name: gastroscopic biopsy, patient1, HGIN

value: Patient 1


title: Patient5_LGIN

source_name: gastroscopic biopsy, patient5, LGIN

value: Patient 5


title: LPS-Roselle_2

city: Taichung

first: Chien-Yun

last: Hsiang

address: 91 Hsueh-Shih Road

country: Taiwan

institute: China Medical University

hyb_protocol: Fluorescent targets were hybridized to Mouse Whole Genome OneArrayTM (Phalanx Biotech Group, Hsinchu, Taiwan).

scan_protocol: The slides were scanned by an Axon 4000 scanner (Molecular Devices, Sunnyvale, CA, USA).

data_processing: The Cy5 fluorescent intensity of each spot was analyzed by Genepix 4.1 software (Molecular Devices, Sunnyvale, CA, USA). The signal intensity of each spot was corrected by subtracting background signals in the surrounding. We filtered out spots that signal-to-noise ratio was less than 0 or control probes. Spots that pass aforementioned criteria were normalized by R program in the limma package.

source_name: Roselle administration and LPS challenge

label_protocol: Fluorescence-labeled RNA targets were prepared from 5 μg of total RNA using MessageAmpTM aRNA kit (Ambion, Austin, TX, USA) and Cy5 dye (Amersham Pharmacia, Piscataway, NJ, USA).

extract_protocol: Total RNAs were extracted from tissues using RNeasy Mini kit (Qiagen, Valencia, CA, USA).

treatment_protocol: Mice were given orally with 0.2 g/kg roselle drink for seven consecutive days and then given intraperitoneally with 1 mg/kg LPS. Four hours after LPS challenge, mice were sacrificed for RNA extraction.

value: BALB/c

tag: Sex

value: renal pelvis


title: LPS-Roselle_3


title: LPS-Roselle_1


title: LPS_3

source_name: LPS challenge


title: Patient1_LGIN

source_name: gastroscopic biopsy, patient1, LGIN

value: Male


title: DT40_H2A.Z_DKO

first: Masahiko

last: Harata

address: 468-1 Aramaki Aza Aoba, Aoba-ku

department: Graduate School of Agricultural Science

description: Gene expression in DT40 H2A.Z DKO cells stably expressing H2A.Z.1

hyb_protocol: 1.65 ug of Cy3-labelled cRNA was fragmented at 60 ºC for 30 min and hybridized by using Gene Expression Hybridization Kit (Agilent) according to the user guide.

scan_protocol: Slides were scanned by using Agilent DNA Microarray Scanner G2565CA.

data_processing: The scanned images were analyzed with Feature Extraction Software.

organism: Gallus gallus

source_name: DT40 H2A.Z isoforms double knockout (DKO) cells, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA by using Low Input Quick Amp labeling kit, one-color (Agilent) according to the provided protocol.

growth_protocol: DT40 cells were cultured at 38 ºC in Dulbecco’s modified medium supplemented with 10% fetal bovine serum, 1% chicken serum, 2-merchaptoethanol, penicillin and streptomycin.

extract_protocol: Total RNAs were extracted with the RNeasy mini kit (QIAGEN) according to the manufacture’s protocol.

treatment_protocol: To suppress expression of the tetracycline repressive H2A.Z.1 transgene, tetracycline was added to the culture medium to a final concentration of 2 µg/ml. Each cell was cultured in the presence of tet for 72 hours.

tag: origin

value: B cell


title: DT40_H2A.Z_DKO/5KR-H2A.Z

description: Gene expression in DT40 H2A.Z DKO cells stably expressing 5KR-H2A.Z

source_name: DT40 H2A.Z DKO cells stably expressing 5KR-H2A.Z, replicate 1


title: Mock_3

source_name: Mock

tag: strain


title: DT40_H2A.Z_DKO/H2A.Z.1

source_name: DT40 H2A.Z DKO cells stably expressing H2A.Z.1, replicate 1


title: LPS_1


title: no NAM, cl.01

description: Maf-DKO no NAM_01

source_name: murine macrophage_untreated

value: double deficiency for MafB and c-Maf (Maf-DKO)

value: murine primary macrophage

value: clone 01

value: untreated (proliferating)


title: Mock_2


title: Mock_1


title: MV4;11 cells treated with DMSO, biological replicate 3

city: Gaithersburg

first: Jingya

last: Wang

state: Maryland

address: 1 Medimmune Way

description: Gene expression data of MV4;11 cells treated with DMSO, biological replicates 3

hyb_protocol: Biotinylated cRNA was hybridized to Affymetrix Gene Atlas U219 Human Genome array strips according to Affymetrix protocols

scan_protocol: The arrays were scanned according to standard Affymetrix GeneAtlas instructions using the GeneAtlas scanner

data_processing: The data were analyzed with affy and limma package of Bioconductor. Raw expression values were RMA normalized and log 2 transformed. Differential expression was tested using Bayesian linear regression model (limma).

source_name: Human leukemia cell line: MV4;11

label_protocol: Total RNA was amplified and labeled according to Affymetrix 3’-IVT labeling protocol

growth_protocol: MV4;11 cells were cultured in RPMI-1640 medium with 10% FBS and 1% penicillin/streptomycin

extract_protocol: Total RNA was extracted from cells using RNeasy mini kit (Qiagen) according to manufacturer instructions, and 1 µg total RNA was submitted for microarray studies.

treatment_protocol: MV4;11 cells were plated in 12-well plates at the initial concentration of 1 mln cells/ml and treated with 4 µM of MI-389 or DMSO, at final DMSO concentration of 0.25%, for 6 days. Media were changed at day three, with viable cell concentration restored to 1 mln cells/ml and compound or DMSO resupplied.

value: MLL leukemia cell line:MV4;11

value: DMSO


title: MV4;11 cells treated with MI389, biological replicate 3

description: Gene expression data of MV4;11 cells treated with MI-389, biological replicate 3


title: DT40_WT_cl18

city: Sendai

description: Gene expression in DT40 wild-type cells cl18

source_name: DT40 wild-type cells cl18, replicate 1

value: wild-type cells cl18


description: Gene expression data of MV4;11 cells treated with DMSO, biological replicate 1


description: Gene expression data of MV4;11 cells treated with DMSO, biological replicate 2


title: MV4;11 cells treated with MI389, biological replicate 2

description: Gene expression data of MV4;11 cells treated with MI-389, biological replicate 2


title: LPS_2


title: CLL B-cells patient B + BM-MSC Evs

status: Public on Aug 20 2017

city: anderlecht

first: Emerence

last: Crompot

state: Bruxelles

address: 808 route de lennik

country: Belgium

institute: Jules Bordet Institute - ULB

description: Gene expression data from CLL B-cells patient B that received EV traetment for 24h

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°c on probe Array

scan_protocol: Probe arrays were scanned with affymetrix genechip scanner 3000

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

source_name: CLL B-cells + 24h incubation with BM-MSC Evs

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 150 ng total RNA

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

tag: patient id

value: patient B

tag: received

value: EV traetment for 24h

value: Chronic Lymphocytic Leukemia B-cells (CLL-B cells)


title: CLL B-cells patient C

description: Gene expression data from CLL B-cells patient C

source_name: CLL B-cells

value: patient C


title: CLL B-cells patient A

description: Gene expression data from CLL B-cells patient A

value: patient A


title: CLL B-cells patient C + BM-MSC Evs

description: Gene expression data from CLL B-cells patient C that received EV traetment for 24h


title: DT40_H2A.Z_DKO/H2A-H2A.Z

institute: Tohoku University

description: Gene expression in DT40 H2A.Z DKO cells stably expressing H2A-H2A.Z

source_name: DT40 H2A.Z DKO cells stably expressing H2A-H2A.Z, replicate 1


title: MV4;11 cells treated with MI389, biological replicate 1

description: Gene expression data of MV4;11 cells treated with MI-389, biological replicate 1

tag: treatment


title: CLL B-cells patient B

description: Gene expression data from CLL B-cells patient B


title: Jejunal explant_DON_10µM_rep3

status: Public on Aug 18 2017

city: Toulouse

first: Yannick

last: Lippi

address: 180 chemin de tournefeuille

department: GeT-TRiX facility

institute: INRAE

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 10x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturers instructions (Agilent Technologies, Santa Clara, CA). On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 INRA Sus scrofa  v1 GE microarray (8X60K, Design 037880)  enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min) and Wash buffer 2 (Agilent Technologies, 37°C, 1 min).

scan_protocol: Slides were scanned immediately after washing on a Agilent G2505C Microarray Scanner with Agilent Scan Control A.8.5.1 software

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent Technologies, Santa Clara, CA) using default parameters (protocol GE1_1010_Sep10 and Grid: 037880_D_F_20120213). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} We selected the spots with a minimal weight of 1 for 36 out of 44 microarrays or with a minimal weight of 3 per group from at least one experimental group. At this step, 44737 spots out of 62976 were selected. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore R library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 44736 rows each corresponding to a unique ProbeName (provided as data Matrix).

organism: Sus scrofa

source_name: Jejunal explant

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng of total RNA using the One-Color Quick Amp Labeling kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer's instructions, followed by Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, Massachusetts) purification. Dye incorporation and cRNA yield were checked using Dropsense™ 96 UV/VIS droplet reader (Trinean, Belgium).

growth_protocol: Jejunal explants obtained from 5 week old crossbred castrated male piglets were incubated in complete Williams medium at 39°C

extract_protocol: The explants were lysed in 1 mL of Extract All reagent (Eurobio, Les Ulis, France) with ceramic beads (Bertin technologies, St Quentin en Yvelines, France). Total RNA was extracted according to the manufacturer's recommendations as already described. RNA concentration was determined by measuring optical density at 260 nm (OD260), and the RNA integrity was assessed by using both a NanoDrop spectrophotometric analysis (Nanodrop ND1000, Labtech International, Paris, France) and Agilent capillary electrophoresis (Agilent 2100 Bioanalyzer, Agilent Technologies Inc., Santa‐Clara, CA).

treatment_protocol: The jejunal explants were treated for 4 hours at 39°C with 2 or 10μM of deoxynivalenol, nivalenol, fusarenon-x, 3-acetyldeoxynivalenol or 15-acetyl deoxynivalenol or vehicle (DMSO) in complete medium. After incubation, treated explants were stored at −80°C for RNA extraction.

value: DON

tag: dose

tag: animal

value: D


title: Jejunal explant_FX_2µM_rep4

value: FX

value: E


title: Jejunal explant_CTRL_0µM_rep2

value: CTRL

value: C


title: Jejunal explant_DON_10µM_rep2


title: Jejunal explant_FX_10µM_rep4


title: Jejunal explant_FX_10µM_rep3


title: Jejunal explant_FX_2µM_rep2


title: CLL B-cells patient A + BM-MSC Evs

description: Gene expression data from CLL B-cells patient A that received EV traetment for 24h

tag: cell type


title: Jejunal explant_FX_10µM_rep1

value: B


title: Jejunal explant_CTRL_0µM_rep1


title: TgUmodC147W F1_1

city: Milano

first: Michela

last: Riba

address: via Olgettina 60

department: COSR, Center for Omics Sciences

country: Italy

institute: IRCCS, Ospdale San Raffaele

description:
SAMPLE 21
Biological replicate, group  6

hyb_protocol: cRNAs were hybridized to the BeadChip Array and stained with streptavidin-Cy3. All procedures were performed following the manufacturer's instructions.

scan_protocol: BeadChips have been imaged using the IlluminaBeadArray Reader, a two-channel 0.8-μm-resolution confocal laser scanner, and the Illumina BeadScan software.

data_processing: The software IlluminaGenomeStudio v.2011.1 was used to elaborate the fluorescence signal to a value whose intensity corresponds to the quantity of the respective transcript in the original sample. The data were normalised using cubic normalisation.

label: biotin-UTP

source_name: total kidney

label_protocol: An amount of 500 ng of total RNA was reverse transcribed into cRNA and biotin-UTP labeled using the Illumina TotalPrep RNA Amplification Kit (Applied Biosystems) according to the manufacturer's protocol.

extract_protocol: Total RNA was extracted from whole kidney with TRIzol reagent according to manufacturer's protocol. RNA extracted was treated with DNase (Qiagen) and purified using columns from RNeasy Mini Kit (Qiagen), according to the manufacturer's protocol.

tag: strain/background

value: FVB

tag: umod transgene

value: mutant

value: 1 month

value: female

value: kidney


title: Jejunal explant_CTRL_0µM_rep4


title: Jejunal explant_FX_10µM_rep2


title: TgUmodwt F1_1

description:
SAMPLE 17
Biological replicate, group  5

value: wild type

tag: tissue


title: Jejunal explant_FX_2µM_rep3


title: Jejunal explant_DON_10µM_rep1


title: TgUmodC147W F1_4

description:
SAMPLE 24
Biological replicate, group  6

tag: age


title: TgUmodC147W M1_3

description:
SAMPLE 15
Biological replicate, group  4

value: male


title: TgUmodwt F1_3

description:
SAMPLE 19
Biological replicate, group  5


title: Jejunal explant_FX_2µM_rep1


title: TgUmodC147W M1_2

description:
SAMPLE 14
Biological replicate, group  4


title: TgUmodC147W M1_4

description:
SAMPLE 16
Biological replicate, group  4


title: TgUmodC147W F1_3

description:
SAMPLE 23
Biological replicate, group  6


title: TgUmodwt F1_2

description:
SAMPLE 18
Biological replicate, group  5


title: TgUmodwt F1_4

description:
SAMPLE 20
Biological replicate, group  5


title: TgUmodC147W F1_2

description:
SAMPLE 22
Biological replicate, group  6


title: TgUmodC147W M1_1

description:
SAMPLE 13
Biological replicate, group  4


title: TgUmodwt M1_4

description:
SAMPLE 12
Biological replicate, group  3


title: Jejunal explant_CTRL_0µM_rep3


title: TgUmodC147W F2_4

description:
SAMPLE 8
Biological replicate, group  2

value: 2 months


title: TgUmodwt M1_1

description:
SAMPLE 9
Biological replicate, group  3


title: TgUmodC147W F2_1

description:
SAMPLE 5
Biological replicate, group  2


title: TgUmodwt M1_3

description:
SAMPLE 11
Biological replicate, group  3


title: TgUmodwt M1_2

description:
SAMPLE 10
Biological replicate, group  3


title: TgUmodC147W F2_2

description:
SAMPLE 6
Biological replicate, group  2


title: TgUmodwt F2_4

description:
SAMPLE 4
Biological replicate, group  1


title: TgUmodwt F2_2

description:
SAMPLE 2
Biological replicate, group  1


title: TgUmodwt F2_3

description:
SAMPLE 3
Biological replicate, group  1


title: TgUmodwt F2_1

description:
SAMPLE 1
Biological replicate, group  1


title: TgUmodC147W F2_3

description:
SAMPLE 7
Biological replicate, group  2


title: IR10

city: Parma

first: Eleonora

last: Derlindati

address: via gramsci, 14

institute: University of Parma

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

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version A.9.5.1.1), LOWESS normalization was applied

source_name: PBMC

label_protocol: 500ng of total RNA were primed with an oligo (d)T-T7 primer and retrotranscribed into dsDNA with MMLV-RT. Then cDNA sample was amplified using T7 RNA Polymerase and labelled with cy5 (Quick Amp Labeling Kit, Agilent) following manifacture instructions

extract_protocol:
[cell isolation protocol] Peripheral blood mononuclear cells (PBMC) were isolated from 20ml of peripheral blood using Ficoll stratification
Total RNA extracted using Rneasy Mini Kit (Qiagen) purification following manufacturer's instructions

value: PBMC

tag: group

value: High HOMA

source_name: Leukocyte reference

value: leukocyte

tag: reference

value: commercial RNA, pool from human leukocyte


title: IR9


title: IR6


title: IR2


title: IR5


title: IR8


title: IS10

value: Low HOMA


title: IS7


title: IS4


title: IR4


title: IS6


title: IS3


title: IS9


title: IR1


title: IS5


title: IS8


title: IR7


title: IR3


title: Jejunal explant_DON_10µM_rep4

value: DON

value: E


title: IS2


title: IS1


title: Statin Intolerant Case C009

city: Memphis

first: Marshall

middle: B

last: Elam

state: TN

address: 1030 Jefferson Avenue

department: Research

institute: VA Medical Center

hyb_protocol: Standard Illumina Protocol. Aliquots of amplified and labeled cRNA (750–1500 ng) were hybridized to Illumina HT-12 V4 Expression BeadChips containing probes to evaluate expression levels of ~47,231 transcripts (Illumina Inc., San Diego, CA).

scan_protocol: Standard Illumina Protocol

data_processing:
Probe level expression signals were loaded to Illumina BeadStudio GX Module software (version 3.4.0) to generate an output file. This was loaded to GeneSpring (version 7.3.1, Silicon Genetics, Redwood, CA) for quality check and data normalization as previously described (13). One sample had low hybridization signal and was dropped. Unsupervised hierarchical clustering identified two outlier samples that were also excluded. For probe quality control, the 47,231 probes from the 23 remaining samples were filtered to identify 21,344 that had a positive expression flag of > 0.99 in at least three samples.  The raw data files have been submitted Geo NCBI (www.ncbi.nlm.nih.gov/geo/).  Gene expression ratios for individual genes corrected for vitamin D level and chip batch (see below) are available in Supplemental Table 1.
We performed principal component analysis on the filtered expression data and this identified three additional outlier samples that were also excluded.  PC analysis on the remaining 20 samples (13 statin intolerant and 7 statin tolerant controls) was then done to derive the major PCs. The first 3 PCs explain over 98.5% of the total variance and we used these to define factors that are major sources of variance in the data (see supplemental figure S1). Specifically, we performed Pearson correlation between the PCs and continuous variables (age of samples, vitamin D and testosterone levels) and ANOVA for categorical variables (statin tolerance status, batch, and diabetes status). From this analysis, we identified vitamin D level as a major source of variation and significantly associated with PC1 and PC3. Another source of variation is batch (i.e., the array slide on which a sample was loaded), which was significantly associated with PC2 and PC3. Statin tolerance status was significantly associated with PC3. Based on this, we performed linear regression analysis to evaluate the association between statin intolerance and gene expression with adjustment for vitamin D levels and batch. Given the large number of genes analysed no single gene association passed stringent genome-wide multiple test correction threshold and we instead applied a nominal cut-off p value of < 0.01 to generate a list of genes sufficient to perform pathway analysis to examine if any specific biological function/pathway is overrepresented among the set of small-effect differentially expressed genes (DEGs).  The nominal p-value of 0.01 yielded a total of 455 genes. In order to analyze the canonical pathways that may be induced in statin intolerant patients, we conducted an Ingenuity IPA and DAVID analysis using this set of DEGs.
Genespring software (11.5.1) computed normalized signal intensity.
Threshold: 1.0, Logbase: 2
Technology: Illumina.SingleColor.HumanHT-12_V4_0_R1_15002873_B
Normalization: Shift to 75 percentile
Baseline Transformation: None
Flag Information:
Lower cutoff for 'Present' call :0.99
Upper cutoff for 'Absent' call : 0.6

source_name: Muscle

label_protocol: The yield and integrity of RNAs were assessed by measuring A260/A280 ratios in a spectrophotometer and by size-fractionation in 1% agarose gels, respectively. Two hundred ng aliquots of total RNA per sample were used for cDNA and cRNA synthesis using Illumina TotalPrep RNA Amplification Kit (Applied Biosystems/Ambion, Austin, TX).

growth_protocol: N/A human study

extract_protocol: Muscle biopsies were taken from the lateral portion of the quadriceps femoris muscle under local anesthetic (xylocaine), using Bergstrom needles (Cadence Science, Cranston R.I.) as described by Mandarino et al. (10). To reduce the risk of bleeding, participants were instructed to avoid aspirin or aspirin containing medications as well as non-steroidal anti-inflammatory medications for at least 5 days prior to biopsy procedure. Muscle specimens were snap-frozen in liquid nitrogen and stored at  –80 °C until used for extraction of mRNA and DNA (11).   Muscle biopsies were taken from the lateral portion of the quadriceps femoris muscle under local anesthetic (xylocaine), using Bergstrom needles (Cadence Science, Cranston R.I.) as described by Mandarino et al. (10). To reduce the risk of bleeding, participants were instructed to avoid aspirin or aspirin containing medications as well as non-steroidal anti-inflammatory medications for at least 5 days prior to biopsy procedure. Muscle specimens were snap-frozen in liquid nitrogen and stored at  –80 °C until used for extraction of mRNA and DNA (11).

treatment_protocol: Patients experiencing myalgia with statin were rechallenged with statin and muscle biopsy performed after 8 weeks treatment or until muscle symptoms required discontinuation.

tag: statintolerancestatus

value: Intolerant

tag: vitamin d (ng/ml)

tag: vitamin d supplement y/n

value: YES

tag: testosterone total (ng/ml)

tag: testosterone free (ng/ml)

tag: testosterone treatment

value: Muscle


title: Statin Intolerant Case C033


title: Statin Intolerant Case C002

value: NO


title: Statin Intolerant Case C020


title: Statin Intolerant Case C021


title: Statin Intolerant Case C027


title: Statin Intolerant Case C014


title: Statin Intolerant Case C037


title: Statin Intolerant Case C029


title: Statin Intolerant Case C026


title: Statin Intolerant Case C010


title: Statin Tolerant Control B022

value: Tolerant


title: Statin Tolerant Control B024


title: Statin Intolerant Case C016


title: Statin Intolerant Case C036


title: Statin Intolerant Case C025


title: Statin Tolerant Control B015


title: Statin Tolerant Control B032


title: Statin Tolerant Control B011


title: Statin Intolerant Case C013


title: H9_1

city: Düsseldorf

first: Wasco

last: Wruck

address: Moorenstr. 5

institute: Universitätsklinikum Düsseldorf

description:
replicate 1
SAMPLE 11

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using rank invariant normalisation with BeadStudio version 3 (Illumina)

source_name: embryonic stem cells

label_protocol: Illumina Gene Expression protocols contain a first- and second-strand  reverse transcription step, followed by a single in vitro transcription  (IVT) amplification that incorporates biotin-labeled nucleotides.  Subsequent steps include array hybridization, washing, blocking, and  streptavadin-Cy3 staining. Fluorescence emission by Cy3 is quantitatively  detected for downstream analysis.

growth_protocol: The fibroblasts were grown in DMEM containing 10 % FBS and 1x penicillin/streptomycin and kept at 37 °C with 5 % CO2 in a standard cell culture incubator. hESCs and iPSCs were grown on MatrigelTM (Becton Dickinson)-coated plates with mTeSR1TM (Stemcell; 05850) medium.

extract_protocol: The RNA was isolated using Direct-zol™ RNA MiniPrep Kit (Zymo Research; #R2050).

treatment_protocol: No special treatment

value: embryonic stem cells

tag: cell line


title: H1_1

description:
replicate 1
SAMPLE 9


title: Statin Tolerant Control B031


title: Statin Tolerant Control B008


title: Statin Tolerant Control B006


title: vBJ_iPS_2

description:
replicate 2
SAMPLE 8

source_name: induced pluripotent stem cells from BJ fibroblasts


title: vBJ_iPS_1

description:
replicate 1
SAMPLE 7

value: induced pluripotent stem cells from BJ fibroblasts


title: H1_2

description:
replicate 2
SAMPLE 10


title: vHFF1_iPS_2

description:
replicate 2
SAMPLE 6

source_name: induced pluripotent stem cells from HFF fibroblasts


title: vHFF1_iPS_1

description:
replicate 1
SAMPLE 5

value: induced pluripotent stem cells from HFF fibroblasts


title: vNBS8_iPS_c2

description:
replicate 2
SAMPLE 4

source_name: induced pluripotent stem cells from NBS patient 9

value: induced pluripotent stem cells

tag: disease state

value: Nijmegen-Breakage Syndrome


title: CCR6p [PAA045]

city: Montréal

first: Jean-Philippe

last: Goulet

state: Québec

address: C.P. 6128, succursale Centre-ville

country: Canada

institute: Université de Montréal

hyb_protocol: High quality RNA was reverse transcribed and hybridized on the Illumina HumanHT12 V4 Expression BeadChip

data_processing: quantile normalisation using Bioconductor

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

extract_protocol: Total cellular RNA was extracted from matched memory CCR6+/CCR6- CD4+ T-cells isolated by FACS using RNeasy columns kit (Qiagen) according to the manufacturer’s protocol.

treatment_protocol: Peripheral blood mononuclear cells (PBMCs) were collected by leukapheresis and cryopreserved until use.

tag: stimulation

value: neg

tag: donor

value: CD4+ T-Cells


title: NBS8_fib_P15

description:
passage 8
SAMPLE 1

source_name: fibroblasts from NBS patient 8, passage 15

tag: cell type

value: fibroblasts

tag: passages

value: passage 15


title: vNBS8_iPS_c1

description:
replicate 1
SAMPLE 3

source_name: induced pluripotent stem cells from NBS patient 8


title: CCR6n [PAA043]


title: HepG2 cells with neuron-like differentiation

city: Nanjing

first: Ying

last: Cao

address: 12 Xuefu Rd., Pukou High-Tech Zone

institute: Nanjing University

description: Gene expression data from HepG2 cells undergoing differentiation

hyb_protocol: Following fragmentation, 10 mg of cRNA were hybridized for 16 hr at 45°C on GeneChip® PrimeView™ Human Gene Expression Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip® Scanner 3000.

data_processing: Normalized probeset data were generated with Robust Multi-array Averaging (RMA) method.

source_name: HepG2 cells treated with a combination of TSA, AZA, EPZ-6438 and SP2509 for nine consecutive days

label_protocol: Biotin-labeled cRNA were prepared using MessageAmp™ Premier RNA Amplification Kit (Ambion) and the protocol of the kit manufacturer from 100 ng total RNA.

growth_protocol: HepG2 cells were cultured in Dulbecco's modified eagle medium (Thermo Fisher Scientific) supplemented with 2% bovine fetal serum (Gibco). Cells were grown at 37°C with 5% CO2.

treatment_protocol: HepG2 cells were treated with 100 nM of TSA, 10 μM of AZA, 150 nM of SP2509 and 1 μM of EPZ-6438 for nine days. HepG2 cells treated with vehicle as control. After treatment, cells were trypsinized and washed twice with PBS, and subjected to total RNA extraction.

value: heptocellular carcinoma cell line

value: 15 years

tag: race

value: Caucasian

tag: gender

value: male


title: CCR6p [PAA041]


title: HepG2 cells

description: Gene expression data from HepG2 cells treated with DMSO for nine days

source_name: HepG2 cells treated with DMSO for nine consecutive days

tag: tissue

tag: age


title: CCR6n [PAA047]


title: CCR6p [PAA038]

value: ATRA


title: CCR6p [PAA042]


title: CCR6n [PAA044]


title: CCR6n [PAA048]


title: NBS8_fib_P8

description:
passage 16
SAMPLE 2

source_name: fibroblasts from NBS patient 8, passage 8

value: passage 8


title: si-HOXD-AS1-1

city: Guangzhou

first: Xu

last: Chen

state: Guangdong

address: 107. W. Yanjiang Road

department: Department of Urology

institute: Sun Yat-sen Memorial Hospital

hyb_protocol: Hybridization was performed at 45℃ with rotation for 16 h (Affymetrix GeneChip Hybridization Oven 640). The GeneChip arrays were washed and then stained (streptavidin-phycoerythrin) on an Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000.

data_processing: The hybridization data were analyzed using GeneChip Operating software (GCOS 1.4). The scanned images were first assessed by visual inspection then analyzed to generate raw data files saved as CEL files using the default setting of GCOS 1.4. An invariant set normalization procedure was performed to normalize the different arrays using DNA-chip analyzer [dChip]

source_name: prostate cancer cell line LNCaP-Bic

label_protocol: An aliquot of 0.1 µg of total RNA was used to synthesize double-stranded cDNA, then produce biotin-tagged cRNA using the MessageAmpTM Premier RNA Amplification Kit. The resulting bio-tagged cRNA were fragmented to strands of 35–200 bases in length according to the protocols from Affymetrix.

growth_protocol: LNCaP cells were cultured in phenol red free RPMI-1640 containing 10% FBS (Shanghai ExCell Biology, China) suppemented with 1% penicillin/streptomycin. Cells were grown in a humidified atmosphere of 5% CO2 at 37°C.

extract_protocol: Total RNA was extracted using Trizol reagent and was further purified using Qiagen RNeasy Mini Kit according to the manufactures’ instructions. The RNA quality was assessed by formaldehyde agarose gel electrophoresis and was quantitated spectrophotometrically.

treatment_protocol: siRNA transfections were done with 75 nM siRNA and Lipofectamine RNAimax (Life technologies) following manufacturer's instructions.

value: LNCaP

tag: tissue type

value: prostate cancer

tag: sirna

tag: sirna target point on wdr5 cds

tag: sirna sequence

value: GAAAGAAGGACCAAAGUAAUU

tag: inhibition rate (relative to control sirna)


title: CCR6p [PAA046]


title: CCR6p [PAA037]


title: CCR6n [PAA040]


title: CCR6p [PAA049]


title: LNCaP-Control

source_name: prostate cancer cell line LNCaP

value: Negative control

value: UUCUCCGAACGUGUCACGUTT


title: CCR6n [PAA051]


title: CCR6n [PAA036]


title: CCR6n [PAA035]


title: CCR6p [PAA050]


title: si-HOXD-AS1-2

source_name: prostate cancer cell line LNCaP-AI

value: GCCCUUUCUGACCUGCUUAUU


title: CCR6n [PAA039]


title: CCR6n [PAA052]


title: CCR6p [PAA034]


title: CCR6p [PAA033]


title: CCR6p [PAA030]


title: CCR6p [PAA029]


title: LNCaP

hyb_protocol: Hybridization was performed at 45℃ with rotation for 16 h (Agilent Hybridization Oven G2545A). The GeneChip arrays were washed on an CapitalBio Slide Washer8.

scan_protocol: GeneChips were scanned using Agilent G2565CA Microarray Scanner.

data_processing: The hybridization data were analyzed using Agilent Feature Extraction(v10.7). Intensity values were then processed with Agilent GeneSpring and normalized.

label_protocol: An aliquot of 0.1 µg of total RNA was used to synthesize double-stranded cDNA,then cRNA was produced by T7 Enzyme Mix.Then cDNA was produced by reverse transcription using CbcScriptⅡ enzyme.The resulting cDNA were fragmented and labled with cy3/cy5 according to the protocols from Affymetrix.

growth_protocol: LNCaP cells were cultured in phenol red free RPMI-1640 containing 10% FBS (Shanghai ExCell Biology, China).LNCaP-AI cells were cultured in phenol red free RPMI-1640 containing 10% charcoal stripped FBS (Gibco, Shanghai, China), whereas LNCaP-Bic were cultured in the same medium as LNCaP-AI with a bicalutmide(Sigma, St. Louis, Missouri, USA) concentration of 20μM. All medium were suppemented with 1% penicillin/streptomycin.Cells were grown in a humidified atmosphere of 5% CO2 at 37°C.

treatment_protocol: LNCaP-Bic and LNCaP-AI cells were constructed by continuously passaged in two different castration mediums for 12 months.

tag: androgen response state

value: androgen dependent(androgen sensitive)


title: NBS7_2

description:
replicate 2
SAMPLE 8

source_name: fibroblasts from NBS patient 7

growth_protocol: The fibroblasts were grown in DMEM containing 10 % FBS and 1x penicillin/streptomycin and kept at 37 °C with 5 % CO2 in a standard cell culture incubator.

value: Nijmegen-Breakage Syndrome


title: NBS7_1

description:
replicate 1
SAMPLE 7


title: CCR6n [PAA032]

value: CD4+ T-Cells