title: GFP minus, biological rep1

status: Public on Oct 31 2017

type: RNA

city: Dublin

first: Breandan

last: Kennedy

address: Belfield

department: UCD School of Biomolecular and Biomedical Science

country: Ireland

institute: UCD Conway Institute, University College Dublin

hyb_protocol: Hybridization, washing and staining were done according to a standard procedure from Affymetrix.

scan_protocol: Scanning was done according to a standard procedure from Affymetrix.

data_processing: The signal intensity of the microarray was normalized and summarized using the Bioconductor package, gcrma, using default setting.

label: Biotin

molecule: total RNA

organism: Danio rerio

source_name: adult zebrafish (GFP-minus) sorted cone photoreceptors

label_protocol: Total RNA were labeled by Affymetrix GeneChip Two-Cycle Target Labeling protocol.

growth_protocol: Zebrafish were kept in transparent 10-liter aquaria, heated to 23ºC-28ºC degrees with a pH between 6.2 to 7.5. Normally, 25 fish were kept in each tank. Fish were maintained with a 14-hour light / 10-hour dark cycle. Fish were fed with ground dry trout pellets, zooplankton, phytoplankton and insect larvae twice a day.

extract_protocol: RNA was isolated with the RNeasy Micro Kit (Qiagen) protocol (Mack et al 2007) in order to increase the final RNA concentration

treatment_protocol: No treatment was done prior to zebrafish euthanasia

tag: age

value: adult

tag: genotype/variation

tag: tissue

value: cone cells

tag: cell population

value: GFP minus


title: GFP minus, biological rep2


title: IV sheilded Lung 2

status: Public on Oct 18 2020

city: Orlando

first: Tara

middle: M.

last: Strutt

state: FL

address: 6900 Lake Nona Blvd.

department: Burnett School of Biomedical Sciences

country: USA

institute: University of Central Florida

description: Gene expression data from donor CD4 T cell effectors from the lung on day 28 post influenza infection

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on M430.2 GeneChip Arrays. Arrays were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: All data included in the resulting publication was generated from Cel files using GeneSpringGX (Agilent) software using default analysis settings and the PLIER normalization method.

organism: Mus musculus

source_name: IV shielded donor memory CD4 T cell effectors from the lung on day 28 post influenza infection

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

growth_protocol: Congenic CD4 T cells were adoptively transferred to naïve mice in 200uL PBS.  Mice were subsequently infected with 0.1 LD50 influenza A virus.

extract_protocol: Total RNA was extracted from cells with RNeasy Mini Kit from QIAGEN and amplified (MessageAmp a RNA; Ambion) according to manufacturers instructions.

treatment_protocol: On day 28 post infection, donor CD4 T cells were sort purifed from adoptive hosts by enrichment with CD4 magnetic beads (Milteny) followed by facs sorting for populations that were either labelled or not with flourescent antibody administered intravenously.

tag: host strain

tag: donor cells

value: Congenic CD4 T cells

tag: time point

value: day 28 post influenza infection

tag: source tissue

value: Lung

tag: sorted memory subset

value: IV sheilded (tissue resident) TCR Tg CD4 T cell


title: GFP minus, biological rep3


title: IV sheilded Lung 3


title: GFP positive, biological rep2

source_name: adult zebrafish (GFP-positive) sorted cone photoreceptors

value: GFP positive


title: GFP positive, biological rep1


title: IV labelled Lung 3

source_name: IV labeled donor memory CD4 T cell effectors from the lung on day 28 post influenza infection

value: IV labelled (circulating) TCR Tg CD4 T cell


title: GFP positive, biological rep3


title: IV labelled Spl2

description: Gene expression data from donor CD4 T cell effectors from the spleen on day 28 post influenza infection

source_name: IV labeled donor memory CD4 T cell effectors from the spleen on day 28 post influenza infection

value: Spleen


title: IV sheilded Lung 1


title: IV labelled Lung 2


title: IV labelled Spl1


title: IV labelled Lung 1


title: SL-22PB

city: Nankoku

first: Tomonori

last: Higuchi

state: Kochi

address: Kohasu, Okpcho

country: Japan

institute: Kochi University

description: primary SMZL cells at the different clinical periods (aggressive phases)

hyb_protocol: see CodeLink application notes and manuals

scan_protocol: GeneChips were scanned using the GenePix® 4000B (Molecular Devices, Sunnyvale, CA, USA) and converted to numerical data with CodeLinkTM Expression Analysis v5.0 (Applied Microarrays, Tempe, AZ, USA).

data_processing: The analysis was performed using the MicroArray Data Analysis Tool Ver3.2 (Filgen, Aichi, Japan). A log base 2 transformation was applied to the microarray raw data, and global normalization was used to median over entire array.

organism: Homo sapiens

source_name: test

extract_protocol: ISOGEN® (NIPPON GENE, Tokyo, Japan) extraction of total RNA was performed according to the manufacturer's instructions. The total RNA was analyzed with the Agilent 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany)

value: primary splenic marginal zone lymphoma (SMZL)

tag: genotype

tag: clinical period

value: aggressive phases


title: MP.post13

city: Beijing

first: tao

middle: bo

last: zhang

address: No. 17 South Panjiayuan, Chaoyang District

country: China

institute: Cancer Hospital

description: Gene expression in Postpartum placental

hyb_protocol: 1.65 ug of Cy3-labeled cRNA (specific activity >9.0 pmol Cy3 per ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 μl containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 55 μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) 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 p/n 5188-5325) and 1 minute with 37°C GE Wash buffer 2 (Agilent p/n 5188-5326).

scan_protocol: After washing, slides were scanned immediately on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5μm, Dye channel is set to Green and Green PMT is set to 100% and 10%, dynamic range is extended).

data_processing: The scanned images were analyzed with the Agilent's Feature Extraction Software (v10.5)  using default parameters (protocol GE1_105_Dec08 and Grid 014850_D_20070207) to obtain background subtracted and spatially detrended processed signal intensities. The raw data was normalized by the GenespringGX Software (Agilent, version 11.5).

source_name: Postpartum placental

label_protocol: 500ng purified total RNA was reverse transcribed into cDNA, transcribed into cRNA and labeled with Cyanine-3 (Cy3) using the Agilent’s Quick Amp Labeling Kit (Agilent p/n 5190-0442) 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: Total RNA was extracted from frozen tissue using TRIzol RNA isolation reagent (Invitrogen, Carlsbad, CA) according to the manufacturer’s specifications, and purified by the RNeasy mini Kit (Cat No.74106, Qiagen, Germany). RNA integrity was detected using a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). RNA concentration was determined using NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies, Wilmington, DE).

treatment_protocol: The villus and mature placenta samples were rinsed with normal saline, then divided into two, one placed in RNAlater RNA Stabilization Reagent (Ambion/ABI,USA) at 4°C through the night and then stored at -80°Cuntil use, and the other placed in formaldehyde solution and then stored at room temperature.

value: Postpartum placenta

tag: gestational age

tag: gender

value: Female


title: SL-15PB

description: primary SMZL cells at the different clinical periods (indolent phases)

source_name: control

label_protocol: see CodeLink application notes and manuals

value: indolent phases


title: MP.post07

description: Gene expression in Postpartum placental


title: MP.post05

description: Gene expression in Postpartum placental


title: MP.post09

description: Gene expression in Postpartum placental


title: MP.post06

description: Gene expression in Postpartum placental


title: SAMPLE_100_1

type: genomic

city: Seattle

first: Sean

last: Maden

state: WA

address: 1100 Fairview Ave N

department: Clinical Research

institute: Fred Hutch

hyb_protocol: Illumina Infinium HD Methylation protocol

scan_protocol: Imaged with iScan+ using Methylation NXT scan setting

data_processing: GenomeStudio v2011.1 with Methylation Module v1.9.0

label: Cy5 and Cy3

molecule: genomic DNA

source_name: Tissue core or slide

extract_protocol: DNA from formalin fixed paraffin-embedded (FFPE) cores or tissue sections

value: SQ

value: Male


title: SAMPLE_99_1

label_protocol: Illumina Infinium HD Methylation protocol


title: MP.post04

description: Gene expression in Postpartum placental


title: SAMPLE_101_1


title: SAMPLE_97_1

value: BE


title: SAMPLE_103_1


title: CV10.P39

description: Gene expression in villi

source_name: chorionic villus

value: chorionic villus

value: 10 weeks


title: SAMPLE_97_2


title: SAMPLE_102_1


title: SAMPLE_104_1


title: SAMPLE_95_1


title: CV10.P52

description: Gene expression in villi


title: CV10.P11

description: Gene expression in villi


title: SAMPLE_96_2


title: SAMPLE_95_2


title: SAMPLE_98_1


title: MP.post02

description: Gene expression in Postpartum placental


title: SAMPLE_98_2


title: CV10.P04

description: Gene expression in villi


title: CV10.P06

description: Gene expression in villi


title: SAMPLE_92_2


title: SAMPLE_96_1


title: SAMPLE_92_1


title: CV09.P73

description: Gene expression in villi

value: 9 weeks


title: SAMPLE_94_1


title: CV09.P76

description: Gene expression in villi


title: SAMPLE_93_2


title: CV09.P69

description: Gene expression in villi


title: SAMPLE_91_2


title: CV09.P67

description: Gene expression in villi


title: CV09.P50

description: Gene expression in villi


title: CV09.P58

description: Gene expression in villi


title: SAMPLE_88_1


title: SAMPLE_89_1


title: SAMPLE_91_1


title: CV08.P71

description: Gene expression in villi

value: 8 weeks


title: SAMPLE_90_2


title: SAMPLE_90_1


title: CV09.P22

description: Gene expression in villi


title: MP.post03

description: Gene expression in Postpartum placental


title: SAMPLE_94_2


title: CV08.P66

description: Gene expression in villi


title: CV08.P21

description: Gene expression in villi


title: CV08.P36

description: Gene expression in villi


title: CV08.P40

description: Gene expression in villi


title: SAMPLE_85_1


title: SAMPLE_84_1


title: SAMPLE_89_2


title: CV08.P13

description: Gene expression in villi


title: SAMPLE_93_1


title: SAMPLE_82_1


title: SAMPLE_87_1


title: CV07.P56

description: Gene expression in villi

value: 7 weeks


title: CV07.P51

description: Gene expression in villi


title: CV07.P44

description: Gene expression in villi


title: CV07.P45

description: Gene expression in villi


title: CV07.P61

description: Gene expression in villi


title: CV07.P64

description: Gene expression in villi


title: SAMPLE_81_1


title: CV07.P35

description: Gene expression in villi


title: SAMPLE_80_1


title: SAMPLE_78_1


title: SAMPLE_77_1


title: SAMPLE_86_1


title: CV07.P25

description: Gene expression in villi


title: SAMPLE_81_2


title: CV09.P42

description: Gene expression in villi


title: CV07.P09

description: Gene expression in villi


title: CV06.P57

description: Gene expression in villi

value: 6 weeks


title: CV06.P60

description: Gene expression in villi


title: CV06.P63

description: Gene expression in villi


title: SAMPLE_79_1


title: SAMPLE_76_5


title: SAMPLE_76_4


title: SAMPLE_76_2


title: SAMPLE_76_3


title: CV06.P47

description: Gene expression in villi


title: SAMPLE_77_2


title: SAMPLE_74_1


title: CV06.P10

description: Gene expression in villi


title: CV06.P48

description: Gene expression in villi


title: CV06.P18

description: Gene expression in villi


title: SAMPLE_83_1


title: SAMPLE_76_1


title: SAMPLE_73_1


title: SAMPLE_75_2


title: SAMPLE_73_2


title: SAMPLE_75_1


title: SAMPLE_72_2


title: SAMPLE_74_2


title: SAMPLE_71_2


title: SAMPLE_71_1


title: SAMPLE_69_1


title: SAMPLE_68_1


title: SAMPLE_70_1


title: SAMPLE_69_2


title: SAMPLE_65_2


title: SAMPLE_72_1


title: SAMPLE_67_2


title: CV06.P41

description: Gene expression in villi


title: SAMPLE_68_2


title: SAMPLE_65_1


title: SAMPLE_66_1


title: SAMPLE_70_2


title: SAMPLE_60_2


title: SAMPLE_63_2


title: SAMPLE_63_1


title: SAMPLE_59_2


title: SAMPLE_64_1


title: SAMPLE_64_2


title: SAMPLE_60_1


title: SAMPLE_61_2


title: SAMPLE_58_2


title: SAMPLE_61_1


title: SAMPLE_59_1


title: SAMPLE_56_1


title: SAMPLE_66_2


title: SAMPLE_67_1


title: SAMPLE_62_2


title: SAMPLE_62_1


title: SAMPLE_57_1


title: SAMPLE_56_2


title: SAMPLE_55_2


title: SAMPLE_55_1


title: SAMPLE_58_1


title: Muscle_nonexercised_12 week_pat2

city: Washington

first: Kanneboyina

last: Nagaraju

state: District of Columbia

address: 111 Michigan Ave NW

institute: Children's National Health System

description: post patient 5

hyb_protocol: Affymetrix Gene-Chip® miRNA 3.0 Array for 16 hr according to the Affymetrix protocol.

scan_protocol: Hewlett Packard G2500A Gene Array Scanner

data_processing: Affymetrix Expression Console Summarization Probe set algorithm for microRNA -RMA+detection above the background (DABG). The gene expression values were filtered based on average signal values, and only microRNAs with average signal values >20% were accepted for further analysis.

label: biotin

source_name: Vastus lateralis, nonexercised, 12 weeks

label_protocol: FlashTag™ Biotin HSR RNA Labeling Kit. Confirmed with enzyme-linked oligosorbent assay (ELOSA).

extract_protocol: Total RNA was extracted with the mirVana miRNA Isolation Kit according to the manufacturer's protocol. Quality control was performed with the Agilent 2100 Bioanalyzer.

treatment_protocol: Myositis patients were randomized into two groups: 1. exercise group and 2. non exercise/control group. Muscle was taken before and after the exercise intervention from both groups.

value: female

tag: diagnosis

value: Polymyositis

tag: disease duration

value: 33 years


title: Muscle_nonexercised_12 week_pat1

description: post patient 4

value: male

value: Dermatomyositis

value: 2 years


title: Muscle_nonexercised_12 week_pat3

description: post patient 6

value: 10 years


title: Muscle_nonexercised_0 week_pat3

description: pre patient 6

source_name: Vastus lateralis, nonexercised, 0 week


title: SAMPLE_53_2


title: SAMPLE_57_2


title: SAMPLE_54_2


title: SAMPLE_54_1


title: SAMPLE_51_1


title: SAMPLE_52_1


title: Muscle_exercised_12 week_pat2

description: post patient 2

source_name: Vastus lateralis, exercised, 12 week

value: 1 year


title: SAMPLE_51_2

value: SQ


title: Muscle_exercised_12 week_pat3

description: post patient 3


title: Muscle_nonexercised_0 week_pat1

description: pre patient 4


title: SAMPLE_50_1

value: Female


title: Muscle_nonexercised_0 week_pat2

description: pre patient 5


title: Muscle_exercised_12 week_pat1

description: post patient 1


title: Muscle_exercised_0 week_pat2

description: pre patient 2

source_name: Vastus lateralis, exercised, 0 week


title: Muscle_exercised_0 week_pat3

description: pre patient 3


title: Muscle_exercised_0 week_pat1

description: pre patient 1


title: SAMPLE_49_2

value: Male


title: MCF-7_FST_si_2

city: Bhubaneswar

first: Sandeep

last: Mishra

state: Odisha

address: Nalco Nagar Road, NALCO Nagar, Chandrasekharpur

country: India

institute: ILS

description: miRNA Expression Data from MCF-7 cell line post FST siRNA

hyb_protocol: hybridization was done for 16 hours at 60 rpm

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

data_processing: Scanned images of microarray chips were analyzed using Affymetrix Expression Console with the default settings. Raw data were processed and Nromalized on basis of organism human using RMA algorithm. The normalized data (CHP files) processed  for the differential miRNA analysis in Affymetrix TAC software.

source_name: MCF-7 post FST siRNA

label_protocol: Complex probes were produced from total RNA using the FlashTag™ Biotin HSR RNA labeling kit (Affymetrix, Santa Clara, CA, USA)

growth_protocol: MCF-7 (ATCC HTB-22) breast cancer cells were purchased from National Centre for Cell Science, Pune and maintained in a humified incubator with 5% CO2 at 37°C. The cells were routinely subcultured in Dulbecco's modified Eagle's medium supplemented with 10% foetal bovine serum (South American Origin) (Pan Biotech, GmBH,Aidenbach, Germany) and antibiotic-antimycotic (Pennicillin/Streptomycin/Amphotericin B) from Himedia Laboratories, Mumbai, India.

extract_protocol: Total RNA were isolated using Trizol Method

treatment_protocol: BCAS2 (F-5’-GAAGGAACUUCAGAAGUUA-3’, R- 5’-UAACUUCUGAAGUUCCUUC-3’), FST (F- 5’-GACCAAUAAUGCCUACUGU-3’, R-5’-ACAGUAGGCAUUAUUGGUC-3’) and control siRNA (against laminin) were purchased from Eurogentec (Seraing, Belgium).  For siRNA transfection, cells were grown upto 70% confluence. Next day, media was changed to serum-free and antibiotic-free media and transfection was performed with ICAFectin 442 (Eurogentec) using manufacterer’s protocol. Transfected cells were harvested for total RNA isolation or isolation of whole cell lysate after 48 hr incubation in 37°C.

tag: cell line

tag: cell type

value: breast cancer

value: breast cancer cell line isolated in 1970 from a 69-year-old Caucasian woman


title: SAMPLE_46_2

tag: age


title: SAMPLE_49_1

value: BE


title: SAMPLE_53_1


title: MCF-7_FST_si_1


title: SAMPLE_48_1


title: SAMPLE_46_1


title: SAMPLE_50_2


title: SAMPLE_44_1


title: MCF-7_FST_si_3


title: SAMPLE_43_1

value: EAC


title: SAMPLE_45_2


title: SAMPLE_47_1


title: SAMPLE_52_2


title: SAMPLE_44_2


title: SAMPLE_42_2


title: SAMPLE_45_1


title: SAMPLE_48_2


title: SAMPLE_47_2


title: MCF-7_BCAS2_si_2

description: miRNA Expression Data from MCF-7 cell line post BCAS2 siRNA

source_name: MCF-7 post BCAS2 siRNA


title: SAMPLE_41_1


title: MCF-7_Control_si_1

description: miRNA Expression Data from MCF-7 cell line post Control siRNA

source_name: MCF-7 post Control siRNA (Lamin B1)


title: MCF-7_BCAS2_si_1


title: MCF-7_BCAS2_si_3


title: SAMPLE_40_2


title: MCF-7_Control_si_3


title: Adult CTCFcKO LSK, biological rep 3

city: Seoul

first: Hyoung-Pyo

last: Kim

address: Yonsei-ro 50-1

country: South Korea

institute: Yonsei University

description: gene expression data from CTCFcKO LSKs from the mouse bone marrow

hyb_protocol: Labeled samples were hybridized to Mouse Gene 2.0 ST array (Affymetrix, Santa Clara, CA, USA) at 48˚C for 16 h, washed, stained with a Streptavidin-PE solution, and scanned.

scan_protocol: Scanning was performed with an Affymetrix Scanner and GeneChip analysis withGeneChip® Command Console® Software (AGCC)

data_processing: Microarray data were analyzed with Bioconductor. Signals were normalized with robust multi-array average (RMA) method within oligo package. (Carvalho BS and Irizarry RA, 2010)

source_name: FACS-sorted BM CTCFcKO LSKs

label_protocol: Target preparation and microarray processing procedures were performed as described in the Affymetrix GeneChip Expression Analysis Manual (Affymetrix, Santa Clara, CA). Briefly, 20 micro gram of the total RNA was used to synthesize 10 mg cRNA as a hybridization sample for the microarray.

growth_protocol: Both CreER and tamoxifen-inducible Ctcf conditional knockout mice were kept in the specific-pathogen free facilities at Avison Biomedical Research Center, Yonsei University College of Medicine.

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

treatment_protocol: Mice were intraperitoneally injected with daily 2mg of tamoxifen for three consecutive days. Twenty-four hours after the last tamoxifen treatment, total bone marrow cells were isolated and suspension cells were stained with antibodies and sorted by the FACSAria II cell sorter (BD Biosciences) at the flow cytometry core in the Avison Biomedical Research Center (Yonsei University College of Medicine).

value: bone marrow Lin−Sca-1+c-Kithi (LSKs)

value: Ctcf conditional KO


title: Adult CTCFcKO LSK, biological rep 2


title: SAMPLE_42_1


title: Adult CTCFcKO LSK, biological rep 1


title: Adult WT LSK, biological rep 1

description: gene expression data from WT LSKs from the mouse bone marrow

source_name: FACS-sorted BM WT LSKs

value: WT


title: Adult WT LSK, biological rep 3


title: Adult WT LSK, biological rep 2


title: MCF-7_Control_si_2

value: female


title: SAMPLE_38_1


title: Muscle_nonexercised_12 week_pat3

description:
post patient 6
SAMPLE 12

hyb_protocol: 750ng cRNA was hybridized to the HumanHT-12v4 BeadChip for 16 hr, followed by washing, blocking, and streptavidin-Cy3 staining according to the Whole-Genone Gene Expression Direct Hybridization protocol.

scan_protocol: HiScanSQ System

data_processing: The data were normalized using Robust Multi-array Average (RMA), log2-transformed with GenomeStudio.

label_protocol: Biotinylated cRNA were prepared with Illumina Total Prep -96 RNA Amplification Kit

value: Polymyositis


title: SAMPLE_34_1


title: SAMPLE_35_1


title: SAMPLE_33_1


title: SAMPLE_37_1


title: Muscle_nonexercised_12 week_pat2

description:
post patient 5
SAMPLE 11

value: 33 years


title: SAMPLE_36_1


title: SAMPLE_29_1


title: SAMPLE_30_1


title: SAMPLE_31_1


title: Muscle_nonexercised_12 week_pat1

description:
post patient 4
SAMPLE 10

value: male

value: Dermatomyositis


title: SAMPLE_31_2


title: SAMPLE_40_1


title: SAMPLE_28_1


title: SAMPLE_39_1


title: Muscle_nonexercised_0 week_pat1

description:
pre patient 4
SAMPLE 7

value: 2 years


title: Muscle_nonexercised_0 week_pat3

description:
pre patient 6
SAMPLE 9

value: 10 years


title: Muscle_nonexercised_0 week_pat2

description:
pre patient 5
SAMPLE 8


title: SAMPLE_32_1


title: SAMPLE_25_2


title: SAMPLE_26_1


title: SAMPLE_35_2


title: SAMPLE_26_2

value: SQ


title: Muscle_exercised_12 week_pat3

description:
post patient 3
SAMPLE 6

value: 1 year


title: SAMPLE_25_1

value: Male


title: SAMPLE_27_1

value: Female


title: Muscle_exercised_12 week_pat2

description:
post patient 2
SAMPLE 5


title: Muscle_exercised_12 week_pat1

description:
post patient 1
SAMPLE 4


title: RL+N+vincristine_rep 2

city: Lyon

first: Taghreed

last: Hirz

address: 8 Avenue Rockefeller

country: France

institute: Cancer research center of Lyon

description:
Replicate 2
RL+N+vincristine_n°2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with GeneSpring Version 1.9.0

source_name: RL+Neutrophils+vincristine

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina TotalPrep RNA Amplification Kit

growth_protocol: RL cells were grown in RPMI medium containing 10% FCS, 2 mM L-glutamine, 100 U/mL penicillin and 100 µg/mL streptomycin. Neutrophils were isolated from fresh peripheral blood of healthy donor at the day of the experiment using dextran (> 90% pure).

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN Qiamp RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with 2100 Bioanalyzer

treatment_protocol: RL cells were cultured alone or co-cultured with neutrophils (N) at N:RL ratio 10:1, in the presence or absence of 10 nM vincristine for 2 h. RL cells were purified (≥ 80 % pure) after labeling with anti-human CD15-Biotin (Miltenyibiotec) then anti-Biotin Microbeads (Miltenyibiotec) followed by magnetic column separation (LD Columns, Miltenyibiotec).

value: RL

value: follicular lymphoma cells

tag: culture type

value: cocultured with neutrophils

tag: exposed to

value: 10 nM vincristine for 2 h


title: Muscle_exercised_0 week_pat2

description:
pre patient 2
SAMPLE 2


title: RL+N+vincristine_rep 3

description:
Replicate 3
RL+N+vincristine_n°3


title: Muscle_exercised_0 week_pat3

description:
pre patient 3
SAMPLE 3


title: 3153A H4pan-ac (Sample 8)

city: Rochester

first: Hironao

last: Wakabayashi

state: NY

address: 601 Elmwood Ave.

department: Biochemistry & Biophysics

institute: University of Rochester

description: Chip-chip 3153A cells H4pan-ac

hyb_protocol: The labeled ChIP DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in 45 ul of buffer containing 20% formamide, 1.2 M betaine, 0.1 ug/ul herring sperm DNA and 10 ug of human COT1 DNA (Invitrogen). Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC. Hybridization buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html)

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction.

organism: Candida albicans

source_name: H4pan-ac ChIP DNA from 3153A cells

label_protocol: 1 µg ChIP DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3 nonamers (ChIP DNA isolated from H3pan-ac or H4pan-ac-immunoprecipitated cells) per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

growth_protocol: Cells of 3,500 colony forming units were plated on each sorbitol plate and cultured until approximately cells count per colony reached  about 100,000 and processed for ChIP-chip experiments.

extract_protocol: 5x10E6 cells were fixed with 1% formaldehyde in culture medium for 10 min at room temperature followed by quenching with 0.125 M glycine for 5 min. The cells were washed twice with ice-cold PBS and lysed in 1 ml of lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris pH8.0) for at least 30 min on ice. The crosslinked chromatin was sheared to an average size of 500 bp by ten 30-second pulses using a BiorupterTM sonicator (Diagenode). The lysate was then centrifuged to remove cell debris, and the chromatin was quantified in a UV spectrophotometer. The chromatin (400 µg) was diluted 10-fold in dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA 16.7 mM Tris pH8.10, 167 mM NaCl) and pre-cleared with 25 µl protein A sepharose beads (pre-absorbed with salmon sperm DNA and BSA) for 2 h at 4C. The chromatin supernatant was then incubated overnight with 5 µg of purified antibody at 4C. After incubation with protein A sepharose beads (50 µl) for 2h at 4C, the immune complexes were collected by centrifugation and washed with the following buffers each for 10 min at 4C; RIPA buffer (150 mM NaCl, 50 mM Tris pH8.0, 0.1% SDS), high-salt buffer (500 mM NaCl, 50 mM Tris pH8.0, 0.1% SDS, 1% NP40) LiCl buffer (250 mM LiCl, 50 mM Tris pH8.0, 0.5% Na deoxycholate, 1% NP40) and 2x TE (20 mM Tris pH8.0, 2 mM EDTA). The protein-DNA complexes were eluted from the beads in 450 µl elution buffer (1% SDS, 100 mM NaHCO3) at 55C for 2 h followed by the addition of proteinaseK to 500 µg/ml and overnight incubaton at 65C. Genomic DNA was isolated from the precipitated material as well as from the sheared chromatin input (1/100 of the material used for ChIP) by phenol extraction and ethanol precipitation.

tag: strain

tag: ch5 ploidy

value: disomic

tag: chip antibody

value: anti-acetyl histone H4 antibody specifically reactive to H4 acetylated at lysines K5, K8, K12, and/or K16 (pan-acetylation) (#06-866, Upstate Biotechnology/Millipore)

source_name: Input DNA from 3153A cells


title: RL+N+vincristine_rep 1

description:
Replicate 1
RL+N+vincristine_n°1


title: Muscle_exercised_0 week_pat1

description:
pre patient 1
SAMPLE 1

value: female


title: 3153A H4pan-ac (Sample 4)

description: Chip-chip 3153A cells H4pan-ac


title: Sor125(55) H4pan-ac (Sample 2)

description: Chip-chip Sor125(55) cells H4pan-ac

source_name: H4pan-ac ChIP DNA from Sor125(55) cells

value: monosomic

source_name: Input DNA from Sor125(55) cells


title: RL+N_rep 3

description:
Replicate 3
RL+N_n°3

source_name: RL+Neutrophils


title: Sor125(55) H4pan-ac (Sample 9)

description: Chip-chip Sor125(55) cells H4pan-ac


title: SAMPLE_23_1

source_name: Tissue core or slide

value: EAC


title: Sor125(55) H3pan-ac (Sample 5)

description: Chip-chip Sor125(55) cells H3pan-ac

source_name: H3pan-ac ChIP DNA from Sor125(55) cells

value: anti-acetyl histone H3 c-terminal antibody specifically reactive to H3 acetylated at K9 and K14 (#61638, Active motif)


title: Sor125(55) H4pan-ac (Sample 6)

description: Chip-chip Sor125(55) cells H4pan-ac


title: SAMPLE_19_1


title: RL+N_rep 2

description:
Replicate 2
RL+N_n°2


title: SAMPLE_20_1


title: SAMPLE_21_1


title: RL+N_rep 1

description:
Replicate 1
RL+N_n°1


title: RL+vincristine_rep 3

description:
Replicate 3
RL+vincristine_n°3

source_name: RL+vincristine

value: cultured alone


title: SAMPLE_18_1


title: SAMPLE_22_1


title: Sor125(55) H3pan-ac (Sample 1)

description: Chip-chip Sor125(55) cells H3pan-ac


title: 3153A H3pan-ac (Sample 3)

description: Chip-chip 3153A cells H3pan-ac

source_name: H3pan-ac ChIP DNA from 3153A cells


title: SAMPLE_15_2


title: SAMPLE_24_1


title: SAMPLE_17_1


title: RL+vincristine_rep 2

description:
Replicate 2
RL+vincristine_n°2


title: SAMPLE_16_1


title: SAMPLE_15_1


title: RL_rep 3

description:
Replicate 3
RL_Ctr_n°3

source_name: RL alone


title: RL+vincristine_rep 1

description:
Replicate 1
RL+vincristine_n°1


title: 3153A H3pan-ac (Sample 7)

description: Chip-chip 3153A cells H3pan-ac


title: SAMPLE_13_1

value: FBE


title: SAMPLE_14_1


title: RL_rep 2

description:
Replicate 2
RL_Ctr_n°2


title: RL_rep 1

description:
Replicate 1
RL_Ctr_n°1


title: SAMPLE_11_1


title: SAMPLE_10_1

value: BE


title: SAMPLE_7_1


title: SAMPLE_12_1


title: SAMPLE_9_1


title: SAMPLE_8_1


title: SAMPLE_2_1


title: SAMPLE_1_1


title: SAMPLE_5_1


title: SAMPLE_6_1


title: SAMPLE_3_1


title: SAMPLE_14_2

value: SQ


title: PMC42-LA EGF Rep 2

city: Clayton

first: Nicholas

middle: C

last: Wong

state: Victoria

address: Wellington Road

department: Monash Bioinformatics Platform, Central Clinical School

country: Australia

institute: Monash University

hyb_protocol: As per Illumina protocol

scan_protocol: As per Illumina protocol

data_processing: Data analysed using R and Bioconductor with the ChAMP Library v2.6.0

source_name: Cell line, PMC42-LA EGF

label_protocol: As per Illumina protocol

growth_protocol: Both PMC42-ET and the PMC42-LA sublines were grown in RPMI, supplemented with 10% FCS and penicillin/streptomycin, at 370C/10% CO2.

extract_protocol: cells were washed with 1 x PBS, dispersed by trypsin digestion, and the cell pellets were lysed in RIPA buffer. Lysates where then digested with proteinase K, followed by phenol-chloroform extraction and isopropanol precipitation

treatment_protocol: EGF treatment was performed on cultures by supplementing EGF at 10ng/ml for 72 hours prior to harvesting


title: PMC42-ET Control Rep 2

source_name: Cell line, PMC42-ET Untreated


title: PMC42-ET EGF Rep 2

source_name: Cell line, PMC42-ET EGF


title: Lu-iPSC6_1

city: Bethesda

first: Paul

last: Meltzer

address: 9100 Rockville Pike

institute: NCI/NIH

description: IPSC

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human methylation450k Beadchip using standard Illumina protocol

scan_protocol: Standard Illumina Protocol

data_processing:
The raw data file 'FinalReport.txt (CMPC121_raw_int.txt)' generated from Illumina 'GenomeStudio' (Illumina) was normalized with 'Simple Scaling Normalization' (SSN) method implemented in the 'lumi' R package following the color-bias adjustment. Two files were produced, one with beta value for individual target and another one with corresponding 'M' values for the beta values.
The file with 'M' values was used for statistical analysis with FDR<0.05 (adjusted based on Benjamini-Hochberg procedure) as significant cutoff unless otherwise indicated, and also the absolute beta value difference greater than 0.2 from the same contrast comparison was applied. Partek Genomics Suite (Partek Inc.), R packages of lumi, methlumi and also other related R packages were used for data processing, analyzing and data presentation.

label_protocol: Standard Illumina Protocol

growth_protocol: Lu-iPSCs  were routinely grown in DMEM medium and stem cell medium,  8TM medium (Life technologies; Cat. no. A1517001) and Rho-associated kinase (Rock) inhibitor (Y-27632; Tocris; Cat. no. 1254) were used to culture the stem cells. SAEC wwre purchased from Lonza and were propagated as described by the Lonza protocol.

extract_protocol: DNA was isolated using QIAamp DNA Mini Kit (Qiagen #51304) and treated with bisulfite using EpiTect Bisulfite Kit (Qiagen). Efficiency of methylation level was measured by Illumina Infinium methylation assays (Illumina).

value: Lung induced pluripotent cells


title: SAEC_3

description: SAEC

source_name: SAEC

value: Small Airway Epithelial Cells


title: PMC42-ET Control Rep 1


title: PMC42-ET EGF Rep 1


title: Lu-iPSC7_1

description: IPSC


title: Lu-iPSC7_3

description: IPSC


title: PMC42-LA EGF Rep 1


title: Lu-iPSC6_2

description: IPSC


title: Lu-iPSC6_3

description: IPSC


title: 1104_1003_0BM

city: Phoenix

first: Bodour

last: Salhia

state: AZ

address: 445 N Fifth Street

department: Integrated Cancer Genomics Division

institute: Translational Genomics Research Institute

description: ARM B

hyb_protocol: Standard Illumina protocol

scan_protocol: Illumina HiScan

data_processing: GenomeStudio V2011.1

source_name: genomic DNA from pediatric AML

label_protocol: Standard Illumina protocol

extract_protocol: All Prep DNA/RNA extraction kit (Qiagen)

value: Acute Myelogenous Leukemia

tag: tissue

value: bone marrow aspirate

tag: tissue type

value: diagnostic marrow


title: SAEC_1

description: SAEC


title: 1104_1003_wk3BM

description: ARM B

value: remission marrow


title: 1104_1002_wk3BM

description: ARM B


title: 1101_1002_0BM

description: ARM B


title: SAEC_2

description: SAEC


title: Lu-iPSC7_2

description: IPSC


title: SAMPLE_4_1

value: Male


title: 1104_1001_0BM

description: ARM A


title: 1104_1002_0BM

description: ARM B


title: PMC42-LA Control Rep 2

source_name: Cell line, PMC42-LA Untreated


title: 1101_1002_wk3BM

description: ARM B


title: 1015_1001_wk3BM

description: ARM A


title: PMC42-LA Control Rep 1


title: 1006_1003_0BM

description: ARM A


title: Macrophage_FO5diet_fish6_pIC

city: St. John's

first: Khalil

last: Eslamloo

state: Newfoundland and Labrador

address: 0 Marine Lab Rd.

department: Ocean Sciences

country: Canada

institute: Memorial University of Newfoundland

hyb_protocol: The labeled aRNA (i.e. 825 ng) of each experimental sample was mixed with an equal amount of labeled aRNA of the common reference, and the resulting pool was fragmented based on the manufacturer's instructions (Agilent, Mississauga, ON). Each labelled aRNA pool (i.e. an individual sample and common reference) was co-hybridized to a cGRASP-designed Agilent 44K salmonid oligonucleotide microarray (GEO accession # GPL11299). The arrays were hybridized at 65°C for 17 h with 10 rpm rotation in an Agilent hybridization oven. The array slides were washed immediately following hybridization as per the manufacturer's instructions.

scan_protocol: The microarray slides were scanned at 5 µm resolution with 90% of laser power using a ScanArray Gx Plus scanner and ScanExpress v4.0 software (Perkin Elmer, Waltham, Massachusetts, USA),  and Photomultiplier tube (PMT) settings of Cy5 and Cy3 were adjusted to balance the  fluorescence signal between the channels.

data_processing: Signal intensity data was extracted from tiff images using Imagene v9.0 (BioDiscovery). In addition to automated quality flagging, spots affected by dust particles, scratches and other local artefacts were flagged manually. Raw data was read into Bioconductor package 'marray', base 2 logratios were calculated from background-corrected median signals and control spots were removed. Data was normalized using print-tip loess. Logratio data for a particular spot was removed when the raw signal value in one of the channels of that spot was lower than the threshold, which was calculated as (median background + 3 * SD) for each channel on each array. Logratio data for a particular spot was also removed if the spot was flagged in Imagene.

organism: Salmo salar

source_name: pIC-exposed macrophages, 5.09% fish oil diet, individual fish 6

label_protocol: Samples from 6 individuals (6 PBS and 6 pIC; 12 samples in total per group) in each dietary group were used for microarray experiment. The microarray experiment was conducted using a common reference design. The mRNA of each sample was amplified and then labelled using 800 ng of DNase-treated and column-purified RNA and Amino Allyl MessageAmp™ II aRNA Amplification kit (Ambion®, Carlsbad, CA, USA), according to the kit’s procedure. A common reference was prepared using a pool of all 24 samples (10 µg aRNA from each sample) involved in microarray experiment. The experimental samples (pIC and PBS of both dietary group) were labelled with Cy5 (GE Healthcare, Buckinghamshire, UK), whereas the common reference samples were labelled with Cy3 (GE Healthcare), based on the manufacturer’s protocol.

growth_protocol: Two different diets (5 mm pellets) with varying levels fish oil [i.e. FO7: 7.38% and FO5: 5.09%], resulting in different levels of DHA and EPA (i.e. FO7: 1.41% and FO5: 1%) were used for this study. Atlantic salmon were randomly distributed into eight 620 L tanks (40 fish per tank and 4 replicate tanks per dietary group). Fish were fed to satiation using the given experimental diet twice a day at ~12° and under 12-h light photoperiod for 16 weeks. Fish were subjected to starvation 24 h before any handling or sampling.

extract_protocol:
cell_isolation_and_stimulation: Two fish per replicate tank in each dietary group were used for pIC stimulation and global gene expression analyses (i.e. 8 biological replicate per group). Each individual was taken and euthanized using an overdose of MS222 (400 mg L-1). After dissection, the head kidney of the fish was removed and transferred into Lebovitz-15+ (L-15+; Gibco, Carlsbad, CA, USA) medium supplemented with 2% fetal bovine serum, 10 U ml-1 heparin and 100 U ml-1 penicillin and 100 µg ml-1 streptomycin. Fish head kidney was then minced using 100 µm nylon cell strainers, and the resulting cell suspension was washed and pelleted by centrifuging at 400 × g for 5 min at 4˚C. The cell suspension was centrifuged on a discontinuous 34/51% Percoll gradient (GE Healthcare, Uppsala, Sweden) at 400 × g for 30 min in 4˚C, and the interface enriched in monocyte/macrophage-like cells was collected. The cells were washed twice and suspended in L-15+ with 2% fetal bovine serum (FBS) and without heparin. The cells were counted using a hemocytometer and then seeded into 6-well plates at an equal density of 3 × 107 viable cells (in 2 ml L-15+) per well. The cells were cultured overnight (16 h) at 15˚C, and the non-adherent cells were removed by washing the plates 3 times with L-15+. The cells were then cultured in L-15+ containing 5% FBS at 15˚C. After 24 h of isolation, Macrophage-like cells (MLCs) isolated from each fish were exposed to PBS (control) or 10 µg ml-1 pIC. Samples from each individual were lysed using 800 µl of TRIzol (Invitrogen, Burlington, Ontario, Canada) at 24 hours post-stimulation.
Total RNA was extracted from TRIzol-lysed samples, following the manufacturer’s instructions. The RNA samples were treated with Dnase-I (Qiagen, Mississauga, Ontario, Canada) for removing any residual genomic DNA contamination, and then purified using RNeasy MinElute Cleanup Kit (Qiagen) according to the manufacturer’s instructions.  The high-purity RNA samples (e.g. A260/230 and A260/280 ratios > 1.8) with tight 18S and 28S ribosomal RNA bands were used for the microarray analysis.

value: Macrophage-like cells

tag: life stage

value: Juvenile

source_name: pool of RNAs from all samples involved in the microarray experiment


title: 1104_1001_wk3BM

description: ARM A


title: 1010_1001_0BM

description: ARM B


title: 1015_1001_0BM

description: ARM A


title: 1010_1001_wk3BM

description: ARM B


title: Macrophage_FO5diet_fish6_PBS

source_name: PBS-exposed macrophages, 5.09% fish oil diet, individual fish 6


title: 1006_1002_0BM

description: ARM A


title: 1003_1008_wk3BM

description: ARM A


title: 1006_1001_0BM

description: ARM A


title: 1006_1001_wk3BM

description: ARM A


title: 1006_1004_wk3BM

description: ARM A


title: Macrophage_FO5diet_fish5_pIC

source_name: pIC-exposed macrophages, 5.09% fish oil diet, individual fish 5


title: 1003_1008_0BM

description: ARM A


title: 12wkb_WT_392.2

city: Nantes

first: Marja

last: Steenman

address: 8 quai Moncousu

institute: L'institut du thorax

hyb_protocol: 1650 ng of Cy3-labeled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 µl of 2x Agilent Hi-RPM hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Microarrays (G4122F) 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). Next, microarrays were washed 30 seconds in acetonitrile and 30 seconds in Stabilization and Drying Solution.

scan_protocol: Slides were scanned immediately after washing on the Agilent G2565CA Microarray Scanner using one color scan setting for 4x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters (protocol GE1-v5_95_Feb07 and Grid: 014868_D_20070820) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Data were normalized using R statistical software. Raw values of all probes on all arrays were normalized against a virtual median chip (median raw intensity per row) using a locally weighted scattered plot smoother analysis (LOWESS). Values for replicate probes were averaged. The data were filtered to 20,000 probes to remove probes with low intensity values.

source_name: heart from 12wk old WT mice

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from100 ng RNA using the Low Input QuickAmp Labeling Kit One-Color (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted using Tri-Reagent. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was assessed using an Agilent 2100 Bioanalyzer.

value: heart

value: male


title: 1006_1005_wk3BM

description: ARM A


title: 1006_1004_0BM

description: ARM A


title: 12wkb_TG1_332.3

source_name: heart from 12wk old mice overexpressing PKR1


title: Macrophage_FO5diet_fish5_PBS

source_name: PBS-exposed macrophages, 5.09% fish oil diet, individual fish 5


title: Macrophage_FO5diet_fish4_pIC

source_name: pIC-exposed macrophages, 5.09% fish oil diet, individual fish 4


title: 1003_1007_wk3BM

description: ARM B


title: 12wkb_TG1_331.3


title: 1003_1005_0BM

description: ARM B


title: Macrophage_FO5diet_fish4_PBS

source_name: PBS-exposed macrophages, 5.09% fish oil diet, individual fish 4


title: 1003_1003_0BM

description: ARM A


title: 1006_1003_wk3BM

description: ARM A


title: 12wkb_WT_330.3


title: Macrophage_FO5diet_fish3_pIC

source_name: pIC-exposed macrophages, 5.09% fish oil diet, individual fish 3


title: 12wkb_WT_329.4


title: 1003_1004_0BM

description: ARM B


title: 1006_1002_wk3BM

description: ARM A


title: Macrophage_FO5diet_fish1_pIC

source_name: pIC-exposed macrophages, 5.09% fish oil diet, individual fish 1


title: 1006_1005_0BM

description: ARM A


title: 1003_1003_wk3BM

description: ARM A


title: 1003_1004_wk3BM

description: ARM B


title: Macrophage_FO5diet_fish2_pIC

source_name: pIC-exposed macrophages, 5.09% fish oil diet, individual fish 2


title: 1002_1001_wk3BM

description: ARM B


title: 1003_1005_wk3BM

description: ARM B


title: Macrophage_FO5diet_fish2_PBS

source_name: PBS-exposed macrophages, 5.09% fish oil diet, individual fish 2


title: 1002_1001_0BM

description: ARM B


title: 1001_1001_0BM

description: ARM B


title: Macrophage_FO7diet_fish4_pIC

source_name: pIC-exposed macrophages, 7.38% fish oil diet, individual fish 4


title: Macrophage_FO5diet_fish1_PBS

source_name: PBS-exposed macrophages, 5.09% fish oil diet, individual fish 1


title: Macrophage_FO7diet_fish5_PBS

source_name: PBS-exposed macrophages, 7.38% fish oil diet, individual fish 5


title: Macrophage_FO7diet_fish5_pIC

source_name: pIC-exposed macrophages, 7.38% fish oil diet, individual fish 5


title: Macrophage_FO7diet_fish6_PBS

source_name: PBS-exposed macrophages, 7.38% fish oil diet, individual fish 6


title: Macrophage_FO5diet_fish3_PBS

source_name: PBS-exposed macrophages, 5.09% fish oil diet, individual fish 3

source_name: pool of RNAs from all samples involved in the microarray experiment


title: 1001_1001_wk3BM

description: ARM B

source_name: genomic DNA from pediatric AML


title: Macrophage_FO7diet_fish1_PBS

source_name: PBS-exposed macrophages, 7.38% fish oil diet, individual fish 1


title: Macrophage_FO7diet_fish3_pIC

source_name: pIC-exposed macrophages, 7.38% fish oil diet, individual fish 3


title: Macrophage_FO7diet_fish6_pIC

source_name: pIC-exposed macrophages, 7.38% fish oil diet, individual fish 6


title: Macrophage_FO7diet_fish3_PBS

source_name: PBS-exposed macrophages, 7.38% fish oil diet, individual fish 3


title: Macrophage_FO7diet_fish2_PBS

source_name: PBS-exposed macrophages, 7.38% fish oil diet, individual fish 2


title: Macrophage_FO7diet_fish1_pIC

source_name: pIC-exposed macrophages, 7.38% fish oil diet, individual fish 1


title: PHF20 gene was koncked down, biological rep1

city: Xi’an

first: Tianlong

last: Liu

address: No. 127 West Changle Road

department: Pharmacy

institute: Xijing Hospital

hyb_protocol: Total RNA was processed for double-strand cDNA synthesis, IVT and aRNA fragmentation with GeneChip 3’IVT Express Kit (Affymetrix, Santa Clara, CA, USA) according to the manufacturer’s instruction. Then, it was processed for hybridization at 45℃ for 17 h with The PrimeView™ Human Gene Expression Array (Affymetrix). The arrays were washed in the GeneChip Fluidic Station 450 (Affymetrix).

scan_protocol: The arrays were scanned by the GeneChip Scanner 3000 (Affymetrix).

data_processing: The raw data were normalized by the log scale robust multi-array analysis (RMA) method with the Expression Console software version 1.1 (Affymetrix).

source_name: U87 cells infected with PHF20-shRNA lentivirus

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol(GeneChip® 3' IVT PLUS Reagent Kit, Affymetrix).

growth_protocol: The cells were cultured in DMEM medium containing 10% FBS, 50U/mL penicillin and 50μg/mL streptomycin at 37℃ with 5% CO2 incubator. The cell line tested negative for any mycoplasma contamination.

extract_protocol: Total RNA in the samples was isolated using Trizol Reagent according to the manufacture's protocol.

treatment_protocol: U87 cells in 6-well plates were infected with lentiviral particles containing either shCON or shPHF20. The virus containing culture medium was replaced with fresh DMEM supplemented with 10% FBS at 12h after infection. 72h post lentivirus infection, two U87 cell groups were set up: KD (knockdown, cells infected with PHF20-shRNA lentivirus) and NC (negative control, cells infected with negative control-shRNA lentivirus).

value: U87 cell

value: human glioblastoma cell

tag: transfection


title: Macrophage_FO7diet_fish4_PBS

source_name: PBS-exposed macrophages, 7.38% fish oil diet, individual fish 4


title: Macrophage_FO7diet_fish2_pIC

source_name: pIC-exposed macrophages, 7.38% fish oil diet, individual fish 2


title: U87 cell as normal control, biological rep1

source_name: U87 cells infected with negative control-shRNA lentivirus

value: shCON


title: 12wkb_TG1_330.4

source_name: heart from 12wk old mice overexpressing PKR1


title: PHF20 gene was koncked down, biological rep3


title: 1800-6

city: Castellón

first: Josep

middle: A

last: Calduch-Giner

address: Ribera de Cabanes

country: Spain

institute: Institute of Aquaculture Torre de la Sal (CSIC)

hyb_protocol: Each sample (600ng) was hybridized to the Custom Sea bream Oligo Microarray Kit (Agilent p/n 067581) at 65 ºC for 17 h using Agilent GE hybridization kit

scan_protocol: Arrays were scanned with Agilent scanner G2565C

data_processing: Spot intensities and other quality control features were extracted with Agilent Feature Extraction software version 11.5.1.1, and was further analyzed, including percentile shift normalization, one-way ANOVA, principal components analysis and k-means clustering of differentially expressed genes, by means of GeneSpring GX 13.0 software (Agilent)

organism: Sparus aurata

source_name: Whole 30-day larva, 9h Zeitgeber time

label_protocol: Total RNA (150 ng) from individual fish (n=6 for each group) were labelled with cyanine 3-CTP (Low Input Quick Amp Labelling Kit, Agilent)

growth_protocol: Gilthead sea bream larvae were reared in four circular 250 L tanks under constant temperature (19 °C), salinity (34 ‰) and 12 h light : 12 h darkness cycle. The larvae were fed ad libitum with rotifers (Brachionus rotundiformis Bs-strain and B. plicatilis S-1-strain) supplied at a density of 10 rotifers/mL and enriched with the microalgae Nannocholopsis gaditana, from day 4 post-hatching (dph) and subsequently with Artemia sp. nauplii from 18 dph until the end of experiment. Larvae were sampled at  30 dph during a 24 h cycle taking 10 individuals every 3 hours (00:00, 03:00, 06:00, 09:00, 12:00, 15:00, 18:00, 21:00 and 24:00 h Zeitgeber time) and preserving them in RNAlater.

extract_protocol: Total RNA was extracted from whole larvae using an Ultra-Turrax T8 and the NucleoSpin RNA II kit, including the on column RNase-free DNase digestion included with the kit. RNA quantity was measured spectrophotometrically at 260 nm with the BioPhotometer Plus giving a yield between 3 and 15 µg

value: Whole 30-day larva

tag: zeitgeber time (hrs)


title: 2050-3

source_name: Whole 30-day larva, 12h Zeitgeber time


title: 2050-4


title: 2050-6


title: 1800-5


title: 2050-1


title: PHF20 gene was koncked down, biological rep2


title: U87 cell as normal control, biological rep3


title: 1003_1007_0BM

description: ARM B


title: U87 cell as normal control, biological rep2


title: 1800-2


title: 1800-1


title: 1500-6

source_name: Whole 30-day larva, 6h Zeitgeber time


title: 1800-3


title: 1200-5

source_name: Whole 30-day larva, 3h Zeitgeber time


title: 1500-1


title: 1200-3


title: 1500-5


title: 1200-4


title: 1800-4


title: 1200-6


title: 1500-3


title: DMSO vehicle 24h (378_C118)

city: Berlin

first: Ralf

last: Lesche

address: Muellerstr 178

country: Germany

institute: Bayer Pharma AG

description: gene expression data from CHL-1 cells vehicle, DMSO, 24h

hyb_protocol: An Affymetrix Human Gene 2.1 ST 96-array plate was hybridized with 3μg of fragmented and labeled ss cDNA, washed, stained, and scanned according to the protocol described in the User Manual GeneTitan®Instrument User Guide for Expression Array Plates  (P/N 702933 Rev.1) and Affymetrix® GeneChip® Command Console™ User’s Guide (P/N 702569 Rev.9)  using the Affymetrix GeneTitan instrument

scan_protocol: GeneChips were scanned using Affymetrix GeneTitan, AGCC 4.2.0

data_processing: Genedata Refiner Array software was used to process the cel files. Antigenomic background probes were used for background subtraction. RMA condensation algorithm was employed to aggregate the probe sets on a meta probe set level. Resulting values were shifted to mean value of 100 and further normalized using LOWESS algorithm.

source_name: CHL-1 cells vehicle, DMSO, 24h

label_protocol: Standard Affymetrix protocol

growth_protocol: Human melanoma cell line, CHL-1 from American Type Culture Collection (ATCC) was cultured using DMEM medium with stable glutamine (Biochrom) supplemented with 10% fetal calve serum (Biochrom)

extract_protocol: Total RNA was extracted using RNeasy Plus Mini kit (Qiagen).

treatment_protocol: CHL-1 cells were seeded on the day before treatment and treated with 75 nM or 468 nM of BAY 1238097 (BET inhibitor) or DMSO (vehicle control) for 4h or 24h.

value: skin

tag: histologic subtype

value: melanoma

tag: treatment

value: vehicle

tag: dose

value: control

tag: time


title: 0900b-4

source_name: Whole 30-day larva, 24h Zeitgeber time


title: 1500-2


title: 1200-1


title: 1500-4


title: BAY1238097 468nM 24h (380_C120)

description: gene expression data from CHL-1 cells treated, 468nM BAY1238097, 24h

tag: cell line


title: BAY1238097 75nM 24h (379_C119)

description: gene expression data from CHL-1 cells treated, 75nM BAY1238097, 24h


title: BAY1238097 75nM 4h (366_C106)

description: gene expression data from CHL-1 cells treated, 75nM BAY1238097, 4h


title: 1200-2


title: BAY1238097 75nM 24h (353_C93)

source_name: CHL-1 cells treated, 75nM BAY1238097, 24h


title: 0900b-5


title: DMSO vehicle 4h (365_C105)

description: gene expression data from CHL-1 cells vehicle, DMSO, 4h

source_name: CHL-1 cells vehicle, DMSO, 4h


title: 0900b-6


title: BAY1238097 468nM 24h (354_C94)

source_name: CHL-1 cells treated, 468nM BAY1238097, 24h


title: 0900b-3


title: 0900b-1


title: 0900a-5

source_name: Whole 30-day larva, 0h Zeitgeber time


title: DMSO vehicle 24h (352_C92)


title: 0900a-6


title: 0900a-4


title: 0900a-3


title: BAY1238097 468nM 4h (341_C81)

description: gene expression data from CHL-1 cells treated, 468nM BAY1238097, 4h


title: BAY1238097 75nM 4h (340_C80)

source_name: CHL-1 cells treated, 75nM BAY1238097, 4h


title: 0900a-2


title: BAY1238097 468nM 24h (328_C68)


title: Nannochloropsis_P-Deplete58h_rep2

city: Trondheim

first: Per

last: Winge

address: Høgskoleringen 5e

department: Department of Biology

country: Norway

institute: Norwegian University of Science and Technology

hyb_protocol: 600 ng cRNA from each sample was fragmented and hybridized on 8x15K custom made N. oceanica whole-genome 60-mer oligonucleotide microarrays (Agilent Technologies, design ID: Agilent-048674) in an Agilent G2545A Hybridization rotary oven (10 rpm, 65°C, 17.5 h). Hybridization was performed with the Gene Expression Hybridization Kit (Agilent p/n 5188-5242). The slides were washed with buffer 1 & 2 from Gene Expression Wash Buffer kit (Agilent p/n 5188-5327) according to manufacturers description.

scan_protocol: The microarray sides were scanned twice at 5 µm resolution on a laser scanner (G2505 B from Agilent Technologies), using the “dynamic range expander” option in the scanner software. The resulting images were processed using Agilent Feature Extraction software v9.5.

data_processing: The median signal intensities (gMedianSignal) were normalized using the quantile method, and no background subtraction was performed. Spots identified as feature outliers were excluded from analysis, and weak or non-detected spots were given reduced weight (0.5). Genes with statistically significant differential expression were identified using the Limma package (version 3.4) and R (version 3.0.3).

organism: Nannochloropsis oceanica

source_name: Nannochloropsis, Phosphate deplete, 58 h

label_protocol: Total RNA (200 ng) from each sample was reverse transcribed, amplified and labelled with Cy3-CTP using the Low Input Quick Amp Labelling Kit, One-Color (Agilent p/n 5190-2305)

growth_protocol: The CCMP1779 strain of N. oceanica was obtained from the National Center for Marine Algae and Microbiota (NCMA, former CCMP, https://ncma.bigelow.org/). N. oceanica pre-cultures were grown in 300 ml of f/2 medium without silica (23°C, 170 rpm, 3 days, constant light of 80 µmoL photons m-2 s-1 (measured by Biospherical instruments Inc. QLS-100, US), and then transferred to 6 L of f/2 medium without silica in three 2 L Nalgene optically clear flasks (Thermo Fisher Nalgene®). Thereafter, N. oceanica was grown in axenic cultures under constant light (350 µmoL photons m-2 s-1), at 23°C. The Nalgene optically clear flasks were aerated with sterile-filtered air. The f/2 medium without silica was prepared from filtered (1 μm, Whatmann GF/C filter), and autoclaved seawater supplemented with macro- and micro-nutrients and vitamins (Guillard, 1975). For the axenic growth culture, 100 μg / mL of Ampicillin was added to the f/2 growth medium.

extract_protocol: For the RNA isolation 50-100 mL samples of the biological replicates were quickly harvested through vacuum filtration on Durapore membrane filters (DVPP, 0.65 µm, Merck Millipore). Three biological replicates were used for the 24h time point, while two biological samples were used for the 48 h, 53 h, 58 h and 70 h samples. After resuspension of the filtered cells in seawater, the cells were centrifuged (13,000xg, 1 min). The supernatant was removed and pellets were flash frozen in liquid nitrogen and stored at -80°C. The supernatant was removed and pellets were flash frozen in liquid nitrogen and stored at -80°C. Precooled (-80°C) 5 mm stainless steel beads (QIAGEN) were added to the tubes with frozen cell pellets, and the samples were mechanically disrupted and homogenized using the TissueLyser system (QIAGEN). Disruption was carried out for 2 x 2 min at 25 Hz. The samples were placed in a precooled (-80°C) adapter set for the first shaking step. Before the second shaking step, the samples were transferred to a room temperate adapter set and 0.5 ml lysis buffer (SpectrumTM Plant Total RNA kit, Sigma-Aldrich) was added to each tube. Total RNA was isolated from the homogenized lysate using the SpectrumTM Plant Total RNA kit (Sigma-Aldrich). On-column digestion of DNA with DNase I (QIAGEN) was included for all RNA preparations. The quantitative total RNA was measured by NanoDrop spectrometer, and the RNA integrity numbers (RINs) assessed by using the 2100 Bioanalyzer (Agilent). Only RIN-values above 7 were used for further analysis.

treatment_protocol: The pre-cultures were grown to the exponential growth phase (OD750nm= 0.40, ~8*106 cells mL-1), mixed, harvested, and washed with sterile seawater by centrifugation (4,700xg, 20 min). The experimental cultures were inoculated to an OD750nm of 0.06 (~2.5*106 cells mL-1) in either f/2 medium without silica (36.38 μM PO43-, +P cells) or f/2 medium without silica with a reduced phosphate concentration (2.79 μM PO43-, -P cells). Three biological replicates of the algal cultures were established for each of the mentioned conditions. For most of the analyses, two technical samples of the three biological replicates were analyzed every 12 h. Two independent experiments were performed. The first experiment was used for transcriptomic and phosphorus footprint studies and the second for lipidomic studies.

tag: clone

tag: harvest timepoint


title: DMSO vehicle 4h (339_C79)


title: 0900b-2

tag: age


title: BAY1238097 75nM 24h (327_C67)


title: 0600-6

source_name: Whole 30-day larva, 21h Zeitgeber time


title: 0600-4


title: BAY1238097 468nM 4h (315_C55)

source_name: CHL-1 cells treated, 468nM BAY1238097, 4h


title: DMSO vehicle 4h (313_C53)


title: Nannochloropsis_P-Deplete70h_rep2

source_name: Nannochloropsis, Phosphate deplete, 70 h


title: 0600-5


title: 0900a-1


title: BAY1238097 75nM 4h (314_C54)


title: 0600-3


title: DMSO vehicle 24h (326_C66)


title: BAY1238097 468nM 24h (302_C42)


title: Nannochloropsis_P-Deplete70h_rep1


title: BAY1238097 75nM 24h (301_C41)


title: Nannochloropsis_P-Deplete53h_rep2

source_name: Nannochloropsis, Phosphate deplete, 53 h


title: Nannochloropsis_P-Deplete58h_rep1


title: DMSO vehicle 24h (300_C40)


title: Nannochloropsis_P-Deplete53h_rep1


title: 0600-2


title: 0600-1


title: Nannochloropsis_P-Deplete48h_rep2

source_name: Nannochloropsis, Phosphate deplete, 48 h


title: BAY1238097 468nM 4h (289_C29)


title: Nannochloropsis_P-Deplete24h_rep3

source_name: Nannochloropsis, Phosphate deplete, 24 h


title: 0300-6

source_name: Whole 30-day larva, 18h Zeitgeber time


title: 0300-5


title: BAY1238097 75nM 4h (288_C28)


title: Nannochloropsis_P-Replete24h_rep3

source_name: Nannochloropsis, Phosphate replete, 24 h


title: Nannochloropsis_P-Deplete48h_rep1


title: Nannochloropsis_P-Deplete24h_rep1


title: Nannochloropsis_P-Replete24h_rep1


title: DMSO vehicle 4h (287_C27)


title: Nannochloropsis_P-Deplete24h_rep2


title: 0300-1


title: 0300-2


title: 0000-4

source_name: Whole 30-day larva, 15h Zeitgeber time


title: BAY1238097 75nM 24h (275_C15)


title: 0000-6


title: 0000-5


title: 2050-2

source_name: Whole 30-day larva, 12h Zeitgeber time


title: BAY1238097 468nM 24h (276_C16)


title: Nannochloropsis_P-Replete24h_rep2


title: LNCaP with miR-33a_1

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

hyb_protocol: After labeling, 2ug of each aRNA was mixed with 2 ug of reference RNA and purified with Qiagen MinElute PCR Purification kit according to manufacturer’s instructions. Eluted sample was mixed with 10× Blocking Solution and 2× HiRPM buffer (Agilent Technologies), incubated for 2 min at 95°C and hybridized on 8× 60K Whole Human Genome Oligo Microarray chip (Agilent Technologies) using SureHyb DNA Microarray Hybridization Chambers in DNA Microarray hybridization oven (Agilent Technologies) at 10 rpm, 65°C for 18 h.

scan_protocol: After hybridization, slides were washed in Gene Expression Wash Buffer 1 and 2 for 1 min. Microarrays were scanned with a dynamic autofocus microarray scanner (Agilent Microarray Scanner–G2565BA, Agilent Technologies) using Agilent-provided parameters (Red and Green photomultiplier tube (PMT) were each set at 100%, and scan resolution was set to 3 μm). The Feature Extraction Software v9.1.3.1 (Agilent Technologies) was used to extract and analyze the signals.

data_processing: Expression arrays were processed and loess-normalized using BioConductor.

source_name: LNCaP with miR-33a

label_protocol: The cDNA reverse transcription and fluorescent labeling reactions were carried out using Invitrogen SuperScript Plus Direct cDNA Labeling System with Alexa Fluor S’-Aminohexylacrylamido-dUTP.Briefly, 2ug of aRNA and Universal Human Reference RNA (Stratagene) were labeled in reverse transcription with Alexa647 and Alexa 555 aha-dUTPs respectively.

growth_protocol: Human PCa LNCaP cells were grown in RPMI-1640 medium (GenDepot) supplemented with 10% fetal bovine serum (FBS, GIBCO) and 100 ug/ml penicillin/ streptomycin (Invitrogen) and VCAP cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM, Invitrogen) supplemented with 10% FBS and 1% penicillin/streptomycin at 37°C in a humidified and 5% CO2 incubator.

extract_protocol: Total RNA samples were extracted with RNeasy Mini Kit (Qiagen) according to the manufacture’s recommendations. RNA quality was assessed with Nanodrop (Invitrogen). The cDNA reverse transcription and fluorescent labeling reactions were carried out using Invitrogen SuperScript Plus Direct cDNA Labeling System with Alexa Fluor S’-Aminohexylacrylamido-dUTP.

treatment_protocol: Mature miR-33a mimic and non-targeting mimic control were purchased from Invitrogen.  Transfection experiments were optimized and performed using Lipofectamine RNAiMAX Transfection Reagent (Invitrogen) following the manufacturer’s protocol.

value: LNCaP

tag: sample type

value: reference


title: 0000-3


title: LNCaP control_2

source_name: LNCaP control

source_name: Universal Human Reference RNA (Stratagene)


title: 0300-3


title: LNCaP with miR-33a_2


title: BAY1238097 75nM 4h (262_C2)


title: 0300-4


title: 0000-2


title: BAY1238097 468nM 4h (263_C3)


title: LNCaP control_1


title: myocardium_4weeks_Non-MI_rep2

city: Beijing

first: Aiming

last: Wu

address: Haiyuncang No.5

institute: Dongzhimen Hospital Affiliated to Beijing University of Chinese Medicine

description: miRNA expression data from left ventricular (LV) tissue of sham-operated rat

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Rat miRNA （8*15K）for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 13.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

organism: Rattus norvegicus

source_name: myocardium, 4 weeks after sham-surgery, Non-myocardial infarction, replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg 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 mirVanaTM RNA Isolation Kit (Applied Biosystem p/n AM1556 ) following the manufacturer's instructions.

value: left ventricular tissue

tag: gender

tag: operation type

value: 4 weeks after sham-surgery

tag: ischemic type

value: Non-myocardial infarction

tag: strain

value: Sprague-Dawley


title: myocardium_4weeks_MI_rep2

description: miRNA expression data from left ventricular (LV) tissue of myocardial infarction rat

source_name: myocardium, 4 weeks after the coronary artery ligation surgery, Myocardial infarction, replicate 2

tag: tissue

value: Myocardial infarction


title: myocardium_4weeks_MI_rep3

source_name: myocardium, 4 weeks after the coronary artery ligation surgery, Myocardial infarction, replicate 3


title: myocardium_4weeks_Non-MI_rep1

source_name: myocardium, 4 weeks after sham-surgery, Non-myocardial infarction, replicate 1


title: myocardium_4weeks_Non-MI_rep3

source_name: myocardium, 4 weeks after sham-surgery, Non-myocardial infarction, replicate 3


title: myocardium_4weeks_MI_rep1

source_name: myocardium, 4 weeks after the coronary artery ligation surgery, Myocardial infarction, replicate 1


title: VCaP with miR-33a_2

source_name: VCaP with miR-33a

value: VCaP


title: VCaP control_1

source_name: VCaP control


title: NS derived from small molecule-treated eKA3

city: Sinjuku-ku, Tokyo

first: Koki

last: Fujimori

address: 35 Shinanomachi

department: Physiology

institute: Keio University

description: small molecule-treated iPSC→NS

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

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

data_processing: The data were 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 500. Normalized data matrices available on the series record contain MAS 5.0 signal. Normalizations were performed on sample subsets.

source_name: Neurosphere (iPSC derived)

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

tag: cell type

value: Neurosphere (NS)

tag: donor

value: KA (healthy)

tag: iPSc source

value: dermal fibroblast

tag: vector for delivery of reprogramming factors

value: episomal vectors


title: small molecule-treated KA11

description: small molecule-treated iPSC

source_name: iPSC

value: iPSC

value: retrovirus


title: EB derived from eKA3

source_name: Embryoid body (iPSC derived)

value: Embryoid body (EB)


title: VCaP with miR-33a_1

tag: treatment


title: NS derived from small molecule-treated KA11

description: small molecule-treated iPSC→NS


title: iPSC (DonorKA-derived, clone #3)


title: BAY1238097 468nM 4h (367_C107)

source_name: CHL-1 cells treated, 468nM BAY1238097, 4h

value: skin

tag: histologic subtype

value: melanoma

tag: dose


title: NS derived from KA11


title: VCaP control_2

tag: cell line

value: control


title: small molecule-treated eKA3

description: small molecule-treated iPSC


title: EB derived from KA11


title: 0000-1

source_name: Whole 30-day larva, 15h Zeitgeber time

value: Whole 30-day larva

tag: zeitgeber time (hrs)


title: NS derived from eKA3


title: FLS_OA_IL-1β_1

first: Bong-Ki

last: Hong

address: 222 Banpo-daero, Seocho-gu

department: School of Medicine

institute: Catholic University of Korea

description: OA-FLS 2-115 + IL-1b

hyb_protocol: RNA was then amplified and hybridized to Agilent-019118 Human miRNA Microarray 2.0 G4470B according to the manufacturers’ standard protocols.

scan_protocol: cRNA on Agilent SurePrint G3 Human Gene Expression 8x60K v2 microarray chip was scanned by SureScan Microarray Scanner

data_processing: Quantile-normalization was performed for the log2-value of gMedianSignal

source_name: OA-FLS IL-1β

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared, followed by RNAeasy Mini Kit (QIAGEN). cRNA was quantified and normalized by using NanoDrop

growth_protocol: FLS were isolated from synovial tissues of patients with rheumatoid arthritis or osteoarthritis and cultured in Dulbecco’s modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 6.0g/L of HEPES, 0.4g/L of L-glutamine, 3.7g/L of Sodium bicarbonate, 1X of antibiotics, 1X of MEM Non-Essential Amino Acids, and 1X of 2-Mercaptoethanol. Experiments were performed between passage 3 and 9.

extract_protocol: We prepared total RNA independently from two (for miRNA) or three (for mRNA) replicate samples using the RNeasy mini kit (Qiagen, Hilden, Germany) and assessed RNA integrity using Bioanalyzer 2100 (Agilent Technologies, CA). The RNA integrity number (PRN) was close to 10 for all samples.

treatment_protocol: Cultured FLS were stimualted with 5%FBS DMEM which containted 10ng/ml of IL-1beta or not for 12 hours.

tag: subject status

value: Osteoarthritis patient

value: Fibroblast like synoviocyte (FLS)

tag: stimulated with

value: interleukin-1 beta


title: FLS_OA_basal_2

description: OA-FLS 2-116


title: FLS_OA_IL-1β_2

description: OA-FLS 2-116 + IL-1b


title: iPSC (DonorKA-derived, clone #11)


title: FLS_OA_basal_1

description: OA-FLS 2-115


title: FLS_RA_basal_2

description: RA-FLS 2-57

value: Rheumatoid Arthritis patient


title: FLS_RA_IL-1β_2

description: RA-FLS 2-57 + IL-1b

source_name: RA-FLS IL-1β


title: FLS_RA_basal_1

description: RA-FLS 2-55


title: FLS_RA_IL-1β_1

description: RA-FLS 2-55 + IL-1b


title: Substantia nigra from intact, levodopa-treated adult male Sprague Dawley rat, biological rep #2

city: Grand Rapids

first: Jack

middle: W

last: Lipton

state: MI

address: 333 Bostwick Ave.

department: TSMM

institute: Michigan State University

description:
38G_LD+_Intact
0.5mm X 1.5 mm punch from substantia nigra

hyb_protocol: 2.5 ug of fragmented cRNA was hybridized for 17 hours at 45C in the GeneChip Hybridization Oven 640 (Affymetrix). Chips were washed and stained in the Fluidics Station 450 (Affymetrix) using fluidix protocol FS450-0007.

scan_protocol: GeneChips were scanned in a GeneChip Scanner 3000 7G (Affymetrix).

data_processing:
Data processing and analysis were performed (N = 3 rats per experimental group) using R v3.2.3 (http://www.R-project.org) and Bioconductor (19). CEL files were imported into R, assessed for quality, and Robust-Multi Array (RMA) normalized at the probeset level using the oligo package (v1.34).
probe group file: Bioconductor package pd.ragene.1.0.st.v1 (version 3.14.1) (target = probeset)
meta-probeset file: Bioconductor package pd.ragene.1.0.st.v1 (version 3.14.1) (target = probeset)

source_name: Intact, levodopa treated substantia nigra

label_protocol: Biotin labeled, cRNA was made using Ambion WT Expression kit (Life Technologies) combined with the GeneChip WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Male, Sprague Dawley rats weighing between 200-225g were given access to food and water ad libitum. They were housed in an AALAC accredited animal facility in a reverse light-dark cycle.

extract_protocol: Rats were sacrificed, brains frozen in isopentane for 30 seconds and stored individually at -80˚C. Structures were dissected using punches at -20˚C in a cryostat. Punches were ejected into an eppendorf tube containing Trizol and gently homogenized using a disposable plastic pestle. Samples were stored at -80˚C. RNA was isolated from Trizol homogenate using RNA Clean and Concentrator kit (Zymo). Quality of total RNA was determined on an Agilent Bioanalyzer. Only samples with RIN values ≥ 7 were used in this study.

treatment_protocol: Rats were anesthetized with 0.3ml/100g chloralpent. Each rat received two injections of 6-OHDA hydrobromide (Sigma-Aldrich, St. Louis, MO), 5ug/ul in 0.2% ascorbic acid in 0.9% saline, or vehicle (0.2% ascorbic acid in 0.9% saline). The two injection coordinates were AP+1.6mm, ML+2.4mm, DV -4.2, and, AP+0.2mm, ML+2.6mm, DV-7.0mm.

tag: strain/background

value: Sprague Dawley

value: Male

tag: age

value: Adult

value: Substantia nigra

tag: lesion

value: Saline

value: Levodopa

tag: animal id


title: Substantia nigra from intact, levodopa-treated adult male Sprague Dawley rat, biological rep #3

description:
39G_LD+_Intact
0.5mm X 1.5 mm punch from substantia nigra

tag: gender


title: Substantia nigra from intact, levodopa-treated adult male Sprague Dawley rat, biological rep #1

description:
10G_LD+_Intact
0.5mm X 1.5 mm punch from substantia nigra

tag: tissue


title: Substantia nigra from lesioned, untreated adult male Sprague Dawley rat, biological rep #3

description:
19G_LD-_6-OHDA
0.5mm X 1.5 mm punch from substantia nigra

source_name: 6-OHDA lesioned, untreated substantia nigra

value: Vehicle


title: Substantia nigra from lesioned, untreated adult male Sprague Dawley rat, biological rep #2

description:
15G_LD-_6-OHDA
0.5mm X 1.5 mm punch from substantia nigra


title: Substantia nigra from lesioned, levodopa-treated, non-dyskinetic adult male Sprague Dawley rat, biological rep #1

description:
5G_LD+_LID-
0.5mm X 1.5 mm punch from substantia nigra

source_name: 6-OHDA lesioned, levodopa treated, LID- substantia nigra

tag: lid

value: non-dyskinetic


title: Substantia nigra from lesioned, untreated adult male Sprague Dawley rat, biological rep #1

description:
6G_LD-_6-OHDA
0.5mm X 1.5 mm punch from substantia nigra


title: THP-1 TNF-a EV 2

city: Oxford

first: Naveed

last: Akbar

state: United Kingdom

address: Radcliffe Department of Medicine, University of Oxford

department: Cardiovascular Medicine

country: United Kingdom

institute: University of Oxford

description:
Cell culture stimulation
SAMPLE 6

data_processing: The normalization and all the data analysis were performed according to the manufacturers instructions    Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]  The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.  Matrix normalized worksheet reports normalized signal (against housekeeping genes).  Fold Change worksheet reports test/control (i.e., NOD1-1IS-/-/WT) ratios.

source_name: Lonza

growth_protocol: THP-1 human monocytes (ATCC®, UK) were cultured in RPMI-medium (Sigma Aldrich) supplemented 10% FBS, 1% antibiotics (Penicillin-Streptomycin) (Sigma Aldrich), 2mM L-glutamine (Sigma Aldrich) and 0.05nM  2-mercaptoethanol.

extract_protocol: Qiagen RNA spin columns

treatment_protocol: Monocytes were differentiated into macrophages by exposure to phorbol myristate acetate (PMA) (200 nM) for 24 hours

tag: cell type

value: THP-1 monocyte


title: THP-1 IL-1b EV 1

description:
Cell culture stimulation
SAMPLE 4


title: THP-1 Basal EV 2

description:
Cell culture stimulation
SAMPLE 5


title: THP-1 IL-1b EV 2

description:
Cell culture stimulation
SAMPLE 7


title: Substantia nigra from lesioned, levodopa-treated, non-dyskinetic adult male Sprague Dawley rat, biological rep #3

description:
16G_LD+_LID-
0.5mm X 1.5 mm punch from substantia nigra


title: THP-1 TNF-a EV 1

description:
Cell culture stimulation
SAMPLE 3


title: THP-1 Basal EV 1

description:
Cell culture stimulation
SAMPLE 2


title: Substantia nigra from lesioned, levodopa-treated, non-dyskinetic adult male Sprague Dawley rat, biological rep #2

description:
13G_LD+_LID-
0.5mm X 1.5 mm punch from substantia nigra


title: THP-1 Control

description:
Cell culture stimulation
SAMPLE 1


title: Striatum from lesioned, levodopa-treated, dyskinetic adult male Sprague Dawley rat, biological rep #3

description:
27C_LD+_LID+
2mm X 2mm punch from lateral striatum

source_name: 6-OHDA lesioned, levodopa treated, LID+ striatum

value: Striatum

value: dyskinetic


title: Striatum from intact, levodopa-treated adult male Sprague Dawley rat, biological rep #3

description:
39C_LD+_Intact
2mm X 2mm punch from lateral striatum

source_name: Intact, levodopa treated striatum


title: Substantia nigra from lesioned, levodopa-treated, dyskinetic adult male Sprague Dawley rat, biological rep #3

description:
27G_LD+_LID+
0.5mm X 1.5 mm punch from substantia nigra

source_name: 6-OHDA lesioned, levodopa treated, LID+ substantia nigra


title: Substantia nigra from lesioned, levodopa-treated, dyskinetic adult male Sprague Dawley rat, biological rep #2

description:
26G_LD+_LID+
0.5mm X 1.5 mm punch from substantia nigra


title: Striatum from lesioned, levodopa-treated, dyskinetic adult male Sprague Dawley rat, biological rep #1

description:
9C_LD+_LID+
2mm X 2mm punch from lateral striatum


title: Striatum from intact, levodopa-treated adult male Sprague Dawley rat, biological rep #1

description:
40C_LD+_Intact
2mm X 2mm punch from lateral striatum


title: Striatum from lesioned, levodopa-treated, dyskinetic adult male Sprague Dawley rat, biological rep #2

description:
26C_LD+_LID+
2mm X 2mm punch from lateral striatum


title: Striatum from lesioned, untreated adult male Sprague Dawley rat, biological rep #2

description:
15C_LD-_6-OHDA
2mm X 2mm punch from lateral striatum

source_name: 6-OHDA lesioned, untreated striatum


title: Substantia nigra from lesioned, levodopa-treated, dyskinetic adult male Sprague Dawley rat, biological rep #1

description:
31G_LD+_LID+
0.5mm X 1.5 mm punch from substantia nigra


title: Striatum from lesioned, levodopa-treated, non-dyskinetic adult male Sprague Dawley rat, biological rep #3

description:
16C_LD+_LID-
2mm X 2mm punch from lateral striatum

source_name: 6-OHDA lesioned, levodopa treated, LID- striatum


title: Striatum from lesioned, levodopa-treated, non-dyskinetic adult male Sprague Dawley rat, biological rep #2

description:
13C_LD+_LID-
2mm X 2mm punch from lateral striatum


title: Striatum from lesioned, levodopa-treated, non-dyskinetic adult male Sprague Dawley rat, biological rep #1

description:
5C_LD+_LID-
2mm X 2mm punch from lateral striatum


title: Striatum from intact, levodopa-treated adult male Sprague Dawley rat, biological rep #2

description:
38C_LD+_Intact
2mm X 2mm punch from lateral striatum


title: Striatum from lesioned, untreated adult male Sprague Dawley rat, biological rep #1

description:
6C_LD-_6-OHDA
2mm X 2mm punch from lateral striatum


title: mPFC from the morphine treated rats 4

city: Shanghai

first: Ming

last: Chen

address: Yixue Road 138

institute: Fudan University

hyb_protocol: After stopping the labeling procedure, the Hy3TM-labeled samples were hybridized on the miRCURYTM LNA Array (v.18.0) (Exiqon) according to array manual. The total 25 μL mixture from Hy3TM-labeled samples with 25 μL hybridization buffer were first denatured for 2 min at 95°C, incubated on ice for 2 min and then hybridized to the microarray for 16–20 h at 56°C in a 12-Bay Hybridization Systems (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA), which provides an active mixing action and constant incubation temperature to improve hybridization uniformity and enhance signal. Following hybridization, the slides were achieved, washed several times using Wash buffer kit (Exiqon), and finally dried by centrifugation for 5 min at 400 rpm. Then the slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

scan_protocol: Scanning is performed with the Axon GenePix 4000B microarray scanner.

data_processing: Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, significant differentially expressed miRNAs were identified through Volcano Plot filtering. Hierarchical clustering was performed using MEV software (v4.6, TIGR).

source_name: mPFC from the morphine treated rats

label_protocol: After RNA isolation from the samples, the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling. One microgram of each sample was 3'-end-labeled with Hy3TM fluorescent label, using T4 RNA ligase by the following procedure: RNA in 2.0 μL of water was combined with 1.0 μL of CIP buffer and CIP (Exiqon). The mixture was incubated for 30 min at 37°C, and was terminated by incubation for 5 min at 95°C. Then 3.0 μL of labeling buffer, 1.5 μL of fluorescent label (Hy3TM), 2.0 μL of DMSO, 2.0 μL of labeling enzyme were added into the mixture. The labeling reaction was incubated for 1 h at 16°C, and terminated by incubation for 15 min at 65°C.

growth_protocol: mPFC dissected from 2 months rat.

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

treatment_protocol: Morphine dependence was induced in rats by repeated intraperitoneal injections of morphine twice daily at 08.00 AM and 19.00 PM. Morphine doses were progressively increased from 10 mg/kg to 40 mg/kg: ﬁrst day 2×10 mg/kg, second day 2×20 mg/kg, third day 2×30 mg/kg, fourth and ﬁfth days 2×40 mg/kg. Control rats were treated with saline following the same procedure.

tag: strain background

tag: genotype/variation

value: wild-type

value: 2 months

tag: treated with

value: morphine

value: brain; medial prefrontal cortex


title: mPFC from the morphine treated rats 3


title: mPFC from the morphine treated rats 2


title: mPFC from the saline treated rats 4

source_name: mPFC from the saline treated rats

value: saline


title: mPFC from the morphine treated rats 1


title: mPFC from the saline treated rats 1


title: mPFC from the saline treated rats 2


title: mPFC from the morphine treated rats 5


title: mPFC from the saline treated rats 3


title: Striatum from lesioned, untreated adult male Sprague Dawley rat, biological rep #3

description:
19C_LD-_6-OHDA
2mm X 2mm punch from lateral striatum

tag: treatment


title: Wnt- rectal tumor 25 [GE]

status: Public on Oct 30 2017

city: HYDERABAD

first: Murali

middle: Dharan

last: Bashyam

state: (Click to Select US State)

address: MJ MARKET

institute: CDFD

description:
2473
Microsatellite stable Wnt- rectal adenocarcinoma

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 sequential

scan_protocol: Scanned on an Agilent G2505B scanner Images were quantified using Agilent Feature Extraction Software (version v10.7)

data_processing: Agilent Feature Extraction Software (v10.7) was used for background subtraction and LOWESS normalization

source_name: Surgically removed rectum

label_protocol: 2μg each of total RNA from tumors along with equal quantity of universal reference RNA (pooled up RNA from 11 cell lines (Bashyam et al., 2005)) were differentially labeled with Cy5 and Cy3 dyes using Quickamp labeling kit (Agilent Technologies, CA, USA) following manufacturer's instructions

growth_protocol: Not applicable

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

tag: Sex

value: Female

value: Rectal adenocarcinoma

tag: Stage

tag: grade

source_name: pooled 11 cell line

tag: reference

value: Universal reference RNA


title: mPFC from the saline treated rats 5

value: Sprague Dawley


title: Wnt- rectal tumor 27 [GE]

description:
2509
Microsatellite stable Wnt- rectal adenocarcinoma


title: Wnt+ rectal tumor 23 [GE]

description:
2495
Microsatellite stable Wnt+ rectal adenocarcinoma

value: Male


title: Wnt+ rectal tumor 25 [GE]

description:
2517
Microsatellite stable Wnt+ rectal adenocarcinoma


title: Wnt- rectal tumor 29 [GE]

description:
2521
Microsatellite stable Wnt- rectal adenocarcinoma


title: Wnt- rectal tumor 28 [GE]

description:
2513
Microsatellite stable Wnt- rectal adenocarcinoma


title: Wnt- rectal tumor 24 [GE]

description:
2455
Microsatellite stable Wnt- rectal adenocarcinoma


title: Wnt- rectal tumor 26 [GE]

description:
2491
Microsatellite stable Wnt- rectal adenocarcinoma


title: Wnt+ rectal tumor 21 [GE]

description:
2413
Microsatellite stable Wnt+ rectal adenocarcinoma


title: Wnt+ rectal tumor 20 [GE]

description:
2403
Microsatellite stable Wnt+ rectal adenocarcinoma


title: Wnt- rectal tumor 17 [GE]

description:
2308
Microsatellite stable Wnt- rectal adenocarcinoma


title: Wnt- rectal tumor 22 [GE]

description:
2409
Microsatellite stable Wnt- rectal adenocarcinoma


title: Wnt+ rectal tumor 24 [GE]

description:
2497
Microsatellite stable Wnt+ rectal adenocarcinoma


title: Wnt+ rectal tumor 18 [GE]

description:
2389
Microsatellite stable Wnt+ rectal adenocarcinoma


title: Wnt+ rectal tumor 19 [GE]

description:
2397
Microsatellite stable Wnt+ rectal adenocarcinoma


title: Peripheral blood mononuclear cells of HC 14

city: Lucknow

first: Sushma

last: Singh

state: Uttar Pradesh

address: Raebareli Road

department: Clinical Immunology

institute: Sanjay Gandhi Post Graduate Institute of Medical Sciences

description: miRNA expression profile in peripheral blood mononuclear cells of healthy control 14

hyb_protocol: The dried sample was resuspended in nuclease free water and mixed with Hybridization Mix containing blocking and Hi-RPM Hybridization Buffer  and incubated at 100oC for 5 minutes followed by snap chill on ice for 5 minutes.  The samples were hybridized on the Human miRNA 8x15k Arrays. The hybridization was carried out at 55°C for 20 hours. After hybridization, the slides were washed using Gene Expression Wash Buffer1 (Agilent Technologies, Part Number 5188-5325) at room temperature for 5 minutes and Gene Expression Wash Buffer 2 (Agilent Technologies, Part Number 5188-5326) at 37oC for 5 minutes. The slides were then washed with Acetonitrile for 30 seconds. The microarray slide was scanned on a G2505C scanner (Agilent Technologies)

data_processing: The normalization was done using GeneSpring GX  Software. 90th Percentile Shift Normalization

source_name: Peripheral blood mononuclear cells of healthy control 14

label_protocol: The miRNA labeling was performed using miRNA Complete Labeling and Hyb Kit (Agilent Technologies, Part Number: 5190-0456). The total RNA sample was diluted to 50ng/ul in nuclease free water. 100ng of total RNA was dephosphorylated using Calf Intestinal Alkaline Phosphatase (CIP) master by incubating at 37oC for 30 minutes. The dephosphorylated miRNA sample was denatured by adding Dimethyl Sulfoxide and heating at 100 oC for 10 minutes and transferred to ice-water bath. The Ligation master mix containing Cyanine 3-pCp was added to the denatured miRNA sample and incubated at 16oC for 2 hours. The Cyanine 3-pCp labeled miRNA sample was dried completely in the vacuum concentrator (Eppendorf, Concentrator Plus) at 45oC for 2 hour.

extract_protocol: Peripheral blood and synovial fluid mononuclear cells (PBMC and SFMCs) were isolated by density gradient centrifugation using Histopaque 1077 (Sigma-Aldrich,  St. Louis, MO, USA). PBMCs and SFMCs were stored at -80ºC in Trizol (Life Technologies Inc., USA) at a concentration of 5-6 x 106/ ml and RNA was isolated using Trizol (Life  Technologies Inc., USA) according to the manufacturer’s protocol. Quantification and purity of RNA was checked by measuring absorbance at 260, 230  and 280 nm using Nanodrop spectrophotometer (Nanodrop Inc., Wilmington, DE, USA) and calculating 260/230 and 260/280 ratio. The quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: diagnosis

value: healthy

value: Peripheral blood

tag: age on collection of sample

value: 21 Yrs

tag: duration of disease

value: 0 Yr


title: Peripheral blood mononuclear cells of HC 13

description: miRNA expression profile in peripheral blood mononuclear cells of healthy control 13

scan_protocol: The microarray slide was scanned on a G2505C scanner (Agilent Technologies)

source_name: Peripheral blood mononuclear cells of healthy control 13

value: 20 Yrs


title: Wnt- rectal tumor 18 [GE]

description:
2353
Microsatellite stable Wnt- rectal adenocarcinoma

tag: age


title: Wnt+ rectal tumor 22 [GE]

description:
2445
Microsatellite stable Wnt+ rectal adenocarcinoma


title: Wnt- rectal tumor 23 [GE]

description:
2433
Microsatellite stable Wnt- rectal adenocarcinoma


title: Wnt- rectal tumor 20 [GE]

description:
2387
Microsatellite stable Wnt- rectal adenocarcinoma


title: Wnt- rectal tumor 21 [GE]

description:
2401
Microsatellite stable Wnt- rectal adenocarcinoma


title: Wnt- rectal tumor 19 [GE]

description:
2379
Microsatellite stable Wnt- rectal adenocarcinoma


title: Peripheral blood mononuclear cells of HC 12

description: miRNA expression profile in peripheral blood mononuclear cells of healthy control 12

source_name: Peripheral blood mononuclear cells of healthy control 12


title: Peripheral blood mononuclear cells of HC 11

description: miRNA expression profile in peripheral blood mononuclear cells of healthy control 11

source_name: Peripheral blood mononuclear cells of healthy control 11

value: 23 Yrs


title: Synovial fluid mononuclear cells of ERA patient 5

description: miRNA expression profile in synovial fluid mononuclear cells of patient 5 with enthesitis related arthritis

source_name: Synovial fluid mononuclear cells of patient 5 with enthesitis related arthritis

value: enthesitis related arthritis

value: Synovial fluid

value: 17 Yrs

value: 2 Yrs


title: Synovial fluid mononuclear cells of ERA patient 12

description: miRNA expression profile in synovial fluid mononuclear cells of patient 12 with enthesitis related arthritis

source_name: Synovial fluid mononuclear cells of patient 12 with enthesitis related arthritis

value: 15 Yrs

value: 6 Yrs


title: Synovial fluid mononuclear cells of ERA patient 11

description: miRNA expression profile in synovial fluid mononuclear cells of patient 11 with enthesitis related arthritis

source_name: Synovial fluid mononuclear cells of patient 11 with enthesitis related arthritis


title: Wnt+ rectal tumor 3 [CGH]

description:
1043
Gender matched control

hyb_protocol: Samples were hybridized to HEEBO arrays and were incubated at 65 °C for 40 hours in rotating microarray hybridization oven. After hybridization, slides were washed sequential.

scan_protocol: Scanned on Genepix 4000B scanner. Images were quantified using Spot Reader (Niles scientific, USA) software.

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. snapCGH package in R was used.

label_protocol: Using Cy-5 and Cy-3 fluorescent dyes (GE Healthcare Lifesciences, NJ, USA) and BioPrime DNA labeling system (Invitrogen Inc., Carlsbad, CA, USA) as per manufacturer’s protocol.

extract_protocol: DNA was isolated using DNeasy blood & tissue kit (Qiagen Gmbh, Hilden, Germany) as per manufacturer’s protocol.

treatment_protocol: DNA was isolated using DNeasy tissue kit (Qiagen Gmbh, Hilden, Germany) as per manufacturer’s protocol and labeled using BioPrime DNA labeling system (Invitrogen Inc., Carlsbad, CA, USA)

source_name: Total DNA from matched gender normal

value: Blood


title: Peripheral blood mononuclear cells of HC 7

description: miRNA expression profile in peripheral blood mononuclear cells of healthy control 7

source_name: Peripheral blood mononuclear cells of healthy control 7


title: Peripheral blood mononuclear cells of ERA patient 10

description: miRNA expression profile in peripheral blood mononuclear cells of patient 10 with enthesitis related arthritis

source_name: Peripheral blood mononuclear cells of patient 10 with enthesitis related arthritis


title: Peripheral blood mononuclear cells of HC 8

description: miRNA expression profile in peripheral blood mononuclear cells of healthy control 8

source_name: Peripheral blood mononuclear cells of healthy control 8

value: 18 Yrs


title: Peripheral blood mononuclear cells of ERA patient 8

description: miRNA expression profile in peripheral blood mononuclear cells of patient 8 with enthesitis related arthritis

source_name: Peripheral blood mononuclear cells of patient 8 with enthesitis related arthritis

value: 19 Yrs


title: Wnt- rectal tumor 16 [GE]

description:
2303
Microsatellite stable Wnt- rectal adenocarcinoma

value: Female

value: Rectal adenocarcinoma

value: Universal reference RNA


title: Wnt+ rectal tumor 17 [GE]

description:
2299
Microsatellite stable Wnt+ rectal adenocarcinoma


title: Wnt+ rectal tumor 16 [GE]

description:
2265
Microsatellite stable Wnt+ rectal adenocarcinoma


title: Wnt+ rectal tumor 15 [GE]

description:
2229
Microsatellite stable Wnt+ rectal adenocarcinoma


title: Wnt- rectal tumor 14 [GE]

description:
2255
Microsatellite stable Wnt- rectal adenocarcinoma


title: Peripheral blood mononuclear cells of ERA patient 9

description: miRNA expression profile in peripheral blood mononuclear cells of patient 9 with enthesitis related arthritis

source_name: Peripheral blood mononuclear cells of patient 9 with enthesitis related arthritis

value: Peripheral blood

value: Male

value: 6 Ys


title: Wnt+ rectal tumor 2 [CGH]

description:
1023
Gender matched control


title: Wnt- rectal tumor 12 [GE]

description:
2243
Microsatellite stable Wnt- rectal adenocarcinoma


title: Wnt- rectal tumor 13 [GE]

description:
2251
Microsatellite stable Wnt- rectal adenocarcinoma


title: Peripheral blood mononuclear cells of ERA patient 5

description: miRNA expression profile in peripheral blood mononuclear cells of patient 5 with enthesitis related arthritis

source_name: Peripheral blood mononuclear cells of patient 5 with enthesitis related arthritis

value: 13 Yrs

value: 2.5 Yrs


title: Peripheral blood mononuclear cells of ERA patient 6

description: miRNA expression profile in peripheral blood mononuclear cells of patient 6 with enthesitis related arthritis

source_name: Peripheral blood mononuclear cells of patient 6 with enthesitis related arthritis

value: enthesitis related arthritis

value: 21 Yrs


title: Wnt- rectal tumor 15 [GE]

description:
2295
Microsatellite stable Wnt- rectal adenocarcinoma

source_name: Surgically removed rectum


title: Wnt- rectal tumor 10 [GE]

description:
2177
Microsatellite stable Wnt- rectal adenocarcinoma

source_name: pooled 11 cell line


title: Synovial fluid mononuclear cells of ERA patient 8

description: miRNA expression profile in synovial fluid mononuclear cells of patient 8 with enthesitis related arthritis

source_name: Synovial fluid mononuclear cells of patient 8 with enthesitis related arthritis

value: Synovial fluid

value: 17 Yrs

value: 10 Yrs


title: Wnt+ rectal tumor 13 [GE]

description:
2161
Microsatellite stable Wnt+ rectal adenocarcinoma