title: Leishmania donovani infected macrophages

city: NEW DELHI

first: Amitabha

last: Mukhopadhyay

state: Delhi

address: Aruna Asaf Ali Marg

department: Cell biology

country: India

institute: National Institute of Immunology

hyb_protocol: Hybridization was done using Agilent miRNA Hybridization kit Cat # 5190-0408  on Human miRNA 8x15k Arrays AMADID: 029297

scan_protocol: The microarray scanning was performed on a G2505C scanner (Agilent Technologies, G2565CA) and image was analyzed using Agilent Feature Extraction software Version 10.7 (Agilent Technologies).

data_processing: The normalization was done using GeneSpring GX 11.5 Software. gTotalGeneSignal is the sum of the total probe signals in the green channel per gene. Expression fold values are provided in terms of log base 2 (included in the 'complete_data.txt'). Expression in uninfected macrophages are taken as 1 and log2 (1) is 0.

label_protocol: Ligation of one cyanine3 –pCp molecule to the 3’ end of RNA molecule was done using Agilent miRNA labeling reagent and used for hybridization to generates fluorescent miRNA molecule with greater than 90% efficiency.

growth_protocol: Human acute monocytic leukemia-derived cells (THP-1) were cultured in complete RPMI (RPMI-1640 containing 10% FCS and 50 μg/ml gentamycin) at 37°C in a humidified incubator with 5% CO2. THP-1 cells were differentiated into macrophages in the presence of Phorbol 12-myristate 13-acetate (100ng/ml) for 24h. Cells were washed and incubated for another 24 h in complete RPMI without PMA and used for experimental purpose.

extract_protocol: Cells were lysed inTRIzol and total RNA was isolated using Biorad MicroBio Spin 6 columns(Cat # 732-6221)

treatment_protocol: THP-1 Differentiated Macrophages were infected with Leishmania donovani promastigotes in RPMI medium at MOI of 1:20 for 3 h at 37°C followed by 3 washes with plain RPMI to remove uninternalized parasites. Infected cells were incubated in complete RPMI at 37°C for 15h.

tag: cell line

tag: source cell type

value: acute monocytic leukemia-derived cell line

tag: cell type

value: PMA-differentiated macrophage

tag: infected with

value: Leishmania donovani promastigotes


title: CRC0129

status: Public on Jun 19 2017

type: RNA

city: Candiolo

first: Enzo

last: Medico

state: TO

address: Strada Prov. 142, km 3,95

department: Oncology

country: Italy

institute: Candiolo Cancer Institute, University of Torino

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data were normalized by Bioconductor (3.0) lumi pipeline with loess normalization

label: biotin-SA Cy3

molecule: total RNA

organism: Homo sapiens

source_name: Liver Metastasis

label_protocol: Synthesis of cDNA and biotinylated cRNA were performed using the Illumina Total-Prep RNA Amplification Kit (Ambion, Austin, TX, USA, cat. no. IL1791), according to the manufacturer’s protocol, for which hybridization was carried out on Illumina HumanHT-12 V3 arrays

growth_protocol: Tumor were collected upon surgical resection and stored in liquid nitrogen

extract_protocol: RNA was extracted using the Trizol Plus purification Kit (Invitrogen, Frederick, MD, USA, cat. no.12183555), according to the manufacturer’s protocol. Quantification and quality analysis of RNA was performed on a Bioanalyzer 2100 (Agilent, Santa Clara, CA, USA).

treatment_protocol: Cryostatic section of the frozen specimens were cut for RNA extraction

tag: tissue type

value: frozen liver metastasis sample

tag: tissue id

tag: kras (1=mut;0=wt,na=not determined)

tag: cris class

value: CRISD

tag: cris distance to template

tag: cris bh.fdr


title: Uninfected macrophages

value: none  (uninfected)


title: CRC0124

value: CRISB


title: CRC0125

value: CRISA


title: CRC0128


title: CRC0123


title: CRC0126


title: CRC0121

value: CRISE


title: CRC0127


title: CRC0122


title: CRC0345-A-1

source_name: LM CRC PDX sample

tag: tissue

value: LM CRC PDX

value: Not assigned

tag: sampling region

value: A


title: CRC0180-A-1


title: CRC0180-A-2


title: CRC0329-B-1

value: B


title: CRC0118


title: CRC0416-A-1


title: CRC0014_rep1

value: CRISC


title: CRC0120


title: CRC0427-A-1


title: CRC0345-A-2


title: CRC0164-B-2


title: CRC0427-A-2


title: CRC0178-0-1


title: CRC0140


title: CRC0119


title: CRC0164-B-1


title: CRC0139


title: CRC0024-B-1


title: CRC0151-B-1


title: CRC0151-0-1


title: CRC0598-B-1


title: CRC0598-A-1


title: CRC0137


title: CRC0576-B-1


title: CRC0559-B-1


title: CRC0576-A-1


title: CRC0136


title: CRC0138


title: CRC0556-B-2


title: CRC0135


title: CRC0134


title: CRC0556-B-1


title: CRC0539-A-2


title: CRC0133


title: CRC0537-B-1


title: CRC0537-A-1


title: CRC0132


title: CRC0535-A-1


title: CRC0529-B-1


title: CRC0535-B-1


title: CRC0131


title: CRC0539-A-1


title: CRC0031


title: CRC0529-A-1


title: CRC0130


title: CRC0527-A-1


title: CRC0527-B-1


title: CRC0525-A-1


title: CRC0516-B-2


title: CRC0027


title: CRC0515-A-1


title: CRC0029


title: CRC0516-B-1


title: CRC0028


title: CRC0508-A-1


title: CRC0512-B-1


title: CRC0024


title: CRC0505-A-1


title: CRC0525-A-2


title: CRC0512-B-2


title: CRC0495-B-2


title: CRC0023_rep2


title: CRC0505-A-2


title: CRC0494-A-1


title: CRC0515-B-1


title: CRC0495-B-1


title: CRC0026


title: CRC0022


title: CRC0494-A-2


title: CRC0508-A-2


title: CRC0493-A-2


title: CRC0488-B-1


title: CRC0490-B-1


title: CRC0018


title: CRC0020


title: CRC0484-B-1


title: CRC0493-A-1


title: CRC0093


title: CRC0490-A-1


title: CRC0039


title: CRC0477-A-1


title: CRC0034


title: CRC0488-A-1


title: CRC0016


title: CRC0035


title: CRC0480-B-1


title: CRC0456-B-1


title: CRC0475-B-2


title: CRC0033


title: CRC0484-A-1


title: CRC0559-A-1


title: CRC0021_rep2


title: CRC0465-A-2


title: CRC0475-B-1


title: CRC0458-B-1


title: CRC0465-A-1


title: CRC0458-B-2


title: CRC0036


title: CRC0480-A-1


title: CRC0477-A-2


title: CRC0456-A-1


title: CRC0442-A-1


title: CRC0441-A-1


title: CRC0087


title: CRC0441-B-1


title: CRC0088


title: CRC0440-A-2


title: CRC0090


title: CRC0442-B-1


title: CRC0092


title: CRC0032


title: CRC0420-A-1


title: CRC0420-A-2


title: CRC0046


title: CRC0435-A-1


title: CRC0045


title: CRC0435-B-1


title: CRC0047


title: CRC0431-B-1


title: CRC0440-A-1


title: CRC0406-B-1


title: CRC0406-A-1


title: CRC0419-A-1


title: CRC0073_rep1


title: CRC0431-A-1


title: CRC0419-B-1


title: CRC0422-B-1


title: CRC0422-B-2


title: CRC0044


title: CRC0400-B-1


title: CRC0403-A-2


title: CRC0075


title: CRC0404-B-2


title: CRC0416-B-1


title: CRC0404-B-1


title: CRC0042


title: CRC0043


title: CRC0399-B-1


title: CRC0403-A-1


title: CRC0041


title: CRC0391-A-1


title: CRC0382-A-2


title: CRC0396-A-2


title: CRC0382-A-1


title: CRC0040


title: CRC0400-A-1


title: CRC0379-A-1


title: CRC0396-A-1


title: CRC0378-A-2


title: CRC0379-A-2


title: CRC0084


title: CRC0391-A-2


title: CRC0074


title: CRC0377-A-1


title: CRC0378-A-1


title: CRC0081


title: CRC0399-A-1


title: CRC0037


title: CRC0082


title: CRC0379-B-1


title: CRC0377-B-1


title: CRC0370-B-1


title: CRC0370-B-2


title: CRC0038


title: CRC0371-B-2


title: CRC0080


title: CRC0362-B-1


title: CRC0371-B-1


title: CRC0079


title: CRC0078


title: CRC0358-B-3


title: CRC0094


title: CRC0358-B-2


title: CRC0354-A-2


title: CRC0358-B-1


title: CRC0348-A-2


title: CRC0077


title: CRC0069


title: CRC0356-A-1


title: CRC0343-B-2


title: CRC0358-A-1


title: CRC0349-A-2


title: CRC0070


title: CRC0348-A-1


title: CRC0076


title: CRC0344-A-2


title: CRC0343-B-1


title: CRC0343-A-2


title: CRC0344-A-1


title: CRC0067


title: CRC0362-A-1


title: CRC0339-A-1


title: CRC0085


title: CRC0339-A-2


title: CRC0356-A-2


title: CRC0343-A-1


title: CRC0095


title: CRC0072


title: CRC0354-A-1


title: CRC0339-A-3


title: CRC0066


title: CRC0334-A-2


title: CRC0334-A-1


title: CRC0334-B-1


title: CRC0065


title: CRC0063


title: CRC0333-A-2


title: CRC0064


title: CRC0333-B-2


title: CRC0332-A-2


title: CRC0330-A-1


title: CRC0330-A-2


title: CRC0329-A-1


title: CRC0333-A-1


title: CRC0060


title: CRC0328-A-2


title: CRC0333-B-1


title: CRC0328-A-1


title: CRC0330-A-3


title: CRC0061


title: CRC0057


title: CRC0332-A-1


title: CRC0058


title: CRC0062


title: CRC0059


title: CRC0321-B-2


title: CRC0324-A-1


title: CRC0323-A-1


title: CRC0321-B-1


title: CRC0324-B-1


title: CRC0313-A-2


title: CRC0323-A-2


title: CRC0056


title: CRC0055


title: CRC0053


title: CRC0051


title: CRC0321-A-2


title: CRC0313-A-1


title: CRC0312-A-1


title: CRC0321-A-1


title: CRC0318-A-1


title: CRC0071


title: CRC0322-A-1


title: CRC0054


title: CRC0052


title: CRC0049


title: CRC0322-A-2


title: CRC0314-A-1


title: CRC0314-A-2


title: CRC0349-A-1


title: CRC0313-B-1


title: CRC0314-B-1


title: CRC0048


title: CRC0318-A-2


title: CRC0310-B-2


title: CRC0150_rep2


title: CRC0312-B-1


title: CRC0306-A-2


title: CRC0146_rep1


title: CRC0309-A-1


title: CRC0145_rep2


title: CRC0306-B-1


title: CRC0141


title: CRC0307-A-1


title: CRC0309-B-1


title: CRC0021_rep1


title: CRC0307-B-1


title: CRC0303-B-1


title: CRC0147_rep2


title: CRC0305-B-3


title: CRC0303-A-2


title: CRC0297-A-1


title: CRC0019_rep1


title: CRC0303-A-1


title: CRC0306-A-1


title: CRC0310-B-1


title: CRC0305-B-1


title: CRC0305-B-2


title: CRC0303-B-2


title: CRC0144_rep1


title: CRC0292-A-2


title: CRC0285-A-1


title: CRC0015_rep2


title: CRC0297-B-1


title: CRC0291-B-1


title: CRC0102


title: CRC0285-B-1


title: CRC0277-A-2


title: CRC0104


title: CRC0101


title: CRC0023_rep1


title: CRC0291-A-1


title: CRC0277-A-1


title: CRC0265-B-2


title: CRC0292-A-1


title: CRC0276-A-2


title: CRC0276-A-1


title: CRC0099


title: CRC0100


title: CRC0257-A-2


title: CRC0097


title: CRC0103


title: CRC0257-A-1


title: CRC0098


title: CRC0105


title: CRC0262-B-1


title: CRC0262-B-2


title: CRC0086


title: CRC0265-B-1


title: CRC0013


title: CRC0015_rep1


title: CRC0253-A-1


title: CRC0243-B-1


title: CRC0246-B-1


title: CRC0012


title: CRC0253-B-1


title: CRC0243-A-1


title: CRC0237-A-1


title: CRC0010


title: CRC0014_rep2


title: CRC0242-B-2


title: CRC0252-A-1


title: CRC0008


title: CRC0005


title: CRC0229-B-1


title: CRC0239-A-1


title: CRC0229-A-1


title: CRC0239-A-2


title: CRC0246-B-2


title: CRC0242-B-1


title: CRC0011


title: CRC0231-A-2


title: CRC0237-A-2


title: CRC0004


title: CRC0231-A-1


title: CRC0252-B-1


title: CRC0009


title: CRC0050


title: CRC0221-B-1


title: CRC0219-B-1


title: CRC0221-B-2


title: CRC0219-A-2


title: CRC0219-A-1


title: CRC0002


title: CRC0218-B-1


title: CRC0217-A-1


title: CRC0218-A-1


title: CRC0216-B-1


title: CRC0001


title: CRC0217-B-1


title: CRC0007


title: CRC0216-A-1


title: CRC0019_rep2


title: CRC0030


title: CRC0089_rep2


title: CRC0214-A-1


title: CRC0091


title: CRC0207-A-2


title: CRC0214-B-1


title: CRC0207-A-1


title: CRC0025_rep1


title: CRC0204-A-1


title: CRC0204-B-1


title: CRC0003_rep2


title: CRC0198-A-1


title: CRC0199-B-2


title: CRC0198-B-1


title: CRC0096_rep1


title: CRC0096_rep2


title: CRC0089_rep1


title: CRC0199-B-1


title: CRC0197-B-1


title: CRC0196-B-2


title: CRC0025_rep2


title: CRC0197-A-1


title: CRC0003_rep1


title: CRC0186-A-1


title: CRC0190-B-1


title: CRC0196-B-1


title: CRC0083


title: CRC0190-A-1


title: CRC0187-B-1


title: CRC0188-A-2


title: CRC0187-A-1


title: CRC0186-B-1


title: CRC0185-B-2


title: CRC0185-B-1


title: 2179

city: Charlottesville

first: Stephen

last: Turner

state: VA

address: 1670 Discovery Drive

country: USA

institute: Signature Science, LLC

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol with Illumina BeadArray Reader.

data_processing: Quantile normalization (no log transformation) using the R beadarray package.

source_name: CD34+ bone marrow cells, healthy

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

extract_protocol: RNA from CD34+ bone marrow cells of healthy donors were purchased from AllCells LLC (Alameda, CA).

tag: disease state

value: normal

value: CD34+ bone marrow cells


title: 2180


title: 2178


title: CRC0184-A-1


title: CRC0178-B-2


title: CRC0184-B-1


title: CRC0178-B-1


title: CRC0176-A-1


title: 2245


title: CRC0177-A-2


title: 2237


title: 250

source_name: PBMCs, AML

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

value: acute myeloid leukemia (AML)

value: peripheral blood mononuclear cells (PBMCs)


title: CRC0177-B-1


title: 2225


title: CRC0188-A-1


title: CRC0174-A-1


title: CRC0176-B-1


title: 2243


title: CRC0175-B-1


title: 2244


title: CRC0177-A-1


title: CRC0175-A-1


title: 280


title: 217


title: CRC0174-B-1


title: CRC0173-B-2


title: CRC0171-B-1


title: CRC0173-B-1


title: 412


title: CRC0171-B-2


title: 194


title: CRC0170-B-1


title: 328


title: CRC0170-A-1


title: 142


title: CRC0169-B-1


title: CRC0169-A-1


title: CRC0168-B-1


title: CRC0167-A-1


title: CRC0165-B-1


title: CRC0168-A-1


title: CRC0166-B-1


title: CRC0166-A-1


title: 387


title: 247


title: CRC0161-A-2


title: 406


title: CRC0167-B-1


title: 176


title: 123


title: CRC0161-A-1


title: CRC0159-A-2


title: CRC0165-A-1


title: CRC0160-B-1


title: CRC0159-A-1


title: 414


title: CRC0162-B-2


title: 166


title: CRC0158-A-1


title: CRC0160-A-1


title: CRC0162-B-1


title: 386


title: CRC0157-A-2


title: 370


title: CRC0158-A-2


title: CRC0157-A-1


title: CRC0154-A-1


title: CRC0156-A-1


title: 267


title: 274


title: CRC0156-A-2


title: CRC0154-A-2


title: CRC0155-B-1


title: 245


title: CRC0149-B-1


title: CRC0150-B-1


title: CRC0153-A-1


title: CRC0148-B-1


title: 141


title: CRC0148-A-1


title: CRC0147-A-1


title: 156


title: 157


title: 202


title: CRC0150-A-1


title: CRC0152-B-2


title: CRC0152-B-1


title: CRC0153-B-1


title: 215


title: CRC0149-A-1


title: CRC0147-B-1


title: 136


title: CRC0146-B-1


title: CRC0146-A-1


title: 126


title: CRC0145-B-1


title: 109


title: CRC0144-B-1


title: 329


title: CRC0144-A-1


title: CRC0141-B-1


title: CRC0141-A-1


title: CRC0140-B-1


title: CRC0139-A-1


title: 307


title: CRC0140-A-1


title: CRC0137-A-1


title: CRC0134-A-1


title: CRC0138-A-1


title: CRC0143-B-2


title: CRC0136-B-2


title: CRC0136-B-1


title: CRC0135-B-1


title: CRC0143-B-1


title: CRC0138-B-1


title: CRC0139-A-2


title: CRC0137-B-1


title: CRC0145-A-1


title: CRC0134-B-1


title: CRC0131-A-1


title: CRC0135-A-1


title: CRC0133-B-1


title: CRC0131-A-2


title: CRC0130-A-1


title: CRC0133-A-1


title: 248


title: CRC0155-A-1


title: CRC0129-B-1


title: CRC0130-B-1


title: CRC0128-A-2


title: CRC0127-A-1


title: CRC0121-B-1


title: CRC0127-B-1


title: CRC0124-A-1


title: CRC0125-B-1


title: CRC0118-A-2


title: CRC0119-A-1


title: CRC0117-A-1


title: CRC0121-A-1


title: CRC0123-A-1


title: CRC0120-B-1


title: CRC0128-A-1


title: CRC0124-B-1


title: CRC0129-A-1


title: CRC0117-B-1


title: CRC0123-B-1


title: CRC0119-B-1


title: CRC0125-B-2


title: CRC0125-A-2


title: CRC0118-A-1


title: CRC0125-A-1


title: CRC0126-B-1


title: CRC0116-A-1


title: CRC0126-A-1


title: CRC0114-B-1


title: CRC0120-A-1


title: CRC0116-B-1


title: CRC0115-A-1


title: CRC0114-A-1


title: CRC0112-B-1


title: CRC0113-B-2


title: CRC0113-B-1


title: CRC0114-B-2


title: CRC0115-B-1


title: CRC0112-A-1


title: CRC0109-A-2


title: CRC0105-A-1


title: CRC0106-B-1


title: CRC0109-A-1


title: CRC0101-A-1


title: CRC0108-B-1


title: CRC0103-B-2


title: CRC0101-B-1


title: CRC0110-B-1


title: CRC0105-B-1


title: CRC0108-B-2


title: CRC0110-A-1


title: CRC0106-B-2


title: CRC0102-B-2


title: CRC0102-B-1


title: CRC0100-B-1


title: CRC0100-A-2


title: CRC0100-A-1


title: CRC0100-B-2


title: CRC0099-B-1


title: CRC0099-A-1


title: CRC0098-B-1


title: CRC0097-B-1


title: CRC0096-B-1


title: CRC0095-B-1


title: CRC0096-A-1


title: CRC0097-B-2


title: CRC0086-B-1


title: CRC0077-A-1


title: CRC0085-B-1


title: CRC0098-A-1


title: CRC0073-A-1


title: CRC0095-A-1


title: CRC0094-B-1


title: CRC0076-B-1


title: CRC0076-B-2


title: CRC0077-B-1


title: CRC0071-A-1


title: CRC0086-A-1


title: CRC0082-B-1


title: CRC0079-A-1


title: CRC0082-A-1


title: CRC0070-B-1


title: CRC0072-B-1


title: CRC0085-A-1


title: CRC0094-A-1


title: CRC0072-A-1


title: CRC0103-B-1


title: CRC0079-A-2


title: CRC0073-B-1


title: CRC0071-B-1


title: CRC0070-A-1


title: CRC0069-A-1


title: CRC0068-A-1


title: CRC0067-B-1


title: CRC0066-B-1


title: CRC0065-B-2


title: CRC0063-A-1


title: CRC0065-B-1


title: CRC0068-A-2


title: CRC0064-B-1


title: CRC0061-A-1


title: CRC0061-B-1


title: CRC0064-A-1


title: CRC0058-B-1


title: CRC0067-B-2


title: CRC0069-B-1


title: CRC0057-B-1


title: CRC0062-A-1


title: CRC0056-B-1


title: CRC0058-A-1


title: CRC0063-B-1


title: CRC0060-B-1


title: CRC0060-A-1


title: CRC0057-A-1


title: CRC0066-A-1


title: CRC0054-A-1


title: CRC0053-B-2


title: CRC0032-A-1


title: CRC0055-A-1


title: CRC0055-B-1


title: CRC0053-B-3


title: CRC0062-B-1


title: CRC0051-A-2


title: CRC0051-A-1


title: CRC0053-A-1


title: CRC0050-A-1


title: CRC0053-B-1


title: Blood_PreRace_Subject16

city: Barcelona

first: Alexandre

last: Perera

state: Barcelona

address: Pau Gargallo 5

department: ESAII

country: Spain

institute: Universitat Politecnica de Catalunya

hyb_protocol: Biotinylated sscDNA was hybridized for 16hour at 45ºC and 60rpm on HuGene2.0st microarrays from Affymetrix in a Hybridization Oven 640 from Affymetrix. Microarrays were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Microarrays were confocal scannes using the GeneChip 3000 7G with Autoloader from Affymetrix.

data_processing: Data was background corrected, quantile normalized and summarized at transcript cluster (TC) level using the Robust Multichip Average (RMA) on the R software platform using oligo package. Positive Quality Control. Only those TCs targeting protein-coding RNA molecules were considered (25272 TCs in total).

label: Biotin

source_name: Peripheral blood sample Subject16 immediately before UMT participation

label_protocol: Biotinylated sscDNA was prepared from 100ng total RNA per sample which was previously processed with GeneChip WT Plus Reagent kit from Affymetrix.

extract_protocol: Total RNA was isolated using the PAXgene Blood RNA kit (PreAnalytiX GmbH/QIAGEN, Switzerland/US). The concentration of the extracted RNA was measured spectrophotometrically (Nanodrop 1000/ Thermo Fisher Scientific, Wilmington, US).

value: Peripheral blood

tag: age

tag: gender

value: Male

tag: umt run distance [km]


title: CRC0050-A-2


title: CRC0031-A-2


title: Blood_PostRace_Subject17

source_name: Peripheral blood sample Subject17 immediately after UMT participation

value: Female


title: CRC0032-B-1


title: CRC0029-B-1


title: Blood_PreRace_Subject15

source_name: Peripheral blood sample Subject15 immediately before UMT participation


title: CRC0056-A-1


title: CRC0029-A-1


title: CRC0031-A-1


title: Blood_PreRace_Subject17

source_name: Peripheral blood sample Subject17 immediately before UMT participation


title: CRC0031-B-2


title: CRC0031-B-1


title: CRC0028-A-1


title: CRC0028-B-1


title: Blood_PreRace_Subject14

source_name: Peripheral blood sample Subject14 immediately before UMT participation


title: Blood_PreRace_Subject13

source_name: Peripheral blood sample Subject13 immediately before UMT participation


title: CRC0027-A-1


title: CRC0025-B-2


title: CRC0027-B-1

value: CRISD


title: CRC0022-B-2


title: Blood_PostRace_Subject14

source_name: Peripheral blood sample Subject14 immediately after UMT participation


title: Blood_PreRace_Subject10

source_name: Peripheral blood sample Subject10 immediately before UMT participation


title: Blood_PostRace_Subject12

source_name: Peripheral blood sample Subject12 immediately after UMT participation


title: Blood_PreRace_Subject12

source_name: Peripheral blood sample Subject12 immediately before UMT participation


title: Blood_PostRace_Subject11

source_name: Peripheral blood sample Subject11 immediately after UMT participation


title: Blood_PostRace_Subject10

source_name: Peripheral blood sample Subject10 immediately after UMT participation


title: CRC0024-A-1


title: CRC0021-B-2


title: CRC0021-B-1


title: CRC0014-B-1


title: CRC0018-B-1


title: CRC0014-A-1


title: CRC0018-B-2


title: CRC0025-B-1


title: Blood_PreRace_Subject11

source_name: Peripheral blood sample Subject11 immediately before UMT participation


title: CRC0019-A-1


title: Blood_PreRace_Subject8

source_name: Peripheral blood sample Subject8 immediately before UMT participation


title: CRC0022-B-1

source_name: LM CRC PDX sample


title: Blood_PostRace_Subject8

source_name: Peripheral blood sample Subject8 immediately after UMT participation


title: Blood_PreRace_Subject7

source_name: Peripheral blood sample Subject7 immediately before UMT participation


title: CRC0019-B-1


title: MYB knockdown mouse 2

city: Durham

first: Wenbin

last: Wei

address: Stockton Road

department: Biosciences

country: United Kingdom

institute: Durham University

description: Gene expression data

hyb_protocol: Affymetrix Standard protocol

scan_protocol: Arrays were scanned with a GeneChip3000 7G scanner

data_processing: Probe level quantile normalisation and robust multi-array analysis on the raw CEL files were performed using Affymetrix Expression Console. Differentially expressed genes were identified using limma with absolute fold change >1.5 and p < 0.01.

label: biotin

organism: Mus musculus

source_name: 4 week old male C57BL6 MYB knockdown mice

label_protocol: Labelled with the Ambion® WT Expression Kit, combined with the GeneChip® WT Terminal Labeling and Controls Kit.

growth_protocol: 4 week old male mice were sacrificed.

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

treatment_protocol: Kit+CD11b+Lin-Low (K11bL) cells were sorted by FACS from bone marrow.

value: bone marrow K11bL cells

tag: mutation

value: MYB knockdown

tag: strain

value: 4 weeks old

value: male


title: MYB knockdown mouse 1

description: Gene expression data


title: MYB knockdown mouse 3

description: Gene expression data


title: Blood_PostRace_Subject7

source_name: Peripheral blood sample Subject7 immediately after UMT participation


title: Wild type mouse 3

description: Gene expression data

source_name: 4 week old male C57BL6 wild type mice

value: wild type


title: Blood_PreRace_Subject4

source_name: Peripheral blood sample Subject4 immediately before UMT participation


title: Blood_PreRace_Subject3

source_name: Peripheral blood sample Subject3 immediately before UMT participation


title: Blood_PreRace_Subject5

source_name: Peripheral blood sample Subject5 immediately before UMT participation


title: Blood_PreRace_Subject6

source_name: Peripheral blood sample Subject6 immediately before UMT participation


title: Preleukemic bone marrow S2.3

city: Munich

first: Tobias

last: Herold

address: Marchioninistr. 15

department: Department of Internal Medicine III

country: Germany

institute: University Hospital Grosshadern, Ludwig-Maximilians-University (LMU)

description: Preleukemic bone marrow

hyb_protocol: Samples were hybridized using Gene chip hybridization kit, Hybridization cocktail was heated at 99°C for 5 min and at 45°C for % min and then was centrifuged for 1 min at full speed. 100 micro liter prehybridization solution was aded to the arrays, and arrays were incubated in a rotation incubato at 45°c for 10 min. After 10 mins pre-hybridization cocktail was removed and arrays were incubated with 80 micro liter hybridization cocktail for 17 hrs at 60 rpm, 45°C. washing was done using FS450_0007 fluidic station.

scan_protocol: Samples were scanned using an Affymetrix GeneChip scanner

data_processing:
Normalization was performed using the Robust Multichip Average (RMA) method. Quality control consisted of visual inspection of the array image for artifacts, assessment of RNA degradation plots, and inspection of rank-vs.-residual plots after normalization and probe set  summarization.
probe group file: mogene10stv1cdf_2.7.0 (ftp://ftp2.uib.no/pub/bioconductor/2.7/data/annotation/html/mogene10stv1cdf.html)

source_name: bone marrow

label_protocol: samples were labelled using Gene chip WT terminal labelling kit

growth_protocol: The tissue specific knock-in mouse line R26LSLCA mice were crossed with vav-Cre, Mb1-Cre, or CD19-Cre mice (all on C57Bl/6-background), to achieve pan-haematopoietic or B cell–specific expression of the C/A fusion gene. Mice were bred and maintained under specific pathogen free (SPF) conditions and received standard rodent chow and drinking water ad libitum.

extract_protocol: Bone marrow  cells were exacted from the femur and the pelvic bones of leukemic, pre-Leukemic and clinically healthy control mice. B220+ Bcells were sorted from the Spleen cells of leukemic or non leukemic control mice using flowcytometry. RNA extraction was done using Trizol reagent from freshly exracted bone marrow cells and FACs sorted B cells..Sample preparation was done using Ambion WT expression kit (Life Technologies).

treatment_protocol: not applicable

tag: genotype/variation

tag: sample type

value: Preleukemic


title: B-cells _ Wildtype S_3.8

description: B-cells _ Wildtype

source_name: B cell

value: Wildtype C57Bl/6

value: Normal/wildtype


title: Wild type mouse 2

description: Gene expression data

tag: cell type


title: B-cells _ Wildtype S_3.9

description: B-cells _ Wildtype


title: Wild type mouse 1

description: Gene expression data


title: Wildtype bone marrow S2.6

description: Wildtype bone marrow


title: B-cells _CA+/Mb1-Cre+ S_3.4

description: B-cells _CA+/Mb1-Cre+

value: Non-leukemic


title: CRC0054-B-1

value: LM CRC PDX

value: CRISE

value: B


title: Blood_PostRace_Subject3

source_name: Peripheral blood sample Subject3 immediately after UMT participation


title: B-cells _ Wildtype S_3.7

description: B-cells _ Wildtype


title: Preleukemic bone marrow S2.1

description: Preleukemic bone marrow


title: B cells _CA+/Vav-Cre+ S_3.3

description: B cells _CA+/Vav-Cre+


title: Blood_PreRace_Subject2

source_name: Peripheral blood sample Subject2 immediately before UMT participation


title: B cells _CA+/Vav-Cre+ S_3.1

description: B cells _CA+/Vav-Cre+


title: Blood_PostRace_Subject6

source_name: Peripheral blood sample Subject6 immediately after UMT participation


title: Preleukemic bone marrow S2.2

description: Preleukemic bone marrow


title: Blood_PostRace_Subject4

source_name: Peripheral blood sample Subject4 immediately after UMT participation


title: Wildtype bone marrow S2.5

description: Wildtype bone marrow


title: B-cells _CA+/Mb1-Cre+ S_3.5

description: B-cells _CA+/Mb1-Cre+


title: Blood_PostRace_Subject5

source_name: Peripheral blood sample Subject5 immediately after UMT participation


title: B-cells _CA+/Mb1-Cre+ S_3.6

description: B-cells _CA+/Mb1-Cre+


title: Wildtype bone marrow S2.4

description: Wildtype bone marrow


title: Blood_PostRace_Subject2

source_name: Peripheral blood sample Subject2 immediately after UMT participation


title: leukemic bone marrow_Biphenotypic S_1-8

description: leukemic bone marrow_Biphenotypic

value: Leukemic Biphenotypic


title: B cells _CA+/Vav-Cre+ S_3.2

description: B cells _CA+/Vav-Cre+


title: leukemic bone marrow_Biphenotypic S_1-6

description: leukemic bone marrow_Biphenotypic


title: leukemic bone marrow_Biphenotypic S_1-5

description: leukemic bone marrow_Biphenotypic


title: Leukemic Bone marrow_Myeloid S_1-4

description: Leukemic Bone marrow_Myeloid

value: Leukemic myeloid


title: Blood_PreRace_Subject1

source_name: Peripheral blood sample Subject1 immediately before UMT participation

value: Peripheral blood


title: leukemic bone marrow_Biphenotypic S_1-7

description: leukemic bone marrow_Biphenotypic


title: Cisp-24A

city: Bethesda

first: WeiPing

last: Chen

state: MD

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

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

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

data_processing: The data were nomanized by RMA with Parteck Genomic Suit 6.6

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: regular human cell culture

treatment_protocol: Cell treated with TM, Cisp and the combined of two drugs in 12 or 24 hours

tag: agent

value: Cisp

tag: time point

tag: cell line


title: Double-12C

value: TM and cisplatin


title: Pancreatic cancer stem cells, NVP-LDE-225 & NVP-BEZ-235, biological rep2

city: Kansas City

first: Sumedha

last: Gunewardena

state: Kansas

address: 3901 Rainbow Boulevard

institute: University of Kansas Medical Center

hyb_protocol: Using the GeneChip 645 Hybridization Oven, labeled target RNA is hybridized overnight  to interrogating oligo probes contained in the GeneChip miRNA 4.0 expression cartridge array (Affymetrix #902017). Hybridized Genechips undergo low and high stringency washing and R-Phycoerythrin-Streptavidin staining procedures using the GeneChip fluidics station 450. After washing, GeneChips undergo a single scan using a GeneChip scanner 3000 7G with autoloader. Fluidics and scan functions are controlled by Affymetrix GeneChip Command Console software (AGCC). Raw expression data is loaded onto the Microarray Data Management System (MDMS) for access by the Investigator and further data analysis.

scan_protocol: Single Scan; Affymetrix GeneChip Scanner 3000 7G with Autoloader; Affymetrix GeneChip Command Console (AGCC) ver. 1.1

data_processing: The data were analyzed with Partek Genomics Suite version 6.5 (RMA) using RMA default analysis settings: RMA Background Correction; Quantile Normalization; Median Polish probeset summarization. Only Homo sapiens brobsets were used throughout the analysis.

source_name: Human PCSCs+NVP-LDE-225+NVP-BEZ-235

label_protocol: 1ug of Total RNA is labeled using the FlashTag Biotin HSR RNA Labeling Kit (Affymetrix #901910). The FlashTag labeling system employs the 3DNA dendrimer signal amplification technology. 3DNA dendrimer is a branched structure of single and double stranded DNA conjugates which incorporates numerous biotin labels for ultrasensitive expression detection.

growth_protocol: Pancreatic cancer stem cells were grown in well defined stem cell medium at 37 degree C with 5% CO2 in the incubator.

extract_protocol: Total RNAs were isolated using the trizol reagent (invitrogen, CA, USA).

treatment_protocol: Pancreatic CSCs were treated with NVP-BEZ-235 (1 µM) and/or NVP-LDE-225 (5 µM) for 36 h.

value: Pancrase

value: Human pancreatic cancer stem cells (CSCs)

tag: treated with

value: NVP-LDE-225 (PI3K/mTOR inhibitor) + NVP-BEZ-235 (Smoothened inhibitor)

tag: treatment duration

value: 36 hrs


title: Double-12B


title: Pancreatic cancer stem cells, NVP-BEZ-235, biological rep1

source_name: Human PCSCs+NVP-BEZ-235

value: NVP-BEZ-235 (Smoothened inhibitor)


title: Cisp-12C


title: Double-12A


title: Pancreatic cancer stem cells, control, biological rep1

source_name: Human PCSCs

value: none (control)


title: TM-12A

value: TM


title: Pancreatic cancer stem cells, NVP-BEZ-235, biological rep2


title: TM-12B


title: Pancreatic cancer stem cells, NVP-LDE-225, biological rep2

source_name: Human PCSCs+NVP-LDE-225

value: NVP-LDE-225 (PI3K/mTOR inhibitor)


title: Pancreatic cancer stem cells, NVP-LDE-225 & NVP-BEZ-235, biological rep1


title: Control-A

value: Control


title: Cisp-12B


title: Control-C


title: Leukemic Bone marrow_Myeloid S_1-1

description: Leukemic Bone marrow_Myeloid


title: Double-24C


title: Control-B


title: Cisp-12A


title: Double-24B


title: Pancreatic cancer stem cells, control, biological rep2


title: Pancreatic cancer stem cells, NVP-LDE-225, biological rep1


title: Double-24A


title: Pho4-6xHis

type: protein

city: Stanford

first: Polly

middle: Morrell

last: Fordyce

state: CA

address: 443 Via Ortega

department: Genetics, Bioengineering

institute: Stanford University

hyb_protocol: Experiments are performed using standard MITOMI 2.0 assay conditions (align and bond custom microfluidic device; pattern device chamber surfaces with anti-pentaHis antibodies in specific locations; passivate device surfaces elsewhere; recruit tagged Pho4-6xHis to antibody-patterned surfaces; solubilize labeled dsDNA in each chamber; allow surface-bound Pho4-6xHis and labeled DNA to interact; trap interactions with a microfluidic valve; wash; and image.

scan_protocol: Device surfaces were scanned via quantitative fluorescence imaging using a Nikon Ti-S microscope and flat-field correcting acquired images.

data_processing:
Images were analyzed using custom MITOMIAnalysis software written in Matlab; each oligonucleotide was spotted 4x within the device. proteinFg signal = median post-wash pixel intensity of 'button' area in eGFP channel; protein Bg signal = median post-wash pixel intensity of surrounding chamber area; surfaceProtein = proteinFg - proteinBg; capturedDNAFg = median post-wash intensity of 'button' area in Cy5 channel; capturedDNABg = median intensity of surrounding chamber post-wash in Cy5 channel; capturedDNA = capturedDNAFg - capturedDNABg; solubleDNAFg = median 'pre-wash' chamber intensity in Cy5 channel; solubleDNABg = median 'post-wash' chamber intensity in Cy5 channel; ratio = capturedDNA/surfaceProtein
sequence = oligonucleotide sequence; sequenceID = oligonucleotide number; surfaceProtein = background-substracted surface-immobilized protein signal (proteinFg - proteinBg)l; capturedDNA = background-subtracted protein-bound DNA signal (capturedDNAFg - capturedDNABg); solubilized DNA = estimated concentration of solubilized DNA available for binding (solubleDNAFg - solubleDNABg); ratio = capturedDNA/surfaceProtein, which is linearly related to fractional occupancy; row = row position in device; col = column position in device.

label: BODIPY

molecule: protein

organism: Saccharomyces cerevisiae

source_name: recombinant Pho4-6xHis

label_protocol: Pho4-6xHis is labeled via stochastic incorporation of Fluorotect Green BODIPY-labeled charged lysine tRNA

extract_protocol: Pho4-6xHis is a C-terminally 6xHis-labeled protein cloned into a Promega TnT vector, produced via in vitro transcription/translation in Promega TnT T7 Quick Coupled Rabbit Reticulocyte extract, and labeled via stochastic incorporation of a BODIPY-labeled charged lysine tRNA (Promega Fluorotect Green).

value: 6xHis-tagged S. cerevisae Pho4 protein (recombinant, tagged protein expressed via transcription/translation in rabbit reticulocyte lysate)


title: TM-24B


title: Cisp-24C


title: Cisp-24B


title: TM-24C


title: TM-24A


title: senescent 02

status: Public on Jun 18 2017

city: Regensburg

first: Stefan

last: Dillinger

address: Universitätsstr. 31

institute: University Regensburg

description: Gene expression data from old, senescent IMR90 cells.

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: R/Bioconductor, rma normalization, default parameters

source_name: senescent IMR90 cells

label_protocol: Standard Affymetrix protocol

growth_protocol: Cells were grown in standard medium DMEM (10% FCS, 1% PenStrep) prior to RNA isolation.

extract_protocol: Total RNA was isolated using TRIzol RNA from two biological replicates of young, proliferating and senescent IMR90 human diploid fibroblasts.

treatment_protocol: Cells were grown until replicative exhaustion in order to reach senescence.

value: human embryonic fibroblast

tag: Stage

value: senescent


title: Colonic tumor_KO_rep4 (mouse #54)

status: Public on Jun 17 2017

city: Essen

first: Elke

last: Cario

state: NRW

address: Virchowstr. 171

department: Division of Gastroenterology and Hepatology

institute: University of Duisburg-Essen, University Hospital of Essen

hyb_protocol: 3,8 µg fragmented and labeled ss cDNA were hybridized to Affymetrix Mouse Gene 2.0 ST arrays for 16 h at 45°C in a GeneChip hybridization oven 640.

scan_protocol: Hybridized arrays were washed and stained in an Affymetrix Fluidics Station FS450, and the fluorescent signals were measured with an Affymetrix GeneChip Scanner 3000 7G. Fluidics and scan functions were controlled by Affymetrix GeneChip Command Console v4.1.3 software.

data_processing: Summarized probe set signals in log2 scale were calculated by using the RMA algorithm with the Affymetrix GeneChip Expression Console v1.4 Software.

source_name: MDR1A KO, Tumor, Colon, AOM/DSS

label_protocol: 200 ng of total RNA was used to generate double-stranded cDNA. 12 µg of subsequently synthesized cRNA was purified and reverse transcribed into sense-strand (ss) cDNA, whereat unnatural dUTP residues were incorporated. Purified ss cDNA was fragmented using a combination of uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) followed by a terminal labeling with biotin.

extract_protocol: Tumor tissue samples were frozen in RNAlater at -80°C. Total RNA from colonic tumors was extracted (RNeasy Micro Kit (Qiagen, Hilden, Germany) or RiboPure plus RNeasy Mini Kit (Qiagen)) including the RNase-free DNase digestion step.

value: FVB/N

value: MDR1A KO

tag: tumor stage

value: adenoma


title: Colonic tumor_WT_rep3 (mouse #62)

source_name: WT, Tumor, Colon, AOM/DSS

value: WT


title: Colonic tumor_WT_rep2 (mouse #49)


title: L2P replicate 3

city: Charleston

first: Philip

middle: H

last: Howe

state: South Carolina

address: 173 Ashley Avenue

department: Biochemistry

institute: Medical University of South Carolina

description: L2P cells isolated from lungs of L1P mammary fat pad injected mice

hyb_protocol: Fragmented cRNA samples were hybridized overnight at 45°C to Affymetrix Mouse Genome 430 2.0 GeneChips®.

scan_protocol: Post hybridization washing, phycoerythrin-streptavidin staining and fluorescence scanning were performed using Affymetrix instrumentation in accordance with manufacturer's protocols.

data_processing: Hybridization data (CEL files) were normalized by RMA algorithm using Affymetrix Expression Console software; detection calls were obtained by Affymetrix MAS5 algorithm. Expression data were compared using dChip software.

source_name: in vivo passaged E1KD-lung metastasis passage 2

label_protocol: cDNA synthesis from 100 ng total RNA, in vitro transcription of biotin-labeled cRNA by 3'IVT Express Plus kit (Affymetrix),  and fragmentation of cRNAs were performed following established Affymetrix procedures.

growth_protocol: All cell lines were maintained in Dulbecco’s modified Eagle’s medium supplemented with 5% fetal bovine serum,  5% calf serum, and 1% antibiotic/antimycotic solution (penicillin G, streptomycin, amphotericin B)

extract_protocol: RNA was extracted with Trizol and purified using an RNeasy minikit (Qiagen) according to manufacturer's instructions.

value: Normal murine mammary gland (NMuMG) cell

value: hnRNP-E1 silenced

tag: selection

value: in-vivo selection


title: Leukemic Bone marrow_Myeloid S_1-2

description: Leukemic Bone marrow_Myeloid

source_name: bone marrow

value: Leukemic myeloid


title: M1P replicate 2

description: M1P cells isolated from E1KD mammary fat pad tumor

source_name: in vivo passaged E1KD-mammary tumor passage 1


title: proliferating 01

description: Gene expression data from young, proliferating IMR90 cells

source_name: proliferating IMR90 cells

value: proliferating


title: L1P replicate 3

description: LIP cells isolated from lungs of E1KD mammary fat pad injected mice

source_name: in vivo passaged E1KD-lung metastasis passage 1


title: L1P replicate 2


title: Colonic tumor_KO_rep2 (mouse #51)


title: Colonic tumor_WT_rep1 (mouse #01)


title: Colonic tumor_KO_rep3 (mouse #52)


title: Colonic tumor_WT_rep4 (mouse #63)


title: Colonic tumor_KO_rep1 (mouse #34)


title: M1P replicate 3


title: L2P replicate 2


title: senescent 01


title: L1P replicate 1


title: proliferating 02


title: L2P replicate 1


title: M1P replicate 1


title: E1KD replicate 3

description: Tumorigenic E1KD cells used for in vivo passaging

source_name: hnRNP E1 silenced NMuMG cells (E1KD)

value: no in-vivo selection


title: E1KD replicate 2


title: IRF.fl_Fast_533

status: Public on Jun 16 2017

city: Chicago

first: Terry

last: Unterman

state: Illinois

address: 820 South Damen Avenue

department: Medical Research Unit

institute: University of Illinois at Chicago and Jesse Brown VA

description:
raw data file: 188_D.gpr
Gene Expression in liver tissue from IR/FoxO1 floxed male mice after 24 hr fast

hyb_protocol: Samples were hybridized in an Agilent Hybridization Cassette according to standard protocols.

scan_protocol: Scanned on an Axon GenePix 4000B scanner; Images were quantified using Axon GenePix 6.1.

data_processing: Median foreground intensites (no background subtraction) were normalized in R (version 3.1.0) using the quantile method in limma (version 3.20.1) . Spots with -100 flags were weighted zero before normalization.

source_name: IRF.fl_Fast_533 Liver RNA

label_protocol: 200 ng of total RNA was labeled using the Agilent's Two-Color Low Input Quick Amp labeling kit according to the manufacturers protocol.

extract_protocol: RNA was prepared using a Qiagen RNeasy kit, with DNAase treatment.

treatment_protocol: mice were fasted overnight and sacrificed  by decapitation following brief sedation with isofluorane 60 min after treatment with glucose or 6 hr after refeeding. Livers were immediately frozen in liquid N2 and stored at -80 C until RNA extraction.

value: Insulin Receptor and Foxo1 floxed (control)

tag: treatment

value: fasted overnight

value: Male

value: 11-12 weeks old

value: Mixed (FVB/N-C57Bl/6)

tag: tissue

value: liver


title: NMuMG replicate 2

description: NMuMG cells (non-tumorigenic cells)

source_name: NMuMG cell line

value: wild-type


title: IR.fl_Fast_491

description:
raw data file: 187_A.gpr
Gene Expression in liver tissue from IR floxed male mice after 24 hr fast

source_name: IR.fl_Fast_491 Liver RNA

value: Insulin Receptor floxed (control)

tag: gender

tag: age


title: IR.KO_GTT_690

description:
raw data file: 188_C.gpr
Gene Expression in liver tissue from LIRKO male mice after 24 hr fast then 60 min after dextrose feeding

source_name: IR.KO_GTT_690 Liver RNA

value: Insulin Receptor knocked out

value: fasted overnight then glucose challenge


title: IR.KO_Fast_550

description:
raw data file: 187_C.gpr
Gene Expression in liver tissue from LIRKO male mice after 24 hr fast

source_name: IR.KO_Fast_550 Liver RNA


title: IRF.KO_GTT_724

description:
raw data file: 188_B.gpr
Gene Expression in liver tissue from LIRFKO male mice after 24 hr fast

source_name: IRF.KO_GTT_724 Liver RNA

value: Insulin Receptor and Foxo1 knocked out


title: IR.KO_GTT_667

description:
raw data file: 187_B.gpr
Gene Expression in liver tissue from LIRKO male mice after 24 hr fast then 60 min after dextrose feeding

source_name: IR.KO_GTT_667 Liver RNA


title: E1KD replicate 1

value: Normal murine mammary gland (NMuMG) cell


title: IR.fl_GTT_691

description:
raw data file: 186_A.gpr
Gene Expression in liver tissue from IR floxed male mice after 24 hr fast then 60 min after dextrose feeding

source_name: IR.fl_GTT_691 Liver RNA


title: IRF.KO_GTT_725

description:
raw data file: 184_C.gpr
Gene Expression in liver tissue from LIRFKO male mice after 24 hr fast then 60 min after dextrose feeding

source_name: IRF.KO_GTT_725 Liver RNA


title: IRF.KO_Refed_524

description:
raw data file: 184_D.gpr
Gene Expression in liver tissue from LIRFKO male mice after 24 hr fast then 6 hr after regular feeding

source_name: IRF.KO_Refed_524 Liver RNA

value: fasted overnight then refed


title: IR.KO_Refed_564

description:
raw data file: 185_C.gpr
Gene Expression in liver tissue from LIRKO male mice after 24 hr fast then 6 hr after regular feeding

source_name: IR.KO_Refed_564 Liver RNA


title: IR.fl_Refed_562

description:
raw data file: 184_B.gpr
Gene Expression in liver tissue from IR floxed male mice after 24 hr fast then 6 hr after regular feeding

source_name: IR.fl_Refed_562 Liver RNA


title: IRF.fl_Refed_467

description:
raw data file: 185_B.gpr
Gene Expression in liver tissue from IR/FoxO1 floxed male mice after 24 hr fast then 6 hr after regular feeding

source_name: IRF.fl_Refed_467 Liver RNA


title: IR.fl_Fast_486

description:
raw data file: 188_A.gpr
Gene Expression in liver tissue from IR floxed male mice after 24 hr fast

source_name: IR.fl_Fast Liver RNA


title: NMuMG replicate 1

description: NMuMG cells (non-tumorigenic cells)


title: IR.fl_Refed_506

description:
raw data file: 184_A.gpr
Gene Expression in liver tissue from IR floxed male mice after 24 hr fast then 6 hr after regular feeding

source_name: IR.fl_Refed_506 Liver RNA


title: IRF.KO_Refed_469

description:
raw data file: 186_D.gpr
Gene Expression in liver tissue from LIRFKO male mice after 24 hr fast then 6 hr after regular feeding

source_name: IRF.KO_Refed_469 Liver RNA


title: IR.KO_Fast_545

description:
raw data file: 186_B.gpr
Gene Expression in liver tissue from LIRKO male mice after 24 hr fast

source_name: IR.KO_Fast_545 Liver RNA


title: IR.KO_Refed_565

description:
raw data file: 186_C.gpr
Gene Expression in liver tissue from LIRKO male mice after 24 hr fast then 6 hr after regular feeding

source_name: IR.KO_Refed_565 Liver RNA


title: IRF.fl_Fast_523

description:
raw data file: 187_D.gpr
Gene Expression in liver tissue from IR/FoxO1 floxed male mice after 24 hr fast

source_name: IRF.fl_Fast_523 Liver RNA


title: NMuMG replicate 3

description: NMuMG cells (non-tumorigenic cells)

source_name: NMuMG cell line


title: IRF.KO_Fast_525

description:
raw data file: 185_D.gpr
Gene Expression in liver tissue from LIRFKO male mice after 24 hr fast

source_name: IRF.KO_Fast_525 Liver RNA


title: IR.fl_GTT_699

description:
raw data file: 187_B.gpr
Gene Expression in liver tissue from IR floxed male mice after 24 hr fast then 60 min after dextrose feeding

source_name: IR.fl_GTT_699 Liver RNA


title: IRF.fl_Refed_473

description:
raw data file: 187_D.gpr
Gene Expression in liver tissue from IR/FoxO1 floxed male mice after 24 hr fast then 6 hr after regular feeding

source_name: IRF.fl_Refed_473 Liver RNA


title: IRF.KO_Refed_478

description:
raw data file: 188_D.gpr
Gene Expression in liver tissue from LIRFKO male mice after 24 hr fast then 6 hr after regular feeding

source_name: IRF.KO_Refed_478 Liver RNA


title: IR.KO_Fast_505

description:
raw data file: 188_A.gpr
Gene Expression in liver tissue from LIRKO male mice after 24 hr fast

source_name: IR.KO_Fast_505 Liver RNA


title: IR.fl_GTT_659

description:
raw data file: 188_B.gpr
Gene Expression in liver tissue from IR floxed male mice after 24 hr fast then 60 min after dextrose feeding

source_name: IR.fl_GTT_659 Liver RNA


title: IR.fl_Refed_566

description:
raw data file: 185_B.gpr
Gene Expression in liver tissue from IR floxed male mice after 24 hr fast then 6 hr after regular feeding

source_name: IR.fl_Refed_566 Liver RNA


title: IRF.KO_Refed_468

description:
raw data file: 186_C.gpr
Gene Expression in liver tissue from LIRFKO male mice after 24 hr fast then 6 hr after regular feeding

source_name: IRF.KO_Refed_468 Liver RNA


title: IR.KO_Refed_558

description:
raw data file: 188_C.gpr
Gene Expression in liver tissue from LIRKO male mice after 24 hr fast then 6 hr after regular feeding

source_name: IR.KO_Refed_558 Liver RNA


title: IRF.KO_Fast_518

description:
raw data file: 187_C.gpr
Gene Expression in liver tissue from LIRFKO male mice after 24 hr fast

source_name: IRF.KO_Fast_518 Liver RNA


title: IRF.KO_GTT_727

description:
raw data file: 186_D.gpr
Gene Expression in liver tissue from LIRFKO male mice after 24 hr fast then 60 min after dextrose feeding

source_name: IRF.KO_GTT_727 Liver RNA


title: IR.fl_Refed_508

description:
raw data file: 186_A.gpr
Gene Expression in liver tissue from IR floxed male mice after 24 hr fast then 6 hr after regular feeding

source_name: IR.fl_Refed_508 Liver RNA


title: IRF.KO_GTT_726

description:
raw data file: 185_D.gpr
Gene Expression in liver tissue from LIRFKO male mice after 24 hr fast then 60 min after dextrose feeding

source_name: IRF.KO_GTT_726 Liver RNA


title: Leukemic Bone marrow_Myeloid S_1-3

description: Leukemic Bone marrow_Myeloid

source_name: bone marrow


title: IR.fl_Fast_552

description:
raw data file: 185_A.gpr
Gene Expression in liver tissue from IR floxed male mice after 24 hr fast

source_name: IR.fl_Fast_552 Liver RNA


title: GYN008

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

hyb_protocol: Biotinylated cRNA was hybridized to the Affymetrix array per manufacturer's instructions

scan_protocol: Standard HT TITAN scanning protocol

data_processing: The data were analyzed with Partek Genomics Suite 6.6 and  in STATA/SE 11.2.

source_name: hMLKL1-181-2Fv-NIH3T3 cell

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol

extract_protocol: Trizol

value: B/B 1h sorted AnnV+ cells then washout for 6h


title: IRF.fl_Refed_472

description:
raw data file: 185_C.gpr
Gene Expression in liver tissue from IR/FoxO1 floxed male mice after 24 hr fast then 6 hr after regular feeding

source_name: IRF.fl_Refed_472 Liver RNA


title: GYN005

value: B/B 1h sorted AnnV+ cells


title: GYN006


title: IR.KO_Refed_553

description:
raw data file: 184_B.gpr
Gene Expression in liver tissue from LIRKO male mice after 24 hr fast then 6 hr after regular feeding

source_name: IR.KO_Refed_553 Liver RNA


title: GYN007


title: GYN009


title: IR.KO_GTT_697

description:
raw data file: 184_C.gpr
Gene Expression in liver tissue from LIRKO male mice after 24 hr fast then 60 min after dextrose feeding

source_name: IR.KO_GTT_697 Liver RNA


title: IRF.KO_Fast_519

description:
raw data file: 184_D.gpr
Gene Expression in liver tissue from LIRFKO male mice after 24 hr fast

source_name: IRF.KO_Fast_519 Liver RNA


title: IR.fl_Fast_542

description:
raw data file: 184_A.gpr
Gene Expression in liver tissue from IR floxed male mice after 24 hr fast

source_name: IR.fl_Fast_542 Liver RNA


title: IRF.fl_Fast_516

description:
raw data file: 187_A.gpr
Gene Expression in liver tissue from IR/FoxO1 floxed male mice after 24 hr fast

source_name: IRF.fl_Fast_516 Liver RNA


title: GYN004


title: GYN003

value: Control treatment


title: GYN002


title: GYN001


title: Hypothalamus_exposed restraint stress_rep6 [re-analysis]

city: Kawasaki

first: Kazushi

last: Yoshida

state: Kanagawa

address: 29-7 Kariyado, Nakahara-ku

country: Japan

institute: T. Hasegawa Co., Ltd.

description: Hypothalamus_Exposed restraint stress-6

hyb_protocol: 15 μg of biotinylated cRNA was fragmented and hybridized to a GeneChip® Rat Genome 230 2.0 Array (Affymetrix, Santa Clara, USA). Following hybridization at 45℃ for 16 h, the array was washed and stained with phycoerythrin using the GeneChip® Fluidics Station 450 (Affymetrix, Santa Clara, CA, USA).

scan_protocol: Fluorescence signals were scanned with a GeneChip® Scanner 3000 7G (Affymetrix, Santa Clara, USA).

data_processing: The Affymetrix® GeneChip® Command ConsoleH (AGCC) software program (Affymetrix, Santa Clara, USA) was used to convert the array images to the intensity values for each probe (CEL files). The CEL files were quantified by the Factor Analysis for Robust Microarray Summarization (qFARMS) in the statistical language R, version 2.12.2.

organism: Rattus norvegicus

source_name: Hypothalamus_exposed restraint stress

label_protocol: Biotinated cRNAs were prepared according to Affymetrix protocol from 500 ng of total RNA (3' IVT PLUS Reagent Kit Assay Manual, 2013, Affymetrix).

growth_protocol: Male Wistar rats aged 7 weeks were housed in a room maintained on a light/dark cycle with lights turned on at 8:00 a.m. and off at 8:00 p.m. They were allowed to get free access to food and water. After acclimatization to the environment and to investigators for one week, 18 rats were divided into three groups (n = 6 each): group C, control; group S, exposure to stress only; and group SO, exposure to both stress and odor. Rats in groups S and SO were placed in steel-wire mesh cages for restraint treatment for 2 h (10:00 - 12:00); they were able to breathe freely but unable to turn around. Twenty microliters of (R,S)-linalool was evaporated and allowed to spread throughout a 40 L box in which the rats (group SO) with the tubes were placed. After the exposure, all the 18 rats were immediately sacrificed by decapitation and then the brains were dissected to isolate the hypothalamic blocks. To look at the brain from the ventral side, two coronal cuts were placed at the apex of the optic chiasm and at the rostral margin of the mammillary bodies using a razor blade. This slab was then placed flat, and two cuts were placed on either side of the optic chiasm. The last cut was placed just above the third ventricle. The block was then put in ice-cold RNAlater (Applied Biosystems Japan, Japan).

extract_protocol: Total RNA was isolated from each hypothalamic block using the TRIzol reagent (Invitrogen Japan K.K., Japan) and then purified with a Maxwell® 16 Instrument using a Maxwell® 16 Total RNA Purification Kit (Promega Corporation, USA) according to manufacturer’s instructions.

treatment_protocol: Hypothalamic blocks were excised and subsequently immersed in RNAlater.

value: Wistar

value: male

value: 7 weeks

tag: exposed to

value: restraint stress only

value: Hypothalamus


title: Treg-injected negative control colon tissue, biological rep1

city: CAMBRIDGE

first: Jesse

last: Lyons

state: Ma

address: 77 Massachusetts Ave 16-343

department: Bioengineering

institute: Massachusetts Institute of Technology

description: Gene expression data from non-inflamed colons

hyb_protocol: Following labeling, biotinylated cRNA was hybridized to the GeneChip® Mouse Exon 1.0 ST Array  for 16 hr at 45C in an Affymetrix HybridizationOven. Hybridized array was washed and stained using fluorescent stain SAPE and Anti-streptavidin antibody.

scan_protocol: The arrays were scanned on GeneChip Scanner 3000 7G

data_processing: The data were extracted and quantified at the gene level using the Affymetrix expression console with RMA processing.

source_name: colon tissue from Treg-injected mice

label_protocol: The targets were prepared using the Affyemtrix GeneChip WT PlUS Reagent Kit and labeled by biotinylation.

growth_protocol: Animals were injected with Tregs or naïve T cells at 10 weeks of age and sacrificed 2-4 months after injection.

extract_protocol: RNA was extracted using the Qiagen RNAeasy tissue microarray tissue mini kit following manufacturers recommended protocol.

treatment_protocol: Colons were excised and distal colon tissue (from rectum to proximal/distal junction) was snap frozen.

tag: strain

tag: genotype

value: Treg-injected

value: non-inflamed colons

value: 4-5 mos


title: Hypothalamus_inhaled (R,S)-linalool and exposed restraint stress_rep6

description: Hypothalamus_Inhaled (R,S)-linalool and exposed restraint stress-6

source_name: Hypothalamus of rat exposed to (R,S)-linalool under restraint stress

value: both stress and odor


title: Hypothalamus_exposed restraint stress_rep5 [re-analysis]

description: Hypothalamus_Exposed restraint stress-5


title: IMR90 senescent 1

type: genomic

description: Nucleolus-associated DNA from proliferating IMR90 cells was labelled with Cy3 and hybridized against non-nucleolar DNA labelled with Cy5 on NimbleGen Human CGH 4.2M Whole-Genome Tiling Array v1.0 arrays.

hyb_protocol: Hybridization was performed at Nimblegen due to their protocols.

scan_protocol: Scanning was perfomred at Nimblegen due to their protocols.

data_processing: Data were preprocessed at Nimblegen, due to their protocols.

molecule: genomic DNA

source_name: nucleolus-associated DNA

label_protocol: 2µg of DNA was submitted to Nimblegen and processed there. Nucleolus-associated DNA was labelled with Cy3 and the control DNA with Cy5.

growth_protocol: 5% CO2, 37°C, 10% FCS, DMEM, 1g/L Glucose

extract_protocol: 1x10^8 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. After washing cells 2 times with ice-cold PBS they were scraped off and pooled in 100 mL 1xPBS and centrifuged (750 g, 5 min, 4°C). Supernatant was discarded or used for DNA precipitation and cells were resuspended in 1 mL HMg buffer (10 mM Hepes pH 7.4, 0.88 M sucrose, 12 mM MgCl2, 1 mM TCEP, PI). Cells were sonicated on ice for 3x10 sec with fine tip (Branson sonifier, 65% output, 70% duty cycle). After centrifugation (15000 g, 30 sec) the supernatant was set aside for DNA precipitation or discarded. The pellet was resuspended in 1 mL LMg buffer (10 mM Hepes pH 7.4, 0.88 M sucrose, 1 mM MgCl2, 1 mM TCEP, PI), sonicated on ice for 2x10 sec (as before) and centrifuged (15000 g, 2 min). Supernatant was set aside for DNA precipitation and the pellet was resuspended in 200 µL 20 mM Tris pH 8.1. RNA was digested by adding 3 µL of RNAse A (10 mg/mL) and incubation for 1 h at 37°C. Proteins were deigested by adding 5 µL Proteinase K and incubation for 8 h at 37°C and the cross-link was reversed for 8 h at 65°C. Finally DNA was precipitated.

treatment_protocol: Nucleolus-associated DNA was isolated as discribed below

tag: sample type

value: isolated, non amplified, nucleolar DNA

source_name: non-nucleolar DNA

treatment_protocol: Non-nucleolar DNA was isolated from supernatants of the nucleolus-isolation with ethanol precipitation

value: non-nucleolar DNA


title: Hypothalamus_exposed restraint stress_rep3 [re-analysis]

description: Hypothalamus_Exposed restraint stress-3


title: Hypothalamus_inhaled (R,S)-linalool and exposed restraint stress_rep2

description: Hypothalamus_Inhaled (R,S)-linalool and exposed restraint stress-2


title: Hypothalamus_inhaled (R,S)-linalool and exposed restraint stress_rep5

description: Hypothalamus_Inhaled (R,S)-linalool and exposed restraint stress-5


title: Hypothalamus_exposed restraint stress_rep1 [re-analysis]

description: Hypothalamus_Exposed restraint stress-1


title: Hypothalamus_exposed restraint stress_rep5

description: Hypothalamus_Exposed restraint stress-5


title: Hypothalamus_inhaled (R,S)-linalool and exposed restraint stress_rep3

description: Hypothalamus_Inhaled (R,S)-linalool and exposed restraint stress-3


title: IMR90 proliferating 2

description: Nucleolus-associated DNA from senescent IMR90 cells was labelled with Cy3 and hybridized against genomic DNA labelled with Cy5 on NimbleGen Human CGH 4.2M Whole-Genome Tiling Array v1.0 arrays.

source_name: genomic DNA

treatment_protocol: Genomic DNA was isolated with standard protocols from proliferating IMR90 cells.

value: genomic DNA


title: Hypothalamus_exposed restraint stress_rep2 [re-analysis]

description: Hypothalamus_Exposed restraint stress-2


title: Hypothalamus_inhaled (R,S)-linalool and exposed restraint stress_rep4

description: Hypothalamus_Inhaled (R,S)-linalool and exposed restraint stress-4


title: Hypothalamus_exposed restraint stress_rep6

description: Hypothalamus_Exposed restraint stress-6


title: Naïve T-injected severely inflamed colon tissue, biological rep2

description: Gene expression data from severely inflamed colons

source_name: colon tissue from Naïve T-injected mice

value: Naïve T-injected

value: severely inflamed colons


title: Hypothalamus_inhaled (R,S)-linalool and exposed restraint stress_rep1

description: Hypothalamus_Inhaled (R,S)-linalool and exposed restraint stress-1


title: Hypothalamus_exposed restraint stress_rep4 [re-analysis]

description: Hypothalamus_Exposed restraint stress-4


title: Treg-injected negative control colon tissue, biological rep5


title: Naïve T-injected severely inflamed colon tissue, biological rep3


title: Naïve T-injected severely inflamed colon tissue, biological rep1


title: Treg-injected negative control colon tissue, biological rep2


title: Hypothalamus_exposed restraint stress_rep4

description: Hypothalamus_Exposed restraint stress-4


title: Treg-injected negative control colon tissue, biological rep3


title: IMR90 senescent 2


title: Hypothalamus_exposed restraint stress_rep3

description: Hypothalamus_Exposed restraint stress-3


title: Hypothalamus_exposed restraint stress_rep1

description: Hypothalamus_Exposed restraint stress-1


title: Hypothalamus_control_rep1

value: control


title: Hypothalamus_control_rep2


title: Hypothalamus_control_rep5


title: Hypothalamus_control_rep6


title: Hypothalamus_exposed restraint stress_rep2

description: Hypothalamus_Exposed restraint stress-2


title: Hypothalamus_control_rep4


title: IMR90 proliferating 1


title: Hypothalamus_control_rep3


title: SAMPLE 4 [IMO-mPFC]

city: Atlanta

first: Raul

last: Andero Gali

state: GA

address: 954 Gatewood Rd

department: Department of Psychiatry and Behavioral Sciences

institute: Emory University

description:
SAMPLE 4
1mm punch used

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: Mouse mPFC

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

extract_protocol: Total RNA was isolated and purified from the tissue with the RNeasy Mini Kit (Catalog #74106) following the manufacturer instructions (Qiagen)

tag: Sex

value: Bilateral mPFC

value: 10 weeks old


title: SAMPLE 12 [IMO-Amygdala-8days]

description:
SAMPLE 12
1mm punch used

source_name: Mouse amygdala

value: Bilateral Amygdala


title: SAMPLE 7 [No stress-Amygdala-6days]

description:
SAMPLE 7
1mm punch used

value: male


title: SAMPLE 14 [No stress-Amygdala-8days]

description:
SAMPLE 14
1mm punch used


title: SAMPLE 6 [No stress-Amygdala-6days]

description:
SAMPLE 6
1mm punch used


title: SAMPLE 5 [No stress-Amygdala-6days]

description:
SAMPLE 5
1mm punch used


title: SAMPLE 3 [IMO-mPFC]

description:
SAMPLE 3
1mm punch used


title: Qingyuan-112d-soleus-rep2

city: Yangzhou

first: Jingting

last: Shu

address: Cangjie Road 58#

country: China

institute: Institute of Poultry Science, Chinese Academy of Agricultural Science

description: gene expression in soleus muscles of Qingyuan partridge chickens

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 55 ul of 2x GEx Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent-026441 Gallus gallus (Chicken) Oligo Microarray v2 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 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

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

organism: Gallus gallus

source_name: Qingyuan partridge chicken, soleus muscle, 112d, replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: The two breeds were reared and had ad libitum access to commercial diets (nutrients levels according to the NRC) under the same conditions during the whole experimental period in National Gene Pool for Chinese indigenous chicken breeds, Yangzhou, P.R.China.

extract_protocol: RNA was extracted by Trizol (Life Technology, 15596-018) following the manufacturer's instructions

treatment_protocol: A 1×1 cm2 section in the middle portion of the left SOL muscle was sampled and immediately frozen in liquid nitrogen and then stored at –80 °C until RNA isolation

value: soleus muscle

tag: breed

value: Qingyuan partridge chicken

value: female


title: Qingyuan-112d-extensor digitorum longusmuscles-rep2

description: gene expression in extensor digitorum longusmuscles muscles of Qinagyuan partridge chickens

source_name: Qingyuan partridge chicken, extensor digitorum longusmuscles muscle, 112d, replicate 2

value: extensor digitorum longusmuscles muscle


title: SAMPLE 9 [IMO-Amygdala-8days]

description:
SAMPLE 9
1mm punch used

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol


title: SAMPLE 8 [No stress-Amygdala-6days]

description:
SAMPLE 8
1mm punch used


title: SAMPLE 10 [IMO-Amygdala-8days]

description:
SAMPLE 10
1mm punch used


title: Qingyuan-112d-soleus-rep3

source_name: Qingyuan partridge chicken, soleus muscle, 112d, replicate 3


title: SAMPLE 2 [IMO-mPFC]

description:
SAMPLE 2
1mm punch used


title: SAMPLE 5 [No stress-mPFC]

description:
SAMPLE 5
1mm punch used


title: SAMPLE 4 [IMO-Amygdala-6days]

description:
SAMPLE 4
1mm punch used


title: SAMPLE 1 [IMO-Amygdala-6days]

description:
SAMPLE 1
1mm punch used


title: SAMPLE 13 [No stress-Amygdala-8days]

description:
SAMPLE 13
1mm punch used


title: SAMPLE 16 [No stress-Amygdala-8days]

description:
SAMPLE 16
1mm punch used


title: SAMPLE 3 [IMO-Amygdala-6days]

description:
SAMPLE 3
1mm punch used


title: Qingyuan-112d-extensor digitorum longusmuscles-rep1

source_name: Qingyuan partridge chicken, extensor digitorum longusmuscles muscle, 112d, replicate 1


title: SAMPLE 15 [No stress-Amygdala-8days]

description:
SAMPLE 15
1mm punch used


title: SAMPLE 7 [No stress-mPFC]

description:
SAMPLE 7
1mm punch used


title: SAMPLE 11 [IMO-Amygdala-8days]

description:
SAMPLE 11
1mm punch used


title: Treg-injected negative control colon tissue, biological rep4

value: Treg-injected

value: non-inflamed colons


title: SAMPLE 1 [IMO-mPFC]

description:
SAMPLE 1
1mm punch used


title: SAMPLE 8 [No stress-mPFC]

description:
SAMPLE 8
1mm punch used


title: SAMPLE 6 [No stress-mPFC]

description:
SAMPLE 6
1mm punch used


title: SAMPLE 2 [IMO-Amygdala-6days]

description:
SAMPLE 2
1mm punch used


title: Qingyuan-112d-extensor digitorum longusmuscles-rep3

source_name: Qingyuan partridge chicken, extensor digitorum longusmuscles muscle, 112d, replicate 3


title: Qingyuan-112d-soleus-rep1

source_name: Qingyuan partridge chicken, soleus muscle, 112d, replicate 1


title: Cobb-42d-extensor digitorum longusmuscles-rep1

description: gene expression in extensor digitorum longusmuscles muscles of Cobb brolier

source_name: Cobb brolier, extensor digitorum longusmuscles muscle, 42d, replicate 1

value: Cobb brolier


title: Longissimus dorsi muscle-Lb106

status: Public on Jun 15 2017

city: Yangli

first: Chuzhao

last: Lei

state: Shannxi

address: Xinong Road

institute: Northwest Agriculture and Forestry University

description: Genomic DNA extracted from Longissimus dorsi muscle tissue was genotyped using illumina GeneSeek HD Bovine 77k Genotyping BeadChips (Illumina).

hyb_protocol: Resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48℃, single-base extension and allele-specific staining was performed on a Teflow chamber rack system.

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

data_processing:
Genomic DNA extracted from longissimus dorsi muscle tissue was genotyped using illumina GeneSeek HD Bovine 77k Genotyping Beadchip (GeneSeek).
Image data was analyzed using Beadstudio 3.1.3 with GT module 3.2.33 (GeneSeek)

organism: Bos taurus

source_name: Longissimus dorsi muscle

label_protocol: 900 ng of genomic DNA was whole-genome amplified in an overnight reaction at 37℃ using amplification master mix and primer/neutralization mix. After incubation the amplified DNA was fragmented with fragmentation mix, precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer.

growth_protocol: All of Qinchuan cattle were raised under the same forage and feeding management conditions

extract_protocol: Extraction of genomic DNA from fresh frozen tissue was performed using proteinase K and repeated phenol-chloroform extraction.

treatment_protocol: Longissimus dorsi muscle tissue was collected after slaughter and conserved in -80℃.

value: Qinchuan

value: Longissimus dorsi muscle

value: Castrated bull


title: Longissimus dorsi muscle-Lb130


title: Longissimus dorsi muscle-Lb085


title: Longissimus dorsi muscle-Lb102


title: Longissimus dorsi muscle-Lb122


title: Longissimus dorsi muscle-Lb125


title: Longissimus dorsi muscle-Lb147


title: Longissimus dorsi muscle-Lb135


title: Cobb-42d-extensor digitorum longusmuscles-rep3

source_name: Cobb brolier, extensor digitorum longusmuscles muscle, 42d, replicate 3


title: Longissimus dorsi muscle-Lb112


title: Cobb-42d-extensor digitorum longusmuscles-rep2

source_name: Cobb brolier, extensor digitorum longusmuscles muscle, 42d, replicate 2


title: Longissimus dorsi muscle-Lb145


title: Apc knockout replicate 1

city: Amsterdam

first: Jarom

last: Heijmans

address: Meibergdreef 69-71

department: Gastroenterology & Hepatology

country: Netherlands

institute: Academic Medical Center

description: replicate 1

source_name: Small intestinal epithelium

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

value: Black 6


title: Longissimus dorsi muscle-Lb140


title: Apc knockout replicate 2

description: replicate 2


title: Apc knockout replicate 4

description: replicate 4


title: Cobb-42d-soleus-rep1

description: gene expression in soleus muscles of Cobb brolier

source_name: Cobb brolier, soleus muscle, 42d, replicate 1


title: Apc knockout replicate 3

description: replicate 3


title: Control replicate 1

description: replicate 1


title: Cobb-42d-soleus-rep2

source_name: Cobb brolier, soleus muscle, 42d, replicate 2


title: Cobb-42d-soleus-rep3

source_name: Cobb brolier, soleus muscle, 42d, replicate 3


title: Longissimus dorsi muscle-Lb124


title: Longissimus dorsi muscle-Lb154


title: Longissimus dorsi muscle-Lb100


title: Longissimus dorsi muscle-Lb038


title: Longissimus dorsi muscle-Lb128


title: Control replicate 3

description: replicate 3


title: Control replicate 4

description: replicate 4


title: Control replicate 2

description: replicate 2


title: Longissimus dorsi muscle-Lb031


title: Longissimus dorsi muscle-Lb012


title: Longissimus dorsi muscle-Lb011


title: Longissimus dorsi muscle-Lb013


title: Longissimus dorsi muscle-Lb008


title: Longissimus dorsi muscle-Lb006


title: Longissimus dorsi muscle-Lb004


title: Longissimus dorsi muscle-Lb245


title: Longissimus dorsi muscle-Lb003


title: Longissimus dorsi muscle-Lb141


title: Longissimus dorsi muscle-Lb279


title: Longissimus dorsi muscle-Lb227


title: Longissimus dorsi muscle-Lb127


title: Longissimus dorsi muscle-Lb281


title: Longissimus dorsi muscle-Lb268


title: Longissimus dorsi muscle-Lb265


title: Longissimus dorsi muscle-Lb068


title: Longissimus dorsi muscle-Lb109


title: Longissimus dorsi muscle-Lb264


title: Longissimus dorsi muscle-Lb257


title: Longissimus dorsi muscle-Lb113


title: Longissimus dorsi muscle-Lb212


title: Longissimus dorsi muscle-Lb044


title: Longissimus dorsi muscle-Lb293


title: Longissimus dorsi muscle-Lb294


title: Longissimus dorsi muscle-Lb010


title: Longissimus dorsi muscle-Lb296


title: Longissimus dorsi muscle-Lb292


title: Longissimus dorsi muscle-Lb007


title: Longissimus dorsi muscle-Lb009


title: Longissimus dorsi muscle-Lb291


title: Longissimus dorsi muscle-Lb290


title: Longissimus dorsi muscle-Lb287


title: Longissimus dorsi muscle-Lb286


title: Longissimus dorsi muscle-Lb284


title: Longissimus dorsi muscle-Lb277


title: Longissimus dorsi muscle-Lb283


title: Longissimus dorsi muscle-Lb282


title: Longissimus dorsi muscle-Lb276


title: Longissimus dorsi muscle-Lb275


title: Longissimus dorsi muscle-Lb272


title: Longissimus dorsi muscle-Lb258


title: Longissimus dorsi muscle-Lb254


title: Longissimus dorsi muscle-Lb274


title: Longissimus dorsi muscle-Lb271


title: Longissimus dorsi muscle-Lb243


title: Longissimus dorsi muscle-Lb241


title: Longissimus dorsi muscle-Lb244


title: Longissimus dorsi muscle-Lb240


title: Longissimus dorsi muscle-Lb253


title: Longissimus dorsi muscle-Lb239


title: Longissimus dorsi muscle-Lb238


title: Longissimus dorsi muscle-Lb232


title: Longissimus dorsi muscle-Lb233


title: Longissimus dorsi muscle-Lb230


title: Longissimus dorsi muscle-Lb229


title: Longissimus dorsi muscle-Lb231


title: Longissimus dorsi muscle-Lb224


title: Longissimus dorsi muscle-Lb228


title: Longissimus dorsi muscle-Lb223


title: Longissimus dorsi muscle-Lb221


title: Longissimus dorsi muscle-Lb219


title: Longissimus dorsi muscle-Lb220


title: Longissimus dorsi muscle-Lb214


title: Longissimus dorsi muscle-Lb210


title: Longissimus dorsi muscle-Lb209


title: Longissimus dorsi muscle-Lb207


title: Longissimus dorsi muscle-Lb208


title: Longissimus dorsi muscle-Lb236


title: Longissimus dorsi muscle-Lb203


title: Longissimus dorsi muscle-Lb177


title: Longissimus dorsi muscle-Lb200


title: Longissimus dorsi muscle-Lb206


title: Longissimus dorsi muscle-Lb187


title: Longissimus dorsi muscle-Lb215


title: Longissimus dorsi muscle-Lb189


title: Longissimus dorsi muscle-Lb175


title: Longissimus dorsi muscle-Lb194


title: Longissimus dorsi muscle-Lb205


title: Longissimus dorsi muscle-Lb162


title: Longissimus dorsi muscle-Lb163


title: Longissimus dorsi muscle-Lb160


title: Longissimus dorsi muscle-Lb164


title: Longissimus dorsi muscle-Lb171


title: Longissimus dorsi muscle-Lb152


title: Longissimus dorsi muscle-Lb155


title: Longissimus dorsi muscle-Lb150


title: Longissimus dorsi muscle-Lb144


title: Longissimus dorsi muscle-Lb216


title: Longissimus dorsi muscle-Lb161


title: Longissimus dorsi muscle-Lb142


title: Longissimus dorsi muscle-Lb139


title: Longissimus dorsi muscle-Lb211


title: Longissimus dorsi muscle-Lb138


title: Longissimus dorsi muscle-Lb136


title: Longissimus dorsi muscle-Lb137


title: Longissimus dorsi muscle-Lb134


title: Longissimus dorsi muscle-Lb126


title: Longissimus dorsi muscle-Lb119


title: Longissimus dorsi muscle-Lb110


title: Longissimus dorsi muscle-Lb118


title: Longissimus dorsi muscle-Lb116


title: Longissimus dorsi muscle-Lb117


title: Longissimus dorsi muscle-Lb107


title: Longissimus dorsi muscle-Lb095


title: Longissimus dorsi muscle-Lb097


title: Longissimus dorsi muscle-Lb094


title: Longissimus dorsi muscle-Lb105


title: Longissimus dorsi muscle-Lb089


title: Longissimus dorsi muscle-Lb093


title: Longissimus dorsi muscle-Lb088


title: Longissimus dorsi muscle-Lb091


title: Longissimus dorsi muscle-Lb086


title: Longissimus dorsi muscle-Lb079


title: Longissimus dorsi muscle-Lb090


title: Longissimus dorsi muscle-Lb084


title: Longissimus dorsi muscle-Lb083


title: Longissimus dorsi muscle-Lb080


title: Longissimus dorsi muscle-Lb078


title: Longissimus dorsi muscle-Lb075


title: Longissimus dorsi muscle-Lb081


title: Longissimus dorsi muscle-Lb072


title: Longissimus dorsi muscle-Lb076


title: Longissimus dorsi muscle-Lb067


title: Longissimus dorsi muscle-Lb066


title: Longissimus dorsi muscle-Lb115


title: Longissimus dorsi muscle-Lb060


title: Longissimus dorsi muscle-Lb064


title: Longissimus dorsi muscle-Lb114


title: Longissimus dorsi muscle-Lb059


title: Longissimus dorsi muscle-Lb058


title: Longissimus dorsi muscle-Lb061


title: Longissimus dorsi muscle-Lb056


title: Longissimus dorsi muscle-Lb057


title: Longissimus dorsi muscle-Lb052


title: Longissimus dorsi muscle-Lb048


title: Longissimus dorsi muscle-Lb053


title: Longissimus dorsi muscle-Lb050


title: Longissimus dorsi muscle-Lb049


title: Longissimus dorsi muscle-Lb046


title: Longissimus dorsi muscle-Lb045


title: Longissimus dorsi muscle-Lb043


title: Longissimus dorsi muscle-Lb041


title: Longissimus dorsi muscle-Lb042


title: Longissimus dorsi muscle-Lb040


title: Longissimus dorsi muscle-Lb039


title: Longissimus dorsi muscle-Lb036


title: Longissimus dorsi muscle-Lb065


title: Longissimus dorsi muscle-Lb035


title: Longissimus dorsi muscle-Lb033


title: Longissimus dorsi muscle-Lb032


title: Longissimus dorsi muscle-Lb030


title: Longissimus dorsi muscle-Lb029


title: Longissimus dorsi muscle-Lb020


title: Longissimus dorsi muscle-Lb005


title: Longissimus dorsi muscle-La259


title: Longissimus dorsi muscle-Lb001


title: Longissimus dorsi muscle-La256


title: Longissimus dorsi muscle-Lb027


title: Longissimus dorsi muscle-Lb028


title: Longissimus dorsi muscle-Lb047


title: Longissimus dorsi muscle-Lb034


title: Longissimus dorsi muscle-La255


title: Longissimus dorsi muscle-La249


title: Longissimus dorsi muscle-La251


title: Longissimus dorsi muscle-La250


title: Longissimus dorsi muscle-La252


title: Longissimus dorsi muscle-La247


title: Longissimus dorsi muscle-Lb037


title: Longissimus dorsi muscle-La242


title: Longissimus dorsi muscle-La225


title: Longissimus dorsi muscle-La226


title: Longissimus dorsi muscle-La235


title: Longissimus dorsi muscle-La237


title: Longissimus dorsi muscle-La222


title: Longissimus dorsi muscle-La218


title: Longissimus dorsi muscle-La217


title: Longissimus dorsi muscle-La204


title: Longissimus dorsi muscle-La199


title: Longissimus dorsi muscle-La198


title: Longissimus dorsi muscle-La193


title: Longissimus dorsi muscle-La197


title: Longissimus dorsi muscle-La195


title: Longissimus dorsi muscle-La192


title: Longissimus dorsi muscle-La196


title: Longissimus dorsi muscle-La191


title: Longissimus dorsi muscle-La188


title: Longissimus dorsi muscle-La190


title: Longissimus dorsi muscle-La186


title: Longissimus dorsi muscle-La183


title: Longissimus dorsi muscle-La184


title: Longissimus dorsi muscle-La234


title: Longissimus dorsi muscle-La246


title: Longissimus dorsi muscle-La185


title: Longissimus dorsi muscle-La180


title: Longissimus dorsi muscle-La182


title: Longissimus dorsi muscle-La179


title: Longissimus dorsi muscle-La181


title: Longissimus dorsi muscle-La176


title: Longissimus dorsi muscle-La213


title: Longissimus dorsi muscle-La173


title: Longissimus dorsi muscle-La172


title: Longissimus dorsi muscle-La170


title: Longissimus dorsi muscle-La201


title: Longissimus dorsi muscle-La169


title: Longissimus dorsi muscle-La174


title: Longissimus dorsi muscle-La168


title: Longissimus dorsi muscle-La156


title: Longissimus dorsi muscle-La154


title: Longissimus dorsi muscle-La165


title: Longissimus dorsi muscle-La158


title: Longissimus dorsi muscle-La159


title: Longissimus dorsi muscle-La153


title: Longissimus dorsi muscle-La149


title: Longissimus dorsi muscle-La151


title: Longissimus dorsi muscle-La147


title: Longissimus dorsi muscle-La146


title: Longissimus dorsi muscle-La135


title: Longissimus dorsi muscle-La178


title: Longissimus dorsi muscle-La148


title: Longissimus dorsi muscle-La143


title: Longissimus dorsi muscle-La145


title: Longissimus dorsi muscle-La133


title: Longissimus dorsi muscle-La131


title: Longissimus dorsi muscle-La123


title: Longissimus dorsi muscle-La130


title: Longissimus dorsi muscle-La120


title: Longissimus dorsi muscle-La129


title: Longissimus dorsi muscle-La121


title: Longissimus dorsi muscle-La132


title: Longissimus dorsi muscle-La108


title: Longissimus dorsi muscle-La166


title: Longissimus dorsi muscle-La106


title: Longissimus dorsi muscle-La111


title: Longissimus dorsi muscle-Lb055


title: Longissimus dorsi muscle-La104


title: Longissimus dorsi muscle-La101


title: Longissimus dorsi muscle-La103


title: Longissimus dorsi muscle-La102


title: Longissimus dorsi muscle-La099


title: Longissimus dorsi muscle-La098


title: Longissimus dorsi muscle-La096


title: Longissimus dorsi muscle-La085


title: Longissimus dorsi muscle-La087


title: Longissimus dorsi muscle-La073


title: Longissimus dorsi muscle-La070


title: Longissimus dorsi muscle-La074


title: Longissimus dorsi muscle-La062


title: Longissimus dorsi muscle-La082


title: Longissimus dorsi muscle-La054


title: Longissimus dorsi muscle-La026


title: Longissimus dorsi muscle-La063


title: Head kidney_spleen_control_rep3

city: Madrid

first: Julio

middle: M

last: Coll

state: Madrid

address: crt Coruna km7

department: Biotechnology

institute: INIA

hyb_protocol: The slides were pre-treated with 1% BSA fraction V, 5 X SSC, 0.1% SDS for 30 min. at 50 ºC and washed with 2 X SSC (3 min) and 0.2 X SSC (3 min) and hybridized overnight in cocktail containing 1.3 X Denhardt's, 3 X SSC, 0.3% SDS, 2.1 ug/ul polyadenylate and 1 ug/ul yeast tRNA.

scan_protocol: Signal was captured and processed using an Agilent scanner (G2565B, Agilent Technologies). The scanner images were segmented by the Agilent Feature Extraction Software (v9.5) with the protocol GE1-v5_95.

data_processing: The gProccesedSignal was chosen for statistical analysis. Normalization within each microarray was carried out by using the sum of all the signals. Data was first filtered by non-uniform pixel distributed outliers and other replicate outliers (glsFeatNonUnifOL, glsBGNonUnifOL, glsFeatPopnOL and glsBGPopnOL) according to the default Agilent feature extraction criteria; ratio between processed signal and its error <2; differentiation from background signal; linear relationship between concentration and intensity below limits according to Spike-In information

organism: Danio rerio

source_name: Head kidney and spleen of 3 zebrafish

label_protocol: RNA were labeled with Cy3 (Amersham Pharmacia) by using SuperScript III reverse transcriptase (InVitroGen) and oligo(dT) primer, and the resulting cDNA was purified with Microcon YM30 (Millipore)

growth_protocol: Adult zebrafish of  2-3 g (~ 4 cm in length) were obtained from a local fish pet shop to study a situation that more closely resembles the variability of natural populations. Zebrafish were maintained at 24-26 ºC in 30 l aquaria with tap-dechlorinated carbon-filtered water with 1 g of CaCl2, 1 g of NaHCO3 and 0.5 g of Instant Ocean sea salts added to water resulting in a conductivity of 200-300 µS pH of 7.8-8.2. The aquaria were provided with biological filters and fish fed with a commercial feed diet. For each experiment, groups of adult zebrafish were moved to 2 l aquaria provided with biological filters.

extract_protocol: RNA was extracted using the RNAeasyPlus kit (Qiagen, Hilden, Germany).

treatment_protocol: Zebrafish were injected with 0,2 μg of polyhistidine or 1 μg of NV (non virion)recombinant protein of VHSV

value: Head kidney and spleen

tag: development stage

value: Adult


title: Longissimus dorsi muscle-La112


title: Head kidney_spleen_NV injected_rep1

value: NV (non virion) recombinant protein of VHSV


title: Head kidney_spleen_NV injected_rep2


title: Head kidney_spleen_NV injected_rep4


title: Head kidney_spleen_control_rep1

value: control


title: Head kidney_spleen_control_rep2


title: Head kidney_spleen_control_rep4


title: Longissimus dorsi muscle-La010


title: leftventricle_aldosalt_2days_rep30

city: Jackson

first: Damian

middle: G.

last: Romero

state: MS

address: 2500 N. State St.

institute: University of Mississippi Medical Center

hyb_protocol: The Hy3-labeled samples and a Hy5-labeled reference RNA sample were mixed pair-wise and hybridized to the miRCURY LNA array version 11.0 (Exiqon), which contains capture probes targeting all miRNAs for human, mouse or rat registered in the miRBASE version 13.0 at the Sanger Institute. The hybridization was performed according to the miRCURY LNA array manual using a Tecan HS4800 hybridization station (Tecan, Austria).

scan_protocol: After hybridization, the microarray slides were scanned using the Agilent G2565BA Microarray Scanner System and the image analysis was carried out using the ImaGene 8.0 software (BioDiscovery).

data_processing: The quantified signals were background corrected (Normexp with offset value 10) and normalized using the global LOWESS (LOcally WEighted Scatterplot Smoothing) regression algorithm.

source_name: left ventricle, Aldosterone/Salt, 2 days

label_protocol: One µg total RNA from sample and reference (a pool of all tested samples) was labelled with Hy3™ and Hy5™ fluorescent labels, respectively, using the miRCURY™ LNA Array power labelling kit (Exiqon) following the procedure described by the manufacturer.

growth_protocol: Eight-week old male Sprague Dawley rats (Harlan Laboratories) were maintained on standard condition with a 12:12h light-dark cycle with ad libitum access to standard rodent chow (Teklad #8640, Harlan Laboratories) and water. Studies were performed in accordance with the National Institutes of Health Guide for the Care and Use of Laboratory Animals, 8th Edition, 2011.

extract_protocol: Total RNA (including miRNAs) was extracted with TRI-Reagent (MRC Gene), resuspended in nuclease free water and subjected to further purification using the RNeasy Mini kit (Qiagen) following an Exiqon modified protocol to preserve miRNAs. Purified total RNA was quantified by UV absorbance using the Nanodrop spectrophotometer (Nanodrop Technolologies) and quality checked by using a 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Animals were uninephrectomized and the next day randomly assigned to Control or Aldosterone/Salt (ALDO/SALT) experimental groups. ALDO (0.75 µg/h, Steraloids) was administered in PEG 300 (vehicle, Fluka) by subcutaneously implanted osmotic minipumps (Alzet 2004, Durect). SALT (1.0 % NaCl) was administered in the drinking fluid instead of tap water. ALDO-treated animals were supplemented with 0.3 % KCl in the drinking fluid to avoid hypokalemia. Animals were treated for 2, 7, 14, 28 or 56 days.

value: left ventricle

value: Aldosterone/Salt

tag: treatment time

value: 2 days

source_name: left ventricle, pooled


title: leftventricle_aldosalt_2days_rep29


title: Longissimus dorsi muscle-La069


title: Longissimus dorsi muscle-La008


title: leftventricle_aldosalt_2days_rep28


title: Head kidney_spleen_NV injected_rep3


title: Longissimus dorsi muscle-La002


title: Longissimus dorsi muscle-La288


title: leftventricle_control_2days_rep27

source_name: left ventricle, Control, 2 days

value: Control


title: Longissimus dorsi muscle-La011


title: leftventricle_control_2days_rep25


title: leftventricle_aldosalt_7days_rep24

source_name: left ventricle, Aldosterone/Salt, 7 days

value: 7 days


title: Longissimus dorsi muscle-La267


title: leftventricle_aldosalt_7days_rep22


title: leftventricle_aldosalt_7days_rep23


title: Longissimus dorsi muscle-La289


title: Longissimus dorsi muscle-La266


title: Longissimus dorsi muscle-La285


title: leftventricle_control_7days_rep21

source_name: left ventricle, Control, 7 days


title: Longissimus dorsi muscle-La260


title: leftventricle_control_7days_rep20


title: leftventricle_control_7days_rep19


title: leftventricle_aldosalt_14days_rep17

source_name: left ventricle, Aldosterone/Salt, 14 days

value: 14 days


title: leftventricle_control_14days_rep15

source_name: left ventricle, Control, 14 days


title: leftventricle_aldosalt_14days_rep16


title: leftventricle_control_14days_rep14


title: leftventricle_aldosalt_28days_rep12

source_name: left ventricle, Aldosterone/Salt, 28 days

value: 28 days


title: Longissimus dorsi muscle-La263


title: Longissimus dorsi muscle-La273


title: HeyA8-PARENTALvsCIS_Resistant

city: Jena

first: Norman

last: Häfner

address: Bachstrasse 18

department: Gynecology

institute: Jena University Hospital

hyb_protocol: The complete workflow of microarray processing followed strictly the Agilent protocol Analysis of methylated DNA immunopreciptiation. Hybridisation was done with Agilent Oligo aCGH hybridisation kit. After combining specific AlexaFluor3 and 5-labelled DNAs, cot1-DNA, blocking solution, deionized formamid and hybridisation buffer samples were denatured 3min at 95°C and incubated for 30min at 37°C. Solutions were then immediately transferred to the microarrays and hybridized for 40h, 67°C at 20rpm in a Agilent hybridisation oven. Arrays were washed using Agilent wash procedure B (including the stabilization and drying solution).

scan_protocol: Scanned on an Agilent G2565CA scanner using Agilent G3_CGH settings at 3µm resolution. Images were quantified using Agilent Feature Extraction Software (version 10.5) and the protocol CGH_105_Jan09.

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used. Log2 ratios of spotted probe duplicates were averaged using Microsoft Excel 2007.

label: Alexa Fluor 3

source_name: HeyA8 parental cell culture

label_protocol: Labelling was done with Invitrogene BioPrime Labelling Kit according to manufacturer protocol. Reaction mixture was denatured for 5min 95°C; after 5min on ice Exo- Klenow fragment was added and samples were incubated 2h at 37°C. After purification (BioPrime Kit) the labelling efficiency was determined by NanoDrop measurements.

extract_protocol:
Genomic DNA extracted by ProteinaseK digestion, phenol-chloroform isolation and ethanol precipitation; 2µg of each sample
gDNA sonicated to fragments of 150-400bp and enrichment of methylated DNA from 2µg of DNA by MethylCollectorUltra Kit (ActiveMotif). Enrichment was validated by qPCR for unmethylated and imprinted (methylated) control regions.

tag: platin sensitivity

value: sensitive, IC50 2.31µM

value: MIRA enriched methylated DNA

label: Alexa Fluor 5

source_name: HeyA8 resistant cell culture

value: resistant, IC50 24.75µM


title: leftventricle_aldosalt_28days_rep11


title: SKOV3-PARENTALvsCIS_Resistant

source_name: SKOV3 parental cell culture

value: sensitive, IC50 5.49µM

source_name: SKOV3 resistant cell culture

value: resistant, IC50 22.73µM


title: Longissimus dorsi muscle-La270

source_name: Longissimus dorsi muscle

value: Qinchuan

value: Longissimus dorsi muscle

value: Castrated bull


title: leftventricle_aldosalt_28days_rep10


title: leftventricle_aldosalt_14days_rep18


title: A2780-PARENTALvsCIS_Resistant

source_name: A2780 parental cell culture

value: sensitive, IC50 2.11µM

source_name: A2780 resistant cell culture

value: resistant, IC50 11.1µM


title: Longissimus dorsi muscle-La295


title: leftventricle_control_28days_rep8

source_name: left ventricle, Control, 28 days

value: left ventricle


title: Longissimus dorsi muscle-La278


title: leftventricle_control_28days_rep9


title: leftventricle_control_14days_rep13


title: reactive Fc-epsilon receptor-crosslinking donor AB10

first: Bernett

last: Lee

address: 8A Biomedical Grove #03-06 Immunos

country: Singapore

institute: Singapore Immunology Network

hyb_protocol: Fragmented samples were hybridized according to Affymetrix guidelines for 18hr in 45°C on GeneChip Human Gene 1.0 ST Array. The arrays were then washed and stained using the standard fluidics protocol (FS450_0007) for gene arrays on the GeneChip Fluidics Station 450.

scan_protocol: The human GeneChips were scanned using GeneChip Scanner 3000. The images were analyzed using Expression Console and standard array quality controls analyses were carried out according to the instructions provided by Affymetrix.

data_processing: CEL files were processed in Bioconductor using the oligo package. Expression data was summarized at the transcript level and normalized using RMA. Log2 transformation was applied to the expression data.

source_name: Isolated basophils, reactive, Fc-epsilon receptor-crosslinking

label_protocol: SPIA cDNA were prepared according to NuGEN Ovation Pico WTA System Kit's protocol from 1ng of Total RNA. ST-cDNA were prepared with 4.5ug of SPIA cDNA according to NuGEN WT-Ovation Exon Module. 5ug of ST-cDNA were fragmented and labelled according to NuGEN Encore Biotin Kit's protocol.

extract_protocol: Total RNA was extracted following the double extraction protocol using Trizol and Qiagen RNeasy Micro Extraction Kit. Total RNA integrity was assessed by Agilent Bioanalyzer.

treatment_protocol: Freshly isolated basophils (75,000 basophils) were incubated with or without 50 ul of anti-FCERIA monoclonal antibody (provided in the Flow2CAST kit) in a total volume 200 ul Stimulation Buffer (Bühlmann Laboratories) for 4 hours.

tag: cell type

value: basophils

value: reactive

tag: stimulation

value: Fc-epsilon receptor-crosslinking

tag: donor


title: leftventricle_control_28days_rep7

value: Control


title: Longissimus dorsi muscle-La262


title: Longissimus dorsi muscle-La261


title: anergic unstimulated donor PB6

source_name: Isolated basophils, anergic, unstimulated

value: anergic

value: unstimulated


title: anergic Fc-epsilon receptor-crosslinking donor PB6

source_name: Isolated basophils, anergic, Fc-epsilon receptor-crosslinking


title: leftventricle_aldosalt_56days_rep5

source_name: left ventricle, Aldosterone/Salt, 56 days

value: Aldosterone/Salt

value: 56 days

source_name: left ventricle, pooled


title: reactive Fc-epsilon receptor-crosslinking donor AB6


title: reactive Fc-epsilon receptor-crosslinking donor AB5


title: reactive unstimulated donor AB10

source_name: Isolated basophils, reactive, unstimulated


title: reactive unstimulated donor AB6


title: anergic Fc-epsilon receptor-crosslinking donor AB4


title: Longissimus dorsi muscle-La269


title: leftventricle_control_56days_rep2

source_name: left ventricle, Control, 56 days


title: leftventricle_aldosalt_56days_rep6


title: anergic unstimulated donor AB4


title: leftventricle_control_56days_rep3


title: leftventricle_control_56days_rep1


title: leftventricle_aldosalt_56days_rep4


title: reactive unstimulated donor AB5


title: LT4 C

status: Public on Jun 14 2017

city: Verona

first: Silvia

last: Dal Santo

address: Strada Le Grazie, 15

department: Department of Biotechnology

institute: University of Verona

hyb_protocol: Hybridization and washing procedures were performed according to the NimbleGen Arrays User’s Guide (V 3.2).

scan_protocol: Each microarray was scanned using a Axon GenePix 4400 A at 532 nm (Cy-3 absorption peak) and GenePix Pro7 software (Molecular Devices, Sunnyvale, CA, USA) according to the manufacturers' instructions.

data_processing: Images were analyzed using NimbleScan v2.5 software (Roche), background correction and standard RMA normalization were selected.

organism: Vitis vinifera

source_name: Stage 4, Skins from berries grown under LT regime, replicate C

label_protocol: cDNA synthesis and labeling reactions were performed according to the NimbleGen Arrays User’s Guide (V 3.2).

growth_protocol: Experiments on grapevine berries were carried out in 2012 on 6-year-old uniformly-potted plants (V. vinifera cv. Sangiovese). The vines, grafted on SO4 rootstocks, were grown in 30-liter pots containing a 1:1 mixture of sand and soil. The number of shoots was standardized to nine shoots per vine. In addition, to achieve a uniform leaf area in all the vines, the tip of each shoot was removed and 15 main leaves were maintained before the experiment started. Before full véraison at the beginning of bunch closure (BBCH 77), 10 vines were selected and cluster numbers were adjusted to 11–12 clusters per vine.

extract_protocol: Total RNA was isolated from approximately 400 mg of berry skins using the Spectrum™ Plant Total RNA kit (Sigma-Aldrich), with modifications as described in Dal Santo et al. (2016).

treatment_protocol: The selected vines were assigned to two treatments: low temperature (LT) and high temperature (HT). Five LT vines were placed from the beginning of bunch closure to harvest in a plastic greenhouse (20 m3) where the air temperature was controlled by a cooler and a fan was used to maintain airflow. During the night, the tunnel was opened. Simultaneously, five HT vines were positioned in an identical plastic greenhouse, whose basal segment was open but all the canopies were covered to maintain similar illumination to the LT vines.

tag: cultivar

value: Sangiovese

tag: sampling timepoints

value: Stage 4, 32 days after véraison

tag: thermal treatment

value: LT, low temperature regime, 21°C as average and 35°C as maximum air daily temperature


title: HT3 C

source_name: Stage 3, Skins from berries grown under HT regime, replicate C

value: Stage 3, 20 days after véraison

value: HT, high temperature regime, 26°C as average and 41.7°C as maximum air daily temperature


title: LT3 B

source_name: Stage 3, Skins from berries grown under LT regime, replicate B


title: LT4 B

source_name: Stage 4, Skins from berries grown under LT regime, replicate B


title: LT3 A

source_name: Stage 3, Skins from berries grown under LT regime, replicate A


title: HT3 B

source_name: Stage 3, Skins from berries grown under HT regime, replicate B


title: HT4 C

source_name: Stage 4, Skins from berries grown under HT regime, replicate C