title: liu-00251: TCGA-02-0432-01A-02R-0280-01


title: liu-00251: TCGA-02-0060-01A-01R-0177-01

status: Public on May 27 2016

type: RNA

city: Rockville

first: Mervi

last: Heiskanen

state: MD

address: 9609 Medical Center Drive, 1W378

department: CBIIT

country: USA

institute: NCI

hyb_protocol: See mage-tab files linked to series entry for additional details

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Brain

tag: diseasestate

value: GLIOBLASTOMA MULTIFORME

tag: organismpart

value: Brain

tag: individual

tag: clinical diagnosis

value: GBM

tag: pathologic status

value: MALIGNANT

tag: histologic diagnosis

tag: tissue anatomic site

value: TEMPORAL LOBE


title: liu-00251: TCGA-02-0085-01A-01R-0202-01

scan_protocol: See mage-tab files linked to series entry for additional details

value: NOT SPECIFIED


title: liu-00251: TCGA-12-0619-01A-01R-0306-01

data_processing: See mage-tab files linked to series entry for additional details

value: OVERLAPPING LESION OF BRAIN


title: liu-00251: TCGA-08-0357-01A-01R-0298-01

label_protocol: See mage-tab files linked to series entry for additional details


title: liu-00251: TCGA-06-0142-01A-01R-0219-01

extract_protocol: See mage-tab files linked to series entry for additional details


title: liu-00251: TCGA-12-0616-01A-01R-0306-01


title: liu-00251: TCGA-06-0179-01A-02R-0280-01


title: liu-00251: TCGA-06-0146-01A-01R-0280-01

value: FRONTAL LOBE


title: liu-00251: TCGA-02-0330-01A-01R-0280-01


title: liu-00251: TCGA-06-0132-01A-02R-0233-01


title: liu-00251: TCGA-08-0512-01A-01R-0280-01


title: liu-00251: TCGA-06-0137-01A-03R-0219-01

value: PARIETAL LOBE


title: liu-00251: TCGA-06-0157-01A-01R-0233-01

value: CEREBRUM


title: liu-00251: TCGA-02-0057-01A-01R-0177-01


title: liu-00251: TCGA-06-0158-01A-01R-0233-01


title: liu-00251: TCGA-02-0106-01A-01R-0280-01


title: liu-00251: TCGA-02-0007-01A-01R-0177-01


title: liu-00251: TCGA-02-0083-01A-01R-0202-01


title: liu-00251: TCGA-08-0529-01A-02R-0280-01


title: liu-00251: TCGA-08-0514-01A-01R-0280-01


title: liu-00251: TCGA-02-0046-01A-01R-0177-01


title: liu-00251: TCGA-06-0648-01A-01R-0306-01


title: liu-00251: TCGA-06-0162-01A-01R-0280-01


title: liu-00251: TCGA-08-0352-01A-01R-0306-01


title: liu-00251: TCGA-02-0070-01A-01R-0298-01


title: liu-00251: TCGA-08-0509-01A-01R-0280-01


title: liu-00251: TCGA-08-0373-01A-01R-0306-01


title: liu-00251: TCGA-02-0058-01A-01R-0177-01


title: liu-00251: TCGA-08-0245-01A-01R-0298-01

value: OCCIPITAL LOBE


title: liu-00251: TCGA-06-0127-01A-01R-0306-01

value: BRAIN, NOS


title: liu-00251: TCGA-06-0137-01A-01R-0219-01


title: liu-00251: TCGA-06-0206-01A-01R-0233-01


title: liu-00251: TCGA-08-0385-01A-01R-0298-01


title: liu-00251: TCGA-06-0152-01A-02R-0306-01


title: liu-00251: TCGA-02-0025-01A-01R-0298-01


title: liu-00251: TCGA-02-0446-01A-01R-0280-01


title: liu-00251: TCGA-08-0390-01A-01R-0298-01


title: liu-00251: TCGA-08-0350-01A-01R-0298-01


title: liu-00251: TCGA-02-0021-01A-01R-0177-01


title: liu-00251: TCGA-08-0244-01A-01R-0298-01


title: liu-00251: TCGA-02-0324-01A-01R-0280-01


title: liu-00251: TCGA-06-0238-01A-02R-0306-01


title: liu-00251: TCGA-08-0359-01A-01R-0298-01


title: liu-00251: TCGA-02-0002-01A-01R-0177-01


title: liu-00251: TCGA-02-0422-01A-01R-0280-01


title: liu-00251: TCGA-02-0332-01A-01R-0280-01


title: liu-00251: TCGA-08-0358-01A-01R-0306-01


title: liu-00251: TCGA-06-0138-01A-01R-0233-01


title: liu-00251: TCGA-02-0333-01A-02R-0280-01


title: liu-00251: TCGA-06-0138-01A-02R-0233-01


title: liu-00251: TCGA-06-0173-01A-01R-0233-01


title: liu-00251: TCGA-02-0289-01A-01R-0280-01


title: liu-00251: TCGA-02-0337-01A-01R-0280-01


title: liu-00251: TCGA-02-0051-01A-01R-0298-01


title: liu-00251: TCGA-08-0510-01A-01R-0280-01


title: liu-00251: TCGA-06-0122-01A-01R-0219-01


title: liu-00251: TCGA-06-0143-01A-01R-0219-01


title: liu-00251: TCGA-06-0171-01A-02R-0233-01


title: liu-00251: TCGA-02-0037-01A-01R-0177-01


title: liu-00251: TCGA-02-0339-01A-01R-0280-01


title: liu-00251: TCGA-02-0028-01A-01R-0177-01


title: liu-00251: TCGA-06-0164-01A-01R-0280-01


title: liu-00251: TCGA-08-0386-01A-01R-0306-01


title: liu-00251: TCGA-02-0054-01A-01R-0177-01


title: liu-00251: TCGA-02-0258-01A-01R-0280-01


title: liu-00251: TCGA-06-0189-01A-05R-0233-01


title: liu-00251: TCGA-02-0059-01A-01R-0298-01


title: liu-00251: TCGA-02-0055-01A-01R-0177-01


title: liu-00251: TCGA-02-0024-01B-01R-0177-01


title: liu-00251: TCGA-06-0211-01A-01R-0233-01


title: liu-00251: TCGA-02-0440-01A-01R-0280-01


title: liu-00251: TCGA-08-0353-01A-01R-0298-01


title: liu-00251: TCGA-02-0039-01A-01R-0298-01


title: liu-00251: TCGA-06-0141-01A-01R-0219-01


title: liu-00251: TCGA-02-0260-01A-03R-0280-01


title: liu-00251: TCGA-06-0214-01A-02R-0233-01


title: liu-00251: TCGA-06-0211-01B-01R-0233-01


title: liu-00251: TCGA-08-0348-01A-01R-0298-01


title: liu-00251: TCGA-08-0351-01A-01R-0298-01


title: liu-00251: TCGA-02-0011-01B-01R-0177-01


title: liu-00251: TCGA-02-0052-01A-01R-0177-01


title: liu-00251: TCGA-02-0079-01A-03R-0306-01


title: liu-00251: TCGA-02-0087-01A-01R-0280-01


title: liu-00251: TCGA-08-0524-01A-01R-0280-01


title: liu-00251: TCGA-06-0221-01A-01R-0233-01


title: liu-00251: TCGA-02-0009-01A-01R-0177-01


title: liu-00251: TCGA-02-0321-01A-01R-0280-01


title: liu-00251: TCGA-02-0064-01A-01R-0202-01


title: liu-00251: TCGA-02-0281-01A-01R-0280-01


title: liu-00251: TCGA-02-0325-01A-01R-0280-01


title: liu-00251: TCGA-02-0015-01A-01R-0298-01


title: liu-00251: TCGA-08-0360-01A-01R-0298-01


title: liu-00251: TCGA-02-0004-01A-01R-0298-01


title: liu-00251: TCGA-08-0380-01A-01R-0298-01


title: liu-00251: TCGA-02-0285-01A-01R-0280-01


title: liu-00251: TCGA-06-0413-01A-01R-0280-01


title: liu-00251: TCGA-02-0116-01A-01R-0202-01


title: liu-00251: TCGA-02-0010-01A-01R-0177-01


title: liu-00251: TCGA-02-0084-01A-03R-0306-01


title: liu-00251: TCGA-12-0615-01A-01R-0306-01


title: liu-00251: TCGA-08-0344-01A-01R-0298-01


title: liu-00251: TCGA-08-0355-01A-01R-0298-01


title: liu-00251: TCGA-02-0027-01A-01R-0177-01


title: liu-00251: TCGA-06-0409-01A-02R-0280-01


title: liu-00251: TCGA-06-0167-01A-01R-0233-01


title: liu-00251: TCGA-06-0241-01A-02R-0233-01


title: liu-00251: TCGA-02-0014-01A-01R-0177-01


title: liu-00251: TCGA-06-0394-01A-01R-0280-01


title: liu-00251: TCGA-02-0071-01A-01R-0202-01


title: liu-00251: TCGA-06-0149-01A-05R-0280-01


title: liu-00251: TCGA-06-0175-01A-01R-0280-01


title: liu-00251: TCGA-06-0168-01A-02R-0233-01


title: liu-00251: TCGA-02-0439-01A-01R-0280-01


title: liu-00251: TCGA-06-0168-01A-01R-0233-01


title: liu-00251: TCGA-02-0430-01A-01R-0280-01


title: liu-00251: TCGA-02-0107-01A-01R-0202-01


title: liu-00251: TCGA-06-0645-01A-01R-0306-01


title: liu-00251: TCGA-02-0269-01B-01R-0280-01


title: liu-00251: TCGA-06-0154-01A-02R-0233-01


title: liu-00251: TCGA-08-0246-01A-01R-0298-01


title: liu-00251: TCGA-07-0249-20A-01R-0280-01


title: liu-00251: TCGA-06-0154-01A-03R-0233-01


title: liu-00251: TCGA-06-0402-01A-01R-0280-01


title: liu-00251: TCGA-06-0129-01A-01R-0219-01


title: liu-00251: TCGA-06-0188-01A-01R-0233-01


title: liu-00251: TCGA-02-0086-01A-01R-0202-01


title: liu-00251: TCGA-06-0133-01A-02R-0219-01


title: liu-00251: TCGA-06-0169-01A-01R-0219-01


title: liu-00251: TCGA-06-0160-01A-01R-0233-01


title: liu-00251: TCGA-06-0210-01A-01R-0233-01


title: liu-00251: TCGA-06-0145-01A-05R-0219-01


title: liu-00251: TCGA-12-0620-01A-01R-0306-01


title: liu-00251: TCGA-06-0145-01A-03R-0219-01


title: liu-00251: TCGA-06-0145-01A-04R-0219-01


title: liu-00251: TCGA-02-0114-01A-01R-0202-01


title: liu-00251: TCGA-06-0145-01A-01R-0219-01


title: liu-00251: TCGA-06-0182-01A-01R-0280-01


title: liu-00251: TCGA-08-0518-01A-01R-0280-01


title: liu-00251: TCGA-06-0126-01A-01R-0219-01


title: liu-00251: TCGA-06-0197-01A-02R-0233-01


title: liu-00251: TCGA-06-0128-01A-01R-0219-01


title: liu-00251: TCGA-02-0034-01A-01R-0177-01


title: liu-00251: TCGA-08-0520-01A-01R-0280-01


title: liu-00251: TCGA-02-0266-01A-01R-0280-01


title: liu-00251: TCGA-02-0003-01A-01R-0177-01


title: liu-00251: TCGA-06-0237-01A-02R-0233-01


title: liu-00251: TCGA-12-0618-01A-01R-0306-01


title: liu-00251: TCGA-08-0389-01A-01R-0298-01


title: liu-00251: TCGA-02-0089-01A-01R-0202-01


title: liu-00251: TCGA-08-0349-01A-01R-0306-01


title: liu-00251: TCGA-06-0148-01A-01R-0219-01


title: liu-00251: TCGA-06-0148-01A-05R-0233-01


title: liu-00251: TCGA-06-0148-01A-04R-0233-01


title: liu-00251: TCGA-06-0147-01A-01R-0219-01


title: liu-00251: TCGA-08-0354-01A-01R-0298-01


title: MCF-10A_SNAI1, biological rep2

city: Beijing

first: Zhihua

last: Liu

address: NO.17 Nanli, Panjiayuan Road, Chaoyang District

country: China

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

description: microRNA expression data from MCF-10A transfected with SNAI1

hyb_protocol: Biotinylated miRNA prepared from 1ug total RNA were hybridized for 16h at 48℃ on GeneChip miRNA 2.0 Array. GeneChips were washed and stained in the Affymetrix ® Fluidics Station 450.

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

data_processing: The data were analyzed with Affymetrix® GeneChip® Command Console™ 1.1 using Affymetrix default analysis settings and global scaling as normalization method.

source_name: MCF-10A transfected with SNAI1

label_protocol: Biotinylated miRNA were prepared using a FlashTag™ Biotin RNA Labeling Kit for Affymetrix® GeneChip® miRNA Arrays (Genisphere, FT30AFYB) from 1ug total RNA.

growth_protocol: MCF-10A mammary epithelial cells were cultured according to the manufacturer's instructions.

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

treatment_protocol: SNAI1 or a vector control was introduced into MCF-10A cells, respectively.

tag: strain

value: MCF-10A mammary epithelial cell line


title: liu-00251: TCGA-02-0099-01A-01R-0202-01


title: MCF-10A_Control, biological rep3

description: microRNA expression data from MCF-10A transfected with a vector control

source_name: MCF-10A transfected with a control vector


title: liu-00251: TCGA-02-0111-01A-01R-0280-01


title: MCF-10A_Control, biological rep2


title: liu-00251: TCGA-08-0525-01A-01R-0280-01

value: ANAPLASTIC ASTROCYTOMA


title: MCF-10A_SNAI1, biological rep3


title: MCF-10A_SNAI1, biological rep1


title: liu-00251: TCGA-06-0148-01A-03R-0233-01


title: M2 macrophages (KO)_rep1

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

description: Macrophages derived from KO mice were stimulated with 50 ng/ml of IL-4 for 2 days.

hyb_protocol: Before hybridization, 600 ng labeled cRNA of each product was fragmented and mixed with hybridization buffer according to the manufacturer's protocol (Agilent Technologies). Hybridizations were done for approximately 17h at 65°C. The slides were washed according to the manufacturer's manual, and scanning of microarrays was performed with 3µm resolution using a DNA microarray laser scanner (Agilent Technologies).

scan_protocol: The array was scanned using Agilent G2505C DNA microarray scanner.

data_processing: The image files were extracted using Agilent Feature Extraction software version 10.5.1.1.

organism: Mus musculus

source_name: M2 macrophages derived from p18 (2400001E08Rik) -/- replicate 1

label_protocol: RNA labeling was performed with a Low Input Quick-Amp Labeling Kit (Agilent Technologies). In brief, cDNA was reverse transcribed from 200ng of total RNA with an oligo-dT-T7 promoter primer and AffinityScript-RT. Second strand synthesis was carried out with random hexamers. Fluorescent antisense cRNA was synthesized with cyanine 3-CTP (Cy3-CTP) and T7 polymerase. The fluorescent-labeled antisense cRNA was purified with RNeasy columns (Qiagen) according to manufacturer's protocols and resuspended in water. The purified products were quantified at A552nm for Cy3-CTP with Agilent 2100 Bioanalyzer (Agilent Technologies).

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

treatment_protocol: Bone marrow cells from each mouse were cultured with L929 sup. for 6 days. They are simulated with 20 ng/ml IFNg and 100 ng/ml LPS (M1), or 50 ng/ml IL-4 (M2) for 2 days. Torin1 treatment was done with IL-4 stimulation in one sample.

tag: genotype

tag: age

value: 10 week-old

tag: treatment


title: Torin1-treated M2 macrophages (WT)_rep1

description: Macrophages derived from WT mice were treated with 50 ng/ml of IL-4 and 250 nM of Torin1 for 2 days.

source_name: Wild type M2 macrophages treated with Torin1 replicate 1

value: wild type


title: liu-00251: TCGA-06-0397-01A-01R-0280-01


title: MCF-10A_Control, biological rep1


title: liu-00251: TCGA-06-0410-01A-01R-0280-01


title: liu-00251: TCGA-08-0516-01A-01R-0280-01


title: liu-00251: TCGA-06-0139-01A-01R-0219-01


title: M2 macrophages (WT)_rep1

description: Macrophages derived from WT mice were stimulated with 50 ng/ml of IL-4 for 2 days.

source_name: M2 macrophages derived from wild type replicate 1


title: liu-00251: TCGA-06-0178-01A-01R-0233-01


title: liu-00251: TCGA-06-0174-01A-01R-0233-01


title: huES9_WTdox_2

city: Philadelphia

first: daniel

last: beiting

state: PA

address: 380 S. University Ave

department: Pathobiology

institute: University of Pennsylvania

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were quantile normalized without background subtraction using Illumina GenomeStudio V1.8

label_protocol: Biotin labeled complementary RNA (cRNA) was made using the EpiCentre Nano Total-Amp kit

growth_protocol: Human ESCs (HUES-7, HUES-9) and human induced pluripotent stem cells were cultured on MEFs at 4% oxygen and passaged manually. To support differentiation, the medium, which lacked β-FGF and contained with 50ng/mL BMP4, 1 µM A83-01 (Tocris), and 0.1 µM PD173074 (Tocris) (B/A/P), was added the next day and refreshed every 48 hours for the course of the differentiation.

extract_protocol: RNA was extracted from individual wells of 6-well plate  using Trizol (Invitrogen)

treatment_protocol: Undifferentiated HUES9 containing the lncRHOXF1 and rtTA3 cDNAs inserted into the AAVS locus of chromosome 19 were used in overexpression experiments. Cells were treated with doxycycline for 7 days.

tag: transgene

value: Wild type with dox

value: doxycycline


title: M1 macrophages (WT)_rep1

description: Macrophages derived from WT mice were stimulated with 20 ng/ml of IFNg and 100 ng/ml of LPS for 2 days.

source_name: M1 macrophages derived from wild type replicate 1


title: huES9_WTdox_1


title: huES9_clone28_untreated_2

value: Clone 28 overexpression no dox

value: untreated


title: liu-00251: TCGA-02-0023-01B-01R-0298-01

value: GLIOBLASTOMA MULTIFORME

value: Brain

value: GBM


title: huES9_clone28_untreated_1


title: liu-00251: TCGA-02-0115-01A-01R-0202-01

value: NOT SPECIFIED


title: SIVneg sooty mangabey, BCG stimulated, 4h (FJa1-B-4h)

city: Seattle

first: Donald

last: Sodora

state: WA

address: 307 Westlake Ave N Ste. 500

institute: Center for Infectious Disease Research

hyb_protocol: Hybridization at 65'C for 16 hours.

scan_protocol: Scanning was done using the nCounter GEN2 Digital Analyzer at High data resolution of 280 Field of Views (FOV)

data_processing: Using nCounter Digital Analyser. See manufacturer's website (http://www.nanostring.com)

organism: Cercocebus atys

source_name: PBMC

growth_protocol: All samples are immediately ex-vivo.

extract_protocol: Following incubation, cells from triplicate wells were pooled and pelleted. 100ul lysis buffer (RLT; Qiagen with Beta-mercaptoethanol), was used to wash/lyse remaining (adherent) cells in the plates before adding it to the cell pellet.  All disrupted cell pellets were stored at -80°C until RNA extraction.

treatment_protocol: PBMC extracted from a Ficoll gradient were resuspended in RPMI+10%FBS.  One million cells were plated in triplicate in 96-well flat-bottom plate and rested 1h at 37°C+5% CO2.  1x106 CFU BCG (RPMI+10% FBS; enumerated via OD600) was then added in 100ul, bringing all final volumes to 200ul.  PBMC were incubated with BCG for 4 hours at 37°C with 5% CO2.

tag: cell type

value: PBMC

tag: status

value: SIV negative

tag: sample


title: SIV+ sooty mangabey, unstimulated (FOo-U-4h)

value: SIV positive


title: SIV+ sooty mangabey, BCG stimulated, 4h (FZs-B)


title: SIV+ sooty mangabey, unstimulated (FZs-U)


title: SIVneg sooty mangabey, unstimulated (FSo-U-4h)


title: SIVneg sooty mangabey, unstimulated (FJa1-U-4h)


title: SIV+ sooty mangabey, BCG stimulated, 4h (FOo-B-4h)


title: SIVneg sooty mangabey, BCG stimulated, 4h (FOz-B)


title: SIVneg sooty mangabey, unstimulated (FOz-U)


title: huES9_clone28_dox_1

value: Clone 28 overexpression with dox


title: SIVneg sooty mangabey, BCG stimulated, 4h (FHq-B)


title: SIVneg sooty mangabey, unstimulated (FHq-U)


title: SIVneg sooty mangabey, BCG stimulated, 4h (FSo-B-4h)


title: SIV+ sooty mangabey, BCG stimulated, 4h (FDu-B)


title: liu-00251: TCGA-02-0456-01A-01R-0280-01


title: liu-00251: TCGA-02-0016-01A-01R-0298-01


title: SIV+ sooty mangabey, unstimulated (FDu-U)


title: HIVneg donor, unstimulated (S237-U-4h)

value: HIVneg donor

value: BCG/Mtb naïve


title: liu-00251: TCGA-02-0075-01A-01R-0202-01


title: liu-00251: TCGA-02-0326-01A-01R-0280-01


title: liu-00251: TCGA-06-0190-01A-01R-0233-01

value: MALIGNANT

value: OVERLAPPING LESION OF BRAIN


title: liu-00251: TCGA-06-0140-01A-01R-0219-01


title: liu-00251: TCGA-06-0646-01A-01R-0306-01

value: TEMPORAL LOBE


title: HIVneg donor, BCG stimulated for 4h (S233-B-4h)


title: huES9_clone28_dox_2


title: liu-00251: TCGA-02-0033-01A-01R-0177-01

value: OCCIPITAL LOBE


title: HIVneg donor, BCG stimulated for 4h (S237-B-4h)


title: HIVneg donor, unstimulated (S233-U-4h)


title: liu-00251: TCGA-02-0102-01A-01R-0202-01


title: HIV infected donor, BCG stimulated for 4h (H087-B-4h)

tag: gender

value: female

value: HIV infected donor

value: Female, ARV-naïve, BCG/Mtb naïve, caucasian


title: HIV infected donor, unstimulated (H087-U-4h)


title: HIVneg donor, BCG stimulated for 4h (S169-B-4h)


title: liu-00251: TCGA-02-0043-01A-01R-0177-01

value: GLIOBLASTOMA MULTIFORME


title: HIVneg donor, unstimulated (S169-U-4h)


title: HIV infected donor, BCG stimulated for 4h (H086-B-4h)

value: male

value: Male, ARV-naïve, BCG/Mtb naïve, African American


title: HIV infected donor, BCG stimulated for 4h (H084-B-4h)

value: Female, ARV-naïve, BCG/Mtb naïve, American Indian


title: HIV infected donor, unstimulated (H086-U-4h)

value: PBMC


title: liu-00251: TCGA-08-0517-01A-01R-0280-01

value: Brain

value: GBM

value: GLIOMA MIXED

value: FRONTAL LOBE


title: MCF-10A_Control, biological rep3

description: gene expression data from MCF-10A transfected with a vector control

hyb_protocol: Following fragmentation, 5ug of cRNA were hybridized for 16h at 45℃ on GeneChip HG-U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix ® Fluidics Station 450.

label_protocol: Biotinylated cRNA were prepared using 1 Poly-A RNA Control Kit (Affymetrix, P/N 900433) and MessageAmp™ Premier RNA Amplification Kit (Ambion,＃1792) from 1ug total RNA, according to the manufacturer's instructions.

value: MCF-10A mammary epithelial cell line


title: MCF-10A_Control, biological rep2


title: MCF-10A_SNAI1, biological rep3

description: gene expression data from MCF-10A transfected with SNAI1


title: MCF-10A_SNAI1, biological rep2


title: MCF-10A_SNAI1, biological rep1


title: HIV infected donor, unstimulated (H083-U)

value: Male, ARV-naïve, BCG/Mtb naïve, Caucasian


title: HIV infected donor, BCG stimulated for 4h (H083-B)


title: HIV infected donor, unstimulated (H084-U-4h)


title: HIVneg donor, unstimulated (SBRI333-U)

value: HIVneg donor

value: BCG/Mtb naïve


title: Myc83

city: Bethesda

first: Maxwell

last: Lee

address: Building 37, Room 5120

department: CCR

institute: National Cancer Institute, NIH

description: Derived from mammary tumor arising in MMTV-Myc transgenic mouse

hyb_protocol: As per Affy protocol

scan_protocol: ffymetrix GeneChip scanner 3000

data_processing:
Affymetrix GCOS software
probe group file: moex-1_0-st-v1.r2.pgf
meta-probeset file: MoEx-1_0-st-v1.r2.dt1.mm9.core.mps

source_name: GEM

label_protocol: Total RNA (1 μg) was reverse transcribed with T7-oligo(dT) primer and labeled with biotin using Affymetrix One Cycle Target Labeling kit

growth_protocol: M6 and M6C cells derived from the C3(1)/Tag model and DB7 cells derived from the MMTV-PyMT model were cultured in Dulbecco’s Modified Eagle’s Media (DMEM), high glucose, with 10% (v/v) fetal calf serum (FCS), Pen/strep and 100 mM Na Pyruvate; 6DT1, Myc83  and cMyc cells  from the MMTV-cMyc model were cultured in DMEM low glucose, and 10% FCS with Pen/Strep.  MVT1 and MVT2 cells derived from the MMTV-cMyc;MMTV-VEGF model  and 69 and 780 cells  from the WAP-cre; BRCA-/-;p53+/- model were cultured in DMEM (high glucose) with 10% FBS, glutamine, Pen/Strep and MEM Non-Essential Amino Acids. 2508 and 2855 cells  from the MMTV-Wnt model were cultured in DMEM/F12 with 2.5 % fetal bovine serum, 12 ng/ml of insulin, 10 ng/ml epidermal growth factor and Pen/Strep.  p877 and p1522 cells derived from the MMTV-cre; p53+/- model were cultured in DMEM (high glucose) with 10% FCS and Pen/Strep.

extract_protocol: The total RNA containing the miRNA species were extracted from tumor samples using a mirVana miRNA Isolation kit (Ambion, Austin, TX, USA).

tag: origin

value: genetically engineered mouse


title: LNCaP-abl cells with si TRIM24 vehicle treated rep1

city: Boston

first: Anna

middle: C

last: Groner

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

hyb_protocol: The fragmented cRNA was hybridized to a HG U133 Plus 2.0 array at 45°C, overnight, in the presence of several biotinylated control oligonucleotides (for quality control).

scan_protocol: After hybridization, bound cRNA was fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors were then added using biotinylated anti-streptavidin antibody and additional SAPE. Each cRNA was excited using a confocal laser scanner, according the Affymetrix protocol.

data_processing: All gene expression data was normalized and log-scaled using the RMA algorithm (RMAExpress) and the RefSeq probe definition.

source_name: LNCaP-abl, siTRIM24, vehicle-treated, rep1

label_protocol: Isolated total RNA was processed by the Dana-Farber Cancer Institute (DFCI) Microarray Core Facility (Boston, MA) according to the standard Affymetrix protocol. In short, cDNA was synthesized using T7 Oligo (dT) primers. Using the double stranded cDNA as a template, biotinylated cRNA was then generated in an in vitro transcription reaction.

growth_protocol: Routinely, LNCaP cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS), penicillin (100 μg/ml), streptomycin (100 units/ml) and L-glutamine (2 mM), at 37 °C with an atmosphere of 5% CO2. For experimental conditions, cells were grown for 48h under hormone-starvation conditions using the media conditions described above but subsituting FBS for charcoal/dextran-treated FBS (CDT). Cells were then treated with vehicle (ETOH) or 10 nM DHT for 24h.

extract_protocol: Total RNA was isolated using the RNAeasy Plus Mini purification kit procedure (Qiagen) according to the manufacturer’s instructions.

treatment_protocol: LNCaP and LNCaP-abl were transfected with siRNA targeting either control or TRIM24 for 48h. The cells were additionally stimulated with 10nM DHT or vehicle for 24h.

tag: cell line

value: LNCaP-abl

tag: transfection

value: vehicle (ETOH)


title: MVT2

description: Derived from mammary tumor arising in MMTV-Myc-VEGF bitransgenic mouse


title: MCF-10A_Control, biological rep1


title: HIV infected donor, BCG stimulated for 4h (H082-B)

value: HIV infected donor


title: NMUMG

description: Derived by outgrowth culture from adult Namru mammary gland

source_name: Immortalized cell line

value: Immortalized cell line


title: p1522

description: Derived from outgrowth froma  mammary tumor arising in p53-/-;MMTV-cre GEM.


title: LNCaP-abl cells with si control vehicle treated rep3

source_name: LNCaP-abl, sicontrol, vehicle-treated, rep3

value: sicontrol


title: LNCaP-abl cells with si control vehicle treated rep2

source_name: LNCaP-abl, sicontrol, vehicle-treated, rep2


title: LNCaP-abl cells with si TRIM24 vehicle treated rep2

source_name: LNCaP-abl, siTRIM24, vehicle-treated, rep2


title: LNCaP-abl cells with si control vehicle treated rep1

source_name: LNCaP-abl, sicontrol, vehicle-treated, rep1


title: LNCaP cells with si TRIM24 DHT treated rep3

source_name: LNCaP, siTRIM24, DHT-treated, rep3

value: LNCaP

value: 10nM DHT


title: M6

description: Cell line derived from a mammary tumor arising in a C3(1)Tag transgenic mouse.


title: HIV infected donor, unstimulated (H082-U)

value: PBMC

value: male

value: Male, ARV-naïve, BCG/Mtb naïve, African American


title: F311

description: Sarcomatoid clone derived from a transplantable ER-negative mammary adenocarcinoma (M3) that arose spontaneously in a Balb/c mouse.  F3II described as giving rise to sarcomatoid carcinomas

source_name: Spontaneous tumor

value: Spontaneous tumor


title: HIV infected donor, BCG stimulated for 4h (H081-B)


title: TSA

description: Derived from a spontaneous BALB/c mammary tumor


title: LNCaP cells with si TRIM24 DHT treated rep2

source_name: LNCaP, siTRIM24, DHT-treated, rep2


title: LNCaP cells with si TRIM24 DHT treated rep1

source_name: LNCaP, siTRIM24, DHT-treated, rep1


title: MVT1


title: LNCaP-abl cells with si TRIM24 vehicle treated rep3

source_name: LNCaP-abl, siTRIM24, vehicle-treated, rep3


title: EPH4

description: Eph4 cells were generated by infecting spontaneously immortalized Ep1 cells (Reichmann 1992) with empty retroviral vector pHMW and subcloning in presence of hygromycin (Fialka, 1996).  Ep1 was a subclone of IM-2  (Reichmann 1989) which was derived from a mid-pregnant Balb/c mouse by spontaneous immortalization.


title: HIVneg donor, BCG stimulated for 4h (SBRI333-B)


title: HIV infected donor, unstimulated (H081-U)


title: LNCaP cells with si control DHT treated rep3

source_name: LNCaP, sicontrol, DHT-treated, rep3


title: EMT6

description: Derived from primary mammary tumor KHJJ arising in BALB/c mouse after implantation of a hyperplastic alveolar nodule.


title: M6C

description: Derived from lung metastasis of M6 cell line derived from a mammary tumor arising in a C3(1)Tag transgenic mouse.


title: HIVneg donor, BCG stimulated for 4h (SBRI111-B)


title: HIVneg donor, unstimulated (SBRI111-U)


title: LNCaP cells with si control DHT treated rep2

source_name: LNCaP, sicontrol, DHT-treated, rep2


title: HIVneg donor, BCG stimulated for 4h (SBRI84-B)


title: LNCaP cells with si control DHT treated rep1

source_name: LNCaP, sicontrol, DHT-treated, rep1


title: HIVneg donor, BCG stimulated for 4h (S185-B-4h)


title: D20R

description: Derived from spontaneous mammary tumor originating from a D2 hyperplastic alveolar nodule line (Rak et al) characterized for metastatic ability


title: LNCaP cells with si TRIM24 vehicle treated rep1

source_name: LNCaP, siTRIM24, vehicle-treated, rep1


title: HIVneg donor, unstimulated (SBRI84-U)

source_name: PBMC


title: D2A1


title: HIVneg donor, unstimulated (S185-U-4h)


title: HIV infected donor, BCG stimulated for 4h (H080-B-4h)


title: cMyc

description: Derived from mammary tumor arising in MMTV-Myc transgenic mouse similar to Myc83 cells.

source_name: GEM


title: LNCaP cells with si TRIM24 vehicle treated rep3

source_name: LNCaP, siTRIM24, vehicle-treated, rep3


title: 67NR

description: Derived from a spontaneous tumor arising in a BALB/cfC3H mouse; transfected to induce geneticin resistance; described as non-disseminating (see also 4T07 and 4T1)


title: LNCaP cells with si control vehicle treated rep3

source_name: LNCaP, sicontrol, vehicle-treated, rep3


title: HIV infected donor, unstimulated (H080-U-4h)


title: 780

description: Derived from a BRCA-/-;p53+/+; Wap-cre GEM spontaneous tumor.


title: 4T1

description: Derived from spontaneous tumor arising in a BALB/cfCH mouse (same tumor as 67NR); selected as spontaneously resistant to thioguanine; fully metastatic (see also 67NR and 4T07)


title: LNCaP cells with si control vehicle treated rep1

source_name: LNCaP, sicontrol, vehicle-treated, rep1


title: SIV+ sooty mangabey, unstimulated (FYs-U-4h)

value: SIV positive


title: 6DT1


title: LNCaP cells with si control vehicle treated rep2

source_name: LNCaP, sicontrol, vehicle-treated, rep2


title: LNCaP cells with si TRIM24 vehicle treated rep2

source_name: LNCaP, siTRIM24, vehicle-treated, rep2


title: 4T07

description: Derived from spontaneous tumor arising in a BALB/cfC3H mouse (same tumor as 67NR); transfected to induce thioguanine and ouabain resistance; described as disseminating to lung but unable to colonize (see also 67NR and 4T1)


title: SIV+ sooty mangabey, BCG stimulated, 4h (FYs-B-4h)


title: 2508

description: Cell line derived from an invasive carcinoma (ZD2508) arising in an MMTV-Wnt transgenic mouse


title: OSKH 3 iPSC

status: Public on May 26 2016

city: San Francisco

first: Akira

last: Kunitomi

state: CA

address: 1650 Owens Street

institute: The J. David Gladstone Institutes

description: SAMPLE 4

hyb_protocol: 600ng of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25ul containing 25x fragmentation and 10x blocking agent following the manufacturers instructions. On completion of the fragmentation reaction,25ul of 2x GE Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse Gene Expression 8x60K Microarrays (G4852A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505CA) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green. No XDR).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters (protocol:GE1_1105_Oct12 and Grid: 028005_D_F_20131202) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: OSKH  iPSC

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

extract_protocol: RNA was prepared using the Trizol and RNeasy Kit following the manufacturer's manuals.  RNA was quantified using a NanoDrop-1000 Spectrophotometer.

value: induced pluripotent stem cell (iPSC)


title: 2855


title: OSK 2 iPSC

description: SAMPLE 7

source_name: OSK iPSC


title: OSK 3 iPSC

description: SAMPLE 8


title: ESC

description: SAMPLE 1

source_name: B6J-23 ESC

value: Embryonic stem cells (ESC)


title: OSK 1 iPSC

description: SAMPLE 6


title: OSKH 1 iPSC

description: SAMPLE 2


title: OSKH 2 iPSC

description: SAMPLE 3


title: lavar-00111: 674

source_name: Neuroblastoma

tag: diseasestate

value: Neuroblastoma

tag: celltype

value: primary tumor

tag: organismpart

value: Adrenal Gland


title: lavar-00111: 610


title: si-hnRNPK_no dox_2

first: Jin

last: Song

address: No.38 shengmingyuan Road

institute: Beijing Institute of Radiation Medicine

hyb_protocol: Mix samples with reaction systems and treat with GEX-HCB, and then hybridize samples with Sentrix BeadChip. Incubate chip with E1BC buffer at room temperature. Wash chip with High-Temp wash buffer, and then wash chip with E1BC buffer at room temperature for the first time.Wash chip with ethanol, and then with E1BC buffer at room temperature for the second time. Block chip with block E1 buffer and detect the cy3 signal, and then wash withE1BC buffer at room temperature for the third time. Finally, dry the chip with centrifuge.

scan_protocol: Read and extractt image with Illumina BeadArray Reader.

data_processing: Expression profile was quantile normalized and log2 transformed by preprocess Core package

source_name: HepG2_si-hnRNPK_no dox

label_protocol: cDNA was synthesized from RNA and amplificated with Ambion Illumina TotalPrep RNA Amplification Kit, And then, was mixed with GEX-HYB in RNAse-free water.

growth_protocol: HepG2 cells were grown in Dulbecco’s modified Eagle’s medium (DMEM) (Gibco), supplemented with 5% fetal bovine serum (Gibco) and 2 mM L-glutamine (Gibco) at 37℃ with 5% CO2.

extract_protocol: The total RNA was extracted from above cells using the Ultrapure RNA Kit (Dnase I) (CWBIO, Beijing, China).

treatment_protocol: For DOX treatment, exponentially growing HepG2 cells were grown in medium containing 400 nM DOX for 8 or 16 hours till harvested.

value: hepatocellular carcinoma (HCC) cell line

tag: transfected with

value: si-hnRNP K

tag: treated with

value: none (no dox)


title: lavar-00111: 1004


title: si-PSTAR_no dox_3

source_name: HepG2_si-PSTAR_no dox

value: si-PSTAR


title: lavar-00111: NB1464


title: lavar-00111: 622


title: si-PSTAR_dox_3

value: 400 nM doxorubicin (DOX) for 16hrs


title: si-hnRNPK_no dox_1


title: si-hnRNPK_no dox_3


title: lavar-00111: 1stNB802


title: lavar-00111: 603


title: lavar-00111: 1389


title: si-PSTAR_dox_1


title: NC_dox_1

value: si-scramble RNAs


title: si-hnRNPK_dox_1


title: lavar-00111: 1614


title: lavar-00111: 2100


title: si-PSTAR_dox_2


title: si-hnRNPK_dox_3


title: NC_no dox_3

source_name: HepG2_NC_no dox


title: NC_no dox_1


title: lavar-00111: 2172


title: NC_dox_3


title: si-PSTAR_no dox_1


title: si-hnRNPK_dox_2


title: NC_dox_2


title: si-PSTAR_no dox_2


title: lavar-00111: 814


title: NC_no dox_2


title: lavar-00111: SST


title: lavar-00111: 1stNBBI


title: lavar-00111: 1stNB1163


title: lavar-00111: 2722


title: lavar-00111: 1332


title: lavar-00111: 1973


title: lavar-00111: 1105


title: lavar-00111: 1stNB1453


title: lavar-00111: 2097


title: lavar-00111: NB1396


title: lavar-00109: NB755

tag: externalid


title: lavar-00109: NB1957


title: lavar-00111: 1986


title: lavar-00109: NB1603


title: lavar-00109: NB1585


title: lavar-00109: NB1670


title: lavar-00111: 1stNB1870


title: lavar-00109: NB1012


title: lavar-00111: NB1646


title: lavar-00109: NB1840


title: DR229

type: genomic

city: Taichung

first: Yng-Tay

last: Chen

address: No 2 Yude road

department: Department of medical research

country: Taiwan

institute: China Medical University Hospital

description:
treatment: none
fraction: promoter

hyb_protocol: Hybridization was performed with an Affymetrix GeneChip Promoter 1.0R array.

scan_protocol: Array was scanned on an Affymetrix GeneChip Scanner 3000.

data_processing: The resulting CHP files are generated by the Affymetrix Tiling Analysis Software. The file processed data(T2D vs CTL).xlsx contains the regions identified with enriched or depleted methylation, including statistics.

molecule: genomic DNA

label_protocol: not provided

growth_protocol: Peripheral blood leukocytes was collected from patients and control.

extract_protocol: One microgram of genomic DNA was sonicated to produce fragments ranging from 100 to 500 bp.  Then, 3.5 mg (7 mL) of MBD-Biotin Protein was added to 10 mL Dynabeads M-280 Streptavidin according to the manufacturer’s instructions.

treatment_protocol: Genomic DNA was extracted from peripheral blood leukocytes by using the Genomic DNA extraction kit (Qiagen, Valencia, CA, USA), according to the manufacturer’s instructions.

tag: tissue

value: Blood

tag: disease


title: lavar-00109: NB1399


title: DR226

description:
treatment: none
fraction: promoter


title: lavar-00109: NB1332


title: lavar-00109: NB1591


title: lavar-00109: NB1637


title: DN314

description:
treatment: none
fraction: promoter


title: DR278

description:
treatment: none
fraction: promoter


title: lavar-00109: NB1581


title: lavar-00109: NB1870


title: lavar-00109: NB941


title: DN304

description:
treatment: none
fraction: promoter


title: lavar-00109: NB1377


title: lavar-00111: 692


title: lavar-00109: NB1877


title: DR248

description:
treatment: none
fraction: promoter


title: DR265

description:
treatment: none
fraction: promoter


title: lavar-00109: NBBI

value: NBBI


title: lavar-00109: NB2242


title: lavar-00109: NB1345


title: DB7

description: Derived from a transplanted MMTV-PyVT Db mammary tumor (Db) passaged in mammary fat pad.  The PyVT Db is a double mutant of the PyVT that leads to uncoupling from the PI3K pathway.

value: genetically engineered mouse


title: lavar-00109: NB802


title: lavar-00109: NB2247


title: lavar-00109: NB1140


title: lavar-00109: NB1370


title: DN195

description:
treatment: none
fraction: promoter


title: DN313

description:
treatment: none
fraction: promoter


title: lavar-00109: NB1327


title: lavar-00109: NB1519


title: DN301

description:
treatment: none
fraction: promoter


title: lavar-00109: NB1456


title: DN147

description:
treatment: none
fraction: promoter


title: DN093

description:
treatment: none
fraction: promoter


title: DN035

description:
treatment: none
fraction: promoter


title: lavar-00109: NB835


title: lavar-00109: NB1646


title: 27385

description:
treatment: none
fraction: promoter

value: Normal


title: lavar-00109: NBEP

value: NBEP


title: 27237

description:
treatment: none
fraction: promoter


title: 27189

description:
treatment: none
fraction: promoter


title: DN297

description:
treatment: none
fraction: promoter


title: lavar-00109: NB1428


title: 27160

description:
treatment: none
fraction: promoter


title: DN097

description:
treatment: none
fraction: promoter


title: mi_static_4_cells

city: Moscow

first: Maxim

last: Shkurnikov

address: 2 bld. 85, Ugreshkaya st.

country: Russia

institute: SRC Bioclinicum

description: miRNA expression data from CaCo2 cells after 24h in Transwell

hyb_protocol: The samples were hybridized on GeneChip miRNA 4.0 Arrays (Affymetrix) for 16 h at 48°C.

scan_protocol: Arrays were washed to remove nonspecifically bound nucleic acids and stained on Fluidics Station 450 (Affymetrix) and then scanned on Gene- Chip Scanner 3000 7G system (Affymetrix).

data_processing: CEL-files were jointly preprocessed in Affymetrix Expression Console (build 1.4.1.46) using RMA-sketch method for Affymetrix HuGene 1.0 ST arrays and RMA+DAGB-Human_only method for Affymetrix miRNA 4.0 arrays.

label_protocol: The procedures for cDNA synthesis and labelling were carried out according to the Ambion WT Expression Kit (Life Technologies, Darmstadt, Germany) using 500 ng total RNA as starting material. ). For miRNA profiling the samples were prepared using FlashTag Biotin HSR RNA Labeling Kit.

growth_protocol: The cells were incubated under conditions for differentiation for 7 days in MEM with 10% FBS, 0.1 mM non-essential aminoacids, 0.1% penicillin-streptomycin (all reagents from Gibco, USA) in 5% CO2, 37° C, changed three times.

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

treatment_protocol: Transwell inserts with CaCo2 monolayers were either kept on the microplate or put into microfluidic chip. The culture medium microcirculation parameters were ±20 kPa and 2 Hz resulting in the pulsatile (0 - 0.85 µl/s) medium flow with mean flow rate of 4.13 μl/min.

value: Transwell


title: lavar-00109: NB603


title: lavar-00109: NB987


title: 27169

description:
treatment: none
fraction: promoter


title: lavar-00109: NB1094_HG_U95Av2


title: lavar-00109: NB1353


title: lavar-00109: NB996


title: lavar-00109: NB1837


title: lavar-00109: NB772


title: lavar-00109: NB2019


title: mi_chip_3_cells

description: miRNA expression data from CaCo2 cells after 24h in microfluidic chip

value: Chip


title: mi_chip_2_cells


title: lavar-00109: NB692


title: mi_static_5_cells


title: mi_static_6_cells


title: OvoAexpressingPGC_rep3

city: Tsukuba

first: Yuko

last: Shinozuka

state: Ibaraki-ken

address: Tennoudai 1-1-1

department: Life Science Center of TARA

institute: University of Tsukuba

description: Gene expression profile in OvoA-expressing PGCs in Drosophila stage 16 embryo.

hyb_protocol: 1.65 ug of Cy3-labelled cDNA was fragmented at 60°C for 30 min in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 µl of 2x Agilent hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Microarrays for 17 hr at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed following the manufacturers instructions.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters (protocol AgilentHD_GX_1Color and Grid: 021791_D_F_20120509) to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Drosophila melanogaster

source_name: OvoA-expressing PGCs, St.16, replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cDNA was prepared from 10 ng total RNA using the Ovation PicoSL WTA System (NuGEN) and NimbleGen One-Color Labeling Kit (Roche) following the manufacture's instructions.

extract_protocol: Total RNAs were extracted using the RNeasy plus micro Kit (QIAGEN) following the manufacture's instructions. The protocol includes an on-column DNase digestion.

treatment_protocol: OvoA-expressing PGCs and control PGCs were isolated from the stage 16 embryos carrying the transgene, EGFP-vasa, which expresses GFP in specifically and continuously in the germline, by using fluorescence-activated cell sorting (FACS)

value: primordial germ cells

tag: developmental stage

value: St.16 embryo


title: mi_chip_1_cells


title: lavar-00109: NB1396

value: Neuroblastoma

value: primary tumor


title: OvoAexpressingPGC_rep2

source_name: OvoA-expressing PGCs, St.16, replicate 2


title: ControlPGC_rep2

description: Gene expression profile in control PGCs in Drosophila stage 16 embryo.

source_name: Control PGCs, St.16, replicate 2


title: OvoAexpressingPGC_rep1

source_name: OvoA-expressing PGCs, St.16, replicate 1


title: lavar-00109: NB1618

value: Adrenal Gland


title: lavar-00109: NB2097


title: lavar-00109: NB1163


title: lavar-00109: NB1614


title: lavar-00109: NB1564


title: lavar-00109: NB674


title: lavar-00109: NB1153


title: lavar-00109: NBSilv

value: NBSilv


title: lavar-00109: NB1615


title: Normal counterpart of CRC oranoid 31

city: Tokyo

first: Mariko

last: Shimokawa

address: 35, Shinanomachi, Shinjuku-Ku

institute: Keio University

description: Batch 1

hyb_protocol: standard Affymetrix procedures

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G

data_processing: The data was analyzed with RMA for normalization. A batch effect was compensated by ComBat algorithm. The pre-processed data was median-centered.

source_name: Patient 42

label_protocol: standard Affymetrix procedures

extract_protocol: Total RNA was extracted using Rneasy Plus Mini Kit according to the manufacturer's instructions.

value: Large intestine


title: OSKH 4 iPSC

description: SAMPLE 5

tag: strain

value: induced pluripotent stem cell (iPSC)


title: Normal counterpart of CRC oranoid 5

description: Batch 1

source_name: Patient 17


title: Normal counterpart of CRC oranoid 12

description: Batch 1

source_name: Patient 23


title: Normal counterpart of Adenoma oranoid 7

description: Batch 1

source_name: Patient 7


title: ControlPGC_rep3

source_name: Control PGCs, St.16, replicate 3


title: ControlPGC_rep1

source_name: Control PGCs, St.16, replicate 1


title: m_Transwell_6_cells

description: Gene expression data from CaCo2 cells after 24h in Transwell


title: CRC organoid 31

description: Batch 1


title: CRC organoid 29

description: Batch 2

source_name: Patient 40


title: m_Transwell_5_cells


title: Normal counterpart of CRC oranoid 25

description: Batch 2

source_name: Patient 36


title: CRC organoid 27

description: Batch 2

source_name: Patient 38


title: CRC organoid 26 subclone a

description: Batch 2

source_name: Patient 37


title: Normal counterpart of CRC oranoid 24

description: Batch 2

source_name: Patient 35


title: m_Chip_3_cells

description: Gene expression data from CaCo2 cells after 24h in microfluidic chip


title: m_Chip_2_cells


title: CRC organoid 28

description: Batch 1

source_name: Patient 39


title: Normal counterpart of Serrated lesion organod 1

description: Batch 1

source_name: Patient 11


title: m_Transwell_4_cells


title: lavar-00111: 1stNB1456

source_name: Neuroblastoma


title: m_Chip_1_cells


title: CRC organoid 25 subclone b

description: Batch 1


title: CRC organoid 24 subclone c

description: Batch 1


title: CRC organoid 23 subclone c

description: Batch 1

source_name: Patient 34


title: CRC organoid 22

description: Batch 2

source_name: Patient 33


title: CRC organoid 25 subclone c

description: Batch 1


title: CRC organoid 26 subclone b

description: Batch 2


title: CRC organoid 23 subclone b

description: Batch 1


title: CRC organoid 23 subclone a

description: Batch 1


title: CRC organoid 17 subclone b

description: Batch 1

source_name: Patient 28


title: CRC organoid 25 subclone a

description: Batch 1


title: CRC organoid 20

description: Batch 1

source_name: Patient 31


title: CRC organoid 18

description: Batch 2

source_name: Patient 29


title: CRC organoid 24 subclone b

description: Batch 1


title: CRC organoid 10

description: Batch 2

source_name: Patient 21


title: CRC organoid 17 subclone a

description: Batch 1


title: CRC organoid 21

description: Batch 2

source_name: Patient 32


title: CRC organoid 16

description: Batch 2

source_name: Patient 27


title: CRC organoid 15

description: Batch 2

source_name: Patient 26


title: CRC organoid 14

description: Batch 1

source_name: Patient 25


title: CRC organoid 12

description: Batch 1

source_name: Patient 23


title: CRC organoid 9

description: Batch 2

source_name: Patient 8


title: CRC organoid 13

description: Batch 1

source_name: Patient 24


title: CRC organoid 4

description: Batch 2

source_name: Patient 16


title: CRC organoid 2

description: Batch 2

source_name: Patient 14


title: CRC organoid 5

description: Batch 1

source_name: Patient 17


title: CRC organoid 6

description: Batch 2

source_name: Patient 18


title: CRC organoid 8

description: Batch 2

source_name: Patient 20


title: CRC organoid 3

description: Batch 2

source_name: Patient 15


title: CRC organoid 11

description: Batch 1

source_name: Patient 22


title: CRC organoid 1 subline b

description: Batch 2

source_name: Patient 13


title: CRC organoid 1 subline a

description: Batch 2


title: CRC organoid 7

description: Batch 1

source_name: Patient 19


title: Adenoma organoid 10

description: Batch 2

source_name: Patient 10


title: Serrated lesion organod 2

description: Batch 2

source_name: Patient 12


title: CRC organoid 19

description: Batch 2

source_name: Patient 30


title: Adenoma organoid 9

description: Batch 1

source_name: Patient 9


title: lau-00212: 386AT

source_name: patient 14

value: Osteoblastoma

tag: follow up months

tag: clinicaltreatment

value: Pre-operative Chemotherapy

tag: Sex

value: male

tag: age

tag: diseasequalifier

value: Nonmetastatic

value: no evidence of disease

tag: histologicresponse

value: good responder

value: Osteoblast

tag: samplingtime

value: definitive surgery

source_name: Reference

value: normal


title: lau-00212: 204AT

source_name: patient 7

tag: diseasestate

value: female

value: poor responder

value: Initial biopsy


title: Serrated lesion organod 1 subclone b

description: Batch 1

source_name: Patient 11


title: lau-00212: 410AT

source_name: patient 6

value: alive with disease


title: lau-00212: 452AT


title: Adenoma organoid 8

description: Batch 2

source_name: Patient 8


title: lau-00212: 197AT

source_name: patient 1


title: lau-00212: 394AT

source_name: patient 5

value: died of disease


title: Adenoma organoid 7

description: Batch 1

source_name: Patient 7


title: lau-00212: 345AT


title: lau-00212: 221AT


title: lau-00212: 680AT

source_name: patient 23


title: lau-00212: 464AT

source_name: patient 16


title: lau-00212: 342AT

source_name: patient 13


title: lau-00212: 392AT

source_name: patient 15


title: Adenoma organoid 4 subclone a

description: Batch 1

source_name: Patient 4


title: Adenoma organoid 3 subclone b

description: Batch 1

source_name: Patient 3


title: Adenoma organoid 6

description: Batch 1

source_name: Patient 6


title: lau-00212: 654AT

source_name: patient 22


title: Adenoma organoid 5

description: Batch 2

source_name: Patient 5


title: Serrated lesion organod 1 subclone a

description: Batch 2


title: Adenoma organoid 2

description: Batch 2

source_name: Patient 2


title: Adenoma organoid 3 subclone a

description: Batch 1


title: lau-00212: 278AT-R

source_name: patient 3

source_name: Reference


title: lau-00212: 308AT


title: lau-00212: 241AT

source_name: patient 8


title: lau-00212: 274AT

source_name: patient 10


title: lau-00212: 479AT

source_name: patient 17


title: lau-00212: 760AT

source_name: patient 26


title: lau-00212: 299AT

source_name: patient 11

value: Metastatic


title: lau-00212: 591AT

source_name: patient 21


title: lau-00212: 300AT

source_name: patient 12


title: lau-00212: 771AT

source_name: patient 28


title: lau-00212: 545AT

source_name: patient 20


title: lau-00212: 691AT

source_name: patient 24


title: lau-00212: 761AT

source_name: patient 27


title: V156D mutant

city: Newcastle Upon Tyne

first: Katarzyna

last: Pirog

address: Central Parkway

department: Institute of Genetic Medicine

country: United Kingdom

institute: Newcastle University

description: gene expression data from chondrocytes at 5 days

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

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

source_name: mouse V156D matn1 mutant chondrocytes at 5 days

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: Mice were kept according to best husbandry practice

treatment_protocol: Mice were sacrificed at 5 days by cervical dislocation, the ribs were dissected and chondrocytes released using collagenase treatment

value: cartilage

tag: genotype

value: V156D mutant

value: 5 days


title: wild type

source_name: mouse wild type chondrocytes at 5 days

value: wild type


title: lau-00212: 481AT

source_name: patient 18

value: Osteoblastoma

value: Pre-operative Chemotherapy

value: male

tag: organismpart


title: lau-00212: 311AT

source_name: patient 4

value: Nonmetastatic


title: lau-00212: 289AT

value: Osteoblast


title: lau-00212: 252AT

source_name: patient 9

value: definitive surgery


title: lau-00212: 759AT-R

source_name: patient 25

value: no evidence of disease

value: good responder

source_name: Reference

value: normal


title: lau-00212: 207AT

source_name: patient 2

value: poor responder

value: Initial biopsy


title: lau-00212: 483AT

source_name: patient 19


title: lau-00212: 236AT


title: HL cell line_4

city: Groningen

first: Masoumeh

last: Tayari

address: Hanzeplein 1, , The Netherlands

department: pathology

country: Netherlands

institute: University of medical center Groningen

description:
mRNA and lncRNA expression analysis HL 4
SUP-HD1

hyb_protocol: According to the manufacturer's instructions

scan_protocol: Agilent DNA Microarray Scanner, Agilent Feature Extraction software version 10.7.3.1.

data_processing: GeneSpring GX 12.5 software (Agilent Technologies); quantile normalization without base line transformation.

source_name: HL cell line

label_protocol: Cy3 labelled using 50-100ng total RNA in combination with the LowInput QuickAmp Labelling Kit, Cyanine 3 CTP Dye Pack and RNA Spike-In kit (all Agilent Technologies).

extract_protocol: Standard Trizol RNA isolation (Life Technologies)

tag: cell line

value: HL cell line SUP-HD1


title: Memory-3

description:
mRNA and lncRNA expression analysis_Memory 3
Mem-3

source_name: Memory B cell

value: tonsil

tag: cell type

value: Memory B cell

tag: markers


title: HL cell line_2

description:
mRNA and lncRNA expression analysis HL 2
L428

value: HL cell line L428


title: HL cell line_3

description:
mRNA and lncRNA expression analysis HL 3
L540

value: HL cell line L540


title: Germinal center B cell_3

description:
mRNA and lncRNA expression analysis_GCB 3
GC-3

source_name: Germinal center B cell

tag: tissue

value: Germinal center B cell


title: Germinal center B cell_1

description:
mRNA and lncRNA expression analysis_GCB 1
GC-1


title: Naive-2

description:
mRNA and lncRNA expression analysis_Naive 2
Naive-2

source_name: Naive B cell

value: Naive B cell

value: CD19+, IgD+


title: Memory-2

description:
mRNA and lncRNA expression analysis_Memory 2
Mem-2


title: Naive-1

description:
mRNA and lncRNA expression analysis_Naive 1
Naive-1


title: HL cell line_1

description:
mRNA and lncRNA expression analysis HL 1
L1236

value: HL cell line L1236


title: YFP-negative rep3

status: Public on May 25 2016

city: Kobe

first: Yuki

last: Kondo

address: 1-1 Rokkodai-cho, Nada-ku

department: Graduate School of Science

institute: Kobe University

hyb_protocol: Hybridization, washing, staining procedures were conducted with Fluidics Station 450 as described in the GeneChip Expression Analysis Techinical Manual (Affymetrix).

scan_protocol: Scanning procedure ws conducted with GeneChip Scanner 3000 7G as described in the GeneChip Expression Analysis Techinical Manual (Affymetrix).

data_processing: RMA algorithm with the Command Console software

organism: Arabidopsis thaliana

source_name: SEOR1pro::SEOR1-YFP, 6-day-old seedlings, cotyledons, protoplasts

label_protocol: Biotinylated cRNA was prepared from total RNA with GeneChip One-Cycle Target Labeling and Control Reagents (Affymetrix).

growth_protocol: Arabidopsis seeds were sterilized with sodium hypochlorite for 5 min, and then washed with sterile water. These seeds were grown with MS liquid medium at 22ºC under the continuous light conditions for 6 days.

extract_protocol: Total RNA was extracted with Rneasy Plant Micro Kit (QIAGEN). Extracted RNA was amplified with Amplification Ovation RNA Amplification System V2 (NuGEN), and then purified using MinElute Reaction Cleanup Kit (QIAGEN).

treatment_protocol: SEOR1pro::SEOR1-YFP cotyledons were cultured with the induction medium containing 2,4-D (1.25 mg/L), kinetin (0.25 mg/L), and bikinin (10 μM). Protoplasts were extracted from samples cultured for 72 hours.

value: cotyledons

tag: time

value: induction after 72h


title: HL cell line_5

description:
mRNA and lncRNA expression analysis HL 5
KM-H2

value: HL cell line KM-H2


title: Naive-3

description:
mRNA and lncRNA expression analysis_Naive 3
Naive-3


title: NLPHL cell line

description:
mRNA and lncRNA expression analysis_NLPHL
DEV

source_name: NLPHL cell line

value: NLPHL cell line DEV


title: Memory-1

description:
mRNA and lncRNA expression analysis_Memory 1
Mem-1


title: YFP-positive rep1

value: phloem


title: YFP-negative rep2


title: YFP-positive rep2


title: YFP-negative rep1


title: YFP-positive rep3


title: apl rep3

description:
apl 72h
Aragene-0598

data_processing: RMA algorithm with Command Console software

source_name: apl, 6-day-old seedlings, cotyledons

extract_protocol: Total RNA was extracted with TRIzol (Invitrogen) and purified with Rneasy Micro Kit (QIAGEN).

treatment_protocol: WT and apl mutants cotyledons were cultured with the induction medium containing 2,4-D (1.25 mg/L), kinetin (0.25 mg/L), and bikinin (10 μM). Samples were collected at 72 hours after induction.

value: apl

value: 6 day-old


title: apl rep1

description:
apl 72h
Aragene-0594


title: WT rep2

description:
WT 72h
Aragene-0595

source_name: Col-0, 6-day-old seedlings, cotyledons

tag: cultivar

value: wildtype


title: WT rep3

description:
WT 72h
Aragene-0597


title: Germinal center B cell_2

description:
mRNA and lncRNA expression analysis_GCB 2
GC-2


title: apl rep2

description:
apl 72h
Aragene-0596


title: WT rep1

description:
WT 72h
Aragene-0593


title: WB_COPD_PT_153

city: Vancouver

first: Bruce

middle: Maxwell

last: McManus

state: BC

address: 1081 Burrard Street

department: UBC James Hogg Research Centre

country: Canada

institute: PROOF Centre of Excellence

hyb_protocol: Affymetrix GeneTitan Hybridization, Wash and Stain Kit for WT Array Plates (Part# 901622)

scan_protocol: Affymetrix GeneChip Command Console (AGCC) version 4.1.2.1567G for scanning, image acquisition and image processing on the Affymetrix GeneTitan Multi-Channel(MC) Instrument.

data_processing: RMA normalization and batch corrected with combat Bioconductor package

source_name: PAXgene whole blood mRNA

label_protocol: Affymetrix GeneChip HT WT Terminal Labeling Kit (Part# 901648)

extract_protocol: Qiagen PAXgene Blood miRNA Kit (Cat# 763134), automated processing using the Qiagen QIAcube robotic workstation (Cat# 9001292). Protocol to amplify RNA-Ambion WT Expression RNA Amplification Kit (Part# 4440536)

tag: disease

value: COPD

value: F

tag: prednisone status

tag: cell prop. granulocyte

tag: cell prop. monocyte

tag: cell prop. b lymphocyte

tag: cell prop. cd4 t lymphocyte

tag: cell prop. cd8 t lymphocyte

tag: cell prop. nk lymphocyte


title: WB_COPD_PT_523

tag: age

tag: Sex

value: M


title: WB_COPD_PT_446


title: WB_COPD_PT_221


title: WB_COPD_PT_984


title: WB_COPD_PT_343


title: WB_COPD_PT_617


title: WB_COPD_PT_838


title: WB_COPD_PT_483


title: WB_COPD_PT_184


title: WB_COPD_PT_848


title: WB_COPD_PT_375


title: WB_COPD_PT_314


title: WB_COPD_PT_330


title: WB_COPD_PT_094


title: WB_COPD_PT_545


title: WB_COPD_PT_329


title: WB_COPD_PT_962


title: WB_COPD_PT_623


title: WB_COPD_PT_210


title: WB_COPD_PT_924


title: WB_COPD_PT_066


title: WB_COPD_PT_183


title: WB_COPD_PT_198


title: WB_COPD_PT_158


title: WB_COPD_PT_422


title: WB_COPD_PT_721


title: WB_COPD_PT_571


title: WB_COPD_PT_720


title: WB_COPD_PT_009


title: WB_COPD_PT_844


title: WB_COPD_PT_940


title: WB_COPD_PT_942


title: WB_COPD_PT_451


title: WB_COPD_PT_888


title: WB_COPD_PT_378


title: WB_COPD_PT_639


title: WB_COPD_PT_774


title: WB_COPD_PT_516


title: WB_COPD_PT_324


title: WB_COPD_PT_976


title: WB_COPD_PT_570


title: WB_COPD_PT_928


title: WB_COPD_PT_978


title: WB_COPD_PT_539


title: WB_COPD_PT_861


title: WB_COPD_PT_124


title: WB_COPD_PT_356


title: WB_COPD_PT_126


title: WB_COPD_PT_080


title: WB_COPD_PT_135


title: WB_COPD_PT_193


title: WB_COPD_PT_486


title: WB_COPD_PT_601


title: WB_COPD_PT_270


title: WB_COPD_PT_840


title: WB_COPD_PT_054


title: WB_COPD_PT_842


title: WB_COPD_PT_638


title: WB_COPD_PT_832


title: WB_COPD_PT_268


title: WB_COPD_PT_366


title: WB_COPD_PT_543


title: WB_COPD_PT_817


title: WB_COPD_PT_131


title: WB_COPD_PT_796


title: WB_COPD_PT_433


title: WB_COPD_PT_856


title: WB_COPD_PT_085


title: WB_COPD_PT_707


title: WB_COPD_PT_964


title: WB_COPD_PT_596


title: WB_COPD_PT_119


title: WB_COPD_PT_312


title: WB_COPD_PT_614


title: WB_COPD_PT_950


title: WB_COPD_PT_383


title: WB_COPD_PT_421


title: WB_COPD_PT_095


title: WB_COPD_PT_325


title: WB_COPD_PT_170


title: WB_COPD_PT_986


title: WB_COPD_PT_594


title: WB_COPD_PT_290


title: WB_COPD_PT_958


title: WB_COPD_PT_224


title: WB_COPD_PT_900


title: WB_COPD_PT_439


title: WB_COPD_PT_540


title: WB_COPD_PT_103


title: WB_COPD_PT_160


title: WB_COPD_PT_299


title: WB_COPD_PT_297


title: WB_COPD_PT_722


title: WB_COPD_PT_808


title: OCI-Ly10 shOCA-B DOX Treated - 2 days - mAdbID:118691

first: Louis

middle: M.

last: Staudt

address: 9000 Rockville Pike, Bldg 10, Rm 4N114

department: Lymphoid Malignancies Branch

institute: National Cancer Institute

description: mAdb experiment ID: 118691

hyb_protocol: Agilent Hybridization Other: According to the manufacture's recommended protocol (Two-Color Microarray-Based Gene Expression Analysis, Agilent).

scan_protocol: Scan_MicronsPerPixelX: 5 Scan_MicronsPerPixelY: 5 Scan_ScannerName: Agilent Technologies Scanner G2505C US45102888 Agilent Scanning Protocol Other: Arrays were scanned at 5um resolution on an Agilent DNA Microarray Scanner (G2505C, Agilent) using the default settings for 4x44k format two-color arrays.

data_processing:
Agilent Data Processing Protocol
Calculation Method: Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction Software. Spot values were normalized using the default linear-lowess normalization.
FeatureExtractor_Version: 10.1.1.1
Protocol_Name: GE2-v5_10_Apr08 (Read Only)

source_name: OCI-Ly10 shControl DOX Treated - 2 days

label_protocol:
Agilent Labeling-Cy5
Other: Total RNA was reverse transcribed to cDNA using T7 Promoter Primer and MMLV-RT. Then the cDNA was converted to aRNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP (Two-Color Microarray-Based Gene Expression Analysis Protocol, Agilent).

extract_protocol:
TRIzol Extraction Protocol
Other: Total RNA was prepared by the TRIzol method (Invitrogen) and purified using RNeasy Mini columns (Qiagen).

treatment_protocol:
Treatment type: shRNA transduction
Treatment dose: 50 ng/mL
Treatment time: 2 days
In-vitro treatment: Cells were transduced with retroviral vectors expressing shControl. shRNA expression was induced with 50 ng/mL doxycycline for 2 days.
Other: Plasmids: OCT2 was cloned from cDNA from BJAB and OCA-B cDNA purchased from Origene. Both were cloned into the vectors pCMV-TOP and pFlagBiopCMV-TOP(30). Site directed mutations were introduced using the QuikChange Lightning kit from Agilent. shRNAs targeting OCT2 or OCA-B were designed and cloned as double stranded oligonucleotides into a retroviral vector (pRSMX_PuroGFP) for doxycycline-inducible shRNA expression. RNAi sequences used are as follows: OCT2 shRNA#1_1196 5'-GCACAACAGTTACTACCTTAT-3', OCT2 shRNA#2_3410 5'-GGATGCTTCTTTCTCTTCACA-3', OCA-B shRNA_3017 5'-CAGCCAGAAGTACCATTAGG-3'. Because OCT2 shRNA#1 targeted the coding region of OCT2, silent mutations were introduced into the recognition site to allow the shRNA to be rescued by OCT2 constructs. Vectors: The pRSMX-PG vector coexpressing GFP and shRNA was introduced into cells and where required selection was carried out with puromycin. Expression of shRNA was induced by addition of doxycycline (50 ng/mL).

value: ABC DLBCL cells

tag: disease state

value: activated B cell-like (ABC) subtype of diffuse large B cell lymphoma (DLBCL)

source_name: OCI-Ly10 shOCA-B DOX Treated - 2 days

label_protocol:
Agilent Labeling-Cy3
Other: Total RNA was reverse transcribed to cDNA using T7 Promoter Primer and MMLV-RT. Then the cDNA was converted to aRNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP (Two-Color Microarray-Based Gene Expression Analysis Protocol, Agilent).

treatment_protocol:
Treatment type: shRNA transduction
Treatment dose: 50 ng/mL
Treatment time: 2 days
In-vitro treatment: Cells were transduced with retroviral vectors expressing shOCA-B. shRNA expression was induced with 50 ng/mL doxycycline for 2 days.
Other: Plasmids: OCT2 was cloned from cDNA from BJAB and OCA-B cDNA purchased from Origene. Both were cloned into the vectors pCMV-TOP and pFlagBiopCMV-TOP(30). Site directed mutations were introduced using the QuikChange Lightning kit from Agilent. shRNAs targeting OCT2 or OCA-B were designed and cloned as double stranded oligonucleotides into a retroviral vector (pRSMX_PuroGFP) for doxycycline-inducible shRNA expression. RNAi sequences used are as follows: OCT2 shRNA#1_1196 5'-GCACAACAGTTACTACCTTAT-3', OCT2 shRNA#2_3410 5'-GGATGCTTCTTTCTCTTCACA-3', OCA-B shRNA_3017 5'-CAGCCAGAAGTACCATTAGG-3'. Because OCT2 shRNA#1 targeted the coding region of OCT2, silent mutations were introduced into the recognition site to allow the shRNA to be rescued by OCT2 constructs. Vectors: The pRSMX-PG vector coexpressing GFP and shRNA was introduced into cells and where required selection was carried out with puromycin. Expression of shRNA was induced by addition of doxycycline (50 ng/mL).


title: OCI-Ly10 shOCA-B DOX Treated - 1 day - mAdbID:118690

description: mAdb experiment ID: 118690

source_name: OCI-Ly10 shControl DOX Treated - 1 day

treatment_protocol:
Treatment type: shRNA transduction
Treatment dose: 50 ng/mL
Treatment time: 1 day
In-vitro treatment: Cells were transduced with retroviral vectors expressing shControl. shRNA expression was induced with 50 ng/mL doxycycline for 1 day.
Other: Plasmids: OCT2 was cloned from cDNA from BJAB and OCA-B cDNA purchased from Origene. Both were cloned into the vectors pCMV-TOP and pFlagBiopCMV-TOP(30). Site directed mutations were introduced using the QuikChange Lightning kit from Agilent. shRNAs targeting OCT2 or OCA-B were designed and cloned as double stranded oligonucleotides into a retroviral vector (pRSMX_PuroGFP) for doxycycline-inducible shRNA expression. RNAi sequences used are as follows: OCT2 shRNA#1_1196 5'-GCACAACAGTTACTACCTTAT-3', OCT2 shRNA#2_3410 5'-GGATGCTTCTTTCTCTTCACA-3', OCA-B shRNA_3017 5'-CAGCCAGAAGTACCATTAGG-3'. Because OCT2 shRNA#1 targeted the coding region of OCT2, silent mutations were introduced into the recognition site to allow the shRNA to be rescued by OCT2 constructs. Vectors: The pRSMX-PG vector coexpressing GFP and shRNA was introduced into cells and where required selection was carried out with puromycin. Expression of shRNA was induced by addition of doxycycline (50 ng/mL).

tag: cell line

source_name: OCI-Ly10 shOCA-B DOX Treated - 1 day

treatment_protocol:
Treatment type: shRNA transduction
Treatment dose: 50 ng/mL
Treatment time: 1 day
In-vitro treatment: Cells were transduced with retroviral vectors expressing shOCA-B. shRNA expression was induced with 50 ng/mL doxycycline for 1 day.
Other: Plasmids: OCT2 was cloned from cDNA from BJAB and OCA-B cDNA purchased from Origene. Both were cloned into the vectors pCMV-TOP and pFlagBiopCMV-TOP(30). Site directed mutations were introduced using the QuikChange Lightning kit from Agilent. shRNAs targeting OCT2 or OCA-B were designed and cloned as double stranded oligonucleotides into a retroviral vector (pRSMX_PuroGFP) for doxycycline-inducible shRNA expression. RNAi sequences used are as follows: OCT2 shRNA#1_1196 5'-GCACAACAGTTACTACCTTAT-3', OCT2 shRNA#2_3410 5'-GGATGCTTCTTTCTCTTCACA-3', OCA-B shRNA_3017 5'-CAGCCAGAAGTACCATTAGG-3'. Because OCT2 shRNA#1 targeted the coding region of OCT2, silent mutations were introduced into the recognition site to allow the shRNA to be rescued by OCT2 constructs. Vectors: The pRSMX-PG vector coexpressing GFP and shRNA was introduced into cells and where required selection was carried out with puromycin. Expression of shRNA was induced by addition of doxycycline (50 ng/mL).


title: WB_COPD_PT_440


title: HT shOCA-B DOX Treated - 1 day - mAdbID:118688

description: mAdb experiment ID: 118688

source_name: HT shControl DOX Treated - 1 day

value: HT

tag: cell type

value: GCB DLBCL cells

value: germinal center B cell-restricted (GCB) subtype of diffuse large B cell lymphoma (DLBCL)

source_name: HT shOCA-B DOX Treated - 1 day


title: HT shOCA-B DOX Treated - 2 days - mAdbID:118689

description: mAdb experiment ID: 118689

source_name: HT shControl DOX Treated - 2 days

source_name: HT shOCA-B DOX Treated - 2 days


title: WB_COPD_PT_204


title: WB_COPD_PT_410


title: WB_COPD_PT_701


title: WB_COPD_PT_584


title: WB_COPD_PT_756


title: WB_COPD_PT_419


title: HBL1 shOCA-B DOX Treated - 2 days - mAdbID:118687

description: mAdb experiment ID: 118687

source_name: HBL1 shControl DOX Treated - 2 days

source_name: HBL1 shOCA-B DOX Treated - 2 days


title: WB_COPD_PT_659


title: BJAB shOCA-B DOX Treated - 2 days - mAdbID:118685

description: mAdb experiment ID: 118685

source_name: BJAB shControl DOX Treated - 2 days

value: BJAB

source_name: BJAB shOCA-B DOX Treated - 2 days


title: WB_COPD_PT_740


title: WB_COPD_PT_257


title: HBL1 shOCT2_1196 DOX Treated, empty vector construct - 2 days - mAdbID:118360

description: mAdb experiment ID: 118360

treatment_protocol:
Other: Plasmids: OCT2 was cloned from cDNA from BJAB and OCA-B cDNA purchased from Origene. Both were cloned into the vectors pCMV-TOP and pFlagBiopCMV-TOP(30). Site directed mutations were introduced using the QuikChange Lightning kit from Agilent. shRNAs targeting OCT2 or OCA-B were designed and cloned as double stranded oligonucleotides into a retroviral vector (pRSMX_PuroGFP) for doxycycline-inducible shRNA expression. RNAi sequences used are as follows: OCT2 shRNA#1_1196 5'-GCACAACAGTTACTACCTTAT-3', OCT2 shRNA#2_3410 5'-GGATGCTTCTTTCTCTTCACA-3', OCA-B shRNA_3017 5'-CAGCCAGAAGTACCATTAGG-3'. Because OCT2 shRNA#1 targeted the coding region of OCT2, silent mutations were introduced into the recognition site to allow the shRNA to be rescued by OCT2 constructs. Vectors: The pRSMX-PG vector coexpressing GFP and shRNA was introduced into cells and where required selection was carried out with puromycin. Expression of shRNA was induced by addition of doxycycline (50 ng/mL).
Treatment type: shRNA transduction
Treatment dose: 50 ng/mL
Treatment time: 2 days
In-vitro treatment: Cells were transduced with retroviral vectors expressing shOCT2_1196 and control empty vector rescue construct. Expression of each was induced with 50 ng/mL doxycycline for 2 days.

source_name: HBL1 shControl DOX Treated, empty vector construct - 2 days

treatment_protocol:
Other: Plasmids: OCT2 was cloned from cDNA from BJAB and OCA-B cDNA purchased from Origene. Both were cloned into the vectors pCMV-TOP and pFlagBiopCMV-TOP(30). Site directed mutations were introduced using the QuikChange Lightning kit from Agilent. shRNAs targeting OCT2 or OCA-B were designed and cloned as double stranded oligonucleotides into a retroviral vector (pRSMX_PuroGFP) for doxycycline-inducible shRNA expression. RNAi sequences used are as follows: OCT2 shRNA#1_1196 5'-GCACAACAGTTACTACCTTAT-3', OCT2 shRNA#2_3410 5'-GGATGCTTCTTTCTCTTCACA-3', OCA-B shRNA_3017 5'-CAGCCAGAAGTACCATTAGG-3'. Because OCT2 shRNA#1 targeted the coding region of OCT2, silent mutations were introduced into the recognition site to allow the shRNA to be rescued by OCT2 constructs. Vectors: The pRSMX-PG vector coexpressing GFP and shRNA was introduced into cells and where required selection was carried out with puromycin. Expression of shRNA was induced by addition of doxycycline (50 ng/mL).
Treatment type: shRNA transduction
Treatment dose: 50 ng/mL
Treatment time: 1 day
In-vitro treatment: Cells were transduced with retroviral vectors expressing shControl and empty vector rescue construct. Expression was induced with 50 ng/mL doxycycline for 2 days.


title: HBL1 shOCT2_3410 DOX Treated, WT OCT2 - 1 day - mAdbID:118359

description: mAdb experiment ID: 118359

treatment_protocol:
Treatment type: shRNA transduction
Treatment dose: 50 ng/mL
Treatment time: 1 day
In-vitro treatment: Expression of upregulated genes from an interferon signature (IFN3) in HBL1 cells depleted of OCT2 by shRNA and rescued with OCT2 WT. Cells were transduced with retroviral vectors expressing shOCT2_3410 and WT OCT2 rescue construct. shRNA expression was induced with 50 ng/mL doxycycline for 1 day.
Other: Plasmids: OCT2 was cloned from cDNA from BJAB and OCA-B cDNA purchased from Origene. Both were cloned into the vectors pCMV-TOP and pFlagBiopCMV-TOP(30). Site directed mutations were introduced using the QuikChange Lightning kit from Agilent. shRNAs targeting OCT2 or OCA-B were designed and cloned as double stranded oligonucleotides into a retroviral vector (pRSMX_PuroGFP) for doxycycline-inducible shRNA expression. RNAi sequences used are as follows: OCT2 shRNA#1_1196 5'-GCACAACAGTTACTACCTTAT-3', OCT2 shRNA#2_3410 5'-GGATGCTTCTTTCTCTTCACA-3', OCA-B shRNA_3017 5'-CAGCCAGAAGTACCATTAGG-3'. Because OCT2 shRNA#1 targeted the coding region of OCT2, silent mutations were introduced into the recognition site to allow the shRNA to be rescued by OCT2 constructs. Vectors: The pRSMX-PG vector coexpressing GFP and shRNA was introduced into cells and where required selection was carried out with puromycin. Expression of shRNA was induced by addition of doxycycline (50 ng/mL).

source_name: HBL1 shControl DOX Treated, WT OCT2 - 1 day

treatment_protocol:
Treatment type: shRNA transduction
Treatment dose: 50 ng/mL
Treatment time: 1 day
In-vitro treatment: Expression of upregulated genes from an interferon signature (IFN3) in HBL1 cells. Cells were transduced with retroviral vectors expressing shControl and WT OCT2 rescue construct. shRNA expression was induced with 50 ng/mL doxycycline for 1 day.
Other: Plasmids: OCT2 was cloned from cDNA from BJAB and OCA-B cDNA purchased from Origene. Both were cloned into the vectors pCMV-TOP and pFlagBiopCMV-TOP(30). Site directed mutations were introduced using the QuikChange Lightning kit from Agilent. shRNAs targeting OCT2 or OCA-B were designed and cloned as double stranded oligonucleotides into a retroviral vector (pRSMX_PuroGFP) for doxycycline-inducible shRNA expression. RNAi sequences used are as follows: OCT2 shRNA#1_1196 5'-GCACAACAGTTACTACCTTAT-3', OCT2 shRNA#2_3410 5'-GGATGCTTCTTTCTCTTCACA-3', OCA-B shRNA_3017 5'-CAGCCAGAAGTACCATTAGG-3'. Because OCT2 shRNA#1 targeted the coding region of OCT2, silent mutations were introduced into the recognition site to allow the shRNA to be rescued by OCT2 constructs. Vectors: The pRSMX-PG vector coexpressing GFP and shRNA was introduced into cells and where required selection was carried out with puromycin. Expression of shRNA was induced by addition of doxycycline (50 ng/mL).


title: HBL1 shOCA-B DOX Treated - 1 day - mAdbID:118686

description: mAdb experiment ID: 118686

source_name: HBL1 shControl DOX Treated - 1 day

source_name: HBL1 shOCA-B DOX Treated - 1 day


title: WB_COPD_PT_758

source_name: PAXgene whole blood mRNA


title: WB_COPD_PT_001


title: WB_COPD_PT_762


title: BJAB shOCA-B DOX Treated - 1 day - mAdbID:118684

description: mAdb experiment ID: 118684

source_name: BJAB shControl DOX Treated - 1 day

source_name: BJAB shOCA-B DOX Treated - 1 day


title: HBL1 shOCT2_3410 DOX Treated, WT OCT2 - 2 days - mAdbID:118363

description: mAdb experiment ID: 118363

treatment_protocol:
Treatment type: shRNA transduction
Treatment dose: 50 ng/mL
Treatment time: 2 days
In-vitro treatment: Expression of upregulated genes from an interferon signature (IFN3) in HBL1 cells depleted of OCT2 by shRNA and rescued with OCT2 WT. Cells were transduced with retroviral vectors expressing shOCT2_3410 and WT OCT2 rescue construct. shRNA expression was induced with 50 ng/mL doxycycline for 2 days.
Other: Plasmids: OCT2 was cloned from cDNA from BJAB and OCA-B cDNA purchased from Origene. Both were cloned into the vectors pCMV-TOP and pFlagBiopCMV-TOP(30). Site directed mutations were introduced using the QuikChange Lightning kit from Agilent. shRNAs targeting OCT2 or OCA-B were designed and cloned as double stranded oligonucleotides into a retroviral vector (pRSMX_PuroGFP) for doxycycline-inducible shRNA expression. RNAi sequences used are as follows: OCT2 shRNA#1_1196 5'-GCACAACAGTTACTACCTTAT-3', OCT2 shRNA#2_3410 5'-GGATGCTTCTTTCTCTTCACA-3', OCA-B shRNA_3017 5'-CAGCCAGAAGTACCATTAGG-3'. Because OCT2 shRNA#1 targeted the coding region of OCT2, silent mutations were introduced into the recognition site to allow the shRNA to be rescued by OCT2 constructs. Vectors: The pRSMX-PG vector coexpressing GFP and shRNA was introduced into cells and where required selection was carried out with puromycin. Expression of shRNA was induced by addition of doxycycline (50 ng/mL).

source_name: HBL1 shControl DOX Treated, WT OCT2 - 2 days

treatment_protocol:
Treatment type: shRNA transduction
Treatment dose: 50 ng/mL
Treatment time: 2 days
In-vitro treatment: Expression of upregulated genes from an interferon signature (IFN3) in HBL1 cells. Cells were transduced with retroviral vectors expressing shControl and WT OCT2 rescue construct. shRNA expression was induced with 50 ng/mL doxycycline for 2 days.
Other: Plasmids: OCT2 was cloned from cDNA from BJAB and OCA-B cDNA purchased from Origene. Both were cloned into the vectors pCMV-TOP and pFlagBiopCMV-TOP(30). Site directed mutations were introduced using the QuikChange Lightning kit from Agilent. shRNAs targeting OCT2 or OCA-B were designed and cloned as double stranded oligonucleotides into a retroviral vector (pRSMX_PuroGFP) for doxycycline-inducible shRNA expression. RNAi sequences used are as follows: OCT2 shRNA#1_1196 5'-GCACAACAGTTACTACCTTAT-3', OCT2 shRNA#2_3410 5'-GGATGCTTCTTTCTCTTCACA-3', OCA-B shRNA_3017 5'-CAGCCAGAAGTACCATTAGG-3'. Because OCT2 shRNA#1 targeted the coding region of OCT2, silent mutations were introduced into the recognition site to allow the shRNA to be rescued by OCT2 constructs. Vectors: The pRSMX-PG vector coexpressing GFP and shRNA was introduced into cells and where required selection was carried out with puromycin. Expression of shRNA was induced by addition of doxycycline (50 ng/mL).


title: HBL1 shOCT2_3410 DOX Treated, empty vector construct - 1 day - mAdbID:118357

description: mAdb experiment ID: 118357

treatment_protocol:
Other: Plasmids: OCT2 was cloned from cDNA from BJAB and OCA-B cDNA purchased from Origene. Both were cloned into the vectors pCMV-TOP and pFlagBiopCMV-TOP(30). Site directed mutations were introduced using the QuikChange Lightning kit from Agilent. shRNAs targeting OCT2 or OCA-B were designed and cloned as double stranded oligonucleotides into a retroviral vector (pRSMX_PuroGFP) for doxycycline-inducible shRNA expression. RNAi sequences used are as follows: OCT2 shRNA#1_1196 5'-GCACAACAGTTACTACCTTAT-3', OCT2 shRNA#2_3410 5'-GGATGCTTCTTTCTCTTCACA-3', OCA-B shRNA_3017 5'-CAGCCAGAAGTACCATTAGG-3'. Because OCT2 shRNA#1 targeted the coding region of OCT2, silent mutations were introduced into the recognition site to allow the shRNA to be rescued by OCT2 constructs. Vectors: The pRSMX-PG vector coexpressing GFP and shRNA was introduced into cells and where required selection was carried out with puromycin. Expression of shRNA was induced by addition of doxycycline (50 ng/mL).
Treatment type: shRNA transduction
Treatment dose: 50 ng/mL
Treatment time: 1 day
In-vitro treatment: Cells were transduced with retroviral vectors expressing shOCT2_3410 and control empty vector rescue construct. Expression of each was induced with 50 ng/mL doxycycline for 1 day.

source_name: HBL1 shControl DOX Treated, empty vector construct - 1 day

treatment_protocol:
Other: Plasmids: OCT2 was cloned from cDNA from BJAB and OCA-B cDNA purchased from Origene. Both were cloned into the vectors pCMV-TOP and pFlagBiopCMV-TOP(30). Site directed mutations were introduced using the QuikChange Lightning kit from Agilent. shRNAs targeting OCT2 or OCA-B were designed and cloned as double stranded oligonucleotides into a retroviral vector (pRSMX_PuroGFP) for doxycycline-inducible shRNA expression. RNAi sequences used are as follows: OCT2 shRNA#1_1196 5'-GCACAACAGTTACTACCTTAT-3', OCT2 shRNA#2_3410 5'-GGATGCTTCTTTCTCTTCACA-3', OCA-B shRNA_3017 5'-CAGCCAGAAGTACCATTAGG-3'. Because OCT2 shRNA#1 targeted the coding region of OCT2, silent mutations were introduced into the recognition site to allow the shRNA to be rescued by OCT2 constructs. Vectors: The pRSMX-PG vector coexpressing GFP and shRNA was introduced into cells and where required selection was carried out with puromycin. Expression of shRNA was induced by addition of doxycycline (50 ng/mL).
Treatment type: shRNA transduction
Treatment dose: 50 ng/mL
Treatment time: 1 day
In-vitro treatment: Cells were transduced with retroviral vectors expressing shControl and empty vector rescue construct. Expression was induced with 50 ng/mL doxycycline for 1 day.


title: HBL1 shOCT2_3410 DOX Treated, empty vector construct - 2 days - mAdbID:118361

description: mAdb experiment ID: 118361

treatment_protocol:
Other: Plasmids: OCT2 was cloned from cDNA from BJAB and OCA-B cDNA purchased from Origene. Both were cloned into the vectors pCMV-TOP and pFlagBiopCMV-TOP(30). Site directed mutations were introduced using the QuikChange Lightning kit from Agilent. shRNAs targeting OCT2 or OCA-B were designed and cloned as double stranded oligonucleotides into a retroviral vector (pRSMX_PuroGFP) for doxycycline-inducible shRNA expression. RNAi sequences used are as follows: OCT2 shRNA#1_1196 5'-GCACAACAGTTACTACCTTAT-3', OCT2 shRNA#2_3410 5'-GGATGCTTCTTTCTCTTCACA-3', OCA-B shRNA_3017 5'-CAGCCAGAAGTACCATTAGG-3'. Because OCT2 shRNA#1 targeted the coding region of OCT2, silent mutations were introduced into the recognition site to allow the shRNA to be rescued by OCT2 constructs. Vectors: The pRSMX-PG vector coexpressing GFP and shRNA was introduced into cells and where required selection was carried out with puromycin. Expression of shRNA was induced by addition of doxycycline (50 ng/mL).
Treatment type: shRNA transduction
Treatment dose: 50 ng/mL
Treatment time: 1 day
In-vitro treatment: Cells were transduced with retroviral vectors expressing shOCT2_3410 and control empty vector rescue construct. Expression of each was induced with 50 ng/mL doxycycline for 2 days.


title: HBL1 shOCT2_1196 DOX Treated, WT OCT2 - 2 days - mAdbID:118362

description: mAdb experiment ID: 118362

treatment_protocol:
Treatment type: shRNA transduction
Treatment dose: 50 ng/mL
Treatment time: 2 days
In-vitro treatment: Expression of upregulated genes from an interferon signature (IFN3) in HBL1 cells depleted of OCT2 by shRNA and rescued with OCT2 WT. Cells were transduced with retroviral vectors expressing shOCT2_1196 and WT OCT2 rescue construct. shRNA expression was induced with 50 ng/mL doxycycline for 2 days.
Other: Plasmids: OCT2 was cloned from cDNA from BJAB and OCA-B cDNA purchased from Origene. Both were cloned into the vectors pCMV-TOP and pFlagBiopCMV-TOP(30). Site directed mutations were introduced using the QuikChange Lightning kit from Agilent. shRNAs targeting OCT2 or OCA-B were designed and cloned as double stranded oligonucleotides into a retroviral vector (pRSMX_PuroGFP) for doxycycline-inducible shRNA expression. RNAi sequences used are as follows: OCT2 shRNA#1_1196 5'-GCACAACAGTTACTACCTTAT-3', OCT2 shRNA#2_3410 5'-GGATGCTTCTTTCTCTTCACA-3', OCA-B shRNA_3017 5'-CAGCCAGAAGTACCATTAGG-3'. Because OCT2 shRNA#1 targeted the coding region of OCT2, silent mutations were introduced into the recognition site to allow the shRNA to be rescued by OCT2 constructs. Vectors: The pRSMX-PG vector coexpressing GFP and shRNA was introduced into cells and where required selection was carried out with puromycin. Expression of shRNA was induced by addition of doxycycline (50 ng/mL).


title: HBL1 shOCT2_1196 DOX Treated, WT OCT2 - 1 day - mAdbID:118358

description: mAdb experiment ID: 118358

treatment_protocol:
Treatment type: shRNA transduction
Treatment dose: 50 ng/mL
Treatment time: 1 day
In-vitro treatment: Expression of upregulated genes from an interferon signature (IFN3) in HBL1 cells depleted of OCT2 by shRNA and rescued with OCT2 WT. Cells were transduced with retroviral vectors expressing shOCT2_1196 and WT OCT2 rescue construct. shRNA expression was induced with 50 ng/mL doxycycline for 1 day.
Other: Plasmids: OCT2 was cloned from cDNA from BJAB and OCA-B cDNA purchased from Origene. Both were cloned into the vectors pCMV-TOP and pFlagBiopCMV-TOP(30). Site directed mutations were introduced using the QuikChange Lightning kit from Agilent. shRNAs targeting OCT2 or OCA-B were designed and cloned as double stranded oligonucleotides into a retroviral vector (pRSMX_PuroGFP) for doxycycline-inducible shRNA expression. RNAi sequences used are as follows: OCT2 shRNA#1_1196 5'-GCACAACAGTTACTACCTTAT-3', OCT2 shRNA#2_3410 5'-GGATGCTTCTTTCTCTTCACA-3', OCA-B shRNA_3017 5'-CAGCCAGAAGTACCATTAGG-3'. Because OCT2 shRNA#1 targeted the coding region of OCT2, silent mutations were introduced into the recognition site to allow the shRNA to be rescued by OCT2 constructs. Vectors: The pRSMX-PG vector coexpressing GFP and shRNA was introduced into cells and where required selection was carried out with puromycin. Expression of shRNA was induced by addition of doxycycline (50 ng/mL).


title: WB_COPD_PT_352


title: HBL1 shOCT2_1196 DOX Treated, empty vector construct - 1 day - mAdbID:118356

description: mAdb experiment ID: 118356

treatment_protocol:
Other: Plasmids: OCT2 was cloned from cDNA from BJAB and OCA-B cDNA purchased from Origene. Both were cloned into the vectors pCMV-TOP and pFlagBiopCMV-TOP(30). Site directed mutations were introduced using the QuikChange Lightning kit from Agilent. shRNAs targeting OCT2 or OCA-B were designed and cloned as double stranded oligonucleotides into a retroviral vector (pRSMX_PuroGFP) for doxycycline-inducible shRNA expression. RNAi sequences used are as follows: OCT2 shRNA#1_1196 5'-GCACAACAGTTACTACCTTAT-3', OCT2 shRNA#2_3410 5'-GGATGCTTCTTTCTCTTCACA-3', OCA-B shRNA_3017 5'-CAGCCAGAAGTACCATTAGG-3'. Because OCT2 shRNA#1 targeted the coding region of OCT2, silent mutations were introduced into the recognition site to allow the shRNA to be rescued by OCT2 constructs. Vectors: The pRSMX-PG vector coexpressing GFP and shRNA was introduced into cells and where required selection was carried out with puromycin. Expression of shRNA was induced by addition of doxycycline (50 ng/mL).
Treatment type: shRNA transduction
Treatment dose: 50 ng/mL
Treatment time: 1 day
In-vitro treatment: Cells were transduced with retroviral vectors expressing shOCT2_1196 and control empty vector rescue construct. Expression of each was induced with 50 ng/mL doxycycline for 1 day.


title: WB_COPD_PT_360


title: OCI-Ly10 shOCT2_3410 DOX Treated - 2 days - mAdbID:118331

description: mAdb experiment ID: 118331

treatment_protocol:
Treatment type: shRNA transduction
Treatment dose: 50 ng/mL
Treatment time: 2 days
In-vitro treatment: Cells were transduced with retroviral vectors expressing shOCT2_3410. shRNA expression was induced with 50 ng/mL doxycycline for 2 days.
Other: Plasmids: OCT2 was cloned from cDNA from BJAB and OCA-B cDNA purchased from Origene. Both were cloned into the vectors pCMV-TOP and pFlagBiopCMV-TOP(30). Site directed mutations were introduced using the QuikChange Lightning kit from Agilent. shRNAs targeting OCT2 or OCA-B were designed and cloned as double stranded oligonucleotides into a retroviral vector (pRSMX_PuroGFP) for doxycycline-inducible shRNA expression. RNAi sequences used are as follows: OCT2 shRNA#1_1196 5'-GCACAACAGTTACTACCTTAT-3', OCT2 shRNA#2_3410 5'-GGATGCTTCTTTCTCTTCACA-3', OCA-B shRNA_3017 5'-CAGCCAGAAGTACCATTAGG-3'. Because OCT2 shRNA#1 targeted the coding region of OCT2, silent mutations were introduced into the recognition site to allow the shRNA to be rescued by OCT2 constructs. Vectors: The pRSMX-PG vector coexpressing GFP and shRNA was introduced into cells and where required selection was carried out with puromycin. Expression of shRNA was induced by addition of doxycycline (50 ng/mL).

source_name: OCI-Ly10 shControl DOX Treated - 2 days


title: OCI-Ly10 shOCT2_1196 DOX Treated - 2 days - mAdbID:118330

description: mAdb experiment ID: 118330

treatment_protocol:
Treatment type: shRNA transduction
Treatment dose: 50 ng/mL
Treatment time: 2 days
In-vitro treatment: Cells were transduced with retroviral vectors expressing shOCT2_1196. shRNA expression was induced with 50 ng/mL doxycycline for 2 days.
Other: Plasmids: OCT2 was cloned from cDNA from BJAB and OCA-B cDNA purchased from Origene. Both were cloned into the vectors pCMV-TOP and pFlagBiopCMV-TOP(30). Site directed mutations were introduced using the QuikChange Lightning kit from Agilent. shRNAs targeting OCT2 or OCA-B were designed and cloned as double stranded oligonucleotides into a retroviral vector (pRSMX_PuroGFP) for doxycycline-inducible shRNA expression. RNAi sequences used are as follows: OCT2 shRNA#1_1196 5'-GCACAACAGTTACTACCTTAT-3', OCT2 shRNA#2_3410 5'-GGATGCTTCTTTCTCTTCACA-3', OCA-B shRNA_3017 5'-CAGCCAGAAGTACCATTAGG-3'. Because OCT2 shRNA#1 targeted the coding region of OCT2, silent mutations were introduced into the recognition site to allow the shRNA to be rescued by OCT2 constructs. Vectors: The pRSMX-PG vector coexpressing GFP and shRNA was introduced into cells and where required selection was carried out with puromycin. Expression of shRNA was induced by addition of doxycycline (50 ng/mL).

treatment_protocol:
Treatment type: shRNA transduction
Treatment dose: 50 ng/mL
Treatment time: 2 days
In-vitro treatment: Cells were transduced with retroviral vectors expressing shControl. shRNA expression was induced with 50 ng/mL doxycycline for 2 days.
Other: Plasmids: OCT2 was cloned from cDNA from BJAB and OCA-B cDNA purchased from Origene. Both were cloned into the vectors pCMV-TOP and pFlagBiopCMV-TOP(30). Site directed mutations were introduced using the QuikChange Lightning kit from Agilent. shRNAs targeting OCT2 or OCA-B were designed and cloned as double stranded oligonucleotides into a retroviral vector (pRSMX_PuroGFP) for doxycycline-inducible shRNA expression. RNAi sequences used are as follows: OCT2 shRNA#1_1196 5'-GCACAACAGTTACTACCTTAT-3', OCT2 shRNA#2_3410 5'-GGATGCTTCTTTCTCTTCACA-3', OCA-B shRNA_3017 5'-CAGCCAGAAGTACCATTAGG-3'. Because OCT2 shRNA#1 targeted the coding region of OCT2, silent mutations were introduced into the recognition site to allow the shRNA to be rescued by OCT2 constructs. Vectors: The pRSMX-PG vector coexpressing GFP and shRNA was introduced into cells and where required selection was carried out with puromycin. Expression of shRNA was induced by addition of doxycycline (50 ng/mL).


title: WB_COPD_PT_625


title: WB_COPD_PT_195


title: WB_COPD_PT_531


title: WB_COPD_PT_843


title: OCI-Ly10 shOCT2_3410 DOX Treated - 1 day - mAdbID:118329

description: mAdb experiment ID: 118329

treatment_protocol:
Treatment type: shRNA transduction
Treatment dose: 50 ng/mL
Treatment time: 1 day
In-vitro treatment: Cells were transduced with retroviral vectors expressing shOCT2_3410. shRNA expression was induced with 50 ng/mL doxycycline for 1 day.
Other: Plasmids: OCT2 was cloned from cDNA from BJAB and OCA-B cDNA purchased from Origene. Both were cloned into the vectors pCMV-TOP and pFlagBiopCMV-TOP(30). Site directed mutations were introduced using the QuikChange Lightning kit from Agilent. shRNAs targeting OCT2 or OCA-B were designed and cloned as double stranded oligonucleotides into a retroviral vector (pRSMX_PuroGFP) for doxycycline-inducible shRNA expression. RNAi sequences used are as follows: OCT2 shRNA#1_1196 5'-GCACAACAGTTACTACCTTAT-3', OCT2 shRNA#2_3410 5'-GGATGCTTCTTTCTCTTCACA-3', OCA-B shRNA_3017 5'-CAGCCAGAAGTACCATTAGG-3'. Because OCT2 shRNA#1 targeted the coding region of OCT2, silent mutations were introduced into the recognition site to allow the shRNA to be rescued by OCT2 constructs. Vectors: The pRSMX-PG vector coexpressing GFP and shRNA was introduced into cells and where required selection was carried out with puromycin. Expression of shRNA was induced by addition of doxycycline (50 ng/mL).

source_name: OCI-Ly10 shControl DOX Treated - 1 day

treatment_protocol:
Treatment type: shRNA transduction
Treatment dose: 50 ng/mL
Treatment time: 1 day
In-vitro treatment: Cells were transduced with retroviral vectors expressing shControl. shRNA expression was induced with 50 ng/mL doxycycline for 1 day.
Other: Plasmids: OCT2 was cloned from cDNA from BJAB and OCA-B cDNA purchased from Origene. Both were cloned into the vectors pCMV-TOP and pFlagBiopCMV-TOP(30). Site directed mutations were introduced using the QuikChange Lightning kit from Agilent. shRNAs targeting OCT2 or OCA-B were designed and cloned as double stranded oligonucleotides into a retroviral vector (pRSMX_PuroGFP) for doxycycline-inducible shRNA expression. RNAi sequences used are as follows: OCT2 shRNA#1_1196 5'-GCACAACAGTTACTACCTTAT-3', OCT2 shRNA#2_3410 5'-GGATGCTTCTTTCTCTTCACA-3', OCA-B shRNA_3017 5'-CAGCCAGAAGTACCATTAGG-3'. Because OCT2 shRNA#1 targeted the coding region of OCT2, silent mutations were introduced into the recognition site to allow the shRNA to be rescued by OCT2 constructs. Vectors: The pRSMX-PG vector coexpressing GFP and shRNA was introduced into cells and where required selection was carried out with puromycin. Expression of shRNA was induced by addition of doxycycline (50 ng/mL).


title: WB_COPD_PT_044


title: WB_COPD_PT_121


title: WB_COPD_PT_815


title: WB_COPD_PT_710


title: WB_COPD_PT_116


title: WB_COPD_PT_089


title: HT shOCT2_3410 DOX Treated - 1 day - mAdbID:118326

description: mAdb experiment ID: 118326

source_name: HT shOCT2_3410 DOX Treated - 1 day

source_name: HT shControl DOX Treated - 1 day


title: HT shOCT2_3410 DOX Treated - 2 days - mAdbID:118328

description: mAdb experiment ID: 118328

source_name: HT shOCT2_3410 DOX Treated - 2 days

source_name: HT shControl DOX Treated - 2 days


title: HBL1 shOCT2_1196 DOX Treated - 1 day - mAdbID:117930

description: mAdb experiment ID: 117930

source_name: HBL1 shOCT2_1196 DOX Treated - 1 day

treatment_protocol:
Treatment type: shRNA transduction
Treatment dose: 50 ng/mL
Treatment time: 1 day
In-vitro treatment: Cells were transduced with retroviral vectors expressing shOCT2_1196. shRNA expression was induced with 50 ng/mL doxycycline for 1 day.
Other: Plasmids: OCT2 was cloned from cDNA from BJAB and OCA-B cDNA purchased from Origene. Both were cloned into the vectors pCMV-TOP and pFlagBiopCMV-TOP(30). Site directed mutations were introduced using the QuikChange Lightning kit from Agilent. shRNAs targeting OCT2 or OCA-B were designed and cloned as double stranded oligonucleotides into a retroviral vector (pRSMX_PuroGFP) for doxycycline-inducible shRNA expression. RNAi sequences used are as follows: OCT2 shRNA#1_1196 5'-GCACAACAGTTACTACCTTAT-3', OCT2 shRNA#2_3410 5'-GGATGCTTCTTTCTCTTCACA-3', OCA-B shRNA_3017 5'-CAGCCAGAAGTACCATTAGG-3'. Because OCT2 shRNA#1 targeted the coding region of OCT2, silent mutations were introduced into the recognition site to allow the shRNA to be rescued by OCT2 constructs. Vectors: The pRSMX-PG vector coexpressing GFP and shRNA was introduced into cells and where required selection was carried out with puromycin. Expression of shRNA was induced by addition of doxycycline (50 ng/mL).


title: WB_COPD_PT_253


title: BJAB shOCT2_1196 DOX Treated - 2 days - mAdbID:117928

description: mAdb experiment ID: 117928

source_name: BJAB shOCT2_1196 DOX Treated - 2 days

source_name: BJAB shControl DOX Treated - 2 days


title: BJAB shOCT2_3410 DOX Treated - 2 days - mAdbID:117929

description: mAdb experiment ID: 117929

source_name: BJAB shOCT2_3410 DOX Treated - 2 days


title: HT shOCT2_1196 DOX Treated - 1 day - mAdbID:118325

description: mAdb experiment ID: 118325

source_name: HT shOCT2_1196 DOX Treated - 1 day


title: WB_COPD_PT_420


title: WB_COPD_PT_757


title: HBL1 shOCT2_3410 DOX Treated - 1 day - mAdbID:117931

description: mAdb experiment ID: 117931

source_name: HBL1 shOCT2_3410 DOX Treated - 1 day

source_name: HBL1 shControl DOX Treated - 1 day


title: BJAB shOCT2_3410 DOX Treated - 1 day - mAdbID:117927

description: mAdb experiment ID: 117927

source_name: BJAB shOCT2_3410 DOX Treated - 1 day

source_name: BJAB shControl DOX Treated - 1 day


title: WB_COPD_PT_444

source_name: PAXgene whole blood mRNA


title: HBL1 shOCT2_1196 DOX Treated - 2 days - mAdbID:117932

description: mAdb experiment ID: 117932

source_name: HBL1 shOCT2_1196 DOX Treated - 2 days

source_name: HBL1 shControl DOX Treated - 2 days


title: WB_COPD_PT_133


title: HBL1 shOCT2_3410 DOX Treated - 2 days - mAdbID:117933

description: mAdb experiment ID: 117933

source_name: HBL1 shOCT2_3410 DOX Treated - 2 days


title: HT shOCT2_1196 DOX Treated - 2 days - mAdbID:118327

description: mAdb experiment ID: 118327

source_name: HT shOCT2_1196 DOX Treated - 2 days


title: BJAB shOCT2_1196 DOX Treated - 1 day - mAdbID:117926

description: mAdb experiment ID: 117926

source_name: BJAB shOCT2_1196 DOX Treated - 1 day


title: WB_COPD_PT_960


title: GapmeR AK156230

city: Dongguan

first: Yu-ning

address: Xin Cheng Avenue 1#, Songshan Lake

institute: Guangdong Medical University

description: Young MEFs were transfected with GapmeR AK156230

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C according to manufacturer’s instructions. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: The GeneChip arrays were scanned immediately after washing and staining using a GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA) and hybridization data were analyzed using GeneChip Operating Software (Affymetrix, Santa Clara, CA).

source_name: Young MEFs

growth_protocol: Primary MEFs were isolated from 13.5-day-old embryos of C57/BL6 mice and maintained in DMEM supplemented with 10%FBS in a humidified incubator with 5% CO2 at 37°C. Serial passage was performed when the cells reached 80% conﬂuence

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

tag: strain

value: Whole embryo

tag: passage

tag: trasnfection

value: GapmeR AK156230


title: GapmeR Control

description: Young MEFs were transfected with GapmeR control

tag: tissue

value: GapmeR control