title: S48-Tp11

tag: cancer type

value: I

value: ductal carcinoma

value: f

tag: diseasecode

tag: diseasedescription

tag: primary / relapse tumor

tag: tumorlocalization

value: IIA

value: malign


title: S58-Tp11

status: Public on Sep 07 2017

type: RNA

city: New York

first: Wei-Yi

last: Cheng

state: New York

address: Roche Translational and Clinical Research Center, 430 East 29th Street

department: Pharma Research and Early Development

country: USA

institute: Roche Innovation Center New York

hyb_protocol: 3 ug (15 ul) labeled cDNA + 105ul  Master Mix. Hybridization was done using GeneTitan Hybridization, Wash and Stain Kit

scan_protocol: Scanning was done using GeneTitan Instrument

data_processing: The CEL files were normalized and summarized into probe-set values using RMA normalization.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Total RNA Seq profiling of sample

label_protocol: Biotin-Labeling and enzymatic fragmentation

growth_protocol: Samples were extracted from tumor or adjacent normal tissue, and then formalin-fixed and paraffin embedded

extract_protocol: Extraction was done using High Pure FFPET RNA Isolation Kits /Cat. No. 06650775001

treatment_protocol: Tumor samples were formalin-fixed and paraffin embedded. RNA amplification: 100ng total RNA

value: BC

tag: normal

value: no

tag: batch i/ii

tag: histology

value: lobular carcinoma

tag: age

tag: gender

tag: weight

tag: bodyheight

tag: bmi

value: malignant neoplasm of central portion of breast

value: primary tumor

tag: tumorsize

tag: ischemiatime

tag: tumorcontent

tag: organ

value: breast right

value: central portion

tag: Stage

tag: radicality

tag: grading

tag: dignity


title: S407-Tp11

tag: cancer type

tag: diseasecode

tag: diseasedescription

value: malignant neoplasm of upper-inner quadrant of breast

tag: primary / relapse tumor

value: breast left

tag: tumorlocalization

value: upper-inner quadrant


title: S70-Tp11

tag: normal

tag: batch i/ii

tag: histology

tag: age

tag: gender


title: S396-Tp11

tag: weight

tag: bodyheight

tag: bmi

tag: tumorsize

tag: ischemiatime


title: S405-Tp11

tag: tumorcontent

tag: organ

tag: Stage

value: IV

tag: radicality

tag: grading


title: S382-Tc15

tag: cancer type

tag: diseasecode

tag: diseasedescription

value: malignant neoplasm of overlapping lesion of breast

tag: primary / relapse tumor

value: several partitions overlapping

value: III A

tag: dignity


title: S392-Tp14

tag: normal

tag: batch i/ii

value: I

tag: histology

value: carcinoma

tag: age

value: f

tag: tumorlocalization


title: S39-Tp11

value: BC

value: ductal carcinoma

tag: gender

tag: weight

tag: bodyheight

tag: bmi

tag: tumorsize

value: malign


title: S33-Tp12

value: no

tag: ischemiatime

tag: tumorcontent

tag: organ

tag: Stage

tag: radicality


title: S362-Tp14

tag: cancer type

tag: diseasecode

tag: diseasedescription

value: malignant neoplasm of upper-outer quadrant of breast

tag: primary / relapse tumor

value: primary tumor

value: upper-outer quadrant

value: III B

tag: grading


title: S393-Tp11

tag: normal

tag: batch i/ii

tag: histology

tag: age

value: breast left

tag: dignity


title: S315-Tp12

tag: gender

tag: weight

tag: bodyheight

tag: bmi

value: malignant neoplasm of lower-outer quadrant of breast

value: breast right

tag: tumorlocalization

value: lower-outer quadrant

value: IIA


title: S212-Tp11

value: malignant neoplasm of breast, unspecified

tag: tumorsize

tag: ischemiatime

tag: tumorcontent

tag: organ

tag: Stage


title: S276-Tp13

tag: cancer type

value: I

tag: diseasecode

tag: diseasedescription

tag: primary / relapse tumor

tag: radicality


title: S399-Tp11

tag: normal

tag: batch i/ii

tag: histology

tag: age

tag: grading


title: S205-Tc15

tag: gender

tag: weight

tag: bodyheight

tag: bmi

value: malignant neoplasm of overlapping lesion of breast

value: several partitions overlapping

value: IV

tag: dignity


title: S253-Tp11

value: BC

value: ductal carcinoma

value: f

tag: tumorsize

tag: ischemiatime

tag: tumorcontent

tag: organ

tag: tumorlocalization


title: S344-Tp11

tag: cancer type

value: no

value: carcinoma

tag: diseasecode

tag: diseasedescription

value: malignant neoplasm of upper-outer quadrant of breast

tag: primary / relapse tumor

tag: Stage

value: malign


title: S199-Tp11

tag: normal

tag: batch i/ii

tag: histology

tag: age

value: malignant neoplasm of lower-inner quadrant of breast

value: primary tumor

value: breast left

value: lower-inner quadrant

tag: radicality


title: S23-Tp11

tag: gender

tag: weight

tag: bodyheight

tag: bmi

value: upper-outer quadrant

value: III B

tag: grading


title: S274-Tp14

value: I

value: mucinous adenocarcinoma

value: malignant neoplasm of upper-inner quadrant of breast

tag: tumorsize

tag: ischemiatime

tag: tumorcontent

tag: organ

value: upper-inner quadrant

value: IIA

tag: dignity


title: S258-Tp11

tag: cancer type

value: BC

value: lobular carcinoma

tag: diseasecode

tag: diseasedescription

value: malignant neoplasm of lower-outer quadrant of breast

tag: primary / relapse tumor

value: breast right

tag: tumorlocalization

value: lower-outer quadrant

value: III A


title: S266-Tp12

tag: normal

value: no

tag: batch i/ii

tag: histology

value: ductal carcinoma

tag: age

value: f

value: malignant neoplasm of upper-outer quadrant of breast

tag: Stage

value: malign


title: S188-Tp11

tag: gender

tag: weight

tag: bodyheight

tag: bmi

value: primary tumor

value: breast left

value: III C

tag: radicality


title: S338-Tp12

value: I

value: malignant neoplasm of upper-inner quadrant of breast

tag: tumorsize

tag: ischemiatime

tag: tumorcontent

tag: organ

tag: grading


title: S17-Tp11

tag: cancer type

value: carcinoma

tag: diseasecode

tag: diseasedescription

value: malignant neoplasm of central portion of breast

tag: primary / relapse tumor

value: central portion

value: III B

tag: dignity


title: S18-Tp14

value: BC

tag: normal

tag: batch i/ii

tag: histology

tag: age

value: breast right

tag: tumorlocalization

value: IV


title: K305-Tp11

value: no

tag: gender

tag: weight

tag: bodyheight

tag: bmi

value: upper-inner quadrant

tag: Stage


title: K277-Tc15

value: lobular carcinoma

value: f

value: malignant neoplasm of lower-outer quadrant of breast

tag: tumorsize

tag: ischemiatime

tag: tumorcontent

tag: organ

value: lower-outer quadrant

value: IIA

tag: radicality


title: K318-Tp12_normal

tag: cancer type

value: yes

value: ductal carcinoma

tag: diseasecode

tag: diseasedescription

tag: primary / relapse tumor

value: primary tumor

tag: grading

value: malign


title: S11-Tp11

tag: normal

tag: batch i/ii

value: I

tag: histology

tag: age

value: III C

tag: dignity


title: K346-Tp11

tag: gender

tag: weight

tag: bodyheight

tag: bmi

tag: tumorlocalization


title: K248-TC15

value: malignant neoplasm of central portion of breast

tag: tumorsize

tag: ischemiatime

tag: tumorcontent

tag: organ

value: breast left

value: central portion

tag: Stage

value: IIB


title: K359-Tc16

tag: cancer type

value: BC

value: no

tag: diseasecode

tag: diseasedescription

value: malignant neoplasm of upper-outer quadrant of breast

tag: primary / relapse tumor

value: upper-outer quadrant

value: III A

tag: radicality


title: K225-Tc16

tag: normal

tag: batch i/ii

tag: histology

tag: age

value: f

value: malignant neoplasm of overlapping lesion of breast

value: breast right

value: several partitions overlapping

tag: grading


title: S144-Tp11

value: ductal carcinoma

tag: gender

tag: weight

tag: bodyheight

tag: bmi

value: primary tumor

value: IIA

tag: dignity


title: K320-Tp13

value: I

value: lobular carcinoma

tag: tumorsize

tag: ischemiatime

tag: tumorcontent

tag: organ

tag: tumorlocalization

value: malign


title: K210-Tp11

tag: cancer type

tag: diseasecode

tag: diseasedescription

tag: primary / relapse tumor

tag: Stage

value: IV


title: K318-Tp12

tag: normal

tag: batch i/ii

tag: histology

tag: age

value: malignant neoplasm of central portion of breast

value: central portion

tag: radicality


title: BC_coex_path_008

value: BC

value: no

tag: gender

tag: weight

tag: bodyheight

tag: bmi

tag: grading


title: BC_coex_path_010

tag: tumorsize

tag: ischemiatime

tag: tumorcontent

tag: organ

tag: dignity


title: BC_coex_path_006

tag: cancer type

tag: diseasecode

tag: diseasedescription

tag: primary / relapse tumor

tag: tumorlocalization


title: BC_coex_path_004

tag: normal

tag: batch i/ii

tag: histology

tag: age

tag: Stage


title: BC_coex_path_002

tag: gender

tag: weight

tag: bodyheight

tag: bmi

tag: radicality


title: K204-Tp11

tag: tumorsize

tag: ischemiatime

tag: tumorcontent

tag: organ

value: breast left

tag: grading


title: BC_coex_path_005

tag: cancer type

tag: diseasecode

tag: diseasedescription

tag: primary / relapse tumor

tag: dignity


title: BC_coex_path_001

tag: normal

tag: batch i/ii

tag: histology

tag: age

tag: tumorlocalization


title: BC_coex_path_009

tag: gender

tag: weight

tag: bodyheight

tag: bmi

tag: Stage


title: BC_coex_path_003

tag: tumorsize

tag: ischemiatime

tag: tumorcontent

tag: organ

tag: radicality


title: BC_coex_path_007

tag: cancer type

tag: diseasecode

tag: diseasedescription

tag: primary / relapse tumor

tag: grading


title: BAM_180d_biol_rep3

city: Bydgoszcz

first: Marta

last: Rasmus

address: Skłodowskiej-Curie 9

country: Poland

institute: Nicolaus Copernicus Univercity in Torun Ludwik Rydygier Collegium Medicum in Bydgoszcz

description: Gene expression analysis of reconstructed bladder wall 180 days after surgury

hyb_protocol: 600 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to the SurePrint G3 Rat Gene Expression 8x60K arrays for 17 hours at 65°C in a rotating hybridization oven. After the 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 on NimbleGen MS 200 Microarray Scanner (Roche, Switzerland) using one color scan setting for 8x60K array slides.

data_processing: Data were extracted from obtained images using the Agilent Feature Extraction software (Agilent Technologies, USA) with default parameters.

organism: Rattus norvegicus

source_name: Reconstructed urinary bladder wall_BAM_180d_biol_rep3

label_protocol: Low Input Quick Amp Labeling Kit, One-Color (Agilent Technologies, USA) was used to generate Cyanine 3-CTP labeled complementary RNA (cRNA) with a sample input of 50ng of total RNA. Amplified cRNA was then purified using the RNeasy Mini Kit (Qiagen, Germany). Cyanine-3 dye concentration, RNA absorbance ratio (260 nm/280 nm) and cRNA concentration were evaluated by the Varioskan LUX (Thermo Scientific, USA).

growth_protocol: Adipose tissue was harvested from the retroperitoneal space from forty ten-weeks male Wistar rats. ADSCs were isolated and cultered in the DMEM/Ham’s F12 supplemented with 10% FBS, 10ng/ml basic fibroblast growth factor (b-FGF, Thermo Fisher Scientific, USA), penicillin (100U/ml, HyClone, USA), streptomycin (100μg/ml, HyClone, USA) and amphotericin B (5µg/ml, BD, USA) at 37°C, 5% CO2 and 95% humidity until the third passage.

extract_protocol: The total RNA was isolated from reconstructed urinary bladder walls using High Pure RNA Tissue Kit (Roche Diagnostics, Switzerland) according to the manufacturer’s protocol. Quantity and purity of RNA were evaluated by A260, A280 and A230 measurements on NanoDrop (Thermo Scientific, USA) and the integrity of RNA was determined using RNA 6000 Nano Kit on the Agilent 2100 BioAnalyzer (Agilent Technologies, USA).

treatment_protocol: Eighty syngeneic male Wistar rats were divided into eight equal groups (n=10). Eighty rats underwent hemicystectomy and bladder augmentation with approximately 1cm2 of graft. In the groups from 1st to 4th urinary bladders were reconstructed with BAM seeded with 10x106 ADSCs. In the gruops from 5th to 8th urinary bladders were reconstructed with unseeded BAM. Animals from groups 1st and 5th, 2nd and 6th, 3rd and 7th, 4th and 8th were sacrificed after 7, 30, 90 and 180 days respectively. Augmented bladders were harvested, placed in RNAlater solution (Thermo Fisher Scientific, USA) and stored at -80°C.

value: male

tag: biomaterial

value: Bladder Acellular Matrix

tag: cells

tag: surgical procedure

value: hemicystectomy

tag: observation time

value: 180 days


title: BAM_180d_biol_rep4

source_name: Reconstructed urinary bladder wall_BAM_180d_biol_rep4

tag: gender


title: BAM_180d_biol_rep6

source_name: Reconstructed urinary bladder wall_BAM_180d_biol_rep6


title: BAM_180d_biol_rep8

source_name: Reconstructed urinary bladder wall_BAM_180d_biol_rep8


title: BAM_180d_biol_rep7

source_name: Reconstructed urinary bladder wall_BAM_180d_biol_rep7


title: BAM_ADSCs_180d_biol_rep8

source_name: Reconstructed urinary bladder wall_BAM_ADSCs_180d_biol_rep8

value: Adipose Derived Stem Cells


title: BAM_180d_biol_rep1

source_name: Reconstructed urinary bladder wall_BAM_180d_biol_rep1


title: BAM_ADSCs_90d_biol_rep8

description: Gene expression analysis of reconstructed bladder wall 90 days after surgury

source_name: Reconstructed urinary bladder wall_BAM_ADSCs_90d_biol_rep8

value: 90 days


title: BAM_ADSCs_180d_biol_rep5

source_name: Reconstructed urinary bladder wall_BAM_ADSCs_180d_biol_rep5


title: BAM_180d_biol_rep2

source_name: Reconstructed urinary bladder wall_BAM_180d_biol_rep2


title: BAM_180d_biol_rep5

source_name: Reconstructed urinary bladder wall_BAM_180d_biol_rep5


title: BAM_90d_biol_rep4

source_name: Reconstructed urinary bladder wall_BAM_90d_biol_rep4


title: BAM_ADSCs_180d_biol_rep1

source_name: Reconstructed urinary bladder wall_BAM_ADSCs_180d_biol_rep1


title: BAM_ADSCs_90d_biol_rep6

source_name: Reconstructed urinary bladder wall_BAM_ADSCs_90d_biol_rep6


title: BAM_ADSCs_180d_biol_rep6

source_name: Reconstructed urinary bladder wall_BAM_ADSCs_180d_biol_rep6


title: BAM_ADSCs_90d_biol_rep5

source_name: Reconstructed urinary bladder wall_BAM_ADSCs_90d_biol_rep5


title: BAM_ADSCs_180d_biol_rep4

source_name: Reconstructed urinary bladder wall_BAM_ADSCs_180d_biol_rep4


title: BAM_ADSCs_180d_biol_rep7

source_name: Reconstructed urinary bladder wall_BAM_ADSCs_180d_biol_rep7


title: BAM_90d_biol_rep1

source_name: Reconstructed urinary bladder wall_BAM_90d_biol_rep1


title: BAM_ADSCs_90d_biol_rep3

source_name: Reconstructed urinary bladder wall_BAM_ADSCs_90d_biol_rep3


title: BAM_90d_biol_rep3

source_name: Reconstructed urinary bladder wall_BAM_90d_biol_rep3


title: BAM_90d_biol_rep8

source_name: Reconstructed urinary bladder wall_BAM_90d_biol_rep8


title: BAM_90d_biol_rep6

source_name: Reconstructed urinary bladder wall_BAM_90d_biol_rep6


title: BAM_ADSCs_180d_biol_rep3

source_name: Reconstructed urinary bladder wall_BAM_ADSCs_180d_biol_rep3


title: BAM_90d_biol_rep2

source_name: Reconstructed urinary bladder wall_BAM_90d_biol_rep2


title: BAM_ADSCs_90d_biol_rep7

source_name: Reconstructed urinary bladder wall_BAM_ADSCs_90d_biol_rep7


title: BAM_ADSCs_90d_biol_rep4

source_name: Reconstructed urinary bladder wall_BAM_ADSCs_90d_biol_rep4


title: BAM_ADSCs_180d_biol_rep2

source_name: Reconstructed urinary bladder wall_BAM_ADSCs_180d_biol_rep2


title: BAM_90d_biol_rep5

source_name: Reconstructed urinary bladder wall_BAM_90d_biol_rep5


title: BAM_90d_biol_rep7

source_name: Reconstructed urinary bladder wall_BAM_90d_biol_rep7


title: BAM_30d_biol_rep6

description: Gene expression analysis of reconstructed bladder wall 30 days after surgury

source_name: Reconstructed urinary bladder wall_BAM_30d_biol_rep6

value: 30 days


title: BAM_30d_biol_rep8

source_name: Reconstructed urinary bladder wall_BAM_30d_biol_rep8


title: BAM_ADSCs_90d_biol_rep2

source_name: Reconstructed urinary bladder wall_BAM_ADSCs_90d_biol_rep2


title: BAM_30d_biol_rep5

source_name: Reconstructed urinary bladder wall_BAM_30d_biol_rep5


title: BAM_30d_biol_rep2

source_name: Reconstructed urinary bladder wall_BAM_30d_biol_rep2


title: BAM_30d_biol_rep7

source_name: Reconstructed urinary bladder wall_BAM_30d_biol_rep7


title: BAM_ADSCs_30d_biol_rep6

source_name: Reconstructed urinary bladder wall_BAM_ADSCs_30d_biol_rep6


title: BAM_ADSCs_90d_biol_rep1

source_name: Reconstructed urinary bladder wall_BAM_ADSCs_90d_biol_rep1


title: BAM_7d_biol_rep1

description: Gene expression analysis of reconstructed bladder wall 7 days after surgury

source_name: Reconstructed urinary bladder wall_BAM_7d_biol_rep1

value: 7 days


title: BAM_7d_biol_rep3

source_name: Reconstructed urinary bladder wall_BAM_7d_biol_rep3


title: BAM_ADSCs_30d_biol_rep3

source_name: Reconstructed urinary bladder wall_BAM_ADSCs_30d_biol_rep3


title: BAM_7d_biol_rep5

source_name: Reconstructed urinary bladder wall_BAM_7d_biol_rep5


title: BAM_30d_biol_rep4

source_name: Reconstructed urinary bladder wall_BAM_30d_biol_rep4


title: BAM_7d_biol_rep8

source_name: Reconstructed urinary bladder wall_BAM_7d_biol_rep8


title: BAM_7d_biol_rep7

source_name: Reconstructed urinary bladder wall_BAM_7d_biol_rep7


title: BAM_7d_biol_rep6

source_name: Reconstructed urinary bladder wall_BAM_7d_biol_rep6


title: BAM_7d_biol_rep2

source_name: Reconstructed urinary bladder wall_BAM_7d_biol_rep2


title: BAM_ADSCs_30d_biol_rep4

source_name: Reconstructed urinary bladder wall_BAM_ADSCs_30d_biol_rep4


title: BAM_ADSCs_30d_biol_rep5

source_name: Reconstructed urinary bladder wall_BAM_ADSCs_30d_biol_rep5


title: BAM_30d_biol_rep3

source_name: Reconstructed urinary bladder wall_BAM_30d_biol_rep3


title: BAM_ADSCs_7d_biol_rep8

source_name: Reconstructed urinary bladder wall_BAM_ADSCs_7d_biol_rep8


title: BAM_ADSCs_7d_biol_rep7

source_name: Reconstructed urinary bladder wall_BAM_ADSCs_7d_biol_rep7


title: BAM_ADSCs_30d_biol_rep1

source_name: Reconstructed urinary bladder wall_BAM_ADSCs_30d_biol_rep1


title: BAM_ADSCs_7d_biol_rep5

source_name: Reconstructed urinary bladder wall_BAM_ADSCs_7d_biol_rep5


title: BAM_ADSCs_30d_biol_rep7

source_name: Reconstructed urinary bladder wall_BAM_ADSCs_30d_biol_rep7


title: BAM_ADSCs_30d_biol_rep8

source_name: Reconstructed urinary bladder wall_BAM_ADSCs_30d_biol_rep8


title: BAM_7d_biol_rep4

source_name: Reconstructed urinary bladder wall_BAM_7d_biol_rep4


title: BAM_30d_biol_rep1

source_name: Reconstructed urinary bladder wall_BAM_30d_biol_rep1


title: BAM_ADSCs_7d_biol_rep6

source_name: Reconstructed urinary bladder wall_BAM_ADSCs_7d_biol_rep6


title: BAM_ADSCs_30d_biol_rep2

source_name: Reconstructed urinary bladder wall_BAM_ADSCs_30d_biol_rep2


title: BAM_ADSCs_7d_biol_rep4

source_name: Reconstructed urinary bladder wall_BAM_ADSCs_7d_biol_rep4


title: placenta-conditioned ECM rep2

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

department: Biology

country: Israel

institute: Tel Aviv University

description: gene expression data after placeta-ECM treatment

hyb_protocol: according to the manufacturer's protocol (Affymetrix, Santa Clara, CA, USA)

data_processing: Gene-level analyses was performed. RMA normalization, summarization by mean and batch effect removal, all were done by Partek Genomics suite (version 6.4) Copyright ©

source_name: Human MCF-7 cells

growth_protocol: MCF-7 breast cancer cells were grown in Dulbecco’s  modified eagle’s medium (DMEM) supplemented  with 10% fetal calf serum (FCS), L-glutamine  (2 mM), and Pen-Strep-Nystatin antibiotics (Biological  Industries, Beit Haemek, Israel). All cell cultures  were maintained in 5% CO2 at 378C.

extract_protocol: RNA was extracted using the RNeasy kit (QAIGEN, Valencia, CA) according to manufacturer’s instructions.

treatment_protocol: Placentae at 6–9 wk of gestation were retrieved from  normal pregnancies terminated for psychosocial  reasons (1,2). Placental villi of 10mg wet weight or  control BCCL (MCF-7) were cultured in  24 well plates previously coated with 10mg/mL  Matrigel (BD Biosciences, Bedford, MA). After 24 h,  explants/cells were removed. BCCL were added to  the conditioned matrixes and cultured for additional  24 h.

tag: tissue

value: Human MCF-7 cells

tag: placenta source

value: Placentae at 6–9 wk of gestation

tag: treatment

value: placenta-conditioned ECM


title: BAM_ADSCs_7d_biol_rep2

source_name: Reconstructed urinary bladder wall_BAM_ADSCs_7d_biol_rep2


title: BAM_ADSCs_7d_biol_rep3

source_name: Reconstructed urinary bladder wall_BAM_ADSCs_7d_biol_rep3


title: BAM_ADSCs_7d_biol_rep1

description: Gene expression analysis in tissue engineered urinary bladder 7 days after the reconstruction

source_name: Reconstructed urinary bladder wall_BAM_ADSCs_7d_biol_rep1


title: Stable lentivirus infected BGC-823 cells with the lentiviral vector containing interference control sequence

city: Jinan

first: Guoying

last: Dong

state: Shandong

address: Jinan lixia district Wenhua west road no. 44

department: Cheeloo College of Medicine

country: China

institute: Shandong University

description: IN-con

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60°C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies).

source_name: Human Gastric cancer

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology). Briefly, total RNA from each sample was linearly amplified and labeled with Cy3-UTP. The Labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: The cells inoculated into cell culture plate of φ3.0cm,adding 0.5ug/ml puromycin.Aafter 48 hours we  collected samples of cells

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

treatment_protocol: Washing three times with 1×PBS ,then Lyse cells directly in a culture dish by adding 1 ml of TRIzol to a 3.5 c Reagent m diameter dish, and passing the cell lysate several times through a pipette.

tag: cell type

value: Gastric cancer

tag: cell line

value: Stomach

tag: lentiviral construct

value: interference control sequence


title: Stable lentivirus infected BGC-823 cells with the lentiviral vector containing interference sequence targeting SIRT1

description: IN-S

value: interference sequence of SIRT1


title: ECM rep1

description: gene expression data after ECM treatment

scan_protocol: according to the manufacturer's protocol (Affymetrix, Santa Clara, CA, USA)

value: ECM


title: Kibble-timepoint9_and_Meat-timepoint9_replicate_1

city: Lincoln

first: Paul

last: Maclean

address: Cnr Springs Road and Gerald Street

country: New Zealand

institute: AgResearch NZ LTD

description: A8; Kibble 9 weeks,Meat 9 weeks replicate 1

hyb_protocol: Samples were hybridized to the microarrays using a loop design, where samples labelled with Cy3 were competitively hybridized with samples labelled with Cy5.

scan_protocol: Microarrays were scanned using an Agilent Technologies Scanner G2505C US81303224

data_processing: Agilent Feature Extraction Software (v 10.10.1.1) was using to calculate fluorescence values.  Loess within array and Aquantile between array normalisation was carried out using the limma package in R (3.2.1)

organism: Canis lupus familiaris

source_name: PBMCs  from adult fed Kibble diet, timepoint 9

label_protocol: 200 ng of sample RNA were linearly amplified with Cy3 and cy 5 labelled CTP using the Agilent Low Input Linear Amplification kit according to the manufacturers instructions.

growth_protocol: Dogs were fed either 1 of 2 diets over a period of 9 weeks

extract_protocol: PBMCs were isolated from the blood samples using the density centrifugation media Lympholyte®-Mammal (Cedarlane Laboratories; CL5110) and stored in RNAprotect Cell Reagent (Qiagen, 74624) at -80C until required. Total RNA was extracted from the PBMC samples using the RNeasy Protect Cell Mini Kit (Qiagen, 74624). All samples passed the technical threshold requirements for amplification and labelling, based on RIN (Agilent 2100 Bioanalyzer; Agilent Technologies).

treatment_protocol: Adult dogs were exclusively fed either a carbohydrate-containing premium kibbled diet (Kibble; n = 8) or a high-protein and high-fat raw red meat diet (Meat; n = 7) for nine weeks.

tag: fed with

value: Kibble diet

tag: time point

value: timepoint 9

value: Peripheral blood mononuclear cell (PBMCs)

source_name: PBMCs  from adult fed Meat diet, timepoint 9

value: Meat diet


title: Stable lentivirus infected BGC-823 cells with the lentiviral expressing vector containing SIRT1 cDNA sequence

description: EX-S

value: SIRT1 cDNA sequence


title: placenta-conditioned ECM rep1

label_protocol: according to the manufacturer's protocol (Affymetrix, Santa Clara, CA, USA)


title: Stable lentivirus infected BGC-823 cells with the lentiviral expressing vector

description: EX-con

value: expression control sequence


title: Kibble-timepoint9_and_Meat-timepoint9_replicate_2

description: D8; Kibble 9 weeks,Meat 9 weeks replicate 2


title: Meat-timepoint0_and_Kibble-timepoint0_replicate_2

description: D5; Meat 0 weeks,Kibble 0 weeks replicate 2

source_name: PBMCs  from adult fed Meat diet, timepoint 0

value: timepoint 0

source_name: PBMCs  from adult fed Kibble diet, timepoint 0


title: Meat-timepoint0_and_Kibble-timepoint0_replicate_1

description: B5; Meat 0 weeks,Kibble 0 weeks replicate 1


title: Kibble-timepoint6_and_Meat-timepoint6_replicate_2

description: D7; Kibble 6 weeks,Meat 6 weeks replicate 2

source_name: PBMCs  from adult fed Kibble diet, timepoint 6

value: timepoint 6

source_name: PBMCs  from adult fed Meat diet, timepoint 6


title: Meat-timepoint9_and_Kibble-timepoint9_replicate_1

description: C7; Meat 9 weeks,Kibble 9 weeks replicate 1


title: Kibble-timepoint0_and_Meat-timepoint0_replicate_1

description: C5; Kibble 0 weeks,Meat 0 weeks replicate 1


title: Kibble-timepoint3_and_Meat-timepoint3_replicate_1

description: A5; Kibble 3 weeks,Meat 3 weeks replicate 1

source_name: PBMCs  from adult fed Kibble diet, timepoint 3

value: timepoint 3

source_name: PBMCs  from adult fed Meat diet, timepoint 3


title: Meat-timepoint9_and_Kibble-timepoint9_replicate_2

description: B7; Meat 9 weeks,Kibble 9 weeks replicate 2


title: Meat-timepoint6_and_Kibble-timepoint6_replicate_1

description: C6; Meat 6 weeks,Kibble 6 weeks replicate 1


title: Meat-timepoint3_and_Kibble-timepoint3_replicate_1

description: A6; Meat 3 weeks,Kibble 3 weeks replicate 1


title: Kibble-timepoint6_and_Meat-timepoint6_replicate_1

description: B6; Kibble 6 weeks,Meat 6 weeks replicate 1


title: ECM rep2

value: Human MCF-7 cells


title: Meat-timepoint6_and_Kibble-timepoint6_replicate_2

description: A7; Meat 6 weeks,Kibble 6 weeks replicate 2


title: Kibble-timepoint3_and_Kibble-timepoint6_replicate_4

description: B4; Kibble 3 weeks,Kibble 6 weeks replicate 4


title: Meat-timepoint6_and_Meat-timepoint3_replicate_4

description: C4; Meat 6 weeks,Meat 3 weeks replicate 4


title: Meat-timepoint3_and_Kibble-timepoint3_replicate_2

description: D6; Meat 3 weeks,Kibble 3 weeks replicate 2


title: Kibble-timepoint3_and_Kibble-timepoint6_replicate_3

description: D4; Kibble 3 weeks,Kibble 6 weeks replicate 3


title: Meat-timepoint6_and_Meat-timepoint3_replicate_3

description: A4; Meat 6 weeks,Meat 3 weeks replicate 3


title: Meat-timepoint6_and_Meat-timepoint3_replicate_2

description: B3; Meat 6 weeks,Meat 3 weeks replicate 2


title: Meat-timepoint9_and_Meat-timepoint0_replicate_2

description: D1; Meat 9 weeks,Meat 0 weeks replicate 2


title: Meat-timepoint9_and_Meat-timepoint0_replicate_1

description: B1; Meat 9 weeks,Meat 0 weeks replicate 1


title: Kibble-timepoint0_and_Kibble-timepoint9_replicate_3

description: B2; Kibble 0 weeks,Kibble 9 weeks replicate 3


title: Meat-timepoint9_and_Meat-timepoint0_replicate_4

description: A2; Meat 9 weeks,Meat 0 weeks replicate 4


title: Kibble-timepoint3_and_Kibble-timepoint6_replicate_1

description: C3; Kibble 3 weeks,Kibble 6 weeks replicate 1


title: Kibble-timepoint3_and_Kibble-timepoint6_replicate_2

description: A3; Kibble 3 weeks,Kibble 6 weeks replicate 2


title: Meat-timepoint6_and_Meat-timepoint3_replicate_1

description: D3; Meat 6 weeks,Meat 3 weeks replicate 1


title: Kibble-timepoint0_and_Kibble-timepoint9_replicate_4

description: D2; Kibble 0 weeks,Kibble 9 weeks replicate 4


title: Kibble-timepoint0_and_Kibble-timepoint9_replicate_2

description: C1; Kibble 0 weeks,Kibble 9 weeks replicate 2


title: Meat-timepoint9_and_Meat-timepoint0_replicate_3

description: C2; Meat 9 weeks,Meat 0 weeks replicate 3


title: Control miRNA mimic, Pull Down, Biological rep 1

status: Public on Sep 06 2017

city: Madision

first: Ashley

last: Strong

state: WI

address: 7418 1111 Highland Drive

department: Dermatology

institute: UW-Madison

description: Biotinylated cel-miR-67 mimic, pulled down RNA fraction

hyb_protocol: RNA quality was assessed prior to performing the microarray analysis on an Agilent 2100 BioAnalyzer (Santa Clara, CA) and samples were hybridized to GeneChip® Human Gene 2.0 ST arrays (#902499, Affymetrix, Santa Clara, CA) according to manufacturer’s instructions.

scan_protocol: Microarrays were scanned using the GeneChip Scanner 3000.

data_processing: The quality of the microarray data was assessed using the affyPLM and Affy Software (Affymetrix). Data pre-processing and normalization were performed using the affy package (https://www.ncbi.nlm.nih.gov/pubmed/12538238). Raw data were normalized by the Robust Multichip Analysis (RMA) approach. To identify differentially expressed genes, the linear modeling approach and empirical Bayes statistics as implemented in the limma package (https://www.ncbi.nlm.nih.gov/pubmed/25605792) were employed. The p-values were adjusted using the Benjamini and Hochberg method (Hochberg and Benjamini 1995). Probes with an absolute fold change of ≥ 1.2 and a p-value < 0.05 were considered as significantly differentially expressed. An enrichment ratio was calculated for each mRNA probe evaluated on the microarray: [Bi-hsa-miR-340 pull-down/Bi-cel-miR-67 pull-down]/[Bi-hsa-miR-340 input/Bi-cel-miR-67 input]. A ratio ≥2.5 was considered significant enrichment.

label: Biotin

source_name: 451 Lu melanoma cells transfected with control miRNA mimic, pull down fraction

label_protocol: Total RNA from miRZip™ and miFAST cleaned-up samples were amplified, using the manufacturer’s protocol, with the Ambion® WT Expression kit (Life Technologies) and labeled, according to manufacturer’s protocol, using the GeneChip® WT Terminal Labeling kit (Affymetrix, Santa Clara, CA) at the University of Wisconsin Madison Biotechnology Center Gene Expression Center core facility (Madison, WI).

growth_protocol: 451 Lu cells were grown in Eagle’s Minimum Essential Medium (EMEM; Corning Cellgro, Manassas, VA) supplemented with 4.5g/L glucose, L-glutamine, 1 mM sodium pyruvate, and 1 mM non-essential amino acids supplemented with 10% (% v/v) heat-inactivated FBS and grown at 37°C in a humidified atmosphere of 5% CO2.

extract_protocol: Total RNA was isolated and extracted using the Direct-zol RNA Mini-prep™ kit (Zymo Research) with TRI Reagent® (Molecular Research Center, Inc.).

treatment_protocol: miRZip™ scrambled hairpin RNA control and miRZip™ miR-340 miRNA inhibiting vectors containing green fluorescent protein (GFP) were transfected into 451 Lu cells using Lipofectamine® 2000 (Life Technologies). 24 h later, transfection medium was removed and cells were collected for cell sorting and GFP analysis. GFP-positive cells were collected using a high-speed FACSAriaIII™ cell sorter (BD Biosciences, San Jose, CA). Cells were washed twice with 1x PBS and pelleted at 1,000 x g for 5 min.

value: 451 Lu melanoma cells


title: miR-340 inhibitor, Biological rep 1

description: miR-340 inhibitor

source_name: 451 Lu melanoma cells transfected with miR-340 miRNA inhibitor


title: miR-340 inhibitor, Biological rep 3

description: miR-340 inhibitor


title: Control miRNA mimic, Input, Biological rep 1

description: Biotinylated cel-miR-67 mimic, total RNA input fraction

source_name: 451 Lu melanoma cells transfected with control miRNA mimic, input fraction


title: Control miRNA inhibitor, Biological rep 1

description: non-targeting control miRNA inhibitor

source_name: 451 Lu melanoma cells transfected with control miRNA inhibitor


title: miR-340 mimic, Pull Down, Biological rep 3

description: Biotinylated miR-340 mimic, pulled down RNA fraction

source_name: 451 Lu melanoma cells transfected with miR-340 mimic, pull down fraction


title: miR-340 mimic, Pull Down, Biological rep 2


title: miR-340 mimic, Input, Biological rep 2

description: Biotinylated miR-340 mimic, total RNA input fraction

source_name: 451 Lu melanoma cells transfected with miR-340 mimic, input fraction


title: miR-340 mimic, Input, Biological rep 3


title: Control miRNA mimic, Input, Biological rep 2


title: miR-340 inhibitor, Biological rep 2

description: miR-340 inhibitor


title: Control miRNA inhibitor, Biological rep 2

description: non-targeting control miRNA inhibitor


title: Control miRNA inhibitor, Biological rep 3

description: non-targeting control miRNA inhibitor


title: Control miRNA mimic, Pull Down, Biological rep 2


title: miR-340 mimic, Pull Down, Biological rep 1


title: Kibble-timepoint0_and_Kibble-timepoint9_replicate_1

description: A1; Kibble 0 weeks,Kibble 9 weeks replicate 1


title: miR-340 mimic, Input, Biological rep 1


title: Control miRNA mimic, Input, Biological rep 3


title: Control miRNA mimic, Pull Down, Biological rep 3


title: KO-2-1 (BAG3-KO HeLa cells, clone 2-1)

city: Toyama

first: Yoshiaki

last: Tabuchi

state: Toyama

address: 2630 Sugitani

department: Life Science Research Center

country: Japan

institute: University of Toyama

description:
KO-2-1
BAG3-KO HeLa cells, clone 2-1
HeLa cell line: Originated from female, 31yr, cervix; infinite lifespan, epithelial-like morphology.

hyb_protocol: After fragmentation, the biotinylated cRNA was hybridized to arrays at 45°C for 16 h.

scan_protocol: The arrays were washed, stained with streptavidin-phycoerythrin and scanned with a probe array scanner (Affymetrix).

data_processing: GeneChip Analysis Suite

source_name: Human cervical carcinoma cell line HeLa, BAG3-KO

label_protocol: 500 ng of total RNA was used to synthesize cRNA with a GeneChip 3’ IVT Express Kit (Affymetrix).

growth_protocol: HeLa cells were cultured in Eagle's Minimum Essential medium supplemented with 10% fetal bovine serum at 37°C in humidified air with 5% CO2 and 95% air.

extract_protocol: Total RNA was extracted from cells using a NucleoSpin® RNA isolation kit (MACHEREY-NAGEL GmbH) along with on-column DNase I treatment. RNA quality was analyzed using a Bioanalyzer 2100 (Agilent Technologies). RNA samples with RIN (RNA integrity number) values >9.5 were considered acceptable.

treatment_protocol: Human cervical carcinoma cell line HeLa cells (wild type), and BAG3-KO HeLa cells (clone 1 and clone 2) were used.

value: HeLa

tag: genotype/variation


title: LMTV_NMuMG-ErbB2/VC_phenformin_3

city: Montreal

first: Julie

last: St-Pierre

state: Quebec

address: 3655 Promenade Sir William Osler

department: Department of Biochemistry

country: Canada

institute: McGill University

description:
cell culture
expression data of explants from LMTV injections of mice injected with control cells. explants treated with phenformin  for 4 days

hyb_protocol: After fragmentation and labeling, 4 µg DNA target was hybridized on GeneChip® Mouse Clariom™ S (ThermoFisher)  and incubated at 450C in the Genechip® Hybridization oven 640 (ThermoFisher) for 17 hours at 60 rpm

scan_protocol: The microarrays were finally scanned on a GeneChip® scanner 3000 (ThermoFisher).

data_processing: Bioconductor. The file 'normalized_data_allcontrols.txt' contains data for all probe sets including controls. The sample table does not include data for AFFX controls or *RPTR controls.

label: Aurum Total RNA Mini Kit

organism: Mus musculus

source_name: LMTV, control,phenformin 4 days

label_protocol: Sense-strand cDNA was synthesized from 10 ng of total RNA and fragmentation and labeling were performed to produce ds DNA with the GeneChip® Pico Labeling Kit according to manufacturer’s instructions (Applied Biosystems)

growth_protocol: LMTV explants were grown as described in this paper, materials and methods

extract_protocol: RNA from LMTV explants were isolated in tissue culture using an Aurum Total RNA Mini Kit.

treatment_protocol: LMTV explants were treated with phenformin (100uM) or dh20 control for 4 days

value: LMTV_NMuMG-ErbB2/VC (control)

value: lung metastatis explants


title: LMTV_NMuMG-ErbB2/VC_phenformin_1


title: KO-1-2 (BAG3-KO HeLa cells, clone 1-2)

description:
KO-1-2
BAG3-KO HeLa cells, clone 1-2
HeLa cell line: Originated from female, 31yr, cervix; infinite lifespan, epithelial-like morphology.


title: LMTV_NMuMG-ErbB2/PGC-1alpha_phenformin_3

description:
cell culture
expression data of explants from LMTV injections of mice injected with PGC1alpha cells. explants treated with phenformin for 4 days

source_name: LMTV, PGC1alpha, phenformin 4 days

value: LMTV_NMuMG-ErbB2/PGC- 1alpha


title: KO-2-2 (BAG3-KO HeLa cells, clone 2-2)

description:
KO-2-2
BAG3-KO HeLa cells, clone 2-2
HeLa cell line: Originated from female, 31yr, cervix; infinite lifespan, epithelial-like morphology.


title: LMTV_NMuMG-ErbB2/PGC-1alpha_phenformin_1


title: LMTV_NMuMG-ErbB2/VC_ctrl_2

description:
cell culture
expression data of explants from LMTV injections of mice injected with control cells. explants treated with dh20  control for 4 days

source_name: LMTV, control,dh20


title: LMTV_NMuMG-ErbB2/VC_phenformin_2


title: LMTV_NMuMG-ErbB2/VC_ctrl_3


title: WT-1 (wild type HeLa cells)

description:
WT-1
Wild type HeLa cells-1
HeLa cell line: Originated from female, 31yr, cervix; infinite lifespan, epithelial-like morphology.

source_name: Human cervical carcinoma cell line HeLa, WT

value: WT


title: LMTV_NMuMG-ErbB2/VC_ctrl_1


title: LMTV_NMuMG-ErbB2/PGC-1alpha_phenformin_2


title: WT-2 (wild type HeLa cells)

description:
WT-2
Wild type HeLa cells-2
HeLa cell line: Originated from female, 31yr, cervix; infinite lifespan, epithelial-like morphology.


title: Rep-iPSC iPSvsHF

city: México

first: Karlen

last: Gazarian

state: Mexico

address: Circuito Exterior 3

department: Genomic Medicine

country: Mexico

institute: Instituto de Investigaciones Biomédicas

description: HDF passage 7

hyb_protocol: Equal quantities of labeled cDNA were hybridized using hybridization solution UniHyb (TeleChem International INC). The arrays were incubated for 14 h at 42°C, and then washed tree times with 1X SCC, 0.05 % SDS at room temperature.

scan_protocol: Acquisition and quantification of array images was performed in GenePix 4100A with its accompanying software GenePix from Molecular Devices. All images were captured using 10µm resolution.

data_processing: For each spot the Alexa555 and Alexa647 density mean value and background mean value were calculated with software ArrayPro Analyzer from Media Cibernetics. Microarray data analysis was performed with genArise, developed in the Computing Unit of Cellular Physiology Institute of UNAM (http://www.ifc.unam.mx/genarise/). GenArise carry out a number of transformations: background correction, lowess normalization, intensity filter, replicates analysis and selecting differentially expressed genes.

source_name: hiPSC at passage 20

label_protocol: 10 µg of total RNA was used for cDNA synthesis, incorporating dUTP-Alexa555 or dUTP-Alexa647 employing the Firs-Strand cDNA labeling kit (Invitrogen). Incorporation of fluorophore was analyzed by using the absorbance at 555 nm for Alexa555 and 650 nm for Alexa647.

growth_protocol: All samples were cultured in TeSR-E8 medium (Stem Cell Technologies) before total RNA extract preparation

extract_protocol: Total RNA extacted using Trizol followed by DNAse treatment and column clean-up

value: Stable iPSC line generated from HDF (ATCC:PCS-201-010) using Sendai vectors (Cytotune 2.0, Life technologies)

source_name: Human dermal fibroblasts

value: Human dermal fibroblasts


title: RepD20-Diff

description: HDF passage 7

source_name: Differentiated colonies at day 20 post-transduction

value: Differentiated colonies and outgrowths within colonies at day 20 after transduction of HDF (ATCC:PCS-201-010) with the lentiviral vectors O2S (Addgene:21162) and K2M (Addgene:21164)


title: RepD20-Comp

description: HDF passage 7

source_name: Compact colonies at day 20 post-transduction

value: Compac ES-like colonies at day 20 after transduction of HDF (ATCC:PCS-201-010) with the lentiviral vectors O2S (Addgene:21162) and K2M (Addgene:21164)


title: NMuMG-ErbB2/VC_Phenformin4

description: expression data of lung metastatic tissue from mice injected with control cells, treated with phenformin

data_processing: Bioconductor Oligo R package. The file 'normalized_data_allcontrols.txt' contains data for all probe sets including controls. The sample table does not include data for AFFX controls or *RPTR controls.

label: pico RNA kit

source_name: lung metastasis, control, Phenformin

growth_protocol: lung metastasis from mice treated with phenformin or PBS was extracted by laser capture microdissection (LCM) from slides

extract_protocol: Lung metastasis RNA was isolated using LCM and pico RNA kit.

treatment_protocol: lung were perfused with 50% optimal cutting temperature solution, diluted in PBS and removed and embedded in OCT at -80degC

value: metastasis lung tissue

value: NMuMG-ErbB2/VC (control)


title: Rep-iPSC HFvsiPS

description: HDF passage 7


title: LMTV_NMuMG-ErbB2/PGC-1alpha_ctrl_1

description:
cell culture
expression data of explants from LMTV injections of mice injected with PGC1alpha cells. explants treated with dh20 control for 4 days

source_name: LMTV, PGC1alpha, dh20


title: NMuMG-ErbB2/VC_PBS_2

description: expression data of lung metastatic tissue from mice injected with control cells, treated with PBS

source_name: lung metastasis, control, PBS


title: NMuMG-ErbB2/VC_Phenformin2


title: LMTV_NMuMG-ErbB2/PGC-1alpha_ctrl_3


title: NMuMG-ErbB2/VC_PBS_1


title: NMuMG-ErbB2/VC_PBS_5


title: NMuMG-ErbB2/VC_PBS_4


title: NMuMG-ErbB2/VC_PBS_3


title: NMuMG-ErbB2/VC_Phenformin3


title: LMTV_NMuMG-ErbB2/PGC-1alpha_ctrl_2


title: NMuMG-ErbB2/VC_Phenformin5


title: NMuMG-ErbB2/VC_Phenformin1


title: KO-1-1 (BAG3-KO HeLa cells, clone 1-1)

description:
KO-1-1
BAG3-KO HeLa cells, clone 1-1
HeLa cell line: Originated from female, 31yr, cervix; infinite lifespan, epithelial-like morphology.


title: NMuMG-ErbB2/PGC-1alpha_Phenformin5

description: expression data of lung metastatic tissue from mice injected with PGC1alpha cells, treated with phenformin

source_name: lung metastasis, PGC1alpha, Phenformin

value: NMuMG-ErbB2/PGC- 1alpha


title: NMuMG-ErbB2/PGC-1alpha_PBS_3

description: expression data of lung metastatic tissue from mice injected with PGC1alpha cells, treated with PBS

source_name: lung metastasis, PGC1alpha, PBS


title: MDAMB231_4175_siPGC1alpha_1

description:
cell culture
expression data from human lung metastatic 4175 cells treated with siPGC1alpha

hyb_protocol: After fragmentation and labeling, 4 µg DNA target was hybridized on  GeneChip® Human Clariom™ S (ThermoFisher)and incubated at 450C in the Genechip® Hybridization oven 640 (ThermoFisher) for 17 hours at 60 rpm

data_processing: Bioconductor. The file 'normalized_data_allcontrols.txt' contains data for all probe sets including controls. The sample table does not include data for AFFX controls, *RPTR controls or probe sets named with 230*.

source_name: 4175 cells, siPGC1alpha

growth_protocol: 4175 cells were cultured and grown as described in this paper, materials and methods

extract_protocol: RNA from 4175 cells were isolated in tissue culture using an Aurum Total RNA Mini Kit.

treatment_protocol: 4175 cells were treated with sicontrol or sipgc1alpha as described here, materials and methods

value: MDA-MB-231 lung variant (4175)


title: NMuMG-ErbB2/PGC-1alpha_Phenformin3


title: NMuMG-ErbB2/PGC-1alpha_PBS_1


title: NMuMG-ErbB2/PGC-1alpha_PBS_4


title: NMuMG-ErbB2/PGC-1alpha_PBS_5


title: MDAMB231_4175_siPGC1alpha_2


title: NMuMG-ErbB2/PGC-1alpha_PBS_2


title: NMuMG-ErbB2/PGC-1alpha_Phenformin6


title: NMuMG-ErbB2/PGC-1alpha_Phenformin4


title: MDAMB231_4175_siPGC1alpha_3


title: NMuMG-ErbB2/PGC-1alpha_Phenformin2


title: MDAMB231_4175_sicontrol_3

description:
cell culture
expression data from human lung metastatic 4175 cells treated with sicontrol

source_name: 4175 cells, sicontrol


title: NMuMG-ErbB2/PGC-1alpha_PBS_6


title: NMuMG-ErbB2/PGC-1alpha_Phenformin1


title: patient44

status: Public on Sep 05 2017

city: Paris

first: Anavaj

last: Sakuntabhai

address: 28 rue du Dr Roux

department: Genome and Genetics

country: France

institute: Institut Pasteur

hyb_protocol: GeneChip hybridization protocol (Affymetrix)

scan_protocol: GeneChip Scanner 3000, AGCC

data_processing: Expression Console v1.3.1 (Affymetrix) SST-RMA default parameters

source_name: asymptomatic_Dengue patient_PBMCs

label_protocol: GeneChip WT terminal labeling kit (Affymetrix)

growth_protocol: no cell growth

extract_protocol: RNA extraction with Rneasy kit (Qiagen)

treatment_protocol: PBMC were separated on Ficoll-Paque density gradient centrifugation and stored in RNA-later

tag: disease state

value: asymptomatic

tag: Sex

value: F

tag: age

tag: viral load

value: peripheral blood mononuclear cells (PBMCs)

tag: scanner

tag: scan date


title: MDAMB231_4175_sicontrol_1


title: patient35

source_name: DFDHF_Dengue patient_PBMCs

value: dengue fever (DF)/dengue hemorrhagic fever (DHF)


title: patient32

source_name: DSS_Dengue patient_PBMCs

value: dengue shock syndrome (DSS)


title: patient43


title: patient30

value: M


title: patient34


title: patient41


title: MDAMB231_4175_sicontrol_2


title: patient38


title: patient28


title: patient33


title: patient29


title: patient20


title: patient25


title: patient8


title: patient23


title: patient21


title: patient9


title: patient13


title: patient15


title: patient14


title: patient22


title: patient7


title: patient6


title: patient11


title: patient12


title: patient10


title: patient26


title: patient5


title: patient2


title: patient1


title: patient3


title: patient4


title: Mock control Human MCF10A cells, rep2 [mRNA profile]

city: GRENOBLE

first: Odile

last: FILHOL

address: 17, rue des martyrs

department: BIG

institute: INSERM-CEA

hyb_protocol: According to Cogenics/Agilent protocol.

scan_protocol: Microarrays were scanned and raw data extracted from the scanned image using Feature Extraction version 10.7.

data_processing: Quantile normalization on the probe values was performed using R version 2.15.0. Data under the background were removed.

source_name: MCF10A cells, control

label_protocol: Five hundred ng of total RNA was converted into labeled cRNA with nucleotides coupled to fluorescent dye Cy3 using the Low RNA Input Linear Amplification Kit (Agilent Technologies, Palo Alto, CA) following the manufacturer’s protocol.

growth_protocol:
MCF-10A is a spontaneously immortalized, but nontransformed human mammary epithelial cell line derived from the breast tissue of a 36-year-old patient with fibrocystic changes.
MCF-10A cells are grown on standard tissue culture plastic in a 5% CO2 humidified incubator at 37°C. The growth medium contains several additives and is composed of DMEM/F12 supplemented with 5% donor horse serum, 20 ng/ml epidermal growth factor (EGF), 10 µg/ml insulin, 0.5 µg/ml hydrocortisone, 100 ng/ml cholera toxin, and antibiotics. MCF-10A cells should not be allowed to grow for more than 2 to 3 days without passage.

extract_protocol: Total RNA extraction was performed using Absolutely RNA Miniprep kit (Agilent).

treatment_protocol: MCF10A cells were grown as described for 3 days. Stable silencing of gene expression in MCF10A cells was accomplished by transduction with lentiviruses pLKO1 (SHVRCS-TRCN000003796, Sigma-Mission) followed by selection with puromycin (# 96). Specificity of the CK2β knockdown was checked by performing a complementation assay using a chicken CK2β which expression is not affected by the shRNA (# F2).The control cells (Mock-) were transduced with an empty pLKO1 vector.

value: Mock control


title: ΔCK2β-modified MCF10A cells, rep2 [mRNA profile]

source_name: MCF10A cells, ΔCK2β

value: CK2beta knockdown


title: wild-type 2D2 T cells, biological rep2

city: Los Angeles

first: Lili

last: Yang

state: CA

address: 610 Charles E. Young Dr. East, TLSB 3032

department: MIMG

institute: University of California, Los Angeles

description: Gene expression data from 2D2 effector T cells

hyb_protocol: Following fragmentation, 10 μg of cRNA was hybridized for 16 hours at 45°C on the microarray.

scan_protocol: GeneChips were washed and stained in the Affymetrix Fluidics Station 450 and then scanned using the GeneChip Scanner 3000 7G.

data_processing: Gene expression level analysis and normalization were performed using the Affymetrix Microarray Suite 5 (mas5.0) method and the Affymetrix Transcriptome Analysis Console (TAC) 2.0 software.

source_name: 2D2 T cells

label_protocol: Biotinylated complementary RNA (cRNA) was prepared from 100 ng total RNA.

growth_protocol: Naïve CD4 T cells sorted from wildtype and miR-146a-deficient 2D2 Tg mice (denoted as 2D2 and 2D2KO T cells, respectively) were cultured in a 24-well plate at 1x10^6 cells per well for 3 days, in the presence of plate-bound anti-CD3 (5 μg/ml) and anti-CD28 (1 μg/ml).

extract_protocol: On day 3, total RNAs were isolated.

treatment_protocol: Plate-bound anti-CD3 (5 μg/ml) and soluble anti-CD28 (1 μg/ml).

tag: genotype

value: wildtype

value: CD4 T cells

tag: background strain

value: 2D2 Tg


title: ΔCK2β-modified MCF10A cells, rep1 [mRNA profile]


title: miR-146a-deficient 2D2 T cells, biological rep1

description: Gene expression data from 2D2KO effector T cells

source_name: 2D2KO T cells


title: miR-146a-deficient 2D2 T cells, biological rep2


title: Mock control Human MCF10A cells, rep1 [mRNA profile]


title: wildtype 2D2 T cells, biological rep1


title: 2 mM IAA treatment, biological rep3

city: Wenjiang, Chengdu city

first: Yunfeng

last: Jiang

state: Sichuan

address: Huiming road No.211

institute: Triticeae Research Institute, Sichuan Agricultural University

description: Gene expression data of common wheat spike after hormone treatments

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

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

data_processing: The data were 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.

organism: Triticum aestivum

source_name: wheat spike heads were collected 24 h after hormone application

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: Plants were grown in climatically controlled chambers under 16: 8 h day-night cycles at 25: 20oC, watered as needed and fertilized weekly with 15-15-15 (N-P-K).

extract_protocol: Total RNA was extracted using aTRIzol reagent (Invitrogen). RNA quality was monitored with a ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE) and by electrophoresis on agarose gel.

treatment_protocol: Only flowering heads were used for hormone treatments. Two florets of each fully developed spikelet of a whole spike at the mid-anthesis stage were treated with 10 μl of a 10% methanol: water solution supplemented or not (control) with either 2 mM IAA, 1 mM SA, 1 mM MeJA, 0.38 mM ABA, 0.5 mM GA3 or 0.5 mM trans-zeatin (one kind of cytokinins). For ethylene treatment, each head was sealed in a plastic bag with 2 ml of freshly prepared 25 mM ethephon solution (pH=11). All of these chemical solutions were inoculated into the florets in less than 1 h after preparation.

value: 2 mM IAA

tag: tissue

value: wheat spike

value: Roblin


title: ET treatment, biological rep1

value: ET


title: ET treatment, biological rep2


title: 2 mM IAA treatment, biological rep2


title: 0.4 mM ABA treatment, biological rep2

value: 0.4 mM ABA


title: 2 mM IAA treatment, biological rep1


title: 0.5 mM CK treatment, biological rep2

value: 0.5 mM CK


title: 0.5 mM CK treatment, biological rep3


title: 0.4 mM ABA treatment, biological rep3


title: ET treatment, biological rep3


title: 0.4 mM ABA treatment, biological rep1


title: 0.5 mM CK treatment, biological rep1


title: 0.5 mM GA treatment, biological rep2

value: 0.5 mM GA


title: 0.5 mM GA treatment, biological rep1


title: 1 mM MeJA treatment, biological rep3

value: 1 mM MeJA


title: Mock control Human MCF10A cells, rep2 [miRNA profile]

data_processing: Raw data were normalized by the average of two LabelingSpikes-InSignal (DMR_285 and DMR_31a) as internal standard, using the GeneSpring software version 7.3.1 (Agilent).

treatment_protocol: MCF10A cells were grown as described for 3 days. Stable silencing of gene expression in MCF10A cells was accomplished by transduction with lentiviruses pLKO1 (SHVRCS-TRCN000003796, Sigma-Mission) followed by selection with puromycin (# 96). Specificity of the CK2β knockdown was checked by performing a complementation assay using a chicken CK2β which expression is not affected by the shRNA (# F2). The control cells (Mock-) were transduced with an empty pLKO1 vector.


title: ΔCK2β-modified MCF10A cells, rep1 [miRNA profile]


title: Mock control Human MCF10A cells, rep1 [miRNA profile]


title: 1 mM MeJA treatment, biological rep2


title: 0.5 mM GA treatment, biological rep3


title: 1 mM SA treatment, biological rep3

value: 1 mM SA


title: 1 mM SA treatment, biological rep2


title: Water treatment, biological rep3

value: Water


title: Water treatment, biological rep1


title: patient42

value: dengue fever (DF)/dengue hemorrhagic fever (DHF)

value: F

value: peripheral blood mononuclear cells (PBMCs)


title: hRPTC-Normal

city: Taipei

first: Tai

middle: Horng

last: Young

address: No.1 Jen Ai Rord Section 1

country: Taiwan

institute: College of Medicine and College of Engineering, National Taiwan University

description: hRPTC-N

hyb_protocol: Fluorescent targets were hybridized to the Mouse Whole Genome OneArray® with Phalanx hybridization buffer using Phalanx Hybridization System. After 16 hrs hybridization at 50 ℃, non-speciﬁc binding targets were washed away by three different washing steps (WashⅠ 42 ℃ 5 mins；Wash Ⅱ 42 ℃, 5 mins, 25 ℃ 5 mins; Wash Ⅲ rinse 20 times)

scan_protocol: The arrays were scanned by Axon GenePix 4000B scanner (635nm power 100 PMT 500) and quantify the fluoresence intensity.

data_processing: The signal intensity of each spot was loaded into Rosetta Resolver System® (Rosetta Biosoftware) to process data analysis. The error model of Rosetta Resolver System® could remove both systematic and random errors form the data. We ﬁltered out spots that the ﬂag is less than 0. Spots that passed the criteria were normalized by 50% media scaling normalization method. Normalize intensities: Median scaling performed on data set without flagged and control data.

source_name: human renal proximal tubule cell

label_protocol: 1 µg of total RNA was reverse-transcribed and amplified using Amino Allyl aRNA Amplification Kit (Phalanx Biotech Group, Taiwan) and Cy5 dyes (Amersham Pharmacia, Piscataway, NJ, USA).

extract_protocol: RNA extraction by Trizol. RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧7).

tag: status after 5 years

value: Alive

tag: histology

value: urothelial carcinoma

value: 62 years

value: Male

tag: Stage

value: human renal proximal tubule cells (RPTCs)

tag: treated with

value: none (normal condition)


title: hRPTC-FIR

description: hRPTC-F

tag: cell type

value: Far infrared radiation (FIR)


title: Control-1 (normal human epidermal keratinocytes)

description: normal human epidermal keratinocytes

data_processing: GeneChip Analysis Suite. RMA

source_name: normal human epidermal keratinocytes

label_protocol: 250 ng of total RNA was used to synthesize cRNA with a GeneChip 3’ IVT Express Kit (Affymetrix).

growth_protocol: Normal human epidermal keratinocytes (NHEK) cells were obtained from Kurabo Ind., Ltd. (Osaka, Japan). NHEK was cultured with HuMedia-KB2 medium (Kurabo Ind., Ltd.) at 37°C in humidified air containing 5% CO2. We enrolled two patients (78- and 83-year-old women) with human basal cell carcinoma of the eyelid. Two patients underwent surgical excision of the tumor at the Toyama University Hospital.

extract_protocol: RNA was extracted from cells using a NucleoSpin® RNA isolation kit (MACHEREY-NAGEL GmbH) along with on-column DNase I treatment. RNA quality was analyzed using a Bioanalyzer 2100 (Agilent Technologies). RNA samples with RIN (RNA integrity number) values >5.0 were considered acceptable.

treatment_protocol: NHEK cells and carcinoma samples were used.

tag: strain

value: female

value: 40 years

value: abdomen

tag: morphology

value: typical keratinocyte morphology


title: Control-2 (normal human epidermal keratinocytes)

description: normal human epidermal keratinocytes


title: Water treatment, biological rep2

tag: treatment

value: wheat spike

value: Roblin


title: 1 mM SA treatment, biological rep1

value: 1 mM SA


title: 1 mM MeJA treatment, biological rep1

value: 1 mM MeJA


title: Patient 1-2 (basal cell carcinoma of the eyelid)

description: Patient 1, basal cell carcinoma of the eyelid

source_name: basal cell carcinoma of the eyelid

value: 78 years

value: eyelid

value: basal cell carcinoma


title: Serum Starved Replicate 2

city: New Delhi

first: Sandeep

last: Saxena

state: New Delhi

address: Aruna Asaf Ali Marg

country: India

institute: National Institute of Immunology

description:
raw data file for Cy3: 1_Exiqon_19716012_S01.txt
raw data file for Cy5: 0_Exiqon_19716012_S01.txt
Biological replicate 2 of 2. HCT116 grown for several passages and starved of serum for 48h before harvesting.
Exp 2 Test 1

hyb_protocol: The Hy3™-labeled samples and a Hy5™-labeled reference RNA sample were mixed pair-wise and hybridized to the miRCURY LNA™ microRNA Array 7th Gen (Exiqon, Denmark). The hybridization was performed according to the miRCURY LNA™ microRNA Array Instruction manual using a Tecan HS4800™ hybridization station (Tecan, Austria).

scan_protocol: The miRCURY LNA™ microRNA Array slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA) and the image analysis was carried out using the ImaGene® 9 (miRCURY LNA™ microRNA Array Analysis Software, Exiqon, Denmark).

data_processing: The quantified signals were background corrected (Normexp with offset value 10, see Ritchie et al. 2007) and normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm.

source_name: HCT116 colon carcinoma cells

label_protocol: All experiments were conducted at Exiqon Services, Denmark. The quality of the total RNA was verified by an Agilent 2100 Bioanalyzer profile. 750 ng total RNA from both sample and reference was labeled with Hy3™ and Hy5™ fluorescent label, respectively, using the miRCURY LNA™ microRNA Hi-Power Labeling Kit, Hy3™/Hy5™ (Exiqon, Denmark) following the procedure described by the manufacturer.

growth_protocol: Cells were grown in Dulbecco’s modified eagle’s medium  supplemented with or without 10% fetal bovine serum and 1% antibiotic-antimycotic at 37°C in a humidified atmosphere with 5% CO2.

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

tag: cell line

value: HCT116 colon carcinoma cells

value: HCT116 cells starved of serum for 48h

tag: sample type

value: reference (total RNA isolated from HCT116 cells)


title: Patient 2-1 (basal cell carcinoma of the eyelid)

description: Patient 2, basal cell carcinoma of the eyelid

tag: age

value: 83 years


title: ΔCK2β-modified MCF10A cells, rep2 [miRNA profile]

value: CK2beta knockdown


title: Niacin 1

city: Calgary

first: Voon

middle: Wee

last: Yong

state: Alberta

address: 3330 Hospital drive NW

department: Clinical Neurosciences

institute: University of Calgary

description:
Niacin 1 (HG-U133_Plus_2).mas5-Signal
Gene expression data from 6h of Niacin treatment

hyb_protocol: Hybridized to Affymetrix GeneChip Human Genome U133 Plus 2.0 Array at 45°C for 16h.  Arrays were stained and washed on Affymetrix GeneChip Fluidics 450 following manufacturer’s protocol.

scan_protocol: Scanned with Affymetrix GeneChip Scanner 3000 7G System.

data_processing: Array data files were generated with GeneChip® Command Console® Software (AGCC) and statistical significant analysis was carried out on software of GeneSpringTM (Agilent Technologies).

label_protocol: One hundred microgram of RNA of each sample with a RIN higher than 9 was labelled with 3' IVT Express Kit (Ambion).

extract_protocol: RNA was extracted using RNeasy MiniKit (Qiagen) as per manufacturer’s instruction.   The RNA quality of integrity number (RIN) was determined with an Agilent RNA 6000 NanoChip on 2100 Bioanalyzer (Agilent Technologies).  The quantity was measured with NanoDrop 1000 (NanoDrop Technologies).

tag: subject status

value: normal adult individual

value: blood

value: monocytes

tag: exposed to

value: niacin (100 μM) for 6h


title: Asynchronous Replicate 2

description:
raw data file for Cy3: 1_Exiqon_19716010_S01.txt
raw data file for Cy5: 0_Exiqon_19716010_S01.txt
Biological replicate 2 of 2. Asnchronously growing HCT116 cells harvested after several passages.
Exp 2 control

value: HCT116 Asynchronous cells


title: Serum re-supplemented Replicate 2

description:
raw data file for Cy3: 1_Exiqon_19716007_S01.txt
raw data file for Cy5: 0_Exiqon_19716007_S01.txt
Biological replicate 2 of 2. HCT116 re-supplemented with 10% FBS after 48h of serum starvation. Cell were harvested after 12h of serum re-supplementation
Exp 2 Test 2

value: HCT116 cells re-supplemented with serum for 12h after 48h of serum starvation


title: Serum re-supplemented Replicate 1

description:
raw data file for Cy3: 1_Exiqon_19716011_S01.txt
raw data file for Cy5: 0_Exiqon_19716011_S01.txt
Biological replicate 1 of 2. HCT116 re-supplemented with 10% FBS after 48h of serum starvation. Cell were harvested after 12h of serum re-supplementation
Exp 1 Test 2


title: Control 1

description:
Control 1 (HG-U133_Plus_2).mas5-Signal
Gene expression data from 6h of vehicle treatment

source_name: monocytes_vehicle control

value: vehicle (control)


title: Control 2

description:
Control 2 (HG-U133_Plus_2).mas5-Signal
Gene expression data from 6h of vehicle treatment


title: Asynchronous Replicate 1

description:
raw data file for Cy3: 1_Exiqon_19716008_S01.txt
raw data file for Cy5: 0_Exiqon_19716008_S01.txt
Biological replicate 1 of 2. Asnchronously growing HCT116 cells harvested after several passages.
Exp 1 control


title: Patient 2-2 (basal cell carcinoma of the eyelid)

value: female


title: Serum Starved Replicate 1

description:
raw data file for Cy3: 1_Exiqon_19716009_S01.txt
raw data file for Cy5: 0_Exiqon_19716009_S01.txt
Biological replicate 1 of 2. HCT116 grown for several passages and starved of serum for 48h before harvesting.
Exp 1 Test 1


title: Niacin 2

description:
Niacin 2 (HG-U133_Plus_2).mas5-Signal
Gene expression data from 6h of Niacin treatment


title: Patient 1-1 (basal cell carcinoma of the eyelid)


title: Niacin 3

description:
Niacin 3 (HG-U133_Plus_2).mas5-Signal
Gene expression data from 6h of Niacin  treatment


title: FFA Case [SK199]

status: Public on Sep 04 2017

city: London

first: John

middle: Alexander

last: McGrath

address: Great Maze Pond

department: St John's Institute of Dermatology

country: United Kingdom

institute: King's College London

description: miRNA expression data

hyb_protocol: Performed at King's FWB Genomics Centre

scan_protocol: Performed at King's FWB Genomics Centre

data_processing: All samples underwent microarray analysis on Affymetrix GeneChip miRNA 4.0 arrays. Data was normalised using Expression Console software (Affymetrix) prior to generating a list of differentially expressed genes using Qlucore Omics Explorer 3.2

source_name: scalp skin

label_protocol: Samples were processed using the FlashTag Biotin HSR RNA Labeling Kit for Affymetrix GeneCip miRNA 4.0 according to the manufacturer's instructions; Performed at King's FWB Genomics Centre

extract_protocol: Total RNA was isolated using RNeasy Plus Universal kit (Qiagen, Valencia, USA) and miRNAs retained according to the manufacturer’s protocol

value: scalp skin


title: Control 3

description:
Control 3 (HG-U133_Plus_2).mas5-Signal
Gene expression data from 6h of vehicle treatment


title: FFA Case [SK197]

description: miRNA expression data


title: FFA Case [SK195]

description: miRNA expression data


title: FFA Case [SK193]

description: miRNA expression data


title: FFA Case [SK194]

description: miRNA expression data


title: Control [SK198]

description: miRNA expression data


title: FFA Case [SK178]

description: miRNA expression data


title: Control [SK202]

description: miRNA expression data


title: Control [SK196]

description: miRNA expression data


title: Control [SK201]

description: miRNA expression data


title: FFA Case [SK175]

description: miRNA expression data


title: Control [SK200]

description: miRNA expression data


title: Control [SK192]

description: miRNA expression data


title: Edited.rep1

status: Public on Sep 03 2017

city: Philadelphia

first: Kyoko

last: Hayakawa

state: PA

address: 333 Cottman Avenue

institute: Fox Chase Cancer Center

description: Gene Expression of 3609t x Vk21 ThyKO_Edited, dye swamp rep1

hyb_protocol: Follow Agilent 60-mer oligo array hybridization protocol.

scan_protocol: Arrays were scanned by following scanning protocol recommended by Agilent, and spot quantifications were done using feature extraction software

data_processing: data were bakcground corrected using normexp method then loess normalized using bioconduction package limma

source_name: VH3609t +/-  x Vk21-5Tg +/- mice, Thy-1 Knockout,edited, Sample 1, rep1

label_protocol: Amplified RNAs were labeled with cy3 or cy5 dye

extract_protocol: RNA was extracted using the acid phenol method. 100ng of total RNA was used for RNA amplificaiton followingAmbion RNA amplification protocol.

value: Follicular B Cell

tag: genotype/variation

source_name: reference

value: six cell lines (R1, RS2, J558, EL4, DN3, and P388d)


title: WT.2.rep1

description: Gene Expression of WT.2, dye swamp rep1

source_name: Wild Type, Sample 2, rep1

value: Wild Type


title: Control [SK167]

description: miRNA expression data


title: Non-edited.rep1

description: Gene Expression of 3609t x Vk21 ThyKO_Non-edited, dye swamp rep1

source_name: VH3609t +/-  x Vk21-5Tg +/- mice, Thy-1 Knockout,Non-edited, Sample 1, rep1


title: Auto.Neg.2.rep1

description: Gene Expression of 3369 ThyKO _Auto.Neg.2, dye swamp rep1

source_name: ATAμκTg (anti-thymocyte/Thy-1 autoreactive, VH3609μ/Vk21-  5κ transgenic ) mice, Thy-1 Knockout, Autoreactive Neg, sample2, rep1

value: anti-thymocyte/Thy-1 autoreactive, VH3609mu/Vkappa21- 5kappa transgenic mice, Thy-1 Knockout, Autoreactive Neg


title: Edited.rep2

description: Gene Expression of 3609t x Vk21 ThyKO_Edited, dye swamp rep2

source_name: VH3609t +/-  x Vk21-5Tg +/- mice, Thy-1 Knockout,edited, Sample 1, rep2


title: Non-edited.rep2

description: Gene Expression of 3609t x Vk21 ThyKO_Non-edited, dye swamp rep2

source_name: VH3609t +/-  x Vk21-5Tg +/- mice, Thy-1 Knockout,Non-edited, Sample 1, rep2


title: Auto.Pos.2.rep2

description: Gene Expression of EP67 AMyIIA_Auto.Pos.2, dye swamp rep2

source_name: AGcAμκTg (anti-intestinal goblet cell autoreactive, VH3609μ/Vk19-17κ transgenic)  mice,Autoreactive Pos, Sample 2, rep2

value: anti-intestinal goblet cell autoreactive, VH3609mu/Vkappa17- 17kappa transgenic)  mice,Autoreactive Pos


title: WT.1.rep2

description: Gene Expression of WT.1, dye swamp rep2

source_name: Wild Type, Sample 1, rep2


title: Auto.Neg.2.rep2

description: Gene Expression of 3369 ThyKO _Auto.Neg.2, dye swamp rep2

source_name: ATAμκTg (anti-thymocyte/Thy-1 autoreactive, VH3609μ/Vk21-  5κ transgenic ) mice, Thy-1 Knockout, Autoreactive Neg, sample2, rep2


title: WT.2.rep2

description: Gene Expression of WT.2, dye swamp rep2

source_name: Wild Type, Sample 2, rep2


title: Auto.Neg.1.rep2

description: Gene Expression of 3369 ThyKO _Auto.Neg.1, dye swamp rep2

source_name: ATAμκTg (anti-thymocyte/Thy-1 autoreactive, VH3609μ/Vk21-  5κ transgenic ) mice, Thy-1 Knockout, Autoreactive Neg, sample1, rep2


title: Auto.Pos.1.rep2

description: Gene Expression of EP67 AMyIIA_Auto.Pos.1, dye swamp rep2

source_name: AGcAμκTg (anti-intestinal goblet cell autoreactive, VH3609μ/Vk19-17κ transgenic)  mice,Autoreactive Pos, Sample 1, rep2


title: Auto.Pos.2.rep1

description: Gene Expression of EP67 AMyIIA_Auto.Pos.2, dye swamp rep1

source_name: AGcAμκTg (anti-intestinal goblet cell autoreactive, VH3609μ/Vk19-17κ transgenic)  mice,Autoreactive Pos, Sample 2, rep1


title: Auto.Neg.1.rep1

description: Gene Expression of 3369 ThyKO _Auto.Neg.1, dye swamp rep1

source_name: ATAμκTg (anti-thymocyte/Thy-1 autoreactive, VH3609μ/Vk21-  5κ transgenic) mice, Thy-1 Knockout, Autoreactive Neg, sample1, rep1


title: Pu3_R

city: Valencia

first: Patricia

last: Diaz Gimeno

state: Valencia

address: Avenida Fernando Abril Martorell 106

department: Reproductive Genomics

country: Spain

institute: Fundacion IVI/Universidad de Valencia

description: Gene expression data from LGCs from PCOS cultured with 5IU/mL hCG in the absence of 100µM Cb2 for 72hours

hyb_protocol: Not provided

scan_protocol: Files were captured using an Affymetrix GeneChip Scanner 3000 7G

data_processing: Bioconductor/R and algorithm RMA

source_name: Untreated PCOS (Patient 3)-Replicate

label_protocol: Biotinylated mRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Lutein granulosa cells from non-PCOS and PCOS women were isolated and seeded in 24-well cell culture plates at a density of 50,000 cells/well and left to rest overnight (37º C, 5% CO2) to allow the cells to attach and remove non-adherent cells. Subsequently, LGCs from each patient were washed and cultured for 72 hours (37ºC, 5% CO2).

extract_protocol: Total mRNA from the cells was extracted using the Quick-RNA Microprep kit (Zymo Research, Freiburg, Germany), according to the manufacturer’s instructions.

treatment_protocol: Lutein granulosa cells from non-PCOS and PCOS women were cultured with 5IU/mL hCG in the absence/presence of 100µM Cb2 for 72hours

value: Ovary

tag: diagnosis

value: polycystic ovarian syndrome (PCOS)

value: lutein granulosa cells (LGCs)


title: Pu3

source_name: Untreated PCOS (Patient 3)


title: Auto.Pos.1.rep1

description: Gene Expression of EP67 AMyIIA_Auto.Pos.1, dye swamp rep1

source_name: AGcAμκTg (anti-intestinal goblet cell autoreactive, VH3609μ/Vk19-17κ transgenic)  mice,Autoreactive Pos, Sample 1, rep1


title: WT.1.rep1

description: Gene Expression of WT.1, dye swamp rep1

source_name: Wild Type, Sample 1, rep1

source_name: reference


title: Pu2

description: Gene expression data from LGCs from PCOS cultured with 5IU/mL hCG in the absence  of 100µM Cb2 for 72hours

source_name: Untreated PCOS (Patient 2)


title: Pt3

description: Gene expression data from LGCs from PCOS cultured with 5IU/mL hCG in the presence of 100µM Cb2 for 72hours

source_name: Cabergoline Treated PCOS (Patient 3)


title: Pt2_R

source_name: Cabergoline Treated PCOS (Patient 2)-Replicate


title: Pu1

source_name: Untreated PCOS (Patient 1)


title: Pt3_R

source_name: Cabergoline Treated PCOS (Patient 3)-Replicate


title: Pt2

source_name: Cabergoline Treated PCOS (Patient 2)


title: Cu3

description: Gene expression data from LGCs from non-PCOS cultured with 5IU/mL hCG in the absence of 100µM Cb2 for 72hours

source_name: Untreated non-PCOS (Control 3)

value: non-polycystic ovarian syndrome (PCOS)


title: Ct2

description: Gene expression data from LGCs from non-PCOS cultured with 5IU/mL hCG in the presence of 100µM Cb2 for 72hours

source_name: Cabergoline Treated non-PCOS (Control 2)


title: Ct1

source_name: Cabergoline Treated non-PCOS (Control 1)


title: Cu1

source_name: Untreated non-PCOS (Control 1)


title: Cu2

source_name: Untreated non-PCOS (Control 2)


title: Pt1

source_name: Cabergoline Treated PCOS (Patient 1)


title: SUM159-CoOE-2

status: Public on Sep 02 2017

city: Graz

first: Martin

last: Pichler

address: Auenbruggerplatz 15

department: Internal medicine, Division of Oncology

country: Austria

institute: Medical University of Graz

hyb_protocol: Affymetrix Human Gene 2.0 ST Array (Cat No. 902112);  Affymetrix GeneChip® HT hybridization, Wash and Stain Kit (Cat No. 900720);   Affymetrix Genechip®  fluidics station 450: protocol FS450_0002 for Cartridge Arrays

scan_protocol: Affymetrix Scanner: GCS3000; AGCC (Command Console Software  AGCC 3.2.)

data_processing:
Affymetrix Genexpression Console (1.3.1) using Affymetrix default analysis settings for generation of CEL-files.
Data Pre-Processing and Filtering (Partek Genomics Suite, v.6.6): RMA  (background correction, quantile normalization across all chips in the experiment, log2 transformation, median polish summarization)

source_name: empty vector

label_protocol: Affymetrix WT PLUS Reagent Kit  P/N 703147 Rev3, (Cat No. 902280); Lot: 4248402

growth_protocol: SUM159 cells were grown in Ham`s F12 containing 1 mmol/L L-glutamine, 2 mmol/L HEPES buffer, 5µg/ml  insulin actrapid, 1µg/ml hydrocortisone, 1% penicillin/streptomycin ( (50 units per ml of penicillin, 50μg/ml of streptomycin) and 5% FBS gold. Cells were incubated in a 5% CO2 humidified atmosphere at 37°C.

extract_protocol: miRNeasy

value: control


title: SUM159-miR1287OE-2

source_name: miR-1287-5p overexpressing cells

value: miR-1287-5p overexpression


title: SUM159-CoOE-3


title: SUM159CoOE-1


title: SUM159-miR1287OE-3


title: Ct3

source_name: Cabergoline Treated non-PCOS (Control 3)


title: control, biological rep3

city: Cambridge

first: Michal

middle: P

last: Wandel

address: Francis Crick Avenue, Cambridge Biomedical Campus

department: PNAC

institute: MRC Laboratory of Molecular Biology

description: Gene expression data from HeLa untreated cells

hyb_protocol: Biotinylated DNA samples were hybridized using Affymetrix Hybridization Kit to Human Affymetrix Gene ST 1.0 cartridge arrays.

scan_protocol: GeneChips were scanned on the Affymetrix GCS3000.

data_processing: The data were analyzed using Affymetrix default analysis settings.

source_name: HeLa cells

label_protocol: RNA samples were manually prepped using the Ambion WT Expression Kit and Affymetrix GeneChip WT Terminal Labeling.

growth_protocol: HeLa cells were grown in IMDM supplemented with 10% FCS at 37°C in 5% CO2.

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

treatment_protocol: HeLa cells were harvested and pelets were stored in -80°C until further processing.

value: HeLa


title: interferon-gamma, biological rep1

description: Gene expression data from HeLa cells treated with interferon-gamma (100mg/ml) for 10h

source_name: HeLa cells + interferon-gamma, 10 ng/ml, 10h


title: interferon-gamma, biological rep3


title: interferon-gamma, biological rep2


title: interferon-beta, biological rep2

description: Gene expression data from HeLa cells treated with interferon-beta (100U/ml) for 10h

source_name: HeLa cells + interferon-beta, 100U/ml, 10h


title: control, biological rep1


title: BY4743_YPD_4

city: Toulouse

first: Marion

last: Schiavone

address: 135 avenue de Rangueil

department: LISBP

institute: INSA-Toulouse

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity > 40 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1 ul Agilent fragmentation buffer and 5 ul Agilent blocking agent following the manufacturers instructions, then hybridized to Agilent Yeast Gene Expression Microarray (V2G4813A-016322) for 12 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed two times for 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the MS200 scanner (NimbleGen Roche Diagnostics, Meylan, France) using one color scan setting for 8x15k array slides.

data_processing: The scanned images were analyzed with Feature Extraction V.11.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Saccharomyces cerevisiae

source_name: BY4743 strain, YPD culture

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Cultures of each strain were carried out in 50 ml of YPD in a 250 mL shake flasks on a rotary shaker set at 200 rpm at 30°C. Yeast cells (about 10 OD600 units) were collected at OD600=1 by centrifugation (3,000 rpm, 4°C, 2 min).

extract_protocol: Frozen cells were mechanically disrupted using a ball mill (MicroDismembrator Braun, Melsungen, Germany). Total RNA was extracted using SV Total RNA Isolation System (Promega) following the protocol of the Manufacturer.

treatment_protocol: The cell pellets were immediately frozen in liquid nitrogen and stored at - 80°C until RNA extraction.


title: control, biological rep2


title: interferon-beta, biological rep3


title: L60_YPD_3

source_name: L60 strain, YPD culture


title: interferon-beta, biological rep1


title: CD271 HIGH population Rat 2

city: Zurich

first: Gaetana

last: Restivo

state: ZH

address: Winterthurerstrasse 190

department: Anatomy

country: Switzerland

institute: University of Zurich

description: CD271 HIGH Rat2

hyb_protocol: Samples were further hybridized for 20 hr at 48ºC on Affymetrix® Human Gene 1.1 ST Array Strip in the Affymetrix GeneAtlas Hybridization Station. Arrays were then washed and stained using Affymetrix GeneAtlas Fluidics Station.

scan_protocol: GAn Affymetrix GeneAtlas Imaging Station was used to measure the fluorescent intensity emitted by the labeled target.

data_processing: Data were RMA processed using Affymetrix Power Tools

source_name: CD271 HIGH population

label_protocol: Single-stranded cDNA (500 ng) was converted into sense target cDNA (ST-cDNA) using WT-OvationT Exon (Cat # 2000-12). Fragmented and biotin-labeled ST-cDNA targets were generated with the FL-Ovation cDNA Biotin Module V2 (NuGEN, 4200-12)

growth_protocol: Melanoma cells were seeded with keratinocytes on rat tail collagen gels containing fibroblasts. The engeenered skin was then transplanted on back of immunocompromised rats

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. Purification of RNA was made with Qiagen Rneasy Mini Plus

treatment_protocol: Melanoma cells prior to be included in the engeneered skin were infected with a lentivirus carrying the Green Fluorescent Protein (GFP)

tag: host organism

value: immunocompromised rat

tag: transplanted with

value: human engeneered skin carrying GFP positive melanoma cells

tag: time point

value: 6 weeks after transplatation

value: engeenered skin

tag: cell population

value: GFP positive, CD271 HIGH melanoma cells


title: CD271 LOW population Rat 1

description: CD271 LOW Rat1

source_name: CD271 LOW population

tag: tissue

value: GFP positive, CD271 LOW melanoma cells


title: Pu2_R

source_name: Untreated PCOS (Patient 2)-Replicate


title: SUM159-miR1287OE-1


title: CD271 LOW population Rat 2

description: CD271 LOW Rat2


title: CD271 HIGH population Rat 1

description: CD271 HIGH Rat1


title: BY4743_YPD_3


title: L62_YPD_3

source_name: L62 strain, YPD culture


title: BY4743_YPD_2


title: L62_YPD_2


title: rat_naive_rep1

city: Krakow

first: Marcin

last: Piechota

address: Smetna 12

department: Molecular Neuropharmacology

institute: Institute of Pharmacology PAS

description:
rat_intact13
Replicate 1

hyb_protocol: Affymetrix GeneChip™ hybridization protocol.

scan_protocol: Affymetrix GeneChip™ scanning protocol.

data_processing: The data were processed using rma function implemented in the oligo R package (v. 1.36.1) with default parameters (background correction and quantile normalization).

source_name: Knee cartilage, control

label_protocol: RNA was labeled using Affymetrix GeneChip™ labeling protocol.

extract_protocol: RNA was isolated following the manufacturer’s protocol and further purified using the RNeasy Mini Kit (Qiagen Inc.). The total RNA concentration was measured using an ND-1000 Spectrometer (NanoDrop Technologies Inc., Montchanin, DE, USA).

treatment_protocol: Knee cartilage samples were collected from individual male Wistar rats with monosodium iodoacetate (MIA) induced OA (0, 2, 14, 28 days after the treatment). MIA-treated (3 mg) animals were compared to intact controls.

tag: strain/background

value: Wistar

tag: gender

value: male

value: knee cartilage

value: naive

tag: day

tag: animal


title: rat_mia_day2_rep3

description:
rat_2d11
Replicate 2

source_name: Knee cartilage, MIA-induced osteoarthritis, day2

tag: treatment

value: monosodium iodoacetate (MIA)


title: L60_YPD_1

tag: strain


title: BY4743_YPD_1


title: L60_YPD_2


title: rat_naive_rep4

description:
rat_intact16
Replicate 4


title: L69_YPD_3

source_name: L69 strain, YPD culture


title: L62_YPD_1


title: L69_YPD_1


title: L71_YPD_3

source_name: L71 strain, YPD culture


title: L71_YPD_2


title: L69_YPD_2


title: rat_naive_rep3

description:
rat_intact15
Replicate 3


title: rat_mia_day2_rep4

description:
rat_2d12
Replicate 3


title: rat_mia_day2_rep1

description:
rat_2d9
Replicate 4


title: rat_naive_rep2

description:
rat_Intact14
Replicate 2


title: rat_mia_day28_rep1

description:
rat_28d1
Replicate 1

source_name: Knee cartilage, MIA-induced osteoarthritis, day28


title: CT26-shCDK8

status: Public on Sep 01 2017

city: Columbia

first: Mengqian

last: Chen

state: SC

address: CLS710, 715 Sumter Street

department: College of Pharmacy

institute: University of South Carolina

hyb_protocol: Samples were hybridized with GeneChip MoGene-2_0-st Arrays (Affymetrix) and scanned at Functional Genomics Core of the Center for Targeted Therapeutics at the University of South Carolina.

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

data_processing:
RMA expression value derived from Expression Console software; core-exon analysis
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0
affymetrix-array-type = MoGene-2_0-st
program-name = Expression Console
program-version = 1.3.1.187

source_name: cells from culture

label_protocol: standard Affymetrix protocol

growth_protocol: CT26 cells were maintained in RPMI-1640 (ThermoFisher Scientific) with 10% fetal bovine serum (FBS) (Atlanta Biologics), 1% penicillin-streptomycin and 2 mM L-glutamine (VWR)

extract_protocol: RNA was isolated from cells in p-6 well plate with the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions.

treatment_protocol: CT26 cells were  treated with DMSO or Senexin B for 24 h.

tag: cell line background


title: rat_mia_day2_rep2

description:
rat_2d10
Replicate 1


title: rat_mia_day28_rep3

description:
rat_28d3
Replicate 3


title: rat_mia_day14_rep3

description:
rat_14d7
Replicate 3

source_name: Knee cartilage, MIA-induced osteoarthritis, day14


title: rat_mia_day28_rep2

description:
rat_28d2
Replicate 2


title: L71_YPD_1


title: rat_mia_day14_rep4

description:
rat_14d8
Replicate 4


title: OGCT3

type: SRA

city: Stockholm

first: Roger

middle: Kae-Jia

last: Chang

address: Karolinska Univ Hospital, R8:04

department: Oncology-Pathology

country: Sweden

institute: Karolinska Institute

description:
35950
raw data unavailable for this sample

library_source: transcriptomic

data_processing:
Adapter sequences were removed, and sequences were filtered using the package Fastx-toolkit
The resultant dataset were aligned to miRBase database version 21 for human mature miRNA using Bowtie short read aligner with settings -f -n 0 -l 15 -k 200 -S –best –chunkmbs 128
Reads were sorted and indexed by SAMtools
For miRNA quantification, the script HTSeq-count of the HTSeq was used
Supplementary_files_format_and_content: txt files, mapped reads to human mature miRNA sequences

extract_protocol:
mirVana miRNA isolation kit (Applied Biosystems/ Ambion, Austin, TX) was used to extract small RNA
for cloning small RNAs were ligated with adenylated 3’-adaptor oligonucleotide [/5rApp/CTGTAGGCACCATCAAT/3ddC; IDT Inc., Coralville, IA, USA] and purified on a 12% denaturing polyacrylamide gel. Second ligation reaction was performed with 5’-adaptor oligonucleotide [5'-ACGCTCTTCCGATCTv-3' (uppercase, DNA; v = barcodes with triple RNA molecules: aaa, ggg, ccc or uuu; IDT)], followed by gel purification. The double ligated product was converted to cDNA using the reverse transcription enzyme SuperScript II (Invitrogen) and the reverse primer [5'-ATTGATGGTGCCTACAG-3'], and then PCR amplified for 16-20 cycles using a forward primer 5'-GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC T-3' and a reverse primer 5'-CAA GCA GAA GAC GGC ATA CGA GCT CTT CCG ATC TAT TGA TGG TGC CTA CAG- 3'.

value: ovarian germ cell tumor

value: benign

tag: histology

value: mature teratoma

tag: patient age

value: 26 year-old

value: female


title: CT26-pLKO.1


title: rat_mia_day28_rep4

description:
rat_28d4
Replicate 4


title: rat_mia_day14_rep1

description:
rat_14d5
Replicate 1


title: CT26 cells treated with Senexin B

tag: treated with

value: 5 µM Senexin B for 24h


title: OGCT1

description:
29079
raw data unavailable for this sample

value: malignant

value: dysgerminoma

value: 73 year-old


title: OGCT2

description:
I033a
raw data unavailable for this sample

value: primitive germ cell tumor

value: 28 year-old


title: OGCT9

description:
39636
raw data unavailable for this sample

value: 54 year-old


title: CT26 cells treated with DMSO

value: DMSO for 24h


title: rat_mia_day14_rep2

description:
rat_14d6
Replicate 2

value: Wistar

value: male


title: Heart, GlycoLo, replicate 2

city: Louisville

first: Bradford

middle: G

last: Hill

state: KY

address: 580 S. Preston St.

department: Medicine

institute: University of Louisville

hyb_protocol: Following fragmentation, cRNA were hybridized, washed and stained in the Affymetrix Fluidics Station 400 according to the standard Affymetrix protocol.

scan_protocol: GeneChips were scanned according to the standard Affymetrix protocol.

data_processing: The data were analyzed using the affy (Gautier et al., 2004) and limma (Ritchie et al., 2015) packages of R for Robust Multi-array Average (RMA) for normalization and for moderate t-statistics to derive p-values, respectively. For the genes with multiple probe set IDs, the probe set with the highest standard deviation among all samples was kept for further analysis.

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

growth_protocol: Mice were aged to 15 weeks prior to euthanasia.

extract_protocol: RNA was extracted using Trizol, according to the manufacturer's instructions.

treatment_protocol: Hearts were excised and immediately snap-frozen in liquid nitrogen for subsequent RNA extraction.

tag: strain background

value: FVB

tag: age

value: 15 weeks

tag: genotype/variation

value: expressing kinase-deficient PFK2

value: heart


title: Heart, GlycoHi, replicate 3

value: expressing phosphatase-deficient PFK2


title: Heart, GlycoHi, replicate 2


title: Heart, WT, replicate 3

value: wild type


title: Heart, WT, replicate 2


title: Heart, GlycoLo, replicate 3


title: Heart, GlycoLo, replicate 1


title: Heart, GlycoHi, replicate 1


title: IECs_InVivo_7day_rep2

city: Seoul

first: June Sung

last: Bae

address: 31, Ttukseom-ro 1-gil, Seongdong-gu

country: South Korea

institute: SG Medical

description:
7 days after tamoxifen injection in Mob1a f/f; Mob1b f/f; Villin-creERT2 mice
ΔD7 #3

hyb_protocol: After checking labeling efficiency, fragmentation of cRNA was performed by adding 10X blocking agent and 25X fragmentation buffer and incubating at 60oC for 30 min. The fragmented cRNA was resuspended with 2X hybridization buffer and directly pipetted onto assembled Agilent’s Human Oligo Microarray (60K). The arrays hybridized at 65oC for 17 hours using Agilent Hybridization oven (Agilent Technology, USA). The hybridized microarrays were washed as the manufacturer’s washing protocol (Agilent Technology, USA).

scan_protocol: The hybridized images were scanned using Agilent’s DNA microarray scanner and quantified with Feature Extraction Software (Agilent Technology, Palo Alto, CA).

data_processing: All data normalization and further analysis were performed using GeneSpringGX 7.3 (Agilent Technology, USA).

source_name: IECs_7days after tamoxifen

label_protocol: Amplified and labeled cRNA was purified on cRNA Cleanup Module (Agilent Technology) according to the manufacturer’s protocol. Labeled cRNA target was quantified using ND-1000 spectrophotometer (NanoDrop Technologies, Inc., Wilmington, DE).

growth_protocol: Mice were backcrossed more than 6 generation to C57BL/6J and raised under SPF conditions.

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

treatment_protocol: Tamoxifen (80mg/kg per day, 2 days) was intraperitoneally injected 8 weeks after birth to induce deletion of the Mob1a/b gene in mouse IECs.

value: conditional knockout of Mob1a/b

value: 8 week old

tag: timepoint

value: 7 days after Tamoxifen injection

value: intestine

tag: cell type

value: intestinal epithelial cells (IECs)


title: Mouse 2 HF TLR2-/-

first: Eric

last: Rullman

address: C1:82 Karolinska University Hospital, Huddinge

department: Laboratory Medicine

institute: Karolinska Institutet

description: Total RNA isolated from Flexor digitorum  brevis muscle from TLR-/- mice. Biological replicate 2

hyb_protocol: Following fragmentation, 5.5 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Mogene 2.1 ST 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 probe-set level intensities of the arrays were normalized using the Robust Multi-array Analysis method (RMA) implemented within the R statistical software environment using the 'AROMA' package (Bioconductor project) and a custom CDF from Brainarray, mouse-ENTREZG 21.

source_name: Flexor digitorum  brevismuscle, Biological replicate 2, TLR2-/-

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA

growth_protocol: From 7-8 weeks of age, male FVB/n mice were fed a high fat diet containing 58% fat, 25.5% carbohydrate and 16.4% protein for 8 weeks. All animals were maintained under pathogen free condition at the York University vivarium on a 12/12h light-dark cycle with food and water available ad libitum.

extract_protocol: Total RNA was using Trizol according to the manufacturer's instructions. Quality/quantity was checked using NanoDrop 2000 spectrophotometer. RNA was dissolved in 20 μl RNAse-free water with no additives.

treatment_protocol: WT C57BL/6 and TLR2-/- mice were used in this study. TLR2-/- mice were on a C57BL/6 background and were kindly provided by Dr S. Akira (Osaka University, Osaka, Japan). WT C57BL/6 mice were purchased from Charles River Laboratories (Wilminton, MA, USA). All the mice used in this study were males and more than 7 weeks old. Animals were kept and bred at Karolinska Institutet animal facility in a specific pathogen-free environment with standard room temperature and a 12-12 hour light/dark cycle. Food and water were provided ad libitum. Mice were killed by rapid neck disarticulation and the flexor digitorum brevis muscles were removed.

value: Flexor digitorum  brevis

value: Skeletal muscle

tag: genotype

tag: Sex

value: Male

tag: subject

value: Biological replicate 2


title: Mouse 4 HF WT

description: Total RNA isolated from Flexor digitorum  brevis muscle from WT mice. Biological replicate 4

source_name: Flexor digitorum  brevismuscle, Biological replicate 4, WT

tag: tissue

value: WT

value: Biological replicate 4


title: IECs_InVivo_10day_rep1

description:
10 days after tamoxifen injection in Mob1a f/f; Mob1b f/f; Villin-creERT2 mice
ΔD10 #2

source_name: IECs_10days after tamoxifen

tag: gender

value: male

value: 10 days after Tamoxifen injection


title: Mouse 3 HF WT

description: Total RNA isolated from Flexor digitorum  brevis muscle from WT mice. Biological replicate 3

source_name: Flexor digitorum  brevismuscle, Biological replicate 3, WT

value: Biological replicate 3


title: Heart, WT, replicate 1

country: USA

value: FVB

value: 15 weeks

value: heart


title: Mouse 1 HF WT

description: Total RNA isolated from Flexor digitorum  brevis muscle from WT mice. Biological replicate 1

source_name: Flexor digitorum  brevismuscle, Biological replicate 1, WT

value: Biological replicate 1


title: IECs_InVivo_7day_rep1

description:
7 days after tamoxifen injection in Mob1a f/f; Mob1b f/f; Villin-creERT2 mice
ΔD7 #1

value: conditional knockout of Mob1a/b

value: 8 week old


title: IECs_InVivo_4day_rep2

description:
4 days after tamoxifen injection in Mob1a f/f; Mob1b f/f; Villin-creERT2 mice
Δ 2

source_name: IECs_4days after tamoxifen

value: 4 days after Tamoxifen injection

value: intestine


title: IECs_InVivo_WT_rep1

description:
7 days after tamoxifen injection in Mob1a f/f; Mob1b f/f mice
WT 1

source_name: IECs_wild type

value: wild type

value: intestinal epithelial cells (IECs)