title: Wt TAC [5511168079_B]

value: TAC


title: Wt TAC [5511168069_D]

status: Public on May 30 2015

type: RNA

city: Groningen

first: Herman

last: Sillje

address: Hanzeplein 1

country: Netherlands

institute: University medical center Groningen

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The raw data were normalised (quantile normalization) by using the Illumina GenomeStudio software (version: 2011.1; Expression Module Version: 1.9.0).

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Mouse heart

label_protocol: During the last step of the amplification procedure using the Illumina TotalPrep -96 RNA Amplification kit, purified cDNA was converted to cRNA inclusive biotinylation through an in vitro transcription step.

extract_protocol: RNA was extracted from left ventricular tissue using Trizol reagent. Quality control was performed with Agilent Bioanalyser.

tag: genotype/variation

value: Wt

tag: protocol

tag: strain

tag: age

value: 4 months

tag: tissue

value: Left ventricle

tag: gender

value: male


title: Vk2 cells_no treatment, biol rep 29

city: Norfolk

first: Irina

middle: A

last: Zalenskaya

state: Virginia

address: 601 Colley ave

department: Ob/Gyn

country: USA

institute: Eastern Virginia Medical School

hyb_protocol: Labeled cRNA was fragmented and hybrized to Affymetrix HG-U133 Plus 2 arrays according to the standard Affymetrix protocol

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

data_processing: A summary of the image signal data, detection calls, and gene annotations for every gene interrogated on the array was generated using the Affymetrix Statistical Algorithm MAS 5.0 (GCOS v1.3) algorithm

organism: Homo sapiens

source_name: Vk2/E6E7, no treatment,  growth medium only

label_protocol: Biotinylated cRNA was prepared from 1  μg total RNA using modified MessageAmp™ -based protocols (Ambion Inc., Austin, TX)

extract_protocol: Total RNA was extracted with Trizol, purified using Qiagen Rneasy according to the manufacturer's instructions

treatment_protocol: Vk2/E6E7 cells were treated for 6 h; compounds: non-inflammatory (carboxymethyl cellulose,  hydroxyethyl cellulose at 1mg/ml, growth medium), pro-inflammatory (imiquimod at 30 mg/ml, macrophage activating lipopeptide 2 (MALP2) at 200 ng/ml, nonoxynol 9 (N9) at 12.5 μg/ml, Pam3CSK4 at 10 μg/ml, TNF-alpha at 40 ng/ml)

tag: cell line

tag: cell type

value: Human vaginal epithelial immortalized cells


title: Cn_WT pH 4.0 vs WT pH 7.2_replicate 1

city: Stony Brook

first: Maurizio

last: Del Poeta

state: NY

address: 150 Life Science Building

department: Molecular Genetics and Microbiology

institute: Stony Brook University

hyb_protocol: 300ng of each sample to be co-hybridized was fragmented and hybridized to an Agilent custom anti-sense probe 8x15K microarray (AMADID 019465) by manufacturer's specifications with the following exception:  5uL of Kreablock (included in the labeling kit) was added after fragmentation.  Hybridization was carried out in a SureHyb chamber in an Agilent hybridization oven at 65C and 10 rpm for 17 hours.

scan_protocol: Slides were washed using Agilent GE wash buffers and scanned on an Agilent C scanner at 5um.

data_processing: Data was extracted using Agilent Feature Extraction v. 10.7.1 software.  The normalization method used for data extraction was Linear-Lowess. Lowess normalized log2 ratio (test/reference) included in supplementary file processed_data.txt.

organism: Cryptococcus neoformans H99

source_name: Whole cell RNA extract

label_protocol: Total RNA integrity was verified by Agilent 2100 Bioanalyzer.  Concentration and sample purity were determined by Nanodrop ND-1000.  Samples with 260/280 < 1.8, 260/230 < 1.8 were column purified and re-quantitated.  1ug of total RNA was direct labeled using Kreatech ULS aRNA Labeling Kit for dual-color hybridization.  Concentrations and dye incorporation data (Cy3: 100-130 pmol/ug, Cy5:  70-100 pmol/ug) were determined by Nanodrop.

growth_protocol: Cryptococcus strains were routinely grown at 30ºC and 0.04% atmospheric CO2 in YPD broth (2% Peptone, 1% yeast extract, 2% Dextrose, BD). Dulbecco’s modified Eagle mediuma high glucose (DMEM high glucose), buffered with 50 mM HEPES, 10% FBS (Fetal Bovine Serum) and 1M sSorbitol at pH 7.2±0.2 and pH 4, were used as conditioned media for growing C. neoformans strains at 37ºC in presence of 5% CO2.

extract_protocol: Overnight YPD grown cultures of WT, ∆gcs1 and ∆smt1 mutant strain, were pelleted, washed twice with sterile Phosphate Buffer Saline (PBS) and inoculated in DMEM high glucose, buffered with 50 mM HEPES, containing 10% Fetal Bovine Serum, 1M Sorbitol at pH 7.2 and pH 4 and shaken-incubated for 20 hours at 37°C, 5% CO2. The cells were harvested by centrifugation at 5,000 g for 10 minutes and washed twice with PBS. The cell-pellets were flash-frozen in dry-ice/ ethanol bath and stored at -80ºC until ready to use. Total RNA was extracted from Cn strains, as described previously [51]. Briefly, the cells were lyophilized overnight and 100 µl of lyophilized cells were transferred in 2 ml screw cap tubes and 1.25 ml of TRI reagent (Molecular Research Center, Inc.) was added. After homogenization, using Bead Beater 16, the tubes were incubated at room temperature for 10 minutes and centrifuged at 8, 000 g to pellet cell debris and unbroken cells. The supernatants were transferred in fresh tubes along with 60 µl of BAN phase separation reagent (Molecular Research Center, Inc.). After mixing for 20-30 seconds and incubating at room temperature for 5 minutes, samples were centrifuged at 8,000 g. The aqueous phases were placed in fresh tubes along with 70% ethanol, and loaded onto RNeasy isolation columns provided by RNeasy Mini Kit (Qiagen, CA, USA). Total RNA was further purified and eluted according to manufacturer’s instructions. Total RNA integrity was verified by Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA). Concentration and sample purity were determined by Nanodrop ND-1000 (Nanodrop, DE, USA).  Samples with 260/280 < 1.8, 260/230 < 1.8 were column purified and re-quantitated.

treatment_protocol: No treatment

tag: genotype

value: WT

tag: ph


title: Cn_WT vs ∆gcs1_pH 4.0_replicate 3


title: LXRα-Tg sham [5511168079_D]

value: LXRα-Tg

value: sham surgery


title: LXRα-Tg TAC [5511168079_A]


title: LXRα-Tg sham [5511168069_G]


title: Vk2 cells_no treatment, biol rep 31


title: LXRα-Tg TAC [5511168069_F]


title: Wt TAC [5511168069_C]


title: LXRα-Tg TAC [5511168079_F]


title: Wt sham [5511168069_B]


title: LXRα-Tg sham [5511168079_C]


title: Cn_WT vs ∆smt1_pH 4.0_replicate 3


title: Vk2 cells_no treatment, biol rep 26


title: Vk2 cells_no treatment, biol rep 28


title: Vk2 cells_N9-treated, biol rep 5

source_name: Vk2/E6E7, nonoxynol 9 (N9) at 12.5 μg/ml


title: Wt sham [5511168069_H]


title: Cn_WT vs ∆gcs1_pH 7.2_replicate 3


title: Cn_WT vs ∆smt1_pH 7.2_replicate 3


title: Vk2 cells_no treatment, biol rep 25


title: Vk2 cells_no treatment, biol rep 24


title: Cn_WT vs ∆gcs1_pH 4.0_replicate 2


title: Vk2 cells_no treatment, biol rep 27


title: Vk2 cells_no treatment, biol rep 23


title: Cn_WT vs ∆smt1_pH 7.2_replicate 2


title: Cn_WT vs ∆smt1_pH 7.2_replicate 1


title: Cn_WT vs ∆smt1_pH 4.0_replicate 2


title: Cn_WT vs ∆smt1_pH 4.0_replicate 1


title: Cn_WT vs ∆gcs1_pH 4.0_replicate 1


title: Cn_WT vs ∆gcs1_pH 7.2_replicate 2


title: Wt TAC [5511168079_H]


title: Cn_WT vs ∆gcs1_pH 7.2_replicate 1


title: Vk2 cells_no treatment, biol rep 18


title: Vk2 cells_no treatment, biol rep 16


title: Vk2 cells_no treatment, biol rep 21


title: Vk2 cells_no treatment, biol rep 22


title: Vk2 cells_no treatment, biol rep 15


title: High fat diet + quercetin + resveratrol HQR 4

city: Shanghai

first: Wang

last: Shidong

address: 151 Libing Road

country: China

institute: SBC

description: Gene expression after 26 weeks HFD plus 0.2% quercetin + 0.2% resveratrol (2g quercetin+ 2g resveratrol per kg diet) feeding

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 2.2ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55ul of 2x GEx Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarray（4×44K）for 17 hours at 65℃ in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37℃ GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: slides were scanned by using an Agilent Microarray Scanner (Agilent Technologies, Santa Clara, USA) with 5-µm resolutions of each slide at photomultiplier tube settings of 100% and 10%.

data_processing: TIFF images were analyzed using Agilent’s feature extraction software (version 9.5.3).

source_name: Liver, HQR

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Low Input Quick Amp Labeling Kit,One-Color (Agilent) and RNA Spike-In Kit, One-Color (Agilent) according to the manufacturer's instructions.  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 UV-VIS Spectrophotometer.

extract_protocol: Total RNA was isolated from 30 individual mouse livers (six members each group) using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) and purified with RNeasy mini Kit (QIAGEN GmBH, Germany). The RNA integrity number was qualified to be more than 7.0 using a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, USA).

treatment_protocol: Thirty 7-week-old male C57/6J mice were seperately fed with standard food (SD), high fat diet (HFD), HFD plus 0.4% quercetin, HFD plus 0.4% resveratrol, HFD plus 0.2% quercetin + 0.2% resveratrol for 26 weeks.

value: Liver

tag: treatment

value: 26 weeks high fat diet plus 0.2% quercetin + 0.2% resveratrol (2g quercetin+ 2g resveratrol per kg diet) feeding

value: 33 wk


title: Vk2 cells_no treatment, biol rep 17


title: High fat diet + resveratrol HR 5

description: Gene expression after 26 weeks HFD plus 0.4% resveratrol (4 g/kg diet) feeding

source_name: Liver, HR

value: 26 weeks high fat diet plus 0.4% resveratrol (4 g/kg diet) feeding


title: Vk2 cells_no treatment, biol rep 19


title: inbR_overexpressing_logphase_rep2

city: wuhan

first: yang

last: min

state: Hubei

address: No. 1, Shizishan Road/Street, Hongshan District

institute: Huazhong Agricultural University

description: log phase gene expression of inbR-overexpressing strain

hyb_protocol: Each Slide was hybridized with 600ng Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=5μm, PMT 100%, 10%, 16bit. Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US).

data_processing: Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

organism: Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2

source_name: inbR overexpressing

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

growth_protocol: M. bovis BCG cells were grown in 7H9 medium at 37℃ to logarithmic growth phase and were collected by centrifugation.

extract_protocol: Total RNA was extracted and purified using RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

value: inbR overexpressing Pasteur 1173P2

tag: medium

tag: Stage

value: log phase


title: Vk2 cells_no treatment, biol rep 20


title: inbR_overexpressing_logphase_rep1


title: High fat diet + quercetin + resveratrol HQR 5


title: High fat diet + quercetin + resveratrol HQR 6


title: Vk2 cells_no treatment, biol rep 14


title: High fat diet + quercetin + resveratrol HQR 2


title: wt_logphase_INH_treatment_24h_rep3

description: wild type gene expression in log phase, but treated by 0.5μg/ml isoniazid for 26 hours.

source_name: 24hrs, 0.5μg/ml INH

value: wild type Pasteur 1173P2

value: 7H9, 0.5μg/ml INH


title: High fat diet + resveratrol HR 4


title: High fat diet + quercetin + resveratrol HQR 1


title: High fat diet + quercetin + resveratrol HQR 3


title: Vk2 cells_no treatment, biol rep 13


title: High fat diet + resveratrol HR 6


title: High fat diet + resveratrol HR 1


title: High fat diet + resveratrol HR 3


title: Vk2 cells_no treatment, biol rep 12


title: Pre-B ALL lymphoma 8

city: Boston

first: yue

last: kang

state: MA

address: 450 Brookline Avenue

department: Medical Oncology

institute: Dana Farber Cancer Institute

hyb_protocol: The biotinylated complementary RNA (cRNA) was purified from the IVT reaction mixture using the RNeasy system (Qiagen). The cRNA was quantified spectrophotometrically and purity of the cRNA was also assessed by spectrophometric measurements. The purified cRNA was fragmented in order to facilitate the subsequent hybridization step. The cRNA was purified from the fragmentation reaction using phenol/chloroform extraction and ethanol precipitation. The fragmented cRNA was added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. The chips were then transferred to a fluidics instrument that performed washes to remove cRNA that had not hybridized to its complementary oligonucleotide probe. The bound cRNA was then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors were then added using biotinylated anti-streptavidin antibody and additional SAPE

scan_protocol: Each cRNA bound at its complementary oligonucleotide was excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions were captured. These measures provided the basis of subsequent biostatistical analysis.

data_processing: Data were processed using Affy R package, and expression signal values were generated using the RMA (Robust Multiarray Average) algorithm (Irizarry et al., 2003) for background adjustment, quantile-normalization and summarization.

source_name: Cre-Ras-INK_pre-B ALL

label_protocol: RNA was converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis was then carried out. The double-stranded cDNA was used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates.

growth_protocol: pre-B ALL tumors isolated from mice were immediatelly processed for total RNA extraction

extract_protocol: Total RNA was isolated from pre-B ALL tumors using TRIzol Reagent.

treatment_protocol: No treatment was included

tag: strain background

value: CD19Cre; KrasG12D/+; Ink4a/ArfL/+

value: Pre-B ALL lymphoma


title: Pre-B ALL lymphoma 9


title: Pre-B ALL lymphoma 10


title: wt_logphase_INH_treatment_24h_rep2

description: wild type gene expression in log phase, but treated by 0.5μg/ml isoniazid for 25 hours.


title: wt_logphase_INH_treatment_24h_rep1

description: wild type gene expression in log phase, but treated by 0.5μg/ml isoniazid for 24 hours.


title: High fat diet + resveratrol HR 2


title: Vk2 cells_no treatment, biol rep 11


title: Pre-B ALL lymphoma 7


title: wt_logphase_rep2

description: wild type gene expression in log phase

source_name: wild type


title: High fat diet + quercetin HQ 5

description: Gene expression after 26 weeks HFD plus 0.4% quercetin (4 g/kg diet) feeding

source_name: Liver, HQ

value: 26 weeks high fat diet plus 0.4% quercetin (4 g/kg diet) feeding


title: High fat diet + quercetin HQ 4


title: High fat diet + quercetin HQ 3


title: Vk2 cells_no treatment, biol rep 9


title: wt_logphase_rep3

description: wild type gene expression in log phase


title: Vk2 cells_no treatment, biol rep 8


title: Pre-B ALL lymphoma 4


title: Vk2 cells_no treatment, biol rep 10


title: Pre-B ALL lymphoma 5


title: wt_logphase_rep1

description: wild type gene expression in log phase


title: Pre-B ALL lymphoma 6


title: High fat diet + quercetin HQ 2


title: Pre-B ALL lymphoma 3


title: Pre-B ALL lymphoma 2


title: Vk2 cells_no treatment, biol rep 6


title: High fat diet + quercetin HQ 1


title: Vk2 cells_no treatment, biol rep 7


title: High fat diet HFD 5

description: Gene expression after 26 weeks HFD feeding

source_name: Liver, HFD

value: 26 weeks high fat diet feeding


title: CD19-positive B-cells from CD19-Cre, KrasG12D, Ink/Arf mice, biological replica rep 2

source_name: CD19-positive B-cells_CD19-Cre, KrasG12D, Ink/Arf mice

growth_protocol: CD19-positive cells were isolated using immunomagnetic beads and immediatelly processed for total RNA extraction

extract_protocol: CD19+ splenic B cells were isolated using magnetic microbeads from Miltenyi Biotec. Total RNA was isolated from control and transgenic CD19+ splenic B-cells using TRIzol Reagent.

value: CD19-Cre, KrasG12D, Ink/Arf

value: 8 weeks

tag: status

value: Pre-malignant

value: spleen

value: CD19-positive B-cells


title: High fat diet HFD 4

value: Liver

value: male


title: Vk2 cells_no treatment, biol rep 4

value: Human vaginal epithelial immortalized cells


title: Vk2 cells_no treatment, biol rep 5


title: High fat diet HFD 6

value: 33 wk


title: SW480 control group

city: Chongqing

first: Xiaorong

last: Yang

address: 1#, Yuzhong Road

institute: Chongqing Medical University

description: T_5_NS; T-5(SW480/CB)

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions。

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, 20bit.

data_processing:
Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US).
Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

organism: Colon

source_name: SW480 control group

growth_protocol: SW-480 human colon cancer cells were cultured in RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum, 100 U/ml Penicillin, and 100μg/ml streptomycin at 37°C in a humidified atmosphere of 5% CO2.

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: SW480 cells were co-cultured with CB (1.5×10^7 CFU/ml) 48 hours which have been identified as a proper CB concentration and treated time by our previous experiments.

value: colon cancer cell line

tag: cocultured with

value: none (control)


title: Pre-B ALL lymphoma 1


title: SW480 co-cultured with CB

description: C_1_NS; C-1(SW480/ctr)

source_name: SW480 co-cultured with CB

value: C. butyricum (1.5×10^7 CFU/ml) for 48 hrs


title: Pop 7, biological rep1

city: Leiden

first: Matthew

middle: James

last: Birket

address: Einthovenweg 20

department: Anatomy and Embryology

institute: Leiden University Medical Center

hyb_protocol: Standard Illumina protocol: Whole-Genome Gene Expression Direct Hybridization Assay.

scan_protocol: Samples were scanned with illumina iscan array scanner using standard Illumina protocol

data_processing: The data was normalized using quantile normalization in Genespring GX  v12.5.

source_name: NKX2-5eGFP/w Tet-ON MYC CPCs (day 6 sorted for NKX2-5+/PDPN-)

label_protocol: Biotin-labeled (Biotin-16-UTP) amplified cRNA was generated using Illumina Totalprep-96 RNA Amplification Kit

growth_protocol: NKX2-5eGFP/w Tet-ON MYC hESCs were differentiated as Ebs for 6 days then dissociated and expanded for 6 more days as CPCs

extract_protocol: RNA extraction was performed with Macherey-Nagel Nucleospin Kit. DNAse treatment was performed on the column and quality of samples was asessed on Agilent bioanalyzer.

treatment_protocol: Cultures were expanded in DSIS+DMH1+SU5402 (Pop1); DSIS+BMP4+SU5402 (Pop2 and Pop3); DSIS+BMP4+bFGF (Pop6 and Pop7)

tag: differentiation

value: Day 6 (EB)+6 days expansion

tag: markers


title: CD19-positive B-cells from CD19-Cre, KrasG12D, Ink/Arf mice, biological replica rep 1

tag: genotype/variation


title: CD19-positive B-cells from CD19-Cre, KrasG12D mice, biological replica rep 2

source_name: CD19-positive B-cells_CD19-Cre, KrasG12D mice

value: CD19-Cre, KrasG12D


title: Vk2 cells_no treatment, biol rep 2


title: Pop 6, biological rep2

source_name: NKX2-5eGFP/w Tet-ON MYC CPCs (day 6 sorted for NKX2-5+/PDPN+)


title: Pop 7, biological rep2


title: Vk2 cells_no treatment, biol rep 3

source_name: Vk2/E6E7, no treatment,  growth medium only


title: CD19-positive B-cells from CD19-Cre, KrasG12D mice, biological replica rep 1


title: Pop 6, biological rep1


title: High fat diet HFD 2

tag: strain


title: High fat diet HFD 1

tag: age


title: adult female on HFD in IH, rep3

city: LA JOLLA

first: Erilynn

last: Heinrichsen

state: CA

address: 9500 Gilman Dr, MC0735

institute: UC-San Diego

description: Adult female Drosophila, after 1 week on high-fat diet (with 20% weight: volume coconut oil) in intermittent hypoxia (1.5-21%, 10 minute cycling)

hyb_protocol: All samples were labeled, hyb'd and scanned by the GeneChip Microarray Core at UCSD following Affymetrix specifications.

data_processing: The raw data were normalized using Bioconductor Affy software (www.bioconductor.org/packages/2.0/bioc/html/affy.html) with the MAS5 algorithm, followed by analysis of the normalized data for each array spot with VAMPIRE microarray suite.  A spot was considered differentially expressed between two samples when the threshold of false discovery rate (fdr) was smaller than 0.05. Significance limits were set at changes of 1.5-fold (for up-regulated genes) and 0.67-fold (for down-regulated genes).

organism: Drosophila melanogaster

source_name: Adult female Drosophila, high-fat diet in intermittent hypoxia

growth_protocol: w1118 flies eclosed in 25 degree incubator and then were kept at room temperature.

extract_protocol: Trizol extraction of total RNA was followed by RNA cleanup using RNeasy kit, according to the manufacturer's instructions.

treatment_protocol: At day 3-5, flies were put on their specific food and oxygen condition for one week.

tag: tissue

value: whole body

value: female

value: adult, d10-12


title: CD19-positive B-cells from CD19-Cre, Ink/Arf mice, biological replica rep2

source_name: CD19-positive B-cells_CD19-Cre, Ink/Arf mice

value: CD19-Cre, Ink/Arf


title: Vk2 cells_no treatment, biol rep 1


title: Pop 3, biological rep2

source_name: NKX2-5eGFP/w Tet-ON MYC CPCs (day 6 sorted for NKX2-5-/PDPN-)


title: Gastric cancer 8 [Agilent-018898]

status: Public on May 29 2015

type: genomic

city: Suwon

first: Dongho

last: Kim

address: #300 Chunchun-dong, Jangan-Ku, Suwon, Kyungggi-do

department: Samsung Biomedical Research Institute

country: South Korea

institute: Sungkyunkwan University School of Medicine

hyb_protocol: The aCGH was performed according to the manufacturer’s recommendations.

scan_protocol: After DNA hybridization and washing, slides were scanned immediately using an Agilent microarray scanner, and raw data were extracted using Feature Extraction Software at the default CGH parameter settings (Agilent Technologies).

data_processing:
Putative CNA intervals in each sample were identified using Agilent Genomic Workbench v7.0.4.0 software. Cy5/Cy3 ratios were converted into log2-transformed values. Centralization and fuzzy zero corrections were applied to the microarray. The Aberration Detection Method 2 (ADM-2) algorithm at threshold 6.0 was used to identify the CNAs in individual samples and to determine aberration frequencies in gastric cancer samples.
The following filters were employed: minimum number of probes in region >= 3, minimum absolute average log ratio of region > = 0.25. gIsSaturated = true OR rIsSaturated = true OR gIsFeatNonUnifOL = true OR rIsFeatNonUnifOL = true OR LogRatio = 0. Homology = 0 OR IsPseudoautosomal = 1

molecule: genomic DNA

source_name: Gastric cancer tissue

label_protocol: Array CGH labeling kit (Invitrogen) using Cy5/Cy3

extract_protocol: A total of 10 patients, who had undergone curative surgical resection for gastric cancer at the Department of Surgery in the Samsung Medical Center, Seoul, Korea, participated in this study.  The tumors were snap-frozen in liquid nitrogen and stored at −80°C until needed. Before DNA was extracted from the fresh frozen tissues, the sections were placed on slides and stained with H&E to evaluate the admixture of tumorous and non-tumorous tissues. Tumor and non-tumor areas were microdissected carefully under a microscope. The microdissected tissues were digested with proteinase K, and the genomic DNA was isolated according to the instructions of the manufacturer (DNeasy Tissue kit, Qiagen, Valencia, CA).

tag: Sex

value: Male

tag: age (years)

source_name: Matched normal tissue


title: Gastric cancer 6 [Agilent-018898]


title: Gastric cancer 7 [Agilent-018898]


title: adult female on HFD in IH, rep1

scan_protocol: All samples were labeled, hyb'd and scanned by the GeneChip Microarray Core at UCSD following Affymetrix specifications.

tag: gender


title: Gastric cancer 10 [Agilent-018898]


title: Gastric cancer 9 [Agilent-018898]


title: Gastric cancer 5 [Agilent-018898]

value: Female


title: Standard Diet SD 5

description: Gene expression after 26 weeks SD feeding

source_name: liver, SD

value: 26 weeks standard diet feeding


title: adult female on RD in IH, rep1

description: Adult female Drosophila, after 1 week on regular diet (Jazz-Mix food) in intermittent hypoxia (1.5-21%, 10 minute cycling)

source_name: Adult female Drosophila, regular diet in intermittent hypoxia

label_protocol: All samples were labeled, hyb'd and scanned by the GeneChip Microarray Core at UCSD following Affymetrix specifications.

tag: genotype


title: CD19-positive B-cells from CD19-Cre, Ink/Arf mice, biological replica rep1

value: 8 weeks

value: Pre-malignant

value: spleen

tag: cell type

value: CD19-positive B-cells


title: Pop 2, biological rep1

source_name: NKX2-5eGFP/w Tet-ON MYC CPCs (day 6 sorted for NKX2-5-/PDPN+)


title: CD19-positive B-cells from CD19-Cre mice, biological replica rep2

source_name: CD19-positive B-cells_CD19-Cre mice


title: Standard Diet SD 3

value: Liver

value: male

tag: treatment

value: 33 wk


title: Gastric cancer 4 [Agilent-018898]


title: Gastric cancer 3 [Agilent-018898]


title: Standard Diet SD 4


title: adult female on RD in IH, rep2


title: adult female on RD in IH, rep3


title: Pop 2, biological rep2


title: Pop 3, biological rep1


title: adult female on HFD in IH, rep2


title: Pop 1, biological rep2

source_name: NKX2-5eGFP/w Tet-ON MYC CPCs (day 6 sorted for NKX2-5-/PDPN++)


title: CD19-positive B-cells from CD19-Cre mice, biological replica rep1


title: Standard Diet SD 2


title: Pop 1, biological rep1


title: Standard Diet SD 1


title: Gastric cancer 2 [Agilent-018898]


title: Primary osteoblasts of mice treated with phosphate

city: Hamburg

first: Thomas

last: Streichert

address: Martinistr. 52, Campus Forschung N27, 2. OG

department: Institute For Clinical Chemistry / Central Laboratories

country: Germany

institute: University Medical Center Hamburg-Eppendorf

description:
Gene expression data from primary murine osteoblasts treated with a-MEM containing a final concentration of 4 mM phosphate (added from a 0.5 M sodium phosphate solution buffered to pH 7.2)
PO4_2- treated osteoblasts

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Affymetrix GeneChip Operating Software GCOS 1.4 (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 200.

source_name: primary osteoblasts_phosphate

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Expression Analysis Technical Manual, Affymetrix).

extract_protocol: Trizol extraction followed by Rneasy purification

treatment_protocol: Cells were serum-starved over night and incubated with fresh serum-free medium for 6 hours.  While the control cultures received non-modified a-MEM (containing 1 mM phosphate, pH 7.2), the treatment was performed with a-MEM containing a final concentration of 4 mM phosphate (added from a 0.5 M sodium phosphate solution buffered to pH 7.2).

value: primary osteoblast


title: Gastric cancer 9 [Agilent-018897]


title: Gastric cancer 1 [Agilent-018898]


title: Untreated primary osteoblasts of mice

description:
Gene expression data from primary murine osteoblasts treated with non-modified a-MEM (containing 1 mM phosphate, pH 7.2)
Untreated primary osteoblasts

source_name: primary osteoblasts_control


title: Gastric cancer 10 [Agilent-018897]


title: Gastric cancer 7 [Agilent-018897]


title: Gastric cancer 8 [Agilent-018897]


title: Gastric cancer 6 [Agilent-018897]


title: Gastric cancer 4 [Agilent-018897]


title: Gastric cancer 1 [Agilent-018897]


title: Gastric cancer 3 [Agilent-018897]


title: Gastric cancer 5 [Agilent-018897]


title: Gastric cancer 2 [Agilent-018897]


title: High fat diet HFD 3

source_name: Liver, HFD

value: 26 weeks high fat diet feeding


title: THP-1 40 degrees, rep 1

city: Camperdown

first: william

last: ritchie

state: NSW

address: Building 93

country: Australia

institute: centenary institute

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: The arrays were normalized using the justRMA suite of algorithms from Bioconductor (http://www.bioconductor.org).

source_name: THP-1 40 degrees

label_protocol: Differential expression of mRNAs was assessed using the GeneChip® Prime View™ Human Gene Expression Array (Affymetrix). Microarray analysis was performed at the Ramaciotti Centre for Genomics (Sydney) according to the manufacturer’s instructions.

growth_protocol: THP-1 cells were maintained in RPMI media supplemented with 10% (v/v) FCS, 0.05 mM 2- mercaptoethanol, 0.1 mg/ml penicillin/streptomycin and 2 mM L-glutamine. Differentiation of THP-1 into macrophages was performed as previously described14. Briefly, cells were plated at a density of 1.5 x 107 cells per 75cm2 culture flask containing supplemented RPMI with 100 ng/ml (PMA) and 50 µM 2-mercaptoethanol for 48 hours. Differentiated THP-1 cells were then maintained at normal (37 °C) or fever-like (40 °C) temperatures up to 24 hours. Cells exposed to 40oC were harvested at two, eight and 24 hours for subsequent small RNA and transcriptomic analyses. K562 cells were maintained in RPMI 1640 supplemented with 10% (v/v) FCS and antibiotics.

extract_protocol: RNA extraction was performed using Trizol (Invitrogen) according to the manufacturer’s instructions. qRT-PCR was performed on cDNA generated from 1μg DNase1-treated total RNA using SuperScript® III First-Strand Synthesis System (Invitrogen), according to the manufacturers’ instructions. qRT-PCR reactions were prepared in 20 μl volumes containing 1IQ SyberGreen supermix and 0.3 μM of the respective forward and reverse primers and analyzed using the CFX96(TM) Real Time PCR Machine (Bio-Rad).

treatment_protocol: THP-1 cells were differentiated into macrophages at 40 °C, harvested and nucleofected with the custom designed 2′-O-methylated miRIDIAN miRNA Hairpin Inhibitor (Dharmacon) directed against miR-142, miR-143, ThermoMIR-1 or non-human miRNA control. These miRNA inhibitors do not necessarily direct degradation of miRNAs but would induce loss of functions as previously published17.  Cells were co-transfected with pmaxGFP vector and GFP expressing cells were purified 24 hours post nucleofection using fluorescence-activated cell sorting for microarray or qRT-PCR analyses.

tag: cell line


title: THP-1 siRNA, rep 1

source_name: THP-1 siRNA

value: siThermomir


title: THP-1 40 degrees, rep 3


title: 3T3-L1 no trasfection, 72 hr after differentiation induction, biological replicate 1

city: Beijing

first: Zhao

last: Renbin

address: 61 Zhichun Road

department: Space Biology Research and Technology Center

institute: China Academy of Space Technology

description: gene expression data from mouse 3T3-L1 cells induced for differentiation

hyb_protocol: Affymetrix instruction.

scan_protocol: Affymetrix instruction.

data_processing: RMA

label_protocol: Affymetrix instruction.

growth_protocol: 3T3-L1 cells were grown in DMEM media.

extract_protocol: Total cellular RNA was isolated from 3T3-L1 cells using RNeasy Protect Mini Kit (Qiagen,Genman).

treatment_protocol: 3T3-L1 cells were grown to % confluency, treated with siRNA with Lipofectamine following manufacturer's instructions. 24 hours after transfection cells were induced to differentiation with cocktail MDI. Cells were harvested at 0, 6, 24 and 72 hours post induction.

value: 3T3-L1 preadipocyte


title: 3T3-L1, transfected with randomized siRNA, 72 hr after differentiation induction, biological replicate 2


title: 3T3-L1, transfected with siFTO-1, 72 hr after differentiation induction, biological replicate 2


title: 3T3-L1, transfected with randomized siRNA, 72 hr after differentiation induction, biological replicate 3


title: 3T3-L1, transfected with siFTO-1, 24 hr after differentiation induction, biological replicate 3


title: 3T3-L1, transfected with siFTO-2, 24 hr after differentiation induction, biological replicate 2


title: THP-1 siRNA, rep 2


title: 3T3-L1, transfected with siFTO-1, 24 hr after differentiation induction, biological replicate 2


title: 3T3-L1, transfected with siFTO-2, 72 hr after differentiation induction, biological replicate 3


title: THP-1 WT, rep 3

source_name: THP-1 WT

value: control


title: THP-1 40 degrees, rep 2


title: THP-1 37 degrees, rep 1

source_name: THP-1 37 degrees


title: 3T3-L1, transfected with siFTO-2, 72 hr after differentiation induction, biological replicate 2


title: THP-1 WT, rep 2


title: THP-1 WT, rep 1


title: THP-1 37 degrees, rep 2


title: 3T3-L1, transfected with siFTO-2, 24 hr after differentiation induction, biological replicate 1


title: 3T3-L1, transfected with siFTO-2, 72 hr after differentiation induction, biological replicate 1


title: THP-1 37 degrees, rep 3


title: 3T3-L1, transfected with siFTO-1, 72 hr after differentiation induction, biological replicate 1


title: 3T3-L1 no trasfection, 72 hr after differentiation induction, biological replicate 2


title: 3T3-L1, transfected with randomized siRNA, 72 hr after differentiation induction, biological replicate 1


title: 3T3-L1 no trasfection, 72 hr after differentiation induction, biological replicate 3


title: 3T3-L1, transfected with siFTO-1, 72 hr after differentiation induction, biological replicate 3


title: THP-1 siRNA, rep 3


title: 3T3-L1, transfected with siFTO-1, 24 hr after differentiation induction, biological replicate 1


title: 3T3-L1, transfected with siFTO-2, 24 hr after differentiation induction, biological replicate 3


title: 3T3-L1, transfected with randomized siRNA, 24 hr after differentiation induction, biological replicate 3


title: 3T3-L1, transfected with randomized siRNA, 24 hr after differentiation induction, biological replicate 1


title: 3T3-L1, transfected with randomized siRNA, 6 hr after differentiation induction, biological replicate 2


title: 3T3-L1, transfected with randomized siRNA, 6 hr after differentiation induction, biological replicate 1


title: 3T3-L1 no trasfection, 24 hr after differentiation induction, biological replicate 3


title: 3T3-L1, transfected with randomized siRNA, 6 hr after differentiation induction, biological replicate 3


title: 3T3-L1, transfected with siFTO-2, 6 hr after differentiation induction, biological replicate 1


title: 3T3-L1, transfected with siFTO-2, 0 hr after differentiation induction, biological replicate 3


title: 3T3-L1, transfected with siFTO-2, 0 hr after differentiation induction, biological replicate 2


title: 3T3-L1, transfected with siFTO-1, 6 hr after differentiation induction, biological replicate 1


title: 3T3-L1, transfected with siFTO-1, 6 hr after differentiation induction, biological replicate 3


title: 3T3-L1, transfected with siFTO-2, 6 hr after differentiation induction, biological replicate 3


title: 3T3-L1 no trasfection, 6 hr after differentiation induction, biological replicate 1


title: 3T3-L1, transfected with randomized siRNA, 24 hr after differentiation induction, biological replicate 2


title: 3T3-L1, transfected with siFTO-1, 0 hr after differentiation induction, biological replicate 3


title: 3T3-L1, transfected with siFTO-1, 0 hr after differentiation induction, biological replicate 2


title: 3T3-L1 no trasfection, 6 hr after differentiation induction, biological replicate 3


title: 3T3-L1 no trasfection, 24 hr after differentiation induction, biological replicate 2


title: 3T3-L1, transfected with siFTO-2, 0 hr after differentiation induction, biological replicate 1


title: 3T3-L1 no trasfection, 24 hr after differentiation induction, biological replicate 1


title: 3T3-L1, transfected with siFTO-1, 6 hr after differentiation induction, biological replicate 2


title: 3T3-L1 no trasfection, 6 hr after differentiation induction, biological replicate 2


title: 3T3-L1, transfected with randomized siRNA, 0 hr after differentiation induction, biological replicate 1


title: 3T3-L1, transfected with siFTO-2, 6 hr after differentiation induction, biological replicate 2


title: 3T3-L1, transfected with randomized siRNA, 0 hr after differentiation induction, biological replicate 3


title: 3T3-L1, transfected with siFTO-1, 0 hr after differentiation induction, biological replicate 1


title: 3T3-L1 no trasfection, 0 hr after differentiation induction, biological replicate 2


title: 3T3-L1, transfected with randomized siRNA, 0 hr after differentiation induction, biological replicate 2


title: 3T3-L1 no trasfection, 0 hr after differentiation induction, biological replicate 1


title: 3T3-L1 no trasfection, 0 hr after differentiation induction, biological replicate 3


title: Ileum_ALI_rep4

city: Houston

first: Frank

last: McKeon

state: TX

address: 3455 Cullen Blvd

department: Biology and Biochemistry

institute: University of Houston

description: Gene expression data from air-liquid interface differentiation

hyb_protocol: GeneChip® Hybridization, Wash, and Stain Kit (affymetrix)

data_processing:
Expression console, Partek Genome Suite 6.6
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: Ileum, ALI

label_protocol: Encore® Biotin Module (Nugen)

growth_protocol: Stem cells are differentiated by air-liquid interface method.

extract_protocol: RNeasy Mini Kit (Qiagen)

value: Fetal ilial tissue


title: TcdB_500pM_8hr_rep1

description:
500pM8hr-1
Colonic stem cells-air liquid interface.
Stem cell differentiation.
TcdB treatment.

hyb_protocol: GeneChip® Hybridization, Wash, and Stain Kit (Affymetrix).

data_processing:
RMA. Expression Console, Partek Genomics Suite 6.6.
Probe group file: HuEx-1_0-st-v2.r2.pgf
Meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

label: Biotin

source_name: Colonic epithelia, TcdB, 500pM, 8hr

label_protocol: Encore® Biotin Module (Nugen).

growth_protocol: Colonic epithelia was generated in air-liquid interface cultures from cloned transverse colon stem cells.

extract_protocol: RNeasy Mini Kit (Qiagen).

treatment_protocol: Colonic stem cells differentiated in air-liquid interface cultures were treated with C. difficile toxin B at different doses (100 pM, 250 pM, and 500 pM) and durations (8 hrs, 16 hrs and 24 hrs).

value: cloned transverse colon stem cells differentiated in air-liquid interface culture

value: TcdB

tag: treatment dosage

tag: treatment duration


title: TcdB_500pM_24hr_rep1

description:
500pM24hr-1
Colonic stem cells-air liquid interface.
Stem cell differentiation.
TcdB treatment.

scan_protocol: GeneChip® Hybridization, Wash, and Stain Kit (Affymetrix).

source_name: Colonic epithelia, TcdB, 500pM, 24hr


title: TcdB_500pM_16hr_rep1

description:
500pM16hr-1
Colonic stem cells-air liquid interface.
Stem cell differentiation.
TcdB treatment.

source_name: Colonic epithelia, TcdB, 500pM, 16hr


title: TcdB_250pM_16hr_rep1

description:
250pM16hr-1
Colonic stem cells-air liquid interface.
Stem cell differentiation.
TcdB treatment.

source_name: Colonic epithelia, TcdB, 250pM, 16hr


title: TcdB_250pM_24hr_rep2

description:
250pM24hr-2
Colonic stem cells-air liquid interface.
Stem cell differentiation.
TcdB treatment.

source_name: Colonic epithelia, TcdB, 250pM, 24hr


title: TcdB_250pM_24hr_rep1

description:
250pM24hr-1
Colonic stem cells-air liquid interface.
Stem cell differentiation.
TcdB treatment.


title: TcdB_100pM_8hr_rep1

description:
100pM8hr-1
Colonic stem cells-air liquid interface.
Stem cell differentiation.
TcdB treatment.

source_name: Colonic epithelia, TcdB, 100pM, 8hr


title: TcdB_500pM_24hr_rep2

description:
500pM24hr-2
Colonic stem cells-air liquid interface.
Stem cell differentiation.
TcdB treatment.


title: TcdB_500pM_16hr_rep2

description:
500pM16hr-2
Colonic stem cells-air liquid interface.
Stem cell differentiation.
TcdB treatment.


title: Control-rep1

description:
Control-1
Colonic stem cells-air liquid interface.
Stem cell differentiation.
TcdB treatment (control).

source_name: Colonic epithelia, control


title: TcdB_100pM_16hr_rep1

description:
100pM16hr-1
Colonic stem cells-air liquid interface.
Stem cell differentiation.
TcdB treatment.

source_name: Colonic epithelia, TcdB, 100pM, 16hr


title: TcdB_100pM_8hr_rep2

description:
100pM8hr-2
Colonic stem cells-air liquid interface.
Stem cell differentiation.
TcdB treatment.


title: Control-rep2

description:
Control-2
Colonic stem cells-air liquid interface.
Stem cell differentiation.
TcdB treatment (control).


title: TcdB_250pM_8hr_rep1

description:
250pM8hr-1
Colonic stem cells-air liquid interface.
Stem cell differentiation.
TcdB treatment.

source_name: Colonic epithelia, TcdB, 250pM, 8hr


title: TcdB_100pM_24hr_rep1

description:
100pM24hr-1
Colonic stem cells-air liquid interface.
Stem cell differentiation.
TcdB treatment.

source_name: Colonic epithelia, TcdB, 100pM, 24hr


title: Ileum_ALI_rep3

scan_protocol: GeneChip® Hybridization, Wash, and Stain Kit (affymetrix)


title: TcdB_250pM_8hr_rep2

description:
250pM8hr-2
Colonic stem cells-air liquid interface.
Stem cell differentiation.
TcdB treatment.


title: TcdB_100pM_24hr_rep2

description:
100pM24hr-2
Colonic stem cells-air liquid interface.
Stem cell differentiation.
TcdB treatment.


title: TcdB_500pM_8hr_rep2

description:
500pM8hr-2
Colonic stem cells-air liquid interface.
Stem cell differentiation.
TcdB treatment.


title: DC_ALI_rep2

description: Differentiation

data_processing:
Expression console, Partek Genome Suite 6.6
probe group file: HuEx-1_0-st-v2.r2.pgf and meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: DC, ALI

extract_protocol: PicoPure® RNA Isolation Kit (life technologies), RNeasy Mini Kit (Qiagen)

value: Fetal

value: DC, ALI


title: DC_ALI_rep1

description: Differentiation


title: AC_ALI_rep2

description: Differentiation

source_name: AC, ALI

value: AC, ALI


title: TcdB_250pM_16hr_rep2

description:
250pM16hr-2
Colonic stem cells-air liquid interface.
Stem cell differentiation.
TcdB treatment.


title: Jejunum_ALI_rep2

description: Differentiation

source_name: Jejunum, ALI

value: Jejunum, ALI


title: TC_ALI_rep1

description: Differentiation

source_name: TC, ALI

value: TC, ALI


title: AC_ALI_rep1

description: Differentiation


title: TC_ALI_rep2

description: Differentiation


title: Ileum_ALI_rep1

description: Differentiation

value: Ileum, ALI


title: Jejunum_ALI_rep1

description: Differentiation


title: AC_stem cell_rep2

description: Stem cell culture

source_name: AC, stem cell

value: AC, stem cell


title: AC_stem cell_rep1

description: Stem cell culture


title: Duodenum_ALI_rep2

description: Differentiation

source_name: Duodenum, ALI

value: Duodenum, ALI


title: Duodenum_ALI_rep1

description: Differentiation


title: Ileum_stem cell_rep2

description: Stem cell culture

source_name: Ileum, stem cell

value: Ileum, stem cell


title: DC_stem cell_rep2

description: Stem cell culture

source_name: DC, stem cell

value: DC, stem cell


title: TcdB_100pM_16hr_rep2

description:
100pM16hr-2
Colonic stem cells-air liquid interface.
Stem cell differentiation.
TcdB treatment.


title: TC_stem cell_rep1

description: Stem cell culture

source_name: TC, stem cell

value: TC, stem cell


title: TC_stem cell_rep2

description: Stem cell culture


title: Ileum_stem cell_rep1

description: Stem cell culture


title: DC_stem cell_rep1

description: Stem cell culture


title: Duodenum_stem cell_rep1

description: Stem cell culture

source_name: Duodenum, stem cell

value: Duodenum, stem cell


title: Jejunum_stem cell_rep2

description: Stem cell culture

source_name: Jejunum, stem cell

value: Jejunum, stem cell


title: U2OS-- vs. U2OS+3

city: Utrecht

first: Marian

last: Groot Koerkamp

state: Utrecht

address: Heidelberglaan 25

department: Research

institute: Princess Maxima Center for Pediatric Oncology

hyb_protocol: * 60 ul labeled sample is combined with 60 ul 2x-hybmix, containing 50% formamide, 10xSSC, 0.2% SDS, 200 ug/ml herring sperm DNA. * Hybridizations of spotted oligo-arrays (Codelink glass) or Agilent microarrays are performed on a HS4800Pro Hybstation (Tecan). * Priming: 5xSSC, 0.1%SDS. * Probe injection: pre-hyb, 5xSSC, 25% formamide, 0.1%SDS, 1%BSA, Volume 110ul. * Hybridization: 45 min at 42C. * Wash 2x: milliQ. * Wash: 5xSSC, 0.1%SDS. * Probe injection: sample. Volume 110ul (Agilent 4packs: 55ul). * Hybridization: 16 hours at 42C. * Wash 2x: 1xSSC, 0.2%SDS at 23C. * Wash 2x: 0.1xSSC, 0.2%SDS at 23C. * Wash 2x: 0.1xSSC at 23C. * Drying: blow with nitrogen for 3min at 30C.

scan_protocol: Scanning of slides using the Agilent G2565BA scanner. Features were extracted using Imagene software from Biodiscovery.

data_processing:
Normalization was done using print-tip LOESS as described in (Yang et al. 2002), for all gene probes using no background subtraction and a span of 0.4. Probes flagged as absent, or with a (nearly) saturated signal (i.e., > 2^15) in either channel were not considered for the estimation of the LOESS curve. Signals were corrected for dye bias using intrinsic gene-specific dye biases estimated from the hybset itself, as described in Margaritis, Lijnzaad et al., MMol. Sys. Biol. 2009.
The supplementary "*derived.txt" file is the single array file containing normalized data for the Cy5 and Cy3 channels.

label_protocol: All amplification and labeling procedures are performed in 96 wells plates (4titude, Bioke) on a customized Sciclone ALH 3000 Workstation (Caliper LifeSciences), supplemented with a PCR PTC-200 (Bio-Rad Laboratories), SpectraMax 190 spectrofotometer (Molecular Devices), and a magnetic bead-locator (Beckman). mRNA amplification protocol description:* all RNAs are diluted to 0.6 ug/ul and 5 ul is put in a 96-wells plate (Abgene). All subsequent steps are performed by the robot script. * mix1 containing 100 ng T7 Mlu VN primer (custom mix) and EC-control RNA per 5 ul is added and mixed in each well. * plate is incubated @ 70C for 10 mins, cooled to 48C. * mix2 containing 4ul 5x 1st strand buffer, 2 ul 0.1M DTT (Invitrogen), 1ul RNAse Inhibitor (Boehringer), 1ul 20mM dNTPs (GE Healthcare), 1ul linear acrylamide, and 1ul SuperScriptIII (Invitrogen) per sample is prewarmed to 48C; 10 ul per sample is added and mixed in each well. * plate is incubated @ 48C for 2 hours and cooled to room temperature. * 106 ul water and subsequently mix3 containing 15ul second strand buffer, 3ul 20mM dNTPs (GE Healthcare), 1 ul T4 DNA ligase, 4 ul E.coli DNA polymerase I and 1 ul RNAseH (Promega) is added and mixed in each well. * plate is incubated @ 16C for 2 hours, @65C for 10 mins. * ds cDNA product is purified and concentrated with RNAClean (Agencourt, GC biotech) according to manufacturers protocol, to an end volume of 25 ul. * 8 ul cDNA is put in a 96 wells plate and mixed with 12 ul IVT mix containing 2 ul 10x rxn-buffer, 2 ul each ATP, CTP, GTP, 0.6 ul UTP, 2 ul T7 enzyme mix (MegaScript kit, Ambion, Applied Biosystems), and 2.1 ul 50 mM 5-(3-aminoallyl)-UTP (Ambion, Applied Biosystems). * Plate is incubated @37C for 4 hours. * cRNA product is purified with RNAClean (Agencourt, Beckman) according to manufacturer's protocol. * Concentration is measured (SpectraMax 190) and adjusted to 600 ng/ul by the robot. * Resulting cRNA plates are sampled for Bioanalyzer QC, snapfrozen and stored at -80C. Labeling protocol description: * NHS-ester Cy3 or Cy5 dye (Amersham PA 23001 and 25001): entire tube is resuspended in 100 ul DMSO (Merck 8.02912.10).  All subsequent steps are performed by the robot script : * 8 ul of each cRNA (0.6 ug/ul) is put in a 96-wells plate (Abgene), the accompanying reference sample is put in the next column (final step combines cy3 and cy5 labeled material ). * 3 ul 0.5 M NaBicarbonate buffer, pH 9 is added and mixed to all wells.* 3 ul cy-dye solution is added and mixed to the appropriate wells, plate is incubated at 18C for 1 hour. * 4.5 ul 5M hydroxylamine is added and mixed, incubated at 18o C for 15 minutes. * Labeled cRNA product is purified with RNA Clean (Agencourt, GC biotech) according to manufacturers protocol.* RNA concentration and labeling incorporation are measured (SpectraMax 190).* 2.5 ug of each labeled sample and reference cRNA are pooled and subjected to fragmentation according to protocol (Ambion, Applied Biosystems), 15 min 70C. * Samples are stored at -20C until hybridization.

growth_protocol: U2OS (ATCC HTB-96) cells and all derived lines were maintained in DMEM with 10% FBS, L-Glutamine and Pen/Strep. Full-length human CTDSP2 (NM_005730.3) was amplified from HEK293T cDNA, BamHI-EcoRI-cloned into pFakeEntry2Dummy (derived from vector pAZ1; containing extended MCS) and sequence verified. The D98E/D101N phosphatase-dead mutant CTDSP2-dead was generated following the Stratagene QuikChange protocol. Using Gateway LR clonase (Invitrogen), CTDSP2 and CTDSP2-dead were transferred into pInducer20 (Addgene plasmid 44012).

extract_protocol: 1. Add 1 ml Trizol per 5 x 10^6 cells in suspension (1 ml trizol per 10 cm culture disk) and mix by pipetting, transfer to 1.5 ml eppendorf tube. 2. Incubate 5 min at room temperature. 3. Add chloroform (200 µl per ml Trizol), mix for 15 seconds by shaking vigorously. Incubate 2-3 min at room temperature. 4. Centrifuge 20 min at 14000 rpm 4°C. After centrifugation, transfer the water-phase to a new 1.5-ml micro centrifuge tube. 5. add isopropanol to precipitate RNA. Use 0.5 ml per 1 ml trizol. Mix by shaking, leave samples at RT for 10 minutes. Centrifuge at 14000 rpm for 15 min. 6. wash pellet with 75% ethanol. Centrifuge at 14000 rpm for 15 min. Carefully pipet off all ethanol (respin briefly and use a P20 for the last microliters). Airdry pellets briefly before dissolving in MilliQ water. Depending on pellet-size, this may take a while. Continue with RNeasy columns (Qiagen) for clean-up of RNA (maximal 100 µg/column) . 7. Adjust each sample to a volume of 300 µl with sterile MilliQ water. Add 160 µl buffer RLT to the samples, and mix (= lysis buffer). 8. Add 240 µl ethanol (100% stored at -20 °C) to the lysate, mix well by pipetting and immediately apply the sample to an RNeasy mini spin column sitting in a 2 ml collection tube (use a second P1000 pipet and work as quick as possible). Next lysate, and so on. 9. Centrifuge at 8000 rpm for 15 seconds in an Eppendorf centrifuge. Discard flowthrough, reuse collection tube. All centrifugation steps at room temperature! DNAse treatment: D1. Pipet 350 µl Buffer RW1 into the RNeasy mini column, and centrifuge for 15 s at 8000 rpm to wash. Discard the flow-through. Reuse the collection tube in step D3. D2. Prepare DNase I incubation mix (80 µl/reaction): add 10 µl DNase I stock solution to 70 µl Buffer RDD. Mix by gently inverting the tube. Buffer RDD is supplied with the RNase-Free DNase Set. Note: DNase I is especially sensitive to physical denaturation. Mixing should only be carried out by gently inverting the tube. Do not vortex. D3. Pipet the DNase I incubation mix (80 µl) directly onto the RNeasy silica-gel membrane, and place on the benchtop (20-30°C) for 15 min. Note: Make sure to pipet the DNase I incubation mix directly onto the RNeasy silica-gel membrane. DNase digestion will be incomplete if part of the mix sticks to the walls or the O-ring of the RNeasy column. D4. Pipet 350 µl Buffer RW1 into the RNeasy mini column, and centrifuge for 15 s at 8000 rpm. Discard the flow-through and collection tube. 10. Transfer the RNeasy column into a new 2 ml collection tube. Add 500 µl buffer RPE, wait 1 minute, and centrifuge at 8000 rpm for 15 seconds. Discard flow-through and reuse the collection tube in next steps.11. Pipet 500 µl buffer RPE onto the RNeasy column, wait 1 minute, and centrifuge at 8000 rpm for 15 seconds. Discard flow-through and reuse collection tube. 12. Centrifuge at 10,000 rpm for 2 minutes (to dry the RNeasy membrane). 13. Transfer the RNeasy column into a new 1.5 ml collection tube. Pipet 100 µl milliQ directly onto the RNeasy membrane and incubate for 4 minutes at room temperature. Centrifuge at 14,000 rpm for 1 minute to elute. Note: When small yields are expected, the elution volume can be lowered to a minimum of 35 µl milliQ. 14. Pipet the eluate of step 13 again onto the RNeasy membrane and incubate for another 4 minutes at room temperature. Centrifuge at 14,000 rpm for 1 minute to elute. After elution, put all RNA-samples on ice. 15. Determine RNA concentration by measuring A260, and RNA intactness by Bioanalyzer. Snap-freeze and store eluate at -80 °C.

treatment_protocol: Protein expression was induced in cells at 20% confluency using sterile filtered doxycycline (Sigma-Aldrich) at a final concentration of 1ug/mL for 48 hours, after which cells were harvested for RNA isolation. As refpool, uninduced U2OS cells were used.

tag: induction

tag: stable expression

tag: sample type

value: reference

value: doxycycline


title: U2OS-- vs. CTDSP2-PD+1

source_name: U2OS, CTDSP2-PD+


title: Duodenum_stem cell_rep2

description: Stem cell culture


title: U2OS-- vs. U2OS+1


title: U2OS-- vs. CTDSP2-PD+3


title: Jejunum_stem cell_rep1

description: Stem cell culture


title: U2OS-- vs. CTDSP2+3

source_name: U2OS, CTDSP2+


title: U2OS-- vs. CTDSP2+1


title: CTDSP2+4 vs. U2OS--


title: U2OS+2 vs. U2OS--


title: CTDSP2-PD+4 vs. U2OS--


title: U2OS+4 vs. U2OS--


title: Human_subline_gastric cancer_SGC7901/VCR

city: Luoyang

first: Ying

last: Wang

address: 24 Jinghua Road

institute: the First Affiliated Hospital of Henan University of Science and Technology

description: SGC7901/VCR is a subline derived from the SGC7901 by supplement with vincristine in the culture media

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

source_name: multidrug resistant subline of SGC7901, SGC7901/VCR

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: The human GC cell line SGC7901 was obtained from the Academy of Military Medical Science (Beijing, China). Two multidrug-resistant sublines, SGC7901/VCR and SGC7901/ADR, were developed in our lab [46]. SGC7901/VCR, SGC7901/ADR and SGC7901 were grown in RPMI1640 medium (Thermo Scientific Co., USA) that was supplemented with 10% fetal calf serum (FCS) (Thermo scientific Co., USA) in a humidiﬁed incubator with 5% CO2 at 37℃. VCR (1.0 μg/ml) or ADR (0.5 μg/ml) was added into the culture medium of the appropriate cells to maintain the drug-resistant phenotype.

extract_protocol: Total RNA was harvested from SGC7901, SGC7901/ADR and SGC7901/VCR using TRIzol reagent (Invitrogen, CA, USA) and the RNeasy Kit(Qiagen Co.,Germany) according to manufacturer's instructions, including a DNase digestion step. Total RNA from each cellline was quantified using a NanoDrop ND-1000(OD 260 nm, NanoDrop,Wilmington, DE), RNA integrity was assessed using standard denaturing agarose gel electrophoresis, and the purity was judged by the ratio of absorbance at 260 nm to 280 nm (A260/A280). Double-strand cDNA (ds-cDNA) was synthesized using 5 μg total RNA by an Invitrogen SuperScript ds-cDNA synthesis kit in the presence of 100 pmol oligo dT primers.

value: gastic cancer


title: CTDSP2-PD+2 vs. U2OS--


title: CTDSP2+2 vs. U2OS--


title: siTLX_IFNg_2

city: Philadelphia

first: daniel

last: beiting

state: PA

address: 380 S. University Ave

department: Pathobiology

institute: University of Pennsylvania

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

source_name: U251 cell line

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

growth_protocol: U251 cells were grown to subconfluency in 6-well plates with DMEM media supplemented with 10% serum and antibiotics.

extract_protocol: RNA was extracted from individual wells of 6-well plate using the Qiagen Rneasy Plus kit.

treatment_protocol: After cells had settled and adhered in 6-well plates, they were transfected with 10 nM siRNA targeting human TLX (or negative control siRNA targeting luciferase) using HiPerfect transfection reagent.  72 hours after transfection, cells were stimulated with 10ng/ml of recombinant IFN-gamma for 8 hours

tag: sirna transfection

value: siRNA targeting TLX

tag: stimulation

value: IFN-gamma

value: astroglioma


title: Human_subline_gastric cancer_SGC7901/ADR

description: SGC7901/ADR is a subline derived from the SGC7901 by supplement with adriamycine in the culture media

source_name: multidrug resistant subline of SGC7901, SGC7902/ADR


title: siTLX_IFNg_1


title: siControl_IFNg_1

value: negative control siRNA


title: Human_cell_line_gastric cancer_SGC7901

description: SGC7901 is a cellline obtained from the human gastric adenocarcinoma

source_name: gastric cancer cell line,SGC7901


title: siTLX_unstim_2

value: unstimulated


title: siTLX_unstim_1


title: siControl_unstim_1


title: siControl_IFNg_2


title: control_unstim_2

source_name: U2OS cell line

growth_protocol: U2OS cells were grown to subconfluency in 6-well plates with DMEM media supplemented with 10% serum and antibiotics.

treatment_protocol: After cells had settled and adhered in 6-well plates, they were transfected with 2ug/well of TLX or control plasmid using Fugene 6 transfection reagent.  24 hours after transfection, cells were stimulated with 10ng/ml of recombinant IFN-gamma for 8 hours

tag: plasmid transfection

value: control vector

value: osteosarcoma


title: control_IFNg_2


title: TLX_unstim_2

value: TLX overexpression vector


title: control_IFNg_1


title: TLX_IFNg_2


title: siControl_unstim_2


title: TLX_IFNg_1


title: control_unstim_1


title: TLX_unstim_1


title: Ileum_ALI_rep2

description: Differentiation

source_name: Ileum, ALI

value: Fetal

value: Ileum, ALI


title: IL7_Wt_rep1

city: Saint Louis

first: Patrick

last: Collins

state: MO

address: 1217 Oakleaf dr

department: Pathology and Immunology

institute: Washington University

hyb_protocol: Products were hybridized to Affymetrix Mouse Gene 1.0 Array according to the manufacturer's instructions.

data_processing: Gene expression levels were determined using the Affymetrix Expression Console software (v1.2.0.20) with exon-level RMA analysis and default settings.

source_name: Setdb1 C/C pro-B cell, cultured in IL-7

label_protocol: Purified RNA was amplified using Nugen Ovation kits and labeled using Nugen Encore Biotin Kit.

growth_protocol: Murine bone marrow-derived pro-B cells were isolated and purified by FACS. Cells were then clutured for four days in media containing 5 ng/µl of IL-7 (Invitrogen, PMC0075).

extract_protocol: RNA was purified using Qiagen Rneasy kits according to the manufacturer's instructions.

value: pro-B cell

value: cultured in IL-7

tag: bcl2 transgene

value: bcl-2 transgenic

value: Floxed


title: IL7_Del_rep1

source_name: Setdb1 Δ/Δ pro-B cell, cultured in IL-7

tag: tissue

value: Deleted


title: IL7_Wt_rep2


title: IL7_Del_rep2


title: Control L25C

first: Zhaohui

last: Gu

state: Shanghai

address: 197 Rui Jin Road II

department: School of Medicine

institute: Shanghai Jiao Tong University

description: Genomic DNA was genotyped using Human660W-Quad v1.0  Genotyping BeadChips (Illumina).

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: Using the Genotyping Module of Illumina Genome Studio software version 2011.1.

label: C-Bio and A-DNP

source_name: Peripheral blood

label_protocol: standard Illumina protocol

growth_protocol: standard Illumina protocol

extract_protocol: standard Illumina protocol  standard Illumina protocol

treatment_protocol: standard Illumina protocol

tag: disease state

value: natural killer/T-cell lymphoma

tag: individual

value: Male

value: Peripheral blood


title: Control L18C

tag: gender


title: Control L07C


title: Control L09C

value: Female


title: Control L24C


title: Control L20C


title: Control L03C


title: Control L22C


title: Control L12C


title: Control L23C


title: Control L19C


title: Control L10C


title: Control L11C


title: Control L06C

description: Genomic DNA was extracted and genotyped using Human660W-Quad v1.0  Genotyping BeadChips (Illumina).


title: Control L15C


title: Control L14C


title: Control L17C


title: Control L16C


title: Case L25A

source_name: NT/T Tumor Cell

value: tumor


title: Control L21C


title: Control L08C


title: Control L13C


title: BM_Wt_rep1

source_name: Setdb1 C/C pro-B cell, bone marrow

value: bone marrow


title: Control L02C


title: BM_Del_rep1

source_name: Setdb1 Δ/Δ pro-B cell, bone marrow


title: BM_Del_rep2


title: FGF23_1

first: Chad

last: Creighton

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

description: Sample name: 71063_1_FGF23_1

hyb_protocol: The sample and reference probes were mixed with GEx hybridization buffer and blocking solution (Agilent, Santa Clara, CA) and denatured by a 2-minute incubation at 95 degC. Probes were hybridized to Agilent 4x44K Whole Mouse Genome arrays and rotating over night at 65 degC.

scan_protocol: Slide were scanned in an Agilent Microarray Scanner and the data were analyzed using Agilent Feature Extraction Software (v.9.1).

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent and Bioconductor software was used.

label_protocol: Complementary DNA (cDNA) reverse transcription and fluorescent labeling reactions were carried out using SuperScript Plus Direct cDNA Labeling system (Invitrogen, Carlsbad, CA).

growth_protocol: Human PCa cells LNCaP were maintained in RPMI-1640 medium (Invitrogen, Grand  Island, NY) supplemented with 10% fetal bovine serum (FBS, Invitrogen) and 100 ug/ml penicillin/streptomycin.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.  Microarray analysis was performed using 2.5 micrograms of total RNA.

treatment_protocol: LNCaP cells were plated at 6-well plates and left to grow for 24 hours. Cells were serum-starved for 24 hours and then stimulated with 25 ng/ml of FGF2 (BD), FGF19(BD) or FGF23 for 24hours.

value: LNCaP

value: FGF23 stimulation

source_name: human, universal reference RNA

value: universal reference RNA


title: Control L05C


title: BM_Wt_rep2


title: FGF19_2

description: Sample name: 71064_2_FGF19_2

value: FGF19 stimulation


title: Control L01C


title: CONTROL_2

description: Sample name: 71064_4_CONTROL_2

value: control


title: FGF2_1

description: Sample name: 71063_3_FGF2_1

value: FGF2 stimulation


title: CONTROL_1

description: Sample name: 71063_4_CONTROL_1


title: FGF2_2

description: Sample name: 71064_3_FGF2_2


title: FGF19_1

description: Sample name: 71063_2_FGF19_1


title: Case L23A


title: Control L04C


title: FGF23_2

description: Sample name: 71064_1_FGF23_2


title: Case L24A


title: DK9-D+S-OHT vs. DK9-DLD1

description: DL23 cells contain FoxO3.A3-ER.

hyb_protocol: * 60 ul labeled sample is combined with 60 ul 2x-hybmix, containing 50% formamide, 10xSSC, 0.2% SDS, 200 ug/ml herring sperm DNA. * Hybridizations of spotted oligo-arrays (Codelink glass) or Agilent microarrays are performed on a HS4800Pro Hybstation (Tecan. * Priming: 5xSSC, 0.1%SDS. * Probe injection: pre-hyb, 5xSSC, 25% formamide, 0.1%SDS, 1%BSA, Volume 110ul. * Hybridization: 45 min at 42C. * Wash 2x: milliQ. * Wash: 5xSSC, 0.1%SDS. * Probe injection: sample. Volume 110ul (Agilent 4packs: 55ul* Hybridization: 16 hours at 42C.* Wash 2x: 1xSSC, 0.2%SDS at 23C. * Wash 2x: 0.1xSSC, 0.2%SDS at 23C. * Wash 2x: 0.1xSSC at 23C. * Drying: blow with nitrogen for 3min at 30C.

source_name: DL23, control, 24hrs

label_protocol: All amplification and labeling procedures are performed in 96 wells plates (4titude, Bioke) on a customized Sciclone ALH 3000 Workstation (Caliper LifeSciences), supplemented with a PCR PTC-200 (Bio-Rad Laboratories), SpectraMax 190 spectrofotometer (Molecular Devices), and a magnetic bead-locator (Beckman). mRNA amplification protocol description:* all RNAs are diluted to 0.6 ug/ul and 5 ul is put in a 96-wells plate (Abgene). All subsequent steps are performed by the robot script. * mix1 containing 100 ng T7 Mlu VN primer (custom mix) and EC-control RNA per 5 ul is added and mixed in each well. * plate is incubated @ 70C for 10 mins, cooled to 48C. * mix2 containing 4ul 5x 1st strand buffer, 2 ul 0.1M DTT (Invitrogen), 1ul RNAse Inhibitor (Boehringer), 1ul 20mM dNTPs (GE Healthcare), 1ul linear acrylamide, and 1ul SuperScriptIII (Invitrogen) per sample is prewarmed to 48C; 10 ul per sample is added and mixed in each well. * plate is incubated @ 48C for 2 hours and cooled to room temperature. * 106 ul water and subsequently mix3 containing 15ul second strand buffer, 3ul 20mM dNTPs (GE Healthcare), 1 ul T4 DNA ligase, 4 ul E.coli DNA polymerase I and 1 ul RNAseH (Promega) is added and mixed in each well. * plate is incubated @ 16C for 2 hours, @65C for 10 mins. * ds cDNA product is purified and concentrated with RNAClean (Agencourt, GC biotech) according to manufacturers protocol, to an end volume of 25 ul . * 8 ul cDNA is put in a 96 wells plate and mixed with 12 ul IVT mix containing 2 ul 10x rxn-buffer, 2 ul each ATP, CTP, GTP, 0.6 ul UTP, 2 ul T7 enzyme mix (MegaScript kit, Ambion, Applied Biosystems), and 2.1 ul 50 mM 5-(3-aminoallyl)-UTP (Ambion, Applied Biosystems). * Plate is incubated @37C for 4 hours. * cRNA product is purified with RNAClean (Agencourt, Beckman) according to manufacturer's protocol. * Concentration is measured (SpectraMax 190) and adjusted to 600 ng/ul by the robot. * Resulting cRNA plates are sampled for Bioanalyzer QC, snapfrozen and stored at -80C. Labeling protocol description: * NHS-ester Cy3 or Cy5 dye (Amersham PA 23001 and 25001): entire tube is resuspended in 100 ul DMSO (Merck 8.02912.10). All subsequent steps are performed by the robot script : * 8 ul of each cRNA (0.6 ug/ul) is put in a 96-wells plate (Abgene), the accompanying reference sample is put in the next column (final step combines cy3 and cy5 labeled material ).* 3 ul 0.5 M NaBicarbonate buffer, pH 9 is added and mixed to all wells.* 3 ul cy-dye solution is added and mixed to the appropriate wells, plate is incubated at 18C for 1 hour.* 4.5 ul 5M hydroxylamine is added and mixed, incubated at 18o C for 15 minutes. * Labeled cRNA product is purified with RNA Clean (Agencourt, GC biotech) according to manufacturers protocol.* RNA concentration and labeling incorporation are measured (SpectraMax 190).* 2.5 ug of each labeled sample and reference cRNA are pooled and subjected to fragmentation according to protocol (Ambion, Applied Biosystems), 15 min 70C.* Samples are stored at -20C until hybridization.

growth_protocol: DLD1 (ATCC CCL-221) and derived DL23 cells were cultured in RPMI-1640 with 10% FBS, L-Glutamine and Pen/Strep.

extract_protocol: 1. Add 1 ml Trizol per 5 x 10^6 cells in suspension (1 ml trizol per 10 cm culture disk) and mix by pipetting, transfer to 1.5 ml eppendorf tube. 2. Incubate 5 min at room temperature. 3. Add chloroform (200 µl per ml Trizol), mix for 15 seconds by shaking vigorously. Incubate 2-3 min at room temperature. 4. Centrifuge 20 min at 14000 rpm 4°C. After centrifugation, transfer the water-phase to a new 1.5-ml micro centrifuge tube. 5. add isopropanol to precipitate RNA. Use 0.5 ml per 1 ml trizol. Mix by shaking, leave samples at RT for 10 minutes. Centrifuge at 14000 rpm for 15 min. 6. wash pellet with 75% ethanol. Centrifuge at 14000 rpm for 15 min. Carefully pipet off all ethanol (respin briefly and use a P20 for the last microliters). Airdry pellets briefly before dissolving in MilliQ water. Depending on pellet-size, this may take a while. Continue with RNeasy columns (Qiagen) for clean-up of RNA (maximal 100 µg/column) . 7. Adjust each sample to a volume of 300 µl with sterile MilliQ water. Add 160 µl buffer RLT to the samples, and mix (= lysis buffer). 8. Add 240 µl ethanol (100% stored at -20 °C) to the lysate, mix well by pipetting and immediately apply the sample to an RNeasy mini spin column sitting in a 2 ml collection tube (use a second P1000 pipet and work as quick as possible). Next lysate, and so on. 9. Centrifuge at 8000 rpm for 15 seconds in an Eppendorf centrifuge. Discard flowthrough, reuse collection tube. All centrifugation steps at roomtemperature! DNAse treatment: D1. Pipet 350 µl Buffer RW1 into the RNeasy mini column, and centrifuge for 15 s at 8000 rpm to wash. Discard the flow-through. Reuse the collection tube in step D3. D2. Prepare DNase I incubation mix (80 µl/reaction): add 10 µl DNase I stock solution to 70 µl Buffer RDD. Mix by gently inverting the tube. Buffer RDD is supplied with the RNase-Free DNase Set. Note: DNase I is especially sensitive to physical denaturation. Mixing should only be carried out by gently inverting the tube. Do not vortex. D3. Pipet the DNase I incubation mix (80 µl) directly onto the RNeasy silica-gel membrane, and place on the benchtop (20-30°C) for 15 min. Note: Make sure to pipet the DNase I incubation mix directly onto the RNeasy silica-gel membrane. DNase digestion will be incomplete if part of the mix sticks to the walls or the O-ring of the RNeasy column. D4. Pipet 350 µl Buffer RW1 into the RNeasy mini column, and centrifuge for 15 s at 8000 rpm. Discard the flow-through and collection tube. 10. Transfer the RNeasy column into a new 2 ml collection tube. Add 500 µl buffer RPE, wait 1 minute, and centrifuge at 8000 rpm for 15 seconds. Discard flow-through and reuse the collection tube in next steps. 11. Pipet 500 µl buffer RPE onto the RNeasy column, wait 1 minute, and centrifuge at 8000 rpm for 15 seconds. Discard flow-through and reuse collection tube. 12. Centrifuge at 10,000 rpm for 2 minutes (to dry the RNeasy membrane). 13. Transfer the RNeasy column into a new 1.5 ml collection tube. Pipet 100 µl milliQ directly onto the RNeasy membrane and incubate for 4 minutes at room temperature. Centrifuge at 14,000 rpm for 1 minute to elute. Note: When small yields are expected, the elution volume can be lowered to a minimum of 35 µl milliQ. 14. Pipet the eluate of step 13 again onto the RNeasy membrane and incubate for another 4 minutes at room temperature. Centrifuge at 14,000 rpm for 1 minute to elute. After elution, put all RNA-samples on ice. 15. Determine RNA concentration by measuring A260, and RNA intactness by Bioanalyzer. Snap-freeze and store eluate at -80 °C.

treatment_protocol: 4-hydroxytamoxifen (4OHT; final concentration 500nM; Sigma-Aldrich) was dissolved in 96% EtOH. At 40% confluency, cells were stimulated with 4OHT or solvent for 24 hrs, after which cells were harvested for RNA isolation. As reference pool, DLD1-cells were used.

value: ethanol solvent

value: 24 hrs

source_name: DLD1 reference

value: reference


title: DL23-8d vs. DL23-0d

description: DL23 cells contain FoxO3.A3-ER.

hyb_protocol: * 60 ul labeled sample is combined with 60 ul 2x-hybmix, containing 50% formamide, 10xSSC, 0.2% SDS, 200 ug/ml herring sperm DNA. * Hybridizations of spotted oligo-arrays (Codelink glass) or Agilent microarrays are performed on a HS4800Pro Hybstation (Tecan. * Priming: 5xSSC, 0.1%SDS. * Probe injection: pre-hyb, 5xSSC, 25% formamide, 0.1%SDS, 1%BSA, Volume 110ul. * Hybridization: 45 min at 42C. * Wash 2x: milliQ. * Wash: 5xSSC, 0.1%SDS. * Probe injection: sample. Volume 110ul (Agilent 4packs: 55ul). * Hybridization: 16 hours at 42C. * Wash 2x: 1xSSC, 0.2%SDS at 23C. * Wash 2x: 0.1xSSC, 0.2%SDS at 23C. * Wash 2x: 0.1xSSC at 23C. * Drying: blow with nitrogen for 3min at 30C.

source_name: DL23, 4OHT induced, 8hrs

label_protocol: All amplification and labeling procedures are performed in 96 wells plates (4titude, Bioke) on a customized Sciclone ALH 3000 Workstation (Caliper LifeSciences), supplemented with a PCR PTC-200 (Bio-Rad Laboratories), SpectraMax 190 spectrofotometer (Molecular Devices), and a magnetic bead-locator (Beckman). mRNA amplification protocol description:* all RNAs are diluted to 0.6 ug/ul and 5 ul is put in a 96-wells plate (Abgene). All subsequent steps are performed by the robot script. * mix1 containing 100 ng T7 Mlu VN primer (custom mix) and EC-control RNA per 5 ul is added and mixed in each well. * plate is incubated @ 70C for 10 mins, cooled to 48C. * mix2 containing 4ul 5x 1st strand buffer, 2 ul 0.1M DTT (Invitrogen), 1ul RNAse Inhibitor (Boehringer), 1ul 20mM dNTPs (GE Healthcare), 1ul linear acrylamide, and  1ul SuperScriptIII (Invitrogen) per sample is prewarmed to 48C; 10 ul per sample is added and mixed in each well. * plate is incubated @ 48C for 2 hours and cooled to room temperature. * 106 ul water and subsequently  mix3 containing 15ul second strand buffer, 3ul 20mM dNTPs (GE Healthcare), 1 ul T4 DNA ligase, 4 ul E.coli DNA polymerase I and 1 ul RNAseH  (Promega) is added and mixed in each well. * plate is incubated @ 16C for 2 hours, @65C for 10 mins. * ds cDNA product is purified and concentrated with RNAClean (Agencourt, GC biotech) according to manufacturers protocol, to an end volume of 25 ul. * 8 ul cDNA is put in a 96 wells plate and mixed with 12 ul IVT mix containing 2 ul 10x rxn-buffer, 2 ul each ATP, CTP, GTP, 0.6 ul UTP, 2 ul T7 enzyme mix (MegaScript kit, Ambion, Applied Biosystems), and 2.1 ul 50 mM 5-(3-aminoallyl)-UTP (Ambion, Applied Biosystems). * Plate is incubated @37C for 4 hours. * cRNA product is purified with RNAClean (Agencourt, Beckman) according to manufacturers protocol. * Concentration  is measured (SpectraMax 190) and adjusted to 600 ng/ul by the robot. * Resulting cRNA plates are sampled for Bioanalyzer QC, snapfrozen and stored at -80C. Labeling protocol description: * NHS-ester Cy3 or Cy5 dye (Amersham PA 23001 and 25001): entire tube is resuspended in 100 ul DMSO (Merck 8.02912.10). All subsequent steps are performed by the robot script : * 8 ul of each cRNA (0.6 ug/ul) is put in a 96-wells plate (Abgene), the accompanying reference sample is put in the next column (final step combines cy3 and cy5 labeled material ). * 3 ul 0.5 M NaBicarbonate buffer, pH 9 is added and mixed to all wells. * 3 ul cy-dye solution is added and mixed to the appropriate wells, plate is incubated at 18C for 1 hour. * 4.5 ul 5M hydroxylamine is added and mixed, incubated at 18o C for 15 minutes. * Labeled cRNA product is purified with RNA Clean (Agencourt, GC biotech) according to manufacturers protocol.* RNA concentration and labeling incorporation are measured (SpectraMax 190).* 2.5 ug of each labeled sample and reference cRNA are pooled and subjected to fragmentation according to protocol (Ambion, Applied Biosystems), 15 min 70C.* Samples are stored at -20C until hybridization.

growth_protocol: DL23 cells were cultured in RPMI-1640 with 10% FBS, L-Glutamine and Pen/Strep.

extract_protocol: 1. Add 1 ml Trizol per 5 x 10^6 cells in suspension (1 ml trizol per 10 cm culture disk) and mix by pipetting, transfer to 1.5 ml eppendorf tube. 2. Incubate 5 min at room temperature. 3. Add chloroform (200 µl per ml Trizol), mix for 15 seconds by shaking vigorously. Incubate 2-3 min at room temperature. 4. Centrifuge 20 min at 14000 rpm 4°C. After centrifugation, transfer the water-phase to a new 1.5-ml micro centrifuge tube. 5. add isopropanol to precipitate RNA. Use 0.5 ml per 1 ml trizol. Mix by shaking, leave samples at RT for 10 minutes. Centrifuge at 14000 rpm for 15 min. 6. wash pellet with 75% ethanol. Centrifuge at 14000 rpm for 15 min. Carefully pipet off all ethanol (respin briefly and use a P20 for the last microliters). Airdry pellets briefly before dissolving in MilliQ water. Depending on pellet-size, this may take a while. Continue with RNeasy columns (Qiagen) for clean-up of RNA (maximal 100 µg/column). 7. Adjust each sample to a volume of 300 µl with sterile MilliQ water. Add 160 µl buffer RLT to the samples, and mix (= lysis buffer). 8. Add 240 µl ethanol (100% stored at -20 °C) to the lysate, mix well by pipetting and immediately apply the sample to an RNeasy mini spin column sitting in a 2 ml collection tube (use a second P1000 pipet and work as quick as possible). Next lysate, and so on. 9. Centrifuge at 8000 rpm for 15 seconds in an Eppendorf centrifuge. Discard flowthrough, reuse collection tube. All centrifugation steps at roomtemperature! DNAse treatment: D1. Pipet 350 µl Buffer RW1 into the RNeasy mini column, and centrifuge for 15 s at 8000 rpm to wash. Discard the flow-through. Reuse the collection tube in step D3. D2. Prepare DNase I incubation mix (80 µl/reaction): add 10 µl DNase I stock solution to 70 µl Buffer RDD. Mix by gently inverting the tube. Buffer RDD is supplied with the RNase-Free DNase Set. Note: DNase I is especially sensitive to physical denaturation. Mixing should only be carried out by gently inverting the tube. Do not vortex. D3. Pipet the DNase I incubation mix (80 µl) directly onto the RNeasy silica-gel membrane, and place on the benchtop (20-30°C) for 15 min. Note: Make sure to pipet the DNase I incubation mix directly onto the RNeasy silica-gel membrane. DNase digestion will be incomplete if part of the mix sticks to the walls or the O-ring of the RNeasy column. D4. Pipet 350 µl Buffer RW1 into the RNeasy mini column, and centrifuge for 15 s at 8000 rpm. Discard the flow-through and collection tube. 10. Transfer the RNeasy column into a new 2 ml collection tube. Add 500 µl buffer RPE, wait 1 minute, and centrifuge at 8000 rpm for 15 seconds. Discard flow-through and reuse the collection tube in next steps. 11. Pipet 500 µl buffer RPE onto the RNeasy column, wait 1 minute, and centrifuge at 8000 rpm for 15 seconds. Discard flow-through and reuse collection tube. 12. Centrifuge at 10,000 rpm for 2 minutes (to dry the RNeasy membrane). 13. Transfer the RNeasy column into a new 1.5 ml collection tube. Pipet 100 µl milliQ directly onto the RNeasy membrane and incubate for 4 minutes at room temperature. Centrifuge at 14,000 rpm for 1 minute to elute. Note: When small yields are expected, the elution volume can be lowered to a minimum of 35 µl milliQ. 14. Pipet the eluate of step 13 again onto the RNeasy membrane and incubate for another 4 minutes at room temperature. Centrifuge at 14,000 rpm for 1 minute to elute. After elution, put all RNA-samples on ice. 15. Determine RNA concentration by measuring A260, and RNA intactness by Bioanalyzer. Snap-freeze and store eluate at -80 °C.

treatment_protocol: 4-hydroxytamoxifen (4OHT; final concentration 500nM; Sigma-Aldrich) was dissolved in 96% EtOH. At 80% confluency, cells were stimulated with 4OHT or solvent for 8 hrs, after which cells were harvested for RNA isolation.

value: 4-hydroxytamoxifen (4OHT)

value: 8 hrs

source_name: DL23, control, 8hrs


title: SI-clone6 P25

description:
Genomic DNA extracted from intestinal stem cells was genotyped using HumanOmniZhongHua-8 Beadchip (Illumina).
HumanOmniZhongHua-8 Beadchip

hyb_protocol: Followed Illumina standard protocol

scan_protocol: Followed Illumina standard protocol

data_processing: GenomeStudio Software (Illumina)

label: cy3, cy5

source_name: Human intestinal stem cells_pedigree 7_Passage 25

label_protocol: Followed Illumina standard protocol

growth_protocol: Intestinal stem cells from human fetus (middle ileum) were cultured on 3T3 feeder layer.

extract_protocol: Genomic DNA from cells were extracted using DNeasy blood and tissue kit (Qiagen)

treatment_protocol: Two independent pedigrees were isolated and collected at passage 5, 10, 15 and 20.

value: human intestinal stem cell

tag: pedigree

tag: passage number

value: Passage 25


title: DL23-0c vs. DL23-8c

description: DL23 cells contain FoxO3.A3-ER.

tag: treatment


title: DL23-8b vs. DL23-0b

description: DL23 cells contain FoxO3.A3-ER.

tag: cell line


title: Case L22A

value: natural killer/T-cell lymphoma

value: Male


title: DK9-B+S+OHT vs. DK9-DLD1

description: DL23 cells contain FoxO3.A3-ER.

source_name: DL23, 4OHT induced, 24hrs


title: DK9-D+S+OHT vs. DK9-DLD1

description: DL23 cells contain FoxO3.A3-ER.


title: DL23-0a vs. DL23-8a

description: DL23 cells contain FoxO3.A3-ER.


title: DK9-B+S-OHT vs. DK9-DLD1

description: DL23 cells contain FoxO3.A3-ER.


title: SI-clone5 P25

source_name: Human intestinal stem cells_pedigree 6_Passage 25

tag: cell type


title: SI-clone6 P5

source_name: Human intestinal stem cells_pedigree 7_Passage 5

value: Passage 5


title: MI P5 #3

description:
Genomic DNA extracted from intestinal stem cells was genotyped using HumanOmniExpress BeadChip Kit (Illumina).
HumanOmniExpress BeadChip Kit

source_name: Human intestinal stem cells_pedigree 2_Passage 5

value: Pedigree 2


title: AS001-refpool vs. AS001-foxo4-c

hyb_protocol: * 60 ul labeled sample is combined with 60 ul 2x-hybmix, containing 50% formamide, 10xSSC, 0.2% SDS, 200 ug/ml herring sperm DNA * Hybridizations of spotted oligo-arrays (Codelink glass) or Agilent microarrays are performed on a HS4800Pro Hybstation (Tecan)* Priming: 5xSSC, 0.1%SDS * Probe injection: pre-hyb, 5xSSC, 25% formamide, 0.1%SDS, 1%BSA, Volume 110ul * Hybridization: 45 min at 42C. * Wash 2x: milliQ * Wash: 5xSSC, 0.1%SDS * Probe injection: sample. Volume 110ul (Agilent 4packs: 55ul) * Hybridization: 16 hours at 42C. * Wash 2x: 1xSSC, 0.2%SDS at 23C * Wash 2x: 0.1xSSC, 0.2%SDS at 23C * Wash 2x: 0.1xSSC at 23C * Drying: blow with nitrogen for 3min at 30C.

source_name: HEK293T, reference

label_protocol: All amplification and labeling procedures are performed in 96 wells plates (4titude, Bioke) on a customized Sciclone ALH 3000 Workstation (Caliper LifeSciences), supplemented with a PCR PTC-200 (Bio-Rad Laboratories), SpectraMax 190 spectrofotometer (Molecular Devices), and a magnetic bead-locator (Beckman). mRNA amplification protocol description: * all RNAs are diluted to 0.6 ug/ul and 5 ul is put in a 96-wells plate (Abgene). All subsequent steps are performed by the robot script. * mix1 containing 100 ng T7 Mlu VN primer (custom mix) and EC control RNA per 5 ul is added and mixed in each well. * plate is incubated @ 70C for 10 mins, cooled to 48C. * mix2 containing 4ul 5x 1st strand buffer, 2 ul 0.1M DTT (Invitrogen), 1ul RNAse Inhibitor (Boehringer), 1ul 20mM dNTPs (GE Healthcare), 1ul linear acrylamide, and  1ul SuperScriptIII (Invitrogen) per sample is prewarmed to 48C; 10 ul per sample is added and mixed in each well. * plate is incubated @ 48C for 2 hours and cooled to room temperature. * 106 ul water and subsequently  mix3 containing 15ul second strand buffer, 3ul 20mM dNTPs (GE Healthcare), 1 ul T4 DNA ligase, 4 ul E.coli DNA polymerase I and 1 ul RNAseH  (Promega) is added and mixed in each well. * plate is incubated @ 16C for 2 hours, @65C for 10 mins. * ds cDNA product is purified and concentrated with RNAClean (Agencourt, GC biotech) according to manufacturer's protocol, to an end volume of 25 ul . * 8 ul cDNA is put in a 96 wells plate and mixed with 12 ul IVT mix containing 2 ul 10x rxn buffer, 2 ul each ATP, CTP, GTP, 0.6 ul UTP, 2 ul T7 enzyme mix (MegaScript kit, Ambion, Applied Biosystems), and 2.1 ul 50 mM 5-(3 aminoallyl)-UTP (Ambion, Applied Biosystems). * Plate is incubated @37C for 4 hours. * cRNA product is purified with RNAClean (Agencourt, Beckman) according to manufacturer's protocol. * Concentration  is measured (SpectraMax 190) and adjusted to 600 ng/ul by the robot. * Resulting cRNA plates are sampled for Bioanalyzer QC, snapfrozen and stored at -80C. Labeling protocol description:  * NHS-ester Cy3 or Cy5 dye (Amersham PA 23001 and 25001): entire tube is resuspended in 100 ul DMSO (Merck 8.02912.10).  All subsequent steps are performed by the robot script : * 8 ul of each cRNA (0.6 ug/ul) is put in a 96-wells plate (Abgene), the accompanying reference sample is put in the next column (final step combines cy3 and cy5 labeled material ). * 3 ul 0.5 M NaBicarbonate buffer, pH 9 is added and mixed to all wells. * 3 ul cy-dye solution is added and mixed to the appropriate wells, plate is incubated at 18C for 1 hour. * 4.5 ul 5M hydroxylamine is added and mixed, incubated at 18o C for 15 minutes. * Labeled cRNA product is purified with RNA Clean (Agencourt, GC biotech) according to manufacturers protocol. * RNA concentration and labeling incorporation are measured (SpectraMax 190). * 2.5 ug of each labeled sample and reference cRNA are pooled and subjected to fragmentation according to protocol (Ambion, Applied Biosystems), 15 min 70C. * Samples are stored at -20C until hybridization

growth_protocol: HEK293T cells (ATCC CRL-11268) were maintained in DMEM with 10% FBS, L-Glutamine and Pen/Strep.

extract_protocol: 1. Add 1 ml Trizol per 5x10^6 cells in suspension (1 ml trizol per 10 cm culture disk) and mix by pipetting, transfer to 1.5 ml eppendorf tube. 2. Incubate 5 min at room temperature. 3. Add chloroform (200 µl per ml Trizol), mix for 15 seconds by shaking vigorously. Incubate 2-3 min at room temperature. 4. Centrifuge 20 min at 14000 rpm 4°C. After centrifugation, transfer the water-phase to a new 1.5-ml micro centrifuge tube. 5. add isopropanol to precipitate RNA. Use 0.5 ml per 1 ml trizol. Mix by shaking, leave samples at RT for 10 minutes. Centrifuge at 14000 rpm for 15 min. 6. wash pellet with 75% ethanol. Centrifuge at 14000 rpm for 15 min. Carefully pipet off all ethanol (respin briefly and use a P20 for the last microliters). Airdry pellets briefly before dissolving in MilliQ water. Depending on pellet-size, this may take a while. Continue with RNeasy columns (Qiagen) for clean-up of RNA (maximal 100 µg/column) . 7. Adjust each sample to a volume of 300 µl with sterile MilliQ water. Add 160 µl buffer RLT to the samples, and mix (= lysis buffer). 8. Add 240 µl ethanol (100% stored at -20 °C) to the lysate, mix well by pipetting and immediately apply the sample to an RNeasy mini spin column sitting in a 2 ml collection tube (use a second P1000 pipet and work as quick as possible). Next lysate, and so on. 9. Centrifuge at 8000 rpm for 15 seconds in an Eppendorf centrifuge. Discard flowthrough, reuse collection tube. All centrifugation steps at roomtemperature! DNAse treatment: D1. Pipet 350 µl Buffer RW1 into the RNeasy mini column, and centrifuge for 15 s at 8000 rpm to wash. Discard the flow-through. Reuse the collection tube in step D3. D2. Prepare DNase I incubation mix (80 µl/reaction): add 10 µl DNase I stock solution to 70 µl Buffer RDD. Mix by gently inverting the tube. Buffer RDD is supplied with the RNase-Free DNase Set. Note: DNase I is especially sensitive to physical denaturation. Mixing should only be carried out by gently inverting the tube. Do not vortex. D3. Pipet the DNase I incubation mix (80 µl) directly onto the RNeasy silica-gel membrane, and place on the benchtop (20-30°C) for 15 min. Note: Make sure to pipet the DNase I incubation mix directly onto the RNeasy silica-gel membrane. DNase digestion will be incomplete if part of the mix sticks to the walls or the O-ring of the RNeasy column. D4. Pipet 350 µl Buffer RW1 into the RNeasy mini column, and centrifuge for 15 s at 8000 rpm. Discard the flow-through and collection tube. 10. Transfer the RNeasy column into a new 2 ml collection tube. Add 500 µl buffer RPE, wait 1 minute, and centrifuge at 8000 rpm for 15 seconds. Discard flow-through and reuse the collection tube in next steps. 11. Pipet 500 µl buffer RPE onto the RNeasy column, wait 1 minute, and centrifuge at 8000 rpm for 15 seconds. Discard flow-through and reuse collection tube. 12. Centrifuge at 10,000 rpm for 2 minutes (to dry the RNeasy membrane). 13. Transfer the RNeasy column into a new 1.5 ml collection tube. Pipet 100 µl milliQ directly onto the RNeasy membrane and incubate for 4 minutes at room temperature. Centrifuge at 14,000 rpm for 1 minute to elute. Note: When small yields are expected, the elution volume can be lowered to a minimum of 35 µl milliQ. 14. Pipet the eluate of step 13 again onto the RNeasy membrane and incubate for another 4 minutes at room temperature. Centrifuge at 14,000 rpm for 1 minute to elute. After elution, put all RNA-samples on ice. 15. Determine RNA concentration by measuring A260, and RNA intactness by Bioanalyzer. Snap-freeze and store eluate at -80 °C.

treatment_protocol: Cells were transfected with a total of 15 microgram DNA (empty vector or FOXO4) using 2 microliter (1 mg/ml) poly(ethylenimine) (PEI) per microgram DNA. Cells were harvested for RNA isolation (using the Qiagen RNeasy kit) 48 hours post transfection.

tag: transfection

source_name: HEK293T, FOXO4

value: FOXO4 expression vector


title: SI-clone5 P5

source_name: Human intestinal stem cells_pedigree 6_Passage 5


title: Case L21A

value: tumor


title: MI P0

source_name: Human intestinal stem cells_pool

value: pool

value: Passage 0


title: AS001-refpool vs. AS001-foxo4-a


title: SI-clone4 P25

source_name: Human intestinal stem cells_pedigree 5_Passage 25


title: MI P5 #2

source_name: Human intestinal stem cells_pedigree 1_Passage 5

value: Pedigree 1


title: SI-clone4 P5

source_name: Human intestinal stem cells_pedigree 5_Passage 5


title: MI P10 #3

source_name: Human intestinal stem cells_pedigree 2_Passage 10

value: Passage 10


title: SI-clone3 P25

source_name: Human intestinal stem cells_pedigree 4_Passage 25


title: MI P10 #2

source_name: Human intestinal stem cells_pedigree 1_Passage 10


title: AS001-EV-d vs. AS001-refpool

source_name: HEK293T, vector

value: empty vector


title: MI P15 #3

source_name: Human intestinal stem cells_pedigree 2_Passage 15

value: Passage 15


title: SI-clone3 P5

source_name: Human intestinal stem cells_pedigree 4_Passage 5


title: Case L19A

source_name: NT/T Tumor Cell


title: Case L20A


title: AS001-foxo4-b vs. AS001-refpool


title: Case L16A


title: AS001-foxo4-d vs. AS001-refpool


title: AS001-EV-b vs. AS001-refpool


title: SI-clone2 P25

source_name: Human intestinal stem cells_pedigree 3_Passage 25


title: AS001-refpool vs. AS001-EV-c


title: DK9-DLD1 vs. DK9-C+S-OHT

description: DL23 cells contain FoxO3.A3-ER.

source_name: DLD1 reference

value: reference

source_name: DL23, control, 24hrs

value: ethanol solvent

tag: treatment duration

value: 24 hrs


title: Case L14A


title: MI P15 #2

source_name: Human intestinal stem cells_pedigree 1_Passage 15

value: human intestinal stem cell


title: AS001-refpool vs. AS001-EV-a

source_name: HEK293T, reference


title: SI-clone2 P5

source_name: Human intestinal stem cells_pedigree 3_Passage 5


title: SI-P0

source_name: Human intestinal stem cells_pool


title: MI P20 #2

source_name: Human intestinal stem cells_pedigree 1_Passage 20

value: Passage 20


title: DK9-DLD1 vs. DK9-A+S-OHT

description: DL23 cells contain FoxO3.A3-ER.


title: DK9-DLD1 vs. DK9-C+S+OHT

description: DL23 cells contain FoxO3.A3-ER.

source_name: DL23, 4OHT induced, 24hrs

value: 4-hydroxytamoxifen (4OHT)


title: Case L15A

value: natural killer/T-cell lymphoma

value: Male


title: Case L17A


title: Replica 3 - LOW-translated_M0471

status: Public on May 28 2015

city: Singapore

first: Igor

middle: V

last: Kurochkin

address: 30 Biopolis street, #07-01 Matrix

country: Singapore

institute: Bioinformatics Institute, A*STAR

description:
RNA from sucrose gradient fractions
RNA associated with low-translated fraction in MRC5 cells treated for 2hr with H2O2
M0471

hyb_protocol: The labeled cRNA was hybridized to the Agilent SurePrint G3 gene expression 8x60K microarray according to the manufacturer's protocol.

scan_protocol: The arrays were washed, and scanned on an Agilent G2565CA microarray scanner at 100% PMT and 3μm resolution.

data_processing: The 24 Agilent features extraction results text files of both, stress and control in triplicates (as mentioned in the Sample section) were imported into Partek Genomics Suite. The gProcessed Signal parameter was imported into the Partek probe intensity spreadsheet and the data was further log2 transformed and quantile normalized.

source_name: MRC5 cells

label_protocol: 100 ng of total RNA from whole cell extracts and polysome fractions was labeled using LowInputQuick Amp Labeling kit (Agilent 5190-2305) following manufacturer instructions. Briefly, mRNA was reverse transcribed in the presence of T7-oligo-dT primer to produce cDNA. cDNA was then in vitro transcribed with T7 RNA polymerase in the presence of Cy3-CTP to produce labeled cRNA.

growth_protocol: MRC5 fibroblasts were cultured in 5% CO2 atmosphere, at 37°C in DMEM/F12 medium supplemented with 10% fetal bovine serum (FBS)

extract_protocol: Cells were incubated with 150μg/ml of cycloheximide (Sigma-Aldrich) for 15 min prior to harvesting. Approximately, 1x10^7 cells were lysed in 500 μl of lysis buffer [5mM Tris-HCl, 2.5mM MgCl2, 1.5mM KCl, 0.5% Triton X, 0.5% Sodium deoxycholate, 2mM DTT, 40 U/µl of RNasin (Fermentas) and 1mM DTT]. Then cell lysates were subjected to centrifugation for 3 min at 14,000 rpm at 4°C to obtain clarified lysate.  The lysates were fractionated by centrifugation in 15-50% linear sucrose gradients at 36,000 x g in a SW41-Ti rotor (Beckman) for two hours at 80C. Twenty three fractions were collected using Piston Gradient Fractionator (Biocomp) and RNA was isolated from the fractions using phenol chloroform extraction. Briefly, RNA was extracted two times in equal volume of 25:24:1 phenol:chloroform:isoamyl alcohol followed by extraction in an equal volume of 49:1 chloroform:isoamyl alcohol. RNA was precipitated at -800C with 2.5 volumes of 100% ethanol and 1/10th volume of 3M sodium acetate, pH5.2.

treatment_protocol: MRC5 fibroblasts were seeded at sub-confluent density and treated the next day for 2 hr with 0.2mM H2O2.

tag: group

value: STRESS

tag: rna translational categories

value: Replica 3 - LOW-translated


title: Case L18A

tag: sample type

value: tumor


title: Case L11A


title: DK9-DLD1 vs. DK9-A+S+OHT

description: DL23 cells contain FoxO3.A3-ER.


title: Replica 3 - HIGH-translated_M0469

description:
RNA from sucrose gradient fractions
RNA associated with high-translated fraction in control cells
M0469

value: Control

value: Replica 3 - HIGH-translated


title: Replica 3 - NON-translated_M0470

description:
RNA from sucrose gradient fractions
RNA associated with non-translated fraction in MRC5 cells treated for 2hr with H2O2
M0470

value: Replica 3 - NON-translated


title: MI P20 #3

source_name: Human intestinal stem cells_pedigree 2_Passage 20

value: Pedigree 2


title: Replica 3 - HIGH-translated_M0472

description:
RNA from sucrose gradient fractions
RNA associated with high-translated fraction in MRC5 cells treated for 2hr with H2O2
M0472


title: Case L02A


title: Case L12A

value: Female


title: Case L06A


title: Case L13A


title: Case L07A


title: Case L10A


title: Replica 3 - LOW-translated_M0468

description:
RNA from sucrose gradient fractions
RNA associated with low-translated fraction in control cells
M0468