title: RNA of normal hippocampus tissue (N1Y)

description:
Sample N1Y
The raw data for former sample is in Row 1 to 155, and the latter is in Row 156 to 349, and between is the space for empty and QC probe.


title: Health Control 2

status: Public on Mar 28 2017

type: RNA

city: Kensington

first: Daniel

middle: D

last: Murray

state: NSW

address: The Kirby Institute, Wallace Wurth Building, UNSW Australia

department: Immunovirology and pathogenesis program

country: Australia

institute: Kirby Institute

data_processing:
Raw data was analysed to see which miRNAs were detectable in serum of HIV infected individuals. No further processing was performed. A miRNA was deemed as 'dectable' if the miRNA was expressed <35CT in more 3 or more samples.
Please note that undetermined values were replaced with a blank in the sample data table.

label: FAM

molecule: total RNA

organism: Homo sapiens

source_name: HIV Negative_serum

label_protocol: cDNA was reversed transcribed and pre-amplified according to manufacturers instructions.

extract_protocol: Total RNA extracted using Trizol methodology

tag: hiv status

value: HIV Negative

tag: tissue

value: serum


title: parental DLD1 colorectal cancer cell line, replicat 1

city: Munich

first: Matjaz

last: Rokavec

address: Thalkirchner Str. 36

department: Institute of Pathology

country: Germany

institute: Ludwig-Maximilians-University Munich

hyb_protocol: Standard Agilent Protocol

scan_protocol: Standard Agilent Protocol

data_processing: Quantile normalization was performed using the preprocessCore package with R version 3.2.0

source_name: colorectal cancer cell line

label_protocol: Standard Agilent Protocol for Cy3 labeling

growth_protocol: Colorectal cancer cell line DLD1 and its derivatives were maintained in McCoy`s 5A Medium (Invitrogen) containing 10% fetal bovine serum (FBS, Invitrogen), 100 units/ml penicillin and 0.1 mg/ml streptomycin.

extract_protocol: Total RNA from cell lines was isolated using the miRNeasy Kit (Qiagen).

treatment_protocol: no treatment

tag: parental cell type

value: colorectal cancer cell line DLD1

tag: cell characteristics

value: epithelial, parental


title: RNA of normal hippocampus tissue (N2W)

city: Nantong

first: cheng

last: xiang

address: Qixiu Road NO.19

country: China

institute: Nantong University

description:
Sample N2W
The raw data for former sample is in Row 1 to 155, and the latter is in Row 156 to 349, and between is the space for empty and QC probe.

hyb_protocol: The microarrays were prehybridized for 1 h at  37℃ based on the designed probe, removed the liquid and hybriedized with 4 ug denatured reversed-transcribed RNA for 16h at the same tempreture.

scan_protocol: Imaging was performed using a laser scanner GenePix4000B (Molecular Device)

data_processing: Normalized intensities were transformed into gene expression log2 values. The ratio and log2 ratio of normalized spot intensities between the test and control samples were calculated. P values were calculated using the analysis of variance (ANOVA) method.

organism: Rattus norvegicus

source_name: normal hippocampus tissue

label_protocol: 2 mg of total RNA was reverse-transcribed using Amino Allyl messageAmp II kit(Life Technologies) and labeled with ULS-Cy5. Labelling efficiency was calculated by the concentration of CyDye and RNA, as measured by spectrophotometry.

extract_protocol: RNA isolated using TRIZOL

tag: strain

value: Sprague-Dawley

tag: protocol

value: control

value: hippocampus


title: Chronic HIV 1

source_name: HIV Positive_serum

value: HIV Positive


title: 20081126 4.08 50

city: Portland

first: Suzy

last: Renn

state: OR

address: 3203 SE Woodstock Blvd

department: Biology

country: USA

institute: Reed College

hyb_protocol: The neutralized color reaction was purified and combined with the appropriate competitive sample in hybridization buffer containing SSC and HEPES buffer with poly(dA)-poly(dT) (Sigma) for blocking and 0.1% for overnight hybridization at 65º C.

scan_protocol: After hybridization arrays were scanned (Axon 4000B: Axon Instruments) using Genepix 5.0 software (Axon Instruments) matching laser power and PMT to roughly normalize the two chanels.

data_processing: Data were filtered for feature quality and diameter, high background intensity, and low feature intensity. Features with demonstrated effects of sequence divergence (poor gDNA hybridization) were also filtered out.

organism: Xenotilapia leptura

source_name: whole brain

label_protocol: 2µg of total RNA from whole brain was reverse transcribed and labeled according to Renn et al. (2004): Briefly, amino-allyl dUTP (Sigma) was incorporated to the cDNA using oligo-dT(12 -18) with SuperScript II (Invitrogen) according to the manufacturer’s protocol, dye-coupling with Cy3 or Cy5 (CyDye Post-Labeling Reactive Dye Pack, Amersham) following RNA hydrolyzation and purification.

growth_protocol: adult

extract_protocol: RNA was extracted with standard trizol protocol

treatment_protocol: brains were extracted from animals captured in the wild. Animals were euthanized as quickly as possible after capture and brains were rapidly removed and stored in RNAlater solution.

tag: Sex

value: male

tag: mating type

value: monogamous

tag: ID

organism: Xenotilapia tenuidentata

value: polygynous


title: Cancer vs health cultured immature MoDC Experiment 2

city: Hefei

first: Rui

last: Li

state: Anhui

address: Huangshan Road 443, USTC West Campus

department: School of Life Sciences

institute: University of Science and Technology of China

description: Cancer serum pool No.2 vs health controls cultured immature MoDCs

hyb_protocol: Equal amount of CY5 and CY3 labeled aRNA were pooled together in Fullmoon hybridization buffer, denaturated at 95ºC for 5 min followed by 1 min on ice. Samples were then applied to pretread microarray slides. The microarray slide was then covered with 22mm×60mm standard glass cover slip and placed in a small sealed humidified chamber. The hybridization would take 16 hours at 42ºC with gentle horizontal shaking in a hybridization incubator. After hybridization, microarray slide was washed with preheated (42ºC) wash buffer for 20 minutes and dried with air blow.

scan_protocol: The microarrays slides were scanned using Generation Ⅲ array scanner (Amersham Pharmacia), and images were processed using Imagequant 5.0 (Amersham Pharmacia Biotech) and Array Vision 6.0 (Imaging Research).

data_processing: Microarray analysis were performed using BRB-ArrayTools (http://brb.nci.nih.gov/BRB-ArrayTools.html) with LOWESS normalization.

source_name: Cancer serum cultured immature MoDC Exp2

label_protocol: Qualified total RNA were used for aRNA synthesis by using Amino Allyl MessageAmp II Kit. aRNA were then labeled with CY5 (health group) or CY3 (cancer group) with purification followed.

growth_protocol: Human monocyte were isolated from the peripheral blood of healthy donors by two step density gradient centrifugation. Human monocyte-derived DCs were generated by culturing the monocytes with rhGM-CSF and rhIL-4 in RPMI 1640 medium with cancer serum or healthy controls added, and incubated at 37°C with 5% CO2 for 5 days. Then, immature DCs cultured with tumor sera or healthy controls were collected for gene expression profiling basing on Operon Human Genome Array-Ready Oligo Set (Version 4.0).

extract_protocol: Total RNA were isolated from experiment samples by TriZol (Invitrogen) and purified by using RNeasy minikit from Qiagen followed with ethanol precipitation. Total RNA quality and quantity were measured with UV spectrum and agarose gel electrophoresis.

tag: cell type

value: Human monocytes-derived dendritic cells

tag: culture media additives

value: Cancer serum pool No.2

tag: brief blood sample protocol

value: Patients in late stage of non-small cell lung cancer (NSCLC) were selected and sampled prior to tumour treatment. There were a total of 56 patients, including 41 males and 15 females, aged 44–76 years. The patient sera were equally and randomly pooled into two groups to obtain a general view of its effects on DCs and to minimize individual variation. All blood serum samples were incubated at 56°C in water bath for 30min to deactivate complement activity prior used in cell growth medium.

source_name: Health plasma cultured immature MoDC

value: Health plasma

value: In the control group, blood plasmas were collected from healthy donors. All blood plasma samples were incubated at 56°C in water bath for 30min to deactivate complement activity prior used in cell growth medium.


title: Patient 2 Glioma

city: Hohhot

first: yong

middle: ping

last: mu

address: No1,Tongdao North Street

institute: Inner Mongolia Medical University

hyb_protocol: Hybridization was performed overnight on a μParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies) (1). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://www.mirbase.org/) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry. The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 L 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.

scan_protocol: Fluorescence images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics)

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal.

source_name: Primary glioma

label_protocol: Labeling of total RNA was performed according to the protocol from LC Science for a single-color experiment with no modification.

extract_protocol: Total RNA from each sample was extracted using TRK1001 (LC Sciences, Cat. TRK-1001, Total RNA Purification Kit) according to the manufacturer's procedure. Total RNA was quantified by the NanoDrop ND-2000 (Thermo Scientific) and the RNA integrity was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies).

tag: age (yrs)

tag: gender

tag: histology

value: glioblastoma

tag: Stage

value: IV

tag: subject status/id

value: control 2

value: brain; non-tumor tissue


title: Patient 1 Glioma

value: anaplasticastroytoma

value: III

value: control 1

value: female


title: Cancer vs health cultured immature MoDC Experiment 1

description: Cancer serum pool No.1 vs health controls cultured immature MoDCs

source_name: Cancer serum cultured immature MoDC Exp1

value: Cancer serum pool No.1


title: Tmub1-Normal Control

status: Public on Mar 27 2017

city: Chongqing

first: Xu

last: jianhua

address: Daping

institute: TMMU

description: Gene expression of Normal cells

hyb_protocol: 1.5 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 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Microarray (Agilent-014879) Hybridization Chambers (Agilent p/n G2530-60029) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (Agilent p/n G2565BA) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Cell line, Tmub1-Normal Control, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1 ug RNA using the Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-0442) according to the manufacturer's instructions, followed by RNeasy Mini Kit (Qiagen p/n 74104). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Normal rat hepatocyte cells (BRL-3A, Cell Bank of Chinese Academy of Sciences, Shanghai, China) were maintained in Dulbecco's modified Eagle's medium (Invitrogen Life Technologies, Carlsbad, CA, USA) containing 10% fetal bovine serum (Invitrogen Life Technologies), 100 units/ml penicillin, and 100 µg/ml streptomycin, and cultured in a humidified atmosphere of 5% CO2 at 37 °C

extract_protocol: The cells were harvested 48 h post-transduction and total RNA for microarray analysis was extracted using an extraction reagent (TRIzol; Invitrogen). Then, complementary DNA was synthesized and labeled before it was purified and hybridized to the microarray (Arraystar, Rockville, MD).

treatment_protocol: BRL-3A cells were divided into five groups and cultured as follows: Tmub1 overexpression lentivirus-transduced (Lv-Tmub1(+)), Tmub1 knockdown lentivirus-transduced (Lv-Tmub1(-)), Lv-Tmub1(+)-Negative Control, Lv-Tmub1(-)-Negative Control and normal control. The cells were harvested 48 h post-transduction and total RNA for microarray analysis was extracted using an extraction reagent (TRIzol; Invitrogen)

tag: cell line


title: Tmub1-overexpression Negative Control

description: Gene expression after Lentivirus of Tmub1-overexpression Negative Control transfected

source_name: Cell line, Lentivirus of Tmub1-overexpression Negative Control transfected, replicate 1


title: Tmub1-knockdown

description: Gene expression after Lentivirus of Tmub1-knockdown transfected

source_name: Cell line, Lentivirus of Tmub1-knockdown transfected, replicate 1


title: Tmub1-overexpression

description: Gene expression after Lentivirus of Tmub1-overexpression transfected

source_name: Cell line, Lentivirus of Tmub1-overexpression transfected, replicate 1


title: Tmub1-knockdown Negative Control

description: Gene expression after Lentivirus of Tmub1-knockdown Negative Control transfected

source_name: Cell line, Lentivirus of Tmub1-knockdown Negative Control transfected, replicate 1


title: Muscle_Pofut1Control_rep3

city: Columbus

first: Paul

middle: T

last: Martin

state: OH

address: 700 Childrens Dr.

department: Center for Gene Therapy

institute: Nationwide Childrens Hospital

hyb_protocol: For each array, 2.2 µg of fragmented and labeled cDNA was hybridized onto 430 2.0 GeneChips® (Affymetrix Inc., USA), for 16 hours at 45°C followed by washing and staining of microarrays in a Fluidics Station 450 (Affymetrix Inc., USA).

scan_protocol: GeneChips were scanned in a GeneChip Scanner 3000 (Affymetrix Inc., USA).

data_processing: CEL files were generated from DAT files using GeneChip® Operating Software (GCOS) (Affymetrix Inc., USA) and probe set signals were generated using the RMA algorithm in ArrayAssist 3.4 (Stratagene) and differential gene expression was determined by pair-wise comparisons.

label: Biotin

organism: Mus musculus

source_name: Quadriceps muscle, Pofut1 Control

label_protocol: The OvationTM Biotin RNA Amplification and Labeling System (NuGen Technologies, Inc.; San Carlos, CA) was used to prepare amplified, biotin-labeled cDNA from 25ng of total RNA from Quadriceps muscle following manufacturer's protocol.

growth_protocol: All mice were maintained in the animal facility of the Research Institute of Nationwide Childrens Hospital following the IACUC guidelines.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's protocol followed by purification on a silica-gel-based membrane (Rneasy-Mini; Qiagen, Valecia, CA).

tag: genotype

value: wildtype

tag: age

value: 2 months

tag: tissue

value: Quadriceps muscle


title: Muscle_Pofut1Knockout_rep3

source_name: Quadriceps muscle, Pofut1 Knockout

tag: strain

value: Pofut1 Knockout


title: Muscle_Pofut1Control_rep2


title: Muscle_Pofut1Knockout_rep2


title: Muscle_Pofut1Control_rep1


title: Muscle_Pofut1Knockout_rep1


title: RNAi RACB Bgh 32h, replicate 4

city: Freising

first: Ralph

last: Hueckelhoven

department: Chair of Phytopathology

institute: TU München

description: Gene expression after 32h in Bgh-treated RNAi RACB

hyb_protocol: 1.65 µg of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 µl containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 µl of 2x Agilent GEx hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Custom Microarrays (20599) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent), 1 minute with 37°C GE Wash buffer 2 (Agilent), 10 seconds with Acetonitril (Agilent) at RT and 30 seconds with Stabilization and Drying solution (Agilent) at RT, then dried immediately by brief centrifugation.

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

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent) using default parameters (protocol GE1_1010_Sep10 and Grid: 020599_D_F_20080612) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Hordeum vulgare

source_name: RNAi RACB Bgh 32h, replicate 4

label_protocol: High-quality cRNA was generated with an input of 100 ng RNA using the Agilent`s Low Input Quick Amp Labeling Kit which produces fluorescent cRNA followed by labeling with cyanine 3-labeled CTP.

growth_protocol: Plants were grown in a growth chamber (Conviron, Winnipeg, Canada) at 18 °C with relative humidity of 65% and a photoperiod of 16 h.

extract_protocol: RNA was extracted using the TRIZOL method (Chomczynski and Sacchi, 1987) out of 14 days old second barley leaves (WT, CA RACB, RNAi RACB each 12 h and 32 h each mock- and Bgh-treated). RNA was eluted in fresh MilliQ H2O and treated with DNaseI according to the manufacture’s manual (RNase-Free DNase set (#79254), Quiagen, Hilden, Germany) before cleaning up with RNeasy® MinElute® Cleanup strictly to the manual (#74204, Quiagen, Hilden, Germany). RNA quality was measured with an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, USA).

treatment_protocol: For inoculation 14 days old plants were inoculated with a density of 100 conidia mm-2 Blumeria graminis f. sp. hordei (Bgh) and the second leaves of five plants per genotype and treatment were harvested and pooled directly after 12 h and 32 h after infection and grinded manually to fine powder.

value: pool of 5 whole second leaves

tag: plant line

value: RNAi RACB 16/2-4


title: RNAi RACB mock 32h, replicate 4

description: Gene expression after 32h in mock-treated RNAi RACB

source_name: RNAi RACB mock 32h, replicate 4


title: RNAi RACB Bgh 32h, replicate 3

description:
Gene expression after 32h in Bgh-treated RNAi RACB
not included in analysis

source_name: RNAi RACB Bgh 32h, replicate 3


title: CA RACB Bgh 32h, replicate 4

description: Gene expression after 32h in Bgh-treated CA RACB

source_name: CA RACB Bgh 32h, replicate 4


title: RNAi RACB mock 32h, replicate 3

description:
Gene expression after 32h in mock-treated RNAi RACB
not included in analysis

source_name: RNAi RACB mock 32h, replicate 3


title: RNAi RACB Bgh 12h, replicate 4

description: Gene expression after 12h in Bgh-treated RNAi RACB

source_name: RNAi RACB Bgh 12h, replicate 4


title: 5-FU resistant cells

city: Seoul

first: Ho-Young

last: Lee

address: 1 Gwanak-ro, Gwanak-gu

department: College of Pharmacy

country: South Korea

institute: Seoul National University

description: Basal gene expression

hyb_protocol: 600ng 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 50

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

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09  and Grid: 028004_D_F_20111107) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: HCT 116 human colon cancer cell line, treated with increasing concentrations of 5-FU more than 6 months

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200ng RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent)

growth_protocol: Sub-confluent cells (70~80% in confluency) were harvested. Cells were incubated for 2~3 days at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: RNA was extracted using TRIzol according to the manufacturer's recommended procedure.

value: Colon cancer

value: 5-FU resistant


title: WT Bgh 32h, replicate 4

description: Gene expression after 32h in Bgh-treated WT

source_name: WT Bgh 32h, replicate 4

value: Golden Promise


title: CA RACB Bgh 12h, replicate 4

description: Gene expression after 12h in Bgh-treated CA RACB

source_name: CA RACB Bgh 12h, replicate 4


title: WT mock 32h, replicate 4

description: Gene expression after 32h in mock-treated WT

source_name: WT mock 32h, replicate 4


title: WT mock 12h, replicate 4

description: Gene expression after 12h in mock-treated WT

source_name: WT mock 12h, replicate 4


title: Parental cells

description: Basal gene expression

source_name: HCT 116 human colon cancer cell line, parental

value: Parental


title: CA RACB mock 12h, replicate 4

description: Gene expression after 12h in mock-treated CA RACB

source_name: CA RACB mock 12h, replicate 4


title: RNAi RACB mock 12h, replicate 4

description: Gene expression after 12h in mock-treated RNAi RACB

source_name: RNAi RACB mock 12h, replicate 4


title: WT mock 32h, replicate 3

source_name: WT mock 32h, replicate 3


title: Lz replicate 4

city: Zurich

first: Nike

last: Krautler

address: Vladimir-Prelog Weg1-5/10

department: Biology, Institute of Microbiology

country: Switzerland

institute: ETH Zurich

hyb_protocol: 3.75 ug of fragmented, labeled cDNA (final concentration in hyb cocktail of 17 ng/ul) was prepared for hybridization. Samples were hybridized to arrays for 16 hours at 45°C rotating at 60 rpm in the Affymetrix Hybridization Oven. Arrays were washed on the Affymetrix Fluidics 4500 Station as per manufacturer’s protocol using program FS450_007.

scan_protocol: Arrays were scanned in the GCS 3000 7G scanner as per manufacturer’s protocol.

data_processing:
Data were processed using GenePattern software, data was RMA-normalized
MoEx-1_0-st-v1.r2.pgf
MoEx-1_0-st-v1.r2.dt1.mm8.mps

label: biotin

source_name: sort purified Lzlo GC SwHEL B cells after immunization with HEL3x-SRBC

label_protocol: Samples were reverse transcribed, amplified, labelled and fragmented using Ovation Pico WTA, WT Ovation Exon Module and Encore Biotin Module (NuGen)

growth_protocol: not applicable

extract_protocol: Sort purified LZ and DZ GC B cells of high or low affinity were sorted into Trizol reagant and snap frozen in liquid nitrogen and stored at -80°C until RNA purification. RNA was purified according to manufacturers instruction (Invitrogen). .  To  improve  recovery,  RNA  was  precipitated  with  GlycoBlue  (Thermo  Fischer).   RNA  quality  and  quantity  was  determined  using  a  Bioanalyzer  2100

treatment_protocol: SwHEL B cells carrying the CD45.1 congenic marker were transferred into C57BL/6J mice (CD45.2) and immunized with sheep red blood cells conjugated to the hen egg lysozyme mutant HEL3x. Day 10 post immunization high and low affinity cells of either LZ (CD86 high, CXCR4 low) or DZ (CXCR4 high, CD86 low) were sort purified from donor-derived GC B cell population (CD45.1+, CD45.2-, IgG1+, CD38 low)

value: spleen

value: LZ GC B cells

tag: affinity

value: low


title: WT Bgh 12h, replicate 4

description: Gene expression after 12h in Bgh-treated WT

source_name: WT Bgh 12h, replicate 4


title: Dz replicate 6

source_name: sort purified Dzlo GC SwHEL B cells after immunization with HEL3x-SRBC

value: DZ GC B cells


title: CA RACB mock 12h, replicate 3

source_name: CA RACB mock 12h, replicate 3


title: CA RACB mock 32h, replicate 4

description: Gene expression after 32h in mock-treated CA RACB

source_name: CA RACB mock 32h, replicate 4


title: Lz replicate 2

source_name: sort purified Lzhi GC SwHEL B cells after immunization with HEL3x-SRBC

value: high


title: WT mock 12h, replicate 3

description:
Gene expression after 12h in mock-treated WT
not included in analysis

source_name: WT mock 12h, replicate 3


title: CA RACB Bgh 32h, replicate 3

source_name: CA RACB Bgh 32h, replicate 3


title: Lz replicate 3

value: female


title: Dz replicate 5


title: Lz replicate 1


title: RNAi RACB Bgh 12h, replicate 3

source_name: RNAi RACB Bgh 12h, replicate 3


title: RNAi RACB mock 12h, replicate 3

source_name: RNAi RACB mock 12h, replicate 3


title: Dz replicate 4


title: 0hMeDIP_rep1_ds2 vs 0hINPUT_rep1_ds2

type: genomic

city: Lyon

first: François

last: ROUDIER

address: 46 Allée d'Italie

department: Biologie

country: France

institute: Ecole Normale Supérieure de Lyon

description: Methylome analysis

hyb_protocol: Co-hybridization was performed using the NimbleGen 3x720K array design and following manufacturer’s instructions

scan_protocol: Data acquisition was performed according to Roche Nimblegen instructions.

data_processing:
Hybridization data were quantile normalized and averaged on the dye-swap to remove technical biases. Normalized data were analysed under stringent criteria using Parsimonious Higher-Order Hidden Markov Models (www.jstacs.de/index.php/PHHMM). Adjacent tiles are joined into domains by requiring a minimal run of 400 bp and allowing a maximal gap of 200 bp.
The processed data are identical for the two co-hybridizations that constitute a dye-swap.

molecule: genomic DNA

organism: Arabidopsis thaliana

label_protocol: Cy3 and Cy5 labeling were performed using the Nimblegen Dual color DNA labeling kit (Roche NimbleGen) …

growth_protocol: Arabidopsis solid growth medium consisted of MS salts with vitamins, supplemented with 0.5 g.L-1 2-(N-morpholino) ethane sulfonic acid (pH5.7), 1 % (w/v) sucrose and 0.6% (w/v) Agarose. Plantlets were germinated and grown in the presence of 1.25 µM 1-N-Naphthylphthalamic acid (NPA) for 6 d prior to NAA treatment. To induce lateral root formation, plantlets were transferred and grown for 42 hours on an auxin medium containing 3.3 µM 1-naphthaleneacetic acid (NAA). To induce shoot meristem formation, primary root segments were excised and transferred on a cytokinin medium containing 8.16 µM N6-[2-isopentenyl]adenine (2-iP), and sucrose was replaced with 2% D-(+)-Glucose.

extract_protocol: 0hMeDIP_rep1:10ug. DNA was extracted as described in Seifert M, Cortijo S, Colomé-Tatché M, Johannes F, Roudier F, Colot V (2012) MeDIP-HMM: genome-wide identification of distinct DNA methylation states from high-density tiling arrays. Bioinforma Oxf Engl 28: 2930–2939.

tag: ecotype

value: root

value: 6 days

tag: developmental stage

value: root explants

tag: antibody

tag: vendor

extract_protocol: 0hINPUT_rep1:10ug. DNA was extracted as described in Seifert M, Cortijo S, Colomé-Tatché M, Johannes F, Roudier F, Colot V (2012) MeDIP-HMM: genome-wide identification of distinct DNA methylation states from high-density tiling arrays. Bioinforma Oxf Engl 28: 2930–2939.


title: CA RACB Bgh 12h, replicate 3

source_name: CA RACB Bgh 12h, replicate 3


title: WT mock 12h, replicate 2

source_name: WT mock 12h, replicate 2


title: WT Bgh 32h, replicate 3

description:
Gene expression after 32h in Bgh-treated WT
not included in analysis

source_name: WT Bgh 32h, replicate 3


title: Lz replicate 6

tag: cell type


title: Dz replicate 3

source_name: sort purified Dzhi GC SwHEL B cells after immunization with HEL3x-SRBC


title: WT Bgh 32h, replicate 2

source_name: WT Bgh 32h, replicate 2


title: Lz replicate 5


title: 58hMeDIP_rep1_ds2 vs 58hINPUT_rep1_ds2

description: Methylome analysis

extract_protocol: 58hMeDIP_rep1:10ug. DNA was extracted as described in Seifert M, Cortijo S, Colomé-Tatché M, Johannes F, Roudier F, Colot V (2012) MeDIP-HMM: genome-wide identification of distinct DNA methylation states from high-density tiling arrays. Bioinforma Oxf Engl 28: 2930–2939.

extract_protocol: 58hINPUT_rep1:10ug. DNA was extracted as described in Seifert M, Cortijo S, Colomé-Tatché M, Johannes F, Roudier F, Colot V (2012) MeDIP-HMM: genome-wide identification of distinct DNA methylation states from high-density tiling arrays. Bioinforma Oxf Engl 28: 2930–2939.


title: Lzlo replicate 2

hyb_protocol: 3.75 ug of fragmented, labeled cDNA (final concentration in hyb cocktail of 17 ng/ul) was prepared for hybridisation. Samples were hybridised to arrays for 16 hours at 45°C rotating at 60 rpm in the Affymetrix Hybridisation Oven. Arrays were washed on the Affymetrix Fluidics 4500 Station as per manufacturer’s protocol using program FS450_007.

scan_protocol: Arrays were scanned in the GCS 3000 7G scanner as per manufacturer's protocol.

data_processing:
Data were processed using GenePattern software, data was RMA-normalized.
Probe group file: MoEx-1_0-st-v1.r2.pgf
Meta-probeset file: MoEx-1_0-st-v1.r2.dt1.mm8.mps

label_protocol: Samples were reverse transcribed, amplified, labelled and fragmented using Ovation Pico WTA, WT Ovation Exon Module and Encore Biotin Module (NuGen).

growth_protocol: Not applicable.

extract_protocol: Sort purified LZ and DZ GC B cells of high or low affinity were sorted into Trizol reagent and snap frozen in liquid nitrogen and stored at -80°C until RNA purification. RNA was purified according to manufacturer's instruction (Invitrogen). To improve recovery, RNA was precipitated with GlycoBlue (Thermo Fischer). RNA quality and quantity were determined using a Bioanalyzer 2100.

treatment_protocol: SwHEL B cells carrying the CD45.1 congenic marker were transferred into C57BL/6J mice (CD45.2) and immunized with sheep red blood cells conjugated to the hen egg lysozyme mutant HEL3x. Day 10 post immunization high and low affinity cells of either LZ (CD86 high, CXCR4 low) or DZ (CXCR4 high, CD86 low) were sort purified from donor-derived GC B cell population (CD45.1+, CD45.2-, IgG1+, CD38 low).

tag: strain/background

value: SWHEL

value: germinal center light zone B cells of low affinity


title: Lzlo replicate 3

tag: gender


title: RNAi RACB mock 32h, replicate 2

source_name: RNAi RACB mock 32h, replicate 2

value: pool of 5 whole second leaves


title: 34hMeDIP_rep2_ds1 vs 34hINPUT_rep2_ds1

description: Methylome analysis

extract_protocol: 34hMeDIP_rep2:10ug. DNA was extracted as described in Seifert M, Cortijo S, Colomé-Tatché M, Johannes F, Roudier F, Colot V (2012) MeDIP-HMM: genome-wide identification of distinct DNA methylation states from high-density tiling arrays. Bioinforma Oxf Engl 28: 2930–2939.

extract_protocol: 34hINPUT_rep1:10ug. DNA was extracted as described in Seifert M, Cortijo S, Colomé-Tatché M, Johannes F, Roudier F, Colot V (2012) MeDIP-HMM: genome-wide identification of distinct DNA methylation states from high-density tiling arrays. Bioinforma Oxf Engl 28: 2930–2939.


title: 34hMeDIP_rep1_ds1 vs 34hINPUT_rep1_ds1

description: Methylome analysis

extract_protocol: 34hMeDIP_rep1:10ug. DNA was extracted as described in Seifert M, Cortijo S, Colomé-Tatché M, Johannes F, Roudier F, Colot V (2012) MeDIP-HMM: genome-wide identification of distinct DNA methylation states from high-density tiling arrays. Bioinforma Oxf Engl 28: 2930–2939.


title: Dz replicate 2


title: Dz replicate 1


title: Lzlo replicate 1


title: Lzhi replicate 4

value: germinal center light zone B cells of high affinity


title: 6hMeDIP_rep1_ds1 vs 6hINPUT_rep1_ds1

description: Methylome analysis

extract_protocol: 6hMeDIP_rep1:10ug. DNA was extracted as described in Seifert M, Cortijo S, Colomé-Tatché M, Johannes F, Roudier F, Colot V (2012) MeDIP-HMM: genome-wide identification of distinct DNA methylation states from high-density tiling arrays. Bioinforma Oxf Engl 28: 2930–2939.

extract_protocol: 6hINPUT_rep1:10ug. DNA was extracted as described in Seifert M, Cortijo S, Colomé-Tatché M, Johannes F, Roudier F, Colot V (2012) MeDIP-HMM: genome-wide identification of distinct DNA methylation states from high-density tiling arrays. Bioinforma Oxf Engl 28: 2930–2939.


title: 34hMeDIP_rep1_ds2 vs 34hINPUT_rep1_ds2

description: Methylome analysis


title: Lzlo replicate 4


title: Lzhi replicate 1


title: RNAi RACB mock 12h, replicate 2

source_name: RNAi RACB mock 12h, replicate 2

value: RNAi RACB 16/2-4


title: 0hMeDIP_rep2_ds1 vs 0hINPUT_rep2_ds1

description: Methylome analysis

extract_protocol: 0hMeDIP_rep2:10ug. DNA was extracted as described in Seifert M, Cortijo S, Colomé-Tatché M, Johannes F, Roudier F, Colot V (2012) MeDIP-HMM: genome-wide identification of distinct DNA methylation states from high-density tiling arrays. Bioinforma Oxf Engl 28: 2930–2939.


title: RNAi RACB Bgh 32h, replicate 2

source_name: RNAi RACB Bgh 32h, replicate 2


title: Lzhi replicate 2


title: CA RACB Bgh 32h, replicate 2

source_name: CA RACB Bgh 32h, replicate 2


title: CA RACB mock 32h, replicate 3

source_name: CA RACB mock 32h, replicate 3


title: 0hMeDIP_rep2_ds2 vs 0hINPUT_rep2_ds2

description: Methylome analysis

extract_protocol: 0hINPUT_rep2:10ug. DNA was extracted as described in Seifert M, Cortijo S, Colomé-Tatché M, Johannes F, Roudier F, Colot V (2012) MeDIP-HMM: genome-wide identification of distinct DNA methylation states from high-density tiling arrays. Bioinforma Oxf Engl 28: 2930–2939.


title: RNAi RACB Bgh 12h, replicate 2

source_name: RNAi RACB Bgh 12h, replicate 2


title: 34hMeDIP_rep2_ds2 vs 34hINPUT_rep2_ds2

description: Methylome analysis

extract_protocol: 34hINPUT_rep2:10ug. DNA was extracted as described in Seifert M, Cortijo S, Colomé-Tatché M, Johannes F, Roudier F, Colot V (2012) MeDIP-HMM: genome-wide identification of distinct DNA methylation states from high-density tiling arrays. Bioinforma Oxf Engl 28: 2930–2939.


title: 6hMeDIP_rep2_ds2 vs 6hINPUT_rep2_ds2

description: Methylome analysis

extract_protocol: 6hMeDIP_rep2:10ug. DNA was extracted as described in Seifert M, Cortijo S, Colomé-Tatché M, Johannes F, Roudier F, Colot V (2012) MeDIP-HMM: genome-wide identification of distinct DNA methylation states from high-density tiling arrays. Bioinforma Oxf Engl 28: 2930–2939.

extract_protocol: 6hINPUT_rep2:10ug. DNA was extracted as described in Seifert M, Cortijo S, Colomé-Tatché M, Johannes F, Roudier F, Colot V (2012) MeDIP-HMM: genome-wide identification of distinct DNA methylation states from high-density tiling arrays. Bioinforma Oxf Engl 28: 2930–2939.


title: 58hMeDIP_rep2_ds1 vs 58hINPUT_rep2_ds1

description: Methylome analysis

data_processing: Hybridization data were quantile normalized and averaged on the dye-swap to remove technical biases. Normalized data were analysed under stringent criteria using Parsimonious Higher-Order Hidden Markov Models (www.jstacs.de/index.php/PHHMM). Adjacent tiles are joined into domains by requiring a minimal run of 400 bp and allowing a maximal gap of 200 bp.!Sample_data_processing = The processed data are identical for the two co-hybridizations that constitute a dye-swap.

extract_protocol: 58hMeDIP_rep2:10ug. DNA was extracted as described in Seifert M, Cortijo S, Colomé-Tatché M, Johannes F, Roudier F, Colot V (2012) MeDIP-HMM: genome-wide identification of distinct DNA methylation states from high-density tiling arrays. Bioinforma Oxf Engl 28: 2930–2939.


title: 58hMeDIP_rep2_ds2 vs 58hINPUT_rep2_ds2

description: Methylome analysis

extract_protocol: 58hINPUT_rep2:10ug. DNA was extracted as described in Seifert M, Cortijo S, Colomé-Tatché M, Johannes F, Roudier F, Colot V (2012) MeDIP-HMM: genome-wide identification of distinct DNA methylation states from high-density tiling arrays. Bioinforma Oxf Engl 28: 2930–2939.


title: Mtb_INH/Cys_rep3

city: Saranac Lake

first: Brian

last: Weinrick

state: NY

address: 154 Algonquin Avenue

institute: Trudeau Institute

description: Biological replicate 3 of 3

hyb_protocol: Slide was hybridized for 16 hours at 42 in water bath with volume of 60 uL in solution of standard gene expression hybridization solution, and blocked in standard prehybridization solution. After hybridization, the slide was washed with standard wash protocol.

scan_protocol: scanned with PMT voltage adjusted for maximum dynamic range on Axon Genepix 4000B scanner

data_processing: Spots were gridded and quantitated in TIGR Spotfinder, data were processed in TIGR MIDAS with lowess normalization, standard deviation regularization, in-slide replicate analysis, one bad channel policy set to generous, all flags on

organism: Mycobacterium tuberculosis

source_name: INH-treated Mtb (Reference)

label_protocol: 2 ug total RNA was used as template for reverse transcription with random hexamer primers and aminoallyl-dUTP in a 2:3 ratio to dTTP in the nucleotide mix. After overnight incubation at 42°C, the reaction was stopped, RNA was hydrolyzed, and unincorporated nucleotides and free amines were removed with the Qiagen MinElute kit as per protocol, with amine-free phosphate wash and elution buffers. cDNA concentration and purity were measured by Nanodrop. Cy3 and Cy5 dyes were coupled to the aminoallyl-cDNA, which was then purified using a MinElute kit. Probe concentration, purity, and dye incorporation were measured by Nanodrop.

growth_protocol: Cultures were prepared by diluting an exponentially growing culture of M. tuberculosis H37Rv to an OD600nm of 0.2 in a 10 mL volume of 7H9 OADC 0.2% glycerol 0.05% tyloxapol broth in a 30 mL ink-well bottle which was incubated shaking at 37°C.

extract_protocol: Cultures were harvested by centrifugation then resuspended in 1mL Qiagen RNA protect and stored at 4°C. Cells were later pelleted and resuspended in 1ml Trizol and transferred to a Fast-Prep lysing matrix B tube. Tubes are processed in Fast-Prep apparatus for 45 seconds at 6.5 M per second then cooled on ice for 1 minute before debris is pelleted by centrifugation. RNA is then purified and sample is DNase-treated following Direct-zol kit manufacturer instructions.

treatment_protocol: Cultures were treated with isoniazid (7.3 μM) with and without cysteine (4.0 mM) for 4 hours.

tag: treatment

value: isoniazid

source_name: INH/Cys-treated Mtb (Test)

value: isoniazid and cysteine


title: Mtb_INH/Cys_rep1

description: Biological replicate 1 of 3


title: 0hMeDIP_rep1_ds1 vs 0hINPUT_rep1_ds1

description: Methylome analysis

extract_protocol: 0hMeDIP_rep1:10ug. DNA was extracted as described in Seifert M, Cortijo S, Colomé-Tatché M, Johannes F, Roudier F, Colot V (2012) MeDIP-HMM: genome-wide identification of distinct DNA methylation states from high-density tiling arrays. Bioinforma Oxf Engl 28: 2930–2939.

extract_protocol: 0hINPUT_rep1:10ug. DNA was extracted as described in Seifert M, Cortijo S, Colomé-Tatché M, Johannes F, Roudier F, Colot V (2012) MeDIP-HMM: genome-wide identification of distinct DNA methylation states from high-density tiling arrays. Bioinforma Oxf Engl 28: 2930–2939.


title: 58hMeDIP_rep1_ds1 vs 58hINPUT_rep1_ds1

description: Methylome analysis

extract_protocol: 58hMeDIP_rep1:10ug. DNA was extracted as described in Seifert M, Cortijo S, Colomé-Tatché M, Johannes F, Roudier F, Colot V (2012) MeDIP-HMM: genome-wide identification of distinct DNA methylation states from high-density tiling arrays. Bioinforma Oxf Engl 28: 2930–2939.

extract_protocol: 58hINPUT_rep1:10ug. DNA was extracted as described in Seifert M, Cortijo S, Colomé-Tatché M, Johannes F, Roudier F, Colot V (2012) MeDIP-HMM: genome-wide identification of distinct DNA methylation states from high-density tiling arrays. Bioinforma Oxf Engl 28: 2930–2939.


title: WT Bgh 32h, replicate 1

source_name: WT Bgh 32h, replicate 1

extract_protocol: RNA was extracted using the TRIZOL method (Chomczynski and Sacchi, 1987) out of 14 days old second barley leaves (WT, CA RACB, RNAi RACB each 12 h and 32 h each mock- and Bgh-treated). RNA was eluted in fresh MilliQ H2O and treated with DNaseI according to the manufacture’s manual (RNase-Free DNase set (#79254), Quiagen, Hilden, Germany) before cleaning up with RNeasy® MinElute® Cleanup strictly to the manual (#74204, Quiagen, Hilden, Germany). RNA quality was measured with an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, USA).

value: Golden Promise


title: 6hMeDIP_rep1_ds2 vs 6hINPUT_rep1_ds2

description: Methylome analysis


title: Dzlo replicate 2

source_name: sort purified Dzlo GC SwHEL B cells after immunization with HEL3x-SRBC

extract_protocol: Sort purified LZ and DZ GC B cells of high or low affinity were sorted into Trizol reagent and snap frozen in liquid nitrogen and stored at -80°C until RNA purification. RNA was purified according to manufacturer's instruction (Invitrogen). To improve recovery, RNA was precipitated with GlycoBlue (Thermo Fischer). RNA quality and quantity were determined using a Bioanalyzer 2100.

value: spleen

value: germinal center dark zone B cells of low affinity


title: Dzlo replicate 3


title: Mtb_INH/Cys_rep2

description: Biological replicate 2 of 3


title: WT Bgh 12h, replicate 3

source_name: WT Bgh 12h, replicate 3


title: CA RACB mock 12h, replicate 2

source_name: CA RACB mock 12h, replicate 2


title: Dzlo replicate 1


title: Dzhi replicate 3

value: germinal center dark zone B cells of high affinity


title: 6hMeDIP_rep2_ds1 vs 6hINPUT_rep2_ds1

description: Methylome analysis


title: WT Bgh 12h, replicate 2

source_name: WT Bgh 12h, replicate 2


title: Dzhi replicate 4


title: Dzhi replicate 2


title: CA RACB mock 32h, replicate 1

source_name: CA RACB mock 32h, replicate 1


title: CA RACB Bgh 32h, replicate 1

source_name: CA RACB Bgh 32h, replicate 1


title: Dzhi replicate 1

source_name: sort purified Dzhi GC SwHEL B cells after immunization with HEL3x-SRBC


title: Batf1/3DKO_10ng_rep3

city: Chiba-shi

first: Arifumi

last: Iwata

state: Chiba

address: 1-8-1 Inohana, Chuou-ku

department: Department of Allergy and Clinical Immunology

country: Japan

institute: Chiba University

hyb_protocol: Hybed onto Mouse Gene 1.0 ST Arrays (Affymetrix)

scan_protocol: not provided.

data_processing: Data was processed using RMA summarization and quartile normalization using Arraystar ver. 5

source_name: cultured TH2 cells

label_protocol: Ambion WT Expression kit, Genechip WT Terminal Labeling and Controls Kit

growth_protocol: Naive CD4 T cells were activated with soluble anti-CD3e at various concentrations and anti-CD28 cross linked by plate-bound anti-hamster IgG under TH2 conditions.

extract_protocol: RNA was extracted using RNAquaous Micro Total RNA Isolation kit (Ambion).

value: cultured TH2 cells

tag: stimulation

value: 4 days 10 ng anti-CD3e


title: RNAi RACB mock 32h, replicate 1

source_name: RNAi RACB mock 32h, replicate 1


title: CA RACB Bgh 12h, replicate 2

description:
Gene expression after 12h in Bgh-treated CA RACB
not included in analysis

source_name: CA RACB Bgh 12h, replicate 2


title: RNAi RACB Bgh 32h, replicate 1

description: Gene expression after 32h in Bgh-treated RNAi RACB

source_name: RNAi RACB Bgh 32h, replicate 1


title: CA RACB mock 32h, replicate 2

description:
Gene expression after 32h in mock-treated CA RACB
not included in analysis

source_name: CA RACB mock 32h, replicate 2


title: Batf1/3DKO_10ng_rep2


title: Batf1/3DKO_10ng_rep1


title: WT mock 32h, replicate 1

source_name: WT mock 32h, replicate 1


title: WT mock 32h, replicate 2

source_name: WT mock 32h, replicate 2


title: RNAi RACB mock 12h, replicate 1

source_name: RNAi RACB mock 12h, replicate 1


title: RNAi RACB Bgh 12h, replicate 1

source_name: RNAi RACB Bgh 12h, replicate 1


title: Batf1/3DKO_2ng_rep3

value: 4 days 2.2 ng anti-CD3e


title: Batf1/3DKO_2ng_rep2


title: ChIP_∆rpoN_wt_2

city: Irvine

first: Michael

last: McClelland

state: CA

address: 132 Med Surge I

department: Microbiology & Molecular Genetics

institute: University of California, Irvine

description:
ChIP_STMpPBHP192_∆rpoN_wt_2
RpoN-specific pulldown
second replicate

hyb_protocol: Labelled ChIP-enriched DNAs were hybridized to S. Typhimurium 14028 high-density oligo arrays in formamide-containing hybridization buffer overnight at 42°C, following standard protocols (Roche Nimblegen).

scan_protocol: Arrays were scanned using the Axon GenePix 4000B scanner (Molecular Devices LLC; Sunnyvale, CA).

data_processing: Image analysis and feature extraction was performed with the Axon GenePix Pro software (Molecular Devices).

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. ATCC 14028

label_protocol: For biological replicate 1, the full range of LM-PCR products was used for labeling with Cy3 and Cy5. For biological replicates 2 and 3, size-selection by agarose gel electrophoresis was used to isolate LM-PCR products of 0.15-0.45 kb for labeling with Cy3 and Cy5. For the labeling reactions, 500-750 ng LM-PCR products were incubated at 98°C for 10 minutes, quick-chilled in ice-water for 2 min, and the following reagents were added: 50 mM Tris pH 6.8, 5 mM MgCl2, 10 mM β-mercaptoethanol, 0.36 ng/µL random hexamers, 0.12 mM each dATP, dGTP, dTTP, 0.06 mM dCTP, 0.4 mM Cy3- or Cy5-labeled dCTP (GE Healthcare), and 10 U Klenow fragment.  The reactions proceeded overnight at 37°C.  Excess hexamers and nucleotides were removed using the PCR Purification Kit (Qiagen) according to the manufacturer’s instructions.

growth_protocol: Wild type and ∆rpoN S. Typhimurium 14028s cells containing pPBHP192 which expresses DctD250 at low levels (WT+DctD250; ∆rpoN+DctD250) were incubated with aeration at 37°C in 40 ml NB-Amp100 until they reached early-to-mid exponential growth phase (OD600≈0.5).

extract_protocol: 50 ml culture was treated with rifampicin (100µg/mL) for 10min at 37°C with shaking to hold holoenzymes in open complex at promoters before the treatment with formaldehyde (1.1%) for 10 min.  Lysate was prepared from the treated cells by French press, cleared of debris by centrifugation, incubated with Protein A bead slurry (USB Corporation) to reduce background due to nonspecific interactions, and then incubated with rabbit polyclonal antiserum against S. Typhimurium σ54 (α-σ54). Antibody-bound protein-DNA complexes were incubated with Protein A beads, washed, and disrupted per the manufacturer’s instruction.  The cross-link between the protein and DNA was reversed, the DNA was isolated and subjected to Ligation-Mediated PCR (LM-PCR) to non-specifically amplify all enriched DNA fragments.  The size range of the LM-PCR products was 0.15-1.0 kb, with most products in the 0.3-0.5 kb range.

value: {delta}rpoN, pPBHP192 (exp)

value: wt, pPBHP192 (control)


title: Batf1/3DKO_day2_rep2

value: 2 days TH2 polarized


title: Batf1/3DKO_day2_rep3


title: Batf1/3DKO_2ng_rep1


title: CA RACB mock 12h, replicate 1

source_name: CA RACB mock 12h, replicate 1


title: CA RACB Bgh 12h, replicate 1

source_name: CA RACB Bgh 12h, replicate 1


title: ChIP_wt_1_3

description:
ChIP_STMpPBHP192_wt_1_3
RpoN-specific pulldown
first & third replicate, control only - to evaluate the effect of sizeclassing

value: polyclonal antiserum against S. Typhimurium σ54


title: WT_10ng_rep3

value: wildtype


title: Batf1/3DKO_day2_rep1


title: Batf1/3DKO_day0_rep1

source_name: naive CD4 T cells

value: naive CD4 T cells

value: unstimulated (day0)


title: Batf1/3DKO_day0_rep2


title: Batf1/3DKO_day0_rep3


title: WT_10ng_rep2


title: WT_10ng_rep1


title: ChIP_∆rpoN_wt_1

description:
ChIP_STMpPBHP192_∆rpoN_wt_1
RpoN-specific pulldown
first replicate


title: WT_2ng_rep2


title: WT_2ng_rep3


title: WT_2ng_rep1


title: WT mock 12h, replicate 1

source_name: WT mock 12h, replicate 1

value: pool of 5 whole second leaves


title: WT_day2_rep3


title: WT_day2_rep2


title: Dzlo replicate 4

source_name: sort purified Dzlo GC SwHEL B cells after immunization with HEL3x-SRBC

value: SWHEL

value: female


title: WT_day0_rep1


title: WT_day0_rep3


title: WT_day0_rep2


title: WT_day2_rep1


title: ∆rpoN_wt_DctD250_2

description:
STMpPBHP192_∆rpoN_wt_2
second replicate

hyb_protocol: Labelled cDNAs were hybridized to S. Typhimurium 14028 high-density oligo arrays in formamide-containing hybridization buffer overnight at 42°C, following standard protocols (Roche Nimblegen).

label_protocol: 25 µg of RNA was combined with 2.4 µg random hexamers, denatured at 70°C, and quick-chilled in ice-water. The remaining components of the reverse transcription reaction were added to the denatured RNA and random hexamers to the following concentrations in a 60 µl reaction: 0.01 M DTT, 1X Superscript II first strand reaction buffer, 0.5 mM dATP, dTTP, dGTP, 0.2 mM dCTP, 0.066 mM Cy3- or Cy5-labeled dCTP (GE Healthcare), RNasin (Roche), and 800 U Superscript II.  After 1 hour at 42°C, an additional 400 U of Superscript II was added and incubated another hour.  Excess random hexamers and nucleotides were removed with a PCR Purification Kit (Qiagen) per manufacturer’s instructions.

extract_protocol: Frozen cell pellets were resuspended in 4 mL of RNA extraction solution [18 mM EDTA, 0.025% SDS, 1% 2-mercaptoethanol, 95% RNA-grade formamide], divided into 4 aliquots and incubated in a 95°C water bath for 10 min.  Cell debris was removed by centrifugation, supernatant was transferred to a fresh tube, and RNA was ethanol precipitated.  RNA was treated with RNase-free DNase I (Ambion) and subjected to a second ethanol precipitation for DNase I removal.


title: Macrphage in Day7 after myocardial infarction vs. control

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner (Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction (Toray Industries Inc., Tokyo, Japan).

data_processing: F635 Median column as Red signal and F532 Median column as Green signal. Global normalized, background subtracted data obtained from log2 of processed Green signal/processed Red signal.

source_name: Sham Heart Macrophage

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

extract_protocol: RNA samples were extracted from cells using miRNesy mini kit (Qiagen).

tag: stress

value: sham

value: Heart

value: Macrophage (CD11b+F4/80+Ly-6G-)

source_name: MI D7 Macrophage

value: myocardial infarction

tag: time

value: day7 after myocardial infarction


title: ∆rpoN_wt_DctD250_1

description:
STMpPBHP192_∆rpoN_wt_1
first replicate

tag: genotype


title: Macrphage in Day1 after myocardial infarction vs. control

source_name: 134-136 MI D1 Macrophage

value: day1 after myocardial infarction


title: Macrphage in Day3 after myocardial infarction vs. control

source_name: 140-142 MI D3 Macrophage

value: day3 after myocardial infarction


title: Non-injected control 2

city: Gent

first: Nicky

last: Wybouw

address: Coupure Links 653

department: Department of Crop Protection

country: Belgium

institute: University of Ghent

description: Replication 2 out of 2

hyb_protocol: Cy3- and Cy5-labeled cRNA were pooled and hybridized using the Gene Expression Hybridization Kit (Agilent Technologies) for 17h in a rotating hybridization oven at 20 r.p.m. and 65 °C; Slides were subsequently washed using the Gene Expression Wash Buffer Kit (Agilent Technologies)

scan_protocol: After standard Agilent washing procedures, hybridized arrays were scanned using an Agilent Microarray High Resolution Scanner.

data_processing: Data was extracted and normalized using Agilent Feature Extraction Software (GE2_107_Sep09 protocol). The data output files were subsequently transferred to limma (Smyth, 2004) for further statistical analysis. After background corrections, within- and between-array normalizations, significant differential expression was identified using cut-offs of log2FC and BH FDR-corrected p-value at 1 and 0.05, respectively. Within the linear modelling of the data, intra-spot correlations were incorporated (Smyth & Altman, 2013).

organism: Tetranychus urticae

source_name: non-injected, whole organism

label_protocol: Using the Agilent Low Input Quick Amp Labeling Kit (version 6.5 Agilent Technologies), Cy3- and Cy5-labeled cRNA was generated using 100 ng of total RNA as starting material (excluding RNA-spike in controls).

growth_protocol: Mite strains were maintained in climatically controlled rooms at 26 °C, 60% RH and 16:8 h light:dark photoperiod

extract_protocol: Total RNA samples were isolated using the RNeasy minikit (Qiagen) and were subsequently treated with DNase (Turbo DNA-free kit, Ambion). RNA was extracted from 300 injected adult female mites in four replicates.

treatment_protocol: Mites were non-injected.

tag: age

value: adult

source_name: LB-buffer injected, whole organism

treatment_protocol: Mites were injected with LB-buffer.


title: ∆rpoN_wt_DctD250_3

description:
STMpPBHP192_∆rpoN_wt_3
third replicate

value: wt, pPBHP192 (control)

value: {delta}rpoN, pPBHP192 (exp)


title: B. megaterium 12 hours 1

description: Replication 1 out of 4, 12 hours post injection of B. megaterium

source_name: B. megaterium injected, whole organism

treatment_protocol: Mites were injected with 1OD of bacteria.

tag: injection

value: LB buffer


title: Macrphage in Day14 after myocardial infarction vs. control

tag: tissue

source_name: MI D14 Macrophage

value: day14 after myocardial infarction


title: QRsP-11 and LV12_1

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

growth_protocol: QRsP-11 and LV12 cells were maintained in Eagle’s minimum essential medium (05900, Nissui Pharmaceuticals, Tokyo, Japan) containing 8% foetal bovine serum (FBS, 1370978, GIBCO, Gaithersburg, MD, USA).

extract_protocol: Total RNA was extracted using the miRNeasy Mini Kit (217004, Qiagen, Valencia, CA, USA).

tag: cell line

value: parental QRsP-11 fibrosarcoma cell line

value: Liver metastatic LV12 subline


title: B. megaterium 3 hours 1

description: Replication 1 out of 4, 3 hours post injection of B. megaterium

value: 3 hours post injection of B. megaterium


title: B. megaterium 3 hours 4

description: Replication 4 out of 4, 3 hours post injection of B. megaterium


title: B. megaterium 12 hours 4

description: Replication 4 out of 4, 12 hours post injection of B. megaterium


title: B. megaterium 12 hours 3

description: Replication 3 out of 4, 12 hours post injection of B. megaterium


title: B. megaterium 12 hours 2

description: Replication 2 out of 4, 12 hours post injection of B. megaterium


title: B. megaterium 6 hours 2

description: Replication 2 out of 4, 6 hours post injection of B. megaterium

value: 6 hours post injection of B. megaterium


title: B. megaterium 6 hours 1

description: Replication 1 out of 4, 6 hours post injection of B. megaterium

value: female


title: E. coli 12 hours 3

description: Replication 3 out of 4, 12 hours post injection of E. coli

source_name: E. coli injected, whole organism

value: 12 hours post injection of E. coli


title: Non-injected control 1

description: Replication 1 out of 2


title: B. megaterium 3 hours 3

description: Replication 3 out of 4, 3 hours post injection of B. megaterium


title: B. megaterium 6 hours 3

description: Replication 3 out of 4, 6 hours post injection of B. megaterium


title: E. coli 12 hours 2

description: Replication 2 out of 4, 12 hours post injection of E. coli


title: B. megaterium 3 hours 2

description: Replication 2 out of 4, 3 hours post injection of B. megaterium


title: E. coli 12 hours 4

description: Replication 4 out of 4, 12 hours post injection of E. coli


title: E. coli 6 hours 3

description: Replication 3 out of 4, 6 hours post injection of E. coli

value: 6 hours post injection of E. coli


title: E. coli 6 hours 4

description: Replication 4 out of 4, 6 hours post injection of E. coli


title: E. coli 12 hours 1

description: Replication 1 out of 4, 12 hours post injection of E. coli


title: E. coli 3 hours 4

description: Replication 4 out of 4, 3 hours post injection of E. coli

value: 3 hours post injection of E. coli


title: E. coli 6 hours 2

description: Replication 2 out of 4, 6 hours post injection of E. coli


title: E. coli 6 hours 1

description: Replication 1 out of 4, 6 hours post injection of E. coli


title: E. coli 3 hours 2

description: Replication 2 out of 4, 3 hours post injection of E. coli


title: E. coli 3 hours 3

description: Replication 3 out of 4, 3 hours post injection of E. coli


title: MV4-11_Chb-50_rep1

status: Public on Mar 26 2017

city: Kyoto

first: Junichi

last: Taniguchi

address: Kitashirakawa-Oiwakecho, Sakyo-Ku

department: Department of Chemistry, Graduate School of Science

institute: Kyoto University

description: Gene expression data from Chb-50-treated cells

hyb_protocol: Following fragmentation, 3.5 ug of cDNA were hybridized for 20 hr at 48°C on Human Gene ST Array Strip. Strip was washed and stained in the Fluidics Station of GeneAtlas System.

scan_protocol: Strip was scanned using the Imaging Station.

data_processing: The data were analyzed with Expression Console 1.3.1 and Transcriptome Analysis Console 1.0 using RMA.

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (WT PLUS Reagent Kit User Manual, 2013, Affymetrix).

growth_protocol: MV4-11 from ATCC was cultured in RPMI1640 medium supplemented with 10% FBS and 1% PS at 37°C, 5% CO2

extract_protocol: RNA was extracted using the RNeasy mini kit (Qiagen, Valencia, CA) following the manufacturer's recommendations. RNA was quantified using a Nanodrop ND1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: For knockdown study (sample 1-8), cells were transduced with each shRNA and subsequently incubated with 3 µM of doxycycline for 24 hours. For PIP treatment study (sample 9-11), cells were treated with 1 µM of Chb-M', Chb-50 or with DMSO for 6 hours.

tag: cell line description

value: Acute Myeloid Leukemia (AML) cell line

value: 6 hours


title: MV4-11_shRx1+shRx2+shRx3_rep1

description: Gene expression data from RUNX1/RUNX2/RUNX3 triple knockdown cells

value: RUNX1 shRNA and RUNX2 shRNA and RUNX3 shRNA

value: 24 hours


title: E. coli 3 hours 1

description: Replication 1 out of 4, 3 hours post injection of E. coli

value: adult


title: MV4-11_shRx1+shRx2_rep1

description: Gene expression data from RUNX1/RUNX2 double knockdown cells

value: RUNX1 shRNA and RUNX2 shRNA


title: MV4-11_shRx2+shRx3_rep1

description: Gene expression data from RUNX2/RUNX3 double knockdown cells

value: RUNX2 shRNA and RUNX3 shRNA


title: MV4-11_shRx3_rep1

description: Gene expression data from RUNX3 knockdown cells

value: RUNX3 shRNA


title: MV4-11_shRx1_rep1

description: Gene expression data from RUNX1 knockdown cells

value: RUNX1 shRNA


title: MV4-11_DMSO_rep1

description: Gene expression data from DMSO-treated cells (control)

value: control treatment (DMSO only)


title: MV4-11_shRx2_rep1

description: Gene expression data from RUNX2 knockdown cells

value: RUNX2 shRNA


title: MV4-11_shRx1+shRx3_rep1

description: Gene expression data from RUNX1/RUNX3 double knockdown cells

value: RUNX1 shRNA and RUNX3 shRNA


title: MV4-11_Chb-Mp_rep1

description: Gene expression data from Chb-M'-treated cells

value: Chb-M' (em prime)


title: MCF7_Four mixture_rep2

city: Shanghai

first: chao

last: lv

state: None Selected

address: No. 325, Guohe Rd

department: School of Pharmacy

institute: Second Military Medical University

description: Gene expression data from human breast cancer cell line MCF7

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US)

data_processing: Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

source_name: MCF7_Four mixture(Tanshinone IIA:Salvianic acid A sodium:Protocatechuic aldehyde:Salvianolic acid B=1:1:1:1）_10μM_rep2

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: The MCF7 cells were cultured in MEM/EBSS supplemented with 10% fetal bovine serum, 1mmol/L sodium pyruvate, 0.1mmol/L MEM non-essential amino acids, 100 unit/mL penicillin, and 100 mg/mL streptomycin in a incubator containing 5% CO2 at 37℃.

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 integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: The MCF7 cells were treated by 102 molecules at 10μM or 1μM, DMSO, and 10μM mixture of four compounds (1:1:1:1) for 12h.

tag: group

value: treatment

tag: perturbagen

value: Four mixture(Tanshinone IIA:Salvianic acid A sodium:Protocatechuic aldehyde:Salvianolic acid B=1:1:1:1)

value: breast cancer cell line MCF7

tag: duration


title: MCF7_Narciclasine_10μM_rep1

source_name: Human breast cancer cell line MCF7

value: Narciclasine


title: MCF7_Sanguinarine_1μM_rep2

value: Sanguinarine


title: MCF7_Chelerythrine_1μM_rep2

value: Chelerythrine


title: MCF7_Santonin_10μM_rep2

value: Santonin


title: MCF7_Santonin_10μM_rep1


title: MCF7_Chelerythrine_1μM_rep1


title: MCF7_Sanguinarine_1μM_rep1


title: MCF7_Four mixture_rep1

source_name: MCF7_Four mixture(Tanshinone IIA:Salvianic acid A sodium:Protocatechuic aldehyde:Salvianolic acid B=1:1:1:1）_10μM_rep1


title: MCF7_vehicle(DMSO)_rep2 [BH14340-3_D]

value: control

value: DMSO


title: MCF7_Ainsliadimer A_1μM_rep1

value: Ainsliadimer A


title: MCF7_Bruceine D_10μM_rep2

value: Bruceine D


title: MCF7_Narciclasine_10μM_rep2


title: WT Bgh 12h, replicate 1

description: Gene expression after 12h in Bgh-treated WT

source_name: WT Bgh 12h, replicate 1

value: pool of 5 whole second leaves

tag: plant line

value: Golden Promise


title: MV4-11_shLuc_rep1

description: Gene expression data from knockdown control cells (sh Luc)

value: Acute Myeloid Leukemia (AML) cell line

value: control shRNA (sh Luciferase)

value: 24 hours


title: MCF7_Bruceine D_10μM_rep1


title: MCF7_(+)2-(1-hydroxyl-4-oxocyclohexyl) ethyl caffeate_10μM_rep2


title: MCF7_Dioscin_1μM_rep1

value: Dioscin


title: MCF7_Dioscin_1μM_rep2

value: treatment


title: MCF7_Oridonin_1μM_rep1

value: Oridonin


title: MCF7_Macrozamin_10μM_rep2

value: Macrozamin

value: breast cancer cell line MCF7


title: MCF7_Oridonin_1μM_rep2


title: MCF7_6-gingerol_10μM_rep2


title: MCF7_Macrozamin_10μM_rep1


title: MCF7_Sennoside A_10μM_rep2

value: Sennoside A


title: MCF7_(+)2-(1-hydroxyl-4-oxocyclohexyl) ethyl caffeate_10μM_rep1


title: MCF7_vehicle(DMSO)_rep1 [BH14340-3_D]


title: MCF7_Ainsliadimer A_1μM_rep2


title: MCF7_Glycyrrhizic acid_10μM_rep2

value: Glycyrrhizic acid


title: MCF7_Hypaconitine_10μM_rep2

value: Hypaconitine


title: MCF7_6-gingerol_10μM_rep1


title: MCF7_L-scopolamine_10μM_rep1

value: L-scopolamine


title: MCF7_Tetrahydropalmatine_10μM_rep1

value: Tetrahydropalmatine


title: MCF7_Benzoylaconitine_10μM_rep1

value: Benzoylaconitine


title: MCF7_Gentiopicroside_10μM_rep1

value: Gentiopicroside


title: MCF7_Sennoside A_10μM_rep1


title: MCF7_L-scopolamine_10μM_rep2


title: MCF7_Benzoylaconitine_10μM_rep2


title: MCF7_Gentiopicroside_10μM_rep2


title: MCF7_Tetrahydropalmatine_10μM_rep2


title: B. megaterium 6 hours 4

description: Replication 4 out of 4, 6 hours post injection of B. megaterium

value: adult

value: female

value: 6 hours post injection of B. megaterium

value: LB buffer


title: MCF7_Benzoylhypaconitine_10μM_rep2

value: Benzoylhypaconitine


title: MCF7_Hypaconitine_10μM_rep1


title: MCF7_Glycyrrhizic acid_10μM_rep1


title: MCF7_Notoginsenoside R1_10μM_rep1

value: Notoginsenoside R1


title: MCF7_Notoginsenoside R1_10μM_rep2

value: treatment


title: MCF7_Liquiritin_10μM_rep1

value: Liquiritin


title: MCF7_Benzoylhypaconitine_10μM_rep1


title: MCF7_Gallic acid_10μM_rep2

value: Gallic acid


title: MCF7_Gallic acid_10μM_rep1

value: breast cancer cell line MCF7


title: MCF7_Liquiritin_10μM_rep2


title: MCF7_Magnolol_10μM_rep2

value: Magnolol


title: MCF7_Geniposide_10μM_rep1

value: Geniposide


title: MCF7_Geniposide_10μM_rep2


title: MCF7_Strychnine_10μM_rep2

value: Strychnine


title: MCF7_Honokiol_10μM_rep1

value: Honokiol


title: MCF7_Magnolol_10μM_rep1


title: MCF7_β-ecdysterone_10μM_rep2

value: β-ecdysterone


title: MCF7_Strychnine_10μM_rep1


title: MCF7_β-ecdysterone_10μM_rep1


title: MCF7_Curculigoside_10μM_rep1

value: Curculigoside


title: MCF7_Curculigoside_10μM_rep2


title: MCF7_Phillyrin_10μM_rep1

value: Phillyrin


title: MCF7_Phillyrin_10μM_rep2


title: MCF7_Scutellarein_10μM_rep2

value: Scutellarein


title: MCF7_Scutellarein_10μM_rep1


title: MCF7_Silybin_10μM_rep2

value: Silybin


title: MCF7_Oleanic acid_10μM_rep2

value: Oleanic acid


title: MCF7_Osthole_10μM_rep1

value: Osthole


title: MCF7_Osthole_10μM_rep2


title: MCF7_Silybin_10μM_rep1


title: MCF7_Matrine_10μM_rep2

value: Matrine


title: MCF7_Schizandrin_10μM_rep2

value: Schizandrin


title: MCF7_Oleanic acid_10μM_rep1

value: treatment


title: MCF7_Matrine_10μM_rep1


title: MCF7_Schisantherin A_10μM_rep2

value: Schisantherin A


title: MCF7_Oxymatrine_10μM_rep1

value: Oxymatrine


title: MCF7_Salidroside_10μM_rep2

value: Salidroside

value: breast cancer cell line MCF7


title: MCF7_Schisantherin A_10μM_rep1


title: MCF7_Honokiol_10μM_rep2


title: MCF7_Daidzin_10μM_rep1

value: Daidzin


title: MCF7_Daidzin_10μM_rep2


title: MCF7_Oxymatrine_10μM_rep2


title: MCF7_vehicle(DMSO)_rep2

value: control

value: DMSO


title: MCF7_Salidroside_10μM_rep1


title: MCF7_Schizandrin_10μM_rep1


title: MCF7_Cinobufotalin_1μM_rep2

value: Cinobufotalin


title: MCF7_Arenobufagin_1μM_rep1

value: Arenobufagin


title: MCF7_Telocinobufagin_1μM_rep1

value: Telocinobufagin


title: MCF7_Arenobufagin_1μM_rep2


title: MCF7_Telocinobufagin_1μM_rep2


title: MCF7_Bufotaline_1μM_rep1

value: Bufotaline


title: MCF7_vehicle(DMSO)_rep1


title: MCF7_Gamabufatalin_1μM_rep2

value: Gamabufatalin


title: MCF7_Gamabufatalin_1μM_rep1


title: MCF7_Bufalin_1μM_rep2

value: Bufalin


title: MCF7_Alantolactone_10μM_rep2

value: Alantolactone


title: MCF7_Resibufogenin_1μM_rep1

value: Resibufogenin


title: MCF7_Resibufogenin_1μM_rep2


title: MCF7_Alantolactone_10μM_rep1


title: MCF7_Cinobufotalin_1μM_rep1


title: MCF7_Bufotaline_1μM_rep2


title: MCF7_Salvianic acid A sodium_10μM_rep2

value: Salvianic acid A sodium


title: MCF7_1β-hydroxyalantolactone_10μM_rep1

value: treatment


title: MCF7_Salvianic acid A sodium_10μM_rep1


title: MCF7_Bufalin_1μM_rep1


title: MCF7_Cinobufogenin_1μM_rep2

value: Cinobufogenin


title: MCF7_Cinobufogenin_1μM_rep1


title: MCF7_Bacopaside I_10μM_rep2

value: Bacopaside I


title: MCF7_Britanin_10μM_rep2

value: Britanin


title: MCF7_Bacopaside I_10μM_rep1

value: breast cancer cell line MCF7


title: MCF7_Britanin_10μM_rep1


title: MCF7_Japonicone A_10μM_rep2

value: Japonicone A


title: MCF7_Isoalantolactone_10μM_rep1

value: Isoalantolactone


title: MCF7_Japonicone A_10μM_rep1


title: MCF7_Isoalantolactone_10μM_rep2


title: MCF7_Protocatechuic aldehyde_10μM_rep1

value: Protocatechuic aldehyde


title: MCF7_1β-hydroxyalantolactone_10μM_rep2


title: MCF7_Ginsenoside Rd_10μM_rep1

value: Ginsenoside Rd


title: MCF7_Ginsenoside Re_10μM_rep1

value: Ginsenoside Re


title: MCF7_Protocatechuic aldehyde_10μM_rep2


title: #1_KD_ES_11_(miRNA-3_0)

city: Cologne

first: Agapios

last: Sachinidis

state: NRW

address: Robert-Kochstr. 39

department: Institute of Neurophysiology

institute: University of Cologne

hyb_protocol: After incubation, the arrays were washed and stained in the fluidics station 450 using fluidics script FS450_0002

scan_protocol: Arrays were scanned using an Affymetrix Gene-Chip Scanner-3000-7G

data_processing: The quality control (QC) matrices were confirmed with expression console software (Affymertix, USA). QC passed CEL files were further analyzed using the Bioconductor package limma . All CEL files were RMA background corrected, quantile normalized and all probe sets were summarized using median polish algorithm.

source_name: KD ESCs first chip

label_protocol: 700 ng total RNA was used as the starting material, and the Affymetrix FlashTag Biotin HSR RNA Labelling kit was used for miRNA ligation (Affymetrix, United Kingdom) according to the manufacturer’s instructions. The labeled samples were  hybridized to the Affymetrix miRNA 3.0 arrays for 16 h at 48 °C in an Affymetrix hybridization oven 645

extract_protocol: WT ESCs, SCR ESCS and KD ESCs were differentiated applying the hanging drop protocol for 4-, 8-, 12- and 16-days (Wagh et al. Fam40b is required for lineage commitment of murine embryonic stem cells. Cell Death Dis 2014, 5: e1320). Total RNA from was isolated using Trizol reagent (Invitrogen) and purified with the RNeasy Plus kit from Qiagen

tag: strain

value: male

tag: genotype/variation

value: Strip2 silenced (KD)

tag: cell type

value: embryonic stem cells (ESCs)


title: MCF7_Nitidine chloride_10μM_rep2

value: Nitidine chloride


title: MCF7_Nitidine chloride_10μM_rep1


title: #1_KD_d4_12_(miRNA-3_0)

source_name: KD4-days EBs first  chip

tag: gender

value: embryoid bodies (EBs)


title: #1_KD_d12_14_(miRNA-3_0)

source_name: KD12-days EBs first  chip


title: #1_KD_d16_15_(miRNA-3_0)

source_name: KD16-days EBs first  chip


title: MCF7_Ginsenoside Rd_10μM_rep2


title: MCF7_Ginsenoside Rb2_10μM_rep2

value: Ginsenoside Rb2


title: #1_Scr_d16_10_(miRNA-3_0)

source_name: SCR 16-days EBs first  chip

value: scrambled control (SCR)


title: #1_Scr_ES_6_(miRNA-3_0)

source_name: SCR ESCs first chip


title: #1_KD_d8_13_(miRNA-3_0)

source_name: KD 8-days EBs first  chip


title: #1_Scr_d4_7_(miRNA-3_0)

source_name: SCR 4-days EBs first  chip


title: MCF7_Ginsenoside Rc_10μM_rep1

value: treatment

value: Ginsenoside Rc


title: #1_Scr_d8_8_(miRNA-3_0)

source_name: SCR 8-days EBs first  chip


title: MCF7_Ginsenoside Rc_10μM_rep2


title: #1_WT_d4-2_(miRNA-3_0)

source_name: WT 4-days EBs first chip

value: wild type


title: MCF7_Ginsenoside Rb2_10μM_rep1


title: #1_Scr_d12_9_(miRNA-3_0)

source_name: SCR 12-days EBs first  chip


title: #1_WT_d12_4_(miRNA-3_0)

source_name: WT 12-days EBs first chip


title: #1_WT_d8_3_(miRNA-3_0)

source_name: WT 8-days EBs first chip


title: #1_WT_d16_5_(miRNA-3_0)

source_name: WT 16-days EBs first chip


title: MCF7_Ginsenoside Rb3_10μM_rep1

source_name: Human breast cancer cell line MCF7

value: Ginsenoside Rb3


title: MCF7_Benzyl benzoate_10μM_rep2

value: Benzyl benzoate

value: breast cancer cell line MCF7


title: MCF7_Borneol_10μM_rep2

value: Borneol


title: #3KD d8_13_(miRNA-3_0)

description: 3KD d8_13_(miRNA-3_0)

source_name: KD 8-days EBs third chip


title: MCF7_Ginsenoside Re_10μM_rep2


title: #3KD d4_12_(miRNA-3_0)

description: 3KD d4_12_(miRNA-3_0)

source_name: KD 4-days EBs third chip


title: #3KD d12_14_(miRNA-3_0)

description: 3KD d12_14_(miRNA-3_0)

source_name: KD 12-days EBs third chip


title: MCF7_Borneol_10μM_rep1


title: MCF7_Ginsenoside Rb3_10μM_rep2


title: MCF7_Isoborneol_10μM_rep2

value: Isoborneol


title: #3KD d16_15_(miRNA-3_0)

description: 3KD d16_15_(miRNA-3_0)

source_name: KD 16-days EBs third chip


title: MCF7_Benzyl benzoate_10μM_rep1


title: MCF7_Muscone_10μM_rep2

value: Muscone


title: MCF7_Muscone_10μM_rep1


title: #3KD ES_11_(miRNA-3_0)

description: 3KD ES_11_(miRNA-3_0)

source_name: KD ESCs third chip


title: MCF7_Cinnamaldehyde_10μM_rep2

value: Cinnamaldehyde


title: MCF7_Cinnamaldehyde_10μM_rep1


title: #3Scr d4_7_(miRNA-3_0)

description: 3Scr d4_7_(miRNA-3_0)

source_name: SCR 4-days EBs third chip

value: male


title: MCF7_Cinnamic acid_10μM_rep1

value: Cinnamic acid


title: #3Scr d8_8_(miRNA-3_0)

description: 3Scr d8_8_(miRNA-3_0)

source_name: SCR 8-days EBs third chip


title: #3Scr d12_9_(miRNA-3_0)

description: 3Scr d12_9_(miRNA-3_0)

source_name: SCR 12-days EBs third  chip


title: MCF7_Cholic acid_10μM_rep2

value: Cholic acid


title: MCF7_Cinnamic acid_10μM_rep2


title: MCF7_Cholic acid_10μM_rep1


title: #3Scr ES_6_(miRNA-3_0)

description: 3Scr ES_6_(miRNA-3_0)

source_name: SCR ESCs third chip

value: embryonic stem cells (ESCs)


title: #3Scr d16_10_(miRNA-3_0)

description: 3Scr d16_10_(miRNA-3_0)

source_name: SCR 16-days EBs third  chip

value: embryoid bodies (EBs)


title: #3Wt ES_1_(miRNA-3_0)

description: 3Wt ES_1_(miRNA-3_0)

source_name: WT ESCs third chip


title: #3Wt d16_5_(miRNA-3_0)

description: 3Wt d16_5_(miRNA-3_0)

source_name: WT 16-days EBs third chip


title: #3Wt d4_2_(miRNA-3_0)

description: 3Wt d4_2_(miRNA-3_0)

source_name: WT 4-days EBs third chip


title: #3Wt d8_3_(miRNA-3_0)

description: 3Wt d8_3_(miRNA-3_0)

source_name: WT 8-days EBs third chip


title: KD_d12_#2_14_(miRNA-3_0)

source_name: KD 8-days EBs second chip

value: Strip2 silenced (KD)


title: MCF7_Chenodeoxycholic acid_10μM_rep2

value: Chenodeoxycholic acid


title: MCF7_Ursodeoxycholic acid_10μM_rep2

value: treatment

value: Ursodeoxycholic acid


title: KD_d8_#2_13_(miRNA-3_0)

source_name: KD 12-days EBs second chip


title: MCF7_Chenodeoxycholic acid_10μM_rep1

source_name: Human breast cancer cell line MCF7


title: KD_d4_#2_12_(miRNA-3_0)

source_name: KD 4-days EBs second chip


title: MCF7_Deoxycholic acid_10μM_rep1

value: Deoxycholic acid


title: MCF7_Ursodeoxycholic acid_10μM_rep1


title: MCF7_Hyodeoxycholic acid_10μM_rep2

value: Hyodeoxycholic acid


title: MCF7_Hyodeoxycholic acid_10μM_rep1


title: MCF7_Deoxycholic acid_10μM_rep2


title: MCF7_Resveratrol_10μM_rep1

value: Resveratrol


title: MCF7_vehicle(DMSO)_rep1 [BH13248-3]

value: control

value: DMSO

value: breast cancer cell line MCF7


title: KD_d16_#2_15_(miRNA-3_0)

source_name: KD 16-days EBs second chip


title: MCF7_Resveratrol_10μM_rep2


title: #3Wt d12_4_(miRNA-3_0)

description: 3Wt d12_4_(miRNA-3_0)

source_name: WT 12-days EBs third chip

value: wild type


title: MCF7_Artemisinin_10μM_rep2

value: Artemisinin


title: MCF7_Isoborneol_10μM_rep1

value: Isoborneol


title: KD_ES_#2_11_(miRNA-3_0)

source_name: KD ESCs second chip

value: male


title: Scr_d4_#2_7_(miRNA-3_0)

source_name: SCR 4-days EBs second chip

value: scrambled control (SCR)


title: MCF7_vehicle(DMSO)_rep2 [BH13248-3]


title: MCF7_Artemisinin_10μM_rep1


title: Scr_d8_#2_8_(miRNA-3_0)

source_name: SCR 8-days EBs second chip


title: Scr_d16_#2_10_(miRNA-3_0)

source_name: SCR 16-days EBs second chip


title: MCF7_Imperatorin_10μM_rep1

value: Imperatorin


title: Scr_ES_#2_6_(miRNA-3_0)

source_name: SCR ESCs second chip

value: embryonic stem cells (ESCs)


title: MCF7_Acteoside_10μM_rep2

value: Acteoside


title: MCF7_Acteoside_10μM_rep1


title: WT_d4_#2_2_(miRNA-3_0)

source_name: WT 4-days EBs second chip

value: embryoid bodies (EBs)


title: Scr_d12_#2_9_(miRNA-3_0)

source_name: SCR 12-days EBs second chip


title: WT_d12_#2_4_(miRNA-3_0)

source_name: WT 12-days EBs second chip


title: WT_d8_#2_3_(miRNA-3_0)

source_name: WT 8-days EBs second chip


title: WT_d16_#2_5_(miRNA-3_0)

source_name: WT 16-days EBs second chip


title: Wt_Es_#1_1Wdh_(miRNA-3_0)

source_name: WT ESCs first chip


title: MCF7_Imperatorin_10μM_rep2

value: treatment


title: WT_ES_#2_1_(miRNA-3_0)

source_name: WT ESCs second chip


title: MCF7_Gastrodin_10μM_rep1

value: Gastrodin


title: MCF7_Gastrodin_10μM_rep2


title: MCF7_Ferulic acid_10μM_rep2

value: Ferulic acid


title: MCF7_Saikosaponin D_10μM_rep1

value: Saikosaponin D


title: MCF7_Ferulic acid_10μM_rep1


title: KD_D8_1

hyb_protocol: 12.5µg of fragmented aRNA was hybridized to the Mouse Genome 430 2.0 microarrays in the Genechip Hybridisation Oven-645 (Affymetrix, United Kingdom) for 16 h at 45º C.

scan_protocol: Arrays were washed and stained with phycoerythrin with Fluidics Station 450 and scanned using the Gene-Chip Scanner 3000 7G (Affymetrix, United Kingdom) according to the manufacturer's instructions

data_processing: The quality control (QC) matrices were confirmed with expression console software (Affymertix, USA) and Partek genomics suite version 6.6 (Partek Inc.St.Louis,USA). QC passed CEL files were further analyzed using Partek genomics suite version 6.6. All CEL files were RMA background corrected, quantile normalized and all probe sets were summarized using median polish algorithm.

source_name: KD 8-days EBs first chip

label_protocol: 100ng total RNA was used for aRNA amplification with GeneChip® 3’ IVT Express Kit (Affymetrix, United Kingdom) according to the manufacturer’s instructions. After 16 h of biotinylated in vitro transcription, aRNA was purified using magnetic beads and 15µg of purified aRNA was fragmented with fragmentation buffer

extract_protocol: Total RNA from the was isolated using Trizol reagent (Invitrogen) and purified with the RNeasy Plus kit from Qiagen

treatment_protocol: WT ESCs, SCR ESCS and KD ESCs were differentiated applying the hanging drop protocol for 4-, 8-, 12- and 16-days (Wagh et al. Fam40b is required for lineage commitment of murine embryonic stem cells. Cell Death Dis 2014, 5: e1320). Total RNA from the undifferentiated and 4-, 8-, 12- and 16-day EBs was isolated and gene expression was analyzed by the Affymetrix (Mouse430 2.0) chip.

value: Strip2 silenced (KD)


title: MCF7_Salvianolic acid B_10μM_rep1

source_name: Human breast cancer cell line MCF7

value: Salvianolic acid B


title: MCF7_Salvianolic acid B_10μM_rep2


title: MCF7_Chlorogenic acid_10μM_rep1

value: Chlorogenic acid


title: MCF7_Saikosaponin A_10μM_rep2

value: Saikosaponin A

value: breast cancer cell line MCF7


title: KD_D4_2

source_name: KD 4-days EBs second chip


title: MCF7_Saikosaponin D_10μM_rep2


title: KD_D8_2

source_name: KD 8-days EBs second chip


title: MCF7_Saikosaponin A_10μM_rep1


title: KD_D4_1

source_name: KD 4-days EBs first chip


title: MCF7_Chlorogenic acid_10μM_rep2


title: MCF7_Astragaloside IV_10μM_rep2

value: Astragaloside IV


title: MCF7_Astragaloside IV_10μM_rep1


title: KD_D12_2

source_name: KD 12-days EBs second chip


title: KD_D16_1

source_name: KD 16-days EBs first  chip


title: MCF7_Ginsenoside Rb1_10μM_rep2

value: Ginsenoside Rb1


title: MCF7_Ginsenoside Rb1_10μM_rep1


title: KD_D4_3

source_name: KD 4-days EBs third chip

value: male


title: MCF7_Ginsenoside Rg1_10μM_rep2

value: Ginsenoside Rg1


title: KD-ES_2

source_name: KD ESCs second chip


title: KD-ES_1

source_name: KD ESCs first chip


title: MCF7_Ginsenoside Rg1_10μM_rep1


title: MCF7_Emodin_10μM_rep2

value: Emodin


title: KD_D12_1

source_name: KD 12-days EBs first chip


title: KD_D8_3

source_name: KD 8-days EBs third chip


title: MCF7_Emodin_10μM_rep1


title: MCF7_Tanshinone IIA_10μM_rep2

value: Tanshinone IIA


title: MCF7_Lobetyolin_10μM_rep1

value: Lobetyolin


title: SCR_D8_5

source_name: SCR 8-days EBs second chip

value: scrambled control (SCR)

value: embryoid bodies (EBs)


title: KD_D16_3

source_name: KD 16-days EBs third chip


title: MCF7_Tanshinone IIA_10μM_rep1

value: treatment


title: KD-ES_3

source_name: KD ESCs third chip

value: embryonic stem cells (ESCs)


title: MCF7_Lobetyolin_10μM_rep2


title: MCF7_Paeoniflorin_10μM_rep1

value: Paeoniflorin


title: SCR_D8_4

source_name: SCR 8-days EBs first chip


title: KD_D16_2

source_name: KD 16-days EBs second chip

value: Strip2 silenced (KD)


title: MCF7_Paeoniflorin_10μM_rep2


title: KD_D12_3

source_name: KD 12-days EBs third chip


title: SCR_D4_5

source_name: SCR 4-days EBs second chip


title: SCR_D4_4

source_name: SCR 4-days EBs first chip


title: SCR_D12_5

source_name: SCR 12-days EBs second chip


title: MCF7_Andrographolide_10μM_rep1

source_name: Human breast cancer cell line MCF7

value: Andrographolide


title: MCF7_Andrographolide_10μM_rep2


title: SCR_D16_4

source_name: SCR 16-days EBs first  chip


title: SCR_D4_6

source_name: SCR 4-days EBs third chip


title: SCR_ES_4

source_name: SCR ESCs first chip


title: MCF7_Ginkgolide B_10μM_rep1

value: Ginkgolide B


title: SCR_ES_5

source_name: SCR ESCs second chip


title: SCR_D16_5

source_name: SCR 16-days EBs second chip


title: MCF7_Berberine hydrochloride_10μM_rep2

value: Berberine hydrochloride


title: SCR_D8_6

source_name: SCR 8-days EBs third chip


title: MCF7_Berberine hydrochloride_10μM_rep1

value: breast cancer cell line MCF7


title: MCF7_Ginkgolide B_10μM_rep2


title: MCF7_Bilobalide_10μM_rep2

value: Bilobalide


title: SCR_D12_4

source_name: SCR 12-days EBs first chip


title: SCR_D12_6

source_name: SCR 12-days EBs third chip


title: SCR_D16_6

source_name: SCR 16-days EBs third chip


title: MCF7_Ephedrine hydrochloride_10μM_rep2

value: Ephedrine hydrochloride


title: WT_D8_2

source_name: WT 8-days EBs second chip

value: male

value: wild type


title: MCF7_Ephedrine hydrochloride_10μM_rep1


title: MCF7_Aconitine_10μM_rep1

value: Aconitine


title: SCR_ES_6

source_name: SCR ESCs third chip


title: WT_D4_2

source_name: WT 4-days EBs second chip


title: WT_D8_1

source_name: WT 8-days EBs first chip


title: WT_D4_1

source_name: WT 4-days EBs first chip


title: MCF7_Bilobalide_10μM_rep1


title: WT_D12_2

source_name: WT 12-days EBs second chip


title: MCF7_Stachydrine hydrochloride_10μM_rep2

value: Stachydrine hydrochloride


title: WT_D12_1

source_name: WT 12-days EBs first chip


title: MCF7_Puerarin_10μM_rep1

source_name: Human breast cancer cell line MCF7

value: Puerarin


title: MCF7_Stachydrine hydrochloride_10μM_rep1


title: MCF7_Hesperidin_10μM_rep2

value: Hesperidin


title: MCF7_Puerarin_10μM_rep2


title: WT_D16_2

source_name: WT 16-days EBs second chip

value: embryoid bodies (EBs)


title: WT_ES_2

source_name: WT ESCs second chip


title: MCF7_Hyperoside_10μM_rep2

value: treatment

value: Hyperoside


title: WT_D16_3

source_name: WT 16-days EBs third chip


title: WT_ES_1

source_name: WT ESCs first chip

value: embryonic stem cells (ESCs)


title: MCF7_Hyperoside_10μM_rep1


title: WT_D16_1

source_name: WT 16-days EBs first  chip


title: MCF7_Anhydroicaritin_10μM_rep2

value: Anhydroicaritin


title: WT_D4_3

source_name: WT 4-days EBs third chip


title: WT_D12_3

source_name: WT 12-days EBs third chip


title: 501mel,204-mimic-repl1

city: Pisa

first: Romina

last: D'Aurizio

state: PI

address: via Moruzzi 1

department: IIT

country: Italy

institute: CNR

description:
9967501162_C
204mimic.1
501 Mel cells transfected with 204-mimic.

hyb_protocol: According to the manufacturer's instructions.

scan_protocol: The HumanHT-12 v4 array (Illumina) was scanned on a BeadScan station.

data_processing: Raw data were normalized using the 'lumi' package (v 2.10), by applying variance stabilizing transformation followed by robust spline normalization. Probes with detected expression above background (detection p-value <0.01) in all samples were retained. In order to reduce the number of false positives, the unannotated probes were excluded after retrieving the nuID of each of them from the lumiHumanAll annotation database (v 1.18). 'annotate' package (v 1.36).

source_name: 501 Mel cells, 204-mimic

growth_protocol: 1.5x10^06 501 Mel cells were seeded in 10cm dishes.

extract_protocol: RNA was extracted using QIAzol reagent (Qiagen), following the manufacturer's instructions.

treatment_protocol: After 24h, 501 Mel cells were transfected with si-CT, 204-mimic or 211-mimic (60nM) using lipofectamine 2000 (Thermo Scientific).

value: melanoma cell line

tag: sirna


title: 501mel,211-mimic,repl2

description:
9967501162_F
211mimic.2
501 Mel cells transfected with 211-mimic.

source_name: 501 Mel cells, 211-mimic

label_protocol: According to the manufacturer's instructions.


title: WT_ES_3

source_name: WT ESCs third chip


title: MCF7_Hydroxysafflor yellow A_10μM_rep1

value: Hydroxysafflor yellow A


title: WT_D8_3

source_name: WT 8-days EBs third chip


title: 501mel,211-mimic,repl1

description:
9967501162_E
211mimic.1
501 Mel cells transfected with 211-mimic.


title: MCF7_Glycyrrhizic acid_10μM_rep2.1-2

value: Glycyrrhizic acid


title: MCF7_Anhydroicaritin_10μM_rep1

value: breast cancer cell line MCF7


title: 501mel,siCT,repl2

description:
9967501162_B
sirnaCT.2
501 Mel cells transfected with siCT.

source_name: 501 Mel cells, siCT

value: siCT


title: MCF7_Hydroxysafflor yellow A_10μM_rep2


title: 501mel,204-mimic,repl2

description:
9967501162_D
204mimic.2
501 Mel cells transfected with 204-mimic.


title: BT3

status: Public on Mar 25 2017

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

state: TX

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

description: Gene expression in the primary undifferentiated carcinoma thyroid tissues of a 78y old female

hyb_protocol: 825 ng from each of the Cy3 or Cy5 labeled samples from two pups were mixed with Gene Expression Hybridization Kit (Agilent Cat # 5188-5242) and the final volume adjusted to 100 µL. The solution was slowly dispensed onto the gasket (Agilent Cat# G2534-60011) placed in the (Agilent) hybridization chamber, the (Agilent) rat (4x44k 60 mer features, 4 microarrays per slide) chip with the active face downward was arranged over the gasket and the “sandwich” firmly closed. The samples were hybridized to the array at 65ºC for 17 h in an (Agilent) oven while vertically rotating (10 rot/min) to wet the gasket and asses the mobility of the bubbles.

scan_protocol: The hybridized chip was washed at room temperature using the Gene Expression Wash Pack (Agilent, Cat# 5188-5327) and Stabilization and drying solution (Agilent, Cat# 5185-5979) then immediately scanned with an Agilent G2565CA microarray scanner system with SureScan high resolution technology at 5µm pixel size and 20-bit scan mode.

data_processing: The resulted Tagged Image File Format (tiffs) obtained through use of (Agilent) Scan Control Software 8.3 were analyzed with (Agilent) Feature Extraction 11.1 software. Data were normalized and analyzed with in-house developed algorithms described in Iacobas et al., Mol Genet Genomics 2012.

source_name: Stably transfected with TMEM194A 8505C cells purchased from DSMZ in Braunschweig, Germany Rep 3

label_protocol: Low Input Quick Amp labeling Kit two-color (Agilent, Cat # 5190-2306) that contains T7 RNA polymerase was used to simultaneously amplify total RNA and the positive controls (RNA Spike in Kit for Two Color, Agilent Cat # 5188-5279), and incorporate cyanine 3 (Cy3) or cyanine 5 (Cy5)-labeled CTP.

growth_protocol: BCPAP cells protocol described in: Fabien N. Fusco A. Santoro M. Barbier Y. Dubois PM. Paulin C. (1994) Description of a human papillary thyroid-carcinoma cell-line—morphologic study and expression of tumoral markers. Cancer. 73:2206–2212. 8505C cells protocol described in: Ito T, Seyama T, Hayashi Y, Hayashi T, Dohi K, Mizuno T, Iwamoto K, Tsuyama N, Nakamura N, Akiyama M. (1994). Establishment of 2 human thyroid-carcinoma cell-lines (8305c, 8505c) bearing p53 gene-mutations. Int J Oncol. 4(3):583-6.

extract_protocol: Total RNA extraction was performed using RNAEasy Minikit (Qiagen, Germantown, MD, USA), following manufacturer's instructions. RNA concentration was determined with a WU-83060-00 Thermo Scientific NanoDrop ND-1000 1-position Spectrophotometer and its quality with a 2100 Bioanalyzer (Agilent, DE) Total RNA extraction was performed using RNAEasy Minikit (Qiagen, Germantown, MD, USA), following manufacturer's instructions. RNA concentration was determined with a WU-83060-00 Thermo Scientific NanoDrop ND-1000 1-position Spectrophotometer and its quality with a 2100 Bioanalyzer (Agilent, DE)

treatment_protocol: Cells were cultured in Rosswell Park Memorial Institute (RPMI)-1640 supplemented with 10% fetal bovine serum (FBS), penicillin 10,000 IU/mL, streptomycin 10 mg/mL, and 2 mM L-glutamine. Cells were stably transfected using pLX304 lentiviral vector (marker blasticidin, V5 epitope tag) with the ORF clone of the nuclear envelope integral membrane protein 1 (NEMP1/TEMP194A, ORF Clone Accession number BC117436,1, BC126300.1). The clone was produced by the shRNA Core Facility of the Albert Einstein College of Medicine (Catalog # HsCD00440155, (https://www.einstein.yu.edu/research/shared-facilities/shrna/resources).

tag: Sex

value: female

value: 78 years old

tag: status

value: primary undifferentiated carcinoma tissues contained residual well differentiated components, suggesting well differentiated to undifferentiated carcinoma progression

value: thyroid gland


title: 501mel,siCT,repl1

description:
9967501162_A
sirnaCT.1
501 Mel cells transfected with siCT.


title: AT4

description: Gene expression in the papillary carcinoma with local and lymph node metastasis of a 76y old female

source_name: Stably transfected with TMEM194A BCPAP cells purchased from DSMZ in Braunschweig, Germany Rep 4

value: 76 years old


title: AT3

source_name: Stably transfected with TMEM194A BCPAP cells purchased from DSMZ in Braunschweig, Germany Rep 3

value: papillary carcinoma with local and lymph node metastasis


title: BT1

source_name: Stably transfected with TMEM194A 8505C cells purchased from DSMZ in Braunschweig, Germany Rep 1


title: MCF7_Hesperidin_10μM_rep1

source_name: Human breast cancer cell line MCF7

value: Hesperidin


title: MCF7_Glycyrrhizic acid_10μM_rep1.1-1


title: BT4

source_name: Stably transfected with TMEM194A 8505C cells purchased from DSMZ in Braunschweig, Germany Rep 4


title: AT1

source_name: Stably transfected with TMEM194A BCPAP cells purchased from DSMZ in Braunschweig, Germany Rep 1


title: BT2

source_name: Stably transfected with TMEM194A 8505C cells purchased from DSMZ in Braunschweig, Germany Rep 2


title: BP3

description: Gene expression in the DDX19B transfected cells from primary undifferentiated  carcinoma thyroid tissues of a 78y old female

source_name: Stably transfected with PANK2 8505C cells purchased from DSMZ in Braunschweig, Germany Rep 3

treatment_protocol: Cells were cultured in Rosswell Park Memorial Institute (RPMI)-1640 supplemented with 10% fetal bovine serum (FBS), penicillin 10,000 IU/mL, streptomycin 10 mg/mL, and 2 mM L-glutamine. Cells were stably transfected using pLX304 lentiviral vector (marker blasticidin, V5 epitope tag) with the ORF clone of PANK2 (pantothenate kinase 2), ORF clone accession number CCSB53315.1. The clone was produced by the shRNA Core Facility of the Albert Einstein College of Medicine (Catalog # HsCD00440361, (https://www.einstein.yu.edu/research/shared-facilities/shrna/resources).


title: AP2

description: Gene expression in the DDX19B transfected cells from papillary carcinoma with local and lymph node metastasis of a 76y old female

source_name: Stably transfected with PANK2 BCPAP cells purchased from DSMZ in Braunschweig, Germany Rep 2


title: BP2

source_name: Stably transfected with PANK2 8505C cells purchased from DSMZ in Braunschweig, Germany Rep 2


title: BP4

source_name: Stably transfected with PANK2 8505C cells purchased from DSMZ in Braunschweig, Germany Rep 4


title: AP4

source_name: Stably transfected with PANK2 BCPAP cells purchased from DSMZ in Braunschweig, Germany Rep 4


title: BP1

source_name: Stably transfected with PANK2 8505C cells purchased from DSMZ in Braunschweig, Germany Rep 1


title: AP1

source_name: Stably transfected with PANK2 BCPAP cells purchased from DSMZ in Braunschweig, Germany Rep 1


title: BD3

description: Gene expression in the DDX19B transfected cells from primary undifferentiated carcinoma thyroid tissues of a 78y old female

source_name: Stably transfected with DDX19B 8505C cells purchased from DSMZ in Braunschweig, Germany Rep 3

treatment_protocol: Cells were cultured in Rosswell Park Memorial Institute (RPMI)-1640 supplemented with 10% fetal bovine serum (FBS), penicillin 10,000 IU/mL, streptomycin 10 mg/mL, and 2 mM L-glutamine. Cells were stably transfected using pLX304 lentiviral vector (marker blasticidin, V5 epitope tag) with the ORF clone of the DDX19B (DEAD (Asp-Glu-Ala-Asp) box polyopeptide 19B, ORF clone accession number BC003626.2. The clone was produced by the shRNA Core Facility of the Albert Einstein College of Medicine (Catalog # HsCD00440155, (https://www.einstein.yu.edu/research/shared-facilities/shrna/resources).


title: AD2

source_name: Stably transfected with DDX19B BCPAP cells purchased from DSMZ in Braunschweig, Germany Rep 2


title: BD4

source_name: Stably transfected with DDX19B 8505C cells purchased from DSMZ in Braunschweig, Germany Rep 4


title: BD2

source_name: Stably transfected with DDX19B 8505C cells purchased from DSMZ in Braunschweig, Germany Rep 2


title: A02

source_name: BCPAP cells purchased from DSMZ in Braunschweig, Germany_Replicate 2

treatment_protocol: Cells were cultured in Rosswell Park Memorial Institute (RPMI)-1640 supplemented with 10% fetal bovine serum (FBS), penicillin 10,000 IU/mL, streptomycin 10 mg/mL, and 2 mM L-glutamine.


title: AD3

source_name: Stably transfected with DDX19B BCPAP cells purchased from DSMZ in Braunschweig, Germany Rep 3


title: B04

description: Gene expression in the primary undifferentiated  carcinoma thyroid tissues of a 78y old female

source_name: 8505C cells purchased from DSMZ in Braunschweig, Germany_ Replicate 4


title: B03

source_name: 8505C cells purchased from DSMZ in Braunschweig, Germany_ Replicate 3


title: AD4

source_name: Stably transfected with DDX19B BCPAP cells purchased from DSMZ in Braunschweig, Germany Rep 4


title: B02

source_name: 8505C cells purchased from DSMZ in Braunschweig, Germany_ Replicate 2


title: B01

source_name: 8505C cells purchased from DSMZ in Braunschweig, Germany_ Replicate 1


title: BD1

source_name: Stably transfected with DDX19B 8505C cells purchased from DSMZ in Braunschweig, Germany Rep 1


title: A04

source_name: BCPAP cells purchased from DSMZ in Braunschweig, Germany_Replicate 4


title: AD1

source_name: Stably transfected with DDX19B BCPAP cells purchased from DSMZ in Braunschweig, Germany Rep 1


title: A01

source_name: BCPAP cells purchased from DSMZ in Braunschweig, Germany_Replicate 1


title: A03

source_name: BCPAP cells purchased from DSMZ in Braunschweig, Germany_Replicate 3


title: AT2

source_name: Stably transfected with TMEM194A BCPAP cells purchased from DSMZ in Braunschweig, Germany Rep 2


title: T3

description: Gene expression in the left lobe of the thyroid gland of a 33y old male with papillary carconoma

source_name: Papillary cancer region of the thyroid tumor_ Replicate 3

growth_protocol: unilateral, single, 32.0 mm papillary carcinoma, classical type in the left thyroid lobe. Pathological stage pT3N0Mx.

treatment_protocol: Lobectomy of the left lobe of the thyroid gland

value: male

value: 33 years old

value: papillary carcinoma

value: left lobe of the thyroid gland


title: N1

source_name: Benign region of the thyroid tumor_Replicate 1


title: N3

source_name: Benign region of the thyroid tumor_Replicate 3


title: T1

source_name: Papillary cancer region of the thyroid tumor_ Replicate 1