title: gamma stim 14T0417 rep 3

city: Newcastle upon Tyne

first: Andrew

middle: James

last: Skelton

state: Tyne and Wear

address: Framlington Place

department: Bioinformatics

country: United Kingdom

institute: Newcastle University

description:
total RNA (200ng)
Biotinylated cRNA (750ng)

hyb_protocol: Per sample, 750ng of biotynilyated cRNA was hybridized onto the Illumina HumanHT-12 v4 (Illumina Inc. San Diego, USA). Each BeadChip contains twelve arrays. Hybridization and washing were performed according to the Illumin Manual Direct Hybridization Assay Guide.

scan_protocol: Scanning was performed on the Illumina iScan (Illumina, San Diego, USA). Image analysis and extraction of raw expression data was performed with Illumina GenomeStudio v2011.1 Gene Expression software with default settings (no background subtraction and no normalization).

data_processing: Data Analysis was carried out using R, utilising packages from the Bioconductor project (Lumi, Limma). Normalisation was carried out using the RSN and VST functions from Lumi.

source_name: patient fibroblast, IFN-gamma stim

label_protocol: RNA quality and integrity was determined using Lab-on-Chip analysis on the Agilent 2100 Bioanalyzer. Biotinylated cRNA was prepared using the Illumina TotalPrep RNA Amplification Kit (Ambrion, Austin Texas, USA) according to manufacturers' specification with an input of 200ng total RNA per sample.

growth_protocol: Dermal fibroblasts were cultured in DMEM with 10% fetal calf serum with 1% penicillin/streptomycin

extract_protocol: RNA was isolated by using the ReliaPrep RNA Cell Miniprep System (Promega) according to manufacturers’ instructions. 200ng total RNA per sample was used.

treatment_protocol: Fibroblasts in 24 well plates were treated in triplicate with media alone, or IFN-alpha, IFN-beta or IFN-gamma (all 1000IU/mL) for 10h

tag: treatment

value: IFN-gamma

tag: cell type

value: dermal fibroblast, patient


title: M-36-1

status: Public on Jun 12 2015

type: RNA

city: Minato

first: Yoshihiro

last: Kawaoka

state: Tokyo

address: Shirokanedai 4-6-1

department: ERATO Influenza-induced Host Responses Project

country: Japan

institute: Japanese Science and Technology Agency

hyb_protocol: Using Agilents Gene Expression Hybridizatoin kit #4 and Gene Expression wash pack #5, Cy3-labeled cRNA preparations were hybridized with rhesus macaque arrays (Agilent Microarray Design Identification Number 015421) for 17 h at 65°C.

scan_protocol: Immediately after washing, Feature Extraction Software, version 7 (Agilent Technologies) was used for image analysis and data extraction.

data_processing: Per chip and per gene normalization was performed using the LIMMA package in R.

molecule: total RNA

organism: Mus musculus

source_name: Lung

label_protocol: Using the Quick Amp Labeling Kit, T7 RNA polymerase was used to simultaneously amplify target material and incorporate cyanine 3-labeled CTP to prepare Cy3-labeled cRNA.

extract_protocol: From the homogenized lung tissues, total RNA was extracted with the RNeasy Mini Kit (Qiagen, Hilden, Germany) in accordance with the manufacturer’s instructions.

treatment_protocol: Mouse lung tissues were placed in RNALater (Ambion, CA), an RNA stabilization reagent and stored at -80°C. All tissues were thawed together and homogenized for 2 minutes at 30 Hz using a TissueLyser (Qiagen, Hilden, Germany) as per the manufacturer’s instructions.

tag: strain

tag: tissue

value: lung

tag: animal number

tag: influenza strain

value: Mock

tag: hours post infection

tag: titer (pfu/g)


title: M-3-2


title: M-3-1


title: gamma stim 120216

label: Biotin

organism: Homo sapiens

source_name: control fibroblast, IFN-gamma stim

value: dermal fibroblast, contol line 3


title: M-18-3


title: M-24-3


title: M-48-1


title: gamma stim 22131

value: dermal fibroblast, contol line 1


title: M-36-2


title: M-30-3


title: gamma stim 14T0417 rep 2


title: beta stim 14T0417 rep 2

source_name: patient fibroblast, IFN-beta stim

value: IFN-beta


title: gamma stim 26025

value: dermal fibroblast, contol line 2


title: M-24-2


title: M-24-1


title: beta stim 14T0417 rep 1


title: M-30-2


title: beta stim 14T0417 rep 3


title: M-30-1


title: gamma stim 14T0417 rep 1


title: beta stim 26025

source_name: control fibroblast, IFN-beta stim


title: M-18-2


title: M-12-3


title: beta stim 22131


title: M-12-2


title: alpha stim 14T0417 rep 3

source_name: patient fibroblast, IFN-alpha stim

value: IFN-alpha


title: beta stim 120216


title: M-18-1


title: M-12-1


title: alpha stim 120216

source_name: control fibroblast, IFN-alpha stim


title: K-D5-2

value: Kawasaki


title: K-D7-2


title: alpha stim 26025


title: M-0-2


title: alpha stim 14T0417 rep 1


title: M-0-3


title: K-D7-1


title: K-72-3


title: K-D7-3


title: 0 stim 14T0417 rep 2

source_name: patient fibloblast, unstim


title: K-9-2


title: 0 stim 120216

source_name: control fibroblast, unstim


title: LAV_2

city: Segrate

first: Francesco

last: Villa

state: MI

address: Via Fratelli Cervi, 93

department: Istituto di Tecnologie Biomediche

country: Italy

institute: Consiglio Nazionale delle Ricerche

description:
replicate 2
9257302079_K

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were processed using Illumina BeadStudio Gene Expression Module v3.4. Imputing of the missing values and rank-invariant normalization were used to obtain p-values and normalized intensities from the raw data.

source_name: HEK293T transfected with vector encoding for LAV-BPIFB4

label_protocol: Illumina TotalPrep RNA Amplification kit Life Technologies

growth_protocol: HEK293T cells were grown in culture medium (DMEM, 10% fetal bovine serum, 2 mM L-glutamine, 100 U penicillin/0.1 mg/ml streptomycin)

extract_protocol: RNA extracted using the small RNA miRNeasy Mini Kit (Qiagen)

treatment_protocol: HEK293T cells were transfected with pRK5 vector encoding WT- or LAV-BPIFB4, or with an empty plasmid, using Lipofectamine 2000 (Life Technologies) according to the manufacturer’s protocol, in triplicates. 24hrs after transfection, cells were serum-starved for 18hrs.

tag: cell line


title: K-9-3


title: M-0-1


title: K-9-1


title: K-D5-3


title: alpha stim 22131


title: 0 stim 22131


title: LAV_3

description:
replicate 3
9257302079_L

value: transfected with vector encoding for LAV-BPIFB4


title: alpha stim 14T0417 rep 2


title: 0 stim 14T0417 rep 3


title: 0 stim 26025


title: 0 stim 14T0417 rep 1


title: LAV_1

description:
replicate 1
9257302079_J


title: K-D5-1


title: K-6-2


title: K-60-3


title: S11 - 14d_L

city: Freiburg

first: Sebastian

last: Grundmann

address: Hugstetter Str. 55

country: Germany

institute: University Hospital Freiburg

description: RNA isolated from the distal adductor muscle group at the specified time point after femoral artery occlusion (right hindlimb) or sham operation (left hindlimb). RNA of five animals was pooled in equal amounts.

hyb_protocol: Hybridization is performed using a micro-circulation pump (Atactic Technologies). The hybridization conditions are 100 µL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide, 34 °C, and overnight.

scan_protocol: Hybridization images are collected using a laser scanner (GenePix 4000B, Molecular Device).

data_processing: Global Normalization across arrays is carried out using a cyclic LOWESS (Locally-weighted Regression) method. For final analysis in the manuscript, only microRNAs with an expression above 500 in any sample were included.

source_name: left hindlimb, sham surgery, 14d

label_protocol: Small RNAs (< 300 nt) are 3’-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag is then ligated to the poly(A) tail for later fluorescent dye staining; two different tags are used for the two RNA samples in dual-sample experiments.

extract_protocol: Total RNA was extracted using Trizol following manufacturer's instructions. Small RNA enrichment and miRNA microarray assays were performed by LC Sciences.

treatment_protocol: Unilateral femoral artery occlusion (right side) and a sham operation on the contralateral (left) side was performed in C57BL/6J mice under anesthesia by double ligation of the superficial femoral artery proximal to the deep femoral artery and distal femoral artery. Total RNA was isolated from the distal adductor muscles at baseline and at 5 time points after femoral artery ligation (6h, 24h, 3 days, 7 days, 14 days) from 5 mice per time point.

tag: strain/background

tag: gender

value: male

value: distal adductor muscles

value: sham surgery

tag: time point


title: WT_1

description:
replicate 1
9257302079_D

source_name: HEK293T transfected with vector encoding for WT-BPIFB4


title: WT_3

description:
replicate 3
9257302079_F

value: transfected with vector encoding for WT-BPIFB4


title: WT_2

description:
replicate 2
9257302079_E


title: S10 - 14d_R

source_name: right hindlimb, femoral artery occlusion, 14d

value: femoral artery occlusion


title: S09 - 7d_L

source_name: left hindlimb, sham surgery, 7d


title: EMPTY_2

description:
replicate 2
9257302079_B

source_name: HEK293T transfected with empty vector

value: transfected with empty vector


title: K-6-1


title: K-6-3


title: K-48-1


title: K-48-3


title: K-48-2


title: K-60-1


title: L-NAME-fed, rep 1

city: Valhalla

first: Caroline

last: Ojaimi

state: NY

country: USA

institute: New York Medical College

description: Gene expression data from left ventricle of L-NAME-fed pregnant rats

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

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

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

label: biotin

organism: Rattus norvegicus

source_name: L-NAME-fed

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Rats were housed in standard cages and supplied with standard chow

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

treatment_protocol: Female Sprague-Dawley rats (200-250g) were purchased from Charles River Laboratories. Day 1 of pregnancy was determined by the day when mucus plugs were found. Drinking water with or without L-methonine (Sigma-Aldrich) (9g/L) or L-NAME (Sigma-Aldrich) (1g/L) was supplied from day 1 to day 20 of pregnancy.  Rats were anesthetized on day 20 or 21 with sodium pentobarbital (50mg/kg, ip), and hearts were immediately harvested for RNA extraction and hybridization on Affymetrix microarrays.

value: female

value: Sprague Dawley

value: Left ventricle


title: methionine-fed, rep 3

description: Gene expression data from left ventricle of methionine-fed pregnant rats

source_name: methionine-fed


title: S08 - 7d_R

source_name: right hindlimb, femoral artery occlusion, 7d


title: K-60-2

source_name: Lung

value: lung


title: L-NAME-fed, rep 2


title: S07 - 3d_L

source_name: left hindlimb, sham surgery, 3d


title: methionine-fed, rep 4


title: L-NAME-fed, rep 3


title: methionine-fed, rep 2


title: S06 - 3d_R

source_name: right hindlimb, femoral artery occlusion, 3d


title: K-3-2


title: EMPTY_3

description:
replicate 3
9257302079_C


title: L-NAME-fed, rep 4


title: K-3-3


title: EMPTY_1

description:
replicate 1
9257302079_A


title: K-36-2


title: S05 - 24h_L

source_name: left hindlimb, sham surgery, 24h


title: K-36-3


title: K-3-1


title: methionine-fed, rep 1


title: control heart, rep 3

description: Gene expression data from left ventricle of control pregnant rats

source_name: control heart


title: control heart, rep 5


title: K-36-1


title: S04 - 24h_R

source_name: right hindlimb, femoral artery occlusion, 24h


title: S03 - 6h_L

source_name: left hindlimb, sham surgery, 6h


title: S02 - 6h_R

source_name: right hindlimb, femoral artery occlusion, 6h


title: 723modA2 vs modA2::kan replicate 4

city: St Lucia

first: Sean

middle: M

last: Grimmond

state: QLD

address: Research Rd

department: Genomics and Bioinformatics

country: Australia

institute: Institute of Molecular Bioscience, Uni of QLD

description:
100932
Biological replicate 4 of 4 (100932)

hyb_protocol: Arrays were hybridized in accordance with the Agilent dual color gene expression handbook

scan_protocol: Arrays were scanned on an Agilent G2565BA scanner with setting in accordance with the manufacurers directions

data_processing:
Features were extracted using Agilent Feature Extraction V9.5. Analysis was preformed using LIMMA as follows. Background correction was applied, spots from duplicate probes were averaged and log transformed. Between-array quantile normalization was then applied to the log transformed spot intensities. A moderated t-test on the normalized log intensities was performed to identify differentially expressed genes and the False Discovery Rate (FDR) used to control for multiple testing.
Processed data file merged_normalized_data.txt is linked as a supplementary file on the Series record.  The file's LogR column reports log2 (modA2ON/modA2 MUTANT) ratios.

organism: Haemophilus influenzae

source_name: modA2 ON

label_protocol: Reverse transcription reactions were performed in 40 ul volumes, containing 10 µg total RNA, 300 ng random hexamers, 0.5mM dNTPs and 300 U SuperScript III Reverse Transcriptase (Invitrogen) at 42ºC for 2.5 h. RNA contamination was removed from the cDNA by the addition of NaOH followed by column purification (Qiagen minElute, Qiagen). A total of 1 µg of purified cDNA was labeled using KREAtech Cy3-ULS or  KREAtech Cy5-ULS (KREAtech, The Netherlands).

growth_protocol: NTHi were routinely cultured in BHI broth (Oxoid) supplemented (sBHI) with hemin (1% v/v) and NAD (2 µg /ml), or sBHI agar (as broth but with 1% w/v bacteriological agar; Oxoid). Liquid cultures were grown aerobically at 37°C with shaking at 90rpm.

extract_protocol: Triplicate cultures of NTHi strains 723 modA2ON, 723 modA2OFF and 723 modA2::kan were grown to exponential phase (optical density at 600 nm = 0.3 to 0.4) in BHI broth prior to RNA extraction. Growth rates of strain pairs used to make RNA for microarray comparison were equivalent, ensuring that the samples taken were in the same growth phase. Culture media for RNA preps were free of antibiotics. Approximately 100 µg of total RNA was prepared from each sample using the RNeasy Midi Kit according to the manufacturer's instructions (Qiagen). The triplicate samples were pooled and the integrity and concentration of RNA was determined via micro-fluidic analysis on a bio-analyser (Agilent Technologies).

source_name: modA2 mutant


title: S01 - 0h_R+L

source_name: right and left hindlimb, baseline


title: control heart, rep 4


title: 723modA2 vs modA2::kan replicate 3

description:
100931
Biological replicate 3 of 4 (100931)


title: 723modA2 vs modA2::kan replicate 2

description:
100929
Biological replicate 2 of 4 (100929)


title: 723modA2 vs modA2::kan replicate 1

description:
100927
Biological replicate 1 of 4 (100927)


title: HEK-293T_DIS3sh: HEK_DIS3 knocked-down

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

institute: IRCCS Istituto Nazionale dei Tumori

description: Global miRNA expression profiling data of  HEK-293T infected with a shRNA specific for DIS3.

hyb_protocol: The labelled RNA was then hybridized to Affymetrix GeneChip® microRNA arrays v1.0 following Affymetrix recommended protocol.

scan_protocol: Genechips were scanned on an Affymetrix GeneChip 3000 7G scanner.

data_processing: The data were extracted using Affymetrix miRNA QC tool software (Affymetrix Inc., Santa Clara, CA, USA) using default analysis settings for normalization and summarization methods.

source_name: Human Embryonic Kidney 293 Cell Line

label_protocol: Total RNA was processed using the FlashTag labeling kit, which uses a tailing reaction followed by ligation of the biotinylated signal molecule to the target RNA sample.

growth_protocol: HEK-293T cells were cultured in Dulbecco's modified Eagle's medium supplemented with 10% fetal bovine serum (FBS) and 1% of Penicillin and Streptomycin antibiotics.

extract_protocol: Total RNA was extracted from cells using TRIzol® RNA Isolation Reagent

treatment_protocol: RNA from RPMI-8226, KMS12-BM, and HEK-293T cell lines knocked-down with a scrambled or hDIS3 sh4 was collected 72 hours after infection.

tag: shRNA

value: shRNA specific for DIS3


title: K-24-3


title: K-30-3


title: RPMI_2_DIS3sh: HMCL_DIS3 knocked-down

description: Global miRNA expression profiling data of RPMI-8226 biological replicate 2 infected with a shRNA specific for DIS3.

source_name: Human Myeloma Cell Line

growth_protocol: RPMI-8226 and KMS12-BM cells were cultured in RPMI medium with 10% FBS and 1% of Penicillin and Streptomycin.


title: control heart, rep 1


title: control heart, rep 2


title: K-30-1


title: RPMI_1_sc: HMCL_control

description: Global miRNA expression profiling data of RPMI-8226 biological replicate 1 infected with a scrambled shRNA.

value: scrambled shRNA


title: K-18-3


title: K-24-1


title: HEK-293T_sc: HEK_control

description: Global miRNA expression profiling data of HEK-293T infected with a scrambled shRNA.


title: K-30-2


title: K-72-1


title: K-18-2


title: K-24-2


title: RPMI_2_sc: HMCL_control

description: Global miRNA expression profiling data of RPMI-8226 biological replicate 2 infected with a scrambled shRNA.


title: RPMI_1_DIS3sh: HMCL_DIS3 knocked-down

description: Global miRNA expression profiling data of RPMI-8226 biological replicate 1 infected with a shRNA specific for DIS3.


title: KMS12_DIS3sh: HMCL_DIS3 knocked-down

description: Global miRNA expression profiling data of KMS12-BM infected with a shRNA specific for DIS3.


title: KMS12_sc: HMCL_control

description: Global miRNA expression profiling data of KMS12-BM infected with a scrambled shRNA.


title: K-18-1


title: K-12-3


title: NK 3

type: genomic

city: Seyagaya-ku

first: Hitomi

last: Ueno

institute: National Center for Child Health and Development

description: genomic DNA from non-neoplastic kidney 3

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using iScan array scanner (illumina) using standard setting.

data_processing: GenomeStudio v2010.1 was used to determine the methylation level at each CpG site as beta value.

label: Cy5 and Cy3

molecule: genomic DNA

source_name: non-neoplastic kidney

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified from fresh-frozen tissues using GE Healthcare Bio-Science illustra tissue & cells genomicprep Mini Spin Kit according to standard instructions

value: Male

tag: sample type

value: frozen tissues

tag: disease state

value: normal


title: Dorsal skin, collagen hydrolysate-containing diet administrated for 12 weeks, biological rep2

city: Aomori

first: Yuji

last: Nakai

state: Aomori

address: 2-1-1, Yanagawa

department: Institute of Regional Innovation

institute: Hirosaki University

description: No additional information

hyb_protocol: Following fragmentation, 12.5 µg cRNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

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

data_processing: CEL files were quantified with theDistribution Free Weighted method (DFW), using the statistical language R (R-2.7.2) and Bioconductor 2.2.

source_name: Dorsal skin, fed  collagen hydrolysate-containing diet for 12 weeks

label_protocol: biotinylated aRNA was obtained from 200 ng of purified total RNA using a GeneChip 3’ IVT Express Kit (Affymetrix, Santa Clara, CA, USA).

extract_protocol: Total RNA was isolated using Trizol reagent (Invitrogen Life Technologies Corp.), then purified with an RNeasy mini kit (Qiagen K.K., Tokyo, Japan).

treatment_protocol: Dorsal skin sample was snap frozen in liquid nitrogen and powdered.

value: Female

value: dorsal skin

tag: age

value: 21 weeks


title: Dorsal skin, control AIN93G diet administrated for 12 weeks, biological rep4

description: No additional information

source_name: Dorsal skin, fed control AIN93G diet for 12 weeks

value: fed control AIN93G diet for 12 week


title: Dorsal skin, collagen hydrolysate-containing diet administrated for 12 weeks, biological rep3

description: No additional information

value: fed  collagen hydrolysate-containing diet for 12 week


title: Potassium chloride treated big neurospheres biological replicate 3

city: St lucia Brisbane

first: Zong-Hong

last: Zhang

state: Queensland

address: QBI Building (#79)

institute: QBI

hyb_protocol: Fragmentation and biotin labelling of the cDNA was carried out using Encore Biotin module (NuGEN) for Affymetrix GeneChip Mouse Gene 1.0 ST arrays. Labelled cDNA was hybridised to arrays in an oven at 45°C.

scan_protocol: Hybridised arrays were scanned using the Affymetrix GeneChip Scanner and the scanned data (.CEL files) was transferred to the Partek Genomics Suite and data analysis

data_processing: CEL files generated by AGCC were uploaded onto Partek software and the data analysis was carried out using the gene expression analysis workflow. Steps performed in Partek included: 1) robust microarray averaging (RMA) to normalize the data; 2) principal component analysis (PCA) to check for sample outliers; 3) analysis ofvariance (ANOVA) to generate p -values

label_protocol: RNA was isolated from neurospheres generatedin presence of either N or K (n=3 each, two biological replicates 249 in common with the RNA-Seq data) and converted to cDNA using Applause WT-Amp ST kit (NuGEN).

growth_protocol: Mouse neurosphere cells treated by potassium chloride (KCl) and norepinephrine. Briefly, adult (8–12 week old) male C57BL/6J mice were used for all in vitro experiments conducted in this study. All mice were housed in groups and maintained on a 12-hour light/dark cycle with ad libitum access to food and water. After mice were sacrificed by cervical dislocation, the neural precursor activity was examined as previous described by our group.

extract_protocol: Total RNA was extracted from neurospheres using TRIzol Reagent (Life Technologies) and chloroform (Sigma-Aldrich) followed by precipitation and washing with isopropanol and ethanol respectively. RNA samples were treated with the Ambion DNA-free kit (Life Technologies) according to the manufacturer’s instructions to remove any contamination from genomic DNA.

treatment_protocol: The isolated hippocampal tissue was minced to obtain a single cell suspension. The cell suspension was cultured in complete neurosphere medium containing EGF and bFGF, in the presence of norepinephrine (10 μM) or potassium chloride (15mM). The primary neurospheres were collected on day 14 for each treatment.

value: hippocampal tissue

value: primary neurospheres

value: male

value: 8-12 week old

value: Potassium chloride


title: K-0-3

value: Kawasaki


title: NK 1

description: genomic DNA from non-neoplastic kidney 1


title: NK 2

description: genomic DNA from non-neoplastic kidney 2


title: K-12-2

value: lung


title: Dorsal skin, collagen hydrolysate-containing diet administrated for 12 weeks, biological rep1

description: No additional information


title: CCSK 3

description: genomic DNA from Clear cell sarcoma of the kidney 3

source_name: Clear cell sarcoma of the kidney

value: Clear cell sarcoma of the kidney


title: Dorsal skin, collagen hydrolysate-containing diet administrated for 12 weeks, biological rep4

description: No additional information


title: Potassium chloride treated big neurospheres biological replicate 1


title: K-0-2

source_name: Lung


title: K-72-2


title: K-0-1


title: Dorsal skin, control AIN93G diet administrated for 12 weeks, biological rep3

description: No additional information


title: RTK 3

description: genomic DNA from Rhabdoid tumor of the kidney 3

source_name: Rhabdoid tumor of the kidney

value: Rhabdoid tumor of the kidney


title: Norepinephrine treated big neurospheres biological replicate 3

source_name: Norepinephrine treated big neurospheres

value: Norepinephrine


title: K-12-1


title: Dorsal skin, control AIN93G diet administrated for 12 weeks, biological rep2

description: No additional information


title: CCSK 2

description: genomic DNA from Clear cell sarcoma of the kidney 2

value: Male

value: frozen tissues


title: Norepinephrine treated big neurospheres biological replicate 2


title: Potassium chloride treated big neurospheres biological replicate 2


title: CCSK 1

description: genomic DNA from Clear cell sarcoma of the kidney 1


title: T20_ICL7

city: Gif-sur-Yvette

first: Olivier

last: ARNAIZ

address: avenue de la terrasse

country: France

institute: CNRS

description:
mating type VIII is a strain carrying an injection-induced macronuclear deletion of the surface antigen A gene and a silencing-induced macronuclear deletion of the ND7 gene
Population of cells 20 hours after T0 with 100% of autogamy (100% visible anlagen)

hyb_protocol: Hybridization by NimbleGen company

scan_protocol: Scanning by PartnerChip company (MS200 Roche-NimbleGen)

data_processing: Images are treated with NimbleScan software from Nimblegen to obtain raw intensities (.RMA.calls) that were then used for analysis with GeneSpring GX11 software.

organism: Paramecium tetraurelia

source_name: T20 time point after ICL7 inactivation

label_protocol: cDNA synthesis and labeling with Cyanine 3: 300ng of total RNA was used to synthesize cDNA according to the Sigma WGA1 TransPlex Whole Transcriptome Amplification kit protocol.

growth_protocol: Silencing media were prepared basically as described in (Galvani and Sperling, 2001) and (Nowak et al., 2011), by inoculating precultures of the appropriate bacterial strains into WGP (wheat grass powder - Pines International Co., Lawrence, USA) medium containing 0.1 mg/mL ampicillin. Following 6–8 hrs of shaking at 37°C, bacterial cultures were diluted six-fold into the same medium containing 0.4 mM IPTG to induce dsRNA synthesis. After overnight induction at 37°C, all silencing media were supplemented with 0.8 µg/mL β-sitosterol (Merck) before use. Paramecium cells were maintained at 27°C during vegetative growth and starvation. Cell growth was monitored by manual counting of cells in 1 mL aliquots of the culture. During starvation, the progression of autogamy through the different stages of nuclear reorganization was monitored by DAPI staining of cells.

extract_protocol: For each sample, total RNA was extracted from ~400,000 Paramecium cells using Trizol.

treatment_protocol: At each time point, 200-600 mL of Paramecium cells were centrifuged at 200 x g for 1 min and total RNA was extracted from unwashed cell pellets.

tag: strain description

value: 51 new mt8 ∆A ∆ND7

value: mating type VIII

tag: caryonide

value: monocaryonide

tag: medium

value: Escherichia coli WGP

tag: assay physiological state

value: autogamy competent


title: T10_ICL7

description:
mating type VIII is a strain carrying an injection-induced macronuclear deletion of the surface antigen A gene and a silencing-induced macronuclear deletion of the ND7 gene
Population of cells 10 hours after T0 with 98% of autogamy (98% visible anlagen)

source_name: T10 time point after ICL7 inactivation

tag: strain


title: Dorsal skin, control AIN93G diet administrated for 12 weeks, biological rep1

description: No additional information

tag: treatment

value: fed control AIN93G diet for 12 week

value: Female

tag: tissue

value: dorsal skin

value: 21 weeks


title: Dorsal skin, collagen hydrolysate-containing diet administrated for 1 week, biological rep2

description: No additional information

source_name: Dorsal skin, fed  collagen hydrolysate-containing diet for 1 week

label_protocol: biotinylated aRNA was obtained from 300 ng of purified total RNA using a GeneChip 3’ IVT Express Kit (Affymetrix, Santa Clara, CA, USA).

value: 10 weeks


title: Dorsal skin, collagen hydrolysate-containing diet administrated for 1 week, biological rep1

description: No additional information

value: fed  collagen hydrolysate-containing diet for 1 week


title: ESFT 1

description: genomic DNA from Ewing's sarcoma family of tumors 1

source_name: Ewing's sarcoma family of tumors

value: Ewing's sarcoma family of tumors


title: Chronic_8W_1

city: Kyoto

first: Kaneyasu

last: Nishimura

address: 53 Shogoin-Kawahara-cho

department: CiRA

institute: Kyto University

hyb_protocol: Following fragmentation, 5.5 ug of cDNA were hybridized for 17 hr at 45˚C on GeneChip Mouse Gene-1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: The data were analyzed with GeneSpring version 12.1 using default analysis settings and global scaling as normalization method (RMA16).

source_name: MPTP chronic administrated mouse striatum

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 200 ng total RNA (Ambion WT Expression Kit, 2011, Affymetrix).

extract_protocol: Total RNA was extracted by Rneasy mini Kit by Qiagen, accoring to manufucture's protocol.

treatment_protocol: Mice were divided into three groups as follows: (i) 1 week after acute administration (four times by every 2 h) of free base MPTP HCl (20 mg/kg, 80 mg/kg in total, intraperitoneally). (ii) 8 weeks after chronic administration (once a day for 20 consecutive days) of free base MPTP HCl (4 mg/kg per day, 80 mg/kg in total). (v) 1 week after injection (four times by every 2 h) of saline.

value: Striatum


title: RTK 1

description: genomic DNA from Rhabdoid tumor of the kidney 1

value: Rhabdoid tumor of the kidney


title: ESFT 2

description: genomic DNA from Ewing's sarcoma family of tumors 2


title: Norepinephrine treated big neurospheres biological replicate 1

value: hippocampal tissue

tag: cell type

value: primary neurospheres

value: male

value: 8-12 week old

value: Norepinephrine


title: T5_ICL7

description:
mating type VIII is a strain carrying an injection-induced macronuclear deletion of the surface antigen A gene and a silencing-induced macronuclear deletion of the ND7 gene
Population of cells 5 hours after T0, with 1% of meiosis and 93% of autogamy (1% skeins, 42% fragmented macs, 49% visible anlagen)

source_name: T5 time point after ICL7 inactivation

value: 51 new mt8 ∆A ∆ND7

value: mating type VIII

value: monocaryonide


title: Acute_1W_2

source_name: MPTP acute administrated mouse striatum


title: Dorsal skin, collagen hydrolysate-containing diet administrated for 1 week, biological rep4

description: No additional information


title: Chronic_8W_2


title: Dorsal skin, collagen hydrolysate-containing diet administrated for 1 week, biological rep3

description: No additional information


title: Acute_1W_3


title: Chronic_8W_3


title: ESFT 3

description: genomic DNA from Ewing's sarcoma family of tumors 3

value: Male

value: frozen tissues


title: RTK 2

description: genomic DNA from Rhabdoid tumor of the kidney 2


title: ST_ICL7

description:
mating type VIII is a strain carrying an injection-induced macronuclear deletion of the surface antigen A gene and a silencing-induced macronuclear deletion of the ND7 gene
Population of cells at 3200 cells per mL, with 14% of meiosis and 30% of autogamy (14% skeins, 16% fragmented macs)

source_name: Starved cells after ICL7 inactivation

value: Escherichia coli WGP

value: autogamy competent


title: Dorsal skin, control AIN93G diet administrated for 1 week, biological rep4

description: No additional information

source_name: Dorsal skin, fed control AIN93G diet for 1 week

value: fed control AIN93G diet for 1 week

value: Female

value: dorsal skin

value: 10 weeks


title: T0_ICL7

description:
mating type VIII is a strain carrying an injection-induced macronuclear deletion of the surface antigen A gene and a silencing-induced macronuclear deletion of the ND7 gene
Population of cells at T0 (autogamy reference timepoint), with 16% of meiosis and 63% of autogamy (14% skeins, 50% fragmented macs)

source_name: T0 time point after ICL7 inactivation


title: VEG_ICL7

description:
mating type VIII is a strain carrying an injection-induced macronuclear deletion of the surface antigen A gene and a silencing-induced macronuclear deletion of the ND7 gene
Population of vegetative cells at 500 cells per mL.

source_name: Vegetative cells - ICL7 inactivation

value: log-phase growth


title: T20_TFIIS4

source_name: T20 time point after TFIIS4 inactivation


title: Dorsal skin, control AIN93G diet administrated for 1 week, biological rep3

description: No additional information


title: Acute_1W_1

value: Striatum


title: Dorsal skin, control AIN93G diet administrated for 1 week, biological rep1

description: No additional information


title: Dorsal skin, control AIN93G diet administrated for 1 week, biological rep2

description: No additional information


title: T10_TFIIS4

description:
mating type VIII is a strain carrying an injection-induced macronuclear deletion of the surface antigen A gene and a silencing-induced macronuclear deletion of the ND7 gene
Population of cells 10 hours after T0 with 100% of autogamy (3% fragmented macs, 97% visible anlagen)

source_name: T10 time point after TFIIS4 inactivation


title: Control_2

source_name: Control mouse striatum


title: Control_3


title: T0_TFIIS4

description:
mating type VIII is a strain carrying an injection-induced macronuclear deletion of the surface antigen A gene and a silencing-induced macronuclear deletion of the ND7 gene
Population of cells at T0 (autogamy reference timepoint), with 18% of meiosis and 69% of autogamy (10% skeins, 58% fragmented macs)

source_name: T0 time point after TFIIS4 inactivation


title: CEF_SE 11_rep1

city: Budapest

first: Ama

last: Szmolka

address: Hungária krt. 21.

department: Enteric Bacteriology and Foodborne Zoonoses

country: Hungary

institute: Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences

description: Biological replicate 1 of 4. Gene expression in chicken embryo fibroblast cells, infected with S. Enteritidis 11.

hyb_protocol: Six hundred ng of Cy3-labeled cRNA were hybridised to Agilent chicken custom 8×15K microarrays. In total, 13,681 probes were designed to characterise the expression of ~9,000 transcripts of Gallus gallus. Hybridisation was performed overnight at 65 °C.

scan_protocol: The slides were washed, treated with Stabilizing and Drying Solution (Agilent Technologies) and scanned with an Agilent DNA Microarray Scanner (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent Technologes) using default parameters (protocol GE1-v5_95 and Grid: 017066_D_F_20070615) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Gallus gallus

source_name: chicken embryo fibroblast (CEF)

label_protocol: One µg of total RNA was transcribed to cDNA with a Low-input RNA Linear Amplification Kit (Agilent Technologies) and then transcribed to cyanine-3 (Cy3)-labelled cRNA according to the One-Color Microarray-Based Gene Expression Manual v5.5 (Agilent Technologies). The fluorescent cRNA probes were purified using the RNeasy Mini Kit (Qiagen), and dye incorporation was determined with a NanoDrop ND-1000 (Thermo Scientific).

growth_protocol: After the preparation cells were maintained in MEM with 5 % fetal calf serum (FCS). One day prior to infection, CEFs were seeded into 36 mm Petri dishes and grown for 18 hours at 37 °C under 5% CO2. Semi-confluent cell cultures were washed three times with HBSS and MEM was replaced with DMEM with 5 % fetal calf serum and 1 % D-mannose.

extract_protocol: After 4 hours of incubation with Salmonella Enteritidis, CEFs were washed 3× with HBSS and lysed directly in a cell-culture vessel by adding 600 µl RLT buffer from the RNA purification kit (see below). Infection with each of the strains was performed in four replicates. The total RNA was extracted from the fibroblasts using a RNeasy Mini Kit according to the manufacturer’s instructions (Qiagen).

treatment_protocol: CEFs were infected for 4 h at 37 °C and 5 % CO2 with overnight bacterial cultures (1:200 dilution).

tag: breed

value: Leghorn

value: embryonic fibroblast cells prepared from 12-day-old chicken embryo


title: CKD Cal MV Set 2

city: Indianapolis

first: Neal

middle: X

last: Chen

state: IN

address: 950 W. Walnut Street

department: Medicine

institute: Indiana University

description: miRNA

hyb_protocol: each sample was hybridized to an Affymetrix miRNA 3.0 array using the standard Affymetrix protocol

scan_protocol: Scanned using the affymetrix GS30007G using Affymetrix Command Console (AGCC)

data_processing: Cel files were generated by AGCC and imported into Partek Genomics Suite  RMA (robust multi-array average) signals were generated using the RMA background correction, Quantile normalization and summarization by Median Polish. RMA data was log base 2 transformed, only core probesets were generated.

source_name: matrix vesicle

label_protocol: 1ug of total RNA was labeled using the Genisphere FlashTag HSR kit.

growth_protocol: VSMC grows in DMEM with 10% FBS (fetal bovine serum)

extract_protocol: Total RNA from VSMC or MV was isolated using miRNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.

treatment_protocol: VSMC treated with calcification media with 5 mM-β-glycerolphosphate

tag: disease status

value: CKD

tag: phenotype

value: cystic

tag: rna source

value: matrix vesicle

tag: rat id

value: vascular smooth muscle


title: CEF_SE 11_rep2

description: Biological replicate 2 of 4. Gene expression in chicken embryo fibroblast cells, infected with S. Enteritidis 11.


title: CEF_SE 11_rep3

description: Biological replicate 3 of 4. Gene expression in chicken embryo fibroblast cells, infected with S. Enteritidis 11.


title: CKD Cal MV Set 1

description: miRNA


title: CEF_SE 11_rep4

description: Biological replicate 4 of 4. Gene expression in chicken embryo fibroblast cells, infected with S. Enteritidis 11.


title: NL Cal MV Set 2

description: miRNA

value: normal


title: T5_TFIIS4

description:
mating type VIII is a strain carrying an injection-induced macronuclear deletion of the surface antigen A gene and a silencing-induced macronuclear deletion of the ND7 gene
Population of cells 5 hours after T0, with 2% of meiosis and 97% of autogamy (6% skeins, 48% fragmented macs, 43% visible anlagen)

source_name: T5 time point after TFIIS4 inactivation

value: 51 new mt8 ∆A ∆ND7

value: mating type VIII

value: monocaryonide


title: CKD Cal MV Set 3

description: miRNA


title: ST_TFIIS4

description:
mating type VIII is a strain carrying an injection-induced macronuclear deletion of the surface antigen A gene and a silencing-induced macronuclear deletion of the ND7 gene
Population of cells at 3100 cells per mL, with 9% of meiosis and 41% of autogamy (26% skeins, 16% fragmented macs)

source_name: Starved cells after TFIIS4 inactivation

value: Escherichia coli WGP

value: autogamy competent


title: 9_1.4a B 3

city: Lund

first: Stefan

last: Schwartz

address: BMC B13, Kilnikagatan 26

country: Sweden

institute: Lund university

description: RNA extraction B

hyb_protocol: 200 ng cDNA was used for hybridization

scan_protocol: Gene array scanner

data_processing: Basic Affymetrix chip and Experimental Quality Analyses were performed using the Expression Console Software v1.1.2.Clara, CA)

label_protocol: cDNA were Labelled with Biotin at  37 degree according to standard protocol by Affymetrix.

growth_protocol: DMEM with 10% heat- inactivated foetal bovine calf serum and penicillin-streptomycin was used as grought medium with G418 at 1mg/ml concentration as selection antibiotic

extract_protocol: Rneasy Kit Qiagen

treatment_protocol: No treatment done any as these are stable cell lines

value: cells permissive for late gene expression of HPV-16  from stable cell line 1.4a

value: Cervical cancer cells

tag: cell line


title: NL Cal MV Set 1

description: miRNA


title: Control_1


title: VEG_TFIIS4

source_name: Vegetative cells - TFIIS4 inactivation


title: 8_1.4a B 2

description: RNA extraction B


title: NL Cal MV Set 3

description: miRNA


title: Butyrate_1

city: Toyama

first: yukihiro

last: furusawa

address: Kurokawa

institute: Toyama Prefectural University

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001.

scan_protocol: Affymetrix GeneChip Scanner G3000.

data_processing:
Data were processed using GeneBASE software. MAT background correction were applied to probe intensities, gene level expression were summarized from the corrected intensities and then quantile normalized.
probe group file: MoEx-1_0-st-v1.r2.pgf
meta-probeset file: MoEx-1_0-st-v1.r2.dt1.mm9.mps

source_name: C57BL/6 Splenic CD4+ Naïve T cells, butyrate

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: RPMI1640 supplemented with 10%FCS, antibiotics, IL-2 and TGF-beta.

extract_protocol: QIAGEN RNeasy micro kit.

treatment_protocol: 0.1 mM Butyrate.

tag: strain/background

tag: genotype/variation

value: wild type

value: splenic CD4+ naïve T cells

value: butyrate


title: CKD Cal VSMC Set 3

description: miRNA

source_name: vascular smooth muscle


title: CEF_SE 147_rep4

description: Biological replicate 4 of 4. Gene expression in chicken embryo fibroblast cells, infected with S. Enteritidis 147.

value: Leghorn


title: Butyrate_2


title: CEF_SE 147_rep3

description: Biological replicate 3 of 4. Gene expression in chicken embryo fibroblast cells, infected with S. Enteritidis 147.

value: embryonic fibroblast cells prepared from 12-day-old chicken embryo


title: 7_1.4a B 1

description: RNA extraction B


title: Control_2

source_name: C57BL/6 Splenic CD4+ Naïve T cells, control

value: vehicle


title: 1.0M Sucrose treated heart_2

city: New York

first: Ross

last: Cagan

address: One Gustave Levy Place, Box 1020

department: Developmental & Regenerative Biology

institute: Icahn School of Medicine at Mount Sinai

description:
Gene expression from sucrose-fed adults
S2

hyb_protocol: Gene expression profiling using Affymetrix Drosophila GeneChip Array (v. 2.0) was performed at Rockefeller University Genomics Resource Center using their standard protocol.

data_processing: Data analysis was performed at Rockefeller University Genomics Resource Center using their standard protocol

organism: Drosophila melanogaster

source_name: Adult females fed 1M sucrose

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

growth_protocol: 30 adult females were fed for 21 days on media supplemented with 0.1M glucosamine or 1.0M sucrose

extract_protocol: Heart/nephrocyte complexes were harvested in 1000 ul Trizol; Total RNA purification was performed using Trizol and RNeasy MinElute kit, following the Stanford PAN Facility Gene Expression Core protocol..

treatment_protocol: Animals were fed for 21 days on media supplemented with 0.1M glucosamine or 1.0M sucrose

tag: gender

value: female

tag: developmental stage

value: adult

value: 1M sucrose

value: heart/nephrocyte complex


title: Control_1


title: CEF_SE 147_rep1

description: Biological replicate 1 of 4. Gene expression in chicken embryo fibroblast cells, infected with S. Enteritidis 147.


title: 1.0M Sucrose treated heart_1

description:
Gene expression from sucrose-fed adults
S1

scan_protocol: Gene expression profiling using Affymetrix Drosophila GeneChip Array (v. 2.0) was performed at Rockefeller University Genomics Resource Center using their standard protocol.


title: 0.1M Glucosamine treated heart_3

description:
Gene expression from glucosamine-fed adults
G3

source_name: Adult females fed 0.1M glucosamine

value: 0.1M glucosame


title: 1.0M Sucrose treated heart_3

description:
Gene expression from sucrose-fed adults
S3


title: CKD Cal VSMC Set 1

description: miRNA

value: CKD

value: cystic

value: vascular smooth muscle


title: NL Cal VSMC Set 1

description: miRNA

value: normal


title: CKD Cal VSMC Set 2

description: miRNA


title: CEF_uninfected_rep3

description: Biological replicate 3 of 4. Gene expression in control chicken embryo fibroblast cells, untreated.


title: CEF_uninfected_rep4

description: Biological replicate 4 of 4. Gene expression in control chicken embryo fibroblast cells, untreated.


title: CEF_SE 147_rep2

description: Biological replicate 2 of 4. Gene expression in chicken embryo fibroblast cells, infected with S. Enteritidis 147.


title: NL Cal VSMC Set 2

description: miRNA


title: 0.1M Glucosamine treated heart_2

description:
Gene expression from glucosamine-fed adults
G2


title: 6_1.4a A 3

description: RNA extraction A

value: cells permissive for late gene expression of HPV-16  from stable cell line 1.4a


title: 5_1.4a A 2

description: RNA extraction A

value: Cervical cancer cells


title: CEF_uninfected_rep2

description: Biological replicate 2 of 4. Gene expression in control chicken embryo fibroblast cells, untreated.


title: NL Cal VSMC Set 3

description: miRNA


title: 0.1M Glucosamine treated heart_1

description:
Gene expression from glucosamine-fed adults
G1


title: Patient 4 M

status: Public on Jun 11 2015

type: protein

city: Daejeon

first: Myung-Shin

last: Lee

address: Yongdu-dong, Jung-gu

department: Microbiology and Immunology

country: South Korea

institute: Eulji University School of Medicine

hyb_protocol: Biotin labeled extract was hybridized with antibody-spotted slide for 2hr at room temperature. After hybridization, slide was washed with 1X wash buffer (Fullmoon Bio) and de-ionized water. Detection Buffer including Cy3-Streptavidin (fullmoon Bio) was treated for 20min at room temperature. And slide was washed with 1X wash buffer (Fullmoon Bio) and de-ionized water.

scan_protocol: Scanned on an Axon 4000B scanner.

data_processing: GenePix Software (v 6.1) was used for data extraction and Genowiz software (v 4.0.5.6) was used for global normalization.

molecule: protein

source_name: Muscle invasive BC

label_protocol: 50ug of Tissue extract was labeled with Biotin and label buffer (Fullmoon Bio).

extract_protocol: 10~40mg of tissues were washed with cold 1X PBS. And tissue samples were homogenized with Extracting buffer (Fullmoon Bio). Debris was removed from tissue extract with centrifuge.

treatment_protocol: All tissue samples were obtained intraiperatively and immedeately frozen in liquid nitrogen and stored at -70 degree until protein extraction

tag: diagnosis

value: Muscle invasive bladder cancer


title: Patient 3 M


title: Patient 5 M


title: Patient 6 M


title: 3_C33A RSVNeo 3

source_name: 3_C33A RSVNeo 3

value: control


title: Patient 5 S

source_name: Superficial BC

value: Superficial bladder cancer


title: Patient 4 S


title: 4_1.4a A 1

description: RNA extraction A


title: CEF_uninfected_rep1

description: Biological replicate 1 of 4. Gene expression in control chicken embryo fibroblast cells, untreated.

value: Leghorn


title: 2_C33A RSVNeo 2

source_name: 2_C33A RSVNeo 2


title: Patient 1 S


title: Patient 2 S


title: Patient 3 S


title: Patient 1 M


title: Patient 7 N

source_name: Bladder normal mucosa

value: Bladder normal mucosa


title: Patient 6 N


title: 1_C33A RSVNeo 1

source_name: 1_C33A RSVNeo 1


title: H1BP p18

city: Columbia

first: Ying

last: Yang

state: MO

address: 1201 East Rollins Street

department: Division of Animal Sciences

institute: University of Missouri-Columbia

description:
SAMPLE 5
replicate 1

data_processing:
The samples of RNA were submitted to University Texas Southwestern Medical Center Microarray Core Facility (https://microarray.swmed.edu/) and microarray analysis performed with Illumina HumanHT-12 v4 expression BeadChips. Raw intensity data were background subtracted by using BeadStudio software and analyzed further by GeneSpring 12.6 software (Agilent Technologies Inc., Santa Clara CA), according to the advanced workflow protocol: percentile shift and filter by flags (detected).
The data were normalized using quantile normalization

source_name: passage 18 of H1BP cells derived from H1 cells treated with BAP for 24h

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

growth_protocol: H1 cells were growing in mTeSR1 medium prior RNA extraction. In order to get H1BP cells, H1 cells were treated with BAP for 24 h and cultured in mouse embryonic fibroblast conditioned medium supplemented with 10ng/ml FGF2. After passage, H1BP colonies emerged and were maintained in mouse embryonic fibroblast conditioned medium supplemented with 10ng/ml FGF2.

extract_protocol: RNA was isolated from control human embryonic stem cells H1 cells, H1 cells exposed to BAP conditions for 24 and 48 h, H1BP colonies picked individually at two different passage numbers (p7 and p18), and H1BP cells that had been allowed to differentiate spontaneously in standard non-conditioned hESC medium in absence of FGF2. In order to collect RNA from cells, medium was removed and RNA STAT60  (I ml; Tel-Test, Friendswood, TX) was immediately added to culture dish and RNA extracted by following the manufacturer’s instructions.

treatment_protocol: H1 cells were treated with BAP for 24 h and 48 h prior RNA extraction. H1BP cells were cultured in standard non-conditioned hESC medium in absence of FGF2 for 10 days prior RNA extraction.

value: H1BP cells (derived from H1 cells treated with BAP for 24h)

tag: passage #


title: differentiated H1BP cells

description:
SAMPLE 6
replicate 1

source_name: H1BP cells allowed to differentiate spontaneously for 10 days

value: H1BP cells (differentiated for 10 days)


title: H1 BAP 48h

description:
SAMPLE 3
replicate 1

source_name: human embryonic stem cells treated with BAP for 48h

value: H1 hESCs

tag: agent

value: BAP

tag: time


title: Patient 5 N


title: Patient 2 M


title: H1BP p7

description:
SAMPLE 4
replicate 1

source_name: passage 7 of H1BP cells derived from H1 cells treated with BAP for 24h


title: Patient 3 N


title: H1

description:
SAMPLE 1
replicate 1

source_name: human embryonic stem cells


title: Patient 1 N


title: Patient 2 N


title: Patient 4 N


title: H1 BAP 24h

description:
SAMPLE 2
replicate 1

source_name: human embryonic stem cells treated with BAP for 24h


title: 17_HDF_T6hA_(HG-U133_Plus_2)

first: Wichmann

last: Barna

address: Szentkirály

institute: SOTE

description: Gene expression data from cell culture samples

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on Affymetrix HGU133 Plus 2.0 chip. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the GeneChip 3000 Scanner

data_processing: The data were preprocessed by the function mas5 from the Bioconductor affy package

source_name: HT29, HDFa cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 microg total RNA

extract_protocol: Qiagen RNeasy Mini extraction of total RNA was performed according to the manufacturer instructions

tag: cell culture

value: HDF Tumor


title: 18_HDF_T6hB_(HG-U133_Plus_2)


title: TAL2073_v2b_rep1

city: Boston

first: Julia

last: Rogers

state: Massachusetts

address: 45 Shattuck Street

department: BCMP

institute: Harvard Medical School

hyb_protocol: First, microarrays were double stranded by on-slide primer extension, as described in Berger et al. (Berger et al. Nat Biotechnol. 2006 (PMID 16998473)). The primer extension mixture contains Cy3-conjugated dUTP, to allow for quantification of the relative amount of double stranded DNA on each spot. Double stranded microarrays were pre-wetted in standard phosphate buffered saline (PBS) (10mM PO43-, 137 mM NaCl, 2.7 mMKCl, pH7.4) / 0.01% Triton-X 100 for 5 minutes. PBS / 2% (wt/vol) nonfat dried milk (Sigma) was applied to individual chambers of an eight-chamber gasket cover slip in a steel hybridization chamber (Agilent), and the assembled microarray was incubated for 1 hour at room temperature. Microarrays were then washed once with PBS / 0.1% (vol/vol) Tween-20 for 5 min and once with PBS / 0.01% (vol/vol) Triton X-100 for 2 min. Proteins were diluted in a 75-μl protein binding mixture containing PBS / 2% (wt/vol) milk, 51.3 ng/μl salmon testes DNA (Sigma), 0.2 μg/μl bovine serum albumin (New England Biolabs). Pre-incubated protein binding mixtures were applied to individual chambers of an eight-chamber gasket cover slip in a steel hybridization chamber (Agilent), and the assembled microarrays were incubated for 1 hour at room temperature. Microarrays were again washed once with PBS/ 0.5% (vol/vol) Tween-20 for 3 min, and then once with PBS/ 0.01% (vol/vol) Triton X-100 for 2 minutes. Alexa-488-conjugated rabbit polyclonal anti-GST antibody (Invitrogen) was diluted to 50μg/ml in PBS / 2% (wt/vol) milk and applied to individual chambers of an eight-chamber gasket cover slip in a steel hybridization chamber (Agilent), and the assembled microarrays were incubated for 30 minutes at room temperature. Microarrays were washed twice with PBS / 0.05% (vol/vol) Tween-20 for 3 min each, and once in PBS for 2 min. After each incubation step, microarrays and cover slips were disassembled in a staining dish filled with the first wash solution. All washes were performed in Coplin jars at room temperature on an orbital shaker at 125 rpm. Following each series of washes, microarrays were rinsed in PBS and slowly removed to ensure removal of detergent and uniform drying.

scan_protocol: Slides were scanned after primer extension to quantify the amount of incorporated Cy3-conjugated dUTP (543 nm ex, 570 nm em). Protein-bound microarrays were scanned to detect Alexa-488 conjugated antibody (488nm ex, 522 nm em) using at least three different laser power settings to capture a broad range of signal intensities and ensure signal intensities below saturation for all spots. Microarray TIF images were analyzed using GenePix Pro software (Molecular Devices), bad spots were manually flagged and removed, and data from multiple Alexa 488 scans of the same slide were combined using masliner (MicroArray LINEar Regression) software.

data_processing: First, we adjusted the Alexa-488 signal for each probe by a constant value so no probe had a negative background-subtracted intensity value. Second, we normalized Alexa-488 signal by the Cy3 signal for each spot to account for the differences in the total amount of double-stranded DNA. Because Cy3-dUTP incorporation is influenced both by the total number of adenines and the sequence context of each adenine, we perform a linear regression over all spots to compute the relative contributions to the total signal of all trinucleotide combinations. Using these regression coefficients, we calculate the ratio of observed-to-expected Cy3 intensity and use that as a normalization factor. Second, to correct for any non-uniformities in protein binding, we further adjust the Cy3-normalized Alexa-488 signal according to their spatial positions on the array. We calculate the median normalized intensity of the 15X15 block centered on each spot and divide the spot’s signal by the ratio of the median within the block to the median over the entire chamber. Here we provide the Cy3 and position normalized Alexa-488 signal intensity.

organism: synthetic construct

source_name: synthetic

label_protocol: All TALE constructs are N-terminally GST-tagged. Arrays were incubated with an Alexa-488-conjugated rabbit polyclonal anti-GST antibody (Invitrogen A-11131).

extract_protocol: All TALE constructs were cloned into the pDEST15 expression vector (Invitrogen), conferring an N-terminal glutathione S-transferase (GST) tag. Proteins were expressed using the PURExpress In Vitro Transcription and Translation Kit (New England Biolabs). Protein quantity and quality was assayed by anti-GST Western blot.

tag: protein name

tag: target site

value: TTGTGGCCGTTTACGTCGCC

tag: pbm concentration (nm)

tag: protein sequence


title: 13_HDF_K6hA_(HG-U133_Plus_2)

value: HDF Control


title: TAL2046_v2b_rep1

value: TGAACCGCATCGAGC


title: 16_HDF_N6hB_(HG-U133_Plus_2)

value: HDF Normal


title: 14_HDF_K6hB_(HG-U133_Plus_2)


title: TAL2072_v2b_rep1

value: TTCACCGGGGTGGTGCCCAT


title: TAL2039_v2b_rep2

value: TTGAAGAAGTCGTG


title: TAL2039_v2b_rep1


title: TAL2036_v2b_rep2

value: TTCAGCGTGTCCGG


title: HDMECs transfected with NUP160/SLC43A3 fusion genes

city: Kumamoto

first: Naoki

last: Shimozono

institute: Kumamoto university

description: test

data_processing:
The raw threshold cycle (Ct) was normalized using the values of housekeeping gene. deltaCt = (Ct_Target − Ct_HKG)]
Fold Change worksheet reports 1/2^ (normalized Ct of HDMEC transfected with the fusion gene – normalized Ct of HDMEC transfected with the control vector). ND, not detected.

label: SYBR Green

source_name: Human Dermal Microvascular Endothelial Cells (HDMEC), (Lonza)

label_protocol: For PCR array, first-strand cDNA was synthesized from RNA using RT2 First Strand Kit (Qiagen). cDNA was mixed with RT2 SYBR Green/Rox qPCR Master Mix (Qiagen), and the mixture was added to 96-well Human Angiogenesis PCR Array (Qiagen).

growth_protocol: Cells were cultured acording to the manufacturer's recommendation with EGM-2 MV Bullet kit (Lonza).

extract_protocol: Total RNA was extracted from culture cells with ISOGEN (Nippon Gene, Tokyo, Japan).

treatment_protocol: To transfected with fusion gene, Cells were cultured in growth media with lentiviral vector for 24h.

tag: cell type

value: HDMECs


title: TAL2037_v2b_rep1

value: TTGCCGTAGGTGGC


title: TAL2036_v2b_rep1


title: 11_HT_T24hA_(HG-U133_Plus_2)

value: HT Tumor


title: TAL2029_v2b_rep1

value: TGCGCTCCTGGAC


title: TAL2029_v2b_rep2


title: 15_HDF_N6hA_(HG-U133_Plus_2)


title: TAL2028_v2b_rep1

value: TCTTCAAGTCCGC


title: 09_HT_N24hA_(HG-U133_Plus_2)

value: HT Normal


title: TAL2024_v2b_rep1

value: TCCTGGTCGAGCT


title: 12_HT_T24hB_(HG-U133_Plus_2)


title: HDMECs transfected with control vector

description: control


title: TAL2023_v2b_rep1

value: TCGGCGAGCTGC


title: TAL2037_v2b_rep2


title: TAL2073_v3_rep2


title: TAL2020_v2b_rep2

value: TGACCTACGGCG


title: 10_HT_N24hB_(HG-U133_Plus_2)


title: 07_HT_K24hA_(HG-U133_Plus_2)

value: HT Control


title: 08_HT_K24hB_(HG-U133_Plus_2)


title: TAL2020_v2b_rep1


title: TAL2073_v3_rep1

value: TTGTGGCCGTTTACGTCGCC


title: TAL2046_v3_rep1


title: TAL2037_v3_rep1


title: TAL2072_v3_rep1


title: TAL2043_v2a_rep1

value: TTGTGGCCGTTTACG


title: TAL2041_v2a_rep5

value: TTCTTCTGCTTGTC


title: TAL2018_v2b_rep1

value: TCCGGCGAGGGC


title: TAL2016_v2a_rep2

value: TAGAGGATCCAC


title: TAL2041_v2a_rep1


title: TAL2041_v2a_rep2


title: TAL2043_v3_rep1


title: MCF7 with 23 IR doses delivered by IOERT-replicate6

city: Cefalù

first: Valentina

last: Bravatà

address: Contrada Pietrapollastra Pisciotto

institute: IBSBC CNR

description: Biological replicate 6 of 6.

hyb_protocol: The microarrays (Agilent Whole Human Genome, 4x44k) were hybridazed according to an established protocol by Agilent Technologies (Santa Clara, CA, USA). Two-channel arrays were hybridized using Cy3 and Cy5 and quantified using Feature Extraction v9.5 software. The Agilent Whole Human Genome Array (4x44K) was used for competitive hybridization and the slides were washed, dried, and scanned in an Agilent microarray scanner (Agilent Technologies, Palo Alto, CA, USA).

scan_protocol: Images were scanned using Agilent scanner, G2505B (Agilent Technologies, Palo Alto, CA, USA).

data_processing: Agilent Data Processing Protocol Calculation Method: Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction Software. FeatureExtractor_Version: 9.5.3.1. Protocol_Name: GE2-v5_95_Feb07.

label_protocol: 500 ng of total RNA was amplified according to the manufacturer’s instructions by double strand cDNA synthesis, followed by T7-based in vitro transcription. Untreated MCF7 breast cancer cell line was used as a control for all samples. Amplified complementary RNA (cRNA) was labeled with cyanine 5 (Cy5)-conjugated dUTP, whereas cRNA from untreated MCF7 was labeled with cyanine 3 (Cy3)-conjugated dUTP.

growth_protocol: MCF7 breast cancer cell line were collected after 24 hours post treatments

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

tag: treatment

value: 23 IR doses delivered by IOERT

tag: harvest time post treatment

value: 24 hours

tag: original tissue

value: breast

value: non exposed to IR treatments


title: MCF7 with 23 IR doses delivered by IOERT-replicate5

description: Biological replicate 5 of 6.

tag: cell line


title: TAL2041_v2a_rep4


title: TAL2025_v2a_rep1

value: TGAACTTGTGGCC


title: TAL2046_v1_rep1

value: TGAACCGCATCGAGC


title: TAL2017_v2a_rep1

value: TCGCCCTTGCTC


title: TAL2029_v3_rep1

value: TGCGCTCCTGGAC


title: TAL2016_v2a_rep1


title: TAL2041_v2a_rep3


title: TAL2036_v3_rep1

value: TTCAGCGTGTCCGG


title: TAL2016_v3_rep1


title: MCF7 with 23 IR doses delivered by IOERT-replicate4

description: Biological replicate 4 of 6.


title: TAL2029_v1_rep1


title: MCF7 with 23 IR doses delivered by IOERT-replicate1

description: Biological replicate 1 of 6.


title: TAL2028_v3_rep1

value: TCTTCAAGTCCGC


title: TAL2034_v1_rep1

value: TCCACCGGTCGCCA


title: TAL2009_v3_rep1

value: TAGGTGGCATC


title: TAL2009_v2a_rep4


title: MCF7 with 23 IR doses delivered by IOERT-replicate3

description: Biological replicate 3 of 6.


title: TAL2009_v2a_rep2


title: TAL2028_v1_rep1


title: MCF7 with 9 IR doses delivered by IOERT-replicate6

description: Biological replicate 6 of 6.

value: 9 IR doses delivered by IOERT


title: TAL2009_v2a_rep1


title: MetII

city: Vienna

first: Robert

last: Bischof

address: Gumpendorferstraße 1a

country: Austria

institute: ACIB GmbH

description: Sample with added L-methionine

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

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

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

organism: Trichoderma reesei QM9414

source_name: Wheat straw culture of T. reesei with L-methionine

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

growth_protocol: Cultures of T. reesei QM9414 (ATCC26921) were pregrown for 48 hours on Mandels Andreotti Medium with pretreated wheat straw as the sole carbon source as previously described (Bischof et. al., Biotechnology for Biofuels 2013, 6:127)

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen, Hilden, Germany) and purified using RNeasy MinElute Kit (Qiagen, Hilden, Germany)

treatment_protocol: After 48 hours, L-methionine resulting in a final concentration of 100µM was added

tag: added gene repressing substance

value: 100µM L-methionine


title: MCF7 with 9 IR doses delivered by IOERT-replicate5

description: Biological replicate 5 of 6.


title: TAL2009_v2a_rep3


title: TAL2024_v1_rep1

value: TCCTGGTCGAGCT


title: MCF7 with 23 IR doses delivered by IOERT-replicate2

description: Biological replicate 2 of 6.


title: QMII

description: Control sample without L-methionine addition

source_name: Wheat straw culture of T. reesei without L-methionine

value: none (control)


title: TAL2025_v1_rep1


title: TAL2020_v1_rep1

value: TGACCTACGGCG


title: MCF7 with 9 IR doses delivered by IOERT-replicate4

description: Biological replicate 4 of 6.


title: MetI

description: Sample with added L-methionine


title: TAL2003_v2a_rep1

value: TTACGTCGCC


title: QMI


title: MCF7 with 9 IR doses delivered by IOERT-replicate2

description: Biological replicate 2 of 6.

value: 24 hours


title: TAL2002_v2a_rep2

value: TGGTGCCCAT


title: TAL2018_v1_rep1

value: TCCGGCGAGGGC


title: zfHeart_atropine_1

city: Cambridge

first: Caitlin

middle: C

last: O'Meara

state: MA

address: 65 landsdowne street

institute: Brigham and Women's hospital

hyb_protocol: The arrays were washed and stained on Fluidics Stations 450 using the Affymetrix Hybe/Wash/Stain

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

data_processing: samples were normalized via the robust multiarray averaging method of normalization. The resulting water values were subracted from the atropine values to give the Log2FC. A 1.5 fold change was used as a cutoff for analysis

organism: Danio rerio

source_name: Adult zebrafish whole hearts

label_protocol: The Affymetrix 3’ IVT Express protocol was used to processing and label samples

extract_protocol: Trizol with quagen clean-up

treatment_protocol: Heart amputation (~20% of the ventricle apex) was performed on adult zebrafish hearts, fish were exposed to either water or atropine and hearts were collected 24 hours post amputations

value: adult

tag: protocol

value: ventricle amputation

value: atropine

tag: tissue

value: whole hearts


title: TAL2003_v2a_rep2


title: TAL2002_v2a_rep1


title: zfHeart_water_1

tag: developmental stage

value: water


title: MCF7 with 9 IR doses delivered by IOERT-replicate1

description: Biological replicate 1 of 6.

value: breast

value: non exposed to IR treatments


title: MCF7 with 9 IR doses delivered by IOERT-replicate3

description: Biological replicate 3 of 6.


title: Serum_pSLE-97A_rep1

status: Public on Jun 10 2015

type: other

city: Stanford

first: Jamie

last: Haddon

state: CA

address: CCSR Rm 2250, 269 Campus Drive West

department: Immunology & Rheumatology

institute: Stanford University

hyb_protocol: Serum was diluted 1:200 from stocks (maintained at -80 deg. C. in) in PBS + 0.5% Tween 20 (Sigma-Aldrich, St. Louis, MO) and 3% fetal calf serum (Omega Scientific, Tarzana CA). Post primary incubation, washed arrays were incubated with Goat anti-Human IgG conjugated to Cy5 (Jackson Immunoresearch, West Grove, PA).

scan_protocol: Arrays were scanned using an Axon digital scanning system (Molecular Devices, Sunnyvale, CA)

data_processing: Array images were analyzed using GenePix 6.0 software (Molecular Devices)

molecule: other

source_name: Serum

tag: diagnosis

value: pSLE

tag: proliferative nephritis

value: No


title: TAL2009_v1_rep1

value: TAGGTGGCATC


title: Serum_pSLE-92A_rep1

label: Goat anti-Human IgG conjugated to Cy5 (Jackson Immunoresearch, West Grove, PA)

value: Unknown


title: Serum_pSLE-91A_rep1


title: Serum_pSLE-94A_rep1


title: Serum_pSLE-90A_rep1

value: Yes


title: TAL2016_v1_rep1

value: TAGAGGATCCAC


title: Serum_pSLE-86A_rep1


title: Serum_pSLE-88A_rep1


title: Serum_pSLE-87A_rep1


title: Serum_pSLE-98A_rep1


title: Serum_pSLE-95A_rep1


title: Serum_pSLE-96A_rep1


title: Serum_pSLE-100A_rep1


title: Serum_pSLE-85A_rep1


title: Serum_pSLE-81A_rep1


title: Serum_pSLE-84A_rep1


title: Serum_pSLE-82A_rep1


title: Serum_pSLE-83A_rep1


title: Serum_pSLE-77A_rep1


title: Serum_pSLE-79A_rep1


title: Serum_pSLE-80A_rep1


title: Serum_pSLE-76A_rep1


title: Serum_pSLE-78A_rep1


title: Serum_pSLE-71A_rep1


title: Serum_pSLE-72A_rep1


title: Serum_pSLE-56A_rep1


title: Serum_pSLE-70A_rep1


title: Serum_pSLE-66A_rep1


title: Serum_pSLE-67A_rep1


title: Serum_pSLE-57A_rep1


title: Serum_pSLE-60A_rep1


title: Serum_pSLE-73A_rep1


title: Serum_pSLE-43A_rep1


title: Serum_pSLE-49A_rep1


title: Serum_pSLE-40A_rep1


title: Serum_pSLE-55A_rep1


title: Serum_pSLE-61A_rep1


title: Serum_pSLE-52A_rep1


title: Serum_pSLE-63A_rep1


title: Serum_pSLE-34A_rep1


title: Serum_pSLE-31A_rep1


title: Serum_pSLE-12A_rep1


title: Serum_pSLE-25A_rep1


title: Serum_pSLE-75A_rep1


title: Serum_Healthy-C19_rep1

value: Healthy


title: Serum_Healthy-C26_rep1


title: Serum_Healthy-C29_rep1


title: Serum_Healthy-C27_rep1


title: Serum_Healthy-C16_rep1


title: Serum_Healthy-C17_rep1


title: Serum_pSLE-29A_rep1


title: Serum_Healthy-C13_rep1


title: Serum_Healthy-C14_rep1


title: GSM-016

city: Shanghai

first: hongxiao

last: han

address: No. 518, Ziyue Road,

department: Shanghai Veterinary Research Institute

country: China

institute: Chinese Academy of Agricultural Sciences

description: sample16 GSM-016

hyb_protocol: The Cy5 dye labeled small RNAs (<300nt) were dissolved in 100 ul 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34℃ overnight.

scan_protocol: Hybridization images were scanned using a laser scanner (GenePix 4000B, Molecular Device) and digitize analysis was performed using Array-Pro software (Media Cybernetics, Bethesda, MD).

data_processing: The data was normalized using a cyclic LOWESS (Locally-weighted Regression) method for further analysis. We definded the differentially expressed miRNA using the ratio of detected signals log2-fold changes [log2(infected/control)] and p values of the t test were calculated.

source_name: infected liver

label_protocol: The assay began with 5ug of RNA from each sample which was size fractionated using an YM-100 Microcon filter (Millipore, Bedford, MA, USA). The small RNAs (<300 nt) extracted were 3’-extended with poly(A) polymerase and labeled with Cy5 dye. Hybridizations were started according to the manual using a μParaflo@ microfluidic technology.

growth_protocol: All animal care and experimental procedures were conducted according to the guidelines for animal use in toxicology.

extract_protocol: The animals were euthanized at 10 days post-infection (p.i.) and the lungs, liver and spleen were harvested and preserved in RNA later (Ambion) at -80℃ until RNA extraction. Total RNA extraction from ~100mg tissues was performed with the mirVana isolation kit, according to instructions of the manufacturer (Ambion, USA). The quality of RNA was measured using a Nanodrop-1000 and the integrity was evaluated by Agilent 2100 Bioanalyzer (Agilent Technologies, USA ).

treatment_protocol: All animals were singly-housed for one week before infection. Food and water was available ad libitum. M.fortis, Rat and BALB/c mice were percutaneously infected with 3000, 2000 and 200 S. japonicum cercariae (Chinese mainland strain, Anhui population), respectively. Three additional animals were used as uninfected controls.

value: liver

tag: Sex

value: Male

tag: infection

value: schistosomes


title: GSM-018

description: sample18 GSM-018

source_name: infected lung

value: lung


title: GSM-017

description: sample17 GSM-017

source_name: infected spleen

value: spleen


title: Serum_Healthy-C12_rep1


title: Serum_pSLE-5A_rep1


title: Serum_Healthy-C11_rep1


title: Serum_Healthy-C18_rep1


title: Serum_Healthy-C8_rep1


title: GSM-014

description: sample14 GSM-014

source_name: control spleen


title: Serum_Healthy-C9_rep1


title: Serum_Healthy-C5_rep1


title: GSM-013

description: sample13 GSM-013

source_name: control liver


title: dcpA knockout rep1

city: Bangalore

first: Dipankar

last: Chatterji

state: Karnataka

address: Malleshwaram

department: Molecular Biphysics Unit

country: India

institute: Indian Institute of Science

description: Gene expression after 48 hours for dcpA knockout strain

hyb_protocol: Agilent’s In situ Hybridzation kit 5188-5242 was used for hybridization

scan_protocol: scanned using the Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D) at 5 micron resolution.

data_processing: Images were quantified using Feature Extraction Software ( Agilent). Feature extracted raw data was analyzed using GeneSpring GX software from Agilent. Normalization of the data was done in GeneSpring GX using the 75th percentile shift (Gene based analysis was performed)

organism: Mycolicibacterium smegmatis MC2 155

source_name: dcpA knockout rep1

label_protocol: Random hexamer method of labeling was done followed by T7 promoter based-linear amplification to generate labeled complementary RNA (One-Color Microarray-Based Gene Expression Analysis). Agilent’s Quick-Amp labeling Kit (p/n5190-0442) was used.

extract_protocol: Qiagen's RNeasy minikit (Cat7410 4)

tag: genotype/variation

value: Strain impaired in c-di-GMP signalling


title: Wild type rep1

description: Gene expression after 48 hours for wild type strain

source_name: Wild type rep1

value: wild type strain of M.smegmatis mc2 155


title: Serum_Healthy-C3_rep1


title: Wild type rep2

source_name: Wild type rep2


title: Serum_Healthy-C15_rep1


title: rel knockout rep1

description: Gene expression after 48 hours for rel knockout strain

source_name: rel knockout rep1

value: Strain impaired in (p)ppGpp signalling


title: dcpA knockout rep2

source_name: dcpA knockout rep2


title: rel knockout rep2

source_name: rel knockout rep2


title: Serum_Healthy-C4_rep1


title: GSM-011

description: sample11 GSM-011

tag: strain

value: BALB/c


title: GSM-015

description: sample15 GSM-015

source_name: control lung


title: GSM-007

description: sample7 GSM-007


title: GSM-008

description: sample8 GSM-008


title: GSM-009

description: sample9 GSM-009


title: GSM-012

description: sample12 GSM-012


title: GSM-002

description: sample2 GSM-002

organism: Alexandromys fortis


title: GSM-006

description: sample6 GSM-006


title: GSM-005

description: sample5 GSM-005


title: GSM-003

description: sample3 GSM-003


title: GSM-001

description: sample1 GSM-001


title: GSM-004

description: sample4 GSM-004


title: LNCaP-truncated-AR-Y267F replicate 1

city: Chapel Hill

first: Office of Genomics Research

last: UNC Lineberger Comprehensive Cancer Center

state: NC

address: 125 Mason Farm Road, CB #7599 5105-5106 Marsico Hall

institute: University of North Carolina at Chapel Hill

hyb_protocol: Described in Hu et al., 2005, BioTechniques, 38:121-125

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with Agilent scanner and image intensity data were extracted and deposited into UNC microarray data base.

data_processing: Data for both channels were Lowess-normalized

source_name: LNCaP-vector cell line

growth_protocol: LNCaP cells expressing vector, truncated-AR-WT, and truncated-AR-Y267F were grown in androgen deprived media supplemented with charcoal-stripped serum.

extract_protocol: Total RNA was isolated by using RNeasy Mini kit (Qiagen) according to the manufacturer's instructions

value: LNCaP

tag: transfection

value: empty vector

source_name: LNCaP-truncated-AR-Y267F cell line

value: truncated (1-660 aa) AR Y267F mutant


title: LNCaP-truncated-AR-WT replicate 1

label_protocol: Described in Hu et al., 2005, BioTechniques, 38:121-125

source_name: LNCaP-truncated-AR-WT cell line

value: truncated (1-660 aa) AR wildtype


title: LNCaP-truncated-AR-WT replicate 2


title: LNCaP-truncated-AR-Y267F replicate 2


title: GSM-010

description: sample10 GSM-010


title: Uninfected U937 derived macrophages, biological replicate 3, technical replicate 2

city: Bogotá D.C.

first: Clemencia

middle: Elena

last: Ovalle-Bracho

state: Bogotá D.C.

address: Avenida 1 # 13A 61

department: Research office

country: Colombia

institute: Centro Dermatológico Federico Lleras Acosta

hyb_protocol: Hybridization was carried out by Almac Diagnostics according to their standard protocols. Fragmented and labelled cDNA was hybridised to an Affymetrix GeneChip® Exon ST Array (Affymetrix Inc.) for 16 hours at 45°C, in accordance with the NuGEN™ guidelines for hybridisation onto Affymetrix GeneChip® arrays. The hybridised arrays were washed and stained.

scan_protocol: The arrays were scanned using the GeneChip® Fluidics Station 450 and GeneChip® Scanner 3000 (Affymetrix Inc.) to generate raw probe level expression data.

data_processing:
Raw microarray profile data has been pre-processed with the Robust Multichip Average (RMA) algorithm (Bolstad et al. 2003) based on standard RMA background correction, quantile normalisation and median polish summarisation. The pre-processed data has been filtered to remove uninformative transcripts based on probeset intensity (background p-value = 0.01) and variance (variance α-value = 0.8), using an ALMAC developed software (FeatureSelection_Workflow version 102), resulting in 15237 probesets passing which comprise the reliably detected genes.
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps
Differentially expressed transcripts have been selected based on fold change differences between the groups of 1.5 and significant adjusted p-values of 0.05 (fold_change.txt)

label: Biotin Allonamide Triphosphate

source_name: U937 derived macrophages

label_protocol: The single-stranded cDNA samples were fragmented and Biotin-labelled using the GeneChip® WT Terminal Labelling Kit (Affymetrix Inc.)

growth_protocol: U937 cell line (American Type Culture Collection -CRL-1593.2) were cultured at a starting density of 100.000 cells/mL in complete RPMI-1640 (Sigma-Aldrich R410) medium supplemented with 10% serum fetal bovine (FBS) at  37 ° C in a 5% CO2 atmosphere. To obtain differentiated macrophages,  6.750.000 U937 cells were stimulated with 100 ng /mL phorbol-12- myristate-13 acetate (PMA) (Sigma P8139) in complete RPMI medium for 120 h, at 37 °C in a  5% CO2 atmosphere. Leishmania braziliensis promastigotes (MHOM/BR/00/M2903)  were cultured in Schneider's insect medium supplemented with 10% FBS and cultured at  26 °C for 6 days until reach stationary phase.

extract_protocol: Isolation of high quantity RNA was made using 500 µL of TRIzol® Reagent (Invitrogen 15596-018) in accordance with manufacturer’s protocol. For purification and precipitation of the isolated RNA, mini spin columns of the RNeasy kit (QIAGEN 74104) were used in accordance with manufacturer’s protocol. Nanodrop 2000 was used to assess RNA concentration and purity. Integrity was assessed using Agilent Bioanalyzer and RNA 6000 Nano Lab Chip kit (Agilent Technologies Ltd.). All samples had 260/280 ratio above 1,9 and RNA integrity numbers (RIN) were above 7,8. Total RNA samples were treated with DNAse-I and ribosomal RNA content was reduced using the RiboMinus™ Human transcriptome isolation kit (Life Technologies), followed by the generation of single-stranded cDNA using the NuGEN Ovation™ RNA amplification system (NuGEN Technologies Inc).

treatment_protocol: Two evaluation groups were considered: Leishmania braziliensis-infected macrophages and uninfected macrophages. Macrophage infection was performed by incubating 15 promastigotes for each U937 derived macrophage at 34°C, in a 5% CO2 atmosphere for 72 h.

tag: cell line background

value: U937 derived macrophages

tag: infected with

value: none (uninfected control)


title: Uninfected U937 derived macrophages, biological replicate 3, technical replicate 3

tag: cell type


title: Uninfected U937 derived macrophages, biological replicate 1, technical replicate 3


title: Uninfected U937 derived macrophages, biological replicate 3, technical replicate 1


title: Uninfected U937 derived macrophages, biological replicate 2, technical replicate 1


title: Uninfected U937 derived macrophages, biological replicate 1, technical replicate 2


title: Infected U937 derived macrophages by Leishmania braziliensis, biological replicate 3, technical replicate 1

source_name: U937 derived macrophages infected by L. braziliensis for 72 h

value: Leishmania braziliensis

tag: leishmania strain


title: Infected U937 derived macrophages by Leishmania braziliensis, biological replicate 3, technical replicate 2


title: Uninfected U937 derived macrophages, biological replicate 2, technical replicate 2


title: Uninfected U937 derived macrophages, biological replicate 2, technical replicate 3


title: Infected U937 derived macrophages by Leishmania braziliensis, biological replicate 3, technical replicate 3


title: Infected U937 derived macrophages by Leishmania braziliensis, biological replicate 2, technical replicate 3


title: Infected U937 derived macrophages by Leishmania braziliensis, biological replicate 2, technical replicate 2


title: duoxa-/- pooled, cage3

city: Ann Arbor

first: Helmut

last: Grasberger

address: 1150 West Medical Center Drive

institute: University of Michigan

description:
duoxa_cage3
gene expression data for RNA pooled from duoxa-/- mice from cage3

hyb_protocol: Hybridization was performed by the UM microarray core facility acoording to standard procedures

scan_protocol: Scanning was performed by the UM microarray core facility acoording to standard procedures

data_processing: Microarray image data were checked for quality and normalized with the RMA procedure using the affy package of Bioconductor implemented in the R statistical language.

source_name: terminal ileum_duoxa-/-

label_protocol: Target labeled cRNA was synthesized using the IVT Express kit

extract_protocol: Total RNA was prepared using TRIzol reagent, treated with deoxyribonuclease and further cleaned up on RNeasy spin columns (Qiagen). RNA quality was checked on RNA 6000 Nano BioAnalyzer

tag: strain background

value: duoxa-/-

tag: gender

value: female

tag: age

value: 3 months

value: ileum


title: wt pooled, cage3

description:
wt_cage3
gene expression data for RNA pooled from wt mice in cage3

source_name: terminal ileum_wt

value: wt


title: Pitx2 8µg transfected Sol8 cells after 48h; probe 3

city: Jaen

first: Francisco

middle: J.

last: Esteban

state: Jaen

address: Campus Las Lagunillas s/n

department: Experimental Biology

country: Spain

institute: University of Jaen

description:
Sample name: pitx_48_8_2
Raw data file: T00342442 Down.gpr; rows 1937 to 2834
30 µg of total RNA was used to hybridize the mirVana miRNA Bioarray

hyb_protocol: mirVana™ miRNA Bioarrays Kit (Cat #AM1566V2)

scan_protocol: Microarrays were scanned on Axon GenePix 4100A scanner (Molecular Devices, Sunnyvale, CA, USA). The GenePix Pro 6.0.1.25 software (Molecular Devices, Sunnyvale, CA, USA) was used to analyse the obtained images.

data_processing: The original raw data file contains quadruplicates of a given microRNA probe. Thus, the raw data for each replicate corresponding to the same probe (F635 Mean - B635 signal intensity value) was splitted to a independent colum (using a custom script run in Python) and, then, normalized using the justvsn function, implemented in the vsn Bioconductor library (run in R). The normalized data for 24h and 48h subsets  were independently uploaded and analyzed in the TM4 microarray software suite (http://www.tm4.org/), where a One-way ANOVA test was carried out using 1000 permutations; the microRNAs selected as significant were those showing a false significant proportion < 0.05. Hierarchical clustering was obtained selecting the Pearson absolute correlation and complete linkage algorithms.

source_name: Sol8 skeletal myogenic (ATCC, CRL-2174) cells

label_protocol: mirVana™ miRNA Labeling Kit (Cat #AM1562)

extract_protocol: mirVana™ miRNA Isolation Kit (Cat #1560, 1561)

tag: cell line

value: Pitx2 8µg

tag: time


title: Pitx2 8µg transfected Sol8 cells after 48h; probe 2

description:
Sample name: pitx_48_8_1
Raw data file: T00342442 Down.gpr; rows 987 to 1936
30 µg of total RNA was used to hybridize the mirVana miRNA Bioarray

value: Sol8 skeletal myogenic (ATCC, CRL-2174) cells


title: Pitx2 8µg transfected Sol8 cells after 48h; probe 4

description:
Sample name: pitx_48_8_3
Raw data file: T00342442 Down.gpr; rows 2835 to 3750
30 µg of total RNA was used to hybridize the mirVana miRNA Bioarray


title: Uninfected U937 derived macrophages, biological replicate 1, technical replicate 1


title: Infected U937 derived macrophages by Leishmania braziliensis, biological replicate 1, technical replicate 2


title: Infected U937 derived macrophages by Leishmania braziliensis, biological replicate 1, technical replicate 3


title: Infected U937 derived macrophages by Leishmania braziliensis, biological replicate 1, technical replicate 1


title: Pitx2 8µg transfected Sol8 cells after 48h; probe 1

description:
Sample name: pitx_48_8_0
Raw data file: T00342442 Down.gpr; rows 89 to 986
30 µg of total RNA was used to hybridize the mirVana miRNA Bioarray


title: Pitx2 4µg transfected Sol8 cells after 48h; probe 4

description:
Sample name: pitx_48_4_3
Raw data file: T00342441 Down.gpr; rows 2835 to 3750
30 µg of total RNA was used to hybridize the mirVana miRNA Bioarray

value: Pitx2 4µg


title: Pitx2 4µg transfected Sol8 cells after 48h; probe 2

description:
Sample name: pitx_48_4_1
Raw data file: T00342441 Down.gpr; rows 987 to 1936
30 µg of total RNA was used to hybridize the mirVana miRNA Bioarray


title: control Sol8 cells after 48h; probe 4

description:
Sample name: control48_3
Raw data file: T00342440 Down.gpr; rows 2835 to 3750
30 µg of total RNA was used to hybridize the mirVana miRNA Bioarray

value: control


title: Infected U937 derived macrophages by Leishmania braziliensis, biological replicate 2, technical replicate 1


title: control Sol8 cells after 48h; probe 2

description:
Sample name: control48_1
Raw data file: T00342440 Down.gpr; rows 987 to 1936
30 µg of total RNA was used to hybridize the mirVana miRNA Bioarray


title: wt pooled, cage2

description:
wt_cage2
gene expression data for RNA pooled from wt mice in cage2

tag: tissue


title: duoxa-/- pooled, cage1

description:
duoxa_cage1
gene expression data for RNA pooled from duoxa-/- mice from cage1


title: duoxa-/- pooled, cage2

description:
duoxa_cage2
gene expression data for RNA pooled from duoxa-/- mice from cage2


title: GF Non-Treg

first: yukihiro

last: furusawa

institute: Toyama Prefectural University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000.

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

source_name: GF Non-Treg

label_protocol: Biotinylated cRNA were prepared according to the Ovation RNA amplification system V2 from at least 20 ng  total RNA/

extract_protocol: TRIZOL LS or QIAGEN RNeasy micro with Dnase

value: IQI

value: germ free

value: colonic lamina propria cells

tag: cell subtype

value: Treg cells; CD3+CD4+FR4-CD25-


title: Pitx2 8µg transfected Sol8 cells after 24h; probe 4

description:
Sample name: pitx_24_8_3
Raw data file: T00342442 Up.gpr; rows 2835 to 3750
30 µg of total RNA was used to hybridize the mirVana miRNA Bioarray


title: control Sol8 cells after 48h; probe 1

description:
Sample name: control48_0
Raw data file: T00342440 Down.gpr; rows 89 to 986
30 µg of total RNA was used to hybridize the mirVana miRNA Bioarray


title: wt pooled, cage1

description:
wt_cage1
gene expression data for RNA pooled from wt mice in cage1


title: Pitx2 8µg transfected Sol8 cells after 24h; probe 3

description:
Sample name: pitx_24_8_2
Raw data file: T00342442 Up.gpr; rows 1937 to 2834
30 µg of total RNA was used to hybridize the mirVana miRNA Bioarray


title: GF Treg

source_name: GF Treg

value: Non-Treg cells; CD3+CD4+FR4+CD25+


title: Pitx2 8µg transfected Sol8 cells after 24h; probe 1

description:
Sample name: pitx_24_8_0
Raw data file: T00342442 Up.gpr; rows 89 to 986
30 µg of total RNA was used to hybridize the mirVana miRNA Bioarray


title: Pitx2 8µg transfected Sol8 cells after 24h; probe 2

description:
Sample name: pitx_24_8_1
Raw data file: T00342442 Up.gpr; rows 987 to 1936
30 µg of total RNA was used to hybridize the mirVana miRNA Bioarray


title: KO Treg

source_name: Uhrf1 KO Treg

value: Uhrf1 knockout

value: Treg cells; CD3+CD4+Foxp3+


title: KO Non-Treg

source_name: Uhrf1 KO Non-Treg

value: Non-Treg cells; CD3+CD4+Foxp3-


title: WT Non-Treg

source_name: Non-Treg

value: wild type (parental control)


title: Pitx2 4µg transfected Sol8 cells after 48h; probe 3

description:
Sample name: pitx_48_4_2
Raw data file: T00342441 Down.gpr; rows 1937 to 2834
30 µg of total RNA was used to hybridize the mirVana miRNA Bioarray


title: control Sol8 cells after 48h; probe 3

description:
Sample name: control48_2
Raw data file: T00342440 Down.gpr; rows 1937 to 2834
30 µg of total RNA was used to hybridize the mirVana miRNA Bioarray


title: Pitx2 4µg transfected Sol8 cells after 48h; probe 1

description:
Sample name: pitx_48_4_0
Raw data file: T00342441 Down.gpr; rows 89 to 986
30 µg of total RNA was used to hybridize the mirVana miRNA Bioarray


title: SPF Treg

source_name: SPF Treg

value: specific-pathogen-free


title: WT Treg

source_name: WT Treg


title: SPF Non-Treg

source_name: SPF Non-Treg


title: Pitx2 4µg transfected Sol8 cells after 24h; probe 4

description:
Sample name: pitx_24_4_3
Raw data file: T00342441 Up.gpr; rows 2835 to 3750
30 µg of total RNA was used to hybridize the mirVana miRNA Bioarray


title: Pitx2 4µg transfected Sol8 cells after 24h; probe 3

description:
Sample name: pitx_24_4_2
Raw data file: T00342441 Up.gpr; rows 1937 to 2834
30 µg of total RNA was used to hybridize the mirVana miRNA Bioarray


title: Pitx2 4µg transfected Sol8 cells after 24h; probe 1

description:
Sample name: pitx_24_4_0
Raw data file: T00342441 Up.gpr; rows 89 to 986
30 µg of total RNA was used to hybridize the mirVana miRNA Bioarray


title: Pitx2 4µg transfected Sol8 cells after 24h; probe 2

description:
Sample name: pitx_24_4_1
Raw data file: T00342441 Up.gpr; rows 987 to 1936
30 µg of total RNA was used to hybridize the mirVana miRNA Bioarray


title: control Sol8 cells after 24h; probe 4

description:
Sample name: control24_3
Raw data file: T00342440 Up.gpr; rows 2835 to 3750
30 µg of total RNA was used to hybridize the mirVana miRNA Bioarray


title: control Sol8 cells after 24h; probe 3

description:
Sample name: control24_2
Raw data file: T00342440 Up.gpr; rows 1937 to 2834
30 µg of total RNA was used to hybridize the mirVana miRNA Bioarray


title: control Sol8 cells after 24h; probe 2

description:
Sample name: control24_1
Raw data file: T00342440 Up.gpr; rows 987 to 1936
30 µg of total RNA was used to hybridize the mirVana miRNA Bioarray


title: control Sol8 cells after 24h; probe 1

description:
Sample name: control24_0
Raw data file: T00342440 Up.gpr; rows 89 to 986
30 µg of total RNA was used to hybridize the mirVana miRNA Bioarray


title: At_shoot_WT_treatment N+, biological rep 1

city: Capital Federal

first: Mariana

last: Obertello

address: Vuelta de Obligado 2490

department: Department of Biology

country: Argentina

institute: INGEBI-CONICET

hyb_protocol: We used 15 µg of labeled cRNA to hybridize the Arabidopsis ATH1 Affymetrix and Rice Affymetrix gene chip for 16 h at 42°C. Washing, staining and scanning were performed as recommended by Affymetrix.

scan_protocol: Scanning were performed as recommended by Affymetrix.

data_processing: All microarray data was processed with Robust Microarray Analysis (RMA) normalization and summarization were done using the R Bioconductor package.

organism: Arabidopsis thaliana

label_protocol: Biotin-labeled cRNA was synthesized using the Enzo BioArray HighYield RNA Transcript Labeling Kit (Enzo, New York, NY).

growth_protocol: Seeds were surface-sterilized in 70% ethanol for 3 minutes followed by commercial H2O2 for 30 minutes with gently agitation, and washed with distilled water. Seeds were sown onto basal MS salts (custom-made; GIBCO) with 0.5 mM ammonium succinate and 3 mM sucrose, 0.8% BactoAgar at pH 5.5 for 3 days in dark conditions at 27°C. Following germination, embryos with developed root system and aerial tissue were dissected from the rest of the seed using a sterile blade and transferred to a hydroponic system (Phytatray II, Sigma Aldrich) containing basal MS salts (custom-made; GIBCO) with 0.5 mM ammonium succinate and 3 mM sucrose at pH 5.5 at light intensity of 180 μE.s-1.m-2 and at 27°C.  Fresh media was exchanged every 3 days. Arabidopsis seeds were placed for 2 days in the dark at 4°C to synchronize germination. Seeds were surface-sterilized and then transferred to a hydroponic system (Phytatray I, Sigma Aldrich) containing the same media previously described for rice (pH 5.7). Growth conditions were the same as in rice, except that plants were under 50 μE.s-1.m-2 light intensity at 22°C.

extract_protocol: RNA was isolated from whole plants using Trizol reagent according to the intructions of the manufacturer (15596; Invitrogen).

treatment_protocol: On day 13,  plants were transiently treated for 2 h at the start of their light cycle by adding N at a final concentration of 20 mM KNO3 and 20 mM NH4NO3. Control plants were treated with KCl at a final concentration of 20 mM. After treatment, whole seedlings were harvest and immediately frozen in liquid nitrogen.

value: wild type

value: 13 days

value: shoot

tag: treated with

value: 20 mM KNO3 and 20 mM NH4NO3 (final conc) for 2hr


title: Cultured iPSC colony 2 from orangutan KB10460

city: Los Angeles

first: Joseph

middle: Gerard

last: Hacia

address: 2250 Alcazar Street, IGM 261

department: Biochemistry and Molecular Biology

institute: University of Southern California

description: Gene expression data of orangutan KB10460 iPSC colony 2

hyb_protocol: followed affymetrix protocol

scan_protocol: followed affymetrix protocol

data_processing: WebArray software was used to generate log2-transformed gene expression values using the RMA algorithm

organism: Pongo abelii

source_name: iPSC from Sumatran orangutan KB10460

label_protocol: followed affymetrix protocol

growth_protocol: Fibroblasts were maintained in Dulbecco’s modified eagle medium (DMEM) containing 10% fetal bovine serum (FBS), 2 mM L-glutamine, 100 µM nonessential amino acids and 0.5% penicillin and streptomycin. iPSCs were cultured in 1:1 ratio of DMEM:F12 medium supplemented with 20% KSR at 37°C, 5% CO2.

extract_protocol: RNA was isolated  using the RNA Stat-60 reagent according to the manusfacturer's suggested protocol (Tel-Test, Inc.).

treatment_protocol: Fibroblasts were dissociated with 0.05% trypsin at 37°C, 5% CO2 for 5minutes and collected by centrifugation; iPSCs were dissociated with 1mg/ml collagenase IV at 37°C, 5% CO2 for 5 minutes, manually detached and collected by centrifugation

value: induced pluripotent stem cells

tag: genotype

value: healthy control

value: 43 year old

tag: Sex

value: female


title: At_shoot_WT_treatment N-, biological rep 1

tag: genotype/variation

value: 20mM KCl (final conc.) for 2hr


title: Cultured iPSC colony 3 from orangutan KB10460

description: Gene expression data of orangutan KB10460 iPSC colony 3


title: Cultured iPSC colony 1 from orangutan KB10973

description: Gene expression data of orangutan KB10973 iPSC colony 1

source_name: iPSC from Sumatran orangutan KB10973

value: 29 year old

value: male


title: At_root_WT_treatment N+, biological rep 1

value: root


title: At_shoot_WT_treatment N+, biological rep 2


title: At_root_WT_treatment N+, biological rep 2


title: At_shoot_WT_treatment N-, biological rep 2


title: Cultured iPSC colony 3 from orangutan KB10973

description: Gene expression data of orangutan KB10973 iPSC colony 3


title: At_root_WT_treatment N-, biological rep 2


title: Cultured iPSC colony 1 from orangutan KB10460

description: Gene expression data of orangutan KB10460 iPSC colony 1


title: Cultured iPSC colony 2 from orangutan KB10973

description: Gene expression data of orangutan KB10973 iPSC colony 2


title: Os_shoot_WT_treatment N+, biological rep 2

organism: Oryza sativa


title: CSES21_T21_Teratoma

city: Jerusalem

first: Yishai

last: Avior

state: Israel

address: Edmond J. Safra Campus, Givat Ram

department: Genetics

country: Israel

institute: Hebrew University of Jeursalem

hyb_protocol: Affymetrix protocol, 11ug cRNA

scan_protocol: GeneChip scanner 3000 7G, GeneChip Operating Software v1.4

data_processing: Affymetrix Expression Console RMA

source_name: Teratroma from aneuploid hESC (trisomy 21)

label_protocol: 200ng total RNA, Affymetrix protocol

extract_protocol: According to the manufacture instruction. RNA was subjected to Human Genome U133 Plus 2.0 microarray platform (Affymetrix); washing and scanning were performed according to the manufacturer’s protocol


title: CSES20_T21_Teratoma


title: CSES32_T21_Teratoma


title: At_root_WT_treatment N-, biological rep 1


title: spleen_Cip2a_rep3

city: Neuherberg

first: Martin

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum München GmbH

description:
SAMPLE 7
replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol using HiScan

data_processing: The data were normalized using cubic spline normalization with Illumina Genomestudio 2011.1

source_name: spleen

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

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up with QIAGEN RNeasy midi kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with gel electrophoreses.

tag: strain

value: C57BL/6Jx 129Ola

value: mutant

value: 18 weeks

tag: mouse id


title: spleen_Cip2a_rep4

description:
SAMPLE 8
replicate 4


title: CSES13_T21_Teratoma


title: Os_shoot_WT_treatment N+, biological rep 1