title: Hiller_S_pneumo_dTprA2_study_mutant_rep3

city: Pittsburgh

first: Anagha

last: Kadam

state: Pennsylvania

address: 4400 Fifth Avenue, Mellon Institute, Room 217

department: Biological Sciences

institute: Carnegie Mellon University

description: This sample is of Streptococcus pneumoniae delta-tprA2 in which tprA2 (SPN23F_12750) is deleted. It is the third of three mutant strain biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Hybridization was performed using NimbleGen hybridization kit components as per the NimbleGen Arrays User's Guide, Gene Expression Analysis Version 6.0

scan_protocol: Scanning was performed using manufacrturer's array software, NimbleScan as per the user's guide

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

organism: Streptococcus pneumoniae

source_name: Streptococcus pneumoniae PN4595-T23 delta-TprA2

label_protocol: Labeling was performed using NimbleGen One Color DNA Labeling Kit as per the NimbleGen Arrays User's Guide, Gene Expression Analysis Version 6.0

growth_protocol: Streptococcus pneumoniae PN4595T-23 was grown to mid-log phase (O.D.600nm 0.5) in Columbia media at 37 degrees C with 5% CO2, without shaking

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by Turbo DNase digestion (Ambion). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer.

treatment_protocol: Streptococcus pneumoniae PN4595T-23 delta-tprA2 was grown to mid-log phase (O.D.600nm 0.5) in Columbia media at 37 degrees C with 5% CO2, without shaking

value: Deletion of tprA2 (SPN23F_12750)


title: HCC827

status: Public on Nov 11 2017

type: RNA

city: Sendagi, Bunkyou-ku

first: Akiko

last: Takahashi

state: Tokyo

department: Pulmonary medicine

country: Japan

institute: Nippon Medical School Hospital

description: the parent cells HCC827

hyb_protocol: Biotin-labeled cDNA was injected into Genechip Human Gene 2.0 ST array and hybridized with probe in Genechip Hybridization Oven 645. The array was washed using Genechip Hybridization, Wash and Stain Kit and stained by phycoerythrin. GeneChip Fluidics Station 450 was used.

scan_protocol: Fluorescent signal by phycoerythrin staining of cDNA hybridized to the probe in the array was measured using a GeneChip Scanner 3000 7G. Data was acquired using analysis software GeneChip Command Console.

data_processing: Data was normalized in a data mining software (GeneSpring GX Version12.6) using the RMA 16 Summarization algorithm. Confidence level was all. Baseline transformation was not performed. All scanned transcript cluster data were obtained.

label: biotin

molecule: total RNA

organism: Homo sapiens

label_protocol: The purified, sense-strand cDNA is fragmented by uracil-DNA glycosylase (UDG) and  apurinic/apyrimidinic endonuclease 1 (APE 1) at the unnatural dUTP residues and breaks the DNA  strand. The fragmented cDNA is labeled by terminal deoxynucleotidyl transferase (TdT) using the  Affymetrix proprietary DNA Labeling Reagent that is covalently linked to biotin. 5.5 μg of singlestranded  cDNA is required for fragmentation and labeling.

extract_protocol: Total RNA from cells was extracted using Rneasy Plus Mini (QIAGEN) Kit according to the manufacturer’s protocol.

tag: cell line

tag: genotype/variation

value: EGFR mutation positive(del.19)


title: c6

status: Public on Nov 10 2017

city: Hangzhou

first: Chengliang

last: Zhou

state: Zhejiang

address: No. 866th, Yuhangtang Road

department: School of Medicine

country: China

institute: Zhejiang University

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: After washing, the arrays were scanned by the Agilent Scanner G2505C(Agilent Technologies).

data_processing: Feature Extraction software (version10.7.1.1, Agilent Technologies) was used to analyze array images to get raw data. Genespring(version 13.1, Agilent Technologies) were employed to finish the basic analysis with the raw data.

source_name: Ovarian granulosa cells, normal control

label_protocol: The sample labeling, microarray hybridization and washing were performed based on the manufacturer’s standard protocols. Briefly, total RNA were transcribed to double strand cDNA, then synthesized into cRNA and labeled with Cyanine-3-CTP.

extract_protocol: RNA was extracted from oGCs using the miRNeasy mini kit (Qiagen).Total RNA was quantified by the NanoDrop ND-2000 (Thermo Scientific)and the RNA integrity was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: Ovarian granulosa cells were obtained by follicular aspiration from women undergoing oocyte retrieval for IVF. For each patient, cells from multiple follicles and consequently follicular fluid were pooled. oGCs from each patient were extracted as described (9) and stored in Trizol (Thermo Fisher Scientific) at −80°C.

tag: gender

value: Female

tag: age

tag: cell type

value: Ovarian granulosa cells

tag: disease state

value: normal control


title: 3097


title: alopecia skin biological rep3

city: Krasnoyarsk

first: Anna

last: Komina

address: Partizana Zheleznyaka

department: Pathological physiology

country: Russia

institute: Krasnoyarsk State Medical University

hyb_protocol: Hybridization on arrays in Affymetrix® miRNA 4.1 Array Strip (Affymetrix, Santa Clara, USA) using the GeneChip® GeneAtlas™ Hybridization and Stain Module (Ref. 902135) reagents (Affymetrix, Santa Clara, CA, USA) 48°C for 20 h

scan_protocol: Washing array strips on the GeneAtlas™ Microarray System Fluidic Station using the GeneChip® GeneAtlas™ Hybridization and Stain Module buffers and solutions (Ref. 902135) (Affymetrix, Santa Clara, CA, USA) and detecting on the Imaging Station of the GeneAtlas™ Microarray System

data_processing:
Data were analyzed using Expression Console and Transcriptome Analysis Console 3.0 software (Affymetrix, USA).
affymetrix-algorithm-name = rma : dabg
affymetrix-algorithm-version = 1.0
affymetrix-array-type = miRNA-4_1
program-name = Expression Console
program-version = 1.4.0.38

source_name: alopecia skin

label_protocol: 8 ul of total RNA samples containing from 130 to 270 ng microRNA were labeled with biotin using Affymetrix® Flash Tag™ Biotin HSR (Ref. 901913, Affymetrix, Santa Clara, CA, USA)

growth_protocol: Skin biopsies were obtained from patients with androgenetic alopecia and healthy volunteers after obtaining informed consent.

extract_protocol: For RNA extraction skin tissues were washed in 0,01M PBS after RNA-later and homogenized mechanically with liquid nitrogen. Total RNA was isolated using RecoverAll™ Total Nucleic Acid Isolation kit (Cat# AM1975, Ambion, Vilnius, Lithuania)

treatment_protocol: Skin samples were stored in RNA-later at -20C before RNA isolation

tag: subject status

value: hair loss patient

value: female

tag: tissue

value: skin biopsy

tag: tissue subtype

value: alopecia skin

tag: molecule subtype

value: microRNA


title: Hiller_S_pneumo_dTprA2_study_mutant_rep2

country: USA

description: This sample is of Streptococcus pneumoniae delta-tprA2 in which tprA2 (SPN23F_12750) is deleted. It is the second of three mutant strain biological replicates used in this experiment, each from separate cultures.

tag: genotype


title: 2094

source_name: Ovarian granulosa cells, PCOS with with normal testosterone level


title: 3084


title: 8.14

source_name: Ovarian granulosa cells, PCOS with hyperandrogenism

value: PCOS with hyperandrogenism


title: XYL


title: 9.7

value: PCOS with with normal testosterone level


title: 8.12


title: 3090


title: Hiller_S_pneumo_dTprA2_study_mutant_rep1

description: This sample is of Streptococcus pneumoniae delta-tprA2 in which tprA2 (SPN23F_12750) is deleted. It is the first of three mutant strain biological replicates used in this experiment, each from separate cultures.


title: 3328


title: Hiller_S_pneumo_dTprA2_study_wild-type_rep2

description: This sample is of wild-type Streptococcus pneumoniae PN4595-T23. It is the second of three wild-type biological replicates used in this experiment, each from separate cultures.

source_name: Streptococcus pneumoniae PN4595-T23 wild-type

value: Wild-type


title: Hiller_S_pneumo_dTprA2_study_wild-type_rep1

description: This sample is of wild-type Streptococcus pneumoniae PN4595-T23. It is the first of three wild-type biological replicates used in this experiment, each from separate cultures.


title: Hiller_S_pneumo_dTprA2_study_wild-type_rep3

description: This sample is of wild-type Streptococcus pneumoniae PN4595-T23. It is the third of three wild-type biological replicates used in this experiment, each from separate cultures.


title: ex vivo human skin, sandalwood oil (0,4%) 9h_C

city: Longjumeau

first: Thomas

middle: M.

last: BADER

address: 1 chemin de Saulxier

country: France

institute: GENEX

description: 0,4% SO gene expression after 9h

hyb_protocol: according to Agilent protocol

scan_protocol: Slides were scannedon the Agilent Technologies Scanner G2505C US83400191 using one color scan setting for 1x44k array slides (20bit depth).

data_processing:
The microarray data were quantified according to the protocol of the quantification software Feature Extraction Software (FeatureExtractor_Version 11.5.1.1, Agilent) using default parameters (protocol GE1_1105_Oct12 and Grid: 039494_D_F_20150612). The data files were normalized and the gProcessedSignal values used as final data set.
After qualitative validation of the microarrays and normalization of the data, the fold-change (FC) between treated versus untreated was calculated. The effects of treatment were evaluated according to a fold change (FC) determined by the following ratio: gene intensity of treated samples versus gene intensity of control samples.

source_name: abdoplasty

label_protocol: RNA (40ng) of each sample was used for reverse transcription, amplification and Cy3 labeling, using the Low Input Labeling kit, one-color (Agilent Technologies). All cRNAs were hybridized to human whole genome microarrays (Agilent Technologies). Labeled cRNA concentrations [ng/μl] and Cy3 incorporation [pmol/μl] were measured using the spectrometer Nanodrop 1000 (ThermoFisher), (cRNA yields> 825ng and AES > 6pmol Cy3/µg cRNA).

growth_protocol: The abdoplasty was immediately transported at room temperature in minimum essential medium 1X (MEM, Gibco life technologies™; Paisley, UK) to BIO-EC laboratory. The hypodermis was removed from the skin, and circular explants (~1cm diameter, 0.2cm thickness, 180mg) were then excised using a sample punch. Explants, dermis face down, were directly placed in a liquid–air interface in BIO-EC’s Explant Medium (BEM), containing gentamicin and fungizone for 24h before treatment. Skin samples were maintained under typical cell culture conditions (37°C in 5% CO2), and half of the medium (1ml) was refreshed every other day.

extract_protocol: Samples were cut in half for storage in RNAlater (Qiagen) or fixation in buffered formol.Total RNA was extracted with ReliaPrep Tissue Miniprep system (fibrous) from Promega.

treatment_protocol: Samples were taken for each timepoint. Triplicates were removed at 9h and 24h for genomic expression analysis and histology, and on day 8 for morphological evaluation. Treatment consisted of excipient alone (sweet almond oil) as control, or 0.1, 0.2, 0.4% (P3), 1.0 and 2% (P1) Santalum album oil in excipient, on day 0 (D0), day 1, day 4 and day 6 on the basis of 2mg per explant.

value: skin

value: 49 years


title: ex vivo human skin, sandalwood oil (0,4%) 24h_A

description: 0,4% SO gene expression after 24h


title: ex vivo human skin, sandalwood oil (0,4%) 24h_B

description: 0,4% SO gene expression after 24h


title: ex vivo human skin, sandalwood oil (2%) 24h_B

description: 2% SO gene expression after 24h


title: ex vivo human skin, sandalwood oil (0,4%) 24h_C

description: 0,4% SO gene expression after 24h


title: ex vivo human skin, sandalwood oil (2%) 24h_C

description: 2% SO gene expression after 24h


title: ex vivo human skin, sandalwood oil (0,4%) 9h_B

description: 0,4% SO gene expression after 9h


title: ex vivo human skin, sandalwood oil (0,4%) 9h_A

description: 0,4% SO gene expression after 9h


title: ex vivo human skin, sandalwood oil (2%) 24h_A

description: 2% SO gene expression after 24h


title: ex vivo human skin,sandalwood oil (2%) 9h_C

description: 2% SO gene expression after 9h


title: p4


title: ex vivo human skin, sandalwood oil (2%) 9h_B

description: 2% SO gene expression after 9h


title: ex vivo human skin, excipient 24h_C

description: excipient gene expression after 24h


title: ex vivo human skin, sandalwood oil (2%) 9h_A

description: 2% SO gene expression after 9h


title: ex vivo human skin, excipient 24h_A

description: excipient gene expression after 24h


title: ex vivo human skin, control 24h_C

description: control gene expression after 24h


title: ex vivo human skin, excipient 9h_B

description: excipient gene expression after 9h


title: ex vivo human skin, excipient 24h_B

description: excipient gene expression after 24h


title: ex vivo human skin, excipient 9h_C

description: excipient gene expression after 9h


title: healthy woman skin biological rep5

source_name: healthy woman skin

value: healthy individual

value: healthy woman skin


title: ex vivo human skin, control 24h_B

description: control gene expression after 24h


title: ex vivo human skin, excipient 9h_A

description: excipient gene expression after 9h


title: ex vivo human skin, control 9h_C

description: control gene expression after 9h


title: ex vivo human skin, control 24h_A

description: control gene expression after 24h


title: 203

status: Public on Nov 09 2017

city: Warsaw

first: Malgorzata

last: Bulkowska

address: Nowoursynowska 159

department: Department of Physiological Sciences

country: Poland

institute: Warsaw University of Life Sciences

description: A total of 317 microRNAs were used for threshold filtering and 122 probes were discarded by the filtering procedure.

hyb_protocol: Labelled samples were hybridized on miRCURY LNA microRNA Array 7th generation − hsa, mmu & rno (Exiqon) using Tecan HS4800TM Hybridization Station (Tecan) according to the manufacturer's protocol.

scan_protocol: Microarray slides were scanned and stored in an ozone free environment (ozone level below 2.0 ppb). Scanning was carried out using Agilent G2565BA Microarray Scanner (Agilent Technologies) according to the manufacturer's protocol. Image analysis was performed using ImaGene 9.0 software (BioDiscovery).

data_processing: Quantified signals were background corrected (Normexp with offset value 10, Ritchie et al., 2007) and normalized using quantile normalization method.

organism: Canis lupus familiaris

source_name: mammary tumour

label_protocol: 750 ng of total RNA was labelled with Hy3 label using miRCURY LNA microRNA Hi-Power Labeling Kit (Exiqon) according to the manufacturer's protocol.

extract_protocol: RNA was isolated from tumour pieces with a diameter of 1 cm. Each piece was washed with RNase Away Reagent (Ambion) and disrupted in Tissue Lyser LT (QIAGEN) at 50 Hz for 30 min. After disruption, total RNA was isolated from samples using miRNeasy Mini Kit (QIAGEN) according to the manufacturer's protocol.

value: mammary tumour

tag: control/tumour type

value: Malignant

tag: grade of malignancy

value: I

tag: metastasis

value: Yes

tag: histological type

value: Tubulopapillary carcinoma

tag: breed

value: Shih-Tzu

tag: age [years]


title: 199

value: III

value: Lipid-rich carcinoma

value: Drever


title: 196

value: Solid carcinoma

value: German Shepherd


title: 155

value: II

value: Borzoi


title: 171

value: Tubulopapillary carcinoma + Bi-phasic carcinoma

value: Samoyed


title: 222

value: Labrador


title: 175

value: Pointer


title: ex vivo human skin, control 9h_B

description: control gene expression after 9h

value: skin

value: female

value: 49 years


title: 124

value: mammary tumour

value: Malignant

value: I

value: Yes

value: Shetland Sheepdog


title: 154

value: Comedocarcinoma

value: Elkhound


title: 120

value: Border Collie


title: 111

value: III

value: Solid carcinoma

value: Poodle


title: 109

value: II

value: Dachshund


title: 86

value: Squamous cell carcinoma

value: Boxer


title: 41


title: 69

value: Cocker Spaniel


title: 137

value: German Shepherd


title: 78

value: mammary tumour


title: 24

value: Malignant

value: Crossbreed


title: 25

value: Yes

value: Anaplastic carcinoma

value: Airedale Terrier


title: 21

value: Comedocarcinoma

value: German Shorthaired Pointer


title: 3B


title: 5


title: 94

value: I

value: Scirrhous carcinoma

value: Elkhound


title: 3848 T/11 I

value: Malignant + Benign

value: Tubulopapillary carcinoma + Complex adenoma

value: Shih-Tzu


title: 38

value: II

value: Solid carcinoma

value: Dunker Hound


title: 3881 T/09 I

value: mammary tumour

value: Unknown


title: 996 T/10 I

value: Malignant

value: Tubulopapillary carcinoma

value: German Shepherd


title: 1060 T/11 I

value: Yes

value: Crossbreed


title: 4588 T/10 I

value: Comedocarcinoma


title: 1953 T/11 I

value: I

value: Rottweiler-mix


title: 5268 T/10 I

value: Dachshund


title: 3112 T/09 I

value: West Highland White Terrier


title: 4116 T/10 I

value: Pointer


title: 42

value: Lhasa Apso


title: 875 T/10 I

value: III


title: healthy woman skin biological rep2

value: healthy individual

value: female

value: skin biopsy

value: healthy woman skin

value: microRNA


title: 28

value: mammary tumour

value: Malignant

value: Tubulopapillary carcinoma


title: 3A

value: II

value: Yes

value: Solid carcinoma

value: Crossbreed


title: 1823 T/07 I

value: Dachshund


title: 2747 T/07 I

value: West Highland White Terrier


title: 2557 T/07 I

value: Golden Retriever


title: ex vivo human skin, control 9h_A

description: control gene expression after 9h

value: skin

value: 49 years


title: 833 T/07 I

value: III

value: Tubulopapillary carcinoma + Solid carcinoma

value: Rottweiler


title: 2243 T/07 I

value: Anaplastic carcinoma

value: Bavarian Mountain Hound


title: 157

value: mammary tumour

value: I

value: Scirrhous carcinoma

value: German Shepherd


title: 61 T/08 I

value: Malignant

value: Yes

value: Special type of carcinoma

value: Poodle


title: 825 T/07 I

value: II

value: Tubulopapillary carcinoma

value: Bobtail


title: 84398

value: No

value: Solid carcinoma

value: Unknown


title: 84464

value: III


title: 83995


title: 83996

value: Comedocarcinoma

value: Dachshund


title: 83994

value: mammary tumour

value: Braque


title: 83993


title: 84692

value: Stafford Shire Bulterier


title: 84134

value: I

value: Carcinoma

value: York


title: 82690

value: Benign

value: Not applicable

value: Complex adenoma

value: Fox Terrier


title: 83731

value: Malignant

value: German Shepherd


title: 82584

value: No

value: Atypical adenoma

value: French Bulldog


title: 83698

value: III

value: Unknown

value: Solid carcinoma

value: Akita


title: 537 T/09 I

value: mammary tumour

value: Afghan Hound


title: 82492

value: II

value: Tubulopapillary carcinoma

value: Crossbreed


title: 84691

value: Carcinosarcoma


title: 83891

value: Bavarian Mountain Hound


title: 82361

value: I

value: Mucinous carcinoma + Tubulopapillary carcinoma

value: Dachshund


title: 82360

value: Benign

value: Not applicable

value: No

value: Complex adenoma

value: Irish Terrier


title: 82363

value: Malignant

value: III

value: Unknown

value: Scirrhous carcinoma


title: 82362

value: mammary tumour

value: II

value: Mucinous carcinoma


title: 82359

value: Complex carcinoma

value: Braque


title: 82408

value: German Shepherd


title: 5404 T/10 II

value: Labrador-mix


title: 5410 T/10 II

value: Squamous cell carcinoma

value: Crossbreed


title: 5268 T/10 II

value: Yes

value: Tubulopapillary carcinoma

value: Dachshund


title: 921 T/11 II

value: I

value: No

value: Cavalier King Charles Spaniel


title: 747 T/11 II

value: Malignant

value: III

value: Comedocarcinoma


title: 960 T/11 II

value: mammary tumour

value: Benign

value: Not applicable

value: Complex adenoma


title: 948 T/11 II

value: Simple adenoma

value: Shepherd-mix


title: 81342


title: 81933

value: II

value: Unknown


title: 1060 T/11 II

value: Yes

value: Crossbreed


title: 81606

value: Complex carcinoma


title: 82186

value: Atypical papilloma


title: 1795 T/11 II

value: No


title: 81932

value: Tubulopapillary carcinoma

value: Boxer


title: 82089

value: Malignant


title: 81684

value: I

value: Dachshund


title: 81683

value: mammary tumour


title: 81895

value: III

value: Welsh Terrier


title: 81896

value: German Shepherd


title: 81340


title: 1394 T/11 II

value: Benign

value: Not applicable

value: Complex adenoma

value: Poodle


title: 81000

value: Crossbreed


title: 81117

value: Solid carcinoma

value: Scent Hound


title: 80999

value: Malignant + Benign

value: No

value: Tubulopapillary carcinoma + Noninfiltrating carcinoma + Benign mixed tumour


title: 1373 T/11 II

value: Malignant

value: Complex carcinoma


title: 81324


title: 80997

value: Basaloid carcinoma

value: Golden Retriever


title: 254 T/11 II

value: mammary tumour

value: I


title: 81341

value: Unknown

value: Tubulopapillary carcinoma


title: 80998

value: Benign

value: Not applicable

value: Benign mixed tumour

value: Pekingese


title: 5120 T/10 II

value: Complex adenoma

value: Fox Terrier


title: 5245 T/10 II

value: Yes

value: German Shepherd


title: 5243 T/10 II

value: II

value: Anaplastic carcinoma

value: Crossbreed


title: 5099 T/10 II

value: No

value: Atypical simple adenoma


title: 4588 T/10 II

value: mammary tumour

value: Malignant

value: Comedocarcinoma


title: 5055 T/10 II

value: Bolognese


title: 4116 T/10 II

value: I

value: Tubulopapillary carcinoma

value: Pointer


title: 2378 T/10 II

value: Benign

value: Not applicable

value: Unknown


title: lncPCL.046

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

description: Gene expression data from plasma cell leukemia primary tumor.

hyb_protocol: The fragmented labeled single-stranded DNA target was hybridized for 16 hours and 30 minutes at 45°C on GeneChip Gene 1.0 ST array, according to the standard Affymetrix protocol, using the GeneChip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Scanning  of the arrays was performed using the GeneChip Scanner 7G.

data_processing: Expression data has been normalized using RMA procedure at the probe cluster ID annotation level. Cross-hybridization probes were filtered-out. We combined annotated probes with both Ensembl transcripts (GRCh37/hg19 assembly) and lncRNAs from v4 database on LNCipedia repository (http://www. lncipedia.org/), based on the chromosome localization of the target sequence identified by each probe; afterwards, we considered only probes univocally referable to lncRNA transcripts (i.e. that do not overlap with Ensembl transcripts). To summarize probes related to each lncRNA, we considered their median expression value

source_name: Plasma cell leukemia patient 046

label_protocol: Biotinylated single stranded cDNA samples were prepared starting from 100 nanograms of purified total RNA, according to the standard Affymetrix protocol (GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions (Gibco BRL). RNA was purified using the Rneasy Mini Kit according to the manufacturer's instruction (Qiagen).

treatment_protocol: Plasma cells were purified from bone marrow samples using CD138 immunomagnetic microbeads according to the manufacturer's instructions (MidiMACS system, Miltenyi Biotec); the purity of the positively selected PCs was assessed by morphology and flow cytometry and was > 90% in all cases.

tag: diagnosis

value: plasma cell leukemia (pPCL)

value: primary tumor


title: 2566 T/08 II

value: II

value: Yes

value: Lipid-rich carcinoma

value: Labrador-mix


title: 2228 T/08 II

value: Spitz-mix


title: 2431 T/08 II

value: mammary tumour

value: III

value: Crossbreed


title: 2416 T/08 II

value: Malignant

value: Beagle


title: 1726 T/08 II

value: I

value: No

value: Comedocarcinoma

value: Yorkshire Terrier


title: 3735 T/10 II

value: Unknown


title: 2652 T/08 II

value: Complex carcinoma

value: Collie-mix


title: lncPCL.049

source_name: Plasma cell leukemia patient 049

value: plasma cell leukemia (pPCL)

value: primary tumor


title: lncPCL.044

source_name: Plasma cell leukemia patient 044

value: plasma cell leukemia (sPCL)


title: 1705 T/08 II

value: Benign

value: Not applicable

value: Simple adenoma

value: Doberman


title: 1822 T/08 II

value: mammary tumour

value: Atypical papilloma

value: Sharpei


title: 2521 T/08 II

value: Malignant

value: III

value: Tubulopapillary carcinoma / Noninfiltrating carcinoma

value: Terrier-mix


title: 2432 T/08 II

value: I

value: No

value: Noninfiltrating carcinoma

value: Crossbreed


title: 1881 T/08 II

value: Yes

value: Squamous cell carcinoma

value: French Bulldog


title: lncPCL.042

source_name: Plasma cell leukemia patient 042

value: plasma cell leukemia (sPCL)

value: primary tumor


title: lncPCL.039

source_name: Plasma cell leukemia patient 039


title: lncPCL.043

source_name: Plasma cell leukemia patient 043

value: plasma cell leukemia (pPCL)


title: lncPCL.037

source_name: Plasma cell leukemia patient 037


title: gallbladder cancer cell_highly metastatic_rep2

city: Shanghai

first: Huaifeng

last: Li

address: NO.1665, kongjiang road, Shanghai, China

department: general surgery

institute: Xinhua hospital affiliated to Shanghai jiaotong university, school of medicine

description: Gene expression in LiM2-NOZ cells

hyb_protocol: Array hybridization was performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications.  1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

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

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 3 out of 6 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering. Hierarchical Clustering and combined analysis were performed using homemade scripts.

source_name: highly metastatic gallbladder cancer cells

label_protocol: Sample labeling was performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: NOZ and LiM2-NOZ cells were cultured in Dulbecco’s modiﬁed Eagle medium (Gibco, Grand Island, NY) supplemented with 10% fetal bovine serum (Gibco)

extract_protocol: Total RNA was extracted using TRIzol Reagent (Invitrogen, Carlsbad, CA). RNA quantity and quality were measured using a NanoDrop ND-1000, and RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

value: gallbladder

value: female


title: 2477 T/08 II

value: mammary tumour

value: Benign

value: Not applicable

value: Complex adenoma

value: American Cocker Spaniel


title: gallbladder cancer cell_highly metastatic_rep3

description: Gene expression in LiM2-NOZ cells

value: highly metastatic gallbladder cancer cells


title: gallbladder cancer cell_parental_rep2

description: Gene expression in NOZ cells

source_name: parental gallbladder cancer cells

value: parental gallbladder cancer cells


title: 1645 T/08 II

value: No

value: Weimaranian


title: 1232 T/08 II

value: Malignant

value: III

value: Yes

value: Comedocarcinoma

value: West Highland White Terrier


title: gallbladder cancer cell_parental_rep3

description: Gene expression in NOZ cells


title: gallbladder cancer cell_parental_rep1

description: Gene expression in NOZ cells


title: lncPCL.034

source_name: Plasma cell leukemia patient 034

value: plasma cell leukemia (pPCL)

value: primary tumor


title: lncPCL.035

source_name: Plasma cell leukemia patient 035


title: 1608 T/08 II

value: Simple adenoma + Complex adenoma

value: Spitz-mix


title: lncPCL.038

source_name: Plasma cell leukemia patient 038


title: lncPCL.036

source_name: Plasma cell leukemia patient 036


title: 1607 T/08 II

value: mammary tumour

value: Benign

value: Labrador-mix


title: lncPCL.033

source_name: Plasma cell leukemia patient 033

value: plasma cell leukemia (sPCL)


title: 992 T/08 II

value: Not applicable

value: Complex adenoma

value: Irish Setter


title: 1010 T/08 II

value: No

value: Basaloid adenoma

value: Kleiner Munsterlander


title: 863 T/08 II

value: Malignant

value: III

value: Complex carcinoma

value: Munsterlander


title: 1076 T/08 II

value: I

value: Solid carcinoma

value: Shepherd-mix


title: lncPCL.032

source_name: Plasma cell leukemia patient 032

value: plasma cell leukemia (pPCL)

value: primary tumor


title: lncPCL.031

source_name: Plasma cell leukemia patient 031


title: lncPCL.030

source_name: Plasma cell leukemia patient 030


title: gallbladder cancer cell_highly metastatic_rep1

description: Gene expression in LiM2-NOZ cells

value: gallbladder

value: female

value: highly metastatic gallbladder cancer cells


title: 1031 T/08 II

source_name: mammary tumour

value: mammary tumour

value: II

value: Simple carcinoma

value: Poodle


title: 862 T/08 II

value: No

value: Solid carcinoma / Lipid-rich carcinoma

value: Dachshund


title: lncPCL.029

source_name: Plasma cell leukemia patient 029


title: 562 T/08 II

value: Malignant

value: Complex carcinoma

value: Cairn-Terrier


title: 500 T/08 II

value: Benign

value: Not applicable

value: Atypical papilloma

value: Dalmatian


title: 379 T/08 II

value: Malignant + Hyperplasia

value: I

value: Complex carcinoma + Mammary ductal ectasia

value: Labrador


title: mRNA_pancreasCancer_rep32

city: Koto

first: Akihisa

last: Takahara

institute: Japanese Foundation For Cancer Research

hyb_protocol: After fragmentation, RNA was hybridized with Affymetrix Hybridization, Wash, and Stain Kit on Affymetrix HG-U133 plus2.0 Array following manufactuer's instruction.

scan_protocol: GeneChip was scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: Data was processed with RMA-dabg using Affymetrix Expression Console software.

label: Biotin

source_name: pancreas Cancer tissue

label_protocol: Biotinylated cRNA was prepared with Affymetrix GeneChip 3'IVT Plus kit according to the manufactuer's instruction.

extract_protocol: Total RNA was extracted using QIAGEN RNeasy Micro Kit following manufacturer's instruction.

value: pancreas cancer

tag: Sex

value: M


title: mRNA_pancreasCancer_rep33


title: mRNA_pancreasCancer_rep35


title: lncPCL.028

source_name: Plasma cell leukemia patient 028

value: plasma cell leukemia (pPCL)

value: primary tumor


title: mRNA_pancreasCancer_rep23


title: mRNA_pancreasCancer_rep22


title: mRNA_pancreasCancer_rep27

value: F


title: mRNA_pancreasCancer_rep34


title: mRNA_pancreasCancer_rep29


title: mRNA_pancreasCancer_rep31


title: mRNA_pancreasCancer_rep20


title: mRNA_pancreasCancer_rep26


title: mRNA_pancreasCancer_rep25


title: mRNA_pancreasCancer_rep28


title: mRNA_pancreasCancer_rep30


title: mRNA_pancreasCancer_rep18


title: 480 T/08 II

value: mammary tumour

value: No

value: Miniature Poodle


title: lncPCL.026

source_name: Plasma cell leukemia patient 026


title: 290 T/08 II

value: Malignant

value: Tubulopapillary carcinoma

value: Unknown


title: mRNA_pancreasCancer_rep19


title: mRNA_pancreasCancer_rep16


title: mRNA_pancreasCancer_rep21


title: mRNA_pancreasCancer_rep17


title: mRNA_pancreasCancer_rep24


title: lncPCL.021

source_name: Plasma cell leukemia patient 021


title: lncPCL.027

source_name: Plasma cell leukemia patient 027


title: mRNA_pancreasCancer_rep15


title: mRNA_pancreasCancer_rep13


title: mRNA_pancreasCancer_rep14


title: 264 T/08 II

value: III

value: Tubulopapillary carcinoma + Solid carcinoma

value: Shepherd-mix


title: 279 T/08 II

value: II

value: Complex carcinoma


title: lncPCL.019

source_name: Plasma cell leukemia patient 019


title: lncPCL.020

source_name: Plasma cell leukemia patient 020


title: lncPCL.017

source_name: Plasma cell leukemia patient 017


title: lncPCL.018

source_name: Plasma cell leukemia patient 018


title: 183 T/08 II

value: Great Dane


title: lncPCL.016

source_name: Plasma cell leukemia patient 016


title: 3100 T/07 II

value: Benign

value: Not applicable

value: Complex adenoma

value: Dachshund


title: lncPCL.013

source_name: Plasma cell leukemia patient 013

value: plasma cell leukemia (sPCL)

value: primary tumor


title: 3167 T/07 II

value: mammary tumour

value: I

value: No

value: Cocker Spaniel


title: mRNA_pancreasCancer_rep11

value: pancreas cancer

value: M


title: 2946 T/07 II

value: Benign mesenchymal tumour (chondroma and osteoma)


title: mRNA_pancreasCancer_rep7


title: mRNA_pancreasCancer_rep12


title: mRNA_pancreasCancer_rep9

value: F


title: 2797 T/07 II

value: Atypical complex adenoma

value: Yorkshire Terrier


title: lncPCL.007

source_name: Plasma cell leukemia patient 007


title: mRNA_pancreasCancer_rep6


title: mRNA_pancreasCancer_rep8


title: mRNA_pancreasCancer_rep5


title: mRNA_pancreasCancer_rep10


title: mRNA_pancreasCancer_rep4


title: mRNA_pancreasCancer_rep1


title: 2280 T/07 II

value: Malignant

value: II

value: Tubulopapillary carcinoma

value: Terrier-mix


title: mRNA_pancreasCancer_rep2


title: 2735 T/07 II

value: Noninfiltrating carcinoma

value: Kerry Blue Terrier


title: mRNA_EsophagusCancer_rep23

source_name: Esophagus Cancer tissue

value: esophagus cancer


title: mRNA_EsophagusCancer_rep22


title: 2118 T/07 II

value: mammary tumour

value: Benign

value: Not applicable

value: Benign mesenchymal tumour (chondroma)

value: West Highland White Terrier


title: mRNA_EsophagusCancer_rep21

value: M


title: lncPCL.011

source_name: Plasma cell leukemia patient 011

value: plasma cell leukemia (sPCL)

value: primary tumor


title: lncPCL.006

source_name: Plasma cell leukemia patient 006


title: mRNA_EsophagusCancer_rep18


title: lncPCL.005

source_name: Plasma cell leukemia patient 005


title: 2332 T/07 II

source_name: mammary tumour

value: I

value: No

value: Complex carcinoma

value: Staffordshire Terrier


title: 3000 N/07 II

source_name: normal mammary gland

value: normal mammary gland

value: Control

value: Shepherd-mix


title: mRNA_EsophagusCancer_rep16


title: mRNA_EsophagusCancer_rep14


title: 1186 T/07 II

value: Malignant

value: Tubulopapillary carcinoma

value: Shih-Tzu


title: 3100 N/07 II

value: Dachshund


title: mRNA_pancreasCancer_rep3

source_name: pancreas Cancer tissue

value: pancreas cancer


title: mRNA_EsophagusCancer_rep17

value: esophagus cancer


title: mRNA_EsophagusCancer_rep19

value: F


title: 2797 N/07 II

value: Not applicable

value: Yorkshire Terrier


title: mRNA_EsophagusCancer_rep20

value: M


title: 2117 T/07 II

value: mammary tumour

value: I

value: Noninfiltrating carcinoma


title: mRNA_EsophagusCancer_rep10


title: mRNA_EsophagusCancer_rep15


title: mRNA_EsophagusCancer_rep12


title: 2747 N/07 II

value: West Highland White Terrier


title: 2946 N/07 II

value: normal mammary gland


title: 2735 N/07 II

value: Control

value: Kerry Blue Terrier


title: mRNA_EsophagusCancer_rep13


title: mRNA_EsophagusCancer_rep8


title: mRNA_EsophagusCancer_rep9


title: mRNA_EsophagusCancer_rep5


title: mRNA_EsophagusCancer_rep2


title: mRNA_EsophagusCancer_rep7


title: 2557 N/07 II

value: Golden Retriever


title: mRNA_EsophagusCancer_rep3


title: mRNA_EsophagusCancer_rep11


title: 2736 N/07 II

value: Shepherd-mix


title: mRNA_EsophagusCancer_rep6


title: 2798 N/07 II


title: 2280 N/07 II

value: Terrier-mix


title: mRNA_EsophagusCancer_rep4


title: mRNA_EsophagusCancer_rep1


title: 2562 N/07 II

value: Kromfohrlander


title: mirPCL.043

description: microRNA expression data from plasma cell leukemia primary tumor.

hyb_protocol: Byotin-labeled RNA samples were hybridized for 16 hours  at 48°C on GeneChip miRNA 3.0 array, according to the standard manifacturer's protocol, using the GeneChip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

data_processing: Raw data were extracted from CEL files and then normalized using robust multi-array average (RMA) procedure in the affy package for Bioconductor and the miRbase Release 18 annotations included in the corresponding cdf definition files available at the University of Michigan Brainarray portal at http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/18.0.0/version.html). Annotations were then updated to miRBase Release 20 definition using the mirna.diff files available at the miRbase website

source_name: Plasma cell leukemia patient 043

label_protocol: 500 ng of total RNA were converted to biotin-labeled RNA using the FlashTag Biotin HSR Labeling kit, according to Affimetrix protocol.

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

value: plasma cell leukemia (pPCL)

value: primary tumor


title: 2380 N/07 II

value: German Shorthaired Pointer


title: 833 N/07 II

value: Not applicable

value: Rottweiler


title: 2332 N/07 II

value: Staffordshire Terrier


title: 2513 N/07 II

value: Poodle


title: mirPCL.032

source_name: Plasma cell leukemia patient 032


title: mirPCL.030

source_name: Plasma cell leukemia patient 030


title: mirPCL.036

source_name: Plasma cell leukemia patient 036


title: 2047 N/07 II

value: Cocker Spaniel


title: mirPCL.026

source_name: Plasma cell leukemia patient 026


title: mirPCL.042

source_name: Plasma cell leukemia patient 042

value: plasma cell leukemia (sPCL)


title: mirPCL.049

source_name: Plasma cell leukemia patient 046


title: mirPCL.027

source_name: Plasma cell leukemia patient 027


title: mirPCL.038

source_name: Plasma cell leukemia patient 038


title: mirPCL.039

source_name: Plasma cell leukemia patient 039


title: 1979 N/07 II

value: Irish Setter


title: 1937 N/07 II

value: normal mammary gland

value: Dalmatian


title: mirPCL.035

source_name: Plasma cell leukemia patient 035


title: mirPCL.044

source_name: Plasma cell leukemia patient 044


title: 825 N/07 II

value: Control

value: Bobtail


title: 830 N/07 II

value: Cocker Spaniel-mix


title: mirPCL.037

source_name: Plasma cell leukemia patient 037


title: mirPCL.033

source_name: Plasma cell leukemia patient 033


title: mirPCL.019

source_name: Plasma cell leukemia patient 019


title: 2194 N/07 II

source_name: normal mammary gland

value: Crossbreed


title: 2117 N/07 II


title: 2168 N/07 II

value: Soft Coated Wheaton Terrier


title: mirPCL.046

value: plasma cell leukemia (pPCL)


title: mirPCL.031

source_name: Plasma cell leukemia patient 031

value: primary tumor


title: mirPCL.034

source_name: Plasma cell leukemia patient 034


title: mirPCL.029

source_name: Plasma cell leukemia patient 029


title: mirPCL.021

source_name: Plasma cell leukemia patient 021


title: mirPCL.017

source_name: Plasma cell leukemia patient 017


title: mirPCL.020

source_name: Plasma cell leukemia patient 020


title: mirPCL.005

source_name: Plasma cell leukemia patient 005


title: mirPCL.007

source_name: Plasma cell leukemia patient 007


title: mirPCL.018

source_name: Plasma cell leukemia patient 018


title: mirPCL.013

source_name: Plasma cell leukemia patient 013


title: mirPCL.016

source_name: Plasma cell leukemia patient 016


title: mirPCL.011

source_name: Plasma cell leukemia patient 011


title: mirPCL.028

source_name: Plasma cell leukemia patient 028


title: 2118 N/07 II

value: West Highland White Terrier


title: mirPCL.006

source_name: Plasma cell leukemia patient 006


title: eugenol_30min_3

city: Irvine

first: Michael

last: McClelland

state: CA

address: 132 Med Surge I

department: Microbiology & Molecular Genetics

institute: University of California, Irvine

description: third replicate

hyb_protocol: Labelled cDNAs were hybridized to PCR product arrays on Corning UltraGAPS slides in 25% formamide / 5xSSC / 0.1% BSA hybridization buffer overnight at 42°C.

scan_protocol: The slides were scanned using the ScanArray 5000 laser scanner (GSI Lumonics).

data_processing: Image analysis and feature extraction was performed with Scanarray 2.1 software, and signals were quantified using Quantarray 3.0 (Packard BioScience).

organism: Salmonella enterica subsp. enterica serovar Enteritidis

label_protocol: 50µg of RNA was combined with 2.4 µg random hexamers, denatured at 70°C, and quick-chilled in ice-water. The remaining components of the reverse transcription reaction were added to the denatured RNA and random hexamers to the following concentrations in a 60 µl reaction: 0.01 M DTT, 1X Superscript II first strand reaction buffer, 0.5 mM dATP, dCTP, dGTP, 0.2 mM dTTP, 0.066 mM Cy3- or Cy5-labeled dUTP (GE Healthcare), RNasin (Roche), and 800 U Superscript II.  After 1 hour at 42°C, an additional 400 U of Superscript II was added and incubated another hour.  Excess random hexamers and nucleotides were removed with a PCR Purification Kit (Qiagen) per manufacturer’s instructions.

growth_protocol: An overnight culture of Salmonella enterica serovar Enteritidis phage type 8 was diluted 1/1000 into 500 ml of LB at 37°C, then grown at 37°C for exactly 6h30min  with vigorous shaking, at which point control samples were taken (OD approx. 0.5). Subsequently, trans-cinnamaldehyde (0.01% final concentration) or eugenol (0.04% final concentration) was added to the cultures, and 100ml samples taken 15min and 30min later. Cells were mixed with 16 ml ice-cold ethanol/phenol stop solution (5% citrate-buffered phenol), centrifuged and stored at -80°C.

extract_protocol: Frozen cell pellets were resuspended in a fresh solution of 10ml 0.5 mg/ml lysozyme in TE (pH 8.0). A volume of 1ml of 10% SDS was added to the resuspended pellet, the solutions mixed and placed in a water bath at 64°C for 2min. Then, phenol/chloroform extraction was performed, followed by isopropanol precipitation. The pellet was resuspended in 2ml of RNase-free DEPC-treated water, split into two and DNAse treated by addition of 500U RNase inhibitor (Ribolock®, Fermentas), 250U DNase (Fermentas), 20µl of 1M Tris (pH 8.3) and 10µl of 1M MgCl, at 37°C for 30 min. The samples were again phenol-chloroform extracted and precipitated with isopropanol before final resuspension in DEPC-treated water.

tag: strain

tag: agent

value: 0.04% eugenol

tag: time

value: 30min exposure

value: control (pre-exposure)


title: trans-cinnamaldehyde_15min_2

description: second replicate

value: 0.04% trans-cinnamaldehyde

value: 15min exposure


title: E11.5 PGC, colony, 5% O2 hypoxia cultivation, rep 2

city: Taipei

first: Yung-Che

last: Kuo

address: 250 Wuxing

country: Taiwan

institute: Taipei Medical University

description:
H010-3111104690
Gene expression after colonies formation of PGC under 5% O2 hypoxia for 7 days

hyb_protocol: Mouse Whole Genome OneArray® (MOA 2.1) arrays were pre-heat at 60℃ for 10 mins, rehydrated by 100% ethanol following with deionized water. The slides were pre-hybridized with 5x SSPE, 0.1% SDS and 1% BSA at 42℃ for 2 hour. After the pre-hybridization, 5 µg Cy5-labeled aRNA were hybridized to the MOA2.1 array with Phalanx hybridization buffer using Phalanx Hybridization System. After 16 hrs hybridization, non-speciﬁc binding targets were washed away.

scan_protocol: The MOA2.1 array scanned using a DNA Microarray Scanner (Model G2505C, Agilent Technologies). The Cy5 ﬂuorescent intensities of each spot were analyzed by GenePix 4.1 software (Molecular Devices).

data_processing: Each single sample was at least performed twice in terms of technical or biological replicates under the reproducibility more than 0.975. The signal intensity was loaded into Rosetta Resolver System® (Rosetta Biosoftware, USA) to do data preprocessing and apply to 75 percentile centering normalization. The errors of the sample were estimated by using the error-weighted approach at the same time.

organism: Mus musculus

source_name: E11.5 PGC_colony_5% O2 hypoxia cultivation

label_protocol: Fluorescent aRNA targets were prepared from 1 µg of total RNA using OneArray® Amino Allyl aRNA Amplification Kit (Phalanx Biotech Group, Taiwan) and Cy5 dye (GE Healthcare).

growth_protocol: The gonadal or testicular cells were seeded on a laminin-coated culture plate (200 ng/cm2, Sigma-Aldrich) at a density of 8 × 10^4 cells/cm2 and cultivated in MCDB-201 medium

extract_protocol: RNA extraction by Trizol Reagent. RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, A260/A230≧1.5, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧6).

treatment_protocol: For formation of PGC and AP+GSC colonies, total gonadal or testicular cells were resuspended in MCDB-201 medium supplemented with 1× insulin, transferrin, and selenium, and 10 ng/mL epidermal growth factor, and culture medium was changed every two days. The gonadal or testicular cells were seeded on a laminin-coated culture plate (200 ng/cm2) at a density of 8 × 104 cells/cm2 and cultivated for 7 days at 37°C under a 5% O2 atmosphere. Finally, picked up colonies prior to RNA extract preparation. The CD49f+GSCs were purified using a magnetic-activated cell sorting system. Briefly, the total testicular cells were incubated with phycoerythrin (PE)-conjugated antibody against CD49f. CD49f-labeled cells were washed and then incubated with anti-PE microbeads. Stained cells were separated using a MACS column, and then subjected to RNA extract preparation.

value: ICR

tag: developmental stage

value: gonad

tag: cell type

value: primordial germ cells (PGCs


title: eugenol_15min_2

description: second replicate


title: eugenol_15min_1

description: first replicate


title: trans-cinnamaldehyde_15min_3

description: third replicate


title: 2dpp GSC, colony, 5% O2 hypoxia cultivation, rep 1

description:
H001-3111104668
Gene expression after colonies formation of GSC under 5% O2 hypoxia for 7 days

source_name: 2dpp GSC_colony_5% O2 hypoxia cultivation

tag: tissue

value: testis

value: Glandular Stem Cells (GSCs)


title: eugenol_30min_2

description: second replicate


title: CD49f+GSC, purified cell, physiological hypoxia, rep 2

description:
H004-3111104674
Gene expression after purification of CD49f+GSC, physiological hypoxia in testis

value: CD49f+ Glandular Stem Cells (GSCs)


title: 2dpp GSC, colony, 5% O2 hypoxia cultivation, rep 2

description:
H002-3111104670
Gene expression after colonies formation of GSC under 5% O2 hypoxia for 7 days


title: E11.5 PGC, colony, 5% O2 hypoxia cultivation, rep 1

description:
H009-3111104686
Gene expression after colonies formation of PGC under 5% O2 hypoxia for 7 days


title: trans-cinnamaldehyde_30min_1

description: first replicate


title: CD49f+GSC, purified cell, physiological hypoxia, rep 1

description:
H003-3111104672
Gene expression after purification of CD49f+GSC, physiological hypoxia in testis


title: eugenol_30min_1

description: first replicate


title: trans-cinnamaldehyde_30min_2

description: second replicate


title: eugenol_15min_3

description: third replicate


title: WeightRegainers9_T2

status: Public on Nov 08 2017

city: Helsinki

first: Miina

last: Ollikainen

address: Tukholmankatu 8

country: Finland

institute: University of Helsinki

description:
adipose tissue 47
WeightRegainer9 at twelfth month (T2)

hyb_protocol: A hybridization cocktail is prepared including the labeled, fragmented target and hybridization controls. The target is  then hybridized to the GeneChip array in a cartridge format and incubated 16 hours at 45 °C. Immediately following  hybridization, the array is washed and stained with streptavidin phycoerythrin conjugate using an automated protocol on  the GeneChip® Fluidics Station 450.

scan_protocol: GeneChip® Scanner

data_processing: Robust Multi-array Average (RMA) algorithm was used to perform background correction followed by quantile normalization.Brainarray customized Chip Description File version 18.0 (hgu133plus2hsentrezgcdf), was used to map probe sets with corresponding genes.

source_name: adipose tissue

label_protocol: Labelling was done according the the manufacturer's instructions using the GeneChip® 3’ IVT PLUS Protocol. 100ng of total RNAwas reverse transcribed and converted into a double-stranded DNA. In vitro transcription was used to synthesize cRNA and to incorporate biotin-conjugated nucleotides.

extract_protocol: Total RNA was isolated using RNeasy Lipid Mini Kit (QIAGEN Nordic, Sollentuna, Sweden), following the manufacturers' instructions. RNA quality was assayed by 2100 Bioanalyzer (Agilent Technologies, Espoo, Finland).

value: Adipose Tissue

tag: gender

value: Male

tag: outcome

value: WeightRegainer


title: WeightLosers6_T2

description:
adipose tissue 57
WeightLoser6 at twelfth month (T2)

value: WeightLoser


title: WeightLosers2_T2

description:
adipose tissue 53
WeightLoser2 at twelfth month (T2)

value: Female


title: trans-cinnamaldehyde_30min_3

description: third replicate


title: WeightLosers1_T2

description:
adipose tissue 52
WeightLoser1 at twelfth month (T2)


title: WeightRegainers10_T2

description:
adipose tissue 48
WeightRegainer10 at twelfth month (T2)


title: WeightLosers4_T2

description:
adipose tissue 55
WeightLoser4 at twelfth month (T2)


title: WeightLosers3_T2

description:
adipose tissue 54
WeightLoser3 at twelfth month (T2)


title: WeightRegainers11_T2

description:
adipose tissue 49
WeightRegainer11 at twelfth month (T2)


title: WeightRegainers13_T2

description:
adipose tissue 51
WeightRegainer13 at twelfth month (T2)


title: WeightRegainers12_T2

description:
adipose tissue 50
WeightRegainer12 at twelfth month (T2)


title: WeightLosers5_T2

description:
adipose tissue 56
WeightLoser5 at twelfth month (T2)


title: WeightRegainers6_T2

description:
adipose tissue 44
WeightRegainer6 at twelfth month (T2)


title: WeightRegainers7_T2

description:
adipose tissue 45
WeightRegainer7 at twelfth month (T2)


title: WeightRegainers8_T2

description:
adipose tissue 46
WeightRegainer8 at twelfth month (T2)


title: WeightLosers6_T1

description:
adipose tissue 38
WeightLoser6 at fifth month (T1)


title: WeightLosers4_T1

description:
adipose tissue 36
WeightLoser4 at fifth month (T1)


title: amp1-13 control, biological rep2

city: Nottingham

first: Marios

last: Georgiou

address: Queen's Medical Centre

department: School of Life Sciences

country: United Kingdom

institute: University of Nottingham

description: Gene expression data from 10-day-old untreated amp1-13 seedlings

hyb_protocol: Labeled samples were hybridized to the Genechip Arabidopsis ATH1 Genome Arrays (Affymetrix, Santa Clara, CA) according to the manufacturer's instructions (Affymetrix; www.affymetrix.com/)

scan_protocol: The GeneArrays were scanned using the Affymetrix GeneChip Scanner (Affymetrix) using standard NASC protocols.

data_processing: The raw CEL files were normalized using the RMA background correction with quantile normalization, log base 2 transformation and mean probe-set summarization with adjustment for GC content.

organism: Arabidopsis thaliana

source_name: Arabidopsis amp1-13 seedlings treated with solvent DMSO

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol (GeneChip® Expression Arrays Technical Manual, 2013, Affymetrix)

growth_protocol: Seeds were surface-sterilized with 70% ethanol + 0.05% SDS for 3 min, rinsed with 96% ethanol for 1 min, and subsequently dried in a laminar flow hood.  Sterile seeds were germinated and grown in 96-well plates (approximately 5 seeds per well) in 100mL liquid half-strength Murashige and Skoog medium containing 1% Sucrose. After stratification at 4°C in darkness for 2 days, seeds were placed in a growth incubator grown at 26°C grown under long d conditions (16 h, 80 mM m-2 s-1 cool-white light/8 h dark).

extract_protocol: Total RNA was extracted using the RNeasy Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions.

treatment_protocol: The indicated genotypes were incubated with either DMSO [1% (v/v)] or 30 µM Hyperphyllin in the medium under the growth conditions described above.

tag: ecotype

value: whole seedlings

tag: genotype

tag: treatment

value: solvent control [DMSO 1% (v/v)]


title: WeightLosers5_T1

description:
adipose tissue 37
WeightLoser5 at fifth month (T1)


title: amp1-13 control, biological rep3


title: WeightRegainers5_T2

description:
adipose tissue 43
WeightRegainer5 at twelfth month (T2)


title: WeightRegainers1_T2

description:
adipose tissue 39
WeightRegainer1 at twelfth month (T2)


title: WeightRegainers3_T2

description:
adipose tissue 41
WeightRegainer3 at twelfth month (T2)


title: WeightRegainers4_T2

description:
adipose tissue 42
WeightRegainer4 at twelfth month (T2)


title: WeightRegainers2_T2

description:
adipose tissue 40
WeightRegainer2 at twelfth month (T2)


title: WeightLosers3 T1

description:
adipose tissue 35
WeightLoser3 at fifth month (T1)


title: amp1-13 control, biological rep1


title: WeightLosers2_T1

description:
adipose tissue 34
WeightLoser2 at fifth month (T1)


title: WeightLosers1_T1

description:
adipose tissue 33
WeightLoser1 at fifth month (T1)


title: Hyperphyllin-treated wild-type, biological rep2

description: Gene expression data from 10-day-old hyperphyllin-treated wild-type seedlings

source_name: Arabidopsis wild-type seedlings treated with 30 µM Hyperphyllin

value: wild type

value: 30 µM Hyperphyllin [in DMSO 1% (v/v)]


title: WeightRegainers7_T1

description:
adipose tissue 26
WeightRegainer7 at fifth month (T1)


title: Hyperphyllin-treated wild-type, biological rep3


title: WeightRegainers6_T1

description:
adipose tissue 25
WeightRegainer6 at fifth month (T1)


title: WeightRegainers13_T1

description:
adipose tissue 32
WeightRegainer13 at fifth month (T1)


title: Hyperphyllin-treated wild-type, biological rep1


title: WeightRegainers9_T1

description:
adipose tissue 28
WeightRegainer9 at fifth month (T1)


title: WeightRegainers8_T1

description:
adipose tissue 27
WeightRegainer8 at fifth month (T1)


title: WeightRegainers12_T1

description:
adipose tissue 31
WeightRegainer12 at fifth month (T1)


title: WeightRegainers10_T1

description:
adipose tissue 29
WeightRegainer10 at fifth month (T1)


title: WeightRegainers11_T1

description:
adipose tissue 30
WeightRegainer11 at fifth month (T1)


title: 2243 N/07 II

description: A total of 317 microRNAs were used for threshold filtering and 122 probes were discarded by the filtering procedure.

source_name: normal mammary gland

value: normal mammary gland

tag: control/tumour type

value: Control

tag: grade of malignancy

value: Not applicable

tag: metastasis

value: Bavarian Mountain Hound


title: WeightRegainers4_T1

description:
adipose tissue 23
WeightRegainer4 at fifth month (T1)


title: wild-type control, biological rep2

description: Gene expression data from 10-day-old untreated wild-type seedlings

source_name: Arabidopsis wild-type seedlings treated with solvent DMSO


title: WeightLosers6_T0

description:
adipose tissue 19
WeightLoser6 at baseline (T0)


title: WeightRegainers2_T1

description:
adipose tissue 21
WeightRegainer2 at fifth month (T1)


title: wild-type control, biological rep3


title: WeightRegainers5_T1

description:
adipose tissue 24
WeightRegainer5 at fifth month (T1)


title: wild-type control, biological rep1


title: WeightLosers3_T0

description:
adipose tissue 16
WeightLoser3 at baseline (T0)


title: WeightRegainers3_T1

description:
adipose tissue 22
WeightRegainer3 at fifth month (T1)


title: WeightLosers4_T0

description:
adipose tissue 17
WeightLoser4 at baseline (T0)


title: WeightRegainers10_T0

description:
adipose tissue 10
WeightRegainer10 at baseline (T0)


title: WeightLosers2_T0

description:
adipose tissue 15
WeightLoser2 at baseline (T0)


title: WeightLosers5_T0

description:
adipose tissue 18
WeightLoser5 at baseline (T0)


title: WeightRegainers11_T0

description:
adipose tissue 11
WeightRegainer11 at baseline (T0)


title: WeightLosers1_T0

description:
adipose tissue 14
WeightLoser1 at baseline (T0)


title: WeightRegainers12_T0

description:
adipose tissue 12
WeightRegainer12 at baseline (T0)


title: WeightRegainers1_T1

description:
adipose tissue 20
WeightRegainer1 at fifth month (T1)


title: WeightRegainers13_T0

description:
adipose tissue 13
WeightRegainer13 at baseline (T0)


title: WeightRegainers6_T0

description:
adipose tissue 6
WeightRegainer6 at baseline (T0)


title: WeightRegainers7_T0

description:
adipose tissue 7
WeightRegainer7 at baseline (T0)


title: WeightRegainers8_T0

description:
adipose tissue 8
WeightRegainer8 at baseline (T0)


title: WeightRegainers9_T0

description:
adipose tissue 9
WeightRegainer9 at baseline (T0)


title: WeightRegainers4_T0

description:
adipose tissue 4
WeightRegainer4 at baseline (T0)


title: WeightRegainers5_T0

description:
adipose tissue 5
WeightRegainer5 at baseline (T0)


title: WeightRegainers2_T0

description:
adipose tissue 2
WeightRegainer2 at baseline (T0)


title: WeightRegainers3_T0

description:
adipose tissue 3
WeightRegainer3 at baseline (T0)


title: WeightLosers5_T2

type: genomic

description:
adipose tissue 56
WeightLoser5 at twelfth month (T2)

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Raw data was exported from BeadStudio and analyzed using minfi package in R. Average Beta obtained from quantile normalization followed by BMIQ normalization.

label: Cy5 and Cy3

molecule: genomic DNA

label_protocol: Standard Illumina Protocol

extract_protocol: High molecular weight DNA was extracted from adipose tissue using QIAamp DNA Mini kit (QIAGEN) following the QIAamp Spin Procedure.


title: HFD-CMPF Liver 2

city: Toronto

first: Kacey

middle: June

last: Prentice

state: ON

address: 1 King's College Circle, MSB3352

department: Physiology

country: Canada

institute: University of Toronto

description: Gene expression from liver of treated mice

hyb_protocol: Following fragmentation, 12.5ug cRNA were hybridized for 16hr at 45C on Affymetrix Mouse430_2 gene chip

scan_protocol: Scanning was performed on the Affymetrix GeneChip® Scanner 3000 7G

data_processing: Data was analyzed using Affymetrix Expression Console (Version 1.1) using default analysis settings and RMA for normalization

source_name: Liver at end of CMPF injections

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200ng RNA

growth_protocol: Wildtype CD1 mice were obtained from Charles River and allowed to acclimate for one week before start of treatment

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

treatment_protocol: Wildtype CD1 mice were treated for one week with vehicle or 6mg/kg/day CMPF and placed on a 60% kcal from fat HFD for 4 weeks before liver isolation. In reversal model, mice were fed a HFD for 6 weeks, then injected with vehicle or 6mg/kg/day CMPF for 2 weeks before liver was isolated.

value: Liver

tag: model

value: reversal

value: HFD-CMPF


title: WeightLosers2_T2

description:
adipose tissue 53
WeightLoser2 at twelfth month (T2)


title: HFD-Control Liver 3

value: HFD-Control


title: HFD-CMPF Liver 1


title: HFD-Control Liver 2


title: HFD-CMPF Liver 3


title: WeightLosers6_T2

description:
adipose tissue 57
WeightLoser6 at twelfth month (T2)

value: Adipose Tissue


title: WeightLosers3_T2

description:
adipose tissue 54
WeightLoser3 at twelfth month (T2)

value: Male


title: WeightLosers1_T2

description:
adipose tissue 52
WeightLoser1 at twelfth month (T2)


title: Chow-Control Liver 1

value: Chow-Control


title: HFD-Control Liver 1


title: Chow-Control Liver 2


title: WeightRegainers11_T2

description:
adipose tissue 49
WeightRegainer11 at twelfth month (T2)

value: WeightRegainer


title: WeightLosers4_T2

description:
adipose tissue 55
WeightLoser4 at twelfth month (T2)

value: WeightLoser


title: Chow-Control Liver 3


title: CMPF-HFD Liver 3

source_name: Liver at end of diet period

value: prevention

value: CMPF-HFD


title: WeightRegainers10_T2

description:
adipose tissue 48
WeightRegainer10 at twelfth month (T2)

value: Female


title: CMPF-HFD Liver 2


title: WeightRegainers1_T0

description:
adipose tissue 1
WeightRegainer1 at baseline (T0)


title: WeightRegainers13_T2

description:
adipose tissue 51
WeightRegainer13 at twelfth month (T2)


title: CMPF-HFD Liver 1


title: WeightRegainers9_T2

description:
adipose tissue 47
WeightRegainer9 at twelfth month (T2)


title: WeightRegainers12_T2

description:
adipose tissue 50
WeightRegainer12 at twelfth month (T2)


title: Control-HFD Liver 3

value: Control-HFD


title: WeightRegainers7_T2

description:
adipose tissue 45
WeightRegainer7 at twelfth month (T2)


title: WeightRegainers4_T2

description:
adipose tissue 42
WeightRegainer4 at twelfth month (T2)


title: WeightRegainers8_T2

description:
adipose tissue 46
WeightRegainer8 at twelfth month (T2)


title: Control-HFD Liver 1


title: WeightRegainers5_T2

description:
adipose tissue 43
WeightRegainer5 at twelfth month (T2)


title: WeightRegainers6_T2

description:
adipose tissue 44
WeightRegainer6 at twelfth month (T2)


title: WeightRegainers2_T2

description:
adipose tissue 40
WeightRegainer2 at twelfth month (T2)


title: WeightRegainers3_T2

description:
adipose tissue 41
WeightRegainer3 at twelfth month (T2)


title: Control-Chow Liver 1

description: Gene expression from liver of treated mice

value: Control-Chow


title: Control-HFD Liver 2


title: MOLM13 shNT_1

city: Heidelberg

first: Simon

last: Raffel

address: INF 280

country: Germany

institute: German Cancer Research Center

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Gene Expression Microarrays were scanned using the Illumina iScan-Scanner according to Standard Illumina Scanning Protocol

data_processing: The data were normalised using quantile normalisation with R using function normalize.quantiles from Bioconductor package preprocessCore

label: Biotin, Cy3-Streptavidin

source_name: MOLM13 CTRL

label_protocol: The Illumina TotalPrep RNA Amplification Kit (life technologie) is used to generate single-stranded cRNA from input amounts of 200ng total RNA

growth_protocol: RPMI, 10% FCS (HL-60) or 20% FCS (SKM1, MOLM13)

extract_protocol: Rneasy (Qiagen)

treatment_protocol: Transduction with shBCAT1-3 or shNT, FACS sort of transduced cells 48hrs after the transduction

tag: cell line

tag: genotype/variation

value: CTRL


title: MOLM13 shNT_3


title: MOLM13 shBCAT1-3_1

source_name: MOLM13 KD BCAT1

value: KD BCAT1


title: MOLM13 shNT_2


title: Control-Chow Liver 2

tag: strain


title: WeightRegainers1_T2

description:
adipose tissue 39
WeightRegainer1 at twelfth month (T2)


title: MOLM13 shBCAT1-3_2


title: MOLM13 shBCAT1-3_3


title: SKM1 shNT_2

source_name: SKM1 CTRL


title: Control-Chow Liver 3


title: SKM1 shBCAT1-3_3

source_name: SKM1 KD BCAT1


title: SKM1 shNT_1


title: SKM1 shNT_3


title: SKM1 shBCAT1-3_2


title: WeightLosers3_T1

description:
adipose tissue 35
WeightLoser3 at fifth month (T1)


title: HL60 shNT_1

source_name: HL-60 CTRL


title: HL60 shNT_2


title: HL60 shNT_3


title: WeightLosers5_T1

description:
adipose tissue 37
WeightLoser5 at fifth month (T1)


title: WeightLosers6_T1

description:
adipose tissue 38
WeightLoser6 at fifth month (T1)


title: WeightLosers2_T1

description:
adipose tissue 34
WeightLoser2 at fifth month (T1)


title: osteoblasts, non-treated, rep3

city: Rehovot

first: Yehiel

last: Zick

address: 234 Herzl st.

department: Molecular Cell Biology

country: Israel

institute: Weizmann Institute of Science

hyb_protocol: 2ug ss cDNA in 80 ul total volume were hybridized to a Mouse Gene 2.0 ST array using Affymetrix hybridization kit materials and hybridized for 17 hours at 45° at 60rpm. Post-hyb washes were done with Affymetrix wash solutions on the FS450 station using FS450_0007 protocol.

scan_protocol: Arrays were scanned on the Affymetrix GeneChip Scanner 3000 7G

data_processing: The analysis was carried out using Partek Genome Suite software (Partek Inc., St. Louis, Missouri 63141, http://www.partek.com), using RMA.

source_name: osteoblasts from calvaria of newborn CD1 mice

label_protocol: 200ng TotalRNA were used for labeling. cDNA samples were generated and labeled using Affymetrix WT-cDNA synthesis and labeling kit

growth_protocol: We isolated primary osteoblasts from the calvaria of newborn (<24 hours old) CD1 mice. Cells were grown at 37°C, 5% CO2 in alpha modified MEM medium (Sigma).

extract_protocol: Total RNA was isolated by PerfectPure RNA tissue kit (5 PRIME, Germany) according to the manufacturer's instructions.

treatment_protocol: cells were treated with 50nM recombinant galectin-8 of rat origin for 24 hours.

value: calvaria

value: osteoblasts


title: WeightRegainers11_T1

description:
adipose tissue 30
WeightRegainer11 at fifth month (T1)


title: HL60 shBCAT1-3_1

source_name: HL-60 KD BCAT1


title: osteoblasts, gal-8 treated, rep1

value: galectin-8 treated (50nM, 24hrs)


title: osteoblasts, gal-8 treated, rep3


title: osteoblasts, non-treated, rep2


title: osteoblasts, gal-8 treated, rep2


title: WeightRegainers9_T1

description:
adipose tissue 28
WeightRegainer9 at fifth month (T1)


title: WeightRegainers13_T1

description:
adipose tissue 32
WeightRegainer13 at fifth month (T1)


title: HL60 shBCAT1-3_3


title: WeightRegainers8_T1

description:
adipose tissue 27
WeightRegainer8 at fifth month (T1)


title: HL60 shBCAT1-3_2


title: WeightRegainers7_T1

description:
adipose tissue 26
WeightRegainer7 at fifth month (T1)


title: CTCL other types, biological rep 2_affymetrix

first: Jie

last: Zheng

address: 197 Ruijin Er Rd

department: Dermatology

institute: Ruijin Hospital

description:
miRNA
CTCL_O_2

hyb_protocol: The sample labeling, microarray hybridization and washing were performed based on the manufacturer’s standard protocols .Briefly, total RNA were tailed with Poly A and then labeled with Biotin. After, the labeled RNAs were hybridized onto the microarray. (This step was performed in core facility of Oebiotech; Address: 1505 Zuchongzhi Rd, Blk 138, Floor 6, Shanghai, China. Tel: 86-21-38762096)

scan_protocol: GeneChips were scanned by the Affymetrix Scanner 3000 (Affymetrix).

data_processing: Affymetrix GeneChip Command Console software (version4.0, Affymetrix) was used to analyze array images to get raw data and then offered RMA normalization. Genespring software (version 12.5; Agilent Technologies) was used to proceed the following data analysis. (This step was performed in core facility of Oebiotech; Address: 1505 Zuchongzhi Rd, Blk 138, Floor 6, Shanghai, China. Tel: 86-21-38762096)

source_name: CTCL other types, biological rep 2

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

value: skin

tag: diagnosis

value: Cutaneous T cell lymphoma (CTCL)

tag: number of patients

tag: number of male patients

tag: number of female patients


title: CTCL other types, biological rep 3_affymetrix

description:
miRNA
CTCL_O_3

source_name: CTCL other types, biological rep 3

label_protocol: This step was performed in core facility of Oebiotech; Address: 1505 Zuchongzhi Rd, Blk 138, Floor 6, Shanghai, China. Tel: 86-21-38762096

tag: tissue


title: WeightLosers4_T1

description:
adipose tissue 36
WeightLoser4 at fifth month (T1)

value: Adipose Tissue

tag: gender

tag: time


title: WeightRegainers10_T1

description:
adipose tissue 29
WeightRegainer10 at fifth month (T1)

tag: outcome


title: CTCL early stage, biological rep 3_affymetrix

description:
miRNA
CTCL_E_3

source_name: CTCL early stage, biological rep 3


title: CTCL other types, biological rep 1_affymetrix

description:
miRNA
CTCL_O_1

source_name: CTCL other types, biological rep 1


title: WeightLosers1_T1

description:
adipose tissue 33
WeightLoser1 at fifth month (T1)

source_name: adipose tissue


title: WeightRegainers12_T1

description:
adipose tissue 31
WeightRegainer12 at fifth month (T1)

value: Male


title: WeightRegainers6_T1

description:
adipose tissue 25
WeightRegainer6 at fifth month (T1)


title: Benign Inflammatory Dermatosis, biological rep 3_affymetrix

description:
miRNA
BID_3

value: Benign Inflammatory Dermatosis (BID)


title: Benign Inflammatory Dermatosis, biological rep 1_affymetrix

description:
miRNA
BID_1


title: CTCL early stage, biological rep 2_affymetrix

description:
miRNA
CTCL_E_2

source_name: CTCL early stage, biological rep 2


title: CTCL early stage, biological rep 1_affymetrix

description:
miRNA
CTCL_E_1

source_name: CTCL early stage, biological rep 1


title: CTCL advanced stage, biological rep 2_affymetrix

description:
miRNA
CTCL_A_2

source_name: CTCL advanced stage, biological rep 2


title: CTCL advanced stage, biological rep 3_affymetrix

description:
miRNA
CTCL_A_3

source_name: CTCL advanced stage, biological rep 3


title: osteoblasts, non-treated, rep1


title: CTCL advanced stage, biological rep 1_affymetrix

description:
miRNA
CTCL_A_1

source_name: CTCL advanced stage, biological rep 1


title: WeightRegainers5_T1

description:
adipose tissue 24
WeightRegainer5 at fifth month (T1)

value: WeightRegainer


title: WeightRegainers4_T1

description:
adipose tissue 23
WeightRegainer4 at fifth month (T1)


title: E.coli_∆ompR pH 7.2+15% sucrose B

city: singapore

first: smarajit

last: chakraborty

address: T-Lab, 5A Engineering Drive 1, NUS

country: Singapore

institute: Mechanobiology Institute

hyb_protocol: 600ng of labeled cRNA was hybridized onto Agilent SurePrint HD E.coli GE 8x15K Microarray for 17 hours at 65oC, 10 rpm in Agilent hybridization oven. After hybridization, the microarray slide was washed in gene expression wash buffer 1 for one minute at room temperature and another minute in gene expression wash buffer 2 at 37oC

scan_protocol: Scanning was performed on Agilent High Resolution Microarray Scanner (C-model).

data_processing:
Raw signal data were extracted from the TIFF image with Agilent Feature Extraction Software (V10.7.1.1). The data analysis is done using a microarray specialized analysis software, Genespring GX. In this experiment, the microarray type used is a slide having 8 arrays with 60 thousand features per array. The exact number of features in the each array, inclusive of control probes, is 10,751 features. The microarray has a specific Agilent identifier called an AMADID which is used to identify what kind of array is being used; in this experiment the AMADID used is the design ID 020097.
Supplementary files contain the following: Raw Signal Values: The term “raw” signal values refer to the linear data after thresholding and summarization Summarization is performed by computing the geometric mean. Raw data filtered on Expression (20.0 - 343943.344)• Normalized Signal Values: ``Normalized'' value is the value generated after log transformation and normalization (Shift to 75 percentile) and baseline transformation.

label: cyanine 3-CTP

organism: Escherichia coli str. K-12 substr. MG1655

source_name: ∆ompR pH 7.2+15% sucrose B

label_protocol: 100 ng of total RNA was labeled with Low Input Quick Amp WT Labeling Kit, One-Color (Agilent p/n 5190-2943) following manufacturer instruction (One-Color Microarray-Based Gene Expression, Analysis Low Input Quick Amp WT Labeling, version 2.0). Briefly, 100 ng of total RNA was converted into double-stranded cDNA by priming with an oligo-dT primer containing the recognition site for T7 RNA polymerase. In vitro transcription with T7 RNA polymerase was used to produce cyanine 3-CTP labeled cRNA.

growth_protocol: E. coli strains was grown in MgM media at pH 5.6, 7.2 and 7.2 with 15% (w/v) sucrose to O.D ~0.6.

extract_protocol: The total RNA was isolated using an RNeasy mini kit (Qiagen).

tag: ph

tag: sucrose status

value: with 15% sucrose

tag: genotype


title: WeightRegainers3_T1

description:
adipose tissue 22
WeightRegainer3 at fifth month (T1)


title: SKM1 shBCAT1-3_1


title: E.coli_∆ompR pH 7.2+15% sucrose A

source_name: ∆ompR pH 7.2+15% sucrose A


title: Benign Inflammatory Dermatosis, biological rep 2_affymetrix

description:
miRNA
BID_2


title: WeightRegainers1_T1

description:
adipose tissue 20
WeightRegainer1 at fifth month (T1)


title: E.coli_WT pH 7.2+15% sucrose C

source_name: WT pH 7.2+15% sucrose C

value: Wildtype


title: E.coli_WT pH 7.2+15% sucrose B

source_name: WT pH 7.2+15% sucrose B


title: WeightLosers4_T0

description:
adipose tissue 17
WeightLoser4 at baseline (T0)

value: WeightLoser


title: WeightLosers3_T0

description:
adipose tissue 16
WeightLoser3 at baseline (T0)


title: Benign Inflammatory Dermatosis, biological rep 4_affymetrix

description:
miRNA
BID_4


title: WeightRegainers2_T1

description:
adipose tissue 21
WeightRegainer2 at fifth month (T1)

value: Female


title: E.coli_∆ompR pH 5.6 C

source_name: ∆ompR pH 5.6 C

value: no sucrose


title: WeightLosers6_T0

description:
adipose tissue 19
WeightLoser6 at baseline (T0)


title: E.coli_∆ompR pH 5.6 B

source_name: ∆ompR pH 5.6 B


title: E.coli_∆ompR pH 5.6 A

source_name: ∆ompR pH 5.6 A


title: E.coli_WT pH 7.2+15% sucrose A

source_name: WT pH 7.2+15% sucrose A


title: E.coli_WT pH 5.6 C

source_name: WT pH 5.6 C


title: WeightLosers5_T0

description:
adipose tissue 18
WeightLoser5 at baseline (T0)


title: CTCL other types, biological rep 1_agilent

description:
miRNA
CTCL_O_1

data_processing:
This step was performed in core facility of Oebiotech; Address: 1505 Zuchongzhi Rd, Blk 138, Floor 6, Shanghai, China. Tel: 86-21-38762096
Normalization was done separately for rep 1 and rep 2 samples due to limited number of patients recruited to study during the course of the study.  The ID_REF column contains a mixture of miRNA ID and probe name. These IDs can be found in the raw data files in the columns "SystematicName" and "ProbeName", respectively. This step was performed in core facility of Oebiotech; Address: 1505 Zuchongzhi Rd, Blk 138, Floor 6, Shanghai, China. Tel: 86-21-38762096.  The normalized data  are available on the series record. The normalization method was not available at the time of data submission.


title: WeightRegainers11_T0

description:
adipose tissue 11
WeightRegainer11 at baseline (T0)


title: E.coli_WT pH 5.6 B

source_name: WT pH 5.6 B


title: CTCL advanced stage, biological rep 1_agilent

description:
miRNA
CTCL_A_1

hyb_protocol: This step was performed in core facility of Oebiotech; Address: 1505 Zuchongzhi Rd, Blk 138, Floor 6, Shanghai, China. Tel: 86-21-38762096


title: E.coli_WT pH 5.6 A

source_name: WT pH 5.6 A


title: WeightRegainers12_T0

description:
adipose tissue 12
WeightRegainer12 at baseline (T0)

source_name: adipose tissue


title: M8 Mice 7 Ileum

city: Lausanne

first: Frederic

last: Raymond

address: Campus EPFL - Quartier de l'Innovation

department: Functional Genomics

country: Switzerland

institute: Nestle Institute of Health Sciences

hyb_protocol: Following fragmentation (Affymetrix procedure), labelled-cRNA were hybridized on GeneChip mouse genome 430A 2.0 chips. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Partek Genomics Suite software. Data were normalized using the Robust Multichip Average (RMA) method.

source_name: Ileum, 6 hrs after OLTT_M8

label_protocol: All cRNA targets were synthesized, labeled, and purified according to the TotalPrep RNA Amplification Kit (Thermo Fisher Scientific, Waltham, MA, USA). 300 ng of ileum total RNA were used to produce cRNA labelled with biotin.

growth_protocol: Germfree male C57BL/6J mice were purchased at 8 weeks of age from Charles River Laboratories (L'Arbresle, France)

extract_protocol: Ileum total RNA was extracted from tissue using RNeasy Mini QIAcube kit (Qiagen, AG, Switzerland), following the manufacturer's instructions. The quality of RNA samples was checked by using the Fragment Analyzer (Advanced Analytical Technologies, Inc., Ankeny, USA).

treatment_protocol: Mice were treated with 10^8 CFU/mL E. coli M8 strain (isolated from the feces of an ob/ob mouse) in drinking water for 14 days. At the end of the treatment, mice were subjected to an oral lipid tolerance test (OLTT) (with 6ml/kg of corn oil) after overnight fasting (14h). All mice were sacrificed 6 hours after the lipid tolerance test and ileum samples were collected for further analysis.

value: Ileum

value: male

tag: microbiome status

value: E. coli M8 strain


title: M8 Mice 6 Ileum


title: CTCL advanced stage, biological rep 2_agilent

description:
miRNA
CTCL_A_2

scan_protocol: This step was performed in core facility of Oebiotech; Address: 1505 Zuchongzhi Rd, Blk 138, Floor 6, Shanghai, China. Tel: 86-21-38762096


title: WeightRegainers7_T0

description:
adipose tissue 7
WeightRegainer7 at baseline (T0)


title: CTCL early stage, biological rep 2_agilent

description:
miRNA
CTCL_E_2

source_name: CTCL early stage, biological rep 2


title: WeightRegainers9_T0

description:
adipose tissue 9
WeightRegainer9 at baseline (T0)


title: CTCL early stage, biological rep 1_agilent

description:
miRNA
CTCL_E_1

source_name: CTCL early stage, biological rep 1


title: M8 Mice 5 Ileum


title: Benign Inflammatory Dermatosis, biological rep 2_agilent

description:
miRNA
BID_2


title: WeightRegainers8_T0

description:
adipose tissue 8
WeightRegainer8 at baseline (T0)


title: WeightRegainers3_T0

description:
adipose tissue 3
WeightRegainer3 at baseline (T0)


title: WeightLosers2_T0

description:
adipose tissue 15
WeightLoser2 at baseline (T0)


title: WeightRegainers10_T0

description:
adipose tissue 10
WeightRegainer10 at baseline (T0)


title: WeightLosers1_T0

description:
adipose tissue 14
WeightLoser1 at baseline (T0)


title: M8 Mice 4 Ileum


title: WeightRegainers5_T0

description:
adipose tissue 5
WeightRegainer5 at baseline (T0)


title: Benign Inflammatory Dermatosis, biological rep 1_agilent

description:
miRNA
BID_1


title: M8 Mice 2 Ileum


title: M8 Mice 3 Ileum


title: WeightRegainers4_T0

description:
adipose tissue 4
WeightRegainer4 at baseline (T0)


title: WeightRegainers2_T0

description:
adipose tissue 2
WeightRegainer2 at baseline (T0)


title: GF Mice 7 Ileum

source_name: Ileum, 6 hrs after OLTT_germfree

value: germ free


title: WeightRegainers13_T0

description:
adipose tissue 13
WeightRegainer13 at baseline (T0)


title: M8 Mice 1 Ileum


title: GF Mice 8 Ileum


title: WeightRegainers1_T0

description:
adipose tissue 1
WeightRegainer1 at baseline (T0)


title: WeightRegainers6_T0

description:
adipose tissue 6
WeightRegainer6 at baseline (T0)


title: GF Mice 4 Ileum


title: GF Mice 5 Ileum


title: GF Mice 6 Ileum


title: GF Mice 3 Ileum


title: GF Mice 2 Ileum


title: Dmel_MN_Day45_Pool5

city: Stony Brook

first: Jorge

last: Azpurua

state: New York

address: 100 Nicolls Rd

department: Anesthesiology

institute: Stony Brook University

description: Gene expression of 45 day old Drosophila motor neurons

hyb_protocol: Cy3-labeled cDNAs were hybridized to an Agilent custom Drosophila microarray (8 x 60K format, Design ID: 065755) at the UTHSCSA Genomics Resource Core using standard protocols.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Agilent Feature Extraction 11 software was used to extract numerical signal values from scan (default settings mapping to Agilent-65755). Data was analyzed using Agilent GeneSpring™ software. Features flagged as compromised were excluded.

organism: Drosophila melanogaster

source_name: Flow cytometry sorted motor neurons, 45 days post-eclosion, replicate 5

label_protocol: cDNA amplification and labeling was performed using a MessageAmp™ II Amino Allyl aRNA Kit (AM1753, Thermo Fisher Scientific). Samples were coupled to Cy3 NHS Ester fluorescent dye (GE Healthcare; Little Chalfont, UK) and purified prior to microarray hybridization.

extract_protocol: GFP positive motor neurons were isolated via flow cytometry

treatment_protocol: Flies were allowed to age normally at 25°C/50% humidity and 12h light/dark cycle for the specified age window.

value: female

tag: age

value: motor neurons


title: Dmel_MN_Day45_Pool6

source_name: Flow cytometry sorted motor neurons, 45 days post-eclosion, replicate 6


title: Dmel_MN_Day45_Pool4

source_name: Flow cytometry sorted motor neurons, 45 days post-eclosion, replicate 4


title: GF Mice 1 Ileum


title: Dmel_MN_Day45_Pool1

source_name: Flow cytometry sorted motor neurons, 45 days post-eclosion, replicate 1


title: Dmel_MN_Day45_Pool2

source_name: Flow cytometry sorted motor neurons, 45 days post-eclosion, replicate 2


title: HL60 BCAT1-OE +DOX_2_12weeks

hyb_protocol: Oxidative bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

data_processing: The data were normalised for red and green channel seperately using quantile normalisation with R using function normalize.quantiles from Bioconductor package preprocessCore

source_name: HL-60 BCAT1-OE_12weeks

growth_protocol: RPMI + 10% FCS (medium change every 3 days)

extract_protocol: genomic DNA was extracted and purified using Qiagen QiAMP Kit according to standard instructions

treatment_protocol: Doxycyclin 10μg/ml


title: Dmel_MN_Day35_Pool5

description: Gene expression of 35 day old Drosophila motor neurons

source_name: Flow cytometry sorted motor neurons, 35 days post-eclosion, replicate 5


title: Dmel_MN_Day35_Pool4

source_name: Flow cytometry sorted motor neurons, 35 days post-eclosion, replicate 4


title: Dmel_MN_Day45_Pool3

source_name: Flow cytometry sorted motor neurons, 45 days post-eclosion, replicate 3


title: Wt+HP-3

description: Gene expression data from 10-day-old hyperphyllin-treated wild-type seedlings

hyb_protocol: Labeled samples were hybridized to the Affymetrix Gene 1.1 ST Arabidopsis Array Plate and washed on an Affymetrix GeneAtlas system

scan_protocol: The GeneArrays were scanned using GeneAtlas Imaging Station (Affymetrix) using standard protocols.

source_name: Hyperphyllin-treated wild-type, biological rep3

extract_protocol: Total RNA was extracted using the E.Z.N.A. Plant RNA Kit (OMEGA Bio-Tek, Norcross, GA) according to the manufacturer's instructions.

tag: ecotype

value: whole seedlings

value: wild type

tag: treatment

value: 30 µM Hyperphyllin [in DMSO 1% (v/v)]


title: HL60 BCAT1-OE -DOX_2_12weeks

source_name: HL-60 CTRL_12weeks

tag: cell line

tag: genotype/variation

value: CTRL


title: Wt+HP-2

source_name: Hyperphyllin-treated wild-type, biological rep2


title: Dmel_MN_Day35_Pool2

source_name: Flow cytometry sorted motor neurons, 35 days post-eclosion, replicate 2


title: Dmel_MN_Day35_Pool3

source_name: Flow cytometry sorted motor neurons, 35 days post-eclosion, replicate 3


title: MOLM13 BCAT1-OE +DOX_1_20weeks

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

source_name: MOLM13 BCAT1-OE_20weeks

growth_protocol: RPMI + 20% FCS (medium change every 3 days)


title: MOLM13 BCAT1-OE -DOX_3_20weeks

source_name: MOLM13 CTRL_20weeks


title: HL60 BCAT1-OE -DOX_1_12weeks


title: MOLM13 BCAT1-OE +DOX_2_20weeks


title: HL60 BCAT1-OE +DOX_1_12weeks


title: MOLM13 BCAT1-OE -DOX_2_20weeks


title: MOLM13 BCAT1-OE -DOX_1_10weeks

source_name: MOLM13 CTRL_10weeks


title: Dmel_MN_Day7_Pool4

description: Gene expression of 7 day old Drosophila motor neurons

source_name: Flow cytometry sorted motor neurons, 7 days post-eclosion, replicate 4


title: Wt+DMSO-2

description: Gene expression data from 10-day-old DMSO treated wild-type seedlings

source_name: wild-type control, biological rep2

value: solvent control [DMSO 1% (v/v)]


title: amp1-13+HP-3

description: Gene expression data from 10-day-old hyperphyllin-treated amp1-13 seedlings

source_name: Hyperphyllin-treated amp1-13, biological rep3


title: Wt+DMSO-3

source_name: wild-type control, biological rep3


title: Dmel_MN_Day35_Pool1

source_name: Flow cytometry sorted motor neurons, 35 days post-eclosion, replicate 1


title: Wt+DMSO-1

source_name: wild-type control, biological rep1


title: Wt+HP-1

source_name: Hyperphyllin-treated wild-type, biological rep1


title: Dmel_MN_Day7_Pool3

source_name: Flow cytometry sorted motor neurons, 7 days post-eclosion, replicate 3


title: Dmel_MN_Day7_Pool5

source_name: Flow cytometry sorted motor neurons, 7 days post-eclosion, replicate 5


title: AML181_shBCAT1_#2

hyb_protocol: 6,6 ug of fragmented and labeled ds-cDNA were hybridized for 17 hr at 45°C on Affymetrix GeneChip® Human Genome U133 Plus 2.0 Arrays

scan_protocol: Gene Expression Microarrays were scanned using the Affymetrix GeneChip® Scanner 3000 according to GeneChip® Expression Wash, Stain and Scan Manual for Cartridge Arrays

label_protocol: The Affymetrix 3’ IVT Pico Reagent Kit is used to generate labeled single-stranded cRNA from input amounts of 500pg total RNA

growth_protocol: AML samples were cultured in StemSpan SFEM (Stemcell Technologies) supplemented with rhIL3 (20 ng/ml), rhFLT3L (100 ng/ml), rhTPO (50 ng/ml), rhSCF (100 ng/ml, all Peprotech), 1% Penicillin/Streptomycin (Sigma) and 2 mM Glutamine (Sigma).

value: KD BCAT1


title: AML181_shBCAT1_#3


title: AML181_shBCAT1_#1


title: HL60 BCAT1-OE +DOX_2_20weeks

source_name: HL-60 BCAT1-OE_20weeks


title: AML181_shNT_#3


title: MOLM13 BCAT1-OE +DOX_1_10weeks

source_name: MOLM13 BCAT1-OE_10weeks


title: MOLM13 BCAT1-OE +DOX_2_10weeks


title: HL60 BCAT1-OE +DOX_2_10weeks

source_name: HL-60 BCAT1-OE_10weeks


title: amp1-13+HP-2

source_name: Hyperphyllin-treated amp1-13, biological rep2


title: MOLM13 BCAT1-OE +DOX_3_20weeks


title: AML181_shNT_#2


title: Dmel_MN_Day7_Pool1

source_name: Flow cytometry sorted motor neurons, 7 days post-eclosion, replicate 1


title: HL60 BCAT1-OE -DOX_1_20weeks

source_name: HL-60 CTRL_20weeks


title: Dmel_MN_Day7_Pool2

source_name: Flow cytometry sorted motor neurons, 7 days post-eclosion, replicate 2


title: amp1-13+HP-1

source_name: Hyperphyllin-treated amp1-13, biological rep1


title: amp1-13+DMSO-3

description: Gene expression data from 10-day-old DMSO treated amp1-13 seedlings

source_name: amp1-13 control, biological rep3


title: MOLM13 BCAT1-OE -DOX_2_10weeks

source_name: MOLM13 CTRL_10weeks


title: S. Typhimurium_∆ompR pH 7.2+15% sucrose D

hyb_protocol: 600ng of labeled cRNA was hybridized onto Agilent SurePrint G3 Custom 8x60K Microarray (G4102A) for 17 hours at 65oC, 10 rpm in Agilent hybridization oven. After hybridization, the microarray slide was washed in gene expression wash buffer 1 for one minute at room temperature and another minute in gene expression wash buffer 2 at 37oC

data_processing:
Raw signal data were extracted from the TIFF image with Agilent Feature Extraction Software (V10.7.1.1). The data analysis is done using a microarray specialized analysis software, Genespring GX.
Supplementary file includes: Raw Signal Values: The term “raw” signal values refer to the linear data after thresholding and summarization Summarization is performed by computing the geometric mean.Raw data  filtered on Expression (20.0 - 731651.375)• Normalized Signal Values: ``Normalized'' value is the value generated after log transformation and normalization (Shift to 75 percentile) and baseline transformation.

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

source_name: ∆ompR pH 7.2+15% sucrose D

growth_protocol: S. Typhimurium strains was grown in MgM media at pH 7.2 with(out) 15% (w/v) sucrose to O.D ~0.6.

tag: strain

value: 15% sucrose


title: amp1-13+DMSO-2

source_name: amp1-13 control, biological rep2


title: HL60 BCAT1-OE -DOX_3_10weeks

source_name: HL-60 CTRL_10weeks


title: AML181_shNT_#1


title: amp1-13+DMSO-1

source_name: amp1-13 control, biological rep1


title: HD48_shBCAT1-2_#4


title: HL60 BCAT1-OE +DOX_3_10weeks


title: MOLM13 BCAT1-OE -DOX_1_20weeks

source_name: MOLM13 CTRL_20weeks


title: HD48_shBCAT1-2_#2


title: HD48_shBCAT1-2_#3


title: S. Typhimurium_∆ompR pH 7.2+15% sucrose A

source_name: ∆ompR pH 7.2+15% sucrose A


title: HL60 BCAT1-OE +DOX_1_10weeks


title: S. Typhimurium_∆ompR pH 7.2+15% sucrose C

source_name: ∆ompR pH 7.2+15% sucrose C


title: HD48_shBCAT1-2_#1


title: HL60 BCAT1-OE +DOX_1_20weeks

source_name: HL-60 BCAT1-OE_20weeks


title: HL60 BCAT1-OE -DOX_1_10weeks


title: HL60 BCAT1-OE -DOX_2_10weeks


title: Dm_DP_knockdown_rep3

city: Charlestown

first: Robert

last: Morris

state: Massachusetts

address: 149 13th Street

institute: Mass. General Hospital Cancer Center

description:
SAMPLE 5
This sample is a transheterozygous dDP mutant

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: Sample raw data was RMA normalized using Oligo R package (Carvalho 2016)

source_name: Drosophila melanogaster Dp knockdown

label_protocol: cDNAs were Cy3 labeled foloowing instructions from Nimblegen standard operating protocols. See www.nimblegen.com.

growth_protocol: Larvae grew in regular Drosophila medium.

extract_protocol: Total RNA was extracted from third instar larvae with Trizol and quality tested with Bioanalyzer.

treatment_protocol: Larvae were washed and not treated with additional reagents prior to RNA extraction.

tag: developmental stage

value: larva

value: dDPa3/dDPa4 (transheterozygous dDP mutant)


title: HL60 BCAT1-OE -DOX_2_20weeks


title: HD48_shNT_#4


title: S. Typhimurium_WT pH 7.2+15% sucrose D

source_name: WT pH 7.2+15% sucrose D

value: Wildtype


title: S. Typhimurium_WT pH 7.2+15% sucrose C

source_name: WT pH 7.2+15% sucrose C


title: S. Typhimurium_WT pH 7.2+15% sucrose B

source_name: WT pH 7.2+15% sucrose B


title: S. Typhimurium_∆ompR pH 7.2+15% sucrose B

source_name: ∆ompR pH 7.2+15% sucrose B


title: HD48_shNT_#3


title: Dm_DP_knockdown_rep2

description:
SAMPLE 4
This sample is a transheterozygous dDP mutant


title: S. Typhimurium_WT pH 7.2+15% sucrose A

source_name: WT pH 7.2+15% sucrose A


title: Dm_wildtype_rep3

description:
SAMPLE 2
This sample is wild-type

source_name: Drosophila melanogaster wildtype

value: w1118; wild type


title: Dm_DP_knockdown_rep1

description:
SAMPLE 3
This sample is a transheterozygous dDP mutant


title: HD48_shNT_#2


title: Dm_wildtype_rep1

description:
SAMPLE 1
This sample is wild-type


title: E7-ca-STAT5A-shSOCS1_2

status: Public on Nov 07 2017

city: Montréal

first: Mathieu

last: Vernier

state: Quebec

address: 2900 Edouard Montpetit

department: Biochemistry

institute: Université de Montréal

description: IMR90 normal human fibroblast cells infected with a vector expressing the E7 protein of human papilloma virus, a constitutively active form of the  transcription factor STAT5A and an shRNA against SOCS1

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Human Gene 2.0 ST Chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 7G/4 Color Early Access.

data_processing: The data were analyzed the Flexarray software using RMA as normalization method. Transcripts with a fold change higher or equal to 1.5 and a p-value˂ 0.05 according to the two-sample student's t-test were selected for final determination.

label_protocol: Biotinylated cRNA were prepared according to the protocol from the Ambion® WT Expression kit for Affymettrix® GeneChip®Whole Transcript (WT) Expression Arrays

growth_protocol: Cells were cultured in DMEM (Wisent, Montréal, QC) supplemented with 10% fetal bovine serum (FBS; Wisent) and 1% penicillin G/streptomycin sulfate (Wisent).

extract_protocol: RNA isolation with RNeasy Mini Kit (QIAGEN) according to manufacturer’s instructions.

treatment_protocol: Cells were infected with a retrovirus expressing the protein E7 from the papillomavirus and a constitutively form of STAT5A, plus either a scrambled shRNA or an shRNA targeting SOCS1. After selection for 6 days with G418 (300 ug/mL), 3 days puromycin (1.5 ug/mL) and 4 days with hygromycin (80 ug/mL) cells were scraped in RLP buffer at day 8 post infection.

tag: cell

value: IMR90 normal human lung fibroblast cell line

value: expressing the protein E7 from the papillomavirus and a constitutively active form of STAT5A, plus an shRNA targeting SOCS1


title: E7-ca-STAT5A-shSOCS1_1


title: E7-ca-STAT5A-shSOCS1_3


title: HD48_shNT_#1


title: E7-ca-STAT5A-shNTC_1

description: IMR90 normal human fibroblast cells infected with a vector expressing the E7 protein of human papilloma virus, a constitutively active form of the  transcription factor STAT5A and a scramble shRNA

value: expressing the protein E7 from the papillomavirus and a constitutively active form of STAT5A, plus a scrambled shRNA


title: E7-ca-STAT5A-shNTC_2


title: E7-ca-STAT5A-shNTC_3


title: BM-MSCs_SCD1 overexpression_endothelial induced_3 days_rep3

last: Tao

address: haining road 100

institute: Shanghai General Hospital

description: Gene expression data from bone marrow mesenchymal stem cells which were transfected by SCD1-lentivirus and endothelial induced for 3 days.

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

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000.

data_processing: The data were analyzed with RMA.

source_name: Bone marrow mesenchymal stem cells transfected by SCD1-lentivirus,endothelial induced,3 days

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

growth_protocol: Bone marrow mesenchymal stem cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) containing 10% fetal bovine serum (FBS) at 37°C in a humidified atmosphere of 5% CO2 and 95% air, according to the standard procedure. The cell lines were routinely passaged using an enzymatic solution consisting of 0.25% (w/v) trypsin for 5 min at 37°C.

treatment_protocol: The third generation cells, with 1 × 10^4 cells/well, were transferred onto a 12-well plate. After 24 h, endothelial cell induction was performed with induction medium (low glucose DMEM containing 10% FBS). Endothelial induced for 3 days. Then rinsed with PBS with 0,7% NaCl, 0,04% triton-X100 and placed on ice in the Trizol solution (GibcoBRL).

value: Human bone marrow

tag: cell type

value: endothelial cells induced from bone marrow mesenchymal stem cells

value: SCD1 overexpression