title: naive primary human hepatocytes (N12-KL14)

source_name: primary human hepatocytes

value: 11 days post infection

value: primary human hepatocytes

value: naïve


title: NCI-H23

status: Public on Oct 08 2016

type: genomic

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

state: Barcelona

address: Hospital Duran i Reynals Av. Gran Via s/n km, 2.7

department: PEBC

country: Spain

institute: IDIBELL

description: NCI60 panel

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 High Scan SQ using standard recommended Illumina scanner setting

data_processing:
Genome Studio V2011.2
Unmethylated and methylated signal intensities

label: Cy3, Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: Lung

label_protocol: Standard Illumina labelling protocol

extract_protocol: unknown

tag: tissue

value: Lung

tag: cell line

tag: cell type

value: Cancer cell line


title: HCV infected primary human hepatocytes (N10-KL8)

status: Public on Oct 07 2016

type: RNA

city: Cambridge

first: Naomi

last: Habib

state: MA

address: 75 Ames st

department: Zhang

country: USA

institute: Broad Institute

hyb_protocol: RNA was hybridized to an Affymetrix GeneChip. Samples were hybridized using Affymetrix hybridization kit (following manufacturer's protocol)

scan_protocol: Affymetrix GeneChip scanner

data_processing: Following robust multi-array average (RMA) procedure and quantile normalization, the probes were filtered using BioDiscovery’s Nexus Expression software (El Segundo, CA). Probes with a variance less than 0.2 and intensity less than 4.0 were removed.

label: biotin

molecule: total RNA

label_protocol: Affymetrix labeling protocol

growth_protocol: Primary human hepatocytes were mixed with lung endothelial cells and seeded in a humidified incubator conditioned by a gas mixture of 95% oxygen and 5% CO2. Following overnight seeding under 95% oxygen the cultures were returned to atmospheric levels of oxygen and 5% CO2.

extract_protocol: Liver biopsy samples were flash frozen, then RNA was extracted for array analysis. RNA from primary samples was collected at day 11 post infection.

treatment_protocol: HCV infection of primaty hepatocytes (JFH-1 virus) was carried 1 day post seeding. Liver biopsy samples were collected from 5 patients, at early stages of HCV infection (genotypes 2B, 1A, 2A, 3A), following an overnight fast.

tag: age

value: liver

tag: infection

value: HCV-infected


title: HT29

description: NCI60 panel

source_name: Large Intestine

value: Large Intestine


title: naive primary human hepatocytes (N11-KL13)


title: H7250303A pancreatic ductal adenocarcinoma

city: ChongQing

first: ShiXiang

last: Guo

state: ChongQing

address: GaoTanYan street No.29，ShaPingBa district

department: Southwest hospital，Third Military Medical University

country: China

institute: institute of Hepatopancreatobiliary Surgery

description: The pancreatic ductal adenocarcinoma sample was collected from the Institute of Hepatopancreatobiliary Surgery, Southwest Hospital, Third Military Medical University, and stored in liquid nitrogen.

hyb_protocol: The labeled cRNAs were hybridized onto an Arraystar Human circRNA Array (8×15K, Arraystar)and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After the slides were washed, the arrays were scanned using an Agilent Scanner 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 using the R software package. Statistical differences in circRNA expression between the two groups were determined with Volcano Plot filtering. Differentially expressed circRNAs between the two sample sets were identified through Fold Change filtering. Hierarchical Clustering was performed to show distinguishable circRNAs expression patterns among samples.

source_name: pancreatic ductal adenocarcinoma

label_protocol: total RNA was digested with RNase R (Epicentre, Inc.) to remove linear RNAs and to enrich for circRNAs. The enriched circRNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar).

extract_protocol: Total RNA from pancreatic ductal adenocarcinoma samples and paracancerous tissues was extracted using the TRIzol reagent (Invitrogen, Carlsbad, CA, USA). The RNA extractions were stored at 80°C. Total RNA from each sample was quantified using a NanoDrop ND-1000. Sample preparation and microarray hybridization were performed based on Arraystar’s standard protocols.

treatment_protocol: Twenty fresh-frozen PDAC samples and twenty paracancerous tissues were collected from the Institute of Hepatopancreatobiliary Surgery, Southwest Hospital, Third Military Medical University. The paracancerous samples were obtained from the same patient. All tissue samples were stored in liquid nitrogen, and pathologists from the Department of Pathology in the Southwest Hospital performed pathologic diagnosis.

value: pancreatic ductal adenocarcinoma sample

tag: gender

value: male


title: H7250303P paracancerous tissue

description: The paracancerous tissue was obtained from the same patient, and stored in liquid nitrogen.

source_name: paracancerous tissue

value: paracancerous tissue


title: CCRF-CEM

description: NCI60 panel

source_name: Haematopoietic and Lymphoid Tissue

value: Haematopoietic and Lymphoid Tissue

value: CCRF-CEM


title: H8741820A pancreatic ductal adenocarcinoma

value: female


title: H5989771P paracancerous tissue


title: M14

description: NCI60 panel

source_name: Skin

value: Skin


title: OVCAR-5

description: NCI60 panel

source_name: Ovary

value: Ovary


title: HCT-116

description: NCI60 panel


title: H5989771A pancreatic ductal adenocarcinoma


title: PC-3

description: NCI60 panel

source_name: Prostate

value: Prostate


title: EKVX

description: NCI60 panel

value: EKVX


title: H5197339A pancreatic ductal adenocarcinoma


title: SW-620

description: NCI60 panel


title: H5187747P paracancerous tissue


title: H5187747A pancreatic ductal adenocarcinoma


title: H55478397A pancreatic ductal adenocarcinoma


title: H4896950P paracancerous tissue


title: H5197339P paracancerous tissue


title: H4896950A pancreatic ductal adenocarcinoma


title: H4782841A pancreatic ductal adenocarcinoma


title: H4782841P paracancerous tissue


title: SI.IEC.SPF.SFB#2

city: Boston

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

hyb_protocol: Ambion WT Expression Kit

scan_protocol: Affymetrix GeneChip Scanner

data_processing: The datasets was pre-filtered to keep only those probesets for which a gene symbol could be found in the Affymetrix annotation. CEL files were normalized using Affymetrix Power Tools on the predefined probeset ID list mentioned above, and using the standard RMA workflow (background adjustment, quantile normalization, median polish probeset summarization). Output on 2^ scale.

label: Biotin

organism: Mus musculus

source_name: Small Intestine

label_protocol: Affymetrix GeneChip WT Terminal Labeling and Controls Kit

extract_protocol: TRIzol

tag: bacterial species

value: SPF (SFB+)

value: 6 Weeks Old

tag: genetic background

tag: Sex

value: Male

tag: phenotype markers

value: EpCAM+

tag: exclusion markers

value: DAPI- CD45-

tag: separation method

value: MoFlo Sorter

tag: amplification technique

value: Ambion WT Expression Kit


title: SI.IEC.SPF.Jax#2

value: SPF (SFB-)


title: SI.IEC.SPF.Jax#1


title: SI.IEC.GF#2

value: Germ-free


title: H4584164P paracancerous tissue

value: paracancerous tissue

value: male


title: SI.IEC.GF#3


title: SI.IEC.Chisto.AO25#2

value: C. histolyticum AO25


title: SI.IEC.SPF.SFB#1


title: SI.IEC.GF#1


title: SI.IEC.Chisto.AO25#1


title: SI.IEC.Badol.L232#4

value: B. adolescentis L2-32


title: SI.IEC.Badol.L232#3


title: SI.IEC.Badol.L232#2


title: UACC-257

description: NCI60 panel

value: Skin

value: Cancer cell line


title: H4476878P paracancerous tissue

value: female


title: H4499473P paracancerous tissue


title: H4499473A pancreatic ductal adenocarcinoma

value: pancreatic ductal adenocarcinoma sample


title: H4584164A pancreatic ductal adenocarcinoma


title: Sp.Treg.10wk#2

source_name: Spleen

value: 10 Weeks Old

value: NOD NRB_SFB+

value: DAPI-

value: Female

tag: cell family

value: Foxp3+ Treg

value: CD4+ TCRb+ CD45+ GFP+


title: H4476878A pancreatic ductal adenocarcinoma


title: H4434313P paracancerous tissue


title: Sp.Treg.10wk#1

value: MoFlo Sorter

value: Ambion WT Expression Kit


title: H4434313A pancreatic ductal adenocarcinoma


title: H4581341P paracancerous tissue


title: Sp.Treg.10wk#3


title: H4581341A pancreatic ductal adenocarcinoma


title: Pa.Treg.10wk#2

source_name: Pancreas


title: SI.IEC.Badol.L232#1

value: 6 Weeks Old

value: Male

value: EpCAM+

value: DAPI- CD45-


title: Pa.Treg.10wk#1


title: Ileum.SFB#2

value: SFB

value: Dissection / Trimming


title: Ileum.Chisto#2

value: C. histolyticum AO25


title: Ileum.GF#2

value: Germ-free


title: Pa.Treg.10wk#3


title: Ileum.SFB#3


title: Ileum.GF#3


title: Ileum.SFB#1


title: Ileum.GF#1


title: Ileum.Chisto#3


title: Liver_HFD-MTX50_rep5

city: Scottsdale

first: Cheryl

middle: E

last: Myers

state: AZ

address: 13400 E Shea Blvd

department: Immunology

institute: Mayo Clinic College of Medicine

hyb_protocol: Agilent hybridization protocol was followed

scan_protocol: GE1-107_SEP09 (Read Only)

data_processing: Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

label_protocol: Agilent Low RNA Input Linear Amplification Kit PLUS, one color,  was used according to manufacturers instructions

growth_protocol: Beginning at 6 weeks of age, C57BL/6 male mice were fed either 10% low fat diet or 60% high fat diet.

extract_protocol: Trizol, followed by Rneasy MiniKit (Qiagen)

treatment_protocol: After 10 weeks on fat diet, treatment cohort mice were injected with methotrexate 50 mg/kg intraperitoneal for 5 rounds. One week after the 5th treatment, mice were euthanized and liver tissue was harvested.

tag: strain

value: Liver

tag: diet

value: high fat

tag: treatment

value: Methotrexate 50mg/kg


title: Liver_HFD-MTX50_rep4

tag: tissue


title: Whole genome gene expression profiles of H1299-shNaa10 and H1299-shRNA negative control

city: Hangzhou

first: Yong

last: Han

address: #158 Shangtang Road

institute: Zhejiang Provincial People's Hospital

hyb_protocol: 0.6 μg of Cy3/Cy5-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Microarray(4*44K)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: Scanned on an Agilent G2505C scanner.

data_processing: Agilent Feature Extraction Software (v 10.7.1.1) was used for background subtraction. Raw data were normalized in quantile algorithm with Genespring 13.0(Agilent).

source_name: shNaa10 transfected H1299 cell line

label_protocol: Cy3/Cy5 labeled cRNA was prepared using the Two-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: H1299 was grown in RPMI1640 (Hyclone UT,USA) supplemented with 10% heat-inactivated fetal bovine serum (FBS).

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

treatment_protocol: Transfection of shRNA plasmid was performed using jetPEITM transfection reagent (Polyplus, NY, USA) according to the manufacturer’s instructions. Cells were then subjected to G418 selection for another two weeks with the concentration of 400 mg/ml.

tag: cell line

tag: transection

value: shNaa10 transfected

source_name: shRNA negative control transfected H1299 cell line

tag: transfection

value: shRNA negative control transfected


title: Ileum.Chisto#1

tag: age


title: Liver_HFD-MTX50_rep2


title: Liver_HFD-MTX50_rep3


title: Ileum.Badol.L232#3

value: B. adolescentis L2-32


title: Ileum.Badol.L232#1


title: Liver_HFD-MTX50_rep1


title: control vs. 2h NaCl treatment replicate 2

city: Busan

first: Yong-Hwan

last: Moon

address: Busandaehak-ro 63Beon-gil 2, Geumjeong-gu

department: Molecular Biology

country: South Korea

institute: Pusan National University

description: Gene expression in 14-day-old seedlings of WT grown under SD conditions (8-h-light and 16-h-dark cycle) with 0h- and 2h-treatment of 300 mM NaCl. Whole seedlings were sampled and total RNA was analyzed.

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing:
Agilent Feature Extraction Software (v 9.3.2.1) was used for background subtraction and LOWESS normalization.
The averages of normalized ratios were calculated by dividing the average of normalized signal channel intensity by the average of normalized control channel intensity.

organism: Arabidopsis thaliana

source_name: NaCl 0h

label_protocol: 0.2ug of total RNA was labeled using Low Input Quick Amp Labeling Kit, Two-Color (Agilent Technology) as following manufacturer's instructions.

growth_protocol: Arabidopsis plants were of the Columbia (Col-0) ecotype background. Arabidopsis seeds were surface-sterilized and water-imbibed in the dark for 3 d at 4°C. The seeds were sown on 0.7% (w/v) agar plates containing one-half-strength Murashige and Skoog (MS) media supplemented with B5 vitamins and 1.5% (w/v) sucrose. They were grown at 22°C under SD conditions (8-h-light/16-h-dark cycle).

treatment_protocol: WT seedlings at 14 DAG were treated with 300 mM NaCl for 0h, 2h, and 5h (on filter paper wetted with 300 mM NaCl).

tag: ecotype

value: 14 days after germination

value: whole seedling

source_name: NaCl 2h #2


title: Liver_HFD_rep1

source_name: Liver_HFD_No Treatment

value: no


title: Liver_HFD_rep2


title: control vs. 2h NaCl treatment replicate 1

source_name: NaCl 2h #1


title: Liver_LFD_rep2

source_name: Liver_LFD_No Treatment

value: low fat


title: Liver_LFD-MTX50_rep4

value: Male


title: Liver_LFD_rep4


title: Liver_LFD_rep1


title: Liver_LFD-MTX50_rep3


title: control vs. 5h NaCl treatment replicate 2

description: Gene expression in 14-day-old seedlings of WT grown under SD conditions (8-h-light and 16-h-dark cycle) with 0h- and 5h-treatment of 300 mM NaCl. Whole seedlings were sampled and total RNA was analyzed.

source_name: NaCl 5h #2


title: Liver_LFD-MTX50_rep2


title: Liver_LFD_rep3


title: Ileum.Badol.L232#2

tag: bacterial species

value: 6 Weeks Old

value: Ambion WT Expression Kit


title: Liver_HFD_rep4


title: Liver_HFD_rep3


title: Liver_LFD-MTX50_rep1


title: CD8_Treated_ Allo-Proliferative_rep3

city: London

first: Caroline

last: Besley

state: - None -

address: John Vane Centre, Charterhouse Sq

department: Haemato-Oncology

country: United Kingdom

institute: Barts Cancer Institute

hyb_protocol: biotin GeneChip hybridisation, Wash and Stain Kit (affymetrix)

scan_protocol: GeneChip fluidics station 450

data_processing: Statistical analysis was performed in R/Bioconductor, gene expression data was normalised using the GC- Robust Multi Array (GCRMA) algorithm. Limma was used for differential expression analysis

source_name: CD8 T cells,Treated,Allo-Proliferative

label_protocol: biotin GeneChip 3'IVT Express Kit (affymetrix)

growth_protocol: Allogeneic co-culture with HLA-mismatched stimulator PBMC in RPMI 1640 Aq Media supplemented with 10%FBS and 1%Pen/Strep

extract_protocol: Direct-zol RNA Mini-Prep kits and TRIzol reagent (Zymo Research)

treatment_protocol: 1 micromolar lenalidomide/vehicle control added at initation of coculture

tag: fraction

value: Alloproliferative

tag: cell type

value: CD8 T cell

value: 1micromolar lenalidomide


title: CD8_Untreated_Non-Allo-Proliferative_rep3

source_name: CD8 T cells,Treated, Non-Allo-Proliferative

value: Non-alloproliferative

value: vehicle control


title: CD8_Untreated_ Allo-Proliferative_rep3


title: CD8_Untreated_Non-Allo-Proliferative_rep2


title: CD8_Treated_ Allo-Proliferative_rep2


title: CD8_Untreated_ Allo-Proliferative_rep2


title: HCV infected primary human hepatocytes (N09-KL7)

source_name: primary human hepatocytes

value: 11 days post infection

value: liver

value: primary human hepatocytes

tag: infection

value: HCV-infected


title: CD8_Untreated_  Non-Allo-Proliferative_rep3

source_name: CD8 T cells,Untreated, Non-Allo-Proliferative


title: CD8_Untreated_  Non-Allo-Proliferative_rep1


title: CD8_Untreated_ Allo-Proliferative_rep1


title: CD8_Treated_ Allo-Proliferative_rep1


title: +S WKO1

city: Fukuoka

first: Akiko

last: Maruyama-Nakashita

address: 6-10-1, Hakozaki, Higashi-ku

country: Japan

institute: Kyushu University

description: Gene expression data from roots of sdi1sdi2 double knockout plants (line 1) vertically grown for 10 days on S1500 medium.

hyb_protocol: Samples were hybridized with GeneChip ATH1-121501.1 Array (Affymetrix) according to the manufacturer’s protocol.

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

data_processing: Raw cell data were parametrically normalized by using SuperNORM data service (Skylight Biotech Inc, Akita, Japan) to obtain z-score for each cell value.

source_name: Roots of sdi1sdi2 double knockout 1

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Arabidopsis thaliana accession Columbia (Col-0) was used as the wild type (WT). Plants were grown at 22˚C under 16 h-light/8 h-dark cycles on mineral nutrient media (MGRL) containing 1% sucrose. For preparation of agar medium, agar was washed twice with 1 l of de-ionized water and vacuum filtrated to remove sulfate. +S agar medium contained 1500 µM MgSO4 as the sulfur source. –S agar medium contained 15 µM MgSO4. The Mg concentration of the –S medium was adjusted to 1500 µM by adding MgCl2. Seeds were sown directly on +S and –S media, and these agar plates were incubated in the same growth chamber under controlled conditions.

extract_protocol: RNA samples were prepared using RNeasy Plant mini kit (QIAGEN).

treatment_protocol: WT, 2 lines of sdi1sdi2 double knockout mutants (sdi1sdi2-1 and sdi1sdi2-4) and 2 lines of SDI1 overexpression plants (SDI1ox-6 and SDI1ox-12) were grown for 10 days under +S (1500 µM sulfate) or –S (15 µM sulfate) conditions. Root tissues were harvested for RNA preparation.

value: Root

tag: plant

value: sdi1sdi2 double knockout 1

tag: sulfate concentration in the media (µm)


title: CD8_Untreated_Non-Allo-Proliferative_rep1


title: +S WKO4

description: Gene expression data from roots of sdi1sdi2 double knockout plants (line 4) vertically grown for 10 days on S1500 medium.

source_name: Roots of sdi1sdi2 double knockout 4

value: sdi1sdi2 double knockout 4


title: CD8_Untreated_  Non-Allo-Proliferative_rep2


title: +S Col 1

description: Gene expression data from roots of Col plants vertically grown for 10 days on S1500 medium.

source_name: Roots of Col

value: Col


title: Shoot apices, Awn primordia, Bowman, replicate3

city: Los Banos

last: Sreenivasulu

address: Metro Manila

country: Philippines

institute: IRRI

description: Gene expression from immature shoot apices at Awn primordia stage of wild type.

hyb_protocol: 600ng of Cy3-labeled, amplified cRNA were hybridized, following the manufacturer's protocol, to a custom-synthesized 60k Barley Microarray (Agilent Technologies).

scan_protocol: Agilent G5761A SureScan Dx.

data_processing:
GeneSpring 12.0.
After doing quantile normalization and baseline transformation to median of all samples, the probe sets (genes) were filtered by Coefficient of Variation <50%, followed by Moderated T-Test and Bonferroni correction. The probe sets which passed the P value cut-off ≤0.01 with the fold change of ≥2.0 were considered for interpreting the data.

organism: Hordeum vulgare

source_name: Immature shoot apices, WT, awn primordia

label_protocol: The RNA was labeled through the application of a Low Input QuickAmp Labeling kit (Agilent Technologies). The labeled cRNA samples were subsequently purified using RNeasy mini spin columns (Qiagen).

growth_protocol: The five vrs2 mutants were obtained from USDA, ARS, USA, Nordic genetic resources center, Sweden and IPK Genebank, Germany. The Bowman near isogenic line of vrs2.e, BW-NIL(vrs2.e), was crossed with Bowman and Golden Promise to generate F2 mapping populations (Bowman × BW-NIL(vrs2.e) and Golden Promise × BW-NIL(vrs2.e)). All plant materials used in this study were grown under greenhouse conditions. The immature shoot apices collected from BW-NIL(vrs2.e) and WT progenitor Bowman at TM, GP, SP, and AP were used for RNA extraction.

extract_protocol: RNA was extracted from tissues using the Plant Mini RNA kit (Qiagen, Hilden, Germany) following the manufacturer's protocol.

treatment_protocol: The seeds were initially germinated in 96-well planting trays under long day conditions, with 16 h light/8 h dark and a temperature of 20±2ºC during the day and 16±2 ºC during the night for 14 days. After 14 days, the plants were vernalized for four weeks at 4˚C. The vernalized plants were hardened for 2 weeks (12/12 h (day/night) and temperature 12±2ºC).

tag: cultivar/background

value: Bowman

tag: genotype/variation

value: Wild type

tag: developmental stage

value: Awn primordia

value: Immature shoot apices


title: +S OX12

description: Gene expression data from roots of SDI1 overexpression plants (line  #12) vertically grown for 10 days on S1500 medium.

source_name: Roots of SDI1 overexpression line 12

value: SDI1 overexpression  line 12


title: +S Col 2


title: -S WKO4

description: Gene expression data from roots of sdi1sdi2 double knockout plants (line 4) vertically grown for 10 days on S15 medium.


title: Shoot apices, Awn primordia, Bowman, replicate1


title: +S OX6

description: Gene expression data from roots of SDI1 overexpression plants (line  #6) vertically grown for 10 days on S1500 medium.

source_name: Roots of SDI1 overexpression line 6

value: SDI1 overexpression line  6


title: control vs. 5h NaCl treatment replicate 1

value: 14 days after germination

value: whole seedling

source_name: NaCl 5h #1


title: Liver_LFD-MTX50_rep5

tag: Sex

value: Male

tag: strain

value: Liver

tag: diet

value: low fat

value: Methotrexate 50mg/kg


title: Shoot apices, Awn primordia, Bowman, replicate2

tag: tissue


title: Shoot apices, Stamen primordia, Bowman, replicate3

description: Gene expression from immature shoot apices at Stamen primordia stage of wild type.

source_name: Immature shoot apices, WT, stamen primordia

value: Stamen primordia


title: Shoot apices, Stamen primordia, Bowman, replicate1


title: Shoot apices, Stamen primordia, Bowman, replicate2


title: -S WKO1

description: Gene expression data from roots of sdi1sdi2 double knockout plants (line 1) vertically grown for 10 days on S15 medium.

value: Root


title: -S Col 2

description: Gene expression data from roots of Col plants vertically grown for 10 days on S15 medium.


title: Shoot apices, Glume primordia, Bowman, replicate2

description: Gene expression from immature shoot apices at Glume primordia stage of wild type.

source_name: Immature shoot apices, WT, glume primordia

value: Glume primordia


title: -S Col 1


title: Shoot apices, Glume primordia, Bowman, replicate1


title: Shoot apices, Triple mound, Bowman, replicate1

description: Gene expression from immature shoot apices at Triple mound stage of wild type.

source_name: Immature shoot apices, WT, triple mound

value: Triple mound


title: Shoot apices, Awn primordia, BW-NIL(vrs2.e), replicate2

description: Gene expression from immature shoot apices at Awn primordia stage of mutant.

source_name: Immature shoot apices, mutant, awn primordia

value: BW-NIL(vrs2.e) mutant


title: HT_NC_rep2

city: Nagasaki

first: TAKEYA

last: NAKAGAWA

address: 1-12-4 sakamoto

department: Biochemistry

institute: Nagasaki unversity

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using rank-invariant normalisation with Illumina GenomeStudio software

source_name: HT1080 fibrosarcoma cells

label_protocol: Biotinylated cRNA were prepared with the Illumina® TotalPrep™‐96 RNA Amplification Kit (Ambion)

growth_protocol: MDA-MB-231 and HT1080 cells were grown at 37 °C in Dulbecco's Modified Eagle Medium (Gibco), supplemented with 10 µg/ml gentamicin and 10% FBS

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: MDA-MB-231 and HT1080 cells (3.5 x 105) were plated in 10 ml of Dulbecco's Modified Eagle Medium with 10 µg/ml gentamicin and 10% FBS in 10-cm dishes. The cells were cultured 24 hr at 37°C, then siRNA-Lipofectamine RNAiMAX complex was added. The cells were then incubated for an additional 42 h to allow for turnover of the target mRNA.

tag: cell line

tag: sirna

value: Scramble siRNA


title: HT_siVRK1_#308_rep1

value: siVRK1 #308


title: Shoot apices, Glume primordia, BW-NIL(vrs2.e), replicate2

description: Gene expression from immature shoot apices at Glume primordia stage of mutant.

source_name: Immature shoot apices, mutant, glume primordia

value: Bowman


title: HT_siVRK1_#308_rep2


title: Shoot apices, Stamen primordia, BW-NIL(vrs2.e), replicate1

description: Gene expression from immature shoot apices at Stamen primordia stage of mutant.

source_name: Immature shoot apices, mutant, stamen primordia

value: Immature shoot apices


title: Shoot apices, Stamen primordia, BW-NIL(vrs2.e), replicate2


title: VCaP siERG Replicate 1

status: Public on Oct 06 2016

city: Ann Arbor

first: Xiaoju

last: Wang

state: MI

address: 1500 E. Medical Center Drive

institute: University of Michigan

description: Biological replicate 1 of 2. VCaP cells were transfected by siERG or siControl individually.

scan_protocol: Scanned on an Agilent G2505B scanner.Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization. Control Features were omitted. The LogRatio columns from each feature file was extracted and converted to log2 ratios then merged into a single processed data matrix.

source_name: Prostate Cancer Cell Line

label_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy5/Cy3-label

growth_protocol: VCaP cells were grown in DMEM-Glutmax (Invitrogen) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin.

value: VCaP

tag: treatment

value: siERG

value: siControl


title: VCaP RI-EIP1 Treatment Replicate 1

description: Biological replicate 1 of 2. VCaP cells were treated by RI-EIP1 or RI-muEIP1 individually.


title: MD_siVRK1_#308_rep2

source_name: MDA-MB-231 breast adenocarcinoma cells


title: HT_NC_rep1


title: MD_NC_rep2


title: MD_siVRK1_#308_rep1


title: Shoot apices, Glume primordia, BW-NIL(vrs2.e), replicate1


title: VCaP RI-EIP1 Treatment Replicate 2

description: Biological replicate 2 of 2. VCaP cells were treated by RI-EIP1 or RI-muEIP1 individually.


title: Shoot apices, Triple mound, BW-NIL(vrs2.e), replicate1

description: Gene expression from immature shoot apices at Triple mound stage of mutant.

source_name: Immature shoot apices, mutant, triple mound


title: Shoot apices, Triple mound, BW-NIL(vrs2.e), replicate3


title: Shoot apices, Awn primordia, BW-NIL(vrs2.e), replicate1

value: Awn primordia


title: MD_NC_rep1


title: SUM149PT, 45 d IH, biological rep1

city: Zurich

first: Katrin

last: Gutsche

address: Winterthurerstrasse 190

country: Switzerland

institute: University of Zurich

description: SUM149PT, 45 d IH, biological rep1

hyb_protocol: Following fragmentation, 180 ng of cDNA were hybridized for 16 hr at 48C onto the GeneChip HuGene 2.1 PEG Array. GeneChips were washed and stained in the GeneTitan Multichannel Instrument.

scan_protocol: GeneChips were scanned using the GeneTitan Multichannel Instrument using AGCC 4.0 software

data_processing: The data was analyzed using robust multi-array average (RMA) analysis using the Bioconductor oligo R package

source_name: SUM149PT cells, 45 d IH

label_protocol: Biotinylated cDNA fragments were prepared according to the standard Affymetrix protocol from 100-150 ng total RNA (GeneAtlas WT Expression Kit Manual, 2012, Affymetrix).

growth_protocol: SUM149PT cells were cultured in equal parts of high-glucose DMEM and Ham`s F-12 Nutrient Mixture, supplemented with 5% heat-inactivated FBS, 1 µg/ml hydrocortisone and 5 µg/ml human insulin.

extract_protocol: The RNeasy mini kit (Qiagen) was used for total RNA extraction according to manufacturer`s protocol.

treatment_protocol: SUM149PT cells were untreated or cultured for 45 days in cycles of hypoxia and reoxygenation (24 h 0.2% O2, 48 h 21% O2).

tag: cell line origin

value: inflammatory breast cancer


title: Shoot apices, Triple mound, BW-NIL(vrs2.e), replicate2


title: AdipoQ-LPL Transgenic  10

city: Lexington

first: Brian

middle: S

last: Finlin

state: KY

address: 900 S. Limestone CTW 575

department: Internal Medicine

institute: University of Kentucky

hyb_protocol: We hybridized the arrays at 45°C for 16-18 hours at 60 rpm.

scan_protocol: Affymetrix 7G Gene Chip Scanner.

data_processing: RMA signal estimates were log2 transformed and analyzed with Partek software. A supplementary data file in excel is included with the submission and available on the series record.  The first tab contains the Partek output for differential gene expression of all genes.  The second tab contains the FDR calculation after unannotated and genes with low expression (less than log transformed expression value of 5 in AdipoQ-LPL mice) were removed.  The third tab contains the analysis of alternative splicing.

source_name: AdipoQ-LPL, Perigonadal Adipose

label_protocol: We used the Affymetrix WT Plus Kit for labeling.

growth_protocol: Perigonadal fat dissected from the abdomen of male mice.

extract_protocol: Qiazol and an Rneasy lipid tissue mini kit (74804, Qiagen).

treatment_protocol: 9.5 Week old mice were placed in TSE calorimetry chambers and switched to high fat diet (60% cal).  The mice were removed from the chambers and individually housed for 3-days on HFD.  Total HFD exposure was 10-days.

value: Perigonadal Adipose

tag: background strain

tag: gender

value: Male

tag: genotype

value: AdipoQ-LpL -/+


title: AdipoQ-LPL Transgenic  7


title: VCaP siERG Replicate 2

description: Biological replicate 2 of 2. VCaP cells were transfected by siERG or siControl individually.


title: AdipoQ-LPL Transgenic  9


title: AdipoQ-LPL Transgenic  8


title: AdipoQ-LPL Transgenic  12


title: AdipoQ-LPL Transgenic  11


title: SUM149PT, 0 h, biological rep1

description: SUM149PT, 0 h, biological rep1

source_name: SUM149PT cells, untreated


title: Grp3_Chip2_THP1-Mo_pre-miRCtrl

city: Berlin

first: Pawel

last: Durek

address: Charitéplatz 1

country: Germany

institute: Deutsches Rheuma-Forschungszentrum

description: Group3, chip2: THP-1 cells transfected with pre-miR-CTRL. Cells of human monocytic cell line THP-1 were transfected with 50 nM pre-miR-CTRL (from lifetechnology) using Lipofectamin 2000 (Invitrogen). RNA samples were harvested at 48 hours post-transfection.

hyb_protocol: The HG-U133A plus 2.0 GeneChip arrays were loaded with the hybridization cocktail, hybridized at 45 °C rotating for 16 h in a hybridization oven 640 (Affymetrix), washed and stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Workstation 400.

scan_protocol: Arrays were scanned with an Affymetrix GeneChip Scanner 3000, using the GCOS software version 1.4 from Affymetrix.

data_processing:
Data were analyzed according to High Performance Chip Data Analysis (HPCDA, unpublished - Joachim R. Grün) with the BioRetis database (http://www.bioretis-analysis.de/) using the default filter parameters for decreased and increased gene lists (description of database c.f. open access paper Menssen et al., 2009; PubMed ID: 19265543). Chip data included in the BioRetis database were analyzed using the GeneChip Operating Software (GCOS, Affymetrix), version 1.4. Microarrays were globally normalized and scaled to a trimmed mean expression value of 150. Quality checks were performed according to the manufacturer's recommendations. All 2 chips of one group were compared to the 2 chips of both other groups. With three different groups of 2 chips there were in total 3 analyses of 2 Experiment- vs. 2 Baseline-chips. The following parameters of absolute and comparative analysis were included in the BioRetis database: expression heights (Signals) and mean, median and standard deviation of Signals of both groups, call for presence of transcripts (Absent, A; Marginal, M; Present, P), p-value for presence or absence of transcripts, log2 value of fold change (Signal Log Ratio, SLR) and the fold change as mean values, call for the significance of differentially expression (Change Call: Increase, I; Marginal I, MI; Decrease, D; Marginal D, MD; No Change, NC), and the p value for that call. Additionally – not calculated with GCOS – t-tests of log Signals and SLRs were included in the database. For each present transcript the significance of differential expression between the groups of arrays was either calculated using strict Bonferroni corrected Welch t-tests between 4 SLR values of Experiment group vs. Baseline group and 4 SLR values within Experiment- and Baseline groups, respectively (the latter 4 giving a mean SLR value of zero; p-value had to be < 1.143E-07) or more than 50% of non-parametrically calculated Change calls (Mann-Whitney U test, GCOS) i.e. 3 or more of all 4 Change calls have to be in the same direction. Significantly differentially expressed genes were filtered using both default parameter sets of filter criteria; these are a combination of four different queries. This was done for all three analyses. Filter criteria were developed with various data sets of GeneChips and validated with the Affymetrix Latin Square dataset as shown in Menssen et al., 2009. You can find these validation experiments in BioRetis without registering, using the public content and public login. Click on view single results, select any existing Analysis beginning with first 3 letters "SGU" and click on "Next". Click on "Chose an existing parameterset" and select "JRG_Increase" for increased or "JRG_Decrease" for decreased probesets and click on "Fill". At the bottom of the site check the box named "* use Bonferroni correction" and click on "Search only" to get the list of significantly changed increased or decreased probesets, respectively. The Affymetrix Latin Square dataset, consisting of 42 chips in 14 experiments with three replicates each were analyzed in BioRetis with all possible 3 vs. 3 chip comparisons (one direction; average true positives are 65 up- or downregulated IDs).
Data tables contain the following: Probe Set ID; VALUE: GCOS Signal, i.e. gene expression height; Detection call: A: gene is detected as Absent, M: as Marginal present, or P: as Present; P-value: Non-parametrical p-value for generation of detection call

source_name: Group3: THP-1 cells transfected with pre-miRNA control

label_protocol: Labeling and hybridization of total RNA was performed using the GeneChip 3’ IVT Expression Kit from Affymetrix according to the manufacturers instruction. Briefly, after total RNA extraction, 100 ng of total RNA from each cell sample was reverse transcribed, cDNA was extracted, biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized to each of the GeneChip arrays.

growth_protocol: THP-1 (American Type Culture Collection) were maintained in RPMI 1640 (Gibco, France) supplemented with 10% heat-inactivated fetal calf serum, 2 mM glutamine (Gibco, France), and 50 g/mL penicillin/streptomycin (Gibco, France) in an atmosphere of 5% CO2 at 37 °C

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instruction, including the recommended DNase digest. The purity and integrity of RNA were assessed for each sample using an Agilent 2100 Bioanalyzer with the RNA 6000 Nano LabChip software and the amount was checked with a NanoDrop ND-1000 spectrophotometer. Contaminating genomic DNA was removed by an on-column DNA digestion step (Qiagen).

tag: cell type

value: Human monocytic cells

tag: cell transfection

value: THP-1 cells transfected with pre-miR-CTRL (lifetechnology); lipofectamin 2000 (invitrogen)

tag: cell cultivation

value: Cells were cultured 48 h in RPMI 1640 media + 10% FBS + 2mM L-Glutamine + Pen/Strept.


title: Grp3_Chip1_THP1-Mo_pre-miRCtrl

description: Group3, chip1: THP-1 cells transfected with pre-miR-CTRL. Cells of human monocytic cell line THP-1 were transfected with 50 nM pre-miR-CTRL (from lifetechnology) using Lipofectamin 2000 (Invitrogen). RNA samples were harvested at 48 hours post-transfection.


title: Grp2_Chip2_THP1-Mo_anti-miR125b

description: Group2, chip2: THP-1 cells transfected with anti-miR125b. Cells of human monocytic cell line THP-1 were transfected with 50 nM anti-miR-125b (from lifetechnology) using Lipofectamin 2000 (Invitrogen). RNA samples were harvested at 48 hours post-transfection.

source_name: Group2: THP-1 cells transfected with anti-miR125b

value: THP-1 cells transfected with anti-miR125b (lifetechnology); lipofectamin 2000 (invitrogen)


title: AdipoQ-LPL Transgenic  6


title: AdipoQ-LPL Transgenic  3


title: root_OBP4_rep2

city: Pozuelo de Alracon

first: Juan

middle: Carlos

last: del Pozo

state: Madrid

address: Campus de Montegancedo, UPM

department: Biotechnology

institute: Centro de Biotecnología y Genómica de Plantas

description: This sample is of roots overexpressing OBP4 for 8 hours. It is the second of three  biological replicates used in this experiment, each from independent in vitro cultured plates.

hyb_protocol: Each microarray was hybridized with the NimbleGen hybridization kit, washed using the NimbleGen wash buffer kit (both from Roche)

scan_protocol: Microarrays were scanned at 2-μm double-pass at 16-bit resolution

data_processing: Data were analyzed through robust multiarray analysis with NimbleGen Scan software (Roche).

source_name: OBP4 overexpressing roots

label_protocol: cDNA was generated with 10 μg RNA using the double-stranded cDNA synthesis kit (Invitrogen), and cDNA was Cy3-labeled with the NimbleGen one-color DNA labeling kit (Roche).

growth_protocol: pER8::GFP and pER8::OBP4 Arabidopsis seedlings were grwon in half strench MS medium for 5 days and then transferred to half strench MS medium with 10 µM of estradiol for 8 hours. Seedlings were grown in a 16 hour light/8 hours dark photoperiod and with a llight intensity of 75 umoles/m2 seg.

extract_protocol: Total RNA was isolated from roots using the Trizol (Lifetechnologies) following the company procedure. This isolated RNA was then purified using the Quiagen RNA isolation kit.

treatment_protocol: pER8::GFP (control) and pER8::OBP4 (treatment) Arabidopsis seedlings were grown in half strench MS medium for 5 days and then transferred to half strench MS medium with 10 µM of estradiol for 8 hours.

value: roots


title: Control 9

source_name: Control, Perigonadal Adipose

value: AdipoQ-LpL -/-


title: AdipoQ-LPL Transgenic  5


title: AdipoQ-LPL Transgenic  4


title: Grp2_Chip1_THP1-Mo_anti-miR125b

description: Group2, chip1: THP-1 cells transfected with anti-miR125b. Cells of human monocytic cell line THP-1 were transfected with 50 nM anti-miR-125b (from lifetechnology) using Lipofectamin 2000 (Invitrogen). RNA samples were harvested at 48 hours post-transfection.


title: AdipoQ-LPL Transgenic  1


title: root_control_rep3

description: This sample is of roots overexpressing GFP-control for 8 hours. It is the third of three  biological replicates used in this experiment, each from independent in vitro cultured plates.

source_name: GFP-control overexpressing roots


title: AdipoQ-LPL Transgenic  2


title: root_OBP4_rep3

description: This sample is of roots overexpressing OBP4 for 8 hours. It is the third of three  biological replicates used in this experiment, each from independent in vitro cultured plates.


title: Control 12


title: Control 11


title: root_OBP4_rep1

description: This sample is of roots overexpressing OBP4 for 8 hours. It is the first of three  biological replicates used in this experiment, each from independent in vitro cultured plates.


title: Control 10


title: Grp1_Chip1_THP1-Mo_pre-miR125b

description: Group1, chip1: THP-1 cells transfected with pre-miR125b. Cells of human monocytic cell line THP-1 were transfected with 50 nM pre-miR-125b (from lifetechnology) using Lipofectamin 2000 (Invitrogen). RNA samples were harvested at 48 hours post-transfection.

source_name: Group1: THP-1 cells transfected with pre-miR125b

value: THP-1 cells transfected with pre-miR125b (lifetechnology); lipofectamin 2000 (invitrogen)


title: Control 8


title: Control 5


title: root_control_rep2

description: This sample is of roots overexpressing GFP-control for 8 hours. It is the second of three  biological replicates used in this experiment, each from independent in vitro cultured plates.


title: Control 4


title: Control 6


title: Control 2


title: Control 1


title: Control 3


title: root_control_rep1

description: This sample is of roots overexpressing GFP-control for 8 hours. It is the first of three  biological replicates used in this experiment, each from independent in vitro cultured plates.


title: Control 7


title: Grp1_Chip2_THP1-Mo_pre-miR125b

description: Group1, chip2: THP-1 cells transfected with pre-miR125b. Cells of human monocytic cell line THP-1 were transfected with 50 nM pre-miR-125b (from lifetechnology) using Lipofectamin 2000 (Invitrogen). RNA samples were harvested at 48 hours post-transfection.


title: L5 Workers/Queens ovaries (dye-swap)

city: Alfenas

first: Angel

middle: Roberto

last: Barchuk

state: Minas Gerais

address: Rua Gabriel Monteiro Silva 700, Campus Unifal

department: Cell and Developmental Biology

country: Brazil

institute: Federal University of Alfenas

hyb_protocol: The RNA was dye-coupled and combined with hybridization buffer (49% Formamide, 49% SSC 20x and 0.2% SDS), pre-heated at 55° C for 3 min, applied to arrays, and hybridized for 17 h at 42 °C in single slide hybridization chambers placed in a water bath. A series of 30s shaking washes in 2× SSC plus 0.1% SDS; 2× SSC; 0.1× SSC and Milli-Q water at room temperature removed excess probe.

scan_protocol: The hybridized slides were scanned using an Axon Genepix 4000B scanner (Molecular Devices, Sunnyvale, CA) with GENEPIX software (Agilent Technologies, Santa Clara, CA), 10-micron resolution, Cy3 with Green Laser (532 nm), and Cy5 with Red Laser (635 nm). GenePix Pro 6.0 software was used for quantification of the spots and image analysis with default parameters.  The hybridized slides were scanned using an Axon Genepix 4000B scanner (Molecular Devices, Sunnyvale, CA) with GENEPIX software (Agilent Technologies, Santa Clara, CA), 10-micron resolution, Cy3 with Green Laser (532 nm), and Cy5 with Red Laser (635 nm). GenePix Pro 6.0 software was used for quantification of the spots and image analysis with default parameters.

data_processing:
The scan results of the slides read in an Axon Genepix 4000B scanner (Molecular Devices) with GenePix® Pro 6.0 software (Agilent Technologies, Santa Clara, CA) were analyzed using the Limma package of Bioconductor software implemented in R The background was corrected by adding to the background intensities a positive constant (offset correction = 50), which restrains spurious variation in log-ratios, particularly at low intensity spots. The “print-tip loess” normalization was used to correct for within-array dye, and spatial effects and single channel normalization was used to facilitate comparison between arrays. (Queen’s sample intensity/Worker’s sample intensity) was determined for each probe in each array. After applying Bayesian statistics to shrink estimated standard errors, we used the moderated t-statistic test for each gene.
The file normalized_data.txt contains the log2 ratio for queen sample intensity/ worker sample intensity that was determined for each probe in each array. The file BeeOligo120406.txt contains block, row and column information with the Gene IDs for the probes on the array.

organism: Apis mellifera

source_name: L5 workers ovaries (pool)

label_protocol: RNA amplification was done with and according to Amino Allyl MessageAmpTM II aRNA Amplification Kit (Ambion). The amplified RNA samples (20 µg) were used for dual channel microarray hibridization with Cy3 and Cy5 dyes (with dye swaps). Dye swaps were done for each comparison and two slides were used to evaluate the differential expression.

growth_protocol: Larvae were obtained from hives of Africanized hybrid Apis mellifera kept in the Experimental Apiary of the University of São Paulo in Ribeirão Preto, Brazil

treatment_protocol: L4 and L5F queen larvae were obtained from queen cells after transfering bipotential L1 larvae to artificial queen cells containing a drop of royal jelly. L4 and L5F worker larvae were obtained from natural worker cells

value: ovary

tag: caste

value: queen

value: worker


title: L5 Workers/Queens ovaries

source_name: L5 queens ovaries (pool)


title: L4 Workers/Queens ovaries (dye-swap)

source_name: L4 workers ovaries (pool)


title: L4 Workers/Queens ovaries

source_name: L4 queen ovaries (pool)


title: PFC_basal_KO_rep2

city: Munich

first: Mira

middle: Alexandra

last: Jakovcevski

state: Bavaria

address: Kraepelin Str. 2-10

department: Stress Neurobiology and Neurogentics

institute: Max Planck Institute of Psychiatry

hyb_protocol: hybridization mix (100 mM MES, 1 M (Na+), 20 mM EDTA, 0.01% Tween-20; containing 1 μL of bovine serum albumin (50 mg/mL) and 1 μL of 10 mg/mL Herring Sperm DNA per 100 μL) was applied  for 16 h.

scan_protocol: Affymetrix GeneChip Scanner 3000 7G.

data_processing:
Affymetrix Expression Console, RMA followed by further processing with Transcriptome Analysis Console v3.0
MoGene-1_0-st-v1.r4.pgf
affymetrix-algorithm-param-apt-opt-meta-ps-file=MoGene-1_0-st-v1.r4.mps

source_name: PFC (cing. Cortex)

label_protocol: according to Affymetrix WT PLUS Reagent kit

growth_protocol: adult Mll1 mutant mice (12 weeks old|) housed under standard housing conditions

extract_protocol: mouse PFC was disected using a brain matrix, tissue was then stored at -80°C until total RNA extraction

treatment_protocol: mice were single housed one week before brain harvest to exclude effects of fighting and to prevent stress-induced gene expression during brain harvest

value: male

value: prefrontal cortex (PFC)

value: Mll1 Ko


title: PFC_basal_KO_rep4


title: PFC_basal_WT_rep3

value: wild-type


title: PFC_basal_WT_rep4


title: CD105_1

city: Copenhagen

first: Mikkel

last: Morsing

state: Nørrebro

address: Blegdamsvej 3b

department: Department of Cellular and Molecular Medicine and Danish Stem Cell Center

country: Denmark

institute: University of Copenhagen

hyb_protocol: Labeled RNA was hybridized to the Affymetrix  GeneChip®Human Gene 2.0 ST Array (Affymetrix) for 16 hours at 45°C at 60 rpm

scan_protocol: Scanned with The GeneChip Scanner 3000 7G (Affymetrix)

data_processing:
Array control probes were used for quality control using the free software Expression Console provided by Affymetrix (affymetrix.com).
Data were imported into the GeneSpring GX 13.0 software and quantile normalized with the RMA16 algorithm using default settings. Only probes designated as 'main’ we used for data analysis in GeneSpring, all data from control probes were removed before this step of the analysis. For variance stabilization 16 was added before log2 transformation. Transcripts were annotated with netaffx annotation build 34.

source_name: Human mammary fibroblasts isolated by FACS as CD105high

label_protocol: 100 ng RNA was labeled using the Ambion® WT Expression Kit (Ambion)

extract_protocol: Total RNA isolated using GenElute Mammalian Total RNA Miniprep Kit (Sigma-Aldrich) according to manufacturers instructions

value: mammary fibroblast

tag: lineage mark


title: PFC_basal_KO_rep1


title: CD105_2


title: CD26_3

source_name: Human mammary fibroblasts isolated by FACS as CD26high


title: PFC_basal_KO_rep3


title: E.coli-20x CORM2-rep4

city: Örebro

first: Robert

last: Kruse

address: S grevrosengatan

department: Medical Sciences

country: Sweden

institute: Örebro University

description: Pre-exposed 20 times to CORM-2

hyb_protocol: Labelled samples were hybridised onto G4813A E. coli gene expression Microarray 8×15K glass slides (Agilent) containing 15 208 E. coli probes.

scan_protocol: Microarrays were scanned with a G2565 CA array laser scanner (Agilent) followed by image analysis and data extraction with Feature Extraction Software version 10.7.3.1 (Agilent).

data_processing: 75th percentile shift normalisation and baseline adjusted

organism: Escherichia coli

source_name: E.coli-20x CORM2-rep4

label_protocol: The cDNA synthesis was performed by using WT Primer Mix and cDNA Master Mix (Agilent).

growth_protocol: Cultures were maintained on tryptic soy agar (TSA) (Becton Dickinson, Le Pont Claix, France). Overnight cultures were grown in Difco Luria-Bertani (LB) broth (Lennox; Franklin Lakes, NJ, USA) at 37 °C aerobically on a shaker at 200 rpm. Bacteria (picked from 5-10 colonies) were suspended in 1 ml of PBS, yielding a suspension corresponding to the turbidity of McFarland 0.5, and diluted 1:100 in minimal salt (MS)-medium (~106 CFU/ml). The suspension was exposed to CORM-2 (250 µM) or vehicle (2.5% DMSO) for 4 hours at 37 °C. A volume (10 µl) was spread onto TSA-agar plates and incubated at 37 °C overnight. This procedure was repeated 10 times (10x, ~45 generations) or 20 times (20x, ~90 generations).

extract_protocol: RNA isolation was performed using an RNeasy mini kit (Qiagen Technologies, Hilden, Germany), according to the manufacturer’s protocol. DNA decontamination treatment was performed using Turbo DNase (Qiagen) and the quantity and purity of the purified RNA samples were determined using a spectrophotometer Nanodrop-1000 (Nanodrop Technologies Inc., Wilmington, DE, USA) by measuring the absorbance (A260, 230, 280) and calculating absorbance ratios (A260/A230 and A260/A280). All samples had A260/A230 and A260/A280 ratios above 1.9. The RNA integrity was analysed using Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) in conjunction with RNA 6000 Nano LabChip kit (Agilent Technologies) according to the manufacturer’s protocol. RNA integrity number (RIN) values were > 8.5 for all samples.

treatment_protocol: Overnight cultures of ESBL7 from the original isolate, or isolates pre-exposed 20 times to CORM-2 or vehicle, were used to inoculate MS-medium, (OD620) of 0.1, followed by exposure to CORM-2 (250 µM) or vehicle for 30 min at 37 °C.

tag: agent

value: 20x CORM2


title: CD105_3


title: E.coli-20x vehicle-rep4

description: Pre-exposed 20 times to vehicle

source_name: E.coli-20x vehicle-rep4

value: 20x vehicle


title: E.coli-1x CORM2-rep4

description: First exposure to sub-inhibitory levels of CORM-2

source_name: E.coli-1x CORM2-rep4

value: 1x CORM2


title: CD26_2


title: CD26_1


title: genomic DNA from GS2-14

city: Houston

first: Erik

middle: P.

last: Sulman

state: TX

address: 1515 Holcombe Blvd

department: Radiation Oncology

institute: The University of Texas M. D. Anderson Cancer Center

description: glioma sphere-forming cells

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: Illumina GenomeStudio

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified from GSC samples using Qiagen DNeasy Kit according to standard instructions

tag: disease

value: Glioblastoma

value: glioma sphere-forming cells

tag: radiation response

value: Sensitive


title: genomic DNA from GSC293

description: glioma sphere-forming cells


title: PFC_basal_WT_rep2

tag: Sex


title: E.coli-20x CORM2-rep3

description: Pre-exposed 20 times to CORM-2

source_name: E.coli-20x CORM2-rep3


title: E.coli-20x vehicle-rep3

description: Pre-exposed 20 times to vehicle

source_name: E.coli-20x vehicle-rep3


title: MDA-MB-231 biological replicate 3

city: Burlington

first: Jonathan

middle: AR

last: Gordon

state: VT

address: 89 Beaumont Ave Given E209

institute: University of Vermont

hyb_protocol: Labeled cDNAs were then hybridized using a GeneChip Hybridization, Wash, and Stain Kit

scan_protocol: Hybridization signals were obtained by GeneChip Scanner (Affymetrix)

data_processing: Analysis was performed in R to execute normalization, quality control, transcript-level reporting, annotation, and contrast tests. The “affy” (Gautier et al., 2004) package was used to read in raw fluorescent values from arrays; values were normalized across all arrays using quantile normalization (Bolstad et al., 2003), robust means average (RMA) background correction and median polish (Irizarry et al., 2003).

source_name: mammary gland/breast epithelial cell

label_protocol: labeled and fragmented with GeneChip WT Terminal Labeling and Controls Kit

growth_protocol: MCF-10A cells, from a lab-maintained stock, were cultured in phenol-free DMEM/F12 media supplemented with EGF, insulin, cholera toxin and hydrocortisone and subcultured as described (Debnath et al., 2002). MDAMB-231 cells, also from a lab-maintained stock, were grown and subcultured as previously described (Pratap et al., 2008). Cell lines are monitored for integrity by STR analysis and are routinely checked for mycoplasma contamination.

extract_protocol: isolated RNA was reversely transcribed into cDNA using WT Expression Kit (Ambion, Austin, TX, USA)

tag: tissue

value: breast

value: metastatic site derived

tag: atcc id

value: ATCC HTB-26


title: E.coli-1x vehicle-rep3

description: First exposure to vehicle

source_name: E.coli-1x vehicle-rep3

value: 1x vehicle


title: Liver_LD64

first: Ghislain

last: Breton

address: 6431 Fannin St MSB 4.216

department: Integrative Biology & Pharmacology

institute: McGovern Medical School

hyb_protocol: cDNA synthesis and labeling, as well as array hybridization (MAUI station) , scanning and RMA data processing were performed by the UCSD/VA GeneChip core according to the NimbleGen Arrays User's guide.

scan_protocol: cDNA synthesis and labeling, as well as array hybridization, scanning (Nimblescan) and RMA data processing were performed by the UCSD/VA GeneChip core according to the NimbleGen Arrays User's guide.

data_processing: cDNA synthesis and labeling, as well as array hybridization, scanning and RMA data processing were performed by the UCSD/VA GeneChip core according to the NimbleGen Arrays User's guide.

organism: Danio rerio

source_name: Danio rerio AB strain

growth_protocol: Zebrafish AB line were mated, staged and raised as described in Westfield , The Zebrafish book 2014

extract_protocol: For expression profiling using microarray, liver samples were immediately submerged in 1mL of RNALater solution (Qiagen). All samples were processed together at the end of the time course for RNA extraction. Tissues were homogenized using a Retsch MM200 mixer mill. Total RNA was extracted using RNA extraction kit from Qiagen using supplier's recommendations for liver samples

value: liver

tag: development stage

value: adult 3-6 months


title: Liver_LD60

label_protocol: cDNA synthesis and labeling, as well as array hybridization, scanning and RMA data processing were performed by the UCSD/VA GeneChip core according to the NimbleGen Arrays User's guide.

value: male


title: Liver_LD68


title: E.coli-20x CORM2-rep2

description: Pre-exposed 20 times to CORM-2

source_name: E.coli-20x CORM2-rep2


title: E.coli-1x vehicle-rep4

description: First exposure to vehicle

source_name: E.coli-1x vehicle-rep4


title: MCF-10A biological replicate 2

tag: cell line

value: luminal ductal cells

value: ATCC CRL-10317


title: MDA-MB-231 biological replicate 2


title: MDA-MB-231 biological replicate 1


title: genomic DNA from GSC262

description: glioma sphere-forming cells


title: E.coli-1x CORM2-rep3

source_name: E.coli-1x CORM2-rep3


title: genomic DNA from GSC267

description: glioma sphere-forming cells


title: KO & HNF6 #2

city: Peoria

first: Kewei

state: IL

address: One Illini Dr.

institute: Univ. of Illinois College of Medicine at Peoria

description: Nuclear DNA

hyb_protocol: Samples were prepared and hybridized to Mouse Promoter 1.0F array according to Affymetrix specifications.

scan_protocol: For instructions on array washing, staining and scanning please refer to the GeneChip® Expression Wash, Stain and Scan User Manual (P/N 702731).

data_processing: The signal intensity data was analyzed with the Affymetrix Tiling Analysis Software (Affymetrix Mouse Promoter 1.0F array).

label: Uracil-DNA

source_name: Knockout liver/HNF6 antibody

extract_protocol: ChIP-DNA preparation. The ChIP process enriches specific cross-linked DNA-protein complexes using an antibody against the protein of interest. Briefly, liver tissues from wild-type and HNF6 knockout mice are fixed in 10 ml 1% Formaldehyde and then added with 0.125M of glycine. The cell pellet is resuspended in 2ml Lysis Buffer (5mM PIPES, 85mM KCl, 0.5% NP-40). The extract is re-suspended in Lysis Buffer High Salt (1 × PBS, 1% NP-40, 0.5% Sodium Deoxycholate, 0.1% SDS) and subsequently sonicated at a power setting of 30%. For the immunoprecipitation, 4µg of mouse monoclonal HNF6 antibody is added using 4µg of mouse IgG as control. Crosslinks are reversed by addition of 400μl Elution Buffer (1% SDS, 0.1 M NaHCO3) and 0.2M NaCl at 65°C overnight. All of samples are treated by10 μg RNase A and then 50μg of Proteinase K. DNA is extracted using an equal volume of phenol/chloroform/isoamyl alcohol.

treatment_protocol: Library preparation. 50µl of reverse crosslinked, QIAquick purified DNA is re-suspended in 10µl of 1X Library Preparation Buffer; Transfer samples to 0.2ml PCR tubes; Add 1µl Library Stabilization Solution, vortex or mix by pipetting. Quick spin and place at 95°C for 2 minutes in thermal cycler; Immediately cool on ice, quick spin again; Add 1µl Library Preparation Enzyme, vortex or mix by pipetting and quick spin; Incubate in thermal cycler as follows: 16°C for 20', 24°C for 20', 37°C for 20', 75°C for 5', 4°C hold; Quick spin and either proceed to first amplification. Amplification (Round one) of immunoprecipitated DNA fragments. Use 10 μl of IP’d or negative control sample for initial round of linear amplification. Set up first round reaction with Primer A (200μM) for random priming. Thereafter, 25mM dNTPs and Sequenase are added. The samples. Re-amplification (Round two). Prepare master mix for each sample containing: 7.5µl of 10X Amplification Master Mix, 47.5µl Nuclease-free H20, 5µl WGA DNA polymerase; Incubate in thermal cycler as follows: 95°C for 3', then 14 cycles of 94°C for 15", 65°C for 5', then 4°C hold, At this point, amplified material is stable and can be stored at -20°C; Purify samples using QIAquick PCR cleanup columns or analogous product The amplified DNA is checked on 1% agarose gel. At this stage, the purification column eluates for total and immunoprecipitated samples should be readily quantifiable. Normally, greater than 9 μg of amplified DNA is obtained from each reaction. At least, 7.5 μg of target DNA is needed. Next, Affymetrix Mouse Promoter 1.0R array is used to perform genome-wide location analysis of binding sites and promoter regions. The Affymetrix GeneChip interrogates over 25,500 mouse promoter regions, yielding insight into the functional elements of gene-regulatory networks. A brief description is as follows: The hybridized samples are analyzed using a Bioanalyzer or agarose gel.15 μL of the Double-Stranded DNA Labeling Mix is added to the DNA samples, flick-mix, and spin them down. To hybridize labeled target on the arrays.

value: HNF6 knockout

tag: antibody

tag: antibody manufacturer

value: Santa Cruz Biotechnology

tag: antibody catalog number

tag: antibody lot number


title: MCF-10A biological replicate 1

tag: cell type


title: Liver_LD48


title: PFC_basal_WT_rep1

value: prefrontal cortex (PFC)

tag: genotype

value: wild-type


title: E.coli-20x vehicle-rep2

description: Pre-exposed 20 times to vehicle

source_name: E.coli-20x vehicle-rep2

value: 20x vehicle


title: Liver_LD56


title: Liver_LD40


title: Liver_LD52


title: genomic DNA from GSC23

description: glioma sphere-forming cells

value: Glioblastoma

value: Resistant


title: genomic DNA from GSC112

description: glioma sphere-forming cells

value: glioma sphere-forming cells

value: Sensitive


title: KO & HNF6 #1

description: Nuclear DNA

label_protocol: Samples were prepared and hybridized to Mouse Promoter 1.0F array according to Affymetrix specifications.

tag: background strain


title: genomic DNA from GSC34

description: glioma sphere-forming cells


title: genomic DNA from GSC20

description: glioma sphere-forming cells


title: IgG-control#1

description: Nuclear DNA

source_name: Wild-type liver/IgG antibody

value: wildtype

value: anti-IgG


title: genomic DNA from GSC274

description: glioma sphere-forming cells


title: IgG-control#2

description: Nuclear DNA


title: HNF6 #2

description: Nuclear DNA

source_name: Wild-type liver/HNF6 antibody


title: E.coli-20x vehicle-rep1

description: Pre-exposed 20 times to vehicle

source_name: E.coli-20x vehicle-rep1


title: Liver_LD44


title: HNF6 #1

description: Nuclear DNA


title: genomic DNA from GSC16

description: glioma sphere-forming cells


title: genomic DNA from GSC107

description: glioma sphere-forming cells


title: genomic DNA from GSC17

description: glioma sphere-forming cells


title: E.coli-1x vehicle-rep1

description: First exposure to vehicle

source_name: E.coli-1x vehicle-rep1

value: 1x vehicle


title: E.coli-20x CORM2-rep1

description: Pre-exposed 20 times to CORM-2

source_name: E.coli-20x CORM2-rep1

value: 20x CORM2


title: E.coli-1x CORM2-rep1

source_name: E.coli-1x CORM2-rep1

value: 1x CORM2


title: E.coli-1x vehicle-rep2

description: First exposure to vehicle

source_name: E.coli-1x vehicle-rep2


title: Liver_LD24

value: liver

value: male

value: adult 3-6 months


title: Liver_LD28


title: E.coli-1x CORM2-rep2

source_name: E.coli-1x CORM2-rep2


title: Liver_LD32


title: Liver_LD36


title: NKT2(B6)_rep2

status: Public on Oct 05 2016

city: Hanover

first: Günter

last: Bernhardt

address: Carl Neuberg Strasse 1

department: Institue of Immunology

institute: Hannover Medical School

hyb_protocol: cRNA fragmentation, hybridization and washing steps were carried-out exactly as recommended in the ‘One-Color Microarray-Based Gene Expression Analysis Protocol V5.7’ (Agilent Technologies), except that 300ng (M4801, M4797, M4803, M5142, M5143), 200ng (M5058-M5060), or 130ng (M4895-M4897) of each cRNA population were used for hybridization. Microarray sample M4930 has been generated in dual-color mode. The procedure was performed as described above with the following modifications: cRNA fragmentation, hybridization and washing steps were carried-out exactly as recommended in the ‘Two-Color Microarray-Based Gene Expression Analysis Protocol V5.7’ (Agilent Technologies), except that 1000ng of each cRNA population were used for hybridization.

scan_protocol: Slides were scanned on the Agilent Micro Array Scanner G2565CA (pixel resolution 3 µm, bit depth 20).

data_processing: Data extraction was performed with the ‘Feature Extraction Software V10.7.3.1’ using the extraction protocol file ‘GE1_107_Sep09.xml’. Processed intensity values of the green channel, ‘gProcessedSignal’ (gPS) were normalized by global linear scaling: All gPS values of one sample were multiplied by an array-specific scaling factor. This factor was calculated by dividing a ‘reference 75th Percentile value’ (set as 1500 for the whole series) by the 75th Percentile value of the particular Microarray (‘Array I’ in the formula shown below). Accordingly, normalized gPS values for all samples (microarray data sets) were calculated by the following formula:   normalized gPSArray i = gPSArray i  x (1500 / 75th PercentileArray i).  Measurements of on-chip replicates (quadruplicates) were averaged using the geometric mean of normalized gPS values to retrieve one resulting value per probe and sample. Single Features were excluded from averaging, if they i) were manually flagged, ii) were identified as Outliers by the Feature Extraction Software, iii) lie outside the interval of ‘1.42 x interquartile range‘ regarding the normalized gPS distribution of the respective on-chip replicate population, or, iv) showed a coefficient of variation of pixel intensities per Feature that exceeded 0.5.  A lower intensity threshold (surrogate value) was defined based on intensity distribution of negative control features. This value was fixed to 20 (15 for M5142 and M5143). All of those normalized gPS values that fell below this intensity border were substituted by the respective surrogate value of 20 (15 for M5142 and M5143).  Microarray sample M4930 has been generated in dual-color mode. The procedure was performed as described above with the following modifications: Data extraction with the ‘Feature Extraction Software V10.7.3.1’ was performed using the extraction protocol file ‘GE2_107_Sep09.xml’. Processing of intensity values as described above was performed for ‘gProcessedSignal’ (gPS) and for ‘rProcessedSignal’ (rPS) independently. Removal of outliers and averaging was performed for each channel separately.  The lower intensity threshold (surrogate value) was fixed to 15 for the dual-color Microarray sample M4930.

source_name: Thymus

label_protocol: 6.5ng or 20ng of total RNA were used to prepare aminoallyl-UTP-modified (aaUTP) cRNA (Amino Allyl MessageAmp™ II Kit; #AM1753; Life Technologies) as directed by the company (applying one-round of amplification). The labeling of aaUTP-cRNA was performed by use of Alexa Fluor 555 Reactive Dye (#A32756; LifeTechnologies). Prior to the reverse transcription reaction, 1µl of a 1:100000 dilution of Agilent’s ‘One-Color spike-in Kit stock solution’ (#5188-5282, Agilent Technologies) was added to each total RNA sample. Microarray sample M4930 has been generated in dual-color mode. Sample processing was performed as described above with the following modifications: 30ng of totalRNA was used as input. Synthesis of AlexaFluor555- or AlexaFluor647 (#A32757; LifeTechnologies) labeled cRNA was performed according to the manufacturer’s recommendations, except that the proportion of aminoallyl-UTP/UTP was adjusted to 1+11 (instead of 1+1).

extract_protocol: Total RNA was extracted by use of the RNeasy Micro Kit (Qiagen).

treatment_protocol: Cells from BALB/c or C57BL/6 thymi were freshly pepared, stained with PBS57-loaded tetramer (Cy5 labeled), anti-CD4 (Pacific Orange labeled), anti-CD122 (FITC labeled), and anti-CD19 (PeCy7 labeled) in parallel. Following washing cells were sorted using a FACSAria into tet+CD19-CD122+ iNKT1,  tet+CD19-CD122-CD4+ iNKT2, and  tet+CD19-CD122-CD4- iNKT17 cells, respectively. Immediatley following sorting, collected fractions of up to 100,000 cells each were spun and taken up in RLT lysis buffer (Qiagen).

value: Thymus

tag: gender

value: female

tag: age

value: 8 weeks

tag: strain

tag: rna input amount

value: 20 ng


title: NKT1(BALB/c_CD4-)_rep1

value: 9 weeks

value: BALB/c


title: NKT2(B6)


title: NKT1(B6)_rep2


title: NKT1(wt)_rep2

treatment_protocol: Cells from BALB/c thymi were freshly pepared, stained with PBS57-loaded tetramer (Cy5 labeled), anti-CD4 (Pacific Orange labeled), anti-CD122 (FITC labeled), and anti-CD19 (PeCy7 labeled) in parallel. Following washing cells were sorted using a FACSAria into tet+CD19-CD122+ iNKT1,  tet+CD19-CD122-CD4+ iNKT2, and  tet+CD19-CD122-CD4- iNKT17 cells, respectively. Immediatley following sorting, collected fractions of up to 100,000 cells each were spun and taken up in RLT lysis buffer (Qiagen).

value: 9.5 weeks


title: NKT1(BALB/c_CD4+)_rep2

value: 30 ng


title: NKT1(BALB/c_CD4-)_rep2


title: NKT2(wt)_rep2


title: NKT1(wt)_rep1


title: NKT17(wt)_rep2


title: NKT17(B6)_rep2


title: NKT1(BALB/c_CD4+)_rep1


title: NKT17(B6)


title: NKT1(B6)


title: NKT17(wt)_rep1


title: DOX-1

city: Gifu

first: Hiroyuki

last: Tomita

address: 1-1 Yanagido

institute: Gifu University

hyb_protocol: 0.6ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 mouse GE 8x60K Microarray  (Agilent) 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).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

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

source_name: tongue tissue

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1ug Total RNA using the Low Input Quick Amp Labeling Kit(Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: total RNA was extracted with the Simply RNA tissue Kit (Promega, Fitchburg, Wisconsin (WI), USA) on a Maxwell RSC instrument.

treatment_protocol: The tongue tissues were obtained from Doxycycline(DOX)-treated mice (n-3) and non-treatede mouse.  DOX treatment kept for two weeks.

tag: strain background

tag: genotype/variation

value: ubiquitous and squamous cell-specific Doxycycline (DOX)- inducible Dek mice (iDek)

tag: treated with

value: none (untreated)

value: tongue


title: Shaziling pig A6

city: Changsha

first: Haiming

last: Ma

state: Hunan

address: Nongda road NO.1

institute: Hunan Agricultural University

description: Gene expression data from longissimus dorsi muscle 25-day-old male pig

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

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.

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

organism: Sus scrofa

source_name: male_longissimus dorsi muscle

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: Three 25-day-old, male full-sibs for each of YS and SZL piglets were from Hunan Xinwufeng Breeding Company in Pig (Xiangtan, China) and Resource Farm of Xiangtan Shaziling pig in Hunan (Xiangtan, China) respectively.

extract_protocol: Total RNAs were isolated from longissimus dorsi muscle using Trizol reagent for gene expression profiles and mirVana™ miRNA Isolation Kit for miRNA sequencing followed the manufacturer’s instructions. The RNA integrity was checked by an Agilent Bioanalyzer 2100 with RIN number > 7.0 on agarose gel electrophoresis. All RNAs were measured for protein contamination and reagent contamination by using Nanodrop2000. Qualified total RNA was purified by RNeasy micro kit and RNase-Free DNase Set.

treatment_protocol: The longissimus dorsi for microarray analysis were harvested and immediately frozen in liquid nitrogen, and then kept at 80℃.

tag: breed

value: Shaziling

tag: Sex

tag: tissue

value: longissimus dorsi muscle


title: Shaziling pig A4


title: DOX+1

value: Doxycycline (DOX) for 2 wks


title: DOX-2


title: Shaziling pig A5


title: DOX+2


title: Yorkshire A1

value: Yorkshire


title: Yorkshire A2

value: male


title: DOX+3


title: NKT2(wt)_rep1


title: XT4699hrcC-, biological rep2

city: Manhattan

first: Sanzhen

last: Liu

state: KANSAS

address: 4024 Throckmorton Plant Sciences Ce

department: Plant Pathology

institute: Kansas State University

description:
Gene Expression Data from wheat leaves inoculated with Xanthomonas translucens
Hrcc-2

hyb_protocol: 15 ug of fragmented biotinylated cRNA was hybridized for 16 hr at 45C on GeneChip Wheat Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000_7G

data_processing: The data was processed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings.

organism: Triticum aestivum

source_name: Wheat leaves inoculated with strain XT 4699hrcC-

label_protocol: Biotinylated cRNA was prepared using GeneChip 3'IVT Express kit from 100ng total RNA according to 3' IVT Express kit user manual (Affymetrix).

growth_protocol: 10-day-old wheat seedlings were grown in the growth chamber at 22 ºC/ 20 ºC (day/night) under a 15-h photoperiod

extract_protocol: RNA samples were isolated from leaf samples using Trizol reagents (Invitrogen) as described by the manufacturer.

treatment_protocol: First fully expanded leaves of 10-day-old ‘Chinese Spring’ wheat plants were inoculated with three different bacterial suspensions (XT4699, XTRocky, Hrcc) with optical density of 0.5 at 600 nm using a needleless syringe. Leaf samples were collected 24 h after inoculation.

tag: cultivar

value: Chinese Spring

value: First fully expanded leaves

tag: inoculated with

value: XT4699hrcC-, type III secretion system mutant of XT4699 strain


title: XT-Rocky, biological rep3

description:
Gene Expression Data from wheat leaves inoculated with Xanthomonas translucens
Rocky-4

source_name: Wheat leaves inoculated with strain XT-Rocky

value: wild type strain XT-Rocky


title: Lgr5-GFP-stem cell vs CD24 hi in mouse colon array_2

city: Utrecht

first: Kay

last: Wiebrands

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

hyb_protocol: according to Agilent guidelines

scan_protocol: according to Agilent guidelines

data_processing: Microarray signal and background information were retrieved using featuere extraction (V.9.5.3, Agilent Technologies).

source_name: FACS sorted Lgr5_GFP positive colonic stem cell

label_protocol: 300 ng of total RNA was labeled using low RNA Input Linear Amp kit (Agilent Technologies, Pato Alto, CA, USA).

growth_protocol: FACS-based cell sorting GFP positive cells and CD24 hi positive cell from mouse colonic crypts

extract_protocol: RNA was isolated using Trizol (invitrogen)

value: normal murin colon

value: adult

source_name: FACS sorted CD24 positive colonic cell


title: XT-Rocky, biological rep1

description:
Gene Expression Data from wheat leaves inoculated with Xanthomonas translucens
Rocky-1


title: DOX-3


title: XT4699, biological rep2

description:
Gene Expression Data from wheat leaves inoculated with Xanthomonas translucens
4699-3

source_name: Wheat leaves inoculated with strain XT4699

value: wild type strain XT4699


title: Lgr5-GFP-stem cell vs CD24 hi in mouse colon array_2 dyeswap


title: XT4699, biological rep3

description:
Gene Expression Data from wheat leaves inoculated with Xanthomonas translucens
4699-4


title: XT-Rocky, biological rep2

description:
Gene Expression Data from wheat leaves inoculated with Xanthomonas translucens
Rocky-3


title: Lgr5-GFP-stem cell vs CD24 hi in mouse colon array_1


title: Lgr5-GFP-stem cell vs CD24 hi in mouse colon array_1 dyeswap


title: XT4699hrcC-, biological rep1

description:
Gene Expression Data from wheat leaves inoculated with Xanthomonas translucens
Hrcc-1


title: nasopharynx tissues obtained from patients with inflamed nasopharyngeal mucosa,N4

city: Guangzhou

first: Zhong-Xi

last: Huang

address: Tonghe

department: Cancer Institute

institute: Southern Medical University

hyb_protocol: Hybridization was performed follow manufacturer's instruction

scan_protocol: Arrays were scanned with a confocal LuxScan 10KA two-channel laser scanner (CapitalBio)

data_processing: Data of obtained images were extracted with LuxScan3.0 software (CapitalBio).A space and intensity-dependent normalization based on LOWESS algorithm was then applied.

source_name: nasopharynx tissues

label_protocol: Five micrograms DNase-treated total RNA was prepared. Sample was labeled by Cy5-dCTP and Cy3-dCTP for human reference.

extract_protocol: After resection, specimens were immediately flash frozen and stored in liquid nitrogen. We selected tumor samples containing more than 70% cancer cells by analysis of corresponding frozen sections.Total cellular RNA was extracted with Trizol (Invitrogen).

value: nasopharynx tissues

source_name: Human reference

tag: sample type

value: reference


title: non-keratinizing nasopharyngeal carcinoma biopsy,C8


title: nasopharynx tissues obtained from patients with inflamed nasopharyngeal mucosa,N8


title: non-keratinizing nasopharyngeal carcinoma biopsy,C6


title: XT4699, biological rep1

description:
Gene Expression Data from wheat leaves inoculated with Xanthomonas translucens
4699-1


title: nasopharynx tissues obtained from patients with inflamed nasopharyngeal mucosa,N6


title: nasopharynx tissues obtained from patients with inflamed nasopharyngeal mucosa,N12


title: nasopharynx tissues obtained from patients with inflamed nasopharyngeal mucosa,N3


title: nasopharynx tissues obtained from patients with inflamed nasopharyngeal mucosa,N9


title: nasopharynx tissues obtained from patients with inflamed nasopharyngeal mucosa,N1


title: non-keratinizing nasopharyngeal carcinoma biopsy,C7


title: nasopharynx tissues obtained from patients with inflamed nasopharyngeal mucosa,N10


title: non-keratinizing nasopharyngeal carcinoma biopsy,C32


title: non-keratinizing nasopharyngeal carcinoma biopsy,C27


title: non-keratinizing nasopharyngeal carcinoma biopsy,C29


title: non-keratinizing nasopharyngeal carcinoma biopsy,C4


title: non-keratinizing nasopharyngeal carcinoma biopsy,C28


title: non-keratinizing nasopharyngeal carcinoma biopsy,C2


title: non-keratinizing nasopharyngeal carcinoma biopsy,C19


title: non-keratinizing nasopharyngeal carcinoma biopsy,C24


title: non-keratinizing nasopharyngeal carcinoma biopsy,C25


title: non-keratinizing nasopharyngeal carcinoma biopsy,C21


title: non-keratinizing nasopharyngeal carcinoma biopsy,C18


title: donor d2 vs donor d4 (E0111:B4)

city: MONTPELLIER

first: Paul

last: CHUCHANA

address: 80 rue Augustin Fliche

country: France

institute: CNRS

hyb_protocol: Prior to hybridization, excess oligonucleotide was removed from the arrays by shaking them twice1min in 0.2% SDS. Arrays were then washed 2 times in distilled water. The two labelled aRNA were added to microarray hybridization buffer version 2 (GE Healthcare) in a final concentration of 50% formamide, denaturated at 95°C for 3 min and applied to the microarrays in individual chambers of an automated slide processor (GE Healthcare). Hybridization was carried out at 37°C for 12 h. Hybridized slides were washed at 37°C successively with 1X SSC, 0.2% SDS for 10 min, twice with 0.1X SSC, 0.2% SDS for 10 min, with 0.1X SSC for 1 min and with isopropanol before air drying.

scan_protocol: Microarrays were immediately scanned at 10 µm resolution in both Cy3 and Cy5 channels with GenePix 4200AL scanner (Molecular Devices) with a variable PMT voltage to obtain maximal signal intensities with <0.1% probe saturation. ArrayVision software was used for feature extraction. Spots with high local background or contamination fluorescence were flagged manually. A local background was calculated for each spot as the median values of the fluorescence intensities of 4 squares surrounding the spot. This background was subtracting from the foreground fluorescence intensity.

data_processing:
Identification of differentially regulated genes was carried out using the EV (Expression Variation) method [Chuchana P., Marchand D., Nugoli M., Rodriguez C., Molinari N. et al. (2007) An adaptation of the LMS method to determine expression variations in profiling data. Nucleic Acids Res 35:e71 doi:10.1093], on paired data, i.e. LPS (Ref Sigma E0111:B4) stimulated macrophages versus unstimulated macrophages from the same donor. This method can be used to analyze the signal with regards to noise by normalizing and constructing confidence bands of gene expression, and by fitting cubic spline curves to the Box–Cox transformation. The confidence bands, fitted to the actual variance of the data, include the genes devoid of significant variation, and are used to calculate EV, based on the confidence bandwidth. Each outlier is positioned according to the dispersion space (DS) and provides a measure of gene EV associated with a p-value. This model allows us to stabilize variance.
To normalize data for this submission, samples treated were compared with untreated matched sample.
There are 6 donors and 6 samples for each donor. A sample without treatment and the 5 other samples were treated with different stimuli.
This corresponds to 5 paired comparisons for 6 donors or 5x6 = 30 columns
[EV normalized Data file "value definition"]: For each spot S, its orthogonal projection to the median O was determined and the distance between O and U d(O,U) (intersection of the segments O,U and the curve of the DS) measured. For each spot located along the O, S line, the value d(O,U) represents the unit of expression. Expression variation Ev#(S) thus corresponds to the d(O,S)/d(O,U) ratio. |EV#(S)| 1/41 defines the baseline for genes presenting no EV. If the ratio is lower than one, the spot do not present expression variation and the measurement in noted NR.
For more precision see:  Chuchana P., Marchand D., Nugoli M., Rodriguez C., Molinari N. et al. (2007) An adaptation of the LMS method to determine expression variations in profiling data. Nucleic Acids Res 35:e71 doi:10.1093
The raw data file is linked as supplementary file on the Series record.
The EV normalized Data file is linked as supplementary file on the Series record.

label_protocol: For the preparation of the labelled Cy3- and Cy5- aRNA target, one microgram of total RNA samples were amplified and synthesised using Amino Allyl Message Amp II aRNA amplification kit (Ambion), according the manufacturer’s instructions.

extract_protocol: Total RNA was then extracted from the fresh pooled monolayer in duplicate experiments, which includes a DNAse step, using the RNeasy® mini kit (Qiagen) according to the manufacturer’s instructions. RNA quantity and purity was quantified using a NanoDrop ND-1000 spectrophotometer (Nanodrop Technologies) and assayed for degradation using an Agilent bioanalyser (Agilent technologies, Santa Clara, USA) according to the manufacturer’s instructions.

treatment_protocol: All samples were processed together the same day. Briefly, the mononuclear cell fraction was obtained by gradient centrifugation over Ficoll (Histopaque 1077, Sigma-Aldrich Chimie, Lyon, France) and monocytes were purified by CD14+ magnetic cell sorting (Miltenyi Biotech) according to manufacturer’s instructions. Monocytes were then seeded in 24-well plates at 106 cells per well (4 wells per donor) in complete Iscove's Modified Dulbecco's Medium (IMDM) supplemented with 10 % heat-inactivated human type AB (Cambrex) serum, ultra-glutamine 2 mM, penicillin 200 U/ml and streptomycin 200 pg/ml. Cells were cultured for 5 days (with pre-warmed complete medium change at day 3) to allow differentiation into macrophages. At day 5, two wells per donor were stimulated with 100 ng/ml lipopolysaccharide (LPS, Escherichia coli, Ref Sigma E0111:B4) whereas the two other wells were left as unstimulated controls (medium change only). After 48 hours, all wells were washed with pre-warmed phosphate-buffered saline (PBS).

tag: donor

value: monocytes/macrophages

tag: treatment


title: non-keratinizing nasopharyngeal carcinoma biopsy,C16


title: donor d2 vs donor d4 (LiLEM75)

tag: cell type


title: non-keratinizing nasopharyngeal carcinoma biopsy,C22


title: non-keratinizing nasopharyngeal carcinoma biopsy,C15


title: donor d2 vs donor d4 (LiITMAP263)


title: non-keratinizing nasopharyngeal carcinoma biopsy,C26


title: non-keratinizing nasopharyngeal carcinoma biopsy,C9


title: donor d2 vs donor d4 (NT)

value: NT


title: donor d5 vs donor d6 (E0111:B4)


title: donor d2 vs donor d4 (TbgB2/7/1)


title: donor d5 vs donor d6 (LiLEM75)


title: non-keratinizing nasopharyngeal carcinoma biopsy,C11


title: donor d2 vs donor d4 (LdLDD8)


title: non-keratinizing nasopharyngeal carcinoma biopsy,C14


title: non-keratinizing nasopharyngeal carcinoma biopsy,C12


title: donor d5 vs donor d6 (LiITMAP263)


title: non-keratinizing nasopharyngeal carcinoma biopsy,C13


title: non-keratinizing nasopharyngeal carcinoma biopsy,C10


title: non-keratinizing nasopharyngeal carcinoma biopsy,C1


title: donor d5 vs donor d6 (TbgB2/7/1)


title: donor d5 vs donor d6 (LdLDD8)


title: hiPSC_OCE1_Day 14_SEM-i_CD235a+

city: Oxford

first: Alison

middle: T

last: Merryweather-Clarke

address: John Radcliffe Hospital, Headley Way, Headington

institute: NHSBT Oxford

hyb_protocol: HTA2 arrays were hybridized with 5 μg of labelled DNA according to manufacturer's instructions.

scan_protocol: The Affymetrix GeneChip Fluidics Station 450 was used to wash and stain the arrays with streptavidin–phycoerythrin, according to the standard protocol for eukaryotic targets (IHC kit, Affymetrix). Arrays were scanned with an Affymetrix GeneChip scanner 3000 at 570nm.

data_processing: Intensity values were determined using GeneChip Operating Software (Affymetrix)and normalized by the Robust Multiarray Average algorithm using Affymetrix Expression Console software. Statistical analysis of differential expression was conducted using the Linear Models for Microarray Data package from the Bioconductor suite in R (www.bioconductor.org). The B values, p-values, and fold changes were used to select differentially expressed (DE) genes reaching a minimum linear expression value of 100 in all replicates of at least one sample group (p ≤ 0.01, fold change (FC) ≥ 2, B > 2.945). Principal component analysis (PCA) was conducted and displayed using Python packages. Hierarchical clustering (HC) analysis was performed using Python SciPy. Heat maps were generated using Python matplotlib. More advanced consensus clustering was conducted using SMART and Bi-CoPaM algorithms in MATLAB, using Biclustering from the biclust package in R. Biopython to fetch 1kb of genomic DNA sequence upstream of the transcriptional start sites (TSS) of each gene in the cluster. MEME suite was used for transcription factor binding site (TFBS) analysis, seeking homology with motifs in the Jolma database. Differentially-expressed genes were examined for enriched functional ontologies using GeneCoDis.

source_name: hiPSC_Day 14_SEM-i_CD235a+

label_protocol: The target was prepared from 100ng DNAsed total RNA for hybridization to Affymetrix GeneChip Human Transcriptome 2.0 ST microarrays (HTA2) using the Ambion WT protocol (Life Technologies) and Affymetrix labelling and hybridization kits (Affymetrix). Labelled DNA mean yield was 13.5 μg (minimum: 8.5 μg; maximum: 20.5 μg).

growth_protocol: Human primary differentiating EBs derived from adult peripheral blood lymphocyte cones (AB) (NHS Blood and Transplant) or cord blood (CB) were obtained with informed consent in accordance with the Declaration of Helsinki. EBs were cultured using a three-phase liquid culture system {Griffiths, 2012 #516} with modifications. HiPSCs were established from fibroblasts or hematopoietic cells transduced with OCT4, SOX2 and KLF4 {Yang, 2014 #522} and EBs were generated by modifying a published protocol {Dias, 2011} in medium optimized for hiPSC-derived EB culture (SEM-i).

extract_protocol: Total RNA including miRNA was extracted using mirVana (Life Technologies) according to the manufacturer’s instructions. RNA quality and quantity was assessed using a Qubit fluorimeter (Life Technologies), a NanoDrop spectrophotometer (Thermo) and an Agilent Bioanalyzer 2100 (Agilent Technologies). RNA integrity numbers were in the range 8.7-10. Before target preparation for hybridization to Affymetrix Human Transcriptome 2.0 (HTA2.0) arrays (Affymetrix), RNA was treated with Turbo DNA-Free DNAse (Life Technologies).

treatment_protocol: AB- and CB-derived EBs were stained and sorted on a MoFlo II (Beckman Coulter) using anti–CD36-PE (BD Biosciences; for EBs cultured for between four and seven days), anti–CD71-FITC (Dako), anti–CD235a-APC (BD Biosciences; for EBs cultured between four and 12 days), and anti–CD235a-RPE (Dako; for EBs cultured for 14 days). At day 0, AB-, CB- and hiPSC-derived HSPCs were isolated using CD34-beads (Miltenyi). HiPSC-derived hematopoietic progenitors were also isolated using CD31 beads at day 0  to incorporate all possible sources of erythroid progenitors. As insufficient cell numbers were obtained for FACS sorting of EBs derived from hiPSCs, CD71 and CD235a-specific magnetic beads were used to isolate hiPSC-EB populations at days 7 and 14 respectively. AB-EBs were isolated using these beads for direct comparison with hiPSC-derived EBs. Maturation of EBs was monitored by staining cytospin preparations from 5x104 cells with Wright-Giemsa and assessed using light microscopy. To visualise hemoglobin expression, cytospins were stained with 1% O-dianisidine in methanol and counterstained with 10% Giemsa (BDH).

tag: days cultured

tag: source

value: hiPSCs

tag: population

tag: media

value: SEM-i

tag: enrichment method

value: Magnetic Beads

value: hiPSC-EB


title: hiPSC_C18_Day 14_SEM-i_CD235a+


title: hiPSC_OC1_Day 14_SEM-i_CD235a+


title: hiPSC_iOCE1-5_Day 7_SEM-i_CD71+

source_name: hiPSC_Day 7_SEM-i_CD71+


title: hiPSC_OC1_Day 7_SEM-i_CD71+


title: donor d1 vs donor d3 (LiITMAP263)


title: donor d1 vs donor d3 (E0111:B4)


title: donor d1 vs donor d3 (LiLEM75)


title: donor d5 vs donor d6 (NT)


title: donor d1 vs donor d3 (LdLDD8)


title: donor d1 vs donor d3 (TbgB2/7/1)


title: donor d1 vs donor d3 (NT)


title: hiPSC_C18_Day 7_SEM-i_CD71+


title: hiPSC_iOCE1-2_Day 0_CD34+

source_name: hiPSC_Day 0_CD34+


title: hiPSC_iOCE1-3_Day 0_CD34+


title: hiPSC_OC1_Day 0_CD31+

source_name: hiPSC_Day 0_CD31+


title: Yorkshire A3

value: Yorkshire

tag: age

value: longissimus dorsi muscle


title: hiPSC_OCE1-6_Day 0_CD31+


title: hiPSC_iOCE1-1_Day 0_CD34+


title: XEZ2OSry rep 2

city: Canterbury

first: Peter

middle: James

last: Ellis

state: Kent

address: Stacey Building

department: School of Biosciences

institute: University of Kent

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data were normalised using Illumina Genome Studio (V.2011.1), quantile normalisation.

source_name: testis

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

extract_protocol: RNA was extracted using TRI reagent followed by cleanup and DNAse I treatment in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: background strain

tag: karyotype

value: XO

tag: transgenes carried

value: Sry, Eif2s3y, Zfy2

tag: gender

value: male

value: 17.5 days post partum

value: testis


title: XT4699hrcC-, biological rep3

description:
Gene Expression Data from wheat leaves inoculated with Xanthomonas translucens
Hrcc-3

value: Chinese Spring

tag: tissue

value: First fully expanded leaves

value: XT4699hrcC-, type III secretion system mutant of XT4699 strain


title: hiPSC_iOCE1-4_Day 7_SEM-i_CD71+


title: CB_CB8_Day 14_SEM-F_CD71+, CD235a+

source_name: CB_Day 14_SEM-F_CD71+,CD235a+

value: CB PBMCs

value: SEM-F

value: Flow Cytometry

value: CB-EB


title: hiPSC_OCE1-7_Day 0_CD31+

value: hiPSCs


title: CB_CB13_Day 7_SEM-F_CD36+, CD71+, CD235a+


title: XEZ2OSry rep 4


title: XEZ2OSry rep 3


title: XEOSry rep 3

value: Sry, Eif2s3y


title: XEOSry rep 2


title: CB_CB13_Day 7_SEM-F_CD36+, CD71+, CD235a-


title: CB_CB1_Day 7_SEM-F_CD36+, CD71+, CD235a-


title: CB_CB10_Day 0_CD34+

source_name: CB_Day 0_CD34+

value: Magnetic Beads


title: CB_CB12_Day 0_CD34+


title: CB_CB2_Day 7_SEM-F_CD36+, CD71+, CD235a-


title: CB_CB2_Day 7_SEM-F_CD36+, CD71+, CD235a+


title: XEOSry rep 4


title: CB_CB9_Day 14_SEM-F_CD71+, CD235a+


title: XEZ2OSry rep 1


title: XEOSry rep 1


title: CB_CB11_Day 0_CD34+


title: MEC-L2-1

city: Silverthorne

first: Margaret

middle: C

last: Neville

state: CO

address: 712 Eveningstar Rd

department: OB/GYN

institute: UC Denver

description: microRNA expression of MECs isolated from Lactation day 2 mice

hyb_protocol: Hybridization was performed as per manufacturer's instructions by UC Denver Microarray core facility

scan_protocol: Scanning was performed as per manufacturer's instructions by UC Denver Microarray core facility

data_processing: All cel files were analyzed in miRNA Affy QC tool (version 1.0.33.0) and RMA normalized signal intensities were exported as text file for further analysis of mouse specific miRNA probesets (609) in GeneSpring.

source_name: Mammary epithelial cells

label_protocol: Labelling was performed as per manufacturer's instructions by UC Denver Microarray core facility

growth_protocol: Eight CD1 mice were bred and day of observation of a vaginal plug was recorded as Day 0 of pregnancy

extract_protocol: Adipose depleted mammary epithelial cells were isolated from mammary gland tissue as described in PMID: 19953310 and RNA was isolated using TRIZOL and subsequently purified with Qiagen RNAeasy columns.

treatment_protocol: 4 mice were euthanized on day 14 of pregnancy and remaining 4 mice were euthanized on Lactation day 2

tag: subject

value: Female CD1 mice


title: MEC-L2-2


title: MEC-L2-3


title: HLA-DR+CD38+ CD8 T cells, Dengue patient 1

city: Atlanta

first: Jaturong

last: Sewatanon

state: GA

address: 1462 Clifton Rd. NE, Room 412

department: Microbiology and Immunology

institute: Emory University School of Medicine

description:
Expression data from naïve (CCR7+CD45RA+) CD8 T cells of healty donor from Thailand
Dengue-1

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Chips were scanned on a seventh−generation GeneChip scanner 3000 (Affymetrix)

data_processing: Affymetrix GCOS software was used to generate the raw intensity data file.

source_name: Activated CD8 T cells (HLA-DR+CD38+) from dengue patient

label_protocol: Standard Affymetrix protocol

growth_protocol: PBMCs isolated from peripheral whole blood of dengue patients and healthy controls were stained with relevant antibodies at 4oC for 30 mins, washed thoroughly and suspended in PBS containg 2% FCS and immediately sorted on a BD FACS Aria III (Becton and Dickenson) with high forward scatter gates to account for the larger blasting effector lymphocytes. CD3+CD8+CD45RA+CCR7+ naïve CD8 T cells and CD3+CD8+HLA-DR+CD38+ activated CD8 T cells were isolated up to a purity of 99%.

extract_protocol: All samples were processed simultaneously for RNA isolation using glycogen as carrier by standard Trizol RNA isolation procedures. Total RNA was evaluated by spectrophotometry to determine quantity, protein concentration and organic solvent contamination and Agilent 2100 bio analyzer was used to determine RNA degradation. Two-rounds of in-vitro transcription were performed to amplify RNA.

treatment_protocol: FACS sorted cells were washed thoroughly and the cell pellet was immediately suspended in Trizol (Invitrogen) and stored at -80oC until RNA extraction.

value: CD8 T cells from PBMCs

tag: disease state

value: Dengue hemorrhagic fever (DHF)

value: 25 years old


title: HLA-DR+CD38+ CD8 T cells, Dengue patient 6

description:
Expression data from activated (HLA-DR+CD38+) CD8 T cells of dengue patient from Thailand
Dengue-6

value: Dengue fever (DF)

value: 17 years old


title: HLA-DR+CD38+ CD8 T cells, Dengue patient 5

description:
Expression data from activated (HLA-DR+CD38+) CD8 T cells of dengue patient from Thailand
Dengue-5

value: 29 years old


title: HLA-DR+CD38+ CD8 T cells, Dengue patient 4

description:
Expression data from activated (HLA-DR+CD38+) CD8 T cells of dengue patient from Thailand
Dengue-4

value: 19 years old