title: Colon, hyperplastic polyp or normal mucosa, replicate 11


title: Colon, hyperplastic polyp or normal mucosa, replicate 9

status: Public on Sep 29 2015

type: RNA

city: Portland

first: Amiee

middle: Bell

last: Potter

state: OR

address: 3181 SW Sam Jackson Park Rd, Mail Code #L581

department: Integrated Genomics Laboratory

country: USA

institute: OHSU

description: miRNA expression in colonic normal mucosa and hyperplastic polyp

hyb_protocol: Labeled RNA was added to the hybridization cocktail following the Genisphere FlashTag technical manual specifically for Affymetrix miRNA microarray. Hyb cocktail was added to the miRNA microarray and hybridized for 16 hrs at 48 degrees C in the Affymetrix GeneChip hybridization Oven 640 with rotation at 60 RPM

scan_protocol: Arrays were washed and stained on the GeneChip Fluidics Station 450 with manufacturer recommended fluidics script. Arrays were scanned using the Affymetrix autoloader carousel and GeneChip Scanner 3000

data_processing: All .cel files as a single set were uploaded to Partek Genomics Suite 6.6 using the default RMA subroutine.  Default RMA includes RMA background correction followed by quantile normalization and median polish summarization. Data QC and array performance assessment was performed in Statistica using the RMA normalized log2 transformed signal data exported from Partek. Differential gene expression was statistically tested using ANOVA in Partek Genomics Suite 6.6 on the RMA normalized log2 transformed signal data.  More advanced statistical testing was conducted on the exported Partek file of RMA normalized log2 transformed signal data using SAS

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: colonic polyp or normal mucosa

label_protocol: Manufacturer's protocol: Genisphere FlashTag Biotin labelin. In sum - RNA was polyadenylated using poly(A) polymerase and ATP in stock reaction buffer. Polyadenylated miRNAs were labeled using the biotin ligation mix and T4 DNA ligase.

extract_protocol: Total RNA, including miRNA, was isolated from the region using the miRNeasy FFPE kit (Catalog #217504; Qiagen, Valencia, CA), per manufacturer’s recommended protocol.

treatment_protocol: Normal colonic mucosa was obtained as part of routine clinical pathology and distant to the adenoma at the time of biopsy. Polyp biopsies were also taken. Polyps were evaluated by two pathologists and classified as normal mucosa, tubular adenoma, sessile serrated adenoma, traditional serrated adenoma, and tubular villous/villous or adenoma with high grade dysplasia. A demarcated hematoxylin and eosin-stained slide was used to guide macrodissection of regions of interest containing the defined predominant histologic feature(s) on which the tissue was classified.

tag: tissue

value: colon

tag: category

value: hyperplastic polyp or normal mucosa


title: Colon, hyperplastic polyp or normal mucosa, replicate 12


title: Colon, hyperplastic polyp or normal mucosa, replicate 8


title: Colon, hyperplastic polyp or normal mucosa, replicate 10


title: Colon, hyperplastic polyp or normal mucosa, replicate 21


title: Colon, hyperplastic polyp or normal mucosa, replicate 20


title: Colon, hyperplastic polyp or normal mucosa, replicate 7


title: Colon, hyperplastic polyp or normal mucosa, replicate 6


title: Colon, hyperplastic polyp or normal mucosa, replicate 3


title: Colon, hyperplastic polyp or normal mucosa, replicate 1


title: Colon, hyperplastic polyp or normal mucosa, replicate 2


title: Colon, hyperplastic polyp or normal mucosa, replicate 5


title: Colon, hyperplastic polyp or normal mucosa, replicate 16


title: Colon, hyperplastic polyp or normal mucosa, replicate 13


title: Colon, hyperplastic polyp or normal mucosa, replicate 4


title: CX3CR1-/- CCL2-/-_Mgl1lo_unt

city: Paris

first: Helene

last: Perrin

address: 91 boulevard de l'hopital

country: France

institute: INSERM

hyb_protocol: Illumina whole mouse genome oligo microarrays WG6 V2.0 following manufacturer’s instructions

scan_protocol: Fluorescence signals were detected using Illumina Beadstation 500

data_processing: Illumina Genome studio software was used to read out and process the microarray image files

organism: Mus musculus

source_name: tibialis anterior muscle untreated

label_protocol: Ovation Pico WTA system V2 (NuGEN, Leek, Netherlands) following manufacturer’s instructions

growth_protocol: Cell subsets sorted by flow cytometry from fresh mouse tibia anterior muscle cell suspensions: CD11b+ Ly6G- NK1.1-  F4/80 Hi Ly6C lo Mgl1 lo, CD11b+ Ly6G- NK1.1-  F4/80 Hi Ly6C lo Mgl1 Hi, CD11b+ Ly6G- NK1.1-  F4/80 lo Ly6C Hi, CD11b+ Ly6G- NK1.1-  F4/80 lo Ly6Clo.  One cell-sorting experiment was performed with a pool of 3 mice per strain and per condition.

extract_protocol: QIAGEN Rneasy minikit following manufacturer’s instructions

treatment_protocol: 4 days following intramuscular injection of notexin or untreated as controls

tag: strain

value: tibialis anterior muscle

tag: cell population

tag: treatment

value: untreated


title: CCL2-/-_Ly6Chi_Nx

source_name: tibialis anterior muscle day 4 post Notexin injection

value: CD11b+ Ly6G- NK1.1-  F4/80 lo Ly6C Hi

value: day 4 post Notexin injection


title: CX3CR1-/- CCL2-/-_F4/80lo_Nx

value: CD11b+ Ly6G- NK1.1-  F4/80 lo Ly6Clo


title: CX3CR1-/- CCL2-/-_Mgl1hi_Nx

value: CD11b+ Ly6G- NK1.1-  F4/80 Hi Ly6C lo Mgl1 Hi


title: CCL2-/-_Mgl1lo_unt

value: CD11b+ Ly6G- NK1.1-  F4/80 Hi Ly6C lo Mgl1 lo


title: CX3CR1-/-_Mgl1lo_Nx


title: CCL2-/-_F4/80lo_Nx


title: CX3CR1-/- CCL2-/-_Mgl1lo_Nx


title: CX3CR1-/-_F4/80lo_Nx


title: WT_F4/80lo_Nx


title: CCL2-/-_Mgl1lo_Nx


title: CX3CR1-/- CCL2-/-_Ly6Chi_Nx


title: CX3CR1-/-_Mgl1hi_unt


title: CX3CR1-/- CCL2-/-_Mgl1hi_unt


title: CCL2-/-_Mgl1hi_unt


title: CX3CR1-/-_Ly6Chi_Nx


title: CX3CR1-/-_Mgl1hi_Nx


title: WT_Ly6Chi_Nx


title: CCL2-/-_Mgl1hi_Nx


title: WT_Mgl1lo_Nx


title: CX3CR1-/-_Mgl1lo_unt


title: WT_Mgl1hi_Nx


title: WT_Mgl1hi_unt


title: HMCL-U266_180K_OGT_PicoPlex_rep2

type: genomic

city: Newcastle upon Tyne

first: Aneta

last: Mikulasova

address: Brewery Lane

department: Biosciences Institute

country: United Kingdom

institute: Newcastle University

hyb_protocol: In total, 3 aCGH platforms were used as follow Human Genome CGH Microarray, 4×44K and SurePrint G3 CGH+SNP Microarray, 4×180K (both Agilent Technologies, Santa Clara, CA, USA); and CytoSure ISCA UPD Array, 4×180K (Oxford Gene Technology, Oxfordshire, UK). HMCL DNA and reference DNA were together with COT Human DNA (F. Hoffman-La Roche, Basel, Switzerland) and hybridization mix (Oligo aCGH Hybridization Kit, Agilent Technologies, Santa Clara, CA, USA) co-hybridize to the array for 24 hour (Agilent platforms) or 48 hour (OGT platform).

scan_protocol: DNA microarrays were scanned by Microarray Scanner (Agilent Technologies, Santa Clara, CA, USA).

data_processing:
Feature Extraction Software 12.0.2.2 (Agilent Technologies, Santa Clara, CA, USA) was used for data extraction and quality control evaluation. Extraction protocol version CGH_1200_Jun14 was applied.
For purpose of CN change analysis, non-segmented L2R data and segmented data was analyzed and exported using Genomic Workbench 7.0.4.0 (Agilent Technologies, Santa Clara, CA, USA) and CytoSure Interpret Software 4.3.2 (Oxford Gene Technology, Oxfordshire, UK). For segmentation, ADM-2 algorithm and following setting: ≥100 kbp size, ≥0.25 fold change of L2R, ≥5 and ≥3 (180K and 44K, respectively) consecutive probes were used. Database of Genomic Variants (http://www.openhelix.com) for hg19 was used to differing somatic copy number alterations (CNAs) and common human population copy number variations (CNVs). Manufacture recommended setting was used for LOH calling as confidence level 0.95 with threshold 6 in case of SurePrint G3 CGH+SNP Microarray, 4×180K Agilent platform; and 80% threshold homozygosity and score above 140 in case of CytoSure ISCA UPD Array, 4×180K OGT platform.

label: Alexa Fluor 5

molecule: genomic DNA

source_name: Human Myeloma Cell Line U266 - PicoPlex

label_protocol: A total of 1.5 µg of tested and reference DNA was used. Unamplified and MDA-based WGA DNA samples were fragmented by AluI and RsaI (both Promega, Madison, WI, USA) restriction enzymes. PCR-based WGA DNA samples were digested only in combination with SurePrint G3 CGH+SNP Microarray, 4×180K (Agilent Technologies, Santa Clara, CA, USA) platform. DNA samples were fluorescent labelled by BioPrime Total for Agilent aCGH Kit (Life Technologies, Paisley, UK); Alexa Fluor 3 for reference DNA and Alexa Fluor 5 for HMCL DNA.

extract_protocol: DNA was isolated from human myeloma cell line (HMCL) U266 using Gentra Puregene Kit (Qiagen, Hilden, Germany). As reference DNA, Human Genomic DNA (Promega, Madison, WI, USA) and Human Reference DNA (Agilent Technologies, Santa Clara, CA, USA) were used. HMCL U266 DNA and reference DNA were amplified by 6 commercial WGA kits as follow REPLI-g Mini Kit, REPLI-g Midi Kit, REPLI-g Single Cell Kit (all Qiagen, Hilden, Germany), illustra GenomiPhi V2 DNA Amplification Kit (GE Healthcare Life Sciences, Piscataway, NJ, USA), GenomePlex Complete WGA Kit (Sigma-Aldrich, St. Louis, MO, USA) and PicoPlex WGA Kit (Rubicon Genomics, Ann Arbor, MI, USA).

tag: gender

value: male

tag: wga type

value: single-cell PCR-based

label: Alexa Fluor 3

source_name: Agilent Euro Reference DNA


title: DPthy_Hdac3KO_rep1

city: Nashville

first: Scott

last: Hiebert

state: TN

address: 2220 Pierce Ave

department: Biochemistry

institute: Vanderbilt University

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
ANOVA
MoGene-1-0-st-v1

source_name: DP thymocytes, Hdac3 KO mouse

label_protocol: Affymetrix Kit: GeneChip® WT Sense Target Labeling and Control Reagents

growth_protocol: thymocytes from 3w old mice

extract_protocol: total RNA purified with PerfectPure RNA extraction kit (5 Prime)

tag: cell type

value: DP thymocyte


title: DPthy_WT_rep3

source_name: DP thymocytes, WT mouse


title: HMCL-U266_180K_OGT_PicoPlex_rep1


title: DPthy_Hdac3KO_rep3


title: DPthy_Hdac3KO_rep2


title: DPthy_WT_rep2


title: Korona 0h vs. Korona 72h: replicate 4

city: Trondheim

first: Per

last: Winge

address: Høgskoleringen 5e

department: Department of Biology

country: Norway

institute: Norwegian University of Science and Technology

description: Two color microarray. Biological replicas are dye-swaped between slides.

hyb_protocol: Hybridizations were performed in a Slide Booster Hybridization Station (Advalytix, Brunnthal, Germany), and the slides were washed according to the manufacturers’ descriptions (Genisphere and Advalytix).

scan_protocol: The slides were scanned at 10 mm resolution on a G2505B Agilent DNA microarray scanner (Agilent Technologies,Palo Alto, CA, USA). The resulting image files were processed using GenePix 5.1 software (Axon Instruments, Union City, CA, USA).

data_processing: Spots identified as not found or which were manually flagged out as bad were filtered out. The data sets were log-transformed and normalized using the printtip-loess approach. Within-array replicated measurements for the same gene were merged by taking the average between the replicates. The low number of spots is because  genes in Fragaria (Strawberry) have diverged so much from Arabidopsis that it is only a small subset of the probes on the Arabidopsis array that hybridize to the labeled cDNA. The data were then scaled so that all array data sets had the same median absolute deviation. No background normalization was done. The differentially expressed genes were identified using the Limma software package. References: Smyth, G. K. Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Statistical Applications in Genetics and Molecular Biology, Vol. 3, No. 1, Article 3 (2004).

organism: Fragaria x ananassa

source_name: Leaf tissue taken from 3 plants grown at 12°C, control sample, harvested before cold exposure (biological replicate 4)

label_protocol: Total RNA (15 mg) and Super-Script III reverse transcriptase (Invitrogen, Carlsbad, CA,USA) were used in a reverse transcription reaction.  Microarray slides were printed by the Norwegian Microarray Consortium (Trondheim, Norway). A 3DNA Array 350 kit with Cy3- and Cy5-labelled dendrimers (Genisphere,Inc., Hatfield, PA, USA) was used for labelling.

growth_protocol: Eight weeks old runner-propagated Fragaria × ananassa Duch. ‘Korona’, were grown on fertilized soil (P-Jord; Emmaljunga Torvmull AB) in plug trays (3 x 6 cells) in a greenhouse at 18°C under natural light and long-day conditions. Plants were short-day adapted for 1 week at 12°C under artificial light (fluorescent tubes, ~90 μmol m-2 sec-1) in a conditioning room.

extract_protocol: Total RNA was isolated with the Spectrum Plant Total RNA Kit (Sigma, St. Louis,MO,USA) and was quantified with NanodropND 1000 (Nanodrop Technologies, Wilmington, DE, USA).

treatment_protocol: Plants were transfered to a cold storage room at 2°C under artificial light (fluorescent tubes, ~90 μmol m-2 sec-1) and relative humidity at average of 80%. Plant sampling was carried out at 24 and 72 hours after initiation of the cold treatment. Control samples (0 h) were harvested prior to the transfer to the cold room. Harvested plant material of leaf from 3 plants per time point was pooled, flash-frozen in liquid N2 and stored at -80°C before sample processing.

tag: cultivar

value: Korona

source_name: Leaf tissue taken from 3 plants, harvested after 72h cold exposure at 2°C (biological replica 4)


title: WT_Mgl1lo_unt


title: Korona 0h vs. Korona 72h: replicate 1

source_name: Leaf tissue taken from 3 plants, harvested after 72h cold exposure at 2°C (biological replicate 1)

source_name: Leaf tissue taken from 3 plants grown at 12°C, control sample, harvested before cold exposure (biological replica 1)


title: Korona 0h vs. Korona 72h: replicate 3

source_name: Leaf tissue taken from 3 plants, harvested after 72h cold exposure at 2°C (biological replicate 3)

source_name: Leaft tissue taken from 3 plants grown at 12°C, control sample, harvested before cold exposure (biological replica 3)


title: DPthy_WT_rep1


title: Korona 0h vs. Korona 24h: replicate 4

source_name: Leaf tissue taken from 3 plants, harvested after 24h cold exposure at 2°C (biological replica 4)


title: HMCL-U266_180K_OGT_RgSC_rep1

source_name: Human Myeloma Cell Line U266 - RgSC

value: single-cell MDA-based


title: HMCL-U266_180K_OGT_RgSC_rep2


title: HMCL-U266_44K_Agilent_PicoPlex_rep1

source_name: Promega genomic DNA

value: female


title: Korona 0h vs. Korona 72h: replicate 2

source_name: Leaf tissue taken from 3 plants grown at 12°C, control sample, harvested before cold exposure (biological replicate 2)

source_name: Leaf tissue taken from 3 plants, harvested after 72h cold exposure at 2°C (biological replica 2)


title: HMCL-U266_180K_OGT_GenomiPhi_rep2

source_name: Human Myeloma Cell Line U266 - GenomiPhi

value: standard MDA-based


title: HMCL-U266_180K_OGT_RgMidi_rep2

source_name: Human Myeloma Cell Line U266 - RgMidi


title: HMCL-U266_44K_Agilent_PicoPlex_rep2

source_name: Human Myeloma Cell Line U266 - PicoPlex


title: HMCL-U266_180K_OGT_RgMini_rep2

source_name: Human Myeloma Cell Line U266 - RgMini


title: HMCL-U266_180K_OGT_GenomiPhi_rep1


title: HMCL-U266_180K_OGT_GenomePlex_rep1

source_name: Human Myeloma Cell Line U266 - GenomePlex

value: standard PCR-based


title: HMCL-U266_44K_Agilent_GenomePlex_rep1


title: HMCL-U266_180K_OGT_GenomePlex_rep2


title: HMCL-U266_44K_Agilent_GenomePlex_rep2


title: HMCL-U266_180K_OGT_RgMidi_rep1

source_name: Agilent Euro Reference DNA


title: HMCL-U266_180K_OGT_Control_rep2

source_name: Human Myeloma Cell Line U266 - Control

value: no WGA


title: HMCL-U266_180K_OGT_Control_rep1


title: Korona 0h vs. Korona 24h: replicate 3

source_name: Leaf tissue taken from 3 plants, harvested after 24h cold exposure at 2°C (biological replicate 3)


title: HMCL-U266_44K_Agilent_RgSC_rep1


title: FTSC, rep2

city: Houston

first: Frank

last: McKeon

state: TX

address: 3455 Cullen Blvd

department: Biology and Biochemistry

institute: University of Houston

description: gene expression of FTSC

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

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

label: Biotin

source_name: human fallopian tube stem cell

label_protocol: Encore® Biotin Module (Nugen)

growth_protocol: stem cells are cultured on 3T3 feeder cells, and stem cells are differentiated using air-liquid interface system

extract_protocol: PicoPure® RNA Isolation Kit (Life Technologies) and RNeasy kit  (Qiagen)

value: human fallopian tube stem cell


title: HMCL-U266_44K_Agilent_RgSC_rep2


title: HMCL-U266_44K_Agilent_RgMini_rep2


title: HMCL-U266_44K_Agilent_Control_rep2


title: HMCL-U266_180K_OGT_RgMini_rep1


title: Korona 0h vs. Korona 24h: replicate 2

description: Two color microarray. Biological replicas are dye-swaped between slides

source_name: Leaf tissue taken from 3 plants, harvested after 24h cold exposure at 2°C (biological replica 2)


title: HMCL-U266_44K_Agilent_RgMini_rep1


title: HMCL-U266_44K_Agilent_GenomiPhi_rep1


title: HMCL-U266_44K_Agilent_GenomiPhi_rep2


title: HMCL-U266_44K_Agilent_Control_rep1


title: patient5_STIC

description: LCM from cryosection (STIC)

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

source_name: STIC (serous tubal intraepithelial carcinoma)

extract_protocol: PicoPure® RNA Isolation Kit (Life Technologies)

tag: patient no.

value: patient 5

value: LCM from cryosection (STIC)


title: patient6_normal

description: LCM from cryosection (normal oviduct)

source_name: normal oviduct

value: patient 6

value: LCM from cryosection (normal oviduct)


title: FTSC-ALI, rep2

description: gene expression of FTSC-ALI

source_name: air-liquid interface differentiation of human fallopian tube stem cell


title: patient6_invasive_SC

description: LCM from cryosection (invasive SC)

source_name: invasive serous ovarian cancer

value: LCM from cryosection (invasive SC)


title: patient5_normal

description: LCM from cryosection (normal oviduct)


title: patient4_invasive_SC

description: LCM from cryosection (invasive SC)

value: patient 4


title: FTSC-ALI, rep1

description: gene expression of FTSC-ALI

value: air-liquid interface differentiation of human fallopian tube stem cell


title: patient6_STIC

description: LCM from cryosection (STIC)


title: patient2_STIC

description: LCM from cryosection (STIC)

value: patient 2


title: patient3_invasive_SC

description: LCM from cryosection (invasive SC)

value: patient 3


title: patient5_invasive_SC

description: LCM from cryosection (invasive SC)


title: patient4_STIC

description: LCM from cryosection (STIC)


title: patient4_normal

description: LCM from cryosection (normal oviduct)


title: FTSC, rep1

description: gene expression of FTSC


title: patient3_STIC

description: LCM from cryosection (STIC)


title: patient3_normal

description: LCM from cryosection (normal oviduct)


title: patient2_normal

description: LCM from cryosection (normal oviduct)


title: patient1_normal

description: LCM from cryosection (normal oviduct)

value: patient 1


title: patient1_invasive_SC

description: LCM from cryosection (invasive SC)


title: patient2_invasive_SC

description: LCM from cryosection (invasive SC)


title: patient1_STIC

description: LCM from cryosection (STIC)


title: HMCL-U266_180K_Agilent_PicoPlex_rep2

value: male

value: single-cell PCR-based


title: HMCL-U266_180K_Agilent_RgSC_rep1

source_name: Human Myeloma Cell Line U266 - RgSC

value: single-cell MDA-based


title: WT_HFD_3

city: Baton Rouge

first: Elizabeth

last: Floyd

state: Louisiana

address: 6400 Perkins Road

institute: Pennington Biomedical Research Center

description: wild-type

hyb_protocol: 750ng labeled RNA was hybridized to MouseRef-8 v2 BeadChip arrays (Illumina) according to manufacturer's protocol.

scan_protocol: Chips were scanned using Illumina iScan system with default settings

data_processing:
Raw data was analyzed using Illumina GenomeStudio with the Gene Expression Module v.1.0.6.  Raw data were background-subtracted and normalized using the quantile normalization method (lumi software package). Normalized data were filtered for genes with significant expression levels compared to negative control beads. GeneSifter (Perkin-Elmer) was used to select differentially expressed genes. It was performed on the basis of arbitrary thresholds for fold changes plus statistical significance.
The file  Non-normalized_data.txt is available on the series record contains background subtracted non-normalized signal data and detection p-values and exported from GenomeStudio. The file Raw_Data_with_decoder_ID.txt includes the background subtracted non-normalized signal data, NBeads and detection p-value with the gene symbol, decoder id information.

source_name: epididymal fat

label_protocol: 400ng total RNA was labeled with Epicentre TargetAmp Nano-g Biotin-aRNA Labeling Kit for Illumina system

extract_protocol: The epididymal adipose tissue was quickly removed, frozen in liquid nitrogen and stored at -80C.  Total RNA was isolated using Tri-Reagent (Molecular Research Center, Inc. Cincinnati, Ohio) with modifications to remove DNA using Qiagen RNAeasy columns.

treatment_protocol: The mice were weaned at 4 weeks of age and randomized to either a low fat (10% fat) diet (Research Diets, New Brunswick, NJ, #D12450B) or high fat (45%) diet (Research Diets, D12451).  The mice remained on these diets until 20 weeks of age.

tag: genotype

value: wildtype

value: epididymal fat

value: Male

tag: diet

value: high fat diet

tag: age

value: 20 weeks


title: WT_LFD_1

description: wild-type

value: low fat diet


title: WT_LFD_2

description: wild-type


title: scrambled control, time point 24h, replicate 1

city: Zurich

first: Beat

last: Schäfer

state: ZH

address: Balgrist Campus Lengghalde 5

department: Oncology

country: Switzerland

institute: University Childrens Hospital

description: Gene expression data from Rh4 cells transduced with scrabmbled shRNA construct after treatment with Dox for 24h

hyb_protocol: Hybridization solution was prepared according to Affymetrix´ GeneChip Expression  Analysis Technical Manual. The final concentration of cRNA is 60 ng/μl.  • Spike-in controls: pre-labelled cRNAs (Affymetrix, Cat. No. 900454) were spiked in at  defined concentrations:  o bioB: 1.5 pM  o bioC: 5 pM  o bioD: 25 pM  o cre: 100 pM  • Hybridization was performed for 16-18 hours at 45°C and 60 rpm in a rotating  hybridization oven (Hybridization Oven 640, Affymetrix).

scan_protocol: Scanning was performed with the GeneChip Scanner 3000 7G (Affymetrix), which is  controlled by Affymetrix´ software GeneChip Operating System (GCOS) v1.4.

data_processing: Data was imported in dCHIP and normalized

source_name: Rh4 cells with scrambled shRNA construct after 24h induction with Dox

label_protocol: cDNA synthesis and in vitro-transcription was done with Ambion´s Message Amp II 96  Kit (Cat. No. 1819) according to the manufacturers’ instructions, starting with 1 μg of  total RNA.

growth_protocol: Rh4 cells were grown in DMEM/10% FBS

extract_protocol: Total RNA was extracted using the RNAeasy kit including the DNAse digestion step

treatment_protocol: shRNA constructs were induced with 100 ng/ml Doxycycline

tag: tumor type

value: alveolar rhadomyosarcoma


title: shRNA 404 directed against CHD4, time point 48h

description: Gene expression data from Rh4 cells transduced with shRNA construct 404 directed against CHD4 after treatment with Dox for 48h

source_name: Rh4 cells with shRNA construct 404 directed against CHD4 after 48h induction with Dox


title: WT_LFD_3

description: wild-type


title: HMCL-U266_180K_Agilent_GenomePlex_rep2

value: standard PCR-based


title: scrambled control, time point 24h, replicate 2


title: scrambled control, time point 72h, replicate 1

description: Gene expression data from Rh4 cells transduced with scrabmbled shRNA construct after treatment with Dox for 72h

source_name: Rh4 cells with scrambled shRNA construct after 72h induction with Dox


title: scrambled control, time point 72h, replicate 2


title: HMCL-U266_180K_Agilent_RgSC_rep2


title: scrambled control, time point 48h, replicate 1

description: Gene expression data from Rh4 cells transduced with scrabmbled shRNA construct after treatment with Dox for 48h

source_name: Rh4 cells with scrambled shRNA construct after 48h induction with Dox


title: shRNA 404 directed against CHD4, time point 0

description: Gene expression data from Rh4 cells transduced with shRNA construct 404 directed against CHD4 before treatment with Dox

source_name: Rh4 cells with shRNA construct 404 directed against CHD4 before induction with Dox


title: shRNA 404 directed against CHD4, time point 24h

description: Gene expression data from Rh4 cells transduced with shRNA construct 404 directed against CHD4 after treatment with Dox for 24h

source_name: Rh4 cells with shRNA construct 404 directed against CHD4 after 24h induction with Dox


title: scrambled control, time point 48h, replicate 2


title: HMCL-U266_180K_Agilent_GenomePlex_rep1

source_name: Human Myeloma Cell Line U266 - GenomePlex

source_name: Agilent Euro Reference DNA


title: HMCL-U266_180K_Agilent_PicoPlex_rep1

source_name: Human Myeloma Cell Line U266 - PicoPlex


title: HMCL-U266_180K_Agilent_GenomiPhi_rep2

source_name: Human Myeloma Cell Line U266 - GenomiPhi

value: standard MDA-based


title: Korona 0h vs. Korona 24h: replicate 1

source_name: Leaf tissue taken from 3 plants, harvested after 24h cold exposure at 2°C (biological replicate 1)

value: Korona

source_name: Leaf tissue taken from 3 plants grown at 12°C, control sample, harvested before cold exposure (biological replica 1)


title: WT_HFD_2

description: wild-type


title: scrambled control, time point 0, replicate 2

description: Gene expression data from Rh4 cells transduced with scrabmbled shRNA construct before treatment with Dox

source_name: Rh4 cells with scrambled shRNA construct before induction with Dox


title: Stress-F1 (3)

city: Shanghai

first: Yan

last: Lu

address: 180 Fenglin Road

department: Department of Endocrinology and Metabolism

country: China

institute: Zhongshan Hospital, Fudan University

hyb_protocol: After stopping the labeling procedure, the Hy3TM-labeled samples were hybridized on the miRCURYTM LNA Array (v.18.0) (Exiqon) according to array manual. The total 25 μL mixture from Hy3TM-labeled samples with 25 μL hybridization buffer were first denatured for 2 min at 95°C, incubated on ice for 2 min and then hybridized to the microarray for 16–20 h at 56°C in a 12-Bay Hybridization Systems (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA)

scan_protocol: Following hybridization, the slides were achieved, washed several times using Wash buffer kit (Exiqon), and finally dried by centrifugation for 5 min at 400 rpm. Then the slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing: Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, significant differentially expressed miRNAs were identified through Volcano Plot filtering.  The file "normalized_data.txt" containing the normalized signal is available on the series record.

label: Hy3TM fluorescent

label_protocol: One microgram of each sample was 3'-end-labeled with Hy3TM fluorescent label, using T4 RNA ligase by the following procedure: RNA in 2.0 μL of water was combined with 1.0 μL of CIP buffer and CIP (Exiqon). The mixture was incubated for 30 min at 37°C, and was terminated by incubation for 5 min at 95°C. Then 3.0 μL of labeling buffer, 1.5 μL of fluorescent label (Hy3TM), 2.0 μL of DMSO, 2.0 μL of labeling enzyme were added into the mixture. The labeling reaction was incubated for 1 h at 16°C, and terminated by incubation for 15 min at 65°C.

growth_protocol: C57BL/6 male mice aged 8 weeks were randomly assigned to control or stress group. Control mice were left undistributed and allowed contact with each other, while stressed mice were individually subjected to 2 hr/day of immobilization stress in 50-mL conical centrifuge tube (Corning Life Sciences, Tewksbury MA, USA) for 2 weeks (between 11:00 AM and 13:00 PM). After 2-week restraint stress, mice were placed with females for 2 days. Then, males were removed, and pregnant females were left alone with a shepherd shack until their offspring were 3 weeks of age. Finally, male offspring aged 12-week were sacrificed and total RNAs were extracted from hepatic tissues.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions.

treatment_protocol: All mice were housed at 21±1°C with a humidity of 55±10% and a 12-hour light–dark cycle.

value: liver

value: 12 weeks


title: HMCL-U266_180K_Agilent_GenomiPhi_rep1


title: Stress-F1 (2)


title: HMCL-U266_180K_Agilent_RgMini_rep2

source_name: Human Myeloma Cell Line U266 - RgMini


title: HMCL-U266_180K_Agilent_RgMini_rep1


title: Xenograft_FTSC_T, rep1

description: Gene expression data from xenografted tumor

data_processing: Expression console, Partek Genome Suite 6.6

source_name: FTSC-xeno

label_protocol: 3' IVT PLUS Kit (affymetrix)

treatment_protocol: FTSC were transformed with retroviral infection of hTERT, SV40 and c-myc and then subcutaneously transplanted into highly immunocompromised NSG (NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ) mice.

tag: sample type

value: xenograft


title: scrambled control, time point 0, replicate 1


title: HMCL-U266_180K_Agilent_RgMidi_rep2

source_name: Human Myeloma Cell Line U266 - RgMidi


title: WT_HFD_1

description: wild-type

source_name: epididymal fat


title: Xenograft_FTSC_T, rep3


title: Siah2KO_LFD_1

description: global knockout of Siah2


title: Siah2KO_LFD_3

description: global knockout of Siah2


title: TrAP-transgenic_seedling 2

city: College Station

first: Claudia

middle: Marcela

last: Castillo-González

state: Texas

department: Biochemistry & Biophysics

institute: Texas A&M University

hyb_protocol: Samples were prepared and hybridized to Affymetrix ATH1 platform according to Affymetrix specifications.

scan_protocol: GeneChip hybridization and scanning were performed at the Genomics Resource Center, Rockefeller University, New York.

data_processing:
Statistical analysis of microarray data was performed using R software. Initially the microarray plates were tested for quality by an M plot and the data normalized by the RMA method from the Affy package. Subsequently, the distribution of the samples was assessed with scatter plots and the normalized data sets were evaluated with the Moderate t-test from R package limma for p-value computation. Then, the eBays method was used to compute moderated t-statistics and log-odds of differential expression by empirical Bayes shrinkage of the standard errors towards a common value.
The moderated t-statistic (t) is the logFC (Fold Change) to its standard error. In our DEG results our thresholds are P.Value < 0.05 and logFC >1 (up-regulated) or logFC < -1 (down-regulated). The False Discovery Rate was approximated from the eBayes adjusted P-value.

organism: Arabidopsis thaliana

source_name: TrAP-transgenic_seedling 2

label_protocol: One mg of total RNA was used for reverse transcription using MessageAmp II aRNA kits (Ambion) and 15 mg of labeled cRNA for hybridization

growth_protocol: 7-days old seedlings grown in MS media supplemented with 1% Sucrose, grown in 12h light/ 12h dark conditions.

extract_protocol: Total RNA was obtained using Trizol reagent following manufactorers instructions.

value: seedling

tag: ecotype


title: Siah2KO_LFD_2

description: global knockout of Siah2


title: Siah2KO_HFD_3

description: global knockout of Siah2


title: HMCL-U266_180K_Agilent_RgMidi_rep1

value: male


title: Siah2KO_HFD_2

description: global knockout of Siah2


title: Siah2KO_HFD_1

description: global knockout of Siah2


title: HMCL-U266_180K_Agilent_Control_rep2

source_name: Human Myeloma Cell Line U266 - Control

value: no WGA


title: FTSC_T, rep1

description: Gene expression data from transformed FTSC

source_name: FTSC-T

value: cell culture (c-Myc, SV40 LT and hTERT)

value: transformed FTSC


title: FTSC_T, rep2


title: Stress-F1 (1)


title: HMCL-U266_180K_Agilent_Control_rep1


title: FTSC_IM, rep1

description: Gene expression data from immortalized FTSC

source_name: FTSC-IM

value: cell culture (SV40 LT and hTERT)

value: immortalized FTSC


title: Control-F1 (3)

value: Male


title: Control-F1 (2)


title: Control-F1 (1)


title: TrAP-transgenic_seedling 1

source_name: TrAP-transgenic_seedling 1


title: Xenograft_FTSC_T, rep2


title: FTSC, rep1

description: Gene expression data from FTSC

source_name: FTSC

value: cell culture

value: FTSC


title: SCC-FAK-/-_rep2

city: Edinburgh

first: Adam

last: Byron

address: Western General Hospital, Crewe Road South

department: Edinburgh Cancer Research UK Centre

institute: University of Edinburgh

description: Gene expression data from SCC FAK-/- cells

hyb_protocol: Fragmented and labelled cDNA was hybridised to GeneChip Mouse Genome 430 2.0 Arrays (Affymetrix) for 16 h at 45 ºC with rotation at 60 rpm. Arrays were washed and stained using the Affymetrix GeneChip Fluidics Station 450 using protocol EukGE-WS2v4_450.

scan_protocol: Arrays were scanned using the Affymetrix GeneChip Scanner 3000 system with autoloader and AGCC software.

data_processing: Gene expression data were analyzed using packages within Bioconductor implemented in the R statistical programming language. The gene expression data were summarised from CEL files using Ensembl gene identifiers  (BRAINARRAY v17.0.0), ENSG and normalized using the Robust Multi-array Average (RMA) algorithm within the ‘affy’ package.

source_name: SCC FAK-/- cells

label_protocol: cDNA synthesis and amplification was performed using the Ovation Pico WTA System V2 (NuGEN Technologies) with an input of 50 ng total RNA according to manufacturer’s instructions. PolyA controls (Affymetrix, part no. 900433) were included at the same concentration as the sample. 5 µg of the cDNA was then fragmented and biotin labelled using an Encore Biotin Module kit (NuGEN) according to manufacturer’s instructions.

growth_protocol: Cells were cultured in Glasgow minimum essential medium (MEM) (Sigma) supplemented with 2 mM L-glutamine, MEM vitamins, 1 mM sodium pyruvate (all Sigma), MEM amino acids, and 10% fetal bovine serum (both Life Technologies). Cell lines re-expressing FAK-wt were maintained under selection using 0.25 mg/ml hygromycin.

extract_protocol: Total RNA extraction and on-column DNase I digestion were performed using an RNeasy kit (Qiagen) according to manufacturer's instructions.

treatment_protocol: Cells were washed three times with ice-cold phosphate-buffered saline.

tag: background strain

value: FVB

value: K14CreER FAKflox/flox

value: Squamous cell carcinoma


title: SCC-FAK-wt_rep3

description: Gene expression data from SCC FAK-wt cells

source_name: SCC FAK-wt cells


title: wilde-type_seedling_2

tag: tissue


title: SCC-FAK-/-_rep1


title: Expression in liver of control mouse line_2

city: Dummerstorf

first: Andreas

last: Hoeflich

address: Wilhelm-Stahl Allee 2

department: Genome Biology

country: Germany

institute: Leibniz Institute for Farm Animal Biology

description: Gene expression data from liver of 70 days old mouse. This mouse model has been generated by thoroughly crossbreeding 4 different outbred (NMRI orig., Han:NMRI, CFW, CF1) and 4 different inbred mouse lines (CBA/Bln, AB/Bln, C57BL/Bln, XVII/Bln) about 40 years ago, thus it is a 'non-inbred' strain. An algorithm is used for mouse breeding to avoid inbreeding.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 42 C on Affymetrix GeneChip Murine Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scanning using the GeneChip scanner 3000 were performed according to Affymetrix protocols

data_processing: Data were analysed with Affymetrix GCOS 1.1.1 software using global scaling to a target signal of 500.

source_name: liver

label_protocol: biotin-labeled cRNAs were prepared according to the standard Affymetrix protocol from 5 µg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was isolated using TRI Reagent (Sigma, Taufkirchen, Germany) according to the manufacturer’s protocol. After DNaseI treatment the RNA was cleaned up using the RNeasy Kit (Qiagen, Hilden, Germany).

value: 70 days

value: DUC

tag: strain selection criteria

value: control line


title: Expression in liver of control mouse line_3

value: liver

tag: strain


title: Expression in liver of high treadmill performance mouse line_3

value: DUhTP

value: long term selection of high treadmill performance


title: WT ovary  eCG

city: Nankoku

first: Katsumi

last: Toda

state: Kochi

address: Oko-cho, Kohasu

country: Japan

institute: Kochi University, School of Medicine

hyb_protocol: Hybridization was done according to manufacturer's instructions, with Affymetrix® GeneChip® Hybridization Oven 640, Affymetrix® GeneChip® Fluidics Station 450

scan_protocol: Affymetrix® GeneChip® Scanner 3000 7G System

data_processing: Affymetrix® GeneChip® Command Console® Software ver. 3.2, Affymetrix® Expression ConsoleTM Softwere ver.1.3.0, RMA-Sketch (RMA-Gene-Default)

source_name: Wil type ovary 4 hours after s.c. injection of 5 IP eCG

label_protocol: With 100 ng total RNA, RNA was labeled with  Affymetrix GeneChip® WT PLUS Reagent Kit (Part# 902280)

growth_protocol: Mice were given water and rodent chow (CE-2; Oriental Yeast Ltd., Tokyo, Japan).

extract_protocol: Total ovarian RNAs were prepared individually using NucleoSpin® RNAII (Macherey-Nagel GmbH & Co., Düren, Germany) according to the manufacturer's instructions.

treatment_protocol: WT mice were injected intraperitoneally (ip) with 5 international units (IU) of eCG (Serotropin®; ASKA Pharmaceutical Co., Ltd., Tokyo, Japan).  ArKO mice received subcutaneous injection of E2 (Sigma-Aldrich Corp., Tokyo, Japan) (18 mg/kg body weight), which was dissolved in sesame oil (Nacalai Tesque, Kyoto, Japan) at a concentration of 1.87 mg/ml, on day 1 of the experimental schedule.  The mice were then injected with E2 and 5 IU or 25 IU of eCG on day 4.   Mice were injected between 1400 and 1600 on the day.  To investigate mRNA expression, the ovaries were collected without treatment or 4 h after the treatments, soaked in RNAlater® (Ambion Inc., Austin, TX) and stored at -20 ºC until use.

value: ovary at 4 weeks of age


title: Expression in liver of control mouse line_1


title: SCC-FAK-wt_rep2


title: KO ovary control

source_name: Estrogen deficient ovary without treatment


title: WT ovary control

source_name: Wild type ovary without treatment


title: Expression in liver of high treadmill performance mouse line_1


title: wilde-type_seedling_1

value: seedling


title: HMCL-U266_44K_Agilent_RgMidi_rep2

value: male

value: standard MDA-based

source_name: Agilent Euro Reference DNA


title: Expression in liver of high treadmill performance mouse line_2


title: FTSC, rep2

description: Gene expression data from FTSC


title: HMCL-U266_44K_Agilent_RgMidi_rep1


title: KO ovary E2

source_name: Estrogen-deficient ovary 4 hours after s.c injection of 17b-estradiol at 18 mg/kg.


title: SCC-FAK-wt_rep1


title: Skin_Ichthyosis

city: Bogota

first: Oscar

middle: Javier

last: Ortega

state: Cundinamarca

address: Carrera 24 N° 63C-69

country: Colombia

institute: Universidad del Rosario

description: Gene expression data from skin affected by Ichthyosis Curth-Macklin

hyb_protocol: Affymetrix PrimeView arrays were hybridized with 8 g of labeled dsDNA, washed, stained and scanned according to the protocol described in GeneChip® 3’ IVT Express Kit User Manual

scan_protocol: Scanning was done on an Affymetrix  GeneChip Scanner 3000

data_processing: The data were analyzed with GeneSpring (RMA) using Agilent default analysis settings. In addition, 75th percentile shift was used to normalize data to gene level expression.

label_protocol: cDNA library synthesized from 100ng total RNA were amplified using the TransPlex® Complete Whole Transcriptome Amplification Kit (Sigma; reference WTA2) and subsequently labeled using GeneChip Mapping 250K Nsp Assay Kit (Affymetrix; catalog # 900766), according to manufacturer's instructions.

extract_protocol: Skin biopsies from patient and healthy controls were obtained and total RNA was extracted using  PureLink RNA Mini Kit (Life technologies) according to the manufacturer. Whole transcriptome amplification was performed from 100 ng of total RNA. cDNA library preparation and amplification were performed following the distributor’s (Sigma-Aldrich) recommendations for WTA2.

value: Female

tag: disease

value: Ichthyosis Curtha-Macklin


title: SCC-FAK-/-_rep3


title: shRNA 404 directed against CHD4, time point 72h

description: Gene expression data from Rh4 cells transduced with shRNA construct 404 directed against CHD4 after treatment with Dox for 72h

source_name: Rh4 cells with shRNA construct 404 directed against CHD4 after 72h induction with Dox

value: alveolar rhadomyosarcoma


title: Skin_Control_2

description: Gene expression data from normal skin

value: normal, control


title: Skin_Control_1

description: Gene expression data from normal skin

value: Male


title: FTSC_IM, rep2

value: cell culture (SV40 LT and hTERT)

value: immortalized FTSC


title: Skin_Control_3

description: Gene expression data from normal skin


title: AGO_2 (gene)

status: Public on Sep 28 2015

city: St. Louis

first: Jinsheng

last: Yu

state: MO

address: 660 S. Euclid Ave.

department: Genetics

institute: Washington University School of Medicine

hyb_protocol: Labeled cDNAs were hybridized onto Affymetrix Human Transcriptome Arrays v2.0 (HTA2.0) following Affymetrix standard protocols.

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

data_processing: Raw data were processed with the Expression Console (Affymetrix) for background correction and normalization, and both probeset (exon) and gene (transcript cluster) level data were generated.

source_name: Original Agilent Human Universal Reference RNA

label_protocol: 100 ng of starting RNAs were amplified with Ambion WT-plus amplification kit and 5,000 ng of biotin-labeled cDNAs were hybridized.

extract_protocol: Samples used in the study are commercially available RNAs derived from mixture of multiple cell lines and RNAs extracted from patient bone marrow specimens

value: pure reference RNA (AGO)


title: AGO_1 (gene)


title: D5.1G4_melanoma_rep1

city: Hampden-Sydney

first: Kristian

middle: Michael

last: Hargadon

state: VA

address: Brown Student Center, Box 837

department: Biology

institute: Hampden-Sydney College

description: Gene expression after 24 hours of culture in normal growth media

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60° C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide (Agilent Mouse 4x44K Gene Expression Microarray v2 [Agilent Design ID 026655]). The slides were incubated for 17 hours at 65° C in an Agilent Hybridization Oven. The hybridized arrays were washed and fixed prior to scanning.

scan_protocol: Slides were scanned on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5 um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze the acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v12.1 software (Agilent Technologies). After quantile normalization of the raw data, genes that at least 3 out of 6 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis. Differentially expressed genes with statistical significance were identified through Volcano Plot filtering. Hierarchical Clustering was performed using R. GO analysis and Pathway analysis were performed in the standard enrichment computation method.

source_name: D5.1G4 melanoma cell line, replicate 1

label_protocol: Sample labeling was performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology). Briefly, total RNA from each sample was linearly amplified and labeled with Cy3-UTP. The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured using a NanoDrop ND-1000.

growth_protocol: 1e6 B16-F1 or D5.1G4 melanoma cells in normal growth media (RPMI-1640 supplemented with 10% FBS) were seeded into 6-well tissue culture plates and grown for 24 hours at 37° C in 5% CO2.

extract_protocol: After 24 hours of culture, B16-F1 and D5.1G4 melanoma cells were collected by cell scraping and centrifuged at 1,500 rpm for 5 minutes.  Cell pellets were lysed with Buffer RLT containing b-ME, and RNA was extracted using an RNeasy Mini Kit (Qiagen, Valencia, CA) according to the manufacturer's recommendations.  Following RNA extraction, samples were treated with Amplification Grade DNase I (Life Technologies, Grand Island, NY)  to digest any residual DNA, and RNA was quantified using an Epoch Spectrophotometer (BioTek, Winooski, VT).  A260/280 ratios for all samples were > 2.0.  RNA samples were diluted to 100 ng/ml, and ~5 mg of RNA was shipped overnight on dry ice to Arraystar, Inc. (Rockville, MD) for analysis using the company's gene expression service.  RNA integrity was assessed by standard denaturing agarose gel electrophoresis

tag: cell line

value: melanoma

tag: cell culture confluence


title: BMO_2 (gene)

source_name: Original Bone Marrow RNA

value: pure bone marrow RNA (BMO)


title: B16-F1_melanoma_rep3

source_name: B16-F1 melanoma cell line, replicate 3


title: BMO_1 (gene)


title: D5.1G4_melanoma_rep3

source_name: D5.1G4 melanoma cell line, replicate 3


title: AG1BM64_2 (gene)

source_name: Mixed RNA of both (1:64)

value: 1:64 mixture of AGO and BMO


title: AG1BM64_1 (gene)


title: AG1BM4_1 (gene)

source_name: Mixed RNA of both (1:4)

value: 1:4 mixture of AGO and BMO


title: B16-F1_melanoma_rep2

source_name: B16-F1 melanoma cell line, replicate 2


title: AG1BM4_2 (gene)


title: AG1BM16_1 (gene)

source_name: Mixed RNA of both (1:16)

value: 1:16 mixture of AGO and BMO


title: B16-F1_melanoma_rep1

source_name: B16-F1 melanoma cell line, replicate 1


title: AG1BM16_2 (gene)


title: D5.1G4_melanoma_rep2

source_name: D5.1G4 melanoma cell line, replicate 2


title: GFP_1

city: Huddinge

first: Karin

last: Dahlman-Wright

address: Blickagången 16

department: Department of Biosciences and Nutrition

country: Sweden

institute: Karolinska Institutet

hyb_protocol: Hybridization to Human Gene 1.1 ST array plates was carried out overnight with biotin-labeled cRNA according to the Affymetrix protocol.

scan_protocol: Array plates were scanned using a GeneTitan scanner.

data_processing: Preprocessing in Affymetrix Expression Console (v. 1.1) using the following methods: Summarization: PLIER, Background Correction: PM-GCBG, Normalization: Global Median.

source_name: GFP control

label_protocol: Total RNA was converted to sense strand cDNA using Ambion WT Expression kit. For fragmentation and labeling WT GeneChip WT target Labeling kit was used.

growth_protocol: Mouse primary hepatocytes were isolated by collagenase perfusion and percoll gradient purification. Cells were seeded on collagen-coated 6-well plates at a density of 450,000 cells/well and maintained in DMEM 4.5 g/L glucose, supplemented with 0.2% BSA, 2 mM sodium pyruvate, 0.1 μM dexamethasone, and 1 nM insulin (maintenance media).

extract_protocol: Total RNA was extracted using Isol reagent, followed by an additional purification using NucleoSpin RNA Kit (Macherey-Nagel). RNA was quantified using a NanoDrop-1000 spectrophotometer and RNA quality was monitored using an Experion Automated Electrophoresis System (Bio-Rad).

treatment_protocol: Cells were transduced overnight in maintenance with adenoviruses expressing GFP alone or together with each FXR isoform. Following transduction, cells were incubated for additional 24 h in maintenance media lacking dexamethasone and insulin, and processed for RNA extraction 36 h post-transduction.

tag: strain background

tag: gender

value: liver

value: Primary hepatocytes

tag: transduced with

value: adenoviruses expressing GFP control

tag: time point

value: 36 h post-transduction


title: GFP_2

value: male

tag: cell type


title: FXRα4_2

source_name: FXRα4 isoform

value: adenoviruses expressing FXRα4 isoform


title: GFP_3


title: FXRα2_3

source_name: FXRα2 isoform

value: adenoviruses expressing FXRα2 isoform


title: FXRα3_3

source_name: FXRα3 isoform

value: adenoviruses expressing FXRα3 isoform


title: FXRα4_3


title: AG1BM64_1 (exon)

hyb_protocol: Labeled cDNAs were hybridized onto Affymetrix Human Gene 1.0 ST Arrays (Gene1.0) following Affymetrix standard protocols.

label_protocol: 50 ng of starting RNAs were amplified with NuGEN Ovation PicoSL WTA V2 kit and 2,500 ng of biotin-labeled cDNAs were hybridized.


title: FXRα3_2


title: FXRα3_1


title: FXRα2_2


title: FXRα2_1


title: FXRα1_3

source_name: FXRα1 isoform

value: adenoviruses expressing FXRα1 isoform


title: FXRα4_1


title: AG1BM64_2 (exon)


title: AG1BM4_1 (exon)


title: AG1BM16_2 (exon)


title: FXRα1_2


title: AG1BM16_1 (exon)


title: FXRα1_1


title: AG1BM4_2 (exon)


title: AG1BM4_rep3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
The image-derived data were processed with Illumina GenomeStudio
Data values are background subtracted and quantile normalized in linear scale for Matrix normalized and are background retained and non-normalized in linear scale for Matrix non-normalized.

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


title: AG1BM16_rep1


title: AG1BM64_rep1


title: AG1BM4_rep2


title: BMO_rep1


title: AGO_1 (exon)


title: AG1BM16_rep2


title: BMO_rep3


title: AG1BM64_rep2


title: AG1BM4_rep1


title: BMO_rep2


title: AGO_2 (exon)


title: BMO_1 (exon)


title: AG1BM4_2

hyb_protocol: 2,000 ng of cy5-labeled aRNA were hybridized following Agilent standard hybridization protocol.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 4x44k array slides.

data_processing:
The scanned images were analyzed with Feature Extraction Software 11.5 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
Data values in Matrix sheet are Feature Extraction generated rProcessedSignal in linear scale without normalization (control probes are removed from the matrix table, so the total data lines are 43376).

label_protocol: 200 ng of starting RNAs were amplified with MessageAmp™ II aRNA Amplification Kit, 3,000 ng of amplified aRNA were labeled with Kreatech ULS™ Fluorescent Labeling Kit (with Cy5).


title: AGO_rep1


title: AG1BM64_2


title: BMO_2 (exon)


title: AG1BM64_1


title: BMO


title: wild-type unstimulated  [17_2155I]

city: Boston

first: Fei

last: Ji

address: 185 Cambridge St

institute: Massachusetts General Hospital

hyb_protocol: 90 μl of cDNA were hybridized for 16 hr at 45⁰C on GeneChip Mouse 1.0 ST Array in an Affymetrix GeneChip Hybridization oven 645

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G running Affymetrix Gene Command Console ver 3.2

data_processing:
The data were normalized using the Robust Multichip Average summary program RMAexpress (Pubmed ID: 12538238)
Differentially expressed genes were identified using the mercury linear fit model

source_name: wild-type unstimulated

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA using amplification kit WT Plus, followed by labeling of 5.5 μg cDNA

growth_protocol: 4x106 wild-type B6 and Toll-like receptor 9 knockout (TLR9KO) immortalized murine macrophages were plated onto 10 cm cell culture dishes. The cells were placed in the 5% CO2 incubator at 37⁰C

extract_protocol: Total RNA was extracted using RNA easy mini kit

treatment_protocol: Cells were stimulated either with β-1,3 glucan beads at MOI of 20:1 for 4 hr or unstimulated

value: immortalized murine macrophages

tag: genotype/variation

value: wild-type


title: wild-type B6 bead stimulated [12_2155D]

source_name: wild-type B6 bead stimulated


title: wild-type unstimulated  [16_2155H]


title: AG1BM16_2


title: AGO_rep2

source_name: Original Agilent Human Universal Reference RNA

value: pure reference RNA (AGO)


title: AG1BM4_1


title: AGO


title: AG1BM16_1


title: TLR9KO Unstimulated [9_2155R]

source_name: TLR9KO Unstimulated


title: wild-type B6 bead stimulated [10_2155B]


title: wild-type B6 bead stimulated [11_2155C]


title: wild-type unstimulated  [18_2155J]


title: TLR9KO Unstimulated [7_2155P]


title: AG1BM64_2 (gene)


title: AG1BM64_1 (gene)


title: TLR9KO bead stimulated [2_2155K]

source_name: TLR9KO bead stimulated


title: AG1BM4_2 (exon)


title: TLR9KO bead stimulated [1_2155A]


title: Mock-treated neurosphere, bio rep 1

city: Columbus

first: Richard

last: Price

state: Ohio

address: 410 W 12th Ave

institute: The Ohio State University

hyb_protocol: 15ug of labeled and fragmented cRNA was hybridized at 45C for 16 hours at 60rpm. GeneChips were then washed and stained on the Affymetrix Fluidics Station 450 according to the manufacturer’s protocol.

scan_protocol: GeneChips were scanned with the Affymetrix GeneChip Scanner 3000 7G.  Data files were generated and processed with Affymetrix AGCC software and Expression Console.

data_processing: The data were analyzed through Bioconductor package, RMA method was used as the background-correction and normalization.

source_name: Mock-treated neurospheres from 4 week old Mut3 mouse

label_protocol: 2ug RNA was used to generate biotinylated-cRNA according to the manufacturer’s protocol in the Affymetrix GeneChip® Expression Analysis Technical Manual.

growth_protocol: The subventricular zone from 4-week-old mice were harvested into a single cell suspension.  These cells were grown in serum free media until they formed spheres.  Neurospheres were then passaged after reaching 100-200 microns.  Neurospheres were passaged 4-5 times before total RNA was harvested.

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

treatment_protocol: Mice were treated with MCMV at perinatal day 2 or Mock-treated (PBS).

tag: infection

tag: age

value: 4 week old

value: neurospheres


title: AGO_2 (gene)

tag: sample type


title: AG1BM16_1 (gene)


title: AG1BM16_2 (gene)


title: BMO_2 (gene)

source_name: Original Bone Marrow RNA

value: pure bone marrow RNA (BMO)


title: AG1BM4_2 (gene)

source_name: Mixed RNA of both (1:4)

value: 1:4 mixture of AGO and BMO


title: AG1BM64_2 (exon)

source_name: Mixed RNA of both (1:64)

value: 1:64 mixture of AGO and BMO


title: differentiated embryoid body, Control (wild type, CD1) mice, Day 11, 9

status: Public on Sep 27 2015

city: Rochester

first: XING

last: LI

state: MN

address: 200 1st street SW

department: Health Sciences Research

institute: Mayo Clinic

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Mouse Genome 430 2.0 Arrays. 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 were analyzed with R/Bioconductor using RMA.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA.

growth_protocol: The study samples consisted of iPSCs (D0) reprogrammed from tail-tip fibroblasts of adult male wild type CD1 and Nos3-/- mice and differentiated embryoid bodies (D11).

extract_protocol: Qiagen RNeasy kit.

treatment_protocol: iPSCs were generated via Sendai viral reprogramming of CD1 and Nos3-/- tail-tip fibroblasts. Cells were cultured on inactive MEF feeders in the pluripotent state and spontaneously differentiated via aggrewell-mediated EB formation to D11.

value: differentiated embryoid body

value: wild type

value: Day 11


title: AGO_1 (gene)


title: MCMV-treated neurosphere, bio rep 2

source_name: MCMV-treated neurospheres from 4 week old Mut3 mouse

value: murine cytomegalovirus


title: AG1BM16_1 (exon)

source_name: Mixed RNA of both (1:16)

value: 1:16 mixture of AGO and BMO


title: Mock-treated neurosphere, bio rep 2


title: AGO_2 (exon)


title: AG1BM4_1 (gene)


title: differentiated embryoid body, Control (wild type, CD1) mice, Day 11, 8


title: differentiated embryoid body, Control (wild type, CD1) mice, Day 11, 5


title: MCMV-treated neurosphere, bio rep 1


title: AG1BM64_1 (exon)


title: Mock-treated neurosphere, bio rep 3


title: BMO_1 (exon)


title: BMO_2 (exon)


title: AG1BM4_1 (exon)


title: AGO_1 (exon)


title: differentiated embryoid body, Nos3-/- mice, Day 11, 4


title: MCMV-treated neurosphere, bio rep 3


title: differentiated embryoid body, Control (wild type, CD1) mice, Day 11, 4


title: differentiated embryoid body, Control (wild type, CD1) mice, Day 11, 2


title: differentiated embryoid body, Nos3-/- mice, Day 11, 2


title: differentiated embryoid body, Control (wild type, CD1) mice, Day 11, 6


title: differentiated embryoid body, Nos3-/- mice, Day 11, 5


title: differentiated embryoid body, Nos3-/- mice, Day 11, 3


title: differentiated embryoid body, Control (wild type, CD1) mice, Day 11, 1


title: differentiated embryoid body, Nos3-/- mice, Day 11, 6


title: iPSCs,control (wild type CD1) mice, Day 0, 6

value: iPSCs

value: Day 0


title: AG1BM16_2 (exon)


title: differentiated embryoid body, Control (wild type, CD1) mice, Day 11, 7


title: iPSCs,control (wild type CD1) mice, Day 0, 10


title: iPSCs,control (wild type CD1) mice, Day 0, 8


title: iPSCs,control (wild type CD1) mice, Day 0, 4


title: iPSCs,control (wild type CD1) mice, Day 0, 7


title: differentiated embryoid body, Control (wild type, CD1) mice, Day 11, 3


title: iPSCs,control (wild type CD1) mice, Day 0, 1


title: iPSCs,control (wild type CD1) mice, Day 0, 2


title: iPSCs,control (wild type CD1) mice, Day 0, 3


title: iPSCs,control (wild type CD1) mice, Day 0, 9


title: iPSCs, Nos3-/- mice, Day 0, 5

description: iPSCs, Nos3-/- mice, Day 0

source_name: iPSCs, Nos3-/- mice, Day 0


title: iPSCs,control (wild type CD1) mice, Day 0, 5


title: differentiated embryoid body, Nos3-/- mice, Day 11, 1


title: iPSCs, Nos3-/- mice, Day 0, 4

description: iPSCs, Nos3-/- mice, Day 0


title: iPSCs, Nos3-/- mice, Day 0, 3

description: iPSCs, Nos3-/- mice, Day 0


title: Nos3-/- mice, right ventricle, 2

description: right ventricle, Nos3-/-

source_name: E14.5 right ventricle heart tissues from Nos3-/- mice

growth_protocol: The study samples consisted of heart tissues (left ventricle and right ventricle) collected from wild type CD1 and Nos3-/- mice at embryonic day 14.5.

treatment_protocol: Left ventricle and right ventricle tissues were collect at E14.5, washed with sterile PBS, and pooled into triplicate samples on ice. Samples were then flash-frozen in liquid nitrogen and stored at -80 degrees Celsius until RNA harvest.

value: right ventricle heart tissue


title: iPSCs, Nos3-/- mice, Day 0, 6

description: iPSCs, Nos3-/- mice, Day 0


title: Wild type CD1 mice, left ventricle, 3

description: left ventricle, CD1

source_name: E14.5 Left ventricle heart tissues from CD1 mice

value: Left ventricle heart tissue


title: Wild type CD1 mice, right ventricle, 3

description: right ventricle, CD1

source_name: E14.5 right ventricle heart tissues from CD1 mice


title: Wild type CD1 mice, right ventricle, 1

description: right ventricle, CD1


title: Wild type CD1 mice, left ventricle, 2

description: left ventricle, CD1


title: BMO_1 (gene)


title: Wild type CD1 mice, right ventricle, 2

description: right ventricle, CD1


title: Nos3-/- mice, left ventricle, 1

description: left ventricle, Nos3-/-

source_name: E14.5 Left ventricle heart tissues from Nos3-/- mice


title: Nos3-/- mice, left ventricle, 2

description: left ventricle, Nos3-/-


title: Nos3-/- mice, left ventricle, 3

description: left ventricle, Nos3-/-


title: iPSCs, Nos3-/- mice, Day 0, 2

description: iPSCs, Nos3-/- mice, Day 0


title: iPSCs, Nos3-/- mice, Day 0, 1

description: iPSCs, Nos3-/- mice, Day 0


title: Nos3-/- mice, right ventricle, 1

description: right ventricle, Nos3-/-


title: Wild type CD1 mice, left ventricle, 1

description: left ventricle, CD1


title: luh over WT replicate 1

city: Daejeon

first: Nayoung

last: Lee

address: 291 Daehak-ro

department: Biological sciences

country: South Korea

institute: KAIST

description: Biological replicate 1 of 3

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: Background correction was performed using the normexp method in LIMMA and intensity data were normalized using LOWESS method

source_name: luh mutant

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. Briefly, each 25ng total RNA was and T7 promoter primer mix and incubated at 65 ℃ for 10min. cDNA master mix (5X First strand buffer, 0.1M DTT, 10mM dNTP mix, RNase-Out, and MMLV-RT) was prepared and added to the reaction mixer. The samples were incubated at 40 ℃ for 2 hours and then the RT and dsDNA synthesis was terminated by incubating at 65 ℃ for 15min.   The transcription master mix was prepared as the manufacturer’s protocol (4X Transcription buffer, 0.1M DTT, NTP mix, 50% PEG, RNase-Out, Inorganic pyrophosphatase, T7-RNA polymerase, and Cyanine 3/5-CTP). Transcription of dsDNA was preformed by adding the transcription master mix to the dsDNA reaction samples and incubating at 40 ℃ for 2 hours. Amplified and labeled cRNA was purified on RNase mini column (Qiagen) according to the manufacturer’s protocol. Labeled cRNA target was quantified using ND-1000 spectrophotometer (NanoDrop Technologies, Inc., Wilmington, DE).

extract_protocol: Total RNAs were isolated from seeds using Spectrum Plant Total RNA Kit (Sigma, www.sigma-aldrich.com), according to the manufacturer's protocol.

treatment_protocol: Seeds were surface sterilized, plated on Murashige and Skoog (MS) medium containing 0.6% phytoagar without sucrose, and imbibed for 1 hr at 22º C. The plates were irradiated with far-red light (2.59 μmol∙m−2∙s−1) for 5 min (phyBoff) and then incubated for 12hr in the dark.

value: seeds

value: luh mutant

source_name: wild type (Col-0)

tag: ecotype


title: luh over WT replicate 3

description: Biological replicate 3 of 3


title: Nos3-/- mice, right ventricle, 3

description: right ventricle, Nos3-/-


title: AcN-Lot1-Rep7

status: Public on Sep 26 2015

city: Cambridge

first: Jay

middle: Lawrence

last: Duffner

state: MA

address: 675 West Kendall St.

department: Research

institute: Momenta Pharmaceuticals

description: A glatiramoid related to, but chemically distinct from Copaxone.

hyb_protocol: Hybridization was performed on the Tecan HS Pro 4800 insturment.  Following a pre-wash with Oligo aCGH hybridization buffer at 65°C, labelled RNA was loaded into the hybridization chambers and incubated at 65°C under agitation for 17 hours.  Slides were twice washed at 23°C with Agilent Gene Expression Wash Buffer 1 and twice washed at 37°C Agilent Gene Expression Wash Buffer 2.  Slides were dried with nitrogen and kept in a low ozone environment until scanning.

scan_protocol: Slides were scanned in an Axon GenePix 4000B scanner at a power of 100%, gain of 547 at 5µm resolution.

data_processing: The gene array list (GAL) file was fit to the slide images in the GenePix Pro software (Axon Instruments Inc). Fluorescence foreground and background were extracted for each spot. Fluorescence data was processed in the R programming environment using functions from the limma package.  Log2-transformed intensiites were background-corrected using the normexp method with an offset of 8.  Background corrected values were normalized using the quantile normalization method.

source_name: AcN control

label_protocol: Sample RNA was first normalized to obtain 99 ng per reaction and then mixed with a spike-in control (5188-5282; Agilent Technologies). Cy3-labeled cRNA was then generated by in vitro transcription using the Agilent Low Input Quick Amp one color labeling kit (5190-2305).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-8000 Spectrophotometer. The concentration was adjusted to 1.65 µg per slide. cRNA, blocking agent and fragmentation buffer were mixed and the mixture was fragmented at 60°C for 30 minutes.  The fragmentation reaction was quenched with GEx Hybridization Buffer (Agilent) and samples were put on ice until they were introduced into the slide hybridization chambers.

growth_protocol: Female Balb.c mice (8-12 weeks old) mice were immunized with Copaxone 250 µg (lot 538455), and lymph nodes were harvested. CD4+ T cells were isolated from the lymph nodes using negative immunomagnetic isolation (EasySep Mouse CD4+ T Cell Isolation Kit, Stem Cell Technologies, Vancouver, BC, Canada). Splenocytes were isolated from naive (nonimmunized) mouse spleens depleted of T cells using positive immunomagnetic isolation. APCs were treated with mitomycin C 50 µg/mL (Calbiochem, EMD Millipore, Billerica, MA, USA) for 25 minutes at 37°C to prevent a proliferative response from residual T cells.  CD4+ T cells were rechallenged ex vivo for 3 to 4 days with Copaxone 20 µg/mL presented using the mitomycin C–treated splenocytes as APCs followed by a period of maintenance for 10 days in the presence of 20 ng/mL murine interleukin-2 (mIL-2; PeproTech, Rocky Hill, NJ, USA). The process of Copaxone restimulation and cell expansion followed by maintenance was repeated for 13 rounds using 20% conditioned media from the cells and mIL-2 as just described; this led to production of a Th2-polarized nonclonal T-cell population.

extract_protocol: RNA processing was performed by blinded operators distinct from those involved in the in vitro stimulation step described in the previous section, and was performed at the same time to minimize the introduction of bias resulting from sample processing. Lysates were thawed and passed through a QiaShredder (Qiagen Inc, Valencia, CA, USA) column. RNA was extracted using the RNEasy standard protocol on the QIACube (Qiagen Inc) instrument. RNA was eluted in 50 µL RNAse/DNAse free water. RNA concentration was measured by absorbance at 260nm, and integrity was measured by Bioanalyzer Nano chip (Agilent Technologies, Wilmington, DE, USA). Only RNAs of acceptable quality (28S/18S ratio close to 2) were subsequently processed.

treatment_protocol: All samples were tested on the same day to minimize the introduction of bias resulting from sample processing. First, APC 0.5 mL (naive Balb/C splenocytes, ReachBio LLC, Seattle, WA, USA) cell suspension (10 X 10^6 cell/mL) was added to each well of a 24-well plate, followed by Th2-455 cell suspension 0.5 mL (2 X 10^6 cell/mL). Then 10 µL media or test article was added for a final concentration of 20 μg/mL. The plates were incubated for 24 hours at 37°C in a 5% CO2 incubator. All cells, both in suspension and adherent, were harvested and spun at 800g at 4°C for 5 minutes. The conditioned media were removed, and 0.35 mL RLT lysis buffer was immediately added to the cell pellet that was then solubilized and frozen at –80°C until RNA purification.

tag: lot

tag: treatment

value: AcN control

value: CD4+ T cell


title: Copaxone-Lot5-Rep2

description: Brand version of glatiramer acetate.

source_name: Copaxone

value: Copaxone


title: embryo treated with SiNPs+B[a]P, biological rep3

city: Beijing

first: Junchao

last: Duan

address: Xi Tou Tiao 10, You An Men street, FengTai, Beijing,100069, China

department: School of Public Health

institute: Capital Medical University

description: 4-3_(ZebGene-1_0-st).rma-gene-full-Signal

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

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000 7G.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Danio rerio

source_name: embryo treated with SiNPs+B[a]P

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

growth_protocol: 2dpf embryos treated with SiNPs, B[a]P, and SiNPs+B[a]P, respectively for 24 h

treatment_protocol: Zebrafish embryos were anesthetized with 0.03% tricaine at 2 dpf. The different concentrations of SiNPs, B[a]P, and SiNPs+B[a]P were loaded into borosilicate pulled glass capillary needlesby an electrode puller, respectively. The injections were performed using a Microinjector. The samples were injected at the ventral end of the Duct of Cuvier under a stereomicroscope and the pulse time was controlled to deliver 10 nL.

value: Ablino embryos

tag: tissue

value: Whole-embryos

tag: developmental stage

tag: treated with

value: SiNPs+B[a]P for 2dpf-3dpf


title: AcN-Lot1-Rep6


title: luh over WT replicate 2

description: Biological replicate 2 of 3


title: AcN-Lot1-Rep8


title: Glatopa-Lot4-Rep4

description: Generic version of glatiramer acetate.

source_name: Glatopa

value: Glatopa


title: Glatopa-Lot2-Rep4

description: Generic version of glatiramer acetate.


title: Glatopa-Lot3-Rep4

description: Generic version of glatiramer acetate.


title: embryo treated with B[a]P, biological rep3

description: 3-3_(ZebGene-1_0-st).rma-gene-full-Signal

source_name: embryo treated with B[a]P

tag: strain

value: B[a]P for 2dpf-3dpf


title: embryo treated with SiNPs+B[a]P, biological rep2

description: 4-2_(ZebGene-1_0-st).rma-gene-full-Signal


title: Copaxone-Lot7-Rep2

description: Brand version of glatiramer acetate.


title: Copaxone-Lot3-Rep2

description: Brand version of glatiramer acetate.


title: Copaxone-Lot6-Rep2

description: Brand version of glatiramer acetate.


title: Copaxone-Lot4-Rep2

description: Brand version of glatiramer acetate.


title: Copaxone-Lot1-Rep2

description: Brand version of glatiramer acetate.


title: embryo treated with SiNPs, biological rep3

description: 2-3_(ZebGene-1_0-st).rma-gene-full-Signal

source_name: embryo treated with SiNPs

value: SiNPs for 2dpf-3dpf


title: embryo treated with B[a]P, biological rep2

description: 3-2_(ZebGene-1_0-st).rma-gene-full-Signal


title: Glatopa-Lot1-Rep4

description: Generic version of glatiramer acetate.


title: Copaxone-Lot9-Rep2

description: Brand version of glatiramer acetate.


title: embryo treated with SiNPs+B[a]P, biological rep1

description: 4-1_(ZebGene-1_0-st).rma-gene-full-Signal


title: embryo treated with B[a]P, biological rep1

description: 3-1_(ZebGene-1_0-st).rma-gene-full-Signal


title: Glatopa-Lot3-Rep3

description: Generic version of glatiramer acetate.


title: Media-Lot1-Rep7

description: Media with mannitol.

source_name: Media

value: Media


title: Copaxone-Lot2-Rep2

description: Brand version of glatiramer acetate.


title: Media-Lot1-Rep6

description: Media with mannitol.


title: root_100d_after_transplantation

city: Guiyan

first: Ruiyuan

last: Li

state: Guizhou

address: No. 116 Baoshanbei Road, Yuanyan District;

institute: Guizhou Normal University

description: root from 5 individual plants were mixed and used to extract total RNA

hyb_protocol: Double-stranded cDNA were synthesized using SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen) with oligo (dT) primers following the manufacturer's protocol, except that the synthesis step was extended to 16 h.

scan_protocol: Scanning was performed by Roche-NimbleGen MS200 (NimbleGen Systems Inc., Madison, WI USA),  NimbleScan 2.6.0.0 was used to extract the signal intensity and stored in files with .pair extention, all the performance were follow the standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.5 (Roche NimbleGen, Inc.). The expression level for each gene was calculated as the ratio of Cy5 and Cy3 after normalized using RMA method.

organism: Nicotiana tabacum

source_name: root, 100d after transplantation

label_protocol: NimbleGen performed Cy-3 and Cy-5 labeling and hybridization steps using standard procedures.

growth_protocol: under normal conditions for tobacco production

extract_protocol: Total RNA were extracted using plant RNA purification reagent (Qiagen) and treated with DNase I (Takara) to remove any DNA contamination according to the manufacturer’s protocols

treatment_protocol: The leaf, stem, root or flower from 5 individual plants were mixed for each sample and were collected as follows: the leaves, stems and roots were harvested at 0, 20, 40, 60, 70 and 100 days after transplantation, and the flowers (F) were harvested at 0, 5 and 10 days after anthesis

tag: germplasm

value: root

source_name: reference RNA mixture of all RNA samples

value: mixture of leaf, stem, root and flower


title: Glatopa-Lot1-Rep3

description: Generic version of glatiramer acetate.


title: embryo treated with SiNPs, biological rep2

description: 2-2_(ZebGene-1_0-st).rma-gene-full-Signal


title: embryo as control, biological rep2

description: 1-2_(ZebGene-1_0-st).rma-gene-full-Signal

source_name: embryo as control

value: none (control) for 2dpf-3dpf


title: Glatopa-Lot4-Rep3

description: Generic version of glatiramer acetate.


title: embryo as control, biological rep3

description: 1-3_(ZebGene-1_0-st).rma-gene-full-Signal


title: Glatopa-Lot2-Rep3

description: Generic version of glatiramer acetate.


title: Media-Lot1-Rep5

description: Media with mannitol.


title: flower_0_days_after_anthesis

description: flowers from 5 individual plants were mixed and used to extract total RNA

source_name: flower, 0 days after anthesis

value: flower


title: AcN-Lot1-Rep5


title: Media-Lot1-Rep4

description: Media with mannitol.


title: Copaxone-Lot7-Rep1

description: Brand version of glatiramer acetate.


title: flower_5_days_after_anthesis

source_name: flower, 5 days after anthesis


title: Media-Lot1-Rep3

description: Media with mannitol.


title: Glatopa-Lot1-Rep2

description: Generic version of glatiramer acetate.


title: root_60d_after_transplantation

source_name: root, 60d after transplantation


title: root_70d_after_transplantation

source_name: root, 70d after transplantation


title: root_40d_after_transplantation

source_name: root, 40d after transplantation


title: Copaxone-Lot6-Rep1

description: Brand version of glatiramer acetate.


title: root_20d_after_transplantation

source_name: root, 20d after transplantation


title: Glatopa-Lot2-Rep2

description: Generic version of glatiramer acetate.


title: embryo as control, biological rep1

description: 1-1_(ZebGene-1_0-st).rma-gene-full-Signal


title: Copaxone-Lot1-Rep1

description: Brand version of glatiramer acetate.


title: Glatopa-Lot2-Rep1

description: Generic version of glatiramer acetate.


title: root_0d_after_transplantation

source_name: root, 0d after transplantation


title: flower_10_days_after_anthesis

source_name: flower, 10 days after anthesis


title: stem_100d_after_transplantation

description: stem from 5 individual plants were mixed and used to extract total RNA

source_name: stem, 100d after transplantation

value: stem


title: Copaxone-Lot5-Rep1

description: Brand version of glatiramer acetate.

source_name: Copaxone


title: Copaxone-Lot9-Rep1

description: Brand version of glatiramer acetate.


title: Glatopa-Lot4-Rep2

description: Generic version of glatiramer acetate.

source_name: Glatopa


title: Copaxone-Lot8-Rep1

description: Brand version of glatiramer acetate.


title: Media-Lot1-Rep1

description: Media with mannitol.


title: Glatopa-Lot3-Rep2

description: Generic version of glatiramer acetate.


title: stem_70d_after_transplantation

source_name: stem, 70d after transplantation


title: Glatopa-Lot1-Rep1

description: Generic version of glatiramer acetate.


title: stem_40d_after_transplantation

source_name: stem, 40d after transplantation


title: Copaxone-Lot3-Rep1

description: Brand version of glatiramer acetate.


title: stem_0d_after_transplantation

source_name: stem, 0d after transplantation


title: Hela cell line after Ies6 knockdown

city: Changchun

first: Yong

last: Cai

address: Qianjin Street

institute: JiLin University

description: replicate 1

data_processing: The data were normalised using BeadStudio Gene Expression Module by EMTD Science and Technology Development Co., Ltd. (Beijing, China)

source_name: Hela

growth_protocol: HeLa cells were cultured in 6-well tissue culture plates (~2x105 cells/well) in DMEM medium containing 10% fetal bovine serum. Arp8 siRNA (sc-60072) was obtained from Santa Cruz, while all specific siRNAs including non-targeting siRNA (D-001206), Ino80 siRNA (D-004176), Ies6 siRNA (D-019327) and Ies2 siRNA (D-009848) SMART pool were from Dharmacon (U.S.A.).

extract_protocol: Total RNA was isolated using TRIzol® LS Reagent (Invitrogen). In addition, cells from 1 well of a 6-well plate were rinsed twice with warm PBS and harvested. Cells were then stored in an RNA hold solution (ER501-01, Beijing Transgen Biotech Co., Ltd.).

treatment_protocol: The cells were transiently transfected with 10~20 pmol specific siRNAs using Lipofetamine RNAMAX transfection kit (Invitrogen, Cat.No-864425) following the manufacture’s instruction. 24 hours after transfection, cells were divided into new 6-well plates for western blot, RT-PCR, and DNA microarray analysis. 48 hours after siRNAs transfection, cells were harvested and lysed.

tag: cell line

value: Hela

tag: sirna


title: embryo treated with SiNPs, biological rep1

description: 2-1_(ZebGene-1_0-st).rma-gene-full-Signal

source_name: embryo treated with SiNPs


title: AcN-Lot1-Rep4

source_name: AcN control


title: stem_60d_after_transplantation

source_name: stem, 60d after transplantation

source_name: reference RNA mixture of all RNA samples


title: AcN-Lot1-Rep3


title: Copaxone-Lot2-Rep1

description: Brand version of glatiramer acetate.


title: Media-Lot1-Rep2

description: Media with mannitol.

source_name: Media


title: Hela cell line after Ies2 knockdown

description: replicate 1


title: stem_20d_after_transplantation

source_name: stem, 20d after transplantation


title: Hela cell line after Arp8 knockdown

description: replicate 1

value: Arp8 siRNA (sc-60072)


title: Copaxone-Lot4-Rep1

description: Brand version of glatiramer acetate.


title: Glatopa-Lot3-Rep1

description: Generic version of glatiramer acetate.


title: AcN-Lot1-Rep2

value: AcN control


title: leaf_100d_after_transplantation

description: leaves from 5 individual plants ( one leaf in the midle of stem) were mixed and used to extract total RNA

source_name: leaf, 100d after transplantation

value: leaf


title: Hela cell line after Ino80 knockdown

description: replicate 1


title: leaf_60d_after_transplantation

source_name: leaf, 60d after transplantation


title: leaf_40d_after_transplantation

source_name: leaf, 40d after transplantation


title: leaf_70d_after_transplantation

source_name: leaf, 70d after transplantation


title: AcN-Lot1-Rep1

description: A glatiramoid related to, but chemically distinct from Copaxone.

value: CD4+ T cell


title: Glatopa-Lot4-Rep1

description: Generic version of glatiramer acetate.


title: leaf_0d_after_transplantation

source_name: leaf, 0d after transplantation


title: PHBECs_MP15_coculture_Array12_replicate3

city: Basel

first: Tim

last: Roloff

address: Maulbeerstrasse 66

department: Functional Genomics

institute: FMI

hyb_protocol: Hybridization was carried out with 5 μg of biotinylated target, which was incubated with a GeneChip human Gene 1.0 ST Array (Affymetrix) at 45°C for 16 h. Following hybridization, non-specifically bound nucleotides were removed by washing and specifically bound target detected using a GeneChip Hybridization, Wash and Stain kit and a GeneChip Fluidics Station 450 (Affymetrix).

scan_protocol: The arrays were scanned using a GeneChip Scanner 3000 7G (Affymetrix) and CEL files acquired using GeneChip Command Console Software (Affymetrix).

data_processing: Arrays were normalized and probeset-level expression values calculated with R/Bioconductor's (v2.14) 'affy' package using the rma() function (www.bioconductor.org).

source_name: primary human breast epithelial cells, dissociated co-culture

label_protocol: Reverse transcription was performed using 4 μM T7- (dT)24/T7- (dN)6 primer mix (Affymetrix) and 150 units of Superscript II reverse transcriptase (Invitrogen). The synthesis of second-strand cDNA was performed by mixing 4 mM dNTPs, 6 units DNA polymerase I, and 0.4 units RNase H in a 20-µL reaction volume. cRNA was produced by in vitro transcription with a T7 RNA polymerase at 37°C for 14 h using the MEGAscript T7 kit (Ambion) as per the manufacturer's instructions. For the second cycle, the first-strand cDNA was synthesized using 0.2 μg random primers from 9 μL of purified cRNA. The second-strand cDNA was produced using 10 µM T7- (dN)6 primer and 40 units DNA polymerase at 16°C for 2 h, after which 10 units T4 DNA polymerase (Invitrogen) were added and the incubation continued for another 10 min. The cDNA was in vitro transcribed with T7 RNA polymerase at 37°C for 16 h. The single-strand cDNA was synthesized using 10 µg purified cRNA in the presence of 4 µg random primers, 0.2 M DTT, 12 mM dNTP + dUTP and 750 units Superscript II (Roche Diagnostics) in a total volume of 20 µL. The cRNA was hydrolyzed with 2 units RNase H at 37°C for 40 min. The sense cDNA was purified and eluted in 28 µL elution buffer. Amplified products were purified using the GeneChip cDNA Sample Cleanup Module (Affymetrix) with a 6,000 g centrifugation during the first two steps. To improve recovery from the columns, water or elution buffer were spun into the matrix at 50 g and left to stand for 4 min before a 16,000 g centrifugation. The quantity and purity of the cRNA and cDNA produced during the first and second rounds were evaluated using a NanoDrop ND-1000 spectrophotometer (Nanodrop Technologies). The cDNA was then fragmented by uracil DNA glycosylase and apurinic/apyrimidic endonuclease 1 and biotin-labeled with terminal deoxynucleotidyl transferase using the GeneChip WT Terminal labeling kit (Affymetrix).

growth_protocol: Human primary epithelial progenitor derived cells and mesenchymal stem cells derived cells bearing fluorescent tags were either co-cultured in novel ex vivo culture conditions on ECM coated meshes in serum free medium (M5) or cultured as monocultures in the same conditions for 30 days.

extract_protocol: RNA was extracted from 300 sorted cells with the PicoPure RNA isolation kit (Arcturus)

treatment_protocol: Serum free medium (M5) was supplemented and/or replaced two to three times a week during the whole ex-vivo culture period. After 30 days the cultures were dissociated with mild proteinase/EDTA (HyQtase, Thermo Scientific) treatment for 20 min. Cells remained thereafter on ice and FACS sorts were performed immediately to isolate viable epithelial or stromal cells, based on their fluorescent protein tag. 300 cells of each condition were directly sorted in 100ul TRIZOL in cooled tubes. The samples were immediately frozen on dry ice and stored at -70°C prior to RNA extraction.

tag: reduction mammoplasty

value: co-culture derived epithelial cells


title: PHBECs_MP15_monoculture_Array10_replicate3

source_name: primary human breast epithelial cells, dissociated monoculture

value: monoculture derived epithelial cells


title: hAMSCs_MP28_coculture_Array11_replicate3

source_name: primary human breast stromal/mesenchymal cells, dissociated co-culture

value: co-culture derived stromal cells


title: hAMSCs_MP22_coculture_Array7_replicate2


title: hAMSCs_MP28_monoculture_Array9_replicate3

source_name: primary human breast stromal/mesenchymal cells, dissociated monoculture

value: monoculture derived stromal cells


title: leaf_20d_after_transplantation

source_name: leaf, 20d after transplantation


title: PHBECs_MP13_coculture_Array8_replicate2


title: PHBECs_MP9_coculture_Array4_replicate1


title: UMUC3 with shRNA control, biological rep1

city: Novato

first: Yuanbin

last: Ru

state: CA

address: 105 Digital Dr

institute: BioMarin Pharmaceutical Inc.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U219 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The raw data were processed by the Robust Multi-array Average (RMA) algorithm implemented in the affy package in R using default settings.

source_name: UMUC3 bladder cancer cell line

growth_protocol: Cells were grown on culture plates at 37C with 5% carbon dioxide in MEM (Gibco) + 10% FBS.

treatment_protocol: Cells growing on culture plates were rinsed with ice-cold PBS and lysed on ice in the Trizol solution (Invitrogen).

value: bladder cancer cell

tag: transfection

value: shRNA control


title: Tgif2 OE replicate3

city: Austin

first: Bum-Kyu

address: 2506 Speedway Stop A5000

institute: University of Texas at Austin

description:
Tgif2 OE replicate3
TGIF2_OE_B3.CEL

hyb_protocol: A hybridization mixture including the fragmented DNA and probe array controls were prepared, and then hybridized to the probe array   during a 16-hour incubation

scan_protocol: GeneChips were scanned by Scanner 3000, Affymetrix

data_processing: Robust multi-array (RMA) normalization method from limma package (lima_3.22.4) of Bioconductor (v.3.0) was applied to calculate averaged expression values from replicates

source_name: ES_Tgif2 overexression

label_protocol: cDNAs were generated using qScript (Qunta) and then labeled with Cy3

growth_protocol: Mouse J1 ES cells were cultivated in 0.1% gelatin coated dishes using DMEM (Dulbecco’s modified Eagle’s medium) supplemented with 20% fetal bovine serum (FBS), 2 mM of L-glutamine, 0.1 mM of non-essential amino acid, 1% of nucleoside mix, 0.1 mM of ß-mercaptoethanol, 1000U/ml of recombinant leukemia inhibitory factor and 50 U/ml of Penicillin/Streptomycin.

extract_protocol: Total RNAs were extracted using RNeasy plus mini kit (Qiagen)

tag: strain background

tag: cell type

value: embryonic stem (ES) cells

value: overexpressing Tgif2


title: Tgif2 OE replicate4

description:
Tgif2 OE replicate4
TGIF2_OE_B4.CEL

tag: genotype/variation


title: hAMSCs_MP29_coculture_Array3_replicate1


title: PHBECs_MP13_monoculture_Array6_replicate2


title: HRA_DW_1

first: Bose

middle: Skaria

last: Kochupurakkal

address: 450 Brookline Avenue

department: Cancer Biology

institute: Dana-Farber Cancer Institute

description: Gene expression form HRA cells treated with Dox to induce RelA expression for 24 hours and then transferred to medium devoid of Dox for 48 hours, replicate 1

hyb_protocol: Recommended Affymetrix protocol was used

scan_protocol: The arrays were scanned using Affymetrix Scanner 3000 7G using recommended settings

data_processing: Summarization and normalization (RMA) was performed in GenePattern using custom CDF files from Brainarray (version 18). Gene symbols for corresponding Ensembl gene IDs were gathered using Biomart. Differentially expressed genes were identified using LIMMA in MEV.

source_name: HRA, DW

growth_protocol: HRA cells were cultured in DMEM-F12 containing Insulin (10 micrograms/ml), EGF (10 nanograms/ml), Cholera toxin (1nanogram/ml), Hydrocortisone (500 nanogram/ml) and 0.6% Fetal Bovine Serum. Doxycycline was used at 1 microgram/ml

extract_protocol: total RNA was extracted using miRNEASY kit from Qiagen using recommended protocol

treatment_protocol: Doxycycline was added to growth medium at 1 microgram/ml.

value: Human Mammary Epithelial Cells conditionally (Doxycycline inducible) expressing NF-kB factor RelA


title: PHBECs_MP9_monoculture_Array2_replicate1


title: HRA_DW_2

description: Gene expression form HRA cells treated with Dox to induce RelA expression for 24 hours and then transferred to medium devoid of Dox for 48 hours, replicate 2

label_protocol: Recommended Affymetrix protocol was used


title: hAMSCs_MP29_monoculture_Array1_replicate1


title: UMUC3 with shRNA specific to AGL, biological rep1

value: shRNA specific to AGL


title: HRA_DW_3

description: Gene expression form HRA cells treated with Dox to induce RelA expression for 24 hours and then transferred to medium devoid of Dox for 48 hours, replicate 3


title: hAMSCs_MP22_monoculture_Array5_replicate2


title: Tgif2 OE replicate1

description:
Tgif2 OE replicate1
TGIF2_OE_B1.CEL


title: UMUC3 with shRNA control, biological rep2


title: UMUC3 with shRNA specific to AGL, biological rep2


title: Tgif2 OE replicate2

description:
Tgif2 OE replicate2
TGIF2_OE_B2.CEL


title: Basal_epithelial_EpCAM_n_MP15_replicate3

data_processing: Arrays were normalized and probeset-level expression values calculated with R/Bioconductor's (v2.14) 'affy' package using the rma() function (www.bioconductor.org). Differential gene expression was determined using linear modeling implemented in the R/Bioconductor package ‘limma’. For general analysis, a cutoff of linear fold change >2, and pvalue <0.005 were used.

source_name: reduction mammoplasty tissue, dissociated organoids

treatment_protocol: Reduction mammoplasty tissue was digested with Collagenase Type A (1 mg/mL, Roche) in DMEM/F12, 15 mM HEPES (1x penicillin/streptomycin, insulin (10 μg/ml), hydrocortisone (0.5 μg/ml)) for 14-16h. Retrieved organoids were dissociated with HyQtase (HyClone, Thermo Scientific) for 10 min at 37˚C and subsequent pipetting. To obtain single cells, cells were filtered twice through 40-μm cell strainers (Falcon). 10^6 cells were blocked for 10 min at 4°C with antibodies against human CD16 (FcRIII, Clone 3G8, 1:50) and CD32 (FcRII, Clone FUN-2, 1:100), washed and labeled in 100 μl medium for 20 min at 4°C with antibodies against human FITC-CD49f (Clone GoH3, 1:25), PerCP/Cy5.5-CD326 (EpCAM, Clone 9C4, 1:25), APC-CD10 (Clone HI10a, 1:20), PE-CD31 (Clone WM59, 1:33), PE-CD45 (Clone HI30, 1:33) and PE-CD235ab (Clone HIR2, 1:33). DAPI (0.2%, Invitrogen) was added (1:250) 2 min before cell sorting. Single cells were gated based on their forward and side scatter profiles. Dead cells (DAPI bright) and Lin+ cells (CD31+, CD45+ and CD235+) were gated out. 300 cells of a luminal epithelial (EpCAM+, CD49f+/-), basal epithelial (EpCAM-, CD49f+), CD10 negative and CD10 positive stromal cell population were directly sorted in 100ul TRIZOL in cooled tubes. The samples were immediately frozen on dry ice and stored at -70°C prior to RNA extraction.

value: basal epithelial (EPCAM-, CD49f+)


title: Luminal_epithelial_EpCAM_p_MP15_replicate3

value: luminal epithelial cells (EpCAM+, CD49f+/-)


title: HRA_72+_1

description: Gene expression form HRA cells treated with Dox to induce RelA expression for 72 hours, replicate 1


title: HRA_72+_3

description: Gene expression form HRA cells treated with Dox to induce RelA expression for 72 hours, replicate 3


title: BirA control replicate4

description: Gene expression data for OE control

data_processing: Robust multi-array (RMA) normalization method was applied to calculate averaged expression values from replicates

source_name: embryonic stem cells

value: ES cells

value: BirA OE


title: HRA_24+_2

description: Gene expression form HRA cells treated with Dox to induce RelA expression for 24 hours, replicate 2


title: HRA_72+_2

description: Gene expression form HRA cells treated with Dox to induce RelA expression for 72 hours, replicate 2


title: Stromal_CD10_n_MP15_replicate3

value: CD10 negative stromal cells


title: HRA_24+_1

description: Gene expression form HRA cells treated with Dox to induce RelA expression for 24 hours, replicate 1


title: HRA_24+_3

description: Gene expression form HRA cells treated with Dox to induce RelA expression for 24 hours, replicate 3


title: HRA_ND_3

description: Gene expression form HRA cells, uninduced, replicate 3

source_name: HRA, ND


title: BirA control replicate3

description: Gene expression data for OE control


title: Stromal_CD10_p_MP15_replicate3

value: CD10 positive stromal cells


title: BirA control replicate1

description: Gene expression data for OE control


title: HRA_ND_2

description: Gene expression form HRA cells, uninduced, replicate 2


title: shControl replicate1

description: Gene expression data upon control KD

value: shControl KD


title: BirA control replicate2

description: Gene expression data for OE control


title: HRA_ND_1

description: Gene expression form HRA cells, uninduced, replicate 1


title: Basal_epithelial_EpCAM_n_MP13_replicate2


title: shControl replicate2

description: Gene expression data upon control KD


title: Luminal_epithelial_EpCAM_p_MP13_replicate2


title: Stromal_CD10_p_MP13_replicate2


title: Stromal_CD10_n_MP13_replicate2


title: Basal_epithelial_EpCAM_n_MP9_replicate1


title: Tgif1 OE replicate4

description: Gene expression data upon Tgif1 OE

value: Tgif1 OE


title: Tgif1 OE replicate2

description: Gene expression data upon Tgif1 OE


title: Tgif1 OE replicate3

description: Gene expression data upon Tgif1 OE


title: Tgif1 KD replicate2

description: Gene expression data upon Tgif1 KD

value: Tgif1 KD


title: Luminal_epithelial_EpCAM_p_MP9_replicate1


title: Stromal_CD10_p_MP9_replicate1


title: Stromal_CD10_n_MP9_replicate1


title: Tgif1 KD replicate1

description: Gene expression data upon Tgif1 KD


title: Tgif1 OE replicate1

description: Gene expression data upon Tgif1 OE


title: CA1 Reconsolidation-impaired, biological rep5

status: Public on Sep 25 2015

city: Cardiff

first: Kerrie

middle: L

last: Thomas

state: Wales

address: Maindy Road

department: Neuroscience & Mental Health Research Institute, & Cardiff School of Biosciences

institute: Cardiff University

hyb_protocol: RNA quality was assessed spectrophotometrically on an Agilent Bioanalyser (Agilent Technologies). Only samples with a RNA Integrity Number (RIN) of 8/10 or more went forward for hybridization to Affymetrix GeneChip Rat Genome 230 2.0 Arrays (Agilent Technologies ) according to the manufacturer’s protocol at the Central Biotechnology Service, Cardiff University, UK. No amplification steps were performed before cDNA synthesis before hybridization because RNA extracted form the individual CA1 samples met the 1 to 5 lg total RNA requirement for the reverse transcription step and subsequent hybridization to the Affymetrix array.

scan_protocol: Agilent GeneChip 3000 scanner.

data_processing: Raw intensity data from each microarray were normalized to expression values using MAS5.0. Analysed with Agilent GCOS 1.4.

organism: Rattus norvegicus

source_name: CA1 2 hr Reconsolidation Control ZIFASO

label_protocol: cRNA were prepared according to the standard Affymetrix protocol  (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: In vivo whole organism.

extract_protocol: Total RNA was isolated with RNeasy (Qiagen Ltd).  Approximately 8 microgramsof total RNA per dorsal CA1 was obtained from one rat.

treatment_protocol: Bilateral microinfusions (1 microlitre/hemisphere) of 2 nmol/microlitre Zif268 antisense ODN (ZIFASO, 5’- GGTAGTTGTCCATGGTGG -3’ in PBS, pH 7.4) or Zif268 missense ODN were (ZIFMSO, 5’ - GTGTTCGGTAGGGTGTCA -3’ in PBS, pH 7.4) into the dorsal hippocampus (AP -3.50, relative to bregma) were given 90 min before a 2 min recall of contextual fear memory. Infusions were made in awake rats via previously surgically implanted indwelling stainless steel cannula. The dorsal CA1 was microdissected 2 hr after recall.

value: Lister hooded

tag: gender

value: Male

tag: age

tag: task

value: Contextual fear conditioning (CFC)

tag: interval cfc and recall

value: 48 hours

tag: recall duration

value: 2 minutes

tag: brain region

tag: time after recall

value: 2 hours

value: ZIFASO


title: CA1 Reconsolidation, biological rep7

source_name: CA1 2 hr Reconsolidation ZIFMSO

tag: treatment

value: ZIFMSO


title: CA1 Reconsolidation, biological rep1

tag: strain


title: CA1 Reconsolidation-impaired, biological rep3


title: CA1 No extinction (NOR), biological rep6

source_name: CA1 2 hr 10 min CS- No recall CFM

extract_protocol: Total RNA was isolated with RNeasy (Qiagen Ltd).  Approximately 8 micrograms of total RNA per dorsal CA1 was obtained from one rat.

treatment_protocol: Rats habituated to two different contexts were CFC in one of the two contexts. 48hr after CFC rats were either exposed to the conditioned context (CS+) or the other context (CS-) for 10 min. The dorsal CA1 was microdissected 2 hr after context re-exposure.

value: 10 minutes

tag: time after reexposure

value: CS-