title: FG_RI3-4_C

city: Ribeirao Preto

first: Neil

last: Brown

address: Av. do Cafe

country: Brazil

institute: USP

hyb_protocol: Fragmented using 200 mM tris-acetate, pH 8.2, 500 mM MgOAc and mixed with the BioArray Eurkaryotic hydridization controls (Enzo Life Science) that included 3 nM control oligo B2, 20x control cRNA cocktail, herring sperma (10 mg / ml), acetylated BSA (50 mg / ml) 2x MES hybridization buffer and water. A final aRNA concentration of 10 µg in 200 µl was hybridized to the F. graminearum Affymetrix array

scan_protocol: GeneChips were scanned using the GeneArray Scanner

data_processing: Gene expression data from infecting hyphae within wheat floral tissue. The data was exported and RMA normalised using the Affymetrix Expression Console. Downstream analyses were performed with software R

organism: Fusarium graminearum

label_protocol: Purified total RNA (> 10 µg) was in vitro transcribed, labelled using the BioArray high yield RNA transcript labelling kit (T7) according to manufacturer’s instructions (Enzo Life Science)

growth_protocol: Wheat plants were grown in a controlled environment with standard light, at 22 degrees and at ambient humidity

extract_protocol: Freeze dried samples were ground in liquid nitrogen with a pestle and mortar. Total RNA was extracted using the TRIzol® reagent (Invitrogen) with minor modifications to manufacturer’s instructions. Total RNA was precipitated at -20oC for 16 hours with 8 M lithium chloride.

treatment_protocol: 200 Fusarium graminearum PH-1 conidia were incoluated into the floral caity of the two florets, of the two spikelets, in the middle of the wheat head at anthesis. Wheat plants were kept at high humidity for the first 3 days, of which the first 24 hours was in the dark. At 7 days post infection the incoluted spikelets and the 7 sequential rachis internodes below the inoculated spikelet were collected and immediately frozen in liquid nitrogen. The individual wheat tissues were pooled for ten wheat heads to form a single biological replicate. Non-infected wheat spikelets and rachis was collected as a negative control. Three biological replicate were collected per treatment.

tag: fusarium strain

tag: infection status

value: infected

tag: wheat tissue

value: Rachis


title: FG_RI1-2_B

status: Public on Aug 01 2017

type: RNA

label: biotin

molecule: total RNA


title: H31

city: Jinan

first: Peng

last: Gao

address: Wen Hua Xi Road 44

country: China

institute: Shandong University

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

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

data_processing: Data were analyzed by first subtracting the background, then the signals were normalized using a Lowess (locally weighted regression) filter. The raw microarray data set was filtered according to a standard procedure to exclude spots with minimum intensity. It was arbitrarily set to an intensity parameter of P100 for the miRNA microarray data. Spots with diameters less than 10 μm and flagged spots were also excluded from the analyses.

organism: Homo sapiens

source_name: human breast cancer tissue

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

extract_protocol: MiRNAs were isolated from breast cancer tissues using a miRNeasy FFPE Kit (Bioteke, Beijing, China) according to the manufacturer's instructions.

tag: drug sensitivity status

value: drug sensitive tissue

tag: tissue

value: human breast cancer tissue


title: FG_SP1_A

value: Spikelet


title: Wheat_rachis

value: non-infected


title: FG_RI3-4_A


title: FG_SP1_B


title: FG_RI3-4_B


title: H19


title: H32


title: FG_RI5-6_A


title: FG_RI1-2_C


title: Wheat_spikelet


title: FG_RI5-6_C


title: C115

value: drug resistant tissue


title: C22


title: H20


title: FG_RI5-6_B


title: C28


title: C17


title: H80


title: C100


title: mouse alveolar macrophage_young_rep4

city: New Haven

first: Koji

last: Sakamoto

state: CT

address: 300 Cedar Street

department: Internal Medicine

country: USA

institute: Yale University

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse Gene Expression v2 8x60k microarray slides (G4852B) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 12.0.0.7 (Agilent) using default parameters (protocol GE1_1200_Jun14 and Grid: 074809_D_F_20150624) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Mus musculus

source_name: alveolar macrophage, from 2-4 month-old, PBS

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.25 ug RNA using the One-Color Low RNA Quick Amp labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was isolated using the miRNeasy micro kit (Qiagen, Valencia CA) by utilizing QIAcube (Qiagen, Valencia CA).  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent Tapestation 2200 Bioanalyzer with High Sensitivity RNA ScreenTape (Agilent Technologies, Santa Clara, CA).

treatment_protocol: C57B/6 mice of either 2-4 months-old or 22-24 months old were obtained from the National Institute of Aging rodent facility. Mice were infected with purified human influenza virus, A/Puerto Rico/8/34 (H1N1) (PR8) (Advanced Biotechnologies Inc.; MD, USA), by instillation of with 50μl PBS containing indicated dose of PR8 virus or 50μl PBS control intranasally. At day 3 post infection, the lungs were harvested and single-cell suspension was obtained by mechanical and enzymatic digestion. . After staining with fluorescent antibodies, Alveolar macrophages were sorted according to their forward- and side-scatter profiles and by their phenotype as follow: CD45+SiglecF+CD11chiF4/80+.

tag: strain

tag: young or aged

value: young

tag: treatment

value: PBS


title: FG_SP1_C


title: FG_RI1-2_A


title: Replicate 1_GU5

type: genomic

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description:
Ncb2 binding profile in Gu5 cells of Candida albicans
GU5_IP_NCB2_1_Cy5 vs. GU5_Input_1_Cy3
ch1-cy3 (WCE) and ch2-cy5(IP)

hyb_protocol: 5 micrograms of cy3 and cy5 labeled samples were hybridized. Hybridizations were done using the Agilent Hybridization kit of (Part Number: 5188-6420) Hybridization was carried out in Agilent's Surehyb Chambers at 65º C for 24 hours. The hybridized slides were washed using Agilent aCGH wash buffers

scan_protocol: Agilent Microarray Scanner

data_processing: Data extraction from Images was done using Feature Extraction software v 10.7 of Agilent. Data analysis was done using Agilent Genomic Workbench Lite Edition 6.5 (Chip-on-Chip Application) and Microsoft Excel.Normalization of the data was done using Lowess normalization

molecule: genomic DNA

organism: Candida albicans

source_name: Input DNA from Gu5 cells

label_protocol: The DNA samples were blunted at 12°C for 20 minutes using T4 DNA polymerase as per the Chip on Chip Protocol of Agilent Technologies. The blunted DNA was cleaned, precipitated and resuspended in 25 microlitres of water. The entire DNA was then ligated to linkers. The linker-ligated DNA was subjected to two rounds of LMPCR and resuspended in water. Two micrograms of each sample was labeled using Agilent Genomic DNA Labeling Kit PLUS with Cy3 or Cy5 dUTP( 5190-0453). DNA yield and incorporation of label (specific activity) was measured using NanoDrop spectrophotometer.

extract_protocol: ChIP experiments were carried out as described earlier (Shukla S et al. 2011). In brief, 15 ml of cultures in YEPD medium [(Gu4 (AS) and Gu5 (AR)] cells were cross-linked with 1% formaldehyde for 20 min at RT with intermittent mixing in between. The cross-linking reaction was quenched with 125 mM glycine and cells were collected by centrifugation at 4K for 5 min. Cells were washed twice with ice cold TBS (Tris Buffered Saline: 20 mM Tris-Cl, pH 7.5, containing 150 mM NaCl) and resuspended in Zymolase buffer (50 mM Tris, pH 7.4, 10 mM MgCl2, 1 M sorbitol, and 30 mM DTT) containing Zymolase 20µg/ml and incubated for 2 hr at 30ºC for the formation of spheroplast. Spheroplasts were washed twice with cold TBS containing 1M sorbitol, resuspended in ChIP lysis buffer (50 mM HEPES-KOH, pH 7.5, 140 mM NaCl, 1 mM EDTA pH 8.0, 1% Triton X-100, 0.1% sodium deoxycholate, and 1 mM PMSF), and incubated on ice for 30 min. SDS was added at a final concentration of 0.5% in each sample. Cells were sonicated for 25 sec at amplitude of 6 for seven cycles with 2 min cooling interval. After sonication cell suspensions were centrifuged at 4ºC for 30 min at 13K rpm and termed soluble total chromatin (STC). 15 µl samples were run on 1% agarose gel to check the size of the fragmented chromatin (approximate size ~250bp to ~500 bp). 50 µl of STC was stored at -20ºC for further use. STC was diluted 5 times with ChIP lysis buffer and pre-cleared by incubating pre-immune serum and 20 µl packed volume of protein-A agarose beads for 2 hrs at 4ºC on rotating rocker. After pre-clearing the samples pre-immune serum (negative control) and anti-Ncb2 antibody was added at a final concentration of 2-5µg and incubated O/N for binding. Next morning 20 µl packed volume of protein-A agarose beads were added and put on rocker for binding, next bead bound immune complexes were precipitated by centrifuging at 3K for 1 min and washed twice with ChIP lysis buffer, TSE 150 (Tris-Cl, pH 8.0, 150 mM NaCl, 1% Triton X-100, 0.1% SDS, 1 mM EDTA, pH 8.0, and 1 mM PMSF), TSE 500 (Tris-Cl, pH 8.0, 500 mM NaCl, 1% Triton X-100, 0.1% SDS, 1 mM EDTA, pH 8.0, and 1 mM PMSF), buffer III (10 mM Tris-Cl, pH 8.0, 1 mM EDTA, pH 8.0, 250 mM LiCl, 1% NP-40, and 1% sodium deoxycholate), and finally with TE (10 mM Tris-Cl, pH 8, and 1 mM EDTA, pH 8.0). After washing, immunoprecipitated complexes were eluted in buffer containing (50 mM Tris-Cl, pH 7.5, 10 mM EDTA, pH 8.0, and 1% SDS) at 65ºC O/N. The immunoprecipitated complexes and input DNA were treated with proteinase-K and incubated for 2 hr at 65ºC. The precipitated DNA was purified by using Qiagen PCR purification kit as instructed by the manufacturer.

tag: clinical isolate

tag: phenotype

value: azole-resistant

tag: chip antibody

value: none, input DNA

source_name: Ncb2 ChIP in Gu5 (AR) Cells

value: Polyclonal anti-Ncb2 antibody (Shukla S et al, 2011)


title: ILC2_IL2_IL7_IL33_rep2

city: Leicester

first: David

middle: John

last: Cousins

address: NIHR BRC Respiratory, Glenfield Hospital

department: Respiratory Sciences

country: United Kingdom

institute: University of Leicester

hyb_protocol: Standard Illumina hybridization protocol except hyb performed at 48 degrees C

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation within Genome Studio without background correction. Data was submitted using Illumina's GEO Data Submission Report Plug-in for Gene Expression

label: Biotin

label_protocol: cDNA synthesis and amplification was performed with the Ovation PicoSL WTA system V2 kit (NuGEN, Leek, Netherlands) as per the manufacturer’s instructions. Purity and yield was then analyzed using the Bioanalyzer platform (Agilent, Stockport, UK) and NanoDrop 2000 spectrophotometer (Thermo Scientific, Loughborough, UK) respectively before amplified cDNA was biotin-labeled with the NuGEN Encore BiotinIL module according to the manufacturer’s instructions

growth_protocol: Human ILC2s were isolated from peripheral blood mononuclear cells by magnetic depletion of Lineage positive cells fololwed by flow cytometric sorting. ILC2s were identified as Lineage (CD2, CD3, CD14, CD16, CD19, CD56, CD235a, CD123) negative,  CD127+, CRTh2+ cells.

extract_protocol: RNA was isolated from cell pellets using the miRNeasy mini kit and RNeasy MinElute cleanup kit (Qiagen, Manchester, UK) according to the manufacturer’s instructions

treatment_protocol: ILC2s were cultured in RPMI 10% FCS for seven days in the presence of the indicated combinations of cytokines.

tag: donor


title: ILC2_IL2_IL7_IL25_IL33_rep3


title: ILC2_IL2_IL7_IL25_rep1


title: ILC2_IL2_IL7_IL25_rep3


title: ILC2_IL2_IL33_rep3


title: ILC2_IL2_IL7_IL33_rep3


title: ILC2_IL2_IL7_IL25_IL33_rep2


title: ILC2_IL2_IL7_IL25_IL33_rep1


title: Replicate 3_GU5

description:
Ncb2 binding profile in Gu5 cells of Candida albicans
GU5_IP_NCB2_3_Cy5 vs. GU5_Input_3_Cy3
ch1-cy3 (WCE) and ch2-cy5(IP)


title: ILC2_IL7_IL33_rep3


title: ILC2_IL2_IL7_IL33_rep1


title: ILC2_IL7_IL33_rep2


title: ILC2_IL2_IL7_rep3


title: ILC2_IL7_IL33_rep1


title: ILC2_IL2_IL7_IL25_rep2


title: UUS patient 7 [aCGH]

city: Stanford

first: Joanna

last: Przybyl

address: 300 Pasteur Drive

department: Department of Pathology

institute: Stanford University

hyb_protocol: Labeled samples were hybridized to Agilent-029830 4x180K CGH+SNP whole-genome microarrays (G4890A) (Agilent Technologies, Santa Clara, CA, USA) according to the manufacturer's protocol.

scan_protocol: The microarray slides were scanned using the Agilent G2565A DNA Microarray Scanner (Agilent Technologies, Santa Clara, CA, USA).

data_processing: Image analysis was done using the Feature Extraction V10.10.1.1 software (Agilent Technologies, Santa Clara, CA, USA). aCGH data were analyzed using Agilent Genomic Workbench 7.0.4.0. software (Agilent Technologies, SantaClara, CA, USA). The ADM-2 algorithm was applied to identify DNA copy number aberrations (CNAs). Aberration Filter: (Minimum Number of Probes for Amplification >= 5 AND Minimum Size (Kb) of Region for Amplification >= 1 AND Minimum Avg. Absolute Log Ratio for Amplification >= 0.25) OR (Minimum Number of Probes for Deletion >= 5 AND Minimum Size (Kb) of Region for Deletion >= 1 AND Minimum Avg. Absolute Log Ratio for Deletion >= 0.25).

source_name: UUS patient

label_protocol: 1ug of genomic DNA was labeled using Cy5 dye, and 1ug reference female DNA was labeled using Cy3 dye, according to the manufacturer's recommendations. Reference female DNA supplied with the SureTag Complete DNA Labeling Kit (cat. no. 5190-4240, Agilent Technologies, Santa Clara, CA, USA) was used for the aCGH experiments.

extract_protocol: Genomic DNA was extracted from the frozen tumour specimens using the Blood & Tissue DNasy kit with the optional RNase treatment (Qiagen).

tag: subject status

value: highly malignant undifferentiated uterine sarcomas (UUS)

tag: gender

value: Female

value: Uterus

tag: tumor subtype

value: undifferentiated uterine sarcoma

source_name: Reference

tag: rerence info.


title: ILC2_IL2_IL33_rep2


title: ILC2_IL2_IL33_rep1


title: UUS patient 6 [aCGH]

value: Reference female DNA supplied with the SureTag Complete DNA Labeling Kit (cat. no. 5190-4240, Agilent Technologies, Santa Clara, CA, USA)


title: Replicate 3_GU4

description:
Ncb2 binding profile in Gu4 cells of Candida albicans
GU4_IP_NCB2_3_Cy5 vs. GU4_Input_3_Cy3
ch1-cy3 (WCE) and ch2-cy5(IP)

source_name: Input DNA from Gu4 cells

value: azole-sensitive

source_name: Ncb2 ChIP in Gu4 (AS) Cells


title: ILC2_IL2_IL7_rep2


title: UUS patient 5 [aCGH]


title: ILC2_IL2_IL7_rep1


title: UUS patient 3 [aCGH]


title: Replicate 2_GU5

description:
Ncb2 binding profile in Gu5 cells of Candida albicans
GU5_IP_NCB2_2_Cy5 vs. GU5_Input_2_Cy3
ch1-cy3 (WCE) and ch2-cy5(IP)


title: UUS patient 2 [aCGH]


title: UUS patient 4 [aCGH]


title: ESS low-grade patient 11 [aCGH]

source_name: ESS low-grade patient

value: low-grade endometrial stromal sarcomas (ESS) patient

value: low-grade endometrial stromal sarcoma


title: Replicate 1_GU4

description:
Ncb2 binding profile in Gu4 cells of Candida albicans
GU4_IP_NCB2_1_Cy5 vs. GU4_Input_1_Cy3
ch1-cy3 (WCE) and ch2-cy5(IP)


title: UUS patient 1 [aCGH]


title: Replicate 2_GU4

description:
Ncb2 binding profile in Gu4 cells of Candida albicans
GU4_IP_NCB2_2_Cy5 vs. GU4_Input_2_Cy3
ch1-cy3 (WCE) and ch2-cy5(IP)


title: Xenopus laevis expression data from juvenile inner ear tissue juv_1

city: Cleveland

first: Selene

last: Virk

state: OH

address: 2103 Cornell Road

institute: Case Western Reserve University

description: Gene expression data from juvenile animals based on Nieuwkoop and Faber (1994) Normal Table of Xenopus laevis (Daudin). Garland Publishing Inc, New York ISBN 0-8153-1896-0.

hyb_protocol: Fragmented cDNA was hybridized according to manufacture's protocol (Affymetrix)

scan_protocol: GeneChip Xenopus laevis 2.0 were scanned using the GeneChip Scanner 3000 7G (Affymetrix)

data_processing: Data processed using JMP Genomics software

organism: Xenopus laevis

source_name: Xenopus juveniles

label_protocol: Labeled antisense single-stranded cDNA was prepared from each RNA replicate (1 ug total RNA) using the Ovation RNA Amplification System V2 in conjunction with the FL-Ovation cDNA Biotin Module V2 (both from NuGEN)

growth_protocol: Juvenile Xenopus laevis (n=5) were approximately 3 months old with an average weight of 9.0 ± 0.2 g and an average length of 4.6 ± 0.5 cm and obtained from Nasco (Fort Atkinson, WI). Animal procedures and protocols were approved by the Institutional Animal Care and Use Committee (IACUC) of New Mexico State University.

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Valencia, CA) as per Trujillo-Provencio C, Powers T, Sultemeier D, Serrano E: RNA isolation from Xenopus inner ear sensory endorgans for transcriptional profiling and molecular cloning. Methods Mol Biol 2009, 493:3-20.

value: inner ear

tag: developmental stage

value: juvenile

tag: age

value: ~3 months


title: plasma of healthy control sample 5

city: Beijing

first: Qinghua

last: Cui

address: 38 Xueyuan Road

institute: Peking University

description: pooled samples from three age and gender matched people

hyb_protocol: The labeled cRNAs were hybridized onto the Human LncRNA Array v2.0 (8 x 60K, Arraystar).

scan_protocol: After having washed the slides, the arrays were scanned by the Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v12.0 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 1 out of 6 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis.

source_name: plasma of healthy control

label_protocol: The sample preparation and microarray hybridization were performed based on the manufacturer’s standard protocols with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method.

extract_protocol: Total RNA from each sample was quantified by the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

value: plasma

tag: disease state

value: healthy control


title: Xenopus laevis expression data from juvenile inner ear tissue juv_2

growth_protocol: Juvenile Xenopus laevis (n=5) were approximately 3 months old with an average weight of 9.6 ± 0.1 g and an average length of 4.7 ± 0.3 cm and obtained from Nasco (Fort Atkinson, WI). Animal procedures and protocols were approved by the Institutional Animal Care and Use Committee (IACUC) of New Mexico State University.


title: SALK_070989 in combined treatment 2, rep 1

city: Urbana

first: Amy

last: Marshall-Colon

state: IL

address: 1201 W Gregory Drive

department: Plant Biology

institute: University of Illinois

description: Gene expression data from shoot

hyb_protocol: labelled cDNA was hybridized, washed and stained on an ATH1-121501 Arabidopsis Genome Array (Affymetrix) using a Hybridization Control Kit (Affymetrix), a GeneChip Hybridization,Wash, and Stain Kit (Affymetrix).

scan_protocol: GeneChips were scanned with the GeneArray Scanner from the Affymetrix GeneChip® Instrument System

data_processing: Microarray intensities were normalized using the GCRMA package in R.

organism: Arabidopsis thaliana

source_name: Arabidopsis, combined dark, N rich treatment, SALK_070989

label_protocol: RNA was converted into cDNA, amplified and labelled with GeneChip 3' IVT Express Kit Assay (Affymetrix)

growth_protocol: Seeds were vapor-phase sterilized, vernalized for 3 days, then grown on basal MS media with 0.5g/l MES hydrate, 0.1% [w/v] sucrose, 1%[w/v] agar at pH 5.7. Plants were grown vertically on plates for 14 days in an Intellus environment controller (Percival Scientific, Perryunder long day (16h light, 8h dark) conditions with light intensity of 50µmol m-2s-1 at a constant temp of 22C.

extract_protocol: RNA as extracted from shoots using an Rneasy Mini Kit with Rnase-free DNaseI Set (QIAGEN)

treatment_protocol: Seedlings were harvested two hours after start of light period and flash frozen in liquid N.

tag: genotype

tag: light treatment

value: Dark

tag: nitrogen treatment

value: pN


title: ESS low-grade patient 10 [aCGH]

tag: tissue


title: SALK_070989 in combined treatment 2, rep 3

description: Gene expression data from shoot


title: ESS low-grade patient 8 [aCGH]


title: plasma of healthy control sample 4


title: ESS low-grade patient 5 [aCGH]


title: ESS low-grade patient 6 [aCGH]


title: ESS high-grade patient 4 [aCGH]

source_name: ESS high-grade patient

value: high-grade endometrial stromal sarcomas (ESS) patient

value: high-grade endometrial stromal sarcoma


title: plasma of healthy control sample 1 (Soutch China)

description: pooled samples from 15 age and gender matched people


title: ESS low-grade patient 4 [aCGH]


title: ESS high-grade patient 2 [aCGH]


title: ESS low-grade patient 2 [aCGH]


title: ESS low-grade patient 7 [aCGH]


title: ESS low-grade patient 9 [aCGH]


title: ESS high-grade patient 1 [aCGH]


title: Xenopus laevis expression data from juvenile inner ear tissue juv_3

growth_protocol: Juvenile Xenopus laevis (n=6) were approximately 3 months old with an average weight of 9.6 ± 0.1 g and an average length of 4.6 ± 0.2 cm and obtained from Nasco (Fort Atkinson, WI). Animal procedures and protocols were approved by the Institutional Animal Care and Use Committee (IACUC) of New Mexico State University.


title: SALK_070989 in combined treatment 2, rep 2

description: Gene expression data from shoot


title: COL-0 in combined treatment 2, rep 1

description: Gene expression data from shoot

source_name: Arabidopsis, combined dark, N rich treatment, COL-0


title: COL-0 in combined treatment 2, rep 2

description:
Gene expression data from shoot
Third replicate was destroyed during liquid nitrogen collection


title: SALK_070989 in combined treatment 1, rep 3

description: Gene expression data from shoot

source_name: Arabidopsis, combined dark, N absent treatment, SALK_070989

value: mN


title: plasma of healthy control sample 3


title: plasma of healthy control sample 2


title: COL-0 in combined treatment 1, rep 2

source_name: Arabidopsis, combined dark, N absent treatment, COL-0


title: plasma of hypertension sample 5

source_name: plasma of hypertension patient

value: hypertension patient


title: plasma of hypertension sample 1  (Soutch China)


title: plasma of hypertension sample 4


title: COL-0 in light treatment, rep 3

description: Gene expression data from shoot

source_name: Arabidopsis, light treatment, COL -0

value: Light


title: plasma of healthy control sample 1


title: SALK_070989 in combined treatment 1, rep 1

description: Gene expression data from shoot


title: COL-0 in combined treatment 1, rep 1

description: Gene expression data from shoot


title: plasma of hypertension sample 1


title: plasma of hypertension sample 3


title: plasma of hypertension sample 2


title: SALK_070989 in light treatment, rep 1

description: Gene expression data from shoot

source_name: Arabidopsis, light treatment, SALK_070989


title: SALK_070989 in dark treatment, rep 1

description: Gene expression data from shoot

source_name: Arabidopsis, dark treatment, SALK_070989

growth_protocol:
At 13 DAP at the start of the light period, seedling plate was wrapped in a double layer of foil to extend darkness then placed back in the same chamber. On 14 DAP,  seedlings were harvested in complete darkness two hours after putative start of light period.
Seeds were vapor-phase sterilized, vernalized for 3 days, then grown on basal MS media with 0.5g/l MES hydrate, 0.1% [w/v] sucrose, 1%[w/v] agar at pH 5.7. Plants were grown vertically on plates for 14 days in an Intellus environment controller (Percival Scientific, Perryunder long day (16h light, 8h dark) conditions with light intensity of 50µmol m-2s-1 at a constant temp of 22C.


title: SALK_070989 in combined treatment 1, rep 2

description: Gene expression data from shoot


title: SALK_070989 in dark treatment, rep 2

description: Gene expression data from shoot


title: SALK_070989 in light treatment, rep 2

description: Gene expression data from shoot


title: COL-0 in light treatment, rep 2

description: Gene expression data from shoot


title: SALK_070989 in N absent treatment, rep 2

description: Gene expression data from shoot

source_name: Arabidopsis, N absent treatment, SALK_070989

growth_protocol:
Seedlings were grown on basal MS media without N (custom GIBCO) and supplemented with 1 mM KNO3, 0.5g/l MES hydrate (Sigma-Aldrich), 0.1% [w/v] sucrose, 1% [w/v] agar at pH5.7. At 14 DAP during the start of the light period seedlings were transferred to control media (basal MS media without N (Phytotech) supplemented with 20mM KCl, 0.5 g/l MES hydrate (Sigma-Aldrich), 0.1% [w/v] sucrose, 1% [w/v] agar at pH 5.7) for two hours and then harvested  and flash frozen in liquid N.
Seeds were vapor-phase sterilized, vernalized for 3 days, then grown on basal MS media with 0.5g/l MES hydrate, 0.1% [w/v] sucrose, 1%[w/v] agar at pH 5.7. Plants were grown vertically on plates for 14 days in an Intellus environment controller (Percival Scientific, Perryunder long day (16h light, 8h dark) conditions with light intensity of 50µmol m-2s-1 at a constant temp of 22C.


title: COL-0 in dark treatment, rep 3

description: Gene expression data from shoot

source_name: Arabidopsis, dark treatment, COL -0


title: COL-0 in dark treatment, rep 2

description: Gene expression data from shoot


title: COL-0 in dark treatment, rep 1

description: Gene expression data from shoot


title: SALK_070989 in dark treatment, rep 3

description: Gene expression data from shoot


title: SALK_070989 in light treatment, rep 3

description: Gene expression data from shoot


title: COL-0 in N absent treatment, rep 3

description: Gene expression data from shoot

source_name: Arabidopsis, N absent treatment, COL-0


title: COL-0 in N absent treatment, rep 2

description: Gene expression data from shoot


title: SALK_070989 in N rich treatment, rep 2

description: Gene expression data from shoot

source_name: Arabidopsis, N rich treatment, SALK_070989

growth_protocol:
Seedlings were grown on basal MS media without N (custom GIBCO) and supplemented with 1 mM KNO3, 0.5g/l MES hydrate (Sigma-Aldrich), 0.1% [w/v] sucrose, 1% [w/v] agar at pH5.7. At 14 DAP during the start of the light period seedlings were transferred to N-rich media (basal MS media without N (Phytotech) supplemented with 20mM NH4NO3, 20 mM KNO3, 0.5 g/l MES hydrate (Sigma-Aldrich), 0.1% [w/v] sucrose, 1% [w/v] agar at pH 5.7) for two hours and then harvested  and flash frozen in liquid N.
Seeds were vapor-phase sterilized, vernalized for 3 days, then grown on basal MS media with 0.5g/l MES hydrate, 0.1% [w/v] sucrose, 1%[w/v] agar at pH 5.7. Plants were grown vertically on plates for 14 days in an Intellus environment controller (Percival Scientific, Perryunder long day (16h light, 8h dark) conditions with light intensity of 50µmol m-2s-1 at a constant temp of 22C.


title: SALK_070989 in N rich treatment, rep 1

description: Gene expression data from shoot


title: SALK_070989 in N rich treatment, rep 3

description: Gene expression data from shoot


title: COL-0 in N absent treatment, rep 1

description: Gene expression data from shoot


title: SALK_070989 in N absent treatment, rep 1

description: Gene expression data from shoot


title: SALK_070989 in N absent treatment, rep 3

description: Gene expression data from shoot


title: COL-0 in N rich treatment, rep 3

description: Gene expression data from shoot

source_name: Arabidopsis, N rich treatment, COL-0


title: COL-0 in light treatment, rep 1

description: Gene expression data from shoot


title: COL-0 in N rich treatment, rep 2

description: Gene expression data from shoot


title: SALK_070989 steady treatment, rep 3

description: Gene expression data from shoot

source_name: Arabidopsis, steady treatment, SALK_070989


title: COL-0 steady treatment, rep3

description: Gene expression data from shoot

source_name: Arabidopsis, steady treatment, COL-0


title: COL-0 in N rich treatment, rep 1

description: Gene expression data from shoot


title: SALK_070989 steady treatment, rep 1

description: Gene expression data from shoot


title: SALK_136009 steady treatment, rep 3

description: Gene expression data from shoot

source_name: Arabidopsis, steady treatment, SALK_136009


title: SALK_070989 steady treatment, rep 2

description: Gene expression data from shoot


title: SALK_016954 steady treatment, rep 2

description: Gene expression data from shoot

source_name: Arabidopsis , steady treatment, SALK_016954


title: COL-0 steady treatment, rep2

description: Gene expression data from shoot


title: SALK_136009 steady treatment, rep 2

description: Gene expression data from shoot


title: SALK_136009 steady treatment, rep 1

description: Gene expression data from shoot


title: SALK_016954 steady treatment, rep 1

description: Gene expression data from shoot


title: SALK_016954 steady treatment, rep 3

description: Gene expression data from shoot


title: hypoxia TH01R008

city: Indianapolis

first: Tim

last: Lahm

address: 980 W Walnut Street

institute: Indiana University

hyb_protocol: standard Affymetrix protocol with hyb for 17 hours

scan_protocol: Scanned by GS3000 7G, using Affymetrix Command console

data_processing: CEL files were imported into Partek, ). RMA (robust multi-array average) signals were generated for the core probe sets using the RMA background correction, Quantile normalization, and summarization by Median Polish. Summarized signals for each probe set were log2 transformed.

organism: Rattus norvegicus

source_name: lung

label_protocol: Ambion WT expression kit

extract_protocol: The lung vasculature was cleared of blood by inserting a catheter into the PA and flushing it with saline. The right lung was snap frozen in liquid nitrogen and used for RNA isolation. Trizol RNA extraction. RNA was isolated from lung homogenates using the TRIzol Plus RNA isolation kit (Ambion, Carlsbad, CA) and further purified for microarray analysis using RNeasy clean up columns (RNeasy mini kit, Qiagen, Germantown, MD).  Quality of the total RNA was assessed by Agilent Bioanalyzer. The RNA integrity number (RIN) for all samples was ≥ 9.

treatment_protocol: A group of four male Sprague-Dawley rats (250-300 g, Charles River, Wilmington, MA) were implanted subcutaneous osmotic pumps (Alzet, Cupertino, CA) containing E2 released at a flow rate of 75 µg/kg/day for three weeks.An additional group of four male rats were implanted with E2 osmotic pumps and concomitantly administered the nonselective ER-antagonist ICI 182,780 (ICI; Tocris, Bristol, United Kingdom) daily via subcutaneous injection (3 mg/kg/day). Following one week of recovery, E2, E2 + ICI treated rats, and four male hypoxic control rats were exposed to two weeks of hypobaric hypoxia (Patm=362 mmHg; equivalent to 10% FiO2 at sea level).  An additional four male rats were used as normoxic controls.

value: hypoxia

tag: estrogen

value: no

tag: fulvestrant


title: WT seedlings, biological rep 1

city: Ikoma

first: Misato

last: Ohtani

address: 8916-5 Takayama-cho

department: Graduate School of Biological Sciences

country: Japan

institute: NAIST

description: Gene expression data from seedlings

hyb_protocol: Following fragmentation, 15 micro g of cRNA were hybridized for 16 hrs at 45 Celsius degree on GeneChip. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data (.cel files) were processed with RMA (Robust Multichip Array, Irizarry and Hobbs, 2003) function of Bioconductor software package of R programming langage (http://www.r-project.org/).

source_name: Arabidopsis seedlings 9-day-old

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 nano g of total RNA.

growth_protocol: Plants were grown on B5-agar (0.8%) plates supplemented with 2% sucrose for 9 days under continuous light (80 µmol photons m-2 sec-1).

extract_protocol: Total RNA was extracted from frozen seedling samples using Sepasol-RNA  (Nacalai tesque, Kyoto, Japan) according to the manufacturer's instructions. They were then purified by RNeasy Plant Mini Kit (QIAGEN, MD, USA).

value: Seedling

value: Wild type (Columbia accession)


title: WT seedlings, biological rep 2

description: Gene expression data from seedlings


title: COL-0 steady treatment, rep1

description: Gene expression data from shoot


title: hypoxia+estrogen TH01R012

tag: treatment


title: hypoxia+estrogen+fulvestrant TH01R013

value: fulvestrant


title: hypoxia+estrogen TH01R011


title: hypoxia+estrogen+fulvestrant TH01R016


title: hypoxia TH01R007


title: hypoxia+estrogen TH01R010


title: hypoxia+estrogen+fulvestrant TH01R015


title: hypoxia+estrogen TH01R009


title: css1 seedlings, biological rep 2

description: Gene expression data from seedlings

value: css1 mutant


title: hypoxia+estrogen+fulvestrant TH01R014


title: hypoxia TH01R006


title: hypoxia TH01R005


title: normoxia TH01R004


title: normoxia TH01R003

value: normal


title: css1 seedlings, biological rep 1

description: Gene expression data from seedlings


title: 80Adenine-2

city: Taipei

first: Guang-Huar

last: Young

state: Taiwan (TWN)

address: 6F.-3, No.21, Ln. 583, Ruiguang Rd., Neihu Dist., Taipei City 114, Taiwan (R.O.C.)

department: Scientific Research

country: Taiwan

hyb_protocol: Each labeled cDNA was hybridized with 135,000 probes and scanned by MS200 microarray scanner performed according to the procedures recommended from Phalanx Biotech Mouse Genome OneArray's user guide.

scan_protocol: Scanning was performed by Phalanx Biotech, following their standard operating protocol.

data_processing: The raw data (.gpr 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).

source_name: Microglial cells BV2

label_protocol: The Cy5 labeled cDNA was then performed using Phalanx Biotech Genome OneArray.

growth_protocol: The murine microglial cell line (BV2) was maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 4 mM L-glutamine, 2 mM sodium pyruvate, and 100 ug/mL penicillin-streptomycin. Cells were incubated at 37∘C under 5% CO2 and 95% relative humidity.  this experiment were between passages 3 and 8.

extract_protocol: Total RNA was extracted by using TRIzol® reagent (Life technology) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer at the Harvard-Partners Center for Genetics and Genomics (Harvard Medical School, Cambridge, MA USA). The extracted RNA passed the quality test done by the Agilent 2100 Bioanalyzer instrument was used for cDNA synthesis.

treatment_protocol: BV2 cells were seeded into 6 cm-dish in a density of 1 × 1000000 cells/dish. After incubation overnight, cells were treated with various concentration of adenine (0, 20, 80 uM) for 1h.

tag: cell line

tag: cell type

value: Immortal microglial cell line

tag: treated with

value: 250 uM adenine


title: 20Adenine-2

value: 80 uM adenine


title: 20Adenine-1


title: Western-Diet-Females-2

city: Kuopio

first: Markus

last: Storvik

address: University of Eastern Finland

department: Pharmacology

country: Finland

institute: University of Eastern Finland

hyb_protocol: The agilent chip labeling, hybridization and scanning were performed at the Biomedicum Functional Genomics Unit, University of Helsinki using standard agilent procedures

data_processing: The data was normalized using mean normalization, and genes with detectable expression in four chips were used in further analyses

source_name: small intestine

growth_protocol: standard conditions

extract_protocol: total RNA extracted from small intestine using the RNeasy Mini kit (Qiagen)

treatment_protocol: an 18 months feeding experiment

tag: strain

value: C57BL/6J Min/+

value: Female

value: small intestine

tag: diet

value: Diet modified from AIN-93G, with high fat and low fiber, vitamin D, calcium and folate. (66.4% of total fat from milk, and 33.6% from rapeseed and sunflower oil)


title: normoxia TH01R001


title: Control 2

description: C

value: none (control)


title: 80Adenine-1


title: Western-Diet-Females-1

scan_protocol: The agilent chip labeling, hybridization and scanning were performed at the Biomedicum Functional Genomics Unit, University of Helsinki using standard agilent procedures

tag: gender


title: Control 1

description: C


title: Control-Males-1

label_protocol: The agilent chip labeling, hybridization and scanning were performed at the Biomedicum Functional Genomics Unit, University of Helsinki using standard agilent procedures

value: Male

value: semisynthetic unmodified AIN-93G diet


title: MS-/EMB-_rep7

city: Victoria

first: Ben

middle: F

last: Koop

state: BC

address: PO Box 3020 STN CSC

department: Biology

country: Canada

institute: The University of Victoria

hyb_protocol: Samples were hybridized to oligonucleotide microarrays as per manufacturers' instructions for Low-Input Quick Amp kits (Agilent; v6.5). Arrays were designed using previously annotated ESTs from both Pacific and Atlantic L. salmonis (Yasuike et al. 2012; eArray design ID 024389; Agilent).

scan_protocol: Scanned at 5 micrometer resolution on a ScanArray Express (Perkin Elmer) and quantified on Imagene (v8.1; BioDiscovery).

data_processing: For each probe on the microarray, the background median was subtracted from the foreground median. Data analysis was performed in GeneSpring GX14.5 (Agilent). Each array was normalized using an intensity-dependent Lowess normalization. All entities on the array are presented in the attached matrix file here, however, for the analysis, quality control filters for each of the three experiments retained probes that pass the following criteria in at least 65% of the samples in any one condition: raw signal ≥ 500 in both channels and no poor quality flags.

organism: Lepeophtheirus salmonis oncorhynchi

source_name: Copepodid larvae_MS-/EMB-

label_protocol: Labeled cRNA was generated from 825ng total RNA using Low-Input Quick Amp kits (Agilent; v6.5). A Cy3-cRNA reference pool to hybridize alongside samples was created for each of the above experiments, ensuring each experimental condition was included in the pool.

growth_protocol: One pigmented egg string collected from ovigerous L. salmonis was placed into a sterile flask containing 300 mL of aerated seawater and incubated at 10°C for six to eight days.

extract_protocol: Total RNA was extracted from frozen tissue using TRIzol reagent® (Life Technologies), on-column DNase digestion (QIAGEN) followed by RNEasy column purification as per manufacturers’ instructions (QIAGEN). Purified total RNA was tested by agarose gel and automated electrophoresis (Experion; Bio-Rad) and spec.

treatment_protocol: Emamectin benzoate was prepared to 1 ug/L (ppb) using fresh sea water. A total of 28 pools of ~75 copepodid larvae derived from individual egg strings were divided into control (0 ppb EMB) and treated (1 ppb EMB) groups, n = 14 for each group. Half of each group (i.e. control and treated) was derived from egg strings that tested positive for F. margolisi infection (n = 7/group). The remaining pools were derived from F. margolisi negative eggs.

tag: species

value: Copepodid lice (Pacific Canada)

tag: presence of f. margolisi

value: Negative

tag: emb concentration (ppb)

source_name: all condition pool_reference

tag: sample type

value: pooled reference


title: Control-Females-2


title: MS+/EMB+_rep6

source_name: Copepodid larvae_MS+/EMB+

value: Positive


title: Western-Diet-Males-1


title: MS-/EMB+_rep6

source_name: Copepodid larvae_MS-/EMB+


title: Control-Males-2


title: MS+/EMB+_rep7


title: normoxia TH01R002

value: no


title: MS+/EMB+_rep5


title: MS-/EMB+_rep7


title: MS+/EMB-_rep7

source_name: Copepodid larvae_MS+/EMB-


title: Control-Females-1


title: MS+/EMB-_rep5


title: MS+/EMB+_rep4


title: MS-/EMB-_rep6


title: MS-/EMB-_rep5


title: MS+/EMB-_rep4


title: MS+/EMB+_rep3


title: MS+/EMB-_rep6


title: Western-Diet-Males-2


title: MS-/EMB+_rep3


title: MS-/EMB-_rep3


title: MS-/EMB-_rep1


title: MS+/EMB-_rep2


title: MS-/EMB+_rep5


title: MS-/EMB+_rep1


title: MS+/EMB-_rep3


title: MS-/EMB-_rep4


title: MS-/EMB+_rep4


title: HFD-NI1

first: Maria

middle: M.

last: Mota

address: Av. Prof Egas Moniz

country: Portugal

institute: IMM Lisboa

description: gene expression of RD versus HFD

hyb_protocol: 45°C for 16h under rotation (60 rpm)

scan_protocol: Affymetrix Genechip Scanner 3000 7G.

data_processing: R/Bioconducter

source_name: liver tissue of HFD fed mice for 2 days

label_protocol: GeneChip WT Terminal Labeling Kit according to manufacturer description

growth_protocol: C57BL/6 mice fed ad libitum on regular diet (RD) or high fat diet (HFD) for 2 days

extract_protocol: Total RNA extracted using Qiagen RNeasy Kit

treatment_protocol: Harvasted tissue immediately frozen in liquid nitrogen

value: liver


title: RD-NI1

description: gene expression of RD versus HFD

source_name: liver tissue of RD fed mice for 2 days


title: RD-NI2

description: gene expression of RD versus HFD


title: HFD-NI2

description: gene expression of RD versus HFD


title: MS+/EMB+_rep2


title: MS+/EMB+_rep1


title: E7R_027f02 -1-

city: Ulm

first: Alexey

last: Ushmorov

address: Albert-Einstein-Allee 11

department: Institute of Physiological Chemistry

country: Germany

institute: Ulm University

description: L1236 cells incubated with 5-Aza-dC for 24 hours, harvested after additional 72h incubation

hyb_protocol: Labeled ssDNA was hybridized to Human Gene 1.0 ST Affymetrix GeneChip arrays (Affymetrix, Santa Clara, CA).

scan_protocol: The chips were scanned with a Affymetrix GeneChip Scanner 3000 according to the Affimetrix protocol.

data_processing: The microarray data were processed using GeneSifter software (http://www.geospiza.com) using RMA normalization protocol.

source_name: L1236, 5-Aza-dC treatment, 24h

label_protocol: The total RNAs were amplified and labeled following the Whole Transcript (WT) Sense Target Labeling Assay (http://www.affymetrix.com).

growth_protocol: L1236 and L428 cells were grown in RPMI1640 medium with addition of 10% FBS, glutamine and antibiotics at 37 ºC, 5% CO2.

extract_protocol: Total RNA was isolated with RNeasy mini kit (QIAGEN) according to the manufacturers instruction.

treatment_protocol: L1236 and L428 cells were incubated with 1 µM 5-Aza-dC. The experiment was done in triplicate. After 24 h of incubation, cells were washed. After additional 72h incubation in normal medium, total RNA was isolated with RNeasy mini kit (QIAGEN).

value: cHL cell line


title: MS-/EMB-_rep2


title: MS-/EMB+_rep2


title: MS+/EMB-_rep1


title: HFD-NI3

description: gene expression of RD versus HFD


title: RD-NI3

description: gene expression of RD versus HFD


title: E7R_027e02 -1-

description: L1236 cells without treatment

source_name: L1236, no treatment


title: KL_8_018Z_F1shR-81-2

description: 018Z transduced with a lentiviral vector expressing FOXO1 shRNA

source_name: 018Z shFOXO1-2

growth_protocol: RS4;11 and 018Z BCP-ALL cells were grown in  RPMI1640 medium with addition of 10% FBS, glutamine and antibiotics at 37 ºC, 5% CO2

treatment_protocol: RS4;11 and 018Z BCP-AL cells were transduced with a lentiviral vector expressing scrambled shRNA of shRNA tageting human FOXO1 mRNA. The infected cells were sorted on Day 5 after transduction.  The experiment was done in duplicate.  Total RNA was isolated with RNeasy mini kit (QIAGEN).

value: BCP-ALL cell  line


title: E7R_027e01 -1-

description: L1236 cells without treatment

source_name: L428, 5-Aza-dC treatment, 24 h

value: cHL cell  line


title: KL_3_RS4_11_F1shR-81-1

description: RS4;11 transduced with a lentiviral vector expressing FOXO1 shRNA

source_name: RS4;11 shFOXO1-1


title: KL_7_018Z_F1shR-81-1

source_name: 018Z shFOXO1-1


title: E7R_027f01 -1-


title: E7R_027e03 -1-

description: L1236 cells without treatment


title: E7R_027d02 -1-

description: L428 cells incubated with 5-Aza-dC for 24 hours, harvested after additional 72h incubation


title: E7R_027d03 -1-


title: E7R_027c03 -1-

description: L428 cells without treatment

source_name: L428, no treatment


title: KL_6_018Z_Scram-2

description: 018Z transduced with a lentiviral vector expressing scrambled shRNA

source_name: 018Z scr2

value: BCP-ALL cell line


title: KL_4_RS4_11_F1shR-81-2

source_name: RS4;11 shFOXO1-2


title: E7R_027f03 -1-


title: E7R_027c02 -1-

description: L428 cells without treatment


title: KL_5_018Z_Scram-1

source_name: 018Z scr1


title: KL_1_RS4_11_Scram-1

description: RS4;11 transduced with a lentiviral vector expressing scrambled shRNA

source_name: RS4;11 scr1


title: KL_2_RS4_11_Scram-2

source_name: RS4;11 scr2


title: BOSS17-V

city: Amsterdam

first: Richard

last: Volckmann

state: Noord-Holland

address: van der Boechorststraat 6a

department: Laboratory of Experimental Oncology and Radiobiology

country: Netherlands

institute: msterdam UMC and University of Amsterdam

hyb_protocol: 10 µg of labeled cRNA was hybridized to Affymetrix Human genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).

scan_protocol: Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protoco

data_processing: Expression data (cel files) were normalized with the MAS5.0 algorithm (target signal = 100) using GCOS software (Affymetrix)

source_name: primary colon cancer resection

label_protocol: RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 200ng of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.

growth_protocol: Human Tissue

extract_protocol: Total RNA was isolated using RNeasy (Qiagen) according to manufacturer’s protocol,

treatment_protocol: Not Applicalbe

value: primary colon cancer resection

tag: specimen id

tag: tumor location

value: ascending colon

tag: disease status

value: AJCC Stage III


title: KB001-DD6 vs. KB001-ref

city: Utrecht

first: Marian

last: Groot Koerkamp

state: Utrecht

address: Heidelberglaan 25

department: Research

institute: Princess Maxima Center for Pediatric Oncology

hyb_protocol: Tecan HS4800 hybridization [details provided in the Series supplementary file 'protocol_details.txt']

scan_protocol: scanning of slides using Agilent G256BA; features were extracted using Imagene software from Biodiscovery. Imagene feature extraction

data_processing: [genes, no bg corr, hybset spec. dye corr]: Normalization was done using print-tip LOESS as described in (Yang et al. 2002), for all gene probes using no background substraction and a span of 0.4. Probes flagged as absent, or with a (nearly) saturated signal (i.e., > 2^15) in either channel were not considered for the estimation of the LOESS curve. Signals were corrected for dye bias using intrinsic gene-specific dye biases estimated from the hybset itself, as described in Margaritis, Lijnzaad et al., Mol. Sys. Biol. 2009

organism: Canis lupus familiaris

source_name: KB001-growth plate-DD

label_protocol: robot amplification and labeling v1.0 [details provided in the Series supplementary file 'protocol_details.txt']

extract_protocol: RNA isolation using Trizol v1.0 (tissue sections) [details provided in the Series supplementary file 'protocol_details.txt']

tag: breed

value: DD

value: growth plate

tag: reference

value: mixed reference (multiple canine organs, including liver, spleen, kidney, lung, heart, intestine, bone)


title: E7R_027c01 -1-

description: L428 cells without treatment


title: E7R_027d01 -1-

source_name: L428, Aza treatment, 24 h


title: KB001-MP2 vs. KB001-ref

source_name: KB001-growth plate-MP

value: MP


title: KB001-MP3 vs. KB001-ref


title: BOSS17-II

tag: tissue


title: BOSS17-IV


title: BOSS13-V

value: caecum

value: AJCC Stage II


title: KB001-DD5 vs. KB001-ref


title: BOSS13-IV


title: KB001-DD3 vs. KB001-ref


title: BOSS13-III


title: BOSS13-II


title: BOSS11-IV

value: AJCC Stage I


title: KB001-DD4 vs. KB001-ref


title: BOSS11-I


title: BOSS11-V


title: KB001-DD1 vs. KB001-ref


title: KB001-DD2 vs. KB001-ref


title: BOSS11-III


title: BOSS11-II


title: BOSS10-V

value: hepatic flexure


title: BOSS10-II


title: BOSS10-IV


title: BOSS09-V

value: AJCC Stage IV


title: BOSS09-IV


title: BOSS10-I


title: BOSS09-II


title: BOSS10-III


title: BOSS07-I

value: sigmoid


title: BOSS07-V


title: BOSS09-I


title: BOSS07-IV


title: BOSS01-V


title: BOSS01-IV


title: BOSS01-III


title: BOSS01-II


title: BOSS01-I


title: tomato leaves at 12 hpi of NPA-pretreated plants, biological rep1

first: Ruey-Fen

last: Liou

address: 1, Sec. 4, Roosevelt Road

department: Plant Pathology and Microbiology

institute: National Taiwan University

description: Gene expression data from NPA-pretreated tomato leaves at 12 hours post inoculation with P. parasitica

hyb_protocol: Following fragmentation, 10 μg of cRNA were hybridized with GeneChip Tomato Genome Array at 45oC for 16 hours. Subsequently, GeneChips were washed and stained in the Affymetrix GeneChip fluidics station 450.

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

data_processing: The raw data were analyzed by using Gene-Spring® GX 10 (Agilent Technologies) based on the Robust Multi-array Average (RMA) algorithm. The processes included background correction, log2 transformation, quantile normalization, and conversion to obtain an expression measure for each probe set on each array. As referring to the histogram of the expression value, normalized probe signal values less than 5.8 in all of the chips were considered to be the result of nonspecific hybridization, and then resulted in 8664 probes.

organism: Solanum lycopersicum

source_name: leaves (with prior NPA treatment for 3 days) at 12 hours post pathogen inoculation

label_protocol: Biotinylated cRNAs were prepared with 10 μg of plant total RNA according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Seedlings of tomato were grown on a mixture of peat moss, perlite, and vermiculite at 27oC under a 12-hour photoperiod. After pathogen inoculation, plants were kept in a moist chamber (humidity > 90%) under a 12-hour photoperiod.

extract_protocol: Total RNAs were isolated by using the Trizol Reagent according to the manufacturer's instructions.

treatment_protocol: The aerial parts of the tomato plants were sprayed with NPA (1 g/L) or water till run-off. For preparation of the NPA solution, 1 g phosphorous acid (Sigma-Aldrich, St. Louis, MO, USA) was mixed with 1 L ddH2O, followed by the addition of 1 g potassium hydroxide (Sigma-Aldrich), to adjust the pH to 6.3. At 3 days post treatment, plants were further inoculated with zoospores of P. parasitica till run-off, and kept in a moist chamber (humidity > 90%) to facilitate disease development.

tag: cultivar

value: Summer sweet

tag: treatment

value: NPA

tag: time (post-treatment)

value: 3 hours

tag: inoculation

value: pathogen Phytophthora parasitica

tag: time (post-inoculation)

value: 12 hours

value: leaves


title: tomato leaves at 12 hpi of water-pretreated plants, biological rep1

description: Gene expression data from water-pretreated tomato leaves at 12 hours post inoculation with P. parasitica

source_name: leaves (with prior water treatment for 3 days) at 12 hours post pathogen inoculation

value: water


title: tomato leaves at 6 hpi of NPA-pretreated plants, biological rep3

description: Gene expression data from NPA-pretreated tomato leaves at 6 hours post inoculation with P. parasitica

source_name: leaves (with prior NPA treatment for 3 days) at 6 hours post pathogen inoculation

value: 6 hours


title: tomato leaves at 12 hpi of NPA-pretreated plants, biological rep2


title: tomato leaves at 6 hpi of NPA-pretreated plants, biological rep2


title: tomato leaves at 12 hpi of NPA-pretreated plants, biological rep3


title: tomato leaves at 12 hpi of water-pretreated plants, biological rep3


title: genomic DNA; HGDP cell lines [HGDP00964]

city: Philadelphia

first: Oana

last: Carja

state: Pennsylvania

address: 204K Lynch Labs, 433 S University Ave

institute: University of Pennsylvania

description:
Standard Illumina Protocol
HGDP00964

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

scan_protocol: BeadChips were imaged  using HiScan with standard recommended Illumina scanner setting.

data_processing: Raw intensities extracted using GenomeStudio v2010.1.

label: Cy3 and Cy5

source_name: HGDP cell lines

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was isolated using Qiagen AllPrep DNA/RNA mini kit according to manufacturer's instructions.

tag: population

value: Yakut


title: genomic DNA; HGDP cell lines [HGDP00967]

description:
Standard Illumina Protocol
HGDP00967


title: tomato leaves at 12 hpi of water-pretreated plants, biological rep2


title: tomato leaves at 6 hpi of NPA-pretreated plants, biological rep1


title: genomic DNA; HGDP cell lines [HGDP00950]

description:
Standard Illumina Protocol
HGDP00950


title: genomic DNA; HGDP cell lines [HGDP00239]

description:
Standard Illumina Protocol
HGDP00239

value: Pathan


title: genomic DNA; HGDP cell lines [HGDP00948]

description:
Standard Illumina Protocol
HGDP00948


title: genomic DNA; HGDP cell lines [HGDP00959]

description:
Standard Illumina Protocol
HGDP00959


title: tomato leaves at 6 hpi of water-pretreated plants, biological rep3

description: Gene expression data from water-pretreated tomato leaves at 6 hours post inoculation with P. parasitica

source_name: leaves (with prior water treatment for 3 days) at 6 hours post pathogen inoculation


title: genomic DNA; HGDP cell lines [HGDP00247]

description:
Standard Illumina Protocol
HGDP00247


title: genomic DNA; HGDP cell lines [HGDP00955]

description:
Standard Illumina Protocol
HGDP00955


title: genomic DNA; HGDP cell lines [HGDP01277]

description:
Standard Illumina Protocol
HGDP01277

value: Mozabite


title: genomic DNA; HGDP cell lines [HGDP00213]

description:
Standard Illumina Protocol
HGDP00213


title: tomato leaves at 3 dpt with NPA, biological rep2

description: Gene expression data from tomato leaves at 3 days post treatment with NPA


title: genomic DNA; HGDP cell lines [HGDP00258]

description:
Standard Illumina Protocol
HGDP00258


title: genomic DNA; HGDP cell lines [HGDP00222]

description:
Standard Illumina Protocol
HGDP00222


title: genomic DNA; HGDP cell lines [HGDP00232]

description:
Standard Illumina Protocol
HGDP00232


title: tomato leaves at 6 hpi of water-pretreated plants, biological rep1


title: genomic DNA; HGDP cell lines [HGDP01274]

description:
Standard Illumina Protocol
HGDP01274


title: genomic DNA; HGDP cell lines [HGDP01259]

description:
Standard Illumina Protocol
HGDP01259


title: genomic DNA; HGDP cell lines [HGDP00237]

description:
Standard Illumina Protocol
HGDP00237


title: tomato leaves at 3 dpt with water, biological rep3

description: Gene expression data from tomato leaves at 3 days post treatment with water


title: tomato leaves at 3 dpt with water, biological rep1

source_name: leaves at 3 days post treatment with water


title: genomic DNA; HGDP cell lines [HGDP01275]

description:
Standard Illumina Protocol
HGDP01275


title: genomic DNA; HGDP cell lines [HGDP01258]

description:
Standard Illumina Protocol
HGDP01258


title: genomic DNA; HGDP cell lines [HGDP01264]

description:
Standard Illumina Protocol
HGDP01264


title: genomic DNA; HGDP cell lines [HGDP00877]

description:
Standard Illumina Protocol
HGDP00877

value: Maya


title: genomic DNA; HGDP cell lines [HGDP01262]

description:
Standard Illumina Protocol
HGDP01262


title: tomato leaves at 12 hpt with NPA, biological rep2

description: Gene expression data from tomato leaves 12 hours after NPA treatment

data_processing: The raw data were analyzed by using Gene-Spring® GX 10 (Agilent Technologies) based on the Robust Multi-array Average (RMA) algorithm. The processes included background correction, log2 transformation, quantile normalization, and conversion to obtain an expression measure for each probe set on each array. As referring to the histogram of the expression value, normalized probe signal values less than 5.5 in all of the chips were considered to be the result of nonspecific hybridization, and then resulted in 8488 probes.

source_name: leaves at 12 hpt with NPA

growth_protocol: Seedlings of tomato were grown on a mixture of peat moss, perlite and vermiculite at 27oC under a 12 hour photoperiod.

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

treatment_protocol: Tomato plants were sprayed thoroughly with NPA or water until run-off. For preparation of NPA, 1 g phosphorous acid (Sigma-Aldrich, St. Louis, MO, USA) was mixed with 1 L ddH2O, followed by the addition of 1 g potassium hydroxide (Sigma-Aldrich) to adjust the pH to 6.3.


title: tomato leaves at 3 dpt with NPA, biological rep3

source_name: leaves at 3 days post treatment with NPA


title: tomato leaves at 12 hpt with water, biological rep2

description: Gene expression data from tomato leaves 12 hours after water treatment

source_name: leaves at 12 hpt with water


title: tomato leaves at 12 hpt with NPA, biological rep1


title: tomato leaves at 3 dpt with water, biological rep2


title: tomato leaves at 12 hpt with water, biological rep1


title: genomic DNA; HGDP cell lines [HGDP00858]

description:
Standard Illumina Protocol
HGDP00858


title: 201B7_D5_SOX-L_rep1

city: Kyoto

first: Junichi

last: Taniguchi

address: Kitashirakawa-Oiwakecho, Sakyo-Ku

department: Department of Chemistry, Graduate School of Science

institute: Kyoto University

description: Gene expression data from SOX-L-treated cells (on day 5)

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

scan_protocol: Strip was scanned using the Imaging Station.

data_processing: The data were analyzed with Expression Console 1.3.1 and Transcriptome Analysis Console 2.0 using RMA.

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

growth_protocol: 201B7 from Riken BRC was cultured in mTeSR1 medium on Matrigel (hESC-qualified) at 37°C, 5% CO2

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

treatment_protocol: After 2 days from plating, the cells were treated with vehicle or 2 µM of SOX-L in Advanced RPMI 1640 supplemented with 0.2% FBS and 2 mM of L-glutamine. The medium was exchanged on day 1 and RNA was extracted on day 5.

tag: cell line

tag: cell type

value: human induced pluripotent stem cell line

value: PIP SOX-L (2 µM)

tag: time

value: Day 5


title: 201B7_D4_vehicle_rep1

description: Gene expression data from control cells (on day 4)

value: non (vehicle only)

value: Day 4


title: 201B7_D5_vehicle_rep1

description: Gene expression data from control cells (on day 5)


title: tomato leaves at 6 hpt with NPA, biological rep2

description: Gene expression data from tomato leaves 6 hours after NPA treatment

source_name: leaves at 6 hpt with NPA

value: Summer sweet


title: tomato leaves at 6 hpt with NPA, biological rep1

value: NPA


title: genomic DNA; HGDP cell lines [HGDP00854]

description:
Standard Illumina Protocol
HGDP00854


title: genomic DNA; HGDP cell lines [HGDP00713]

description:
Standard Illumina Protocol
HGDP00713

value: Cambodian


title: genomic DNA; HGDP cell lines [HGDP00857]

description:
Standard Illumina Protocol
HGDP00857


title: genomic DNA; HGDP cell lines [HGDP00868]

description:
Standard Illumina Protocol
HGDP00868


title: 201B7_D3_SOX-L_rep1

description: Gene expression data from SOX-L-treated cells (on day 3)

value: Day 3


title: tomato leaves at 6 hpi of water-pretreated plants, biological rep2

value: 3 hours

value: pathogen Phytophthora parasitica


title: genomic DNA; HGDP cell lines [HGDP00721]

description:
Standard Illumina Protocol
HGDP00721


title: genomic DNA; HGDP cell lines [HGDP00715]

description:
Standard Illumina Protocol
HGDP00715


title: 201B7_D3_vehicle_rep1

description: Gene expression data from control cells (on day 3)


title: genomic DNA; HGDP cell lines [HGDP00856]

description:
Standard Illumina Protocol
HGDP00856


title: tomato leaves at 3 dpt with NPA, biological rep1

value: leaves


title: genomic DNA; HGDP cell lines [HGDP00720]

description:
Standard Illumina Protocol
HGDP00720


title: genomic DNA; HGDP cell lines [HGDP00855]

description:
Standard Illumina Protocol
HGDP00855


title: genomic DNA; HGDP cell lines [HGDP00716]

description:
Standard Illumina Protocol
HGDP00716


title: genomic DNA; HGDP cell lines [HGDP00711]

description:
Standard Illumina Protocol
HGDP00711


title: genomic DNA; HGDP cell lines [HGDP00712]

description:
Standard Illumina Protocol
HGDP00712


title: BLOOD64

city: Vancouver

first: Michael

middle: S.

last: Kobor

address: 950 West 28th Avenue

department: Medical Genetics

institute: Centre for Molecular Medicine and Therapeutics / University of British Columbia

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Infinium HumanMethylation450k Beadchip using standard Illumina protocol

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

data_processing: GenomeStudio software V2011.1 with GenomeStudio Methylation Analysis Module Version 1.9.1000 (background-subtraction, colour-correction)

label: Cy5 and Cy3

source_name: BLOOD

extract_protocol: DNA was extracted from samples using the Qiagen DNAeasy DNA extraction kit (Qiagen, Valencia, CA, USA)

tag: well

tag: replicate

value: N

tag: gender

value: M

tag: age

tag: ph

tag: refrigerationdelayhrs


title: BLOOD250rep

value: Y


title: KB001-ref vs. KB001-MP6

tag: reference

value: mixed reference (multiple canine organs, including liver, spleen, kidney, lung, heart, intestine, bone)

tag: breed

value: MP

value: growth plate


title: KB001-ref vs. KB001-MP4


title: KB001-ref vs. KB001-MP5


title: BLOOD245


title: tomato leaves at 6 hpt with water, biological rep2

description: Gene expression data from tomato leaves 6 hours after water treatment

source_name: leaves at 6 hpt with water

tag: cultivar

value: water

value: 6 hours

tag: tissue


title: 201B7_D4_SOX-L_rep1

description: Gene expression data from SOX-L-treated cells (on day 4)

value: human induced pluripotent stem cell line

tag: treatment

value: PIP SOX-L (2 µM)


title: KB001-ref vs. KB001-DD6

value: DD


title: BLOOD94


title: tomato leaves at 6 hpt with water, biological rep1

value: Summer sweet

tag: time (post-treatment)


title: KB001-ref vs. KB001-MP2


title: KB001-ref vs. KB001-DD5


title: BLOOD250


title: KB001-ref vs. KB001-DD4


title: KB001-ref vs. KB001-MP3


title: KB001-ref vs. KB001-DD2


title: BLOOD248

value: F


title: IL-17C x IL-6KO Involved 14 weeks

city: Ann Arbor

first: William

middle: R

last: Swindell

state: MI

address: 1500 E. Medical Center Drive

department: Dermatology

institute: University of Michigan

description:
male and female pooled dorsal skin n=5
17C 6KO In 14

hyb_protocol: Standard Affymetrix protocol 45oC, 16 hrs, 60rpm

scan_protocol: Std GeneChip Scanner 3000

data_processing: Cel files were converted into spreadsheets of observation data using the RMA normalization feature in Affymetrix's Expression Console.

source_name: Skin, IL-17C Overexpression cross IL-6 knock-out Sample, Involved area, 14 weeks old

label_protocol: WT plus labelling protocol

growth_protocol: Control and transgenic mice were bred and housed in full barrier facility with vented racks and provided with food and water ad libitum. Mice were euthanized at 10 or 14 weeks of age and involved and uninvolved areas of dorsal skin collected for use in the analyses. Similar anatomical regions were collected for C57Bl/6 and IL-6KO mice.

extract_protocol: RNA was isolated from skin adjacent to that used for histology and immunostaining as previously described (Wolfram et al. 2009, Am J Pathol 174:1443-1458).

treatment_protocol: Mice were euthanized with an overdose of ketamine/xylazine followed by cervical dislocation.

tag: strain

value: 14 weeks

value: dorsal skin

tag: skin type

value: involved

tag: genotype

value: male and female


title: IL-17C Uninvolved 14 weeks

description:
male and female pooled dorsal skin n=5
17C Un 14

source_name: Skin, IL-17C Overexpression Sample, Uninvolved area, 14 weeks old

value: uninvolved


title: KB001-ref vs. KB001-DD3

source_name: KB001-growth plate-DD

tag: cell type


title: KB001-MP6 vs. KB001-ref


title: KB001-MP5 vs. KB001-ref


title: IL-17C Involved 14 weeks

description:
male and female pooled dorsal skin n=5
17C In 14

source_name: Skin, IL-17C Overexpression Sample, Involved area, 14 weeks old


title: BLOOD189

value: N


title: IL-6KO 14 weeks

description:
male and female pooled dorsal skin n=5
6KO 14

source_name: Skin, IL-6 knock-out Sample, 14 weeks old


title: IL-17C x IL-6KO Uninvolved 14 weeks

description:
male and female pooled dorsal skin n=5
17C 6KO Un 14

source_name: Skin, IL-17C Overexpression cross IL-6 knock-out Sample, Uninvolved area, 14 weeks old


title: BLOOD216

value: M


title: IL-17C x IL-6KO Uninvolved 10 weeks

description:
male and female pooled dorsal skin n=5
17C 6KO Un 10

source_name: Skin, IL-17C Overexpression cross IL-6 knock-out Sample, Uninvolved area, 10 weeks old

value: 10 weeks


title: BLOOD234


title: BLOOD169

value: Y


title: BLOOD135


title: BLOOD169rep


title: KB001-MP4 vs. KB001-ref

source_name: KB001-growth plate-MP

value: MP

value: growth plate

value: mixed reference (multiple canine organs, including liver, spleen, kidney, lung, heart, intestine, bone)


title: BLOOD104


title: BLOOD242


title: BLOOD221


title: KB001-ref vs. KB001-DD1


title: BLOOD101


title: BA7250rep


title: BLOOD163


title: IL-6KO 10 weeks

description:
male and female pooled dorsal skin n=4
6KO 10

source_name: Skin, IL-6 knock-out Sample, 10 weeks old


title: BLOOD133


title: BA7250


title: BA794


title: WT 14 weeks

description:
male and female pooled dorsal skin n=5
Control 14

source_name: Skin, Control Sample, 14 weeks old

value: WT


title: IL-17C Uninvolved 10 weeks

description:
male and female pooled dorsal skin n=5
17C Un 10

source_name: Skin, IL-17C Overexpression Sample, Uninvolved area, 10 weeks old


title: WT 10 weeks

description:
male and female pooled dorsal skin n=4
Control 10

source_name: Skin, Control Sample, 10 weeks old


title: IL-17C Involved 10 weeks

description:
male and female pooled dorsal skin n=5
17C In 10

source_name: Skin, IL-17C Overexpression Sample, Involved area, 10 weeks old


title: BA7248


title: Brain_Transgenic_rep2

first: Robert

middle: H

last: Miller

address: 10900 Euclid Avenue

department: Neurosciences

description: RMA normalized gene expression data from lesioned transgenic mouse brain

hyb_protocol: 15 ug of biotinylated cRNA were fragmented and added to a hybridization cocktail along with bacterial hybridization controls and buffers. This hybridization cocktail was hybridized  overnight at 45°Cin a genechip hybridization Oven 320. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Genechip 3000 scanner A.

data_processing: Scanned fluorescent images of the hybridized chips were converted into spreadsheets of RMA-normalized gene expression signals uning with Affymetrix proprietary Expression Console (EC) ver. 2.0.

source_name: Macrodissected lesion from mouse transgenic brain

label_protocol: Biotinylated cRNA were prepared according to current (2014) Affymetrix protocol from  total RNA

growth_protocol: 5-6 weeks old animals (transgenic and wildtype), sacrificed 7 days post lesion

extract_protocol: The total RNA from each macrodissected brain lesion using mirVana Total RNA extraction kit (Life Technologies, Inc., Gaithersburg, MD, USA) per the manufacturer's instructions.

treatment_protocol: LPC-mediated lesions at 5-6 weeks, followed by CID injection (astrocyte ablation) 48 hrs later; analysis and brains harvested 7 days post lesion

value: transgenic that allows for the selective elimination of non-proliferative GFAP+ astrocytes

value: Lesioned brain


title: Brain_WT_rep3

description: RMA normalized gene expression data from lesioned wildtype mouse brain

source_name: Macrodissected lesion from WT mouse brain

value: wild type


title: Brain_WT_rep1


title: Brain_Transgenic_rep1


title: BCC Histamine-treated - repeat 3

city: Bethesda

first: Babru

middle: Bahan

last: Samal

state: MD

address: 9000 Rockville Pike

department: SMN

institute: NIMH/NIH

description: No additional information.

hyb_protocol: Affy Hybridization Protocol Other: The hybridization cocktail containing biotin-labeled cDNAs was added to the Affymetrix GeneChip Bovine Genome Array (P/N 900562). Using the Affymetrix Fluidics Station and following standard Affymetrix protocol, chips were hybridized and washed and then stained with streptavidin phycoerythrin solution (Molecular Probes), and enhanced with a 0.5 mg/mL biotinylated anti-streptavidin antibody solution (Vector Laboratories).

scan_protocol: Scanning Protocol Other: The probe arrays were scanned using an Affymetrix Gene Chip Scanner 3000.

data_processing:
Data Processing Protocol
Calculation Method: Scanned arrays were analyzed to identify transcripts significantly up- or down-regulated by various treatments applying robust multichip analysis (RMA) normalization.

organism: Bos taurus

source_name: Histamine-treated BCC

label_protocol:
Sample Labeling Protocol
Other: 5 ug of total RNA was employed for One-Cycle Target Labeling according to the Affymetrix recommended protocol (Affymetrix P/N 900493).

extract_protocol:
Sample Extraction Protocol
Other: Total RNA was isolated from cultured chromaffin cells using Trisol and RNAqueous kit (Ambion Life Technologies) and RNA quality and quantity were evaluated by Bioanalyzer (Agilent, Inc).

treatment_protocol:
Treatment type: compound
Agent: histamine
Treatment dose: 10 uM
Treatment time: 6 hours

value: adrenal glands

value: bovine chromaffin cell (BCC)

tag: agent

value: histamine

tag: treatment dose

value: 10 uM

tag: treatment time

value: 6 hours


title: Brain_WT_rep2

institute: Case Western Reserve University


title: Brain_Transgenic_rep3


title: BA7245

tag: well

tag: replicate

tag: gender


title: BA7216

tag: age

tag: ph

tag: refrigerationdelayhrs


title: BCC IFNalpha-treated - repeat 3

description: No additional information.

source_name: IFNalpha-treated BCC

treatment_protocol:
Treatment type: compound
Agent: human interferon-α (PeproTech) (IFNalpha)
Treatment dose: 1 nM
Treatment time: 24 hours

value: IFNalpha (PeproTech)

value: 1 nM

value: 24 hours


title: BCC Histamine-treated - repeat 2

description: No additional information.


title: BA7189

value: N

value: F


title: BCC IFNalpha-treated - repeat 2

description: No additional information.


title: BCC IFNalpha-treated - repeat 1

description: No additional information.


title: BCC Histamine-treated - repeat 1

description: No additional information.


title: BCC IL6-treated - repeat 3

description: No additional information.

source_name: IL6-treated BCC

treatment_protocol:
Treatment type: compound
Agent: Interleukin-6 (IL6)
Treatment dose: 10 nM
Treatment time: 24 hours

value: Interleukin-6 (IL6)

value: 10 nM


title: BA7173

value: M


title: BA7234


title: BCC IL6-treated - repeat 1

description: No additional information.


title: BCC IL6-treated - repeat 2

description: No additional information.


title: BA7169


title: IL-17C x IL-6KO Involved 10 weeks

description:
male and female pooled dorsal skin n=5
17C 6KO In 10

source_name: Skin, IL-17C Overexpression cross IL-6 knock-out Sample, Involved area, 10 weeks old

value: 10 weeks

value: dorsal skin

value: involved

value: male and female


title: BA7104


title: BA7221


title: BCC Untreated Control - repeat 2

description: No additional information.

source_name: Untreated BCC

value: adrenal glands


title: BA7163


title: BA7133


title: BA20248


title: BA7135


title: BCC Untreated Control - repeat 3

description: No additional information.

value: bovine chromaffin cell (BCC)


title: BA764


title: Batf+/+ Treg_3

city: Yokohama

first: Shohei

last: Hori

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

institute: RIKEN Center for Integrative Medical Sciences

description: freshly sorted from FoxP3hCD2.Batf+/+ mice

hyb_protocol: The labeled cDNA was hybridized to Affymetrix GeneChip Mouse Genome 430 2.0 Arrays using Affymetrix standard procedures.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: Expression values for each probe set were calculated with rma method in a GeneSpring GX software package (version 13.0) (Agilent).

source_name: Batf+/+ Treg cells

label_protocol: RNA was subjected to biotinylated cDNA synthesis by using GeneChip 3'IVT Express Kit.

growth_protocol: ex vivo isolated cells

extract_protocol: Total RNA was extracted using Isogen reagent (Nippon Gene) followed by RNeasy mini kit (Qiagen).

value: lymph node and spleen

value: hCD2(+)CD4(+) cells

tag: sorted from

value: FoxP3hCD2.Batf+/+ mice


title: Batf-/- Treg_2

description: freshly sorted from FoxP3hCD2.Batf-/- mice

source_name: Batf-/- Treg cells

tag: tissue

value: FoxP3hCD2.Batf-/- mice


title: Batf-/- Treg_1


title: BA20245


title: Batf+/+ Treg_1


title: BCC Untreated Control - repeat 1

description: No additional information.


title: BA20250


title: BA20234


title: BA2064


title: BA20242


title: R397W Treg_3

description: freshly isolated cells

source_name: hCD2(+)GFP(-)CD4(+) cells sorted from FoxP3R397W:hCD2/WT:GFP mice

label_protocol: RNA was subjected to biotinylated cDNA synthesis by using GeneChip Two-Cycle Target Labeling and Control Reagents.

value: lymph nodes and spleen

value: hCD2(+)GFP(-)CD4(+) cells

value: FoxP3R397W:hCD2/WT:GFP mice


title: I363V Treg_2

description: freshly isolated cells

source_name: hCD2(+)GFP(-)CD4(+) cells sorted from FoxP3I363V:hCD2/WT:GFP mice

value: FoxP3I363V:hCD2/WT:GFP mice


title: R397W Treg_2

description: freshly isolated cells


title: BA20133

value: N


title: I363V Treg_1

description: freshly isolated cells


title: BA20163


title: BA2094


title: Batf-/- Treg_3


title: BA20135


title: A384T Treg_2

description: freshly isolated cells

source_name: hCD2(+)GFP(-)CD4(+) cells sorted from FoxP3A384T:hCD2/WT:GFP mice

value: FoxP3A384T:hCD2/WT:GFP mice


title: BA7101

value: M


title: BA20104


title: A384T Treg_3

description: freshly isolated cells


title: BA20101


title: BA20216


title: BA10250


title: BA1094


title: BA20173


title: A384T Treg_1

description: freshly isolated cells


title: WT Treg (GFP+ from A384T:hCD2/WT:GFP mice)_3

description: freshly isolated cells

source_name: hCD2(-)GFP(+)CD4(+) cells sorted from FoxP3A384T:hCD2/WT:GFP mice

value: hCD2(-)GFP(+)CD4(+) cells


title: WT Treg (GFP+ from A384T:hCD2/WT:GFP mice)_2

description: freshly isolated cells


title: BA102482

value: Y

value: F


title: R397W Treg_1

description: freshly isolated cells


title: WT Treg (hCD2+ from WT:hCD2/WT:GFP mice)_4

description: freshly isolated cells

source_name: hCD2(+)GFP(-)CD4(+) cells sorted from FoxP3WT:hCD2/WT:GFP mice

value: FoxP3WT:hCD2/WT:GFP mice


title: BA102481


title: BA10245


title: BA20169


title: WT Treg (hCD2+ from WT:hCD2/WT:GFP mice)_3

description: freshly isolated cells


title: BA7242


title: Tconv_2

description: freshly isolated cells

source_name: hCD2(-)GFP(-)CD4(+) cells sorted from FoxP3WT:hCD2/WT:GFP mice

value: hCD2(-)GFP(-)CD4(+) cells


title: WT Treg (GFP+ from WT:hCD2/WT:GFP mice)_1

description: freshly isolated cells

source_name: hCD2(-)GFP(+)CD4(+) cells sorted from FoxP3WT:hCD2/WT:GFP mice


title: BA10242


title: WT Treg (GFP+ from WT:hCD2/WT:GFP mice)_2

description: freshly isolated cells


title: Batf+/+ Treg_2


title: Tconv_1

description: freshly isolated cells


title: I363V Treg_3

description: freshly isolated cells


title: R397W FoxP3-transduced T cells_2

description: Naïve CD4(+) T cells were transduced with R397W FoxP3/MIGR1 retroviral vector and GFP(high) CD4(+) cells were sorted on day 7.

source_name: GFP(high) CD4(+) T cells transduced with R397W FoxP3/MIGR1 retroviral vector

label_protocol: RNA was subjected to biotinylated cDNA synthesis by using GeneChip One-Cycle Target Labeling and Control Reagents.

growth_protocol: Retrovirally transduced T cells were cultured in RPMI1640 medium supplemented with 10% FBS, 10 mM HEPES, 1 mM Sodium Pyruvate, 50 uM 2-ME, PN/ST, and 10 ng/ml recombinant mouse IL-2.

treatment_protocol: Sorted naïve CD4(+) T cells were stimulated with 0.5 ug/ml anti-CD3e (145-2C11) in the presence of 10 ng/ml recombinant mouse IL-2 and syngeneic T cell-depleted and irradiated (20Gy) spleen cells, and spin-infected with retroviral supernatants 24 hr later.

value: BALB/cA

value: In vitro activated CD4(+) T cells

tag: transduction

value: R397W FoxP3/MIGR1 retroviral vector


title: R397W FoxP3-transduced T cells_1


title: A384T FoxP3-transduced T cells_3

description: Naïve CD4(+) T cells were transduced with A384T FoxP3/MIGR1 retroviral vector and GFP(high) CD4(+) cells were sorted on day 7.

source_name: GFP(high) CD4(+) T cells transduced with A384T FoxP3/MIGR1 retroviral vector

value: A384T FoxP3/MIGR1 retroviral vector


title: BA20189


title: BA10221


title: WT FoxP3-transduced T cells_1

description: Naïve CD4(+) T cells were transduced with WT FoxP3/MIGR1 retroviral vector and GFP(high) CD4(+) cells were sorted on day 7.

source_name: GFP(high) CD4(+) T cells transduced with WT FoxP3/MIGR1 retroviral vector

value: WT FoxP3/MIGR1 retroviral vector


title: WT FoxP3-transduced T cells_3

value: lymph nodes and spleen


title: A384T FoxP3-transduced T cells_2


title: BA10216


title: WT FoxP3-transduced T cells_2


title: BA10234


title: Mock-transduced T cells_2

description: Naïve CD4(+) T cells were transduced with MIGR1 retroviral vector and GFP(high) CD4(+) cells were sorted on day 7.

source_name: GFP(high) CD4(+) T cells transduced with MIGR1 retroviral vector

value: MIGR1 retroviral vector


title: Mock-transduced T cells_3


title: Mock-transduced T cells_1


title: Sca6 CtmKO/CtmKO mouse_replicate 3

city: Bunkyo-ku

first: Kaoru

last: Mogushi

state: Tokyo

address: 2-1-1 Hongo

department: Intractable Disease Research Center

institute: Juntendo University

description: Gene expression profile of mouse cerebellum

hyb_protocol: Hybridization and signal detection of Mouse Genome 430 2.0 arrays (Affymetrix) was performed following the manufacturer's instruction using the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 3000.

data_processing: The data was normalized by robust multichip analysis (RMA) using justRMA function in R/Bioconductor.

source_name: Sca6 CtmKO/CtmKO mouse

label_protocol: cRNA was prepared using one-cycle target labeling and control reagents kit (Affymetrix, Santa Clara, CA).

extract_protocol: Total RNA was extracted from tissue specimens using RNeasy kit (Qiagen, Hilden, Germany). Integrity of obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).

treatment_protocol: Sca6 CtmKO/CtmKO, MPI 118Q/118Q and MPI 11Q/11Q mice as well as their WT littermates (n = 3 in each group) were used.

value: cerebellum

value: CtmKO


title: Sca6 CtmKO/CtmKO mouse_replicate 2


title: shTMS1AS-2/shTMS1, biological rep2

city: chengdu

first: Tao

last: Liu

address: 24th,yihuan road

institute: Sichuan University

description: Gene expression data from SKBR3 cells infected with shTMS1AS-2 and shTMS1

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

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

data_processing: The hybridization data were analyzed using Affymetrix GeneChip Command Console Software (AGCC), which uses statistical criteria to generate a ‘present’ or ‘absent’ call for genes represented by each probe set on the array. Afterwards, genes with ‘absent’ scores were filtered out and the remaining genes were analyzed.

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: SKBR3 cells were cultured in RPMI-1640 with 10% fetal bovine serum

treatment_protocol: SKBR3 cells were infected with shNC, shTMS1AS or shTMS1.

tag: cells

value: breast cancer cells


title: WT Treg (GFP+ from A384T:hCD2/WT:GFP mice)_1

description: freshly isolated cells

tag: strain

value: FoxP3A384T:hCD2/WT:GFP mice


title: BA10189

value: N


title: BA10169

value: M


title: shTMS1AS-1/shTMS1, biological rep2

description: Gene expression data from SKBR3 cells infected with shTMS1AS-1 and shTMS1


title: BA10173


title: BA10101


title: BA10135


title: BA10133


title: BA10104


title: Sca6 CtmKO/CtmKO mouse_replicate 1


title: Wild type littermate for Sca6 CtmKO/CtmKO_replicate 2

value: CtmWT


title: BA1064


title: shTMS1AS-1/shTMS1, biological rep1

source_name: SKBR3 cells infected with shTMS1AS-1 and shTMS1


title: BA10163


title: A384T FoxP3-transduced T cells_1


title: LV-miR-495 infused rat, biological replicate 3

city: Albuquerque

first: Nora

last: Perrone-Bizzozero

state: NM

address: 1 University of New Mexico MSC08 4740

institute: University of New Mexico

description: Gene expression data from miR-495 OE LV-miR-495 rat

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

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. Also, we used RMA for normalization of the signal.

source_name: Rat nucleus accumbens

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions polling both nuclie accumbens of each animal.

treatment_protocol: Control rats were infused bilaterally with 2.0 ul of LV-GFP viral particles (8.28 x 10^8 IUF/mL) into nucleus accumbens and miR-495 OE rats were infused with 2.0 ul LV-miR-495 (1.39 x10^9 IU/ml). Viral contructs were from System Biosciences

tag: genotype/variation

value: miR-495 OE

tag: lentivirus


title: LV-miR-495 infused rat, biological replicate 1


title: MPI 118Q/118Q knockin mouse_replicate 3

source_name: MPI 118Q/118Q knockin mouse

tag: genotype


title: shTMS1AS-1, biological rep2

description: Gene expression data from SKBR3 cells infected with shTMS1AS-1

source_name: SKBR3 cells infected with shTMS1AS-1


title: shTMS1AS-2/shTMS1, biological rep1

source_name: SKBR3 cells infected with shTMS1AS-2 and shTMS1


title: LV-GFP infused rat, biological replicate 3

description: Gene expression data from control LV-GFP rat

value: control

value: LV-GFP


title: Wild type littermate for Sca6 CtmKO/CtmKO_replicate 1


title: shTMS1AS-2, biological rep1

description: Gene expression data from SKBR3 cells infected with shTMS1AS-2

source_name: SKBR3 cells infected with shTMS1AS-2


title: LV-GFP infused rat, biological replicate 1


title: shTMS1AS-1, biological rep1


title: MPI 118Q/118Q knockin mouse_replicate 2


title: Wild type littermate for Sca6 CtmKO/CtmKO_replicate 3


title: MPI 118Q/118Q knockin mouse_replicate 1


title: shNC, biological rep2

description: Gene expression data from SKBR3 cells infected with shNC

source_name: SKBR3 cells infected with shNC


title: Wild type littermate for MPI 118Q/118Q knockin_replicate 2


title: Wild type littermate for MPI 118Q/118Q knockin_replicate 3


title: shNC, biological rep1


title: LV-miR-495 infused rat, biological replicate 2


title: MPI 11Q/11Q knockin mouse_replicate 1

source_name: MPI 11Q/11Q knockin mouse


title: MPI 11Q/11Q knockin mouse_replicate 3


title: naringenin treatment 2

city: Beijing

first: Qinghua

last: Cui

address: 38 Xueyuan Road

institute: Peking University

hyb_protocol: The labeled cRNAs were hybridized onto the Mouse LncRNA Array v2.0 (8 x 60K, Arraystar).

scan_protocol: After having washed the slides, the arrays were scanned by the Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v12.0 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 1 out of 6 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis.

source_name: mouse abdominal aorta

label_protocol: The sample preparation and microarray hybridization were performed based on the manufacturer’s standard protocols with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method.

extract_protocol: Total RNA from each sample was quantified by the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

value: aorta

tag: Sex

value: Male

tag: treatment

value: naringenin


title: Wild type littermate for MPI 118Q/118Q knockin_replicate 1


title: naringenin treatment 1


title: CaPO4 treatment 2


title: CaPO4 treatment 1


title: wild type 3


title: Wild type littermate for MPI 11Q/11Q knockin_replicate 1


title: Wild type littermate for MPI 11Q/11Q knockin_replicate 3


title: naringenin treatment 3


title: wild type 1


title: Wild type littermate for MPI 11Q/11Q knockin_replicate 2


title: MPI 11Q/11Q knockin mouse_replicate 2


title: wild type 2


title: NC

city: Jinan

first: Peng

last: Gao

address: Wen Hua Xi Road 44

institute: Shandong University

description: MCF-7/ADM transfected with negative control

hyb_protocol: Microarrays were hybridized at 42°C during 16 to 20h with 4 μg of Cy3 labeled ds-cDNA in NimbleGen hybridization buffer/hybridization component A in a hybridization chamber (Hybridization System - NimbleGen Systems, Inc., Madison, WI, USA). Following hybridization, washing was performed using the NimbleGen Wash Buffer kit (NimbleGen Systems, Inc., Madison, WI, USA). After being washed in an ozone-free environment, the slides were scanned using the Axon GenePix 4000B microarray scanner.

scan_protocol: Slides were scanned at 5 μm/pixel resolution using an Axon GenePix 4000B scanner (Molecular Devices Corporation) piloted by GenePix Pro 6.0 software (Axon).Scanned images (TIFF format) were then imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis.

data_processing: Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software. The Probe level (*_norm_RMA.pair) files and Gene level (*_RMA.calls) files were generated after normalization.All gene level files were imported into Agilent GeneSpring GX software (version 11.5.1) for further analysis. Differentially expressed genes were identified through Fold Change filtering.

source_name: human breast cancer cell line_negative_control

label_protocol: Double-strand cDNA (ds-cDNA) was synthesized from total RNA using an Invitrogen SuperScript ds-cDNA synthesis kit in the presence of 100 pmol oligo dT primers. ds-cDNA was cleaned and labeled in accordance with the NimbleGen Gene Expression Analysis protocol (NimbleGen Systems, Inc., Madison, WI, USA). Briefly, ds-cDNA was incubated with 4 μg RNase A at 37°C for 10 min and cleaned using phenol:chloroform:isoamyl alcohol, followed by ice-cold absolute ethanol precipitation. The purified cDNA was quantified using a NanoDrop ND-1000. For Cy3 labeling of cDNA, the NimbleGen One-Color DNA labeling kit was used according to the manufacturer's guideline detailed in the Gene Expression Analysis protocol (NimbleGen Systems, Inc., Madison, WI, USA). One μg ds-cDNA was incubated for 10 min at 98°C with 1 OD of Cy3-9mer primer. Then, 100 pmol of deoxynucleoside triphosphates and 100U of the Klenow fragment (New England Biolabs, USA) were added and the mix incubated at 37°C for 2 hours. The reaction was stopped by adding 0.1 volume of 0.5 M EDTA, and the labeled ds-cDNA was purified by isopropanol / ethanol precipitation.

growth_protocol: MCF-7/ADM cells were cultured in RPMI-1640 medium (Gibco) supplemented with 10% FBS.

extract_protocol: Total RNA were extracted using Trizol. The RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: MCF-7/ADM cells were transfected with SPIN1 siRNA or negative control.

tag: cell line

tag: cell type

value: breast cancer


title: P45 D-5

city: Trondheim

first: Lene

middle: Christin

last: Olsen

address: Erling Skjalgsons gt. 1

department: Medical Faculty

country: Norway

institute: Norwegian University of Science and Technology - NTNU

description: miRNA expression in entorhinal cortex deep layers at postnatal age P45

hyb_protocol: The Cy3-labeled miRNA samples were hybridized for 20hrs  at  55°C onto separate Rat miRNA Microarrays, Release 15.0 (Agilent Technologies, AMADID 029200, 8x15K format). The microarrays were then washed with increasing stringency using Gene Expression Wash Buffers (Agilent Technologies) followed by drying  with  acetonitrile  (SIGMA)

scan_protocol: Fluorescent signal intensities were detected with  Scan Control A.8.4.1  Software (Agilent Technologies) on the Agilent DNA Microarray Scanner

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) to obtain QC stats of Feature Outliers, Background and Non-Uniformity.  The additive error was below 12 for all samples, and the Hyb Spike-In signal was above the recommended threshold of 2.50 for all arrays.
The raw values were processed using the AgiMicroRna Bioconductor package, filtering according to the quality flag (filterMicroRna function with settings wellaboveNEG = FALSE, limIsGeneDetected = 50, limNEG = 25), and normalizing using the quantile method.

source_name: Entorhinal cortex, deep layers, P45, replicate 5

label_protocol: 100 ng of total RNA from each sample was spiked with MicroRNA Spike-In Kit (Agilent Technologies), treated with calf intestinal phosphatase, and labeled with Cy3 using the miRNA Complete Labeling and Hyb Kit according to the manufacturer's recommendations.

extract_protocol: Total RNA was extracted using Ambion's RNAqueous®-Micro kit, following the manufacturer's recommendations except for an extra 1 minute incubation with wash buffer, and the ethanol added for precipitation was increased to 1.25x lysis buffer volume to include small RNAs. RNA was eluted with 2x10μl RNAqueous Elution Buffer. The RNA in four samples  (RS-198_20, RS-198_25, RS-198_27, RS-198_28) was extracted using Ambion's mirVana kit according to the manufacturer's recommendations and eluted in 2x50 µl mirVana Elution Buffer.  The amount of RNA in all samples was analyzed on the Nano Drop, and the quality of the RNA on the BioAnalyzer Nano Chip

treatment_protocol: Long Evans rats were deeply anesthetized and sacrificed by guillotine. The brain was immediately placed in oxygenated ACSF, sliced on a microtome (400μm) and placed in RNAlater. Layer slices were then dissected under a microscope.

tag: layer

value: Deep

value: Long Evans


title: P45 II-5

description: miRNA expression in entorhinal cortex layer II at postnatal age P45

source_name: Medial entorhinal cortex, layer II, P45, replicate 5

value: II


title: Tg2576 hippocampus + LXR agonist TO901317, biological rep 9

city: Cambridge

first: Andrew

last: Hill

state: MA

address: 300 Technology Square

department: Research Business Technology

institute: Pfizer

description: Gene expression data from transgenic mouse Tg2576 hippocampus treated 7d with LXR agonist TO901317

hyb_protocol: Ten micrograms of cRNA was fragmented and hybridized to the MOE430 2.0 array (Affymetrix, Santa Clara, CA).

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

source_name: Mus musculus hippocampus Tg2576, TO901317 treated

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 2ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Tg2576 mice express hAPP with the Swedish familial AD mutation (Lys-670-Asn; Met-671-Leu) under the control of the prion promoter 28 , and were maintained on a SJL × C57BL/6J genetic background.

extract_protocol: The hippocampus was dissected and immediately placed in RNAlater solution. Total RNA was isolated using a FastPrep Homogenizer and Isolation System (Thermo Fisher Scientific, Waltham, MA) and further purified using RNeasy spin columns (Qiagen, CA), with on-column DNase I digestion (RNase-free DNAse Set; Qiagen, CA).  RNA quantity and quality were assessed using the Agilent Technologies (Palo Alto, CA) Bioanalyzer and the NanoDrop ND-1000 spectrophotometer (Wilmington, DE).

treatment_protocol: Five-month-old heterozygous male Tg2576 mice (n=11-12 group) treated with vehicle or 50 mg/kg/d TO901317 for 5 days and age-matched, vehicle-dosed, wild-type littermate controls were anesthetized using isoflurane, saline perfused and the brains removed.

value: SJL × C57BL/6J

value: LXR agonist TO901317


title: Tg2576 hippocampus + LXR agonist TO901317, biological rep 11


title: 512

description: MCF-7/ADM transfected with SPIN1 siRNA

source_name: human breast cancer cell line_SPIN1_siRNA


title: Tg2576 hippocampus + LXR agonist TO901317, biological rep 7


title: Tg2576 hippocampus + LXR agonist TO901317, biological rep 6


title: Tg2576 hippocampus + LXR agonist TO901317, biological rep 8