title: L2 colon cancer cells

city: Houston

first: Mien-chie

last: Hung

state: Texas

address: 1515 Holcomb Blvd

department: Molecular and Cellular Oncology

institute: M.D. Anderson Cancer Center

description: Metastatic colorectal cancer-derived cell line.

hyb_protocol: Samples were hybridized using the Affymetrix hybridization kit.

scan_protocol: GeneChip Operating System (Affymetrix).

data_processing:
GeneChip Analysis Software.

Supplementary *.txt file:
Column 1: Affymetrix probe set
Column 2: Number of paired probes in array
Column 3: Number of paired probes used in array
Column 4: Signal intensity
Column 5: Detection call
Column 6: Detection p-value

source_name: metastatic colorectal cancer

label_protocol: Samples were biotinylated using the One-Cycle Target Labeling Kit (Affymetrix).

extract_protocol: Trizol extraction.

treatment_protocol: None.

value: metastatic colorectal cancer cells


title: BY4741 120min_3AT_2

status: Public on Dec 31 2011

type: RNA

city: singapore

first: Xiaowei

last: XUE

address: 60 Biopolis Street, #02-01, Genome

department: systems biology 1

country: Singapore

institute: Genome Institute of Singapore

hyb_protocol: Afer fragmentation, 10 μg of cRNA were hybridized for 16 hr at 45ºC on GeneChip Yeast Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450. The protocol used for infividual module array stain is EuKGE_WS2v4_450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner GCS3000.

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

label: biotin

molecule: total RNA

organism: Saccharomyces cerevisiae

source_name: BY4741 wild-type

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

growth_protocol: Yeast strain was precultured in SC medium at 28ºC overnight and transferred into fresh SC medium to dilute to 1.4 liter (6  time points) or 1.6 liter (8 time points).

extract_protocol: Extraction of total RNA was performed as manufacture's instractions

treatment_protocol: 200ml cells were collected and harvested when cells grew in SC medium to reach OD600nm=0.5 as time point 0. 3-aminotriazol was added to a final concentration of 100mM to induce amino acid starvation. 200ml cells were taken and pelleted at each time point after 3AT treatment.

tag: genotype

value: WT

tag: collection time after 3at treatment

tag: genetic background

tag: treatment


title: Whole Tissue_SD DARK_bhlh93_rep2

city: Austin

first: Enamul

last: Huq

state: TX

address: 24th St. and Whitis BIO labs ,

department: MCDB

country: USA

institute: University of Texas at Austin

description:
394517_A09_22Feb10_532.pair
394517_A09_22Feb10_532_RMA.calls

hyb_protocol: Microarray hybridization experiment was performed according to user manual of Roche Nimbelgen Arabidopsis thaliana 12x135K Array (090717 Athal TAIR9 exp HX12; Cat No. 05543746001). 4 micrograms of labeled product were resuspended in sample tracking control, applied to the arrays, and hybridized overnight in a Maui 4-position hybridization chamber, according to Roche Nimblegen protcol version 2.3. The arrays were then washed and dried according to the same protocol.

scan_protocol: Arrays were scanned and analyzed according to Roche Nimblegen protcol version 2.3. Briefly, the arrays were scanned on an Axon 4000B scanner set at 5 micron resolution with 100% laser power and PMT gain between 500 and 600. The resulting TIF images were post-processed using Nimblescan version 2.3 to identify probe locations and each array was visually inspected for proper grid alignment.

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

organism: Arabidopsis thaliana

source_name: Whole tissue, 10d old in SD

label_protocol: Double stranded cDNA was created using the Invitrogen double stranded-cDNA synthesis kit(Cat #11917010) according to Roche Nimblegen instructions (Roche protocol version 2.3) using an oligo-dT primer. Double-stranded cDNA was then labeled using Cy3-labeled nonamers (TriLink, San Diego, CA) and Klenow (large fragment, NEB cat #M0210M) also according to the Roche protocol version 2.3).

growth_protocol: Seeds were surface sterilized and plated on Murashige and Skoog growth medium (GM) containing 0.9% agar without Suc (GM - Suc) as described (Shen et al., 2005). After 4 d of stratification at 4oC, seeds were exposed to SD.

extract_protocol: For microarray, total RNA was isolated from 10d-old bhlh93-1 mutant and wild-type Col-0 seedlings grown under SD using the RNeasy plant mini kit (Qiagen). Five µg RNA from 10d old SD grown seedling of Wt and bhlh93-1 mutants was reverse transcribed using the RT-PCR kit from Invitrogen.

treatment_protocol: Samples were harvested in dark and after 4h light treatment in SD growth conditions.

tag: cultivar

value: bhlh93-1 mutant

tag: time

value: 0 hr


title: BY4741 120min_3AT_1


title: Whole Tissue_SD 4h Light_bhlh93_rep3

description:
394517_A12_22Feb10_532.pair
394517_A12_22Feb10_532_RMA.calls

value: 4 hr


title: sw620 colon cancer cells

description: Non-metastatic colorectal cancer-derived cell line.

organism: Homo sapiens

source_name: non-metastatic colorectal cancer

tag: cell line

tag: cell type

value: non-metastatic colorectal cancer cells


title: sw480 colon cancer cells


city: Halle (Saale)

first: Martin

middle: Sebastian

last: Staege

state: Sachsen-Anhalt

address: Ernst-Grube-Str. 40

department: Universitätsklinik u. Poliklinik für Kinder- u. Jugendmedizin

country: Germany

description: Gene expression data from established Hodgkin's lymphoma cell line after treatment with vorinostat

hyb_protocol: Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45C on HG_U133A Microarrays. 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 using the MAS5.0 algorithm and Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: Hodgkin’s lymphoma cell line L-540, treated with vorinostat

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 10 ug total RNA.

growth_protocol: Established Hodgkin's lymphoma cells were grown under standard conditions.

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

treatment_protocol: Cells were treated with vorinostat or left untreated.

value: Hodgkin’s lymphoma cells

value: vorinostat


title: Whole Tissue_SD DARK_bhlh93_rep3

description:
394517_A11_22Feb10_532.pair
394517_A11_22Feb10_532_RMA.calls


title: 1C5HX

city: Bordeaux

first: eric

last: chevet

address: 146 rue Leo Saignat

country: France

institute: inserm

description: Gene expression data from U87_IRE1DN cells under hypoxia

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A 2.0  Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: standard Affy protocol

data_processing: GCOS 1.2 software (Affymetrix).

source_name: U87 glioma cells

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: U87 control and IRE1DN cells subjected to severe hypoxia (0.1%), glucose deprivation, glutamine deprivation and tunicamycin treatment (5ug/ml) for 16h

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

treatment_protocol: cells were washed with ice cold PBS

tag: plasmid

value: under hypoxia


title: Whole Tissue_SD 4h Light_Col-0_rep2

description:
394517_A04_22Feb10_532.pair
394517_A04_22Feb10_532_RMA.calls


title: 1C5_tun

description: Gene expression data from U87_IRE1DNcells upon tunicamycin treatment

value: upon tunicamycin treatment


title: Whole Tissue_SD 4h Light_bhlh93_rep2

description:
394517_A10_22Feb10_532.pair
394517_A10_22Feb10_532_RMA.calls


title: 1C5GLUT

description: Gene expression data from U87_IRE1DN cells under glutamine deprivation

value: under glutamine deprivation


title: 1C5Contr

description: Gene expression data from U87_IRE1DN cells under basal conditions

value: under basal conditions


title: Whole Tissue_SD DARK_bhlh93_rep1

description:
394517_A07_22Feb10_532.pair
394517_A07_22Feb10_532_RMA.calls


title: BY4741 90min_3AT_1


title: Whole Tissue_SD 4h Light_Col-0_rep3

description:
394517_A06_22Feb10_532.pair
394517_A06_22Feb10_532_RMA.calls


title: T1P5_tun

description: Gene expression data from U87 ctrl cells upon tunicamycin treatment


title: BY4741 90min_3AT_2


title: cell line L-540, untreated

description: Gene expression data from established Hodgkin's lymphoma cell line

source_name: Hodgkin’s lymphoma cell line L-540, untreated


title: 1C5HG

description: Gene expression data from U87_IRE1DN cells under glucose deprivation

value: under glucose deprivation


title: L1 colon cancer cells

description: Metastatic colorectal cancer-derived cell line.


title: BY4741 60min_3AT_3


title: T1P5GLUT

description: Gene expression data from U87 ctrl cells under glutamine deprivation


title: Whole Tissue_SD 4h Light_Col-0_rep1

description:
394517_A02_22Feb10_532.pair
394517_A02_22Feb10_532_RMA.calls


title: Whole Tissue_SD DARK_Col-0_rep2

description:
394517_A03_22Feb10_532.pair
394517_A03_22Feb10_532_RMA.calls


title: Whole Tissue_SD DARK_Col-0_rep3

description:
394517_A05_22Feb10_532.pair
394517_A05_22Feb10_532_RMA.calls


title: BY4741 60min_3AT_2


title: BY4741 45min_3AT_1


title: Mouse GIST imatinib rep 3

city: New York

first: Jeffrey

last: Zhao

state: NY

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

description:
Tumor3
replicate 3

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalized using quantile normalization with Partek software based on the MouseWG6_V2_0_R0_11278593_A.txt annotation

organism: Mus musculus

source_name: Mouse GIST

label_protocol: 200 ng of total RNA were labeled using the Illumina TotalPrep RNA Amplification kit (Ambion), according to manufacturer’s instructions.

extract_protocol: We harvested organs from GIST mice and isolated total RNA using Trizol. Quality of RNA was ensured before labeling by analyzing 20-50 ng of each sample using the RNA 6000 NanoAssay and a Bioanalyzer 2100 (Agilent). Samples with a 28S/18S ribosomal peak ratio of 1.8–2.0 were considered suitable for labeling.

tag: strain

tag: genotype/variation

value: Kit V558Δ/+

tag: age

value: 6 weeks

tag: tissue

value: GIST tumor


title: T1P5HX

description: Gene expression data from U87 ctrl cells under hypoxia


title: T1P5Contr

description: Gene expression data from U87 ctrl cells under basal conditions


title: BY4741 30min_3AT_3


title: BY4741 45min_3AT_3


title: BY4741 60min_3AT_1


title: Whole Tissue_SD DARK_Col-0_rep1

description:
394517_A01_22Feb10_532.pair
394517_A01_22Feb10_532_RMA.calls


title: T1P5HG

description: Gene expression data from U87 ctrl cells under glucose deprivation


title: BY4741 45min_3AT_2


title: Mouse GIST imatinib rep 2

description:
Tumor2
replicate 2


title: RH30_untreated_12hr

city: Bologna

first: Andrea

last: Pession

state: BO

address: Massarenti 11

department: Pediatrics

country: Italy

institute: University of Bologna

hyb_protocol: Affymetrix protocol for sample hybridization

scan_protocol: Affymetrix protocol for sample scanning

data_processing: CEL files were analyzed by the MAS5 algorithm implemented in GCOS and signal values were scaled to 500.

source_name: RH30 cell line - treated with mutated PNA anti-MYCN

label_protocol: Affymetrix one-cycle protocol

growth_protocol: cells were grown in RPMI supplemented with 1% penicillin and streptomycin, 1% L-glutamine and 10% foetal bovine serum

extract_protocol: RNA was extracted by TRI-Zol reagent following manufacturer's instructions.

treatment_protocol: cells are untreated

tag: RH30 - untreated

tag: alveolar rhabdomyosarcoma cell line


title: Mouse GIST vehicle rep 3

description:
Tumor6
replicate 3


title: BY4741 30min_3AT_2


title: RH30_anti-MYCN-PNA_12hr

source_name: RH30 cell line - treated with anti-MYCN PNA

treatment_protocol: cells were treated for 12 hours with a 10uM concentration of anti-MYCN PNA.

tag: RH30 - treated with anti-MYCN PNA


title: Thalamus_animal N254_0.2 mL saline_no seize_no drugs_24hr

city: Aberdeen Proving Ground

first: James

middle: F

last: Dillman

state: MD

address: 3100 Ricketts Point Rd

department: Cell and Molecular Biology Branch

institute: U.S. Army Medical Research Institute of Chemical Defense

description: Gene expression data from Thalamus of animal N254_0.2 mL saline_no seize_no drugs_24hr

hyb_protocol: Spike controls were added to 15 µg fragmented cRNA before hybridization (36h) using 10 µg of cRNA.  Arrays were washed and stained with streptavidin-phycoerythrin before being scanned on an Affymetrix GeneChip Scanner.

scan_protocol: After scanning, array images were assessed by eye to confirm scanner alignment and the absence of significant bubbles or scratches on the chip surface. The 3'/5' ratios for GAPDH and B-actin were checked for quality. BioB, BioC, BioD and CreX spike controls were also examined to determine sample quality. All arrays were scaled to a target intensity of 150 using Affymetrix GeneChip Operating System (GCOS) software.

data_processing: Raw signal intensities were imported into Partek Genomics Solutions v6.3 (Partek, St. Louis, MO) and normalized using the robust multi-array averaging (RMA) algorithm (Irizarry et al., 2003)

organism: Rattus norvegicus

label_protocol: Total RNA was processed for hybridization to GeneChip® Rat Genome 230 2.0 oligonucleotide arrays (Affymetrix, Inc., Santa Clara, CA) using the BioArray Single-Round RNA Amplification and Biotin Labeling System (Enzo Life Sciences, Inc., Farmingdale, NY) as previously described [20].  In brief, 1 µg of total RNA was used to generate first strand cDNA by using a T7-linked oligo(dT) primer.  After second strand synthesis, in vitro transcription was performed with biotinylated UTP and CTP for cRNA amplification.

extract_protocol: Tissues were homogenized in RNeasy lysis buffer (QIAGEN, Valencia, CA) for three seconds at 5,000 rpm and ramped to 17,000 rpm for 30 sec using an Omni Programmable Digital Homogenizer (Omni International, Kennesaw, GA).  Each homogenate was subsequently centrifuged for 10 min at 16,110 x g at room temperature, and the supernatant was transferred to a new microcentrifuge tube.  Total RNA was then extracted and DNase I-treated using the RNeasy Mini Kit and RNase-Free DNase Set (QIAGEN) according to the manufacturer’s protocol.  The quantity and quality of the RNA was determined with a NanoDrop ND-1000 UV-vis spectrophotometer (Thermo Scientific, Wilmington, DE) and an Agilent bioanalyzer (Agilent Technologies, Santa Clara, CA) throughout sample processing.

treatment_protocol: Male Sprague-Dawley rats (350-500 g) were obtained from Charles River Laboratories (Wilmington, MA).  They were housed in a temperature-controlled room with a 12-h light/12-h dark cycle and given food and water ad libitum.  The research for this study was conducted at the United States Army Medical Research Institute of Chemical Defense (USAMRICD; Aberdeen Proving Ground, MD), which is fully accredited by the Association for Assessment and Accreditation of Laboratory Animal Care, International.  All of the animal procedures were approved by the Institute Animal Care and Use Committee at USAMRICD and conducted in accordance with the principles stated in the Guide for the Care and Use of Laboratory Animals (National Research Council, 1996) and the Animal Welfare Act of 1966 (P.L. 89-544), as amended.    PhysioTel® F40-EET transmitters (Data Sciences International, St. Paul, MN) were surgically implanted into the animals to record bi-hemispheric cortical electroencephalogram (EEG) activity, body temperature, and gross motor activity throughout the study.  After a two-week recovery period, the animals were challenged with 1 x LD50 sarin (108 µg/kg, sc) that was obtained and diluted in sterile saline at USAMRICD.  One minute after seizure onset, animals were treated with atropine sulfate (2 mg/kg; Sigma-Aldrich, St. Louis, MO) and 2-pyridine aldoxime methylchloride (2-PAM; 25 mg/kg; Sigma-Aldrich), both administered in a single injection (im).  Thirty minutes later, animals were given the anticonvulsant diazepam (10 mg/kg, sc; TW Medical Veterinary Supply, Austin, TX).  Control animals received an equivalent volume of vehicle (saline), atropine sulfate, 2-PAM, and diazepam at time points corresponding to the injections administered to sarin-exposed animals.  Drug treatments were not given to sarin-exposed non-seizure animals or their matched controls.  Naïve animals received no injections.  Animals were euthanized by decapitation at 0.25, 1, 3, 6, and 24 h after seizure onset.  Each tissue was immediately snap-frozen in liquid nitrogen and stored at -80°C until use.

tag: animal number

value: Thalamus

tag: agent

value: Saline

tag: amount administered

tag: agent dose

value: Sprague-Dawley

tag: atropine, 2-pam, diazepam

value: N

tag: time point (hr)

tag: date injected

tag: time injected

tag: date sacrificed

tag: time sacrificed

tag: presence of seizure

tag: animal weight (g)


title: Mouse GIST vehicle rep 2

description:
Tumor5
replicate 2

tag: strain

tag: genotype/variation

tag: age


title: RH30_mutatedPNA_12hr

treatment_protocol: cells were treated for 12 hours with a 10uM concentration of a mutated anti-MYCN PNA.

tag: RH30 - treated with mutated PNA anti-MYCN

tag: alveolar rhabdomyosarcoma cell line


title: Thalamus_animal N260_0.21 mL saline_no seize_no drugs_0.25hr

description: Gene expression data from Thalamus of animal N260_0.21 mL saline_no seize_no drugs_0.25hr

tag: animal number

tag: tissue


title: Thalamus_animal N257_naive_no agent_0hr

description: Gene expression data from Thalamus of animal N257_naive_no agent_0hr

source_name: Thalamus_animal N257_naive_no agent_0hr

tag: agent

value: Naive


title: Thalamus_animal N259_naive_no agent_0hr

description: Gene expression data from Thalamus of animal N259_naive_no agent_0hr

source_name: Thalamus_animal N259_naive_no agent_0hr


title: Thalamus_animal N258_naive_no agent_0hr

description: Gene expression data from Thalamus of animal N258_naive_no agent_0hr

source_name: Thalamus_animal N258_naive_no agent_0hr


title: Thalamus_animal N256_0.2 mL saline_no seize_no drugs_24hr

description: Gene expression data from Thalamus of animal N256_0.2 mL saline_no seize_no drugs_24hr

tag: amount administered

tag: agent dose


title: Mouse GIST imatinib rep 1

description:
Tumor1
replicate 1


title: Thalamus_animal N252_0.2 mL saline_no seize_no drugs_24hr

description: Gene expression data from Thalamus of animal N252_0.2 mL saline_no seize_no drugs_24hr

tag: atropine, 2-pam, diazepam

tag: time point (hr)


title: Thalamus_animal N251_0.21 mL saline_no seize_no drugs_1hr

description: Gene expression data from Thalamus of animal N251_0.21 mL saline_no seize_no drugs_1hr

tag: date injected

tag: time injected


title: BY4741 20min_3AT_2

tag: genotype

value: WT

tag: collection time after 3at treatment

tag: genetic background

tag: treatment


title: BY4741 20min_3AT_3


title: Mouse GIST vehicle rep 1

description:
Tumor4
replicate 1

tag: strain

tag: genotype/variation


title: Thalamus_animal N250_0.21 mL saline_no seize_no drugs_3hr

description: Gene expression data from Thalamus of animal N250_0.21 mL saline_no seize_no drugs_3hr

tag: date sacrificed

tag: time sacrificed

tag: presence of seizure

tag: animal weight (g)


title: BY4741 20min_3AT_1


title: Thalamus_animal N246_0.18 mL saline_no seize_no drugs_6hr

description: Gene expression data from Thalamus of animal N246_0.18 mL saline_no seize_no drugs_6hr

tag: animal number

tag: tissue

tag: agent


title: Thalamus_animal N248_0.2 mL saline_no seize_no drugs_1hr

description: Gene expression data from Thalamus of animal N248_0.2 mL saline_no seize_no drugs_1hr

tag: amount administered

tag: agent dose

tag: atropine, 2-pam, diazepam


title: Thalamus_animal N247_0.2 mL saline_no seize_no drugs_0.25hr

description: Gene expression data from Thalamus of animal N247_0.2 mL saline_no seize_no drugs_0.25hr

tag: time point (hr)

tag: date injected

tag: time injected


title: Thalamus_animal N245_0.2 mL saline_no seize_no drugs_3hr

description: Gene expression data from Thalamus of animal N245_0.2 mL saline_no seize_no drugs_3hr


title: Thalamus_animal N249_0.21 mL saline_no seize_no drugs_0.25hr

description: Gene expression data from Thalamus of animal N249_0.21 mL saline_no seize_no drugs_0.25hr


title: BY4741 30min_3AT_1

tag: genotype

tag: collection time after 3at treatment

tag: genetic background


title: BY4741 10min_3AT_3

tag: treatment


title: Thalamus_animal N244_0.18 mL saline_no seize_no drugs_1hr

description: Gene expression data from Thalamus of animal N244_0.18 mL saline_no seize_no drugs_1hr

tag: strain

tag: date sacrificed


title: BY4741 10min_3AT_2


title: BY4741 10min_3AT_1


title: C2C12 differentiated for 3 day (rep1)

city: Hong Kong

first: Hao

last: Sun

address: 306G LiHS biomedical Sciences Building

department: Chemical Pathology

country: Hong Kong

institute: The Chinese University of Hong Kong

description:
miRNA profiling by array
C2C12-DM-3day-1
P4954_HW-5_pmt800_010809.gpr

hyb_protocol: The hybridization with miRNA-labled targets is performed on the Tecan HS4800 hybridization station. In general, the labeled targets of first-strand biotin-cDNA from 2.5 to 5 ug of total RNA are used to hybridize miRNA arrays in 6xSSPE/30% formamide at 25C for 18h. Hybridized slides are washed post-hybridyzation and signals on slides are detected using indirect detection of Streptavidin-Alexa 647 conjugate (Invitrogen/Molecular Probes).

scan_protocol: The processed slides are scanned in 10 um resolution by using Axon 4000B Scanner (Molecular Devices) with 635 nm qred laser at Power 100% and PMT 800 setting.

data_processing: Microarray was processed by limma package in R. Two functions in the limma package,  backgroundCorrect and normalizeBetweenArrays were used to normalize the array.

source_name: C2C12 time5

label_protocol: 2.5 to 5.0 ug of total RNA was used as starting material. The labeled targets are directly generated as the first strand biotin-cDNA that is complementary to oligo probe on array, by using custom biotin-end-labeled randome octomer DNA oligo primer (5'-biotin-(dA)12-(dT-biotin)-(dA)12-(N)8-3') in reverse transcrition.

growth_protocol: C2C12 cells were grown in DMEM supplemented with 10% FBS, 2 mM L-glutamine, 100 U/ml penicillin, and 100 µg of Streptomycin at 37 C in 5% CO2.

extract_protocol: Total RNAs were isolated from C2C12 cells using TRIZOL (Invitrogen) according to manufacturer’s manual.

treatment_protocol: C2C12 cells were induced to differentiate in DMEM  containing 2% horse serum.

tag: cell line

tag: time

value: 3 day


title: Thalamus_animal N243_0.21 mL saline_no seize_no drugs_3hr

description: Gene expression data from Thalamus of animal N243_0.21 mL saline_no seize_no drugs_3hr

tag: animal number

tag: time sacrificed

tag: presence of seizure

tag: animal weight (g)


title: C2C12 differentiated for 1 day (rep2)

description:
miRNA profiling by array
C2C12-DM-1day-2
P4954_HW-4_pmt800_010809.gpr

source_name: C2C12 time4

value: 1 day


title: C2C12 differentiated for 3 day (rep2)

description:
miRNA profiling by array
C2C12-DM-3day-2
P4954_HW-6_pmt800_010809.gpr

source_name: C2C12 time6


title: Thalamus_animal N241_0.2 mL saline_no seize_no drugs_6hr

description: Gene expression data from Thalamus of animal N241_0.2 mL saline_no seize_no drugs_6hr

tag: tissue

tag: agent

tag: amount administered

tag: agent dose


title: Thalamus_animal N173_0.22 mL sarin_seize (10 min latency)_drugs_24hr

description: Gene expression data from Thalamus of animal N173_0.22 mL sarin_seize (10 min latency)_drugs_24hr

value: Sarin

tag: atropine, 2-pam, diazepam

value: Y

tag: time point (hr)

tag: date injected

tag: time injected

tag: seizure time

tag: seizure latency


title: Thalamus_animal N174_0.21 mL saline_no seize_drugs_0.25hr

description: Gene expression data from Thalamus of animal N174_0.21 mL saline_no seize_drugs_0.25hr

tag: strain

tag: date sacrificed


title: Thalamus_animal N242_0.2 mL saline_no seize_no drugs_6hr

description: Gene expression data from Thalamus of animal N242_0.2 mL saline_no seize_no drugs_6hr


title: Thalamus_animal N170_0.21 mL sarin_seize (5 min latency)_drugs_24hr

description: Gene expression data from Thalamus of animal N170_0.21 mL sarin_seize (5 min latency)_drugs_24hr


title: C2C12 differentiated for 1 day (rep1)

description:
miRNA profiling by array
C2C12-DM-1day-1
P4954_HW-3_pmt800_010809.gpr

source_name: C2C12 time3

tag: cell line

tag: time


title: Thalamus_animal N81_0.24 mL saline_no seize_drugs_1hr

description: Gene expression data from Thalamus of animal N81_0.24 mL saline_no seize_drugs_1hr

tag: animal number

tag: time sacrificed


title: Thalamus_animal N80_0.22 mL sarin_no seize_no drugs_0.25hr

description: Gene expression data from Thalamus of animal N80_0.22 mL sarin_no seize_no drugs_0.25hr

tag: presence of seizure

tag: animal weight (g)


title: BY4741 0min_3AT_2

tag: genotype

tag: collection time after 3at treatment

tag: genetic background

tag: treatment

value: baseline


title: C2C12 differentiated for 0 day (rep2)

description:
miRNA profiling by array
C2C12-DM-0day-2
P4954_HW-2_pmt800_010809.gpr

source_name: C2C12 time2

value: 0 day


title: Thalamus_animal N78_0.23 mL saline_no seize_drugs_6hr

description: Gene expression data from Thalamus of animal N78_0.23 mL saline_no seize_drugs_6hr

tag: tissue

tag: agent

tag: amount administered

tag: agent dose

tag: atropine, 2-pam, diazepam

tag: time point (hr)


title: C2C12 differentiated for 0 day (rep1)

description:
miRNA profiling by array
C2C12-DM-0day-1
P4954_HW-1_pmt800_010809.gpr

source_name: C2C12 time1


title: BY4741 90min_3AT_3

source_name: BY4741 wild-type


title: Thalamus_animal N82_0.2 mL saline_no seize_drugs_1hr

description: Gene expression data from Thalamus of animal N82_0.2 mL saline_no seize_drugs_1hr

tag: strain

tag: date injected

tag: time injected

tag: date sacrificed


title: Thalamus_animal N172_0.21 mL sarin_no seize_no drugs_24hr

description: Gene expression data from Thalamus of animal N172_0.21 mL sarin_no seize_no drugs_24hr

tag: animal number

tag: time sacrificed


title: Thalamus_animal N77_0.21 mL saline_no seize_drugs_0.25hr

description: Gene expression data from Thalamus of animal N77_0.21 mL saline_no seize_drugs_0.25hr

tag: presence of seizure

tag: animal weight (g)


title: Thalamus_animal N79_0.22 mL sarin_no seize_no drugs_1hr

description: Gene expression data from Thalamus of animal N79_0.22 mL sarin_no seize_no drugs_1hr


title: Thalamus_animal N74_0.22 mL sarin_seize (8 min latency)_drugs_3hr

description: Gene expression data from Thalamus of animal N74_0.22 mL sarin_seize (8 min latency)_drugs_3hr

tag: seizure time

tag: seizure latency


title: HT-29 human cells challenged 3h with Bifidobacterium longum R0175

city: Montreal

first: Thomas

middle: Allan

last: Tompkins

state: Qc

address: 6100 Royalmount Avenue

department: R&D

country: Canada

institute: Lallemand Health Solutions Inc.

hyb_protocol: Cy3 and Cy5 labelled cDNA were mixed and hybridized at 50 Celcius degrees during 18h on the Immune Array chips in an ArrayBooster (Advalytix, Beckman Coulter, Germany).

scan_protocol: Each array was scanned in a ScanArray 5000 instrument (Perkin Elmer, Waltham, MA) and acquired images were quantified with QuantArray software (Perkin Elmer).

data_processing: Statistical analyses were done with R software (v. 2.13.0) and the Limma package from Bioconductor. Normalization within slide was obtained by LOWESS correction and between slides normalization was done with Aquantile method.

source_name: HT-29 + Bifidobacterium longum R0175

label_protocol: Poly A mRNA were reverse transcribed from 15 µg of total RNA with SuperScript III (Invitrogen) and labelled with Cy3 (GE Healthcare Life Sciences, Buckinghamshire, England) before cDNA purification with PCR Purification Kit (QIAGEN).

extract_protocol: Total RNA was extracted by TRIzol Reagent (Invitrogen, Burlington, ON, Canada) following manufacturer's protocol and with PhaseLock tubes (5 Prime, Gaithersburg, MD) for nucleic acids separation. Purification was achieved with RNeasy (QIAGEN, Germantown, MD). Quality was assessed by Bioanalyzer (Agilent Technologies, Mississauga, ON, Canada). RIN over 9.0 were considered good quality RNA for reverse transcription.

tag: cell type

value: HT-29 intestinal epithelial cells (IEC)

tag: treatment

value: stimulated with a 100:1 bateria to cell ratio of B. longum R0175

source_name: Control (HT-29 cells only)

label_protocol: Poly A mRNA were reverse transcribed from 15 µg of total RNA with SuperScript III (Invitrogen) and labelled with Cy5 (GE Healthcare Life Sciences, Buckinghamshire, England) before cDNA purification with PCR Purification Kit (QIAGEN).

value: not stimulated with anything (bacteria to cell ration of 0:1)


title: HT-29 human cells challenged 3h with Lactobacillus rhamnosus R0011

source_name: HT-29 + L. rhamnosus R0011

value: stimulated with a 100:1 bateria to cell ratio of L. rhamnosus R0011


title: BY4741 0min_3AT_3

tag: genotype

tag: collection time after 3at treatment

tag: genetic background


title: HT-29 human cells challenged 3h with Saccharomyces cerevisiae boulardii SB (I-1079)

source_name: HT-29 + S. cerevisiae boulardii SB (I-1079)

value: stimulated with a 100:1 bateria to cell ratio of S. cerevisiae boulardii SB (I-1079)


title: HT-29 human cells challenged 3h with Lactobacillus farciminis R1127

source_name: HT-29 + L. farciminis R1127

value: stimulated with a 100:1 bateria to cell ratio of L. farciminis R1127


title: Thalamus_animal N75_0.2 mL sarin_no seize_no drugs_3hr

description: Gene expression data from Thalamus of animal N75_0.2 mL sarin_no seize_no drugs_3hr

tag: tissue

value: Thalamus

tag: agent

tag: amount administered

tag: agent dose

tag: atropine, 2-pam, diazepam


title: Thalamus_animal N72_0.21 mL sarin_seize (7 min latency)_drugs_6hr

description: Gene expression data from Thalamus of animal N72_0.21 mL sarin_seize (7 min latency)_drugs_6hr

tag: strain

value: Sprague-Dawley

tag: time point (hr)

tag: date injected

tag: time injected

tag: date sacrificed


title: HT-29 human cells challenged 3h with Bifidobacterium longum subsp. infantis R0033

source_name: HT-29 + Bifidobacterium longum subsp. infantis R0033

value: stimulated with a 100:1 bateria to cell ratio of R0033


title: Thalamus_animal N69_0.23 mL sarin_no seize_no drugs_24hr

description: Gene expression data from Thalamus of animal N69_0.23 mL sarin_no seize_no drugs_24hr

tag: animal number

value: N

tag: time sacrificed

tag: presence of seizure

tag: animal weight (g)


title: BY4741 0min_3AT_1

tag: genotype

value: WT

tag: treatment


title: HT-29 human cells challenged 3h with Lactobacillus helveticus R0052

source_name: HT-29 + L. helveticus R0052

tag: cell type

value: stimulated with a 100:1 bateria to cell ratio of L. helveticus R0052


title: Thalamus_animal N70_0.21 mL sarin_seize (12 min latency)_drugs_0.25hr

description: Gene expression data from Thalamus of animal N70_0.21 mL sarin_seize (12 min latency)_drugs_0.25hr

tag: tissue

tag: seizure time

tag: seizure latency


title: Thalamus_animal N73_0.2 mL sarin_no seize_no drugs_1hr

description: Gene expression data from Thalamus of animal N73_0.2 mL sarin_no seize_no drugs_1hr

tag: agent

tag: amount administered

tag: agent dose


title: HT-29 human cells challenged 3h with Bifidobacterium bifidum R0071

source_name: HT-29 + B. bifidum R0071

value: stimulated with a 100:1 bateria to cell ratio of B. bifidum R0071


title: Thalamus_animal N76_0.2 mL saline_no seize_drugs_24hr

description: Gene expression data from Thalamus of animal N76_0.2 mL saline_no seize_drugs_24hr

value: Saline

tag: strain

tag: atropine, 2-pam, diazepam

tag: time point (hr)


title: Thalamus_animal N67_0.2 mL sarin_seize (9 min latency)_drugs_1hr

description: Gene expression data from Thalamus of animal N67_0.2 mL sarin_seize (9 min latency)_drugs_1hr

value: Sarin

value: Y

tag: date injected

tag: time injected

tag: date sacrificed


title: Thalamus_animal N68_0.22 mL saline_no seize_drugs_24hr

description: Gene expression data from Thalamus of animal N68_0.22 mL saline_no seize_drugs_24hr

tag: animal number

tag: time sacrificed

tag: presence of seizure


title: Thalamus_animal N65_0.21 mL sarin_seize (16 min latency)_drugs_24hr

description: Gene expression data from Thalamus of animal N65_0.21 mL sarin_seize (16 min latency)_drugs_24hr

tag: animal weight (g)


title: Thalamus_animal N71_0.2 mL sarin_no seize_no drugs_6hr

description: Gene expression data from Thalamus of animal N71_0.2 mL sarin_no seize_no drugs_6hr


title: HT-29 human cells challenged 3h with Lactobacillus plantarum 299v

source_name: HT-29 + Lactobacillus plantarum 299v

tag: cell type

tag: treatment

value: stimulated with a 100:1 bateria to cell ratio of L. plantarum 299v


title: Thalamus_animal N66_0.23 mL sarin_seize (11 min latency)_drugs_3hr

description: Gene expression data from Thalamus of animal N66_0.23 mL sarin_seize (11 min latency)_drugs_3hr

tag: tissue

tag: seizure time


title: Thalamus_animal N63_0.2 mL sarin_no seize_no drugs_24hr

description: Gene expression data from Thalamus of animal N63_0.2 mL sarin_no seize_no drugs_24hr

tag: agent


title: Thalamus_animal N60_0.2 mL sarin_no seize_no drugs_3hr

description: Gene expression data from Thalamus of animal N60_0.2 mL sarin_no seize_no drugs_3hr

tag: amount administered


title: Thalamus_animal N62_0.21 mL sarin_seize (13.5 min latency)_drugs_6hr

description: Gene expression data from Thalamus of animal N62_0.21 mL sarin_seize (13.5 min latency)_drugs_6hr

tag: agent dose

tag: seizure latency


title: HT-29 human cells challenged 3h with LPS

source_name: HT-29 + LPS from E. coli

value: HT-29 intestinal epithelial cells (IEC)

value: stimulated with 1 µg per mL of LPS from E. coli


title: Thalamus_animal N61_0.21 mL sarin_no seize_no drugs_1hr

description: Gene expression data from Thalamus of animal N61_0.21 mL sarin_no seize_no drugs_1hr

tag: strain

tag: atropine, 2-pam, diazepam


title: HT-29 human cells challenged 3h with an isolate of Salmonella enterica ser Enteritidis

source_name: HT-29 + an isolate of Salmonella enterica ser Enteritidis

value: stimulated with a 5:1 bateria to cell ratio of an isolate of S. enterica ser Enteritidis

value: not stimulated with anything (bacteria to cell ration of 0:1)


title: Thalamus_animal N59_0.2 mL sarin_no seize_no drugs_6hr

description: Gene expression data from Thalamus of animal N59_0.2 mL sarin_no seize_no drugs_6hr

tag: time point (hr)

tag: date injected


title: Thalamus_animal N57_0.21 mL sarin_seize (25 in latency)_drugs_3hr

description: Gene expression data from Thalamus of animal N57_0.21 mL sarin_seize (25 in latency)_drugs_3hr

tag: time injected

tag: date sacrificed


title: 21 day old bLR strain rat nucleus accumbens, biological replicate 6

city: Birmingham

first: Sarah

middle: Megan

last: Clinton

state: Alabama

address: 1720 7th Avenue South, SC 745

department: Psychiatry and Behavioral Neurobiology

institute: University of Alabama-Birmigham

description:
P21_LR_Nacc_L06
Gene expression data from nucleus accumbens of selectively-bred sprague dawley rats (Low Reponder strain), 21 days after birth

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: To account for recent advances in annotation and accuracy of rat genome bioinformatics, GeneChip data were interpreted using a custom cdf (filename RUG34A_Rn_UG), which groups individual probes from the GeneChip into newly defined probe sets based on a very recent version of UniGene (build updated 6th July 2010). Data were analyzed by RMA in Bioconductor.

source_name: Selectively-bred Low responder rat strain derived from Sprague Dawley stock, 21 days after birth

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

value: Selectively bred Low Responder (derived from an original Sprague Dawley)

value: Nucleus Accumbens

tag: age

value: 21 days after birth


title: 21 day old bLR strain rat nucleus accumbens, biological replicate 3

description:
P21_LR_Nacc_L03
Gene expression data from nucleus accumbens of selectively-bred sprague dawley rats (Low Reponder strain), 21 days after birth


title: HT-29 human cells challenged 3h with Salmonella enterica ser Typhimurium (ATCC 14028)

source_name: HT-29 + Salmonella enterica ser Typhimurium ATCC 14028

value: stimulated with a 5:1 bateria to cell ratio of Salmonella enterica ser Typhimurium ATCC 14028


title: 21 day old bLR strain rat nucleus accumbens, biological replicate 1

description:
P21_LR_Nacc_L01
Gene expression data from nucleus accumbens of selectively-bred sprague dawley rats (Low Reponder strain), 14 days after birth


title: 21 day old bLR strain rat nucleus accumbens, biological replicate 5

description:
P21_LR_Nacc_L05
Gene expression data from nucleus accumbens of selectively-bred sprague dawley rats (Low Reponder strain), 21 days after birth


title: 21 day old bLR strain rat nucleus accumbens, biological replicate 4

description:
P21_LR_Nacc_L04
Gene expression data from nucleus accumbens of selectively-bred sprague dawley rats (Low Reponder strain), 21 days after birth


title: 21 day old bLR strain rat nucleus accumbens, biological replicate 2

description:
P21_LR_Nacc_L02
Gene expression data from nucleus accumbens of selectively-bred sprague dawley rats (Low Reponder strain), 21 days after birth


title: HT-29 human cells challenged 3h with E. coli (ATCC 25922)

source_name: HT-29 + E. coli ATCC 25922

value: stimulated with a 5:1 bateria to cell ratio of E. coli ATCC 25922


title: Thalamus_animal N54_0.2 mL saline_no seize_drugs_6hr

description: Gene expression data from Thalamus of animal N54_0.2 mL saline_no seize_drugs_6hr

tag: animal number

value: Thalamus

value: Sprague-Dawley

tag: time sacrificed

tag: presence of seizure

value: N


title: Thalamus_animal N58_0.21 mL sarin_no seize_no drugs_0.25hr

description: Gene expression data from Thalamus of animal N58_0.21 mL sarin_no seize_no drugs_0.25hr

tag: animal weight (g)


title: 14 day old bLR strain rat nucleus accumbens, biological replicate 6

description:
P14_LR_Nacc_L06
Gene expression data from nucleus accumbens of selectively-bred sprague dawley rats (Low Reponder strain), 14 days after birth

source_name: Selectively-bred Low responder rat strain derived from Sprague Dawley stock, 14 days after birth

tag: tissue

value: 14 days after birth


title: Thalamus_animal N51_0.22 mL sarin_no seize_no drugs_0.25hr

description: Gene expression data from Thalamus of animal N51_0.22 mL sarin_no seize_no drugs_0.25hr


title: 14 day old bLR strain rat nucleus accumbens, biological replicate 5

description:
P14_LR_Nacc_L05
Gene expression data from nucleus accumbens of selectively-bred sprague dawley rats (Low Reponder strain), 14 days after birth


title: Thalamus_animal N46_0.2 mL sarin_no seize_no drugs_3hr

description: Gene expression data from Thalamus of animal N46_0.2 mL sarin_no seize_no drugs_3hr


title: Thalamus_animal N55_0.22 mL sarin_seize (10 min latency)_drugs_0.25hr

description: Gene expression data from Thalamus of animal N55_0.22 mL sarin_seize (10 min latency)_drugs_0.25hr

tag: seizure time


title: Thalamus_animal N48_0.18 mL sarin_seize (11 min latency)_drugs_1hr

description: Gene expression data from Thalamus of animal N48_0.18 mL sarin_seize (11 min latency)_drugs_1hr

tag: agent


title: Thalamus_animal N52_0.22 mL sarin_seize (9 min latency)_drugs_24hr

description: Gene expression data from Thalamus of animal N52_0.22 mL sarin_seize (9 min latency)_drugs_24hr

tag: amount administered


title: 14 day old bLR strain rat nucleus accumbens, biological replicate 4

description:
P14_LR_Nacc_L04
Gene expression data from nucleus accumbens of selectively-bred sprague dawley rats (Low Reponder strain), 14 days after birth


title: Thalamus_animal N47_0.2 mL saline_no seize_drugs_1hr

description: Gene expression data from Thalamus of animal N47_0.2 mL saline_no seize_drugs_1hr

value: Saline

tag: agent dose


title: 24 hr shikonin-2

city: Taipei

first: Ning-Sun

last: Yang

state: Taiwan

address: No.128 Sec.2, Academia Rd.

department: Agricultural Biotechnology Research Center

country: Taiwan

institute: Academia Sinica

hyb_protocol: MOA v1.1 arrays were pre-heat at 60℃ for 10 mins, rehydrated by 100% ethanol following with deionized water. The slides were pre-hybridized with 5x SSPE, 0.1% SDS and 1% BSA at 42℃ for 2 hour. After the pre-hybridization, 5 µg Cy5-labeled aRNA was hybridize on MOA in the presentation of the Phalanx OneArray hybridization buffer in duplication.

scan_protocol: The arrays were scanned by Axon GenePix 4000B scanner (635nm power 100 PMT 550~570 ; 532nm power 10, PMT 460) and quantify the fluoresence intensity.

data_processing: The raw intensity was filtered (SNR>5) and normalized by Quantile normalization method. Calculate average ratios of the hybridization replicates and find significant values for each gene by pairwise comparision (Ranking and hypothesis testing).

source_name: 24 hr shikonin

label_protocol: 2.5 µg of total RNA was reverse-transcribed and amplified using MessageAmpTM aRNA Amplification Kit (Ambion).  Indirect labeling the aa-UTP whereon by NHS-CyDye (Cy5, Amershan).

extract_protocol: RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧8).

treatment_protocol: Solutions containing 10 μg/μl shikonin or 100 μnM phorbol 12-myristate 13-acetate (TPA) in acetone were prepared immediately before use. A volume of 100 μl of the test chemicals was pipetted onto the abdominal skin area of mice and allowed to completely air dry. The skin treated with solvent (acetone) alone was used as negative control.

tag: tissue type

value: abdominal skin

tag: stimulation

value: shikonin

tag: time period

value: 24 hr


title: Thalamus_animal N45_0.2 mL sarin_seize (8 min latency)_drugs_1hr

description: Gene expression data from Thalamus of animal N45_0.2 mL sarin_seize (8 min latency)_drugs_1hr

value: Sarin

tag: strain

tag: atropine, 2-pam, diazepam

value: Y

tag: time point (hr)

tag: seizure latency


title: 24 hr shikonin-1


title: 14 day old bLR strain rat nucleus accumbens, biological replicate 3

description:
P14_LR_Nacc_L03
Gene expression data from nucleus accumbens of selectively-bred sprague dawley rats (Low Reponder strain), 14 days after birth

tag: age


title: 24 hr acetone-2

source_name: 24 hr acetone

value: acetone


title: Thalamus_animal N44_0.21 mL sarin_no seize_no drugs_6hr

description: Gene expression data from Thalamus of animal N44_0.21 mL sarin_no seize_no drugs_6hr

tag: animal number

tag: date injected

tag: time injected

tag: date sacrificed


title: Thalamus_animal N42_0.2 mL sarin_seize (8 min latency)_drugs_3hr

description: Gene expression data from Thalamus of animal N42_0.2 mL sarin_seize (8 min latency)_drugs_3hr

tag: tissue

tag: time sacrificed

tag: presence of seizure

tag: animal weight (g)


title: 14 day old bLR strain rat nucleus accumbens, biological replicate 2

description:
P14_LR_Nacc_L02
Gene expression data fromnucleus accumbens of selectively-bred sprague dawley rats (Low Reponder strain), 14 days after birth


title: 14 day old bLR strain rat nucleus accumbens, biological replicate 1

description:
P14_LR_Nacc_L01
Gene expression data from nucleus accumbens of selectively-bred sprague dawley rats (Low Reponder strain), 7 days after birth


title: 24 hr acetone-1


title: 7 day old bLR strain rat nucleus accumbens, biological replicate 4

description:
P7_LR_Nacc_L04
Gene expression data from nucleus accumbens of selectively-bred sprague dawley rats (Low Reponder strain), 7 days after birth

source_name: Selectively-bred Low responder rat strain derived from Sprague Dawley stock, 7 days after birth

value: 7 days after birth


title: Thalamus_animal N43_0.21 mL sarin_seize (9 min latency)_drugs_6hr

description: Gene expression data from Thalamus of animal N43_0.21 mL sarin_seize (9 min latency)_drugs_6hr

tag: agent

tag: amount administered

tag: agent dose

tag: seizure time


title: 7 day old bLR strain rat nucleus accumbens, biological replicate 5

description:
P7_LR_Nacc_L05
Gene expression data from nucleus accumbens of selectively-bred sprague dawley rats (Low Reponder strain), 7 days after birth

tag: strain

value: Selectively bred Low Responder (derived from an original Sprague Dawley)


title: 7 day old bLR strain rat nucleus accumbens, biological replicate 3

description:
P7_LR_Nacc_L03
Gene expression data from nucleus accumbens of selectively-bred sprague dawley rats (Low Reponder strain), 7 days after birth

value: Nucleus Accumbens


title: Thalamus_animal N40_0.21 mL saline_no seize_drugs_3hr

description: Gene expression data from Thalamus of animal N40_0.21 mL saline_no seize_drugs_3hr

tag: atropine, 2-pam, diazepam


title: K562 NF-E2

type: genomic

city: Bei Jing

first: Jia

last: Yu

address: Dong Dan San Tiao #5

department: Biochemistry

country: China

institute: Peking Union Medical College

hyb_protocol: The Cy5-ChIP and Cy3-input labelled DNA samples were co-hybridized to NimbleGen HG18 RefSeq promoter arrays for 18 hours, post hybridization washes were carried out.

scan_protocol: microRNA promoter arrays were scanned using an Axon 4000B microarray scanner with GenePix 6.0.

data_processing: Raw data were extracted as pair files by NimbleScan software. We performed Median-centering, quantile normalization, and linear smoothing by Bioconductor packages Ringo, limma and MEDME. After normalization, a normalized log2-ratio data (*_ratio.gff file) was created for each sample. From the normalized log2-ratio data, a permutation-based peak-finding algorithm provided by NimbleScan v2.5 (Roche-NimbleGen) was applied to find peaks which represent significant positive enrichment. NimbleScan detects peaks by searching for 4 or more probes whose signals were above the specified cutoff values, ranging from 90% to 15%, using a 500bp sliding window. The cutoff values are a percentage of a hypothetical maximum, which is the mean + 6 [standard deviation]. The ratio data is then randomized 20 times to evaluate the probability of “false positives”. Each peak is then assigned a false discovery rate (FDR) score based on the randomization. After getting the *_peaks.gff files, the identified peaks with an FDR ≤ 0.2 were mapped to genomic features: transcripts.

molecule: genomic DNA

source_name: NF-E2 ChIP DNA from hemin induced K562 cells at 48h

label_protocol: Ampliﬁed genomic DNA from puriﬁed ChIP and input DNA was fluorescently labelled using the NimbleGen Dual-Color DNA Labeling Kit as the Cy5-ChIP and Cy3-input labelled DNA samples

growth_protocol: K562 cells were cultured in RPMI1640

extract_protocol: 5x10E6 K562 cells were cross-linked with 1% formaldehyde for 10 min, washed in cold PBS buffer, resuspended in lysis buffer, and sonicated to obtain chromatin fragments between 200 bp and 1000 bp. Sonicated chromatin was resuspended in IP buffer and incubated overnight at 4°C with magnetic beads conjugated antibodies ( Santa Cruz Biotechnologies). The IP was then washed with lysis buffer, LiCl buffer and TE buffer, eluted in elution buffer. The DNA was then recovered by reversing the crosslinks, and purified by QIAGEN Purification Kit. An un-enriched sample of DNA was treated in a similar manner to serve as input. The immunoprecipitated DNA was tested for enrichment of control loci by qPCR. To obtain sufficient DNA for hybridization, puriﬁed ChIP and input DNA was ampliﬁed with the WGA ampliﬁcation kit

treatment_protocol: K562 cells were treated by hemin into erythroid differentiation for 48h

tag: cell line

tag: cell type

value: pro-Erythroid cells

tag: chip antibody

tag: chip antibody vendor

value: Abcam Company

tag: chip antibody cat. number

source_name: NF-E2 ChIP input DNA from hemin induced K562 cells at 48h


title: Thalamus_animal N37_0.19 mL saline_no seize_drugs_3hr

description: Gene expression data from Thalamus of animal N37_0.19 mL saline_no seize_drugs_3hr

tag: animal number

tag: time point (hr)

tag: date injected

tag: time injected


title: 4 hr shikonin-2

source_name: 4 hr shikonin

tag: tissue type

tag: stimulation

tag: time period

value: 4 hr


title: Thalamus_animal N41_0.2 mL saline_no seize_drugs_24hr

description: Gene expression data from Thalamus of animal N41_0.2 mL saline_no seize_drugs_24hr

tag: tissue

value: Thalamus

tag: agent

tag: amount administered

tag: date sacrificed

tag: time sacrificed

tag: presence of seizure

tag: animal weight (g)


title: 4 hr acetone-2

source_name: 4 hr acetone


title: Thalamus_animal N38_0.2 mL sarin_no seize_no drugs_24hr

description: Gene expression data from Thalamus of animal N38_0.2 mL sarin_no seize_no drugs_24hr

tag: agent dose

tag: strain

value: Sprague-Dawley

tag: atropine, 2-pam, diazepam


title: 4 hr shikonin-1


title: 7 day old bLR strain rat nucleus accumbens, biological replicate 2

description:
P7_LR_Nacc_L02
Gene expression data from nucleus accumbens of selectively-bred sprague dawley rats (Low Reponder strain), 7 days after birth

tag: age


title: Thalamus_animal N36_0.2 mL saline_no seize_drugs_0.25hr

description: Gene expression data from Thalamus of animal N36_0.2 mL saline_no seize_drugs_0.25hr

tag: animal number

tag: time point (hr)

value: N


title: Myometrium Prok1, 6 hrs, rep 4

city: Edinburgh

first: Roberto

last: Catalano

address: 47 Little France Crescent

department: The Queen's Medical Research Institute

country: United Kingdom

institute: MRC Human Reproductive Sciences Unit

data_processing:
Raw data: The numerical results were extracted with GenomeStudio v. 2010.1 without any normalization or background subtraction.
Normalized data: The data were normalized using quantile normalization with limma in R.

source_name: Human myometrium explant, PROK1, 6 hrs

label_protocol: 300 ng of purified total RNA was amplified and biotinylated in an overnight in vitro transcription reaction using the Illumina RNA TotalPrepTM amplification kit (Ambion, Applied Biosystems).

growth_protocol: Explants cultured in RPMI medium (GIBCO, Invitrogen, Paisley, UK) supplemented with 100 IU penicillin and 100 μg/ml streptomycin (Sigma, Poole, UK) at 37 °C and 5% CO2.

extract_protocol: RNA was extracted with QIAzol (QIAGEN, Crawley, UK) and on-column DNase I treatment with the QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyzer.

treatment_protocol: Myometrial explants treated with either vehicle or 40 nM PROK1 for 6 and 24 hours.

value: myometrium explant

tag: gestation stage

value: term non-labor

tag: treatment

value: prokineticin 1

tag: treatment duration

value: 6 hrs


title: 7 day old bLR strain rat nucleus accumbens, biological replicate 1

description:
P7_LR_Nacc_L01
Gene expression data from nucleus accumbens of selectively-bred sprague dawley rats (Low Reponder strain), 7 days after birth


title: Thalamus_animal N35_0.2 mL saline_no seize_drugs_6hr

description: Gene expression data from Thalamus of animal N35_0.2 mL saline_no seize_drugs_6hr

value: Saline

tag: date injected

tag: time injected


title: 4 hr acetone-1

tag: tissue type

value: abdominal skin

tag: stimulation

tag: time period


title: 21 day old bHR strain rat nucleus accumbens, biological replicate 6

description:
P21_HR_Nacc_H06
Gene expression data from nucleus accumbens of selectively-bred sprague dawley rats (High Reponder strain), 21 days after birth

source_name: Selectively-bred High responder rat strain derived from Sprague Dawley stock, 21 days after birth

value: Selectively bred High Responder (derived from an original Sprague Dawley)

tag: tissue

value: 21 days after birth


title: K562 EKLF

source_name: EKLF ChIP DNA from hemin induced K562 cells at 48h

tag: cell line

tag: cell type

tag: chip antibody

value: EKLF

tag: chip antibody vendor

value: Santa Cruz Biotechnology

tag: chip antibody cat. number

source_name: EKLF ChIP DNA input from hemin induced K562 cells at 48h


title: K562 GATA-1

source_name: GATA-1 ChIP DNA from hemin induced K562 cells at 48h

source_name: GATA-1 ChIP input DNA from hemin induced K562 cells at 48h


title: 21 day old bHR strain rat nucleus accumbens, biological replicate 5

description:
P21_HR_Nacc_H05
Gene expression data fromnucleus accumbens of selectively-bred sprague dawley rats (High Reponder strain), 21 days after birth

tag: strain

value: Nucleus Accumbens

tag: age


title: Thalamus_animal N56_0.22 mL sarin_seize (4 min latency)_drugs_0.25hr

description: Gene expression data from Thalamus of animal N56_0.22 mL sarin_seize (4 min latency)_drugs_0.25hr

tag: animal number

tag: agent

value: Sarin

tag: amount administered

tag: agent dose

tag: atropine, 2-pam, diazepam

value: Y

tag: time point (hr)

tag: date sacrificed

tag: time sacrificed

tag: presence of seizure

tag: seizure time

tag: seizure latency

tag: animal weight (g)


title: Myometrium Vehicle, 6 hrs, rep 1

source_name: Human myometrium explant, vehicle, 6 hrs

tag: tissue

tag: gestation stage

tag: treatment

value: vehicle

tag: treatment duration


title: Myometrium Vehicle, 24 hrs, rep 6

source_name: Human myometrium explant, vehicle, 24 hrs

value: 24 hrs


title: Thalamus_animal N34_0.22 mL saline_no seize_drugs_3hr

description: Gene expression data from Thalamus of animal N34_0.22 mL saline_no seize_drugs_3hr

value: Thalamus

tag: strain

value: Sprague-Dawley

tag: date injected

tag: time injected


title: Thalamus_animal N33_0.2 mL saline_no seize_drugs_1hr

description: Gene expression data from Thalamus of animal N33_0.2 mL saline_no seize_drugs_1hr

tag: animal number

tag: agent

tag: amount administered

value: N


title: Myometrium Vehicle 4 hrs, rep 2

source_name: Human myometrium explant, vehicle, 4 hrs

value: myometrium explant

value: term non-labor

value: 4 hrs


title: 21 day old bHR strain rat nucleus accumbens, biological replicate 3

description:
P21_HR_Nacc_H03
Gene expression data from nucleus accumbens of selectively-bred sprague dawley rats (High Reponder strain), 21 days after birth

tag: age


title: Septum_animal N260_0.21 mL saline_no seize_no drugs_0.25hr

description: Gene expression data from Septum of animal N260_0.21 mL saline_no seize_no drugs_0.25hr

value: Septum

value: Saline

tag: agent dose

tag: atropine, 2-pam, diazepam

tag: time point (hr)

tag: date sacrificed


title: Myometrium Vehicle, 24 hrs, rep 3


title: 21 day old bHR strain rat nucleus accumbens, biological replicate 2

description:
P21_HR_Nacc_H02
Gene expression data from nucleus accumbens of selectively-bred sprague dawley rats (High Reponder strain), 21 days after birth

value: Selectively bred High Responder (derived from an original Sprague Dawley)


title: 21 day old bHR strain rat nucleus accumbens, biological replicate 1

description:
P21_HR_Nacc_H01
Gene expression data from nucleus accumbens of selectively-bred sprague dawley rats (High Reponder strain), 21 days after birth

value: 21 days after birth


title: Myometrium Vehicle, 6 hrs, rep 3

value: 6 hrs


title: 21 day old bHR strain rat nucleus accumbens, biological replicate 4

description:
P21_HR_Nacc_H04
Gene expression data from nucleus accumbens of selectively-bred sprague dawley rats (High Reponder strain), 21 days after birth


title: Septum_animal N256_0.2 mL saline_no seize_no drugs_24hr

description: Gene expression data from Septum of animal N256_0.2 mL saline_no seize_no drugs_24hr

tag: time sacrificed

tag: presence of seizure


title: 14 day old bHR strain rat nucleus accumbens, biological replicate 6

description:
P14_HR_Nacc_H06
Gene expression data from nucleus accumbens of selectively-bred sprague dawley rats (High Reponder strain), 14 days after birth

source_name: Selectively-bred High responder rat strain derived from Sprague Dawley stock, 14 days after birth

tag: tissue

value: 14 days after birth


title: 14 day old bHR strain rat nucleus accumbens, biological replicate 4

description:
P14_HR_Nacc_H04
Gene expression data from nucleus accumbens of selectively-bred sprague dawley rats (High Reponder strain), 14 days after birth

value: Nucleus Accumbens


title: Septum_animal N257_naive_no agent_0hr

description: Gene expression data from Septum of animal N257_naive_no agent_0hr

source_name: Septum_animal N257_naive_no agent_0hr

value: Naive

tag: animal weight (g)


title: Myometrium Vehicle, 6 hrs, rep 5

tag: gestation stage

tag: treatment


title: 14 day old bHR strain rat nucleus accumbens, biological replicate 5

description:
P14_HR_Nacc_H05
Gene expression data from nucleus accumbens of selectively-bred sprague dawley rats (High Reponder strain), 14 days after birth

tag: strain


title: Septum_animal N258_naive_no agent_0hr

description: Gene expression data from Septum of animal N258_naive_no agent_0hr

source_name: Septum_animal N258_naive_no agent_0hr


title: Myometrium Prok1, 24 hrs, rep 4

source_name: Human myometrium explant, PROK1, 24 hrs

value: prokineticin 1

tag: treatment duration


title: Septum_animal N259_naive_no agent_0hr

description: Gene expression data from Septum of animal N259_naive_no agent_0hr

source_name: Septum_animal N259_naive_no agent_0hr


title: Septum_animal N254_0.2 mL saline_no seize_no drugs_24hr

description: Gene expression data from Septum of animal N254_0.2 mL saline_no seize_no drugs_24hr

tag: date injected

tag: time injected


title: 14 day old bHR strain rat nucleus accumbens, biological replicate 3

description:
P14_HR_Nacc_H03
Gene expression data from nucleus accumbens of selectively-bred sprague dawley rats (High Reponder strain), 14 days after birth


title: Myometrium Vehicle, 24 hrs, rep 5

value: vehicle


title: 14 day old bHR strain rat nucleus accumbens, biological replicate 2

description:
P14_HR_Nacc_H02
Gene expression data from nucleus accumbens of selectively-bred sprague dawley rats (High Reponder strain), 14 days after birth


title: Myometrium Prok1, 6 hrs, rep 6


title: Septum_animal N252_0.2 mL saline_no seize_no drugs_24hr

description: Gene expression data from Septum of animal N252_0.2 mL saline_no seize_no drugs_24hr

tag: animal number

tag: agent


title: Myometrium Vehicle, 24 hrs, rep 4

value: 24 hrs


title: Septum_animal N251_0.21 mL saline_no seize_no drugs_1hr

description: Gene expression data from Septum of animal N251_0.21 mL saline_no seize_no drugs_1hr

tag: amount administered


title: 14 day old bHR strain rat nucleus accumbens, biological replicate 1

description:
P14_HR_Nacc_H01
Gene expression data from nucleus accumbens of selectively-bred sprague dawley rats (High Reponder strain), 14 days after birth

tag: age


title: Septum_animal N250_0.21 mL saline_no seize_no drugs_3hr

description: Gene expression data from Septum of animal N250_0.21 mL saline_no seize_no drugs_3hr

tag: agent dose

tag: atropine, 2-pam, diazepam


title: Myometrium Prok1, 24 hrs, rep 3


title: Septum_animal N249_0.21 mL saline_no seize_no drugs_0.25hr

description: Gene expression data from Septum of animal N249_0.21 mL saline_no seize_no drugs_0.25hr

tag: time point (hr)

tag: date sacrificed


title: 7 day old bHR strain rat nucleus accumbens, biological replicate 6

description:
P7_HR_Nacc_H06
Gene expression data from nucleus accumbens of selectively-bred sprague dawley rats (High Reponder strain), 7 days after birth

source_name: Selectively-bred High responder rat strain derived from Sprague Dawley stock, 7 days after birth

value: 7 days after birth


title: Myometrium Prok1, 6 hrs, rep 5


title: Myometrium Prok1, 24 hrs, rep 6


title: 7 day old bHR strain rat nucleus accumbens, biological replicate 3

description:
P7_HR_Nacc_H03
Gene expression data from nucleus accumbens of selectively-bred sprague dawley rats (High Reponder strain), 7 days after birth


title: Myometrium Prok1, 24 hrs, rep 2


title: Septum_animal N248_0.2 mL saline_no seize_no drugs_1hr

description: Gene expression data from Septum of animal N248_0.2 mL saline_no seize_no drugs_1hr

value: Sprague-Dawley

tag: time sacrificed

tag: presence of seizure


title: 7 day old bHR strain rat nucleus accumbens, biological replicate 5

description:
P7_HR_Nacc_H05
Gene expression data from nucleus accumbens of selectively-bred sprague dawley rats (High Reponder strain), 7 days after birth

tag: tissue


title: 7 day old bHR strain rat nucleus accumbens, biological replicate 2

description:
P7_HR_Nacc_H02
Gene expression data from nucleus accumbens of selectively-bred sprague dawley rats (High Reponder strain), 7 days after birth


title: 7 day old bHR strain rat nucleus accumbens, biological replicate 4

description:
P7_HR_Nacc_H04
Gene expression data from nucleus accumbens of selectively-bred sprague dawley rats (High Reponder strain), 7 days after birth


title: Myometrium Prok1, 24 hrs, rep 5

tag: gestation stage


title: Myometrium Vehicle, 6 hrs, rep 4

tag: treatment


title: Septum_animal N246_0.18 mL saline_no seize_no drugs_6hr

description: Gene expression data from Septum of animal N246_0.18 mL saline_no seize_no drugs_6hr

tag: strain

value: N

tag: animal weight (g)


title: Myometrium Prok1, 6 hrs, rep 2

value: myometrium explant

tag: treatment duration


title: 7 day old bHR strain rat nucleus accumbens, biological replicate 1

description:
P7_HR_Nacc_H01
Gene expression data from nucleus accumbens of selectively-bred sprague dawley rats (High Reponder strain), 7 days after birth


title: Myometrium Prok1, 6 hrs, rep 1

value: term non-labor


title: 21 day old bLR strain rat hippocampus, biological replicate 6

description:
P21_LR_HPC_L06
Gene expression data from hippocampus of selectively-bred sprague dawley rats (Low Reponder strain), 21 days after birth

source_name: Selectively-bred Low responder rat strain derived from Sprague Dawley stock, 21 days after birth

value: Selectively bred Low Responder (derived from an original Sprague Dawley)

value: Hippocampus


title: Septum_animal N247_0.2 mL saline_no seize_no drugs_0.25hr

description: Gene expression data from Septum of animal N247_0.2 mL saline_no seize_no drugs_0.25hr

value: Septum

value: Saline

tag: date injected

tag: time injected


title: Septum_animal N245_0.2 mL saline_no seize_no drugs_3hr

description: Gene expression data from Septum of animal N245_0.2 mL saline_no seize_no drugs_3hr

tag: animal number

tag: agent


title: Septum_animal N243_0.21 mL saline_no seize_no drugs_3hr

description: Gene expression data from Septum of animal N243_0.21 mL saline_no seize_no drugs_3hr

tag: amount administered


title: TM_Meiosis_Thiamine

city: Salamanca

first: Luis

last: Quintales

address: Calle Zacarías González, 2

department: Universidad de Salamanca / CSIC

country: Spain

institute: Instituto de Biología Funcional y Genómica (IBFG)

description:
RNA Meiosis 3h + Thiamine
All the results files are in Wiggle Track Format (WIG) containing: log2(IP fraction/input fraction) for ChIP* samples, log2(mononucleosomal fraction/input fraction) for NUC* samples, and RNA raw signal for TM* samples (transcription mapping). The WIG file coordinates are mapped against the Sanger September 2008 Schizosaccharomyces pombe genome version.

hyb_protocol: 220 ml 1x hybridization mixture containing 5.5 mg of fragmented and labeled DNA target, 7% DMSO, 1.5, 5, 25 and 100 pM of Eukaryotic Hibridization Controls (bioB, bioC, bioD, cre) respectively, and 50 pM control oligonucleotide B2 were prepared using the Affymetrix GeneChip Hybridization Kit as described in the Affymetrix GeneChip Whole Transcript (WT) Sense Target Assay Labeling Manual. The final DNA target mixture was hybridized to Affymetrix S. pombe Tiling 1.0FR arrays and incubated in a hybridization oven at 45 °C and 60 rpm for 17 h ±1h.

scan_protocol: Affymetrix standard protocol using Affymetrix Fluidics 450 and Scanner 3000

data_processing: The five M*.CEL  were quantile normalized (PMID:12538238). After this, individual raw signals were reported in WIG files.

organism: Schizosaccharomyces pombe

source_name: RNA Meiosis 3h + Thiamine

label_protocol: 5.5 mg of the fragmented single-stranded DNA samples resuspended in 45 ml were incubated with a labeling master mix containing DNA Labeling Reagent (5 mM), terminal deoxynucleotidyl transferase (30 U/ul) and 1× Terminal Deoxynucleotidyl Transferase Buffer in a thermal cycler as described in the Affymetrix GeneChip Whole Transcript (WT) Sense Target Assay Labeling Manual.

growth_protocol: Minimal Medium (MM) at 25 ºC (asynchronous) until OD595=0.8 followed by transfer to MM without nitrogen for 14 h after which NH4Cl was added to 0.5 g/l and cells were transferred to 34 ºC to induce synchronous meiosis

extract_protocol: Total RNA was prepared by resuspending the cell pellets in 20 μl extraction buffer (100 mM EDTA, pH 8.0, 100 mM NaCl, 50 mM Tris-HCl, pH 8.0), 20 μl phenol/chloroform, 2 μl 10% SDS, 200 μl glass beads (425-600 μm, SIGMA G-8772). Cells were mechanically disrupted in a Fast-Prep device (Savant BIO 101) and the cell lysate was extracted with phenol, phenol/chloroform and chloroform/isoamyl alcohol before precipitation with 0.3 M sodium acetate and ethanol. RNA was resuspended in 50 μl of sterile water with diethyl pyrocarbonate (SIGMA D-5758) and was further purified with the RNeasy mini kit (Quiagen) following the supplier's specifications.

treatment_protocol: Minimal Medium (MM) with thiamine (5 microgrames/ml) at 25 ºC (asynchronous) until OD595=0.8 followed by transfer to MM without nitrogen for 14 h after which NH4Cl was added to 0.5 g/l and cells were transferred to 34 ºC to induce synchronous meiosis

tag: genotype

tag: culture type

value: Synchronous Meiosis


title: TM_Mitosis

description:
RNA Mitosis
All the results files are in Wiggle Track Format (WIG) containing: log2(IP fraction/input fraction) for ChIP* samples, log2(mononucleosomal fraction/input fraction) for NUC* samples, and RNA raw signal for TM* samples (transcription mapping). The WIG file coordinates are mapped against the Sanger September 2008 Schizosaccharomyces pombe genome version.

source_name: RNA Mitosis

growth_protocol: Yeast extract (YE) medium at 32 ºC until OD595=0.8

value: Asynchronous Mitosis


title: TM_Meiosis_Ox

description:
RNA Meiosis 2.5h + H202
All the results files are in Wiggle Track Format (WIG) containing: log2(IP fraction/input fraction) for ChIP* samples, log2(mononucleosomal fraction/input fraction) for NUC* samples, and RNA raw signal for TM* samples (transcription mapping). The WIG file coordinates are mapped against the Sanger September 2008 Schizosaccharomyces pombe genome version.

source_name: RNA Meiosis 2.5h + H202

treatment_protocol: Minimal Medium (MM) at 25 ºC (asynchronous) until OD595=0.8 followed by transfer to MM without nitrogen for 14 h after which NH4Cl was added to 0.5 g/l and cells were transferred to 34 ºC to induce synchronous meiosis. H202 was added to a final concentration of 0.5 mM 2 h after transference to 34 ºC to induce meiosis.


title: 21 day old bLR strain rat hippocampus, biological replicate 5

description:
P21_LR_HPC_L05
Gene expression data from hippocampus of selectively-bred sprague dawley rats (Low Reponder strain), 21 days after birth

tag: age

value: 21 days after birth


title: Myometrium Prok1, 6 hrs, rep 3

source_name: Human myometrium explant, PROK1, 6 hrs

value: 6 hrs


title: Septum_animal N244_0.18 mL saline_no seize_no drugs_1hr

description: Gene expression data from Septum of animal N244_0.18 mL saline_no seize_no drugs_1hr

tag: agent dose

tag: atropine, 2-pam, diazepam

tag: time point (hr)

tag: date sacrificed


title: Myometrium Prok1, 24 hrs, rep 1

tag: tissue

tag: gestation stage


title: Myometrium Vehicle, 24 hrs, rep 2

tag: treatment


title: Septum_animal N242_0.2 mL saline_no seize_no drugs_6hr

description: Gene expression data from Septum of animal N242_0.2 mL saline_no seize_no drugs_6hr

tag: strain

tag: time sacrificed

tag: presence of seizure

tag: animal weight (g)


title: 21 day old bLR strain rat hippocampus, biological replicate 4

description:
P21_LR_HPC_L04
Gene expression data from hippocampus of selectively-bred sprague dawley rats (Low Reponder strain), 21 days after birth


title: Septum_animal N241_0.2 mL saline_no seize_no drugs_6hr

description: Gene expression data from Septum of animal N241_0.2 mL saline_no seize_no drugs_6hr

tag: animal number

tag: date injected

tag: time injected


title: Myometrium Vehicle 4 hrs, rep 1

tag: treatment duration

value: 4 hrs


title: TM_Meiosis

description:
RNA Meiosis 3h
All the results files are in Wiggle Track Format (WIG) containing: log2(IP fraction/input fraction) for ChIP* samples, log2(mononucleosomal fraction/input fraction) for NUC* samples, and RNA raw signal for TM* samples (transcription mapping). The WIG file coordinates are mapped against the Sanger September 2008 Schizosaccharomyces pombe genome version.

source_name: RNA Meiosis 3h

treatment_protocol: Minimal Medium (MM) at 25 ºC (asynchronous) until OD595=0.8 followed by transfer to MM without nitrogen for 14 h after which NH4Cl was added to 0.5 g/l and cells were transferred to 34 ºC to induce synchronous meiosis

tag: genotype

tag: culture type


title: 21 day old bLR strain rat hippocampus, biological replicate 1

description:
P21_LR_HPC_L01
Gene expression data from hippocampus of selectively-bred sprague dawley rats (Low Reponder strain), 21 days after birth

tag: age


title: 14 day old bLR strain rat hippocampus, biological replicate 6

description:
P14_LR_HPC_L06
Gene expression data from hippocampus of selectively-bred sprague dawley rats (Low Reponder strain), 14 days after birth

source_name: Selectively-bred Low responder rat strain derived from Sprague Dawley stock, 14 days after birth

value: 14 days after birth


title: 21 day old bLR strain rat hippocampus, biological replicate 3

description:
P21_LR_HPC_L03
Gene expression data from hippocampus of selectively-bred sprague dawley rats (Low Reponder strain), 21 days after birth


title: 21 day old bLR strain rat hippocampus, biological replicate 2

description:
P21_LR_HPC_L02
Gene expression data from hippocampus of selectively-bred sprague dawley rats (Low Reponder strain), 21 days after birth


title: Septum_animal N173_0.22 mL sarin_seize (10 min latency)_drugs_24hr

description: Gene expression data from Septum of animal N173_0.22 mL sarin_seize (10 min latency)_drugs_24hr

tag: agent

value: Sarin

tag: amount administered

tag: agent dose

tag: atropine, 2-pam, diazepam

value: Y

tag: seizure time

tag: seizure latency


title: NUC_Mitosis

type: mixed

description:
Mononucleosomal DNA Mitosis
All the results files are in Wiggle Track Format (WIG) containing: log2(IP fraction/input fraction) for ChIP* samples, log2(mononucleosomal fraction/input fraction) for NUC* samples, and RNA raw signal for TM* samples (transcription mapping). The WIG file coordinates are mapped against the Sanger September 2008 Schizosaccharomyces pombe genome version.

hyb_protocol: 200 ml 1x hybridization mixture containing 4.5 mg of fragmented and labeled DNA target, 7% DMSO and 50 pM control oligonucleotide B2 (Affymetrix P/N 900720) were prepared according to the Affymetrix hibridization  protocol for single tiling arrays described in the Affymetrix GeneChip Whole Transcript (WT) Double-Stranded Target Assay Manual. The final DNA target mixture was hybridized onto Affymetrix S. pombe Tiling 1.0FR arrays and incubated in a hybridization oven at 45 °C and 60 rpm for 16 h.

data_processing: The five NUC*.CEL and NAKED_DNAtotal.CEL were quantile normalized (PMID:12538238). After this, individual log2(test/control) fold changes were reported in WIG files.

molecule: other

source_name: Mononucleosomal DNA Mitosis

label_protocol: 4.5 mg of the fragmented double-stranded DNA samples resuspended in 45 mg were incubated with a labeling master mix containing DNA Labeling Reagent (5 mM), terminal deoxynucleotidyl transferase (30 U/ml) and 1× Terminal Deoxynucleotidyl Transferase Buffer in a thermal cycler as described in the Affymetrix GeneChip Whole Transcript (WT) Double-Stranded Target Assay Manual.

extract_protocol: Chromatin was prepared from formaldehyde crosslinked log phase cells and digested with micrococcal nuclease (Fermentas #ENO181) to a final concentration of 180 units/ml for 40 minutes at 37 ºC to yield about 90% mononucleosomes. DNA of mononucleosomal size was purified from agarose gels, fragmented to an average size of about 50 bp with DNaseI. DNAseI fragmented genomic DNA from S. pombe was used as hybridization control.

treatment_protocol: Yeast extract (YE) medium at 32 ºC until OD595=0.8

tag: sample type

value: Mononucleosomal DNA

source_name: Naked DNA


title: NUC_Meiosis_Thiamine

description:
Mononucleosomal DNA Meiosis 3h + thiamine
All the results files are in Wiggle Track Format (WIG) containing: log2(IP fraction/input fraction) for ChIP* samples, log2(mononucleosomal fraction/input fraction) for NUC* samples, and RNA raw signal for TM* samples (transcription mapping). The WIG file coordinates are mapped against the Sanger September 2008 Schizosaccharomyces pombe genome version.


title: NUC_Meiosis_Ox

description:
Mononucleosomal DNA Meiosis 2.5h + H202
All the results files are in Wiggle Track Format (WIG) containing: log2(IP fraction/input fraction) for ChIP* samples, log2(mononucleosomal fraction/input fraction) for NUC* samples, and RNA raw signal for TM* samples (transcription mapping). The WIG file coordinates are mapped against the Sanger September 2008 Schizosaccharomyces pombe genome version.

source_name: Mononucleosomal DNA Meiosis 2.5h + H202

value: mononucleosomal DNA


title: Septum_animal N170_0.21 mL sarin_seize (5 min latency)_drugs_24hr

description: Gene expression data from Septum of animal N170_0.21 mL sarin_seize (5 min latency)_drugs_24hr

tag: tissue

tag: strain

value: Sprague-Dawley

tag: time point (hr)

tag: date sacrificed

tag: time sacrificed


title: Myometrium Vehicle, 24 hrs, rep 1

source_name: Human myometrium explant, vehicle, 24 hrs

value: myometrium explant

tag: gestation stage

tag: treatment

value: vehicle

value: 24 hrs


title: NUC_Meiosis

description:
Mononucleosomal DNA Meiosis 3h
All the results files are in Wiggle Track Format (WIG) containing: log2(IP fraction/input fraction) for ChIP* samples, log2(mononucleosomal fraction/input fraction) for NUC* samples, and RNA raw signal for TM* samples (transcription mapping). The WIG file coordinates are mapped against the Sanger September 2008 Schizosaccharomyces pombe genome version.

source_name: Mononucleosomal DNA Meiosis 3h

tag: genotype


title: Septum_animal N174_0.21 mL saline_no seize_drugs_0.25hr

description: Gene expression data from Septum of animal N174_0.21 mL saline_no seize_drugs_0.25hr

tag: animal number

tag: date injected

tag: time injected

tag: presence of seizure

value: N

tag: animal weight (g)


title: Septum_animal N172_0.21 mL sarin_no seize_no drugs_24hr

description: Gene expression data from Septum of animal N172_0.21 mL sarin_no seize_no drugs_24hr

value: Septum

tag: agent

tag: amount administered

tag: agent dose

tag: atropine, 2-pam, diazepam


title: 14 day old bLR strain rat hippocampus, biological replicate 5

description:
P14_LR_HPC_L05
Gene expression data from hippocampus of selectively-bred sprague dawley rats (Low Reponder strain), 14 days after birth

value: Selectively bred Low Responder (derived from an original Sprague Dawley)

tag: tissue

value: Hippocampus

tag: age


title: 14 day old bLR strain rat hippocampus, biological replicate 4

description:
P14_LR_HPC_L04
Gene expression data from hippocampus of selectively-bred sprague dawley rats (Low Reponder strain), 14 days after birth

tag: strain


title: ChIP_Orc4

description:
Orc4 ChIP DNA
All the results files are in Wiggle Track Format (WIG) containing: log2(IP fraction/input fraction) for ChIP* samples, log2(mononucleosomal fraction/input fraction) for NUC* samples, and RNA raw signal for TM* samples (transcription mapping). The WIG file coordinates are mapped against the Sanger September 2008 Schizosaccharomyces pombe genome version.

data_processing: Data was quantile normalized (PMID:12538238). log2(test/control) fold changes were reported in WIG files.

source_name: Orc4 ChIP DNA

extract_protocol: Orc4 was immunoprecipitated with 5 microgrames of polyclonal anti Orc4 raised against the last 14 carboxy-terminal aminoacids of the protein. Ten microliters of immunoprecipitate and control DNA from whole cell extract (WCE) were amplified 4 times with Sequenase (70775Y, USB) and primer A (GTTTCCCAGTCACGGTC(N)9), followed by 20 rounds of amplification with Taq polymerase (Biotools) in the presence of 8 mM dUTP and primer B (GTTTCCCAGTCACGGTC).

tag: antibody

value: Rabbit polyclonal

tag: culture type

value: Asynchronous Mitosis

tag: sample type

value: IP DNA

source_name: Whole cell extract (WCE)


title: Bovine adrenocortical cells transduced with pBabe and pLNCX2, biological rep1

city: Grenoble

first: Michaël

last: Thomas

address: 17 rue des martyrs

department: iRTSV/BCI

institute: Inserm U1036

description: Gene expression from cells transduced first by pBabe followed by pLNCX2

hyb_protocol: Following fragmentation, 10ug of labeled cRNA were hybridized for 16 hours at 45C on Affymetrix GeneChip Bovine Genome Array. Arrays were washed and stained with streptavidin-phycoerythrin in a fluidic 450 (Affymetrix).

scan_protocol: The arrays were read with a confocal laser (GeneChip scanner 3000, Affymetrix).

data_processing: The obtained data were normalized with Affymetrix Expression Console software using MAS5 statistical algorithm.Normalized data were compared and filtered using partek Genomic Suite software 6.5.

organism: Bos taurus

source_name: Primary bovine adrenocortical cells

label_protocol: One microgram of total RNA was amplified and biotin-labeled using GeneChip Expression 3' Amplification one-Cycle Target Labeling and Control Reagents kit

extract_protocol: Total RNA was extracted using Rneasy kit

value: adrenal cortex

tag: transducer

value: pBabe and pLNCX2


title: 14 day old bLR strain rat hippocampus, biological replicate 3

description:
P14_LR_HPC_L03
Gene expression data from hippocampus of selectively-bred sprague dawley rats (Low Reponder strain), 14 days after birth

value: 14 days after birth


title: Septum_animal N82_0.2 mL saline_no seize_drugs_1hr

description: Gene expression data from Septum of animal N82_0.2 mL saline_no seize_drugs_1hr

value: Saline

value: Y

tag: time point (hr)

tag: date sacrificed

tag: time sacrificed


title: Septum_animal N81_0.24 mL saline_no seize_drugs_1hr

description: Gene expression data from Septum of animal N81_0.24 mL saline_no seize_drugs_1hr

tag: animal number

tag: date injected

tag: time injected


title: Septum_animal N80_0.22 mL sarin_no seize_no drugs_0.25hr

description: Gene expression data from Septum of animal N80_0.22 mL sarin_no seize_no drugs_0.25hr

tag: agent

value: Sarin

tag: presence of seizure

tag: animal weight (g)


title: Bovine adrenocortical cells transduced with pLNCX2 and pBabe, biological rep2

description: Gene expression from cells transduced first by pLNCX2 followed by pBabe

value: pLNCX2 and pBabe


title: 14 day old bLR strain rat hippocampus, biological replicate 2

description:
P14_LR_HPC_L02
Gene expression data from hippocampus of selectively-bred sprague dawley rats (Low Reponder strain), 14 days after birth


title: ChIP_Orc1

description:
Orc1 ChIP DNA
All the results files are in Wiggle Track Format (WIG) containing: log2(IP fraction/input fraction) for ChIP* samples, log2(mononucleosomal fraction/input fraction) for NUC* samples, and RNA raw signal for TM* samples (transcription mapping). The WIG file coordinates are mapped against the Sanger September 2008 Schizosaccharomyces pombe genome version.

source_name: Orc1 ChIP DNA

extract_protocol: Orc1-HA was immunoprecipitated with 10 microgrames of HA antibody (12CA5, Roche). Ten microliters of IP and control DNA from whole cell extract (WCE) were amplified 4 times with Sequenase (70775Y, USB) and primer A (GTTTCCCAGTCACGGTC(N)9), followed by 20 rounds of amplification with Taq polymerase (Biotools) in the presence of 8 mM dUTP and primer B (GTTTCCCAGTCACGGTC).

tag: genotype

value: HA monoclonal

tag: vendor/catalog

value: Roche, 12CA5


title: Septum_animal N79_0.22 mL sarin_no seize_no drugs_1hr

description: Gene expression data from Septum of animal N79_0.22 mL sarin_no seize_no drugs_1hr

tag: tissue

tag: amount administered

tag: agent dose

value: Sprague-Dawley

tag: atropine, 2-pam, diazepam


title: Bovine adrenocortical cells transduced with Ras and p53, biological rep3

description: Gene expression from cells transduced first by oncogenic Ras followed by p53

value: Ras and p53


title: Bovine adrenocortical cells transduced with pBabe and pLNCX2, biological rep2


title: Bovine adrenocortical cells transduced with Ras and p53, biological rep2


title: 7 day old bLR strain rat hippocampus, biological replicate 5

description:
P7_LR_HPC_L05
Gene expression data from hippocampus of selectively-bred sprague dawley rats (Low Reponder strain), 7 days after birth

source_name: Selectively-bred Low responder rat strain derived from Sprague Dawley stock, 7 days after birth

tag: strain

tag: age

value: 7 days after birth


title: Septum_animal N78_0.23 mL saline_no seize_drugs_6hr

description: Gene expression data from Septum of animal N78_0.23 mL saline_no seize_drugs_6hr

value: Septum

tag: time point (hr)

value: N


title: 14 day old bLR strain rat hippocampus, biological replicate 1

description:
P14_LR_HPC_L01
Gene expression data from hippocampus of selectively-bred sprague dawley rats (Low Reponder strain), 14 days after birth

value: Selectively bred Low Responder (derived from an original Sprague Dawley)

value: Hippocampus


title: 7 day old bLR strain rat hippocampus, biological replicate 6

description:
P7_LR_HPC_L06
Gene expression data from hippocampus of selectively-bred sprague dawley rats (Low Reponder strain), 7 days after birth


title: Septum_animal N77_0.21 mL saline_no seize_drugs_0.25hr

description: Gene expression data from Septum of animal N77_0.21 mL saline_no seize_drugs_0.25hr

tag: date sacrificed


title: Septum_animal N76_0.2 mL saline_no seize_drugs_24hr

description: Gene expression data from Septum of animal N76_0.2 mL saline_no seize_drugs_24hr

tag: time sacrificed


title: Bovine adrenocortical cells transduced with pLNCX2 and pBabe, biological rep1

tag: transducer


title: Bovine adrenocortical cells transduced with p53 and Ras, biological rep2

description: Gene expression from cells transduced first by p53 followed by oncogenic Ras

value: p53 and Ras


title: Bovine adrenocortical cells transduced with Ras and p53, biological rep1

value: adrenal cortex


title: Bovine adrenocortical cells transduced with p53 and Ras, biological rep1


title: total microRNAs in LNCaP cells treated with DHT at 24h

city: Shanghai

first: Wenjuan

last: Mo

address: No. 220 Handan Road

department: Life School

institute: Fudan University

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: LNCaP cell line

growth_protocol: The androgen-sensitive human prostate cancer cell line LNCaP was obtained from ATCC and maintained in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) and penicillin (100 units/ml)-streptomycin (100g/ml) at 37 ℃ in a humidified 5% CO2 cell incubator.

extract_protocol: For cell samples at each time point, the total RNA was extracted and purified using the RNeasy Mini kit following the manufacturer’s instructions. The isolated RNA was stored at -70℃ for the Illumina microarrays.

treatment_protocol: Before androgen treatment, the LNCaP cells were cultivated with Phenol Red -free RPMI 1640 (GIBCO/ BRL) supplemented with 10% charcoal-dextran-stripped FBS for 5 days. Then the cells were induced with androgen dihydrotestosterone (DHT), at ultimate concentration 10 nM, which has been proven by pre-experiment to be optimum for LNCaP cell growth (data not shown). The cell response to androgen treatment was analyzed at ten time points — 0h, 20min, 40min, 1h, 2 h, 4 h, 8 h, 16h, 24 h and 48 h, where ‘0h’ refers to cell status before androgen action.

tag: treatment group

value: dihydrotestosterone (DHT) at 24h

tag: hormone status

value: androgen-sensitive

value: prostate cancer

tag: cell line

value: LNCaP


title: total microRNAs in LNCaP cells treated with DHT at 48h

description: replicate 1

label_protocol: The isolated RNA was stored at -70℃ for the Illumina microarrays.

value: dihydrotestosterone (DHT) at 48h


title: 7 day old bLR strain rat hippocampus, biological replicate 4

description:
P7_LR_HPC_L04
Gene expression data from hippocampus of selectively-bred sprague dawley rats (Low Reponder strain), 7 days after birth


title: 7 day old bLR strain rat hippocampus, biological replicate 2

description:
P7_LR_HPC_L02
Gene expression data from hippocampus of selectively-bred sprague dawley rats (Low Reponder strain), 7 days after birth


title: 7 day old bLR strain rat hippocampus, biological replicate 3

description:
P7_LR_HPC_L03
Gene expression data from hippocampus of selectively-bred sprague dawley rats (Low Reponder strain), 7 days after birth


title: total microRNAs in LNCaP cells treated with DHT at 16h

description: replicate 1

value: dihydrotestosterone (DHT) at 16h


title: 7 day old bLR strain rat hippocampus, biological replicate 1

description:
P7_LR_HPC_L01
Gene expression data from hippocampus of selectively-bred sprague dawley rats (Low Reponder strain), 7 days after birth


title: total microRNAs in LNCaP cells treated with DHT at 8h

description: replicate 1

value: dihydrotestosterone (DHT) at 8h


title: total microRNAs in LNCaP cells treated with DHT at 4h

description: replicate 1

value: dihydrotestosterone (DHT) at 4h


title: Septum_animal N74_0.22 mL sarin_seize (8 min latency)_drugs_3hr

description: Gene expression data from Septum of animal N74_0.22 mL sarin_seize (8 min latency)_drugs_3hr

tag: animal number

tag: agent

value: Sarin

value: Sprague-Dawley

value: Y

tag: date injected

tag: time injected

tag: presence of seizure

tag: seizure time

tag: seizure latency


title: total microRNAs in LNCaP cells treated with DHT at 2h

description: replicate 1

value: dihydrotestosterone (DHT) at 2h

tag: tissue


title: Septum_animal N72_0.21 mL sarin_seize (7 min latency)_drugs_6hr

description: Gene expression data from Septum of animal N72_0.21 mL sarin_seize (7 min latency)_drugs_6hr

value: Septum

tag: amount administered

tag: agent dose

tag: strain

tag: atropine, 2-pam, diazepam

tag: animal weight (g)


title: Septum_animal N71_0.2 mL sarin_no seize_no drugs_6hr

description: Gene expression data from Septum of animal N71_0.2 mL sarin_no seize_no drugs_6hr

value: N

tag: time point (hr)

tag: date sacrificed

tag: time sacrificed


title: Septum_animal N73_0.2 mL sarin_no seize_no drugs_1hr

description: Gene expression data from Septum of animal N73_0.2 mL sarin_no seize_no drugs_1hr


title: Sample 8, BTV-uninfected red deer Cervus elaphus

city: Ciudad Real

first: Ruth

middle: Cecilia

last: Galindo

state: Ciudad Real

address: Ronda de Toledo s/n

department: Animal Health

institute: Instituto de Investigacion en Recursos Cinegéticos

description:
CE10
Control 4.

hyb_protocol: Standard Affymetrix hybridization protocol.

scan_protocol: Scanner 300 7G and Microarray Analysis Suite 5.0.

data_processing: RMA normalization and statistical analyses were done using the free statistical language R and the libraries developed by the Bioconductor Project (www.bioconductor.org). The selection of differentially expressed genes was performed using a linear model approach following the methodology (Empirical Bayes and Linear Models for Microarrays) described by G. Smyth and implemented in the limma Bioconductor package.

label: Biotin

organism: Cervus elaphus

source_name: Skin biopsy, uninfected

label_protocol: GeneChip® HT IVT Labeling Kit (Affymetrix).

growth_protocol: Skin biopsies were taken at 14 days post-infection in experimentally infected deer and in controls.

extract_protocol: RNA was extracted with TriReagent Sigma (St. Louis MO, USA) according to the manufacturer's instructions.  RNA was purified using the Qiagen purification kit according to the instructions.

treatment_protocol: 8 hinds eleven months old were kept in a P3 installation. 4 of the hinds were inoculated intravenously (iv) with 2.5x10^6 TCID50 of BTV-1 strain Algeria/2006 and 4 were kept as controls. 14 days post-infection, skin biopsies were taken to extract RNA from both experimentally infected and controls.

tag: gender

value: female

tag: age

value: 7 months

value: skin

tag: treatment


title: 21 day old bHR strain rat hippocampus, biological replicate 6

description:
P21_HR_HPC_H06
Gene expression data from hippocampus of selectively-bred sprague dawley rats (High Reponder strain), 21 days after birth

source_name: Selectively-bred High responder rat strain derived from Sprague Dawley stock, 21 days after birth

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

value: Selectively bred High Responder (derived from an original Sprague Dawley)

value: Hippocampus

value: 21 days after birth


title: Sample 7, BTV-uninfected red deer Cervus elaphus

description:
CE9
Control 3.


title: total microRNAs in LNCaP cells treated with DHT at 1h

description: replicate 1

tag: treatment group

value: dihydrotestosterone (DHT) at 1h

tag: hormone status

value: androgen-sensitive

value: prostate cancer

tag: cell line

value: LNCaP


title: Septum_animal N70_0.21 mL sarin_seize (12 min latency)_drugs_0.25hr

description: Gene expression data from Septum of animal N70_0.21 mL sarin_seize (12 min latency)_drugs_0.25hr

tag: animal number

tag: agent

tag: date injected

tag: time injected

tag: presence of seizure

tag: seizure time


title: Sample 6, BTV-uninfected red deer Cervus elaphus

description:
CE8
Control 2.

tag: tissue


title: Sample 4, BTV-infected red deer Cervus elaphus

description:
CE6
Bluetongue virus-infected deer 4.

source_name: Skin biopsy, infected

value: Bluetongue virus infection


title: Sample 3, BTV-infected red deer Cervus elaphus

description:
CE4
Bluetongue virus-infected deer 3.


title: Sample 5, BTV-uninfected red deer Cervus elaphus

description:
CE7
Control 1.


title: 21 day old bHR strain rat hippocampus, biological replicate 5

description:
P21_HR_HPC_H05
Gene expression data from hippocampus of selectively-bred sprague dawley rats (High Reponder strain), 21 days after birth

tag: strain


title: total microRNAs in LNCaP cells treated with DHT at 40min

description: replicate 1

value: dihydrotestosterone (DHT) at 40min


title: total microRNAs in LNCaP cells treated with DHT at 20min

description: replicate 1

value: dihydrotestosterone (DHT) at 20min


title: Septum_animal N69_0.23 mL sarin_no seize_no drugs_24hr

description: Gene expression data from Septum of animal N69_0.23 mL sarin_no seize_no drugs_24hr

value: Sarin

tag: amount administered

tag: agent dose

value: Sprague-Dawley

tag: atropine, 2-pam, diazepam

tag: time point (hr)

tag: animal weight (g)


title: total microRNAs in LNCaP cells treated with DHT at the beginning

description: replicate 1

value: dihydrotestosterone (DHT) at the beginning


title: 21 day old bHR strain rat hippocampus, biological replicate 4

description:
P21_HR_HPC_H04
Gene expression data from hippocampus of selectively-bred sprague dawley rats (High Reponder strain), 21 days after birth

tag: age


title: Septum_animal N68_0.22 mL saline_no seize_drugs_24hr

description: Gene expression data from Septum of animal N68_0.22 mL saline_no seize_drugs_24hr

value: Septum

value: Saline

value: Y

tag: date sacrificed

tag: time sacrificed

value: N


title: 21 day old bHR strain rat hippocampus, biological replicate 1

description:
P21_HR_HPC_H01
Gene expression data from hippocampus of selectively-bred sprague dawley rats (High Reponder strain), 21 days after birth

value: Selectively bred High Responder (derived from an original Sprague Dawley)


title: Sample 2, BTV-infected red deer Cervus elaphus

description:
CE3
Bluetongue virus-infected deer 2.

tag: gender

value: female

value: 7 months

value: skin

tag: treatment


title: Septum_animal N67_0.2 mL sarin_seize (9 min latency)_drugs_1hr

description: Gene expression data from Septum of animal N67_0.2 mL sarin_seize (9 min latency)_drugs_1hr

tag: animal number

tag: agent

tag: seizure latency


title: 14 day old bHR strain rat hippocampus, biological replicate 6

description:
P14_HR_HPC_H06
Gene expression data from hippocampus of selectively-bred sprague dawley rats (High Reponder strain), 14 days after birth

source_name: Selectively-bred High responder rat strain derived from Sprague Dawley stock, 14 days after birth

value: Hippocampus

value: 14 days after birth


title: 21 day old bHR strain rat hippocampus, biological replicate 2

description:
P21_HR_HPC_H02
Gene expression data from hippocampus of selectively-bred sprague dawley rats (High Reponder strain), 21 days after birth

value: 21 days after birth


title: Septum_animal N66_0.23 mL sarin_seize (11 min latency)_drugs_3hr

description: Gene expression data from Septum of animal N66_0.23 mL sarin_seize (11 min latency)_drugs_3hr

tag: date injected

tag: time injected

tag: presence of seizure


title: 21 day old bHR strain rat hippocampus, biological replicate 3

description:
P21_HR_HPC_H03
Gene expression data from hippocampus of selectively-bred sprague dawley rats (High Reponder strain), 21 days after birth

tag: strain

tag: tissue


title: Septum_animal N65_0.21 mL sarin_seize (16 min latency)_drugs_24hr

description: Gene expression data from Septum of animal N65_0.21 mL sarin_seize (16 min latency)_drugs_24hr

tag: amount administered

tag: agent dose

tag: seizure time


title: melanoma patient 2 sample 10

city: Granada

first: Rafael

last: Carretero

address: Avenida del Hospicio

institute: Universidad de Granada

hyb_protocol: 6 ug of labeled, fragmented cRNA per sample was applied to microarrays in Kreatech's Hybridization buffer, and hybridized for 16 h at 42C. After hybridization, slides were washed three four times with wash solutions containg gradually decreased concentrations of SSC (1x-0x)

scan_protocol: Scanned on an Agilent DNA Microarray Scanner. Images were quantified using Agilent Feature Extraction Software (version A.9.5.3).

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used for feature extraction.

source_name: melanoma metastasis 10

label_protocol: 0.5 µg of total RNA was primed with 0.25 ug oligo dT-T7 primer (5’ AAA CGA CGG CCA GTG AAT TGT AAT ACG ACT CAC TAT AGG CGC T(15) 3’) at 70°C for 3 min, then reverse transcribed at 42°C for 90 min in the presence of 200 U SuperScript II RTase (Invitrogen), and 1 mM dNTP. Second strand synthesis was done with the 5’ primer switch method using 0.25 ug Ts/SMARTII primers (5’ AAG CAG TGG TAA CAA CGC AGA GTA CGC GGG 3’) for priming at 65°C for 1 min, and subsequent primer extension at 75°C for 30 min using the Advantage cDNA Polymerase Mix (Clontech) and 0.2mM dNTP. Double stranded cDNA subjected to in vitro transcription at 42°C for 6h using Megascript T7 kit (Ambion). After two rounds of linear amplification, cRNA was chemically labeled using ULS Cy3/Cy5 Fluorescent Labeling Kit (Kreatech), and fragmented by Fragmentation Reagents kit (Ambion).

extract_protocol: Total RNA extracted using Qiagen's RNEasy Mini kit following manufacturer's instructions

value: melanoma

tag: treatment protocol

value: M-VAX

tag: status

value: regressing

tag: patient

source_name: Total RNA from pooled PBMC

value: Blood

tag: preservation

value: cryopreservation

tag: reference

value: Total RNA from pooled PBMC


title: 14 day old bHR strain rat hippocampus, biological replicate 5

description:
P14_HR_HPC_H05
Gene expression data from hippocampus of selectively-bred sprague dawley rats (High Reponder strain), 14 days after birth

tag: age


title: Septum_animal N62_0.21 mL sarin_seize (13.5 min latency)_drugs_6hr

description: Gene expression data from Septum of animal N62_0.21 mL sarin_seize (13.5 min latency)_drugs_6hr

tag: animal number

value: Septum

value: Sarin

value: Sprague-Dawley

tag: atropine, 2-pam, diazepam

tag: time point (hr)

tag: date sacrificed

tag: time sacrificed

tag: animal weight (g)


title: melanoma patient 2 sample 9

source_name: melanoma metastasis 9


title: Sample 1, BTV-infected red deer Cervus elaphus

description:
CE1
Bluetongue virus-infected deer 1.

tag: gender

tag: treatment

value: Bluetongue virus infection