title: cortical neurons_E14.5 electroporated_150623_FACS sorted at E17.5-2


title: WTC1H_replicate2

status: Public on Aug 23 2017

type: RNA

city: Jena

first: Klaus

last: Gase

address: Hans-Knoell-Strasse 8

department: Molecular Ecology

country: Germany

institute: Max-Planck-Institute for Chemical Ecology

description:
WT plant leaves, 1 h, not treated
WTC1HR2

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent platform GPL13527 for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed at room temperature with GE Wash Buffer 1 (Agilent) and at 37°C with GE Wash buffer 2 (Agilent) as outlined in the One-Color Microarray-Based Gene Expression Analysis manual (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Data was acquired with the Agilent Scan Control software (version A.7.0.1 for the B scanner) and extracted using the Agilent Feature Extraction software (version 9.5). Quantile normalization and log2 transformation was performed for all raw microarray data using the R package “Agi4x44PreProcess”. All probes with signal within 95% confidence interval of the signal of negative control probes were discared from down-stream analysis.  All replicated probes were averaged.

molecule: polyA RNA

organism: Nicotiana attenuata

source_name: WT plant leaves, 1 h, not treated, replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Quick Amp labeling kit (Agilent, Santa Clara, CA) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Hilden, Germany).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Seeds from N. attenuata wild type and ir-MYB8 plants were grown in the glasshouse under high-pressure sodium lamps (200-300 µmol s-1 m-2 light) with a day/night cycle of 16 h(26-28°C)/8 h(22-24°C) and 45 to 55% humidity.

extract_protocol: Total RNA was extracted from leaves using the Plant RNeasy kit (Qiagen, Hilden, Germany) and its quality checked by spectrophotometry (NanoDrop, Wilmington, DE). Genomic DNA was removed by DNAse treatment following commercial instructions (Turbo DNase; Ambion, Europe), RNA was cleaned up with RNeasy MinElute columns (Qiagen) and the RNA quality was checked with the RNA 6000 Nano kit (Agilent, Santa Clara, CA) using an Agilent 2100 Bioanalyzer (Agilent).

treatment_protocol: For elicitation treatment, leaves were wounded by rolling a fabric-pattern wheel three times on each side of the midvein and the wounds were supplemented with 20 microliters of M. sexta oral secretion diluted 1/5 (v/v) in water.

tag: tissue

value: leaves

tag: genotype

value: wildtype

tag: treatment

value: not treated

tag: timepoint

value: 1 h


title: cortical neurons_E14.5 electroporated_150623_FACS sorted at E16.5-2

city: Setagaya-ku

first: Chiaki

last: Ohtaka-Maruyama

state: Tokyo

address: 2-1-6 Kamikitazawa

department: Department of brain development and neural regeneration

country: Japan

institute: Tokyo Metropolitan Institute of Medical Science

description: GFP expression plasmids were electroporated in utero at E14.5 and GFP labeled migrating cells were collected at E16.5 by FACS sorting from dissiciated cell mixture of dorsal part of celebral cortex

hyb_protocol: 1.65 µg of Cy3-labeled cRNA was fragmented and hybridized to Agilent Mouse Gene Expression v2 Microarray (G4846A) using Agilent Gene Expression Hybridization Kit. Hybridization was performed for 17 hours at 65ºC at 10 rpm in a rotating hybridization oven.

scan_protocol: Slides were scanned with SureScan Microarray Scanner (Agilent Technologies) using a scan resolution of 5µm and dye channel of Green with PMT set to 100%.

data_processing: Data was obtained using the Agilent Feature Extraction software (v11.5.1.1) with set to default for all parameters.

molecule: total RNA

organism: Mus musculus

source_name: Cortical neurons

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200ng of total RNA using the Low Input Quick Amp Labeling Kit  (Agilent Technologies) according to the manufacturer's protocol.

extract_protocol: Total RNA was purified from the collected GFP-positive cells using Trizol (Invitrogen) according to the manufacturer’s   protocol.  The quality of RNA was assessed with a 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Brains electroporated in utero with GFP plasmids at E14.5  were collected at E15.5, E16.5, and E17.5, respectively.    GFP-positive dorsal cortical areas were dissected out under a dissection microscope with a fluorescent lamp.  The   tissue fragments were treated with 8-10 U/ml papain (Worthington Biochemical) and 10 μg/ml DNase I (TAKARA Bio),   and then triturated by pipetting in 10% FCS/ DMEM.  Dissociated cortical cells were collected by centrifugation (1,000×g   for 5 min), and then re-suspended in HBS at a concentration of 1-2×106 cells/ml.  Dissociated cells were stained with   2 μg/ml propidium iodide (PI) prior to sorting to distinguish dead cells.  The gating parameters were determined using   the side and forward scatters to eliminate debris and aggregated cells, using red fluorescence (633 nm) to eliminate   dead cells, and green fluorescence (488 nm) to separate the positive from negative cells.  Cells prepared from the   brains not electroporated with pCAGGS-EGFP were used as the negative controls.

value: cerebral cortex

tag: age


title: Heart-heterozygote-3wk-rep1

city: Vermillion

first: Kathleen

middle: M

last: Eyster

state: SD

address: 414 E. Clark St.

department: Basic Biomedical Sciences

country: USA

institute: University of South Dakota

description:
The heart was dissected into RNAlater (Ambion/Thermofisher) immediately upon euthanasia of the animal.
T00351795_2012-3-5

hyb_protocol: 10 micrograms of cRNA was mixed with fragmentation buffer and heated to 94C for 20 min.  The fragmented cRNA was mixed with CodeLink hybridization buffer, loaded on the microarray slides, and hybridized for 18 hours at 37C.  The slides were washed in 0.75x TNT (Tris-HCl, NaCl, Tween-20) at 46C for 1h then incubated with streptavidin-Alexa 647 fluorescent dye for 30 min at room temperature.  The Alexa fluor was prepared in TNB blocking buffer (0.1M Tris-HCl, 0.15M NaCL, 0.5% NEN Blocking Reagent-PerkinElmer)  The slides were then washed 4 times for 5 min each in 1x TNT and once in 0.05% Tween 20 for 5 sec each.  The slides were dried by centrifugation and scanned in an Axon GenePix 4000B scanner.

scan_protocol: The slides were scanned in an Axon GenePix 4000B scanner using GenePix Pro 4.1 to align and acquire the microarray image.  CodeLink Expression Analysis 4.1.0.4163 was used to apply the background correction.

data_processing:
Data in the matrix table were prepared by global median normalization applied by CodeLink Expression Analysis 4.1.0.4163.
CodeLink Expression Analysis 4.1.0.4163 was used to compute the normalized signal intensity.

label: streptavidin Alexa Fluor 647

source_name: ventricular cardiac tissue

label_protocol: Labeled cRNA was prepared using the MessageAmp II-Biotin enhanced kit (Ambion).  1.0 microgram of heart total RNA was mixed with bacterial control RNA spikes and primed with T7 oligo(dT) primer for 10 min at 70C.  (The bacterial control spikes included araB, entF, fixB, gnd, hisB, and leuB.)  The first strand of cDNA was synthesized with first strand buffer, dNTP mix, RNase inhibitor, and reverse transcriptase for 2 h at 42C.  The second strand cDNA synthesis reaction was prepared using second strand buffer, dNTP mix, DNA polymerase mix, and RNase H; the reaction was carried out for 2h at 16C.  The double-stranded cDNA was purified on QIAquick columns (Qiagen).  The double-stranded cDNA was mixed with T7 reaction buffer, T7 ATP, T7 GTP, T7 UTP, T7 CTP, biotin-11-UTP, and T7 enzyme mix for the synthesis of cRNA.  The cRNA synthesis reaction was terminated after 14h at 37C by purifying the cRNA.  The concentration of cRNA was determined by spectrophotometry. Streptavidin Alexa fluor 647 was incubated with the slides after hybridization to complete the labeling reaction.  One sample was hybridized with each slide so no dye swaps were necessary.

extract_protocol: 30-50 micrograms of cardiac ventricular tissue was homogenized in TRI reagent, bromochloropropane and sodium acetate were added, and the samples were centrifuged to separate the phases.  The RNA-containing layer was removed and the RNA purified on an RNeasy extraction column (Qiagen).  The sample was treated with an on-column DNase treatment (RNase-free DNase, Qiagen) and the purified RNA was eluted.  The purity and quantity of RNA were evaluated by an Agilent Bioanalyzer using the RNA 6000 Nanoassay LabChip.

treatment_protocol: RNA samples were obtained from FVB/N inbred mice. In this Cops8 floxed allele (Csn8flox/+), exon 4 to 6 of the Cops8 gene are flanked by two loxP sites. The Csn8flox/+ mice were created using standard homologous recombination. The CR-CSN8KO mice were generated with the use of the Cre-loxP system in which transgenic Cre expression is driven by the mouse α-myosin heavy chain (Myh6) promoter. From the cross-breeding of  Csn8flox/flox and Csn8flox/+::Myh6-CreTG mice, Csn8flox/flox::Myh6-CreNTG (Control)  and Csn8flox/+::Myh6-CreTG (Heterozygous Cops8 cardiac knockout or Het-CKO) littermates of homozygous Csn8-CKO (Csn8flox/flox::Myh6-CreTG or Homozygous cardiac knockout or Hom-CKO) mice were used. The knockout of Cops8 gene was confirmed in RT2-PCR experiment where primers for 5’UTR region and exon 5 of the Cops8 gene were used.

tag: strain

value: FVB/N

tag: genotype/variation

value: heterozygous knockout

value: three weeks

tag: transgene expression

value: cardiac restricted

tag: transgene


title: Heart-ko-3wk-rep3

description:
The heart was dissected into RNAlater (Ambion/Thermofisher) immediately upon euthanasia of the animal.
T00351794_2012-3-5

value: homozygous knockout


title: Heart-heterozygote-3wk-rep2

description:
The heart was dissected into RNAlater (Ambion/Thermofisher) immediately upon euthanasia of the animal.
T00351796_2012-3-5


title: Heart-heterozygote-3wk-rep3

description:
The heart was dissected into RNAlater (Ambion/Thermofisher) immediately upon euthanasia of the animal.
T00351797_2012-3-5


title: Pfs25-EPA+GLA-LSQ Pre-bleed [E14_14 prebleed]

city: Stockholm

first: Elizabeth

middle: Anne

last: Thompson

department: Department of Medicine, Solna

country: Sweden

institute: Karolinska Institutet

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Rhesus Macaque Gene Expression Microarrays v2 (part number G2519F-026806) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x44K array slides (Scan Area 61x21.6 mm, Scan resolution 3 µm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Raw images were analyzed using the Agilent Feature Extraction software, and background corrected gProcessed signals were subjected to quantile normalization.

organism: Macaca mulatta

source_name: Pfs25-EPA+GLA-LSQ Pre-bleed

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using the Low Input One-Color Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the PAXgene® Blood RNA Kit, PreAnalytiX, Qiagen following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2200 Tapestation (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: Blood was collected directly into PAXgene® tubes prior to and 24 hours after immunization and stored at -20C until ready for analysis.

value: Whole blood


title: irMYB8OS5H_replicate3

description:
irMYB8 plant leaves, 5 h after Manduca sexta oral secretion treatment
irMYB8OS5HR3

source_name: irMYB8 plant leaves, 5 h after Manduca sexta oral secretion treatment, replicate 3

value: Manduca sexta oral secretion treatment

value: 5 h


title: irMYB8OS1H_replicate1

description:
irMYB8 plant leaves, 1 h after Manduca sexta oral secretion treatment
irMYB8OS1HR1

source_name: irMYB8 plant leaves, 1 h after Manduca sexta oral secretion treatment, replicate 1


title: irMYB8OS5H_replicate1

description:
irMYB8 plant leaves, 5 h after Manduca sexta oral secretion treatment
irMYB8OS5HR1

source_name: irMYB8 plant leaves, 5 h after Manduca sexta oral secretion treatment, replicate 1


title: irMYB8OS1H_replicate2

description:
irMYB8 plant leaves, 1 h after Manduca sexta oral secretion treatment
irMYB8OS1HR2

source_name: irMYB8 plant leaves, 1 h after Manduca sexta oral secretion treatment, replicate 2


title: irMYB8OS5H_replicate2

description:
irMYB8 plant leaves, 5 h after Manduca sexta oral secretion treatment
irMYB8OS5HR2

source_name: irMYB8 plant leaves, 5 h after Manduca sexta oral secretion treatment, replicate 2


title: WTC1H_replicate1

description:
WT plant leaves, 1 h, not treated
WTC1HR1

source_name: WT plant leaves, 1 h, not treated, replicate 1


title: irMYB8OS1H_replicate3

description:
irMYB8 plant leaves, 1 h after Manduca sexta oral secretion treatment
irMYB8OS1HR3

source_name: irMYB8 plant leaves, 1 h after Manduca sexta oral secretion treatment, replicate 3


title: Heart-ko-3wk-rep2

description:
The heart was dissected into RNAlater (Ambion/Thermofisher) immediately upon euthanasia of the animal.
T00351793_2012-3-5


title: Heart-control-3wk-rep2

description:
The heart was dissected into RNAlater (Ambion/Thermofisher) immediately upon euthanasia of the animal.
T00351789_2012-3-5

value: control


title: Heart-control-3wk-rep1

description:
The heart was dissected into RNAlater (Ambion/Thermofisher) immediately upon euthanasia of the animal.
T00351788_2012-3-5


title: Heart-ko-3wk-rep1

description:
The heart was dissected into RNAlater (Ambion/Thermofisher) immediately upon euthanasia of the animal.
T00351792_2012-3-5


title: irMYB8C5H_replicate2

description:
irMYB8 plant leaves, 5 h, not treated
irMYB8C5HR2

source_name: irMYB8 plant leaves, 5 h, not treated, replicate 2


title: irMYB8C5H_replicate3

description:
irMYB8 plant leaves, 5 h, not treated
irMYB8C5HR3

source_name: irMYB8 plant leaves, 5 h, not treated, replicate 3


title: irMYB8C5H_replicate1

description:
irMYB8 plant leaves, 5 h, not treated
irMYB8C5HR1

source_name: irMYB8 plant leaves, 5 h, not treated, replicate 1


title: H3K27ac_siCtrl_ChIPSeq (UV)

status: Public on Aug 22 2017

type: SRA

city: Shanghai

first: Min

last: Xia

address: 320 YueYang Road

country: China

institute: SIBCB

description: ctrl_k27_UV_treat_chr(1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,M,X,Y).wig.gz

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie with the following configurations: -v1, -best, -strata, -k2, and -m1.
peaks were called using MACS by P-value threshold of 10-5.
called peaks were annotated using R package ChIPpeakAnno and the average ChIP-seq intensity between 2 kb upstream of TSS and 2 kb downstream of TSS was calculated.
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using MACS; Scores represent ChIP intensity.

molecule: genomic DNA

source_name: Melanoma cell line

growth_protocol: Cells are culturing in DMEM with 10% FBS and 1% P/S.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
ChIP DNA was prepared for DNA library using ChIP-seq Sample Prep Kit (illumina).

tag: cell type

tag: chip antibody

value: H3K27ac: Abcam, ab4729


title: H3K27ac_siMed23B_ChIPSeq (UV)

description: 23b_k27_UV_treat_chr(1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,M,X,Y).wig.gz


title: H3K27ac_siMed23A_ChIPSeq (UV)

description: 23a_k27_UV_treat_chr(1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,M,X,Y).wig.gz


title: siCtrl_input (UV)

description: ctrl_input_UV_treat_chr(1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,M,X,Y).wig.gz


title: Pol II_siMed23B_ChIPSeq (no UV)

description: 23b_pol2_no_treat_chr(1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,M,X,Y).wig.gz

value: Pol II: Santa Cruz, sc-899


title: Heart-heterozygote-2wk-rep3

description:
The heart was dissected into RNAlater (Ambion/Thermofisher) immediately upon euthanasia of the animal.
T00351786_2012-3-5

value: two weeks


title: Heart-ko-2wk-rep3

description:
The heart was dissected into RNAlater (Ambion/Thermofisher) immediately upon euthanasia of the animal.
T00351783_2012-3-5


title: Heart-heterozygote-2wk-rep1

description:
The heart was dissected into RNAlater (Ambion/Thermofisher) immediately upon euthanasia of the animal.
T00351784_2012-3-5


title: irMYB8C1H_replicate3

description:
irMYB8 plant leaves, 1 h, not treated
irMYB8C1HR3

source_name: irMYB8 plant leaves, 1 h, not treated, replicate 3

value: leaves


title: siMed23B_input (no UV)

description: 23b_input_no_treat_chr(1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,M,X,Y).wig.gz


title: Heart-heterozygote-2wk-rep2

description:
The heart was dissected into RNAlater (Ambion/Thermofisher) immediately upon euthanasia of the animal.
T00351785_2012-3-5


title: Pol II_siCtrl_ChIPSeq (no UV)

description: ctrl_pol2_no_treat_chr(1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,M,X,Y).wig.gz


title: Heart-control-2wk-rep3

description:
The heart was dissected into RNAlater (Ambion/Thermofisher) immediately upon euthanasia of the animal.
T00351780_2012-3-5


title: irMYB8C1H_replicate1

description:
irMYB8 plant leaves, 1 h, not treated
irMYB8C1HR1

source_name: irMYB8 plant leaves, 1 h, not treated, replicate 1


title: Heart-control-2wk-rep2

description:
The heart was dissected into RNAlater (Ambion/Thermofisher) immediately upon euthanasia of the animal.
T00351779_2012-3-5


title: Heart-control-2wk-rep1

description:
The heart was dissected into RNAlater (Ambion/Thermofisher) immediately upon euthanasia of the animal.
T00351778_2012-3-5


title: siCtrl_input (no UV)

description: ctrl_input_no_treat_chr(1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,M,X,Y).wig.gz


title: Heart-ko-2wk-rep1

description:
The heart was dissected into RNAlater (Ambion/Thermofisher) immediately upon euthanasia of the animal.
T00351781_2012-3-5


title: Heart-ko-2wk-rep2

description:
The heart was dissected into RNAlater (Ambion/Thermofisher) immediately upon euthanasia of the animal.
T00351782_2012-3-5


title: Pol II_siCtrl_ChIPSeq (UV)

description: ctrl_pol2_UV_treat_chr(1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,M,X,Y).wig.gz


title: Heart-control-3wk-rep3

description:
The heart was dissected into RNAlater (Ambion/Thermofisher) immediately upon euthanasia of the animal.
T00351790_2012-3-5


title: siMed23A_input (UV)

description: 23a_input_UV_treat_chr(1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,M,X,Y).wig.gz


title: H3K27ac_siMed23B_ChIPSeq (no UV)

description: 23b_k27_no_treat_chr(1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,M,X,Y).wig.gz


title: H3K27ac_siCtrl_ChIPSeq (no UV)

description: ctrl_k27_no_treat_chr(1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,M,X,Y).wig.gz


title: irMYB8C1H_replicate2

description:
irMYB8 plant leaves, 1 h, not treated
irMYB8C1HR2

source_name: irMYB8 plant leaves, 1 h, not treated, replicate 2


title: Pol II_siMed23B_ChIPSeq (UV)

description: 23b_pol2_UV_treat_chr(1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,M,X,Y).wig.gz


title: siMed23A_input (no UV)

description: 23a_input_no_treat_chr(1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,M,X,Y).wig.gz


title: Uninfected Salmonella speG mutant 2

city: Taipei

first: Ke-Chuan

last: Wang

address: 250 Wu-Hsing Street

country: Taiwan

institute: Taipei medical university

description: Salmonella speG mutnat

hyb_protocol: All labeled nucleic acids were hybridized to Agilent Custom Salmonella GE 8x15k Microarray (Design ID:061231) that had been tiled with 50599 probes of human genes (Agilent) at 65oC for 17 h. After washing and drying, the array chips were scanned using an Agilent microarray scanner at 535 nm for Cy3-CTP.

scan_protocol: The scanned images were quantified and analyzed by Feature Extraction 10.5.1.1 software (Agilent). The background values were corrected by spatial detrend surface value, and normalized by quantile

data_processing: The expression levels of the genes on each array group were analyzed using DAVID database (http://david.abcc.ncifcr.gov). The heap map with those more than 2 fold-change up- or down-regulated genes of each group was constructed based on their normalized values using GeneSpring multi-omic analysis software (Agilent).

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

source_name: Salmonella speG mutnat

label_protocol: The total RNA samples were reverse transcribed to cDNAs that were then labeled with Cy3-CTP (CyDye, Agilent) with an Agilent Low Input Quick-Amp Labeling kit (Agilent) according to the manufacturer’s instruction. Thus, the Cy3-labled cRNAs were fragmented into 50-100 nucleotides by incubation with fragmentation buffer at 60oC for 30 min.

growth_protocol: The S. Typhimurium wild-type strain SL1344, its isogenic speG-deleted mutant ΔspeG, and the speG-complemented strain of ΔspeG (ΔspeG′) were cultured in LB broth for 18-h.

extract_protocol: The total RNAs of both cells from the above three conditions were isolated using TRIzol reagent (Invitrogen) according to the manufacturer’s instruction, and preformed RNA clean-up by using RNeasy Mini Kit (Qiagen, Valencia, CA). The RNA concentration was quantified using a NanoDrop ND-1000 spectrophotometer (Thermo Scientific, Waltham, MA) and the integrity of RNA samples were validated by the ratio of absorbance at 260 nm and 280 nm as well as RIN (RNA integrity number) using a Bioanalyzer 2100 (Agilent Technology, Palo Alto, CA) with an RNA 6000 Nano LabChip kit (Agilent).

treatment_protocol: The prepared confluent  Caco-2 cells in 12-well plates were infected with overnight cultures of the three S. Typhimurium strains (wild-type strain SL1344, its isogenic speG-deleted mutant ΔspeG, and the speG-complemented strain of ΔspeG) (MOI = 5) for 2 h and treated with gentamicin (100 μg/mL) for 1 h. After washing with PBS three times, the cells were incubated for an additional 15 h. Finally, the cells were lysed with 1% Triton X-100.

value: speG mutnat

tag: sample type

value: Salmonella speG mutnat


title: Salmonella SL1344 infected in vitro cells 1

description: SL1344-infected Caco-2 cells

source_name: SL1344-infected Caco-2 cells

value: wild type

value: SL1344-infected Caco-2 cells


title: Salmonella speG mutant infected in vitro cells 2

description: speG mutant-infected Caco-2 cells

source_name: speG mutant-infected Caco-2 cells

value: speG mutant-infected Caco-2 cells


title: Gene expression data from BALB/3T3 cells infected by Ectromelia virus at 12 hours post infection

city: Lanzhou

first: Wenyu

last: Cheng

state: Gansu

department: State Key Laboratory of Veterinary Etiological Biology

institute: Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45℃ 60 rpm on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with CapitalBio® Molecule Annotation System V3.0 (MAS3.0) using CapitalBio (Beijing, China) default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

source_name: BALB/3T3 cells of ECTV infected at 12 hours post infection

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

growth_protocol: BALB/3T3 cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM, Gibco) supplemented with 10% fetal bovine serum (FBS, Gibco), 100 IU of penicillin/mL, and 100 µg streptomycin/mL and incubated at 37 °C in the presence of 5% CO2.

extract_protocol: Trizol (Invitrogen, Carlsbad, CA,USA) extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: 5×10^5 BALB/3T3 cells were seeded in each well of a 6-well plate and infected in triplicate with ECTV at a multiplicity of infection (MOI) of 1. Control cells were mock infected with virus-free DMEM. All infected and control cells were incubated in complete DMEM at 37 °C in 5% CO2 and harvested for total RNA extraction at 6, 12, 24, 48, and 96 h post infection (hpi). For cell harvesting, cells were washed three times with cold PBS and lysed with 1 mL of TRIzol reagent (Invitrogen).

tag: cell line

value: MEF

tag: infection

value: ECTV

tag: time

value: 12 hours post infection


title: TIG113 blackcurrant

city: Aomori

first: Naoki

last: Nanashima

state: Aomori

address: 58-1 Mase, Hamadate

department: Department of Nutrition

institute: Aomori University of Health and Welfare

description: Gene expression treatment with BCE

hyb_protocol: Following fragmentation, 1.65 ug of cRNA were hybridized to the Agilent expression microarray according to the protocols provided by the manufacturer.

scan_protocol: Arrays were scanned using the Agilent Technologies G4900DA SG12494263.

data_processing: Array data export processing and analysis was performed using Agilent Feature Extraction v11.0.1.1.

organism: Homo sapiens

source_name: TIG113 blackcurrant

label_protocol: Labeled cRNA were prepared from 1~5 ug total RNA using the Agilent’s Quick Amp Labeling Kit

growth_protocol: TIG113 cells were purchased from Japanese Collection of Research Bioresources Cell Bank. The TIG113 were routinely cultured in DMEM medium supplemented with 10% fetal bovine serum at 37ºC in 5% CO2.

extract_protocol: Total RNA was extracted by using the RNeasy mini kit (Qiagen, Tokyo, Japan).

treatment_protocol: Then medium replace with phenol-red-serum-free DMEM medium with or without BCE (1.0μg/ml). After the cells were incubated for 24 h at 37 °C 5% CO2.

value: Human normal fibroblast from skin (TIG113)


title: Gene expression data fromBALB/3T3 cells infected by Ectromelia virus at 24 hours post infection

source_name: BALB/3T3 cells of ECTV infected at 24 hours post infection

value: 24 hours post infection


title: MDA-MB-231 Cells Control  Triplicate3

city: Tallahassee

middle: A

last: Mazzio

state: Florida

address: 1515 MLK Blvd

department: College of Pharmacy & Pharmaceutical Science

institute: Florida Agricultural & Mechanical University

description: Gene expression data from MDA-MB-231 cells grown under variable experimental treatment

hyb_protocol: Hybrization was conducted according to manufacturer's instructions as per the GeneChipTM WT PLUS Reagent Manual for Whole Transcript (WT) Expression Arrays. (Affymetrix, ThermoFisher Scientific).

scan_protocol: Arrays were scanned with GeneAtlas Imaging station scanner  (Affymetrix, ThermoFisher Scientific)

data_processing: The data was processed using Affymetrix expression console and evaluated by Affymetrix transcription console software (Affymetrix, ThermoFisher Scientific)

label: Biotin

source_name: MDA-MB-231 ATCC® HTB-26™ cells

label_protocol: cDNA was labeled using according to manufacturer's instructions as per the GeneChipTM WT PLUS Reagent Manual for Whole Transcript (WT) Expression Arrays. (Affymetrix, ThermoFisher Scientific).

growth_protocol: MDA-MB-231 cells were cultured in Dulbecco’s Modified Eagle’s Medium - high glucose with 4500 mg/L glucose, L-glutamine, sodium pyruvate, and sodium bicarbonate, supplemented with 10% FBS and 100 U/ml penicillin G sodium /100 μg/ml streptomycin sulfate. Cells were grown at 37°C with 95% air and 5% CO2 and sub-cultured every three to five days.

extract_protocol: After treatment, cells were washed three times in HBSS, rapidly frozen and stored at -80 C. Total RNA was isolated/ purified using the TRIzol/chloroform method, quality was assessed and concentration was equalized to 82ng/ul in nuclease free water

treatment_protocol: 3-OAβBA was dissolved in DMSO [20mg/mL], where  Boswellia Serrata was prepared in absolute ethanol [50 mg/mL] after being diced, macerated and powdered prior to being stored at –20 °C.  All dilutions were prepared in sterile HBSS + 5 mM HEPES, adjusted to a pH of 7.4, ensuring solvent concentration of DMSO or absolute ethanol at less than 0.5%. LC50s were determined by regression analysis at 24 hours: Boswellia Serrata 128 ug/ml and 3-O-Acetyl-β-boswellic acid 46 ug/ml.  For whole transcriptome microarray studies, the LC50 of Boswellia Serrata and 3-OAβBA were applied to fully viable cells at Time 0 (zero minutes), and morphological changes were monitored every hour, to ensure no cell death was evident. At 6-8 hours, the cells retained morphological shape, flask attachment and had no obvious signs of cell death.  At this point, cells were rapidly washed in HBSS 3x, spun and frozen at -80C.

value: mammary gland/breast; derived from metastatic site:pleural effusion


title: Gene expression data fromBALB/3T3 cells infected by Ectromelia virus at 96 hours post infection

source_name: BALB/3T3 cells of ECTV infected at 96 hours post infection

value: 96 hours post infection


title: TIG113 control

description: Gene expression control

source_name: TIG113 control


title: Salmonella speG mutant infected in vitro cells 1

description: speG mutant-infected Caco-2 cells


title: MDA-MB-231 Cells Boswellia Serrata Triplicate3

value: Boswellia Serrata Extract 128 ug/ml


title: Gene expression data from BALB/3T3 cells infected by Ectromelia virus at 48 hours post infection

source_name: BALB/3T3 cells of ECTV infected at 48 hours post infection

value: 48 hours post infection


title: Salmonella wild-type (WT) SL1344 2

description: Salmonella WT SL1344

source_name: Salmonella WT SL1344

value: Salmonella WT SL1344


title: MDA-MB-231 Cells 3-O-Acetyl-β-boswellic acid Triplicate3

value: 3-O-Acetyl-β-boswellic acid 46ug/ml


title: Salmonella SL1344 infected in vitro cells 2

description: SL1344-infected Caco-2 cells


title: Uninfected Salmonella speG mutant 1

description: Salmonella speG mutnat


title: MDA-MB-231 Cells 3-O-Acetyl-β-boswellic acid Triplicate1


title: Salmonella wild-type (WT) SL1344 1

description: Salmonella WT SL1344


title: MDA-MB-231 Cells Boswellia Serrata Triplicate2


title: Gene expression data from BALB/3T3 cells infected by Ectromelia virus at 6 hours post infection

source_name: BALB/3T3 cells of ECTV infected at 6 hour post infection

value: 6 hour post infection


title: MDA-MB-231 Cells 3-O-Acetyl-β-boswellic acid Triplicate2


title: MDA-MB-231 Cells Boswellia Serrata Triplicate1


title: MDA-MB-231 Cells Control  Triplicate2

value: control


title: Gene expression data from BALB/3T3 cell non-infected at 0 hour

source_name: BALB/3T3 cells,non-infected


title: PCC6803_Δslr0242_slr1658c_24h_iron_repletion_1

city: Freiburg

first: Jens

last: Georg

address: Schänzlestr. 1

institute: University of Freiburg

hyb_protocol: Fragmentation and hybridization was performed with 600 ng of labeled RNA according to the Agilent protocol for 8×60k single color microarrays.

scan_protocol: Arrays were scanned on the Agilent Technologies Scanner G2505C US90900275, using Agilent Feature Extraction Software 10.7.3.1 and the protocols GE1_107_Sep09  for Cy3 labelled arrays

data_processing: Raw data were processed with the R package Limma. Median signal intensities were normexp background substracted (offset=50) and quantile normalized.

organism: Synechocystis sp. PCC 6803

label_protocol: DNAse treated RNA was labeled directly, without cDNA synthesis in 2 µg aliquots with the Kreatech “ULS labeling kit for Agilent gene expression arrays” with Cy3 according to the manufacturers protocol.

growth_protocol: Stock cultures of the glucose tolerant strain of Synechocystis sp. PCC 6803 and mutants were grown in YBG11 (Shcolnick et al., 2007) medium containing 10 mM iron (10Fe - YBG11 media). Stock cultures of Dslr0242_slr1658m, Δslr0242-2, Δslr0243 and sll0221 strains were supplemented with 50 μg/ml kanamycin. Dslr0242_slr1658c strains were supplemented with 50 μg/ml kanamycin and 25 μg/ml ampicillin.

extract_protocol: Cultures of Dslr0242_slr1658m and Dslr0242_slr1658c used for transcript analysis were collected at several time points before and after the 0Fe→10Fe transition, centrifuged at 1700 g for 10 min at 30 °C and frozen in liquid nitrogen. Samples were then resuspended in PGTX and incubated for 15 min at 65 °C in a water bath (Pinto et al., 2009). After addition of 700 µl of chloroform/isoamylalcohol (24:1) and thorough agitation samples were incubated at room temperature for 10 min. Samples were centrifuged with a swing out rotor at 5,000 rpm, 23 °C for 5 min. The upper aqueous phase was transferred into a new vial and the same volume of chloroform/isoamylalcohol (24:1) was added and mixed. Samples were centrifuged as described above and the aqueous phase transferred again and mixed with an equal volume of isopropanol. After gently inverting the tube, RNA was allowed to precipitate overnight at -20°C. RNA was pelleted through centrifugation (13,000 rpm, 4 °C, 30 min). The pellet was washed with 200 µl of 70% ethanol (13,000 rpm, 4 °C, 10 min), allowed to air dry for approximately 10 min and resuspended in 20 µl H2O.

treatment_protocol: To achieve iron depletion (0Fe conditions) cells were spun down, re-suspended in a MES-EDTA solution (20 mM MES, 10 mM Ethylenediaminetetraacetic acid (EDTA), pH 5) and placed on a shaker for 20 minutes. The procedure was repeated twice. Subsequently, cells were re-suspended in YBG11 medium with or without added iron (10Fe or 0Fe, respectively). Cultures were grown in 250 ml Erlenmeyer flasks at 30 °C with constant shaking. Light intensity was set to 60 μmol photons m−2 s−1.

value: iron repletion


title: PCC6803_Δslr0242_slr1658c_6h_iron_repletion_2


title: MDA-MB-231 Cells Control  Triplicate1


title: PCC6803_Δslr0242_slr1658c_24_iron_repletion_2


title: PCC6803_Δslr0242_slr1658c_3h_iron_repletion_1


title: PCC6803_Δslr0242_slr1658c_3h_iron_repletion_2


title: PCC6803_Δslr0242_slr1658c_-1h_iron_repletion_2


title: PCC6803_Δslr0242_slr1658m_24h_iron_repletion_1


title: PCC6803_Δslr0242_slr1658m_24_iron_repletion_2


status: Public on Aug 21 2017

city: Stadt Seeland

first: Renate

middle: Hanna

last: Schmidt

state: Sachsen-Anhalt

address: Corrensstrasse 3

department: Breeding Research

institute: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)

description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line R206, 10-11 days after flower opening
A_R206

hyb_protocol: Hybridisation was performed by ATLAS Biolabs GmbH, Berlin Germany (Affymetrix authorised service provider)

scan_protocol: Scanning was performed by ATLAS Biolabs GmbH, Berlin Germany (Affymetrix authorised service provider)

data_processing: The raw hybridisation intensity data files (‘CEL’ files) were directly imported into the RMAExpress 1.0.5 program (Irizarry et al. 2003) in order to carry out background correction, quantile normalisation and the transformation to log2 values with the normalisation approach robust multi-array average.

organism: Arabidopsis thaliana

source_name: Arabidopsis thaliana recombinant inbred line R206 developing seeds, 10-11 days after flower opening

label_protocol: Labeling was performed by ATLAS Biolabs GmbH, Berlin Germany (Affymetrix authorised service provider)

growth_protocol: A. thaliana seeds of 116 recombinant inbred lines were sown in pots with substrate 1 (Klasmann‐Deilmann GmbH, Geeste, Germany) and grown after stratification for 3 days at 4°C in long‐day conditions (16 h light at 20°C and 70% relative humidity/8 h dark at 16°C and 60% relative humidity). Light intensity during the light phase amounted to approximately 250 µE m−2 s−1. At least six plants per accession were grown.

extract_protocol: RNA was isolated from 200 mg samples of seeds. After grinding for 45 s at 27 Hz with Mixer Mill MM400 (Retsch GmbH, Haan, Germany) the samples were mixed with 0.7 ml extraction buffer (1 M Tris-HCl (pH 9.0), 1% (v/v) SDS, 10 mM EDTA (pH 8.0), 0.5% (v/v) β-mercaptoethanol in DEPC-H2O (0.1% (v/v)) and subsequently with 0.7 ml of phenol/chloroform/isoamyl alcohol (25:24:1). After centrifugation for 10 min, the aqueous phases were extracted once more with phenol/chloroform/isoamyl alcohol and then with chloroform. After adding 0.1 volume of 3 M sodium acetate (pH 5.4) and 2.5 volumes of 96% ethanol the samples were kept for 45 min at -80°C and then centrifuged for 5 min. The resulting RNA pellets were dissolved in 0.4-0.5 ml of DEPC-H2O (0.1% (v/v) and after centrifugation the supernatants were mixed with 1 volume of 4 M LiCl. After an overnight incubation on ice, RNA pellets were collected by centrifugation, washed in 1 ml each of 2 M LiCl, 96% and 70% ethanol, dried and dissolved in ribonuclase-free water. All centrifugation steps were carried out at 14,000 rpm and 4°C. Purification of RNA samples was achieved with RNeasy columns (Qiagen) and the peqGOLD OptiPure reagent (Peqlab Biotechnologie GmbH, Erlangen, Germany) according to manufacturer’s instructions.

treatment_protocol: Siliques of plants were harvested ten or eleven days after flower opening and immediately frozen in liquid nitrogen. Eight siliques each from six different plants were pooled for each of the recombinant inbred lines. The siliques were dissected and only the seeds were used for RNA extraction. For each of the recombinant inbred lines one sample was prepared.

value: developing seeds

value: Recombinant inbred line R206

tag: Stage

value: 10-11 days after flower opening


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line R205, 10-11 days after flower opening
A_R205

source_name: Arabidopsis thaliana recombinant inbred line R205 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line R205


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line R211, 10-11 days after flower opening
A_R211

source_name: Arabidopsis thaliana recombinant inbred line R211 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line R211


title: PCC6803_Δslr0242_slr1658m_3h_iron_repletion_2


title: PCC6803_Δslr0242_slr1658c_-1h_iron_repletion_1


title: PCC6803_Δslr0242_slr1658m_-1h_iron_repletion_1


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line R204, 10-11 days after flower opening
A_R204

source_name: Arabidopsis thaliana recombinant inbred line R204 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line R204


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line R177, 10-11 days after flower opening
A_R177

source_name: Arabidopsis thaliana recombinant inbred line R177 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line R177


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line R199, 10-11 days after flower opening
A_R199

source_name: Arabidopsis thaliana recombinant inbred line R199 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line R199


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line R215, 10-11 days after flower opening
A_R215

source_name: Arabidopsis thaliana recombinant inbred line R215 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line R215


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line R183, 10-11 days after flower opening
A_R183

source_name: Arabidopsis thaliana recombinant inbred line R183 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line R183


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line R197, 10-11 days after flower opening
A_R197

source_name: Arabidopsis thaliana recombinant inbred line R197 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line R197


title: PCC6803_Δslr0242_slr1658m_6h_iron_repletion_2


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line R174, 10-11 days after flower opening
A_R174

source_name: Arabidopsis thaliana recombinant inbred line R174 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line R174


title: PCC6803_Δslr0242_slr1658m_3h_iron_repletion_1


title: PCC6803_Δslr0242_slr1658c_6h_iron_repletion_1


title: PCC6803_Δslr0242_slr1658m_6h_iron_repletion_1


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line R162, 10-11 days after flower opening
A_R162

source_name: Arabidopsis thaliana recombinant inbred line R162 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line R162


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line R202, 10-11 days after flower opening
A_R202

source_name: Arabidopsis thaliana recombinant inbred line R202 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line R202


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line R165, 10-11 days after flower opening
A_R165

source_name: Arabidopsis thaliana recombinant inbred line R165 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line R165


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line R222, 10-11 days after flower opening
A_R222

source_name: Arabidopsis thaliana recombinant inbred line R222 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line R222


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line R194, 10-11 days after flower opening
A_R194

source_name: Arabidopsis thaliana recombinant inbred line R194 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line R194


title: PCC6803_Δslr0242_slr1658m_-1h_iron_repletion_2

value: control


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line R218, 10-11 days after flower opening
A_R218

source_name: Arabidopsis thaliana recombinant inbred line R218 developing seeds, 10-11 days after flower opening

value: developing seeds

value: Recombinant inbred line R218


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line R186, 10-11 days after flower opening
A_R186

source_name: Arabidopsis thaliana recombinant inbred line R186 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line R186

value: 10-11 days after flower opening


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line R161, 10-11 days after flower opening
A_R161

source_name: Arabidopsis thaliana recombinant inbred line R161 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line R161


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line R155, 10-11 days after flower opening
A_R155

source_name: Arabidopsis thaliana recombinant inbred line R155 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line R155


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line R114, 10-11 days after flower opening
A_R114

source_name: Arabidopsis thaliana recombinant inbred line R114 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line R114


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line R116, 10-11 days after flower opening
A_R116

source_name: Arabidopsis thaliana recombinant inbred line R116 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line R116


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line R152, 10-11 days after flower opening
A_R152

source_name: Arabidopsis thaliana recombinant inbred line R152 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line R152


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line R123, 10-11 days after flower opening
A_R123

source_name: Arabidopsis thaliana recombinant inbred line R123 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line R123


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line R103, 10-11 days after flower opening
A_R103

source_name: Arabidopsis thaliana recombinant inbred line R103 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line R103


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line R125, 10-11 days after flower opening
A_R125

source_name: Arabidopsis thaliana recombinant inbred line R125 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line R125


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line R064, 10-11 days after flower opening
A_R064

source_name: Arabidopsis thaliana recombinant inbred line R064 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line R064


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line R099, 10-11 days after flower opening
A_R099

source_name: Arabidopsis thaliana recombinant inbred line R099 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line R099


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line R067, 10-11 days after flower opening
A_R067

source_name: Arabidopsis thaliana recombinant inbred line R067 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line R067


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line R069, 10-11 days after flower opening
A_R069

source_name: Arabidopsis thaliana recombinant inbred line R069 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line R069


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line R113, 10-11 days after flower opening
A_R113

source_name: Arabidopsis thaliana recombinant inbred line R113 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line R113


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line R105, 10-11 days after flower opening
A_R105

source_name: Arabidopsis thaliana recombinant inbred line R105 developing seeds, 10-11 days after flower opening

value: developing seeds

value: Recombinant inbred line R105


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line R063, 10-11 days after flower opening
A_R063

source_name: Arabidopsis thaliana recombinant inbred line R063 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line R063


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line R111, 10-11 days after flower opening
A_R111

source_name: Arabidopsis thaliana recombinant inbred line R111 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line R111

value: 10-11 days after flower opening


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line R086, 10-11 days after flower opening
A_R086

source_name: Arabidopsis thaliana recombinant inbred line R086 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line R086


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line R098, 10-11 days after flower opening
A_R098

source_name: Arabidopsis thaliana recombinant inbred line R098 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line R098


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line R079, 10-11 days after flower opening
A_R079

source_name: Arabidopsis thaliana recombinant inbred line R079 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line R079


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line R148, 10-11 days after flower opening
A_R148

source_name: Arabidopsis thaliana recombinant inbred line R148 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line R148


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line R060, 10-11 days after flower opening
A_R060

source_name: Arabidopsis thaliana recombinant inbred line R060 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line R060


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line R061, 10-11 days after flower opening
A_R061

source_name: Arabidopsis thaliana recombinant inbred line R061 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line R061


title: PD12-1: iPSC-derived dopamine neuron progenitor, day 26

city: Kyoto

first: Tetsuhiro

last: Kikuchi

state: Kyoto

address: 53 Kawahara-cho Shogoin Sakyo-ku

institute: Kyoto University

hyb_protocol: Following fragmentation, 5.5 ug of cDNA were hybridized for 17 hr at 45C on GeneChip Human Gene-1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with GeneSpring version 14.5 using default analysis settings and global scaling as normalization method (RMA16).

source_name: iPSC-derived dopamine neuron progenitor

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 200 ng total RNA (Ambion WT Expression Kit, 2011, Affymetrix).

growth_protocol: The iPSCs were cultured on chemically definced matrix before cell sorting, and then the cells were cultured on aggregative sphere.

extract_protocol: Total RNA was extracted by Rneasy mini Kit by Qiagen, accoring to manufucture's protocol.

treatment_protocol: Cultured cells were harvested after an enzymatic dissociation.

tag: tissue type

value: cultured cell

value: iPSC-derived dopamine neuron progenitor


title: Adult Substantia_Nigra: Adult substantia nigra

source_name: human adult substantia nigra

value: brain (substantia nigra)

tag: developmental stage

value: adult


title: N117-11: iPSC-derived dopamine neuron progenitor, day 26


title: fVM_pc7.5w: fetal ventral mesencephalon

source_name: human fetal ventral mesenchephalon (7.5w)

value: brain (ventral mesencephalon)

value: fetal (7.5wks)


title: fDM_pc7.5w: fetal dorsal mesencephalon

value: brain (dorsal mesencephalon)


title: 836B3_D0: Undifferentiated iPSC

source_name: undifferentiated iPSC

value: undifferentiated iPSC


title: 836B3: iPSC-derived dopamine neuron progenitor, day 26


title: Adult_Whole_Brain: Adult whole brain

source_name: human adult whole brain

value: brain (whole)


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line R075, 10-11 days after flower opening
A_R075

source_name: Arabidopsis thaliana recombinant inbred line R075 developing seeds, 10-11 days after flower opening

tag: tissue

value: developing seeds

tag: genotype

value: Recombinant inbred line R075


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line R059, 10-11 days after flower opening
A_R059

source_name: Arabidopsis thaliana recombinant inbred line R059 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line R059

value: 10-11 days after flower opening


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line R046, 10-11 days after flower opening
A_R046

source_name: Arabidopsis thaliana recombinant inbred line R046 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line R046


title: 1263A18: iPSC-derived dopamine neuron progenitor, day 26


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line R043, 10-11 days after flower opening
A_R043

source_name: Arabidopsis thaliana recombinant inbred line R043 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line R043


title: 783E2: iPSC-derived dopamine neuron progenitor, day 26


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line R055, 10-11 days after flower opening
A_R055

source_name: Arabidopsis thaliana recombinant inbred line R055 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line R055


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line R002, 10-11 days after flower opening
A_R002

source_name: Arabidopsis thaliana recombinant inbred line R002 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line R002


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line R041, 10-11 days after flower opening
A_R041

source_name: Arabidopsis thaliana recombinant inbred line R041 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line R041


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line R035, 10-11 days after flower opening
A_R035

source_name: Arabidopsis thaliana recombinant inbred line R035 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line R035


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line R009, 10-11 days after flower opening
A_R009

source_name: Arabidopsis thaliana recombinant inbred line R009 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line R009


title: 1275A3: iPSC-derived dopamine neuron progenitor, day 26

value: cultured cell

value: iPSC-derived dopamine neuron progenitor


title: 1231A3_D0: Undifferentiated iPSC


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line R024, 10-11 days after flower opening
A_R024

source_name: Arabidopsis thaliana recombinant inbred line R024 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line R024


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line R005, 10-11 days after flower opening
A_R005

source_name: Arabidopsis thaliana recombinant inbred line R005 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line R005


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line R042, 10-11 days after flower opening
A_R042

source_name: Arabidopsis thaliana recombinant inbred line R042 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line R042


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line R013, 10-11 days after flower opening
A_R013

source_name: Arabidopsis thaliana recombinant inbred line R013 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line R013


title: 1231A3: iPSC-derived dopamine neuron progenitor, day 26

source_name: iPSC-derived dopamine neuron progenitor


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line R006, 10-11 days after flower opening
A_R006

source_name: Arabidopsis thaliana recombinant inbred line R006 developing seeds, 10-11 days after flower opening

value: developing seeds

value: Recombinant inbred line R006


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line R034, 10-11 days after flower opening
A_R034

source_name: Arabidopsis thaliana recombinant inbred line R034 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line R034


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line R038, 10-11 days after flower opening
A_R038

source_name: Arabidopsis thaliana recombinant inbred line R038 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line R038

value: 10-11 days after flower opening


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line R008, 10-11 days after flower opening
A_R008

source_name: Arabidopsis thaliana recombinant inbred line R008 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line R008


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line Q217, 10-11 days after flower opening
A_Q217

source_name: Arabidopsis thaliana recombinant inbred line Q217 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line Q217


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line Q213, 10-11 days after flower opening
A_Q213

source_name: Arabidopsis thaliana recombinant inbred line Q213 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line Q213


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line Q220, 10-11 days after flower opening
A_Q220

source_name: Arabidopsis thaliana recombinant inbred line Q220 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line Q220


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line R025, 10-11 days after flower opening
A_R025

source_name: Arabidopsis thaliana recombinant inbred line R025 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line R025


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line Q218, 10-11 days after flower opening
A_Q218

source_name: Arabidopsis thaliana recombinant inbred line Q218 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line Q218


title: 1147F1: iPSC-derived dopamine neuron progenitor, day 26

value: cultured cell


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line Q221, 10-11 days after flower opening
A_Q221

source_name: Arabidopsis thaliana recombinant inbred line Q221 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line Q221


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line Q226, 10-11 days after flower opening
A_Q226

source_name: Arabidopsis thaliana recombinant inbred line Q226 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line Q226


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line Q219, 10-11 days after flower opening
A_Q219

source_name: Arabidopsis thaliana recombinant inbred line Q219 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line Q219


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line Q202, 10-11 days after flower opening
A_Q202

source_name: Arabidopsis thaliana recombinant inbred line Q202 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line Q202


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line Q173, 10-11 days after flower opening
A_Q173

source_name: Arabidopsis thaliana recombinant inbred line Q173 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line Q173


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line Q203, 10-11 days after flower opening
A_Q203

source_name: Arabidopsis thaliana recombinant inbred line Q203 developing seeds, 10-11 days after flower opening

value: developing seeds

value: Recombinant inbred line Q203


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line Q189, 10-11 days after flower opening
A_Q189

source_name: Arabidopsis thaliana recombinant inbred line Q189 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line Q189


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line Q153, 10-11 days after flower opening
A_Q153

source_name: Arabidopsis thaliana recombinant inbred line Q153 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line Q153


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line Q191, 10-11 days after flower opening
A_Q191

source_name: Arabidopsis thaliana recombinant inbred line Q191 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line Q191

value: 10-11 days after flower opening


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line Q168, 10-11 days after flower opening
A_Q168

source_name: Arabidopsis thaliana recombinant inbred line Q168 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line Q168


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line Q148, 10-11 days after flower opening
A_Q148

source_name: Arabidopsis thaliana recombinant inbred line Q148 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line Q148


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line Q129, 10-11 days after flower opening
A_Q129

source_name: Arabidopsis thaliana recombinant inbred line Q129 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line Q129


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line Q170, 10-11 days after flower opening
A_Q170

source_name: Arabidopsis thaliana recombinant inbred line Q170 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line Q170


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line Q108, 10-11 days after flower opening
A_Q108

source_name: Arabidopsis thaliana recombinant inbred line Q108 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line Q108


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line Q139, 10-11 days after flower opening
A_Q139

source_name: Arabidopsis thaliana recombinant inbred line Q139 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line Q139


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line Q178, 10-11 days after flower opening
A_Q178

source_name: Arabidopsis thaliana recombinant inbred line Q178 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line Q178


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line Q132, 10-11 days after flower opening
A_Q132

source_name: Arabidopsis thaliana recombinant inbred line Q132 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line Q132


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line Q163, 10-11 days after flower opening
A_Q163

source_name: Arabidopsis thaliana recombinant inbred line Q163 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line Q163


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line Q140, 10-11 days after flower opening
A_Q140

source_name: Arabidopsis thaliana recombinant inbred line Q140 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line Q140


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line Q134, 10-11 days after flower opening
A_Q134

source_name: Arabidopsis thaliana recombinant inbred line Q134 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line Q134


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line Q088, 10-11 days after flower opening
A_Q088

source_name: Arabidopsis thaliana recombinant inbred line Q088 developing seeds, 10-11 days after flower opening

value: developing seeds

value: Recombinant inbred line Q088


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line Q120, 10-11 days after flower opening
A_Q120

source_name: Arabidopsis thaliana recombinant inbred line Q120 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line Q120


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line Q111, 10-11 days after flower opening
A_Q111

source_name: Arabidopsis thaliana recombinant inbred line Q111 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line Q111


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line Q080, 10-11 days after flower opening
A_Q080

source_name: Arabidopsis thaliana recombinant inbred line Q080 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line Q080


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line Q106, 10-11 days after flower opening
A_Q106

source_name: Arabidopsis thaliana recombinant inbred line Q106 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line Q106

value: 10-11 days after flower opening


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line Q192, 10-11 days after flower opening
A_Q192

source_name: Arabidopsis thaliana recombinant inbred line Q192 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line Q192


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line Q118, 10-11 days after flower opening
A_Q118

source_name: Arabidopsis thaliana recombinant inbred line Q118 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line Q118


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line Q073, 10-11 days after flower opening
A_Q073

source_name: Arabidopsis thaliana recombinant inbred line Q073 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line Q073


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line Q087, 10-11 days after flower opening
A_Q087

source_name: Arabidopsis thaliana recombinant inbred line Q087 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line Q087


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line Q143, 10-11 days after flower opening
A_Q143

source_name: Arabidopsis thaliana recombinant inbred line Q143 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line Q143


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line Q127, 10-11 days after flower opening
A_Q127

source_name: Arabidopsis thaliana recombinant inbred line Q127 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line Q127


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line Q090, 10-11 days after flower opening
A_Q090

source_name: Arabidopsis thaliana recombinant inbred line Q090 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line Q090


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line Q113, 10-11 days after flower opening
A_Q113

source_name: Arabidopsis thaliana recombinant inbred line Q113 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line Q113


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line Q013, 10-11 days after flower opening
A_Q013

source_name: Arabidopsis thaliana recombinant inbred line Q013 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line Q013


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line Q033, 10-11 days after flower opening
A_Q033

source_name: Arabidopsis thaliana recombinant inbred line Q033 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line Q033


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line Q072, 10-11 days after flower opening
A_Q072

source_name: Arabidopsis thaliana recombinant inbred line Q072 developing seeds, 10-11 days after flower opening

value: developing seeds

value: Recombinant inbred line Q072


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line Q055, 10-11 days after flower opening
A_Q055

source_name: Arabidopsis thaliana recombinant inbred line Q055 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line Q055


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line Q025, 10-11 days after flower opening
A_Q025

source_name: Arabidopsis thaliana recombinant inbred line Q025 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line Q025


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line Q070, 10-11 days after flower opening
A_Q070

source_name: Arabidopsis thaliana recombinant inbred line Q070 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line Q070


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line Q018, 10-11 days after flower opening
A_Q018

source_name: Arabidopsis thaliana recombinant inbred line Q018 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line Q018


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line Q047, 10-11 days after flower opening
A_Q047

source_name: Arabidopsis thaliana recombinant inbred line Q047 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line Q047

value: 10-11 days after flower opening


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line Q003, 10-11 days after flower opening
A_Q003

source_name: Arabidopsis thaliana recombinant inbred line Q003 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line Q003


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line Q000, 10-11 days after flower opening
A_Q000

source_name: Arabidopsis thaliana recombinant inbred line Q000 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line Q000


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line Q002, 10-11 days after flower opening
A_Q002

source_name: Arabidopsis thaliana recombinant inbred line Q002 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line Q002


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line Q009, 10-11 days after flower opening
A_Q009

source_name: Arabidopsis thaliana recombinant inbred line Q009 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line Q009


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line Q016, 10-11 days after flower opening
A_Q016

source_name: Arabidopsis thaliana recombinant inbred line Q016 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line Q016


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line Q021, 10-11 days after flower opening
A_Q021

source_name: Arabidopsis thaliana recombinant inbred line Q021 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line Q021


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line Q050, 10-11 days after flower opening
A_Q050

source_name: Arabidopsis thaliana recombinant inbred line Q050 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line Q050


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line Q022, 10-11 days after flower opening
A_Q022

source_name: Arabidopsis thaliana recombinant inbred line Q022 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line Q022


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line Q039, 10-11 days after flower opening
A_Q039

source_name: Arabidopsis thaliana recombinant inbred line Q039 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line Q039


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line Q005, 10-11 days after flower opening
A_Q005

source_name: Arabidopsis thaliana recombinant inbred line Q005 developing seeds, 10-11 days after flower opening

value: developing seeds

value: Recombinant inbred line Q005


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line Q029, 10-11 days after flower opening
A_Q029

source_name: Arabidopsis thaliana recombinant inbred line Q029 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line Q029


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line Q007, 10-11 days after flower opening
A_Q007

source_name: Arabidopsis thaliana recombinant inbred line Q007 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line Q007


title: Slc6a3_Ip_rep4

status: Public on Aug 20 2017

city: St Louis

first: Joseph

middle: D

last: Dougherty

state: Missouri

address: 4566 Scott Ave, box 8232

department: Genetics and Psychiatry

institute: Washington University

hyb_protocol: Standard Affymetrix protocol for mouse 430 2.0 platform

data_processing: Data were processed in R as described (see PMID: 20308160) using GC-RMA for normalization and identification of specific and enriched genes using the pSI package (see PMID: 20308160) with default settings, compared to a large set of prior cell types analyzed by TRAP on the same microarray platform.

source_name: TRAP'd RNA from Slc6a3 neurons

label_protocol: Affymetrix two-cycle amplification kit, using up to 10ng of total RNA per sample

extract_protocol: Five adult mice per replicate were euthanized with CO2, and midbrains were dissected in ice cold buffer in the presence of cyclohexamide to stall translation.  TRAP was conducted as described (see PMID: 24810037). Parallel input fractions were collected from each replicate as a measure of whole midbrain tissue RNA composition. RNA quantity and quality were determined with a Nanodrop 1000 spectrophotometer and Agilent 2100 Bioanalyzer with PicoChip reagents. All RINs were above 7.

value: midbrain

tag: rna type

value: TRAP

tag: Sex

value: both

value: adult (6-12 weeks)

tag: number of mice

tag: line

value: Slc6a3 JD1640 TRAP line


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line Q068, 10-11 days after flower opening
A_Q068

source_name: Arabidopsis thaliana recombinant inbred line Q068 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line Q068

value: 10-11 days after flower opening


title: Slc6a3_Ub_rep2

scan_protocol: Standard Affymetrix protocol for mouse 430 2.0 platform

source_name: unbound (total) RNA

value: unbound

tag: age


title: Slc6a3_Ip_rep2


title: Slc6a3_Ub_rep1


description:
Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line Q052, 10-11 days after flower opening
A_Q052

source_name: Arabidopsis thaliana recombinant inbred line Q052 developing seeds, 10-11 days after flower opening

value: Recombinant inbred line Q052


title: C. elegans_DGLA_rep2

status: Public on Aug 19 2017

city: Pamplona

first: David

last: Navarro-Herrera

state: Navarra

address: C/ Irunlarrea s/n, Ed. Investigación

department: Biochemistry & Genetics

country: Spain

institute: University of Navarra

hyb_protocol: Following fragmentation, cRNA were hybridized for Affymetrix® GeneChip® C. elegans Gene 1.0 ST arrays (Affymetrix Inc., Santa Clara, CA)

data_processing:
Background correction and normalization were performed by Robust Multiarray Analysis (RMA) algorithm and then evaluated using the Affymetrix® Transcriptome Analysis Console (TAC) v3. (Affymetrix Inc., Santa Clara, CA).
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0
affymetrix-array-type = EleGene-1_0-st
program-name = Expression Console
program-version = 1.4.1.46

organism: Caenorhabditis elegans

source_name: C. elegans L4 larvae grown in NGM medium supplemented with 1000 µM DGLA

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

growth_protocol: Escherichia coli OP50 was used as normal nematode diet. The experiment was performed on worms grown and maintained on Nematode Growth Medium (NGM) at 20 °C.

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

treatment_protocol: All assays were performed in triplicate in 6-well cell culture plates with 4 mL of NGM (supplemented or not with fatty acids (FAs) per well. FAs were tested at concentration of 1000 µM and, as they were stored as stock solutions in ethanol, the same quantity of this vehicle (1% v/v) were added to non-supplemented plates (NGM). Once FAs were added to NGM, plates were allowed to solidify and dried for two days in the dark to protect them from light oxidation. Subsequently, 200 µL of an overnight culture of E. coli OP50 were seeded and plates were again incubated in the dark at room temperature until dried. Age-synchronized N2 worms were obtained by standard hypochlorite treatment of gravid animals. The eggs were allowed to hatch overnight in M9 medium and about 2000 L1 larvae were transferred onto plates and grown until L4 state.

tag: strain

tag: devolpmental state

value: L4 larvae

tag: treated with

value: NGM + 1000 µM dihomo-gamma-linolenic acid (DGLA)


title: C. elegans_DGLA_rep3


title: C. elegans_GLA_rep3

source_name: C. elegans L4 larvae grown in NGM medium supplemented with 1000 µM GLA

value: NGM + 1000 µM gamma-linolenic acid (GLA)


title: C. elegans_DGLA_rep1


title: C. elegans_GLA_rep2


title: C. elegans_NGMcontrol_rep2

source_name: C. elegans L4 larvae grown in NGM medium (Control)

value: NGM (control)


title: 23436-24455T-Neg [P2538_11]

city: St. Louis

first: DAvid

last: DeNardo

state: Mo

address: 660 S. Euclid Ave

department: Medicine

hyb_protocol: Hybridization of the labeled cDNAs was done in Agilent 2x gene expression hybridization buffer, Agilent 10x blocking reagent and kreatech Kreablock onto Agilent microarrays at 65oC for 20 min.

scan_protocol: Slides were scanned on an Agilent C-class Microarray scanner.

data_processing:
Gridding and analysis of images was performed using Agilent Feature Extraction V11.5.1.1.
Intensity values were Feature Extraction processed signal values (called rProcessedSignal) in log2 scale. Control probes were filtered off and duplicate probes were averaged before quantile-normalization. There are 4 data sets, and each of them was normalized by the quantile method separately.

source_name: pancreas tumor macrophage YFP-

label_protocol: cDNAs were amplified using the Sigma-WTA2 kit, and chemically labeled with Kreatech ULS RNA labeling kit (Kreatech Diagnostics) and Cy5-labeled cDNAs were hybridized to Agilent Mouse Gene Expression Microarrays either 8x60K (G4852B-07809) or 4x44K (G4846A-026655).

extract_protocol: Total RNA was isolated using ENZO total RNA kit.

treatment_protocol: Animals were implanted with tumors and cells were isolated by FACS directly into RNA Lysis buffer.

tag: strain/background

tag: genotype/variation

value: Not provided

value: pancreas tumor

tag: cell type

value: macrophage YFP-

tag: gender

value: female

value: 8-10 weeks


title: 23430-24455T-Pos [P2538_10]

source_name: pancreas tumor macrophage YFP+

value: macrophage YFP+


title: 23433-24452T-Neg [P2538_12]


title: 23431-24456T-Pos [P2538_8]


title: C. elegans_LNA_rep1

source_name: C. elegans L4 larvae grown in NGM medium supplemented with 1000 µM LNA

value: NGM + 1000 µM  linoleic acid (LNA)


title: C. elegans_LNA_rep2


title: 23434-24453T-Neg [P2538_6]


title: C. elegans_LNA_rep3


title: 23429-24454T-Pos [P2538_9]


title: 23428-24453T-Pos [P2538_1]


title: C. elegans_GLA_rep1


title: 23547 YFP+ [P1991_16]


title: 23547 YFP(-) [P1991_13]


title: C. elegans_NGMcontrol_rep1


title: 23435-24454T-Neg [P2538_4]


title: 23427-24452T-Pos [P2538_7]


title: 23438-24457T-Neg [P2538_2]


title: 23912 YFP(-) [P1991_12]

source_name: normal pancreas macrophage YFP-

value: normal pancreas


title: C. elegans_NGMcontrol_rep3


title: 23916 YFP(-) [P1991_15]


title: 23551 YFP+ [P1991_14]


title: 23432-24457T-Pos [P2538_3]


title: 23437-24456T-Neg [P2538_5]


title: 23917 YFP+ [P1991_11]

source_name: normal pancreas macrophage YFP+


title: 23548 YFP(-) [P1991_8]


title: 23677 YFP(-) [P1991_10]


title: 23677 YFP+ [P1991_7]


title: 23550 YFP+ [P1991_9]


title: 23912 YFP+ [P1991_5]


title: 23551 YFP(-) [P1991_4]


title: 23548 YFP+ [P1991_1]


title: LM3 [P1301_10]

source_name: normal pancreas macrophage

value: macrophage

value: 4-5 months


title: 868 [P1301_7]

source_name: pancreas tumor macrophage


title: LM6 [P1301_8]


title: LM5 [P1301_12]


title: 868 [P1301_11]


title: 23550 YFP(-) [P1991_2]


title: LM1 [P1301_1]


title: 877 [P1301_2]


title: 964 [P1301_9]


title: 23917 YFP(-) [P1991_6]


title: 23916 YFP+ [P1991_3]


title: 20442 Low [P1750_6]

source_name: pancreas tumor macrophage MHCIIl Low

value: FvBn

value: macrophage MHCIIl Low


title: 20439 High [P1750_7]

source_name: pancreas tumor macrophage MHCIIl High

value: macrophage MHCIIl High


title: LM2 [P1301_3]


title: 242 [P1301_4]


title: 74 [P1301_5]


title: LM2 [P1301_6]


title: 20435 High [P1750_8]


title: 20436 Low [P1750_4]


title: FG-L-2

city: Tsukuba

first: Akemi

last: Ohmiya

state: Ibaraki

address: Fujimoto 2-1

department: Institute of Vegetable and Floriculture Science

institute: National Agriculture and Food Research Organization

description: Gene expression of mature leaves

hyb_protocol: The labeled cRNA (1.65 ug) was hybridized to the Chrysanthemum moliforium custom 180K oligo microarray (GPL13124) with the Gene Expression Hybridization kit (Agilent) according to the manufacturer’s instructions. Hybridization was performed at 65 ◦C for 17 h in a hybridization chamber. After hybridization, the array slides were washed with the Gene Expression Wash Buffer Kit (Agilent).

scan_protocol: After washing, dried slides were immediately scanned with an Agilent microarray scanner (G2505C).

data_processing: Raw scan data were captured by Agilent Feature Extraction software (v.10.7.1.1).

organism: Chrysanthemum x morifolium

source_name: Feeling Green, Leaf, mature, replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100ng total RNA with a Low Input Quick Amp Labeling Kit, one color (Agilent) according to the manufacturer’s instructions.

growth_protocol: Plants were grown under natural daylight conditions in a greenhouse

extract_protocol: Total RNAs were extracted using TRIzol reagent (Thermo Fisher Scientific, Waltham, MA) and RNeasy Mini Kit (Qiagen, Hilden, Germany). RNA integrity was evaluated using an Agilent 2100 Bioanalyzer (Agilent Technologies).

value: Leaf


title: FGD-P-3

description: Gene expression in ray petals at middle stage of flower development

source_name: Feeling Green Dark, Ray petal, middle stage of flower development, replicate 3

value: Ray petal


title: 20442 High [P1750_5]


title: FGD-P-1

source_name: Feeling Green Dark, Ray petal, middle stage of flower development, replicate 1


title: FG-L-3

description: Gene expression of mature leaves

source_name: Feeling Green, Leaf, mature, replicate 3


title: 20435 Low [P1750_3]


title: FGD-P-2

source_name: Feeling Green Dark, Ray petal, middle stage of flower development, replicate 2


title: FW-P-2

source_name: Feeling White, Ray petal, middle stage of flower development, replicate 2


title: FW-P-3

source_name: Feeling White, Ray petal, middle stage of flower development, replicate 3


title: 20436 High [P1750_2]


title: Mammary fat pad tumor from MDA-MB-231 cells ablated with DHHC3 shRNA, Replicate 2

status: Public on Aug 18 2017

city: Boston

first: Chandan

last: Sharma

state: MA

address: 450 Brookline Avenue

department: Cancer Immunology and Virology

institute: Dana Farber Cancer Institute

hyb_protocol: The biotinylated cRNAs were hybridized to microarray chip containing complementary oligonucleotide probes

scan_protocol: Affymatrix gene chip scanner 7G was used for scanning the microrarray chip for signal intensity.

data_processing:
The data were analyzed using dCHIP software. The signficant changes (P<0.05) in expression, with 1.5 fold increase or decreases, were finally selected.
The values in the sample data table were normalized intensities of gene expression

label_protocol: RNAs were converted into cDNA, then amplified and labeled with biotinylated nucleotides by in vitro transcription, to produce biotinylated cRNAs.

growth_protocol: Orthotopic tumor were generated by injecting MDA-MB-231 cells, ablated for control and DHHC3 expression, into mammary fat pads of nude mice

extract_protocol: Total RNA from xenograft tumors were extracted using Qiagen RNA isolation kit

tag: host strain

value: athymic nude mice

tag: host strain gender

tag: host strain genotype/variation

tag: injected with

value: MDA-MB-231 cells

value: ablated with DHHC3 shRNA

value: xenograft tumor after 35 days


title: Mammary fat pad tumor from MDA-MB-231 cells ablated with control shRNA, Replicate 1

value: ablated with control shRNA

tag: tissue


title: Mammary fat pad tumor from MDA-MB-231 cells ablated with DHHC3 shRNA, Replicate 1

value: female


title: Mammary fat pad tumor from MDA-MB-231 cells ablated with control shRNA, Replicate 2


title: 20439 Low [P1750_1]

value: Not provided

value: pancreas tumor

value: 8-10 weeks


title: FW-P-1

source_name: Feeling White, Ray petal, middle stage of flower development, replicate 1


title: FG-P-3

source_name: Feeling Green, Ray petal, middle stage of flower development, replicate 3


title: IR-BMI10

city: Parma

first: Eleonora

last: Derlindati

address: via gramsci, 14

country: Italy

institute: University of Parma

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

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version A.9.5.1.1), LOWESS normalization was applied

source_name: PBMC_High HOMA

label_protocol: 500ng of total RNA were primed with an oligo (d)T-T7 primer and retrotranscribed into dsDNA with MMLV-RT. Then cDNA sample was amplified using T7 RNA Polymerase and labelled with cy5 (Quick Amp Labeling Kit, Agilent) following manifacture instructions

extract_protocol:
[cell isolation protocol] Peripheral blood mononuclear cellss (PBMC) were isolated from 20ml of peripheral blood using Ficoll stratification
Total RNA extracted using Rneasy Mini Kit (Qiagen) purification following manifacture instructions

tag: group

value: High HOMA

value: PBMC

value: Leucocyte

tag: sample type

value: commercial RNA, pool from human leucocyte


title: IR-BMI9

extract_protocol: Total RNA extracted using Rneasy Mini Kit (Qiagen) purification following manifacture instructions


title: FG-P-2

source_name: Feeling Green, Ray petal, middle stage of flower development, replicate 2


title: IR-BMI6


title: IR-BMI5


title: IS-BMI8

source_name: PBMC_Low HOMA

value: Low HOMA


title: IR-BMI2


title: IR-BMI8


title: IR-BMI4


title: IR-BMI7


title: IR-BMI3


title: IR-BMI1


title: IS-BMI7


title: FG-P-1

source_name: Feeling Green, Ray petal, middle stage of flower development, replicate 1


title: IS-BMI4


title: IS-BMI10


title: IS-BMI5


title: IS-BMI9


title: IS-BMI3


title: IS-BMI1


title: IS-BMI2


title: IS-BMI6


title: HEK293_SnxATnf_12hr

city: Columbia

first: Mengqian

last: Chen

state: SC

address: CLS710, 715 Sumter Street

department: College of Pharmacy

institute: University of South Carolina

hyb_protocol: 300 ng of Cy3-labelled cRNA and 300 ng of Cy5-labelled cRNA was mixed and fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to  Agilent SurePrint G3 Human Gene Expression 8x60K Microarrays (G4851A-28004) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then immersed in acetonitrile and dried immediately by slowly removing the slide.

scan_protocol: Slides were scanned immediately after washing on an Agilent DNA Microarray Scanner (G2505C) using two color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3 um, Dye channels set to 20 bit).

data_processing: The scanned images were analyzed with Feature Extraction Software  10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid 039494_D_F_20140813) to obtain background subtracted and spatially detrended Processed Signal intensities.  Data was uploaded into Genespring version 11.5.1 where was thresholded to 1.0, log2 transformed, quantile normalized and base line transformed using the median of all samples. Data was filtered by flags in a way that at least 75% of the samples in any of the 2 experimental groups had DETECTED flags. Then, differentially expressed genes were determined using a moderated t-test statistics with p-value 0.01 and fold change 1.5 as cutoffs.

source_name: HEK293 cells, treated with 5μM Senexin A for 60 minutes and then treated with 10ng/mL TNFα for 12 hours

label_protocol: Cyanine-3 (Cy3) and Cyanine-5 (Cy5) labeled cRNA was prepared from 200 ng RNA using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with a NanoDrop 2000c Spectrophotometer.

growth_protocol: HEK293 cells were grown in DMEM (High-glucose) media with 10% FBS, 1% penicillin-streptomycin and 2 mM L-glutamine. The cells were plated in 12-well plate at the density of 3x10^5 cells per well 24 hours prior to treatment.

extract_protocol: Total RNA was extracted using RNAeasy Mini Kit (Qiagen) and RNA quality was tested using Bioanalyser.

treatment_protocol: Cells were first pre-treated with 5μM Senexin A or 0.1% DMSO (control) for 1 hour and then treated with or without 10 ng/mL TNFα for 2hr, 6hr, 12hr and 24hr.

tag: cell line


title: HEK293_DMSO_25hr

source_name: HEK293 cells, treated with 0.1% DMSO for 25 hours


title: HEK293_SnxA_25hr

source_name: HEK293 cells, treated with 5μM Senexin A for 25 hours


title: HEK293_SnxA_7hr

source_name: HEK293 cells, treated with 5μM Senexin A for 7 hours


title: HEK293_SnxA_13hr

source_name: HEK293 cells, treated with 5μM Senexin A for 13 hours


title: HEK293_SnxATnf_24hr

source_name: HEK293 cells, treated with 5μM Senexin A for 60 minutes and then treated with 10ng/mL TNFα for 24 hours


title: HEK293_Tnf_12hr

source_name: HEK293 cells, treated with 0.1% DMSO for 60 minutes and then treated with 10ng/mL TNFα for 12 hours


title: FG-L-1

description: Gene expression of mature leaves

source_name: Feeling Green, Leaf, mature, replicate 1


title: HEK293_DMSO_13hr

source_name: HEK293 cells, treated with 0.1% DMSO for 13 hours


title: HEK293_SnxATnf_30min_Rep3

source_name: HEK293 cells, treated with 5μM Senexin A for 60 minutes and then treated with 10ng/mL TNFα for 30min, Rep-3

treatment_protocol: Cells were first pre-treated with 5μM Senexin A or 0.1% DMSO (control) for 1 hour and then treated with or without 10 ng/mL TNFα for 30min.


title: HEK293_Tnf_24hr

source_name: HEK293 cells, treated with 0.1% DMSO for 60 minutes and then treated with 10ng/mL TNFα for 24 hours


title: HEK293_Tnf_2hr

source_name: HEK293 cells, treated with 0.1% DMSO for 60 minutes and then treated with 10ng/mL TNFα for 2 hours


title: HEK293_SnxA_3hr

source_name: HEK293 cells, treated with 5μM Senexin A for 3 hours


title: HEK293_Tnf_6hr

source_name: HEK293 cells, treated with 0.1% DMSO for 60 minutes and then treated with 10ng/mL TNFα for 6 hours


title: HEK293_DMSO_7hr

source_name: HEK293 cells, treated with 0.1% DMSO for 7 hours


title: HEK293_Tnf_30min_Rep4

source_name: HEK293 cells, treated with 0.1% DMSO for 60 minutes and then treated with 10ng/mL TNFα for 30min, Rep-4


title: HEK293_SnxATnf_30min_Rep2

source_name: HEK293 cells, treated with 5μM Senexin A for 60 minutes and then treated with 10ng/mL TNFα for 30min, Rep-2


title: HEK293_Tnf_30min_Rep2

source_name: HEK293 cells, treated with 0.1% DMSO for 60 minutes and then treated with 10ng/mL TNFα for 30min, Rep-2


title: HEK293_SnxATnf_6hr

source_name: HEK293 cells, treated with 5μM Senexin A for 60 minutes and then treated with 10ng/mL TNFα for 6 hours


title: HEK293_Tnf_30min_Rep3

source_name: HEK293 cells, treated with 0.1% DMSO for 60 minutes and then treated with 10ng/mL TNFα for 30min, Rep-3


title: HEK293_SnxATnf_30min_Rep1

source_name: HEK293 cells, treated with 5μM Senexin A for 60 minutes and then treated with 10ng/mL TNFα for 30min, Rep-1


title: HEK293_DMSO_3hr

source_name: HEK293 cells, treated with 0.1% DMSO for 3 hours


title: HEK293_Tnf_30min_Rep1

source_name: HEK293 cells, treated with 0.1% DMSO for 60 minutes and then treated with 10ng/mL TNFα for 30min, Rep-1


title: HEK293_SnxA_90min_Rep4

source_name: HEK293 cells, treated with 5μM Senexin A for 90 minutes, Rep-4


title: HEK293_SnxATnf_30min_Rep4

source_name: HEK293 cells, treated with 5μM Senexin A for 60 minutes and then treated with 10ng/mL TNFα for 30min, Rep-4


title: HEK293_SnxA_90min_Rep3

source_name: HEK293 cells, treated with 5μM Senexin A for 90 minutes, Rep-3


title: HEK293_SnxA_90min_Rep2

source_name: HEK293 cells, treated with 5μM Senexin A for 90 minutes, Rep-2


title: HEK293_SnxATnf_2hr

source_name: HEK293 cells, treated with 5μM Senexin A for 60 minutes and then treated with 10ng/mL TNFα for 2 hours