title: Tgfb_17_454

status: Public on Sep 15 2020

city: Philadelphia

first: Robert

middle: Joesph

last: Norgard

state: PA

address: 421 Curie Blvd, 531 BRB II/III

institute: University of Pennsylvania

data_processing:
Illumina Casava was used for baseCalling
Raw sequence reads were filtered for quality (Q > 30) and trimmed by minimum length 30bp using Trimmomatic (version 0.32), and then mapped to mouse genome (mm10) using one leading fast aligner STAR (Dobin  A, et al., 2013).
The count matrix was generated using FeatureCounts tool (Liao Y, et al, 2014), and filtered by applying threshold of the presence in >=3 samples.
Genome_build: mm10
Supplementary_files_format_and_content: raw count

source_name: PD454_48 hours with 10ng/ml TGFB

growth_protocol: Cell lines were grown in PDAC mediaMurine cell lines were cultured in Dulbecco’s Modified Eagle Medium/F12 medium supplemented with 5 mg/mL D-glucose (Invitrogen), 0.1 mg/mL soybean trypsin inhibitor type I (Invitrogen), 5 mL/L insulin-transferrin-selenium (ITS Premix; BD Biosciences), 25 µg/mL bovine pituitary extract (Gemini Bio-Products), 5 nmol/L 3,3′,5-triiodo-L-thyronine (Sigma), 1 µmol/L dexamethasone (Sigma), 100 ng/mL cholera toxin (Sigma), 10 mmol/L nicotinamide (Sigma), 5% Nu-serum IV culture supplement (ThermoFisher Scientific), and antibiotics (gentamicin 150 µg/mL, Gibco; amphotericin B 0.25 µg/mL, Invitrogen). These cells were passaged 1-2 times per week when reaching near confluency.

extract_protocol:
RNA was prepared from cultured tumor cells using RNeasy Mini Kit (Qiagen) or NucleoSpin RNA (Takara).
Library was constructed by NOVOGENE

treatment_protocol: Murine pancreatic cancer cells were treated with either DMSO, ionomycin, or TGFb for 48 hours

tag: strain background

value: Mixed

value: Pancreas

tag: tissue/cell type

value: Pancreatic ductal adenocarcinoma

value: 48 hours with 10ng/ml TGFB


title: Tgfb_12_883

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

source_name: PD883_48 hours with 10ng/ml TGFB

tag: cell line

tag: tissue

tag: treatment


title: Tgfb_6_7591

source_name: PD7591_48 hours with 10ng/ml TGFB


title: TgfB_5_7591


title: Iono_3_7591

source_name: PD7591_48 hours with 2.5uM Ionomycin

value: 48 hours with 2.5uM Ionomycin


title: Iono_9_883

source_name: PD883_48 hours with 2.5uM Ionomycin


title: Tgfb_11_883


title: HBEC-6KT-media-only-rep3

status: Public on Sep 16 2020

type: RNA

city: Waterloo

first: Jennifer

middle: A.

last: Aguiar

state: ON

address: 200 University Avenue East

department: Biology

country: Canada

institute: University of Waterloo

hyb_protocol: Labeled cDNA was hybridized to GeneChip™ Clariom_S_Human arrays according to ThermoFisher Scientific instructions.

scan_protocol: Arrays were scanned GeneChip Scanner 3000 7G using AGCC software.

data_processing: Raw intensity values from the microarray experiment using the Affymetrix Clariom S Human chip-type were imported into the R statistical language environment (version 3.6.1). Probe definition files were obtained from the Brainarray database (version 24). The Single Channel Array Normalization (SCAN) method was used to obtain log2-transformed normalised expression values with the SCAN.UPC R package (version 2.26.0), with annotation data from the Bioconductor project (version 3.9). Determination of statistically significant differential gene expression was performed using the empirical Bayes method via the eBayes function from the limma R package (version 3.40.0). P values were adjusted using the Benjamini & Hochberg method, with a significance cutoff of 0.05.

label: Biotin

organism: Homo sapiens

source_name: Human airway epithelial cell line HBEC-6KT culture exposed to media only

label_protocol: cDNA was amplified using GeneChip™ WT PLUS Reagent Kit, from ThermoFisher Scientific following manufacturers instructions.

growth_protocol: An immortalized human airway epithelial cell line (HBEC-6KT) over expressing human telomerase reverse transcriptase (hTERT) and cyclin-dependent kinase 4 (Cdk4) was cultured as a submerged monolayer. HBEC-6KT were grown in keratinocyte serum free medium supplemented with 0.8 ng/mL epithelial growth factor, 50 μg/mL bovine pituitary extract and 1X penicillin/streptomycin. All cells were grown at 37℃ at 5% CO2  and all experiments were performed within 5 passages.

extract_protocol: Cells were harvested directly in culture plates using the Buffer RLT mixed with 2-ME. Following harvest, total RNA was extracted as instructed by the RNeasy Mini Kit manual.

treatment_protocol: All in vitro knockdown experiments in HBEC-6KT were done using siRNA transfected with DharmaFECT Transfection Reagent according to the manufacturer’s instructions. Cells were transfected with siABCF1 or siCTRL for 24 hours. After knockdown, cells were transfected with an immunostimulatory ligand for 24h followed by outcome measurements of cell viability (LDH and cell morphology), function (CXCL10 secretion), protein expression (immunoblot), or gene transcription (microarray). For  VACV-70 stimulation experiments, a concentration-response study was performed using  0.1-3.16 mg/ml (VACV-70) followed by incubation for 24h.


title: HBEC-6KT-media-only-rep1


title: Iono_15_454

source_name: PD454_48 hours with 2.5uM Ionomycin


title: Iono_10_883


title: Dmso_7_883

source_name: PD883_48 hours with DMSO

value: 48 hours with DMSO


title: Dmso_2_7591

source_name: PD7591_48 hours with DMSO


title: Iono_16_454


title: Dmso_8_883


title: Tgfb_18_454


title: Dmso_1_7591


title: Dmso_14_454

source_name: PD454_48 hours with DMSO


title: Dmso_13_454


title: CEMBA190627_10E_3_CEMBA190627_10E_4_H9_ad002

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

molecule: genomic DNA

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

value: CA

tag: Sex

value: male

tag: age

tag: strain


title: CEMBA190627_10E_3_CEMBA190627_10E_4_H9_ad001


title: CEMBA190627_10E_3_CEMBA190627_10E_4_H9_ad004


title: CEMBA190627_10E_3_CEMBA190627_10E_4_H9_ad007


title: CEMBA190627_10E_3_CEMBA190627_10E_4_H9_ad008


title: CEMBA190627_10E_3_CEMBA190627_10E_4_H9_ad012


title: CEMBA190627_10E_3_CEMBA190627_10E_4_H9_ad010


title: CEMBA190627_10E_3_CEMBA190627_10E_4_H8_ad004


title: CEMBA190627_10E_3_CEMBA190627_10E_4_H8_ad012


title: CEMBA190627_10E_3_CEMBA190627_10E_4_H9_ad006


title: CEMBA190627_10E_3_CEMBA190627_10E_4_H8_ad008


title: Iono_4_7591


title: CEMBA190627_10E_3_CEMBA190627_10E_4_H8_ad001


title: CEMBA190627_10E_3_CEMBA190627_10E_4_H8_ad002


title: CEMBA190627_10E_3_CEMBA190627_10E_4_H8_ad007


title: CEMBA190627_10E_3_CEMBA190627_10E_4_H8_ad006


title: CEMBA190627_10E_3_CEMBA190627_10E_4_H7_ad012


title: CEMBA190627_10E_3_CEMBA190627_10E_4_H7_ad006


title: CEMBA190627_10E_3_CEMBA190627_10E_4_H7_ad008


title: CEMBA190627_10E_3_CEMBA190627_10E_4_H7_ad004


title: CEMBA190627_10E_3_CEMBA190627_10E_4_H7_ad002


title: CEMBA190627_10E_3_CEMBA190627_10E_4_H7_ad001


title: CEMBA190627_10E_3_CEMBA190627_10E_4_H6_ad007


title: CEMBA190627_10E_3_CEMBA190627_10E_4_H6_ad008


title: CEMBA190627_10E_3_CEMBA190627_10E_4_H6_ad012


title: CEMBA190627_10E_3_CEMBA190627_10E_4_H8_ad010


title: CEMBA190627_10E_3_CEMBA190627_10E_4_H6_ad006


title: CEMBA190627_10E_3_CEMBA190627_10E_4_H6_ad010


title: CEMBA190627_10E_3_CEMBA190627_10E_4_H7_ad007


title: CEMBA190627_10E_3_CEMBA190627_10E_4_H6_ad001


title: CEMBA190627_10E_3_CEMBA190627_10E_4_H5_ad002


title: CEMBA190627_10E_3_CEMBA190627_10E_4_H5_ad006


title: CEMBA190627_10E_3_CEMBA190627_10E_4_H6_ad004


title: CEMBA190627_10E_3_CEMBA190627_10E_4_H4_ad010


title: CEMBA190627_10E_3_CEMBA190627_10E_4_H4_ad001


title: CEMBA190627_10E_3_CEMBA190627_10E_4_H4_ad004


title: CEMBA190627_10E_3_CEMBA190627_10E_4_H5_ad001


title: CEMBA190627_10E_3_CEMBA190627_10E_4_H4_ad006


title: CEMBA190627_10E_3_CEMBA190627_10E_4_H3_ad008


title: CEMBA190627_10E_3_CEMBA190627_10E_4_H4_ad002


title: CEMBA190627_10E_3_CEMBA190627_10E_4_H4_ad008


title: CEMBA190627_10E_3_CEMBA190627_10E_4_H4_ad007


title: CEMBA190627_10E_3_CEMBA190627_10E_4_H2_ad004


title: CEMBA190627_10E_3_CEMBA190627_10E_4_H2_ad007


title: CEMBA190627_10E_3_CEMBA190627_10E_4_H2_ad002


title: CEMBA190627_10E_3_CEMBA190627_10E_4_H12_ad012


title: CEMBA190627_10E_3_CEMBA190627_10E_4_H2_ad001


title: CEMBA190627_10E_3_CEMBA190627_10E_4_H12_ad010


title: CEMBA190627_10E_3_CEMBA190627_10E_4_H2_ad010


title: CEMBA190627_10E_3_CEMBA190627_10E_4_H12_ad007


title: CEMBA190627_10E_3_CEMBA190627_10E_4_H12_ad002


title: CEMBA190627_10E_3_CEMBA190627_10E_4_H11_ad012


title: CEMBA190627_10E_3_CEMBA190627_10E_4_H12_ad004


title: CEMBA190627_10E_3_CEMBA190627_10E_4_H5_ad007


title: CEMBA190627_10E_3_CEMBA190627_10E_4_H4_ad012


title: CEMBA190627_10E_3_CEMBA190627_10E_4_H11_ad010


title: CEMBA190627_10E_3_CEMBA190627_10E_4_H11_ad004


title: CEMBA190627_10E_3_CEMBA190627_10E_4_H11_ad006


title: CEMBA190627_10E_3_CEMBA190627_10E_4_H11_ad007


title: CEMBA190627_10E_3_CEMBA190627_10E_4_H11_ad001


title: CEMBA190627_10E_3_CEMBA190627_10E_4_H10_ad012


title: CEMBA190627_10E_3_CEMBA190627_10E_4_H10_ad008


title: CEMBA190627_10E_3_CEMBA190627_10E_4_H10_ad010


title: CEMBA190627_10E_3_CEMBA190627_10E_4_H1_ad012


title: CEMBA190627_10E_3_CEMBA190627_10E_4_H10_ad001


title: CEMBA190627_10E_3_CEMBA190627_10E_4_H1_ad006


title: CEMBA190627_10E_3_CEMBA190627_10E_4_H1_ad007


title: CEMBA190627_10E_3_CEMBA190627_10E_4_H11_ad008


title: CEMBA190627_10E_3_CEMBA190627_10E_4_H10_ad006


title: CEMBA190627_10E_3_CEMBA190627_10E_4_G9_ad010


title: CEMBA190627_10E_3_CEMBA190627_10E_4_H1_ad004


title: CEMBA190627_10E_3_CEMBA190627_10E_4_H1_ad010


title: CEMBA190627_10E_3_CEMBA190627_10E_4_H12_ad006


title: CEMBA190627_10E_3_CEMBA190627_10E_4_H12_ad001


title: CEMBA190627_10E_3_CEMBA190627_10E_4_H10_ad004


title: CEMBA190627_10E_3_CEMBA190627_10E_4_G9_ad012


title: CEMBA190627_10E_3_CEMBA190627_10E_4_H1_ad001


title: CEMBA190627_10E_3_CEMBA190627_10E_4_G9_ad008


title: CEMBA190627_10E_3_CEMBA190627_10E_4_G9_ad002


title: CEMBA190627_10E_3_CEMBA190627_10E_4_G9_ad004


title: CEMBA190627_10E_3_CEMBA190627_10E_4_H1_ad002


title: CEMBA190627_10E_3_CEMBA190627_10E_4_G9_ad007


title: CEMBA190627_10E_3_CEMBA190627_10E_4_G9_ad001


title: CEMBA190627_10E_3_CEMBA190627_10E_4_H10_ad002


title: CEMBA190627_10E_3_CEMBA190627_10E_4_G8_ad008


title: CEMBA190627_10E_3_CEMBA190627_10E_4_G8_ad007


title: CEMBA190627_10E_3_CEMBA190627_10E_4_G8_ad002


title: CEMBA190627_10E_3_CEMBA190627_10E_4_G8_ad001


title: CEMBA190627_10E_3_CEMBA190627_10E_4_G7_ad012


title: CEMBA190627_10E_3_CEMBA190627_10E_4_G7_ad007


title: CEMBA190627_10E_3_CEMBA190627_10E_4_G7_ad008


title: CEMBA190627_10E_3_CEMBA190627_10E_4_G7_ad006


title: CEMBA190627_10E_3_CEMBA190627_10E_4_G7_ad002


title: CEMBA190627_10E_3_CEMBA190627_10E_4_G6_ad006


title: CEMBA190627_10E_3_CEMBA190627_10E_4_G7_ad001


title: CEMBA190627_10E_3_CEMBA190627_10E_4_G6_ad010


title: CEMBA190627_10E_3_CEMBA190627_10E_4_G5_ad010


title: CEMBA190627_10E_3_CEMBA190627_10E_4_G6_ad007


title: CEMBA190627_10E_3_CEMBA190627_10E_4_G6_ad002


title: CEMBA190627_10E_3_CEMBA190627_10E_4_G5_ad006


title: CEMBA190627_10E_3_CEMBA190627_10E_4_G5_ad004


title: CEMBA190627_10E_3_CEMBA190627_10E_4_G5_ad007


title: CEMBA190627_10E_3_CEMBA190627_10E_4_G5_ad001


title: CEMBA190627_10E_3_CEMBA190627_10E_4_G4_ad012


title: CEMBA190627_10E_3_CEMBA190627_10E_4_G5_ad002


title: CEMBA190627_10E_3_CEMBA190627_10E_4_G4_ad010


title: CEMBA190627_10E_3_CEMBA190627_10E_4_G4_ad006


title: CEMBA190627_10E_3_CEMBA190627_10E_4_G4_ad008


title: CEMBA190627_10E_3_CEMBA190627_10E_4_G4_ad004


title: CEMBA190627_10E_3_CEMBA190627_10E_4_G4_ad002


title: CEMBA190627_10E_3_CEMBA190627_10E_4_G3_ad012


title: CEMBA190627_10E_3_CEMBA190627_10E_4_G7_ad010


title: CEMBA190627_10E_3_CEMBA190627_10E_4_G3_ad006


title: CEMBA190627_10E_3_CEMBA190627_10E_4_G9_ad006


title: CEMBA190627_10E_3_CEMBA190627_10E_4_G3_ad004


title: CEMBA190627_10E_3_CEMBA190627_10E_4_G3_ad008


title: CEMBA190627_10E_3_CEMBA190627_10E_4_G2_ad010


title: CEMBA190627_10E_3_CEMBA190627_10E_4_G2_ad012


title: CEMBA190627_10E_3_CEMBA190627_10E_4_G2_ad008


title: CEMBA190627_10E_3_CEMBA190627_10E_4_G2_ad006


title: CEMBA190627_10E_3_CEMBA190627_10E_4_G6_ad001


title: CEMBA190627_10E_3_CEMBA190627_10E_4_G2_ad007


title: CEMBA190627_10E_3_CEMBA190627_10E_4_G12_ad012


title: CEMBA190627_10E_3_CEMBA190627_10E_4_G2_ad004


title: CEMBA190627_10E_3_CEMBA190627_10E_4_G12_ad007


title: CEMBA190627_10E_3_CEMBA190627_10E_4_G2_ad002


title: CEMBA190627_10E_3_CEMBA190627_10E_4_G2_ad001


title: CEMBA190627_10E_3_CEMBA190627_10E_4_G12_ad008


title: CEMBA190627_10E_3_CEMBA190627_10E_4_G12_ad006


title: CEMBA190627_10E_3_CEMBA190627_10E_4_G12_ad004


title: HBEC-6KT-media-only-rep2


title: CEMBA190627_10E_3_CEMBA190627_10E_4_G12_ad002


title: CEMBA190627_10E_3_CEMBA190627_10E_4_G11_ad012


title: CEMBA190627_10E_3_CEMBA190627_10E_4_G11_ad008


title: CEMBA190627_10E_3_CEMBA190627_10E_4_G11_ad004


title: CEMBA190627_10E_3_CEMBA190627_10E_4_G3_ad007


title: CEMBA190627_10E_3_CEMBA190627_10E_4_G11_ad007


title: CEMBA190627_10E_3_CEMBA190627_10E_4_G11_ad001


title: CEMBA190627_10E_3_CEMBA190627_10E_4_G11_ad002


title: CEMBA190627_10E_3_CEMBA190627_10E_4_G10_ad008


title: CEMBA190627_10E_3_CEMBA190627_10E_4_G10_ad012


title: CEMBA190627_10E_3_CEMBA190627_10E_4_G10_ad004


title: CEMBA190627_10E_3_CEMBA190627_10E_4_G10_ad007


title: CEMBA190627_10E_3_CEMBA190627_10E_4_G10_ad010


title: CEMBA190627_10E_3_CEMBA190627_10E_4_G10_ad002


title: CEMBA190627_10E_3_CEMBA190627_10E_4_G1_ad010


title: CEMBA190627_10E_3_CEMBA190627_10E_4_G10_ad001


title: CEMBA190627_10E_3_CEMBA190627_10E_4_G1_ad007


title: CEMBA190627_10E_3_CEMBA190627_10E_4_G1_ad002


title: CEMBA190627_10E_3_CEMBA190627_10E_4_G1_ad012


title: CEMBA190627_10E_3_CEMBA190627_10E_4_G11_ad010


title: CEMBA190627_10E_3_CEMBA190627_10E_4_G1_ad004


title: CEMBA190627_10E_3_CEMBA190627_10E_4_G1_ad001


title: CEMBA190627_10E_3_CEMBA190627_10E_4_F9_ad010


title: CEMBA190627_10E_3_CEMBA190627_10E_4_G11_ad006


title: CEMBA190627_10E_3_CEMBA190627_10E_4_F9_ad007


title: CEMBA190627_10E_3_CEMBA190627_10E_4_F9_ad008


title: CEMBA190627_10E_3_CEMBA190627_10E_4_F9_ad012


title: CEMBA190627_10E_3_CEMBA190627_10E_4_F9_ad002


title: CEMBA190627_10E_3_CEMBA190627_10E_4_F9_ad001


title: CEMBA190627_10E_3_CEMBA190627_10E_4_F8_ad010


title: CEMBA190627_10E_3_CEMBA190627_10E_4_F8_ad008


title: CEMBA190627_10E_3_CEMBA190627_10E_4_F9_ad004


title: CEMBA190627_10E_3_CEMBA190627_10E_4_F8_ad006


title: CEMBA190627_10E_3_CEMBA190627_10E_4_F8_ad002


title: CEMBA190627_10E_3_CEMBA190627_10E_4_F8_ad001


title: CEMBA190627_10E_3_CEMBA190627_10E_4_F7_ad012


title: CEMBA190627_10E_3_CEMBA190627_10E_4_F7_ad010


title: CEMBA190627_10E_3_CEMBA190627_10E_4_F7_ad008


title: CEMBA190627_10E_3_CEMBA190627_10E_4_G1_ad006


title: CEMBA190627_10E_3_CEMBA190627_10E_4_F7_ad007


title: CEMBA190627_10E_3_CEMBA190627_10E_4_F7_ad002


title: CEMBA190627_10E_3_CEMBA190627_10E_4_F7_ad001


title: CEMBA190627_10E_3_CEMBA190627_10E_4_F6_ad007


title: CEMBA190627_10E_3_CEMBA190627_10E_4_F6_ad004


title: CEMBA190627_10E_3_CEMBA190627_10E_4_F6_ad002


title: CEMBA190627_10E_3_CEMBA190627_10E_4_F6_ad001


title: CEMBA190627_10E_3_CEMBA190627_10E_4_F5_ad008


title: CEMBA190627_10E_3_CEMBA190627_10E_4_F5_ad002


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title: CEMBA190627_10E_1_CEMBA190627_10E_2_B10_ad008


title: CEMBA190627_10E_1_CEMBA190627_10E_2_B10_ad010


title: CEMBA190627_10E_1_CEMBA190627_10E_2_B10_ad007


title: CEMBA190627_10E_1_CEMBA190627_10E_2_B10_ad002


title: CEMBA190627_10E_1_CEMBA190627_10E_2_B1_ad010


title: CEMBA190627_10E_1_CEMBA190627_10E_2_B1_ad008


title: CEMBA190627_10E_1_CEMBA190627_10E_2_B1_ad007


title: CEMBA190627_10E_1_CEMBA190627_10E_2_B1_ad002


title: CEMBA190627_10E_1_CEMBA190627_10E_2_B1_ad004


title: CEMBA190627_10E_1_CEMBA190627_10E_2_B1_ad006


title: CEMBA190627_10E_1_CEMBA190627_10E_2_A9_ad012


title: CEMBA190627_10E_1_CEMBA190627_10E_2_A9_ad004


title: CEMBA190627_10E_1_CEMBA190627_10E_2_A9_ad006


title: CEMBA190627_10E_1_CEMBA190627_10E_2_A9_ad008


title: CEMBA190627_10E_1_CEMBA190627_10E_2_A9_ad002


title: CEMBA190627_10E_1_CEMBA190627_10E_2_B1_ad001


title: CEMBA190627_10E_1_CEMBA190627_10E_2_A8_ad010


title: CEMBA190627_10E_1_CEMBA190627_10E_2_A8_ad008


title: CEMBA190627_10E_1_CEMBA190627_10E_2_A7_ad012


title: CEMBA190627_10E_1_CEMBA190627_10E_2_A9_ad001


title: CEMBA190627_10E_1_CEMBA190627_10E_2_A8_ad001


title: CEMBA190627_10E_1_CEMBA190627_10E_2_A7_ad010


title: CEMBA190627_10E_1_CEMBA190627_10E_2_A7_ad007


title: CEMBA190627_10E_1_CEMBA190627_10E_2_A7_ad008


title: CEMBA190627_10E_1_CEMBA190627_10E_2_A8_ad006


title: CEMBA190627_10E_1_CEMBA190627_10E_2_A8_ad007


title: CEMBA190627_10E_1_CEMBA190627_10E_2_A7_ad004


title: CEMBA190627_10E_1_CEMBA190627_10E_2_A6_ad012


title: CEMBA190627_10E_1_CEMBA190627_10E_2_A7_ad002


title: CEMBA190627_10E_1_CEMBA190627_10E_2_A6_ad008


title: CEMBA190627_10E_1_CEMBA190627_10E_2_A7_ad006


title: CEMBA190627_10E_1_CEMBA190627_10E_2_A6_ad006


title: CEMBA190627_10E_1_CEMBA190627_10E_2_A6_ad007


title: CEMBA190627_10E_1_CEMBA190627_10E_2_A6_ad002


title: CEMBA190627_10E_1_CEMBA190627_10E_2_A6_ad001


title: CEMBA190627_10E_1_CEMBA190627_10E_2_A5_ad010


title: CEMBA190627_10E_1_CEMBA190627_10E_2_A5_ad008


title: CEMBA190627_10E_1_CEMBA190627_10E_2_A8_ad004


title: CEMBA190627_10E_1_CEMBA190627_10E_2_A5_ad001


title: CEMBA190627_10E_1_CEMBA190627_10E_2_A5_ad002


title: CEMBA190627_10E_1_CEMBA190627_10E_2_A5_ad007


title: CEMBA190627_10E_1_CEMBA190627_10E_2_A4_ad004


title: CEMBA190627_10E_1_CEMBA190627_10E_2_A3_ad010


title: CEMBA190627_10E_1_CEMBA190627_10E_2_A7_ad001


title: CEMBA190627_10E_1_CEMBA190627_10E_2_A4_ad002


title: CEMBA190627_10E_1_CEMBA190627_10E_2_A3_ad008


title: CEMBA190627_10E_1_CEMBA190627_10E_2_A5_ad004


title: CEMBA190627_10E_1_CEMBA190627_10E_2_A3_ad012


title: CEMBA190627_10E_1_CEMBA190627_10E_2_A4_ad010


title: CEMBA190627_10E_1_CEMBA190627_10E_2_A3_ad004


title: CEMBA190627_10E_1_CEMBA190627_10E_2_A3_ad006


title: CEMBA190627_10E_1_CEMBA190627_10E_2_A3_ad002


title: CEMBA190627_10E_1_CEMBA190627_10E_2_A3_ad001


title: CEMBA190627_10E_1_CEMBA190627_10E_2_A3_ad007


title: CEMBA190627_10E_1_CEMBA190627_10E_2_A2_ad007


title: CEMBA190627_10E_1_CEMBA190627_10E_2_A2_ad004


title: CEMBA190627_10E_1_CEMBA190627_10E_2_A5_ad012


title: CEMBA190627_10E_1_CEMBA190627_10E_2_A2_ad006


title: CEMBA190627_10E_1_CEMBA190627_10E_2_A2_ad001


title: CEMBA190627_10E_1_CEMBA190627_10E_2_A12_ad012


title: CEMBA190627_10E_1_CEMBA190627_10E_2_A12_ad010


title: CEMBA190627_10E_1_CEMBA190627_10E_2_A2_ad008


title: CEMBA190627_10E_1_CEMBA190627_10E_2_A12_ad007


title: CEMBA190627_10E_1_CEMBA190627_10E_2_A5_ad006


title: CEMBA190627_10E_1_CEMBA190627_10E_2_A12_ad008


title: CEMBA190627_10E_1_CEMBA190627_10E_2_A12_ad006


title: CEMBA190627_10E_1_CEMBA190627_10E_2_A12_ad004


title: CEMBA190627_10E_1_CEMBA190627_10E_2_A11_ad008


title: CEMBA190627_10E_1_CEMBA190627_10E_2_A10_ad010


title: CEMBA190627_10E_1_CEMBA190627_10E_2_A10_ad012


title: CEMBA190627_10E_1_CEMBA190627_10E_2_A10_ad008


title: CEMBA190627_10E_1_CEMBA190627_10E_2_A11_ad001


title: CEMBA190627_10E_1_CEMBA190627_10E_2_A11_ad004


title: CEMBA190627_10E_1_CEMBA190627_10E_2_A10_ad002


title: CEMBA190627_10E_1_CEMBA190627_10E_2_A10_ad001


title: CEMBA190627_10E_1_CEMBA190627_10E_2_A1_ad012


title: CEMBA190627_10E_1_CEMBA190627_10E_2_A11_ad006


title: CEMBA190627_10E_1_CEMBA190627_10E_2_A10_ad007


title: CEMBA190627_10E_1_CEMBA190627_10E_2_A2_ad002


title: CEMBA190627_10E_1_CEMBA190627_10E_2_A10_ad006


title: CEMBA190627_10E_1_CEMBA190627_10E_2_A10_ad004


title: CEMBA190627_10E_1_CEMBA190627_10E_2_A1_ad006


title: CEMBA190627_10E_1_CEMBA190627_10E_2_A1_ad007


title: CEMBA190627_10E_1_CEMBA190627_10E_2_A1_ad004


title: CEMBA190627_10E_1_CEMBA190627_10E_2_A1_ad001


title: CEMBA190627_10E_1_CEMBA190627_10E_2_A1_ad002


title: CEMBA190627_10E_1_CEMBA190627_10E_2_A11_ad012


title: C8161_ATF3_OE_3_1

city: Boston

first: Natasha

last: Frank

state: MA

address: 77 Avenue Louis Pasteur

department: Medicine

institute: Brigham and Women's Hospital

description: Transcriptome expression levels from ATF-3 overexpressing cells

data_processing:
Bowtie2 was used to align the reads and RSEM to quantify gene expression.
The three C8161 technical replicates were averaged.
RPKM values < 1 were assigned a value of 1 before log2 transformation.
Genes expressed at < 5 RPKM in all samples (row sums) were excluded from further analysis.
Genome_build: hg38
Supplementary_files_format_and_content: Row names consist of Gene IDs and column names are the samples.

source_name: Melanoma cell line C8161 overexpressing ATF-3

growth_protocol: All melanoma cells were cultured in DMEM supplemented with 10% FBS and 0.1% penicillin/streptomycin.

extract_protocol:
An RNeasy mini kit was used to extract the RNA.
RNA libraries were prepared for sequencing using standard DNA nanoball protocols.

treatment_protocol: ATF-3 overexpression was induced by retroviral transduction with corresponding neomycin controls.

tag: cell type

value: melanoma

tag: atf-3 status

value: ATF-3 overexpressing


title: C8161_ATF3_OE_2_1


title: C8161_NEO_1_1

description: Transcriptome expression levels from neomycin control cells

source_name: Melanoma cell line C8161 neomycin control

value: Neomycin control


title: CEMBA190627_10E_1_CEMBA190627_10E_2_A4_ad001


title: CEMBA190627_10E_1_CEMBA190627_10E_2_A11_ad007


title: C8161_ATF3_OE_1_1


title: CEMBA190627_10E_1_CEMBA190627_10E_2_A12_ad002


title: A2058_NEO_1

source_name: Melanoma cell line A2058 neomycin control


title: A2058_ATF3_OE_1

source_name: Melanoma cell line A2058 overexpressing ATF-3


title: H2O Control 2

city: Charlottesville

first: David

middle: Michael

last: Johanson

state: VA

address: 200 Jeanette Lancaster Way

department: Department of Neuroscience

institute: UVa School of Medicine

data_processing:
Demultiplexed FASTQ files were processed with the Dada2 v1.12.1 function "filterAndTrim": truncLen = c(300,250), maxN = 0, maxEE = c(10,10), truncQ = 2, rm.phix = TRUE, compress = TRUE, multithread = TRUE
Error learning with Dada2 v1.12.1 "learnErrors" for R1 and R2 reads: multithread = TRUE, Dereplication with "derepFastq": verbose = TRUE
Amplicon Sequence Variant Identification with  Dada2 v1.12.1 "dada" from learned error rates and dereplicated FASTQ reads: multithread = TRUE
Read pair merging with  Dada2 v1.12.1 "mergePairs": verbose = TRUE
Chimera identification and removal with  Dada2 v1.12.1 "removeBimeraDenovo": nethod = "consensus", multithread = TRUE, verbose = TRUE
Taxonomy assignment with  Dada2 v1.12.1 "assignTaxonomy": multithread = TRUE
Genome_build: Taxonomy was assigned manually with input from the following 16S reference databases: Silva v132, Greengenes v13_8_set_97, GTDB bac-arc_ssu_r86, and RefSeq RDB16S v2_May2018
Supplementary_files_format_and_content: comma separated files (.csv) containing: 1. ASV abundances per sample, 2. Taxonomy of each ASV, and 3. Sample parameter data and Identification

organism: blank sample

source_name: 16S sequencing control with water only

growth_protocol: Female C57BL/6 mice were maintained on a 12 hours light/dark cycle with lights on at 7am and provided with standard food and water ad libitum. Mice were housed at 2-3 per cage and experimental treatment was assigned randomly to each cage.

extract_protocol:
Fecal samples were collected from live mice restrained with a tail scruff. DNA for 16S amplification was extracted with a phenol-chloroform method: Fecal pellets were placed in 2 mL tubes containing 200 μL silica-zirconia beads (0.1 mm). The tubes were filled with 750 μL extraction buffer, 200 μL 20% SDS and 750 μL phenol-chloroform-isoamyl alcohol (25:24:1). After disruption, the aqueous phase was separated by centrifugation and cleaned up with two washes of chloroform-isoamyl alcohol (24:1). The DNA was precipitated and resuspended in 10 mM Tris solution.
The V3-V4 region of the 16S rRNA gene was amplified for 25 cycles using specific primers with adapter overhangs as per the Illumina library preparation guide (Forward Primer: TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGCCTACGGGNGGCWGCAG, Reverse Primer: GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGGACTACHVGGGTATCTAATCC). Following purification of the PCR products, individual indexes were added to the amplicons by PCR. The amplicons were purified, pooled in equal quantities, and then sequenced on the Illumina MiSeq platform.
V3-V4 16S-seq

treatment_protocol: Each group recieved different treatments: naïve mice recieved no treatment, EAE (MOG+CFA) mice were immunized subcutaneously with 50 μg of myelin oligodendrocyte glycoprotein peptide 35–55 (MOG35–55) (CSBIO #CS0681) emulsified at a 1:1 ratio in Complete Freud’s Adjuvant (Sigma Aldrich #F5881). On days 0 and 2, 250 ng of pertussis toxin (List Biologicals #180) was administered intraperitoneally. CFA imce recieved only the equivalent dose of Complete Freud’s Adjuvant.

tag: molecule subtype

value: 16S Amplicon

tag: sample type

value: 16S sequencing control with water only


title: H2O Control 1


title: DSM01-G3

city: Daejeon

first: Wonjae

last: Seong

address: Gwahak-ro 125

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

data_processing:
Illumina BaseSpace for configurations
Bowtie2 for mapping onto reference genome sequence
StringTie v1.3.3b for assembling mapped read into transcripts and determine their abundance
DESeq2 for determining Differentiaily expressed genes
Genome_build: Escherichia coli K-12 MG1655 (NC_000913.3)
Supplementary_files_format_and_content: xlsx files include FPKM values for each Sample and raw gene counts for every gene and every sample

molecule: polyA RNA

organism: Escherichia coli

source_name: wildtype Escherichia coli DSM01 in the glucose M9 (rep3)

growth_protocol: SBA01 and DSM01 were growed in 3g/L M9 sodium acetate meida and 5g/L M9 glucose, DSM01 was in 5g/L M9 glucose media

extract_protocol:
Total RNA for RNA-seq was extracted from log phase cultures using Qiagen's RNeasy Plus Mini kit
Libraries were prepared according to Illumina's instructions accompanying the TruSeq Stranded mRNA Library PrepKit.


title: SBA01-G1

source_name: evolved Escherichia coli DSM01 (SBA01) in the glucose M9 (rep1)


title: CEMBA190627_10E_1_CEMBA190627_10E_2_A1_ad010


title: SBA01-A1

source_name: evolved Escherichia coli DSM01 (SBA01) in the sodium acetate M9 (rep1)


title: DSM01-G1

source_name: wildtype Escherichia coli DSM01 in the glucose M9 (rep1)


title: SBA01-A3

source_name: evolved Escherichia coli DSM01 (SBA01) in the sodium acetate M9 (rep3)


title: SBA01-G2

source_name: evolved Escherichia coli DSM01 (SBA01) in the glucose M9 (rep2)


title: C8161_NEO_3_1


title: SBA01-G3

source_name: evolved Escherichia coli DSM01 (SBA01) in the glucose M9 (rep3)


title: C8161_NEO_2_1


title: DSM01-G2

source_name: wildtype Escherichia coli DSM01 in the glucose M9 (rep2)


title: mir-284 KO 3d replicate 2

city: Oxford

first: Aron

last: Szabo

address: John Radcliffe Hospital, Headley Way

department: Radcliffe Department of Medicine

country: United Kingdom

institute: Weatherall Institute of Molecular Medicine, University of Oxford

data_processing:
Sequencing quality was assessed in BaseSpace and later by FastQC. Reads were aligned to the Drosophila melanogaster iGenome dm6 using STAR version 2.4.2a.
Reads on both strands were counted using featureCounts: "featureCounts" "-T" "5" "-a" "/databank/igenomes/Drosophila_melanogaster/UCSC/dm6/Annotation/Genes/genes.gtf" "-t" "exon" "-g" "gene_id" "-o" "features_counted_284_strand0.txt" "-p" "-s" "0" "w25d1Aligned.out.sam" "w25d2Aligned.out.sam" "w25d3Aligned.out.sam" "ko25d1Aligned.out.sam" "ko25d2Aligned.out.sam" "ko25d3Aligned.out.sam" "w3d1Aligned.out.sam" "w3d2Aligned.out.sam" "w3d3Aligned.out.sam" "ko3d1Aligned.out.sam" "ko3d2Aligned.out.sam" "ko3d3Aligned.out.sam"
Genome_build: dm6
Supplementary_files_format_and_content: comma-separated values file, raw read counts per gene prior to normalization

organism: Drosophila melanogaster

source_name: antennal third segment

growth_protocol: Flies were aged according to standard protocols on cornmeal-yeast-agar medium, flipped every 2-3 days.

extract_protocol:
Third antennal segments were removed, washed into Qiazol, homogenized and stored at -80 C until extraction. Total RNA extraction was performed with the miRNEasy kit (Qiagen). 150 ng RNA was Turbo DNAse-treated, 100 ng of this RNA was polyA-selected (NEBNext Poly(A) mRNA Magnetic  Isolation Module, NEB #E7490).
Sequencing libraries were prepared using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB #E7420).

value: antennal third segment

value: 3d after eclosion

tag: genotype

value: w1118;;mir-284 KO (7 times outcrossed to w1118)


title: mir-284 KO 25d replicate 2

value: 25d after eclosion


title: mir-284 KO 25d replicate 1


title: mir-284 KO 3d replicate 1


title: w 25d replicate 3


title: w 25d replicate 1


title: w 25d replicate 2


title: w 3d replicate 3


title: w 3d replicate 2


title: w 3d replicate 1


title: mir-284 KO 3d replicate 3


title: SBA01-A2

source_name: evolved Escherichia coli DSM01 (SBA01) in the sodium acetate M9 (rep2)


title: HL-60: Group 6, 1

city: SERI KEMBANGAN

first: VAHID

last: HOSSEINPOUR SARMADI

state: SELANGOR

address: C-12-06, THE HERITAGE RESIDENCY, JALAN DAGANG

department: Pathology

country: Malaysia

institute: University Putra Malaysia

description: Agilent SurePrint G3 Catalog Human GE 8x 60 K Microarrays

hyb_protocol: Gene Expression Hybridization Kit (5188-5242), Lot: 0006130573

scan_protocol: After hybridization, the microarray slide was washed in gene expression wash buffer 1 for one minute at room temperature and another minute in gene expression wash buffer 2 at 37oC before scanning on Agilent High Resolution Microarray Scanner (C-model).

data_processing: Raw signal data were extracted from the TIFF image with Agilent Feature Extraction Software (V10.7.1.1).

source_name: HL-60 cell line

label_protocol: Low Input Quick Amp Labeling Kit (Agilent: 5190-2305), Lot: 0006183781

growth_protocol: Leukemic tumor cells were cultured with UC-MSCs as experiment and alone as a control for 72 hours in RPMI1640.

extract_protocol: Total RNA were extracteted by using Total RNA of HL-60 and BV173 cell lines were extracted using the RNeasy Plus Mini kit (Qiagen, CA, USA) according to the manufacturer’s instructions

treatment_protocol: MSC derived from umbilical cord were used as treatment

value: Leukemic Cell Line


title: HL-60: Group 6, 3


title: HL-60: Group 5, 7

source_name: HL-60 cell line in co culture UC-MSC


title: BV173: Group 4, 32

source_name: BV173 cell line


title: BV173: Group 4, 31


title: BV173: Group 3, 30

source_name: BV173 cell line in co culture UC-MSC


title: BV173: Group 4, 33


title: BV173: Group 3, 29


title: HL-60: Group 5, 9


title: FL5_IDELA

city: Barcelona

first: Patricia

last: Pérez-Galán

state: Barcelona

address: Centre Esther Koplowitz, Hemato-oncology dept, Rosello 149-153, 2nd floor

department: Hemato-oncology

country: Spain

institute: IDIBAPS

description: Gene expression data control cells

hyb_protocol: RNA samples were processed to Affymetrix GeneChip HT HG-U219 arrays.

scan_protocol: Scanning was processed in the Gene Titan instrument.

data_processing: Determination of the signal value for each probe set of the array were obtained with GeneChip® Command Console® Software (AGCC) (Affymetrix).

label: biotin

source_name: Follicular lymphoma primary sample from lymph node

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 150 ng total RNA

growth_protocol: FL primary samples were seed onto  preestablised layesr of FDC

extract_protocol: RNA was obtained by using the TRIzol reagent followed by a cleaning step with the RNAeasy kit. RNA integrity was examined with the Agilent 2100 Bioanalyzer

treatment_protocol: FL and FL-FDC cultures  were treated with 500nM  idelalisib for 48h

value: Idelalisib


title: BV173: Group 3, 6


title: FL5

description: Gene expression data control cells

value: control


title: FL2_FDC_IDELA

description: Gene expression data control cells

value: cocultured with FDC +Idelalisib


title: FL3_IDELA

description: Gene expression data control cells


title: FL4

description: Gene expression data control cells


title: FL2

description: Gene expression data control cells


title: FL3_FDC_IDELA

description: Gene expression data control cells


title: FL1_IDELA

description: Gene expression data control cells


title: FL3

description: Gene expression data control cells


title: FL1

description: Gene expression data control cells


title: FL4_IDELA

description: Gene expression data control cells


title: FL4_FDC_IDELA

description: Gene expression data control cells


title: FL3_FDC

description: Gene expression data control cells

value: cocultured with FDC


title: FL5_FDC

description: Gene expression data control cells


title: FL4_FDC

description: Gene expression data control cells


title: FL2_FDC

description: Gene expression data control cells


title: FL5_FDC_IDELA

description: Gene expression data control cells


title: FL2_IDELA

description: Gene expression data control cells


title: FL1_FDC_IDELA

description: Gene expression data control cells


title: FL1_FDC

description: Gene expression data control cells


title: 26EDLWt

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

country: Italy

institute: University of Padova

hyb_protocol: Cy3-labeled cRNA (1.65 μg; specific activity of >9.0 pmol Cy3/μg of cRNA) was fragmented at 60 °C for 30 min in a reaction volume of 55 μl containing 1× Agilent fragmentation buffer and 2× Agilent blocking agent, following the manufacturer's instructions. On completion of the fragmentation reaction, 55 μl of 2× GEx Hybridization buffer HI-RPM was added to the fragmentation mixture, and mixtures were hybridized to Agilent Whole-Human Genome Oligo Microarrays (G4845A) for 17 h at 65 °C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 min at room temperature with GE Wash Buffer 1 (Agilent Technologies) and 1 min at 37 °C with GE Wash buffer 2 (Agilent Technologies) and then dried

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using the one-color scan setting for 1 × 44 k array slides (scan area of 61 × 21.6 mm; scan resolution of 5 μm; dye channel set to green; green PMT set to 100%).

data_processing: Scanned images were analyzed with Feature Extraction Software 12.0.0.7 (Agilent Technologies) using default parameters (protocol GE1_107_Sep09 and Grid:  014868_D_20070820 ) to obtain background-subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Signal intensities were normalized using quantile normalization for GE .

label_protocol: Cy3-labeled cRNA was prepared from 1 μg of RNA using One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) (Agilent Technologies) according to the manufacturer's instructions, and RNeasy column purification was performed (Qiagen). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: RyR1 I4895T knock-in mice on a 129S2/SvPasCrl background were kindly provided by the S. Hamilton laboratory, Texas, USA. These founder mice were rederived using C57BL/6J for breeding. This resulted in a new sub-line with a mixed genetic background (approximately 50% 129S2/SvPasCrl and 50% C57BL/6J after rederivation). Since homozygotes have a perinatal lethal phenotype (Zvaritch et al. 2007), heterozygotes (HET) were crossed with wild type (WT) littermates or C57BL/6J mice (Charles River) to maintain the colony. At least five such crosses had occurred before the experiments. Ear snips from adult mice and tail snips from sacrificed neonates were retained for genotyping. DNA was extracted from tissue samples using the Extract-N-Amp kit (Sigma) and PCR was used to amplify the fragment covering the mutation site. Forward and reverse primers were 5’-GGTCTTCCTGTCTCAATAACCCGATCTAGAAAC-3’ and 5’-GATGGAGAAACCAAAGCTCAGAGAGACCAC-3’ respectively. Since the inserted mutation site also contains an Age I target sequence, only samples containing the mutated allele undergo Age I digestion.

extract_protocol: Total RNA was prepared from biopsies using TRIzol (Life Technologies) following the manufacturer's instructions.

treatment_protocol: no treatment

value: EDL muscle

tag: gender

tag: mutation


title: 28SWt

value: Soleo muscle


title: 28EDLWt

value: male


title: 26SWt


title: 29EDLEt


title: 25EDLEt


title: 27EDLWt


title: 30SEt

value: female


title: WT-A-E, biological rep1

city: Wuhan

first: Feng

last: Zhu

address: No.1,Shizishan Street

department: College of Horticulture & Forestry Sciences

country: China

institute: Huazhong Agricultural University

description: Gene expression data from the flavode of the wild type citrus  at 170 days after flowering after ABA+ETH treatment

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

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

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

organism: Citrus reticulata

source_name: The flavode of the citrus were collected at 170 days after flowering after  ABA+ETH treatment

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

extract_protocol: The  RNA samples were isolated according to the method described by Liu et al. (2009)

value: The flavode of the citrus  at 170 days after flowering after ABA+ETH treatment

tag: culitvar

value: Suavissima


title: 25SEt


title: 30EDLEt


title: 27SWt


title: WT-A-E, biological rep2

source_name: The flavode of the citrus were collected at 170 days after flowering after ABA+ETH treatment


title: MT-A-E, biological rep1


title: WT-ETH, biological rep2

description: Gene expression data from the flavode of the wild type citrus  at 170 days after flowering after ETH treatment

source_name: The flavode of the citrus were collected at 170 days after flowering after ETH treatment

value: The flavode of the citrus  at 170 days after flowering after ETH treatment


title: amp1-13, biological rep3

city: Freising

first: Tobias

last: Sieberer

address: Liesel-Beckmann-Strasse 1

department: Plant Sciences

country: Germany

institute: Technical University of Munich

description: Gene expression data from 10-day-old amp1-13 seedlings

hyb_protocol: Labeled samples were hybridized to the Genechip Arabidopsis ATH1 Genome Arrays (Affymetrix, Santa Clara, CA) according to the manufacturer's instructions (Affymetrix; www.affymetrix.com/)

scan_protocol: The GeneArrays were scanned using the Affymetrix GeneChip Scanner (Affymetrix) using standard NASC protocols.

data_processing: Microarray Suite 5.0

organism: Arabidopsis thaliana

source_name: Arabidopsis amp1-13 seedlings

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol (GeneChip® Expression Arrays Technical Manual, 2013, Affymetrix)

growth_protocol: Seeds were surface-sterilized with 70% ethanol + 0.05% SDS for 3 min, rinsed with 96% ethanol for 1 min, and subsequently dried in a laminar flow hood.  Sterile seeds were germinated and grown in 96-well plates (approximately 5 seeds per well) in 100mL liquid half-strength Murashige and Skoog medium containing 1% Sucrose and 1% DMSO. After stratification at 4°C in darkness for 2 days, seeds were placed in a growth incubator grown at 26°C grown under long d conditions (16 h, 80 mM m-2 s-1 cool-white light/8 h dark).

extract_protocol: Total RNA was extracted using the RNeasy Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions.

value: whole seedlings

tag: ecotype

value: 10 days


title: WT-ABA, biological rep2

description: Gene expression data from the flavode of the wild type citrus  at 170 days after flowering after ABA treatment

source_name: The flavode of the citrus were collected at 170 days after flowering after ABA treatment

value: The flavode of the citrus  at 170 days after flowering after ABA treatment


title: MT-ETH, biological rep2


title: cyp78a5,7, biological rep2

description: Gene expression data from 10-day-old cyp78a5,7 seedlings

source_name: Arabidopsis cyp78a5,7 seedlings


title: MT-A-E, biological rep2


title: amp1-13, biological rep2


title: cyp78a5,7, biological rep3


title: MT-ABA, biological rep2


title: WT-ETH, biological rep1


title: amp1-13, biological rep1


title: MT-ABA, biological rep1


title: cyp78a5,7, biological rep1


title: fetal cord tissue, A1172

type: genomic

city: Singapore

first: Jonathan

middle: Yinhao

last: Huang

state: « choose one »

address: 30 Medical Drive

country: Singapore

institute: Singapore Institute for Clinical Sciences

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing:
GenomeStudio; R/Rstudio
green (RAW_ID_Grn.idat) and red (RAW_ID_Red.idat) channels provided
[value definition]  chip position, DNA extraction, and bisulfite conversion batch, and celltype-adjusted residuals provided

label: Cy3, Cy5

source_name: cord tissue

label_protocol: Standard Illumina Protocol

extract_protocol: Prior to purification, 250 mg crushed cord tissue was enzymatically digested with hyaluronidase (~2.7U in 250 µl PBS) for 30 minutes at 37 C, mixed with 250 µl TNES lysis buffer, transferred to gentleMACS M Tubes (Miltenyi 130-093-236) for 1-minute homogenization followed by overnight treatment with 200 µg Proteinase K at 55 C. QIASymphony SP was used for automated purification of (buffy coat/cord tissue) DNA in combination with QIASymphony DSP DNA Midi Kit (Qiagen #937255) and DNA was bisulfite converted using the EZ DNA Methylation Kit™ (Zymo Research).

value: fetal cord tissue

tag: art treatment status (0 = spontaneous; 1 = assisted reproduction)

tag: maternal age at delivery (years)

tag: maternal ethnicity (0 = chinese; 1 = indian; 2 = malay)

tag: child sex (male = 0; female = 1)

tag: pre-pregnancy bmi (kg/m^2)


title: fetal cord tissue, A1173

tag: tissue


title: fetal cord tissue, A1178


title: fetal cord tissue, A1169


title: fetal cord tissue, A1170


title: fetal cord tissue, A1177


title: fetal cord tissue, A1174


title: fetal cord tissue, S1168


title: fetal cord tissue, S1167


title: fetal cord tissue, S1166


title: fetal cord tissue, S1164


title: fetal cord tissue, S1163


title: WT-ABA, biological rep1

tag: treatment


title: fetal cord tissue, S1162


title: MT-ETH, biological rep1


title: wild type, biological rep3

description: Gene expression data from 10-day-old wild-type seedlings

source_name: Arabidopsis wild-type seedlings

value: wild type

tag: age


title: fetal cord tissue, A1176


title: fetal cord tissue, S1156


title: fetal cord tissue, S1161


title: fetal cord tissue, S1159


title: fetal cord tissue, S1160


title: fetal cord tissue, S1158


title: fetal cord tissue, S1155


title: fetal cord tissue, S1165


title: wild type, biological rep1


title: fetal cord tissue, A1175


title: fetal cord tissue, S1154


title: fetal cord tissue, S1153


title: fetal cord tissue, S1146


title: fetal cord tissue, S1144


title: fetal cord tissue, S1147


title: fetal cord tissue, S1149


title: fetal cord tissue, S1143


title: fetal cord tissue, S1145