title: MCF7 AF, biological rep3

city: Solna

first: Sylvain

last: Peuget

state: Stockholm

address: Solnavägen 9

department: MTC

country: Sweden

institute: Karolinska Institute

description: MCF7 treated with AF 1µM

hyb_protocol: Following fragmentation, cRNA was hybridized on HT-Human Genome U133+ PM Array.

scan_protocol: GeneChips were scanned using a confocal scanner (Affymetrix).

data_processing: The data were analyzed with geneXplain platform, and RMA method was used for background correction, normalization, and summarization.

source_name: MCF7 cell line

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

growth_protocol: MCF7 cells were maintained in Dulbecco's Modified Eagle Medium supplemented with 10% fetal bovine serum and penicillin/streptomycin (10 units/ml)

extract_protocol: Total RNA was isolated with the Aurum total RNA mini kit (Bio-Rad) according to the manufacturer's instructions.

treatment_protocol: MCF7 cells were treated with 1 μM AF for 8h or 5 μM Onc1 for 16h.

tag: treatment

value: 1µM AF for 8 h


title: MCF7 ONC1, biological rep3

status: Public on Dec 31 2019

type: RNA

description: MCF7 treated with Onc1 5µM

label: biotin

molecule: total RNA

organism: Homo sapiens

tag: cell line

value: 5µM Onc1 for 16 h


title: Brain, Pooled Repo>UAS-RNAi R1

city: Memphis

first: Daniel

middle: Lee

last: Johnson

state: Tennessee

address: 71 S Manassas

department: Molecular Informatics Core

country: USA

institute: UTHSC

hyb_protocol: Done according to Affymetrix protocols

scan_protocol: Scanned on Affymetrix GCS 3000 scanner

data_processing: Processed Expression Console using GMT normalization

organism: Drosophila melanogaster

source_name: Whole Brain

label_protocol: Used WT amplification and Labeling kit (Life Technologies) according to Affymetrix protocols

growth_protocol: All flies were raised at 25deg in a humidity controled biochamber. Approximately 3-5 day old flies were used for expression studies.

extract_protocol: TRI reagent and Directzol miniPrep for total RNA

treatment_protocol: Total RNA was isolated from control (repo>36303-emptyvector-RNAi) and gliopathic seizure lines by removing 15-25 fly heads per genotype and homogenizing in TRI Reagent (Applied Biosystems) and followed by RNA purification with Directzol RNA MiniPrep Plus (Zymo Research Corp) according to the manufacturer’s instructions. Purity and concentration was verified using NanoDrop spectrophotometer (ThermoFisher Scientific) and Qubit (ThermoFisher Scientific). RNA integrity was measured using a Bioanalyzer (Agilent). mRNA from the gliopathic seizure flies was pooled into a single group by adding equal amounts of mRNA from each sample. Samples were run on a GeneChip Drosophila Gene 1.0 ST Array (ThermoFisher Scientific, #902155).

tag: tissue

value: Brain

tag: genotype

value: Experimental pool


title: Brain, Pooled Repo>UAS-RNAi R2


title: Brain, Repo-GAL4 R3

value: Control


title: MCF7 ONC1, biological rep2

description: MCF7 treated with Onc1 5µM


title: MCF7 AF, biological rep2

description: MCF7 treated with AF 1µM


title: WT_Hip

type: SRA

first: Maxim

middle: N.

last: Artyomov

state: MO

address: 660 S. Euclid Avenue, Campus Box 8118

department: Immunology&Pathology

institute: Washington University in St.Louis

library_source: transcriptomic

data_processing:
quality control, Cell Ranger Single Cell Software Suite (v2.1.0)
sample de-multiplexing,  Cell Ranger Single Cell Software Suite (v2.1.0)
barcode processing, Cell Ranger Single Cell Software Suite (v2.1.0)
single-cell 3′ gene counting , Cell Ranger Single Cell Software Suite (v2.1.0)
alignment, Cell Ranger Single Cell Software Suite (v2.1.0)
Genome_build: mm10
Supplementary_files_format_and_content: Filtered matrix of gene by cell expression, file with barcodes and file with expressed genes. Files are ready to be imported to Seurat package.

molecule: polyA RNA

organism: Mus musculus

source_name: Isolated single nuclei from brain of wild type mice

extract_protocol:
Mice were aged to 15 months of age. Upon tissue harvest, mice were euthanized and perfused with 1U/ml heparin in PBS. Left hemisphere of the brains were dissected out and flash frozen on dry ice. Flash frozen brain tissue was homogenized in a Dounce homogenizer in Lysis Buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, and 0.025% NP-40), and incubated on ice 15 minutes. The suspension was filtered through a 30 um filter to remove debris and pelleted at 500 x g 5 min at 4o C. Nuclei were washed and filtered twice with Nuclei Wash (1% BSA in PBS with 0.2 U/uL RNasin (Promega)). Nuclei pellets were resuspended in 500 uL Nuclei Wash and 900 uL 1.8 M Sucrose. This 1400 uL mixture was carefully layered on top of 500 uL 1.8 M sucrose and centrifuged at 13,000 x g 45 min 4oC to separate the nuclei from myelin debris. The nuclei pellet was resuspended in Nuclei wash at 1000 nuclei/uL and filtered through a 40 um FlowMi Cell Strainer.
Isolated single nuclei were subjected to droplet-based 3’ end massively parallel single-cell RNA sequencing using Chromium Single Cell 3’ Reagent Kits as per manufacturer’s instructions (10x Genomics) The generated scRNAseq libraries were sequenced using an Illumina sequencer.

tag: strain

tag: mouse genotype

value: wt

value: nuclei of brain

tag: age

value: 15 months


title: Brain, Pooled Repo>UAS-RNAi R3


title: Trem2_KO_5XFAD_Cor

source_name: Isolated single nuclei from brain of Trem2 KO 5XFAD mice

value: Trem2-/- 5XFAD


title: MCF7 AF, biological rep1

description: MCF7 treated with AF 1µM


title: MCF7 DMSO, biological rep2

description: MCF7 control


title: Trem2_KO_Hip

source_name: Isolated single nuclei from brain of Trem2 KO mice


title: pup normoxia no treatment-rep3

city: Indianapolis

first: Leni

last: Moldovan

state: IN

address: 980 W Walnut St., Rm. C422

department: Ophthalmology

institute: Indiana University

hyb_protocol: Three Mouse genome 430A v2 per experimental condition were hybridized and stained using the Hybridization Oven 645 and Fluidics station 450, using standard protocols, in the Center for Medical Genomics at Indiana University School of Medicine.

scan_protocol: GeneChip Scanner 3000 7G (Affymetrix), standard protocol

data_processing: Partek Genomic Suite (Partek Inc., Chesterfield, MO)

source_name: pup retina @ P17

label_protocol: 100 ng total RNA were further used for cDNA synthesis and labeling, using Ovation® PicoSL WTA System V2 and Encore® Biotin Module, respectively (NuGEN Technologies, Inc., San Carlos, CA), according to manufacturer’s protocols.

extract_protocol: One retina from each pup was used for total RNA isolation with the RNeasy Mini Kit and post-lysis processing was done with QiaCube (both from Qiagen).

treatment_protocol: 7-day-old mice are placed with their nursing dams in a 75% oxygen atmosphere for 5 days. Pups were intravitreally injected with either CD34+ cells (10,000 cells), ECFCs (100,000 cells) or a combination thereof (110,000 cells). The injections were done either on P5, before placing in 75% oxygen, or on P12, upon return to normoxic conditions. The mice were euthanized on either P12 or P17.

value: retina

tag: developmental stage

tag: disease state

value: normoxia

value: no treatment


title: MCF7 ONC1, biological rep1

description: MCF7 treated with Onc1 5µM


title: WT_5XFAD_Cor

source_name: Isolated single nuclei from brain of 5XFAD mice


title: Trem2_KO_Cor


title: MCF7 DMSO, biological rep3

description: MCF7 control


title: Brain, Repo-GAL4 R2


title: S31_181_KO

city: Baltimore

first: Yazmin

last: Rovira Gonzalez

state: MD

address: 707 N Broadway

institute: Johns Hopkins University School of Medicine

data_processing:
Quality check: fastqc --extract -t 2 -o FastQC Fastq/${i}_1.fastq.gz Fastq/${i}_2.fastq.gz
Trimming: seqtk trimfq  -e50 ${i}_1.fq.gz > Trimmed/${i}_1.fastq
High-quality reads were imported into Tophat v2.1.1 (uses bowtie2 v2.2.6) for alignment into BAM files
Cufflinks (version 2.2.1, http://cole-trapnell-lab.github.io/cufflinks/) was used to estimate the expression level for each gene based on high-quality reads that have been uniquely mapped to the mouse genome mm10.
Cufflinks reported the abundance of a transcript in Fragments Per Kilobase of transcript per Million (FPKM) mapped reads.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each sample

source_name: Quadriceps muscle

extract_protocol:
6mo Mss51 WT and KO animals were maintained under a 12:12 hour light:dark schedule with ad libitum access to food and water. Quadriceps muscle were isolated from each mouse and frozen in cold isopentane (#M32631, Sigma-Aldrich). Muscle tissues were homogenized in TRIzol (15596018, Life Technologies) and 2 ug of total RNA was isolated using the Direct-zol RNA MiniPrep Kit (R2052, Zymo Research, Irvine, CA, USA) for the construction of sequncing libraries.
After the QC procedures, mRNA from eukaryotic organisms was enriched using oligo(dT) beads. rRNA was removed using the Ribo-Zero kit that leaves the mRNA. First, the mRNA was fragmented randomly by adding fragmentation buffer, then the cDNA was synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina), dNTPs, RNase H and DNA polymerase I were added to initiate the second-strand synthesis. Second, after a series of terminal repairs, ligation and sequences adapter ligation, the double-stranded cDNA library was completed through size selection and PCR enrichment. Captured library was sequenced on Illumina HiSeq 4000 (Illumina) platform according to manufacturer’s instructions for paired-end 150 bp sequencing with sequence coverage of 50 million read-pairs.

tag: gender

value: Female

value: Quadriceps muscle


title: S31_180_KO


title: pup normoxia no treatment-rep2


title: S31_171_KO


title: S31_203_WT

value: wild type


title: S31_193_WT


title: S31_163_WT


title: HIF-3a2_ChIPseq

city: Oulu

first: Jussi-Pekka

middle: Matteus

last: Tolonen

address: Aapistie 7A

department: Faculty of Biochemistry and Molecular Medicine

country: Finland

institute: University of Oulu

library_source: genomic

data_processing:
Raw fastq files were trimmed by ngsShoRT program with parameter 'lqr_5adpt_tera' and analyzed by FastQC for quality
Reads were aligned to hg19 by Bowtie2 with default parameters
Peaks were called using the MACS algorithm with input as control
The bedGraph format from MACS was converted to bigWig using the UCSC pro-compiled utilities bedGraphToBigWig provided with chromosome sizes
bigWigToWig utility was used to produce Wig files that were visualized using the Integrative Genomic Viewer
Genome_build: hg19
Supplementary_files_format_and_content: HIF-3a2 binding sites against input in WIG format

molecule: genomic DNA

source_name: Isogenic Hep3B cells

growth_protocol: 1.6 million Hep3B cells were seeded at approx. 70 % confluency  in EMEM on a 10 cm plate under normoxic conditions for the first 24 h and then 24 h in 1 % hypoxia.

extract_protocol:
The cells were prepared in triplicate and pooled for ChIP. Cells were crosslinked with 1 % (v/v) formaldehyde (10 min. at 22 degrees Celsius) and washed twice with PBS, after which they were collected in a cold room in Farham Lysis Buffer. After centrifugation, the cell pellets were resuspended in RIPA buffer. Chromatin was sonicated to an average fragment size of 200-400 bp using Bioruptor UCD-300-TO (Diagenode). The chromatin was immunoprecipitated for ChIP-seq with V5-tag antibody (R960-25, Invitrogen).
ChIP-seq samples were processed according to Illumina's instructions and DNA libraries were sequenced using Illumina HiSeq System (Illumina) in the EMBL Gene Core Facility (Heidelberg, Germany).

treatment_protocol: The cells were co-transfected with 6 000 ng of HIF-3a2-V5 and 4 000 ng of HIF-beta overexpression plasmids and cultured under normoxia and then hypoxia as described above.

value: liver, hepatoma

tag: passages

value: up to 10

tag: chip-antibody

value: V5 (R960-25, Invitrogen)

tag: transfection

value: V5-tagged HIF-3alpha2


title: pup normoxia no treatment-rep1


title: pup OIR-treatment @ P5-ECFC+CD34-rep3

value: OIR model

value: treatment @ P5-ECFC+CD34


title: input_DNA

value: wildtype HIF-beta overexpression plasmid


title: S31_161_WT


title: S31_182_KO


title: pup OIR no treatment-rep1


title: pup OIR no treatment-rep2


title: pup OIR no treatment-rep3


title: WT_Cor

value: wt


title: MCF7 DMSO, biological rep1

description: MCF7 control


title: pre_subject21

city: Tokushima

first: Kensei

last: Nishida

state: Tokushima

address: 3-18-15 Kuramoto-cho

country: Japan

institute: Tokushima University Graduate school

hyb_protocol: Hybridizations were performed using GE Hybridization Kit (P/N 5188-5242) and GE Wash Buffer 1 and 2 (P/N 5188-5325, -5326) as following Agilent's protocol. The fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4858A) for 17 hours at 65C in a rotating Agilent hybridization oven.

scan_protocol: Microarrays were scanned using Agilent’s DNA Microarray Scanner (P/N G2600D).

data_processing: Data extracted using Agilent's Feature Extraction software. Raw data output was imported into Genespring GX14.9 (Agilent) and normalized each chip to the 75th percentile of all measurements (per chip normalization).

source_name: whole blood from athlete, pre-intervention

label_protocol: Sample labeling, array processing and scanning, and data extraction were performed as described in One-Color Microarray-Based Gene Expression Analysis’ Protocol. These protocols are available for download from Agilent's DNA Microarray Manuals website. For microarray analysis, total RNA (150 ng) was used for amplification and labeling of complementary RNA (cRNA) using a Low RNA Input Liner Amplification Kit PLUS and a succinimide-containing fluorescent dye (Cy3)-CTP according to the manufacturer’s protocol (Agilent).

extract_protocol: The total RNA from whole blood was extracted using PAXgene according to the manufacturer's protocol (QIAGEN).

treatment_protocol: Dairy intake of Lactobacillus gasseri CP2305 strain for 12 weeks

value: male

tag: cell type

value: peripheral blood leukocytes

value: placebo


title: pup OIR-treatment @ P5-ECFC-rep1

value: retina

value: treatment @ P5-ECFC


title: pup OIR-treatment @ P5-CD34-rep2

value: treatment @ P5-CD34


title: GR MUT DexLPS rep3

city: Freising

first: Franziska

last: Greulich

address: Gregor-Mendel-Str. 2

department: Metabolic Programming

country: Germany

institute: TU München

description:
GAR1245
C437G_DexLPSEffect_MEFs_unfiltered_DESeq.txt

data_processing:
The reads were mapped to the mouse genome mm10 (Ensembl build 38.91) and reads per gene counted using STAR version 2.4.2a with the following settings: --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 -- alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 100000 --quantMode GeneCounts.
Quality control was performed by fastQC and unsupervised sample clustering by PCA to identify outliers.
Counts were filtered for their expression strength by selecting only genes with counts above 200 as expressed. Gene count normalization and differential expression analysis was performed with DESeq2. Thresholds for genes being differential expressed were abs(log2FoldChange)>0.58 (approx. 1.5x fold-change) and an adjusted p-value < 0.05.
For gene annotation Ensembl Transcript Ids were mapped to mgi_symbol using the Bioconductor package biomaRt version 2.32.1 and information from Ensembl (build 38.91).
Genome_build: mm10
Supplementary_files_format_and_content: „_STARReadsPerGene.out“ files contain the raw read counts per transcript as determined by STAR aligner version 2.4.2.   column1 = gene ID; column2 = read counts if strandness is ignored (the sum of columns 3 and 4); column3 = read counts covering all exons of the specified gene mammping the 1st strand of the DNA (e.g: sense mRNA); column4 = read counts covering all exons of the specified gene mammping the 2nd strand of the DNA (e.g. anti-sense mRNA); „_DESeq.txt“ files contain the unfiltered results from the DESeq2 analysis for differential expression on Dex-treated vs. Vehicle-treated wild-type and GR Zn/Zn mutant MEFs or on Dex+LPS-treated vs. LPS-treated wild-type and GR Zn/Zn mutant MEFs , respectively (as indicated in the file name).

source_name: 16h 1µM Dex in EtOH + 6h 100ng/ul LPS in PBS

growth_protocol: MEFs generation: C57BL/6 male mouse embryos from either wild-type or GR Zn/Zn were harvested at 13.5 days after vaginal plug formation. Internal organs (mainly heart and liver) and head were removed and embryos were minced and digested with Trypsin 10-15min at 37°C. MEFs were cultured for 7 days in high glucose DMEM incl. 10% FBS and 1% Pen/Strep.

extract_protocol:
RNA was extracted with RNeasy minikit (Qiagen). All samples were DNAse-treated using DNaseI from the Qiagen kit.  The quality of the RNA was verified by Agilent 2100 Bioanalyzer with RNA 6000Nano Reagents (Agilent Technologies).
Library preparation and rRNA depletion was performed using the TruSeq Stranded mRNA Library Prep Kit (Illumina) according to manufacture's manual. 500 ng RNA were used as input for each sample.

treatment_protocol: 16h EtOH (vehicle), 16h 1uM Dex in EtOH (Dex), 16h 1uM Dex in EtOH + 6h 100ng/ul LPS (Dex+LPS) or 16h EtOH + 6h 100 ng/ul LPS (LPS) as indicated in sample description

value: mouse embryonic fibroblasts (MEFs)

value: GR Zn / Zn

tag: Sex


title: pup OIR-treatment @ P5-CD34-rep3


title: GR MUT DexLPS rep2

description:
GAR1244
C437G_DexLPSEffect_MEFs_unfiltered_DESeq.txt


title: pup OIR-treatment @ P12-ECFC-rep3

value: treatment @ P12-ECFC


title: pup OIR-treatment @ P5-ECFC-rep2


title: pup OIR-treatment @ P5-saline-rep1

value: treatment @ P5-saline


title: pup OIR-treatment @ P5-CD34-rep1


title: pup OIR-treatment @ P5-saline-rep3


title: GR MUT LPS rep3

description:
GAR1242
C437G_DexLPSEffect_MEFs_unfiltered_DESeq.txt

source_name: 6h 100ng/ul LPS in PBS


title: GR MUT DexLPS rep1

description:
GAR1243
C437G_DexLPSEffect_MEFs_unfiltered_DESeq.txt


title: pup OIR-treatment @ P5-ECFC+CD34-rep2


title: pup OIR-treatment @ P5-ECFC-rep3


title: GR MUT LPS rep2

description:
GAR1318
C437G_DexLPSEffect_MEFs_unfiltered_DESeq.txt


title: pup OIR-treatment @ P5-ECFC+CD34-rep1


title: pup OIR-treatment @ P12-ECFC+CD34-rep3

value: treatment @ P12-ECFC+CD34


title: GR MUT LPS rep1

description:
GAR1240
C437G_DexLPSEffect_MEFs_unfiltered_DESeq.txt


title: pup OIR-treatment @ P12-ECFC+CD34-rep1


title: pup OIR-treatment @ P12-CD34-rep2

value: treatment @ P12-CD34


title: pup OIR-treatment @ P12-CD34-rep1


title: pup OIR-treatment @ P12-ECFC-rep1


title: pup OIR-treatment @ P12-saline-rep3

value: treatment @ P12-saline


title: pup OIR-treatment @ P12-ECFC-rep2

value: OIR model


title: GR MUT Dex rep3

description:
GAR1239
C437G_DexEffect_MEFs_unfiltered_DESeq.txt

source_name: 16h 1µM Dex in EtOH


title: pup OIR-treatment @ P12-CD34-rep3


title: pup OIR-treatment @ P12-saline-rep2


title: pup OIR-treatment @ P12-saline-rep1


title: pup OIR-treatment @ P5-saline-rep2


title: GR MUT Dex rep2

description:
GAR1238
C437G_DexEffect_MEFs_unfiltered_DESeq.txt


title: GR MUT CTR rep1

description:
GAR1317
C437G_DexEffect_MEFs_unfiltered_DESeq.txt

source_name: vehicle, EtOH


title: GR MUT CTR rep2

description:
GAR1235
C437G_DexEffect_MEFs_unfiltered_DESeq.txt


title: pup OIR-treatment @ P12-ECFC+CD34-rep2


title: Lactoferrin knockout (Lf-/-) mouse 1, paracancerous lung tissue

city: Changsha

first: Jian

last: Ma

state: Hunan

address: 110  Xiangya  Road

department: Cancer  Research Institute

country: China

institute: Central South University

description:
Lf-/- mouse 1 injected with B16-F10 cells
KO1

data_processing:
Raw data (raw reads) were processed using NGS QC Toolkit. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads. Then the clean reads were mapped to reference human genome using Tophat.
FPKM value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq-count. DEGs were identified using the DESeq functions estimate Size Factors and nbinomTest. P value < 0.05 was set as the threshold for significantly differential expression. Hierarchical cluster analysis of DEGs was performed to explore genes expression pattern. GO enrichment and KEGG pathway enrichment analysis of DEGs were respectively performed using R based on the hypergeometric distribution.
Genome_build: mouse genome GRCm38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each samples

source_name: Lf-/- mouse injected with B16-F10 cells

growth_protocol: Mice were maintained in Central Sourth University Animal Facility according to the Institutional Animal Care Guidelines. All animals were housed in plastic cages (5 mice/cage) with free access to distilled water and a standard diet under specific-pathogen free (SPF) conditions of humidity (50±10%), lightning (12-h light/dark cycle) and temperature (24±0.5℃).

extract_protocol:
mirVana miRNA ISOlation Kit (Ambion#1561) extraction of RNA was performed according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Solexa protocols.

treatment_protocol: 8-week-old male  WT or Lf-/-mice were injected  2×10^5 B16-F10 cells through tail vein (each group has 10 mice). Mice were killed at the end of the third week. Lung tissues around the metastatic colonies (but without tumor cells) were harvested.

value: paracancerous lung tissue


title: Lactoferrin knockout (Lf-/-) mouse 2, paracancerous lung tissue

description:
Lf-/- mouse 2 injected with B16-F10 cells
KO2


title: GR WT DexLPS rep1

description:
GAR1231
wt_DexLPSEffect_MEFs_unfiltered_DESeq.txt

value: GR wt / wt


title: GR WT LPS rep3

description:
GAR1230
wt_DexLPSEffect_MEFs_unfiltered_DESeq.txt


title: GR WT Dex rep3

description:
GAR1227
Wt_DexEffect_MEFs_unfiltered_DESeq.txt


title: GR WT DexLPS rep2

description:
GAR1232
wt_DexLPSEffect_MEFs_unfiltered_DESeq.txt


title: GR WT LPS rep2

description:
GAR1229
wt_DexLPSEffect_MEFs_unfiltered_DESeq.txt


title: WT mouse 1, paracancerous lung tissue

description:
WT mouse 1 injected with B16-F10 cells
WT1

source_name: WT mouse injected with B16-F10 cells

value: WT


title: GR WT Dex rep2

description:
GAR1226
Wt_DexEffect_MEFs_unfiltered_DESeq.txt

value: male


title: GR WT DexLPS rep3

description:
GAR1316
wt_DexLPSEffect_MEFs_unfiltered_DESeq.txt


title: GR MUT Dex rep1

description:
GAR1237
C437G_DexEffect_MEFs_unfiltered_DESeq.txt


title: GR WT CTR rep2

description:
GAR1223
Wt_DexEffect_MEFs_unfiltered_DESeq.txt


title: GR WT CTR rep3

description:
GAR1224
Wt_DexEffect_MEFs_unfiltered_DESeq.txt


title: GR WT Dex rep1

description:
GAR1225
Wt_DexEffect_MEFs_unfiltered_DESeq.txt


title: GR WT CTR rep1

description:
GAR1222
Wt_DexEffect_MEFs_unfiltered_DESeq.txt


title: control group, rep1

city: Valencia

first: Francisco

middle: García

last: García

address: Eduardo Primo Yúfera, 3

department: Bionformatics & Biostatistics Unit

country: Spain

institute: CIPF

description: non-alcoholic fatty liver disease

hyb_protocol: All samples were hybridized using a Hybridization Oven 645 (Affymetrix) for 16h at 45°C. GeneChips were washed in the Fluidics Station 450 (Affymetrix), using fluidics script FS450_0002 (Affymetrix).

scan_protocol: All samples were scanned using GeneChip Scanner 3000 7G (Affymetrix).

data_processing: Data was standardized using Robust Multi-array Average method and quantile normalization.  Differential gene expression was carried out using the limma  package  from Bioconductor.

source_name: liver

label_protocol: RNA 6000 Nano Lab-on-a-Chip kit and the Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA) were used to determine the integrity of the samples. Afterwards, Affimetrix  WT Plus Reagent Kit was used and all samples were normalized to 300 ng of RNA.

growth_protocol: Wild-type C57BL/6 mice were fed with normal of high fat (60%) diet for 3 months, and treated with RPV (p.o.) on a daily basis at clinically relevant doses (equivalent to those used in humans)

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. Afterwards Genequant Pro Classic spectrophotometer (GE Healthcare, Little Chalfont, UK) kit was used to assess the purity and RNA concentration of the samples

treatment_protocol: After extraction of animal liver tissue, samples were rapidly snap-frozen in liquid nitrogen and kept at -80 °C until further manipulation

value: liver

value: control


title: control group, rep3

description: non-alcoholic fatty liver disease


title: rilpivirine group, rep4

description: non-alcoholic fatty liver disease + rilpivirine

value: rilpivirine treatment


title: rilpivirine group, rep3


title: control group, rep2

description: non-alcoholic fatty liver disease


title: rilpivirine group, rep2


title: KURC3_Tem_P4_#1

type: genomic

city: Kyoto

first: Hiromasa

last: sakamoto

address: 54 Shogoinkawahara-cho, Sakyo-ku,

institute: Kyoto University Graduate School of Medicine

description: DNA methylation data from patient-derived xenograft tumor (KURC3) treated with temsirolimus.

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to the Illumina Infinium HumanMethylation450 BeadChip using standard Illumina protocol

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

data_processing: Data processing was performed using Illumina GenomeStudio V2011.1 and Methylation Module version 1.9.0.

label: Cy5 and Cy3

source_name: KURC3 (temsirolimus)

label_protocol: Standard Illumina protocol

growth_protocol: We kept a patient-derived xenograft models (KURC;Kyoto University Renal Cancer-3) derived from human renal cell carcinoma tissues.

extract_protocol: Total DNA was extracted using QIAamp DNA mini kit (Qiagen, Hilden, Germany), according to the manufacturer’s instructions.

treatment_protocol: Ten mg/kg temsirolimus or vehicle only was intraperitoneally administered once a week.Once xenograft tumors had developed sufficiently, they were removed and transplanted into other SCID mice. Two weeks later, temsirolimus was re-administered to these mice, and this was repeated until tumors became completely resistant to temsirolimus

value: renal cancer patient-derived xenograft tumor


title: rilpivirine group, rep1


title: control group, rep4

description: non-alcoholic fatty liver disease


title: Ex6DEL_GN3

city: Ottawa

first: David

last: Picketts

address: 501 Smyth Rd

country: Canada

institute: Ottawa Hospital Research Institute

data_processing:
Pseudoalignment to GRCm38 (release 88) with kallisto (v0.44.0)
Quantification by Sleuth (v0.29.0)
Genome_build: GRCm38
Supplementary_files_format_and_content: Paired reads were merged with bowtie2, sorted and normalized to RPKM

source_name: Cerebellar Granule Neuron

growth_protocol: GNPs were isolated from P4-P6 murine cerebella and plated in serum-free NeurobasalA media (Lee et al., 2009)

extract_protocol:
RNA was extracted in Trizol and purified by PureLink RNA cleanup kit (Thermo Fisher, cat 12183020) with in-column DNaseI treatment
NEB mRNA stranded library preparation was carried out following Bioanalyser analysis of RNA

treatment_protocol: GNPs collected either 2h after plating or allowed to differentiate into GNs in vitro for 72h

value: Cerebellar Granule Neuron

value: FVB/N

value: loss of Snf2l activity (Ex6DEL)

tag: differentiation

value: differentiated


title: KURC3_Veh_P4_#1

description: DNA methylation data from patient-derived xenograft tumor (KURC3) treated with vehicle.

source_name: KURC3 (vehicle)


title: Ex6DEL_GN2


title: Ex6DEL_GN1


title: Ex6DEL_GNP3

source_name: Cerebellar Granule Neuron Progenitor

value: Cerebellar Granule Neuron Progenitor

value: undifferentiated


title: Ex6DEL_GNP2


title: genomic DNA from normal colon sample 121

city: Seattle

first: Ting

last: Wang

state: WA

address: 1100 Fairview Ave. N.

department: Clinical Research

institute: Fred Hutchinson Cancer Research Center

description: normal colon sample

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation450 and EPIC Beadchip arrays using standard Illumina protocol

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

data_processing: Raw IDAT files of the two methylation arrays were read into R with the minfi package separately, the combineArrays function was utilized to combine the two arrays’ data together. Then the data was preprocessed with background and dye bias correction using the Noob method, following by the Functional normalization. CpG probes that were SNP-associated, cross-reactive, located on sex chromosomes and unreliably detected (>10% of samples with detection P-value > 0.01), with the exception of those epigenetic clock CpGs, were excluded from the analysis

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA samples were extracted from the fresh frozen normal colon mucosa tissue samples using the DNeasy Blood and Tissue Kit (Qiagen). Genomic DNA quantification was performed using the Quant-iT PicoGreen DNA assay kit (Life Technologies). 500 ng of DNA from each sample was bisulfite converted using the EZ DNA Methylation Kit (Zymo Research, Irvine, USA)

tag: source

value: GICaRes

tag: array platform_id

tag: run date

value: M

tag: crc risk

value: Low


title: genomic DNA from normal colon sample 125

description: normal colon sample

value: ColoCare

value: High


title: Ex6DEL_GNP1

tag: tissue

tag: genotype


title: genomic DNA from normal colon sample 119

description: normal colon sample


title: genomic DNA from normal colon sample 115

description: normal colon sample


title: genomic DNA from normal colon sample 116

description: normal colon sample

value: F


title: genomic DNA from normal colon sample 111

description: normal colon sample

value: Medium


title: genomic DNA from normal colon sample 122

description: normal colon sample


title: GR WT LPS rep1

description:
GAR1228
wt_DexLPSEffect_MEFs_unfiltered_DESeq.txt

value: mouse embryonic fibroblasts (MEFs)

tag: strain

value: GR wt / wt

value: male


title: WT mouse 2, paracancerous lung tissue

description:
WT mouse 2 injected with B16-F10 cells
WT2

value: WT

value: paracancerous lung tissue


title: genomic DNA from normal colon sample 114

description: normal colon sample

tag: age


title: genomic DNA from normal colon sample 127

description: normal colon sample


title: WT_GN3

value: Cerebellar Granule Neuron

value: FVB/N

value: wild type


title: genomic DNA from normal colon sample 113

description: normal colon sample


title: genomic DNA from normal colon sample 120

description: normal colon sample


title: genomic DNA from normal colon sample 112

description: normal colon sample


title: WT_GN2

value: differentiated


title: WT_GN1


title: genomic DNA from normal colon sample 118

description: normal colon sample


title: genomic DNA from normal colon sample 107

description: normal colon sample


title: genomic DNA from normal colon sample 117

description: normal colon sample


title: genomic DNA from normal colon sample 126

description: normal colon sample


title: genomic DNA from normal colon sample 128

description: normal colon sample


title: genomic DNA from normal colon sample 124

description: normal colon sample


title: genomic DNA from normal colon sample 106

description: normal colon sample


title: genomic DNA from normal colon sample 110

description: normal colon sample


title: WT_GNP2

value: Cerebellar Granule Neuron Progenitor

value: undifferentiated


title: genomic DNA from normal colon sample 103

description: normal colon sample

value: GICaRes

value: M


title: genomic DNA from normal colon sample 105

description: normal colon sample


title: genomic DNA from normal colon sample 108

description: normal colon sample

value: Low


title: WT_GNP1


title: genomic DNA from normal colon sample 123

description: normal colon sample

value: ColoCare

value: High


title: genomic DNA from normal colon sample 109

description: normal colon sample

value: F

value: Medium


title: genomic DNA from normal colon sample 104

description: normal colon sample


title: genomic DNA from normal colon sample 101

description: normal colon sample


title: genomic DNA from normal colon sample 102

description: normal colon sample


title: genomic DNA from normal colon sample 99

description: normal colon sample


title: genomic DNA from normal colon sample 96

description: normal colon sample


title: genomic DNA from normal colon sample 93

description: normal colon sample


title: genomic DNA from normal colon sample 84

description: normal colon sample


title: WT_GNP3


title: genomic DNA from normal colon sample 85

description: normal colon sample


title: genomic DNA from normal colon sample 97

description: normal colon sample


title: genomic DNA from normal colon sample 88

description: normal colon sample


title: genomic DNA from normal colon sample 92

description: normal colon sample


title: genomic DNA from normal colon sample 86

description: normal colon sample


title: genomic DNA from normal colon sample 94

description: normal colon sample


title: genomic DNA from normal colon sample 98

description: normal colon sample


title: genomic DNA from normal colon sample 83

description: normal colon sample


title: genomic DNA from normal colon sample 81

description: normal colon sample


title: genomic DNA from normal colon sample 80

description: normal colon sample


title: genomic DNA from normal colon sample 91

description: normal colon sample


title: genomic DNA from normal colon sample 77

description: normal colon sample


title: genomic DNA from normal colon sample 87

description: normal colon sample


title: genomic DNA from normal colon sample 90

description: normal colon sample


title: genomic DNA from normal colon sample 78

description: normal colon sample


title: genomic DNA from normal colon sample 89

description: normal colon sample


title: genomic DNA from normal colon sample 72

description: normal colon sample


title: genomic DNA from normal colon sample 79

description: normal colon sample


title: genomic DNA from normal colon sample 82

description: normal colon sample


title: genomic DNA from normal colon sample 74

description: normal colon sample


title: genomic DNA from normal colon sample 100

description: normal colon sample


title: genomic DNA from normal colon sample 76

description: normal colon sample


title: genomic DNA from normal colon sample 71

description: normal colon sample


title: genomic DNA from normal colon sample 73

description: normal colon sample


title: genomic DNA from normal colon sample 75

description: normal colon sample


title: genomic DNA from normal colon sample 95

description: normal colon sample


title: genomic DNA from normal colon sample 69

description: normal colon sample


title: RND3_S48_166

city: Bergen

first: Laurence

middle: William-Joseph

last: Dyer

address: Haukelandsveien 22

department: Clinical Institute

country: Norway

institute: University of Bergen

data_processing:
Illumina Casava v1.8
Reads were aligned to the Human reference genome (GrCH38) using HiSat (Version 2.10.0), with options “hisat2-align-s --wrapper basic-0 -p 140”
Aligned reads were then put into featureCounts (Version 1.5.2) with options “featureCounts -T 64 -p -t exon -g gene_id”
Differential expression analysis was performed via DESeq2 (Version 1.14.1)
Genome_build: GrCH38
Supplementary_files_format_and_content: tab-delimited text files include DESeq2 normalised counts for each Sample ...

source_name: Adipose

growth_protocol: The stromal vascular fraction (SVF) from subcutaneous adipose tissue was isolated as previously described (Lee and Fried, 2014) with some modifications. Briefly, KRP-buffer containing Liberase Blendzyme 3 (Roche) and DNase was used to enzymatically digest the liposuction aspirate. Following a 1-hour incubation at 37°C, the digested fat tissue was filtered and the SVF was extracted by repetitive washing with 0.9% NaCl followed by pelleting cells by centrifugation. Red blood cells were lysed using a buffer containing NH 4 Cl (155 mM), K 2 HPO 4 (5.7 mM) and EDTA (0.1 mM). Thereafter, SVF was cultured in GlutaMAX DMEM (Thermo Fisher) supplemented with 10% fetal bovine serum (FBS) and 50 μg/ml gentamicin (Sigma) and grown at 37°C with 5% CO 2 . Adipocyte progenitor cells were counted before seeding. The day after seeding of isolated SVF, adipogenic differentiation was induced by supplementing the culture medium with 33 μM biotin, 1 nM triiodothyronine, 17 μM DL-pantothenate, 10 μg/ml transferrin, 66 nM insulin, 100 nM cortisol, 15 mM Hepes and 10 μM rosiglitazone. Rosiglitazone was discontinued after 6 days and terminal differentiation was defined at 12-13 days.

extract_protocol:
Total RNA from human cell cultures was obtained using RNeasy kit (QIAGEN) and quality checked by QIAxpert spectrophotometer (QIAGEN) prior to cDNA synthesis with 200 ng RNA input using a high-capacity cDNA reverse transcription kit (Applied Biosystems). Sample cDNA was analyzed by Lightcycler480 (Roche) quantitative real-time PCR using SYBR Green dye (Roche) and target primers (Table S3). Relative mRNA expression was determined by standard curves and normalized to reference genes (Table S3) as indicated. qPCR was performed with duplicate technical reactions per biological sample and averaged for further analyses.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Individual samples were treated with either a control/vehicle RNA treament (siNT) or a targetted siRND3 KD treatment

value: Adipose

tag: treatment

value: 12 days

tag: patient


title: RND3_S28_162


title: RND3_S21_161


title: RND3_S34_163


title: RND3_S41_165


title: RND3_S14_160


title: NT_S44_166

value: siNT


title: genomic DNA from normal colon sample 67

description: normal colon sample

tag: gender


title: genomic DNA from normal colon sample 65

description: normal colon sample


title: genomic DNA from normal colon sample 70

description: normal colon sample


title: NT_S37_165


title: NT_S24_162


title: genomic DNA from normal colon sample 66

description: normal colon sample


title: genomic DNA from normal colon sample 64

description: normal colon sample


title: NT_S10_160


title: NT_S31_163


title: genomic DNA from normal colon sample 61

description: normal colon sample


title: genomic DNA from normal colon sample 54

description: normal colon sample


title: genomic DNA from normal colon sample 55

description: normal colon sample


title: genomic DNA from normal colon sample 60

description: normal colon sample


title: genomic DNA from normal colon sample 57

description: normal colon sample


title: genomic DNA from normal colon sample 56

description: normal colon sample


title: genomic DNA from normal colon sample 63

description: normal colon sample


title: genomic DNA from normal colon sample 58

description: normal colon sample


title: genomic DNA from normal colon sample 50

description: normal colon sample


title: genomic DNA from normal colon sample 59

description: normal colon sample


title: genomic DNA from normal colon sample 62

description: normal colon sample


title: genomic DNA from normal colon sample 48

description: normal colon sample


title: genomic DNA from normal colon sample 51

description: normal colon sample


title: genomic DNA from normal colon sample 52

description: normal colon sample


title: genomic DNA from normal colon sample 68

description: normal colon sample


title: PC3 ATAC-seq replicate 2

city: La Jolla

first: Paul

middle: S

last: Mischel

address: 9500 Gilman Dr.

institute: Ludwig Institute for Cancer Research

description: DNA

data_processing:
Bowtie2 for mapping, MarkDuplicates from Picard tools v1.119 to remove PCR duplicates, Samtools v1.3.1, MACS2 2.1.2 for peak calling.
Genome_build: hg19
Supplementary_files_format_and_content: tdf

growth_protocol: Human prostate cancer cell line PC3, colon cancer cell line COLO320DM and glioblastoma cell line U87 were purchased from ATCC and cultured in DMEM/F12 with 10% FBS. Human glioblastoma GBM39 tumor spheroid was derived from patient tissue, and cultured in DMEM/F12 with GlutaMAX, B27, 20 ng/ml EGF, 20 ng/ml FGF and 5 μg/ml heparin.

extract_protocol:
ATAC-seq: Briefly, 100-500K cell nuclei were extracted by NPB buffer (5% BSA, 0.2% IGEPAL-CA630, 1 mM DTT, EDTA-free protease, in PBS) at 4°C for 10 min. Tagmentation was done in TB buffer (33 mM Tris-acetate pH 7.8, 66 mM K-acetate, 11 mM Mg-acetate, 16% DMF) with Tn5 transposase (Illumina), at 37°C for 30 min. DNA samples were then extracted and DNA libraries were generated by PCR. ChIP-seq: Formaldehyde crosslinked chromatin from 5 million cells per ChIP was sheared to small fragments by Covaris M220 Focused-ultrasonicator. The following antibodies were used for chromatin pull-down in RIPA buffer with protease inhibitor cocktail: anti-H3K27ac (Active Motif 39685, 5 µg), anti-H3K4me1 (Active Motif 39297, 10 µl), anti-CTCF (Abcam ab70303, 5 µg), anti-SMC3 (Abcam ab9263, 5 µg). After capturing by Protein A/G magnetic beads, chromatin was washed 6 times and reverse-crosslinked for 3 hr with RNase A and Proteinase K.
DNA library was constructed by NEBNext Ultra II DNA Library Prep kit for paired-end sequencing.

treatment_protocol: No

value: Human prostate tumor


title: NT_S17_161


title: genomic DNA from normal colon sample 47

description: normal colon sample


title: PC3 ATAC-seq replicate 1

description: DNA


title: GBM39 ATAC-seq replicate 2

description: DNA

value: Human brain tumor


title: GBM39HSR ATAC-seq replicate 2

description: DNA


title: GBM39HSR ATAC-seq replicate 1

description: DNA


title: COLO320HSR ATAC-seq replicate 2

description: DNA

value: Human colon tumor


title: GBM39 ATAC-seq replicate 1

description: DNA


title: genomic DNA from normal colon sample 53

description: normal colon sample


title: genomic DNA from normal colon sample 36

description: normal colon sample


title: genomic DNA from normal colon sample 45

description: normal colon sample


title: genomic DNA from normal colon sample 44

description: normal colon sample


title: genomic DNA from normal colon sample 35

description: normal colon sample


title: genomic DNA from normal colon sample 38

description: normal colon sample


title: genomic DNA from normal colon sample 39

description: normal colon sample


title: COLO320DM ATAC-seq replicate 1

description: DNA


title: genomic DNA from normal colon sample 46

description: normal colon sample


title: genomic DNA from normal colon sample 34

description: normal colon sample


title: genomic DNA from normal colon sample 42

description: normal colon sample


title: genomic DNA from normal colon sample 49

description: normal colon sample


title: genomic DNA from normal colon sample 40

description: normal colon sample


title: genomic DNA from normal colon sample 37

description: normal colon sample


title: genomic DNA from normal colon sample 41

description: normal colon sample


title: COLO320HSR ATAC-seq replicate 1

description: DNA


title: genomic DNA from normal colon sample 31

description: normal colon sample


title: genomic DNA from normal colon sample 43

description: normal colon sample


title: genomic DNA from normal colon sample 29

description: normal colon sample


title: genomic DNA from normal colon sample 27

description: normal colon sample


title: genomic DNA from normal colon sample 23

description: normal colon sample


title: COLO320DM ATAC-seq replicate 2

description: DNA


title: genomic DNA from normal colon sample 33

description: normal colon sample


title: genomic DNA from normal colon sample 26

description: normal colon sample


title: genomic DNA from normal colon sample 28

description: normal colon sample


title: genomic DNA from normal colon sample 24

description: normal colon sample


title: genomic DNA from normal colon sample 22

description: normal colon sample


title: genomic DNA from normal colon sample 30

description: normal colon sample


title: genomic DNA from normal colon sample 32

description: normal colon sample


title: B6D2F1_beta-cell_rep2

city: Saga City

first: Keiichiro

last: Mine

state: Saga

address: 5-1-1 Nabeshima

institute: Saga university

hyb_protocol: cRNA was hybridized to Affymetrix  Clariom D Assay Mouse array, washed and stained according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Affymetrix scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The data were analyzed with median polish summarization and quantile normalization by Affymetrix® Expression Console™ 1.1 software, and obtained normalized intensity values.

source_name: Pancreatic beta-cell from B6D2F1, 2days after EMC-D virus infection, replicate2

label_protocol: The cRNA was amplified, labeled using GeneChip WT PLUS Reagent Kit according to the manufacturer's instructions.

extract_protocol: Total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions.

value: Pancretic beta-cell

value: male

value: 48hr after EMC-D virus infection


title: B6D2F1_beta-cell_rep3

source_name: Pancreatic beta-cell from B6D2F1, 2days after EMC-D virus infection, replicate3


title: genomic DNA from normal colon sample 21

description: normal colon sample


title: B6D2F1_beta-cell_rep1

source_name: Pancreatic beta-cell from B6D2F1, 2days after EMC-D virus infection, replicate1


title: genomic DNA from normal colon sample 20

description: normal colon sample


title: genomic DNA from normal colon sample 17

description: normal colon sample


title: genomic DNA from normal colon sample 14

description: normal colon sample


title: genomic DNA from normal colon sample 25

description: normal colon sample


title: genomic DNA from normal colon sample 10

description: normal colon sample


title: genomic DNA from normal colon sample 11

description: normal colon sample


title: DBA/2_beta-cel_rep3

source_name: Pancreatic beta-cell from DBA/2, 2days after EMC-D virus infection, replicate3


title: genomic DNA from normal colon sample 16

description: normal colon sample


title: genomic DNA from normal colon sample 19

description: normal colon sample


title: DBA/2_beta-cel_rep2

source_name: Pancreatic beta-cell from DBA/2, 2days after EMC-D virus infection, replicate2


title: genomic DNA from normal colon sample 4

description: normal colon sample


title: genomic DNA from normal colon sample 15

description: normal colon sample


title: genomic DNA from normal colon sample 8

description: normal colon sample


title: genomic DNA from normal colon sample 3

description: normal colon sample


title: genomic DNA from normal colon sample 12

description: normal colon sample


title: genomic DNA from normal colon sample 9

description: normal colon sample


title: genomic DNA from normal colon sample 13

description: normal colon sample


title: DBA/2_beta-cel_rep1

source_name: Pancreatic beta-cell from DBA/2, 2days after EMC-D virus infection, replicate1


title: B6_beta-cell_rep3

source_name: Pancreatic beta-cell from C57BL/6J, 2days after EMC-D virus infection, replicate3


title: genomic DNA from normal colon sample 6

description: normal colon sample


title: B6_beta-cell_rep2

source_name: Pancreatic beta-cell from C57BL/6J, 2days after EMC-D virus infection, replicate2


title: ID547_Control

city: Penrith

first: Christine

last: Chiu

state: NSW

address: Locked Bag 1797

country: Australia

institute: Western Sydney University

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation450 Beadchip using standard Illumina protocol

data_processing: Illumina Genome Studio software was used to extract the raw signal intensities of each probe (without background correction or normalization). Data was then pre-processed in the R package wateRmelon using the dasen function. processed data: dasen normalized beta

source_name: Saliva

extract_protocol: Genomic DNA was extracted using a DNeasy Blood & Tissue Kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol.

value: Female

tag: disease status

value: Control


title: B6_beta-cell_rep1

source_name: Pancreatic beta-cell from C57BL/6J, 2days after EMC-D virus infection, replicate1


title: KO-COLD-5

city: Shanghai

first: Yuli

last: Lin

address: No.130, Dong'an Road, Xuhui

institute: Fudan University

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using SOAPnuke, then mapped to reference whole genome using bowtie.
Mapped reads were count, and Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: inguinal fat

extract_protocol:
The inguinal white adipose was collected and total RNA was harvested with RNeasy Lipid Tissue Mini Kit (Qiagen, Hilden, Germany) according to the instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

value: iWAT


title: KO-COLD-4


title: genomic DNA from normal colon sample 5

description: normal colon sample


title: KO-COLD-6


title: genomic DNA from normal colon sample 7

description: normal colon sample

value: M


title: genomic DNA from normal colon sample 1

description: normal colon sample

value: ColoCare


title: ID507_Control

value: Male


title: genomic DNA from normal colon sample 18

description: normal colon sample

value: GICaRes


title: WT-COLD-1

value: WT


title: WT-COLD-3


title: ID510_Control


title: WT-COLD-2


title: ID500_Coeliac

value: Coeliac


title: ID535_Control


title: ID501_Coeliac


title: ID506_Control


title: ID497_Coeliac


title: ID493_Coeliac


title: ID472_Coeliac


title: ID483_Control


title: ID479_Control


title: ID471_Coeliac


title: spleen_2_3

city: Zurich

first: giancarlo

last: russo

state: Schweiz

address: winterthurerstrasse 190

department: Functional Genomics Center Zurich

country: Switzerland

institute: ETH/University of Zurich

data_processing:
bcl2Fastq v2.19 software used for demultiplexing + basecalling.
reads trimmed with trimmomatic, options: ILLUMINACLIP:adapters.fa:1:20:7:5:true AVGQUAL:10 MINLEN:20
reads mapped with STAR  v2.3, options: --sjdbOverhang 150 --twopassMode None --runThreadN 8 --outFilterType BySJout --outFilterMatchNmin 30 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05 --outMultimapperOrder Random --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMultimapNmax 50 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --chimScoreMin 15 --chimScoreSeparation 10 --outSAMstrandField intronMotif --outSAMattributes All --outStd BAM_Unsorted --outSAMtype BAM Unsorted
count: CountOvelap (Bioconductor), options minFeatureOverlap=10; minMapQuality= 10 ; keepMultiHits=true
differential expression analysis: EdgeR, options: normMethod = TMM; backgroundExpression =10; testMethod = glm; deTest =QL
Genome_build: Mm10
Supplementary_files_format_and_content: tab-separated value files with the output from countOverlap

source_name: spleen

extract_protocol:
Brains were removed, flash frozen on liquid nitrogen, and RNA was harvested using Trizol reagent and cleaned up using RNeasy kit. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 500ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: spleen

value: 2 months

value: AC H6


title: ID444_Control


title: ID446_Control


title: ID454_Control


title: spleen_2_2


title: spleen_2_1


title: ID443_Control


title: ID415_Control


title: spleen_1_3

value: isotype


title: ID412_Control


title: ID398_Control


title: duodenum_2_3

source_name: duodenum

value: duodenum


title: spleen_1_1


title: duodenum_2_2


title: ID429_Control


title: ID457_Control


title: spleen_1_2


title: duodenum_2_1


title: ID319_Coeliac


title: ID411_Control


title: ID463_Control


title: ID417_Control


title: ID313_Coeliac


title: duodenum_1_2


title: genomic DNA from normal colon sample 2

description: normal colon sample

value: High


title: duodenum_1_3


title: duodenum_1_1


title: ID393_Control


title: ID302_Coeliac


title: ID270_Coeliac


title: ID271_Coeliac


title: ID388_Coeliac


title: ID238_Coeliac


title: ID416_Control


title: ID401_Control


title: ID458_Control


title: ID447_Control


title: ID287_Coeliac


title: ID256_Coeliac


title: EGFRdEP-K5-SOS [JK-1_12]

city: Vienna

first: Thomas

last: Mohr

address: Borschkegasse 8a

department: Institute of Cancer Research

country: Austria

institute: Medical University of Vienna

data_processing:
BaseSpace Workflow 1.1.0
STAR (2.5.0b) Alignment, params: outSAMtype BAM SortedByCoordinate  limitBAMsortRAM 12000000000  outSAMunmapped Within  OutSAMmapqUnique 50  outFilterType BySJout  outSJfilterCountUniqueMin -1 2 2 2  outSJfilterCountTotalMin -1 2 2 2  outFilterIntronMotifs RemoveNoncanonical  twopassMode Basic
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text file with gene symbol and counts

source_name: Skin biopsy

extract_protocol:
Trizol extraction according to the instructions of the manufacturer (RNeasy Kit, Qiagen)
NEBNext Ultra™ Directional RNA Library Prep Kit for Illumina according to manufacturer’s protocols (New England Biolabs)

tag: mouse

tag: genotype/variation


title: EGFRdEP-K5-SOS [JK-1_11]


title: ID178_Coeliac


title: ID205_Coeliac


title: EGFdEP-AB [JK-1_9]

value: antibiotics

value: EGFdEP-AB


title: ID63_Coeliac

value: Female


title: ID125_Coeliac


title: EGFdEP-AB [JK-1_8]


title: ID47_Coeliac


title: ID27_Control

value: Control


title: ID43_Coeliac


title: ID175_Coeliac


title: ID52_Coeliac


title: ID30_Control


title: ID194_Coeliac


title: ID257_Coeliac


title: ID68_Coeliac


title: ID237_Coeliac


title: EGFdEP-AB [JK-1_7]


title: ID239_Coeliac


title: EGFRdEP [JK-1_6]

value: EGFRdEP


title: EGFRdEP [JK-1_5]


title: EGFRdEP-K5-SOS [JK-1_10]


title: ID6_PostGFDiet

tag: diet status

value: Post GF Diet


title: ID24_Control


title: Wildtype [JK-1_3]

value: Wildtype


title: ID5_PostGFDiet

value: Male


title: ID5_Control


title: ID2_PostGFDiet


title: ID241_Coeliac


title: EGFRdEP [JK-1_4]


title: Wildtype [JK-1_1]


title: ID3_PostGFDiet


title: Wildtype [JK-1_2]


title: ID251_Coeliac


title: ID1_PostGFDiet


title: ID67_Coeliac


title: 24-B-7

city: Chuo-ku

first: Yusuke

last: Yamamoto

state: Tokyo

address: 5-1-1, Tsukiji, Chuo-ku

institute: National cancer center research institute

description: Isolation of total RNA, 100 ng RNA for analysis

hyb_protocol: Gene Expression Hybridization Kit and Gene Expression Wash Pack (Agilent)

scan_protocol: Agilent SureScan G4900DA

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: primary tumor tissue needle-biopsy

label_protocol: Low Input Quick Amp Labeling Kit (Agilent Technologies)

extract_protocol: Total RNA was extracted using QIAzol and the RNeasy Mini Kit (Qiagen, Hilden, Germany) according to manufacturer’s protocols. RNA was quantified using a NanoDrop-1000 spectrophotometer and a Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, Calif.).

treatment_protocol: Isolation of total RNA from ER-positive breast primary tumor tissues.

tag: cell

value: breast invasive ductal carcinoma

tag: recurrence status

value: recurrence

tag: subtype

value: Luminal B


title: 21-B-5


title: 23-B-6-2


title: ID4_PostGFDiet


title: 25-B-8


title: 19-B-3

value: Luminal A


title: 18-B-2


title: 20-B-4


title: 13-A-13

value: non-recurrence


title: 17-B-1-2


title: 15-A-14-2


title: ID5_PreGFDiet

value: Pre GF Diet


title: ID6_PreGFDiet


title: ID2_PreGFDiet


title: ID3_PreGFDiet


title: 252364710493___2

city: St Lucia

first: Sean

last: McWilliam

state: Queensland

address: 306 Carmody Road

department: Agriculture and Food

institute: CSIRO

description:
LDM_HER_PAST_2
gene expresson after 259 d in a feedlot

hyb_protocol: 1.65 ug of fragmented, labeled cRNA  was prepared for hybridisation. Samples were hybridised to arrays for 17 hours at 45 degree C rotating at 10 rpm in the Agilent hybridisation oven. Arrays were washed using Gene Expression Wash buffer kit in a slide staining dish with slide rack.

scan_protocol: Arrays were scanned in the Agilent C scanner using the AgilentHD_GX_1 color protocol

data_processing: We applied the base-2 log-transformation followed by a normalization using a previously described mixed model approach (Reverter et al. 2004.  Bioinformatics 21:1112-1120. https://doi.org/10.1093/bioinformatics/bti124). In brief, the mixed model contained the fixed effect of library sample with 96 levels and the random effects of gene, gene by breed interaction, gene by tissue interaction and residual.

organism: Bos taurus

label_protocol: We used the Agilent one colour microarray based gene expression analysis low input Quick Amp labeling. We used an input of 50 ng of total RNA

growth_protocol: 259 d in a feedlot

extract_protocol: RNA was prepared using the phenol chloroform extraction methodology with Trizol reagent

treatment_protocol: post-slaughter tissue samples were dissected in an abattoir and snap frozen prior to RNA extraction

tag: fat depot

tag: breed

value: HEREFORD

tag: feeding protocol

tag: replicate number

value: 259 days


title: 252364710493___4

description:
LDM_HER_PAST_4
gene expresson after 259 d in a feedlot


title: 12-A-12


title: 11-A-11


title: 252364710493___3

description:
LDM_HER_PAST_3
gene expresson after 259 d in a feedlot


title: ID1_PreGFDiet


title: 252364710492___4

description:
LDM_ANG_PAST_4
gene expresson after 259 d in a feedlot

value: ANGUS


title: 7-A-7


title: 26-B-9


title: 252364710492___3

description:
LDM_ANG_PAST_3
gene expresson after 259 d in a feedlot


title: 4-A-4


title: 10-A-10


title: 252364710491___2

description:
KID_WAG_PAST_2
gene expresson after 259 d in a feedlot


title: 6-A-6


title: 252364710491___3

description:
KID_HER_PAST_3
gene expresson after 259 d in a feedlot


title: 5-A-5


title: 252364710491___4

description:
KID_HER_PAST_4
gene expresson after 259 d in a feedlot


title: 8-A-8


title: 3-A-3


title: 9-A-9


title: 27-B-10

value: breast invasive lobular carcinoma


title: 252364710493___1

description:
LDM_HER_PAST_1
gene expresson after 259 d in a feedlot


title: 2-A-2


title: 252364710492___1

description:
LDM_ANG_PAST_1
gene expresson after 259 d in a feedlot


title: 252364710492___2

description:
LDM_ANG_PAST_2
gene expresson after 259 d in a feedlot


title: 252364710491___1

description:
KID_WAG_PAST_1
gene expresson after 259 d in a feedlot


title: 1-A-1


title: 252364710490___4

description:
KID_WAG_PAST_4
gene expresson after 259 d in a feedlot


title: 252364710490___3

description:
KID_WAG_PAST_3
gene expresson after 259 d in a feedlot


title: 252364710489___1

description:
LDM_WAG_PAST_1
gene expresson after 259 d in a feedlot


title: 252364710489___3

description:
LDM_WAG_PAST_3
gene expresson after 259 d in a feedlot


title: 252364710489___2

description:
LDM_WAG_PAST_2
gene expresson after 259 d in a feedlot


title: 252364710489___4

description:
LDM_WAG_PAST_4
gene expresson after 259 d in a feedlot


title: 252364710488___2

description:
KID_ANG_PAST_2
gene expresson after 259 d in a feedlot


title: 252364710486___3

description:
SCF_HER_PAST_3
gene expresson after 259 d in a feedlot


title: 252364710488___4

description:
OME_HER_PAST_4
gene expresson after 259 d in a feedlot


title: 252364710490___1

description:
KID_HER_PAST_1
gene expresson after 259 d in a feedlot


title: ID4_PreGFDiet


title: 252364710488___3

description:
OME_ANG_PAST_3
gene expresson after 259 d in a feedlot


title: 252364710487___3

description:
IMF_WAG_PAST_3
gene expresson after 259 d in a feedlot


title: 252364710487___2

description:
IMF_ANG_PAST_2
gene expresson after 259 d in a feedlot


title: 252364710487___4

description:
IMF_HER_PAST_4
gene expresson after 259 d in a feedlot


title: 252364710486___4

description:
KID_ANG_PAST_4
gene expresson after 259 d in a feedlot


title: 252364710487___1

description:
IMF_ANG_PAST_1
gene expresson after 259 d in a feedlot


title: 252364710486___1

description:
SCF_ANG_PAST_1
gene expresson after 259 d in a feedlot


title: 252364710485___4

description:
SCF_HER_PAST_4
gene expresson after 259 d in a feedlot


title: 252364710485___3

description:
SCF_WAG_PAST_3
gene expresson after 259 d in a feedlot


title: 252364710485___2

description:
SCF_WAG_PAST_2
gene expresson after 259 d in a feedlot


title: 252364710488___1


title: 252364710484___3


title: 252364710486___2

description:
SCF_HER_PAST_2
gene expresson after 259 d in a feedlot


title: 252364710484___4

description:
SCF_ANG_PAST_4
gene expresson after 259 d in a feedlot


title: Total RNA 3

city: Philadelphia

first: Austin

middle: Lewis

last: Good

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

description: Total RNA

data_processing:
Illumina used for basecalling
Data was aligned to mm10 using TopHat2
Read counts per gene were determined using featureCounts
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files of raw counts

source_name: Mouse insulinoma cell line

growth_protocol: Min6 cells were grown in high glucose DMEM

extract_protocol:
Min6 cells were lysed in buffer containing 50mM Tris pH 8.0, 150mM NaCl, and 1% NP-40 with RNase, protease, and phosphatase inhibitors. Total RNA was extracted from lysate (10% input) using RNeasy Mini Kit. Lysate encompassing 200ug of protein was added to beads bound to antibody for hnRNPK (Bethyl Laboratories, A300-674A), then incubated overnight at 4C. The next day, IPs were washed with buffer containing 20mM HEPES pH 7.4, 5mM MgCl2, 350mM KCl, 2mM DTT, 1% NP-40, and RNase inhibitors. RNA was eluted from beads in RLT buffer and RNA was isolated using RNeasy Mini Kit, including on-column DNase digestion.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Min6 cells were treated with 25mM glucose and 500uM palmitic acid for 30 hours prior to harvesting.

tag: cell line

value: Min6 cells

tag: passage

value: glucolipotoxicity


title: Total RNA 2

description: Total RNA


title: 252364710484___2

tag: age


title: Total RNA 1

description: Total RNA

tag: treatment


title: hnRNPK IP 3

description: IP RNA


title: hnRNPK IP 2

description: IP RNA


title: 252364710483___4

description:
LDM_HER_PAST_4
gene expresson after 259 d in a feedlot


title: 252364710483___3

description:
LDM_WAG_PAST_3
gene expresson after 259 d in a feedlot


title: 252364710484___1

description:
SCF_WAG_PAST_1
gene expresson after 259 d in a feedlot


title: hnRNPK IP 1

description: IP RNA


title: 252364710485___1


title: 252364710483___2

description:
LDM_WAG_PAST_2
gene expresson after 259 d in a feedlot


title: 252364710482___4


title: 252364710482___3

description:
LDM_HER_PAST_3
gene expresson after 259 d in a feedlot


title: 252364710482___1

description:
LDM_WAG_PAST_1
gene expresson after 259 d in a feedlot


title: 252364710481___4

description:
LDM_HER_SUPP_4
gene expresson after 259 d in a feedlot


title: WT

first: Xingguang

last: Liu

address: Xiangyin road 800

department: National Key Laboratory of Immunity & Inflammation

institute: Naval medical university

data_processing:
Sequencing raw reads were preprocessed by filtering out rRNA reads, sequencing adapters, short-fragment reads and other low-quality reads using Seqtk.
Hisat2 (version:2.0.4) was used to map the cleaned reads to the mouse GRCm38.p4 (mm10) reference genome with two mismatches.
After genome mapping, Stringtie (version:1.3.0) was run with a reference annotation to generate FPKM values (Fragments Per Kilobase of exon model per Million mapped reads) for known gene models.
Differentially expressed genes were identified using edgeR. The p-value significance threshold in multiple tests was set by the false discovery rate (FDR).
Genome_build: GRCm38.p4 (mm10)
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include FPKM values.

source_name: peritoneal macrophage

growth_protocol: Peritoneal macrophages were harvested from mice 4 days after thioglycollate (BD, Sparks, MD) injection.

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany). Total RNA was quantified using a NanoDrop ND-2000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA), and RNA integrity was determined using an Agilent 2100 system and an RNA 6000 Nano kit (Agilent Technologies, Santa Clara, CA, USA).
Paired-end libraries were synthesized by using the TruSeq® RNA Sample Preparation Kit (Illumina, USA) following TruSeq® RNA Sample Preparation Guide. Briefly, the poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under 94°C for 8 min. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then go through an end repair process, the addition of a single base, and then ligation of the adapters. The products are then purified and enriched with PCR to create the final cDNA library.
Purified libraries were quantified by Qubit® 2.0 Fluorometer (Life Technologies, USA) and validated by Agilent 2100 bioanalyzer (Agilent Technologies, USA) to confirm the insert size and calculate the mole concentration. Cluster was generated by cBot with the library diluted to 10 pM and then were sequenced on the Illumina HiSeq 2500 (Illumina, USA).

treatment_protocol: LPS 100ng/ml for 3 hours.

tag: strain/background

value: wild type

tag: cell type

value: peritoneal macrophages

tag: stimulation

value: LPS 100ng/ml 4h


title: Kdm2b-KO


title: 252364710482___2

description:
LDM_HER_PAST_2
gene expresson after 259 d in a feedlot


title: 252364710481___1

description:
LDM_HER_SUPP_1
gene expresson after 259 d in a feedlot


title: 252364710483___1


title: 252364710476___4

description:
OME_WAG_PAST_4
gene expresson after 259 d in a feedlot


title: 252364710481___3

description:
LDM_HER_SUPP_3
gene expresson after 259 d in a feedlot


title: 252364710476___2

description:
OME_HER_PAST_2
gene expresson after 259 d in a feedlot


title: HBMSCs treated with F-53B, biological rep3

city: Dalian

first: Yifan

last: Pan

address: Ganjingzi District，Ruanjianyuan street

institute: Dalian University of Technology

description:
Gene expression data from HBMSCs
HBMSCs_F-53B-3

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 4.0 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by RMA algorithm, Affy packages in R.

source_name: Human bone mesenchymal stem cells treated with F-53B for 7 days

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip PLUS Reagent Kit (Cat#902416, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: Cells were grown at 37°C with 5% humidified CO2, fed every 2–3 days.

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by NucleoSpin RNA Clean-up XS kit (Cat#740903, MN, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: Human bone mesenchymal stem cells were treat separately with DMSO vehicle, 100 nM PFOS, 100 nM PFOA, 100 nM PFHxS or100 nM F-53B for 7 days.

tag: tissue

value: bone marrow

value: HBMSC

value: passage 6

tag: agent


title: 252364710476___3

description:
OME_ANG_PAST_3
gene expresson after 259 d in a feedlot


title: 252364710475___4

description:
OME_ANG_PAST_4
gene expresson after 259 d in a feedlot


title: 252364710481___2

description:
LDM_HER_SUPP_2
gene expresson after 259 d in a feedlot


title: HBMSCs treated with PFHxS, biological rep3

description:
Gene expression data from HBMSCs
HBMSCs_PFHxS-3

source_name: Human bone mesenchymal stem cells treated with PFHxS for 7 days

value: PFHxS


title: HBMSCs treated with F-53B, biological rep2

description:
Gene expression data from HBMSCs
HBMSCs_F-53B-2


title: HBMSCs treated with F-53B, biological rep1

description:
Gene expression data from HBMSCs
HBMSCs_F-53B-1


title: 252364710475___2

description:
INT_HER_PAST_2
gene expresson after 259 d in a feedlot


title: 252364710475___3


title: HBMSCs treated with PFOA, biological rep3

description:
Gene expression data from HBMSCs
HBMSCs_PFOA-3

source_name: Human bone mesenchymal stem cells treated with PFOA for 7 days

value: PFOA


title: 252364710476___1

description:
OME_WAG_PAST_1
gene expresson after 259 d in a feedlot


title: 252364710468___3

description:
IMF_HER_PAST_3
gene expresson after 259 d in a feedlot


title: HBMSCs treated with PFOS, biological rep3

description:
Gene expression data from HBMSCs
HBMSCs_PFOS-3

source_name: Human bone mesenchymal stem cells treated with PFOS for 7 days

value: PFOS


title: HBMSCs treated with PFOA, biological rep1

description:
Gene expression data from HBMSCs
HBMSCs_PFOA-1


title: HBMSCs treated with PFOA, biological rep2

description:
Gene expression data from HBMSCs
HBMSCs_PFOA-2


title: 252364710468___4

description:
IMF_ANG_PAST_4
gene expresson after 259 d in a feedlot


title: 252364710467___4

description:
IMF_WAG_PAST_4
gene expresson after 259 d in a feedlot


title: 252364710468___2

description:
IMF_HER_PAST_2
gene expresson after 259 d in a feedlot


title: 252364710468___1

description:
IMF_HER_PAST_1
gene expresson after 259 d in a feedlot


title: HBMSCs treated with PFHxS, biological rep1

description:
Gene expression data from HBMSCs
HBMSCs_PFHxS-1


title: HBMSCs treated with PFOS, biological rep1

description:
Gene expression data from HBMSCs
HBMSCs_PFOS-1


title: 252364710467___2

description:
IMF_WAG_PAST_2
gene expresson after 259 d in a feedlot


title: 252364710475___1

description:
INT_HER_PAST_1
gene expresson after 259 d in a feedlot


title: HBMSCs treated with PFOS, biological rep2

description:
Gene expression data from HBMSCs
HBMSCs_PFOS-2


title: HBMSCs treated with PFHxS, biological rep2

description:
Gene expression data from HBMSCs
HBMSCs_PFHxS-2


title: HBMSCs treated with DMSO vehicle, biological rep3

description:
Gene expression data from HBMSCs
HBMSCs_vehicle-3

source_name: Human bone mesenchymal stem cells treated with DMSO vehicle

value: vehicle


title: 252364710467___1

description:
IMF_ANG_PAST_1
gene expresson after 259 d in a feedlot


title: 252364710490___2

description:
KID_ANG_PAST_2
gene expresson after 259 d in a feedlot


title: 252364710467___3

description:
IMF_WAG_PAST_3
gene expresson after 259 d in a feedlot


title: 252364710466___4

description:
OME_HER_PAST_4
gene expresson after 259 d in a feedlot


title: 252364710466___3

description:
OME_HER_PAST_3
gene expresson after 259 d in a feedlot


title: HBMSCs treated with DMSO vehicle, biological rep2

description:
Gene expression data from HBMSCs
HBMSCs_vehicle-2


title: 252364710466___2

description:
OME_WAG_PAST_2
gene expresson after 259 d in a feedlot


title: HBMSCs treated with DMSO vehicle, biological rep1

description:
Gene expression data from HBMSCs
HBMSCs_vehicle-1


title: 252364710465___4

description:
LDM_WAG_SUPP_4
gene expresson after 259 d in a feedlot


title: 252364710466___1

description:
OME_WAG_PAST_1
gene expresson after 259 d in a feedlot


title: 252364710465___3

description:
LDM_WAG_SUPP_3
gene expresson after 259 d in a feedlot


title: 252364710465___1

description:
LDM_WAG_SUPP_1
gene expresson after 259 d in a feedlot


title: 252364710459___3

description:
INT_WAG_PAST_3
gene expresson after 259 d in a feedlot


title: 252364710459___1

description:
INT_WAG_PAST_1
gene expresson after 259 d in a feedlot


title: 252364710459___2

description:
INT_WAG_PAST_2
gene expresson after 259 d in a feedlot


title: 252364710458___4

description:
INT_ANG_PAST_4
gene expresson after 259 d in a feedlot


title: 252364710458___2

description:
KID_HER_PAST_2
gene expresson after 259 d in a feedlot


title: 252364710465___2

description:
LDM_WAG_SUPP_2
gene expresson after 259 d in a feedlot


title: 252364710458___1

description:
KID_ANG_PAST_1
gene expresson after 259 d in a feedlot


title: 252364710458___3

description:
INT_ANG_PAST_3
gene expresson after 259 d in a feedlot


title: 252364710457___2


title: 252364710457___4

description:
INT_HER_PAST_4
gene expresson after 259 d in a feedlot


title: 252364710456___4

description:
LDM_ANG_PAST_4
gene expresson after 259 d in a feedlot


title: 252364710457___1

description:
INT_ANG_PAST_1
gene expresson after 259 d in a feedlot


title: 252364710459___4


title: 252364710456___3

description:
LDM_ANG_PAST_3
gene expresson after 259 d in a feedlot


title: HCC827 cells, pLX303-lacZ SNAIL-V5, rep2

city: Burjassot

first: Julian

last: Carretero

state: Valencia

address: Ave. Vicent Andres Estelles s/n

department: Physiology

institute: University of Valencia

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Genepattern's IlluminaExpressionFileCreator

source_name: HCC827 cell line

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

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: SNAIL, lentiviral overexpression


title: 252364710456___1

description:
LDM_ANG_PAST_1
gene expresson after 259 d in a feedlot


title: 252364710455___2

description:
LDM_ANG_SUPP_2
gene expresson after 259 d in a feedlot


title: 252364710456___2

description:
LDM_ANG_PAST_2
gene expresson after 259 d in a feedlot


title: HCC827 cells, pLKO1 shRNA non target NT, rep2

description: replicate 1

value: shRNA control, CDH1 experiment


title: 252364710455___4

description:
LDM_ANG_SUPP_4
gene expresson after 259 d in a feedlot

value: 259 days


title: 252364710455___3

description:
LDM_ANG_SUPP_3
gene expresson after 259 d in a feedlot

value: ANGUS


title: HCC827 cells, pLX303-lacZ SNAIL-V5, rep3

description: replicate 2


title: 252364710455___1

description:
LDM_ANG_SUPP_1
gene expresson after 259 d in a feedlot


title: HCC827 cells, pLKO1 shRNA non target NT, rep3

description: replicate 2


title: 252364710457___3

description:
INT_HER_PAST_3
gene expresson after 259 d in a feedlot

value: HEREFORD


title: HCC827 cells, pLX303-lacZ SNAIL-V5, rep1

description: replicate 1


title: HCC827 cells, pLKO1 shRNA CDH1, rep3

description: replicate 2

value: shRNA against CDH1


title: HCC827 cells, pLKO1 shRNA non target NT, rep1

description: replicate 1


title: MCF10A R702R2 rep2

city: Baltimore

first: William

middle: Brian

last: Dalton

state: Maryland

address: 1650 Orleans St.

department: Oncology

institute: Johns Hopkins University School of Medicine

data_processing:
Casava
The reads are quality trimmed. The original untrimmed reads were not available.
TopHat (Version 2.0.10)
Cufflinks
HTSeq (htseq-count)
RSeQC (Version 2.6.4)
DEXseq
Genome_build: GRCh38
Supplementary_files_format_and_content: bed and gtf. Bed columns are: 1. chrom  2. chromStart  3. chromEnd  4. Known or partial/complete novel exon-exon junction (wrt GENCODE v25)  5. Number of reads that span exon-exon junction  6. strand  7. thickStart  8. thickEnd  9. itemRgb  10. blockCount  11. blockSizes  12. blockStarts

source_name: MCF10A cell line

growth_protocol: MCF-10A cells were from ATCC and grown in DMEM/F12 with 5% horse serum, 20 ng/ml EGF, 10 μg/ml insulin, 0.5 μg/ml hydrocortisone, and 0.1 μg/ml cholera toxin.

extract_protocol:
Total RNA was harvested from cultured cells using RNeasy and Qiashredder kits (Qiagen).
RNA-seq libraries were constructed using the Illumina TruSeq RNA Sample Preparation Kit v3.

tag: genotype

value: SF3B1 R702R

tag: replicate


title: MCF10A R702R1 rep1


title: MCF10A K700E1 rep2

value: SF3B1 K700E


title: MCF10A K700E2 rep1


title: MCF10A TWT1R2 rep2


title: MCF10A TWT1R1 rep1


title: HCC827 cells, parental, rep2

description: replicate 1

value: parental


title: HCC827 cells, pLX303-lacZ control, rep3

description: replicate 2

value: Control lentivirus, SNAIL experiment


title: HCC827 cells, parental, rep3

description: replicate 2


title: HCC827 cells, TGFB1-treated rep2

description: replicate 1

value: TGFB1-treated (30 days)


title: HCC827 cells, pLKO1 shRNA CDH1, rep1

description: replicate 1


title: HCC827 cells, pLX303-lacZ control, rep1

description: replicate 1


title: HCC827 cells, TGFB1-treated rep3

description: replicate 2


title: HCC827 cells, pLKO1 shRNA CDH1, rep2

description: replicate 1


title: HCC827 cells, pLX303-lacZ control, rep2

description: replicate 1


title: HCC827 cells, TGFB1-treated rep1

description: replicate 1


title: MCF10A K700E2 rep2


title: primary bovine trophoblast giant cells from cow 4

city: Dummerstorf

first: Rainer

last: Fuerbass

address: Wilhelm-Stahl-Allee

institute: Leibniz Institute for Farm Animal Biology

hyb_protocol: The RNA was hybridized overnight (45°C) in the GeneChipR Hybridization Oven (Affymetrix) to the Affymetrix Bovine Gene 1.0 ST arrays. Washing and staining were performed according to the Affymetrix standard protocol.

scan_protocol: The scanning of the microarray was done with the GeneChip Scanner 3000 7G (Affymetrix) and image processing was done with the software AGCC (Affymetrix).

data_processing: Raw data were processed with the Expression Console (V1.4.1.46; Affymetrix), where normalization, background reduction and a gene-level summary was done using the RMA method (Robust Multichip Average).

label: Biotin

source_name: primary bovine trophoblast giant cells

label_protocol: RNA from each cell sample was used to generate single strand DNA (Ambion WT Expression Kit). Fragmentation and labeling was performed with the Affymetrix Gene Chip WT Terminal Labeling and Hybridization Kit

extract_protocol: Total RNA was prepared using the NucleoSpin RNA Kit including removal of genomic DNA with RNAse free rDNAse (Macherey-Nagel).

treatment_protocol: Primary UTC and TGC isolates were analyzed without further treatment.

value: primary bovine trophoblast giant cells


title: KURC3_Tem_P4_#3

city: Kyoto

first: Hiromasa

last: sakamoto

address: 54 Shogoinkawahara-cho, Sakyo-ku,

institute: Kyoto University Graduate School of Medicine

description: Gene expression data from patient-derived xenograft tumor (KURC3) treated with temsirolimus.

hyb_protocol: Hybridization cocktails containing fragmented, end-labelled cDNA were prepared and applied to GeneChip Human Gene 2.0 ST arrays. Hybridization was performed in 45°C GeneChip®Hybridization Oven 645 at 60 rpm for 16 hours. The hybridized GeneChip® Human Gene 2.0 ST Arrays were washed and stained using GeneChip® Fluidics Station 450.

scan_protocol: Arrays were scanned using Affymetrix GeneChip® Scanner 3000 7G controlled by GeneChip® Command Console® to produce CEL files.

data_processing: Data were analyzed using GeneSpring GX ver. 12.6 (Agilent Technologies).

source_name: KURC3 (temsirolimus)

label_protocol: Total RNA from each model were processed using GeneChip® WT PLUS Reagent Kit (Affymetrix, Inc., Santa Clara, CA) to generate amplified sense-strand cDNA. Fragmentation and labeling was done usingGeneChip® WT PLUS Reagent Kit (Affymetrix, Inc., Santa Clara, CA).

growth_protocol: We kept 2 types of patient-derived xenograft models (KURC;Kyoto University Renal Cancer-1,3) derived from human renal cell carcinoma tissues.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit and QIAamp DNA mini kit (Qiagen, Hilden, Germany), respectively, according to the manufacturer’s instructions.

value: renal cancer patient-derived xenograft tumor


title: primary bovine uninucleate trophoblast cells from cow 3


title: primary bovine trophoblast giant cells from cow 2


title: primary bovine trophoblast giant cells from cow 3


title: HCC827 cells, parental, rep1

description: replicate 1


title: KURC3_Tem_P4_#1


title: KURC3_Veh_P4_#2

description: Gene expression data from patient-derived xenograft tumor (KURC3) treated with vehicle.

source_name: KURC3 (vehicle)


title: KURC3_Tem_P4_#2


title: primary bovine uninucleate trophoblast cells from cow 2


title: KURC3_Veh_P4_#1


title: KURC3_Tem_P4_#4


title: KURC1_Tem_P4_#1

description: Gene expression data from patient-derived xenograft tumor (KURC1) treated with temsirolimus.

source_name: KURC1 (temsirolimus)


title: KURC1_Tem_P4_#2


title: KURC1_Veh_P4_#1

description: Gene expression data from patient-derived xenograft tumor (KURC1) treated with vehicle.

source_name: KURC1 (vehicle)


title: TF1, KIT D816V, 2

city: Strassen

first: Tony

last: KAOMA

address: 1 A-B Rue Thomas Edison

department: Quantitative Biology Unit

country: Luxembourg

institute: Luxembourg Institute of Health

hyb_protocol: Labeled cRNA products were randomly fragmented and hybridized onto Affymetrix GeneChips.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000

data_processing: CEL files were preprocessed into Partek GS with default partek options.

source_name: TF1, KIT D816V, replicate 3

label_protocol: 250 ng of total RNAs were reverse transcribed into cDNA, then transcribed into cRNAs and labeled into biotinylated cRNA using the GeneChip WT PLUS Reagent kit (Affymetrix) according to the manufacturer’s standard protocols (P/N 4425209 Rev.B 05/2009 and P/N 702808 Rev.6).

growth_protocol: TF-1 was grown in RPMI containing 10% fetal calf serum supplemented with 2 ng/ml GM-CSF (Miltenyi Biotec, France). At 4 h before the experiments, cells were washed and maintained in GM-CSF-free medium. TF-1 KITD816V were cultured in RPMI 1640 medium with Glutamax (Gibco, Life Technologies) supplemented with fetal bovine serum (Sigma) and 100 units/mL of penicillin and streptomycin (Invitrogen).

extract_protocol: Total RNA were extracted form TF-1 cells expressing either the wild-type KIT or the mutant KITD816V in independent triplicate using the Qiagen kit according to manufacturer’s instructions.


title: WholeBlood_CRC305DGENT1683046_Day0

city: London

first: David

last: Lewis

address: Du Cane Road

department: ICRF

country: United Kingdom

institute: Imperial College London

description: Whole blood gene expression of participant on day

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented and hybridized to custom whole genome human 8 × 60K multipack microarrays (Agilent-048908) following the manufacturers instructions. 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) according the manufacturers protocol.

scan_protocol: Slides were scanned immediately after washing using a high resolution DNA Microarray Scanner (G2505B, Agilent Technologies) with 3 µm resoltion and 20 bit image depth

data_processing: The scanned microarray images were processed with the Image Analysis/Feature Extraction software G2567AA v. A.11.5.1.1 (Agilent Technologies) using default settings and the GE1_1105_Oct12 extraction protocol.

source_name: Peripheral Blood, PaxGene

label_protocol: Total RNA was amplified and labeled with the low input Quick-Amp Labelling Kit (Agilent Technologies) with cyanine 3-CTP followed by precipitation, purification, and quantification.

extract_protocol: mRNA was reverse transcribed and amplified using an oligo-dT-T7 promoter primer

treatment_protocol: Microarray experiments were performed as single-color hybridization. Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng total RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

tag: participant

tag: gender

value: female

tag: race

value: white

tag: ethnicity

value: not american hispanic or latino

tag: protocol

value: FLUADD

tag: day

value: whole blood


title: TF1, Control, 2

source_name: TF1, Control, replicate 2

tag: cell line

value: wild type


title: WholeBlood_CRC305DGENT0263008_Day21


title: TF1, KIT D816V, 1


title: WholeBlood_CRC305DGENT1581031_Day1

value: male


title: WholeBlood_CRC305DGENT1773058_Day0


title: WholeBlood_CRC305DGENT1211029_Day7


title: WholeBlood_CRC305DGENT1563035_Day7


title: WholeBlood_CRC305DGENT0131009_Day21


title: WholeBlood_CRC305DGENT0263008_Day7


title: WholeBlood_CRC305DGENT2313050_Day7


title: WholeBlood_CRC305DGENT2303051_Day7


title: WholeBlood_CRC305DGENT0233014_Day21


title: WholeBlood_CRC305DGENT2351058_Day0

value: other


title: WholeBlood_CRC305DGENT0131009_Day7


title: TF1, KIT D816V, 3


title: TF1, Control, 1

source_name: TF1, Control, replicate 1


title: MCF10A K700E1 rep1


title: WholeBlood_CRC305DGENT1361021_Day0


title: WholeBlood_CRC305DGENT0063016_Day1


title: WholeBlood_CRC305DGENT2303051_Day3


title: WholeBlood_CRC305DGENT2321056_Day21


title: WholeBlood_CRC305DGENT1511040_Day7

value: PLACEBOD


title: WholeBlood_CRC305DGENT1461019_Day3


title: WholeBlood_CRC305DGENT0343002_Day21


title: WholeBlood_CRC305DGENT0313004_Day21


title: WholeBlood_CRC305DGENT2371051_Day0


title: Lung, HDM + MM (53)

city: Fulda

first: Daniela

last: Fussbroich

address: Leipziger Str. 123

institute: University of Applied Sciences Fulda

data_processing:
PhiX Sequencing Control v3 and the MiSeq™ Desktop Sequencer (all Illumina Inc., San Diego, USA) for Base Calling
Results were processed according to Bioo Scientific Small RNA analysis pipeline.
Cutadapt V1.14 was used to remove adapter sequences and random bases and to discard too short reads
bowtie 2 (V2.2.9; http://www.bowtie-bio.sourceforge.net) was used to align readouts to murine mature miRNAs from miRBase (mature.fs, v21, June 2014; http://www.mirbase.org)
miRUtils (v1.0.0; http://www.mirutils.sourceforge.net) was used to process the aligned files
Genome_build: Mus musculus GRCm38 (v21)
Supplementary_files_format_and_content: coverage files including total reads per mapped miRNA

source_name: Lung

growth_protocol: Mice were purchased at the age of 6-8 weeks.

extract_protocol:
Lungs were removed, stored immediately in RNA later, and RNA was harvested using miRNeasy Mini Kit.
RNA libraries were prepared with 1 ug of total RNA for sequencing using standard NEXTflex Small RNA-Seq Kit v3.

treatment_protocol: Mice were first sensitized for 10 consecutive days with 40 µg house dust mite extract to induce allergic asthma and thereafter supplemented with the LCPUFA combination for 24 days. Within the last 3 days, mice daily received repetitive doses of HDM (recall).

tag: strain

value: Lung

value: HDM + MM


title: Lung, HDM + MM (54)


title: TF1, Control, 3

source_name: TF1, Control, replicate 3


title: Lung, HDM + MM (50)


title: Lung, HDM + MM (49)


title: Lung, HDM + MM (52)


title: WholeBlood_CRC305DGENT2401055_Day3

tag: age


title: WholeBlood_CRC305DGENT1233028_Day1

tag: treatment


title: WholeBlood_CRC305DGENT1653039_Day7


title: primary bovine uninucleate trophoblast cells from cow 4


title: WholeBlood_CRC305DGENT1551038_Day7


title: Lung, HDM + Normal Diet (48)

value: HDM + Normal Diet


title: Lung, PBS + Normal Diet (45)

value: PBS + Normal Diet


title: Lung, HDM + Normal Diet (47)


title: WholeBlood_CRC305DGENT2361060_Day1


title: WholeBlood_CRC305DGENT0351013_Day3


title: WholeBlood_CRC305DGENT1843044_Day7


title: Lung, HDM + Normal Diet (46)


title: Lung, PBS + Normal Diet (43)


title: WholeBlood_CRC305DGENT1301023_Day21


title: WholeBlood_CRC305DGENT0153020_Day0


title: WholeBlood_CRC305DGENT0213015_Day3


title: WholeBlood_CRC305DGENT2343042_Day21


title: WholeBlood_CRC305DGENT0011001_Day1


title: WholeBlood_CRC305DGENT1823053_Day1


title: WholeBlood_CRC305DGENT0403011_Day0


title: WholeBlood_CRC305DGENT1611036_Day3


title: WholeBlood_CRC305DGENT1773058_Day7


title: WholeBlood_CRC305DGENT2463060_Day7


title: WholeBlood_CRC305DGENT0123021_Day21


title: Lung, HDM + Normal Diet (27)


title: Lung, PBS + Normal Diet (23)


title: WholeBlood_CRC305DGENT1471032_Day0


title: WholeBlood_CRC305DGENT1331025_Day1


title: mESC 12h chase Rep 1

first: Brian

last: Reichholf

address: Doktor-Bohr-Gasse 3

institute: IMBA

description:
artificial_chromosome_targetedRNAseq.bed
artificial_chromosome_targetedRNAseq.fa

data_processing:
Basecalls performed using "Real Time Analysis RTA" V.1.18.64.0
Demultiplexed reads were adapter-trimmed using cutadapt; 12nt were trimmed from the 5' during the alignment process
Trimmed reads were aligned using SLAMdunk v0.3.0: Reads were aligned to the artificial chromosome (artificial_chromosome_targetedRNAseq.fa) using local alignment scoring and multimapping reads were discarded. In the filtering step, alignments with a minimum identity of 95% and a minimum of 50% of the read bases mapped were retained. SNPs exceeding a coverage cutoff of 10x and a variant fraction cutoff of 0.8 were called using VarScan2.4.1 using default parameters. Non-SNP overlapping T>C mutations with a base quality of Phred score >26 were identified. T>C containing reads and total reads aligning within the custom defined amplicon regions (artificial_chromosome_targetedRNAseq.bed) were reported. T>C conversion rate was determined for each position along the custom defined intervals by normalizing to genomic T content and coverage of each position and averaged per region.
The artifical_chromosome_targetedRNAseq.bed file was manually created by extracting the genome coordinates and sequences (for fasta file) of the expected amplicons of the custom-designed primers
Genome_build: artificial_chromosome_targetedRNAseq.fa
Supplementary_files_format_and_content: artificial_chromosome_targetedRNAseq.fa: Genomic sequences of the expected amplicons of the custom-designed primers. artificial_chromosome_targetedRNAseq.bed: Relative Coordinates of the amplicons of the custom-designed primers. *.tsv files: Count file output from SLAMdunk containing the relative chromosomal coordinates (from the "artificial chromosome"), Gene Name and Strand of the sequenced amplicons, T>C conversion rate, Expression (ReadsCPM), T content of the amplicon interval, Coverage on Ts within the amplicon interval, T>C Conversions on Ts, Read Count, T>C Read Count and Multimap Counts

source_name: mouse embryonic stem cells AN3-12

growth_protocol: Mouse embryonic stem (mES) cells (clone AN3-12) were cultured in 15 % FBS (Gibco), 1x Penicillin-Streptomycin solution (100 U/ml Penicillin, 0.1 mg/ml Streptomycin, Sigma), 2 mM L-Glutamine (Sigma), 1x MEM Non-essential amino acid solution (Sigma), 1 mM sodium pyruvate (Sigma), 50 µM 2-Mercaptoethanol (Gibco) and 20 ng/ml LIF (in-house produced). Cells were maintained at 37°C with 5% CO2 and passaged every second day.

extract_protocol:
total RNA extraction and IAA-derivatization
Targeted mRNA 3' end cDNA libraries were prepared using a protocol described in the Quantseq Flex kit. For details see associated manuscript. Gene-specific forward primers were as follows (sequence in 5  -3  ): ActB,ENSMUSG00000029580, CACGACGCTCTTCCGATCTNNNNNNCCCACTCCTAAGAGGAGGATG; GusB, ENSMUSG00000025534, CACGACGCTCTTCCGATCTNNNNNNGTGGTCTTTGGGAAGGTGAA; Hspa1b, ENSMUSG00000090877, CACGACGCTCTTCCGATCTNNNNNNGGACTGGATGTTCCTCTCCA; Nat10, ENSMUSG00000027185, CACGACGCTCTTCCGATCTNNNNNNTGAAGGGTGGTGTTTTCTCA; Sox2, ENSMUSG00000074637, CACGACGCTCTTCCGATCTNNNNNNATGGCCAACTTTGGCAGTAG; Tnrc6b, ENSMUSG00000047888, CACGACGCTCTTCCGATCTNNNNNNTTTTAGGGGCATCACTGGAG;

treatment_protocol: Mouse embryonic stem cells were incubated with 100 µM s4U for 12h; followed by a wash out with incubation with standard medium supplemented with 10 mM uridine for the times indicated before they were directly lysed in Trizol® (Ambion).

value: 12h s4U treatment; 12h uridine chase


title: mESC 6h chase Rep 2

value: 12h s4U treatment; 6h uridine chase


title: WholeBlood_CRC305DGENT1511040_Day1


title: mESC 6h chase Rep 1


title: WholeBlood_CRC305DGENT0351013_Day1


title: Lung, PBS + Normal Diet (22)


title: mESC 12h chase Rep 2


title: Lung, HDM + Normal Diet (28)


title: mESC 1h chase Rep 1

value: 12h s4U treatment; 1h uridine chase


title: mESC 0.5h chase Rep 2

value: 12h s4U treatment; 0.5h uridine chase


title: mESC 1h chase Rep 2


title: mESC 3h chase Rep 2

value: 12h s4U treatment; 3h uridine chase


title: mESC 3h chase Rep 1


title: WholeBlood_CRC305DGENT1483036_Day7

value: female

value: white


title: mESC 0h chase Rep 2

value: 12h s4U treatment


title: mESC no s4U Rep 2

value: no s4U treatment


title: mESC 0h chase Rep 1


title: mESC no s4U Rep 1


title: WholeBlood_CRC305DGENT1503022_Day3

value: not american hispanic or latino

value: FLUADD

value: whole blood


title: mESC 0.5h chase Rep 1


title: WholeBlood_CRC305DGENT2241042_Day0

value: male


title: WholeBlood_CRC305DGENT2281049_Day1


title: WholeBlood_CRC305DGENT1653039_Day0


title: WholeBlood_CRC305DGENT2351058_Day7

value: other


title: WholeBlood_CRC305DGENT1301023_Day7


title: Haploids and DamP collection Ethylzingerone (1250 ug/ml) treatment

city: Paris

first: Cosmin

last: Saveanu

address: 25-28 rue du docteur Roux

department: Genomes and Genetics

country: France

institute: Institut Pasteur

hyb_protocol: Hybridization was done in Roche RapidHyb buffer at 24°C overnight.

scan_protocol: Genepix 4200AL and GenePix Pro v7

data_processing: The scans were processed using GenePix Pro, v7. The values from the obtained gpr files were filtered to keep only values for spots with an SNR > 10. Next, we performed a loess normalization on groups of probes (UP/DAMP, UP/DELETION, DOWN/DAMP, DOWN/DELETION), followed by aggregation of values for each mutant and a second loess normalization on the aggregated data.

organism: Saccharomyces cerevisiae

source_name: Haploid, homozygous yeast deletion collection + DamP collection (Decourty et al., Cell Rep. 2014)

label_protocol: Cy3 and Cy5 5' tagged oligonucleotides were used to amplify the barcode region with universal primers. PCR products were then mixed, precipitated in the presence of linear poly-acrylamide and prepared for hybridization

growth_protocol: Cells were thawed from -80°C aliquots and left to recover for 8 hours in YPD medium. An aliquot of the pool of strains was diluted to a DO of 0.002 in 1 liter of YPD medium with the indicated concentrations of products or without (control, solvent only). Cells were recovered after overnight growth, when reaching a 600 nm OD of 2 (after about 10 generations).

extract_protocol: Genomic DNA was extracted through mechanical lysis (vortexing with glass beads). PCR amplification of the barcode region was followed by a second PCR amplification with Cy3 5' tagged oligonucleotide.

treatment_protocol: Cells in exponential growth were recovered by centrifugation, washed once in cold water and stored at -80°C until DNA extraction

value: Mix of haploid strains derived from BY4741 (yeast deletion collection)

value: YPD+Ethylzingerone(HEPB) 1250ug/ml

source_name: Barcoded DNA from haploid, homozygous yeast deletion collection + DamP collection (Decourty et al., Cell Rep. 2014)

value: untreated control (YPD)


title: WholeBlood_CRC305DGENT0421004_Day21


title: Haploids and DamP collection Ethylzingerone (937 ug/ml) treatment

value: YPD+Ethylzingerone(HEPB) 937ug/ml

value: Mix of haploid strains derived from BY4741


title: WholeBlood_CRC305DGENT0141011_Day1


title: WholeBlood_CRC305DGENT1471032_Day7


title: WholeBlood_CRC305DGENT1371020_Day0


title: WholeBlood_CRC305DGENT1593031_Day7


title: Haploids and DamP collection Methylparaben (300 ug/ml) treatment

value: YPD+Methylparaben 300ug/ml


title: WholeBlood_CRC305DGENT0103017_Day0


title: WholeBlood_CRC305DGENT1551038_Day1


title: WholeBlood_CRC305DGENT0223019_Day21


title: WholeBlood_CRC305DGENT2433059_Day1


title: WholeBlood_CRC305DGENT2233045_Day0


title: WholeBlood_CRC305DGENT0103017_Day7


title: WholeBlood_CRC305DGENT1713056_Day0


title: WholeBlood_CRC305DGENT2453055_Day3


title: Haploids and DamP collection Methylparaben (400 ug/ml) treatment

value: YPD+Methylparaben 400ug/ml


title: Haploids and DamP collection Triclosan (20 ug/ml) treatment

value: YPD+Triclosan 20ug/ml


title: WholeBlood_CRC305DGENT0421004_Day1


title: Haploids and DamP collection Triclosan (15 ug/ml) treatment

value: YPD+Triclosan 15ug/ml


title: WholeBlood_CRC305DGENT1703047_Day7

value: female

value: white

value: PLACEBOD


title: WholeBlood_CRC305DGENT0011001_Day7

value: not american hispanic or latino


title: WholeBlood_CRC305DGENT0343002_Day7

value: FLUADD


title: WholeBlood_CRC305DGENT1823053_Day21

value: whole blood