title: P_23_3

hyb_protocol: The Nanostring assay used was the human V3a assay, which has 829 miRNA probes. Nanostring assays can accommodate twelve samples/run, so samples were split into two runs, with two samples from each time in each run.

scan_protocol: not provided

data_processing:
The Nanostring software program, nSolver, was used for initial data processing and normalization. Both runs passed all Nanostring Quality Control tests.
Counts from the Nanostring assay were normalized to the average of all miRNA detected above background (determined on the basis of background binding in negative control lanes), on a per sample basis, to account for differences in RNA loading across lanes.
All miRNA that were detected above background in all 16 samples were analyzed for differential abundance and in the cluster analysis.
For analysis of differential abundance, normalized counts of miRNA detected above background were box-cox transformed in JMP (SAS, Inc), to improve normality of distribution of data. The linear, quadratic, and cubic effects of time, with Nanostring run as a block, were assessed by ANOVA in R. Interaction of block*day was tested, and in no case was the interaction term significant for a miRNA that was differentially abundant (main effect of day), so that term was removed. The Benjamini-Hochberg correction was used to correct for false discovery rate, with miRNA considered significantly differentially abundant with Padj < 0.15.

label_protocol: not provided

extract_protocol: Samples of RNA were isolated using the miRcury tissue total RNA isolation kit (Exiqon) according to the manufacturer’s protocol. This kit isolates miRNA with total RNA. RNA quantity and quality were assessed using a Biorad Experion; all samples had an RNA quantity index (RQI) greater than 8.5, which is well within the range of good quality samples. A260/230 ratios were all >2.00, and 260/280 ratios were all >1.98.

value: Corpus luteum

tag: day of pregnancy

tag: nanostring run

value: run 2


title: P_23_4

status: Public on Mar 28 2020

type: RNA

city: University Park

first: Camilla

middle: H. K.

last: Hughes

state: PA

address: 439 Shortlidge Rd

department: Animal Science

country: USA

institute: Penn State University

molecule: total RNA

organism: Bos taurus

source_name: Corpus luteum (ovary)

tag: tissue


title: P_23_1

value: run 1


title: Plate 1009901003

type: SRA

city: Stanford

first: Yuan

last: Xue

state: CA

address: 318 Campus Drive

institute: Stanford University

description:
NS24_schistosome_atlas_reads_v13.tsv.gz
NS24_schistosome_atlas_TPM_v13.tsv.gz

library_source: transcriptomic

data_processing:
Paired-end reads were mapped to S. mansoni genome version WBPS13 (WormBase Parasite) using Salmon (version 0.14.0) with â--validateMappingsâ flag. Read counts from the two separate sequencing lanes were then summed for samples that originated from the same well during sort.
We performed downstream preprocessing and analysis on the estimated read counts in the Salmon output. Reads were initially mapped to exonic regions of the genome. To calculate total gene counts, exonic read counts corresponding to each gene were summed together.
To eliminate low-quality cells, we filtered out cells with fewer than 520 genes detected, leaving 7,657 cells remaining. This number was arbitrarily chosen based on the histogram of number of genes detected per cell.
Genome_build: Schitosoma mansoni WBPS 13
Supplementary_files_format_and_content: Gzip compressed tab-separated values (tsv.gz). Contains read count matrix, estimated TPM, and other meta output of Salmon

molecule: polyA RNA

organism: Schistosoma mansoni

source_name: S. mansoni juveniles retrieved from infected female Swiss Webster mice at 3.5 weeks post-infection

growth_protocol: Worms were cultured at 37ËC in Basch Media 169 supplemented with 1X Antibiotic-Antimycotic.

extract_protocol:
S. mansoni juveniles were retrieved from infected female Swiss Webster mice (NR-21963) by hepatic portal vein perfusion with 37Â°C DMEM + 5% heat inactivated FBS at 3.5 weeks post-infection.
Smart-seq2 followed by Illumina Nextera XT library construction kit.
Each sample was sequenced on two separate lanes on a NovaSeq 6000, thus producing two pairs of fastqs for each single cell.

tag: developmental stage

value: S. mansoni juveniles

tag: host

value: Swiss Webster female mice (NR-21963)

tag: time

value: retrieved from infected female mice at 3.5 weeks post-infection

tag: cell type

value: all body cells


title: Plate 1009901002


title: Rfc1-Pk in HU:  BrdU-IP-ssSeq

city: London

first: Hon Wing

last: Liu

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Institute

library_source: genomic

data_processing:
Raw reads from each sample were adapter-trimmed using cutadapt (version 1.9.1) (Martin M, 2011) with parameters “-a AGATCGGAAGAGC -A AGATCGGAAGAGC --minimum-length=25 –quality-cutoff=20”. As a result of the protocol used for the library preparation, a second round of trimming was performed using cutadapt with the parameter “-U 10” to remove the last 10bp of read 2.
BWA (version 0.6.2) (Li and Durbin, 2009) with default parameters was used to perform genome-wide mapping of the trimmed reads to the yeast sacCer3 genome assembly downloaded from the UCSC (Karolchik et al., 2004).
Alignments were filtered to remove read pairs that were discordant, mapped to different chromosomes, ambiguously mapped, had an insert size outside the range 120-200 bp, and mismatch > 4 in any reads.
Alignments were split by strand using a custom script, and normalised bedGraph coverage tracks representing the signal per million mapped paired-reads were generated using BEDTools genomeCoverageBed (version 2.26.0) (Quinlan & Hall, 2010) with the parameters “-bg -pc -du -strand <STRAND> -scale <SCALE_FACTOR>”. BedGraph files were converted to bigWig using the wigToBigWig binary available from the UCSC with the "-clip" parameter (Kent et al., 2010).
Genome_build: sacCer3
Supplementary_files_format_and_content: Genome-wide strand-specific bigWig files were generated by treating each pair of reads as a single fragment, and normalised to 1 million reads.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: yeast strains in small batch culture

growth_protocol: Cells were grown in rich YPD media, arrested into G1 for 2 hours 45 minutes with alpha-factor, and either released to medium containing YPD either without HU for 26 minutes (S phase), or released into YPD supplemented with 0.1M HU for 40 minutes (HU).

extract_protocol:
Preparation of BrdU-IP, ChIP and eSPAN DNA according to a published eSPAN protocol (Yu et al., 2018).  Briefly, cells were grown under the specified conditions and then fixed with 1% formaldehyde.  Cells were lysed and nuclear extracts harvested, followed by chromatin immunoprecipitation.  Purified ChIP DNA was then denatured and subject to another round of BrdU-IP.  In parallel, BrdU-IP was also performed with Input DNA.  Libraries were then amplified from purified eSPAN DNA, alongside ChIP, BrdU-IP and Input DNA, and were subject to high throughput sequencing by the Ilumina HiSeq 2500 and 4000 platforms.
Sequencing libraries were prepared using the Accel-NGS® 1S Plus DNA Library Kit as per manufacturer's protocol.

treatment_protocol: Cells were cross-linked with 1% Formaldehyde for 20 minutes at room temperature. The reaction was stopped with 0.125 M Glycine for 5 minutes.

value: yeast cells

tag: strain

tag: genotype

value: MATa, ade2-1, trp1-1, can1-100, leu2-3, 112, his3-11,15, ura3-52, GAL, psi+ pADH1-hENT1-TK::TRP1 RFC1-Pk9::KANMX6

tag: chip antibody

value: anti-BrdU (B44, BD Biosciences)


title: P_20_4


title: cranial meningioma 19

type: genomic

city: Beijing

first: Dake

last: Zhang

address: NO.1 Beichen West Road, Chaoyang District

country: China

institute: Beijing Institute of Genomics, Chinese Academy of Sciences

description: Genomic DNA extracted from meningioma samples  was genotyped using Illumina Human Infinium CoreExome BeadChips (Illumina, San Diego, CA, USA).

hyb_protocol: DNA was amplified, fragmented and hybridized to BeadChip arrays according to the manufacturer's instructions.

scan_protocol: The BeadChip arrays were scanned using the iScan (Illumina).

data_processing: Raw intensity values were processed to obtain a normalized B allele frequency (BAF) and a Log R ratio (LRR) for each probe using the Genome Studio Software v2.0.4 (illumina, San Diego, USA)

label: Cy3 and Cy5

organism: Homo sapiens

source_name: cranial meningioma

label_protocol: The single base extension reaction uses chain-terminating dideoxynucleotides. The A and T nucleotides are labeled with dinitrophenyl (abbreviated as DNP)and the G and C nucleotides are labeled with biotin.

extract_protocol: Genomic DNA was purified from tumor samples using a Biomek 3000 automated workstation with an E.Z.N.A Mag-Bind Tissue DNA Kit (Omega Bio-Tek, Norcross, GA, USA).

tag: gender

value: F

tag: age

tag: grade

value: II


title: Plate 1009901001


title: cranial meningioma 30

value: I


title: Ctf18-HA in rfc1-aid cells in HU:  eSPAN

value: MATa, ade2-1, trp1-1, can1-100, leu2-3, 112, his3-11,15, ura3-52, GAL, psi+ pADH1-hENT1-TK::TRP1 ade2::pADH1-OsTir1-Myc9 RFC1-PK3-miniAID3::KANMX6  CTF18-HA6::HIS3

value: anti-HA followed by anti-BrdU (B44, BD Biosciences)


title: Ctf18-HA in rfc1-aid cells in HU:  Input


title: P_20_3


title: cranial meningioma 31

value: M


title: P_20_2


title: Ctf18-HA in rfc1-aid cells in HU:  BrdU-IP-ssSeq


title: Ctf18-HA in rfc1-aid cells in HU:  ChIP-ssSeq

value: anti-HA (ab9110, abcam)


title: wblC Tet rep2

city: Seoul

first: Jung-Hye

last: Roe

address: 1 Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

data_processing:
Adapter sequences were trimmed from raw read data using Trimmomatic v0.36.
Processed reads were mapped to S. coelicolor A3(2) reference genome using Bowtie v2.3.2.
Raw counts for features were obtained using featureCounts of Subread package v1.5.3.
Count was normalized and differential expression was assessed for features using DESeq2 v3.5.
Genome_build: GCF_000203835.1
Supplementary_files_format_and_content: The tab-delimited text file includes normalized abundance measurements by DESeq2 of each genes on RefSeq NC_003888.3 (excluding pseudogenes), denoted by locus tag, for all samples.

organism: Streptomyces coelicolor

source_name: Streptomyces coelicolor A3(2) strain M145

growth_protocol: Spores were inoculated in YEME liquid media with 5 mM MgCl2 and 10% sucrose and were grown to OD600 of 0.3~0.4.

extract_protocol:
Total RNA was extracted by SDS and hot phenol method and was treated with Dnase I. rRNA were removed using Ribo-Zero rRNA Removal Kit (Bacteria) (Epicentre) following manufacturer's protocol.
Library was constructed using TruSeq Stranded Total RNA Sample Prep Kit (Illumina) according to manufacturer's protocol.

value: A3(2) strain M145

value: wblC mutant

tag: treatment

value: 2 microgram/ml tetracycline, 30 minutes


title: Rfc1-Pk in HU:  ChIP-ssSeq

value: anti-Pk (ab15828, abcam)


title: cranial meningioma 29


title: P_23_2

value: Corpus luteum

value: run 1


title: wblC Tet rep1


title: cranial meningioma 17


title: WT Tet rep2

value: wild type


title: P_17_4

value: run 2


title: P_20_1


title: cranial meningioma 28


title: Ctf18-HA in Pol2EDD cells in HU:  eSPAN

value: yeast cells


title: P_17_3


title: WT Tet rep1


title: P_17_2


title: Ctf18-HA in Pol2EDD cells in HU:  ChIP-ssSeq


title: WT rep2


title: cranial meningioma 15


title: cranial meningioma 16


title: cranial meningioma 27


title: Ctf18-HA in Pol2EDD cells in HU:  Input


title: P_17_1


title: Ctf18-HA in Pol2EDD cells in HU:  BrdU-IP-ssSeq

value: anti-BrdU (B44, BD Biosciences)


title: input DNA

data_processing:
Adapter sequences were trimmed from raw read data using Trimmomatic v0.36.
Processed reads were mapped to S. coelicolor A3(2) reference genome using Bowtie v2.3.2.
Duplicated reads were identified and removed using MarkDuplicates of Picard v1.133.
Significantly enriched peaks of ChIP sample compared to input DNA were determined using MACS v2.1.1.
Genome_build: GCF_000203835.1
Supplementary_files_format_and_content: The tab-delimeted text file lists information of MACS2-identified peaks.

extract_protocol:
A portion of sonicated and clarified lysate was set aside for input DNA preparation, and WblC-bound DNA were immunoprecipitated from the remainder. Both ChIP eluate and 'input DNA' lysate were reverse-crosslinked and DNA were extracted.
Library was constructed using KAPA DNA Library Preparation Kit (Roche) according to manufacturer's protocol.

treatment_protocol: Cultures were treated with 2 μg/ml tetracycline for 1 hour, followed by formaldehyde treatment for protein-DNA crosslinking and quenching by glycine.

value: 2 microgram/ml tetracycline, 1 hour


title: cranial meningioma 18

value: II


title: Ctf18-HA in HU:  eSPAN


title: P_14_3


title: P_14_2


title: Ctf18-HA in HU:  BrdU-IP-ssSeq


title: Ctf18-HA in HU:  ChIP-ssSeq


title: cranial meningioma 14

value: F

value: I


title: Ctf18-HA in HU:  Input


title: P_14_1


title: WblC ChIP

value: anti-WblC polyclonal rabbit IgG


title: S3

status: Public on Mar 27 2020

city: wenzhou

first: kankai

last: wang

address: wenzhou medical university

institute: wenzhou medical university

description: from melatonin pre-treatment rat

data_processing:
After sequencing was completed, the original reads were screened using Solexa CHASTITY quality control to obtain clean reads.
Cutadapt (v 1.14) was used to obtain trimmed reads, which were then compared to the reference genome using bowtie.
The miRNA expression was quantified by the software mirdeep2 (v  0.0.8) through the comparison results to the known genome and statistically obtained. The miRNA expression threshold is the miRNA with a CPM average of more than 1 in each group, which is considered to be expressed in the group and statistically analyzed.
Differential expression analysis of miRNAs between groups was performed using edgeR (v 3.18.1). The threshold was set to 1.5 times the difference, p-value was less than or equal to 0.05, and the average CPM in the group was greater than or equal to 1 to screen differentially expressed miRNAs.
Genome_build: Rnor6
Supplementary_files_format_and_content: Xlsx include CPM values for all samples

organism: Rattus norvegicus

source_name: plasma

extract_protocol:
Rat plasma was centrifuged at 10,000 g for 70 min to isolate exosomes. The total RNA sample was extracted and subjected to agarose electrophoresis and Nanodrop quality inspection and quantification, and then a library was constructed. The quality of the library was determined using an Agilent 2100 Bioanalyzer. The sequencing libraries of different samples were mixed, and single-stranded DNA was generated by denaturing with 0.1M NaOH. Vendor instructions Perform 51-cycle sequencing on the Illumina NextSeq 500 sequencer.
miRNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Adult male rats (200-250g) received intraperitoneal injections for 7 consecutive days with a control solvent (5% DMSO + PBS) or melatonin (10 mg/kg, dissolved in 5% DMSO + PBS) respectively. On day 8, plasma exosomes (Exo1 represented basic plasma exosome and EXO2 presented melatonin-treated plasma exosome) were isolated and identified.

value: Sprague Dawley

tag: weight

value: plasma

tag: agent

value: melatonin


title: S2_polysome

city: Seville

first: Juan

middle: Pablo

last: Couso

address: Carretera de Utrera, Km 1

country: Spain

institute: Centro Andaluz de Biologia del Desarrollo

description: ribosome footprint

data_processing:
Library strategy: Ribo-Seq
Sequencing reads were clipped, trimmed and aligned to an rRNA, snoRNA, snRNA & tRNA reference using Bowtie, discarding the alignments and collecting unaligned reads (Ingolia et al 2012).
Unaligned reads were mapped to the whole genome of Drosophila melanogaster FlyBase (Release 6.13) using HISAT2, default setiings.
Profiles of ribosome footprints  were constructed by quantifying the number of footprint reads aligned at each position within the feature (ORF) of interest. Ribosome density was computed by scaling read counts for each feature-by-feature length and by the total number of genome-aligned reads, using Rsamtool package (http://www.bioconductor.org/packages/release/bioc/html/Rsamtools.html).
For framing analyses, all ribosome footprints were aligned to a custom transcriptome assembly consisting of every ORF studied in its -18 and +15 mRNA context.
For each ORF, the number of reads per frame was counted using the R package "riboSeqR", and the probability of randomly obtaining framing as good or better that the observed was calculated using the R expression "pbinom([framed_reads]-1, [all_reads], 1/3, lower.tail=FALSE)"
Genome_build: FB2016_05 Dmel (Release r6.13)
Supplementary_files_format_and_content: Summary of ribosome density (expressed as RPKM) , framing (expressed as a p-value derived from a binomial test), transcription, ribosome-binding and translation calls, as well as Z-score analysis of translational regulation for annotated canonical protein-coding genes, short coding-sequences (shortCDSs) and upstream ORFs.

organism: Drosophila melanogaster

source_name: S2 cell

growth_protocol: Wild-type Drosophila melanogaster flies (Oregon-R) were grown in standard cages with molasses egg-laying plates containing yeast paste.

extract_protocol:
We purified mRNAs in polysomes, away from monosomes (80S), ribosomal subunits (40S, 60S). Footprinting was performed overnight at 4°C with RNaseI (Invitrogen), stopped with SUPERase·In TM RNase inhibitor (Invitrogen) and precipitated. mRNA from total cytoplasmic lysate, was purified using oligo (dT) Dynabeads (Invitrogen) and fragmented by alkaline hydrolysis.
28-34 nt ribosome footprints and 50-80 nt mRNA fragments were gel purified and prepared as previously described (Ingolia et al, 2012; Ingolia et al, 2009; Ingolia et al, 2011) for Next Generation Sequencing.
Libraries were sequenced on Illumina NextSeq and MiSeq machines with 50, 75 and 150bp SingleEnd read protocol.

treatment_protocol: After removing pre-laying plates, embryos were flash frozen, turned into powder using a pre-chilled pestle and mortar and homogenized in Lysis Buffer at 4°C for 20 min.

tag: developmental window

tag: replicate


title: late_cyt_RNA_T

description: cytoplasmic poly-A RNA

source_name: Embryo

value: 16-24 hours

value: late

value: replicate T


title: WT rep1

value: A3(2) strain M145


title: S2

description: from melatonin pre-treatment rat


title: S1

description: from melatonin pre-treatment rat


title: cranial meningioma 26


title: early_cyt_RNA_T

description: cytoplasmic poly-A RNA

value: 0-8 hours

value: early


title: N3

description: from PBS pre-treatment rat

value: PBS


title: early_polysome_T

description: ribosome footprint


title: N2

description: from PBS pre-treatment rat


title: N1

description: from PBS pre-treatment rat


title: mid_cyt_RNA_T

description: cytoplasmic poly-A RNA

value: 8-16 hours

value: mid


title: wblC rep2

value: wblC mutant


title: hSMC_growth medium_1

city: Hannover

first: Simona

last: Weisheit

address: Carl-Neuberg-Strasse 1

department: Cardiology and Angiology

country: Germany

institute: Hannover Medical School

hyb_protocol: cRNA fragmentation, hybridization and washing steps were carried-out as recommended in the ‘One-Color Microarray-Based Gene Expression Analysis Protocol V5.7’. 600ng of labelled cRNA were used for hybridization.

scan_protocol: Slides were scanned on the Agilent Micro Array Scanner G2565CA (pixel resolution 3 µm, bit depth 20).

data_processing: Data extraction was performed with the ‘Feature Extraction Software V10.7.3.1’ using the extraction protocol file ‘GE1_107_Sep09.xml’. Measurements of on-chip replicates were averaged using the geometric mean of processed intensity values of the green channel, ‘gProcessedSignal’ (gPS) to retrieve one resulting value per unique non-control probe. Single Features were excluded from averaging, if they i) were manually flagged, ii) were identified as Outliers by the Feature Extraction Software, iii) lay outside the interval of ‘1.42 x interquartile range‘ regarding the normalized gPS distribution of the respective on-chip replicate population, or, iv) showed a coefficient of variation of pixel intensities per Feature that exceeded 0.5.   Averaged gPS values were normalized by global linear scaling: All gPS values of one sample were multiplied by an array-specific scaling factor. This factor was calculated by dividing a ‘reference 75th Percentile value’ (set as 1500 for the whole series) by the 75th Percentile value of the particular Microarray to be normalized (‘Array I’ in the formula shown below). Accordingly, normalized gPS values for all samples (microarray data sets) were calculated by the following formula:   normalized gPSArray i = gPSArray i  x (1500 / 75th PercentileArray i)  Finally, a lower intensity threshold (surrogate value) was defined based on intensity distribution of negative control features. This value was fixed at 15 normalized gPS units. All of those measurements that fell below this intensity cutoff were substituted by the respective surrogate value of 15.

source_name: Human coronary artery smooth muscle cells

label_protocol: Synthesis of Cy3-labeled cRNA was performed with the ‘Quick Amp Labeling kit, one color’ (#5190-0442, Agilent Technologies) using 500ng of total RNA as input and according to the manufacturer’s recommendations, except that reaction volumes were halved.

growth_protocol: Human coronary artery SMCs were purchased from Lonza (Switzerland) and cultured at 37 °C with 5 % CO2 in the appropriate growth medium (Provitro, Germany or Lonza) containing 10 % FCS (GM).  Every medium additionally contained 1 % Penicillin-Streptomycin (Gibco, USA). Cell culture expansion was performed by detaching cells with 0,25 % Trypsin/EDTA (Gibco, USA).

extract_protocol: Total RNA was isolated using the RNeasy mini kit (Qiagen) according to the manufacturer’s instructions. RNA concentrations were measured using Nanodrop 2000c (Thermo Fisher, USA) and Agilent 2100 Bioanalyzer (Agilent Technologies, USA) according to the manufacturer’s instructions.

treatment_protocol: SMCs were serum starved over night and then treated with basal medium, growth medium or (+)-JQ1. After 6 h total RNA was isolated.

value: coronary artery smooth muscle cells


title: hSMC_JQ1_3


title: hSMC_growth medium_3


title: hSMC_growth medium_2


title: P_14_4

value: Corpus luteum

tag: day of pregnancy

tag: nanostring run

value: run 2


title: hSMC_basal medium_2


title: RIPK1E-KO_5

city: Cologne

first: Manolis

last: Pasparakis

state: NRW

address: Joseph Stelzmann Strasse, 26

department: Institute for Genetics

institute: University of Cologne

data_processing:
Base calling:Illumina RTA v3.4.4
Adaptor trimming:Illumina bcl2fastq2 v2.20.0
RNA-Seq data alignment to Mouse Genome GRCm38.78
Genome_build: GRCm38.78
Supplementary_files_format_and_content: log2normalisedcounts.csv

organism: Mus musculus

source_name: Total skin

extract_protocol:
Qiagen RNA Isolation kit
Illumina TruSeq totalRNA pus ribo-zero gold

tag: tissue

value: Total skin


title: RIPK1E-KO_4


title: hSMC_JQ1_1


title: hSMC_JQ1_2


title: hSMC_basal medium_3


title: hSMC_basal medium_4


title: RIPK1E-KO_2


title: Internal_mammary arteries_DM_Not treated A07_Pt5_C

city: Oxford

first: Nadia

last: Akawi

address: Headley Way

institute: John Radcliffe Hospital

description: Internal mammary arteries_DM_Not treated

hyb_protocol: As per manufacturer (Affymetrix)

scan_protocol: The GeneTitan System (Affymetrix)

data_processing:
Microarray data analyses and identification of the differentially expressed genes were performed using the GeneChip Expression Analysis Software (version 4, Affymetrix).
CEL format was analyzed using Affymetrix Expression Console, which performs the normalization of signal intensity, quality control and performs statistical analysis. For background adjustment, quantile normalization and summarization, a Robust Multichip Analysis (RMA) was used.

label: biotin

source_name: Primary internal mammary arteries from patients

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Internal mammary artery (IMA) samples were harvested with a “no touch” technique at the time of CABG. Vascular segments were transferred and incubated into oxygenated (95%O2 / 5% CO2) ice-cold Krebs Hensleit buffer.

extract_protocol: RNA was isolated by the QIAGEN microarray tissue kit as per manufacturer’s instructions and its quality tested with an Agilent bioanalyzer.

treatment_protocol: Internal mammary artery (IMA) segments from n=6 patients (3 non-diabetic patients & 3 diabetic patients) were inculbated with insulin 10nM for 6h

value: Internal mammary arteries

tag: cell line

value: Primary


title: Internal_mammary arteries_DM_Treated with M1 B07_Pt5_M1

description: Internal mammary arteries_DM_Treated with M1


title: Internal_mammary arteries_Non DM_Not treated A07_Pt2_C

description: Internal mammary arteries_Non DM_Not treated


title: RIPK1E-KO_1


title: Internal_mammary arteries_Non DM_Treated with M1 B09_Pt3_M1

description: Internal mammary arteries_Non DM_Treated with M1


title: Internal_mammary arteries_DM_Not treated A09_Pt6_C


title: Internal_mammary arteries_Non DM_Treated with M1 B05_Pt1_M1


title: RIPK1E-KO_3


title: Internal_mammary arteries_DM_Not treated A05_Pt4_C


title: Internal_mammary arteries_Non DM_Not treated A05_Pt1_C


title: hSMC_basal medium_1


title: Internal_mammary arteries_Non DM_Treated with M1 B07_Pt2_M1


title: Internal_mammary arteries_DM_Treated with M1 B09_Pt6_M1


title: Wild type_5

value: Wild type


title: Wild type_3


title: Wild type_1


title: Wild type_2


title: Internal_mammary arteries_DM_Treated with M1 B05_Pt4_M1


title: RIPK1E-KO_RTi treated_1

value: RTi drug


title: RIPK1E-KO_RTi treated_3


title: Wild type_4


title: RIPK1E-KO_RTi treated_2


title: RIPK1E-KO_RTi treated_5


title: RIPK1E-KO_RTi treated_4


title: Internal_mammary arteries_Non DM_Not treated A09_Pt3_C


title: c-MYC liver tumour 4

first: Mariia

last: Yuneva

address: 1, Midland Road

description: c-MYC liver tumour 4

hyb_protocol: Following fragmentation, 10ug of cRNA were hybridised for 16hrs at 45c on Genechip Human Gene 2.0 ST arrays. Genechips were washed and stained in the Affymetrix Fludics station 450.

scan_protocol: Genechips were scanned using the Affymetrix Genechip Scanner 3000G

data_processing: Data were analyzed using Bioconductor 2.13 running on R 3.0.2. Probeset expression measures were calculated using the Affymetrix package’s Robust Multichip Average (RMA) default method.

source_name: Liver tumour

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

growth_protocol: c-MYC driven tumours were harvested when tumours reached the humane endpoint. Normal livers from matched mice were used as control.

extract_protocol: RLT buffer (+beta-ME) extraction of total RNA was performed and purified further with the Rneasy kit (Qiagen) according to the manufacturers instructions

treatment_protocol: Liver-specific Human c-MYC overexpression (CEBPB-LAP promoter under the control of doxycycline)

value: c-MYC driven Liver tumour


title: c-MYC liver tumour 1

description: c-MYC liver tumour 1


title: c-MYC liver tumour 3

description: c-MYC liver tumour 3


title: c-MYC liver tumour 2

description: c-MYC liver tumour 2


title: Control Liver 3

description: Control Liver 3

source_name: Liver

value: Liver


title: Control Liver 4

description: Control Liver 4


title: Control Liver 2

description: Control Liver 2


title: Control Liver 1

description: Control Liver 1


title: TRI415-002

city: Sendai

first: Shin

last: Takahashi

address: 4-1, Seiryo-machi, Aobaku

department: Clinical Oncology

country: Japan

institute: Tohoku University

hyb_protocol: The labeled cDNA was hybridized to the Whole Human Genome 4 × 44 K Microarray (Agilent) following manual instraction.

scan_protocol: Scanning and image analysis of the microarray were performed using a DNA microarray scanner (Agilent). Raw fluorescence intensities were quantified and normalized using Feature Extraction Software (Agilent).

data_processing: The data were normalized by percentile shift (all samples were normalized to the signal value of the 75th percentile of all probes on the microarray). Genes with low signals that could not be detected in all samples were ruled out.

source_name: Colorectal cancer

label_protocol: cDNA was amplified from total RNA (300 ng) using a TransPlex Complete Whole Transcriptome Amplification Kit (Sigma, St Louis, MO, USA). The amplified cDNA was then purified using a QIAquick PCR Purification Kit (Qiagen). The purified cDNA (1.5 μg) was labeled with Cy3 using a Genomic DNA ULS Labeling Kit (Agilent).

extract_protocol: Tumor cells were collected by macrodissection under the guidance of a hematoxylin-eosin-stained tissue slide. Total RNA was extracted using an Absolutely RNA FFPE Kit (Agilent, Santa Clara, CA, USA).

value: Primary tumor

tag: disease state

value: Colorectal cancer


title: TRI410-004-2


title: TRI413-002


title: TRI413-003


title: TRI413-010


title: TRI415-003


title: TRI409-022


title: TRI413-011


title: TRI410-003


title: TRI415-005


title: TRI409-023


title: TRI410-002


title: TRI413-006


title: TRI415-004


title: TRI415-001


title: TRI409-024


title: TRI409-017


title: TRI409-008


title: TRI409-004


title: TRI409-007


title: TRI409-005


title: TRI409-002


title: TRI409-016


title: TRI409-019


title: TRI409-011


title: TRI409-014


title: TRI409-009


title: TRI409-003


title: TRI409-015


title: TRI409-001


title: TRI408-012


title: TRI408-011


title: TRI408-009


title: TRI408-010


title: TRI408-008


title: TRI408-005


title: TRI407-002


title: TRI408-007


title: TRI408-001


title: TRI408-006


title: TRI402-004


title: TRI403-001


title: TRI402-001


title: TRI401-012


title: TRI401-014


title: TRI408-004


title: TRI401-016


title: TRI401-013


title: TRI408-003


title: TRI408-002


title: TRI402-003


title: TRI407-005


title: TRI404-002


title: TRI407-001


title: TRI402-005


title: TRI407-004


title: TRI402-002


title: wblC rep1

value: A3(2) strain M145


title: TRI404-001


title: TRI401-009


title: TRI401-008


title: TRI401-011


title: TRI401-005


title: TRI401-010


title: TRI401-007


title: TRI401-001


title: TRI401-004


title: TRI321-017


title: TRI321-016


title: TRI401-002


title: TRI401-003


title: TRI321-018


title: TRI321-014


title: TRI321-006


title: TRI321-009


title: TRI321-011


title: TRI321-013


title: TRI321-008


title: TRI312-001


title: TRI321-012


title: TRI321-015


title: TRI321-002


title: TRI321-005


title: TRI321-007


title: TRI312-002


title: TRI312-005


title: TRI312-004


title: TRI321-010


title: TRI312-003


title: TRI321-004


title: TRI321-003


title: TRI321-001


title: TRI311-057


title: TRI311-058


title: TRI311-047


title: TRI311-051


title: TRI311-049


title: TRI311-054


title: TRI311-053


title: TRI311-046


title: TRI311-042


title: TRI311-037


title: TRI311-033


title: TRI311-035


title: TRI311-056


title: TRI311-030


title: TRI311-048


title: TRI311-031


title: TRI311-036


title: TRI311-025


title: TRI311-024


title: TRI311-026


title: TRI311-052


title: TRI311-022


title: TRI311-043


title: TRI311-014


title: TRI311-015


title: TRI311-028


title: TRI311-032


title: TRI311-023


title: TRI311-021


title: TRI311-011


title: TRI311-027


title: TRI311-008


title: TRI311-003


title: TRI311-009


title: TRI311-002


title: TRI310-004


title: TRI309-001


title: TRI308-044


title: TRI311-029


title: TRI309-012


title: TRI309-010


title: TRI310-001


title: TRI308-022


title: TRI308-041


title: TRI308-032


title: TRI308-025


title: TRI308-035


title: TRI309-004


title: TRI308-036


title: TRI308-024


title: TRI308-046


title: TRI308-030


title: TRI310-003


title: TRI308-049


title: TRI308-037


title: TRI308-045


title: TRI308-048


title: TRI308-020


title: TRI311-007


title: TRI308-031


title: TRI308-018


title: TRI308-029


title: TRI310-002


title: TRI308-021


title: TRI308-017


title: TRI308-016


title: TRI308-008


title: TRI308-010


title: TRI308-019


title: TRI308-004


title: TRI308-011


title: TRI306-001


title: TRI308-001


title: TRI308-003


title: TRI303-005


title: TRI306-004


title: TRI306-003


title: TRI305-001


title: TRI308-005


title: TRI305-002


title: TRI303-002


title: TRI304-001


title: TRI304-002


title: TRI303-003


title: TRI306-002


title: TRI304-008


title: TRI308-013


title: TRI303-004


title: TRI307-001


title: TRI304-005


title: TRI303-001


title: TRI304-003


title: TRI308-006


title: TRI302-021


title: TRI302-020


title: TRI302-015


title: TRI302-010


title: TRI302-014


title: TRI302-019


title: TRI302-016


title: TRI302-018


title: TRI302-013


title: TRI302-012


title: TRI301-035


title: TRI302-005


title: TRI301-030


title: TRI301-038


title: TRI301-031


title: TRI301-034


title: TRI301-039


title: TRI302-009


title: TRI302-003


title: TRI302-007


title: TRI302-006


title: TRI302-001


title: TRI302-004


title: TRI302-002


title: TRI302-008


title: TRI302-011


title: TRI301-037


title: TRI301-036


title: TRI301-019


title: TRI301-027


title: TRI301-017


title: TRI301-018


title: TRI301-013


title: TRI301-026


title: TRI301-025


title: TRI301-032


title: TRI301-028


title: TRI301-023


title: TRI301-010


title: TRI301-016


title: TRI301-020


title: TRI301-006


title: TRI301-024


title: TRI301-029


title: TRI301-021


title: TRI301-022


title: TRI301-004


title: TRI301-015


title: TRI301-009


title: TRI301-003


title: TRI217-001


title: TRI210-001


title: TRI301-012


title: TRI301-007


title: TRI301-011


title: TRI205-002


title: TRI209-002


title: TRI301-005


title: TRI203-002


title: TRI202-001


title: TRI301-008


title: TRI203-003


title: TRI301-002


title: TRI210-002


title: TRI205-004


title: TRI217-004


title: TRI209-001


title: TRI205-005


title: TRI209-005


title: TRI205-001


title: TRI209-004


title: TRI210-004


title: TRI111-003


title: TRI203-001


title: TRI111-002


title: TRI203-005


title: TRI203-006


title: TRI108-021


title: TRI111-001


title: TRI203-004


title: TRI108-015


title: TRI108-019


title: TRI108-020


title: TRI108-017


title: TRI108-013


title: TRI108-002


title: TRI108-007


title: TRI108-014


title: TRI108-009


title: TRI108-006


title: TRI106-003


title: TRI106-004


title: TRI108-005


title: TRI108-018


title: TRI106-001


title: TRI108-001


title: TRI105-001


title: TRI103-002


title: TRI102-022


title: TRI103-001


title: TRI106-002


title: TRI102-016


title: TRI103-003


title: TRI108-008


title: TRI102-023


title: TRI102-018


title: TRI102-014


title: TRI102-010


title: TRI102-013


title: TRI102-008


title: TRI108-003


title: TRI102-011


title: TRI102-004


title: TRI102-001


title: TRI102-003


title: TRI102-012


title: TRI101-001


title: TRI102-006


title: Rice (IKP)-root-NaCl (Ref: control)-replicate 1

city: Louvain-la-Neuve

first: Willy

last: IRAKOZE

state: Belgium

address: 5 (Bte 7.07.13) Place Croix du Sud

department: Earth and Life Institute-Agronomy

country: Belgium

institute: UCLouvain

description: Biological replicate 1 of 2

hyb_protocol: Hybridization of the labeled cDNA (0.3 microg per sample) were added to hybridization buffer (Agilent In Situ Hybridization Kit Plus)  and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially according to Agilent instructions.

scan_protocol: Scanned on an Agilent Scanner G2565B Images were quantified using Agilent Feature Extraction Software (version 9.1).

data_processing: Agilent Feature Extraction Software (v 9.1) was used for background subtraction and LOWESS normalization.

label: Alexa Fluor 555

organism: Oryza sativa

source_name: IKP-control, root

label_protocol:
First strand cDNA was synthetized from 10 microg RNA. Synthesized cDNA were purified and labeled with Alexa Fluor 555 and Alexa Fluor 647. Experiments were carried out according to instructions of the Superscript Plus Indirect cDNA Labeling system (Invitrogen).
The quality of the labeled cDNA and its concentration were respectively measured with the 2100 Bioanalyser (Agilent Technologies, Santa Clara, CA) and ND-1000 spectrophotometer (NanoDrop Technologies, Isogen Life Science, De Meern, The Netherlands).

growth_protocol: plants where grown in hydroponic solution (Yoshida, 1976) in phytotron (heated and extra lighting  to expose plants to a minimum 12 h day length at a minimum PAR of 120 µmol m-2 s-1 at the top of the canopy).

extract_protocol: Total RNA was prepared from 100 mg of roots or shoots (of pooled plants) using tthe RNeasy Plant Mini Kit (Qiagen) following the manufacturer’s instructions.

treatment_protocol: Twenty five days old rice seedlings were exposed to 0, 200 mM NaCl or 100 mM Na2SO4 for 48 hours in hydroponic culture.

value: Root

value: No salt stress

label: Alexa Fluor 647

source_name: IKP-NaCl, root

tag: organ

value: 200 mM NaCl


title: Rice (IKP)-root-NaCl (Ref: control)-replicate 2

description: Biological replicate 2 of 2


title: Rice (IKP)-shoot-NaCl (Ref: control)-replicate 2

description: Biological replicate 2 of 2

source_name: IKP-control, shoot

value: Shoot

source_name: IKP-NaCl, shoot


title: Rice (IKP)-root-Na2SO4 (Ref: control)-replicate 2

description: Biological replicate 2 of 2

source_name: IKP-Na2SO4, root

value: 100 mM Na2SO4


title: Rice (IKP)-shoot-Na2SO4 (Ref: NaCl)-replicate 2

description: Biological replicate 2 of 2

source_name: IKP-Na2SO4, shoot


title: TRI102-005


title: TRI102-002


title: Rice (IKP)-root-Na2SO4 (Ref: NaCl)-replicate 1

description: Biological replicate 1 of 2


title: Rice (IKP)-root-Na2SO4 (Ref: control)-replicate 1

description: Biological replicate 1 of 2


title: Rice (IKP)-root-Na2SO4 (Ref: NaCl)-replicate 2

description: Biological replicate 2 of 2


title: TRI102-019


title: CeA-ZT9-Rep15

city: Glassboro

first: Mary

last: Staehle

state: NJ

address: 201 Mullica Hill Road

department: Biomedical Engineering

institute: Rowan University

description:
ZT9
S244 CeA

data_processing:
Raw CT values were calculated using default settings in the Real-Time PCR Analysis Software (Fluidigm) and software-designated failed reactions were discarded from analysis.  For each sample, the raw CT values were quantile-normalized (∆CT) in R version 2-11-1.  Quantile normalized data are presented as the normalized data herein.
Normalized data presented is quantile normalized data.  Fold Change data is not typical 2^ddCt fold change values, but rather the ddCt values that are normalized to the average ZT5 expression.

label: UPL (FAM)

source_name: bilateral brain punch of CeA

label_protocol: Reverse transcription was performed from 100ng total RNA using SuperScript II (Invitrogen, Carlsbad, CA). The standard BioMark™ protocol was used to pre-amplify cDNA samples for 14 cycles (TaqMan® PreAmp Master Mix: Applied Biosystems, Foster City, CA).  qRT-PCR reactions were performed with 96.96 BioMark™ Dynamic Arrays (Fluidigm, South San Francisco, CA), enabling simultaneous quantitative measurement of up to 96 transcripts in 96 samples each (Orina et al., 2009; Spurgeon et al., 2008).  Runs were 40 cycles (15s at 95C; 5s at 70C; 60s at 60C).

growth_protocol: Forty young, male, Sprague Dawley rats (35-45g, Harlan Laboratories, Indianapolis, IN) were housed individually in the Thomas Jefferson University Alcohol Research Center Animal Core Facility and fed standard chow and water until their weight reached 120 grams (approximately 10 days).  Upon achievement of the weight criteria, the rats were given an alcohol-free, maltose-dextrin substituted, Lieber DeCarli liquid diet (BioServ, Frenchtown, NJ) ad libitum for three days.  This diet is a liquid control diet that is nutritionally balanced to provide all necessary nutrients without supplementation (Lieber and Decarli, 1994).  On subsequent days, each rat received a restricted quantity of the liquid diet such that the 24-hour delayed caloric intake equaled the previous day’s intake of matched alcohol-fed animals. Only the calorie-restricted, alcohol-naïve animals were used in this study.

extract_protocol: RNA was extracted with either the RNeasy or the AllPrep DNA/RNA extraction kit (Qiagen, Valencia, CA).  Total RNA was DNAse treated (DNA-Free RNA kit, Zymo Research, Orange, CA)

treatment_protocol: Animals considered here were not subjected to any treatments.

tag: strain

value: Sprague Dawley

tag: brain region

value: CeA

tag: time

tag: Sex

value: male


title: Rice (IKP)-shoot-Na2SO4 (Ref: NaCl)-replicate 1

description: Biological replicate 1 of 2


title: Rice (IKP)-shoot-Na2SO4 (Ref: control)-replicate 1

description: Biological replicate 1 of 2


title: TRI102-007


title: Rice (IKP)-shoot-NaCl (Ref: control)-replicate 1

description: Biological replicate 1 of 2


title: CeA-ZT9-Rep11

description:
ZT9
S208 CeA


title: CeA-ZT9-Rep14

description:
ZT9
S238 CeA


title: CeA-ZT9-Rep13

description:
ZT9
S220 CeA


title: CeA-ZT9-Rep12

description:
ZT9
S211 CeA


title: CeA-ZT9-Rep3

description:
ZT9
S121 CeA


title: CeA-ZT9-Rep9

description:
ZT9
S157 CeA


title: CeA-ZT9-Rep5

description:
ZT9
S136 CeA


title: CeA-ZT9-Rep7

description:
ZT9
S145 CeA


title: CeA-ZT9-Rep1

description:
ZT9
S106 CeA


title: CeA-ZT5-Rep13

description:
ZT5
S262 CeA


title: CeA-ZT5-Rep18

description:
ZT5
S259 CeA


title: CeA-ZT5-Rep16

description:
ZT5
S184 CeA


title: CeA-ZT5-Rep15

description:
ZT5
S181 CeA


title: CeA-ZT9-Rep10

description:
ZT9
S163 CeA


title: CeA-ZT5-Rep12

description:
ZT5
S229 CeA


title: TRI102-009


title: CeA-ZT9-Rep2

description:
ZT9
S112 CeA


title: CeA-ZT5-Rep5

description:
ZT5
S130 CeA


title: CeA-ZT5-Rep3

description:
ZT5
S115 CeA


title: CeA-ZT5-Rep14

description:
ZT5
S175 CeA


title: CeA-ZT5-Rep6

description:
ZT5
S139 CeA


title: CeA-ZT3-Rep7

description:
ZT3
S250 CeA


title: CeA-ZT5-Rep2

description:
ZT5
S109 CeA


title: CeA-ZT3-Rep1

description:
ZT3
S169 CeA


title: CeA-ZT3-Rep2

description:
ZT3
S178 CeA


title: CeA-ZT5-Rep1

description:
ZT5
S103 CeA


title: CeA-ZT3-Rep6

description:
ZT3
S241 CeA


title: CeA-ZT3-Rep4

description:
ZT3
S193 CeA


title: DVC-ZT9-Rep15

description:
ZT9
S244 DVC

source_name: bilateral brain punch of DVC

value: DVC


title: CeA-ZT3-Rep3

description:
ZT3
S187 CeA


title: CeA-ZT3-Rep5

description:
ZT3
S205 CeA


title: Rice (IKP)-shoot-Na2SO4 (Ref: control)-replicate 2

description: Biological replicate 2 of 2


title: DVC-ZT9-Rep13

description:
ZT9
S220 DVC


title: DVC-ZT9-Rep9

description:
ZT9
S157 DVC


title: DVC-ZT9-Rep11

description:
ZT9
S208 DVC


title: DVC-ZT9-Rep7

description:
ZT9
S145 DVC


title: DVC-ZT9-Rep14

description:
ZT9
S238 DVC


title: CeA-ZT5-Rep11

description:
ZT5
S226 CeA


title: DVC-ZT9-Rep10

description:
ZT9
S163 DVC


title: TRI101-002


title: DVC-ZT9-Rep12

description:
ZT9
S211 DVC


title: CeA-ZT5-Rep17

description:
ZT5
S253 CeA


title: DVC-ZT9-Rep6

description:
ZT9
S142 DVC


title: CeA-ZT5-Rep10

description:
ZT5
S223 CeA


title: DVC-ZT9-Rep5

description:
ZT9
S136 DVC


title: DVC-ZT9-Rep8

description:
ZT9
S154 DVC


title: DVC-ZT9-Rep3

description:
ZT9
S121 DVC


title: DVC-ZT9-Rep4

description:
ZT9
S133 DVC


title: DVC-ZT9-Rep1

description:
ZT9
S106 DVC


title: DVC-ZT9-Rep2

description:
ZT9
S112 DVC


title: DVC-ZT5-Rep18

description:
ZT5
S259 DVC


title: DVC-ZT5-Rep16

description:
ZT5
S184 DVC


title: DVC-ZT5-Rep15

description:
ZT5
S181 DVC


title: DVC-ZT5-Rep17

description:
ZT5
S253 DVC


title: DVC-ZT5-Rep6

description:
ZT5
S139 DVC


title: DVC-ZT5-Rep5

description:
ZT5
S130 DVC


title: DVC-ZT5-Rep14

description:
ZT5
S175 DVC


title: DVC-ZT3-Rep7

description:
ZT3
S250 DVC


title: DVC-ZT5-Rep7

description:
ZT5
S166 DVC


title: DVC-ZT5-Rep13

description:
ZT5
S262 DVC


title: DVC-ZT5-Rep4

description:
ZT5
S124 DVC


title: DVC-ZT5-Rep8

description:
ZT5
S172 DVC


title: DVC-ZT5-Rep12

description:
ZT5
S229 DVC


title: DVC-ZT5-Rep2

description:
ZT5
S109 DVC


title: DVC-ZT5-Rep3

description:
ZT5
S115 DVC


title: DVC-ZT3-Rep5

description:
ZT3
S205 DVC


title: DVC-ZT5-Rep1

description:
ZT5
S103 DVC


title: DVC-ZT3-Rep6

description:
ZT3
S241 DVC


title: DVC-ZT3-Rep1

description:
ZT3
S169 DVC


title: DVC-ZT3-Rep3

description:
ZT3
S187 DVC


title: DVC-ZT3-Rep2

description:
ZT3
S178 DVC


title: DVC-ZT5-Rep10

description:
ZT5
S223 DVC


title: WHEL ID 5304

city: La Jolla

first: Loki

last: Natarajan

address: 3855 Health Sciences DR

institute: University of California, San Diego

description:
NanoString reporter probe
X2895625922_10

hyb_protocol: Transcript expression was quantified with 250 ng of total RNA using the NanoString nCounter analysis system with a custom miRGE CodeSet. Assay reactions were assembled per manufacturer’s specifications (NanoString Technologies, INC Seattle, WA).

scan_protocol: See manufacturer's website http://www.nanostring.com for procedures.  Digital Analyzer was set to scan at 1155 FOV (fields of view).

data_processing: R-NanoStringNorm package was used to normalize data. Code count normalization used 6 positive controls and background subtraction used 8 negative controls. All expression values were first log2 transformed.  For mRNAs, five (ACTB, PSMC4, MRPL19, RPLPO, SF3A1) genes were used as housekeepers; the data matrix elements are relative gene expression values (log2 transformed) compared to log2 value of the geometric mean of the five house-keepers within each sample. For miRNAs, log2 expression values are presented.  For miRNAs, quantile normalization was performed. Normalized datasets for both mRNA and miRNA are available on the series record. Sample data tables include data only for mRNAs.

source_name: primary breast cancer

extract_protocol: Unstained slides from archival specimens with ≥ 40% tumor cellularity were incubated at 65 °C for 30 minutes and deparaffinized using Citrisolv  (Fisher Scientific, Pittsburgh, PA) followed by ethanol wash. Tumor tissues were macrodissected into RNAse-free microfuge tubes, and nucleic acids isolated using the Qiagen AllPrep FFPE kit (#80234).  Manufacturer’s instructions were followed with the exception that the proteinase K digestion step was extended to an overnight incubation for the DNA isolation.

value: primary breast cancer


title: WHEL ID 7418

description:
NanoString reporter probe
X2895625923_12

label_protocol: See manufacturer's website http://www.nanostring.com for procedures


title: WHEL ID 7202

description:
NanoString reporter probe
X2895473660_11


title: WHEL ID 7465

description:
NanoString reporter probe
X2895625924_9


title: WHEL ID 13157

description:
NanoString reporter probe
X2895514930_3


title: WHEL ID 1279

description:
NanoString reporter probe
X2895625921_11


title: WHEL ID 3152

description:
NanoString reporter probe
X2895473659_10


title: DVC-ZT5-Rep9

description:
ZT5
S217 DVC


title: DVC-ZT3-Rep4

description:
ZT3
S193 DVC


title: WHEL ID 9176

description:
NanoString reporter probe
X2895473656_8


title: WHEL ID 7411

description:
NanoString reporter probe
X2895473658_9


title: WHEL ID 1219

description:
NanoString reporter probe
X2895473650_7


title: WHEL ID 3141

description:
NanoString reporter probe
X2895473652_6


title: WHEL ID 7191

description:
NanoString reporter probe
X2895473654_2


title: WHEL ID 11168

description:
NanoString reporter probe
X2895473651_8


title: WHEL ID 13020

description:
NanoString reporter probe
X2895473657_12


title: WHEL ID 1133

description:
NanoString reporter probe
X2895473649_6


title: WHEL ID 9010

description:
NanoString reporter probe
X2895473648_5


title: WHEL ID 7427

description:
NanoString reporter probe
X2895473646_2


title: WHEL ID 3139

description:
NanoString reporter probe
X2895473643_10


title: WHEL ID 7475

description:
NanoString reporter probe
X2895473640_7


title: WHEL ID 1109

description:
NanoString reporter probe
X2895473639_6


title: WHEL ID 13006

description:
NanoString reporter probe
X2895473644_11


title: WHEL ID 1105

description:
NanoString reporter probe
X2895473641_8


title: WHEL ID 3135

description:
NanoString reporter probe
X2895473647_4


title: WHEL ID 3140

description:
NanoString reporter probe
X2895473642_9


title: WHEL ID 9198

description:
NanoString reporter probe
X2895473638_5


title: WHEL ID 3127

description:
NanoString reporter probe
X2895473637_4


title: WHEL ID 7367

description:
NanoString reporter probe
X2895473636_3


title: WHEL ID 5208

description:
NanoString reporter probe
X2895473632_11


title: WHEL ID 7158

description:
NanoString reporter probe
X2895473633_12


title: WHEL ID 7259

description:
NanoString reporter probe
X2895473630_9


title: WHEL ID 7160

description:
NanoString reporter probe
X2895473629_7


title: WHEL ID 5527

description:
NanoString reporter probe
X2895473653_10


title: WHEL ID 3130

description:
NanoString reporter probe
X2895473634_1


title: WHEL ID 5404

description:
NanoString reporter probe
X2895473635_2


title: WHEL ID 7047

description:
NanoString reporter probe
X2895473628_6


title: WHEL ID 3084

description:
NanoString reporter probe
X2895473645_1


title: WHEL ID 3040

description:
NanoString reporter probe
X2895473627_5


title: WHEL ID 5129

description:
NanoString reporter probe
X2895473626_4


title: WHEL ID 13152

description:
NanoString reporter probe
X2895473624_2


title: WHEL ID 5455

description:
NanoString reporter probe
X2895473625_3


title: WHEL ID 7359

description:
NanoString reporter probe
X2895473623_1


title: WHEL ID 7256

description:
NanoString reporter probe
X2895473619_9


title: WHEL ID 9121

description:
NanoString reporter probe
X2895473618_8


title: WHEL ID 13205

description:
NanoString reporter probe
X2895473621_11


title: WHEL ID 9248

description:
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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title: WHEL ID 1100

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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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title: WHEL ID 1397

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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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title: WHEL ID 7123

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NanoString reporter probe
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title: WHEL ID 7199

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NanoString reporter probe
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title: WHEL ID 7177

description:
NanoString reporter probe
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title: WHEL ID 7144

description:
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title: SHPC36 DUHi mX 239

city: Lyon

first: Sophie

last: PANTALACCI

address: 46 Allée d'Italie

department: Ecole Normale Supérieure de Lyon

country: France

institute: LBMC

data_processing:
Reads were then mapped to the mouse genome using Kallisto ((Bray et al., 2016), version 0.44.0, options -l 200, -s 20). The reference cDNA sequences and annotation files for M. musculus are based on C57B6 strain. They were collected from Ensembl 88 (10 5129 cDNAs, (Zerbino et al., 2018), GRCm38). Reads were independently mapped to the FVB/NJ strain cDNAs, collected from Ensembl strains 94, using biomart (10 1520 cDNAs, strain FVB_NJ_v1, accession GCA_001624535.1).
Tximport was used to import and summarize transcript-level estimates at gene level (version 1.6, (Soneson et al., 2016)).
Differentially expressed genes were detected with DESeq2 (Love et al., 2014), version 1.18.1) with design  (jaw+strain), and using FDR significance threshold = 0.05.
Genome_build: Ensembl 88 - GRCm38
Supplementary_files_format_and_content: normalized basemean from DEseq2, p-adj

source_name: molar tooth germ

growth_protocol: Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.

extract_protocol:
Following dissection in culture medium, tooth germs were stored in RNA later at -20°C. RNA was extracted with RNAeasy micro kit (Qiagen), and controlled with Q-bit (Invitrogen) and Tapestation (Agilent technologies).
RNA-Seq samples were prepared following the TruSeq® RNA Sample Preparation v2 Guide, starting from 100ng of total RNA of top quality (RINe>9.5).

treatment_protocol: Carefull dissection of first molar germ

value: DUHi strain

tag: location

value: upper molar germ

value: 239 mg embryo


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title: SHPC35 DUHi mX 219

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title: SHPC34 DUHi mX 196

value: 196mg embryo


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title: SHPC31 FVB mX 195

value: FVB strain

value: 195mg embryo


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title: SHPC29 FVB mD 215

value: lower molar germ

value: 215mg embryo


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title: SHPC27 DUHi mD 239


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title: SHPC32 FVB mX 215


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title: UBE1L+IFN rep2

first: Junbao

last: Fan

address: 3855, Health Sciences Drive

department: Moores Cancer Center

data_processing:
Raw transcriptomic data were trimmed using Trimmomatic 0.36 and quantified with Salmon 0.9.1 on M16 genome annotation. Differential expression (DE) analysis was performed with the edgeR package on RStudio. Hierarchical clustering and volcano plot of top results from DE analysis was performed on Matlab software.
Genome_build: M16 genome annotation

source_name: MECs

extract_protocol:
Total RNA from MECs was isolated using Trizol reagent (ThermoFisher) according to the manufacturer’s instructions. Total RNA was assessed for quality using an Agilent Tapestation, and RNA Integrity Numbers (RIN) ranged from 9.2 to 10.0. Libraries were generated using Illumina’s TruSeq Stranded mRNA Sample Prep Kit following manufacturer’s instructions, modifying the shear time to 5 minutes. RNA libraries were multiplexed and sequenced with 50 base pair (bp) single reads (SR50) to a depth of approximately 25 million reads per sample on an Illumina HiSeq4000.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: FVB

tag: genotype/variation

value: Uba7 KO


title: Ctrl+IFN+LPS rep2

tag: treatment

value: Control (empty vector) + LPS (100ng/mL) for 6 hours


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description:
NanoString reporter probe
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title: Ctrl+IFN+LPS rep1


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description:
NanoString reporter probe
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title: UBE1L+IFN rep1


title: WHEL ID 11044

description:
NanoString reporter probe
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title: Ctrl+IFN rep2

value: Control (empty vector)


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description:
NanoString reporter probe
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title: WHEL ID 11194

description:
NanoString reporter probe
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title: UBE1L+IFN+LPS rep1

value: Uba7 KO + LPS (100ng/mL) for 6 hours


title: UBE1L+IFN+LPS rep2


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NanoString reporter probe
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NanoString reporter probe
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NanoString reporter probe
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description:
NanoString reporter probe
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description:
NanoString reporter probe
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title: Ctrl+IFN rep1


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description:
NanoString reporter probe
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description:
NanoString reporter probe
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description:
NanoString reporter probe
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description:
NanoString reporter probe
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description:
NanoString reporter probe
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description:
NanoString reporter probe
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description:
NanoString reporter probe
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description:
NanoString reporter probe
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description:
NanoString reporter probe
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description:
NanoString reporter probe
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description:
NanoString reporter probe
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description:
NanoString reporter probe
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title: MCF7, Tamoxifen, replicate N4

city: Trieste

first: Silvano

last: Piazza

address: localita' Padriciano 99

country: Italy

institute: ICGEB

description: Gene expression of MCF7 cells grown for 24 hours with Tamoxifen (5 uM) added to the cell medium

hyb_protocol: 1.65 mg of Cy3-labeled cRNA (specific activity: 19.4 ±1.6 pmol Cy3 per mg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ml containing 1x Fragmentation Buffer and 2x GE (Gene Expression) Blocking Agent (Gene Expression Hybridization Kit, p/n 5188-5242, Agilent Technologies) following manufacturer’s instructions. On completion of the fragmentation reaction, 55 ml of 2x Hi-RPM Hybridization Buffer were added to the fragmentation mixture and hybridized to Agilent Mouse GE 4x44K V2 Microarray kit (G4846A, Agilent Technologies) for 17 hours at 65°C in a rotating hybridization oven.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C, Agilent Technologies) using the AgilentHD_GX_1Color Profile (Scan Area: 61x21.6 mm; Scan resolution: 5 mm, dye channel set to 100% Green PMT) of Agilent ScanControl software 8.1.3 (Agilent Technologies).

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent Technologies) using default parameters protocol GE1_107_Sep09).
Background signal has been correct using Edwards method as implemented in limma package. Normalization between samples has been performed using quantile method as implemented in limma package.

source_name: MCF7, Tamoxifen, replicate N4

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 g RNA using the One-Color Low Input Quick Amp Labeling Kit (p/n 5190-2331, Agilent Technologies)

growth_protocol: MCF7 breast cancer cells were plated in 10 cm dishes in regular DMEM medium containing 10% FBS and 1.0 g/L glucose

extract_protocol: TRIZOL RNA Isolation Protocol was followed.

treatment_protocol: The DMEM cell medium was removed and cells were incubated for 24h either in the same medium or in low-glucose (0.5 g/L) DMEM medium with 1 % FBS (short-term starvation conditions). 24h later, tamoxifen (5 uM) or vehicle were added to the culture medium. 24 h later, cells were used for RNA extraction and gene expression was assessed by standard gene expression microarrays.

tag: protocol

value: Tamoxifen


title: MCF7, starvation and Tamoxifen, replicate N4

description: Gene expression of MCF7 cells grown for 24 hours in low-glucose (0.5 g/L) DMEM medium with 1 % FBS and for other 24 hours with Tamoxifen (5 uM) added to the cell medium

value: starvation and Tamoxifen


title: MCF7, starvation and Tamoxifen, replicate N3


title: MCF7, starvation and Tamoxifen, replicate N2


title: MCF7, Tamoxifen, replicate N3

source_name: MCF7, Tamoxifen, replicate N3


title: MCF7, Tamoxifen, replicate N2

source_name: MCF7, Tamoxifen, replicate N2


title: MCF7, starvation and Tamoxifen, replicate N1


title: MCF7, Tamoxifen, replicate N1

source_name: MCF7, Tamoxifen, replicate N1


title: MCF7, starvation, replicate N1

description: Gene expression of MCF7 cells grown for 24 hours in low-glucose (0.5 g/L) DMEM medium with 1 % FBS

source_name: MCF7, starvation, replicate N1

value: starvation


title: WHEL ID 11159

description:
NanoString reporter probe
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value: primary breast cancer


title: MCF7, starvation, replicate N3

source_name: MCF7, starvation, replicate N3


title: MCF7, starvation, replicate N2

source_name: MCF7, starvation, replicate N2


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NanoString reporter probe
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NanoString reporter probe
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