title: A rep2

description:
treat with AFB1
A2

value: 28 day old


title: Met-Met replicate 4

status: Public on Apr 02 2022

type: SRA

city: Hangzhou

first: Qiong

last: Chen

state: Zhejiang

address: Yuhangtang Road 866

department: animal science

country: China

institute: Zhejiang University

library_source: transcriptomic

data_processing:
Clustering and sequencing:The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina, San Diego, California, USA) according to the manufacturer’s instructions. After cluster generation, the libraries were sequenced on an Illumina Hiseq 4000 platform and 150 bp paired-end reads were generated.
Quality control :Raw sequencing data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter or ploy-N and low quality reads. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Mapping to the reference genome:Reference genome and gene model annotation files were downloaded from genome  website directly (FA Download Link: ftp://ftp.ensembl.org/pub/release-90/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.primary_assembly.fa.gz; GTF Download Link: ftp://ftp.ensembl.org/pub/release-90/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.primary_assembly.fa.gz). Index of the reference genome was built using bowtie 2 v 2.2.8, and paired-end clean reads were aligned to the reference genome using HISAT2 (Langmead et al., 2012) v2.0.4. HISAT2 was run with ‘--rna-strandness RF’, other parameters were set as default.
Transcriptome assembly:The mapped reads of each sample were assembled by StringTie (v1.3.1) (Pertea et al., 2016) in a reference-based approach. StringTie uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full length transcripts representing multiple splice variants for each gene locus.
Conservative analysis:Phast (v1.3) is a software package contains statistical programs, most used in  phylogenetic analysis (Hubisz et al., 2011), and phastCons (Siepel et al., 2005) is a conservation scoring and identification program of conserved elements. We used phyloFit to compute phylogenetic models for conserved and non-conserved regions among species and then gave the model and HMM transition parameters to phyloP to compute a set of conservation scores of coding genes.
Genome_build: mm9
Supplementary_files_format_and_content: FPKM

molecule: total RNA

organism: Mus musculus

source_name: The 4th inguinal mammary gland

extract_protocol:
RNA was isolated with TRIzol (Invitrogen, CA, USA). RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA) and gel electotrophoresis. The concentration was measured using Qubit ® RNA Assay Kit in Qubit ® 2.0 Flurometer (Life Technologies, CA, USA). Then, RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: In the Met group, pregnant mice at pregnant day (P) 0 were fed a methionine-deficient diet with i.p. injection of 35% methionine contained in the control diet. The Met-Met group was treated as the Met group, except that 25% of injected methionine was replaced with methionyl-methionine dipeptide. At P 17, mammary gland was collected, n=4.

tag: strain

value: ICR

tag: tissue

value: The 4th inguinal mammary gland

tag: condition

value: Pregnant day 17


title: M145Dgbn_45h 1

city: Ledien

first: Gilles

middle: P.

last: van Wezel

address: Sylviusweg 72

department: Institute of Biology Leiden

country: Netherlands

institute: Leiden University

description: 45 hours sample on MM plate with cellophane

data_processing:
Raw data (raw reads) of FASTQ format were firstly processed through fastqc version 0.11.9. In this step, clean data (clean reads) were obtained by triming reads containing adapter and removing poly-N sequences and reads with low quality from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Both building index of reference genome and aligning clean reads to reference genome were used Bowtie2 version 2.4.4. (Langmead, B. and S.L. Salzberg, 2012)
featureCounts (version 2.0.1) from subreads used to generate count table

organism: Streptomyces coelicolor

source_name: bacteria culture

growth_protocol: 10e8 spores were plated on MM medium covered with cellophane at 30°C for 24 or 45 h before extraction.

extract_protocol:
At time of harvest, mycelium scraped off from cellophane, snap freeze in liquid N2, bioruptor 30 s at 30 Hz for two times, extract using Kirby mix and then phenol/chloroform extraction. Treated with DNaseI and phenol/chloroform extracted again.
Sequencing libraries were generated using NEBNext® Ultra TM RNA Library Prep Kit for Illumina® (NEB, USA)
First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptor ligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

tag: genotype

tag: time

value: 45 hours


title: Primary_Input

city: Cambridge

first: Haiting

last: Ma

state: MA

address: 455 Main Street

country: USA

institute: Whitehead Institute

description: H3K27Ac ChIP-input from primary human hepatocytes

library_source: genomic

data_processing:
Images analysis and base calling was done using the Illumina standard pipeline.
ChIP-seq datasets were aligned using bowtie (Langmead et al., 2009) to the hg38 reference genome using only the standard chromosomes (i.e. chr1 through chr19, chrX, chrY and chrM) with parameter –k 1 –m1 –best and –l set to read length.
Peaks were called using MACS (Zhang et al., 2008) with parameters -p 1e-9 –keep-dup=auto and input control. These files were subsequently normalized to the millions of mapped reads and displayed in the UCSC Genome Browser (Kent et al., 2002). Peaks from H3K27Ac ChIP-Seq were used for super-enhancer analyses were performed suing ROSE (Whyte et al., 2013) (https://bitbucket.org/young_computation/rose) with parameters –s 12500 –t 2000. Stitched enhancers were assigned to the single expressed RefSeq gene whose transcription start site was nearest the center of the stitched enhancer.
Genome_build: hg38
Supplementary_files_format_and_content: Bed files of called peaks

molecule: genomic DNA

organism: Homo sapiens

source_name: Primary human hepatocytes

growth_protocol: H1 ES cell were routinely cultured in mTeSR medium in matrigel-coated 6-well plates, and passaged every 3-4 days with versene passaging. Differentiation to hepatocytes-like cells were describe in the manuscript.

extract_protocol:
The H3K27Ac ChIP-seq and library preparation methods were described in the manuscript.
Crosslinked material was resuspended in 0.1% SDS (50mM Tris-HCl (pH 8), 10mM EDTA) and sonicated for 5min with a Covaris E220 instrument (5% duty cycle, 140 Peak Incident Power, 200 cycles per burst, 1ml AFA Fiber milliTUBEs). Soluble chromatin (5 µg) is immunoprecipitated with Protein A/G Dynabeads (Thermo Fisher Scientific, 10002D, 10004D) and 10μg of H3K27ac (Diagenode, C15410196).
ChIP-seq libraries were constructed using Accel-NGS 2S DNA library kit from Swift Biosciences. Fragments of the desired size were enriched using AMPure XP beads (Beckman Coulter). Libraries were sequenced on an Illumina NovaSeq 6000 instrument with 50 bp paired-end sequencing.

treatment_protocol: The 2D, 3D hepatocytes differentiation were described in the manuscript.

tag: cell type

value: Primary human hepatocytes

tag: chip antibody

value: none (input)


title: C rep3

city: Harbin

first: Sihong

last: Li

address: 600 Changjiang Road

institute: Northeast Agricultural University

description:
Control
C3

data_processing:
Illumina Casava software used for basecalling.
The sequencing data obtained from Illumina Hiseq™ was filtered to get clean reads using Trimmomatic.
Index of the reference genome was built using bowtie2 v2.3.2 and paired-end clean reads were aligned to the reference sequence (Gallus_gallus-5.0, NCBI) using HISAT2 v2.1.0.
FPKM was calculated with StringTie v1.3.3b.
Genome_build: Gallus_gallus-5.0
Supplementary_files_format_and_content: csv files include RPKM values for each Sample.

organism: Gallus gallus

source_name: Control

growth_protocol: 32 (1 day old) commercial Arbor Acres broilers were bought from Yi Nong Commercial hatchery (Harbin, Heilongjiang, China) and were assigned randomly to three groups namely control group, AFB1 group, AFB1+curcumin group.Broilers were provided fresh, clean water, free diet and 12 hours dark/light cycle。On day 28, broilers were euthanized by heart puncture and liver samples were collected.

extract_protocol:
Livers were removed, flash frozen on dry ice, and RNA was harvested using Total RNA Extractor (Trizol).
RNA libraries were prepared for sequencing using standard Illumina protocols and was validated on the Illumina HiSeq™ 2000.

treatment_protocol: Control group (C): No treatment control, fed with the same environment, keeping up with the end of the experiment. AFB1 group (A): diet with 1mg/kg AFB1. AFB1+curcumin group (T): diet with 1mg/kg AFB1 and 300mg/kg curcumin. Chickens were continuously fed 28 days.

value: liver

value: Arbor Acres broilers

tag: age


title: Control replicate 4


title: Liver, Tem, 1

city: Stanford

first: Julia

last: Belk

state: California

address: 450 Serra Mall

institute: Stanford University

data_processing:
scATAC-seq fastq files were processed using cellranger atac pipeline
Assembly: mm10
Supplementary files format and content: fragments file containing trimmed, deduplicated, high quality atac-seq fragments and cell barcodes

source_name: liver

extract_protocol:
Nuclei were isolated from frozen, flow cytometry sorted CD8+ T cell subsets
scATAC-seq libraries were constructed using 10X genomics reagents and protocols
10X genomics single cell ATAC-seq

tag: sorted

value: yes

tag: infection

value: LCMV

tag: days p.i.

tag: phenotype

value: T cell


title: C rep2

description:
Control
C2


title: A rep1

description:
treat with AFB1
A1

source_name: treat with AFB1


title: Control replicate 3


title: Control replicate 2


title: Met replicate 2


title: M145Dgbn_24h 1

description: 24 hours sample on MM plate with cellophane

value: 24 hours


title: Naive, 1

source_name: spleen

value: spleen

value: n


title: Met replicate 1


title: M145_45h 3


title: Liver REG-2

city: Chengdu

first: zilong

last: zhang

state: Sichuan

address: Western Section 2, 1st Ring Rd

department: Hepatobiliary-Pancreatic Surgery Center, Cell Transplantation Cente

institute: Sichuan Academy of Medical Sciences & Sichuan Provincial People’s Hospital

data_processing:
Quality control， Samples are sequenced on the platform to get image files, which are transformed by the software of the sequencing platform, and the original data in FASTQ format (Raw Data) is generated. Sequencing data contains a number of connectors, low-quality Reads, so we use Cutadapt (v1.15) software to filter the sequencing data to get high quality sequence（Clean Data）for further analysis
The reference genome and gene annotation files were downloaded from genome website. The filtered reads were mapping to the reference genome using HISAT2 v2.0.5.
Differential expression analysis: we used HTSeq(0.9.1) statistics to compare the Read Count values on each gene as the original expression of the gene, and then used FPKM to standardize the expression.
Assembly: Mus_musculus.GRCm38.dna.primary_assembly.fa
Supplementary files format and content: Then difference expression of genes was analyzed by DESeq (1.30.0) with screened conditions as follows: expression difference multiple |log2FoldChange| > 1, significant P-value < 0.05. At the same time, We used R language Pheatmap(1.0.8) software package to perform bi-directional clustering analysis of all different genes of samples. We geted heatmap according to the expression level of the same gene in different samples and the expression patterns of different genes in the same sample with Euclidean method to calculate the distance and Complete Linkage method to cluster.
Supplementary files format and content: we mapped all the genes to Terms in the Gene Ontology database and calculated the numbers of differentially enriched genes in each Term. Using topGO to perform GO enrichment analysis on the differential genes, calculate P-value by hypergeometric distribution method (the standard of significant enrichment is P-value <0.05), and find the GO term with significantly enriched differential genes to determine the main biological functions performed by differential genes. ClusterProfiler (3.4.4) software was used to carry out the enrichment analysis of the KEGG pathway of differential genes, focusing on the significant enrichment pathway with P-value <0.05.

source_name: Liver

extract_protocol:
Total RNA was isolated using the Trizol Reagent (Invitrogen Life Technologies), after which the concentration, quality and integrity were determined using a NanoDrop spectrophotometer (Thermo Scientific). Three micrograms of RNA were used as input material for the RNA sample preparations.
The sequencing library was then sequenced on NovaSeq 6000 platform(Illumina)

tag: disease state

value: Chronic Liver Fibrosis

tag: treatment

value: 200μl PBS


title: Liver REG-1


title: M145_45h 2


title: Liver MSC-3

value: 1×10^6 ADMSCs in 200μl PBS


title: Liver MSC-2


title: Liver MSC-1


title: M145_24h 3


title: M145_45h 1


title: M145_24h 2


title: MP - 35k

city: Montréal

first: Abderrahim

last: Benmoussa

state: Québec

address: 240 Murray Street

department: Nutrition

country: Canada

institute: Université de Montréal

description: short RNA - 8-15 nt window

data_processing:
Quality control (QC) of our total RNA samples was assessed by gel electrophoresis and NanoDrop ND-1000 (Thermo Fisher Scientific, Waltham, MA, USA) analyses (Supplementary QC data). The
Squencing : small RNA-seq libraries, containing RNA species between 8 and 30 nt in length, were prepared as described previously [78]. Briefly, total RNA of each sample was used to prepare the small non-coding RNA sequencing library, which included the following steps: (1) 3′-adapter ligation, (2) 5′-adapter ligation, (3) cDNA synthesis, (4) PCR amplification, and (5) size selection of approximately 120 to 150 bp of PCR-amplified fragments (corresponding to approximately 8 to 30 nt of small RNA). The QC of the sequencing libraries was assessed by Agilent 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany) (Supplementary QC data).
Samples were diluted to a final concentration of 8 pM, denatured as single-stranded DNA, and cluster generation was performed on the Illumina cBot using TruSeq Rapid SR cluster kit (GD-402-4001, Illumina, San Diego, CA, USA). Afterward, the clusters were sequenced for 51 cycles on Illumina HiSeq 2000 using TruSeq Rapid SBS Kits (FC-402-4002, Illumina, San Diego, CA, USA), as per the manufacturer’s instructions.
Bioinformatics Analysis : Clean reads matching the quality standards were processed to remove the adaptor sequence, leading to sRNA trimmed reads. All reports displayed here were generated through the Arraystar Inc. (https://www.arraystar.com/ accessed on December 2015) standard analysis pipeline and refined using R (Free Software Foundation). Only the reads that were identical, both in length and sequence, were considered as a unique read. sRNA read counts were expressed as reads per million (RPM) sRNA alignments. Trimmed sRNA reads were mapped to the RefSeq database of the corresponding organism using the NCBI Basic Local Alignment Search Tool (BLAST) (https://blast.ncbi.nlm.nih.gov/Blast.cgi accessed on 2016).
Assembly: N/A
Supplementary files format and content: RPM

organism: Bos taurus

source_name: Lactantia purefilter commercial cow's milk

growth_protocol: Not applicable

extract_protocol:
Total RNA was isolated using Trizol LS and treated with DNAse on column with RNeasy mini-kit and treated on-column with DNase, according to the manufacturer’s protocol (Qiagen, Hilden, Germany)
Library preparations were performed following modified SOPs at ArrayStar platform to allow for larger RNA size window (8–35 nt). The purity, quality, and concentration of total RNA samples were determined with NanoDrop ND-1000 (Thermo Fisher Scientific) and 2100 Bioanalyzer (Agilent, Santa Clara, CA). MiRNA sequencing library was prepared from total RNA through: (1) 3′-adapter ligation, (2) 5′-adapter ligation, (3) cDNA synthesis, (4) PCR amplification, and (5) size selection of approximately 120 to 155 bp of PCR-amplified fragments (corresponding to approximately 8 to 35 nt of small RNA). The complete libraries were quantified by Agilent 2100 Bioanalyser.
nc-RNAseq, The cDNA library samples were then diluted to a final concentration of 8 pM and denatured as single-stranded DNA. Cluster generation was performed on the Illumina cBot using TruSeq Rapid SR cluster kit (#GD-402–4001, Illumina, San Diego, CA) and sequenced for 51 cycles on Illumina HiSeq 2000, using TruSeq Rapid SBS Kits (#FC-402–4002, Illumina), following the manufacturer’s instructions.

treatment_protocol: Not applicable

tag: subtype

value: Holstein

tag: sample

value: Pasteurized homogeineized Skimmed filtered milk

tag: processing

value: commercially available - food


title: M145Dgbn_24h 2

tag: strain


title: MP - 70k

description: short RNA - 8-15 nt window


title: Liver REG-3


title: Liver Exo-3

value: 250μg ADMSCs-Exo in 200μl PBS


title: MP - 100k

description: short RNA - 8-15 nt window


title: M145_24h 1


title: Control replicate 1

value: ICR

tag: tissue

value: The 4th inguinal mammary gland

value: Pregnant day 17


title: gDNA_48h

description: Whole sample without ChIP

data_processing:
Alignment of raw sequence to genome (bowtie2 version 2.3.4): bowtie2 -p 8 -x M145Genome_bowtie2 -U sample.fq.gz -S sample.sam
Sort sam file (samtools version 1.9): samtools sort -m 8G -o sample.bam -O bam -@ 8 sample.sam
Peak calling (MACS2 version 2.1.2):macs2 callpeak -t inputFile -c controlFile -n sample --outdir outputDir -f BAM --gsize 8.67e6 -s 50 -q 1e-20 --extsize 147 --call-summits -B --keep-dup all
Genome_build: NC_003888.3
Supplementary_files_format_and_content: .txt file - peak calling result

growth_protocol: 10e8 spores of strain GAD043 were plated on MM medium covered with cellophane at 30°C for 25 or 48 h before extraction.

extract_protocol:
After 25 h or 48 h growth, cellophane disks were soaked up-side-down in PBS solution containing 1% formaldehyde for 20 min allowing DNA-protein crosslink. Ten plates were collected for 25 h samples; four plates were collected for 48 h samples. Then the disks were moved to PBS solution containing 0.5 M glycine for 5 min to stop crosslinking reaction. The mycelium was then collected, washed in PBS and resuspended in 0.5 mL lysis buffer (10 mM Tris-HCl pH 8.0, 50 mM NaCl, 15 mg·mL-1 lysozyme, 1× protease inhibitor (Roche, Bavaria, Germany) and incubated at 37°C for 20 min. After incubation, 0.5 mL IP buffer (100 mM Tris-HCl pH 8.0, 250 mM NaCl, 0.8% v/v Triton-X-100) was added to the sample, and chromosomal DNA sheared to 100 to 500 bp using Bioruptor Plus water bath sonication system (Diagenode, Liège, Belgium). After centrifugation to remove cell debris, lysates were incubated with 40 uL Anti-FLAG M2 affinity gel (cat A2220, Sigma-Aldrich, St. Louis, U.S.) suspension according to the manufacturer’s instructions and incubated at 4°C overnight. After centrifugation and washing, the pellets and 50 uL of untreated total extracts (controls) were incubated in 100 uL IP elution buffer (50 mM Tris-HCl pH7.5, 10 mM EDTA, 1% m/v SDS) at 65°C overnight to reverse cross-links. Beads were then removed by centrifugation before DNA extraction with phenol-chloroform. The DNA sample was then extracted with chloroform and the water layer was further purified using DNA Clean & Concentrator kit (Cat. D4029, Zymo Research, California, U.S.).
The libraries were prepared by BGI for sequencing using BGISEQ-500 platform. Briefly, the fragmented DNA was end-repaired and 3’-dA overhang was added to the product. Methylated sequencing adaptors were then ligated and the library was PCR amplified and size selected (100-300bp, including adaptor sequence).
DNA-end repair, 3’-dA overhang and ligation of methylated sequencing adaptors. PCR amplification and size selection (100-300bp, including adaptor sequence).

value: 48 hours


title: MP - 12k

description: short RNA - 8-15 nt window


title: Liver Exo-1


title: Milk - 3

description: short RNA - 8-15 nt window


title: Tumor tissue low dose TRT rep 3

type: RNA

city: Jette

first: Thomas

last: Ertveldt

state: Brussels

address: Laarbeeklaan 103, E206

department: BMWE

country: Belgium

institute: Vrije Universiteit Brussel

description:
RNA isolated from whole B16-huCD20 melanoma tissue
RNA-samples from 9 whole B16-huCD20 tumor from mice treated with 50 (Low dose TRT) or 140MBq (High dose TRT) of 177Lu-9079, or 140MBq of 177Lu-R3B23 (control condition) were isolated when they reached 250±100mm3. These were subjected to multiplex analysis to study the tumor immune signature upon performing RNA-isolation (RNeasy® Plus Mini Kit, Qiagen), quality control on the Qubit4 (Qubit™ RNA HS Assay Kit, Thermo Fisher Scientific) and 2100 Bioanalyzer (RNA6000 Nano Kit, Agilent, RRID:SCR_019715), and analysis using the nCounter® PanCancer Immune Profiling Panel on an nCounter® Analysis System (Nanostring Technologies) was performed. Raw counts were normalized by the RuvSeq method adapted for Nanostring analysis .

hyb_protocol: Probes and target transcripts were hybridized overnight at 65°C for 20 hours as described in the manufacturer’s protocol.

scan_protocol: Samples are loaded onto the nCounter Prep Station for further purification and immobilization onto the sample cartridge. After transfer to the Digital Analyzer (MAX Analysis System, Brightcore, VUB) absolute counts are quantified.

data_processing: For quality control the nSolver_analysis_software_4.0 was used. Raw counts were processed in R and normalized using the RUVSeq method adjusted for NanoString analysis. The DESeq R-package was used for differential expression analysis.

label: Biotin

source_name: Whole B16-huCD20 melanoma tissue

label_protocol: After RNA was converted to cDNA and amplified using target-specific primers samples were mixed with a 3′ biotinylated capture probe and a 5′ reporter probe tagged with a fluorescent barcode from the nCounter Myeloid Innate Immunity Panel.

growth_protocol: Female, 6-12 week old C57BL/6 mice (Charles River) were transplanted subcutaneous (s.c.) in the right thigh with 10E5 B16-huCD20 cells after cultivation in DMEM-medium. These mice were then followed up over time and their welfare evaluated.

extract_protocol: Tumors were cut in 5mm pieces and immersed in 5mL RPMI1640-medium (Sigma-Aldrich) with 5% fetal clone I serum (HyClone), 100U/mL penicillin, 100µg/mL streptomycin, 2mM L-glutamine, 1mM sodium pyruvate, 1mM non-essential amino acids and 50µM β-mercaptoethanol (Sigma-Aldrich). An enzymatic digestion with 2000U/mL DNase I (Sigma-Aldrich), 1mg/mL Dispase II (Roche) and 300U/mL Collagenase I (Sigma-Aldrich) was performed for 1 hour at 37°C. The cell suspension was passed over a 70µm cell strainer (Falcon) to obtain a single cell suspension. Red blood cell lysis was performed using 0.15M NH4Cl-0.017M Tris-solution.

treatment_protocol: On days 3, 9 and 14 of B16-huCD20 s.c. tumor growth, mice received an i.v. injection of 3.3µg 177Lu-9079 co-infused with 150mg/kg Gelofusin with a total cumulative radioactive dose of 50.7±0.4MBq (low-dose) or 141.3±1.3MBq (high-dose). Control mice received i.v. injections of 3.3µg 177Lu-R3B23 co-infused with 150mg/kg Gelofusin with a total cumulative radioactive dose of 143.2±1.5MBq. Gelofusin was employed to limit kidney toxicity by attenuating sdAb retention in kidneys.

tag: Sex

value: Female

tag: tumor size

tag: experimental condition

value: 50MBq (Low dose TRT) of 177Lu-9079


title: Tumor tissue high dose TRT rep 2

value: 140MBq (High dose TRT) of 177Lu-9079


title: Tumor tissue high dose TRT rep 3


title: Tumor tissue low dose TRT rep 2


title: Gbn_ChIP_48h

description: DNA fragments after ChIP

tag: genotype

tag: time


title: Liver LFG-3

value: sacrifice


title: Tumor tissue low dose TRT rep 1


title: Milk - 2

description: short RNA - 8-15 nt window


title: gDNA_25h

description: Whole sample without ChIP

value: 25 hours


title: Tumor tissue high dose TRT rep 1


title: Liver LFG-2


title: Milk - 1

description: short RNA - 8-15 nt window


title: Tumor tissue control rep 3


title: Liver LFG-1


title: Gbn_ChIP_25h

description: DNA fragments after ChIP


title: Liver Exo-2


title: WD-1 R6 field rep2

status: Public on Apr 01 2022

city: Columbus

first: Tu

last: Huynh

state: OH

address: 2021 Coffey Rd

department: Horticulture and Crop Science

institute: Ohio State University

data_processing:
Short reads were assessed for quality control using the FastQC program (version 0.11.5).
High-quality reads were loaded to kallisto (version 0.43.1) available as a graphic user interface on Cyverse (www.cyverse.org) with bootstrap value set at 100 and k-mer length at 31. AtWRI1 and AtDGAT sequences used in the transformation vector were added to the G. max cDNA database corresponding to the Wm82.a2.v1 genome retrieved from Ensembl (http://plants.ensembl.org). This cDNA library served as the transcriptome reference for pseudo-alignment and read quantification.
Results from kallisto were used as input for differential expression analysis at gene level via the sleuth package (version 0.30.0) in R (version 3.6.3).
Raw count files (.csv) were generated via extracting information in the kallisto "abundance.tsv" file of each sample into a matrix in R, matching transcript IDs with gene IDs, and summing estimated counts (marked as "est_counts") of all transcript of the same gene.
Genome_build: Glycine max [L.] Merr Wm82.a2.v1
Supplementary_files_format_and_content: Tab-delimited .csv files include raw gene counts for each sample

organism: Glycine max

source_name: seed

growth_protocol: Field Condition: Field trials were conducted on homozygous transgenic events and lineages of T4, and T5 generations of transgenic plants, WD-1 and WD-2, in crop seasons 2019. All evaluations were conducted in completely randomized plots with three replications. Each plot consisted of four 10 ft rows in a four-row plot design in which two border rows were the wildtype (WT) Thorne. One hundred seeds were sown in each row. Irrigation was provided when necessary using a sprinkler system. Seeds were collected at R5, R5/6, and R6 from three replications. A small portion of twelve seeds from each sample were used for genotyping for the presence of the transgenes and the rest portion of the seeds were bulked to extract RNA.  Greenhouse condition: The seeds were planted in 30 by 26 cm plastic pots (Nursery supplies Inc., Orange, CA, USA) containing Baccto, Horticultural sphagnum peat and perlite (Michigan peat company, Houston, TX, USA). After planting, the pots were placed in a greenhouse maintained at 30° and 25° C, day and night, respectively, with a photo-period of 16 h. The light intensity varied but was, on  average,  approximately  450  μmol.m–2.s–1. The three genotypes, WD-1, WD-2 and the control WT,  were potted every two weeks (four pots each). The plants were separated in the greenhouse using pollen screens to avoid cross-pollination between genotypes. After the first 45 days, the plants were fertilized every 2 weeks with 6 g of 15-5-15 fertilizer (Everris NA Inc., Dublin, OH, USA).  Once the plants start flowering, each day the flowers  that open were tagged in order to identify the correct developmental stages. Samples for biomass, metabolomics and transcriptomic analysis were collected at different points of development: 21, 24, 27, 30, 33, 36 days after flowering (DAF) and at maturity. The collected immature seeds were peeled, removing the seed coat and endosperm and then were frozen under liquid N2. Each replicate consisted in one embryo per tube, except for 21 and 24 DAF, where three embryos were used and at least four replicates were collected for each time point and line. For the mature stage, embryos were ground for each replicate and 4 replicates were analyzed. Finally, all the samples were freeze dried in a liophilator for 3 days.

extract_protocol:
Regarding field samples, twelve seeds from each pot sample were genotyped and four seeds were bulked for RNA extraction using the QIAGEN RNAEseay Kit (QIAGEN, INC.). The purified RNA was checked for quality on 1% agarose gel. Concentration was quantified using the Nanodrop. The RNA was cleaned from any DNA contamination by DNAse treatment using the Turbo DNA free kit (Invitrogen, INC.).  Regarding greenhouse samples, immature embryos of the same green-house grown plants as the metabolomics analysis were used to collect RNA for the transcriptomics analysis. For each of the three genotypes, RNA was extracted at four timepoints of 24, 27, 30, and 33 DAP and from three plants as three replicates. For each replicate, a single embryo was flash-frozen with liquid nitrogen and ground with pestle and mortar into fine powder from which RNA was isolated and cleaned using the Macherey-Nagel NucleoSpin RNA Plant Mini kit (MACHEREY-NAGEL Inc.).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: growth condition

value: field

tag: time point

value: seed


title: WD-1 R6 field rep1


title: WD-1 R6 field rep3


title: Tumor tissue control rep 1


title: W-1 R6 field rep3


title: WT R6 field rep3

value: Thorne (WT)


title: W-1 R6 field rep2


title: WD-1 R5/6 field rep1


title: WD-1 R5/6 field rep3


title: W-1 R6 field rep1


title: WD-1 R5/6 field rep2


title: W-1 R5/6 field rep3


title: WD-1 R5 field rep3


title: WT R6 field rep1


title: Tumor tissue control rep 2


title: W-1 R5/6 field rep2


title: W-1 R5 field rep2


title: WD-1 R5 field rep1


title: WT R5/6 field rep1


title: WT R5/6 field rep2


title: WT R5/6 field rep3


title: WT R5 field rep1


title: WD-2 33DAP greenhouse rep3

source_name: immature embryos

value: greenhouse

value: 33 DAP

value: immature embryos


title: W-1 R5 field rep3


title: WT R6 field rep2


title: rpd3Δ_G1_rep2

city: Los Angeles

first: Yiwei

last: He

state: CA

address: 1050 Childs Way RRI 203

department: Molecular Biology

institute: University of Southern California

description: Sample 29

data_processing:
Barcode-splitting: Sequenced reads were first processed using ea-utils which de-multiplexes the reads based on the specified barcode sequences.
Alignment: The raw sequencing reads were then aligned to the indexed genome of S288C from Saccharomyces Genome Database using bowtie2.
Data-cleaning: Filterred reads that were mapped to more than one region in the genome using samtools view. Reads were sorted by coordinates of the reference genome using samtools sort. PCR duplicates were removed using samtools rmdup
Binning: sequencing reads were binned over 50bp bins across the genome using coverageBed.
Assembly: R64
Supplementary files format and content: binned.bed files

organism: Saccharomyces cerevisiae

source_name: Yeast cells

growth_protocol: ~100 mL of cells were grown per sample to OD ~ 0.5 in YEPD at 23 °C

extract_protocol:
Cells were resuspend in 500 μL ChIP lysis buffer and disrupted by bead-beating with FastPrep. Followed by PCI extractracion and ethanol precipitaion.
Samples were end-labeled using KAPA Hyper prep kit with unique barcoded adapters that are compatible with the subsequent library-amplification and sequencing primers for the Illumina sequencing platform.

treatment_protocol: Cells were arrested with α-factor (~5 nM ) and incubated for ~4 h at 23 °C. Chrmatin was cross-linked with formaldehyde solution (1 % final concentration)

tag: phase

tag: chip antibody

value: anti-FLAG M2 (Sigma F1804)

tag: arrest

value: alpha-factor


title: rpd3Δ_G1_rep1

description: Sample 28


title: WD-1 33DAP greenhouse rep3


title: WT_G1-rep3

description: Sample 27

value: WT


title: WD-1 R5 field rep2


title: WD-1 33DAP greenhouse rep1


title: WT 33DAP greenhouse rep3


title: WT R5 field rep2


title: W-1 R5 field rep1


title: W-1 R5/6 field rep1


title: WD-2 33DAP greenhouse rep2


title: rpd3Δ_G1_rep3

description: Sample 30


title: WT 33DAP greenhouse rep2


title: WT R5 field rep3


title: WT_G1-rep2

description: Sample 26


title: WT_G1-rep1

description: Sample 25


title: WD-2 33DAP greenhouse rep1


title: P2 whole kidneys [RNA-Seq]

city: New Orleans

first: Samir

middle: S

last: El-Dahr

state: Louisiana

address: 1430 Tulane Avenue

department: Pediatric Nephrology

institute: Tulane University

data_processing: Cell Ranger pipeline v1.2.0 for processing scATAC seq data and cellranger-arc-1.0.1 with v1 chemistry for processing multiomic single nuclei ATAC+GEX sequencing.  The major steps involved were Fastq generation, Alignment, Duplicate Marking, Peak calling, Cell Calling, UMI counting  ArchR 1.0.1  Cicero 1.3.4.11  chromVAR 1.8.0  circlize 0.4.13  Genome_build: mm10  Supplementary_files_format_and_content: atac_fragments.tsv.gz and filtered_feature_bc_matrix.h5 files

source_name: Postnatal Kidneys

extract_protocol: CG000169 for scATAC-seqand CG000366 for Multiomic scATAC+GEX assay  (1) 10X Genomics CG000169 RevB (Nuclei Isolation for Single Cell ATAC Sequencing.) (2) 10X Genomics CG000366 RevB (Nuclei Isolation from Embryonic Mouse Brain for Single Cell Multiome ATAC + Gene Expression Sequencing)  Libraries were prepared from individual nuclei (for the respective genotypes) using the droplet-based method as was outlined by10X Genomics. Indexed libraries were sequenced on a NextSeq500 (Illumina) sequencer to obtain paired-end reads.

tag: developmental stage


title: P2 whole kidneys [Multiomic scATAC]

description: single cell  Multiomic ATAC + Gene Expression


title: P2 Six2TGC NPCs [SH3]

description: scATAC-seq

data_processing:
Cell Ranger pipeline v1.2.0 for processing scATAC seq data and cellranger-arc-1.0.1 with v1 chemistry for processing multiomic single nuclei ATAC+GEX sequencing.
The major steps involved were Fastq generation, Alignment, Duplicate Marking,  Peak calling, Cell Calling, UMI counting
ArchR 1.0.1
Cicero 1.3.4.11
chromVAR 1.8.0
circlize 0.4.13
Genome_build: mm10
Supplementary_files_format_and_content: atac_fragments.tsv.gz and filtered_feature_bc_matrix.h5 files

extract_protocol:
CG000169 for scATAC-seqand CG000366 for Multiomic  scATAC+GEX assay
(1) 10X Genomics CG000169 RevB (Nuclei Isolation for Single Cell ATAC Sequencing.) (2) 10X Genomics CG000366 RevB (Nuclei Isolation  from Embryonic Mouse Brain for Single Cell Multiome ATAC + Gene Expression Sequencing)
Libraries were prepared from individual nuclei  (for the respective genotypes) using the droplet-based method as was outlined by10X Genomics. Indexed libraries were sequenced on a NextSeq500 (Illumina) sequencer to obtain paired-end reads.

value: Six2TGC (Six2-GFP::CreTg)


title: WD-2 30DAP greenhouse rep3

value: 30 DAP


title: P2 Six2TGC NPCs [SH7]

description: scATAC-seq


title: E16.5 Six2TGC NPCs [SH9]

description: scATAC-seq

source_name: Embryonic Kidneys


title: WD-1 30DAP greenhouse rep3


title: WD-1 30DAP greenhouse rep2


title: WT 33DAP greenhouse rep1


title: WD-1 33DAP greenhouse rep2


title: WD-2 30DAP greenhouse rep2


title: WD-1 30DAP greenhouse rep1


title: WT 30DAP greenhouse rep3


title: WT 30DAP greenhouse rep1


title: WT 30DAP greenhouse rep2


title: Flax variety JRF-2 seedlings - heat stress exposed

city: Kolkata

first: Dipnarayan

last: Saha

state: West Bengal

address: Biotechnology Unit, Division of Crop Improvement, ICAR- Central Research Institute for Jute and Allied Fibres, Nilgunj, Barrackpore

country: India

institute: Indian Council of Agricultural Research - Central Research Institute for Jute and Allied Fibres

description:
High-quality genomic DNA converted using Bisulfite conversion kit and size fractionated
JH

data_processing:
Raw paired-end reads were filtered using Trimmomatic and quality checked using FastQC tools.
Processed reads were aligned to the reference chromosome-scale flax genome of cv. CDC Bethune using bwa-meth software
MethylDackel software was used to call 5-mC bases in CG, CHG and CHH contexts
Differentially methylation regions (DMRs) identification and annotations were performed using the methylKit in pairwise manner using the control (JC) methylome sample
Genome_build: CDC Bethune
Supplementary_files_format_and_content: bedGraph and text files

organism: Linum usitatissimum

source_name: var. JRF-2

growth_protocol: Flax (JRF-2) seeds were surface sterilized, germinated on sterile Soilrite mix, and grown in culture room at 22±2°C, 16 h of light and 8h dark for 21 days. Seedlings were irrigated with Hoagland solution every alternate days.

extract_protocol:
Shoot apices (3-5 cm) of 10 randomly chosen treated and untreated seedlings were sample-wise pooled and extracted genomic DNA using the DNeasy Blood and Tissue Kit (Qiagen Inc., USA) as per the manufacturer's instructions
1µg of purified genomic DNA was treated with Bisulfite conversion kit from Active Motif Inc., as per the manufacturer's instructions. About 200ng of Bisulfite converted genomic DNA was size fractionated (450–500 bp) in sonicator. Ligation of sequencing adapters and paired-end (PE) sequencing libraries were prepared using the NEBNext® Ultra™ DNA Library Prep Kit for Illumina® (New England Biolabs Inc.) as per manufacturer's instructions. A high-fidelity PCR amplication  of the librraies was performed using NEBNext High-Fidelity PCR Master Mix (New England Biolabs Inc.) to ensure enrichment of libraries. The amplified libraries were quality checked on Bioanalyzer 2100 using the High Sensitivity (HS) DNA kit (Agilent Technologies Inc.) as per manufacturer's instructions. Cluster generation and paired-end library sequencing performed on Illumina HiSeq 2500 platform (2x150bp chemistry).

treatment_protocol: A subset of JRF-2 seeds was treated with a 5-Azacytidine (1mM)) for 24 hours in the dark at 20°C. After 21 days after sowing, subsets of flax seedlings with or without 5-Aza treatment were exposed to heat stress (40±2°C; 70% RH) for 4h for five consecutive days in a plant growth chamber. The heat stress exposed seedlings were allowed to recover in culture room (22±2°C) after the stress treatment.

tag: developmental satge

value: Seedling

tag: age

tag: treatment

value: untreated seedling-heat exposure (40+/- 2C 4 h for 5 consecutive days


title: WD-2 30DAP greenhouse rep1


title: Flax variety JRF-2 seedlings treated with 5-Azacytidine - heat stress exposed

description:
High-quality genomic DNA converted using Bisulfite conversion kit and size fractionated
JAH

value: 5-Azacytidin seedling-heat exposure (40+/- 2C 4 h for 5 consecutive days


title: E16.5 whole kidneys [RNA-Seq]


title: E16.5 Six2TGC NPCs [SH2]

description: scATAC-seq


title: E16.5 whole kidneys [Multiomic scATAC]


title: WD-2 27DAP greenhouse rep2

value: 27 DAP


title: Flax variety JRF-2 seedlings - control

description:
High-quality genomic DNA converted using Bisulfite conversion kit and size fractionated
JC

value: untreated seedling-control (22+/- 2C)


title: WD-2 27DAP greenhouse rep3


title: Flax variety JRF-2 seedlings treated with 5-Azacytidine - control

description:
High-quality genomic DNA converted using Bisulfite conversion kit and size fractionated
JAC

value: 5-Azacytidine treated seedling-control (22+/- 2C)


title: WD-1 24DAP greenhouse rep2

value: 24 DAP


title: WD-1 27DAP greenhouse rep1


title: WT 27DAP greenhouse rep3


title: WD-1 27DAP greenhouse rep3


title: WT 27DAP greenhouse rep2


title: WD-2 24DAP greenhouse rep3


title: WT 27DAP greenhouse rep1


title: WD-2 24DAP greenhouse rep2


title: DamRing1B  - EB and ESC day10 (KIN5599_index12)

city: Utrecht

first: Jop

last: Kind

address: Uppsalalaan 8

institute: Hubrecht Institute

description: Raw data files include both DamID and CEL-seq reads

data_processing:
Library strategy: scDam&T-seq
Libraries are demultiplexed based on the sample-specific and readout-specific barcode present in R1, using custom pipelines (available at: https://github.com/KindLab/scDamAndTools).
DamID alignment: DamID reads are aligned using bowtie2 (v. 2.3.3.1) with the following parameters: “--seed 42 --very-sensitive -N 1”.
DamID filtering: Alignments with a MAPQ < 10 are removed.
DamID procesing: Using our own custom pipeline (see KindLab GitHub), aligned reads are matched to known GATC positions in the genome to get the number of observations per (strand-specific) GATC position.
DamID processing: GATC-position counts are deduplicated using UMI information to allow a maximum of 4 unique UMIs per GATC position.
DamID processing: Unique GATC counts are summarized in genomic intervals at the desired resolution.
CELseq alignment: CELseq reads are aligned using GRCm38 (v. 89) transcript models and tophat2 (v. 2.1.1) with the following paramters: : “--segment-length 22 --read-mismatches 4 --read-edit-dist 4 --min-anchor 6 --min-intron-length 25 --max-intron-length 25000 --no-novel-juncs --no-novel-indels --no-coverage-search --b2-very-sensitive --b2-N 1 --b2-gbar 200”.
CELseq filtering: Alignments with a MAPQ < 10 are removed.
CELseq processing: Using our own custom pipeline (see KindLab GitHub), we assign alignments to genes using a method similar to htseq-count with mode "intersection_strict".
CELseq processing: Transcript counts are deduplicated using UMI information, allowing an unlimited number of UMI-unique counts per gene.
Genome_build: mm10
Supplementary_files_format_and_content: celseq count table: count table containing UMI-unique transcript counts per gene for all single-cell samples; damid count table: count table containing UMI-unique GATC counts per 10-kb interval for all single-cell samples; sample annotation: table containing detailed sample information for all single-cell samples; sample barcodes: sample-specific and readout-specific barcodes that can be used to demultiplex the raw data. Barcodes follow a 3-NNN-3-NNN format, where "N" positions indicate the barcode-specific sequence, and the "3" indicates positions of a 3nt UMI sequence.

source_name: Embryoid Bodies and 2i-cultured ESC (day 10)

growth_protocol: For the EB differentiation the stable knockin F1ES lines were cultured for 2 weeks on 0.1% gelatin coated plates in 2i ES cell culture medium: 48% DMEM/F12 (Gibco) and 48% Neurobasal (Gibco), supplemented with 1x N2 (Gibco), 1x B27 supplement + vitA (Gibco), 1x non-essential amino acids, 1% FBS, 1% Pen/Strep, 0.1mM β-mercaptoethanol, 1 μM PD0325901 (Axon Medchem, PZ0162-5MG), 3 μM CHIR99021 (Tocris, SML1046-5MG) and 10^3U/ml ESGRO mLIF medium before plating for EB differentiation according to ATCC protocol. On day1 of the differentiation 2x10^6 cells are grown in suspension on a non-coated bacterial 10cm dish with 15ml CM +/- (with β-mercaptoethanol without LIF) and 0.5mM IAA. The next day half the cell suspension is divided over 5 non-coated bacterial 10cm dishes with 15ml CM+/- medium and 0.5mM IAA and plates are refreshed every other day.

extract_protocol:
Cells were trypsinized and harvested in medium with 20 μg/mL Hoechst 34580 (Sigma 63493) per 1x10^6 cells for 45 minutes at 37°C. The cells were stained for live/dead gating with 1ug/ml propidium iodide and singlets were index sorted based on their Hoechst profile. One cell per well was sorted into 384-well plates (Biorad, HSP3801) using the BD FACS Jazz cell sorter. Wells contained 5 μL filtered mineral oil (Sigma) and 50nL of 0.5uM unique CELseq primer.
The scDam&T protocol and library preparation was performed as previously described in detail (PMID: 32350457).

treatment_protocol: Two days before single cell sorting the EB’s are shifted to CM+/- medium with 1mM IAA, and before single cell sorting on day 7, 10 and 14 the Dam-POI constructs are induced in the following way: 6hrs no IAA (Ring1B), 20hrs no IAA + 7hrs 1uM 4-OH Tamoxifen (Dam-ScFv-H3K27me3) and 7hrs no IAA + 4hrs 1uM 4-OH Tamoxifen (Dam-only), and the best developed embryonic bodies were handpicked and pooled together.

value: 129S1/SvImJ x CAST/Eij

tag: dam-fusion protein

value: Ring1B (full protein)

tag: molecule subtypes

value: genomic DNA; mRNA


title: WD-2 24DAP greenhouse rep1

value: greenhouse

tag: tissue


title: DamH3K27me3  - EB and ESC day07 (KIN5599_index10)

source_name: Embryoid Bodies and 2i-cultured ESC (day 7)

value: anti-H3K27me3 (mintbody)


title: DamRing1B  - EB day07 (KIN5600_index13)

source_name: Embryoid Bodies (day 7)


title: DamH3K27me3  - EB and ESC day10 (KIN5599_index13)


title: WD-2 27DAP greenhouse rep1

value: immature embryos


title: WD-1 24DAP greenhouse rep3


title: WD-1 27DAP greenhouse rep2


title: WD-1 24DAP greenhouse rep1


title: WT 24DAP greenhouse rep3

value: Thorne (WT)


title: study2_1604_Duodenum

city: Madison

first: Bryan

last: Zabel

state: wi

address: 3329 Agriculture Dr

department: GEM

institute: International Flavors & Fragrances Inc

data_processing:
The threshold baseline of the qPCR assay was manually set at 200 for all plates if the automatically calculated (by the CFX Maestro 1.1 software) threshold baseline was >200. The 200-threshold baseline value was determined at the development/qualification stage of RT-qPCR assays of genes of interest. However, if the automatically calculated threshold baseline was < 200, then the threshold baseline was directly used. Cq value in each well was also automatically calculated by the Maestro 1.1 software based on the threshold baseline. Data generated by the software were exported to a Microsoft Excel (Microsoft Corporation; Redmond, WA) spreadsheet for data processing.
dCq was calculated by subtracting cytokine mRNA gene level from that of GAPDH. Then ddCq was obtained by subtracting dCq from placebo group results. The distribution of dCq (grouped by gene, tissue, and day) was then examined for normality (Shapiro test and qq plot) and extremes (< 1Q-3×IQR or > 3Q+3×IQR). After removal of extremes, mixed effects models were performed for each gene.

label: FAM

organism: Mustela putorius furo

source_name: ferret tissue lysate

label_protocol: Two step RT qPCR were used to analyze the gene expression in ferret lung and duodenum total RNA samples. Reverse transcription was performed with iScript Reverse Transcription Supermix (Bio-Rad). For lungs, 1250 ng RNA per 50 ul RT reaction and for duodenum, 625 ng RNA per 50 ul RT reaction was used.  The total RT reaction volume was 50 µL and RT was performed in a 96 well plate on a Bio-Rad CFX96 Touch Real Time PCR Detection System.

growth_protocol: Outbred male ferrets (Triple F Farms, Sayre, PA), Animals were quarantined at IIT Reseacrh Institute (IITRI), Chicago, USA for approximately 6-7 days before initiation of the dosing. Animals were approximately 8-11 months of age and were approximately 1.0 to 2.0 kg at the initiation of dosing.

extract_protocol: Lung and duodenum were collected and stored in trizol. Tissue RNA was isolated using Direct-Zol RNA Miniprep Plus kit.

treatment_protocol:
Study1: From D-21 through study D21, ferrets in group 1 received a daily oral gavage with the OL-1 consortia (20B CFU/ strain), and ferrets in group 3 received a daily oral gavage with the Placebo. Ferrets in group 2 received a daily oral gavage with the OL-2 consortia (20B CFU/ strain) from study D1 through study D21. Five ferrets from each OL-1 and placebo groups were necropsied on D0 and five ferrets from each group were necropsied on D5 and D21 in the pilot study.
Study2: From study D-7 through study D10, ferrets in group 1 received a daily oral gavage with the OL-1 consortia (20B CFU/ strain), ferrets in group 2 received a daily oral gavage with the OL-2 consortia (20B CFU/ strain), and ferrets in group 3 received a daily oral gavage with the Placebo. Each probiotic capsule was opened and content diluted in 3mL sterile PBS for each daily oral gavage.

tag: day

tag: dose

value: Duodenum

tag: study

value: neg


title: WT 24DAP greenhouse rep1

tag: genotype


title: study2_1807_Duodenum


title: WT 24DAP greenhouse rep2


title: DamRing1B  - EB and ESC day14 (KIN5599_index04)

source_name: Embryoid Bodies and 2i-cultured ESC (day 14)


title: study2_1806_Duodenum


title: study2_1630_Duodenum


title: study2_1578_Duodenum


title: DamRing1B  - EB and ESC day07 (KIN5578_index14)


title: DamOnly  - EB and ESC day14 (KIN5599_index06)

value: untethered Dam


title: DamOnly  - EB and ESC day07 (KIN5599_index11)


title: DamH3K27me3 DamOnly DamRing1B  - EB and ESC day14 (KIN5599_index02)

value: anti-H3K27me3 (mintbody); untethered Dam; Ring1B (full protein)


title: study2_1625R_Duodenum


title: study2_1575_Duodenum


title: DamH3K27me3  - EB and ESC day14 (KIN5599_index05)


title: study2_1821_Duodenum


title: study2_1583_Duodenum


title: DamH3K27me3  - EB and ESC day07 (KIN5599_index09)


title: study2_1606_Duodenum


title: study2_1589_Duodenum


title: study2_1609_Duodenum


title: study2_1648_Duodenum


title: study2_1640_Duodenum


title: study2_1819_Duodenum


title: study2_1822_Duodenum


title: study2_1634_Duodenum


title: study2_1577_Duodenum


title: study2_1602_Duodenum


title: study2_1633_Duodenum


title: study2_1820_Duodenum


title: study2_1649_Duodenum


title: study2_1811_Duodenum


title: study2_5872_Duodenum


title: study2_1611_Duodenum


title: study2_1621_Duodenum


title: study2_1589_Lung

value: Lung


title: study2_1604_Lung


title: study2_1613_Duodenum


title: study2_1641_Duodenum


title: study2_1807_Lung


title: study2_1572_Duodenum


title: study2_1630_Lung


title: study2_1578_Lung


title: study2_1609_Lung


title: study2_1811_Lung


title: study2_1577_Lung


title: study2_1575_Lung


title: study2_1648_Lung


title: study2_1649_Lung


title: study2_1625R_Lung


title: study2_1806_Lung


title: study2_1641_Lung


title: study2_1640_Lung


title: study2_1821_Lung


title: study2_5872_Lung


title: study2_1606_Lung


title: study2_1822_Lung


title: study2_1819_Lung


title: study2_1611_Lung


title: study2_1583_Lung


title: study2_1621_Lung


title: study2_1634_Lung


title: study2_1602_Lung


title: study2_1613_Lung


title: study2_1633_Lung


title: study2_1820_Lung


title: study1_1814_Duodenum


title: study2_1572_Lung


title: study1_1580_Duodenum


title: study1_1599_Duodenum


title: study1_1579_Duodenum


title: study1_1590_Duodenum


title: study1_1592_Duodenum


title: study1_1823_Duodenum


title: study1_1582_Duodenum


title: study1_1645_Duodenum


title: study1_1587_Duodenum


title: study1_1610_Duodenum


title: study1_1573_Duodenum


title: study1_1627_Duodenum


title: study1_1629_Duodenum


title: study1_1605_Duodenum


title: study1_1593_Duodenum


title: study1_1616_Duodenum


title: study1_1810_Duodenum


title: study1_1581_Duodenum


title: study1_1643_Duodenum


title: study1_1614_Duodenum


title: study1_1598_Duodenum


title: study1_1571_Duodenum


title: study1_1588_Duodenum


title: study1_1647_Duodenum


title: study1_1636_Duodenum


title: study1_1608_Duodenum


title: study1_1638_Duodenum


title: study1_1615_Duodenum


title: study1_1603_Duodenum


title: study1_1815_Duodenum


title: study1_1600_Duodenum


title: study1_1574_Duodenum


title: study1_1809_Duodenum


title: study1_1596_Duodenum


title: study1_1585_Duodenum


title: study1_1644_Duodenum


title: study1_1594_Duodenum


title: study1_1595_Duodenum


title: study1_1612_Duodenum


title: study1_1823_Lung


title: study1_1580_Lung


title: study1_1590_Lung


title: study1_1817_Duodenum


title: study1_1642_Duodenum


title: study1_1592_Lung


title: study1_1645_Lung


title: study1_1599_Lung


title: study1_1579_Lung


title: study1_1627_Lung


title: study1_1587_Lung


title: study1_1582_Lung


title: study1_1629_Lung


title: study1_1605_Lung


title: study1_1812_Lung


title: study1_1593_Lung


title: study1_1616_Lung


title: study1_1610_Lung


title: study1_1810_Lung


title: study1_1581_Lung


title: study1_1814_Lung


title: study1_1573_Lung


title: study1_1571_Lung


title: study1_1588_Lung


title: study1_1614_Lung


title: study1_1615_Lung


title: study1_1598_Lung


title: study1_1647_Lung


title: study1_1608_Lung


title: study1_1643_Lung


title: study1_1815_Lung


title: study1_1638_Lung


title: study1_1603_Lung


title: study1_1600_Lung


title: study1_1636_Lung


title: study1_1574_Lung


title: study1_1809_Lung


title: LungCa_277

city: Tokyo

first: Shogo

last: Yamamoto

address: 4-6-1 Komaba, Megro-ku

department: Research Center for Advanced Science and Technology

country: Japan

institute: The University of Tokyo

description:
Histology : Large cell neuroendocrine carcinoma
Expression profile : group 2 (favorable prognosis)

hyb_protocol: 10 micrograms of fragmented cRNA were hybridised (45degree CelsiusC, 16 hours). Hybridization was controled by use of the GeneChip Eukaryotic Hybridization Control Kit (Affymetrix). Washing and staining was performed in a Fluidics Station 450 (Affymetrix) using the protocol EukGE-WS2v4.

scan_protocol: Scanning was performed in an Affymetrix GeneChip scanner 3000 7G.

data_processing: Affymetrix Microarray Suite v5.0 with target intensity=100

label: biotin

source_name: Lung cancer

label_protocol: In vitro transcription was performed on 1 microgram of cDNA using the Enzo BioArray High Yield RNA transcript labelling kit (Enzo Diagnostics). The cRNA was cleaned using RNAeasy clean-up columns (Qiagen). The cRNA was fragmented by heating in 40 mM Tris-acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc.

extract_protocol: Total RNAs were extracted using Isogen (Nippon Gene, Osaka, Japan). 3 micrograms of total RNA was reverse transcribed using the SuperScript III system for cDNA synthesis (Invitrogen) according to the protocol recommended by Affymetrix.

tag: Lung cancer


title: LungCa_269


title: LungCa_267


title: study1_1594_Lung


title: study1_1644_Lung


title: LungCa_265


title: LungCa_271


title: LungCa_263


title: LungCa_261


title: LungCa_255

description:
Histology : Small cell lung cancer
Expression profile : group 2 (favorable prognosis)


title: study1_1595_Lung


title: study1_1596_Lung


title: study1_1585_Lung


title: LungCa_253


title: LungCa_251


title: LungCa_237


title: study1_1612_Lung


title: LungCa_239


title: LungCa_247


title: LungCa_231


title: LungCa_275

description:
Histology : Small cell lung cancer
Expression profile : group 1 (unfavorable prognosis)


title: LungCa_215


title: LungCa_279

description:
Histology : Large cell neuroendocrine carcinoma
Expression profile : group 1 (unfavorable prognosis)


title: study1_1642_Lung


title: study1_1817_Lung


title: 22RV1_IVM12_rep2

city: Guangzhou

first: Shidong

last: Lv

address: Guangzhou Ave. North No. 1838

department: Urology

institute: Nanfang Hospital, Southern Medical University

data_processing:
Basecalling
Sequencing trimming
Sequencing mapping
Read count analyzing and FPKM calculating
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: 22RV1 cells

growth_protocol: Prostate cancer cells were cultured in RPMI 1640 with 10% FBS (Atlanta Biologicals)

extract_protocol:
Total RNA was extracted by TRIzol Reagent for RNA-Seq analysis
The library is constructed by NEBNext Ultra RNA Library Prep Kit for Illumina.

treatment_protocol: C4-2 and 22RV1 cells were treated with 8 or 12 μM ivermectin for 48 hours and the transcription profiling was analyzed by RNA-seq

tag: sample type

value: Human prostate cancer cell line

value: 12 uM ivermectin for 48 hours


title: 22RV1_IVM12_rep3


title: 22RV1_IVM12_rep1


title: 22RV1_IVM8_rep2

value: 8 uM ivermectin for 48 hours


title: 22RV1_IVM8_rep1


title: 22RV1_DMSO_rep3

value: DMSO


title: 22RV1_DMSO_rep2


title: ONX-5

city: Tokushima

first: Yuki

last: Sasaki

address: 3-18-15 Kuramoto-cho

department: Department of Immunology and Parasitology

institute: Tokushima University Graduate school of Medicine

hyb_protocol: standard Agilent protocol

scan_protocol: standard Agilent protocol

data_processing: The resulting data were normalized using GeneSpring (Agilent Technologies) software.

label_protocol: standard Agilent protocol

growth_protocol: The mouse monocyte-macrophage cell line J774.1 was cultured in 10% FBS-RPMI medium (Nakalai Tesque) supplemented with a penicillin/streptomycin solution (Gibco)

extract_protocol: RNA was extracted from cultured J774 cells, with genomic DNA degradation, using ReliaPrep RNA Cell Miniprep Systems (Promega)

treatment_protocol: in the presence of the proteasome inhibitor MG132 (LifeSensors, PA, USA), the 20S proteasome inhibitor epoxomicin (PEPTIDE INSTITUTE, Osaka, Japan), or the β5/β5i inhibitor ONX 0914 (Adooq Bioscience) at 1 μM or DMSO (Sigma-Aldrich) as a control solvent for 4 hours.

tag: cell line

tag: cell type

value: monocyte-macrophage cell line


title: N4 [heart, B6 control]

city: Philadelphia

first: Patrick

middle: Michael

last: Schaefer

state: PA

address: 3501 Civic Center Blvd

institute: Children's Hospital of Philadelphia

data_processing:
Base calling was done using [Genewiz NGS Laboratory]
Sequenced reads mapped to mm10 whole transcriptome and Gencode M17 annotation using STAR v2.5.2b with parameters --readFilesCommand zcat --outSAMtype None --outSAMunmapped Within --quantMode TranscriptomeSAM --outSAMattributes NH HI AS NM MD --outFilterType BySJout --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --sjdbScore 1 --limitBAMsortRAM 50000000000
Expected counts and Fragments Per Kilobase of transcript per Million mapped reads (FPKM) for all genes in Gencode M17 annotation were obtained from aligned bams using RSEM v1.2.28 with parameters --paired-end --no-bam-output --no-qualities -p 4 --forward-prob 0.5 --seed-length 25 --fragment-length-mean -1.0
Assembly: mm10
Supplementary files format and content: tab-delimited matrix table with Expected counts for every gene and every sample
Supplementary files format and content: tab-delimited matrix table with FPKM values for every gene and every sample

source_name: heart, B6 control

growth_protocol: Mice were maintained on a 12:12h light-dark cycle and fed 5L0D diet from PicoLab

extract_protocol:
Total RNA was extracted using Qiagen RNeasy Plus Universal mini kit following manufacturer’s instructions (Qiagen, Hilden, Germany).
Extracted RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked using Agilent TapeStation 4200 (Agilent Technologies, Palo Alto, CA, USA). RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were first enriched with Oligo(dT) beads.  Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by limited-cycle PCR. The sequencing libraries were validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA). The sequencing libraries were clustered on 3 flowcell lanes. After clustering, the flowcell was loaded on the Illumina HiSeq instrument (4000 or equivalent) according to manufacturer’s instructions.  The samples were sequenced using a 2x150bp Paired End (PE) configuration. Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.

treatment_protocol: Starting at 16 weeks mice performed initial exercise testing and then were either handled (non-exercised) or run every 2nd day at 50% of max capacity for 45min for a total of 8 weeks. Following the post exercise testing, mice were sacrificed using cervical dislocation and heart and soleus muscle were disected, flash frozen and stored at -80C until the experiment

value: exercised

tag: exercise response

value: heart

tag: strain

value: B6 control


title: N62 [heart, B6 control]


title: N68 [heart, B6 control]


title: 22RV1_IVM8_rep3


title: LungCa_233


title: LungCa_257


title: LungCa_241


title: LungCa_249


title: EPOX-4

value: epoxomicin


title: C4-2_IVM12_rep3

source_name: C4-2 cells


title: C4-2_IVM12_rep2


title: DMSO-1


title: LungCa_227


title: LungCa_235


title: N69 [heart, B6 control]


title: N7 [heart, B6 control]


title: 22RV1_DMSO_rep1


title: N8 [heart, B6 control]

value: non-exercised


title: C4-2_IVM12_rep1


title: LungCa_229


title: LungCa_259


title: N66 [heart, B6 control]


title: MG132-3

description: MG132-3.txt:gProcessedSignal(normalized)


title: LungCa_213


title: LungCa_207


title: LungCa_205

extract_protocol: Total RNAs were extracted using Isogen (Nippon Gene, Osaka, Japan). 3 micrograms of total RNA was reverse transcribed using the SuperScript III system for cDNA synthesis (Invitrogen) according to the protocol recommended by Affymetrix. The oligonucleotide used for priming was 5'-ggccagtgaattgtaatacgactcactatagggaggcgg-(t)24-3' (Invitrogen). Double-stranded cDNA was cleaned by phenol:chloroform extraction and the aqueous phase removed by centrifugation through Phase-lock Gel (Eppendorf).


title: N1 [heart, B6 control]


title: C4-2_IVM8_rep1


title: C4-2_IVM8_rep2


title: N5 [heart, B6 control]


title: N63 [heart, B6 control]


title: C4-2_DMSO_rep3


title: I95 [heart, ND6P25L]

source_name: heart, ND6P25L


title: N2 [heart, B6 control]


title: I76 [heart, ND6P25L]


title: LungCa_209


title: I63 [heart, ND6P25L]


title: I59 [heart, ND6P25L]


title: I57 [heart, ND6P25L]


title: N65 [heart, B6 control]


title: I58 [heart, ND6P25L]


title: AJNT100

city: Suwon

first: Hyun Goo

last: Woo

address: 164 Worldcup-ro Yeongtong-gu

country: South Korea

institute: Ajou University School of Medicine

data_processing:
Illumina BeadStudio software
The low quality sequence reads with less than 30 PHRED score and adapter sequence reads were trimmed using a Trim Galore tool
Sequence reads were mapped to the human reference genome (hg38) using TopHat2 tool with default parameters
RNA abundance was estimated by as the FPKM values according to GENCODE database (version 22) using Cufflinks tool
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text files include log2(FPKM+1) values for each sample

source_name: Non-tumor

extract_protocol:
Total RNA was extracted from each sample using the mirVana total RNA extraction kit (Ambion, Austin, TX).
The sequencing library for RNA was constructed using TruSeq RNA sample preparation kit (illumina, San Diego, CA) according to manufacturer’s instruction

value: Liver

tag: molecular subtype

tag: disease state

value: non-tumor


title: AJNT079


title: AJNT081


title: AJNT052


title: I56 [heart, ND6P25L]


title: C4-2_DMSO_rep2


title: AJNT080


title: I55 [heart, ND6P25L]


title: C4-2_DMSO_rep1


title: AJNT040


title: AJNT039


title: AJHCC099

source_name: Hepatocellular carcinoma

value: HCC


title: AJNT038


title: I62 [heart, ND6P25L]


title: I50 [heart, ND6P25L]


title: I4 [heart, ND6P25L]


title: AJNT098


title: E80 [heart, CO1V421A]

source_name: heart, CO1V421A


title: AJHCC097


title: E74 [heart, CO1V421A]


title: E75 [heart, CO1V421A]


title: AJHCC098


title: AJNT048


title: AJHCC095


title: E69 [heart, CO1V421A]


title: E55 [heart, CO1V421A]


title: I53 [heart, ND6P25L]


title: E64 [heart, CO1V421A]


title: AJHCC096


title: E56 [heart, CO1V421A]


title: AJHCC079


title: E52 [heart, CO1V421A]


title: AJHCC094


title: AJHCC082


title: E53 [heart, CO1V421A]


title: AJHCC081


title: AJHCC100


title: E50 [heart, CO1V421A]


title: B83 [heart, ND5S204F]

source_name: heart, ND5S204F


title: E44 [heart, CO1V421A]


title: AJHCC075


title: AJHCC076


title: AJHCC078


title: AJHCC072


title: B71 [heart, ND5S204F]


title: E42 [heart, CO1V421A]


title: AJHCC080


title: B80 [heart, ND5S204F]


title: B81 [heart, ND5S204F]


title: AJHCC073


title: AJHCC070


title: B69 [heart, ND5S204F]


title: B70 [heart, ND5S204F]


title: B13 [heart, ND5S204F]


title: B21 [heart, ND5S204F]


title: AJHCC067


title: AJHCC068


title: AJHCC064


title: B11 [heart, ND5S204F]


title: AJHCC062


title: AJHCC065


title: AJHCC063


title: B5 [heart, ND5S204F]


title: B9 [heart, ND5S204F]


title: A80 [heart, ANT1-/-]

source_name: heart, ANT1-/-


title: AJHCC061


title: A73 [heart, ANT1-/-]


title: AJHCC060


title: A76 [heart, ANT1-/-]


title: A69 [heart, ANT1-/-]


title: AJHCC066


title: A71 [heart, ANT1-/-]


title: A70 [heart, ANT1-/-]


title: A64 [heart, ANT1-/-]


title: AJHCC054


title: B10 [heart, ND5S204F]


title: C4-2_IVM8_rep3


title: A63 [heart, ANT1-/-]


title: A72 [heart, ANT1-/-]


title: AJHCC052


title: AJHCC059


title: AJHCC050


title: A58 [heart, ANT1-/-]


title: AJHCC058


title: AJHCC046


title: A17 [heart, ANT1-/-]


title: A23 [heart, ANT1-/-]


title: N4 [soleus muscle, B6 control]

source_name: soleus muscle, B6 control

value: responder

value: soleus muscle


title: AJHCC048


title: N68 [soleus muscle, B6 control]


title: N7 [soleus muscle, B6 control]

value: non-responder


title: AJHCC043


title: AJHCC041


title: AJHCC044


title: AJHCC051


title: AJHCC040


title: AJHCC057


title: N8 [soleus muscle, B6 control]


title: N69 [soleus muscle, B6 control]


title: AJHCC074


title: AJHCC056


title: N65 [soleus muscle, B6 control]


title: N1 [soleus muscle, B6 control]


title: N5 [soleus muscle, B6 control]


title: AJHCC034


title: AJHCC053


title: AJHCC036


title: N62 [soleus muscle, B6 control]


title: I100 [soleus muscle, ND6P25L]

source_name: soleus muscle, ND6P25L


title: AJHCC031


title: AJHCC038


title: N63 [soleus muscle, B6 control]


title: AJHCC030


title: I94 [soleus muscle, ND6P25L]


title: AJHCC039


title: AJHCC033


title: AJHCC028


title: I75 [soleus muscle, ND6P25L]


title: N66 [soleus muscle, B6 control]


title: I84 [soleus muscle, ND6P25L]


title: I63 [soleus muscle, ND6P25L]


title: AJHCC042


title: N2 [soleus muscle, B6 control]


title: I95 [soleus muscle, ND6P25L]


title: AJHCC029


title: AJHCC025


title: I85 [soleus muscle, ND6P25L]


title: AJHCC027


title: AJHCC017


title: AJHCC026


title: I62 [soleus muscle, ND6P25L]


title: I18 [soleus muscle, ND6P25L]


title: I59 [soleus muscle, ND6P25L]


title: I13 [soleus muscle, ND6P25L]


title: AJHCC019


title: AJHCC016


title: I50 [soleus muscle, ND6P25L]


title: AJHCC013


title: AJHCC020


title: REH_ETV6-RUNX1_rep2

city: Rennes

first: Gilles

last: Salbert

address: 263 Av. Gal. Leclerc

department: IGDR UMR6290

country: France

institute: University Rennes 1

data_processing:
ChIP-seq reads were aligned to the reference human genome version GRCh37 (hg19).
The .sam files were converted to .bam files using SAMtools.
The .bam files were then processed to yield .wig files using MACS.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: wig files

source_name: Pre-B lymphoblast cells

growth_protocol: REH cells were maintained in RPMI 1640 medium (Gibco, Thermo Fisher Scientific) containing 10% heat-inactivated fetal calf serum (FCS) (Eurobio) supplemented with antibiotics (100 U/mL penicillin-G and 100 U/mL streptomycin, Gibco).

extract_protocol:
Cells were fixed in 1% formaldehyde (648336, Polysciences) at room temperature for 10 min and then quenched in 100 mM glycine for 1 min. Cells were washed twice in PBS and lysed 15 min in 50 mM Tris-HCl ph8.1/10 mM EDTA/0.5% Empigen BB/1% SDS. Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP-seq libraries were generated using TruSeq® ChIP Library Preparation Kit (Illumina) according to the manufacturer’s protocol.

value: REH

value: Pre-B lymphoblast cells

value: Peripheral blood

tag: chip antibody

value: HPA00026 (Sigma Aldrich)


title: AJHCC014


title: AJHCC012


title: E100 [soleus muscle, CO1V421A]

source_name: soleus muscle, CO1V421A

tag: treatment


title: AJHCC010


title: E98 [soleus muscle, CO1V421A]


title: E78 [soleus muscle, CO1V421A]


title: hippo_saline_litter 2

first: Heath

last: Schmidt

address: 125 South 31st Street

institute: University of Pennsylvania

hyb_protocol: All sample labeling, hybridization, and scanning were conduced according to standard protocols developed by the Next Generation Sequencing Core (NGSC) at the University of Pennsylvania and followed the Affymetrix GeneChip Expression Analysis Technical Manual.

scan_protocol: Affymetrix Rat Genome 230 2.0 arrays were scanned using a GeneArray Scanner

data_processing: Data were analyzed with Microarray Suite version 5.0 using Affymetrix default analysis.

organism: Rattus norvegicus

source_name: drug-naïve offspring dorsal hippocampal tissue from saline father 2

label_protocol: Biotinylated cDNA was prepared according to standard Affymetrix protocols.

growth_protocol: Tissue was harvested from drug-naïve, young adult first generation male rats

extract_protocol: Extraction of total RNA was performed according to the manufacturer's instructions from bilateral 1 mm^3 micropunches of the dorsal hippocampus collected using a Leica cryostat (Leica 3050S)

treatment_protocol: First generation male offspring from sires that self-administered nicotine (0.03 mg/kg, i.v.) for 60 days. Male control rats from yoked saline sires.

value: Sprague-Dawley

tag: Sex

value: Male

value: dorsal hippocampal

tag: paternal sire

value: saline


title: hippo_saline_litter 4

source_name: drug-naïve offspring dorsal hippocampal tissue from saline father 4

tag: tissue


title: AJHCC009


title: AJHCC007


title: hippo_nicotine_litter 4

source_name: drug-naïve offspring dorsal hippocampal tissue from nicotine father 4

value: nicotine


title: hippo_saline_litter 1

source_name: drug-naïve offspring dorsal hippocampal tissue from saline father 1


title: hippo_saline_litter 3

source_name: drug-naïve offspring dorsal hippocampal tissue from saline father 3


title: hippo_nicotine_litter 2

source_name: drug-naïve offspring dorsal hippocampal tissue from nicotine father 2


title: hippo_nicotine_litter 3

source_name: drug-naïve offspring dorsal hippocampal tissue from nicotine father 3


title: AJHCC005


title: E76 [soleus muscle, CO1V421A]

value: exercised


title: E64 [soleus muscle, CO1V421A]

value: non-exercised


title: E56 [soleus muscle, CO1V421A]


title: hippo_nicotine_litter 1

source_name: drug-naïve offspring dorsal hippocampal tissue from nicotine father 1


title: AJHCC004

value: Liver


title: E53 [soleus muscle, CO1V421A]


title: 1385-TE: Tumour epithelium_sample_1385

city: Edinburgh

first: Andrew

middle: H

last: Sims

address: Carrington Crescent

department: Institute of Genetics and Molecular Medicine

country: United Kingdom

institute: University of Edinburgh

hyb_protocol: SurePrint G3 Human GE 8x60K microarray kit with SurePrint technology (Agilent Technologies, #G4851-60510) were used for all the experiments. Two-color microarray-based gene expression hybridization kit was used to perform the hybridizations (Agilent, #5188-5242). The 2 dyes used were Cy3 and Cy5. The aRNA of interest (300 ng) was labelled with Cy3. The reference sample used (300 ng) was a universal human reference RNA sample (Stratagene, #740000, La Jolla, California, USA) that was previously amplified using the RiboAmp HS plus kit and labelled with Cy5 dye using the Arcturus Cy5 Turbo Labeling Kit (Life Technologies, #KIT0610).

scan_protocol: Microarray data were feature extracted using Feature Extraction Software (v. 9.5.3) from Agilent with the default parameters.

data_processing: The microarray experiments were carried out in 3 batches and pre-processed using Agilent GeneSpring Software. Raw data was normalised, log2 transformed and filtered, and quality control analyses were carried out. HGNC gene annotations were applied and the mean was taken when multiple probes were present for the same gene. Finally, the batch effect was corrected using ComBat.

source_name: Invasive Lobular Carcinoma fresh frozen tumor

label_protocol: RNA was amplified using the T-7 based RiboAmp HS Plus RNA amplification kit (Arcturus) and quality control Agilent RNA 6000 Nano kit was used (Agilent). RNA was labelled with Cy3 dye (Turbo labeling kit Cy3, Life Technologies) according to the manufacturer’s procedure. The amount of Cy3-labeled aRNA was quantified using a NanoDrop.

growth_protocol: Breast tumor tissue samples were obtained at primary surgery from patients providing written informed consent.

extract_protocol: Total RNA was extracted from each population of microdissected cells in RNase-free eppendorf containing 50 µl of extraction buffer and placed for 30 min at 42 ºC (Arcturus). After RNA extraction, RNA was isolated and subjected to DNaseI treatment (PicoPure RNA isolation kit, Arcturus). Samples were concentrated to a final volume of 6 µl using a refrigerated CentriVap concentrator (LabConco) at 4 ºC for 10 min. Agilent RNA 6000 Pico kit was used for Bioanalyzer quality control (Agilent).

treatment_protocol: Tissue specimens were microdissected into epithelium and stroma using a PixCell IIe LCM system (Arcturus). All microdissections were performed within two hours following tissue staining.

value: Tumour epithelium

tag: patient age

tag: tumor size

tag: nuclear grade

value: II

tag: er status

value: pos

tag: pr status

value: neg

tag: her2 status

source_name: Universal Human Reference RNA Sample

tag: supplier


title: 1780-TE: Tumour epithelium_sample_1780

value: Stratagene, #740000, La Jolla, California, USA


title: 1751-TE: Tumour epithelium_sample_1751

value: equivocal. (neg by FISH)


title: 1775-TS: Tumour stroma_sample_1775

value: Tumour stroma


title: 1739-TS: Tumour stroma_sample_1739


title: 1780-TS: Tumour stroma_sample_1780


title: 1775-TE: Tumour epithelium_sample_1775


title: 1859-TS: Tumour stroma_sample_1859


title: 1332-TS: Tumour stroma_sample_1332

value: I


title: 1816-TE: Tumour epithelium_sample_1816


title: AJHCC003

source_name: Hepatocellular carcinoma

value: HCC


title: 1830-TE: Tumour epithelium_sample_1830

value: III


title: 1830-TS: Tumour stroma_sample_1830


title: E50 [soleus muscle, CO1V421A]

value: non-responder

value: soleus muscle


title: E42 [soleus muscle, CO1V421A]


title: blmp1_rep_3

city: Taipei

first: Yi-Chun

last: Wu

address: No. 1 Sec. 4 Roosevelt Road

department: Institute of Molecular and Cellular Biology

country: Taiwan

institute: National Taiwan University

data_processing:
Transcriptome sequence reads were initially quality and adaptor trimmed using Trimmomatic (v0.36; parameter used: ILLUMINACLIPTruSeq2-PE.fa:2:40:12:8:true LEADING:10 TRAILING:10 SLIDINGWINDOW:3:15 MINLEN:34)
Pair-end reads were mapped to C. elegans reference with HISAT2 (v2.1.0)
Read counts of individual genes were obtained using featureCounts (v1.6.3)
Differential expressions between wild type and blmp-1 mutant strain were determined with DESeq2 (v1.22.0; padj < 0.05 and FDR > 2)
Genome_build: Wormbase (WS267)
Supplementary_files_format_and_content: CPM and TPM of genes were listed in csv file

organism: Caenorhabditis elegans

source_name: young adult animal

growth_protocol: Embryos were isolated by bleach treatment and synchronized L1 were grown on NGM plates to the young adult stage

extract_protocol:
Total RNA was extracted with Invitrogen TRIzol Reagent
Library construction was created using TruSeq RNA Sample Preparation Kits (Illumina)

tag: developmental stage

value: young adult animal


title: 1037-TE: Tumour epithelium_sample_1037

value: ND


title: blmp1_rep_2


title: 1037-TS: Tumour stroma_sample_1037


title: 1756-TE: Tumour epithelium_sample_1756


title: 436-TE: Tumour epithelium_sample_436


title: 826-TE: Tumour epithelium_sample_826


title: E12 [soleus muscle, CO1V421A]

value: exercised

tag: exercise response

value: responder


title: E7 [soleus muscle, CO1V421A]

value: non-exercised

tag: strain


title: blmp1_rep_1


title: E1 [soleus muscle, CO1V421A]


title: wt_rep_3


title: 1332-TE: Tumour epithelium_sample_1332

value: Tumour epithelium


title: wt_rep_2


title: wt_rep_1


title: B85 [soleus muscle, ND5S204F]

source_name: soleus muscle, ND5S204F


title: B98 [soleus muscle, ND5S204F]


title: B80 [soleus muscle, ND5S204F]


title: U-RT1 cell line #3

city: Ulm

first: Julia

last: Maier

address: Albert-Einstein-Allee 23

country: Germany

institute: Institute of Pathology

description: basic gene expression of U-RT1

hyb_protocol: 100 ng of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s protocol. On completion of the fragmentation reaction, 25 µl of 2x Agilent HiRPM hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Human 4x44K Whole Genome Microarray (G412F) for 17 hours at 65°C in a rotating hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent), 1 minute with 37°C GE Wash buffer 2 (Agilent) and 30 seconds with Acetonitril.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA microarray Scanner G2505B (5micron) with the the Agilent Scan Control Version A.8.4.1 .

data_processing: The scanned images were analyzed with Feature Extraction Software 12.0.1.1(Agilent) using Default Parameters (protocol GE1_1200_Jun14 and grid: 014850_D_F_20110325) to obtain Background subtracted and spatially detrended processed signal intensities

source_name: U-RT1 cell line

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's protocol, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with a NanoPhotometer

growth_protocol: The cell lines were cultured in Iscove’s Modified Dulbecco’s Medium/RPMI 1640 (4:1; Lonza, Basel, Switzerland) with 10 % fetal bovine serum (Biochrom AG, Berlin, Germany), 2 mM glutamine, and penicillin/streptomycin

extract_protocol: RNA was isolated using the RNeasy Mini Kit (Qiagen) following the manufacturer's protocol. RNA was quantified using a NanoPhotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: The cell lines were not treated with any reagents.

tag: cell type

value: stable Richter Syndrome cell line

tag: original tissue

value: lymph node with Richter Syndrome

tag: cell line


title: 1859-TE: Tumour epithelium_sample_1859

value: II

value: pos

value: neg


title: 031-TS: Tumour stroma_sample_031

value: Tumour stroma

value: Stratagene, #740000, La Jolla, California, USA


title: 384-TE: Tumour epithelium_sample_384

value: I


title: 1789-TS: Tumour stroma_sample_1789

value: equivocal. (neg by FISH, ratio 1.11)


title: 549-TE: Tumour epithelium_sample_549


title: U-RT1 cell line #2

description: basic gene expression of U-RT1


title: 031-TE: Tumour epithelium_sample_031


title: U-RT1 cell line #1

description: basic gene expression of U-RT1


title: B70 [soleus muscle, ND5S204F]

tag: treatment


title: B69 [soleus muscle, ND5S204F]


title: 583-TS: Tumour stroma_sample_583


title: RPE1 Dam-Taf3_3 (set10.samplenr_010) DamID

data_processing:
Library strategy: DamID-seq
Samples are demultiplexed based on the sample barcode present in R1, using custom pipelines (available at: https://github.com/KindLab/scDamAndTools).
DamID reads are aligned using bowtie2 (v. 2.3.3.1) with the following parameters: “--seed 42 --very-sensitive -N 1”.
Alignments with a MAPQ < 10 are removed.
Using our own custom pipeline (see KindLab GitHub), aligned reads are matched to known GATC positions in the genome to get the number of observations per (strand-specific) GATC position.
GATC-position counts are deduplicated using UMI information to allow a maximum of 64 unique UMIs per GATC position.
Unique GATC counts are summarized in genomic intervals at the desired resolution.
Genome_build: hg19
Supplementary_files_format_and_content: Hdf5 files contain per chromosome the observed number of UMI-unique counts within genomic intervals of a resolution indicated by the bin size.

growth_protocol: Human hTERT-immortalized RPE-1 cells were grown in DMEM: F12 supplemented with 10% fetal bovine serum and 1% Pen/Strep (100 U/mL penicillin and 100 ug/mL streptomycin).

extract_protocol:
Cells were harvested by trypsinization, and genomic DNA was extracted by column purification.
DamID sequencing was performed as previously described (doi 10.1038/s41596-020-0314-8). Briefly, genomic DNA was digested with DpnI, followed by indexed adapter ligations, bead cleanup and amplification by T7 RNA polymerase. RNA sequencing libraries were prepared by reverse transcription, PCR-based amplification of cDNA, and single-ended size selection. Libraries were sequenced on the Illumina HiSeq 2500 or NextSeq 500.

treatment_protocol: hTERT-RPE1 cells grown in DMEM/F12 (Gibco) 10% FBS (Hyclone) and 1% Pen/Strep (Gibco) on 6 well to 30% confluency were transduced in 1500ul total volume with lentiviral amounts ranging between 0.1-40ul concentrated or 20-1500ul unconcentrated lentivirus in the presence of 10ug/ml of polybrene, and collected for gDNA isolation 48hrs after transduction.

tag: dam-fusion protein

value: Taf3 (PHD domain)

tag: dam type

value: DamWT


title: B47 [soleus muscle, ND5S204F]

tag: tissue

value: soleus muscle


title: 826-TS: Tumour stroma_sample_826

tag: patient age


title: 549-TS: Tumour stroma_sample_549

tag: tumor size


title: RPE1 Dam-Taf3_3 (set10.samplenr_011) DamID


title: 1751-TS: Tumour stroma_sample_1751

tag: nuclear grade

value: equivocal. (neg by FISH)


title: B19 [soleus muscle, ND5S204F]


title: 1789-TE: Tumour epithelium_sample_1789

tag: er status


title: RPE1 Dam-Taf3_3 (set14.samplenr_013) DamID


title: 583-TE: Tumour epithelium_sample_583

tag: pr status


title: RPE1 Dam-Ring1B_full (set14.samplenr_041) DamID

value: Ring1B (full protein)


title: B11 [soleus muscle, ND5S204F]

value: exercised

value: responder


title: B10 [soleus muscle, ND5S204F]

value: non-exercised


title: 281-TS: Tumour stroma_sample_281

tag: her2 status


title: 040-TS: Tumour stroma_sample_040

tag: supplier


title: 281-TE: Tumour epithelium_sample_281

value: Tumour epithelium


title: 040-TE: Tumour epithelium_sample_040


title: RPE1 Dam-Ring1B_full (set14.samplenr_042) DamID


title: 344-TS: Tumour stroma_sample_344


title: 222-TE: Tumour epithelium_sample_222


title: 344-TE: Tumour epithelium_sample_344


title: RPE1 Dam-Ring1B_full (set14.samplenr_040) DamID


title: 222-TS: Tumour stroma_sample_222


title: ADBR3 overexpressing heart 6

city: Nantes

first: Marja

last: Steenman

address: 8 quai Moncousu

institute: L'institut du thorax

hyb_protocol: 600 ng of Cy3-labeled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent Hi-RPM hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Microarrays (G4122F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent). Next, microarrays were washed 30 seconds in acetonitrile and 30 seconds in Stabilization and Drying Solution.

scan_protocol: Slides were scanned immediately after washing on the Agilent G2565CA Microarray Scanner using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters (protocol GE1-107_Sep09 and Grid: 028279_D_20131202) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Data were normalized using R statistical software. Raw values of all probes on all arrays were normalized against a virtual median chip (median raw intensity per row) using a locally weighted scattered plot smoother analysis (LOWESS). Values for replicate probes were averaged. The data were filtered to 20,000 probes to remove probes with low intensity values.

source_name: left ventricle from 45wk old ADBR3 overexpressing rats

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the Low Input QuickAmp Labeling Kit One-Color (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted using Tri-Reagent. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was assessed using an Agilent 2100 Bioanalyzer.

tag: genotype/variation

value: left ventricle

tag: gender

value: male


title: B9 [soleus muscle, ND5S204F]

tag: exercise response

value: non-responder

tag: strain


title: ADBR3 overexpressing heart 5


title: B4 [soleus muscle, ND5S204F]


title: ADBR3 overexpressing heart 7


title: 820-TE: Tumour epithelium_sample_820

value: pos

value: neg


title: B3 [soleus muscle, ND5S204F]


title: RPE1 Dam-PolR2F_full (set10.samplenr_045) DamID

value: Polr2f (full protein)


title: RPE1 Dam-PolR2F_full (set10.samplenr_043) DamID


title: A88 [soleus muscle, ANT1-/-]

source_name: soleus muscle, ANT1-/-


title: ADBR3 overexpressing heart 3


title: ADBR3 overexpressing heart 4

description: 286c is a replicate hybridization of 286


title: ADBR3 overexpressing heart 1

description: 285a is a replicate labeling of 285


title: RPE1 Dam-PolR2F_full (set3.samplenr_021) DamID


title: ADBR3 overexpressing heart 2

description: 285b is a replicate labeling of 285


title: RPE1 Dam-PolR2F_full (set3.samplenr_003) DamID


title: A82 [soleus muscle, ANT1-/-]


title: A81 [soleus muscle, ANT1-/-]


title: 820-TS: Tumour stroma_sample_820

value: Tumour stroma

value: I

value: Stratagene, #740000, La Jolla, California, USA


title: 1A_3: H3K4me2 edited de-differentiated vascular smooth muscle cell_rep3

city: Pittsburgh

first: Delphine

last: Gomez

address: 200 Lothrop St

department: Department of Medicine, Division of Cardiology

institute: University of Pittsburgh

data_processing:
Analysis performed on CLC Genomics Workbench 21
Small RNA were mapped to Rnor_6.0
Grouping and analysis were performed under default setting in CLC Genomics Workbench 21 by normalization of TMM
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: xlsx spreadsheet

source_name: Aortic vascular smooth muscle cell

growth_protocol: VSMC was routinely cultured in DMEM/F12 supplemented with FBS, antibiotics and L-glutamin as described in methods section.

extract_protocol:
RNA isolation was performed using miRNeasy kit following manufacturer's instructions.
The library was prepared by QIAseq small RNA according to manufacturer’s protocol and sequencing was performed with illumina NextSeq High Output 75 cycle kit (1 x 75 bp) with reading depth of 30 million reads per sample.

treatment_protocol: VSMC was starved in serum-free medium for 24 h prior to treatment. VSMC was treated with PDGF-BB for 24 h at a concentration of 30 ng/ml.

tag: cell type

value: Aortic vascular smooth muscle cell

value: Lentiviral transduction with expressing sequence of Myocardin-F-LSD1


title: WT heart 4

source_name: left ventricle from 45wk old WT rats

value: WT


title: 1A_1: H3K4me2 edited de-differentiated vascular smooth muscle cell_rep1


title: WT heart 5

description: 296c is a replicate hybridization of 296


title: WT heart 3


title: BB_3: PDGF-BB induced de-differentiated vascular smooth muscle cell_rep3

value: Millipore #01-305 @ 30ng/ml


title: RPE1 Dam-Mphosph8_3 (set7.samplenr_017) DamID

tag: cell line

value: Mphosph8 (chromodomain)

value: DamWT


title: WT heart 6


title: RPE1 Dam-PolR2F_full (set10.samplenr_044) DamID


title: BB_2: PDGF-BB induced de-differentiated vascular smooth muscle cell_rep2

tag: treatment


title: WT heart 1

description: 282a is a replicate labeling of 282


title: A75 [soleus muscle, ANT1-/-]

value: non-exercised

value: soleus muscle


title: RPE1 Dam-Mphosph8_3 (set14.samplenr_038) DamID

tag: dam-fusion protein


title: A76 [soleus muscle, ANT1-/-]

value: exercised


title: 518_3: Differentiated vascular smooth muscle cell_rep3


title: BB_1: PDGF-BB induced de-differentiated vascular smooth muscle cell_rep1


title: 1A_2: H3K4me2 edited de-differentiated vascular smooth muscle cell_rep2


title: 518_2: Differentiated vascular smooth muscle cell_rep2


title: A43 [soleus muscle, ANT1-/-]

value: responder


title: 8x pooled E17 SCN, maternal SCN lesion, mother on time-restricted feeding regime killed at time 21

city: Prague 4

first: Martin

last: Sládek

address: Videnska 1083

country: Czech Republic

institute: Institute of Physiology of the Czech Academy of Sciences

data_processing:
nf-core/rnaseq workflow pipeline
Reads were mapped to the latest UCSC rn6 (RGSC Rnor_6.0) rat genome assembly by HISAT2 v.2.1.0
FPKM were calculated by Salmon and Stringtie
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: comma-delimited csv file includes read counts for each sample

source_name: 8x pooled E17 SCN

extract_protocol:
Fetal SCN samples collected at each of the 8 time points (time 0-21) were pooled from the same mother (n = 8 for Group A, n = 5-10 for Group B). RNA was isolated by RNeasy Micro Kit (Qiagen, Germany) according to manufacturer’s instructions, treated with On-Column DNAse I digestion set (Sigma) for 15 minutes at 37°C, then quantified by spectrophotometry. RNA integrity was tested by capillary electrophoresis (Agilent Tech., USA).
RNA libraries were prepared for sequencing by rRNA depletion, polyA RNA enrichment and using Smarter Stranded low input tot-RNA-Seq kit v2 (Takara, Japan).
Illumina NextSeq 500/550 High output kit v2 (150 cycles, SE)

value: Wistar

value: suprachiasmatic nuclei (SCN)

tag: circadian time

value: 21 hr

tag: developmental stage

value: fetus

tag: age

value: embryonic age 17

tag: mother treatment

value: SCN lesion, time-restricted feeding regime

tag: mother group

value: B


title: WT heart 2

description: 282b is a replicate labeling of 282

tag: tissue

value: left ventricle

value: male


title: RPE1 Dam-Mphosph8_3 (set7.samplenr_016) DamID

tag: dam type


title: 8x pooled E17 SCN, maternal SCN lesion, mother on time-restricted feeding regime killed at time 18

value: 18 hr


title: RPE1 Dam-Mphosph8_3 (set14.samplenr_037) DamID


title: A30 [soleus muscle, ANT1-/-]

value: non-responder


title: A58 [soleus muscle, ANT1-/-]


title: 8x pooled E17 SCN, maternal SCN lesion, mother on time-restricted feeding regime killed at time 6

value: 6 hr


title: 8x pooled E17 SCN, maternal SCN lesion, mother on time-restricted feeding regime killed at time 9

value: 9 hr


title: 8x pooled E17 SCN, maternal SCN lesion, mother on time-restricted feeding regime killed at time 12

value: 12 hr


title: RPE1 Dam-H4K20me1 (set4.samplenr_021) DamID

value: anti-H4K20me1 (mintbody)

value: DamWT


title: A17 [soleus muscle, ANT1-/-]

value: exercised

value: soleus muscle


title: A18 [soleus muscle, ANT1-/-]

value: non-exercised


title: RPE1 Dam-H4K20me1 (set2.samplenr_010) DamID


title: A13 [soleus muscle, ANT1-/-]

value: responder


title: 8x pooled E17 SCN, maternal SCN after sham surgery, ad libitum fed mother killed at time 21

value: Wistar

value: suprachiasmatic nuclei (SCN)

value: 21 hr

value: fetus

value: SCN sham surgery, ad libitum feeding regime

value: A


title: A4 [soleus muscle, ANT1-/-]


title: 8x pooled E17 SCN, maternal SCN lesion, mother on time-restricted feeding regime killed at time 3

value: 3 hr

value: embryonic age 17

value: SCN lesion, time-restricted feeding regime

value: B


title: 518_1: Differentiated vascular smooth muscle cell_rep1

value: Aortic vascular smooth muscle cell


title: RPE1 Dam-Mphosph8_3 (set14.samplenr_039) DamID

value: Mphosph8 (chromodomain)


title: 8x pooled E17 SCN, maternal SCN after sham surgery, ad libitum fed mother killed at time 18

value: 18 hr


title: 8x pooled E17 SCN, maternal SCN after sham surgery, ad libitum fed mother killed at time 15

value: 15 hr


title: 8x pooled E17 SCN, maternal SCN after sham surgery, ad libitum fed mother killed at time 12

value: 12 hr


title: RPE1 Dam-H4K20me1 (set2.samplenr_004) DamID

value: anti-H4K20me1 (mintbody)

value: DamWT


title: 8x pooled E17 SCN, maternal SCN lesion, mother on time-restricted feeding regime killed at time 15

value: Wistar


title: 8x pooled E17 SCN, maternal SCN after sham surgery, ad libitum fed mother killed at time 9

value: suprachiasmatic nuclei (SCN)

value: 9 hr


title: 8x pooled E17 SCN, maternal SCN after sham surgery, ad libitum fed mother killed at time 3

value: fetus


title: KO 3

city: NEW YORK

first: Jesus

middle: Maria

last: Gomez Salinero

state: NY

address: 1300 York Avenue

institute: Weill Cornell Medicine

data_processing:
FastQC (v0.11.5) to check FASTQ quality.
Skewer (v0.2.2) for adapter trimming
Minion from Kraken tool (reaper-13-100) for adapter diagnosis
STAR (v2.7.6a) for alignment and gene count quantification using --quantMode GeneCounts
Genome_build: GRCm38
Supplementary_files_format_and_content: Gene count matrix

molecule: polyA RNA

source_name: Liver endothelium

extract_protocol:
ECs were isolated by fluorescence-activated cell sorting and subjected to RNA extraction using RNeasy Mini Kit from Qiagen.
RNA-seq libraries of polyadenylated RNA were prepared using the TruSeq RNA Library Prep Kit v2 (Illumina) or TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer’s instructions.

value: Liver

tag: genotype

value: c-Maf KO


title: KO 4


title: RPE1 Dam126-H4K20me1 (set4.samplenr_020) DamID


title: RPE1 Dam-H4K20me1 (set4.samplenr_022) DamID


title: KO 1


title: 8x pooled E17 SCN, maternal SCN lesion, mother on time-restricted feeding regime killed at time 0

value: 0 hr


title: 8x pooled E17 SCN, maternal SCN after sham surgery, ad libitum fed mother killed at time 0

value: embryonic age 17

value: SCN sham surgery, ad libitum feeding regime

value: A


title: RPE1 Dam126-H4K20me1 (set5.samplenr_017) DamID


title: Ctl 3

value: Control


title: KOPALM3

city: MADRID

last: VALDECANTOS

state: MADRID

address: C/ARTURO DUPERIER, 4

country: Spain

institute: IIB ALBERTO SOLS

data_processing:
RNA-Seq paired-end reads were mapped against the mouse reference genome using STAR (RRID:SCR_015899, version 2.5.2a) with ENCODE parameters for long RNA. Genes were quantified using RSEM (RRID:SCR_013027, version 1.2.2.8) and GENCODE (RRID:SCR_014966, version 24).
Mapping quality metrics were calculated with GEMtools (http://gemtools.github.io/) and RSeQC (RRID:SCR_005275).
Normalization and transformation of the expression data for plotting and analysis were done with the variance stabilizing transformation function of DESeq2 (RRID:SCR_015687). Only the protein coding genes from the normalized count matrix were selected for further analysis.
After low-expressed genes were filtered out (at least 1 count in 70% of samples) and genes with duplicated gene symbol were averaged by the median of their expression.
Finally, counts were log2 transformed for Limma analysis.
Assembly: RNA-Seq paired-end reads were mapped against the mouse reference genome using STAR (RRID:SCR_015899, version 2.5.2a) with ENCODE parameters for long RNA.
Supplementary files format and content: Processed data file are presented as normalized counts in microsoft excel  format

source_name: Liver progenitor cells

growth_protocol: Cells were mantained in DMEM 10% with 10% FBS and passed twice a week

extract_protocol:
RNA was extracted using the miRNeasy Mini kit (QIAGEN 217004, Hilden, Germany) following the manufacturer’s instructions and assessed for quality. The starting input material for the construction of the RNA library was DNA-free total RNA from FFPE samples, obtained using the KAPA RNA HyperPrep Kit with RiboErase (HMR; Kapa Biosystems, Wilmington, MA, USA), according to the manufacturer´s protocol. Briefly, the ribosomal RNA (rRNA) was depleted from 0.8 to 1 μg of total RNA using RiboErase. rRNA-depleted RNA samples were fragmented in the presence of divalent ions at 65°C for 1 min due to the low quality of the initial total RNA. Following RNA fragmentation (first- and second-strand synthesis), the Illumina-compatible bar-coded adapters were ligated at a concentration of 1.5 μM.
The libraries were sequenced on HiSeq2000 (Illumina, San Diego, CA, USA) in paired-end mode with a read length of 2 × 76 bp using TruSeq SBS Kit v4. Each sample was sequenced in a fraction of a sequencing v4 flow cell lane, following the manufacturer's protocol.

treatment_protocol: Cells were treated with Palmitic Acid 400 µM in DMEM  supplemented with 5% FBS and 1% of BSA

value: Hepatic progenitor cells

tag: agent

value: Palmitic acid 400 microM 8h


title: KOPALM4