title: LCN_REP1

city: Los Angeles

first: Calvin

last: Pan

address: 675 Charles Young Dr South

institute: UCLA

data_processing:
Alignment was performed using HISAT2 against genome build GRCm38
Quantification and differential expression was performed using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: feature counts were generated using DESeq2

source_name: gonadal fat

extract_protocol:
Upon sacrifice, tissues were instantly frozen in liquid nitrogen. Frozen tissues were homogenized in QIAzol, and following chloroform phase separation RNA was prepared from the pink phase using Qiagen miRNeasy kits as per original protocol. Total RNA quality was validated with BioAnalyzer (all samples had eRIN >8.2).
RNA libraries were prepared using KAPA Stranded mRNA-Seq Kit.

tag: aav


title: LCN_REP3

status: Public on Oct 11 2018

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: strain


title: LCN_REP4


title: LCN_REP2


title: F-RIG-I Input, replicate1

city: Nashville

first: Jeff

last: Rathmell

state: TN

address: 1211 Medical Center Drive

department: PMI

institute: Vanderbilt University Medical Center

description: Total RNA

data_processing:
The fastq raw reads were evaluated using fastqc
Then the reads were mapped to GRCh38 p10 reference genome using STAR_2.5.3a
The the aligned reads were assembled using gencode.v27 annotation with cufflinks _2.2.1
Then the enrichment of features were analysis with cuffquant and cuffdiff.
Genome_build: GRCh38.p10; GQ994935 (HHV8 genome)
Supplementary_files_format_and_content: cuffdiff output in plain text

organism: Homo sapiens

source_name: patient-derived PEL cell line

extract_protocol:
BC-3 cells were crosslinked with 1% formaldehyde for 10 min in PBS, and unreacted formaldehyde was neutralized with 0.3 M glycine, pH 7, for 5 min. Cells were washed 2X with PBS, then resuspended in RIPA buffer (50 mM Tris, pH 8, 1% IGEPAL CA 630, 0.5% sodium deoxycholate, 0.05% SDS, 1 mM EDTA, 150 mM NaCl, 1 mM DTT, and RNAse and protease inhibitors) and kept on ice for 10 min. Soluble cell extracts were incubated with anti-FLAG M2 magnetic resin at 4 °C for 2 h. Resin was washed three times for 10 min and then two times for 5 min at room temperature in RIPA buffer containing 0.1% SDS, 1 M NaCl, and 1 M urea. Resin was eluted with 1xFLAG peptide in RIPA buffer for 45 min at 4 °C. Protein–RNA crosslinks were reversed by adding 100 mM Tris, pH 8, 10 mM EDTA, 1% SDS, and 2 mM DTT to eluted samples and heating to 70 °C for 45 min. RNA was recovered by extraction with TRIzol and then again with phenol:chloroform:isoamyl alcohol [25:24:1 (vol/vol)] followed by ethanol precipitation.
Paired-end RNA-sequencing libraries were prepared from the recovered RNA using the NEBNext Ultra II Directional RNA Library Prep Kit (NEB) according to the manufacture recommendations. Libraries were then subjected to paired-end sequencing on a HiSeq3000 with 150 cycles at the Vanderbilt Technologies for Advanced Genomics (VANTAGE).

tag: cell type

value: inducible F-RIG-I BC-3 cells

tag: cell line


title: GFP_REP4

value: GFP


title: GFP_REP3


title: GFP_REP2


title: Huh7.5_BMP6_Replicate3

type: RNA

city: Oxford

first: Hal

last: Drakesmith

address: John Radcliffe Hospital

department: MRC Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

description:
Huh7.5 cells treated for 24h with 18nMBMP6
SAMPLE 6

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using the Lumi package (Bioconductor) and compared using LIMMA (Bioconductor)

label: biotin

source_name: Huh7.5 cells, BMP6 18nM for 24h

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

growth_protocol: Huh7.5 cells were cultured in DMEM media supplemented with 10% FCS, 2mM glutamine, 100U/mL penicillin, 0.1mg/mL streptomycin prior to trypsinisation and plating in tissue culture plates

extract_protocol: Total RNA was isolated using Qiagen RNeasy mini spin columns, then converted into labelled cRNA and used for hybridisation; quality control was performed with Agilent Bioanalyser.

treatment_protocol: Cells were plated at 3x10e5/well in 12-well plates, allowed to adhere overnight, and were then treated for 24h with 18nM recombinant human BMP6 or media vehicle (untreated)


title: GFP_REP1


title: Huh7.5_Untreated_Replicate2

description:
Untreated control
SAMPLE 4

source_name: Huh7.5 cells, untreated, 24h


title: Huh7.5_Untreated_Replicate3

description:
Untreated control
SAMPLE 5


title: Huh7.5_BMP6_Replicate2

description:
Huh7.5 cells treated for 24h with 18nMBMP6
SAMPLE 3


title: pESC_early

city: Beijing

first: Qi

last: Zhou

address: Datun Road, Chaoyang District

country: China

institute: Institute of Zoology,CAS

library_source: genomic

data_processing:
The sequencing reads were mapped to the mouse genome (version mm9) by Bismark v0.13.1 (Babraham Bioinformatics) after trimming by Trim Galore (Babraham Bioinformatics) with the "-rrbs" option.
The methylation levels of covered cytosine sites were calculated by dividing the number of reported C with the total number of reported C and T. CpG sites covered by more than ten reads were used for the analysis.
Genome_build: mm9
Supplementary_files_format_and_content: Methylation percentage of the CpG sites

molecule: genomic DNA

growth_protocol: The details of animal and cell culture were described in manuscript.

extract_protocol:
Genomic DNA was isolated from the tissues and cells with Universal Genomic DNA Extraction Kit (TaKaRa).
Reduced representation bisulfite sequencing (RRBS) libraries were constructed as described previously with some modifications.Briefly, about 1 ug genomic DNA was digested with the MspI enzyme. Digested DNA was then purified, end-repaired, and adenylated, followed by ligation to Illumina TruSeq barcode adapters. Fragments of 150-300 bp in size were selected, bisulfite-treated, and sequenced using an Illumina Hiseq 4000.

value: parthenogenetic haploid ESCs

tag: passage

value: early

tag: variation

value: WT


title: phESC_late

value: late


title: WT_adult_brain

tag: tissue

value: brain

tag: developmental stage

value: adult


title: WT15.5embryo

value: whole embryo


title: Huh7.5_Untreated_Replicate1

description:
Untreated control
SAMPLE 1


title: Untreated mouse 1: Lrg5-Lrig1+  population

city: Bruxelles

first: Adriana

last: Sanchez-Danes

address: Route de Lennik 808

country: Belgium

institute: Université Libre de Bruxelles

hyb_protocol: Affymetrix MG-430 PM array strips were hybridized with 8 mg of labeled cDNA, washed, stained and scanned according to the protocol described in GeneAtlas 3’IVT express kit User Manual.

scan_protocol: Arrays were scanned with GeneAtlasImaging station scanner (Affymetrix, Santa Clara, CA)

data_processing: Normalized expression signals were calculated from Affymetrix CEL files using RMA algorithm (Irizarry et al., 2003)

label: Biotin

source_name: Untreated_ Lrg5-Lrig1+  population

label_protocol: cDNA was labeled using GeneChip Mapping 250K Nsp Assay Kit (Affymetrix; catalog # 900766), according to manufacturer's instructions.

growth_protocol: Mouse colonies were maintained in a certified animal facility in accordance with the European guidelines.

extract_protocol: RNA isolation and cDNA amplification was performed as described in Gonzalez-Roca et al. (2010).

treatment_protocol: Sample preparation was performed as previously described in Jensen et al, Nature Protocols 2010.The back skin of mice bearing basal cell carcinomas and drug-tolerant lesions was placed in a petri dish and a sterile scalpel was used to remove the adipose tissue and muscle. The skin was incubated in thermolysin (Sigma) for 1h at 37oC and after a scalpel was used to separate epidermis from the dermis. The epidermal tissue was chopped in little pieces and resuspended in PBS supplemented with 5% chelated fetal calf serum and filtered in 70um and 40um cell strainers (BD). Cells were stained using the anti-Lrig1 (goat polyclonal, R&D) followed by the secondary  donkey anti-Goat-Alexa 647 ( Invitrogen). Living cells were selected by forward scatter, side scatter, doublets discrimination and by Hoechst dye exclusion. Tumour cell subpopulations were selected based on the expression of endogenous Lgr5-GFP and Lrig1-Alexa647.The cell sorting  was performed using FACSAria I at high pressure (70 psi) and FACSDiva software (BD Biosciences).

tag: genotype/variation

tag: treatment

value: Untreated

value: Back skin

value: basal cell carcinoma tumour cells

tag: cell population


title: ESC_late

value: diploid ESC


title: Huh7.5_BMP6_Replicate4

description:
Huh7.5 cells treated for 24h with 18nMBMP6
SAMPLE 7


title: Medial neurogenic zone, no lesion, biological replicate 2

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum Muenchen

description: Gene expression data from medial neurogenic zone from zebrafish without after stab-wound injury

hyb_protocol: According to the Affymetrix expression protocol (HWS kit)

scan_protocol: According to the Affymetrix expression protocol (GeneChip Scanner 3000 7G)

data_processing: RMA probeset summary with standard settings of the Affymetrix Expression Console software (v.1.2) including median polish and Sketch-Quantile normalisation

organism: Danio rerio

source_name: Medial neurogenic zone from zebrafish without after stab-wound injury

label_protocol: Ovation PicoSL WTA System V2 and Encore Biotin Module (Nugen)

growth_protocol: Normal husbandry conditions

extract_protocol: RNeasy Plus Micro Kit (Qiagen)

treatment_protocol: Cerebroventricular microinjections (CMVI) in the telencephalic region of the brain were performed as described (Kizil and Brand, 2011, Barbosa et al., 2015). Fish were anaesthetized in 0.02% MS222 and held in a sponge. A small hole in the skull was made in the region between the telencephalon and the optic tectum using a micro-knife (Fine Science Tools). After the injections, fish were woken up in the aerated tank water and kept in their normal husbandry conditions.

value: Medial neurogenic zone

tag: age

value: 3-6 months

tag: genotype

value: Tg(gfap:gfp)mi2001 transgenic line


title: Medial neurogenic zone, day 7 post lesion, biological replicate 3

description: Gene expression data from medial neurogenic zone from zebrafish, 7 days after stab-wound injury

source_name: Medial neurogenic zone from zebrafish, 7 days after stab-wound injury


title: ESC_early


title: Medial neurogenic zone, day 7 post lesion, biological replicate 1


title: Huh7.5_BMP6_Replicate1

description:
Huh7.5 cells treated for 24h with 18nMBMP6
SAMPLE 2


title: BP15.5embryo

tag: embryo type

value: bipaternal embryo

value: DMR-KO


title: BM_adult_brain

value: bimaternal embryo


title: BM19.5brain


title: Medial neurogenic zone, day 2 post lesion, biological replicate 4

description: Gene expression data from medial neurogenic zone from zebrafish, 2 days after stab-wound injury

source_name: Medial neurogenic zone from zebrafish, 2 days after stab-wound injury


title: Medial neurogenic zone, no lesion, biological replicate 1


title: ahESC_late

value: androgenetic haploid ESCs


title: BM15.5embryo


title: Medial neurogenic zone, day 7 post lesion, biological replicate 2


title: ahESC_early

value: early


title: H3K27ac_reg

city: Barcelona

first: Montserrat

last: Corominas

state: Catalonia

address: Diagonal 643

department: Genètica, Microbiologia i estadística

country: Spain

institute: University of Barcelona

description: PolyA RNA

data_processing:
Data was processed using chip-nf pipeline (available at https://github.com/guigolab/chip-nf).
Reads were continuously mapped to the fly genome (dm6) using GEM mapper.
Duplicated reads were removed using Picard (http://broadinstitute.github.io/picard/).
Fragment length was estimated using SPP.
Peak calling was performed using MACS2.
Genome_build: dm6 (Release 6 plus ISO1 MT)
Supplementary_files_format_and_content: bigWig, narrowPeak (bed)

organism: Drosophila melanogaster

source_name: Regenerating Wing Disc

growth_protocol: Flies were grown on standard media.

extract_protocol:
We isolated 100 wing discs per sample (early control and regeneration). Discs were fixed, pooled in 700 μl of sonication buffer (10 mM Tris-HCl, pH 8.0, 2 mM EDTA and 1 mM EGTA) and processed as described (Pérez-Lluch et al. 2011). Immunoprecipitations were performed in RIPA buffer and using 1 μg of the corresponding antibody. Immunocomplexes were recovered by incubation with Invitrogen Protein A magnetic beads for 2 h. The beads were washed three times in RIPA, once in lithium chloride buffer and twice in TE buffer. After, an RNase treatment was done and samples were decrosslinked at 65⁰C overnight by adding Proteinase K. Samples were purified with Qiagen MinElute Kit and eluted in Gibco water.
HiSeq2000

value: Wing Disc

value: Third instar larvae

tag: condition

value: Regenerating

tag: chip antibody


title: H3K4me1_reg

description: PolyA RNA


title: H3K4me1_Ctrl

description: PolyA RNA

source_name: Undamaged Wing Disc

value: Undamaged


title: H3K27ac_Ctrl

description: PolyA RNA


title: Medial neurogenic zone, day 2 post lesion, biological replicate 3


title: RNApol-II_Ctrl

description: PolyA RNA

value: RNA polII


title: RNApol-II_reg

description: PolyA RNA


title: Lentiviruses expressing mtDRBD DGCR8 rep3

first: Zunpeng

last: Liu

address: Beichen West Road

department: Institute of Zoology, Chinese Academy of Sciences

institute: State Key Laboratory of Stem Cell and Reproductive Biology

description: Lentiviruses expressing mtDRBD DGCR8

data_processing:
Reads were trimmed to remove the adapter sequences and low quality bases.
Clean reads were aligned to mm10 genome using hisat2 software.
Reads were counted by Htsseq-count.
Differentially expressed genes were calculated by DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: The fomat of processed data is tab seprated file. And, the content is HTseq reads count.

source_name: knee joints

growth_protocol: Human MSCs (hMSCs) derived from hESCs were cultured in MEMa (Thermo Fisher Scientific) medium supplemented with 10% fetal bovine serum (FBS, Thermo Fisher Scientific (Cat:10099-141, Lot:1616964)), 0.1 mM non-essential amino acids (Thermo Fisher Scientific), 1% penicillin/streptomycin (Thermo Fisher Scientific), and 1 ng/mL bFGF (Joint Protein Central, JPC).

extract_protocol:
Total cellular RNA was extracted using TRIzol (Thermo Fisher Scientific) and genomic DNA was removed using a DNA-free kit (Thermo Fisher Scientific). Quality control and sequencing was done by Novogene Bioinformatics Technology Co.Ltd.
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

treatment_protocol: An OA mouse model was generated as previously described20. Briefly, anterior cruciate ligament transection (ACLT) was performed on male C57BL/6 mice aged 8 weeks. For the ACLT surgery, after opening the joint capsule, the ACL was transected with microscissors under a surgical micro¬scope. One week after surgery, lentiviruses expressing Luc, DR8-WT, or DR8-mtDRBD were injected into the articular cavity. 7 weeks after lentivirus injection, the mice knee joints were examined by microCT analysis. The mice were then euthanized and the joints were collected for mRNA quantification and histological assessment of the medial tibial plateau joint.

value: knee joints

value: Lentiviruses expressing mtDRBD DGCR8


title: SC_Mix-E6_100nM_6hrs_1

city: Boston

first: Marina

middle: V

last: Kasaikina

state: MA

address: 450 Brookline avenue SM944

department: Cancer Biology

institute: Dana Farber Cancer Institute

data_processing:
alignment using TopHat (v 2.1.1)aligner against mm10 assembly
cufflinks (v2.1.1)
cuffmerge (v 2.1.1)
cuffdiff (v2.1.1)
differential expression of the detected genes in merged biological replicates
Supplementary_files_format_and_content: gene_exp.diff

source_name: Macrophages

growth_protocol: Mouse femurs and tibias were homogenized in DMEM (Corning cellgro) containing 2% FBS. Bone marrow cells were filtered through a 70-μm strainer (Falcon, REF352350) and further purified on a gradient of NycoPrep A-1.077 (Axis-Shield PoC AS, Oslo, Norway). Purified bone marrow cells were cultured in DMEM/F12 containing 10% FBS, 1 ng/mL recombinant mouse interleukin-3 (rmIL-3, R&D Systems, Minneapolis, MN, USA), and 10% L-929 cell conditioned medium as a source of colony stimulation factor-1 (CSF-1) for 3 days. Non-adherent cells were collected and expanded in DMEM/F12 containing 10% FBS and 20% L-929 cell conditioned medium in the ultra-low cluster plates (Corning, Acton, MA, USA) for additional 3 days. Cells were plated in tissue culture plastic ware in DMEM/F12 containing 10% FBS and 10% L-929 conditioned medium to form a monolayer of macrophages for 4 days with a media change on day 2.

extract_protocol:
RNA was isolated using Qiagen RNeasy Plus Mini Kit (74136)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: day of differentiation

value: Bone Marrow derived  Macrophages

value: 100nM Rocaglate


title: SC_Mix-E6_100nM_6hrs_2


title: SC_Mix-E6_100nM_6hrs_3


title: Lentiviruses expressing mtDRBD DGCR8 rep2

description: Lentiviruses expressing mtDRBD DGCR8


title: Lentiviruses expressing mtDRBD DGCR8 rep1

description: Lentiviruses expressing mtDRBD DGCR8


title: Lentiviruses expressing WT DGCR8 rep3

description: Lentiviruses expressing WT DGCR8

value: Lentiviruses expressing WT DGCR8


title: Untreated3

value: untreated


title: Medial neurogenic zone, day 2 post lesion, biological replicate 1

value: Medial neurogenic zone

value: 3-6 months

value: Tg(gfap:gfp)mi2001 transgenic line


title: Lentiviruses expressing WT DGCR8 rep2

description: Lentiviruses expressing WT DGCR8


title: Dorsal subventricular zone, no lesion, biological replicate 2

description: Gene expression data from dorsal subventricular zone from zebrafish without after stab-wound injury

source_name: Dorsal subventricular zone from zebrafish without after stab-wound injury

value: Dorsal subventricular zone


title: Medial neurogenic zone, day 2 post lesion, biological replicate 2


title: Dorsal subventricular zone, day 2 post lesion, biological replicate 3

description: Gene expression data from dorsal subventricular zone from zebrafish, 2 days after stab-wound injury

source_name: Dorsal subventricular zone from zebrafish, 2 days after stab-wound injury


title: Infected_CS-NC_Donor3

city: Paris

first: Juan Manuel

last: Coya

address: 25-28 Rue du Dr Roux

country: France

institute: Institut Pasteur

data_processing:
STAR v2.5.0b was used to map RNA-seq reads to the hg38 reference genome and quantify  gene expression (option--quantMode GeneCounts) by counting the fragments overlapping the Ensembl genes (GRCh38 v. 83).
Differential expression analysis was performed using a generalized linear model with the R Bioconductor package edgeR v3.16.5 [61] on the genes with more than one count per million (CPM) in at least two samples. The model formula used in edgeR (~Donor + Infection + Infection:Donor + Infection:Treatment + Donor:Treatment) contained: the main effects for Donor and Infection, interactions of Donor with Infection and Treatment to adjust for various responses to infection and treatment between donors, and a nested interaction of Infection with Treatment because we were interested in the infection-status-specific treatment effects. The latter was used to extract differentially expressed genes between NC-treated and untreated samples under the infected and uninfected conditions.
Genome_build: hg38
Supplementary_files_format_and_content: The raw counts were generated using STAR v2.5.0b for GRCh38 Ensembl genes

growth_protocol: Blood mononuclear cells were isolated by Ficoll-Paque centrifugation (GE Healthcare Life Sciences). CD14+ monocytes were isolated by positive selection using CD14 microbeads (Miltenyi Biotec) and allowed to differentiate into Mφs in the presence of granulocyte-macrophage colony-stimulating factor (GM-CSF) (20 ng/mL; R&D Systems) over a six-day period. RPMI medium + GM-CSF was added to the cell cultures every two days.

extract_protocol:
Total RNA from macrophages was extracted using QIAzol reagent (Life Technologies) and purified over RNeasy columns (Qiagen). The quality of all samples was assessed with an Agilent 2100 bioanalyzer (Agilent Technologies) to verify RNA integrity. Only samples with a good RNA yield and no RNA degradation (ratio of 28S to 18S, > 1.7; RNA integrity number > 9) were used for further experiments.
cDNA libraries were prepared with the Illlumina TruSeq RNA Sample Preparation Kit v2 and were sequenced on an Illumina HiSeq 2500

treatment_protocol: Macrophages from 3 donors were left untreated (control) or treated with 10 µg/mL ungrafted or grafted CS-NCs for 18 h. Concerning infected cells, M. tuberculosis H37Rv was grown from a frozen stock to mid-log phase in 7H9 medium (Becton Dickinson), supplemented with albumin-dextrose-catalase (ADC, Difco). Before infection, bacteria were washed three times and re-suspended in 1 ml PBS. Clumps were dissociated by 30 passages through a needle and then allowed to sediment for 5 min. The density of bacteria in the supernatant was verified by measuring the OD600 and aliquot volumes defined to allow one bacterium-per two cell infections. Cells were infected in 24-well plates with each well containing 0.5 × 10^6 cells in 1 ml medium containing GM-CSF (R&D Systems). After 2 h of incubation at 37°C, infected cells were washed three times in PBS to remove extracellular bacteria and incubated in fresh medium. After 18h, macrophage from 3 donnors were treated with 10 µg/mL ungrafted or grafted CS-NCs for 18 h. After incubation, the cell transcriptome was analyzed by mRNA sequencing.

tag: individual

value: Monocyte-derived macrophages

tag: infection

value: Mycobacterium tuberculosis

value: CS-NC


title: Infected_Untreated_Donor3

tag: cell type

value: control


title: Infected_CS-NC-tri_Donor3

value: CS-NC-tri


title: Uninfected_CS-NC-tri_Donor3


title: Uninfected_CS-NC_Donor3


title: Lentiviruses expressing WT DGCR8 rep1

description: Lentiviruses expressing WT DGCR8


title: Untreated2

tag: strain

value: Bone Marrow derived Macrophages


title: Dorsal subventricular zone, no lesion, biological replicate 1


title: Dorsal subventricular zone, no lesion, biological replicate 3


title: Dorsal subventricular zone, day 7 post lesion, biological replicate 2

description: Gene expression data from dorsal subventricular zone from zebrafish, 7 days after stab-wound injury

source_name: Dorsal subventricular zone from zebrafish, 7 days after stab-wound injury


title: Dorsal subventricular zone, day 7 post lesion, biological replicate 3


title: Dorsal subventricular zone, day 7 post lesion, biological replicate 1


title: Infected_CS-NC_Donor2


title: Infected_CS-NC-tri_Donor2


title: Dorsal subventricular zone, day 2 post lesion, biological replicate 2


title: Lentiviruses expressing Luc rep3

description: Lentiviruses expressing Luc

value: Lentiviruses expressing Luc


title: Uninfected_Untreated_Donor3


title: Lentiviruses expressing Luc rep2

description: Lentiviruses expressing Luc

value: knee joints


title: Infected_Untreated_Donor2


title: Dorsal subventricular zone, day 2 post lesion, biological replicate 1


title: Dorsal parenchyma, no lesion, biological replicate 2

description: Gene expression data from dorsal parenchyma from zebrafish without after stab-wound injury

source_name: Dorsal parenchyma from zebrafish without after stab-wound injury

value: Dorsal parenchyma


title: Uninfected_CS-NC-tri_Donor2


title: Dorsal parenchyma, no lesion, biological replicate 1


title: Uninfected_CS-NC_Donor2


title: Lentiviruses expressing Luc rep1

description: Lentiviruses expressing Luc


title: Non invasive rep3

description: Non invasive

value: Non invasive


title: Infected_CS-NC-tri_Donor1


title: Uninfected_Untreated_Donor2


title: Infected_CS-NC_Donor1


title: Infected_Untreated_Donor1


title: Uninfected_CS-NC-tri_Donor1


title: Uninfected_CS-NC_Donor1


title: Non invasive rep1

description: Non invasive


title: Untreated1


title: Spermidine treated replicate 1

city: Cork

first: Patrick

last: O' Connor

address: Western Gateway building

country: Ireland

institute: UCC

data_processing:
Initial processing; Cutadapt was used for the removal of the adapter sequence (CTGTAGGCACCATCAATAGATCGGAAGAGCACACGTCTGAACTCCAGTCA). Reads that aligned to rRNA were removed. Reads were aligned to the Human RefSeq gene catalogue downloaded from NCBI on September 2015 (ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/mRNA_Prot/) with bowtie. The alignment parameters used where (-a -m 100 -v 2 –norc).
Gene level quantification; For quantification of gene RNA levels the RNA-seq reads aligning to all RefSeq transcripts deriving from the same gene locus were used. For genes that had transcripts with annotated coding regions we used only ribo-seq reads aligning to them, otherwise those mapped to the entire transcript were included. Ribo-seq reads were assigned to mRNA coordinates based on the inferred location of the A-site. The location of the A-site was taken to be 17th nucleotide downstream of the first nucleotide of the mapped read for reads whose read length was between 29 and 33 inclusive. The A-site was taken to be the 18th nucleotide downstream for reads whoes read length was 34 or 35. Those of length less than 29 or greater than 35 were discarded. Reads which aligned to transcripts from more than 3 genes were discarded while the value of 'ambiguous' reads that aligned to 2 or 3 genes was downweighed proportionally (i.e. the count of a read mapped to two genes was reduced by half). To reduce the effects of misalignment on a genes estimated level of expression we excluded coordinates corresponding to the three highest density peaks of the ribosome density from each transcript.
Differential expression analysis; To identify differentially expressed genes we carried out the Z-score transformation of log ratios in read counts by calculating local Z-scores for the groups of 300 genes clustered based on the lowest signal of their expression mRNA-seq, ribo-seq or both depending on what is being compared. The gene was classified as upregulated if (Z1+Z2)/2 > T and downregulated if (Z1+Z2)/2 < -T, where Z1 and Z2 are Z-scores for the same gene obtained in two replicas and T is the threshold. The threshold T was set based on the desired false discovery rate (FDR). The number of false positives was estimated as the number of genes for which (|Z1|+|Z2|)/2>T when Z1Z2<0.
Supplementary_files_format_and_content: These tab delimited csv files record the number of mapped reads that aligned the gene in the RefSeq catalogue after the alignment step. Each row contains the record of a Gene with first 3 columns indicating its Gene symbol, its annotation classification (coding, ncRNA, rRNA,transcript,pseudo,linc) and the number of alignments. Three more columns are used for coding transcripts. These columns indicates the number of alignments to the 5'leader, the acORF and the 3'UTR.

growth_protocol: Hek293T cells were grown in DMEM + 10% FBS

extract_protocol:
Detergent lysis was performed in the dish, and after DNAse treatment sample  were subjected to ribosome footprinting by RNAse I treatment. Monosomes were isolated using Illustra MicroSpin S-400 HR Columns (GE Healthcare).
Library preparation was carried out as described in Ingolia et al (2012),Nature Protocols

treatment_protocol: 2.5 mM DFMO for 5 days and then the cells were either left untreated or stimulated with 2 mM spermidine for 24 hr

tag: sample type

value: ribosome protected fragments

value: Spermidine


title: Spermidine treated replicate 2

data_processing:
Initial processing; Cutadapt was used for the removal of the adapter sequence (CTGTAGGCACCATCAATAGATCGGAAGAGCACACGTCTGAACTCCAGTCA). Reads that aligned to rRNA were removed. Reads were aligned to the Human RefSeq gene catalogue downloaded from NCBI on September 2015 (ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/mRNA_Prot/) with bowtie. The alignment parameters used where (-a -m 100 -v 2 –norc).
Gene level quantification; For quantification of gene RNA levels the RNA-seq reads aligning to all RefSeq transcripts deriving from the same gene locus were used.
For genes that had transcripts with annotated coding regions we used only ribo-seq reads aligning to them, otherwise those mapped to the entire transcript were included. Ribo-seq reads were assigned to mRNA coordinates based on the inferred location of the A-site. The location of the A-site was taken to be 17th nucleotide downstream of the first nucleotide of the mapped read for reads whose read length was between 29 and 33 inclusive. The A-site was taken to be the 18th nucleotide downstream for reads whoes read length was 34 or 35. Those of length less than 29 or greater than 35 were discarded. Reads which aligned to transcripts from more than 3 genes were discarded while the value of 'ambiguous' reads that aligned to 2 or 3 genes was downweighed proportionally (i.e. the count of a read mapped to two genes was reduced by half). To reduce the effects of misalignment on a genes estimated level of expression we excluded coordinates corresponding to the three highest density peaks of the ribosome density from each transcript.
Differential expression analysis; To identify differentially expressed genes we carried out the Z-score transformation of log ratios in read counts by calculating local Z-scores for the groups of 300 genes clustered based on the lowest signal of their expression mRNA-seq, ribo-seq or both depending on what is being compared. The gene was classified as upregulated if (Z1+Z2)/2 > T and downregulated if (Z1+Z2)/2 < -T, where Z1 and Z2 are Z-scores for the same gene obtained in two replicas and T is the threshold. The threshold T was set based on the desired false discovery rate (FDR). The number of false positives was estimated as the number of genes for which (|Z1|+|Z2|)/2>T when Z1Z2<0.
Supplementary_files_format_and_content: These tab delimited csv files record the number of mapped reads that aligned the gene in the RefSeq catalogue after the alignment step. Each row contains the record of a Gene with first 3 columns indicating its Gene symbol, its annotation classification (coding, ncRNA, rRNA,transcript,pseudo,linc) and the number of alignments. Three more columns are used for coding transcripts. These columns indicates the number of alignments to the 5'leader, the acORF and the 3'UTR.


title: Non invasive rep2

description: Non invasive


title: Uninfected_Untreated_Donor1


title: DFMO treated replicate 2

value: DFMO


title: Auxin-treated, no Cu. Experiment 2

city: Bethesda

first: Razvan

middle: V.

last: Chereji

state: Maryland

address: 6 Center Drive, Room 2A14

department: NICHD

institute: National Institutes of Health

description: Biological replicate 2

data_processing:
Paired reads were aligned to the yeast genome (sacCer3) using Bowtie2 with default settings.
The sequenced DNA fragments were size selected: fragments with lengths between 120 and 180 bp were retained.
Genome-wide coverage profiles were computed in MATLAB, and they were normalized such that the average coverage for every chromosome is 1.
IGV tracks (tdf files) were generated using igvtools.
Genome_build: sacCer3
Supplementary_files_format_and_content: tdf files containing the normalized occupancy profiles, for the IGV browser

organism: Saccharomyces cerevisiae

source_name: S. cerevisiae

growth_protocol: Cells of haploid strain YTK1460 were grown overnight in 10 ml CSM-uracil medium and diluted to OD600=0.2 in 400 ml of fresh CSM-uracil. Cells were grown for 270 min to OD600 0.8 at 30°C and 230 rpm.

extract_protocol:
Nuclei were prepared from cells and digested with different amounts of MNase (units given in filenames). The extent of digestion was determined by gel electrophoresis of the purified DNA.
The DNA was repaired using the DNA PreCR kit (M0309) from New England Biolabs (NEB). Paired-end libraries were constructed and indexed using Illumina kits from NEB (E7370 and E7335).

treatment_protocol: For auxin-induced Rsc2p depletion, auxin was added to the culture medium 240 min before Cu treatment to a final concentration of 1 mM. For copper activation, cells were treated for 10 min with 100 μM copper (II) sulphate. Cells were harvested by filtration.

tag: strain name

value: MAT alpha  his3-d1 leu2-d0 lys2-d0 ura3-d0 pdr5-d::LoxP-KAN-LoxP ACE1-HaloTag::URA3 RSC2-AID*-6HA::Hyg trp1d::pADH-AFB2::LEU2


title: Auxin-treated, Cu-induced. Experiment 2

description: Biological replicate 2


title: DFMO treated replicate 1

data_processing:
Initial processing; Cutadapt was used for the removal of the adapter sequence (CTGTAGGCACCATCAATAGATCGGAAGAGCACACGTCTGAACTCCAGTCA). Reads that aligned to rRNA were removed. Reads were aligned to the Human RefSeq gene catalogue downloaded from NCBI on September 2015 (ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/mRNA_Prot/) with bowtie. The alignment parameters used where (-a -m 100 -v 2 –norc).
Gene level quantification;  For quantification of gene RNA levels the RNA-seq reads aligning to all RefSeq transcripts deriving from the same gene locus were used.
For genes that had transcripts with annotated coding regions we used only ribo-seq reads aligning to them, otherwise those mapped to the entire transcript were included. Ribo-seq reads were assigned to mRNA coordinates based on the inferred location of the A-site. The location of the A-site was taken to be 17th nucleotide downstream of the first nucleotide of the mapped read for reads whose read length was between 29 and 33 inclusive. The A-site was taken to be the 18th nucleotide downstream for reads whoes read length was 34 or 35.  Those of length less than 29 or greater than 35 were discarded. Reads which aligned to transcripts from more than 3 genes were discarded while the value of 'ambiguous' reads that aligned to 2 or 3 genes was downweighed proportionally (i.e. the count of a read mapped to two genes was reduced by half). To reduce the effects of misalignment on a genes estimated level of expression we excluded coordinates corresponding to the three highest density peaks of the ribosome density from each transcript.
Differential expression analysis; To identify differentially expressed genes we carried out the Z-score transformation of log ratios in read counts by calculating local Z-scores for the groups of 300 genes clustered based on the lowest signal of their expression mRNA-seq, ribo-seq or both depending on what is being compared. The gene was classified as upregulated if (Z1+Z2)/2 > T and downregulated if (Z1+Z2)/2 < -T, where Z1 and Z2 are Z-scores for the same gene obtained in two replicas and T is the threshold. The threshold T was set based on the desired false discovery rate (FDR). The number of false positives was estimated as the number of genes for which (|Z1|+|Z2|)/2>T when Z1Z2<0.
Supplementary_files_format_and_content: These tab delimited csv files record the number of mapped reads that aligned the gene in the RefSeq catalogue after the alignment step. Each row contains the record of a Gene with first 3 columns indicating its Gene symbol, its annotation classification (coding, ncRNA, rRNA,transcript,pseudo,linc) and the number of alignments. Three more columns are used for coding transcripts. These columns indicates the number of alignments to the 5'leader, the acORF and the 3'UTR.


title: No auxin, Cu-induced. Experiment 2

description: Biological replicate 2


title: No auxin, no Cu. Experiment 2

description: Biological replicate 2


title: Auxin-treated, no Cu. Experiment 1

description: Biological replicate 1


title: Auxin-treated, Cu-induced. Experiment 1

description: Biological replicate 1


title: Dorsal parenchyma, day 7 post lesion, biological replicate 3

description: Gene expression data from dorsal parenchyma from zebrafish, 7 days after stab-wound injury

source_name: Dorsal parenchyma from zebrafish, 7 days after stab-wound injury

tag: tissue

value: 3-6 months


title: No auxin, Cu-induced. Experiment 1

description: Biological replicate 1


title: Dorsal parenchyma, day 2 post lesion, biological replicate 2

description: Gene expression data from dorsal parenchyma from zebrafish, 2 days after stab-wound injury

source_name: Dorsal parenchyma from zebrafish, 2 days after stab-wound injury

value: Tg(gfap:gfp)mi2001 transgenic line


title: Dorsal parenchyma, day 2 post lesion, biological replicate 1


title: Dorsal parenchyma, day 2 post lesion, biological replicate 3


title: Dorsal parenchyma, day 7 post lesion, biological replicate 2


title: Dorsal parenchyma, day 7 post lesion, biological replicate 1


title: Cpa3-Cre;miR-9∆fl/∆fl #3

city: Columbus

first: Joelle

middle: Marie

last: Fenger

state: Ohio

address: 601 Vernon L Tharp Street, OSU Veterinary Medical Center

department: Veterinary Clinical Sciences

institute: The Ohio State University

data_processing:
Alignment/filtering - AdapterRemover was used to trim adapter sequences and the remaining reads were aligned using STAR to the mouse GRCm38/mm10 genome.  Quality control was performed using RNA-SeQC, in order to check for samples needing additional sequencing reads.
Processing equipment - .  Differential expression was determined using two different pipelines. First, gene expression counts were generated by HTSeq-Count and fed into DESeq2, which compared several sample groups using a likelihood-ratio test (LRT). Second, expression of individual transcripts was quantified by cuffquant with comparisons between pairs of conditions performed by cuffdiff.  Statistical analysis relative to mRNA expression data was performed using DESeq2 Software. Differential gene expression was determined by one-way ANOVA and p-values of <0.0001 were considered statistically significant.
Read alignment software - STAR
Genome_build: GRCm38/mm10 genome
Supplementary_files_format_and_content: Raw and normalized counts/output was generated from DeSeq; processed data file is an excel file and it includes: raw counts of sequencing reads and group comparisons Cpa3-Cre vs Cpa3-Cre/miR-9  normalized abundance measurements (DESeq)

source_name: bone marrow-cultured mast cells

growth_protocol: BMCMCs  were cultured for 6-8 weeks in RPMI-1640 (Gibco Life Technologies, Grand Island, NY, USA) supplemented with 10% fetal bovine serum, non-essential amino acids, sodium pyruvate, penicillin, streptomycin, L-glutamine, HEPES (4-(2-dydroxethyl)-1 piperazineethanesulfonic acid) (Gibco) and 50 ng/mL rmIL-3 (R & D Systems, Minneapolis, MN, USA)  at 37ºC with 5% CO2

extract_protocol:
RNA was isolated using the RNeasy Isolation Kit (Qiagen Inc, Valencia, CA, USA) according to manufacturer’s instructions; RNA was heparinase treated with 40 U Heparinase I for 2 hrs at room temperature and subsequently column cleaned using the Rneasy Isolation Kit according to manufacturer's protocols
Total RNA was treated by Ribo-Zero Gold Subtraction reagents from TruSeq stranded total RNA (Illumina; RS-122-2201) to remove cytoplasmic and mitochondrial rRNAs and for the subsequent construction of the RNA-seq library according to the manufacturer’s instructions. .  Stranded total transcriptome libraries were quantified and qualified by Qubit and RIN analysis, respectively. Sequencing was performed on an Illumina HiSEq 2500 instrument at a depth of ∼70 million paired-end, 50 bp long, strand-specific reads per sample.

treatment_protocol: No treatments


title: No auxin, no Cu. Experiment 1

description: Biological replicate 1


title: Cpa3-Cre;miR-9∆fl/∆fl #1


title: Cpa3-Cre #2


title: Cpa3-Cre;miR-9∆fl/∆fl #2


title: E195_WT-2

data_processing:
Basecalls performed by Casava using default settings
For the bulk cells RNA-Seq data, the clean reads were mapped to at mm9 genome assembly by TopHat2 (version 2.1.1).
Cufflinks (version 2.2.1)  with default settings was used for gene expression level calculation.
Fragments per Kilobase of exon per Megabase of library size (FPKM) was calculated using Cufflinks
Genome_build: mm9
Supplementary_files_format_and_content: FPKM files estimated by Cufflinks

growth_protocol: The animal and cells were cultured as described in manuscript

extract_protocol:
Total RNA was extracted from tissues with TRIzol (Invitrogen). Following extraction, 1 μg of purified RNA was used for reverse transcription polymerase reaction each time (Invitrogen). For RNA-seq library construction, two rounds of PolyA+ tailed RNA purification were performed for each sample.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: brain

tag: developmental stage

tag: variation

value: wildtype


title: E195_WT-1


title: E195_KO2-2

value: H19-DMR and IG-DMR KO


title: E195_KO7-1

value: Nespas-DMR, Grb10-DMR, Igf2r-DMR, Snrpn-DMR, Kcnq1-DMR, Peg3-DMR and Gnas-DMR KO


title: E195_KO7-2


title: E195_KO2-1


title: adultWT2-2

value: adult


title: adultWT2-1


title: adultWT1-2


title: Adult_KO3-2

value: H19-DMR, IG-DMR, and Rasgrf1-DMR KO


title: adultWT1-1


title: UB_RNASeq

city: North Hills

first: Masaki

last: Nishikawa

state: CA

address: 16111 Plummer st

institute: UCLA / VA

data_processing:
For ChIP-seq analysis, the replicate was concatenated and mapped using Bowtie2 at default setting.
ChIP-seq peaks were called using MACS14 against the input control data. The parameter set used in MACS14 was as follows: H3K4me3 (Band width 300, Pvalue cutoff 1e-05, the nearby regions to calculate dynamic lambda 1000-10000) and H3K27me3 (Band width 2900, Pvalue cutoff 1e-04 (mES and MM(Cited1)) or 1e-03 (UB), the nearby regions to calculate dynamic lambda 1000-20000).
Peaks were annotated with overlapping genes using AnnotateGenomicRegions (  https://sourceforge.net/projects/annotatelocus/files/webarchive/JSFversion/AnnotateGenomicRegions.war/download)
For RNA-seq analysis, all sequencing reads were mapped using Tophat at default setting.
Aligned RNA-seq reads were further analyzed using Cufflinks, Cuffmerge, and Cuffdiff
Genome_build: mm10
Supplementary_files_format_and_content: ChIP-seq: BED files with called peaks on sample records and peak annotation files on series record.
RNA-seq: text file with FPKM

source_name: Ureteric epithelium

extract_protocol: Libraries were prepared using SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian (Clontech Laboratories)

value: Ureteric epithelium

value: Ureteric epithelium (manually dissected)

value: wild type


title: MM_RNASeq

source_name: Metanephric mesenchyme

value: Metanephric mesenchyme

value: Metanephric mesenchyme (manually dissected)


title: Cpa3-Cre #1


title: WT_5_Fat_Mouse

city: Sydney

first: Carsten

last: Schmitz-Peiffer

state: NSW

address: 384 Victoria St, Darlinghurst

department: Diabetes and Obesity Division

country: Australia

institute: Garvan Institute of Medical Research

data_processing:
The sequenced sample libraries were trimmed with Trim Galore (v.0.2.8),
mapped to the mouse genome and transcriptome with STAR (v.2.4.0d)
counted with RSEM (v.1.2.12)
The counts reported with RSEM were normalized with R package DESeq2
Genome_build: Mus_musculus.GRCm38.85
Supplementary_files_format_and_content: tab-delimited text file as count matrix (countdata.txt)

source_name: WT_gonadal fat pad

extract_protocol:
Qiagen RNeasy extraction kit
TruSeq Stranded mRNA Sample Preparation Kit (Illumina)

treatment_protocol: High fat diet feeding

tag: strain background

tag: genotype/variation

value: WT

tag: diet

value: High fat diet feeding

value: gonadal fat pad


title: WT_4_Liv_Mouse

value: liver


title: WT_4_Fat_Mouse


title: WT_2_Liv_Mouse


title: WT_2_Fat_Mouse


title: WT_3_Fat_Mouse


title: WT_1_Liv_Mouse


title: KO_5_Liv_Mouse

value: AdEpsKO


title: WT_1_Fat_Mouse


title: control

city: Suita

first: Keisaku

last: Wakabayashi

state: Osaka

address: 1-6 Yamadaoka

country: Japan

institute: Osaka University

description: SAMPLE 1

hyb_protocol: The labeled samples were hybridized and washed using the Agilent Gene Expression Hybridization Kit and Wash Buffers Kit (Agilent Technologies).

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using an Agilent SureScan microarray scanner (Agilent Technologies).

data_processing: The Agilent Feature Extraction Software was used to read out and to process the microarray image files.

source_name: HeLa cells transfected with control mimic

label_protocol: One hundred ng of each total RNA sample was amplified and labeled using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol.

growth_protocol: Hela cells were cultured in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum (FBS), streptomycin (100 mg/ml), and penicillin (100 U/ml).

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

treatment_protocol: The cells were transfected with control or 3'-mivaRNAII-138 mimic. After 48-h incubation, total RNA was extracted using Isogen (Nippongen).

tag: cell line

value: HeLa

tag: transfected with

value: control


title: KO_4_Liv_Mouse


title: 3'-mivaRNAII-138

description: SAMPLE 2

source_name: HeLa cells transfected with 3'-mivaRNAII-138 mimic

value: 3'-mivaRNAII-138 mimic


title: KO_4_Fat_Mouse

source_name: AdEpsKO_gonadal fat pad


title: KO_2_Liv_Mouse


title: KO_5_Fat_Mouse


title: KO_1_Liv_Mouse


title: Adult_KO3-1

value: brain


title: Adult_KO2-2

value: H19-DMR and IG-DMR KO


title: KO_1_Fat_Mouse


title: WT_5_Liv_Mouse


title: HCC-LM3 shPLAGL2-2

city: Nanjing

first: Hu

last: Weiwei

address: No. 639, long Mian Road, Jiangning District, Nanjing

institute: China Pharmaceutical University

data_processing:
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions
Raw 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, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.16.1)
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: HCC-LM3 cell

growth_protocol: HCCLM3 cells were cultivated in DMEM (Biological Industries, USA) supplemented with 10% fetal bovine serum (FBS) (Biological Industries, USA) and 1% Penicillin-Streptomycin (Gibico, USA) at 37 °C in a humidified 5% CO2 incubator.

extract_protocol:
Total RNA was prepared by using TRIzol reagent (Invitrogen) according to the manufacturer’s instructions. cDNA was synthesized from 2 μg of total RNA by reverse transcriptase (Takara). Quantitative real-time RT-PCR (qRT-PCR) analysis was performed with LightCycler (Roche Diagnostics) and the SYBR RT-PCR kit (Takara)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: sh-hPLAGL2-Luc-Puro and sh-negative control-Luc-Puro (shctrl) lentiviruses were purchased from HanBio Technology Co.Ltd. (HanBio, Shanghai, China). Lentiviral supernatants incubated with HCC-LM3 cells for 24h, These infected cells were treated with 2 μg/ml of puromycin (Invitrogen) to generate stable transfectants.

tag: lentivirus


title: Adult_KO2-1

value: adult


title: WT_3_Liv_Mouse


title: hem3

city: Heidelberg

first: Fanny

last: Gatzmann

address: Im Neuenheimer Feld 580

department: A130 Epigenetics

institute: DKFZ

description: processed data file: merged-atac_macs2_peaks.broadPeak

data_processing:
Illumina Casava1.8.1 software used for basecalling.
Preprocessing, read trimming: TrimGalore
DNA mapping: bowtie2
Calling ATAC peaks with MACS2.
Genome_build: Pvir0.4
Supplementary_files_format_and_content: merged-atac_macs2_peaks.broadPeak: Peaks file.

organism: Procambarus virginalis

source_name: Wild catches from lake Reilingen

extract_protocol:
Approximately 500 µL of hemolymph was collected from three independent animals. After washing the cell pellet twice with sterile and cold PBS 1X, 50.000 hemocytes were immediately used for the ATAC library preparation.
The transposase reaction was optimized and a 20 min reaction was used to avoid DNA “over transposition”. The subsequent steps were as described in the original protocol (Buenrostro 2015).
ATAC-Seq on Illumina HiSeq X platform.

value: hemocytes


title: hem2


title: hem1


title: HCC-LM3 shCtrl-2

value: sh-negative control-Luc-Puro


title: KO_3_Fat_Mouse


title: hem

data_processing:
Illumina Casava1.8.1 software used for basecalling.
Preprocessing, read trimming: Trimmomatic 0.35
Preprocessing, quality filtering: Trimmomatic 0.35
WGBS mapping: BSMAP 2.73
methylation calling: BSMAP-provided script methratio.py
select for CpGs and calculate total coverage and ratio at each CpG site
Genome_build: Pvir0.4
Supplementary_files_format_and_content: sample_cov.bed: bed file for each CpG site with chrom, start, end, coverage
Supplementary_files_format_and_content: sample_ratio.bed: bed file for each CpG site with chrom, start, end, methylation ratio (#methylated reads/#total reads at this position)

source_name: P.virginalis_wild catch, lake Reilingen

extract_protocol:
Samples of organs and tissues from adult crayfish for DNA and RNA preparation were taken under a dissection microscope, snap-frozen in liquid nitrogen and stored at -80°C until extraction of nucleic acids. Embryonized eggs and juveniles were frozen in liquid nitrogen as a whole. Genomic DNA was isolated using the Blood & Cell Culture DNA Kit (Qiagen, Hilden, Germany)
The TruSeq PCR-Free Library Prep Kit (LT) was used for library preparation, and the Epitect Kit (Qiagen) for bisulfite conversion. Library amplification was performed using the Kapa HiFi HotStart Uracil+ ReadyMix (2X).
WGBS on an Illumina HiSeq platform

value: wild catch, lake Reilingen


title: Mora_abdM

source_name: P.virginalis_wild catch, Madagascar

value: wild catch, Madagascar

value: abdominal musculature


title: e.17

value: Heidelberg laboratory strain

value: embryonic stage 1.7


title: hem37 [RNA-seq]

data_processing:
Illumina Casava1.8.1 software used for basecalling.
Preprocessing, read trimming: shore 0.6.2
Preprocessing, quality filtering: shore 0.6.2
RNA mapping: hisat2 2.0.4
calculating expression levels: RSEM-1.2.30
Genome_build: Pvir0.4
Supplementary_files_format_and_content: rsem genes.results files

source_name: Pooled wild catches from lake Reilingen

extract_protocol:
Total RNA was isolated from 20-60 mg frozen tissues. Thawed tissues were homogenized in 1 ml Trizol (Ambion), precipitated with isopropanol and resuspended in 20-100 µl RNase-free water (Gibco Life Technologies). Total RNA was treated with DNase using the RNeasy Mini Kit (Qiagen) following the manufacturer's RNeasy Mini Protocol for RNA Cleanup in combination with the On-Column DNase Digestion Protocol.
Sequencing libraries were prepared using 1µg of DNAse-treated total RNA in the first step of the TruSeq RNA Sample Preparation v2 protocol (Illumina, Part# 15026495 Rev. A) as recommended by the manufacturer.


title: hem40 [RNA-seq]


title: hem39 [RNA-seq]


title: KO_2_Fat_Mouse

value: High fat diet feeding


title: KO_3_Liv_Mouse


title: Pvir#3_abdM

source_name: P.virginalis_wild catch, lake Moosweiher

value: wild catch, lake Moosweiher


title: Pvir#7_hep [RNA-seq]

value: hepatopancreas


title: HCC-LM3 shCtrl-1


title: Pvir#6_hep [RNA-seq]


title: Pfal#4_abdM [RNA-seq]

organism: Procambarus fallax

source_name: P.fallax_female from aquarium supply

value: female from aquarium supply


title: Pfal#3_abdM [RNA-seq]


title: Pvir#6_abdM [RNA-seq]


title: Pvir#2_abdM [RNA-seq]


title: Pvir#2_abdM


title: Pfal#1_abdM [RNA-seq]


title: Pvir#2_hep [RNA-seq]


title: Pfal#4_abdM


title: HCC-LM3 shPLAGL2-1


title: Pvir#6_hep


title: Pfal#4_hep


title: Pvir#3_hep


title: Pfal#3_hep


title: Pvir#7_abdM [RNA-seq]


title: 8dpf WT2

status: Public on Oct 10 2018

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

description:
WT2
processed data file: 8dpf.counts.matrix.norm.txt

data_processing:
Raw reads were assessed for quality, adapter content and duplication rates with FastQC (Andrews 2010). Trimmomatic version 0.33 was employed to trim reads after a quality drop below a mean of Q18 in a window of 5 nucleotides (Bolger, Lohse et al. 2014). Only reads above 30 nucleotides were cleared for further analyses.
Trimmed and filtered reads were aligned versus the Ensembl Zebrafish genome version DanRer10 (GRCz10.87) using STAR 2.4.0a with the parameter “--outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%.
The number of reads aligning to genes was counted with featureCounts 1.4.5-p1 tool from the Subread package (Liao, Smyth et al. 2014). Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded.
The batch effect correction for 8dpf samples was done using removeBatchEffect function from edgeR package version 3.16.5 on log-transformed expression matrix with a minimum combined mean of 5 reads. Differentially expressed genes were identified using DESeq2 version 1.62.
Only genes with a minimum fold change of log2 <=> 0,9, a maximum Benjamini-Hochberg corrected p-value of 0.05, and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed.
Genome_build: DanRer10 (GRCz10)
Supplementary_files_format_and_content: *.counts.matrix.norm txt: Library size and batch effect normalized count tables; tab-delimited text files.

source_name: larvae

growth_protocol: Zebrafish husbandry was performed under standard conditions following institutional and national ethical and animal welfare guidelines. Larvae used in 8 dpf experiments were subjected to external feeding from 5dpf before being collected for the analysis at 8dpf.

extract_protocol:
RNA was isolated from a pool of 5 zebrafish larvae at 5dpf and 8dpf using the miRNeasy micro Kit (Qiagen) combined with on-column DNase digestion (DNase-Free DNase Set, Qiagen) to avoid contamination by genomic DNA.
1-2 µg of total RNA was used as input for TruSeq Stranded mRNA Library preparation following the low sample protocol (Illumina).

tag: line/background

value: AB

value: WT

value: pool of 5 whole larvae

tag: age


title: 8dpf Mut1

description:
Mut1
processed data file: 8dpf.counts.matrix.norm.txt


title: 8dpf Mut3

description:
Mut3
processed data file: 8dpf.counts.matrix.norm.txt


title: 8dpf WT1

description:
WT1
processed data file: 8dpf.counts.matrix.norm.txt


title: 8dpf WT3

description:
WT3
processed data file: 8dpf.counts.matrix.norm.txt


title: 5dpf Mut3

description:
mut3
processed data file: 5dpf.counts.matrix.norm.txt


title: 5dpf WT3

description:
wt3
processed data file: 5dpf.counts.matrix.norm.txt


title: 8dpf Mut2

description:
Mut2
processed data file: 8dpf.counts.matrix.norm.txt


title: 5dpf Mut1

description:
mut1
processed data file: 5dpf.counts.matrix.norm.txt


title: 5dpf WT1

description:
wt1
processed data file: 5dpf.counts.matrix.norm.txt


title: Pvir#2_hep


title: 5dpf Mut2

description:
mut2
processed data file: 5dpf.counts.matrix.norm.txt


title: 5dpf WT2

description:
wt2
processed data file: 5dpf.counts.matrix.norm.txt


title: Liver_vehicle_24 h_pooled

city: Nagoya-shi

first: Yuya

last: Urano

state: Aichi-ken

address: 65, Tsurumai-cho, Showa-ku

institute: Nagoya University

hyb_protocol: Hybridization were performed using Gene Expression Hybridization Kit (Agilent) according to manufacturer's instruction.

scan_protocol: Slides were scanned using Agilent Technologies Microarray Scanner (Agilent).

data_processing:
The scanned images were analyzed with Agilent Feature Extraction Software 12.0.3.1 (Agilent).  All raw signal intensities were normalized by 75 percentile-shift and log-2-transformed and then fold changes to the vehicle control group were calculated using Subio Platform ver. 1.21 (Subio, Kagoshima, Japan).
After data processing, probes that have positive and certain signal intensity (gIsBGNonUnifOL = 0, gIsWellAboveBG = 1, gIsFeatNonUnifOL = 0, gIsBGPopnOL = 0) are used in enrichment analysis described in the paper.

source_name: Liver, vehicle, i.p., 24 hr, pooled

label_protocol: Labelling of cRNA were performed using Low Input Quick Amp Labeling Kit (Agilent) according to manufacturer's instruction.

extract_protocol: Total RNA was extracted from each liver sample collected at 24 hours after the administration of TAK-875, AMG-837, TUG-770 or vehicle using an RNeasy Mini kit according to manufacturer’s instruction.

value: ICR

tag: agent

value: vehicle

value: Liver

value: 6 weeks old

tag: gender

value: female


title: Liver_TUG-770_24 h_pooled

source_name: Liver, 200 mg/kg TUG-770, i.p., 24 hr, pooled


title: Liver_TAK-875_24 h_pooled

source_name: Liver, 200 mg/kg TAK-875, i.p., 24 hr, pooled


title: Liver_AMG-837_24 h_pooled

source_name: Liver, 200 mg/kg AMG-837, i.p., 24 hr, pooled


title: 12_C07: Sham-LAN4

city: Venlo

first: Anne-Loes

last: Opperhuizen

address: Deken van Oppensingel 23

country: Netherlands

institute: Maastricht University

description: Experiment 2

hyb_protocol: The labeled samples were hybridized to GeneChip HT RG-230 PM arrays (Thermo Fisher Scientific). GeneTitan Wash and Stain Kit for 3' IVT Array Plates were used to perform washing and staining steps.

scan_protocol: Scanning was performed with the GeneTitan Instrument (Thermo Fisher Scientific).

data_processing: The raw data per experiment were subjected to a set of quality controls. The quality checks revealed no significant hybridization and experimental blocking effects. All arrays used in the final analysis passed the quality control and were annotated. Normalized expression values were calculated using the robust multi-chip average (RMA) algorithm. Differential gene expression between the experimental groups and the control group were statistically analyzed using the Limma package in R-3.2.1 (http://cran.r-project.org). False Discovery Rate correction was performed as described by John D. Storey.

label: Alexa

organism: Rattus norvegicus

source_name: liver of LAN exposed SHAM

label_protocol: Amplification of 100 ng total RNA was done using the GeneChip 3' IVT Plus Reagent kit (Thermo Fisher Scientific, Massachusetts, USA) generating biotinylated complementary RNA.

growth_protocol: Male Wistar rats (Charles River Breeding Laboratories, Sulzfeld, Germany) weighing 280-300 g were housed in constant conditions with a controlled 12:12/light:dark cycle (lights on at 7:00, lights off at 19:00), constant temperature (21±2°C), humidity (60±5%) and background noise (radio). Animals had ad libitum access to water and regular chow (Teklad Global Diet, Harlan, Horst, the Netherlands) during the complete experiment, unless stated otherwise.

extract_protocol: Liver tissue was cut on dry ice with a razor blade (max. 5 mm), added to 1 mL of TRIzol (Macherey-Nagel Ltd., Oensingen, Switzerland) and homogenized by Ultra Turrax homogenizer (IKA, Staufen, Germany). Total RNA was isolated from tissues using TRIzol reagent (Macherey-Nagel Ltd., Oensingen, Switzerland). RNA concentration was determined using Nanodrop DS (Thermo Scientific, Wilmington, USA) and RNA quality was determined using BioAnalyzer (Agilent, Santa Clara, USA). Ten microliter of RNA was used for microarray analysis. Samples included in the microarray analysis had RNA concentration >100 ng/μl and RIN values for RNA quality >8.0.

treatment_protocol: At the experimental day, two weeks after surgery, food was removed at 21:00 until sacrifice (22:00). Light exposure was done with mixed white TL-light from the ceiling of ~125±25 photopic lux and animals remained in their own cage and were not touched or moved during the exposure. After the light exposure or darkness (Sham-DARK), all animals were sacrificed. Tissue collection of 13 animals was finished within 1h, and collection of all tissues from all animals (n=26) was spread and randomized over two days to minimize variation in the daily timing of sacrifice. The same experimenter (ALO) obtained all liver samples.

value: male

value: Wistar

value: liver


title: 24_F07: Sham-DARK8

description: Experiment 2

source_name: liver of unexposed control


title: 13_F05: Sham-LAN5

description: Experiment 2


title: 20_C09: Sham-LAN7

description: Experiment 2


title: 15_A07: Sham-LAN6

description: Experiment 2


title: 16_B05: Tx-LAN5

description: Experiment 2

source_name: liver of LAN exposed denervated


title: 23_H07: Tx-LAN8

description: Experiment 2


title: 22_H09: Sham-LAN8

description: Experiment 2


title: 17_F09: Sham-DARK6

description: Experiment 2


title: 19_D09: Tx-LAN6

description: Experiment 2


title: 21_A09: Tx-LAN7

description: Experiment 2


title: 14_B07: Tx-LAN4

description: Experiment 2


title: 11_G07: Tx-LAN3

description: Experiment 2


title: 18_C05: Sham-DARK7

description: Experiment 2


title: 10_G05: Sham-DARK5

description: Experiment 2


title: 09_H05: Sham-DARK4

description: Experiment 2


title: 06_G09: Sham-LAN2

description: Experiment 2


title: 07_E07: Sham-LAN3

description: Experiment 2


title: 08_B09: Tx-LAN2

description: Experiment 2


title: 03_E09: Sham-DARK1

description: Experiment 2


title: 23_C05: Sx5

description: Experiment 1

source_name: liver of sympathectomy

growth_protocol: Animals in all groups were anesthetized with with 80 mg/kg ketamine (Eurovet Animal Health, Bladel, Netherlands) and 8 mg/kg Rompun (xylaxine, Bayer Health Care, Mijdrecht, Netherlands). Intact animals only received anaesthesia and were left to recover. Sham surgery included the laparotomy and destruction of connective tissue but did not include destruction of any parasympathetic or sympathetic nerve branches to the liver. Hepatic sympathectomy (Sx) and parasympathectomy (Px) were performed as previously reported. Total denervation (Tx) included removal of both sympathetic and parasympathetic branches to the liver. The same, very experienced, experimenter (EFo) performed all surgeries. After surgery, animals were monitored in an incubator (30˚C) until wakening. Afterwards animals were returned to their home cage and left to recover in group-housing and monitored closely.


title: 04_D05: Sham-DARK2

description: Experiment 2


title: 22_D05: Tx4

description: Experiment 1

source_name: liver of hepatectomy


title: 19_B05: Intact3

description: Experiment 1

source_name: intact liver


title: 24_E09: Tx5

description: Experiment 1


title: 02_D07: Tx-LAN1

description: Experiment 2


title: 16_F05: Sx3

description: Experiment 1


title: 15_G07: Tx3

description: Experiment 1


title: 07_F09: Sham2

description: Experiment 1

source_name: liver of sham-hepathectomy


title: 14_C07: Px3

description: Experiment 1

source_name: liver of parasympathectomy


title: 11_B09: Sham3

description: Experiment 1


title: 08_A07: Sx2

description: Experiment 1


title: 17_G05: Px4

description: Experiment 1


title: 21_H05: Px5

description: Experiment 1


title: 18_C09: Sx4

description: Experiment 1


title: 06_F07: Intact1

description: Experiment 1


title: 05_E05: Sham-DARK3

description: Experiment 2


title: 05_D09: Sx1

description: Experiment 1


title: 01_A05: Sham-LAN1

description: Experiment 2


title: 20_E07: Intact4

description: Experiment 1


title: 12_D07: Sham4

description: Experiment 1


title: 13_A05: Sham5

description: Experiment 1


title: 09_H09: Intact2

description: Experiment 1


title: 04_B07: Sham1

description: Experiment 1


title: 01_G09: Px1

description: Experiment 1


title: 10_A09: Tx2

description: Experiment 1


title: 02_H07: Tx1

description: Experiment 1


title: 100 mg/kg/day of PCN for 7 days, biological rep2

city: Osaka

first: Ayako

last: Ohara

address: 1-98, Kasugade-naka 3-chome, Konohana-ku

institute: Sumitomo Chemical Co., Ltd.

description: Gene expression data from liver of rats administered for 7 days by oral gavage with 100 mg/kg/day of pregnenolone-16α-carbonitrile(PCN)

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes using the Gene Expression Hybridization Kit (Agilent) following the manufacturers instructions. On completion of the fragmentation reaction, mixtures were hybridized to SurePrint G3 Rat Gene Expression 8x60K Microarrays 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) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (Agilent) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 3 um, Dye channel is set to Green and Green PMT is set to 100%). The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

data_processing: By using Excel VBA, the signal intensity (gProcessedSignal) was normalized by dividing all data points with the signal value of the 75th percentile of all of non-control probes (gPercentileIntensityProcessedSignal).

source_name: liver of rats administered for 7 days by oral gavage with 100 mg/kg/day of PCN

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the Low Input Quick Amp Labeling Kit, one-color (Agilent) according to the manufacturer's instructions, followed by RNeasy Mini Kit (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: RCCHanTM:WIST male rats at the age of 4 weeks were purchased and quarantined for 1 weeks. The animal rooms were automatically controlled to maintain the following environmental conditions: room temperature, 24+2°C; relative humidity, 55+15%; ventilation, not less than 10 air exchanges per hour; and artificial lighting from 8:00 am to 8:00 pm. A pelleted diet and tap water were provided ad libitum.

extract_protocol: The livers were stored in RNAlater RNA Stabilization Reagent (QIAGEN, Valencia, CA) at room temperature. Total RNA was prepared using the mirVanaTM miRNA Isolation Kit (Life Technologies, Carlsbad, CA) following the manufacturer's instructions. RNA was quantified using a NanoDrop 2000/2000c Spectrophotometer (Thermo Fisher Scientific, Waltham, MA) and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Animals were administered for 7 days by oral gavage with vehicle (corn oil) or 100 mg/kg/day of pregnenolone-16α-carbonitrile(PCN).

value: Wistar Hannover


title: 0 (control) for 7 days, biological rep1

description: Gene expression data from liver of rats administered for 7 days by oral gavage with vehicle (corn oil)


title: 0 (control) for 7 days, biological rep2

source_name: liver of rats administered for 7 days by oral gavage with vehicle (corn oil)


title: 03_E05: Px2

description: Experiment 1


title: 0 (control) for 7 days, biological rep3


title: 100 mg/kg/day of PCN for 7 days, biological rep3


title: Heart_E9.5_Hdac3 Mutant vs WT_rep4

city: Philadelphia

first: Michael

middle: Patrick

last: Morley

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

description: Biological replicate 4 of 4. Control embryonic stem cells, untreated, harvested after several passages.

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed in Agilent GE wash buffers 1-3.

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

source_name: E9.5 Mutant Hearts 4

label_protocol: cDNA labeled at 40°C for 2 hours with 25 µM dCTP or 25 µM Cy3-label in the prescence of T7 RNA Polymerase (Agilent)

growth_protocol: Mice were maintained on mixed CD1/B6/129 genetic backgrounds separated by 4-8 generations of interbreeding from pure parental strains. Littermate embryos were analyzed in all experiments unless otherwise noted. Institutional Animal Care and Use Committee approved all animal protocols.

extract_protocol: 100ng of total RNA were primed with 7 µl of 100 µM T7 DNA primer at 65°C for 10 min, then reversed transcribed at 40°C for 2 h in the presence of 1.2ul of Affinity Script BlockMix (Agilent) and 100 µM each dATP, dTTP, dGTP

treatment_protocol: Nkx2.5Cre; Hdac3f/+ mice were crossed to Hdac3f/f, embryos dissected at 9.5dpc, hearts microdissected on ice, we obtained 4 independent replicates of Nkx2.5Cre; Hdac3f/f mutants and littermate controls.

value: Embryonic hearts

tag: genotype

value: Nkx2.5Cre; Hdac3f/f mutants

tag: background strain

value: mixed CD1/B6/129

source_name: E9.5 Wild-type Hearts 4

value: Hdac3f/f controls


title: 100 mg/kg/day of PCN for 7 days, biological rep1

tag: strain


title: Heart_E9.5_Hdac3 Mutant vs WT_rep2

description: Biological replicate 2 of 4. Control embryonic stem cells, untreated, harvested after several passages.

source_name: E9.5 Mutant Hearts 2

source_name: E9.5 Wild-type Hearts 2


title: pancreas_WT_6_64_0hr_sham group

city: Munich

first: Alexander

last: Graf

address: Feodor-Lynen-Str. 25

department: Gene Center Munich

institute: Ludwig-Maximilians-Universität München

description: Gene expression of a control mouse without pancreatitis

hyb_protocol: Microarray analysis was performed using Agilent SurePrint G3 Mouse GE 8x60K microarrays (AMADID 028005). Labeled cRNA was hybridized to the microarrays according the manufacturer’s instructions.

scan_protocol: Hybridized and washed slides were scanned at 2-µm resolution with an Agilent DNA Microarray Scanner (G2505C, Agilent Technologies).

data_processing: Image processing was performed with the Feature Extraction Software 10.7.3.1 (Agilent Technologies). The signals were filtered based on “Well above background” flags where two out of each experimental group must be above background signal. The data was normalized with the vsn package from BioConductor.

source_name: pancreas_WT_No6_ID64_0hr_sham group

label_protocol: cRNA (Cy3-labeled ) was produced with the Low-Input QuickAmp Labeling Kit; one-color (Agilent Technologies) according the manufacturer’s instructions.

growth_protocol: not applicable

extract_protocol: Total RNA was isolated, after homogenizing the preserved tissue samples in TRIzol (Invitrogen) according to the manufacturer’s protocol. The quality and purity of the RNA were measured with a NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific). The quality of total RNA was analyzed with an Agilent 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany).

treatment_protocol: After fasting for 18 h, all animals received one intraperitoneal applications of 50 µg/kg body weight cerulein in saline or saline only.  Mice were killed 3 hours after cerulein (saline) injection, and the whole pancreas was removed and immediately perfused by an injection of 1 ml RNAlater. The perfused pancreas was incubated in 5ml RNAlater at 4°C for 24h and subsequently frozen at -80°C until further processing.


title: Heart_E9.5_Hdac3 Mutant vs WT_rep1

description: Biological replicate 1 of 4. Mutant vs WT embryonic hearts, pooled 3 hearts per condition.

source_name: E9.5 Mutant Hearts 1

source_name: E9.5 Wild-type Hearts 1


title: pancreas_WT_12_47_3hr_cerulein group

description: Gene expression of a control mouse with pancreatitis


title: Heart_E9.5_Hdac3 Mutant vs WT_rep3

description: Biological replicate 3 of 4. Control embryonic stem cells, untreated, harvested after several passages.

source_name: E9.5 Mutant Hearts 3

source_name: E9.5 Wild-type Hearts 3


title: pancreas_WT_11_85_3hr_cerulein group


title: pancreas_WT_9_93_3hr_cerulein group

source_name: pancreas_WT_No9_ID93_3hr_cerulein group


title: pancreas_TG_16_90_3hr_cerulein group

description: Gene expression of a transgenic mouse with pancreatitis


title: pancreas_WT_10_83_3hr_cerulein group


title: pancreas_WT_8_68_0hr_sham group

source_name: pancreas_WT_No8_ID68_0hr_sham group


title: pancreas_TG_13_81_3hr_cerulein group


title: pancreas_WT_5_31_0hr_sham group

source_name: pancreas_WT_No5_ID31_0hr_sham group


title: Con1

city: Hiroshima-shi

first: Yasuo

last: Kitajima

state: Hiroshima

address: 1-2-3 Kasumi, Minami-ku

department: Graduate School of Biomedical and Health Sciences

institute: Hiroshima University

hyb_protocol: cDNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Mouse Gene Expression Microarray 8×60K ; Agilent Technologies) according to the manufacturer's instructions.

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

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of all samples were normalized by the quantile algorithm with the Bioconductor.

source_name: satellite cell_control_1

label_protocol: Whole transcriptome amplificaton was carried out by using 5 ng of total RNA with Ovation RNA Amplification System V2（NuGEN Techonologies）.The amplified DNA was labelled with SureTag DNA Labeling Kit (Agilent technology).

extract_protocol: Total RNA was isolated from tissues using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega)

value: muscle satellite cell


title: Con3

source_name: satellite cell_control_3


title: MDA-MB-231_VitC_3_RNA

city: Provo

first: David

middle: Wayne

last: Sant

state: UT

address: 1712 South East Bay Blvd, Building 5 Suite 300

department: Biomedical Informatics

institute: Noorda College of Osteopathic Medic

description:
Ribodepleted RNA
Counts of reads in each gene

data_processing:
Basecalls performed using CASAVA version 1.4
Bases were quality trimmed to q20 and adaptors were removed using Trim_Galore!
RNA-seq reads were aligned to the HG38 transcriptome using STAR
RNA-seq counts were generated during alignment using STAR
Genome_build: HG38
Supplementary_files_format_and_content: Count files were generated using STAR.

extract_protocol:
Qiagen RNEasy
Epicentre RiboZero

treatment_protocol: 100 micromolar sodium ascorbate (Vitamin C)

value: MDA-MB-231 Cells

tag: treatment

value: 100 micromolar Vitamin C 3 Days


title: pancreas_TG_14_91_3hr_cerulein group


title: MDA-MB-231_Control_1_RNA

value: Control


title: pancreas_WT_7_67_0hr_sham group

source_name: pancreas_WT_No7_ID67_0hr_sham group


title: pancreas_TG_2_24_0hr_sham group

description: Gene expression of a transgenic mouse without pancreatitis

source_name: pancreas_TG_No2_ID24_0hr_sham group


title: pancreas_TG_15_92_3hr_cerulein group


title: pancreas_TG_3_29_0hr_sham group

source_name: pancreas_TG_No3_ID29_0hr_sham group


title: KO2

source_name: satellite cell_Rpt3 null_2

tag: tissue


title: pancreas_TG_4_30_0hr_sham group

source_name: pancreas_TG_No4_ID30_0hr_sham group


title: A2058_Control_3_RNA

data_processing:
Basecalls performed using CASAVA version 1.4
Bases were quality trimmed to q20 and adaptors were removed using Trim_Galore!
RNA-seq reads were aligned to the HG38 transcriptome using STAR
Genome_build: HG38
Supplementary_files_format_and_content: Count files were generated using STAR.

treatment_protocol: 50 micromolar sodium ascorbate (Vitamin C)

value: A2058 Cells


title: A2058_VitC_3_RNA

value: 100 micromolar Vitamin C 48 Hours


title: A2058_Control_2_RNA


title: Con2

source_name: satellite cell_control_2


title: A2058_VitC_1_RNA


title: A2058_VitC_2_RNA


title: Per2_Mock

city: Fukuoka

first: Satoru

last: Koyanagi

state: Fukuoka

address: 3-1-1 Maidashi, Higashi-ku

department: Pharmaceutics

institute: Kyushu University

description: SAMPLE 5

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Mouse Gene Expression Microarray 8x60K ; Agilent Technologies) according to the manufacturer's instructions.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. The raw signal intensities of all samples were  normalized by the quantile algorithm with the Bioconductor.

source_name: MEFs_Per2 mock

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

growth_protocol: Cells were maintained in Dulbecco’s mod- ified Eagle’s medium supplemented with 10% FBS

extract_protocol: The total RNA was isolated from cells using ReliaPrep TM  RNA Cell Miniprep System (Promega) according to the manufacturer's instructions.

value: ICR

tag: cell type

value: mouse embryonic fibroblasts (MEFs)

value: mock


title: WT_H_Ras_SV40

description: SAMPLE 2

source_name: MEFs_wild type_H-Ras and SV40 induced

value: wild type

value: H-Ras and SV40T expressing vector


title: Per2_H_Ras_SV40

description: SAMPLE 6

source_name: MEFs_Per2 and H-Ras induced


title: M364_TM

city: Boston

first: Jiantao

last: Shi

address: 3 Blackfan Circle

institute: dana farber cancer institute

data_processing:
RNA-seq data was processed by Bcbio_nextgen pipeline (https://github.com/bcbio/bcbio-nextgen). Briefly, alignment was performed using TopHat2 against human genome assembly GRCh37 with default settings. Bioconductor package ‘Rsubread’ was used to generate gene-level read counts, which were further used for differential expression analysis by DESeq2.
Kallisto was used for quantification of transcript-level expression, which was reported as TPM.
Genome_build: GRCh37
Supplementary_files_format_and_content: *.tsv: text file contains transcript-level expression, represented as TPM.

growth_protocol: MM.1S, IM-9, OPM2 cells were genetically modified to carry firefly luciferase, fluorescent proteins, and/or Cas9. All cells were cultured in RPMI or DMEM medium (Corning) supplemented with 10% fetal calf serum (FCS) (Gibco), 2 mM glutamine and 1% pen/strep (Corning). All cells were treated with Plasmocin (InvivoGen) to exclude potential mycoplasma contaminations and maintained under 5% CO2.

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy plus Mini or Micro kit (Qiagen). Quality of the RNA was checked by an Agilent 2100 Bioanalyzer. Genomic DNA was extracted using QIAamp DNA Mini or Micro kit (Qiagen) according to manufacturer’s instruction.
For RNA sequencing, poly-A selection and cDNA synthesis were performed, followed by library preparation using Illumina TruSeq RNA Sample Prep Kit, sequencing (75-bp paired reads), and sample identification for quality control.

treatment_protocol: Mice were euthanized when they exhibit signs of hind-limb paralysis. Primary tumors, femur and tibias were dissected and the BM cells were harvested by flushing the implanted bone chip, femur and tibia bones with Hanks balanced salt solution (HBSS). Tumors outgrown the implanted bone chip were minced with a razor blade and treated with collagenase/Dispase, then were mixed with BM flush from the bone chip. Isolated tumor cells were immediately underwent flow-cytometry and tumor cells that express at least one fluorescent protein were sorted.

tag: site

value: bone chip

tag: femur

value: left and right


title: Clk_Clk_Mock

description: SAMPLE 3

source_name: MEFs_Clk/Clk mock

tag: genotype/variation

value: Clk/Clk


title: KO1

source_name: satellite cell_Rpt3 null_1


title: KO3

source_name: satellite cell_Rpt3 null_3


title: MDA-MB-231_VitC_1_RNA


title: MDA-MB-231_VitC_2_RNA


title: A2058_Control_1_RNA


title: MDA-MB-231_Control_3_RNA


title: Clk_Clk_H_Ras_SV40

description: SAMPLE 4

source_name: MEFs_Clk/Clk_H-Ras and SV40 induced


title: M368_TM


title: M361_TM


title: M368_BM

value: bone marrow


title: M364_BM


title: MM1S_M2_TM


title: M361_BM


title: MM1S_M3_BM


title: MM1S_M1_BM


title: MM1S_M1_TM


title: M964_T_LS

value: left


title: MM1S_M2_BM


title: M964_BM_LS


title: M962_T_RS

value: right


title: M964_BM_RS


title: WT_Mock

description: SAMPLE 1

source_name: MEFs_wild type_mock


title: MM1S_M3_TM


title: M962_BM_RS


title: M962_BM_LS


title: A-549 rep1

city: Halle

first: Markus

last: Glaß

address: Kurt-Mothes-Str. 3a

department: Institute of Molecular Medicine

institute: Martin Luther University Halle-Wittenberg

data_processing:
Sequenced reads were trimmed for adaptor sequences and low quality sequence using Cutadapt (v 1.14) with parameters -q 20 -O 7 -m 16
Trimmed reads were mapped against the human genome (hg38 UCSC) using Bowtie2 (v 2.3.2) with parameters  -N 1
Mapped reads were summarized using featureCounts (v 1.5.3) with parameters -s 1 -t miRNA -g ID and annotated using miRBase (v 21)
Differential gene expression was assessed using R/edgeR (v 3.18.1) using TMM normalization
Genome_build: hg38
Supplementary_files_format_and_content: Comma-separated text file including CPM, log2 fold change and false discovery rate values for each sample

source_name: lung adenocarcinoma derived cell line

growth_protocol: Cells were cultured in DMEM supplemented with 10% FBS. Cells were grown at 37°C in 5% CO2.

extract_protocol:
RNA extraction was performed using TRIZOL according to manufacturer's protocol.
50ng of total RNA served as input using the NEXTflex Small RNA Library Prep Kit v3 (Bioo Scientific). Sequencing was performed on the Illumina HighSeq 2000 platform

treatment_protocol: Parental cells were seeded for 48 hours for RNA extraction.

tag: passages

value: harvested upon 48 hours


title: IM9_GFP_1

value: Cell line


title: MM1S_Luc_GFP


title: A-549 rep2

tag: cell line


title: OPM2


title: Huh-7 rep1

source_name: hepatocellular carcinoma derived cell line


title: Huh-7 rep2


title: MV-3 rep2

source_name: melanoma derived cell line


title: MV-3 rep1


title: M964_T_RS


title: ES-2 rep1

source_name: ovarian cancer derived cell line


title: ES-2 rep2


title: LUGI: 32960

type: genomic

city: Bethesda

middle: Christian

last: Harris

address: 50 South Drive

department: National Human Genome Research Institute

institute: National Institutes of Health

hyb_protocol: Resuspended DNA was loaded onto BeadChips arrays and hybridized overnight at at 48oC.  Single-base extension and allele-specific staining was performed by hand.

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing: Image data was analyzed using GenomeStudio with GT module (Illumina).

label: Cy3, Cy5

organism: Canis lupus familiaris

source_name: whole blood

label_protocol: 200ng of genomic DNA was amplified in an overnight reaction at 37oC. The amplified DNA was enzymatically fragmented, precipitated with isopropanol, and resuspended in hybridization buffer.

extract_protocol: Genomic DNA was extracted from whole blood using Proteinase K and phenol/chloroform with standard protocols.

tag: breed

value: Lupino del Gigante

value: whole blood


title: LUGI: 32961


title: LUGI: 32956


title: LUGI: 32959


title: LUGI: 32952


title: LUGI: 32951


title: LUGI: 32955


title: LUGI: 32953


title: LUGI: 32948


title: LUGI: 32947


title: M962_T_LS


title: LUGI: 32945


title: LUGI: 32949


title: LUGI: 32944


title: LUGI: 32942


title: LUGI: 32946


title: PALA: 32939

value: Pastore della Lessinia e del Lagorai


title: PALA: 32933


title: PALA: 32937


title: PALA: 32932


title: PALA: 32938


title: PALA: 32935


title: PALA: 32934


title: PALA: 32930


title: PALA: 32936


title: APWF: 32929

value: Apennine Wolf


title: APWF: 32923


title: APWF: 32926


title: APWF: 32927


title: APWF: 32924


title: APWF: 32928


title: VPIN: 31590

value: Volpino Italiano


title: APWF: 32922


title: VPIN: 31589


title: LUGI: 32941


title: VPIN: 31582


title: VPIN: 31586


title: VPIN: 31588


title: VPIN: 31585


title: VPIN: 31587


title: VPIN: 31580


title: VPIN: 31583


title: VPIN: 31581


title: VPIN: 31579


title: PALA: 32931


title: SPIN: 31577

value: Spinone Italiano


title: SPIN: 31576


title: SPIN: 31573


title: SPIN: 31574


title: VPIN: 31578


title: SPIN: 31572


title: SPIN: 31570


title: SPIN: 31571


title: SPIN: 31568


title: SPIN: 31569


title: SPIN: 31575


title: SIPR: 31559

value: Segugio Italiano Pelo Raso


title: SIPR: 31558


title: SPIN: 31561


title: SPIN: 31566


title: SPIN: 31567


title: SIPR: 31557


title: SPIN: 31563


title: SIPR: 31554


title: SIPR: 31552


title: SIPR: 31556


title: SPIN: 31564


title: SIPR: 31555


title: SPIN: 31562


title: SIPR: 31550


title: SIPR: 31549


title: SIPR: 31551


title: SIPR: 31548


title: SIPR: 31547


title: HJURP_ChIP-2_New_S4

last: Sturgill

state: MARYLAND

address: Building 41, Rm B622

department: NCI

institute: NIH

data_processing:
Reads were demultiplexed with the bacl2fastq2 program (v2.17.1.4, Illumina, San Diego, USA). Raw reads that passed Illumina quality filters were trimmed for adapter sequence and low quality using Trimmomatic.
These processed reads were aligned to the hg19 assembly with Bowtie2 v2.2.6 with default alignment parameters, reporting a single best alignment where there are multiple alignments possible.  To reduce spurious peak calling in repetitive sequence, we filtered these alignments for alignment quality (which incorporates uniqueness) using samtools with a quality criterion of ten or greater.
Depth normalized browser tracks were generated from these data using Deeptools
Peaks were called using the MACS peak caller, using default parameters, comparing each ChIP sample to its respective input as control.
Genome_build: hg19
Supplementary_files_format_and_content: BED files contain peaks called
Supplementary_files_format_and_content: BW files contain depth-normalized read counts

growth_protocol: Cells were cultured in RPMI 1640 medium (Thermo Fisher) supplemented with 10% FBS and 1% PenStrep (Thermo Fisher).

extract_protocol:
Libraries were constructed using the Illumina TruSeq ChIP Sample Prep Kit (#IP-202-1012-1024).
The soluble fraction of CENP-A was obtained by suspending cells in PBS with 0.5% NP-40 for 5 minutes on ice. Nuclei were then pelleted via centrifugation for 1 minute at 1000 RPM. Nuclei were once again resuspended in PBS NP-40 buffer and pelleted via centrifugation as before. Supernatants were pre-cleared via centrifugation at 12000 RPM for 10 minutes and the resulting supernatant was used in the IP.
Native ChIP was performed as in (Bui et al., Epigenetics Chromatin 2017) with the exception of a longer MNase digest of 15 minutes. For each of four independent replicates (or duplicates for double knockdowns), libraries were constructed using the Illumina TruSeq ChIP Sample Prep Kit (#IP-202-1012-1024).

treatment_protocol: SW480 cells were transfected with siRNAs for 72-hours total. siRNAs were transfected using electroporation Lonza Kit V, program L-024 into 1x10^6 SW480 cells. Before harvesting the cells were treated with the CDK inhibitor RO-3306 for 16 hours to arrest cells in G2 phase (Janssen et al., Science, 2011). The cells were released from G2 by washing the cells 3 times with warm media. Anaphase cells were obtained after a 1.5 hour release then treated with DAPI to analyze mitotic defects. For G1 phase, cells were released for 2 hours then immunofluorescence was performed as in (Zhao et al., J Am Chem Soc 2016). Mitotic cells were obtained by treating cells with 100 ng/ml colcemid for 6-8 hours. Cell synchronization by double thymidine block performed as in (Athwal et al., Epigenetics Chromatin 2015). Monastrol treatment performed as in (Barnhart et al., J Cell Biol 2011).

tag: sirna treatment

value: siHJURP

tag: antibody

value: α-ACA Serum (Centromere Ab Pos. Serum, BBI Solutions)


title: HJURP_INP-1_S2

value: Input


title: HJURP_Input-2_New_S4

description: x


title: HJURP_ChIP-1_S2


title: SIPR: 31544


title: SIPR: 31545


title: SIPR: 31543


title: SIPF: 31541

value: Segugio Italiano Pelo Forte


title: HJP_HIRA_Input-2_New_S4


title: HJP_HIRA_ChIP_1_New_S2


title: SIPF: 31540


title: SIPR: 31542


title: HJP_HIRA_ChIP_-2_New_S4


title: SIPF: 31537


title: SIPF: 31539


title: HIRA_INP-2_S1

value: siHIRA


title: HIRA_INP-1_S3


title: HIRA_DAXX_INP-2_S3


title: dendritic cells transfected with negative control - donor 3

city: Cosenza

first: Cirino

last: Botta

address: Via Migliori

department: Hematology Unit

country: Italy

institute: "Annunziata" Hospital of Cosenza

description: gene expression data from dendritic cells transfected with negative control

hyb_protocol: cDNA was hybridized on GeneChip® Human Transcriptome Array 2.0  at 45C for 16-18 hours. The arrays were washed and stained on Affymetrix Fluidics Stations 450.

scan_protocol: The arrays were scanned with an Affymetrix GeneChip Scanner 3000

data_processing: Data were processed using Affymetrix Expression Console for quality control after summarization and Robust Multi-array Average (RMA) normalization

source_name: healthy donor 3

label_protocol: cDNA was processed for fragmentation and labeling using the Affymetrix® GeneChip® WT Terminal Labeling Kit (Affymetrix Inc.) according to the Affymetrix’s procedures

growth_protocol: DCs were generated from healthy donors'  CD14+ monocytes isolated by immunomagnetic separation. These cells were then cultured for 6 days in RPMI-1640 medium containing 10% FBS, 1% penicillin/streptomycin, 100 ng/ml recombinant human GM-CSF  and 50 ng/ml IL-4 . Half-medium was replaced every 48 hours.

extract_protocol: total RNA (tRNA) from DCs was extracted through column purification with RNeasy kit (Qiagen, Hilden, Germany)

treatment_protocol: After 6 days, 3x106 DCs, obtained from three different healthy donors, were transfected with either miR-29b or NC and co-cultured with U266 MM cells. 24 hours after transfection, cell were harvested and separated with immuno-magnetic microbeads.

value: Dendritic cells

tag: transfection

value: negative control


title: SIPF: 31536


title: dendritic cells transfected with miR-29b mimics - donor 2

description: gene expression data from dendritic cells transfected with miR-29b mimics

source_name: healthy donor 2

value: miR-29b mimic


title: dendritic cells transfected with miR-29b mimics - donor 3


title: dendritic cells transfected with negative control - donor 2


title: dendritic cells transfected with miR-29b mimics - donor 1

source_name: healthy donor 1


title: HIRA_DAXX_ChIP-2_resent_S3


title: HIRA_DAXX_ChIP-1_resent_S1


title: HIRA_DAXX_INP-1_S1


title: dendritic cells transfected with negative control - donor 1


title: SIPF: 31535


title: HJP_HIRA_Input-1_New_S2


title: SIPF: 31533


title: HIRA_ChIP-1_resent_S3


title: HIRA_ChIP-2_resent_S1


title: SIPF: 31538


title: SIPF: 31531


title: SIPF: 31532


title: DAXX_INP-2_S2

value: siDAXX


title: DAXX_ChIP-2_resent_S2


title: DAXX_INP-1_S4


title: SIPF: 31530


title: SIPF: 31529


title: Rep2_HJURP_IP_S6


title: DAXX_ChIP-1_S4


title: Control_ChIP-1_resent_S1

value: Untreated


title: SIPF: 31528


title: MDA-MB-231_Control_2_RNA

value: MDA-MB-231 Cells

value: Control


title: Control_INP-1_S1


title: SIPF: 31525

value: whole blood


title: Rep2_DAXX_IP_S8


title: SILA: 31516

value: Pastore della Sila


title: SILA: 31515


title: SILA: 31520


title: Rep2_HIRA_IP_S7


title: Control_ChIP-2_S3


title: SILA: 31523


title: SIPF: 31524


title: SILA: 31511


title: SILA: 31522


title: Rep2_HIRA_Input_S3


title: SILA: 31521


title: Rep2_HJURP_Input_S2


title: SILA: 31509


title: SILA: 31518


title: Control_INP-2_S3


title: SIPF: 31527


title: SILA: 31508


title: SILA: 31507


title: Rep2_DAXX_Input_S4


title: Rep2_Control_IP_S5


title: SILA: 31517


title: SILA: 31514


title: Rep2_Control_Input_S1


title: DORO: 31504

value: Pastore d'Oropa


title: DORO: 31502


title: Rep1_HJURP_IP_S6


title: Rep1_HJURP_Input_S2


title: DORO: 31501


title: Huh-7 siImp1 rep4

data_processing:
Sequenced reads were trimmed for adaptor sequences and low quality sequence using Cutadapt (v 1.14) with parameters -q 20 -O 7 -m 20
Trimmed reads were mapped against the human genome (hg38 UCSC) using HiSat2 (v 2.1.0) with parameters  -p 6 --dta --strandness RF -k 5
secondary alignments were filtered out using samtools (v 1.5)
Mapped reads were summarized using featureCounts (v 1.5.3) with parameters -p -s 2 -M -t exon -g gene_id and Ensembl gene annotations (GRCh 38.89)
Differential gene expression was assessed using R/edgeR (v 3.18.1) using TMM normalization
Genome_build: hg38
Supplementary_files_format_and_content: Comma-separated text file including FPKM, log2 fold change and false discovery rate values for each sample

growth_protocol: Huh-7 cells were cultured in DMEM supplemented with 10% FBS. Cells were grown at 37°C in 5% CO2.

extract_protocol:
RNA extraction was performed using TRIZOL according to manufacturer's protocol.
1µg of total RNA served as input for rRNA depletion using RiboCop v1.2 (Lexogen). NEBNext Ultra Directional RNA Library kit (NEB) was used for library generation. Sequencing was performed on the Illumina NextSeq 500 platform

treatment_protocol: 72 hours upon transfection cells were harvested for RNA extraction.

tag: sirna

value: siRNA pool against IGF2BP1

value: harvested 72 hours upon transfection


title: DORO: 31500


title: SILA: 31510


title: Rep1_HIRA_IP_S7


title: DORO: 31499


title: Rep1_DAXX_IP_S8


title: Rep1_HIRA_Input_S3


title: DORO: 31498


title: DORO: 31506


title: Rep1_DAXX_Input_S4


title: Rep1_Control_IP_S5


title: DORO: 31505


title: DORO: 31497


title: Huh-7 siImp1 rep3


title: Rep1_Control_Input_S1


title: Huh-7 siC rep1

value: Control siRNA


title: Huh-7 siImp1 rep2


title: Huh-7 siC rep3


title: ES-2 siSRF rep1

growth_protocol: ES-2 cells were cultured in DMEM supplemented with 10% FBS. Cells were grown at 37°C in 5% CO2.

value: siRNA pool against SRF

value: harvested 72h upon transfection


title: ES-2 siImp1 rep3


title: DORO: 31496


title: DORO: 31494


title: ES-2 siSRF rep3


title: DORO: 31492


title: DORO: 31495


title: ES-2 siSRF rep2


title: Huh-7 siC rep2


title: DORO: 31493


title: Huh-7 siImp1 rep1


title: ES-2 siImp1 rep2


title: BERG: 31489

value: Bergamasco


title: ES-2 siImp1 rep1


title: ES-2 siC rep2

description:
DE_ES2_C_vs_IMP1_all.csv
DE_ES2_C_vs_SRF_all.csv


title: BERG: 31485


title: BERG: 31486


title: ES-2 siC rep1


title: BERG: 31483


title: BERG: 31482


title: BERG: 31480


title: BERG: 31481


title: DORO: 31491