title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_A2_AD007_indexed


title: tongue10-A64036

status: Public on Sep 07 2020

type: SRA

city: New York

first: Igor

last: Dolgalev

state: New York

address: 550 1st Ave

country: USA

institute: NYU Grossman School of Medicine

library_source: transcriptomic

data_processing:
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
The sequencing reads were adapter- and quality-trimmed with Trimmomatic.
The sequencing reads were aligned to the human genome (build hg38/GRCh38) using the splice-aware STAR aligner.
The raw counts were normalized using the DESeq2 R package.
The featureCounts program was utilized to generate counts for each gene based on how many aligned reads overlap its exons.
Genome_build: hg38/GRCh38
Supplementary_files_format_and_content: CSV files contain raw and normalized counts for all genes and samples.

molecule: total RNA

organism: Homo sapiens

source_name: tongue

extract_protocol:
Total RNA was extracted from 30 mg of fresh frozen oral cancer tissue and clinically normal contralateral gingiva or tongue tissues from oral cancer patients using the Qiagen RNeasy kit (Catalog No: 74104) following the manufacturer’s protocol including the recommended DNase treatment.  Homogenized tissue lysates were prepared by using a small hand-held pestle followed by passing the lysate at least five times through a blunt 20-gauge needle fitted to an RNase-free syringe.  The RNA concentration and integrity were determined using an Agilent 2100 Bioanalyzer, equipped with an RNA 6000 Nano kit (part number 5067-1511), following the manufacturer’s instructions.
Ribodepleted strand specific RNA libraries were prepared from 24 total RNA samples.  Samples were pooled and 125 base paired end sequencing was performed on the Illumina 2500.

tag: tissue

value: tongue

tag: patient id

tag: diagnosis

value: cancer tissue

tag: ptnm stage

tag: pain score


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_A10_AD012_indexed

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

library_source: genomic

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

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

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

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

tag: brain region

value: PAL

tag: Sex

value: male

tag: age

tag: strain


title: rna_PVpos_striatum_DD_rep3

city: Pittsburgh

first: Alyssa

middle: J

last: Lawler

state: PA

address: 4400 Fifth Ave

department: Computational Biology

institute: Carnegie Mellon University

data_processing:
RNA-Seq alignment:  Fastq files were mapped to the mm10 genome (downloaded from UCSC in November 2015) using Hisat2 with default parameters.
RNA-Seq filtering:  Duplicate UMIs were removed using NuDup (https://github.com/tecangenomics/nudup).
Generation of RNA-Seq count matrix:  A counts per gene per sample matrix was constructed using Subread featureCounts version 1.6.4 with GRCm38 gene annotations (Ensembl version 79).
ATAC-seq alignment:  Reads were mapped to the mm10 genome with Bowtie2 using the ENCODE ATAC-seq pipeline (https://github.com/kundajelab/atac_dnase_pipelines) with default parameters.
ATAC-seq filtering:  Duplicate reads, mitochondrial reads, and blacklist region reads were filtered out as a part of the ENCODE ATAC-seq pipeline.
ATAC-seq peak calling:  Peaks were called on each sample individually using MACS2 within the ENCODE ATAC-seq pipeline workflow and reproducible peaks were determined on biological replicates with an IDR threshold of 0.1.
Generation of ATAC-seq count matrix:  The IDR peaks across all biological replicates were merged to create the genomic ranges of interest. Read counts per sample in these regions were computed with Rsubread featureCounts version 1.28.1 on the filtered bam alignments.
More information on all data processing and conclusions can be found in the publication.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw read counts for every gene and every sample
Supplementary_files_format_and_content: Genomic coordinates of merged ATAC-seq peak regions
Supplementary_files_format_and_content: Matrix table with raw read counts for every peak region and every sample
Supplementary_files_format_and_content: ATAC-seq peaks called in each sample
Supplementary_files_format_and_content: MACS2 pval signal tracks for each sample in bigwig format

extract_protocol:
PV neuron nuclei were tagged and isolated using cSNAIL, a virus-based adaptation of the INTACT method. Nuclei populations were then partitioned for total RNA extraction with the Qiagen RNeasy Micro Kit or ATAC-seq tagmentation with tn5 transposase.
RNA libraries were constructed using the Ovation SoLo RNA-seq System with Mouse AnyDeplete to remove ribosomal RNA. To retain immature nuclear transcripts, no polyA selection was performed. ATAC-seq libraries were constructed with standard amplification and size selection methods. See publication for more details.

treatment_protocol: Mice underwent dopamine depletion with bilateral, acute 6-OHDA lesion to the medial forebrain bundle or received a sham surgery injecting saline instead of the toxin.

value: striatum

tag: cell type

value: PVpos

tag: treatment

value: DD

tag: dopamine remaining

value: F

value: 9 to 12 weeks


title: tongue2-A64025


title: rna_PVpos_striatum_DD_rep4


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_A10_AD008_indexed


title: tongue1-A64024


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_A2_AD006_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_A3_AD004_indexed


title: tcont3-A64037

value: Clinically normal tissue from cancer patient

value: Not applicable


title: rna_PVpos_striatum_DD_rep1

value: M


title: rna_PVpos_striatum_DD_rep2


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_A1_AD012_indexed


title: rna_PVneg_cortex_Sham_rep2

value: cortex

value: PVneg

value: Sham


title: tongue3-A64027


title: tcont2-A64035


title: MOLT4_SK391_8h-03

city: Boston

first: Eric

middle: S

last: Fischer

state: Massachusetts

address: 450 Brookline Ave

department: Cancer Biology

institute: Dana-Farber Cancer Institute

data_processing:
Sequencing reads were aligned to the human genome (BSgenome.Hsapiens.UCSC.hg19 Bioconductor package, using splicedAlignment = FALSE) and quantified at the level of genes (TxDb.Hsapiens.UCSC.hg19.knownGene Bioconductor package) using the QuasR package with default parameters (Gaidatzis et al., 2015)
Expressed genes were identified using the edgeR Bioconductor package (Robinson et al., 2010).
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with RPKKM values for every Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: cell line

growth_protocol: Cells were grown in RPMI1640 supplemented with 10% FBS

extract_protocol:
Cells were harvested using CellStripper Dissociation reagent (Corning), washed twice with PBS, followed by snap freezing in liquid nitrogen. Total RNA was isolated from cell pellets using the RNeasy Mini Kit (Qiagen) following the manufacturer’s directions.
Samples were submitted to BGI Group for RNA-seq library preparation.
Next Generation Sequencing using the BGISEQ-500 platform producing 50 base-pair single-end reads.

treatment_protocol: Cells were treated with either SK-3-91 or DMSO for the indicated amount of time

tag: cell line

tag: time

value: 8 h


title: MOLT4_SK391_8h-04


title: MOLT4_DMSO_8h-04

value: DMSO


title: MOLT4_SK391_8h-01


title: MOLT4_SK391_8h-02


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_A12_AD010_indexed


title: gingiva9-A64048

source_name: gingiva

value: gingiva


title: rna_PVneg_cortex_Sham_rep1


title: gingiva8-A64047

value: cancer tissue


title: MOLT4_DMSO_8h-03


title: gingiva7-A64046


title: rna_PVneg_cortex_DD_rep3


title: rna_PVneg_cortex_DD_rep4


title: MOLT4_SK391_4h-04

value: 4 h


title: MOLT4_SK391_4h-02


title: rna_PVneg_cortex_DD_rep2


title: gingiva6-A64045


title: rna_PVneg_cortex_DD_rep1


title: gingiva5-A64044


title: MOLT4_SK391_4h-03


title: MOLT4_DMSO_4h-02


title: MOLT4_SK391_4h-01


title: MOLT4_DMSO_4h-04


title: tcont1-A64026

value: tongue


title: gingiva4-A64043

value: Not available


title: MOLT4_DMSO_4h-03


title: MOLT4_DMSO_4h-01


title: MOLT4_DMSO_8h-01


title: MOLT4_DMSO_8h-02


title: MOLT4_SK391_1h-03

value: 1 h


title: MOLT4_SK391_1h-04


title: rna_PVpos_cortex_DD_rep4

value: PVpos

value: DD


title: gingiva3-A64041


title: MOLT4_DMSO_1h-04


title: MOLT4_DMSO_1h-02


title: rna_PVpos_cortex_DD_rep2

value: 9 to 12 weeks


title: rna_PVpos_cortex_Sham_rep1


title: gingiva2-A64040


title: rna_PVpos_cortex_DD_rep3

value: F


title: gingiva1-A64039


title: MOLT4_SK391_1h-01


title: gcont2-A64042

value: Clinically normal tissue from oral cancer patient

value: Not applicable


title: MOLT4_DMSO_1h-01


title: PHH_HUM183221_LCA_CsA

city: Tokyo

first: Masaru

last: Koido

address: 4-6-1, Shirokanedai, Minato-ku

country: Japan

institute: Institute of Medical Science, The University of Tokyo

data_processing:
From the sequencing output, quality control, alignment reads on hg19 (hg19_AmpliSeq_Transcriptome_21K_v1.bed), read counts and the normalization (reads per million, RPM) for each gene were obtained using the Torrent ampliSeqRNA plugin (hg19 AmpliSeq Transcriptome ERCC v1) in Torrent Suite Software v5.2.1.
Genome_build: hg19
Supplementary_files_format_and_content: Row counts file is the tab-delimited text file including row gene counts, which were generated from Torrent Suite Software v5.2.1.

source_name: primary human hepatocytes

extract_protocol:
Total RNA was extracted from cultured cells, using a PureLink RNA Mini Kit (Thermo Fisher Scientific).
A cDNA library was generated from 10 ng of total RNA, using a SuperScript VILO cDNA Synthesis Kit (Thermo Fisher Scientific). Amplification, primer digestion, and adapter ligation were performed using an Ion AmpliSeq Transcriptome Human Gene Expression Kit (Thermo Fisher Scientific). The cDNA library was purified using Agencourt AMPure XP Reagent (Beckman Coulter) and quantified using Ion Library TaqMan Quantitation Kit (Thermo Fisher Scientific), followed by dilution to 75 pM with water and pooled equally. Eight samples per pool were sequenced using an Ion 540 Chip Kit (Thermo Fisher Scientific) simultaneously, using IonS5 XL (Life technologies) and Ion Chef instrument systems (Life technologies) with Ion 540 Kit-Chef (Life technologies). All procedures were performed per the manufacturers’ protocols.

value: primary human hepatocytes

tag: drug treatment

value: CsA&LCA

tag: basal expression profiling

tag: donor


title: gcont1-A64038

tag: tissue

value: Clinically normal tissue from cancer patient


title: PHH_HEP187276_LCA_CsA


title: rna_PVpos_cortex_DD_rep1

value: cortex

value: M


title: rna_PVpos_cortex_Sham_rep2

value: Sham


title: PHH_HUM181551A_LCA_CsA


title: PHH_LHuf17905A_LCA_CsA


title: PHH_HU1652_LCA_CsA


title: MOLT4_SK391_1h-02


title: MOLT4_DMSO_1h-03

value: DMSO


title: PHH_HUM183231_LCA_CsA


title: 8b_P06

city: Freiburg

first: Nina

last: Hensel

address: Hugstetterstr. 55

country: Germany

institute: UNIVERSITÄTSKLINIKUM FREIBURG

data_processing:
The mapping tool STAR (version 2.5.2b) was used employing a 2-pass alignment.
Reads were position sorted using SAMtools (version 1.6).
Duplicate read marking was performed using sambamba (version 0.6.5) with 8 threads. BAM file indexes were generated using sambamba.
Quality control was performed using the rnaseqc tool (version v1.1.8.1)  with the 1000 genomes assembly and gencode 19 gene models and no depth of coverage analysis, and also using samtools flagstat.
For gene strand unspecific read counting over exon (gencode v19 gene models), featureCounts (version 1.5.1) was used on only uniquely mapping reads (indicated by a mapping quality 255 reported by.
For calculation of total library abundance, (for FPKM/TPM calculations), every gene on chromosomes X, Y, MT and rRNA and tRNA were omitted to avoid library size estimation biases they may introduce.
Genome_build: build 37, version hs37d5 from the 1000 Genome Project Phase 3

source_name: Cryopreserved PBMCs, Department of Medicine II of the University Hospital Freiburg, Germany

extract_protocol: PBMCs from EDTA anticoagulated patient blood were isolated by density gradient centrifugation using Pancoll (Pan-Biotech, Germany). Magnetic bead-based enrichment of antigen-specific CD8 T cells was further performed. For magnetic bead-based enrichment of HCV-specific CD8+ T cells PBMCs were incubated with peptide-loaded HLA- tetramers coupled to phycoerythrin (PE). Subsequent enrichment was performed with anti-PE beads using the MACS technology (Miltenyi Biotec, Germany) according to the manufacturer’s protocol. Enriched HCV-specific CD8+ T cells were used for multiparametric flow cytometry and transcriptome analysis. Epitope-specific HLA tetramers were generated by conjugation of biotinylated peptide-MHC class I monomers with PE-conjugated streptavidin at a HLA:Strepatividin molar ratio of 5:1. The following peptide-loaded HLA tetramers were used: NS31073(CINGVCWTV)/HLA-A*02:01; NS31406(KLVALGINAV/KLSGLGLNAV)/HLA-A*02:01; NS52594(ALYDVVTKL)/HLA-A*02:01; and NS5B2841(ARMILMTHF)/HLA-B*27:05.

tag: disease status

value: spontaneously resolved HCV infection

value: Peripheral Blood

value: HCV-specific CD8+ T cells

tag: population subset

value: CD127+PD1+ subset

tag: sequence variation

value: no

tag: cell count

tag: manuscript sample id


title: 8a_P06

value: CD127+PD1- subset


title: 7_P05

value: cured HCV infection

value: yes


title: PHH_HU1591_LCA_CsA


title: zinc supplemented drinking water, GrWT, rep5 [WT_ZN2-2]

city: Gent

first: Steven

last: Timmermans

address: Technologiepark 71

country: Belgium

institute: VIB-UGent

data_processing:
Pre-processing to remove adpater sequences and low quality reads: Trimmomatic; version: 0.33; parameters:ILLUMINACLIP:/TruSeq3-SE.fa:2:30:10 AVGQUAL:20 TRAILING:20 MINLEN:33
Data were mapped to the mm10 reference genome with hisat2 v2.0.4 with Ensembl release 85 derived splice sites (--known-splicesite-infile) and strandedness 'R'
mapped read were stired as position sorted bam files by diretly piping hisat output through samtools (| samtools view -bu - | samtools sort -@ 4 -o out.bam )
read counting was performed with featurecounts (-a Ensemb85.gtf -s 2 -T 6 --primary *.bam)
Differential expressed genes were obtained with DESeq2 with standard analysis settings
Genome_build: mm10
Supplementary_files_format_and_content: processed files are a count matrix containg the counts output from featurecouts for all samples

source_name: wild type GR_7 days of 25 mM zinc in drinking water_IEC

extract_protocol:
ileum was isolated, washed with PBS and stored in RNAlater for RNA extraction, IEC samples for RNA-isolations were prepared as follow: +/- 5 cm of the distal ileum was dissected, flushed with ice-cold PBS and incubated with lysis buffer (732 6802, Bio-Rad) supplemented with 2-mercaptoethanol on ice for 5 min, after which the inner part of the bowel was scraped out and snap-frozen in liquid nitrogen. RNA extractions were done with RNeasy Mini Kit (Qiagen)
Illumina truseq RNA stranded library protocol (for single end sequencing)

treatment_protocol: mice recieved 7 days of normal dinking water or drinking water with 25 mM ZnSO4

value: FVB/N mice

tag: genotype

value: wild type GR

value: 7 days of 25 mM zinc in drinking water

value: IEC


title: zinc supplemented drinking water, GrWT, rep4 [WT_ZN2-1]


title: PHH_HUM190131_LCA_CsA

value: primary human hepatocytes

value: CsA&LCA


title: zinc supplemented drinking water, GrWT, rep3 [WT_ZN1-3]

source_name: wild type GR_7 days of 25 mM zinc in drinking water_ileum

value: ileum


title: PHH_HUM183221

value: Control


title: zinc supplemented drinking water, GrWT, rep2 [WT_ZN1-2]


title: PHH_HUM181551A


title: PHH_HEP187276


title: 6_P05

value: chronic HCV infection


title: PHH_LHuf17905A


title: normal drinking water, GrWT, rep5 [WT_NI2-2]

source_name: wild type GR_normal drinking water_IEC

value: normal drinking water


title: PHH_HU1591


title: zinc supplemented drinking water, GrWT, rep1 [WT_ZN1-1]


title: 4b_P04

value: Peripheral Blood

value: CD127-PD1+ subset


title: 5_P04

value: HCV-specific CD8+ T cells

value: CD127+PD1+ subset


title: normal drinking water, GrWT, rep4 [WT_NI2-1]


title: PHH_HUM183231


title: PHH_HUM190131


title: 4a_P04

value: no


title: normal drinking water, GrWT, rep3 [WT_NI1-3]

source_name: wild type GR_normal drinking water_ileum


title: HLO_75A

source_name: human liver bud organoids

value: human liver bud organoids


title: 21b_P11

value: spontaneously resolved HCV infection


title: HLO_10A


title: HLO_45A


title: normal drinking water, GrWT, rep2 [WT_NI1-2]

value: FVB/N mice


title: HLO_73B


title: HLO_CW10027


title: PHH_HEP187239_2day


title: normal drinking water, GrWT, rep1 [WT_NI1-1]

value: wild type GR


title: 21a_P11

value: CD127+PD1- subset


title: PHH_HU1652


title: 18_P08

value: cured HCV infection


title: PHH_HEP187310_2day

value: primary human hepatocytes


title: zinc supplemented drinking water, Grdim, rep6 [DIM_ZN2-3]

source_name: GRDIM_7 days of 25 mM zinc in drinking water_IEC

value: GRDIM

value: 7 days of 25 mM zinc in drinking water

value: IEC


title: 17b_P08

value: chronic HCV infection


title: PHH_HEP187269_2day


title: zinc supplemented drinking water, Grdim, rep5 [DIM_ZN2-2]


title: PHH_HEP187344_2day


title: PHH_HEP187319_2day


title: zinc supplemented drinking water, Grdim, rep4 [DIM_ZN2-1]


title: PHH_HEP187277_2day


title: PHH_HUM4182_2day


title: 17a_P08


title: PHH_HUM4133_2day


title: 14b_P09


title: PHH_HEP187348_2day


title: PHH_HUM4115B_2day


title: 14a_P09


title: zinc supplemented drinking water, Grdim, rep3 [DIM_ZN1-3]

source_name: GRDIM_7 days of 25 mM zinc in drinking water_ileum

value: ileum


title: PHH_HUM4182_1day_4


title: 13_P08

value: Peripheral Blood

value: yes


title: PHH_HEP187277_1day_2


title: zinc supplemented drinking water, Grdim, rep1 [DIM_ZN1-1]


title: PHH_HUM4182_1day_2


title: 12_P08

value: HCV-specific CD8+ T cells


title: normal drinking water, Grdim, rep6 [DIM_NI2-3]

source_name: GRDIM_normal drinking water_IEC

value: normal drinking water


title: PHH_HUM4133_1day_2


title: 11_P07

value: CD127+PD1+ subset

value: no


title: PHH_HUM4182_1day_1


title: PHH_HUM4133_1day_1


title: 10b_P07

value: CD127-PD1+ subset


title: PHH_HUM4182_1day_3


title: normal drinking water, Grdim, rep5 [DIM_NI2-2]

value: FVB/N mice


title: LSEC

source_name: liver sinusoidal endothelial cell

value: liver sinusoidal endothelial cell

value: LSEC


title: normal drinking water, Grdim, rep3 [DIM_NI1-3]

source_name: GRDIM_normal drinking water_ileum


title: normal drinking water, Grdim, rep2 [DIM_NI1-2]


title: HSC

source_name: hepatic stellate cell

value: hepatic stellate cell

value: HSC


title: ALT_1

source_name: adult liver tissue

value: adult liver tissue

value: ALT


title: 10a_P07


title: HOM Zebrafish 1

city: Belfast

first: Guilherme

last: Costa

address: 97 Lisburn Road

country: United Kingdom

institute: Queen's University of Belfast

data_processing:
The stranded paired-end RNA-seq reads were quality assessed using FastQC (v0.11.3) and FastQ Screen (v0.9.2).
The raw reads were processed with BBDuk (part of the BBMap suite; v36.32) to trim the adapter sequences and low-quality bases.
Processed reads from the human-derived samples were mapped against the reference assembly hg38 using STAR (v2.7.2b) with “–quantMode GeneCounts” option to obtain read count for each gene annotated in GENCODE v32, whereas reads from the zebrafish-derived samples were mapped against the reference assembly GRCz11 and gene annotation from Ensembl v99.
Genome_build: hg38 (HUVEC samples); GRCz11 (zebrafish samples)
Supplementary_files_format_and_content: bigWig files include RPKM values for each sample

organism: Danio rerio

source_name: Zebrafish embryo

growth_protocol: HUVECs were cultured in complete ECGM2 in gelatin-coated dishes. Zebrafish were maintained and bred according to standard conditions.

extract_protocol:
Zebrafish – zygote stage embryos were injected with sgRNA-Cas9 ribonucleoproteins and grown to adult stages. Germline transmission of targeted deletion was performed by PCR and 1 desired founder animal (F0) was identified. The F0 was outcrossed to Wt animals to generate F1 heterozygous animals. F1 animals were incrossed and the resulting offspring was grown 28 hours stage embryos. Heads were dissected for PCR-genotyping and the trunks of 2 WT and 2 HOM embryos were processed for RNA extraction.
RNA-seq library prepared with TruSeq Stranded mRNA (Illumina)

treatment_protocol: HUVECs – cells were transfected with sgRNA-Cas9 ribonucleoproteins and a GFP expressing plasmid. GFP+ cells were harvested 48 hours later and single cell FACS sorted in 96 well plates.  After amplification, cells were PCR genotyped and RNA was extracted from 1 non-edited exemplar clone (WT) and 1 exemplar clone with bi-allelic targeted deletion.

value: 28 hpf embryo trunk

value: Homozygous RAB13 3' UTR mutant

tag: passage


title: FLT

source_name: fetal liver tissue

value: fetal liver tissue

value: FLT


title: WT Zebrafish 2

value: Wild type


title: normal drinking water, Grdim, rep1 [DIM_NI1-1]

tag: strain

value: GRDIM

value: ileum


title: HOM Zebrafish 2


title: WT Zebrafish 1


title: normal drinking water, Grdim, rep4 [DIM_NI2-1]

value: normal drinking water

value: IEC


title: ALT_2


title: zinc supplemented drinking water + PBS injection,  rep2

source_name: ileum

extract_protocol:
ileum was isolated, washed with PBS and stored in RNAlater for RNA extraction with RNeasy Mini Kit (Qiagen)
Illumina truseq RNA stranded library protocol (for single end sequencing)

treatment_protocol: mice recieved 7 days of normal dinking water or drinking water with 25 mM ZnSO4, aftwards an injection of 200 µg DEX in 200 ml PBS OR just 200 ml of PBS was given. Sampeling occured 2 hours after the injections

value: C57BL/6J mice

value: 7 days of 25 mM ZNSO4, 200ml PBS 2h before sampling


title: S4 2x (βA-globin+ β-actin)

city: Paris

first: Caroline

last: Brossas

address: 15 rue Hélène Brion

country: France

institute: Institut Jacques Monod, Université de Paris, CNRS UMR 7592

description: Nascent strands of DNA

data_processing:
Library strategy: Repli-Seq
Paired-end sequencing data were mapped on the galGal5 chicken genome using bowtie2 (Langmead & Salzberg, 2012). For each timing fraction, replication timing was computed using 50kb sliding windows at 10kb intervals, normalized by the global and local genomic coverage of the asynchonous cell population, to normalize for total and local coverage variations. Then the centered and standardized timing profiles were smoothed using cubic splines (smooth.spline function of R). In order to provide a single RT profile combining all fractions, we used the method proposed by (Du et al, 2019), by computing the weighted average WA = (0.917*G1) + (0.750*S1) + (0.583*S2) + (0.417*S3) + (0.250*S4) + (0*G2). An increase in WA indicates an earlier timing.
Genome_build: galGal5 chicken genome
Supplementary_files_format_and_content: Bed Graph files were generated

organism: Gallus gallus

source_name: DT40 Chicken cell line

growth_protocol: DT40 cells were grown in RPMI 1640 Glutamax (Thermo Fisher Scientific #61870010) containing 10% FBS, 1% chicken serum, 0.1 mM β-mercaptoethanol, 200 U/mL penicillin, 200 µg/mL streptomycin and 1.75 µg/mL amphotericin B, at 37°C, under an atmosphere containing 5% CO2.

extract_protocol:
Exponentially growing cells were pulse-labeled with 5-Bromo-2’-deoxyuridine for 1h and four S-phase fractions (S1 to S4) were collected by flow cytometry or from an asynchronous cell population (AS). The cells were treated with lysis buffer (50 mM Tris pH 8.0; 10 mM EDTA pH 8.0; 300 mM NaCl; 0.5% SDS, 0.2 mg/ml of freshly added proteinase and 0.5 mg/ml of freshly added RNase A), incubated at 65°C for 2 h and stored at -20°C, in the dark. Genomic DNA was isolated from each sample by phenol-chloroform extraction and alcohol precipitation and sonicated four times for 30s each, at 30s intervals, in the high mode at 4°C in a Bioruptor water bath sonicator (Diagenode), to obtain fragments of 500 to 1000 bp in size. The sonicated DNA was denatured by incubation at 95°C for 5 minutes. We added monoclonal anti-BrdU antibody (BD Biosciences #347580) at a final concentration of 3.6 μg/ml in 1x IP buffer (10 mM Tris pH 8.0, 1 mM EDTA pH 8.0, 150 mM NaCl, 0.5% Triton X-100, and 7 mM NaOH). We used 30 μl or 50 µl of protein-G-coated magnetic beads (from Ademtech #4342 or Thermo Fisher Scientific #10004D, respectively) per sample to pull down the anti-BrdU antibody. Beads and BrdU-labeled nascent DNA were incubated for 2-3 hours at 4°C, on a rotating wheel. The beads were then washed once with 1x IP buffer, twice with wash buffer (20 mM M Tris pH 8.0, 2 mM EDTA pH 8.0, 250 mM NaCl, 0.25% Triton X-100) and then twice with 1x TE buffer pH 8.0. The DNA was eluted by incubating the beads at 37°C for 2 h in 250 µl 1x TE buffer pH 8.0, to which we added 1% SDS and 0.5 mg/ml proteinase K. DNA was purified by phenol-chloroform extraction and alcohol precipitation and resuspended in 50 µl TE. Immunoprecipitated NS were amplified by whole-genome amplification (GenomePlex Complete Whole Genome Amplification kit #WGA2; Sigma) according to the manufacturer’s recommendations to obtain sufficient DNA amount.
Libraries were constructed with the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB #E7645S) following the manufacturer’s instructions with minor modifications. For the adaptor ligation, undiluted adaptor and no size selection were used. The library amplification was performed using NEB-Next Multiplex Oligos for Illumina (NEB #E7710S) with nine different NEB-Next index primer and the NEB-Next Universal PCR Primer (NEB #E6861A) with three PCR cycles. Library purification was performed with the SPRI-select Reagent kit (Beckman coulter #B23317), and the final elution step was reduced to 33µl of 0.1×TE. The mean size of the library molecules determined on an Agilent Bio-analyser High Sensitivity DNA chip (Agilent technologies, #5067–4626) was 330-350 bp. Sequencing was performed on a NextSeq 500 Illumina sequencer with a High Output 150 cycles flow cell (paired-end reads of 75 bp) according to standard procedures. For each sample, 15-20 M of reads were generated.

tag: cell type

value: dervived from a Bursal lymphoma

value: 2x (betaA-globin+ beta-actin)

tag: fraction


title: AML #3 DENATONIUM [304]

type: RNA

city: Meldola

first: Giorgia

last: Simonetti

state: FC

address: Via Piero Maroncelli, 40

country: Italy

institute: IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori"

description: Gene expression data from denatonium-treated cells from AML patient #3 (0.5 mM) after 24h of culture

hyb_protocol: Sample hybridization was performed for 16 hours at 45°C according to standard Affymetrix protocol. Washing and staining was performed on an Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip scanner 3000.

data_processing: The data were analyzed with Expression Console software (Affymetrix). Normalization was performed using the Signal Space Transformation-Robust multiple-array average normalization method (SST-RMA).

label: biotin

source_name: Denatonium-treated cells from AML patient #3 (0.5 mM) after 24h of culture

label_protocol: ss-cDNA was prepared according to the standard Affymetrix protocol from 100 ng total RNA (GeneChip® WT PLUS Reagent Kit User Manual, 2013, Affymetrix).

growth_protocol: Cells were cultured in RPM1 1640 medium supplemented with 10% fetal bovine serum, 2 mM L-glutamine, 100 U/ml of penicillin and 100 μg/ml of streptomycin

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

treatment_protocol: Cells were treated with 0.1 or 0.5 mM denatonium for 24h before harvesting.

value: primary AML cells

tag: treatment

value: Denatonium-treated (0.5 mM)


title: zinc supplemented drinking water + PBS injection, rep1


title: S3 2x (βA-globin+ β-actin)

description: Nascent strands of DNA

tag: cell line


title: S1 2x (βA-globin+ β-actin)

description: Nascent strands of DNA


title: S4 Wt

description: Nascent strands of DNA

value: Wt


title: S2 Wt

description: Nascent strands of DNA


title: S1 Wt

description: Nascent strands of DNA


title: zinc supplemented drinking water + DEX injection, rep2

value: 7 days of 25 mM ZNSO4, 200 µg (in 200ml PBS) DEX 2h before sampling


title: AS Wt

description: Nascent strands of DNA

value: AS


title: zinc supplemented drinking water, Grdim, rep2 [DIM_ZN1-2]

value: FVB/N mice

value: 7 days of 25 mM zinc in drinking water


title: zinc supplemented drinking water + PBS injection,  rep3


title: normal drinking water + PBS injection,(control)  rep3

value: 7 days water, 200ml PBS 2h before sampling


title: Arp5-FRB CHIP-seq rapamycin rep1

city: Worcester

first: Salih

last: Topal

state: MA

address: 373 Plantation Street

institute: UMass Medical School

data_processing:
FASTQ files from single end libraries were collapsed by barcode and the Illumina adapter sequence was trimmed from the 3’ end.
Reads were aligned to S. cerevisiae genome (SacCer3, SGD) using Bowtie2. After filtering out clonal reads, the IP and input samples were shuffled to similar reads, IP samples were normalized to input using a custom script.
S. cerevisiae genome was divided into 50-bp windows, and significant windows with a p-value lower than 0.001 were selected as described in (Ferrari et al., 2012).
The log2 ratio of ChIP versus input at significant windows was used to generate metagene profiles around the TSS and TTS or profiles centered at the TSS or TTS.
Genome_build: SacCer3
Supplementary_files_format_and_content: bed file of peaks

organism: Saccharomyces cerevisiae

source_name: log phase S. cerevisiae

growth_protocol: Yeast strains were grown in YPD at 30°C with shaking from an initial OD of 0.1 to mid-log phase with an OD of 1.

extract_protocol:
Cells were collected and crosslinked with 1% formaldehyde. Samples were lysed with glass beads in lysis buffer (50 mM HEPES, 140 mM NaCl, 10 mM EDTA, 5 mM EGTA, 1% Triton X-100, 0.1% Na-deoxycholate, 0.5% N-Lauroyl Sarcosine) with protease inhibitors. Chromatin was collected by centrifugation, resuspended in lysis buffer and subjected to sonication.
ChIP was performed as described in (Kitada et al., 2012) using commercial antibodies (α-V5 (Invitrogen); α-Arp5 (Abcam)). Libraries were prepared as previously described in (Xue et al., 2017) and sequenced using the Illumina HiSeq 2000 for 50 bp single end reads

treatment_protocol: 0.2M nocodazole was added for 1 hour, and Orc2 was depleted by 8 µg/ml rapamycin for 1 hour, and then cells were arrested in G1 by 5 µg/ml α-factor for 1 hour prior to harvest.

tag: protocol

value: ChIP-seq


title: Arp5-FRB CHIP-seq rapamycin rep2


title: normal drinking water + PBS injection,(control)  rep2


title: zinc supplemented drinking water + DEX injection, rep3


title: AML #2 DENATONIUM [302]

description: Gene expression data from denatonium-treated cells from AML patient #2 (0.5 mM) after 24h of culture

source_name: Denatonium-treated cells from AML patient #2 (0.5 mM) after 24h of culture


title: Arp5-FRB CHIP-seq no rapamycin rep2


title: AML #1 CNTRL [297]

description: Gene expression data from vehicle-treated cells from AML patient #1 (0.5 mM) after 24h of culture

source_name: Vehicle-treated cells from AML patient #1 (0.5 mM) after 24h of culture

value: vehicle control


title: S3 Wt

description: Nascent strands of DNA


title: C3H10 ASO MALAT1

city: Shanghai

first: LEI

last: SHEN

state: State...

address: Feng lin road 180

department: Department of General Surgery

country: China

institute: Zhongshan Hospital, Fudan University

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
HISAT2.1.0 mapping to reference genome
count counting
Genome_build: GRCm38
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: C3H10 ASO MALAT1

growth_protocol: C3H10 cells were cultured in high-glucose Dulbecco’s modified Eagle medium (DMEM)  supplemented with 10% fetal bovine serum (FBS). C3H10 cells were differentiated in induction medium (0.5 mM isobutyl-1-methylxanthine (IBMX), 5 mM dexamethasone, 0.5 mg/L troglitazone, 10 ng/mL insulin). Cells were switched to maintenance medium (10 ng/mL insulin) after 2 days for further differentiation.

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.Part of RNA was utilized to construct rRNA depletion(NEBNext Ultra Directional RNA Library Prep Kit),The RNA with RIN >8.0 is right for cDNA library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: C3H10 cells at 70% confluence were transfected with 100 nM ASO using RNAiMAX Transfection Reagent according to instructions. Eight hours post-transfection, cells were recovered in full culture medium, grown to confluence, and induced to differentiation as described above.

value: fibroblast precursor cell with adipogenic ability

value: MALAT1 knockdown


title: C3H10 ASO NC

source_name: C3H10 ASO NC

value: negative control


title: normal drinking water + PBS injection,(control) rep1

value: C57BL/6J mice


title: OCI-AML3 DENATONIUM [261]

description: Gene expression data from denatonium-treated (0.1 mM) OCI-AML3 cells after 24h of culture

source_name: Denatonium-treated (0.1 mM) OCI-AML3 cells after 24h of culture

value: Denatonium-treated (0.1 mM)


title: AML #3 CNTRL [303]

description: Gene expression data from vehicle-treated cells from AML patient #3 (0.5 mM) after 24h of culture

source_name: Vehicle-treated cells from AML patient #3 (0.5 mM) after 24h of culture


title: OCI-AML3 DENATONIUM [260]


title: PHH_HEP187277_1day_1

source_name: primary human hepatocytes

value: primary human hepatocytes

tag: drug treatment


title: OCI-AML3 DENATONIUM [259]


title: AML #1 DENATONIUM [298]

description: Gene expression data from denatonium-treated cells from AML patient #1 (0.5 mM) after 24h of culture

source_name: Denatonium-treated cells from AML patient #1 (0.5 mM) after 24h of culture


title: Orc5-FRB ChIP-seq no rapamycin


title: S2 2x (βA-globin+ β-actin)

description: Nascent strands of DNA

value: dervived from a Bursal lymphoma

value: 2x (betaA-globin+ beta-actin)


title: OCI-AML3 CNTRL [257]

description: Gene expression data from vehicle-treated THP-1 cells after 24h of culture

source_name: Vehicle-treated OCI-AML3 cells after 24h of culture


title: normal drinking water + DEX injection, rep2

value: 7 days water, 200 µg (in 200ml PBS) DEX 2h before sampling


title: OCI-AML3 CNTRL [256]


title: Arp5-FRB CHIP-seq no rapamycin rep1


title: MNC-1011 +PMP rep2

city: Beijing

first: Mingyi

last: Qu

state: Beijing

address: 27 Taiping Road

institute: Institute of Health Service and Transfusion Medicine

description: gene expression data from CB-MNC after PMP trearment

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the  manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Affymetrix PrimeView™ Human Gene Expression for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%)

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 13.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

source_name: healthy human CB-MNC

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/n AM1556 ) following the manufacturer's instructions.

value: cord clood

value: CB-MNC


title: normal drinking water + DEX injection, rep1


title: Scramble_rep2

city: Rozzano

first: Simone

last: Serio

state: Milano

address: Via Alessandro Manzoni, 56

department: Cardiovascular Medicine

institute: Humanitas Research Hospital

data_processing:
RNA-seq reads were aligned to the mm10 genome assembly using STAR v2.7 (PMID: 23104886)
Transcript abundance was obtained using the internally  developed RNA read counter of STAR v2.7 (PMID: 23104886)
Differentially expressed genes were identified using R and edgeR (PMID: 19910308)
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigWig were generated using STAR v2.7(PMID: 22743226)

molecule: polyA RNA

extract_protocol:
RNA was isolated using Zymo extraction Kit (EuroClone) plus DNAse treatment on columns according to the manufacture’s protocol.
DNase I-treated RNA analysed on the Tape Station 4200 (Agilent) shown an RNA integrity number (RIN) of 9.7-9.8. SMART-Seq v4 Ultra Low Input RNA Kits (Takara Bio USA) was used for cDNA amplification. Indexed sequencing libraries were generated using Nextera XT DNA Library Preparation Kits (Illumina) following manufacture’s instruction. Electrophoresis of the libraries on a LabChip GX instrument showed average library size of 500-555 bp. Single-end multiplexed libraries were sequenced using NextSeq500 instrument. 19-34 million reads for each sample were obtained.
Single end sequence reads (75-bp in length) were generated on an Illumina NextSeq 500 (Samples 1 to 9)

tag: strain background

tag: age

value: neonatal

value: cardiomyocyte

value: Gapmer Scramble


title: Scramble_rep3


title: Orc5-FRB ChIP-seq rapamycin


title: normal drinking water + DEX injection, rep3


title: Granulosa cells, eCG48h_2 ChIP-Seq

city: Sainte-Anne-de-Bellevue

first: Raj

last: Duggavathi

state: Quebec

address: 21111 Rue Lakeshore

department: Animal Science

country: Canada

institute: McGill University

data_processing:
Adapters were trimmed using Trimmomatic - 0.36 with the following configurations TRAILING: 30, MINLEN:36
ChIP-seq reads were aligned to the mm10 genome assembly using Bowtie 2 version 2.2.9
peaks were called using Macs2 version 2.2 with the following setting: callpeak --broad --broadcutoff 0.000001 --bdg --nomodel
Peaks were annotated using ChIPseeker Version 1.18.0
Differential enrichment analyses was carried out using Network Analyst Version 2.0
Genome_build: mm10
Supplementary_files_format_and_content: Matrix of counts provided in a text file

source_name: Granulosa cells

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with H3K4me3 antibody (Abcam ab98580) or not (input)
Libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were either left untreated or treated with follicle stimulating hormone (FSH) for 48 hours

value: Granulosa cells

tag: tissue

value: Ovary

tag: chip antibody

value: H3K4me3 (Abcam ab8580)

value: 48h eCG


title: OCI-AML3 CNTRL [258]

value: vehicle control


title: Granulosa cells, Input DNA


title: Scramble_rep1


title: zinc supplemented drinking water + DEX injection, rep1

value: 7 days of 25 mM ZNSO4, 200 µg (in 200ml PBS) DEX 2h before sampling


title: Granulosa cells, eCG48h_1 ChIP-Seq


title: THP1 DENATONIUM [295]

description: Gene expression data from denatonium-treated (0.5 mM) THP-1 cells after 24h of culture

source_name: Denatonium-treated (0.5 mM) THP-1 cells after 24h of culture

value: Denatonium-treated (0.5 mM)


title: THP1 DENATONIUM [296]


title: MNC-1011+PMP rep1


title: THP-1 CNTRL [292]

source_name: Vehicle-treated THP-1 cells after 24h of culture


title: KD_IRENE_SS_rep3

value: Gapmer anti-IRENE-SS


title: MNC-0803 +PMP rep2


title: MNC-0920 +PMP rep1


title: MNC-0920 +PMP rep2


title: THP1 DENATONIUM [294]


title: MNC-0920 con

description: gene expression data from CB-MNC


title: MNC-0803 con

description: gene expression data from CB-MNC


title: MNC-0803 +PMP rep1


title: Granulosa cells, eCG0h_2 ChIP-Seq

value: 0h eCG


title: KD_IRENE_SS_rep2


title: sep1sep2sep3 SEP3 line 2

city: Grenoble

first: Veronique

last: Hugouvieux

address: 17 rue des Martyrs

department: IRIG

institute: CEA Grenoble

description: triple mutant expressing SEP3 line2

data_processing:
Mapping onto the Arabidopsis genome was done using STAR (no multimapping mismatch < 10),  available in the Galaxy platform.
Read count per gene was done using FeatureCount (default parameters)  available in the Galaxy platform.
Statistical analysis were done using  EdgeR (default parameters),  available in the Galaxy platform.
Genome_build: Arabidopsis_thaliana_TAIR10
Supplementary_files_format_and_content: comparison data

organism: Arabidopsis thaliana

source_name: flower

growth_protocol: Description of the Arabidopsis lines , growth condition and RNA extraction protocoles are found in the following paper: Hugouvieux et al, Nucleic Acid Research, 2018:1;46(10):4966-4977. doi: 10.1093/nar/gky205.

extract_protocol: Poly A selection,  Construction of the libraries and  sequencing were perfomed by Genewiz

value: infloresence meristem flower buds

tag: developmental stage

value: stages 10-11

value: sep1sep2sep3 expressing SEP3


title: KD_IRENE_SS_rep1


title: KD_IRENE_div_rep3

value: Gapmer anti-IRENE-div


title: THP-1 CNTRL [293]


title: sep1sep2sep3 replicate 1

description: triple mutant replicat 1


title: mir128_repB

description: Sample 6

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data exported from GenomeStudio V2011.1  were analysed with Lumi/Limma in R.                 Data preprocessing was performed using lumi package:                                                                          - Background Correction: bgAdjust  - Variance Stabilizing Transform method: vst  - Normalization method: rsn (Robust Spline Normalization)                                                                                The differentianly expressed genes were identified using limma package.

source_name: Primary VSMC

label_protocol: Biotinylated cRNA were prepared with the Ambion TotalPrep RNA Amplification Kit for Illumina arrays

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

treatment_protocol: Primary VSMCs were infected with lentiviral particles expressing miR-128 or scrambled miRNA, selected with puromycin for two days and then RNA collected after five days.

value: 8 weeks

value: vascular smooth muscle cell

value: mir128 overexpression


title: MNP-DT40-1-3-16-2p-R1-T1

description: DT40 cell line modified clone 16

data_processing:
Fastq files were mapped to the gal5Gal5 (and gal5Gal5 modified allele) genome using the distiller pipeline (github.com/mirnylab/distiller-nf). Hi-C interaction data was stored in the cooler format (Abdennur, N., and Mirny, L. (2019).
WT replicates and clones were combined into one multires.cool file.
Genome_build: galGal5 chicken genome
Supplementary_files_format_and_content: Multiresolution cooler files (.mcool) containing pairwise interactions.

source_name: DT40 Chicken cell line

extract_protocol:
10M formaldehyde cross-linked cells were lysed and digested overnight at 37°C with 400 units of DpnII (NEB). Next, the DNA ends were marked with biotin-14-dATP (Thermo Fisher Scientific #19524016) for 4 hours at 23°C and ligated for 4 hours at 16°C. To remove proteins and reverse crosslink, DNA was treated with proteinase K overnight at 65°C. DNA was then purified using phenol:chloroform and biotin was removed from unligated ends. Ligation products were fragmented by sonication to an average size of 200bp and size selected with Ampure XP beads (Beckman Coulter, # A63880) to fragments ranging from 100 to 350 bp.
End repair was performed on the DNA fragments to obtain blunt ends and biotinylated ligation products were purified using streptavidin beads (Thermo Fisher Scientific #65001). dA-tailing was then performed and the TruSeq DNA LT kits Set A (Illumina, #15041757) was used for adapter ligation and PCR amplification. PCR primers were removed using Ampure XP beads.
The Hi-C libraries were sequenced using 50 bp paired end reads on Illumina HiSeq4000.

value: derived from a Bursal lymphoma

value: modified

tag: enzyme

value: DpnII


title: Granulosa cells, eCG0h_1 ChIP-Seq

value: Granulosa cells

value: Ovary

value: H3K4me3 (Abcam ab8580)


title: mir128_repA

description: Sample 5


title: shScr2_repB

description: Sample 4

value: scrambled miRNA


title: KD_IRENE_div_rep2

value: neonatal

value: cardiomyocyte


title: MNP-DT40-WT2-R1-T1

description: WT DT40 cell line

value: WT


title: sep1sep2 replicate 2

description: double mutant replicat 2

value: infloresence meristem flower buds


title: sep1sep2sep3 SEP3 line 1

description: triple mutant expressing SEP3 line1

value: stages 10-11


title: shScr2_repA

description: Sample 3


title: AML #2 CNTRL [301]

description: Gene expression data from vehicle-treated cells from AML patient #2 (0.5 mM) after 24h of culture

source_name: Vehicle-treated cells from AML patient #2 (0.5 mM) after 24h of culture

value: primary AML cells

value: vehicle control


title: MNP-DT40-1-3-17-2p-R1-T1

description: DT40 cell line modified clone 17


title: sep1sep2 replicate 1

description: double mutant replicat 1


title: MNC-1011 con

description: gene expression data from CB-MNC

value: cord clood

value: CB-MNC


title: sep1sep2sep3 replicate 2

description: triple mutant replicat 2


title: KD_IRENE_div_rep1

value: Gapmer anti-IRENE-div


title: 189_Gill_B32_CT29_DD

status: Public on Sep 06 2020

city: Tromsø

first: Alexander

middle: Christopher

last: West

state: Troms

address: Framstredet 39, Tromsø

department: Arctic Chronobiology and Physiology

country: Norway

institute: Universitetet i Tromsø

description: A bespoke Atlantic salmon (Salmo salar) clock gene Nanostring CodeSet was used to measure the abundance of target mRNA

hyb_protocol: Following manufacurers instructions

scan_protocol: Using a Nanostring nCounter analysis system, following manufacturers instructions

data_processing: nSolver software

label: Nanostring hydridisation

organism: Salmo salar

source_name: Gill fillaments

label_protocol: Nanosting hybridisation was used to quantify transcript abundance

growth_protocol: Atlantic salmon (Salmo salar) were raised under LL, fed daily

extract_protocol: From optic tectum and gill RNA was extracted using QIAgen RNeasy mini kit following the manufacturers instructions. SV RNA was extracted using an QIAgen RNeasy micro kit.

treatment_protocol: Pre-smolt salmon were transferred to a light:dark cycle (LD, 8:16) for 8 weeks then transferred to either constant light or constant darkness. Tissue samples were collected under LD, LL and DD conditions at a 4 hour resolution. Food was removed 48h before the first sampling point. Water temperature was maintained at 14oC throughout.

value: DD

tag: time

tag: weight and life-stage

value: ~45g pre-smolt


title: 184_Gill_B25_CT25_DD


title: 185_Gill_B26_CT25_DD


title: 186_Gill_B27_CT25_DD


title: 188_Gill_B31_CT29_DD


title: 183_Gill_B23_CT21_DD


title: 182_Gill_B22_CT21_DD


title: 180_Gill_B19_CT17_DD


title: 181_Gill_B21_CT21_DD


title: MNP-DT40-WT1-R1-T1

description: WT DT40 cell line

value: derived from a Bursal lymphoma

tag: genotype

value: DpnII


title: 177_Gill_B16_CT13_DD


title: 179_Gill_B18_CT17_DD


title: shScr1_repB

description: Sample 2

value: 8 weeks

value: vascular smooth muscle cell


title: THP-1 CNTRL [291]


title: 171_Gill_B7_CT5_DD


title: 174_Gill_B11_CT9_DD


title: 175_Gill_B13_CT13_DD


title: 187_Gill_B29_CT29_DD


title: 172_Gill_B9_CT9_DD


title: shScr1_repA

description: Sample 1

value: scrambled miRNA


title: 170_Gill_B6_CT5_DD


title: 173_Gill_B10_CT9_DD


title: 168_Gill_B3_CT1_DD


title: 169_Gill_B5_CT5_DD


title: 178_Gill_B17_CT17_DD


title: 165_Gill_A55_CT29_LL

value: LL


title: 167_Gill_B2_CT1_DD


title: 166_Gill_B1_CT1_DD


title: 161_Gill_A50_CT25_LL


title: 159_Gill_A47_CT21_LL


title: 164_Gill_A54_CT29_LL


title: 158_Gill_A46_CT21_LL


title: 162_Gill_A52_CT25_LL


title: 176_Gill_B14_CT13_DD


title: 160_Gill_A49_CT25_LL


title: 163_Gill_A53_CT29_LL


title: 155_Gill_A42_CT17_LL


title: 157_Gill_A45_CT21_LL


title: 156_Gill_A43_CT17_LL


title: 153_Gill_A39_CT13_LL


title: 154_Gill_A41_CT17_LL


title: 150_Gill_A35_CT9_LL


title: 148_Gill_A33_CT9_LL


title: 151_Gill_A37_CT13_LL


title: 142_Gill_A25_CT1_LL


title: 146_Gill_A30_CT5_LL


title: 143_Gill_A26_CT1_LL


title: 141_Gill_A23_ZT21_LD

value: LD


title: 147_Gill_A31_CT5_LL


title: 145_Gill_A29_CT5_LL


title: 139_Gill_A21_ZT21_LD


title: 144_Gill_A28_CT1_LL


title: 140_Gill_A22_ZT21_LD


title: 137_Gill_A19_ZT17_LD


title: 138_Gill_A20_ZT17_LD


title: 136_Gill_A18_ZT17_LD


title: 152_Gill_A38_CT13_LL


title: 149_Gill_A34_CT9_LL


title: 132_Gill_A11_ZT9_LD


title: 130_Gill_A9_ZT9_LD


title: 133_Gill_A13_ZT13_LD


title: 126_OT_B32_CT29_DD

source_name: Optic tectum


title: 131_Gill_A10_ZT9_LD


title: 128_Gill_A6_ZT5_LD


title: 129_Gill_A7_ZT5_LD


title: 127_Gill_A5_ZT5_LD


title: 123_OT_B27_CT25_DD


title: 124_OT_B29_CT29_DD


title: 120_OT_B23_CT21_DD


title: 118_OT_B21_CT21_DD


title: 122_OT_B26_CT25_DD


title: 121_OT_B25_CT25_DD


title: 135_Gill_A15_ZT13_LD


title: 117_OT_B19_CT17_DD


title: 116_OT_B20_CT17_DD


title: 134_Gill_A14_ZT13_LD


title: 115_OT_B17_CT17_DD


title: 114_OT_B16_CT13_DD


title: 113_OT_B14_CT13_DD


title: 112_OT_B13_CT13_DD


title: 125_OT_B31_CT29_DD


title: 107_OT_B6_CT5_DD


title: 111_OT_B11_CT9_DD


title: 108_OT_B7_CT5_DD


title: 109_OT_B9_CT9_DD


title: 110_OT_B10_CT9_DD


title: 106_OT_B5_CT5_DD


title: 103_OT_B1_CT1_DD


title: 101_OT_A54_CT29_LL


title: 104_OT_B2_CT1_DD


title: 100_OT_A53_CT29_LL


title: 105_OT_B3_CT1_DD


title: 98_OT_A50_CT25_LL


title: 99_OT_A52_CT25_LL


title: 97_OT_A49_CT25_LL


title: 102_OT_A55_CT29_LL


title: 119_OT_B22_CT21_DD


title: 96_OT_A47_CT21_LL


title: 95_OT_A46_CT21_LL


title: 94_OT_A45_CT21_LL


title: 91_OT_A41_CT17_LL


title: 92_OT_A42_CT17_LL


title: 93_OT_A43_CT17_LL


title: 89_OT_A38_CT13_LL


title: 88_OT_A37_CT13_LL


title: 90_OT_A39_CT13_LL


title: 83_OT_A30_CT5_LL


title: 82_OT_A29_CT5_LL


title: 80_OT_A26_CT1_LL


title: 84_OT_A31_CT5_LL


title: 78_OT_A23_ZT21_LD


title: 85_OT_A33_CT9_LL


title: 87_OT_A35_CT9_LL


title: 81_OT_A28_CT1_LL


title: 75_OT_A20_ZT17_LD


title: 86_OT_A34_CT9_LL


title: 74_OT_A19_ZT17_LD


title: 77_OT_A22_ZT21_LD


title: 73_OT_A18_ZT17_LD


title: 76_OT_A21_ZT21_LD


title: 72_OT_A15_ZT13_LD


title: 69_OT_A11_ZT9_LD


title: 70_OT_A13_ZT13_LD


title: 71_OT_A14_ZT13_LD


title: 67_OT_A9_ZT9_LD


title: 66_OT_A7_ZT5_LD


title: 64_OT_A5_ZT5_LD


title: 63_SV_B31_CT29_DD

source_name: saccus vasculosus


title: 61_SV_B29_CT29_DD


title: 60_SV_B27_CT25_DD


title: 79_OT_A25_CT1_LL


title: 58_SV_B25_CT25_DD


title: 59_SV_B26_CT25_DD


title: 57_SV_B23_CT21_DD


title: 56_SV_B22_CT21_DD


title: 52_SV_B17_CT17_DD


title: 53_SV_B18_CT17_DD


title: 47_SV_B10_CT9_DD


title: 49_SV_B13_CT13_DD


title: 44_SV_B6_CT5_DD


title: 43_SV_B5_CT5_DD


title: 62_SV_B32_CT29_DD


title: 50_SV_B14_CT13_DD


title: 55_SV_B21_CT21_DD


title: 54_SV_B19_CT17_DD


title: 45_SV_B7_CT5_DD


title: 46_SV_B9_CT9_DD


title: 68_OT_A10_ZT9_LD


title: 42_SV_B3_CT1_DD


title: 40_SV_B1_CT1_DD


title: 41_SV_B2_CT1_DD


title: 48_SV_B11_CT9_DD


title: 51_SV_B16_CT13_DD


title: 38_SV_A54_CT29_LL


title: 39_SV_A55_CT29_LL


title: 65_OT_A6_ZT5_LD


title: 34_SV_A49_CT25_LL


title: 32_SV_A46_CT21_LL


title: 37_SV_A53_CT29_LL


title: 33_SV_A47_CT21_LL


title: 35_SV_A50_CT25_LL


title: 36_SV_A52_CT25_LL


title: 29_SV_A42_CT17_LL


title: 31_SV_A45_CT21_LL


title: 30_SV_A43_CT17_LL


title: 28_SV_A41_CT17_LL


title: 26_SV_A38_CT13_LL


title: 27_SV_A39_CT13_LL


title: 25_SV_A37_CT13_LL


title: 23_SV_A34_CT9_LL


title: 22_SV_A33_CT9_LL


title: 20_SV_A30_CT5_LL


title: 21_SV_A31_CT5_LL


title: 19_SV_A29_CT5_LL


title: Osteoblastoma_7

type: genomic

city: London

first: Adrienne

middle: M

last: Flanagan

state: Middlesex

address: Huntley Street

institute: University College London

hyb_protocol: Samples were hybridised using the standard Illumina Protocol

scan_protocol: standard Illumina Protocol

data_processing: idat files were processed in R (version 3.5) using the minfi package ( 1.26.2)

label: cy3 and cy5

source_name: Fresh frozen tumour

label_protocol: Samples were labelled according to standard Illumina Protocol

extract_protocol: Genomic DNA was extracted using the Qiagen QIAmp DNA mini kit

tag: disease

value: Osteoblastoma


title: 18_SV_A28_CT1_LL


title: Osteoblastoma_11


title: 17_SV_A26_CT1_LL


title: 24_SV_A35_CT9_LL


title: Osteoblastoma_10


title: 16_SV_A25_CT1_LL


title: Osteoblastoma_9


title: Osteoblastoma_6


title: Osteoblastoma_12


title: 15_SV_A23_ZT21_LD


title: Osteoblastoma_2


title: Osteoblastoma_8


title: Nonossifying_Fibroma_12


title: Osteoblastoma_3


title: Nonossifying_Fibroma_3


title: 13_SV_A21_ZT21_LD


title: Nonossifying_Fibroma_11


title: Nonossifying_Fibroma_2


title: Nonossifying_Fibroma_10


title: 14_SV_A22_ZT21_LD


title: Osteoblastoma_5


title: Osteoblastoma_4


title: 12_SV_A19_ZT17_LD


title: 10_SV_A20_ZT17_LD


title: Nonossifying_Fibroma_5


title: Nonossifying_Fibroma_7


title: Nonossifying_Fibroma_8


title: Chordoma_5

value: Chordoma


title: 8_SV_A14_ZT13_LD


title: 9_SV_A15_ZT13_LD


title: Nonossifying_Fibroma_9


title: Nonossifying_Fibroma_4


title: Chordoma_4


title: Nonossifying_Fibroma_6


title: Longyan-input (Replicate 3)

city: Nanjing

first: Shahid

last: Iqbal

state: Jiangsu

address: Nanjing, China

institute: Nanjing Agriculture University

data_processing:
The primary raw reads obtained by Illumina HiSeqTM3000/4000 were filtered to remove low quality reads which were low complexity or containing adaptor sequence
The cleaned reads were aligned to the Prunus mume referance genome using Bowtie aligner .
MACS (Model-based Analysis of ChIP-Seq) software (Zhang et al., 2008) with standard parameters was used for peak calling to locate the enriched regions of binding sites.
A motif analysis was performed based on the location of detected peaks and enrichment positions using MEME software (Bailey et al., 2006)
GO functional enrichment analysis and KEGG pathway analysis was continued with Blast2Go. KEGG pathway analysis is also used for the target gene candidates. In organisms, genes usually interact with each other to play different roles in certain biological function. The analysis based on pathways could facilitate the understanding of biological functions of genes. KEGG is the major public pathway-related database[8]. KEGG pathway analysis identifies significantly enriched metabolic pathways or signal transduction pathways in target gene candidates comparing with the whole reference gene background. The calculating formula is the same as that in GO analysis. Here N is the number of all genes with KEGG annotation, n is the number of target gene candidates in N, M is the number of all genes annotated to a certain pathway, and m is the number of target gene candidates in M. Genes with FDR<=0.05 are considered as significantly enriched in target gene candidates

organism: Prunus mume

source_name: Prunus mume Longyan flower buds

growth_protocol: All plants were grown at National Field Gene Bank for ‘Prunus mume’ located in Nanjing, Jiangsu Province, China

extract_protocol: ChIP-Seq libraries were contructed for sequencing using llumina HiSeq 3000/4000 standard Illumina protocols

treatment_protocol: ChIP-Seq samples were prepared using the method described by Kaufmann et al., 2010

tag: common name

value: Japanese Apricot

tag: cultivar

value: Longyan

value: pistil


title: Osteoblastoma_1


title: 6_SV_A11_ZT9_LD


title: Nonossifying_Fibroma_1


title: Chordoma_3


title: 5_SV_A10_ZT9_LD


title: 7_SV_A13_ZT13_LD


title: 3_SV_A7_ZT5_LD


title: Longyan-PmTCP4 chIP (Replicate 3)


title: 2_SV_A6_ZT5_LD


title: 1_SV_A5_ZT5_LD


title: 4_SV_A9_ZT9_LD


title: Chordoma_2


title: Longyan-input (Replicate 2)


title: Longyan-PmTCP4 chIP (Replicate 2)


title: 11_SV_A18_ZT17_LD


title: 12w MI Drug2

city: Houston

first: Jong

middle: H

last: Kim

state: TX

address: One Baylor Plaza

institute: Baylor College of Medicine

description: processed data Sample ID in count matrix : barcode_8

data_processing:
10x Cell Ranger count
Single cell data was analyized using Seurat v3
Raw count data matrix files were extracted from Seurat object
Genome_build: mm10
Supplementary_files_format_and_content: Raw data count matrix text file

source_name: Adult Cardiac Interstitual Cells

extract_protocol:
Interstitual cells were extracted from heart tissue using landgendorff
10x Chromium v3

value: Heart

tag: cell type

value: Interstitual Cells

tag: strain


title: 12w MI Control2

description: processed data Sample ID in count matrix : barcode_6


title: Chondrosarcoma_5

value: Chondrosarcoma


title: 12w MI Drug1

description: processed data Sample ID in count matrix : barcode_7


title: 12w MI Control1

description: processed data Sample ID in count matrix : barcode_5


title: Longyan-input (Replicate 1)


title: 24hr MI Drug2

description: processed data Sample ID in count matrix : barcode_4


title: 24hr MI Drug1

description: processed data Sample ID in count matrix : barcode_3


title: Longyan-PmTCP4 chIP (Replicate 1)


title: 24hr MI Control2

description: processed data Sample ID in count matrix : barcode_2


title: Daqiandi-input (Replicate 3)

source_name: Prunus mume Daqiandi flower buds

value: Daqiandi


title: Chondrosarcoma_3


title: RNAseq in EB-Day4[D0+RA+SAG][D2+48hDox(iFlag.Hoxc9)] replicate 2

city: University Park

first: Shaun

last: Mahony

address: 404 South Frear Bldg

department: Biochemistry & Molecular Biology

institute: Penn State University

data_processing:
Basecall conversion to fastq files was performed using Picard (v 2.8.2)
Alignment: Fastq files obtained from RNA-sequencing were aligned to the genome using the splice-aware STAR (v2.7.0c) (Spliced Transcripts Alignment to a Reference) aligner (Dobin & Gingeras, 2016).
Computing Abundance: Mapped reads were assigned to NCBI RefSeq annotated mm10 genes using the featureCount function in Rsubread (v1.30.9) (Liao, Smyth, & Shi, 2019). RefSeq genes with matching Entrez IDs were merged into a single gene by Rsubread. Following read summarization, read counts were normalized using the ‘rlog’ or regularized log transformation in DESeq2 (Love, Huber, & Anders, 2014) (v1.20.0).
Differential Expression Analysis: The log2 fold change (LFC) in gene expression levels between iHox motor neuron vs. progenitor motor neurons was estimated using DESeq2. A q-value < 0.01 and LFC > 2 was used to define differentially expressed genes between progenitor motor neurons, noDox controls, iHoxc6 MNs, iHoxc8 MNs, iHoxc9 MNs, and iHoxc10 MNs.
Genome_build: mm10
Supplementary_files_format_and_content: Unnormalized Read Counts at mm10 annotated genes

source_name: ES-derived embryoid bodies+4D RA+SAG with induced transcription factors

growth_protocol: mESC lines were cultured in 2-inhibitors based medium (Advanced DMEM/F12:Neurobasal (1:1) medium (Gibco), supplemented with 2.5% ESC-grade fetal bovine serum (vol/vol, Corning), N2 (Gibco), B27 (Gibco), 2mM L-glutamine (Gibco), 0.1 mM β-mercaptoethanol (Gibco), 1000 U/mL leukemia inhibitory factor (Millipore), 3μM CHIR (BioVision) and 1 μM PD0325901 (Sigma)) on 0.1% gelatin (Millipore) coated plates at 37 °C, 8% CO2.

extract_protocol:
Cells were collected prior to TF induction (day 2 of RA/SAG differentiation) and 48h after Doxycycline (Dox) treatment. RNA was extracted by using TRIzol LS Reagent (Life Technologies) and purified using the RNAeasy mini kit (Qiagen). Agilent High Sensitivity RNA Screentape (Agilent, 5067-5579) was used to check RNA integrity.
500ng of RNA was used to prepare RNA-seq libraries and spiked-in with ERCC Exfold Spike-in mixes (Thermo Fisher, 4456739). RNA-seq libraries were prepared using TruSeq Stranded mRNA Library Preparation kit (Illumina, 20020594). Library size was verified using High Sensitivity DNA ScreenTape (Agilent, 5067-5584). The KAPA library amplification kit was used on Roche Lightcycler 480 for library quantification before pooling.

treatment_protocol: Embryoid bodies (EBs) were obtained by plating trypsinized (Gibco) mESCs in AK medium (Advanced DMEM/F12:Neurobasal (1:1) medium (Gibco), 7% KnockOut SR (vol/vol) (Gibco), 2 mM L-glutamine, 0.1 mM ß-mercaptoethanol and penicillin–streptomycin (Gibco),) at 37 °C, 5% CO2 (day -2). On day 0, EBs were split 1:2 and AK medium was replenished and supplemented with 1 μM all-trans retinoic acid and 0.5 μM smoothened agonist (SAG) (Millipore, 566660). TF induction was performed by adding 3 μg/mL of Doxycycline (Sigma, D9891) on day 2. For RNA-seq experiments, 3.5x10^5 mESCs were plated in 100mm suspension dishes (Corning).

tag: strain genotype/variation

tag: treatment

value: EB + 4 Days RA + SAG, +48hours Dox

value: Embryoid Bodies


title: Chondrosarcoma_1


title: Daqiandi-input (Replicate 2)


title: RNAseq in EB-Day4[D0+RA+SAG][D2+48hDox(iFlag.Hoxc9)] replicate 1


title: RNAseq in EB-Day4[D0+RA+SAG][D2+48hDox(iFlag.Hoxc9)] replicate 3


title: Chondromyxoid_Fibroma_14


title: Daqiandi-PmTCP4 chIP (Replicate 2)


title: RNAseq in EB-Day4[D0+RA+SAG][D2+48hDox(iFlag.Hoxc10)] replicate 2


title: RNAseq in EB-Day4[D0+RA+SAG][D2+48hDox(iFlag.Hoxc8)] replicate 3


title: RNAseq in EB-Day4[D0+RA+SAG][D2+48hDox(iFlag.Hoxc10)] replicate 3


title: RNAseq in EB-Day4[D0+RA+SAG][D2+48hDox(iFlag.Hoxc10)] replicate 1


title: 24hr MI Control1

description: processed data Sample ID in count matrix : barcode_1


title: Chondrosarcoma_4


title: Daqiandi-PmTCP4 chIP (Replicate 1)


title: Daqiandi-PmTCP4 chIP (Replicate 3)


title: Chondromyxoid_Fibroma_10


title: RNAseq in EB-Day4[D0+RA+SAG][D2+48hDox(iFlag.Hoxc6)] replicate 2


title: RNAseq in EB-Day4[D0+RA+SAG][D2+48hDox(iFlag.Hoxc8)] replicate 2


title: Chondromyxoid_Fibroma_15


title: Chondrosarcoma_2


title: RNAseq in EB-Day4[D0+RA+SAG][noDox(iFlag.Hoxc6)]_replicate3

source_name: ES-derived embryoid bodies+4D RA+SAG

value: EB + 4 Days RA + SAG, +48h NO Dox


title: RNAseq in EB-Day4[D0+RA+SAG][D2+48hDox(iFlag.Hoxc8)] replicate 1


title: sham mice #4 - CL

city: Barcelona

first: Alba

last: Simats

state: Catalunya

address: Passeig Vall d'Hebron, 119-129

country: Spain

institute: Vall d'Hebron Institute of Research

description: Gene expression data from mouse brain.

hyb_protocol: cDNA was hybridized in GeneChip Mouse Clariom S Affymetrix microarrays for 16 hours at 45 ºC with rotation.

scan_protocol: Microarrays were scanned in Affymetrix GeneChip Scanner 3000.

data_processing: The images were processed with the Affymetrix GeneChip Command Console software for CEL file generation. To check the array image quality, Affymetrix Expression Console was used. Samples that demonstrated good quality results (pm mean, bgrd mean, pos vs neg auc,...) were subjected to subsequent analysis.

source_name: mouse brain, contralateral hemisphere (CL)

label_protocol: Samples were amplified and labeled using GeneChip WT Plus Reagent Kit.

growth_protocol: Saline-perfused mouse brain samples were isolated; IP and CL hemispheres were separated and flash frozen with liquid N2 until RNA isolation.

extract_protocol: RNA was isolated from frozen brain samples with the MirVana™ Paris™ (Thermo Fisher Scientific Inc., USA) and kept at -80ºC until the array was performed.

treatment_protocol: Flash frozen at -80ºC.

tag: strain/background

value: 8-10 weeks

tag: Sex

value: Male

value: Sham surgery

value: Contralateral hemisphere (CL)


title: Chondromyxoid_Fibroma_12


title: RNAseq in EB-Day2[D0+RA+SAG][iCre]_replicate2

source_name: ES-derived embryoid bodies+2D RA+SAG

value: EB + 2 Days RA + SAG


title: Chondromyxoid_Fibroma_13


title: Daqiandi-input (Replicate 1)


title: Chondromyxoid_Fibroma_11


title: sham mice #4 - IP

description: Gene expression data from mouse brain.

source_name: mouse brain, ipsilateral hemisphere (IP)

tag: age

value: Ipsilateral hemisphere (IP)


title: RNAseq in EB-Day4[D0+RA+SAG][D2+48hDox(iFlag.Hoxc6)] replicate 3


title: Chondromyxoid_Fibroma_4


title: RNAseq in EB-Day4[D0+RA+SAG][noDox(iFlag.Hoxc6)]_replicate2


title: RNAseq in EB-Day4[D0+RA+SAG][noDox(iFlag.Hoxc6)]_replicate1


title: Chondromyxoid_Fibroma_9


title: RNAseq in EB-Day2[D0+RA+SAG][iCre]_replicate1


title: Chondromyxoid_Fibroma_8


title: ChIPseq Hoxc9 in EB+12hDox(iFlag.Hoxc9) replicate 2

description:
H7KNHBGX3_n01_mb36
ES-derived embryoid bodies with induced transcription factors

data_processing:
Basecall conversion to fastq files was performed using Picard (v 2.8.2)
Alignment: ChIP-seq reads were aligned to the mm10 genome using Bowtie (v1.0.1) (Langmead, Trapnell, Pop, & Salzberg, 2009), using options “-q --best --strata -m 1 --chunkmbs 1024”.
Binding Event Detection: Genome-wide TF binding events were called in each condition using MultiGPS (v0.74) (Mahony et al., 2014). EdgeR (v3.22.5) was used within the MultiGPS framework to test whether genomic sites were differentially bound by TFs (Robinson, McCarthy, & Smyth, 2010). A genomic site was defined as shared by TFs if significant binding events were called in both TF ChIP-seq experiments (q-value < 0.001), and the TFs did not display differential read enrichment at that site as estimated by EdgeR (q-value > 0.01). A binding event was defined as “TF1>TF2” if a MultiGPS peak was called in TF1 ChIP-seq (q-value < 0.001), TF1 exhibited a greater log fold-change with respect to the input ChIP-seq than TF2, and TF1 and TF2 were significantly differentially bound as defined by EdgeR (q-value < 0.01). A similar strategy was applied to perform multi-way ChIP-seq comparisons.
Genome_build: mm10
Supplementary_files_format_and_content: MultiGPS: MultiGPS output files
Supplementary_files_format_and_content: BED: Conversion of MultiGPS output files to BED format, centered on the MultiGPS binding event location

source_name: ChIPseq Hoxc9 in EB+12hDox(iFlag.Hoxc9)

extract_protocol:
Cells were collected 24h and 48h after Doxycycline (Dox) treatment. Crosslinking was performed at room temperature in 1mM DSG (ProteoChem) for 15min, followed by the addition of 1% FA (vol/vol) for an additional 15min. After quenching with Glycine, cells were divided into ~25-30x106 aliquots, pelleted by centrifugation and frozen at -80°C. After thawing cells on ice, lysis was performed in 5mL of 50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA pH 8.0, 10% glycerol (vol/vol), 0.5% Igepal (vol/vol), 0.25% Triton X-100 (vol/vol) with 1× protease inhibitors (Roche, 11697498001) for 10 min at 4 °C. Cells were centrifuged for 5min, resuspended in 5mL of 10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA pH 8.0, 0.5 mM EGTA pH 8.0 with 1× protease inhibitors, and incubated for 10 min at 4 °C on a rotating platform. Cells were centrifuged for 5min and resuspended in 2mL of Sonication Buffer (50 mM Hepes pH 7.5, 140 mM NaCl, 1 mM EDTA pH 8.0, 1 mM EGTA pH 8.0, 1% Triton X-100 (vol/vol), 0.1% sodium deoxycholate (wt/vol), 0.1% SDS (vol/vol) with 1× protease inhibitors). Sonication was performed by splitting each sample to 2 Bioruptor tubes with sonication beads and using the Bioruptor Pico (Diagenode) for 18 cycles of 30 sec on and 30 sec off into an average size of approximately 200 bp. Immunoprecipitation was performed for 16h at 4 °C on a rotating platform by incubating with Dynabeads protein-G (Thermo Fisher Scientific) conjugated with 5 µg of one of the following antibodies: mouse monoclonal antibody to Flag (Sigma, F1804) or rabbit polyclonal antibody to HA (Abcam, ab9110).
lllumina DNA sequencing libraries were prepared with one third of the ChIP sample or a 1:100 dilution of the input sample in water. Library preparation was performed by end repair, A-tailing and ligating Illumina-compatible Bioo Scientific multiplexed adapters. Unligated adapters were removed using Agencourt AmpureXP beads (Beckman Coulter). Amplification was performed by PCR with Phusion polymerase (New England Biolabs) and TruSeq primers (Sigma). Libraries were gel purified (Qiagen) between 250 and 550bp in size. Final quantification of the library was performed using the KAPA library amplification kit on the Roche Lightcycler 480 before pooling.

treatment_protocol: Embryoid bodies (EBs) were obtained by plating trypsinized (Gibco) mESCs in AK medium (Advanced DMEM/F12:Neurobasal (1:1) medium (Gibco), 7% KnockOut SR (vol/vol) (Gibco), 2 mM L-glutamine, 0.1 mM ß-mercaptoethanol and penicillin–streptomycin (Gibco),) at 37 °C, 5% CO2 (day -2). On day 0, EBs were split 1:2 and AK medium was replenished and supplemented with 1 μM all-trans retinoic acid and 0.5 μM smoothened agonist (SAG) (Millipore, 566660). TF induction was performed by adding 3 μg/mL of Doxycycline (Sigma, D9891) on day 2. For ChIP-seq experiments, 3-3.5x10^6 mESCs were plated in 245mm x 245mm square dishes (Corning).

value: EB + 12hours Dox

tag: chip target

value: Sigma, F1804


title: RNAseq in EB-Day2[D0+RA+SAG][iCre]_replicate3


title: ChIPseq Hoxc9 in EB+12hDox(iFlag.Hoxc9) replicate 1

description:
H7KNHBGX3_n01_mb35
ES-derived embryoid bodies with induced transcription factors

tag: chip antibody

value: Sigma. F1804


title: Chondromyxoid_Fibroma_2


title: Chondromyxoid_Fibroma_7


title: ChIPseq Hoxc6 in EB+12hDox(iFlag.Hoxc6) replicate 1

description:
H7KNHBGX3_n01_mb33
ES-derived embryoid bodies with induced transcription factors

source_name: ChIPseq Hoxc6 in EB+12hDox(iFlag.Hoxc6)


title: Chordoma_1

value: Chordoma


title: sham mice #2 - CL

description: Gene expression data from mouse brain.

tag: tissue


title: ChIPseq Hoxc10 in EB-Day4[D0+RA+SAG][D2+48hDox(iFlag.Hoxc10)] replicate 4

description:
HWLMWBGX5_n01_mb119
ES-derived embryoid bodies+4D RA+SAG with induced transcription factors

value: EB + 4 Days RA + SAG, D2+48hours Dox


title: sham mice #3 - CL

description: Gene expression data from mouse brain.


title: ChIPseq Hoxc10 in EB-Day4[D0+RA+SAG][D2+48hDox(iFlag.Hoxc10)] replicate 3

description:
HWLMWBGX5_n01_mb118
ES-derived embryoid bodies+4D RA+SAG with induced transcription factors


title: Chondromyxoid_Fibroma_1


title: ChIPseq Hoxc10 in EB-Day4[D0+RA+SAG][D2+48hDox(iFlag.Hoxc10)] replicate 2

description:
H5CL7BGX5_n01_mb68
ES-derived embryoid bodies+4D RA+SAG with induced transcription factors


title: Chondromyxoid_Fibroma_3


title: RNAseq in EB-Day4[D0+RA+SAG][D2+48hDox(iFlag.Hoxc6)] replicate 1


title: ChIPseq Hoxc10 in EB-Day4[D0+RA+SAG][D2+48hDox(iFlag.Hoxc10)] replicate 1

description:
H5CL7BGX5_n01_mb62
ES-derived embryoid bodies+4D RA+SAG with induced transcription factors


title: sham mice #3 - IP

description: Gene expression data from mouse brain.


title: Chondromyxoid_Fibroma_5


title: Chondroblastoma_17

value: Chondroblastoma


title: ChIPseq Hoxc9 in EB-Day4[D0+RA+SAG][D2+48hDox(iFlag.Hoxc9)] replicate 2

description:
H5CL7BGX5_n01_mb67
ES-derived embryoid bodies+4D RA+SAG with induced transcription factors


title: sham mice #2 - IP

description: Gene expression data from mouse brain.


title: Chondromyxoid_Fibroma_6


title: ChIPseq Hoxc9 in EB-Day4[D0+RA+SAG][D2+48hDox(iFlag.Hoxc9)] replicate 1

description:
H5CL7BGX5_n01_mb66
ES-derived embryoid bodies+4D RA+SAG with induced transcription factors


title: sham mice #1 - CL

description: Gene expression data from mouse brain.


title: sham mice #1 - IP

description: Gene expression data from mouse brain.


title: Chondroblastoma_14


title: ChIPseq input in EB-Day4[D0+RA+SAG][D2+48hDox(iFlag.Hoxc8)] replicate 1

description:
H2GJMBGX2_n01_mb15
ES-derived embryoid bodies+4D RA+SAG with induced transcription factors

value: input


title: ChIPseq Hoxd9 in EB-Day3[D0+RA+SAG][D2+24hDox(iHoxd9.HA)] replicate 2

description:
HFJFLBGXC_n01_mb263
ES-derived embryoid bodies+3D RA+SAG with induced transcription factors

value: EB + 3 Days RA + SAG, D2+24hours Dox

value: Abcam, ab9110


title: ChIPseq Hoxc6 in EB-Day4[D0+RA+SAG][D2+48hDox(iFlag.Hoxc6)] replicate 1

description:
HKW5JBGX3_n01_mb64
ES-derived embryoid bodies+4D RA+SAG with induced transcription factors

value: Embryoid Bodies


title: ischemic mice #7 - CL

description: Gene expression data from mouse brain.

source_name: mouse brain, healthy hemisphere (CL)

value: Middle cerebral artery occlusion

value: Healthy hemisphere (CL)


title: ChIPseq antiFlag in EB-Day3[D0+RA+SAG][D2+24hDox(iHoxc10.V5)] replicate 1

description:
45382555-5_s_3_sequence
ES-derived embryoid bodies+3D RA+SAG with induced transcription factors

value: Flag


title: ChIPseq Hoxc6 in EB-Day4[D0+RA+SAG][D2+48hDox(iFlag.Hoxc6)] replicate 2

description:
H5CL7BGX5_n01_mb61
ES-derived embryoid bodies+4D RA+SAG with induced transcription factors


title: ChIPseq Hoxc13 in EB-Day3[D0+RA+SAG][D2+24hDox(iHoxc13.HA)] replicate 2

description:
HFJFLBGXC_n01_mb264
ES-derived embryoid bodies+3D RA+SAG with induced transcription factors


title: ischemic mice #8 - CL

description: Gene expression data from mouse brain.

value: 8-10 weeks

value: Male


title: ischemic mice #8 - IP

description: Gene expression data from mouse brain.

source_name: mouse brain, ischemic hemisphere (IP)

value: Ischemic hemisphere (IP)


title: ChIPseq Hoxc13 in EB-Day3[D0+RA+SAG][D2+24hDox(iFlag.Hoxc13)] replicate 1

description:
HFJFLBGXC_n01_mb261
ES-derived embryoid bodies+3D RA+SAG with induced transcription factors


title: ChIPseq Hoxc6 in EB+12hDox(iFlag.Hoxc6) replicate 2

description:
H7KNHBGX3_n01_mb34
ES-derived embryoid bodies with induced transcription factors


title: ChIPseq Hoxd9 in EB-Day3[D0+RA+SAG][D2+24hDox(iFlag.Hoxd9)] replicate 1

description:
HFJFLBGXC_n01_mb260
ES-derived embryoid bodies+3D RA+SAG with induced transcription factors


title: ChIPseq Hoxa9 in EB-Day3[D0+RA+SAG][D2+24hDox(iFlag.Hoxa9)] replicate 1

description:
HFJFLBGXC_n01_mb259
ES-derived embryoid bodies+3D RA+SAG with induced transcription factors


title: ischemic mice #7 - IP

description: Gene expression data from mouse brain.


title: Chondroblastoma_15


title: Chondroblastoma_12


title: ischemic mice #5 - CL

description: Gene expression data from mouse brain.


title: ChIPseq Hoxc9 in EB-Day3[D0+RA+SAG][D2+24hDox(iFlag.Hoxc9)] replicate 2

description:
PPG_Day5_iHoxc9-FLAG_1-101201
ES-derived embryoid bodies+3D RA+SAG with induced transcription factors


title: Chondroblastoma_10


title: ischemic mice #5 - IP

description: Gene expression data from mouse brain.


title: ChIPseq Hoxa9 in EB-Day3[D0+RA+SAG][D2+24hDox(iHoxa9.HA)] replicate 2

description:
HFJFLBGXC_n01_mb262
ES-derived embryoid bodies+3D RA+SAG with induced transcription factors


title: ischemic mice #6 - CL

description: Gene expression data from mouse brain.


title: Chondroblastoma_9


title: ChIPseq Hoxc10 in EB-Day3[D0+RA+SAG][D2+24hDox(iFlag.Hoxc10)] replicate 2

description:
PPG_Day5_iHoxc10_2-101201.fq.gz
ES-derived embryoid bodies+3D RA+SAG with induced transcription factors


title: ChIPseq Hoxc10 in EB-Day3[D0+RA+SAG][D2+24hDox(iHoxc10.V5)] replicate 1

description:
PPG_Day5_iHoxc10_1.fq.gz
ES-derived embryoid bodies+3D RA+SAG with induced transcription factors

value: Abcam, ab15828


title: Chondroblastoma_16


title: ischemic mice #6 - IP

description: Gene expression data from mouse brain.


title: ChIPseq Hoxc8 in EB-Day3[D0+RA+SAG][D2+24hDox(iFlag.Hoxc8)] replicate 2

description:
HWLMWBGX5_n01_mb110
ES-derived embryoid bodies+3D RA+SAG with induced transcription factors


title: ischemic mice #4 - CL

description: Gene expression data from mouse brain.


title: Chondroblastoma_8


title: ischemic mice #3 - CL

description: Gene expression data from mouse brain.


title: Chondroblastoma_11


title: Chondroblastoma_5


title: Chondroblastoma_2


title: Chondroblastoma_3


title: ChIPseq Hoxc6 in EB-Day3[D0+RA+SAG][D2+24hDox(iFlag.Hoxc6)] replicate 2

description:
HKW5JBGX3_n01_mb63
ES-derived embryoid bodies+3D RA+SAG with induced transcription factors


title: Chondroblastoma_7


title: Chondroblastoma_4


title: Chondroblastoma_6


title: Chondroblastoma_13


title: ischemic mice #2 - IP

description: Gene expression data from mouse brain.


title: ChIPseq Hoxc9 in EB-Day3[D0+RA+SAG][D2+24hDox(iFlag.Hoxc9)] replicate 1

description:
HWFTLBGX2_n01_mb41
ES-derived embryoid bodies+3D RA+SAG with induced transcription factors


title: ischemic mice #3 - IP

description: Gene expression data from mouse brain.


title: ischemic mice #4 - IP

description: Gene expression data from mouse brain.


title: ChIPseq Hoxc6 in EB-Day3[D0+RA+SAG][D2+24hDox(iFlag.Hoxc6)] replicate 1

description:
H5CL7BGX5_n01_mb65
ES-derived embryoid bodies+3D RA+SAG with induced transcription factors


title: Mesenchyme cells (-Ve CTRL)

city: Kansas City

first: Sumedha

last: Gunewardena

state: Kansas

address: 2146 West 39th Avenue

department: Dept. of Molecular and Integrative Physiology

institute: University of kansas medical center

description: from whole cell lysate

data_processing:
base calling was performed using Illumina’s Real Time Analysis (RTA) software
Sequence reads were mapped to the mouse reference genome (GRCh38/hg38) using STAR (STAR_2.4.0e) with default parameters
Transcript abundance estimates were generated using Cufflinks (cufflinks-2.2.1)
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: tab-delimited text files of FPKM values for each Sample

source_name: Primary Cells

growth_protocol: Proliferating vCTBs and mesenchymal cells were isolated through enzymetic digestion, percoll gradient separation followed by culture in the specilized medium that promotes growth of CTB cells, as described earlier. Mesenchyme cells were cultured in vitro in a RPMI based medium with 10% FBS under standard ambient cell culture condition.

extract_protocol:
Total RNA from the whole cell-extract was isolated using RNeasy Mini Kit (#74104) from Qiagen per the manufacturer’s protocol.  RNA concentrations were quantified using a NanoDrop Spectrophotometer at a  wavelength of 260nm. Integrity of the total RNA samples was evaluated using an Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Santa Clara, CA) and the samples with RNA integrity values above 7.0 were used for the sequencing experiments.
Total RNA was used to construct RNA-seq libraries using the Illumina TruSeq RNA Sample Preparation Kit v3 according to manufacturer's instructions

value: mesenchymal cells


title: hCTBP0

description: from whole cell lysate

value: Proliferating vCTBs


title: ChIPseq Hoxc10 in EB-Day3[D0+RA+SAG][D2+24hDox(iFlag.Hoxc10)] replicate 3

description:
HWFTLBGX2_n01_mb45
ES-derived embryoid bodies+3D RA+SAG with induced transcription factors

value: Sigma, F1804


title: VM2: exvivoblood-vestibulermigraine-female-31y

status: Public on Sep 05 2020

city: haerbin

first: lin

last: jinghan

address: 23 Postoffice Street, Nangang District

department: neurology

institute: The First Affiliated Hospital of Harbin Medical University

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide.

scan_protocol: The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.

data_processing:
Quantile normalization of raw data and subsequent data processing were performed using the R software limma package. After quantile normalization of the raw data, low intensity filtering was performed, and the circRNAs that at least 4 out of 10 samples have flags in “P” or “M” (“All Targets Value”) were retained for further analyses.
When comparing two groups of profile differences (such as disease versus control), the “fold change” (i.e. the ratio of the group averages) between the groups for each circRNA is computed. The statistical significance of the difference may be conveniently estimated by t-test. circRNAs having fold changes 1.5 and p-values  0.05 are selected as the significantly differentially expressed. One can filter the analysis outputs and rank the differentially expressed circRNAs according to fold change, p-value etc, using Microsoft Excel’s Data/Sort & Filter functionalities.

source_name: peripheral blood of vestibuler migraine patient

label_protocol: The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Then, the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar).

treatment_protocol: Sample labeling and array hybridization were performed according to the manufacturer’s protocol (Arraystar Inc.). Briefly, total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs.

value: peripheral blood

tag: gender

value: female


title: ischemic mice #1 - CL

description: Gene expression data from mouse brain.


title: Rat 24 Adipose microRNA seq

city: Ames

first: Joe

last: Webb

state: IA

address: 2302 Osborn drive, 220 Mackay Hall

institute: Iowa State University

description:
microRNA seq
S4.xlsx
S3.xlsx

data_processing:
Basecalls performed by the ISU DNA facility and data processing steps were followed according to the manufacturers guidelines here: https://www.lexogen.com/wp-content/uploads/2015/11/015UG009V0211_QuantSeq-Illumina.pdf
Briefly, fastq quality control tool FastQC was used to examine the quality of the sequencing run.
Next, adapters were trimmed using BBDUK and sequences were reanalyzed using FastQC
Reads were mapped to the RNO_6 genome using RNA STAR and read counts were simultaneously quantified using the --read-counts flag
Genome_build: RNO_6
Supplementary_files_format_and_content: mRNA DESEQ results.xlsx
Supplementary_files_format_and_content: mRNA Raw Reads.xlsx
Supplementary_files_format_and_content: microRNA DESEQ results.xlsx
Supplementary_files_format_and_content: microRNA Raw Reads.xlsx

organism: Rattus norvegicus

source_name: Adipose

extract_protocol:
Tissue samples were homogenized on ice and total RNA was extracted using a Lexogen SPLIT RNA Extraction kit following the manufacturers instructions.
Libraries were prepared according to Lexogens instructions accompanying the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina and small RNA sequencing kits. Briefly, the Quantseq kit uses total RNA as input, hence no prior poly(A) enrichment  or rRNA depletion is needed. Library generation starts with oligodT priming containing the  Illumina-specific Read 2 linker sequence.  After first strand synthesis the RNA is removed. Second strand synthesis is initiated by random priming and a DNA  polymerase. The random primer contains the Illumina-specific Read 1  linker sequence. At this step Unique Molecular Identifiers (UMIs)  can be introduced by exchanging the Second Strand Synthesis Mix 1  (SS1) from the standard QuantSeq FWD Kit with UMI Second Strand  Synthesis Mix (USS). No purification is required between first and second strand synthesis.  Second strand synthesis is followed by a magnetic bead-based  purification step rendering the protocol compatible with automation. During the library amplification step sequences required  for cluster generation are introduced. NGS reads are generated towards the poly(A) tail and directly  correspond to the mRNA sequence. To pinpoint the exact 3’ end,  Libraries were sequenced on the Illumina HiSeq 3000 following the manufacturer's protocols.
RNA-seq, miRNA-seq

treatment_protocol: Animals were fed their respective diets, either Whole Egg or Casein.

tag: animal number

value: Casein

value: Lean


title: ischemic mice #1 - IP

description: Gene expression data from mouse brain.


title: Rat 24 Liver microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx

source_name: Liver


title: Rat 24 Kidney microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx

source_name: Kidney


title: VM3: exvivoblood-vestibulermigraine-female-39y


title: VM1: exvivoblood-vestibulermigraine-female-40y


title: Aneurysmal_Bone_Cyst_9

source_name: Fresh frozen tumour


title: Aneurysmal_Bone_Cyst_8


title: Rat 24 Adipose Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Aneurysmal_Bone_Cyst_7


title: C2: exvivoblood-control-female-23y

source_name: peripheral blood of healthy control


title: M1: exvivoblood-migraine-female-30y

source_name: peripheral blood of migraine patient


title: M4: exvivoblood-migraine-female-35y


title: M3: exvivoblood-migraine-male-35y

value: male


title: Rat 24 Brain microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx

source_name: Brain


title: ChIPseq Hoxc8 in EB-Day3[D0+RA+SAG][D2+24hDox(iFlag.Hoxc8)] replicate 1

description:
HWFTLBGX2_n01_mb43
ES-derived embryoid bodies+3D RA+SAG with induced transcription factors

value: EB + 3 Days RA + SAG, D2+24hours Dox


title: Rat 24 Liver Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Rat 24 Kidney Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: C3: exvivoblood-control-male-30y


title: C1: exvivoblood-control-female-47y


title: Rat 22 Kidney microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx

value: Whole Egg


title: Rat 23 Brain Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Rat 23 Adipose microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Rat 22 Adipose microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Rat 23 Kidney microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Rat 23 Brain microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Rat 23 Liver microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Rat 23 Liver Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Rat 24 Brain Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: M2: exvivoblood-migraine-female-24y


title: Rat 22 Brain microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Rat 22 Adipose Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Rat 22 Liver Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Rat 22 Kidney Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Rat 22 Brain Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Rat 23 Adipose Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Rat 21 Brain microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Rat 21 Adipose Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Rat 21 Kidney Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Chondroblastoma_1

value: Chondroblastoma


title: Rat 21 Adipose microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Rat 22 Liver microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Rat 21 Liver microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Rat 23 Kidney Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Rat 21 Brain Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Rat 20 Kidney microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Rat 20 Adipose microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Rat 21 Kidney microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Rat 20 Liver microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Rat 20 Brain microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Aneurysmal_Bone_Cyst_4


title: Rat 20 Adipose Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Rat 20 Brain Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Rat 20 Kidney Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Aneurysmal_Bone_Cyst_5


title: Rat 19 Adipose microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Rat 19 Kidney microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Rat 19 Liver microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Rat 20 Liver Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Aneurysmal_Bone_Cyst_2


title: Rat 19 Adipose Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Rat 19 Liver Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Rat 18 Liver microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Rat 18 Brain microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Rat 19 Brain Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Rat 18 Adipose microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Aneurysmal_Bone_Cyst_3


title: Rat 17 Adipose microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Rat 17 Kidney microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Rat 18 Brain Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Rat 17 Liver microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Rat 18 Kidney Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Rat 19 Brain microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Rat 17 Brain microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Aneurysmal_Bone_Cyst_1


title: Rat 17 Kidney Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Rat 18 Adipose Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Rat 17 Liver Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Rat 16 Adipose microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Rat 17 Adipose Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Rat 18 Kidney microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Rat 17 Brain Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Rat 16 Liver microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Rat 16 Brain microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Aneurysmal_Bone_Cyst_6


title: Rat 16 Adipose Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Rat 16 Kidney Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Rat 16 Liver Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Rat 16 Brain Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Rat 15 Kidney microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Rat 15 Adipose microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Rat 15 Brain microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Rat 15 Adipose Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Rat 15 Kidney Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Rat 15 Brain Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Rat 15 Liver Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Rat 14 Adipose microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Rat 15 Liver microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Rat 14 Adipose Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Rat 16 Kidney microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Rat 14 Liver Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Rat 14 Kidney microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: ischemic mice #2 - CL

description: Gene expression data from mouse brain.

value: Middle cerebral artery occlusion

value: Healthy hemisphere (CL)


title: Rat 14 Brain Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Rat 14 Liver microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Rat 14 Kidney Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Rat 13 Kidney microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Rat 14 Brain microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Rat 13 Liver microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Rat 13 Adipose microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Rat 13 Brain microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Rat 13 Kidney Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Rat 13 Adipose Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Rat 12 Adipose microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx

value: ZDF


title: Rat 12 Kidney microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Rat 12 Liver microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Rat 11 Adipose microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Rat 12 Adipose Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Rat 12 Kidney Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Rat 11 Kidney microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Rat 12 Brain Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Rat 19 Kidney Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Rat 11 Kidney Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Rat 11 Adipose Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Rat 11 Brain Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Rat 10 Adipose microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Rat 10 Kidney microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Rat 12 Liver Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Rat 10 Liver microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Rat 10 Adipose Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Rat 11 Liver Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Rat 11 Liver microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Rat 11 Brain microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Rat 10 Kidney Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Rat 10 Liver Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Rat 10 Brain Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Rat 13 Brain Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Rat 13 Liver Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Rat 9 Adipose microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Rat 12 Brain microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Rat 9 Liver microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Rat 9 Kidney microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Rat 9 Kidney Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Rat 10 Brain microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Rat 9 Adipose Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Rat 9 Brain microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Rat 9 Brain Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Rat 8 Adipose microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Rat 9 Liver Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Rat 8 Kidney microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Rat 8 Kidney Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Rat 8 Adipose Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Rat 8 Liver microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Rat 8 Brain microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Rat 8 Liver Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Rat 8 Brain Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx


title: Rat 7 Adipose microRNA seq

description:
microRNA seq
S4.xlsx
S3.xlsx


title: Rat 7 Kidney Quantseq

description:
Quantseq
S2.xlsx
S1.xlsx