title: EU Seq of ESC. Experiment ID7, 120min 0.5uM JQ1 tx, replicate1.

description: Nascent RNA

data_processing:
Library strategy: EU-Seq
Trimming of adaptors and low-quality sequences (-q 20) was performed using Cutadapt. Read sequences were aligned to mm10 (mouse), using bwa aln with default parameters (BWA version 0.7.10) (Li and Durbin, 2010). Low mapping quality (MAPQ < 10) reads, and reads with more than 3 mismatches were removed using samtools (version 1.4) (Li et al., 2009). Reads mapped to rRNA and tRNA region are removed as described in the RNA-seq section. The number of reads mapped to gene body was counted using HTseq (Anders et al., 2015), and log2 fold-change (FC) and p-values were calculated using DEseq2 (Love et al., 2014). The HTseq default scaling method (median of relative abundance) was used as a scaling factor for the analysis for the mouse cell line data.
Genome_build: mm10
Supplementary_files_format_and_content: Normalized gene track files (bigwig).

growth_protocol: Unless indicated otherwise, E14Tg2A Rosa26-Cre Oct4-IRES-Puro mouse ESCs were used for all experiments (Ying et al., 2002). ESCs were cultured in the standard N2B27 medium consisting of 1:1 mix of DMEM/F12 and Neurobasal medium (Thermo Fisher Scientific), or in a SILAC compatible N2B27 medium lacking L-lysine and L-arginine (custom-made, C.C.Pro GmbH, Oberdorla), supplemented with 1000 units/ml leukemia inhibitory factor (LIF) (Merck Millipore), 1μM PD0325901, 3μM CT-99021 (custom-made by ABCR GmbH, Karlsruhe), 100μM 2-mercaptoethanol, 150μM sodium pyruvate, 0.5x B27 supplement (Thermo Fisher Scientific), 0.5x N2 supplement (made in house or from Thermo Fisher Scientific), and where relevant with L-lysine and L-arginine. Unless indicated otherwise, the cells were treated with the following inhibitor concentrations: A-485 10μM, dTAG13 0.1 μM, JQ1 0.5μM, and TSA 2 μM.

extract_protocol:
Following 5-EU labelling, cells were quickly washed (1x) with PBS, and immediately lysed in RLT buffer and RNA was prepared using RNeasy Mini Kit (Qiagen).
The labelled RNA was subsequently enriched using the Click-iT® Nascent RNA Capture Kit (Thermo Fisher Scientific) according to the manufacturer’s instructions. Where indicated, rRNA was depleted using NEBNext® rRNA Depletion Kit (NEB) before the enrichment of labelled RNA. RNA-seq libraries were prepared using the NEBNext Ultra kit (NEB) as per manufacturer’s instructions and subsequently sequenced using a Next-Seq 500 Sequencer (Illumina).

treatment_protocol: Cells were treated with DMSO or with the indicated inhibitors for the specified time points. Unless indicated otherwise, cells were treated with 10μM A-495, 2μM TSA, and 0.5μM JQ1. The inhibitors were added prior to or simultaneous to adding 5-ethynyl uridine (5-EU), as specified. Cells were pulse-labelled with 0.5 mM 5-EU for 20 min before sample collection.

value: ES cells

value: wild type

value: 120min 0.5uM JQ1


title: EU Seq of ESC. Experiment ID4, 120min 0.5uM JQ1 tx, replicate2.

status: Public on Mar 24 2021

type: SRA

city: Copenhagen N

first: Chunarum

last: Choudhary

state: --- Select a state ---

address: Blegdamsvej 3B

department: Novo Nordisk Foundation Center for Protein Research

country: Denmark

institute: University of Copenhagen

description: Nascent RNA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

source_name: mouse ES cells

tag: cell type

tag: cell line

tag: genotype/variation

tag: treatment


title: MZ-TR-Rep1

city: Davis

first: Siobhan

last: Brady

state: CA

address: 451 Health Sciences Dr

department: Genome Center and Plant Biology

country: USA

institute: University of California Davis

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
M
processed data file: Tomato_Field_raw_counts.csv
protocols used: growth protocol 3, extract protocol 1 and library construction protocol 1

data_processing:
Library strategy: TRAP-seq
Sequences were pooled, and then trimmed and filtered using Trim Galore! (v0.4.5) with parameter -a GATCGGAAGAGCACA. Trimmed reads were pseudo-aligned to ITAG3.2 transcriptome (cDNA) using Kallisto (v0.43.1), with the parameters -b 100 --single -l 200 -s 30, to obtain count estimates and transcript per million (TPM) values.
ATAC-seq raw reads were aligned to each species' corresponding genome using Bowtie2 with default parameters.
ATAC-seq mapped reads were filtered to remove 1) reads that mapped to organelle genomes and 2) reads with a mapping quality score of q<2.
Transposase Hypersensitive Sites were identified using the Findpeaks function of the HOMER package, with the parameters "-minDist 150" "-region" and "-regionRes 1".
Filtered ATAC-seq bam files for each sample were converted to the bigwig format using a bin size resolution of 1 base pair and the "--normalizeUsingRPKM" option.
For accurate visualization, all filtered ATAC-seq bam files for a given tissue were scaled to the same number of reads and combined per condition to create a single merged bam file for a condition in a tissue type. The merged bam file was converted to a bigwig file using a bin size resolution of 1 base pair and the "--normalizeUsingRPKM" option.
Filtered ATAC-seq bam files from genomic DNA samples were scaled to the total number of reads present in the merged bam files for a given tissue type. The scaled bam file was converted to a bigwig file using a bin size resolution of 1 base pair and the "--normalizeUsingRPKM" option.
Rice TRAP-seq. Barcoded libraries were pooled together and sequenced on Illumina HiSeq 3000 at the UC Davis DNA Technologies Core to obtain 50-bp reads.
Rice TRAP-seq. R/Bioconductor (version 3.2.1) and FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) were used in short read quality control and grep for filtering of oligo dT for PolyA RNA libraries.
Rice TRAP-seq. Sequences were pooled, and then trimmed and filtered using Trim Galore! (v0.4.5) with parameter -a GATCGGAAGAGCACA. Trimmed reads were pseudo-aligned to IRGSP-1.0 transcriptome (CDS, https://rapdb.dna.affrc.go.jp/index.html) using Kallisto (v0.43.1), with the parameters -b 100 --single -l 200 -s 30, to obtain count estimates and transcript per million (TPM) values. Splice variants were summed to assess transcript values.
Genome_build: Tomato: SOLANUM LYCOPERSICUM: ITAG3.20 (ftp://ftp.solgenomics.net/tomato_genome/assembly/build_3.00/)
Genome_build: Rice: IRGSP-1.0 (https://rapdb.dna.affrc.go.jp/download/irgsp1.html)
Supplementary_files_format_and_content: .bed files contain Transposase Hypersensitive Site (THS) coordinates for individual samples or for each tissue type they are organized as (All) all the replicated THSs identified in that sample set in either control or submergence samples, (Up) THSs upregulated in submergence samples, and (Down) THSs downregulated in submergence samples.
Supplementary_files_format_and_content: .bw files contain aligned reads for individual samples, or combined samples for a specific condition of a given tissue, at a resolution of 1 bp bin sized windows.
Supplementary_files_format_and_content: .csv files contain raw counts.

organism: Solanum lycopersicum

source_name: Whole root system of 2-month-old tomato plants.

growth_protocol:
growth protocol 1: Transgenic Solanum lycopersicum seeds from transgenic lines were surface sterilized in 50% (v/v) bleach solution for 20 min (S. lycopersicum) and then rinsed three times with sterile distilled water. Seven seeds were plated on 10 cm x 10 cm plates containing full-strength Murashige and Skoog standard medium (MS) agar (1% w/v) and 1% w/v sucrose and germination was scored daily after plating. Seedlings were grown for 3-5 days after germination in a growth chamber (16 h day / 8 h night;  at 22°C/22°C day/night; 60-65 ?Em-2s-1) and 1cm primary root tips were harvested and flash frozen into liquid nitrogen.
growth protocol 2: 1-month-old control plants: Transgenic Solanum lycopersicum seeds were germinated on 1xMS media with 1% sucrose and 200ug/ml Kanamycin. After 7d, seedlings were transplanted into pots with Turface Athletic Profile Field & Fairway clay substrate (Turface Athletics, 2017) that was pre-wetted with a nutrient water solution containing 4% nitrogen, 18% phosphoric acid, and 38% soluble potash. Plants were grown in a randomized design for 31 d in a Conviron Growth Chamber at 22°C, 70% RH, 16/8 h light/dark cycle, light intensity of 150-200 µmol/m2/s.
growth protocol 3: Field: Transgenic Solanum lycopersicum seeds were germinated on 1xMS plate (0-7d), screened for correct GFP pattern from root tip, transplanted on soil and grown in a growth chamber for one week (7-14d) ,  grown in a screenhouse for two weeks (14-28d), and finally transplanted into the field and grown for one month (29-60d)  with drip watering and weekly removal of flower buds.
growth protocol 4: Rice seeds from transgenic lines were dehulled and surface sterilized in 50% (v/v) bleach solution for 30 min and then rinsed with sterile distilled water. Seedlings were grown on plates (10 cm x 10 cm) containing half-strength Murashige and Skoog standard medium (MS) agar (1% w/v) and 1% w/v sucrose, during 7 days in a growth chamber (16 h day / 8 h night;  at 28°C/25°C day/night; 110 ?Em-2s-1). The whole root system was placed immediately into liquid nitrogen upon harvesting.

extract_protocol:
extract protocol 1: Translating Ribosome Affinity Purification (TRAP) was performed as previously described (Reynoso et al, 2019).
extract protocol 2: Nuclei were purified from frozen and pulverized tissue as previously described (Reynoso et al, 2019). Tissue was resuspended in an ice-cold mortar containing 10 mL of freshly prepared nuclei purification buffer (NPB: 20 mM MOPS, 40 mM NaCl, 90 mM KCl, 2 mM EDTA, 0.5 mM EGTA, 0.5 mM spermidine, 0.2 mM spermine, pH, 7.0) containing 200 uL Protease Inhibitor Cocktail (0.4X, Sigma, P9599) per 50 mL of buffer. The homogenized extracts were filtered through a 30 µM nylon mesh to remove cell debris and centrifuged at 1000 x g for 15 min at 4° C to pellet nuclei. Nuclei were resuspended in 1 mL of NPB and 25 µL of  streptavidin-coated beads (NEB) were added to the nuclei. This mixture was slowly rotated in a cold room at 4° C for 30 min. The nuclei/beads suspension was diluted to 14 mL with NPB supplemented with 0.1% (v/v) Triton X-100 (NPB-T), in a 15 mL Falcon tube, mixed thoroughly and placed in a 15 ml magnet  to capture bead-bound nuclei for 1 min at 4° C. The supernatant was carefully removed using a plastic Pasteur pipette, taking care to remove bubbles to avoid disturbing the beads. Beads were resuspended in 14 ml of cold NPB-T, placed on a rotating mixer for 30 sec, and then placed back in the 15 ml magnet to capture the beads-nuclei at 4° C for 1 min. This wash step was repeated and bead-bound nuclei were resuspended in 1 mL of NPB-T and transferred to a new tube
extract protocol 3: For Rice: TRAP was performed as previously described (Reynoso et al, 2019)
library construction protocol 1: RNA-seq libraries  were prepared from poly(A)+ selected total and TRAP mRNA as described by Townsley et al. (2014) for random primer primed libraries.
library construction protocol 2: RNA-seq libraries  were prepared from poly(A)+ selected total and TRAP mRNA as described by Townsley et al. (2014) for random primer primed libraries.

tag: cultivar

tag: line

tag: age

value: 2 months

tag: tissue

value: Whole root system


title: EN-TR-Rep4

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
J
processed data file: Tomato_Field_raw_counts.csv
protocols used: growth protocol 3, extract protocol 1 and library construction protocol 1


title: EU Seq of ESC. Experiment ID7, 60min 0.5uM JQ1 tx, replicate2.

description: Nascent RNA

value: 60min 0.5uM JQ1


title: X35S-TR-Rep2

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
B
processed data file: Tomato_Field_raw_counts.csv
protocols used: growth protocol 3, extract protocol 1 and library construction protocol 1


title: S15_02_H01 CD49a-NKG2C- CD56bright

city: Stockholm

first: Jakob

last: Michaelsson

address: Alfred Nobels allé 8, ANA Futura, level 7

department: Department of Medicine

country: Sweden

institute: Karolinska Institutet

description:
210210__GEO_counts.csv
S15_02_H01

data_processing:
Read pairs were trimmed from Illumina adapters using cutadapt (version 1.14), and UrQt was used to trim all bases with a phred quality score below 20
Read pairs were aligned to the protein coding sequences of the human transcriptome (gencode.v26.pc_transcripts.fa) using Salmon (version 0.8.2) and gene annotation using gencode.v26.annotation.gtf
Genome_build: Homo sapiens, GRCh38
Supplementary_files_format_and_content: Comma-separated text file include counts for each sample

organism: Homo sapiens

source_name: Blood

extract_protocol:
Cells were sorted directly into lysis buffer (0.2% Triton X-100, 2.5uM oligo-dT (5′-AAGCAGTGGTATCAACGCAGAGTACT30VN-3′), 2.5mM dNTP, RNAse Inhibitor (Takara), and ERCC RNA spike in controls (Ambion)) in a 96-well V-bottom PCR plate.
Standard SMART-Seq2 protocol with 22 cycles of cDNA amplification. Sample quality was determined using a bioanalyzer (Agilent, High Sensitivity DNA chip). 5ng of amplified cDNA was taken for tagmentation using a customized in-house protocol) and Nextera XT primers.

treatment_protocol: Fresh human lung tissue was digested using collagenase II and DNAse and enriched for lymphocytes by density gradient centrifugation using Ficoll. Peripheral blood mononuclear cells from healthy donors were isolated from buffy coats by density gradient centrifugation using Ficoll. All cells were cryopreserved in FCS with 10% DMSO in liquid nitogen until sorting of NK cell subsets by FACS.

value: CD49a-NKG2C- CD56bright

tag: donor

value: H

tag: replicate


title: EU Seq of ESC. Experiment ID4, 120min 0.5uM JQ1 tx, replicate1.

description: Nascent RNA


title: ESC_Ctrl_Med1_ChIP_rep1

description: processed data file: ChIP.ESC_Ctrl_Med1_TC0.n2.rpkm.smooth.bw

library_source: genomic

data_processing:
Read alignment was performed using BWA with default parameters. Low mapping quality read (MAPQ 10) and duplicated reads were removed using samtools.  The DAC Blacklisted Regions  were also omitted from the bam file using bedtools. Peaks were called using epic with the following parameters: --fragment-size 200 --gaps-allowed 5.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

molecule: genomic DNA

growth_protocol: E14Tg2A Rosa26-Cre Oct4-IRES-Puro mouse ESCs were used for all experiments 11932748. ESCs were cultured in a custom-made N2B27 medium consisting of 1:1 mix of DMEM/F12 and Neurobasal medium, without L-arginine and L-lysine (C.C.Pro GmbH, Oberdorla). The media was supplemented with L-arginine, L-lysine, 1000 units/ml leukemia inhibitory factor (LIF) (Merck Millipore), 1µM PD0325901, 3µM CT-99021 (custom-made by ABCR), 100µM 2-mercaptoethanol, 150µM sodium pyruvate, 0.5x B27 supplement (Thermo Fisher Scientific), as well as with 0.5x N2 supplement (made in house; or from Thermo Fisher Scientific).

extract_protocol:
Cells were cross-linked for 10 min at room temperature with 1% formaldehyde solution with gentle agitation and quenched with 0.125 M glycine. Cross-linked cells were washed once with PBS, added swelling buffer (10 mM Tris-HCl pH8.0, 1.5 mM MgCl2, 10 mM NaCl, 0.5% NP-40) and incubated on ice for 10 minutes. After centrifugation, pellets were suspended with RIPA buffer (10 mM Tris-HCl pH8.0, 1 mM EDTA, 140 mM NaCl, 1% Triton X-100, 0.1% SDS, 0.1% Sodium Deoxycholate) containing proteinase inhibitor cocktail (Roche), and then were sonicated by using a BioRuptor sonicator (Diagenode). After centrifugation, solubilized chromatin was recovered and incubated with 5 µg of antibody bound to protein A/G magnetic beads (Pierce). After overnight incubation at 4ºC, the magnetic beads were washed with RIPA buffer twice, RIPA high salt buffer (10 mM Tris-HCl pH8.0, 1 mM EDTA, 500 mM NaCl, 1% Triton X-100, 0.1% SDS, 0.1% Sodium Deoxycholate), LiCl buffer (10 mM Tris-HCl pH8.0, 1 mM EDTA, 250 mM LiCl, 0.5% NP-40, 0.5% Sodium Deoxycholate) and TE buffer. The bound materials were eluted with elution buffer (10 mM Tris-HCl pH8.0, 5 mM EDTA, 300 mM NaCl, 0.1% SDS) overnight at 65ºC and treated with RNaseA for 30 min for 37°C and further incubation with Proteinase K for 1 hour at 37ºC. Then DNA was purified with a PCR purification kit (Qiagen).
ChIP-seq libraries were prepared by using the NEBNext Ultra II DNA prep kit (NEB E7645) following the manufacturer's instruction and sequenced on a Next-Seq 500 Sequencer (Illumina).

treatment_protocol: A-485 (10uM) or JQ1(0.5mM) were treated for 60 min if not indicated. For control samples, 0.1 % DMSO was added.

tag: antibody

value: MED1 (Sigma-Aldrich 17-10530)

value: Control


title: EU Seq of ESC. Experiment ID7, 120min 0.5uM JQ1 tx, replicate2.

description: Nascent RNA


title: scr1_30h

city: PARIS

first: Anne Laure

last: Todeschini

address: 15 rue hélène brion

country: France

institute: CNRS/Université Paris Cité

data_processing:
Demultiplexing using bcl2fastq2 V2.15.0
adapters were removed with Cutadapt1.9.1.
Only reads longer than 10pb were kept for analysis (about 10,000,000 reads per sample). Reads mapped on the mouse genome (mm10) with TopHat2.
Mapped reads were assigned to features with features count (1.5.0-p2)
differential analysis  performed with DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample.

source_name: ovarian granulosa cells

extract_protocol:
RNA extraction was performed 30h after transfection, following the TRI-reagent supplier’s instructions (MRC). 1.3 µg of total RNAs underwent high throughput sequencing
Directional RNA-Seq Libraries were constructed using the TruSeq mRNA Stranded library prep kit (Illumina), following the manufacturer’s instructions. Final library quality was assessed on an Agilent Bioanalyzer 2100, using an Agilent High Sensitivity DNA Kit.
Libraries were pooled in equimolar proportions and sequenced on Single Read 75pb runs, on an Illumina NextSeq500 instrument, using NextSeq 500 High Output 75 cycles kits.

treatment_protocol: Lipofectamine RNAiMax

value: primary ovarian granulosa cells

tag: strain

value: 8-week-old female


title: S25_02_H02 CD49a+NKG2C+ CD56bright

description:
210210__GEO_counts.csv
S25_02_H02

value: CD49a+NKG2C+ CD56bright


title: X35S-TR-Rep1

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
A
processed data file: Tomato_Field_raw_counts.csv
protocols used: growth protocol 3, extract protocol 1 and library construction protocol 1


title: S25_02_G02 CD49a+NKG2C+ CD56bright

description:
210210__GEO_counts.csv
S25_02_G02

value: G


title: MCOTRAPT

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
T08
processed data file: Tomato_ATLAS_raw_counts.csv
protocols used: growth protocol 1, extract protocol 1 and library construction protocol 1

source_name: 3-5 days-old seedling 1 cm roots tips

value: 3-5 days

value: Roots tips


title: S15_02_H02 CD49a-NKG2C- CD56bright

description:
210210__GEO_counts.csv
S15_02_H02


title: ESC_A485_10uM_5min_TBP_ChIP_rep2

description: processed data file: ChIP.ESC_A485_10uM_TBP_TC5.n2.smooth.bw

value: 10uM A-485 for 5 min.


title: S25_02_H01 CD49a+NKG2C+ CD56bright

description:
210210__GEO_counts.csv
S25_02_H01


title: XYTRAPT

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
T07
processed data file: Tomato_ATLAS_raw_counts.csv
protocols used: growth protocol 1, extract protocol 1 and library construction protocol 1


title: EU Seq of ESC. Experiment ID4, 60min 0.5uM JQ1 tx, replicate1.

description: Nascent RNA

value: ES cells


title: S25_02_I02 CD49a+NKG2C+ CD56bright

description:
210210__GEO_counts.csv
S25_02_I02

value: I


title: S15_02_I02 CD49a-NKG2C- CD56bright

description:
210210__GEO_counts.csv
S15_02_I02


title: EU Seq of ESC. Experiment ID7, 60min 10uM JQ1 tx, replicate2.

description: Nascent RNA

value: wild type

value: 60min 10uM JQ1


title: EU Seq of ESC. Experiment ID7, 60min 10uM JQ1 tx, replicate1.

description: Nascent RNA


title: PHTRAPT

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
T06
processed data file: Tomato_ATLAS_raw_counts.csv
protocols used: growth protocol 1, extract protocol 1 and library construction protocol 1


title: S25_02_I01 CD49a+NKG2C+ CD56bright

description:
210210__GEO_counts.csv
S25_02_I01


title: EU Seq of ESC. Experiment ID7, 60min 0.5uM JQ1 tx, replicate1.

description: Nascent RNA


title: CORTRAPT

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
T05
processed data file: Tomato_ATLAS_raw_counts.csv
protocols used: growth protocol 1, extract protocol 1 and library construction protocol 1


title: VTRAPTb

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
T04
processed data file: Tomato_ATLAS_raw_counts.csv
protocols used: growth protocol 1, extract protocol 1 and library construction protocol 1


title: S15_02_I01 CD49a-NKG2C- CD56bright

description:
210210__GEO_counts.csv
S15_02_I01


title: EU Seq of ESC. Experiment ID4, 60min 10uM JQ1 tx, replicate2.

description: Nascent RNA


title: VTRAPTa

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
T03
processed data file: Tomato_ATLAS_raw_counts.csv
protocols used: growth protocol 1, extract protocol 1 and library construction protocol 1


title: WOXTRAPTa

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
T01
processed data file: Tomato_ATLAS_raw_counts.csv
protocols used: growth protocol 1, extract protocol 1 and library construction protocol 1


title: MCOTRAPS

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
S01
processed data file: Tomato_ATLAS_raw_counts.csv
protocols used: growth protocol 1, extract protocol 1 and library construction protocol 1


title: WOXTRAPTb

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
T02
processed data file: Tomato_ATLAS_raw_counts.csv
protocols used: growth protocol 1, extract protocol 1 and library construction protocol 1


title: H1_in_mTESR1_3

city: Beijing

first: Hongkui

last: Deng

address: Summer Palace Road No. 5

country: China

institute: Peking University

data_processing:
The ATAC-seq reads were trimmed with Trimmomatic-0.39 to remove sequencing adapters. The clean reads were next mapped to human reference genome hg19 using bowtie2 version 2.3.5 with parameter ‘very sensitive’. Low quality mapped reads were removed using samtools version 1.10. The peaks were called using MACS2-2.2.6 with parameters ‘-g hs --nomodel --shift -100 --extsize 200’.
The differential binding analysis of peak data was analyzed with R package DiffBind. The differential binding peaks (FDR < 0.05) between groups were used to perform motif enrichment analysis with Homer version 4.10.3. The genes whose transcription start sites within 10 kb of differential binding peaks were collected to perform GO analysis with R package clusterProfiler. The mitochondrial peaks are not included in all analysis above.
Genome_build: hg19

source_name: Human  pluripotent stem cells

growth_protocol: Xeno-free human EPS  cells were cultured in chemically defined LCDM medium under 20% O2 and 5% CO2 at 37°C. Feeder-cultured human EPS cells were cultured in serum-free LCDM medium in 20% O2, 5% CO2 conditions on mitomycin C-inactivated MEF feeder cells. H1 were cultured in mTESR1 medium in  20% O2, 5% CO2 conditions on matrigel

extract_protocol:
Cells were prepared by using the TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD502-01) following the manufacture’s guideless.
Cells were prepared by using the TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD502-01) following the manufacture’s guideless.

value: Human  pluripotent stem cells

tag: culture condition


title: MZTRAPR

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
R04
processed data file: Tomato_ATLAS_raw_counts.csv
protocols used: growth protocol 1, extract protocol 1 and library construction protocol 1


title: EU Seq of ESC. Experiment ID4, 60min 10uM JQ1 tx, replicate1.

description: Nascent RNA


title: VTRAPR

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
R03
processed data file: Tomato_ATLAS_raw_counts.csv
protocols used: growth protocol 1, extract protocol 1 and library construction protocol 1


title: EU Seq of ESC. Experiment ID4, 60min 0.5uM JQ1 tx, replicate2.

description: Nascent RNA

value: 60min 0.5uM JQ1


title: EU Seq of ESC. Experiment ID7, 60min TSA tx, replicate2.

description: Nascent RNA

value: 60min TSA


title: ENTRAPR

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
R01
processed data file: Tomato_ATLAS_raw_counts.csv
protocols used: growth protocol 1, extract protocol 1 and library construction protocol 1


title: H1_in_mTESR1_2


title: EU Seq of ESC. Experiment ID7, 60min TSA tx, replicate1.

description: Nascent RNA


title: X35STRAPQ

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
Q04
processed data file: Tomato_ATLAS_raw_counts.csv
protocols used: growth protocol 1, extract protocol 1 and library construction protocol 1


title: EPTRAPQ

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
Q03
processed data file: Tomato_ATLAS_raw_counts.csv
protocols used: growth protocol 1, extract protocol 1 and library construction protocol 1


title: XYTRAPQ

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
Q02
processed data file: Tomato_ATLAS_raw_counts.csv
protocols used: growth protocol 1, extract protocol 1 and library construction protocol 1


title: H1_in_mTESR1_1


title: H1-EPS_in_XF_LCDM_3

source_name: Human extended pluripotent stem cells

value: Human extended pluripotent stem cells

value: Xeno-free


title: EU Seq of ESC. Experiment ID4, 60min TSA tx, replicate2.

description: Nascent RNA


title: PHTRAPQ

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
Q01
processed data file: Tomato_ATLAS_raw_counts.csv
protocols used: growth protocol 1, extract protocol 1 and library construction protocol 1


title: H1-EPS_in_XF_LCDM_1


title: WOXTRAPP

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
P03
processed data file: Tomato_ATLAS_raw_counts.csv
protocols used: growth protocol 1, extract protocol 1 and library construction protocol 1


title: EU Seq of ESC. Experiment ID4, control, replicate2.

description: Nascent RNA

value: DMSO


title: H1-EPS_in_XF_LCDM_2


title: MZTRAPO

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
O04
processed data file: Tomato_ATLAS_raw_counts.csv
protocols used: growth protocol 1, extract protocol 1 and library construction protocol 1


title: X35STRAPO

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
O01
processed data file: Tomato_ATLAS_raw_counts.csv
protocols used: growth protocol 1, extract protocol 1 and library construction protocol 1


title: WOXTRAPO

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
O03
processed data file: Tomato_ATLAS_raw_counts.csv
protocols used: growth protocol 1, extract protocol 1 and library construction protocol 1


title: H1-EPS_in_F_LCDM_2

value: Feeder-cultured


title: EXOTRAPP

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
P01
processed data file: Tomato_ATLAS_raw_counts.csv
protocols used: growth protocol 1, extract protocol 1 and library construction protocol 1


title: ACTTRAPP

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
P07
processed data file: Tomato_ATLAS_raw_counts.csv
protocols used: growth protocol 1, extract protocol 1 and library construction protocol 1


title: EU Seq of ESC. Experiment ID7, control, replicate2.

description: Nascent RNA


title: ACTTRAPN

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
N07
processed data file: Tomato_ATLAS_raw_counts.csv
protocols used: growth protocol 1, extract protocol 1 and library construction protocol 1


title: EU Seq of ESC. Experiment ID7, control, replicate1.

description: Nascent RNA


title: CORTRAPO

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
O02
processed data file: Tomato_ATLAS_raw_counts.csv
protocols used: growth protocol 1, extract protocol 1 and library construction protocol 1


title: ENTRAPN

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
N03
processed data file: Tomato_ATLAS_raw_counts.csv
protocols used: growth protocol 1, extract protocol 1 and library construction protocol 1


title: EU Seq of ESC. Experiment ID4, control, replicate1.

description: Nascent RNA


title: H1-EPS_in_F_LCDM_1


title: EPTRAPN

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
N01
processed data file: Tomato_ATLAS_raw_counts.csv
protocols used: growth protocol 1, extract protocol 1 and library construction protocol 1


title: XYTRAPN

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
N02
processed data file: Tomato_ATLAS_raw_counts.csv
protocols used: growth protocol 1, extract protocol 1 and library construction protocol 1


title: Sample 30, from female blood donor [BST_39]

city: Badalona

first: Lauro

last: Sumoy

state: Barcelona

address: Ctra. Can Ruti, Camí de les escoles s/n

department: High Content Genomics and Bioinformatics

country: Spain

institute: IGTP

data_processing:
BCL basecall files were converted to FASTQ per sample using CASAVA v1.8.2 (Illumina) with default parameters to generate demultiplexed per sample fastq raw sequencing data files.
Per sample read quality was assessed using FastQC.
Trimming, quality filtering, mapping and raw read counting data processing steps were performed with XICRA pipeline developed in house, with miraligner software (Pantano L, et al Nucleic Acids Res. 38(5):e34, 2010) to map the reads.
Statistically significant differences in miRNA expression were determined both by DESeq2 (Love, M. et al, Genome Biology, 15:550, 2014) with multiple testing adjustment. A dataset consistency step was perfomed by principal components analysis (PCA) to detect outliers. Data were renormalized after outlier removal prior to the final analysis.
Genome_build: Reads were mapped to GRCh38.87  and annotated with miRBase 21 mature database.
Supplementary_files_format_and_content: Processed miRNA expression profiling data table is provided as a supplementary file in excel workbook (.xlsx) format. It includes a single worksheet. This contains annotation columns (Gene:  unique identifier of miRNA isoform; miRNA: corresponding mature miRNA miRBase identifier; isomir: full isomir identifier;  iso_type: isomir type; iso_suffix: bases extended or removed relative to canonical reference, miRTOP: unique identifier using miRTOP nomenclature,  and DESeq2 outputs including normalized counts for all samples (identified by sample name), log2 FC  (logarithm in base 2 of the fold changes), pvalue (nominal p value), padj (adjusted pvalue by default Benjamini and Hochberg method) for the comparisons, followed by baseMean (average normalized counts). the file contains four worksheets corresponding to the 4 analysis modalities presented in the publication (PE_0: mapping of paired end reads joined with fastqjoin allowing 0% errors; PE_8: mapping of paired end reads joined with fastqjoin allowing 8% errors; SR1: mapping of single reads using R1 only; SR2, mapping of single reads using R2 only).

source_name: Circulating total RNA from serum of anonymous female blood donor

extract_protocol:
Blood samples were collected in red cap clot activating tubes by venous extraction from anonymous healthy blood donors after informed conset obtained by the Blood and Tissue Bank of Catalonia (Banc de Sang i Teixits, Hospital Germans Trias i Pujol, Badalona, Spain). After 30 minutes at room temperature, serum samples were obtained by a single centrifugation (1000g, 15min. at room temperature). For RNA extraction from 200ul of serum, miRCURY RNA insolation kit-Biofluids (#300112) was used following manufacturer indications with modifications that included using glycogen as carrier and a 1:50 dilution of spike in RNA.
Barcoded sequencing libraries were prepared using the TruSeq SmallRNA library kit (Illumina) with slight modifications from the default recommendations (Part # 15004197 Rev. F, February 2014). Modifications included using all RNA extracted from 200 ul of serum, in the subnanogram range, and increasing the number of cycles in the final PCR reaction (from 12 to 15).
Libraries were quality assessed with Bioanalyzer DNA 1000 assays (Agilent). Bioanalyzer concentration estimates were used to generate an equimolar library mix. The library pool was automatically size selected (135-160bp) using 3% agarose dye free cassettes with 3% DF marker F on a Pippin Prep system with software v.6.0 (Sage Science). QIAquick (Qiagen) column purifications were performed prior and after to size selection. The library pool was quantified by PCR with theKAPA Library Quantification Kit following manufacturer’s instructions (Roche). The library pool was run on 2 lanes of 2x50 bp sequencing was performed on HiSeq2500 platform (Illumina) using adapted protocols for TruSeq PE cluster kit v3 (Part#15037931) following cBot™ (Part#15006165) and HiSeq2500 System (Part#15035786) user guidelines. Raw data were analysed by Real Time Analysis software v. 1.17.21.3 and Sequence Analysis Viewer software v. 1.8.20 (Illumina.).

tag: gender

value: female

value: Blood serum


title: PHTRAPM

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
M03
processed data file: Tomato_ATLAS_raw_counts.csv
protocols used: growth protocol 1, extract protocol 1 and library construction protocol 1


title: EU Seq of ESC. Experiment ID3, 120min JQ1 tx, replicate1.

description: Nascent RNA

value: 120min JQ1


title: Sample 29, from female blood donor [BST_38]


title: EU Seq of ESC. Experiment ID4, 60min TSA tx, replicate1.

description: Nascent RNA


title: MCOTRAPM

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
M02
processed data file: Tomato_ATLAS_raw_counts.csv
protocols used: growth protocol 1, extract protocol 1 and library construction protocol 1

value: 3-5 days


title: EU Seq of ESC. Experiment ID2, 120min JQ1 tx, replicate1.

description: Nascent RNA


title: EXOTRAPM

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
M01
processed data file: Tomato_ATLAS_raw_counts.csv
protocols used: growth protocol 1, extract protocol 1 and library construction protocol 1

value: Roots tips


title: PHTRAPL

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
L02
processed data file: Tomato_ATLAS_raw_counts.csv
protocols used: growth protocol 1, extract protocol 1 and library construction protocol 1


title: MZTRAPL

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
L03
processed data file: Tomato_ATLAS_raw_counts.csv
protocols used: growth protocol 1, extract protocol 1 and library construction protocol 1


title: ENTRAPL

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
L01
processed data file: Tomato_ATLAS_raw_counts.csv
protocols used: growth protocol 1, extract protocol 1 and library construction protocol 1


title: Sample 27, from female blood donor [BST_36]


title: EU Seq of ESC. Experiment ID2, 60min JQ1 tx, replicate2.

description: Nascent RNA

value: 60min JQ1


title: Sample 28, from female blood donor [BST_37]


title: VTRAPM

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
M04
processed data file: Tomato_ATLAS_raw_counts.csv
protocols used: growth protocol 1, extract protocol 1 and library construction protocol 1


title: EU Seq of ESC. Experiment ID3, 60min JQ1 tx, replicate1.

description: Nascent RNA

value: ES cells


title: ACTTRAPL

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
L09
processed data file: Tomato_ATLAS_raw_counts.csv
protocols used: growth protocol 1, extract protocol 1 and library construction protocol 1


title: Sample 24, from female blood donor [BST_32]


title: EU Seq of ESC. Experiment ID2, 60min JQ1 tx, replicate1.

description: Nascent RNA


title: XYTRAPK

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
K04
processed data file: Tomato_ATLAS_raw_counts.csv
protocols used: growth protocol 1, extract protocol 1 and library construction protocol 1


title: Sample 26, from female blood donor [BST_35]


title: Sample 25, from female blood donor [BST_33]


title: Sample 23, from male blood donor [BST_31]

source_name: Circulating total RNA from serum of anonymous male blood donor

value: male


title: CORTRAPK

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
K02
processed data file: Tomato_ATLAS_raw_counts.csv
protocols used: growth protocol 1, extract protocol 1 and library construction protocol 1


title: MCOTRAPK

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
K01
processed data file: Tomato_ATLAS_raw_counts.csv
protocols used: growth protocol 1, extract protocol 1 and library construction protocol 1


title: X35STRAPJ

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
J04
processed data file: Tomato_ATLAS_raw_counts.csv
protocols used: growth protocol 1, extract protocol 1 and library construction protocol 1


title: VTRAPJ

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
J03
processed data file: Tomato_ATLAS_raw_counts.csv
protocols used: growth protocol 1, extract protocol 1 and library construction protocol 1


title: EXOTRAPJ

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
J02
processed data file: Tomato_ATLAS_raw_counts.csv
protocols used: growth protocol 1, extract protocol 1 and library construction protocol 1


title: EU Seq of ESC. Experiment ID2, 120min JQ1 tx, replicate2.

description: Nascent RNA

value: wild type


title: EPTRAPJ

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
J01
processed data file: Tomato_ATLAS_raw_counts.csv
protocols used: growth protocol 1, extract protocol 1 and library construction protocol 1


title: EU Seq of ESC. Experiment ID3, 30min JQ1 tx, replicate1.

description: Nascent RNA

value: 30min JQ1


title: Sample 22, from male blood donor [BST_30]


title: EU Seq of ESC. Experiment ID2, 30min JQ1 tx, replicate2.

description: Nascent RNA


title: WOXTRAPK

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
K03
processed data file: Tomato_ATLAS_raw_counts.csv
protocols used: growth protocol 1, extract protocol 1 and library construction protocol 1


title: EU Seq of ESC. Experiment ID2, 30min JQ1 tx, replicate1.

description: Nascent RNA


title: Sample 21, from male blood donor [BST_28]


title: Sample 20, from female blood donor [BST_27]


title: VTRAPI

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
I01
processed data file: Tomato_ATLAS_raw_counts.csv
protocols used: growth protocol 1, extract protocol 1 and library construction protocol 1


title: XYTRAPI

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
I03
processed data file: Tomato_ATLAS_raw_counts.csv
protocols used: growth protocol 1, extract protocol 1 and library construction protocol 1


title: EU Seq of ESC. Experiment ID3, 150min A-485 tx and co-tx with TSA in the last 120min, replicate1.

description: Nascent RNA

value: 150min A-485 and co-tx with TSA in the last 120min


title: EU Seq of ESC. Experiment ID6, 150min A-485 tx and co-tx with TSA in the last 120min, replicate1.

description: Nascent RNA


title: ACTTRAPH

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
H09
processed data file: Tomato_ATLAS_raw_counts.csv
protocols used: growth protocol 1, extract protocol 1 and library construction protocol 1


title: MZTRAPH

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
H02
processed data file: Tomato_ATLAS_raw_counts.csv
protocols used: growth protocol 1, extract protocol 1 and library construction protocol 1


title: X35STRAPH

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
H01
processed data file: Tomato_ATLAS_raw_counts.csv
protocols used: growth protocol 1, extract protocol 1 and library construction protocol 1


title: EU Seq of ESC. Experiment ID6, 90min A-485 tx and co-tx with TSA in the last 60min, replicate1.

description: Nascent RNA

value: 90min A-485 and co-tx with TSA in the last 60min


title: EU Seq of ESC. Experiment ID3, 90min A-485 tx and co-tx with TSA in the last 60min, replicate1.

description: Nascent RNA


title: ENTRAPG

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
G04
processed data file: Tomato_ATLAS_raw_counts.csv
protocols used: growth protocol 1, extract protocol 1 and library construction protocol 1


title: MCOTRAPI

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
I04
processed data file: Tomato_ATLAS_raw_counts.csv
protocols used: growth protocol 1, extract protocol 1 and library construction protocol 1


title: CORTRAPG

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
G03
processed data file: Tomato_ATLAS_raw_counts.csv
protocols used: growth protocol 1, extract protocol 1 and library construction protocol 1


title: Sample 16, from male blood donor [BST_22]


title: Sample 17, from female blood donor [BST_23]


title: EXOTRAPG

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
G02
processed data file: Tomato_ATLAS_raw_counts.csv
protocols used: growth protocol 1, extract protocol 1 and library construction protocol 1


title: EPTRAPG

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
G01
processed data file: Tomato_ATLAS_raw_counts.csv
protocols used: growth protocol 1, extract protocol 1 and library construction protocol 1


title: EU Seq of ESC. Experiment ID6, 60min A-485 tx and co-tx with TSA in the last 30min, replicate1.

description: Nascent RNA

value: 60min A-485 and co-tx with TSA in the last 30min


title: Sample 19, from male blood donor [BST_26]


title: pasRNA_ABAT_replicateB (1M7)

city: La Jolla

first: MICHAEL

middle: G

last: ROSENFELD

address: 9500 Gilman Drive

institute: HHMI/UCSD

description:
pasRNA_ABAT_replicateB.map
pasRNA_ABAT_replicateB.profile.txt
pasRNA_ABAT_replicateB.shape

data_processing:
Library strategy: SHAPE-MaP
Quality control: FASTQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was used to inspect the quality of the sequencing reads
ShapeMapper 2.1.5 pipeline (https://github.com/Weeks-UNC/shapemapper2) was used to generate the shape, map and profile files.
RNAfold webserver (http://rna.tbi.univie.ac.at/cgi-bin/RNAWebSuite/RNAfold.cgi) was used to build and visualize the RNA structure.
Genome_build: hg38 (the sequence of ABAT pasRNA)
Supplementary_files_format_and_content: profile, shape, map

molecule: other

organism: synthetic construct

source_name: pasRNA of ABAT human gene (in vitro)

extract_protocol:
The ABAT PAS RNA used in SHAPE-MaP experiment was synthesized by MAXIscript™ SP6/T7 Transcription Kit according to manufacturer's protocol. After purification, 500 ng ABAT PAS RNA for each SHAPE sample was refolded before being treated with DMSO or 100 mM 1-Methyl-7-nitroisatoic anhydride (1M7) for 75 second. RNA was then isolated and subject to SHAPE-MaP reverse transcription with gene specific primer. Second-strand synthesis was performed with Q5 hot start high-fidelity DNA polymerase.
Deep sequencing was performed by Illumina MiSeq PE250.

tag: sample type

value: pasRNA of ABAT human gene (in vitro)


title: pasRNA_ABAT_replicateB (DMSO)


title: Sample 13, from female blood donor [BST_17]


title: PHTRAPI

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
I02
processed data file: Tomato_ATLAS_raw_counts.csv
protocols used: growth protocol 1, extract protocol 1 and library construction protocol 1


title: pasRNA_ABAT_replicateA (1M7)

description:
pasRNA_ABAT_replicateA.map
pasRNA_ABAT_replicateA.profile.txt
pasRNA_ABAT_replicateA.shape


title: Sample 15, from male blood donor [BST_20]


title: WOXTRAPH

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
H03
processed data file: Tomato_ATLAS_raw_counts.csv
protocols used: growth protocol 1, extract protocol 1 and library construction protocol 1


title: EU Seq of ESC. Experiment ID6, 60min TSA and A-485 tx , replicate1.

description: Nascent RNA

value: 60min TSA and A-485


title: Sample 12, from female blood donor [BST_16]


title: pasRNA_ABAT_replicateA (DMSO)

value: DMSO


title: GA_affy_SNP of homo sapiens_blood [JX10-IP19D2302]

type: genomic

city: Linhai

first: Xuejiao

last: Chen

address: chichen

institute: Taizhou Hospital of Zhejiang Province affiliated to Wenzhou Medical University

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
Affymetrix®Chromosome Analysis Suite (ChAS) Software for data visualization and analysis. As per manufacturer (Affymetrix).
primary data description: Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

label: Biotin

source_name: GA_affy_SNP of homo sapiens_blood

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Human genomic DNA was extracted from whole blood or amniotic fluid using a QIAamp DNA Mini Kit

value: 11p11.12p12 duplication

value: blood


title: GA_affy_SNP of homo sapiens_blood [JX8-IP19D2301]


title: Sample 10, from male blood donor [BST_13]

value: Blood serum


title: EU Seq of ESC. Experiment ID6, 120min TSA tx, replicate1.

description: Nascent RNA

value: AID-Ctcf

value: 120min TSA


title: EU Seq of ESC. Experiment ID3, 120min TSA tx, replicate1.

description: Nascent RNA


title: Sample 8, from female blood donor [BST_11]

value: female


title: EU Seq of ESC. Experiment ID3, 60min A-485 tx and co-tx with TSA in the last 30min, replicate1.

description: Nascent RNA


title: Sample 9, from male blood donor [BST_12]


title: EU Seq of ESC. Experiment ID6, 60min TSA tx, replicate1.

description: Nascent RNA

value: 60min TSA


title: EU Seq of ESC. Experiment ID3, 60min TSA tx, replicate1.

description: Nascent RNA

value: ES cells


title: Sample 7, from male blood donor [BST_10]

value: male


title: Sample 6, from male blood donor [BST_9]


title: EU Seq of ESC. Experiment ID6, 30min TSA tx, replicate1.

description: Nascent RNA

value: wild type

value: 30min TSA


title: Sample 11, from female blood donor [BST_15]


title: Sample 5, from male blood donor [BST_8]


title: U0126-Light  at CT22, biological replicate 3

type: RNA

city: Columbus

first: Diego

middle: Fernando

last: Alzate Correa

state: OH

address: 333 W 10th Avenue

department: Neuroscience

institute: The Ohio State University

description:
UL.3.22
Gene Expression data from Mouse Suprachiasmatic Nucleus treated with U0126 and  Light Pulse collected at CT22

hyb_protocol: cRNA was hybridized to GeneChip Mouse Transcriptome Assay 1.0 following the manufacturer’s guidelines (Affymetrix, Santa Clara, CA).

scan_protocol: GeneChips were scanned using the Affy GeneChip Scanner 3000 according to the manufacturer's instruction (Affymetrix)

data_processing: All analyses were undertaken using the R platform for statistical computing (version 3.1.0)  library packages were implemented in Bioconductor. Global changes in RNA in samples were analyzed by Oligo, and differential expression of genes (DEGs) were identified by a standard limma pipeline using a generalized linear model.

source_name: Mouse SCN from 2 mice pool together after treatment with U0126, Light Pulse and collected at CT22

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix). Probes were prepared with 100 ng of total RNA as starting material using the GeneChip WT Plus Reagent Kit

growth_protocol: A 24gauge cannula was placed in the Lateral Ventricle of Adult C57BL/6J wild type (WT) mice (8 to 14 weeks old). Sterotaxic coordiantes (anterio-posterior -0.22mm. from bregma; and medial-lateral +1.0 mm from the midline; dorso-ventral -2.00 mm from dura).Mice were mantained on a 12h light/12h dark (LD) cycle for two weeks after sterotaxic surgery.

extract_protocol: SCN from two animals under the same treatment were pooled in conical tubes and stored at -80°C. RNA from each pooled sampled was isolated by pestle disruption in 500μL of Trizol (Invitrogen), followed by the addition and mixing with 125μL of chloroform, and centrifugation at 16,000xg for 15 minutes at 4°C. The aqueous phase was recovered and mixed in a 1:1 proportion with chloroform and centrifuged at 16,000xg for 5 minutes at 4°C, this final aqueous phase was mixed 1:1 with 70% ethanol and applied to RNAesy minikit columns (Qiagen). RNA in the columns was washed successively with buffer RW1, buffer RPE x2, and 80% ethanol. The RNA was eluted and resuspended in 20μL of RNase Free water.

treatment_protocol: Two days before the drug-light treatment mice were transferred to a 12h dark/12h dark (DD) cycle, where by convention circadian time 0 (CT0) corresponds to the expected beginning of the subjective day, and CT12 correspond to the expected time of the subjective night.  Infusions were performed under dim red light (<2 lux) at one of three time points: CT4, CT15 or CT22.  For infusion of vehicle (DMSO) or U0126 (10mM), mice were manually restrained and a 10.5 mm 30-gauge injector placed in the guide cannula was used to infuse a total of 3uL at a rate of 0.6uL/min. After the infusion, the injector was kept in the guide cannula for one additional minute to prevent the drug from seeping back out. For each of the three time points mice were divided in four groups: DMSO-No Light Pulse (DMSO-Sham); DMSO-Light Pulse (DMSO-Light); U0126-No Light Pulse (U0126-Sham); and U0126-Light Pulse (U0126-Ligth). 30 minutes after the corresponding infusion, mice were placed in a lightproof chamber and either exposed to a light pulse of 100 lux for 10 minutes (light groups) or kept in the dark for the same amount of time (sham groups). Tissue for RNA isolation was collected 60 minutes after the end of the light/sham pulse.

tag: drug treatment

tag: light ttreatment

value: Light Pulse

tag: circadian time

value: Brain Suprachiasmatic Nucleus (SCN)


title: Sample 4, from male blood donor [BST_7]


title: EU Seq of ESC. Experiment ID8, control, replicate2.

description: Nascent RNA

tag: cell type

tag: cell line


title: Sample 3, from male blood donor [BST_6]


title: EU Seq of ESC. Experiment ID8, control, replicate1.

description: Nascent RNA

tag: genotype/variation

tag: treatment


title: U0126-Sham  at CT22, biological replicate 3

description:
US.3.22
Gene Expression data from Mouse Suprachiasmatic Nucleus treated with U0126 and Sham Light Pulse collected at CT22

source_name: Mouse SCN from 2 mice pool together after treatment with U0126, Sham Light Pulse and collected at CT22

value: Sham Pulse


title: U0126-Sham  at CT22, biological replicate 1

description:
US.1.22
Gene Expression data from Mouse Suprachiasmatic Nucleus treated with U0126 and Sham Light Pulse collected at CT22


title: EU Seq of ESC. Experiment ID3, 30min TSA tx, replicate1.

description: Nascent RNA


title: U0126-Light  at CT22, biological replicate 1

description:
UL.1.22
Gene Expression data from Mouse Suprachiasmatic Nucleus treated with U0126 and  Light Pulse collected at CT22


title: EU Seq of ESC. Experiment ID6, control, replicate1.

description: Nascent RNA


title: EU Seq of ESC. Experiment ID8, 20min A-485 tx, replicate2.

description: Nascent RNA


title: DMSO-Light  at CT22, biological replicate 2

description:
DL.2.22
Gene Expression data from Mouse Suprachiasmatic Nucleus treated with DMSO and  Light Pulse collected at CT22

source_name: Mouse SCN from 2 mice pool together after treatment with DMSO, Light Pulse and collected at CT22


title: Sample 2, from male blood donor [BST_5]


title: DMSO-Sham  at CT22, biological replicate 2

description:
DS.2.22
Gene Expression data from Mouse Suprachiasmatic Nucleus treated with DMSO and Sham Light Pulse collected at CT22

source_name: Mouse SCN from 2 mice pool together after treatment with DMSO, Sham Light Pulse and collected at CT22


title: DMSO-Light  at CT22, biological replicate 3

description:
DL.3.22
Gene Expression data from Mouse Suprachiasmatic Nucleus treated with DMSO and  Light Pulse collected at CT22


title: U0126-Sham  at CT22, biological replicate 2

description:
US.2.22
Gene Expression data from Mouse Suprachiasmatic Nucleus treated with U0126 and Sham Light Pulse collected at CT22


title: DMSO-Sham  at CT22, biological replicate 3

description:
DS.3.22
Gene Expression data from Mouse Suprachiasmatic Nucleus treated with DMSO and Sham Light Pulse collected at CT22


title: U0126-Light  at CT22, biological replicate 2

description:
UL.2.22
Gene Expression data from Mouse Suprachiasmatic Nucleus treated with U0126 and  Light Pulse collected at CT22


title: U0126-Light  at CT15, biological replicate 1

description:
UL.1.15
Gene Expression data from Mouse Suprachiasmatic Nucleus treated with U0126 and  Light Pulse collected at CT15

source_name: Mouse SCN from 2 mice pool together after treatment with U0126, Light Pulse and collected at CT15


title: Sample 1, from female blood donor [BST_2]


title: U0126-Sham  at CT15, biological replicate 2

description:
US.2.15
Gene Expression data from Mouse Suprachiasmatic Nucleus treated with U0126 and Sham Light Pulse collected at CT15

source_name: Mouse SCN from 2 mice pool together after treatment with U0126, Sham Light Pulse and collected at CT15


title: U0126-Light  at CT15, biological replicate 2

description:
UL.2.15
Gene Expression data from Mouse Suprachiasmatic Nucleus treated with U0126 and  Light Pulse collected at CT15


title: DMSO-Light  at CT22, biological replicate 1

description:
DL.1.22
Gene Expression data from Mouse Suprachiasmatic Nucleus treated with DMSO and  Light Pulse collected at CT22


title: U0126-Light  at CT15, biological replicate 3

description:
UL.3.15
Gene Expression data from Mouse Suprachiasmatic Nucleus treated with U0126 and  Light Pulse collected at CT15


title: U0126-Sham  at CT15, biological replicate 1

description:
US.1.15
Gene Expression data from Mouse Suprachiasmatic Nucleus treated with U0126 and Sham Light Pulse collected at CT15


title: EU Seq of ESC. Experiment ID8, 20min A-485 tx, replicate1.

description: Nascent RNA

source_name: mouse ES cells


title: DMSO-Light  at CT15, biological replicate 3

description:
DL.3.15
Gene Expression data from Mouse Suprachiasmatic Nucleus treated with DMSO and  Light Pulse collected at CT15

source_name: Mouse SCN from 2 mice pool together after treatment with DMSO, Light Pulse and collected at CT15


title: U0126-Sham  at CT15, biological replicate 3

description:
US.3.15
Gene Expression data from Mouse Suprachiasmatic Nucleus treated with U0126 and Sham Light Pulse collected at CT15


title: ChIP on POLR2A  and with estradiol treatment of MCF-7 cells (40min) [POL2_shctrl_plusE2_Fan118]

data_processing:
The image analysis and base calling were performed by using Illumina's Genome Analysis pipeline.
Quality control: FASTQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and TRIMMOMATIC (http://www.usadellab.org/cms/?page=trimmomatic) were used to inspect the quality of the sequencing reads, and to trim the sequencing adaptors, if necessary.
Read alignment: Bowtie2 (Langmead et al., Nature Methods 2012) was employed to align ChIP-seq and ChIRC-seq samples to hg38 genome and we have kept 1 copy/read per genome position.
Peak finding: we have called the ChIP-seq and ChiRC-seq peaks by using HOMER findPeaks subroutine (Heinz et al., 2010, http://homer.ucsd.edu/homer/). For the CHIP-seq analysis, we have used the default settings in HOMER. For the ChIRC-seq analysis, we have used the input samples in order to estimate the background.
Generation of bedgraph files: we have used the HOMER scripts makeUCSCfile and makeMultiWigHub.pl in order to generate bedgraph files for visualization in the UCSC genome browser.
Genome_build: hg38
Supplementary_files_format_and_content: bedgraph

growth_protocol: MCF-7 cells were cultured in DMEM, 10% FBS and 1% penicillin-streptomycin in a humidified incubator with 5% CO2 at 37C.

extract_protocol:
ChIP was performed as previously described, with minor modifications. Briefly, approximately 5 x 10^7 cells were crosslinked with 1% formaldehyde at room temperature for 15 min and quenched with 0.125M glycine for 5 min. Cells were then harvested and incubated with nuclei preparation buffer (50 mM Tris pH 7.5, 150 mM NaCl , 5 mM EDTA, 0.5% NP-40, 1% TX-100), with protease inhibitor (Sigma, Cat#P2714-1BTL) included, for 10 min. After centrifugation, the pellet was suspended in sonication buffer (10 mM Tris, pH8.0, 100 mM NaCl, 1mM EDTA, 0.5 mM EGTA, 0.1% Na-Deoxycholate and 0.5% N-lauroylsarcosine, with protease inhibitor included) for sonication. After sonication, 1/10 volume of 10% Triton X-100 was added to sonicated lysate. The supernatant, after centrifugation, was then incubated with 5μg of antibody at 4°C overnight. Immunoprecipitated complexes were collected using Protein G magnetic beads (Invitrogen, Cat#10004D). Immuno-complexes were washed with RIPA buffer (50 mM Hepes-KOH, pH 7.6, 500 mM LiCl, 1 mM EDTA, 1% NP-40 and 0.7% Na-Deoxycholate, with protease inhibitor included) for at least 5 times and TE buffer containing 50 mM Nacl once. After de-crosslinking, DNA was then purified by QIAquick Spin columns (Qiagen).
For Bio-ChIP, 5x10^7 MCF-7 cells stably expressing BirA and biotin acceptor peptide (BAP)-HP1α (4A) or BAP- HP1α (4E) were crosslinked with 1% formaldehyde at room temperature for 15 min, and then incubated with 0.125M glycine for 5 min. To isolate nuclei, cells were incubated with nuclei preparation buffer (50 mM Tris pH 7.5, 150 mM NaCl , 5 mM EDTA, 0.5% NP-40, 1% TX-100), with protease inhibitor (Sigma, Cat#P2714-1BTL) included, for 10 min. The obtained nuclei were suspended in immunoprecipitation buffer (50 mM HEPES pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate and 1% Triton X-100, with protease inhibitor included) for sonication. The sonicated chromatin in immunoprecipitation buffer was then incubated with 50 ul of pre-blocked Pierce™ Streptavidin Magnetic Beads (Thermo Fisher, Cat#88816) overnight at 4°C on a rotating wheel. Beads were extensively washed with SDS buffer (10 mM Tris, pH 8, 1 mM EDTA, 2% SDS, protease inhibitor included) twice, high salt buffer (50 mM HEPES pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate and 500 mM NaCl) twice, DOC buffer (250 mM LiCl, 0.5%, NP-40, 0.5% deoxycholate, 1 mM EDTA and 10 mM Tris pH 8) once and TE buffer containing 50 mM Nacl once. Beads were then treated with RNase A (Thermo Fisher Scientific, Cat# AM2270) and Proteinase K (Thermo Fisher Scientific, Cat# AM2548) before de-crosslinking overnight at 65°C. DNA was finally purified by QIAquick Spin columns (Qiagen, Cat#28106).
The library construction protocol followed the manufacturer’s instructions.

treatment_protocol: For estrogen stimulation, these cells were cultured in phenol-red free DMEM with 5% charcoal stripped FBS for at least 3 days and then treated with 100nM 17β-estradiol (E2) for 40 minutes. Control samples were treated with ethanol.

tag: chip antibody

value: POLR2A (RPB1)


title: DMSO-Sham  at CT22, biological replicate 1

description:
DS.1.22
Gene Expression data from Mouse Suprachiasmatic Nucleus treated with DMSO and Sham Light Pulse collected at CT22


title: CORTRAPR

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
R02
processed data file: Tomato_ATLAS_raw_counts.csv
protocols used: growth protocol 1, extract protocol 1 and library construction protocol 1

tag: cultivar

tag: line

tag: age

value: 3-5 days

value: Roots tips


title: EU Seq of ESC. Experiment ID3, 60min A-485 tx, replicate1.

description: Nascent RNA


title: ChIP on POLR2A  and with estradiol treatment of MCF-7 cells (40min) [POL2_plusE2_Fan44]


title: ChIP on POLR2A  and with no estradiol treatment of MCF-7 cells [POL2_shctrl_minusE2_Fan117]


title: ChIP on POLR2A  and with no estradiol treatment of MCF-7 cells [POL2_minusE2_Fan43]


title: EU Seq of ESC. Experiment ID3, control, replicate1.

description: Nascent RNA

value: DMSO


title: EU Seq of ESC. Experiment ID3, 30min A-485 tx, replicate1.

description: Nascent RNA


title: ChIP on H3K9me3 and with estradiol treatment of MCF-7 cells (40min) [H3K9me3_plusE2_Fan96]


title: EU Seq of ESC. Experiment ID2, 120min A-485 tx, replicate2.

description: Nascent RNA


title: EU Seq of ESC. Experiment ID2, 120min A-485 tx, replicate1.

description: Nascent RNA


title: ChIP on H3K9me3 and with no estradiol treatment of MCF-7 cells [H3K9me3_minusE2_Fan95]


title: DMSO-Light  at CT15, biological replicate 2

description:
DL.2.15
Gene Expression data from Mouse Suprachiasmatic Nucleus treated with DMSO and  Light Pulse collected at CT15

tag: tissue


title: KO_ATM_2

city: fuzhou city

first: guo

last: Li

state: fujian province

address: shangjie road

institute: Fujian medical university

description: Mice were kept under specific pathogen-free conditions at the animal facilities of University of Illinois Urbana-Champaign (UIUC) or Fijian Medical University (FJMU). For all experiments, 4-5 weeks old male mice were fed with a normal diet (no. 5058; Lab-Diet) or a high-fat diet (no. D12455; Research Diets Inc.).

data_processing:
none provided by the submitter
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: adipose tissue macrophages,Brd4-CKO

extract_protocol:
Total RNA was extracted from adipose tissue macrophages (ATMs) of WT or Brd4-CKO mice fed HFD for 20 weeks.
RNA was checked for quality using agilent 2100 bioanalyzer and processed for RNA-seq by the Beijing Genomic Institute (BGI) according to their standard protocols.

treatment_protocol: For all experiments, 4-5 weeks old male mice were fed with a normal diet (no. 5058; Lab-Diet) or a high-fat diet (no. D12451; Research Diets Inc.).

tag: genotype

value: adipose tissue


title: DMSO-Sham  at CT15, biological replicate 2

description:
DS.4.15
Gene Expression data from Mouse Suprachiasmatic Nucleus treated with DMSO and Sham Light Pulse collected at CT15

source_name: Mouse SCN from 2 mice pool together after treatment with DMSO, Sham Light Pulse and collected at CT15

tag: strain


title: KO_ATM_3

description: Mice were kept under specific pathogen-free conditions at the animal facilities of University of Illinois Urbana-Champaign (UIUC) or Fijian Medical University (FJMU). For all experiments, 4-5 weeks old male mice were fed with a normal diet (no. 5058; Lab-Diet) or a high-fat diet (no. D12456; Research Diets Inc.).


title: KO_ATM_1

description: Mice were kept under specific pathogen-free conditions at the animal facilities of University of Illinois Urbana-Champaign (UIUC) or Fijian Medical University (FJMU). For all experiments, 4-5 weeks old male mice were fed with a normal diet (no. 5058; Lab-Diet) or a high-fat diet (no. D12454; Research Diets Inc.).


title: iPS-EPS in XF-LCDM

data_processing:
The generated sequencing reads were mapped against human genome build hg19 for human using TopHat alignment software tools.
The read counts for each gene were calculated, and the expression values of each gene were normalized using FPKM.
Genome_build: hg19

growth_protocol: Xeno-free human EPS  cells were cultured in chemically defined LCDM medium under 20% O2 and 5% CO2 at 37°C. Feeder-cultured human EPS cells were cultured in serum-free LCDM medium in 20% O2, 5% CO2 conditions on mitomycin C-inactivated MEF feeder cells

extract_protocol:
Total RNA from each sample was isolated using the RNeasy Plus Mini Kit (QIAGEN).
RNA sequencing libraries were constructed by using magnetic beads with oligo (DT) enriched mRNA. After that, added fragment buffer to break the mRNA into short segments. Using mRNA as template, then synthesized a strand of cDNA with six base random primers. Then added buffer, dNTPs, DNA polymer I and RNase H to synthesize a two strand cDNAs, purified the two strand cDNA with AMPURE XP beads. The purified double stranded cDNA was first repaired, a-tailed and sequenced, and then the fragment size was selected by AMPURE XP beads. Finally, PCR amplification was carried out and PCR products were purified with AMPURE XP beads to obtain the final library.

tag: culture condition

value: Xeno-free


title: U0126-Light  at CT4, biological replicate 3

description:
UL.3.4
Gene Expression data from Mouse Suprachiasmatic Nucleus treated with U0126 and  Light Pulse collected at CT4

source_name: Mouse SCN from 2 mice pool together after treatment with U0126, Light Pulse and collected at CT4


title: U0126-Light  at CT4, biological replicate 1

description:
UL.1.4
Gene Expression data from Mouse Suprachiasmatic Nucleus treated with U0126 and  Light Pulse collected at CT4


title: U0126-Sham  at CT4, biological replicate 3

description:
US.3.4
Gene Expression data from Mouse Suprachiasmatic Nucleus treated with U0126 and Sham Light Pulse collected at CT4

source_name: Mouse SCN from 2 mice pool together after treatment with U0126, Sham Light Pulse and collected at CT4


title: DMSO-Sham  at CT15, biological replicate 1

description:
DS.1.15
Gene Expression data from Mouse Suprachiasmatic Nucleus treated with DMSO and Sham Light Pulse collected at CT15


title: U0126-Sham  at CT4, biological replicate 2

description:
US.2.4
Gene Expression data from Mouse Suprachiasmatic Nucleus treated with U0126 and Sham Light Pulse collected at CT4


title: U0126-Light  at CT4, biological replicate 2

description:
UL.2.4
Gene Expression data from Mouse Suprachiasmatic Nucleus treated with U0126 and  Light Pulse collected at CT4


title: WT_ATM_3

description: Mice were kept under specific pathogen-free conditions at the animal facilities of University of Illinois Urbana-Champaign (UIUC) or Fijian Medical University (FJMU). For all experiments, 4-5 weeks old male mice were fed with a normal diet (no. 5058; Lab-Diet) or a high-fat diet (no. D12453; Research Diets Inc.).

source_name: adipose tissue macrophages,wile type


title: EU Seq of ESC. Experiment ID2, 60min A-485 tx, replicate2.

description: Nascent RNA


title: H1-EPS in XF-LCDM

source_name: Human extended pluripotent stem cells


title: DMSO-Light  at CT4, biological replicate 3

description:
DL.3.4
Gene Expression data from Mouse Suprachiasmatic Nucleus treated with DMSO and  Light Pulse collected at CT4

source_name: Mouse SCN from 2 mice pool together after treatment with DMSO, Light Pulse and collected at CT4


title: U0126-Sham  at CT4, biological replicate 1

description:
US.1.4
Gene Expression data from Mouse Suprachiasmatic Nucleus treated with U0126 and Sham Light Pulse collected at CT4


title: ES2-EPS in XF-LCDM


title: EU Seq of ESC. Experiment ID2, 60min A-485 tx, replicate1.

description: Nascent RNA


title: ES1-EPS in XF-LCDM


title: DMSO-Light  at CT4, biological replicate 1

description:
DL.1.4
Gene Expression data from Mouse Suprachiasmatic Nucleus treated with DMSO and  Light Pulse collected at CT4


title: WT_ATM_1

description: Mice were kept under specific pathogen-free conditions at the animal facilities of University of Illinois Urbana-Champaign (UIUC) or Fijian Medical University (FJMU). For all experiments, 4-5 weeks old male mice were fed with a normal diet (no. 5058; Lab-Diet) or a high-fat diet (no. D12451; Research Diets Inc.).


title: WT_ATM_2

description: Mice were kept under specific pathogen-free conditions at the animal facilities of University of Illinois Urbana-Champaign (UIUC) or Fijian Medical University (FJMU). For all experiments, 4-5 weeks old male mice were fed with a normal diet (no. 5058; Lab-Diet) or a high-fat diet (no. D12452; Research Diets Inc.).


title: EU Seq of ESC. Experiment ID2, 30min A-485 tx, replicate2.

description: Nascent RNA


title: EU Seq of ESC. Experiment ID2, 30min A-485 tx, replicate1.

description: Nascent RNA


title: H1-EPS in F-LCDM

value: Feeder-cultured


title: ES1-EPS in F-LCDM


title: S3G2Str

city: Tel-Aviv

first: Leah

last: Houri-Ze'evi

address: Haim Levanon

department: Neurobiology

country: Israel

institute: Tel-Aviv University

description: small RNA

data_processing:
Adapter trimming - cutadapt
Quality examination - fastQC
Alignment - Shortstack
Counting - HTseq_count
Comparisons - DESeq2
Genome_build: WS235/ce11
Supplementary_files_format_and_content: HTseq_count output files

organism: Caenorhabditis elegans

source_name: Pmex-5::gfp::h2b::tbb-2 (mjIs134 II)

growth_protocol: 20C fed on E.coli OP-50 bacteria

extract_protocol:
TRIzol®
NEBNext® Small RNA Library Prep Set for Illumina®

tag: generation

tag: stress condition

value: Starvation


title: ES2-EPS in F-LCDM


title: EU Seq of ESC. Experiment ID2, control, replicate1.

description: Nascent RNA


title: S3G2Osm

description: small RNA

value: Hyperosmotic conditions


title: DMSO-Light  at CT15, biological replicate 1

description:
DL.1.15
Gene Expression data from Mouse Suprachiasmatic Nucleus treated with DMSO and  Light Pulse collected at CT15

tag: drug treatment


title: SCN_r1r2V.4

city: Houston

first: Zheng

last: Sun

address: One Baylor Plaza

institute: Baylor College of Medicine

data_processing:
The samples were sequenced using BGISEQ-500 platform. The internal software SOAPnuke(v1.5.2) was used to filter reads to get clean reads.
The clean reads were mapped onto reference genome using HISAT(V2.0.4).
The novel transcripts were constructed using StringTie(v1.0.4) and compared to reference annotation using Cufflinks(v.2.2.1). The coding potential of novel transcipts was predicted using CPC(V0.9-r2).
SNP and INDEL were called using GATK. Differentially splicing genes were detected using rMATs(v3.2.5).
Clean reads were mapped using Bowtie2(v2.2.5), and then calculated gene expression levels with RSEM(V1.2.12). DEGs were detected with DEseq2.
Genome_build: mm10
Supplementary_files_format_and_content: xls. files with FPKM values for each sample.

source_name: Suprachiasmic nucleus

extract_protocol: Brains were embedded in OCT and snap-frozen in -80°C. Coronal brain sections containing SCN region were collected. SCN was isolated using a 26G needle on 1ml syringe. Isolated SCN was immediately put into 1 ml TRI reagent ® (Molecular Research Center, Inc) and shear the tissue through needle 30 strokes. RNA was extracted using RNeasy mini kit (QIAGEN) following manufactuer’s protocol.

treatment_protocol: Mice were sacrificed ar ZT12-14 in dark.

value: Brain

tag: Sex

value: Female

tag: developmental stage


title: DMSO-Light  at CT4, biological replicate 2

description:
DL.2.4
Gene Expression data from Mouse Suprachiasmatic Nucleus treated with DMSO and  Light Pulse collected at CT4

tag: light ttreatment

tag: circadian time


title: DMSO-Sham  at CT4, biological replicate 2

description:
DS.2.4
Gene Expression data from Mouse Suprachiasmatic Nucleus treated with DMSO and Sham Light Pulse collected at CT4

source_name: Mouse SCN from 2 mice pool together after treatment with DMSO, Sham Light Pulse and collected at CT4


title: DMSO-Sham  at CT4, biological replicate 3

description:
DS.3.4
Gene Expression data from Mouse Suprachiasmatic Nucleus treated with DMSO and Sham Light Pulse collected at CT4


title: DMSO-Sham  at CT4, biological replicate 1

description:
DS.1.4
Gene Expression data from Mouse Suprachiasmatic Nucleus treated with DMSO and Sham Light Pulse collected at CT4


title: S3G2HS

description: small RNA

value: Heat


title: EU Seq of ESC. Experiment ID1, 120min A-485 tx, replicate2.

description: Nascent RNA

tag: cell type

value: ES cells

tag: cell line

tag: genotype/variation

value: wild type


title: SCN_V.3


title: SCN_r1r2V.5


title: EU Seq of ESC. Experiment ID1, 120min A-485 tx, replicate1.

description: Nascent RNA

tag: treatment


title: S3G2Ctrl

description: small RNA

value: Control


title: SCN_V.2


title: EU Seq of ESC. Experiment ID2, control, replicate2.

description: Nascent RNA


title: ChIP on  SUV39H1 (KMT1A) and with estradiol treatment of MCF-7 cells (40min) [SUV39h1_plusE2_dsgf_Fan68]

data_processing:
The image analysis and base calling were performed by using Illumina's Genome Analysis pipeline.
Quality control: FASTQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and TRIMMOMATIC (http://www.usadellab.org/cms/?page=trimmomatic) was used to inspect the quality of the sequencing reads, and to trim the sequencing adaptors, if necessary.
Read alignment: Bowtie2 (Langmead et al., Nature Methods 2012) was employed to align ChIP-seq and ChIRC-seq samples to hg38 genome and we have kept 1 copy/read per genome position.
Peak finding: we have called the ChIP-seq and ChiRC-seq peaks by using HOMER findPeaks subroutine (Heinz et al., 2010, http://homer.ucsd.edu/homer/). For the CHIP-seq analysis, we have used the default settings in HOMER.
Generation of bedgraph files: we have used the HOMER scripts makeUCSCfile and makeMultiWigHub.pl in order to generate bedgraph files for visualization in the UCSC genome browser.
Genome_build: hg38
Supplementary_files_format_and_content: bedgraph

tag: chip antibody

value: SUV39H1 (KMT1A)


title: ChIP on  SUV39H1 (KMT1A) and with estradiol treatment of MCF-7 cells (40min) [SUV39h1_plusE2_Fan65]


title: EU Seq of ESC. Experiment ID1, 60min A-485 tx, replicate3.

description: Nascent RNA


title: ChIP on  SUV39H1 (KMT1A) and with no estradiol treatment of MCF-7 cells [SUV39h1_minusE2_Fan66]


title: ChIP on  SUV39H1 (KMT1A) and with no estradiol treatment of MCF-7 cells [SUV39h1_minusE2_dsgf_Fan67]


title: S2G2Osm

description: small RNA


title: SCN_r1r2V.1


title: EU Seq of ESC. Experiment ID1, 120min A-485 tx, replicate3.

description: Nascent RNA


title: EU Seq of ESC. Experiment ID1, 60min A-485 tx, replicate2.

description: Nascent RNA


title: NaBu2

first: Liuhui

last: Fu

address: Zhongguancun North Street

department: Institute for Immunology

institute: Tsinghua university

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie2
FPKM were calculated using RSEM tool
Genome_build: mm10
Supplementary_files_format_and_content: xls files include FPKM values for each Sample

source_name: CD8+ T cells

growth_protocol: OT-I CD8+ T cells were purified by MACS negative selection to obtain purities >95% and cultured in complete RPMI-1640 culture medium with 10 ng/ml recombinant mouse IL-2 in plate pre-coated with 1 μg/ml anti-CD3 and 2 μg/ml anti-CD28 for 2 d. Cells were then washed once and cultured in a new plate with 10 ng/ml recombinant mouse IL-2 for another 2 d.

extract_protocol:
Total RNA was isolated with the RNeasy Micro Kit (QIAGEN)
RNA libraries were prepared for sequencing using standard protocols

treatment_protocol: OT-I CD8+ T cells were then treated with control or 1 mM NaBu for 12 hr.

value: LN

value: OT-I

value: 1mM NaBu for 12hr


title: NaBu1


title: S2G2Ctrl

description: small RNA


title: EU Seq of ESC. Experiment ID1, 60min A-485 tx, replicate1.

description: Nascent RNA

data_processing:
Library strategy: EU-Seq
Trimming of adaptors and low-quality sequences (-q 20) was performed using Cutadapt. Read sequences were aligned to mm10 (mouse), using bwa aln with default parameters (BWA version 0.7.10) (Li and Durbin, 2010). Low mapping quality (MAPQ < 10) reads, and reads with more than 3 mismatches were removed using samtools (version 1.4) (Li et al., 2009). Reads mapped to rRNA and tRNA region are removed as described in the RNA-seq section. The number of reads mapped to gene body was counted using HTseq (Anders et al., 2015), and log2 fold-change (FC) and p-values were calculated using DEseq2 (Love et al., 2014). The HTseq default scaling method (median of relative abundance) was used as a scaling factor for the analysis for the mouse cell line data.
Genome_build: mm10
Supplementary_files_format_and_content: Normalized gene track files (bigwig).


title: ChIP on POLR2A Ser2P and with estradiol treatment of MCF-7 cells (40min) and shKAP1 [Pol2S2P_shKAP1_plusE2_C137]

value: POLR2A (RPB1) Ser2P


title: S2G2HS

description: small RNA


title: SCN_V.4


title: S2G2Str

description: small RNA


title: Ctrl2

value: control


title: ChIP on POLR2A Ser2P and with no estradiol treatment of MCF-7 cells and shKAP1 [Pol2S2P_shKAP1_minusE2_C136]


title: S1G2Str

description: small RNA


title: ChIP on POLR2A Ser2P and with estradiol treatment of MCF-7 cells (40min) and shCTRL [Pol2S2P_shCtrl_plusE2_C134]


title: Ctrl1


title: EU Seq of ESC. Experiment ID1, 30min A-485 tx, replicate2.

description: Nascent RNA


title: EU Seq of ESC. Experiment ID1, 30min A-485 tx, replicate3.

description: Nascent RNA


title: EU Seq of ESC. Experiment ID1, control, replicate3.

description: Nascent RNA

value: DMSO


title: S1G2HS

description: small RNA


title: EU Seq of ESC. Experiment ID1, 30min A-485 tx, replicate1.

description: Nascent RNA


title: S1G2Osm

description: small RNA


title: ChIP on POLR2A  and with no estradiol treatment of MCF-7 cells and shKDM4B_shKDM4C [Pol2_shKDM4B4C_minusE2_Fan105]

value: POLR2A (RPB1)


title: S3G1Str

description: small RNA


title: EU Seq of ESC. Experiment ID1, control, replicate2.

description: Nascent RNA


title: S1G2Ctrl

description: small RNA


title: EU Seq of ESC. Experiment ID1, control, replicate1.

description: Nascent RNA


title: ChIP on POLR2A  and with no estradiol treatment of MCF-7 cells and shCTRL [Pol2_shctrl_minusE2_Fan107]


title: ATAC_mESC_A485_1hr_rep2

description:
Cells were treated with A-485 for 60 min.
processed data file: ATAC_mESC_A485_1hr.bw

data_processing:
Read alignment was performed using BWA with default parameters. Low mapping quality read (MAPQ 10) and duplicated reads were removed using samtools.
For differential peak accessibility analysis, all the bam files from the previous steps were merged, and consensus peaks were called using macs2 callpeak (PMID: 18798982) with the following parameter: --nomodel --shift -37 --extsize 73 –broad.
The consensus peak and aligned bam files in each experiment were the input for Diffbind.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigWig

extract_protocol:
Cells were washed once in pre-warmed PBS, disaggregated using TrypLE (Thermo Fisher Scientific), and trypsinization was stopped by adding cold media. Two hundred thousand cells were transferred to LoBind microfuge tube (Eppendorf) and centrifuged at 500g for 5min at 4ºC. After centrifugation, the cells were suspended in buffer A (10mM HEPES pH 7.9, 10mM KCl, 1.5mM MgCl2, 0.34M Sucrose, 10% Glycerol, 10% Triton-X), mixed by tapping and incubated on ice for 7min. After centrifugation, buffer A was removed, and nuclei were suspended in lysis buffer (10mM Tris-HCl pH7.4, 10mM NaCl, 3mM MgCl2, 0.3% Igepal). A quarter of nuclei was transferred to a new Lobind tube, briefly vortexed, incubated on ice for 15min, vortexed briefly again, and pelleted down at 600g for 10min at 4ºC. After removing lysis buffer, nuclei were recovered with 2.5 μL 2X TD buffer and 2.5 μL transposase (TDE1) mixture (Illumina). After pipetting several times, the nuclei were incubated for 30min at 37 ºC on a rocking mixer. The transposed DNA was purified using the MinElute PCR Purification kit (Qiagen) following the manufacturer's protocol.
The transposed genomic region was PCR-amplified using Nextera Primers (https://www.encodeproject.org/documents/860c95a8-fdc4-46bd-b9b5-d44242ff20ef/@@download/attachment/ATAC_garberlab_protocol.pdf) and NEBNext High-Fidelity 2x PCR Master Mix (NEB). PCR product was purified using Agencourt® AMPure® XP beads (Beckman Coulter) and sequenced on a Next-Seq 500 Sequencer (Illumina).

value: A-485 for 60 min


title: ChIP on  NELFA and with no estradiol treatment of MCF-7 cells and shHP1a_shHP1b [NELFA_shHP1ab_minusE2_Fan116]

value: NELFA


title: S3G1HS

description: small RNA


title: ChIP on POLR2A Ser2P and with no estradiol treatment of MCF-7 cells and shCTRL [Pol2S2P_shCtrl_minusE2_C135]


title: ChIP on POLR2A  and with estradiol treatment of MCF-7 cells (40min) and shKDM4B_shKDM4C [Pol2_shKDM4B4C_plusE2_Fan106]


title: EU Seq of ESC. Experiment ID3, 120min A-485 tx, replicate1.

description: Nascent RNA

extract_protocol:
Following 5-EU labelling, cells were quickly washed (1x) with PBS, and immediately lysed in RLT buffer and RNA was prepared using RNeasy Mini Kit (Qiagen).
The labelled RNA was subsequently enriched using the Click-iT® Nascent RNA Capture Kit (Thermo Fisher Scientific) according to the manufacturer’s instructions. Where indicated, rRNA was depleted using NEBNext® rRNA Depletion Kit (NEB) before the enrichment of labelled RNA. RNA-seq libraries were prepared using the NEBNext Ultra kit (NEB) as per manufacturer’s instructions and subsequently sequenced using a Next-Seq 500 Sequencer (Illumina).


title: ATAC_mESC_A485_1hr_rep1


title: HK2 cell treated with rLRR20 rep2

city: Taoyuan

first: Shen-Hsing

last: Hsu

address: 5 Fu-Shing St.

department: Kidney Research Center

country: Taiwan

institute: Chang Gung Memorial Hospital

description: Gene expression data from HK2 cell treated with rLRR20

hyb_protocol: Standard Applied Biosystems GeneChip WT PLUS Reagent Kit protocol

scan_protocol: Standard Applied Biosystems protocol

data_processing: Normalize with SST-RMA by Applied Biosystems Transcriptome Analysis Console Ver 4.0

label: biotin

source_name: HK2 cell treated with rLRR20

growth_protocol: HK2 cell were incubated at 37 ℃ in a humidified atmosphere of 5% (v/v) CO2 to 70% confluence and serum-starved overnight before stimulation .

extract_protocol: The total RNA was extracted by Trizol extraction methods according to the manufacturer's instructions.

treatment_protocol: HK2 cell were stimulated with 10 μM purified rLRR20 for 4 h. The control groups were treated with PBS buffer.

value: HK2 cell (ATCC #CRL-2190)


title: S3G1Ctrl

description: small RNA


title: miRNA MOCK-3

city: Hangzhou

first: Haimin

state: zhejiang

address: yuhangtang Road

department: College of Animal Science

institute: Zhejiang University

description:
MOCK-3
control

data_processing:
Poly-N, adapter and low-quality were removed by in-house perl scripts ，Quality control analysis was performed by ng_qc.
Clean reads were aligned to the Sus scrofa ensembl 76 using Tophat v2.0.9 with the following configurations two passMode Basic --hhlibraryhtypecfrhfirststrand.
Sus scrofa ensembl 76
circRNAs were identified using find-circ. It was considered to be a circRNA when  the read count was no less than 2.
bowtie was used to aligne the miRNAs to the Sus scrofa ensemble 76
Genome_build: tab-delimited excel files include  normalized  values for each Sample

organism: Sus scrofa

source_name: porcine kidney epithelial cells

extract_protocol:
Total RNA was isolated from infected cells using SuPerfecTRITM Total RNA Isolation Reagent (Pufei) according to the manufacturer.
A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Firstly, ribosomal RNA was removed by Epicentre Ribo-zeroTM rRNA Removal Kit (Epicentre, USA), and rRNA free residue was cleaned up by ethanol precipitation. Then, linear RNA was removed by RNaseR digeston.  Subsequently, sequencing libraries were generated using the rRNA-depleted RNA by NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations. For miRNA, sequencing libraries were generated using Small RNA Sample Pre Kit according to the manufacture.

treatment_protocol: PK-15 cells were infected with PRV-DX, and gE-TK- PRV-DX at a multiplicity of infection (MOI) of 5 and harvested at 11 hour post infection or without, respectively.

value: uninfected


title: ChIP on  NELFA and with estradiol treatment of MCF-7 cells (40min) and shCTRL [NELFA_shctrl_plusE2_Fan113]


title: ATAC_mESC_A485_30min_rep2

description:
Cells were treated with A-485 for 30 min.
processed data file: ATAC_mESC_A485_30min.bw

value: A-485 for 30 min


title: HK2 cell treated with rLRR20 rep1

label_protocol: Standard Applied Biosystems GeneChip WT PLUS Reagent Kit protocol


title: ChIP on POLR2A  and with estradiol treatment of MCF-7 cells (40min) and shCTRL [Pol2_shctrl_plusE2_Fan108]


title: HK2 cell treated with rLRR20 rep3


title: S3G1Osm

description: small RNA

value: Hyperosmotic conditions


title: S2G1Str

description: small RNA

value: Starvation


title: miRNA MOCK-1

description:
MOCK-1
control


title: miRNA MOCK-2

description:
MOCK-2
control


title: ChIP on  NELFA and with no estradiol treatment of MCF-7 cells and shCTRL [NELFA_shctrl_minusE2_Fan114]


title: S2G1HS

description: small RNA

value: Heat


title: HK2 cell treated with PBS rep3

description: Gene expression data from HK2 cell treated with PBS

source_name: HK2 cell treated with PBS


title: HK2 cell treated with PBS rep2


title: S2G1Osm

description: small RNA


title: HK2 cell treated with PBS rep1


title: ATAC_mESC_Ctrl_rep2

description:
Cells were treated with DMSO for 60 min.
processed data file: ATAC_mESC_Ctrl.bw

value: ES cells

value: DMSO for 60 min


title: ChIP on  NELFA and with estradiol treatment of MCF-7 cells (40min) [NELFA_plusE2_Fan151]


title: miRNA gE-TK-PRV-DX-2

description:
gE-TK-PRV-DX-2
infected at MOI=5 and harvested at 11 hour post infection

value: infected gE-TK-PRV-DX

value: attenuated gE/TK gene dual-deficiency


title: S2G1Ctrl

description: small RNA

value: Control


title: ATAC_mESC_Ctrl_rep1


title: EU Seq of ESC. Experiment ID3, 60min TSA and A-485 tx , replicate1.

description: Nascent RNA

value: wild type

value: 60min TSA and A-485


title: ChIP on KDM4C and with estradiol treatment of MCF-7 cells (40min) [KDM4C_plusE2_FanC102]


title: ChIP on  NELFA and with no estradiol treatment of MCF-7 cells [NELFA_minusE2_Fan150]


title: ESC_JQ1_Pol2_TC60_1

description:
Cells were treated with 0.5 mM JQ1 for 60 min.
processed data file: ChIP.ESC_JQ1_Pol2_TC60.n.bw

data_processing:
Read alignment was performed using BWA with default parameters. Low mapping quality read (MAPQ 10) and duplicated reads were removed using samtools. The DAC Blacklisted Regions were also omitted from the bam file using bedtools. Peaks were called using epic with the following parameters: --fragment-size 200 --gaps-allowed 5.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigWig

extract_protocol:
Cells were cross-linked for 10 min at room temperature with 1% formaldehyde solution with gentle agitation and quenched with 0.125 M glycine. Cross-linked cells were washed once with PBS, added swelling buffer (10 mM Tris-HCl pH8.0, 1.5 mM MgCl2, 10 mM NaCl, 0.5% NP-40) and incubated on ice for 10 minutes. After centrifugation, pellets were suspended with RIPA buffer (10 mM Tris-HCl pH8.0, 1 mM EDTA, 140 mM NaCl, 1% Triton X-100, 0.1% SDS, 0.1% Sodium Deoxycholate) containing proteinase inhibitor cocktail (Roche), and then were sonicated by using a BioRuptor sonicator (Diagenode). After centrifugation, solubilized chromatin was recovered and incubated with 5 µg of antibody bound to protein A/G magnetic beads (Pierce). After overnight incubation at 4ºC, the magnetic beads were washed with RIPA buffer twice, RIPA high salt buffer (10 mM Tris-HCl pH8.0, 1 mM EDTA, 500 mM NaCl, 1% Triton X-100, 0.1% SDS, 0.1% Sodium Deoxycholate), LiCl buffer (10 mM Tris-HCl pH8.0, 1 mM EDTA, 250 mM LiCl, 0.5% NP-40, 0.5% Sodium Deoxycholate) and TE buffer. The bound materials were eluted with elution buffer (10 mM Tris-HCl pH8.0, 5 mM EDTA, 300 mM NaCl, 0.1% SDS) overnight at 65ºC and treated with RNaseA for 30 min for 37°C and further incubation with Proteinase K for 1 hour at 37ºC. Then DNA was purified with a PCR purification kit (Qiagen).
ChIP-seq libraries were prepared by using the NEBNext Ultra II DNA prep kit (NEB E7645) following the manufacturer's instruction and sequenced on a Next-Seq 500 Sequencer (Illumina).

treatment_protocol: A-485 (10uM) or JQ1 (0.5mM) were treated for 60 min if not indicated. For control samples, 0.1% DMSO was added.

value: 05 mM JQ1 for 60 min

value: Pol2 (Abcam, ab817)


title: miRNA gE-TK-PRV-DX-1

description:
gE-TK-PRV-DX-1
infected at MOI=5 and harvested at 11 hour post infection


title: ESC_JQ1_Pol2_TC60_2


title: S1G1Str

description: small RNA


title: ATAC_mESC_A485_30min_rep1


title: DMSO-Sham  at CT15, biological replicate 3

description:
DS.3.15
Gene Expression data from Mouse Suprachiasmatic Nucleus treated with DMSO and Sham Light Pulse collected at CT15

value: DMSO

value: Sham Pulse

value: Brain Suprachiasmatic Nucleus (SCN)


title: ChIP on KDM4C and with estradiol treatment of MCF-7 cells (40min) [KDM4C_plusE2_Fan70]


title: ChIP on KDM4C and with no estradiol treatment of MCF-7 cells [KDM4C_minusE2_FanC101]


title: miRNA PRV-DX-3

description:
PRV-DX-3
infected at MOI=5 and harvested at 11 hour post infection

value: infected with PRV-DX


title: ESC_JQ1_Pol2_TC30_2

description:
Cells were treated with 0.5 mM JQ1 for 30 min.
processed data file: ChIP.ESC_JQ1_Pol2_TC30.n.bw

value: 05 mM JQ1 for 30 min


title: miRNA PRV-DX-2

description:
PRV-DX-2
infected at MOI=5 and harvested at 11 hour post infection


title: S1G1Osm

description: small RNA

value: Hyperosmotic conditions


title: S1G1HS

description: small RNA


title: ESC_JQ1_Pol2_TC30_1


title: S1G1Ctrl

description: small RNA


title: ChIP on KDM4C and with no estradiol treatment of MCF-7 cells [KDM4C_minusE2_Fan69]


title: ChIP on KDM4B  and with estradiol treatment of MCF-7 cells (40min) [KDM4B_plusE2_FanC104]


title: miRNA PRV-DX-1

description:
PRV-DX-1
infected at MOI=5 and harvested at 11 hour post infection


title: ESC_JQ1_Pol2_TC15_2

description:
Cells were treated with 0.5 mM JQ1 for 15 min.
processed data file: ChIP.ESC_JQ1_Pol2_TC15.n.bw

value: 05 mM JQ1 for 15 min


title: miRNA gE-TK-PRV-DX-3

description:
gE-TK-PRV-DX-3
infected at MOI=5 and harvested at 11 hour post infection


title: ChIP on KDM4B  and with estradiol treatment of MCF-7 cells (40min) [KDM4B_plusE2_Fan90]


title: circRNA MOCK-3

description:
MOCK-3
control

value: uninfected


title: ChIP on KDM4B  and with no estradiol treatment of MCF-7 cells [KDM4B_minusE2_FanC103]


title: circRNA MOCK-2

description:
MOCK-2
control


title: ChIP on KDM4B  and with no estradiol treatment of MCF-7 cells [KDM4B_minusE2_Fan89]


title: ESC_Ctrl.JQ1_Pol2_TC0_1

description:
Cells were treated with DMSO for 60 min.
processed data file: ChIP.ESC_Ctrl.JQ1_Pol2_TC0.n.bw

value: ES cells


title: ESC_JQ1_Pol2_TC15_1


title: ESC_A485_Pol2_TC60_2

description:
Cells were treated with 10uM A-485 for 60 min.
processed data file: ChIP.ESC_A485_Pol2_TC60.n.bw

value: 10uM A-485 for 60 min


title: circRNA gE-TK-PRV-DX-3

value: infected gE-TK-PRV-DX


title: ESC_Ctrl.JQ1_Pol2_TC0_2

value: DMSO for 60 min


title: circRNA MOCK-1

description:
MOCK-1
control


title: circRNA gE-TK-PRV-DX-2

value: attenuated gE/TK gene dual-deficiency


title: ChIP on KAP1 (TRIM28)  and with estradiol treatment of MCF-7 cells (40min) [KAP1_plusE2_C141]

value: KAP1 (TRIM28)


title: ESC_A485_Pol2_TC60_1


title: ChIP on KAP1 (TRIM28) and with no estradiol treatment of MCF-7 cells [KAP1_minusE2_Fan137]


title: ESC_A485_Pol2_TC30_2

description:
Cells were treated with 10uM A-485 for 30 min.
processed data file: ChIP.ESC_A485_Pol2_TC30.n.bw

value: 10uM A-485 for 30 min


title: circRNA gE-TK-PRV-DX-1


title: circRNA PRV-DX-3

value: wild type


title: ESC_A485_Pol2_TC30_1

value: Pol2 (Abcam, ab817)


title: ChIP on HP1a (CBX5) and with estradiol treatment of MCF-7 cells (40min) [HP1_plusE2_Fan93]

value: HP1A (CBX5)


title: ESC_A485_Pol2_TC15_2

description:
Cells were treated with 10uM A-485 for 15 min.
processed data file: ChIP.ESC_A485_Pol2_TC15.n.bw

value: 10uM A-485 for 15 min


title: ChIP on HP1a (CBX5) and with no estradiol treatment of MCF-7 cells [HP1_minusE2_Fan94]


title: Control [3634-7]

city: Halle

first: Edith

last: Willscher

state: Deutschland

address: Ernst-Grube-Straße 40

department: Internal Medicine IV

country: Germany

institute: Martin Luther University of Halle-Wittenberg

hyb_protocol: From each probe 750 ng of cRNA were hybridised to Human HT-12 v4 Expression BeadChips

scan_protocol: scanned on the Illumina HiScan instrument

data_processing: Raw probe data was quantile normalized and background corrected by Illumina GenomeStudio

source_name: Human Gut

label_protocol: 250ng RNA per sample were ethanol precipitated with GlycoBlue (Invitrogen) as carrier and dissolved at a concentration of 100-150 ng/µl prior to probe synthesis using the TargetAmp™- Nano Labeling Kit for Illumina Expression BeadChip.

extract_protocol: Fresh tissue samples were snap frozen and stored in liquid nitrogen until preparation. Frozen biopsies were disrupted and homogenized by TissueLyzer from Quiagen (Hilden, Germany). Total RNA was isolated using AllPrep® DNA/RNA Micro kit (QIAGEN, Hilden, Germany) and stored at -70°C.  Before microarray analysis RNA integrity and concentration was examined on an Agilent 2100 Bioanalyzer

tag: disease

value: Control

tag: marsh stage

tag: age


title: Control [4107-1_2]


title: Celiac disease [7259-7]

value: Celiac disease


title: circRNA PRV-DX-1

value: infected with PRV-DX

tag: strain


title: Celiac disease [0047-7_2]


title: ChIP on KAP1 (TRIM28)  and with estradiol treatment of MCF-7 cells (40min) [KAP1_plusE2_Fan138]


title: Control [2684-X]


title: Control [4445-0]


title: ChIP on HEXIM1 and with estradiol treatment of MCF-7 cells (40min) [HEXIM1_plusE2_FanC124]


title: ESC_A485_Pol2_TC5_1

description:
Cells were treated with 10uM A-485 for 5 min.
processed data file: ChIP.ESC_A485_Pol2_TC5.n.bw

source_name: mouse ES cells

value: 10uM A-485 for 5 min


title: ChIP on KAP1 (TRIM28) and with no estradiol treatment of MCF-7 cells [KAP1_minusE2_C140]


title: ESC_A485_Pol2_TC5_2


title: ChIP on H3K9me3 and with no estradiol treatment of MCF-7 cells and shKDM4B_shKDM4C [H3K9me3_shKDM4B4C_minusE2_FanC113]


title: Np95 knockout spermatocytes Rep_2

city: Yokohama-shi

first: Jafar

last: Sharif

state: Kanagawa-ken

address: 1-7-22 Suehiuro-cho, Tsurumi-ku

department: IMS

country: Japan

institute: RIKEN

data_processing:
Fastq raw reads were mapped to the mm9 genome with Bowtie2.
RPKM values were calculated using VisR (https://visrsoftware.github.io/)
Genome_build: mm9
Supplementary_files_format_and_content: RPKM, csv

source_name: Spermatocytes

growth_protocol: Spermatocytes collected from the testes of 21 dpc mice

extract_protocol:
RNA was extracted using the QIAGEN DNA/RNA allprep kit (80204)
Poly-A RNA was enriched by NEBNext® Poly(A) mRNA Magnetic Isolation Module (E7490), and library was prepared with NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (E7770). 50-bp paired-end reads were generated by Novaseq 6000.

treatment_protocol: Seminiferous tubules were chopped into small pieces and treated with accutase, and the cell suspension was passed through a 95um mesh, to obtain spermatocyte single cell suspension.

value: Np95 knock out


title: Np95 knockout spermatocytes Rep_1


title: ChIP on H3K9me3 and with no estradiol treatment of MCF-7 cells and shKDM4B_shKDM4C [H3K9me3_shKDM4B4C_minusE2_FanC109]


title: Control [2029-0]


title: circRNA PRV-DX-2


title: ChIP on HEXIM1 and with no estradiol treatment of MCF-7 cells [HEXIM1_minusE2_FanC123]


title: ESC_Ctrl_Pol2_TC0_2

first: Chunarum

address: Blegdamsvej 3B

institute: University of Copenhagen

description:
Cells were treated with DMSO for 60 min.
processed data file: ChIP.ESC_Ctrl_Pol2_TC0.n.bw


title: ESC_A485_Pol2_TC15_1


title: Control spermatocytes RNAseq Rep_2

value: control


title: ESC_Ctrl_Pol2_TC0_1

value: ES cells


title: Celiac disease [5691-4]


title: ChIP on H3K9me3 and with no estradiol treatment of MCF-7 cells and shCTRL [H3K9me3_shctrl_minusE2_FanC111]


title: Control spermatocytes RNAseq Rep_1


title: Control [4107-1_1]


title: ChIP on H3K9me3 and with no estradiol treatment of MCF-7 cells and shCTL [H3K9me3_shctrl_minusE2_FanC107]


title: Celiac disease [7049-0]


title: Celiac disease [4938-8]


title: ESC_JQ1_BRD4_TC60_2

description:
Cells were treated with 0.5 mM JQ1 for 60 min.
processed data file: ChIP.ESC_JQ1_BRD4_TC60.n.bw

value: 05 mM JQ1 for 60 min


title: Celiac disease [9482-5]


title: ESC_A485_BRD4_TC60_2

description:
Cells were treated with 10uM A-485 for 60 min.
processed data file: ChIP.ESC_A485_BRD4_TC60.n.bw

value: 10uM A-485 for 60 min


title: ChIP on H3K9me3 and with no estradiol treatment of MCF-7 cells [H3K9me3_minusE2_rep2_Fan104]


title: ESC_A485_BRD4_TC15_2

description:
Cells were treated with 10uM A-485 for 60 min.
processed data file: ChIP.ESC_A485_BRD4_TC15.n.bw


title: ChIP on H3K9me3 and with estradiol treatment of MCF-7 cells (40min) [H3K9me3_plusE2_rep2_Fan103]


title: Klf2KD/Snd1KD_rep1_RNA-seq

city: Daejeon

first: Lin

last: Seo

address: Basic Science Bld Rm414, 291 Daehak-ro, Yuseong-gu, KAIST

department: Department of Biological Sciences

country: South Korea

institute: KAIST

data_processing:
Reads were aligned to mm39 using HISAT2
Genome_build: mm39
Supplementary_files_format_and_content: Bigwig files were generated using deeptools2 bamCoverage

source_name: Embryonic stem cells

growth_protocol: E14Tg2a cells were cultured in 0.1% gelatin coated dishes with KnockOut DMEM (Gibco) with 15% FBS, NEAA, L-glutamine, 2-mercaptoethanol, and 1,000 U/ml LIF.

extract_protocol:
RNA samples were lyesed with total RNA extraction kit.
Libraries were prepared according to Illumina's instructions.

treatment_protocol: From HEK 293T cells, shControl, shKlf2 and shSnd1 lentiviruses were harvested. Lentiviral particles (MOI 10) with hexadimethrine bromide were infected in E14TG2a and selected with 2 ug/ml puromycin.

tag: background strain

tag: genotype

value: Wild-type

value: shKlf2, shSnd1

tag: cell types


title: Klf2KD/Snd1KD_rep2_RNA-seq


title: ESC_A485_BRD4_TC60_1

city: Copenhagen N

last: Choudhary


title: Snd1KD_rep1_RNA-seq


title: ESC_JQ1_BRD4_TC60_1


title: Snd1KD_rep2_RNA-seq


title: Celiac disease [2861-7]


title: Klf2KD_rep2_RNA-seq


title: ESC_A485_BRD4_TC15_1


title: ChIP on H3K9K14ac and with estradiol treatment of MCF-7 cells (40min) [H3K9K14ac_plusE2_Fan86]