title: MG_DM3_BR3_RNAseq

city: Charlottesville

first: Roza

middle: Kamila

last: Przanowska

state: Virginia

department: Biomedical Engineering

institute: University of Virginia

data_processing:
STAR
HTSeq
DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: .txt: table with fpkm for all samples

source_name: Murine myoblasts C2C12

growth_protocol: C2C12 PAX7 NEG cells were maintained in HyClone Dulbecco’s High Glucose Modified Eagles Medium (GE #SH30081.01) with 20% FBS. For differentiation to myotubes serum was exchanged to 2%HS.

extract_protocol:
Cells were grown to ~80% confluency for GM or differentiated for 3 days for DM3 and washed briefly twice with ice-cold PBS. Total RNA was extracted by Trizol reagent (Invitrogen #15596018) and purified with column-based Direct-zol RNA Miniprep kit (Zymo Research #R2051).
RNA-seq was performed by Hudson Alpha on poly(A) enriched RNA using the Illumina HiSeq 2500 instrument.

tag: genotype/variation

value: MUNC genomic overexpressing

value: Myotubes


title: 0.25X Dox, Input

status: Public on Jan 21 2022

type: SRA

city: Pasadena

first: Mario

middle: R

last: Blanco

state: CA

address: 1200 E California Blvd

country: USA

institute: Caltech

description: DNA associated with Xist RNA captured using hybridization capture

library_source: genomic

data_processing:
Raw fastq reads were trimmed and removed of Illumina adapters and low quality reads.
Filtered paired-end reads were aligned using STAR aligner and uniquely mapped reads kept for analysis.
Bigwig files were created using Deeptools suite to summarize read coverage.
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files summarizing read-depth coverage per sample.

molecule: genomic DNA

organism: Mus musculus

source_name: mouse embryonic stem cells

extract_protocol:
Lysate was prepared and diluted to hybridization conditions containing 3M guanidine thiocyanate, precleared by adding streptavidin-coated magnetic beads and incubating for 30 minutes at 37°C, mixed with biotin-labeled single stranded DNA capture probes, and incubated at 37°C for 2 hours. Streptavidin beads were used to capture the hybridized complexes. Next, captured chromatin complexes were eluted with RNaseH and crosslinks were reversed by adding Proteinase K to the probe-bead complexes and incubating overnight at 65°C.
DNA from captures was purified and subjected to standard Illumina sequencing procedures.

treatment_protocol: Cells were crosslinked with 3% Formaldehyde +DSG

tag: cell type

value: mouse embryonic stem cells

tag: genotype

value: expressing Xist under a Dox inducible promoter

tag: treatment

value: Dox induction, 0.25X

tag: crosslinking

value: 3% Formaldehyde + DSG

tag: fraction

value: input


title: 0.25X Dox, Rep2

value: DNA from captures


title: 0.25X Dox, Rep1


title: 14-EndoC-E2-Val-SiQ-IFNa.14

city: Anderlecht

first: Valerie

last: Vandenbempt

state: Vlaams-Brabant

address: Lenniksebaan 808

country: Belgium

institute: Université Libre de Bruxelles

library_source: transcriptomic

data_processing:
STAR alignment
HTseq count
DE analysis
analysis using Degust for log fold changes and statistics (limma-voom)
batch effect removal
LogfoldChange calculations
Genome_build: GRCh38

molecule: total RNA

organism: Homo sapiens

source_name: EndoC-𝛽H1 cells

growth_protocol: The human β-cell line EndoC-βH1 (kindly provided by Dr. R. Scharfmann, University of Paris, France) was cultured in Matrigel-fibronectin-coated plates

extract_protocol:
RNAeqsy mini kit (Qiagen #741014)
Tru stranded mRNA kit (illumina #20020594)

treatment_protocol: EndoC-βH1 and dispersed human islets have been transfected with small interfering RNAs (siRNAs) against STAT3, STAT1 or allstars Negative Control siRNA (negative control), Qiagen, Venlo, the Netherlands) (30nM) using Lipofectamine RNAiMAX (Invitrogen, Carlsbad, CA, USA)

value: Control

value: Interferon-alpha


title: 13-EndoC-E2-Val-SiQ-Ctl.13


title: MG_DM3_BR2_RNAseq

molecule: polyA RNA

tag: cell line

tag: tissue


title: CLAP, FLSHARP, Rescue, RepB

source_name: CLAP, FLSHARP, Rescue

extract_protocol:
Cells were lysed in RIPA lysis buffer and bound to Halo-link resin to purify Halo-tagged SHARP variants.
RNA from Halo captures were purifed and subjected to stranded RNA-seq library prepartion by the ligation of 3' adapter to RNA and cDNA prior to PCR amplification.

treatment_protocol: Cells were crosslinked 0.25 J cm−2 (UV2.5k) of UV at 254 nm in a Spectrolinker UV Crosslinker.

value: UV

tag: variants of sharp protein

value: FL (full length sharp protein)

tag: fusion protein

value: N-terminal Halo-tag

tag: purification of halo-tagged sharp variants

value: Halo-link resin


title: 12-EndoC-E1-Val-SiPTPN2-IFNY.12

value: PTPN2 silencing

value: Interferon-gamma


title: 11-EndoC-E1-Val-SiPTPN2-IFNa.11


title: CLAP, EndoSHARP, RepB

source_name: CLAP, EndoSHARP

value: Endo (endogenous SHARP protein)


title: MG_DM3_BR1_RNAseq

source_name: Murine myotubes C2C12

value: MUNC genomic overexpressing


title: CLAP, dRRM, Rescue, RepB

source_name: CLAP, dRRM, Rescue

value: dRRM (deletion of RRM domain)


title: 10-EndoC-E1-Val-SiPTPN2-Ctl.10


title: CLAP, dIDR, Rescue, RepB

source_name: CLAP, dIDR, Rescue

value: dIDR (deletion of IDR region)

value: mouse embryonic stem cells


title: 8-EndoC-E1-Val-SiQ-IFNa.8


title: MS_DM3_BR3_RNAseq

value: MUNC spliced overexpressing

value: Myotubes


title: MS_DM3_BR2_RNAseq


title: MS_DM3_BR1_RNAseq


title: 17-EndoC-E2-Val-SiPTPN2-IFNa.17


title: Control_DM3_BR3_RNAseq

value: Wild-type


title: 10-day old cecum control 3

city: Yangzhou

first: 金俊

middle: 许金俊

last: 许

address: Floor 29, campus of Wenhui Road

country: China

institute: College of Veterinary Medicine, Yangzhou University

data_processing:
Illumina Casava1.8 software used for basecalling
The raw reads obtained by sequencing contains low-quality reads with connectors. In order to ensure the quality of information analysis, rawreads must be processed to get cleanreads.
The clean reads of each sample was screened, and the sRNA within a certain length was selected for follow-up analysis.
Reference sequence alignment analysis
The expression levels of known and new miRNAs in each sample were counted, and transcripts per million clean tags (TPM)
Genome_build: gallus_gallus_Ensembl_97
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: cecum

extract_protocol:
The cecum samples aseptically collected from chickens were thoroughly rinsed in PBS and immediately frozen in liquid nitrogen. Then the cecum samples were stored at −80°C until RNA extraction.Total RNA was prepared from individual cecum samples using TRIzol Reagent according to the manufacturer's instruction. The small RNA libraries were prepared from a total of 2 μg total RNA isolated from each sample using NEBNext® Multiplex Small RNA Library Prep Set for Illumina®
smallRNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Histomonas meleagridis infect/control

tag: age

value: 10-day old

tag: agent

value: control

value: cecum


title: 7-EndoC-E1-Val-SiQ-Ctl.7

value: Control


title: CLAP, EndoSHARP, RepA

value: UV


title: Control_DM3_BR2_RNAseq


title: 6-EndoC-E1-10-IFNY.6


title: CLAP, dRRM, Rescue, RepA

value: N-terminal Halo-tag


title: Control_DM3_BR1_RNAseq


title: CLAP, dIDR, Rescue, RepA

value: Halo-link resin


title: MG_GM_BR3_RNAseq

value: Myoblasts


title: INPUT, FLSHARP, Rescue, RepB

source_name: INPUT, FLSHARP, Rescue

value: FL (full length sharp protein)

value: none (input)


title: INPUT, EndoSHARP, RepB

source_name: INPUT, EndoSHARP

value: Endo (endogenous SHARP protein)


title: MG_GM_BR1_RNAseq

value: MUNC genomic overexpressing


title: 2-EndoC-E1-SiQ-IFNa.2

value: Interferon-alpha


title: INPUT, dRRM, Rescue, RepB

source_name: INPUT, dRRM, Rescue

value: dRRM (deletion of RRM domain)

value: mouse embryonic stem cells


title: MS_GM_BR3_RNAseq

value: MUNC spliced overexpressing


title: 1-EndoC-E1-SiQ-Ctl.1


title: INPUT, dIDR, Rescue, RepB

source_name: INPUT, dIDR, Rescue

value: dIDR (deletion of IDR region)


title: INPUT, EndoSHARP, RepA


title: MS_GM_BR2_RNAseq


title: 9-EndoC-E1-Val-SiQ-IFNY.9

value: Interferon-gamma


title: INPUT, FLSHARP, Rescue, RepA


title: CLAP, FLSHARP, Rescue, RepA


title: HcordbloodN1_2

city: Lausanne

first: Nadine

last: Fournier

state: Vaud

address: Agora Cancer Research Center, Bugon 25A

country: Switzerland

institute: Agora Cancer Research Center & Swiss Institute of Bioinformatics

description: HcordbloodN1_2_FKDL202595134-1a_HC25CDSXY_L1

data_processing:
Illumina bcl2fastq 2.19.1 software was used for base calling.
Reads were trimmed using atropos (1.1.21) to remove the Illumina TruSeq adapter sequences.
Trimmed reads were aligned to the human genome (hg38) using BWA-MEM (0.7.17).
The aligned reads were filtered to include reads from chromosomes 1 - 22, X, and Y using samtools (1.9) and duplicates were marked using “MarkDuplicates” from Picard (2.18.27).
ATAC-seq peaks were called with MACS2 (2.1.1.20160309).
Genome_build: hg38
Supplementary_files_format_and_content: bedGraph file for each ChIP sample - generated by MACS2

source_name: CD34- CD38+ CD5- CD7+ GFP+

extract_protocol:
20'000 induced immature cells were isolated from cultured human cord blood and processed as in Current Protocol in Molecular Biology by Buenrostro et al. in 2015 ATAC-Seq: A Method for Assaying Chromatin Accessibility Genome-Wide.
Library was amplify using NEBNext High-Fidelity 2X PCR Master Mix and size selection was performed using Agencourt AMPure XP beads. The primer list can be found in Current Protocol in Molecular Biology by Buenrostro et al. in 2015 ATAC-Seq: A Method for Assaying Chromatin Accessibility Genome-Wide.
sequencing protocol: Sequencing was performed by Novogene using the Illumina NovaSeq and the 150-bp paired-end configuration to obtain at least 100 million reads per sample.

value: cord blood CD34 cells

tag: group

tag: replicate

tag: batch


title: HcordbloodN1_1

description: HcordbloodN1_1_FKDL202595133-1a_HHGCHDSXY_L4


title: Control_GM_BR3_RNAseq

value: Wild-type


title: INPUT, dRRM, Rescue, RepA


title: Control_GM_BR2_RNAseq


title: SC328 Pulp 2 scRNA-seq

city: Wuhan

first: Wei

last: Yin

address: 237 Luoyu road

institute: Wuhan Unuversity

description: *** Raw data not provided due to patient privacy concerns ***

data_processing: Raw sequencing reads of the cDNA library were processed through the BD Rhapsody Whole Transcriptome Analysis pipeline.

source_name: Dental pulp 2

extract_protocol: Transcriptome of single cells were obtained through BD Rhapsody System. Microbeads-captured single cell transcriptome sequences were generated into cDNA library containing cell labels and unique molecular identifiers (UMI) information. Briefly, double strand cDNA was firstly generated from microbeads-captured single cell transcriptome through several steps including reverse transcription, second strand synthesis, end preparation, adapter ligation and whole transcriptome amplification. Then final cDNA library was generated from double strand full length cDNA by random priming amplification with BD Rhapsody cDNA Kit (BD Biosciences, Cat. No. 633773) and BD Rhapsody Targeted mRNA & AbSeq Amplification Kit (BD Biosciences, Cat No. 633774).

tag: gender

value: Female

value: Dental pulp


title: INPUT, dIDR, Rescue, RepA

value: UV

value: N-terminal Halo-tag


title: SC327 Pulp 1 scRNA-seq

source_name: Dental pulp 1


title: Control_GM_BR1_RNAseq

tag: genotype/variation

value: Myoblasts


title: S100A4 1

status: Public on Jan 20 2022

city: Geneva

first: Sylvain

last: LEMEILLE

address: 1 rue Michel-Servet

department: Department of Pathology and Immunology

institute: University of Geneva Medical School

description:
S100A4_rep1
processed data file: Raw_counts.txt

data_processing:
Basecalls performed using CASAVA version 1.8.2.
Reads were mapped to the reference genome using STAR 2.4 with --outFilterMultimapNmax 1.
Raw count measurements were obtained with featureCounts 1.4.6 keeping only unambiguous reads.
Genome_build: Sscrofa11.1.96
Supplementary_files_format_and_content: Raw_counts.txt: Tab-delimited text file includes raw counts.

organism: Sus scrofa

source_name: porcine smooth muscle cells

extract_protocol:
Total RNA was extracted from treated SMCs by using the NucleoSpin kit (Macherey-Nagel).
Libraries were prepared according to Illumina's instructions using the TruSeq RNA-seq protocol.
Libraries were sequenced using single-end reads (100 nt-long) on an Illumina HiSeq4000.

treatment_protocol: SMCs between the 6th and 11th passages were plated at a density of 60 cells/mm2 in 35 mm culture dishes containing Dulbecco's modiﬁed eagle medium supplemented with 10% fetal calf serum and after 24 hours they were treated for 4 hours with 30 ng/ml of PDGF-BB, 1µg/ml of S100A4 or both together.

tag: cell type

value: smooth muscle cells

tag: cell source

value: porcine coronary artery

tag: cell phenotype

value: differentiated/contractile

tag: sample type

value: primary cell culture


title: S100A4 3

description:
S100A4_rep3
processed data file: Raw_counts.txt

tag: treatment


title: 4-EndoC-E1-10-Ctl.4

tag: genotype

value: PTPN2 silencing

value: Control


title: 5-EndoC-E1-10-IFNa.5

value: Interferon-alpha


title: PDGFS100A4 2

description:
PDGFS100A4_rep2
processed data file: Raw_counts.txt

value: PDGF-BB + S100A4


title: PDGFS100A4 3

description:
PDGFS100A4_rep3
processed data file: Raw_counts.txt


title: MG_GM_BR2_RNAseq

tag: cell line

value: MUNC genomic overexpressing

tag: tissue


title: PDGFS100A4 1

description:
PDGFS100A4_rep1
processed data file: Raw_counts.txt


title: PDGF-BB 2

description:
PDGF_rep2
processed data file: Raw_counts.txt

value: PDGF-BB


title: YHO-1701

type: RNA

city: Niigata

first: Naohiro

last: Yanagimura

address: 1–757 Asahimachi-dori, Chuo-ku

department: Respiratory Medicine and Infectious Diseases

country: Japan

institute: Niigata University

description: ALK-rearranged human lung cancer cells (EML4-ALK variant1), treated with YHO-1701 (3 μM) for 24 h

hyb_protocol: Following fragmentation, biotinylated cDNA were hybridized on microarrays (Clariom™ S Array, human; Thermo Fisher Scientific) using hybridization chambers (Hybridization Oven 645; Affymetrix). The GeneChips were washed and stained using GeneChip™ Hybridization, Wash, and Stain Kit (Thermo Fisher Scientific) in Fluidics Station 450 (Affymetrix).

scan_protocol: Gene expression signal intensities were scanned using GeneChip scanner (Scanner 3000 7G; Affymetrix), and CEL files were created using the Analysis software GeneChip® Command Console® (Thermo Fisher Scientific).

data_processing: The signal intensities in the CEL files were normalized using  the Analysis software Transcriptome Analysis Console (Thermo Fisher Scientific) and according to the guanine cytosine count normalization-signal space transformation-robust multichip analysis (GCCN-SST-RMA) algorithms to create CHP files. The signal values were log2 transformed.

label: biotin

source_name: primary lung cancer

label_protocol: Biotinylated cDNA were prepared according to the protocol of GeneChip™ WT PLUS Reagent Kit (Thermo Fisher Scientific).

growth_protocol: H3122 cells were cultured in RPMI 1640 medium supplemented with 10% FBS and 1% penicillin-streptomycin in a humidified CO2 incubator at 37 °C.

extract_protocol: Total RNA was extracted using RNeasy® Lipid Tissue Mini Kit (QIAGEN) following manufacturer's instructions.

treatment_protocol: H3122 cells were treated with DMSO or YHO-1701 (3 μM) for 24 h.

value: Lung adenocarcinoma


title: 3-EndoC-E1-SiQ-IFNY.3

value: Interferon-gamma


title: PDGF-BB 3

description:
PDGF_rep3
processed data file: Raw_counts.txt


title: CTRL 3

description:
Ctrl_rep3
processed data file: Raw_counts.txt


title: PDGF-BB 1

description:
PDGF_rep1
processed data file: Raw_counts.txt


title: CTRL 2

description:
Ctrl_rep2
processed data file: Raw_counts.txt


title: Control

description: ALK-rearranged human lung cancer cells (EML4-ALK variant1), untreated


title: LNCaP2_enza_d5 (ATAC-seq)

city: Houston

first: Filippo

last: Giancotti

state: Texas

address: 1881 East Road

department: Cancer Biology

institute: UT MD Anderson Cancer Center

data_processing:
We utilized cutadapt (v1.18) (Martin, 2011) for the raw reads to remove the adaptor sequence or the reads shorter than 35bp.
The trimmed reads were aligned to the human reference genome (hg19) using default parameters in Bowtie2 (v2.4.1)
The aligned reads were subsequently filtered for quality and uniquely mappable reads were retained for further analysis using Samtools (v1.10)
Relaxed peaks were called using MACS2 (v2.1.2) with a p value of 1X10-2. Consensus peaks were calculated by taking the overlap of peaks for samples.
Genome_build: hg19
Supplementary_files_format_and_content: The bedGraph format is line-oriented. BedGraph data are preceded by a track definition line, which adds a number of options for controlling the default display of this track.

source_name: prostate

growth_protocol: Cells were cultured as adherent cells in RPMI-1640 supplemented with 10% FBS, 50 U/mL penicillin and 50 mg/mL streptomycin.

extract_protocol:
5x10e5 LNCaP cells were prepared and collected. Cells were then washed once with cold 1xPBS and spinned down at 500g for 5min at 4C. Cells were kept on ice and subsequently resuspended in 25ul 2xTD buffer (Illumina Nextera kit), 2.5ul Transposase enzyme (Illumina Nextera kit, 15028252) and 22.5ul Nuclease-free water in total of 50ul reaction for 1hr at 37C. DNA was then purified using Qiangen MinElute PCR purification kit (28004) in a final volume of 10ul.
ATAC-seq Libraries were prepared following the Buenrostro protocol (http://www.ncbi.nlm.gov/pmc/articles/PMC4374986/)

treatment_protocol: Cells were treated with 10uM enzalutamide.

value: prostate

value: LNCaP

value: prostate adenocarcinoma

value: 10uM enzalutamide treatment for 5days


title: CTRL 1

description:
Ctrl_rep1
processed data file: Raw_counts.txt


title: LNCaP1_enza_d14 (ATAC-seq)

value: 10uM enzalutamide treatment for 14days


title: LNCaP1_enza_d5 (ATAC-seq)


title: LNCaP2_enza_d7 (ATAC-seq)

value: 10uM enzalutamide treatment for 7days


title: LNCaP1_enza_d7 (ATAC-seq)


title: LNCaP2_enza_d1 (ATAC-seq)

value: 10uM enzalutamide treatment for 1day


title: MS_GM_BR1_RNAseq

source_name: Murine myoblasts C2C12

value: MUNC spliced overexpressing

value: Myoblasts


title: LNCaP2_enza_d14 (ATAC-seq)


title: LNCaP2_enza_d3 (ATAC-seq)

value: 10uM enzalutamide treatment for 3days


title: LNCaP2_enza_d0 (ATAC-seq)

value: untreated


title: LNCaP1_enza_d0 (ATAC-seq)


title: LNCaP1_brca1_sh1 (RNA-seq)

data_processing:
The raw reads from .fastq files were trimmed by trimmomatic/0.33
The trimmed reads were aligned to the human reference genome (hg19) using Tophat/2.1.1
Gene models of Refgene were downloaded from the Illumina's iGenomes project.
FPKM (Fragments Per Kilobase of transcript per Million mapped reads) values were generated using cufflinks/v2.2.1
Further differential expression analysis was using cuffdiff function which is in cufflinks.
Genome_build: hg38
Supplementary_files_format_and_content: genes.fpkm_tracking files are tab delimited text files output by cufflinks in a generic FPKM tracking format with estimated gene-level expression values in the form of FPKM values. htseq.txt files are  tab delimited text files output by HTSeq with aligned reads count per genes.

extract_protocol:
Total RNA were extracted from samples using TRIzol (Invitrogen, USA) according to manufactures's instructions
1 µg total RNA was sent to BGI for quality testing and library construction based on the standard workflow.


title: LNCaP2_brca1_sh1 (RNA-seq)


title: LNCaP2_brca1_sh2 (RNA-seq)


title: LNCaP1_brca1_sh2 (RNA-seq)


title: LNCaP3_brca1_sh1 (RNA-seq)


title: LNCaP3_brca1_sh2 (RNA-seq)


title: LNCaP3_brca1ctrl (RNA-seq)

value: ctrl knockdown


title: LNCaP1_brca1ctrl (RNA-seq)


title: LNCaP3_p53_sh2 (RNA-seq)


title: LNCaP2_p53_sh2 (RNA-seq)


title: LNCaP1_p53_sh2 (RNA-seq)


title: LNCaP2_p53_sh1 (RNA-seq)


title: LNCaP3_p53_sh1 (RNA-seq)


title: LNCaP3_p53ctrl (RNA-seq)


title: LNCaP1_p53_sh1 (RNA-seq)


title: LNCaP1_p53ctrl (RNA-seq)


title: LNCaP3_LDN (RNA-seq)

value: 100nM LDN193189 treatment for 8 days


title: LNCaP1_LDN (RNA-seq)


title: LNCaP2_LDN (RNA-seq)


title: LNCaP3_un_LDN (RNA-seq)


title: LNCaP1_enza_d3 (ATAC-seq)


title: LNCaP1_un_LDN (RNA-seq)


title: LNCaP2_p53ctrl (RNA-seq)


title: LNCaP1_enza_d1 (ATAC-seq)


title: LNCaP3_NRG1 (RNA-seq)

value: sequential treatment of 2ng/ul neuregulin for 7days


title: LNCaP1_NRG1 (RNA-seq)


title: LNCaP2_NRG1 (RNA-seq)


title: LNCaP2_un_LDN (RNA-seq)


title: LNCaP2_enza (RNA-seq)


title: LNCaP3_FBS (RNA-seq)


title: LNCaP2_FBS (RNA-seq)


title: LNCaP1_enza (RNA-seq)


title: LNCaP1_FBS (RNA-seq)


title: LNCaP2_brca1ctrl (RNA-seq)


title: DRy5 (Young, Rep 5)

city: Jena

first: Philipp

last: Koch

address: Beutenbergstraße 11

department: Core Facility Life Science Computing

country: Germany

institute: Leibniz Institute on Aging - Fritz Lipmann Institute

data_processing:
Reads were extracted in FastQ format using Illumina’s bcl2FastQ v2.20.0.422
Reads were aligned to the Zebrafish reference genome (GRCz11 with the Ensembl genome annotation Release 95) using STAR 2.5.4b (parameters: --alignIntronMax 100000, --outSJfilterReads Unique, --outSAMmultNmax 1, --outFilterMismatchNoverLmax 0.04) (PMID: 23104886)
For each gene, all reads that map uniquely to one genomic position were counted with FeatureCounts 1.6.3 (multi-mapping or multi-overlapping reads were discarded, stranded mode was set to “–s 2”) (PMID: 24227677)
Genome_build: GRCz11
Supplementary_files_format_and_content: csv file containing read counts per gene over all samples

organism: Danio rerio

source_name: Heart ventricle

extract_protocol:
Total RNA was extracted from zebrafish ventricles using Trizol.
Preparation of libraries was done using NEBNext Ultra II directional RNA library preparation kit including enrichment of polyA RNAs using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB)  according the manufacturer‘s description.

value: ventricle

value: 7 months


title: DRo5 (Old, Rep 5)

value: 4 years


title: DRo1 (Old, Rep 1)


title: DRy1 (Young, Rep 1)


title: DRo3 (Old, Rep 3)


title: DRy2 (Young, Rep 2)


title: H3K4me3 ChIP in KO decidualized stromal cells

city: Xiamen

first: Wenbo

last: Deng

state: Fujian

address: Xiang'an Road

department: School of Medicine

institute: Xiamen University

description: D8 decidua tissue

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using STAR with default parameters
MACS2 was used to call the peaks of Menin and H3K4me3 binding using default parameters.
Genome_build: mm10

source_name: decidualized mouse stromal cells

growth_protocol: Mice were housed in the animal care facility of Xiamen University according to the guidelines for the care and use of laboratory animals. All experimental procedures were approved by the Animal Welfare Committee of Research Organization (X200811), Xiamen University.

extract_protocol:
Decidual tissue wetted with PBS quickly cut into small pieces with an iris scissor. The pieces should not be bigger than 0.5 cm3. Snipped tissue was fixed with 1% formaldehyde (CST) for 10 mins at RT (for H3K4me3 ChIP), or fixed with disuccinimidyl glutarate (DSG, Santa Cruz, 2 mM) for 30 mins at RT, washed twice with PBS and then double fixed with 1% formaldehyde for another 10 mins at RT (for Menin ChIP). Fixation was stopped by adding glycine (0.125 M). Tissue homogenate obtained by using Dounce Tissue Grinder was filtered through a 200 μm cell strainer to remove connective tissue. Fixed cells were lysed by Lysis Buffer 1 (50 mM HEPES pH 7.5, 1 mM EDTA, 140 mM NaCl, 0.5% NP-40, 10% glycerol, 0.25% Triton X-100) and Lysis Buffer 2 (10 mM Tris-HCl pH8.0, 1 mM EDTA, 0.5 mM EGTA, 200 mM NaCl) and Lysis Buffer 3 (10 mM Tris-HCl pH8.0, 1 mM EDTA, 0.5 mM EGTA, 100 mM NaCl, 0.1% Sodium Deoxycholate, 0.1% N-lauroylsarcosine). All lysis buffers should be supplemented with protease inhibitors cocktail (Roche) before use. Chromatin DNA was sheared to 300-500 bp average in size by using a BioRuptor sonicator (Diagenode). Solubilized chromatin was was centrifuged to remove debris and incubated overnight at 4°C with antibody against Menin (Bethyl, 10 μg) and H3K4me3 (Abcam, 1 μg) bound to 20 μl protein A magnetic beads (Invitrogen). After washing and elution, the protein-DNA complex was reversed by heating at 65°C overnight. Immunoprecipitated DNA was purified by using QIAquick spin columns (Qiagen). Immunoprecipitated and input DNA were quantified using Qubit 4.0 fluorometer. ChIP-seq libraries were prepared by using the KAPA DNA Hyper Prep Kit (KK8502) following the manufacturer’s instruction and sequenced with an Illumina Nova PE150. For ChIP-qPCR, chromatin was sheared by sonication until the average length of 500-1000 bp.
The ChIP libraries were prepared using KAPA HyperPrep Kits (Roche, 07962347001) and then run on the Illumina sequencer Hiseq-Xten PE150 using standard Illumina protocols

tag: strain

value: Mouse uteri on pregnant day 8

tag: chip antibody

value: H3K4me3 Rabbit pAb, vendor:Abcam; catalog number:#ab8580; lot/batch number:GR134451-3

value: KO


title: M_AD-2

city: Beijing

first: Lin

last: He

address: Xueyuan Road 38

institute: Peking University

data_processing:
Library strategy: CUT&Tag
Raw data were preprocessed by using fastp version0.19.6.
Filtered reads were aligned to the genome (GRCm38, mm10) assembly using Bowtie2.
Peaks were called using MACS version2.
Genome_build: GRCm38, mm10.
Supplementary_files_format_and_content: bigwig files were generated using deepTools.
Supplementary_files_format_and_content: peak txt files containing the specific binding region.

source_name: Microglia

extract_protocol:
CUT&Tag was performed using Hyperactive In-Situ ChIP Library Prep Kit for Illumina (pG-Tn5) (Vazyme Biotech) according to manufacturer’s instructions. In brief, total brain cells and microglia were collected and bounded to Concanavalin A–coated beads. Subsequently, cells were resuspended in antibody buffer and incubated with primary antibodies against H4K12la and secondary antibodies in order. The samples were incubated with pA-Tn5 transposase. After transposon activation and tagmentation, DNA was isolated, amplified, and purified to construct library.
The library for sequencing was constructed and VAHTS DNA Clean beads were used for purification steps. The library was quantified with VAHTS Library Quantification Kit for Illumina and sequenced on an Illumina novaseq 150PE.

treatment_protocol: WT and 5XFAD mice were deeply anesthetized with pentobarbital sodium and perfused transcardially with ice-cold saline. Whole brain without cerebellum was immediately removed and washed with prechilled PBS. The brain tissue was mechanically and enzymatically dissociated using the Adult Brain Dissociation Kit (Miltenyi Biotec) according to the manufacture’s instruction. After myelin was removed by using the cell debris removal buffers, total cell pellet was resuspended. Microglia were purified by anti-CD11b-coated MicroBeads (Miltenyi Biotec).

value: brain

value: Microglia

value: 5XFAD mice


title: H3K4me3 ChIP in WT decidualized stromal cells

description: D8 decidua tissue

value: WT


title: M_WT-2

value: WT mice


title: M_AD-1


title: T_AD-2

source_name: Total cells

value: Total cells


title: T_AD-1


title: M_WT-1


title: LNCaP3_enza (RNA-seq)

value: prostate

value: LNCaP

value: prostate adenocarcinoma

value: 10uM enzalutamide treatment for 7days


title: T_WT-2


title: T_WT-1


title: H3K4me3 ChIP_Seq in WT decidualized stromal cells

description: D8 decidua tissue

value: C57 mouse decidua


title: H3K4me3 ChIP_Seq in KO decidualized stromal cells

description: D8 decidua tissue


title: XBP VP16, replicate 3

city: New York

first: Anna

last: Di Gregorio

state: NY

address: 345 E 24th Street, room 804A

department: Basic Science and Craniofacial Biology

institute: NYU College of Dentistry

description: 100-300 fluorescent embryos

hyb_protocol: Hybridization to customized Ciona intestinalis GeneChipTM was performed by the Weill Cornell Genomics Resources Core Facility using standard Affymetrix protocols.

scan_protocol: Standard Affymetrix procedure as performed by the Weill Cornell Genomics Resources Core Facility.

data_processing: Results were RMA summarized from raw data and quantile normalized using GeneSpring GX 11 as carried out by the Weill Cornell Epigenomics Core Facility.

organism: Ciona intestinalis

source_name: whole Bra>XBP VP16 expressing embryos at iTb

label_protocol: Total RNA was amplified and labeled using the Ambion MessageAmpTM Premier RNA Amplification Kit (Life Technologies #AM1792) by the Weill Cornell Genomics Resources Core Facility.

growth_protocol: Adult Ciona intestinalis were purchased from Marine Research and Educational Products (M-REP; Carlsbad, CA) and kept in an aquarium in recirculating artificial sea water at 18°C.  In vitro fertilization, electroporation and embryo culturing were carried out as previously described (Oda-Ishii I, Di Gregorio A, 2007.  Lineage-independent mosaic expression and regulation of the Ciona multidom gene in the ancestral notochord.  Dev Dyn.  236, 1806–1819 (PMID 17576134).).  Embryos expressing Bra>XBPDBD::GFP or Bra>XBPVP16::GFP fusion transgenes or Bra>GFP were grown to the initial tailbud I/II stage (~8.5 hpf) according to the staging outlined in Hotta, K., Mitsuhara, K., Takahashi, H., Inaba, K., Oka, K., Gojobori, T., Ikeo, K., 2007. A web-based interactive developmental table for the ascidian Ciona intestinalis, including 3D real-image embryo reconstructions: I. From fertilized egg to hatching larva. Dev Dyn. 236 (PMID 17557317).

extract_protocol: Total RNA was extracted using the RNeasy micro kit (Qiagen #74004), following the manufacturer's instructions.  Samples were eluted in 13µl pre-warmed ddH2O.

treatment_protocol: Approximately 100-300 fluorescent Bra>XBPDBD::GFP, Bra>XBPVP16::GFP or Bra>GFP embryos were manually selected utilizing a Zeiss SteReo Discovery V12 microscope at the initial tailbud stage prior to RNA extraction.

tag: Stage

value: initial tailbud (iTb); ~8.5hpf

tag: electroporated construct

value: Bra>XBP VP16::GFP


title: XBP DBD, replicate 3

description: 100-300 fluorescent embryos

source_name: whole Bra>XBP DBD expressing embryos at iTb

value: Bra>XBP DBD::GFP


title: XBP DBD, replicate 2

description: 100-300 fluorescent embryos


title: control, replicate 3

description: 100-300 fluorescent embryos

source_name: whole Bra>GFP expressing embryos at iTb

value: Bra>GFP


title: Input decidualized stromal cells

description: D8 decidua tissue

value: Mouse uteri on pregnant day 8


title: T_RNASeq

city: Chicago

first: Zhe

last: Ji

state: ILLINOIS

address: 303 E Superior St, Lurie 6-107

institute: Northwestern University

data_processing:
For RNase footprinting libraries, we performed paired-end sequencing (2 x 151 nt). Because the footprint lengths are short (< 35 nt for ribosome footprints), we used the first ends of reads to perform mapping and gene expression calculation. We first trimmed the 3’ sequencing adapters of reads (AGATCGGAAG for the datasets generated by linker ligation methods, and AAAAAAAAAA for the A-tailing methods). For the libraries using SMARTer-oligo based template switch, we trimmed the first 7 nts, including the random 4 nts and 3 locked Gs in the 5’ sequencing adapters. The trimmed reads were first mapped to the NCBI rRNA sequences (5S: NR_023363.1, 5.8S: NR_003285.3, 18S: NR_003286.4, and 28S: NR_003287.4) using bowtie2 (version 2.2.6). The unmappable reads were then mapped to reference human genome (hg38) and transcriptome using tophat (version 2.1.0). The transcriptome annotation was based on GENCODE (v28), and we modified the annotation by incorporating the mitochondrial transcripts annotated by the UCSC Genome Browser. For ribosome footprints and ribosome profiling data, only the uniquely mappable reads with lengths of 18-35 nt were used for the downstream expression calculations because ribosome footprints show these defined lengths. For RNA-seq data, uniquely mappable reads with lengths all sizes were used for the downstream expression calculations. To obtain read counts in protein-coding regions, we excluded the regions overlapping with uORFs and used HTSeq (version 0.9.1) to generate gene-level read counts. We used the same data analyses procedures for ribosome profiling and RNA-seq. Except that we used all reads with different fragment lengths from RNA-seq to calculate RNA expression.
Genome_build: hg38
Supplementary_files_format_and_content: HTSeq gene-level count in txt format

source_name: Peripheral blood mononuclear cell

growth_protocol: Fresh human whole peripheral blood was purchased from Stemcell Technologies, which was standard blood draw from one healthy donor (61-year-old female). PBMCs were isolated using Ficoll-Paque PREMIUM (GE Healthcare) following the manufacturer’s protocol. PBMCs were maintained at 37 °C using RPMI 1640 supplemented with 10% FBS. CD3+ T cells, CD3-CD19+ B cells, and CD14+CD16- Monocytes were isolated from PBMCs using immunomagnetic isolation kits (Stemcell Technologies, cat. no. 17951, 17954, and 19359, respectively) following the manufacturer’s instructions. For each cell population, 100,000 cells were counted to generate the RNase footprinting library, and 300,000 cells were counted to generate the RNA sequencing library.

extract_protocol:
For RNase footprinting, cells were treated with 100 ug/ml cycloheximide for 3 min before harvesting. Cells were then rinsed twice with PBS and lysed using cold lysis buffer. The cell lysis was digested with RNase 1 (cat. no. N6901K, Lucigen) at room temperature for 1.5 hour. We added 400 ul of TRIzol (Ambion) and then 100 ul of chloroform (Sigma) to extract RNase footprints. The footprints were precipitated overnight with isopropanol.
For RNA-seq, total RNA was isolated using the Direct-zol RNA kit (Zymo Research), and mRNAs were purified using Oligo(dT)25 magnetic beads (New England Biolabs) according to the manufacturer’s instructions. Purified mRNAs were fragmented with NEBNext Mg2+ RNA fragmentation module (New England Biolabs) at 94 for 6 min. Fragmented RNAs were then precipitated overnight at -20C by adding 0.1 volumes of 3M sodium acetate, 10 mg of glycoblue, and 1.2 volumes of isopropanol.
We use the same procedures for RNase footprinting and RNA-seq, precipitated RNA fragments were suspended in 5 ul of TNK reaction mixture and end-repaired at 37 C for 90 min followed by incubating at 65 C for 5 min to inactive PNK. The end-repaired fragments were 3’ polyadenylated with 5 U of E. coli poly (A) polymerase (New England Biolabs) by incubating at 37 C for 2-4 hrs. The resulting polyadenylated RNA was next reverse transcribed by a modified SMAT-RT reaction with customized template-switching oligos and incubated at 42 C for 1 h, followed by 3 cycles of heating to 50 C for 2 min and then cooling to 42 C for 2 min. The enzyme was inactivated by heating at 70 C for 10 min. The RNA fragments hybridized to DNA were then removed by incubating reaction mixture at 37 C for 15 min with 5 U of RNase H (New England Biolabs). The resulting cDNA was then amplified by two rounds of PCR to generate the sequencing library. DNA library was separated and visualized in a 4% agarose gel. DNA with 15-35 bp-insert was excised and recovered using the DNA gel recover kit (Zymo Research).

value: Peripheral blood

value: Isolated CD3+ T cells from PBMCs


title: XBP DBD, replicate 1

description: 100-300 fluorescent embryos


title: Menin ChIP_Seq in decidualized stromal cells repeat 2

description: D8 decidua tissue

value: Menin Rabbit pAb, vendor:Bethyl; catalog number:#A300-105A; lot/batch number:A300-105A-7


title: XBP VP16, replicate 2

description: 100-300 fluorescent embryos


title: control, replicate 2

description: 100-300 fluorescent embryos


title: XBP VP16, replicate 1

description: 100-300 fluorescent embryos


title: Monocyte_RNASeq

value: Isolated CD14+CD16- Monocytes from PBMCs


title: PBMC_RFP_rep1

value: PBMCs


title: PBMC_RFP_rep2


title: T_RFP_rep1


title: control, replicate 1

description: 100-300 fluorescent embryos


title: Menin ChIP_Seq in decidualized stromal cells repeat 1

description: D8 decidua tissue


title: Parva KO-2

city: Freiburg

first: Manuel

last: Rogg

state: Baden Wuerttemberg

address: Breisacher Straße 115a

department: Institute of Surgical Pathology

institute: University Medical Center Freiburg

data_processing:
Demultiplexing and adapter trimming were performed with bcl2fastq v2.19. No quality trimming was performed for deposited fastq files.
Sequenced reads were quality trimmed using Cutadapt v1.16.5.
Reads were mapped to mm10 whole genome using HISAT2 v2.1 with default settings for paired-end reverse strand specific libraries.
featureCounts v1.6.4 and DESeq2 v2.11.40.6 were applied for differentially expression analysis
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized counts for all Sample

source_name: renal glomeruli

extract_protocol:
Isolation of glomeruli form 9 week old male mice with mild proteinuria was performed based on perfusion with magnetic beads (Dynabeads) as previously described in detail (Boerries, Melanie et al. “Molecular fingerprinting of the podocyte reveals novel gene and protein regulatory networks.” Kidney international vol. 83,6 (2013): 1052-64. doi:10.1038/ki.2012.487). RNA was isolated from whole glomeruli using the Qiagen RNAeasy midi Kit (74104, Quiagen) according to the suppliers instructions.
RNA libraries were prepared for sequencing using the NEBnext ultra II RNA directional kit. Libraries were sequenced on the Illumina NovaSeq 6000 sequencer following the manufacturer's protocols.

value: C57BL/6 mixed

value: renal glomeruli

tag: age

value: 9 weeks


title: Parva KO-3


title: Parva KO-1


title: B_RFP_rep1

value: Isolated CD3-CD19+ B cells from PBMCs


title: Parva WT-2

value: Parva-fl/fl


title: Parva WT-3


title: Parva WT-1


title: T_RFP_rep2


title: HeLa_RNASeq_gTUFM2

source_name: HeLa Cells

growth_protocol: HeLa cells were cultured in DMEM medium supplemented with 10% FBS.

treatment_protocol: HeLa cells were infected with lentivirus expressing control gRNA or gRNA against TUFM.

value: Cervix

value: HeLa

value: TUFM knockout


title: HeLa_RNASeq_gTUFM1


title: Monocyte_RFP_rep2


title: PBMC_RNASeq


title: B_RFP_rep2


title: HeLa_RNASeq_gCtrl2

value: Control


title: HeLa_RFP_gTUFM2


title: HeLa_RNASeq_gCtrl1


title: HeLa_RFP_gTUFM1


title: HeLa_RFP_gCtrl1


title: K562_RiboSeq_rep2

growth_protocol: HEK293T and HeLa cells were cultured in DMEM medium supplemented with 10% FBS. K562 cells were cultured using IMDM medium supplemented with 10% FBS.

extract_protocol:
For low-input RNase footprinting, cells were treated with 100 ug/ml cycloheximide for 3 min before harvesting. Cells were then rinsed twice with PBS and lysed using cold lysis buffer. The cell lysis was digested with RNase 1 (cat. no. N6901K, Lucigen) at room temperature for 1.5 hour. We added 400 ul of TRIzol (Ambion) and then 100 ul of chloroform (Sigma) to extract RNase footprints. The footprints were precipitated overnight with isopropanol.   To compare RNA fragments after digestion with different doses of RNase, we used 0.5 million HEK293T cells for the experiments. We treated the cell lysate containing 10 ug total RNA with different RNase doses (cat. no. N6901K, Lucigen): 0.5 U (low dose), 5 U (medium dose), and 500 U (high dose), respectively, at the room temperature for 1 hr. The RNA fragments were precipitated overnight with isopropanol.  For Ribosome profiling, libraries were prepared based on the published protocol in (McGlincy and Ingolia, Methods, 2017).   For RNA-seq, total RNA was isolated using the Direct-zol RNA kit (Zymo Research), and mRNAs were purified using Oligo(dT)25 magnetic beads (New England Biolabs) according to the manufacturer’s instructions. Purified mRNAs were fragmented with NEBNext Mg2+ RNA fragmentation module (New England Biolabs) at 94 for 6 min. Fragmented RNAs were then precipitated overnight at -20 C by adding 0.1 volumes of 3M sodium acetate, 10 mg of glycoblue, and 1.2 volumes of isopropanol.
We use the same procedures for low-input RNase footprinting and RNA-seq, precipitated RNA fragments were suspended in 5 ul of TNK reaction mixture and end-repaired at 37 C for 90 min followed by incubating at 65 C for 5 min to inactive PNK. The end-repaired fragments were 3’ polyadenylated with 5 U of E. coli poly (A) polymerase (New England Biolabs) by incubating at 37 C for 2-4 hrs. The resulting polyadenylated RNA was next reverse transcribed by a modified SMAT-RT reaction with customized template-switching oligos and incubated at 42 C for 1 h, followed by 3 cycles of heating to 50 C for 2 min and then cooling to 42 C for 2 min. The enzyme was inactivated by heating at 70 C for 10 min. The RNA fragments hybridized to DNA were then removed by incubating reaction mixture at 37 C for 15 min with 5 U of RNase H (New England Biolabs). The resulting cDNA was then amplified by two rounds of PCR to generate the sequencing library. DNA library was separated and visualized in a 4% agarose gel. DNA with 15-35 bp-insert was excised and recovered using the DNA gel recover kit (Zymo Research).
For Ribosome profiling, the adapter ligation were carried out based on the published protocol in (McGlincy and Ingolia, Methods, 2017).
To compare RNA fragments after digestion with different doses of RNase, for the medium and high dose conditions, we selected RNA fragments with 10-40 nt to generate the sequencing library, using the same adapter ligation procedures described in ribosome profiling. For the low dose RNase condition, we extracted all RNA fragments and used A-tailing and SMARTer oligo-based template switch described above to generate the sequencing library.

value: Bone marrow


title: K562_RiboSeq_rep1


title: K562_RFP_1kCells_rep1


title: Monocyte_RFP_rep1


title: K562_RFP_50kCells_rep2


title: K562_RNASeq_rep2


title: HeLa_RFP_gCtrl2


title: B_RNASeq


title: K562_RNASeq_rep1


title: HEK293T_RNASeq_rep1

source_name: Human embryonic kidney cells

value: Embryonic kidney


title: HEK293T_RiboSeq_rep2


title: HEK293T_RiboSeq_rep1


title: HEK293T_RFP_1kCells_rep2


title: HEK293T_RFP_50kCells_rep2


title: HEK293T_RFP_50kCells_rep1


title: HEK293T_RNaseHigh_rep2


title: HEK293T_RNaseLow_rep1


title: HEK293T_RNaseLow_rep2


title: HEK293T_RNaseMed_rep2


title: HEK293T_RNaseMed_rep1


title: K562_RFP_1kCells_rep2


title: P0_2

city: Hangzhou

first: Yishan

last: Chen

address: #866 Yuhangtang Road

institute: Zhejiang University

data_processing:
Illumina Casava1.7 software used for basecalling.
Alignment was conducted with bowtie2
ATAC peaks were called using MACS2 with default parameters for each sample, and peaks in the same group were merged for downstream analysis
Chipseeker was utilized to annotate the peak locations. Group specific peaks were identified by DiffBind. De novo motif search was performed using HOMER package
Genome_build: mm10
Supplementary_files_format_and_content: Processd data-2 and 3 include peak calling profiles in P0 and P8 respectively. Processed data-4 includes differentially enriched peaks in P0 and P8 chondrocytes

source_name: articular cartilage

growth_protocol: Mouse chondrocytes were isolated from knee cartilage of C57Bl/6 mice (postnatal 0-4 days) following the previously published method. The digested cells was resuspended and culture with DMEM/F12 medium (Gibico), supplemented with 10% fetal bovine serum, at 37 ¡ãC with 5% CO2. P0 chondrocytes represents the primary chondrocytes having been cultured in vitro less than 24 hours (h). For dedifferentiation model, chondrocytes were passaged after a doubling of cell quantity (seeding density: 24000/cm2; collecting density: 48000/cm2).

extract_protocol:
ATAC-seq was performed as previously described. Briefly, 5¡Á104 cells were harvested for each sample, centrifuged into pellet, and washed in 50¦Ìl cold PBS. Then we gently resuspended the cell pellet in 50¦Ìl cold lysis buffer. The samples were centrifuged immediately at 500 ¡Ág for 10 min, 4¡ãC. After discarded the supernatant, we resuspended the samples in the transposition reaction mix (25 ¦Ìl TD (2x reaction buffer), 2.5 ¦Ìl TDE1 (Nextera Tn5 Transposase), 22.5 ¦Ìl nuclease free H2O), and incubated them at 37¡ãC for 30 min. We purified the transposed DNA with a Qiagen MinElute PCR Purification Kit.
The transposed DNA was amplified by PCR. The amplified library was purified with Qiagen MinElute PCR Purification Kit. The quality of purified libraries was further assessed using a Bioanalyzer High Sensitivity DNA Analysis kit (Agilent). Libraries were sequenced on the Illumina HiSeq 2500 with 50 bp paired-end reads and aligned to the reference genome with bowtie2.

value: cartilage

tag: passage

value: passage 0


title: P8_1

value: passage 8


title: P0_1


title: P8_2


title: K562_RFP_50kCells_rep1


title: HEK293T_RNASeq_rep2


title: H4K5Ac_epl1a/b rep1

first: Xin-Jian

address: No. 7, zhongguancun life science park road, changping district

institute: National Institute of Biological Sciences

data_processing:
Basecalls performed using bcl2fastq version 2.16.
Adapter and low-quality sequences were trimmed, and the clean reads were aligned to the Arabidopsis genome (TAIR10) using Bowtie2 (v2.4.2) allowing one mismatch.
SICER (v2.0) was used to identify ChIP-enriched peaks between the WT type and epl1a/b mutant.
Differentially expressed peaks in all mutants were identified based on the change of read counts at peaks.
Genome_build: TAIR10
Supplementary_files_format_and_content: bigWig files were generated using bamCoverage.

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Arabidopsis seedlings were grown on MS (Murashige and Skoog) medium plates at 23°C with a 16-h light/8-h dark photoperiod.

extract_protocol:
After chromatin was extracted and sonicated, the extraction was immunoprecipitated with anti-histone H3 acetylation antibody (Millipore, 06-599) and anti-H4K5 acetylation antibody (Abcam, ab51997). Protein A agarose was used for conjugation followed by immunoprecipitation.
Libraries were built for ChIP-seq (Illumina NovaSeq 6000; 150-bp paired-end sequencing)

treatment_protocol: Fourteen-day-old seedlings were cross-linked in 0.5% formaldehyde under vacuum.

value: seedlings

value: Abcam, ab51995


title: Col-0 rep3

value: wild type


title: Col-0 rep2


title: Col-0 rep1


title: H4K5Ac_epl1a/b rep3


title: E-micA323-48h_1

first: Yilong

last: Wang

state: Zhejiang

address: NO.3333 binsheng Road

department: Department of Neurology

institute: Children’s Hospital, Zhejiang University School of Medicine

data_processing:
Raw reads were deduplication by UMI
Remove reads of tRNA, rRNA, snRNA, snoRNA
miRNA quantification with miRDeep2
Count matrix were converted to TPM
Genome_build: hg38
Supplementary_files_format_and_content: miRNA TPM expression matrix

source_name: plasma samples

extract_protocol:
Total RNA samples were extracted and purified from sEVs by the miRNeasy Mini kit
For small RNA libraries, a total of 1–  500 ng of RNA per sample was prepared as the input  material. Sequencing libraries were constructed using QIAseq  miRNA Library Kit

value: plasma small extracellular vesicles

tag: molecule subtype

value: miRNA

tag: disease state

value: healthy


title: H4K5Ac_epl1a/b rep2


title: E-micA323-49h_1


title: E-micA323-50h_1


title: E-micA323-47h_1


title: E-micA323-45h_1


title: E-micA323-46h_1


title: E-micA323-44h_1


title: HEK293T_RFP_1kCells_rep1


title: E-micA323-42h_1


title: E-micA323-41h_1


title: E-micA323-43h_1


title: HEK293T_RNaseHigh_rep1


title: E-micA323-40h_1

value: pediatric epilepsy


title: E-micA323-39h_1


title: E-micA323-35h_1


title: E-micA323-37h_1


title: E-micA323-38h_1


title: E-micA323-28h_1


title: E-micA323-29h_1


title: E-micA323-34h_1


title: E-micA323-22h_1


title: E-micA323-19h_1


title: E-micA323-24h_1


title: E-micA323-18h_1


title: E-micA323-17h_1


title: E-micA323-11h_1


title: E-micA323-04h_1


title: E-micA323-08h_1


title: E-micA323-15h_1


title: E-micA323-02h_1


title: E-micA323-06h_1


title: E-micA323-05h_1


title: E-micA323-12h_1


title: E-micA323-16h_1


title: Sample_119978

city: Ann Arbor

first: Lam

last: Tsoi

state: MI

address: Medical Sciences 1 Bldg. 1301 E. Catherine

institute: University of Michigan

data_processing:
Illumina standard primers were trimmed
Reads were mapped to the human reference genome using STAR
Number of reads for each gene was counted using HTSeq
Genome_build: hg19
Supplementary_files_format_and_content: raw read count matrix (genes x samples)

source_name: Skin

extract_protocol:
The processing of RNA was performed using the RNeasy kit (Qiagen, RNeasy plus mini kit, Cat.No.: 74136).
Samples were processed for sequencing using the SMARTer Stranded Total RNA-seq Kit v2 – Pico Input Mammalian (Takara, Cat#634411).  Parallel samples were processed using the Lexogen 3’ QuantSeq mRNA-seq Library Prep Kit FWD (Lexogen).

treatment_protocol: Tape stripping was performed on lesional and distal non-lesional psoriatic skin (buttocks) and on site-matched healthy control skin.  Three 6mm punch biopsies were obtained from each patient: 1) an intact psoriatic plaque, 2) underneath the tape-stripped area, and 3) non-lesional skin

tag: protocol

tag: patient id

value: Lesional Skin


title: E-micA323-03h_1


title: Sample_119977


title: Sample_119976


title: Sample_119975


title: Sample_119973


title: Sample_119971


title: Sample_119969


title: Sample_119972


title: Sample_119974


title: Sample_119970


title: Sample_119968


title: Sample_119967

value: Uninvolved Skin


title: Sample_119966


title: Sample_119964


title: E-micA323-01h_1


title: Sample_119961


title: Sample_119962


title: Sample_119960


title: Sample_119963


title: E-micA323-07h_1


title: Sample_119965


title: Sample_119959


title: Sample_119957


title: Sample_119953


title: Sample_119954


title: Sample_119955


title: Sample_119958


title: Sample_119952


title: Sample_119951


title: Sample_119949


title: AKO rep3

city: Xiangyang

first: lanting

last: zhou

address: No.296, Longzhong Road, Xiangyang City, Hubei Province

institute: Hubei university of arts and science

data_processing:
Illumina Casava1.7 software used for basecalling.
The RNAseq was conducted by using Illumina HiSeq2000 platform. The ribosomal RNA was removed from the total RNA which blasted with the Mus musculus genome by HISAT, and the gene expression was calculated by FPKM. Differentially expressed RNAs were analyzed by the DESeq2 package.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

extract_protocol:
The brain was dissected and followed by 20 μm cryosection. The hippocampus CA3 was isolated from brain slides by using laser capture microdissection. Then the samples were stored on dry ice until RNA extraction by Trizol. The RNAseq was conducted by using Illumina HiSeq2000 platform.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Hippocampus

value: Adora1 knockout


title: Sample_119946

value: Normal


title: Sample_119947


title: Sample_119948


title: Sample_119945


title: AKO rep1


title: Sample_119944


title: WT rep2


title: Sample_119943


title: Sample_119942

value: Biopsy


title: Sample_119956


title: Sample_119937


title: Sample_119935


title: Sample_119941


title: Sample_119934


title: Sample_119940


title: Sample_119936


title: Sample_119933


title: Sample_119938


title: Sample_119939


title: MSCs, Ipr_2

city: Montréal

first: Moutih

last: Rafei

state: Québec

address: 2900 Boul. Édouard-Montpetit

country: Canada

institute: Université de Montréal

data_processing:
Sequencing was performed with the Illumina HiSeq 2000 and basecalls analyzed using Illumina RTA 1.17.21.3.
Samples demultiplexed using Illumina Casava 1.8.2 using adapter masking.
Sequenced reads were trimmed for masked adapters and low quality extremities using Trimmomatic 0.35 and then mapped to the reference genome using Tophat version 2.1.0, guided by transcript annotations from RefSeq.
Expression values were computed usingHTseq-count version 0.6.1 and RefSeq annotations.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited file where columns correspond to each sample (first line identifies the columns) and lines identifies genes.

source_name: Mesenchymal stem cells (MSCs)

growth_protocol: Cells grown in AMEM + 10% FBs + PS

extract_protocol:
Trizol extraction and Qiagen Rneasy column purification
KAPA RNA Stranded PolyA
RNAseq (poly-A purification)

tag: cell type

value: Bone marrow-derived Mesenchymal stem cells (MSCs)

value: IPr subunit expression


title: MSCs, Ipr_3


title: MSCs, Ipr_1


title: MSCs, AP2_3

description: MSC

value: control


title: Sample_119950


title: Sample_119931


title: AKO rep2


title: Sample_119932


title: MSCs, AP2_2

description: MSC


title: WT rep3


title: Sample_119930


title: Sample_119929


title: MSCs, AP2_1

description: MSC


title: Sample_119927


title: Sample_119928


title: Sample_119926


title: CD4+ T cells, d4_Sh5

city: Galveston

first: Steven

middle: G

last: Widen

address: 301 University Blvd

department: BMB

institute: University of Texas Medical Branch

data_processing:
Base calling was using Illumina's bcl2fastq2-v2.20 converter
Reads were aligned to the GRCh38 reference using the STAR software version 2.5.2b with the parameters recommended for the ENCODE consortium.
Gfold software, version 1.1.4, was used to count reads per gene and estimate expression differences between samples. The GENCODE V24 basic annotation file was used for the gene models.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab delimited file with RPKM values for samples and estimated differences.

source_name: Human primary CD4+ T cells

growth_protocol: Purified CD4 positive cells were grown in RPMI medium supplemented with 20% FBS and 100ng/ml human recombinant IL-2

extract_protocol:
Total RNA was isolated from cells using ReliaPrep RNA Cell Miniprep System (Promega) and treated in-column with Dnase I following the manufacturer's recommendations
Poly-A plus RNA was enriched from 1 ug of total RNA and used to generate libraries using the Illumina TruSeq RNA kit.

treatment_protocol: Cells were ransduced with lentiviruses for 3 days, followed by 4 days of puromycin selection and 1 day without puromycin

tag: individual

value: Donor 4

value: primary CD4+ T cells

value: Sh5 DDX39B Knock down


title: CD4+ T cells, d4_Sh3

value: Sh3 DDX39B Knock down


title: Sample_119924


title: WT rep1

value: wild type


title: Sample_119923


title: CD4+ T cells, d1_Sh3

value: Donor 1


title: CD4+ T cells, d1_Sh5


title: Sample_119920


title: Sample_119922


title: Sample_119918


title: Sample_119915


title: Sample_119919


title: CD4+ T cells, d4_NTC

value: NTC Control


title: Sample_119912


title: Sample_119911


title: hakai_3 IP

city: Nottingham

first: Nigel

middle: P

last: Mongan

address: University Park

department: Biodiscovery Institute

country: United Kingdom

institute: University of Nottingham

description: hakai  IP

data_processing:
Raw reads in fastq format were processed to remove contaminating adapter sequences and reads with phred score <30 using the Trimgalore wrapper for Cutadapt and FastQC.
The resultant QC fastq files were aligned to the Arabidposis thaliana reference genome (TAIR10) using the STAR aligner.
BAM files from input and m6A immunoprecipitated samples were analyzed using the m6AViewer. Peaks identified in all samples were recorded and peak summits reported in BED format.
Genome_build: TAIR10.49
Supplementary_files_format_and_content: BED

source_name: 2 weeks old seedlings

growth_protocol: Arabidopsis seeds were cultured in plates. Seeds planted in plates were sterilized by soaking in 5% NaClO for 4 min and then washed with sterile water for 5 times before being planted onto 0.5 × MS medium plus 1% sucrose. Plates were placed in the cold room (4°C, dark) for 2 days and then kept in the tissue culture room (16 h light: 8 h dark, 22°C) until used.

extract_protocol:
Total RNA was isolated using hot phenol extration. Poly(A) RNA was prepared according to the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, NEB). m6A levels were measured by two-dimensional thin layer chromatography (TLC) analysis as described previously
The immunoprecipitation was carried out using the EpiMark N6-Methyladenosine Enrichment Kit (NEB),following manufacturers’ instruction. We omitted the final elution step as we carried out the cDNA synthesis on the magnetic beads using ScriptSeq v2 RNA-Seq Library Preparation Kit (Illumina). The libraries were size selected using E-Gel SizeSelect II (Invitrogen), and quality checked on Agilent High Sensitivity DNA Chips (Agilent).

tag: developmental stage

value: whole seedlings

tag: ecotype

value: Columbia

tag: antibody for merip

value: Epimark Monoclonal anti-m6A NEB


title: Sample_119913

value: Uninvolved Skin


title: hakai_3 input

description: hakai  input


title: hakai_2 IP

description: hakai  IP


title: Sample_119909


title: Sample_119907

value: Lesional Skin


title: hakai_2 input

description: hakai  input


title: Sample_119904


title: Sample_119906


title: hakai_1 input

description: hakai  input


title: Sample_119910


title: CD4+ T cells, d1_NTC

tag: genotype


title: Sample_119908

tag: tissue


title: Sample_119925


title: Sample_119903

value: Normal


title: Sample_119901


title: Sample_119905


title: Sample_119900

value: Biopsy


title: hakai_1 IP

description: hakai  IP


title: Sample_119914


title: Sample_119921


title: vir_2 input

description: virilizer input


title: Sample_119917


title: LE24_D14_K27_rep2 (ChIP-seq)

data_processing:
Sequencing reads from H3K4me3 and H3K27me3 ChIP-seq were trimmed by using trimmomatic (v0.39)
The trimmed reads were then aligned to the human genome (hg19) using the Bowtie2 software.
PRC duplication reads were removed by Samtools.
Relaxed peaks were called using MACS2 (v2.1.2) with a p value of 1X10-2. Consensus peaks were calculated by taking the overlap of peaks for samples.
Genome_build: hg19
Supplementary_files_format_and_content: The bedGraph format is line-oriented. BedGraph data are preceded by a track definition line, which adds a number of options for controlling the default display of this track.

source_name: prostate

extract_protocol:
1x10e6 Cells were crosslinked by using 2mM DSG for 45 min, then by using 1% formaldehyde for 15 min, which were both performed at room temperature (RT). To stop crosslink, glycine was added to final concentration of 0.125M, then incubate at RT for 5 min. Cells were collected by scraping from dishes, then washed with PBS 3 times. Resuspend pellets in 0.5ml of SDS lysis buffer (1% SDS, 10mM EDTA, 50mM Tris-HCl, pH8.0)/PIC/PMSF/Sodium butyrate mix, then incubate on ice for 10 min. Sonicate the crosslinked cellular lysate with Diagnode sonicator. After sonication, aliquot samples into a 1.7ml tube. Centrifuge at max speed for 10 min at 4C. Transfer supernatant to a new 1.7ml tube. To prepare chromatin immunoprecipitation sample, per 0.1ml of sonicated sample, add 0.9ml of dilution buffer (50mM Tris-HCl, pH8.0, 0.167M NaCl, 1.1% Triton X-100, 0.11% sodium deoxycholate)/PIC/PMSF/Sodium butyrate mix, and then add antibody bound Dynabeads. Gently mix and place on rocker O/N at 4C. Place tube in magnetic stand.  Invert several times.  Allow beads to clump.  Discard supernatant. Perform the following wash steps with 0.8ml of cold buffer.  Flick tubes to resuspend beads and incubate each wash for 5min on rocker at 4C.  Place tube in magnetic stand.  Invert several times.  Allow beads to clump and discard supernatant. 1 time with RIPA-150, 1 time with RIPA-500, 1 time with RIPA-LiCl, 2 times with 1xTE Buffer, pH8.0. Resuspend beads in 200ul freshly made Direct Elution Buffer (10mM Tris-HCl pH8.0, 0.3M NaCl, 5mM EDTA, 0.5% SDS). Add 1ul of RNase A and incubate O/N at 65C to reverse crosslink. Quick spin sample.  Place in magnetic stand.  Allow beads to clump and transfer supernatant to a new low-bind tube. Add 3ul of Proteinase K and incubate for 1-2hrs at 55C. Purify the reverse-crosslinked ChIP DNA sample using phase lock tubes and EtOH precipitation. Resuspend sample in 25ul of Qiagen elution buffer.
Libraries were prepared according to standard illumina protocol.

value: prostate

tag: cell line

value: LNCaP

value: prostate adenocarcinoma

value: H3K27me3 (Millipore, 07-449)

tag: treatment

value: 10uM enzalutamide treatment for 14days


title: Sample_119894


title: vir_1 input

description: virilizer  input


title: LE22_D7_K27_rep2 (ChIP-seq)

tag: chip antibody

value: 10uM enzalutamide treatment for 7days


title: Sample_119902


title: vir_2 IP

description: virilizer IP


title: Sample_119899


title: Sample_119898


title: Sample_119897


title: vir_3 input

description: virilizer input


title: Sample_119895


title: LE20_D5_K27_rep2 (ChIP-seq)

value: 10uM enzalutamide treatment for 5days


title: LE23_D14_K27_rep1 (ChIP-seq)


title: vir_3 IP

description: virilizer IP


title: LE21_D7_K27_rep1 (ChIP-seq)


title: vir_1 IP

description: virilizer  IP


title: LE19_D5_K27_rep1 (ChIP-seq)


title: LE18_D3_K27_rep2 (ChIP-seq)

value: 10uM enzalutamide treatment for 3days


title: Sample_119896


title: LE17_D3_K27_rep1 (ChIP-seq)


title: fip37_5 IP

description: fip37  IP


title: fip37_4 IP

description: fip37  IP


title: fip37_5 input

description: fip37  input


title: fip37_2 IP

description: fip37  IP


title: KO_MI_1

city: Seattle

first: Jennifer

last: Davis

state: WA

address: 850 Republican St, Brotman #343

department: Lab Medicine and Pathology

institute: University of Washington

data_processing:
The Cell Ranger Single-Cell Software Suit (Zheng et al., 2017) was used to perform sample demultiplexing, barcode processing and single-cell 3′ gene counting.
For each sample, reads were aligned to the Mouse (mm10) 2020-A premRNA reference genome using CellRanger count v6.1.1. CellRanger Aggr (v6.1.1) was used to aggregate count matrices across samples with normalize=none. Only confidently mapped reads with valid barcodes and unique molecular identifiers were used to generate the gene-barcode matrix.
Further analyses for quality filtering was performed using the Seurat R package (Butler et al., 2018) .We calculated the distribution of detected genes per cell and removed cells in the top 1% quantile or those which had fewer than 200 detected genes. We also removed cells with more than 15% of the transcripts coming from mitochondrial genes.
After quality filtering, we normalized reads to account for technical variation in the dataset including sequencing depth. To do this, we implemented the SCTransform function (Hafemeister and Satija, 2019) with the “glmGamPoi” method (Ahlmann-Eltze and Huber, 2021); mitochondrial mapping percentage was also regressed out using the vars.to.regress argument.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with SCTransform normalized gene counts [normalized_counts.csv] or raw RNA counts [raw_counts.csv] for every gene and every cell from every sample. Genes are rows and cells are columns. Cell barcodes include sample name in the following pattern: "CELLBARCODE.samplename"

source_name: Isolated cardiac fibroblasts

extract_protocol:
For single cell RNA sequencing, isolated cardiac fibroblasts were subjected to magnetic bead sorting using a Miltenyi QuadroMACS magnetic cell separation kit. Briefly, cells were strained through a 70 µm cell strainer and resuspended in 180uL of sorting buffer (1XPBS, 0.5%BSA, 2µM EDTA) and 20µL of Cd11b microbeads. Samples were mixed well and incubated for 15 minutes at 4oC. Samples were washed through the magnetic columns and the flow through (containing the Cd11b- fraction) was collected. The cells were spun and resuspend in 160uL of sorting buffer with 40µL of MEFSK4 (Anti-feeder) microbeads. Cells were again incubated for 15 minutes at 4oC and sorted using magnetic columns. The flow through was discarded, and the magnetic columns containing the MEFSK4+ fraction were removed and rinsed with sorting buffer. Viability was assessed at this point for all preps. Viability was greater than 90% for all samples. Cells were lysed as previously described (Alexanian et al., 2021). Briefly cells were spun and rinsed in 1x HBSS with no FBS. Pellets were resuspended in 200uL of Lysis buffer (Tris-HCl 10mM pH 7.4, NaCl 10mM, MgCl2 3mM, Tween-20 0.1%, NP40 0.1%, Digitonin 0.01%, in Nuclease-free water), pipetted 10 times and kept on ice for 5 minutes. Nuclei were wash with 1 mL of wash buffer [Tris-HCl 10mM pH 7.4, NaCl 10mM, MgCl2 3mM, Tween-20 0.1%, in Nuclease-free water] inverting 3 times to mix. Nuclei were spun at 5000g for 3 minutes at 4oC. Nuclei were further washed in 1.2mL of 1X PBS with 1%BSA and filtered through a 30µm filter to remove any debris. Nuclei were counted using Trypan blue and a hemocytometer. Nuclei were resuspended at a concentration of 1000nuclei/µL in 1XPBS with 1%BSA with 8300 nuclei being loaded for subsequent 10X Genomics Chromium single cell RNAseq preparation.
Single-cell droplet libraries were generated in the 10X Genomics Chromium controller according to the manufacturer’s instructions in the Chromium Single Cell 3′ Reagent Kit v.3.1 with Dual Indexing User Guide. Additional components used for library preparation include the Chromium Single Cell 3′ Library and Gel Bead Kit v.3.1 (PN- 2000164) and the Chromium Single Cell 3′ Chip kit v.3.1 (PN-120236). Libraries were prepared according to the manufacturer’s instructions using the Chromium Single Cell 3′ Library and Gel Bead Kit v.3.1 (PN- 2000164) and Chromium i7 Multiplex Kit (PN- 1000213). Final libraries were sequenced on the NextSeq 2000. All 14 samples were pooled and sequenced in one single lane. Sequencing parameters were selected according to the Chromium Single Cell v.3.1 specifications. Libraries were sequenced to a mean read depth of at least 20,000 total aligned reads per cell.

treatment_protocol: The surgical model was previously described (Bugg et al., 2020; Molkentin et al., 2017), but briefly 8-week-old mice were anesthetized using injectable ketamine and xylazine. Mice were mechanically ventilated through oral intubation and a lateral thoracotomy was performed to expose the left ventricle. The pericardium was removed, and the left anterior descending artery was permanently ligated more apically to reduce risk of rupture, using 8-0 Surgipro tapered suture. Two days prior to surgery mice were taken off Tam chow for 2 days to prevent any adverse effects of Tam during the surgical procedure and then put back on Tam chow until the studies end point. Experimentalists remained blinded to the genotypes until analysis was complete. Both male and female mice were used in all experiments and mice were randomly assigned to groups. Echocardiography was performed on a Vevo2100 or Vevo3100 under isoflurane anesthetic.

value: heart

value: Isolated cardiac fibroblasts

tag: surgery

value: MI

tag: strain


title: Tg_SHAM_1

value: SHAM


title: Tg_MI_2


title: Tg_MI_1


title: Tg_SHAM_2


title: fip37_2 input

description: fip37  input

value: whole seedlings

value: Columbia


title: KO_MI_2


title: LE16_D1_K27_rep2 (ChIP-seq)

value: 10uM enzalutamide treatment for 1day


title: KO_SHAM_2


title: wt_6 IP

description: wild type IP

value: Epimark Monoclonal anti-m6A NEB


title: LE15_D1_K27_rep1 (ChIP-seq)


title: KO_SHAM_1


title: LE14_D0_K27_rep2 (ChIP-seq)

value: untreated


title: wt_6 input

description: wild type input


title: Ntg_MI_4

value: NTG


title: wt_5 IP

description: wild type IP


title: LE13_D0_K27_rep1 (ChIP-seq)

value: prostate

value: LNCaP


title: Ntg_MI_3


title: fip37_3 input

description: fip37 input


title: wt_4 IP

description: wild type IP


title: Ntg_MI_2


title: Ntg_MI_1


title: wt_4 input

description: wild type input


title: LE10_D7_K4_rep2 (ChIP-seq)

value: prostate adenocarcinoma

value: H3K4me3 (Cell Signaling, 9751)


title: LE9_D7_K4_rep1 (ChIP-seq)

value: 10uM enzalutamide treatment for 7days


title: LE12_D14_K4_rep2 (ChIP-seq)

value: 10uM enzalutamide treatment for 14days


title: wt_5 input

description: wild type input


title: LE11_D14_K4_rep1 (ChIP-seq)


title: LE8_D5_K4_rep2 (ChIP-seq)

value: 10uM enzalutamide treatment for 5days


title: Ntg_SHAM_2

value: heart


title: Ntg_SHAM_1

value: Isolated cardiac fibroblasts


title: LE7_D5_K4_rep1 (ChIP-seq)


title: LE6_D3_K4_rep2 (ChIP-seq)

value: 10uM enzalutamide treatment for 3days


title: Spleen_RFP_rep2

data_processing:
For RNase footprinting libraries, we performed paired-end sequencing (2 x 151 nt). Because the footprint lengths are short (< 35 nt for ribosome footprints), we used the first ends of reads to perform mapping and gene expression calculation. We first trimmed the 3’ sequencing adapters of reads (AGATCGGAAG for the datasets generated by linker ligation methods, and AAAAAAAAAA for the A-tailing methods). For the libraries using SMARTer-oligo based template switch, we trimmed the first 7 nts, including the random 4 nts and 3 locked Gs in the 5’ sequencing adapters. The trimmed reads were first mapped to the NCBI rRNA sequences using bowtie2 (version 2.2.6). The unmappable reads were then mapped to reference mouse genome (mm10) and transcriptome using tophat (version 2.1.0). The transcriptome annotation was based on GENCODE (v20). For ribosome footprints and ribosome profiling data, only the uniquely mappable reads with lengths of 18-35 nt were used for the downstream expression calculations because ribosome footprints show these defined lengths. For RNA-seq data, uniquely mappable reads with lengths all sizes were used for the downstream expression calculations. To obtain read counts in protein-coding regions, we excluded the regions overlapping with uORFs and used HTSeq (version 0.9.1) to generate gene-level read counts. We used the same data analyses procedures for ribosome profiling and RNA-seq. Except that we used all reads with different fragment lengths from RNA-seq to calculate RNA expression.
Genome_build: mm10
Supplementary_files_format_and_content: HTSeq gene-level count in txt format

source_name: Fresh frozen spleen

growth_protocol: Snap frozen mouse tissues were powdered using a pre-cooled mortar and pestle under the continuous addition of liquid nitrogen. For each tissue type, we collected 1mg powdered tumor and spleen tissues for RNase footprinting profiling, and 5 mg powdered tissue for total RNA extraction and RNA-seq.

extract_protocol:
For RNase footprinting, cells were then rinsed twice with PBS and lysed using cold lysis buffer. The cell lysis was digested with RNase 1 (cat. no. N6901K, Lucigen) at room temperature for 1.5 hour. We added 400 ul of TRIzol (Ambion) and then 100 ul of chloroform (Sigma) to extract RNase footprints. The footprints were precipitated overnight with isopropanol.   For RNA-seq, total RNA was isolated using the Direct-zol RNA kit (Zymo Research), and mRNAs were purified using Oligo(dT)25 magnetic beads (New England Biolabs) according to the manufacturer’s instructions. Purified mRNAs were fragmented with NEBNext Mg2+ RNA fragmentation module (New England Biolabs) at 94 for 6 min. Fragmented RNAs were then precipitated overnight at -20C by adding 0.1 volumes of 3M sodium acetate, 10 mg of glycoblue, and 1.2 volumes of isopropanol.
We use the same procedures for RNase footprinting and RNA-seq, precipitated RNA fragments were suspended in 5 ul of TNK reaction mixture and end-repaired at 37 C for 90 min followed by incubating at 65 C for 5 min to inactive PNK. The end-repaired fragments were 3’ polyadenylated with 5 U of E. coli poly (A) polymerase (New England Biolabs) by incubating at 37 C for 2-4 hrs. The resulting polyadenylated RNA was next reverse transcribed by a modified SMAT-RT reaction with customized template-switching oligos and incubated at 42 C for 1 h, followed by 3 cycles of heating to 50 C for 2 min and then cooling to 42 C for 2 min. The enzyme was inactivated by heating at 70 C for 10 min. The RNA fragments hybridized to DNA were then removed by incubating reaction mixture at 37 C for 15 min with 5 U of RNase H (New England Biolabs). The resulting cDNA was then amplified by two rounds of PCR to generate the sequencing library. DNA library was separated and visualized in a 4% agarose gel. DNA with 15-35 bp-insert was excised and recovered using the DNA gel recover kit (Zymo Research).
RNase footprinting, and RNA-seq.

value: Mouse 4T1 breast tumor model

value: Fresh frozen spleen


title: Tumor_RFP_rep2

source_name: Fresh frozen tumor

value: Fresh frozen tumor


title: HUDEP2_dTATA_r2

city: Guangzhou

first: Peng

last: Huang

state: Guangdong

address: Xinzao, Panyu District

department: GMU-GIBH Joint School of Life Sciences

institute: Guangzhou Medical University

data_processing:
library strategy: Capture-C
Basecalls using DRAGEN BCL Data Conversion (version 3.7.4), bcl2fastq2 v2.20, and parameters --no-eamss --mismatches 1
Reads were processed using the published pipeline (https://github.com/telenius/captureC/releases).
Genome_build: hg38
Supplementary_files_format_and_content: bigwig file with the normalized Capture-C interaction signals was generated from both samples and is linked to the corresponding *r1 sample records.

source_name: HUDEP2 cells

growth_protocol: HUDEP2 cells were cultured with StemSpan SFEM (Stem Cell Technologies) supplemented with 1 μg/ml doxycycline, 1 μM dexamethasone, 100 ng/ml human SCF, 3 units/ml erythropoietin and 1% penicillin/streptomycin.

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 minutes at room temperature. Fixed cells were lysised in 1mL Cell Lysis Buffer (10mM Tris-HCl pH 8, 10mM NaCl, 0.2% NP-40/Igepal).
Capture-C libraries were generated as described (Davies et al. 2016 Nature Methods).

treatment_protocol: HUDEP2 cells were differentiated for 5 days in Iscove’s Modified Dulbecco’s Medium (IMDM) supplemented with 330 μg/ml holo-transferrin, 10 μg/ml insulin, 2 units/ml heparin, 5% FBS, 3 units/ml erythropoietin, 1 μg/ml doxycycline and 1% penicillin/streptomycin.

tag: tissue source

value: Immortalized Human Erythroid Progenitor

value: Erythroid cells

tag: differentiation

value: Differentiated for 5 days

value: TATA deletion


title: HUDEP2_dTATA_r1


title: HUDEP2_dPromoter_r2

value: Promoter deletion


title: HUDEP2_dPromoter_r1


title: Tumor_RFP_rep1

tag: disease state


title: LE4_D1_K4_rep2 (ChIP-seq)

first: Filippo

address: 1881 East Road

institute: UT MD Anderson Cancer Center

value: prostate

value: LNCaP

value: 10uM enzalutamide treatment for 1day


title: LE3_D1_K4_rep1 (ChIP-seq)

value: prostate adenocarcinoma

value: H3K4me3 (Cell Signaling, 9751)


title: Smooth muscle cell - D148_Quiescent

city: Charlottesville

first: Mete

last: Civelek

address: 21 Hospital Drive, Old Medical School Room 3836

institute: University of Virginia

description: Quiescent.tsv

data_processing:
RNA-seq reads trimmed the with low average Phred scores (<20) using Trim Galore
Reads were mapped to the hg38 version of the human reference genome using the STAR Aligner in two-pass mode
Only uniquely mapped read pairs were kept.
Expression values were calculated as transcripts per million (TPM) for each gene using RNA-SeQC based on GENCODE v32 transcript annotations
Genome_build: grch38
Supplementary_files_format_and_content: Transcript per Million Gene Expression Quiescent SMCs
Supplementary_files_format_and_content: Transcript per Million Gene Expression Proliferative SMCs

source_name: Smooth Muscle Cell

growth_protocol: SMCs were grown till 80% confluence

extract_protocol:
RNeasy Mini Kit (Qiagen) and the RNase-free DNase Set
Illumina TruSeq Stranded mRNA Library Prep Kit

treatment_protocol: proliferative SMCs were grown in the presence of 5% FBS while quiescent SMCs were cultered without FBS for 24 hours

value: ascending aorta

value: Quiescent


title: HUDEP2_WT_r1

value: WT


title: LE2_D0_K4_rep2 (ChIP-seq)

last: Giancotti

value: untreated


title: Smooth muscle cell - D148_Proliferative

description: Proliferative.tsv

value: Proliferative


title: Smooth muscle cell - D147_Quiescent

description: Quiescent.tsv


title: Spleen_RNASeq

value: Mouse 4T1 breast tumor model

value: Fresh frozen spleen


title: H4K5Ac_epl1a/b_rep2

data_processing:
Zebracall software used for basecalling.
After removing adapter and filtering low-quality reads, the clean reads were aligned to the Arabidopsis genome (TAIR10) using HISAT2 with the default parameters.
The reads mapped on the exon were counted using featureCounts.
The differentially expressed genes were identified with log2(fold change) >1 or <-1 and p-value<0.01 using edgeR.
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab-delimited text file include normalized reads or reads count for each sample.

extract_protocol:
Total RNA was extracted with TRI Reagent (Sigma, T9424) from 2-week-old seedlings and was then used for reverse transcription or RNA deep sequencing.
Sequencing libraries were built for RNA-seq (the single-ended 50-bp and paired-end 150-bp strategy).

treatment_protocol: MS plates with seedlings were wrapped in foil for dark treatment.

value: seedlings


title: LNCaP3_enza_d14 (RNA-seq)

data_processing:
The raw reads from .fastq files were trimmed by trimmomatic/0.33
The trimmed reads were aligned to the human reference genome (hg19) using Tophat/2.1.1
Gene models of Refgene were downloaded from the Illumina's iGenomes project.
FPKM (Fragments Per Kilobase of transcript per Million mapped reads) values were generated using cufflinks/v2.2.1
Further differential expression analysis was using cuffdiff function which is in cufflinks.
Genome_build: hg38
Supplementary_files_format_and_content: genes.fpkm_tracking files are tab delimited text files output by cufflinks in a generic FPKM tracking format with estimated gene-level expression values in the form of FPKM values. htseq.txt files are  tab delimited text files output by HTSeq with aligned reads count per genes.

extract_protocol:
Total RNA were extracted from samples using TRIzol (Invitrogen, USA) according to manufactures's instructions
1 µg total RNA was sent to BGI for quality testing and library construction based on the standard workflow.

value: 10uM enzalutamide treatment for 14days


title: LE1_D0_K4_rep1 (ChIP-seq)


title: Smooth muscle cell - D147_Proliferative

description: Proliferative.tsv


title: Col-0 rep 2

value: wild type


title: Smooth muscle cell - D146_Quiescent

description: Quiescent.tsv


title: LNCaP2_enza_d14 (RNA-seq)


title: LNCaP1_enza_d14 (RNA-seq)


title: Tumor_RNASeq

value: Fresh frozen tumor


title: Spleen_RFP_rep1


title: Smooth muscle cell - D146_Proliferative

description: Proliferative.tsv


title: Smooth muscle cell - D145_Quiescent

description: Quiescent.tsv


title: Smooth muscle cell - D145_Proliferative

description: Proliferative.tsv


title: LNCaP3_enza_d7 (RNA-seq)

value: 10uM enzalutamide treatment for 7days


title: LNCaP2_enza_d7 (RNA-seq)

value: prostate


title: LE5_D3_K4_rep1 (ChIP-seq)

value: LNCaP

value: 10uM enzalutamide treatment for 3days


title: RNAseq_Ythdc2_WLA_homo_243

first: Yuhki

last: Saito

address: 1230 York avenue

institute: The Rockefeller University

description: total RNA

data_processing:
Alignment with STAR
DESeq2 were used for RNA abundance analysis and RiboWaltz and anota2seq were for ribosome profiling.
Genome_build: mm10
Supplementary_files_format_and_content: File containing gene symbol, fold change, pValue, FDR, and translation efficiency.

source_name: Testis

growth_protocol: Mouse testis from Ythdc2 mutants and wild-type mice

extract_protocol:
Trizol extraction
Illumina High-throughput TruSeq RNA Sample preparation: ribozero or poly(A) selection

value: Testis

tag: age

value: 20 weeks

value: Ythdc2 WLA/WLA (homo)


title: RNAseq_Ythdc2_WLA_homo_226

description: total RNA

value: 24 weeks


title: RNAseq_Ythdc2_WLA_homo_225

description: total RNA


title: Smooth muscle cell - D144_Quiescent

description: Quiescent.tsv

value: ascending aorta

value: Quiescent


title: HUDEP2_WT_r2

value: Immortalized Human Erythroid Progenitor

value: Erythroid cells

value: Differentiated for 5 days

value: WT


title: LNCaP1_enza_d7 (RNA-seq)

value: prostate adenocarcinoma


title: RNAseq_Ythdc2_WLA_het_242

description: total RNA

value: Ythdc2 WLA/+ (het)


title: Smooth muscle cell - D144_Proliferative

description: Proliferative.tsv

value: Proliferative


title: LNCaP3_enza_d5 (RNA-seq)

value: 10uM enzalutamide treatment for 5days


title: Smooth muscle cell - D143_Quiescent

description: Quiescent.tsv


title: RNAseq_Ythdc2_WLA_het_227

description: total RNA


title: H4K5Ac_epl1a/b_rep1

value: seedlings


title: LNCaP2_enza_d5 (RNA-seq)

value: prostate

value: LNCaP


title: LNCaP1_enza_d5 (RNA-seq)


title: ribo_8dpp_Ythdc2-WT_DJ34

description: total RNA

data_processing:
Library strategy: Ribo-seq
Alignment with STAR
DESeq2 were used for RNA abundance analysis and RiboWaltz and anota2seq were for ribosome profiling.
Genome_build: mm10
Supplementary_files_format_and_content: File containing gene symbol, fold change, pValue, FDR, and translation efficiency.

value: Testis

value: Postnatal day 8

value: Ythdc2 +/+


title: Smooth muscle cell - D142_Quiescent

description: Quiescent.tsv


title: Smooth muscle cell - D143_Proliferative

description: Proliferative.tsv


title: RNAseq_Ythdc2_WLA_het_224

description: total RNA

value: 24 weeks


title: LNCaP3_enza_d3 (RNA-seq)

value: 10uM enzalutamide treatment for 3days


title: ribo_8dpp_Ythdc2-WT_DJ138

description: total RNA


title: Col-0 rep 1

value: wild type


title: LNCaP2_enza_d3 (RNA-seq)


title: Smooth muscle cell - D142_Proliferative

description: Proliferative.tsv

value: ascending aorta


title: Smooth muscle cell - D141_Quiescent

description: Quiescent.tsv

value: Quiescent


title: ribo_8dpp_Ythdc2-WT_DJ134

description: total RNA


title: ribo_8dpp_Ythdc2KO_homo_DJ32

description: total RNA

value: Ythdc2 -/- (homo)


title: LNCaP1_enza_d3 (RNA-seq)


title: Smooth muscle cell - D141_Proliferative

description: Proliferative.tsv


title: Smooth muscle cell - D140_Quiescent

description: Quiescent.tsv


title: ribo_8dpp_Ythdc2KO_homo_DJ139

description: total RNA


title: ribo_8dpp_Ythdc2KO_homo_DJ132

description: total RNA


title: Smooth muscle cell - D140_Proliferative

description: Proliferative.tsv


title: LNCaP2_enza_d1 (RNA-seq)

value: 10uM enzalutamide treatment for 1day


title: LNCaP3_enza_d1 (RNA-seq)

value: prostate adenocarcinoma


title: LNCaP1_enza_d1 (RNA-seq)


title: ribo_10dpp_Ythdc2-WT_DJ395

description: total RNA

value: Postnatal day 10


title: Smooth muscle cell - D139_Quiescent

description: Quiescent.tsv


title: LNCaP3_enza_d0 (RNA-seq)

value: untreated


title: ribo_10dpp_Ythdc2KO_homo_DJ391

description: total RNA


title: LNCaP2_enza_d0 (RNA-seq)


title: Smooth muscle cell - D139_Proliferative

description: Proliferative.tsv

value: Proliferative


title: Smooth muscle cell - D138_Quiescent

description: Quiescent.tsv


title: ribo_10dpp_Ythdc2KO_homo_DJ363

description: total RNA


title: ribo_10dpp_Ythdc2KO_homo_DJ358

description: total RNA


title: Smooth muscle cell - D137_Quiescent

description: Quiescent.tsv


title: LNCaP1_enza_d0 (RNA-seq)


title: Smooth muscle cell - D138_Proliferative

description: Proliferative.tsv


title: ribo_10dpp_Ythdc2KO_het_DJ364

description: total RNA

value: Ythdc2 +/- (het)


title: ribo_10dpp_Ythdc2KO_het_DJ359

description: total RNA


title: input_8dpp_Ythdc2-WT_DJ34

description: total RNA


title: Smooth muscle cell - D136_Quiescent

description: Quiescent.tsv


title: input_8dpp_Ythdc2-WT_DJ138

description: total RNA


title: Smooth muscle cell - D136_Proliferative

description: Proliferative.tsv


title: input_8dpp_Ythdc2-WT_DJ134

description: total RNA


title: Smooth muscle cell - D135_Quiescent

description: Quiescent.tsv


title: Smooth muscle cell - D135_Proliferative

description: Proliferative.tsv


title: input_8dpp_Ythdc2KO_homo_DJ139

description: total RNA


title: input_8dpp_Ythdc2KO_homo_DJ32

description: total RNA


title: Smooth muscle cell - D134_Quiescent

description: Quiescent.tsv


title: Smooth muscle cell - D134_Proliferative

description: Proliferative.tsv


title: input_10dpp_Ythdc2-WT_DJ395

description: total RNA


title: Smooth muscle cell - D133_Quiescent

description: Quiescent.tsv


title: Smooth muscle cell - D133_Proliferative

description: Proliferative.tsv


title: input_10dpp_Ythdc2KO_homo_DJ391

description: total RNA


title: input_10dpp_Ythdc2KO_homo_DJ363

description: total RNA


title: Smooth muscle cell - D132_Quiescent

description: Quiescent.tsv


title: input_10dpp_Ythdc2KO_homo_DJ358

description: total RNA


title: input_10dpp_Ythdc2KO_het_DJ364

description: total RNA


title: Smooth muscle cell - D131_Quiescent

description: Quiescent.tsv


title: input_10dpp_Ythdc2KO_het_DJ359

description: total RNA


title: D8_Menin_KO_2

first: Wenbo

last: Deng

address: Xiang'an Road

institute: Xiamen University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using HISAT2 with default parameters
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using EdgeR package of R.
Genome_build: mm10

source_name: decidualized mouse stromal cells

extract_protocol:
D8 decidualized stromal cells were harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: C57 mouse decidua

tag: time point

value: pregnant day 11

value: Mouse uterus

tag: genotype/variation

value: Menin KO


title: Smooth muscle cell - D131_Proliferative

description: Proliferative.tsv


title: D8_Menin_KO_1

value: pregnant day 10


title: Smooth muscle cell - D130_Proliferative

description: Proliferative.tsv


title: Smooth muscle cell - D130_Quiescent

description: Quiescent.tsv


title: Smooth muscle cell - D137_Proliferative

description: Proliferative.tsv


title: Smooth muscle cell - D129_Proliferative

description: Proliferative.tsv


title: D8_WT_1

value: pregnant day 8

value: WT


title: Smooth muscle cell - D129_Quiescent

description: Quiescent.tsv


title: Smooth muscle cell - D128_Quiescent

description: Quiescent.tsv


title: RNA-Seq shCTCF_Rep2

city: Shanghai

first: Ji

last: Wu

address: No.800, Dongchuan Road, Minhang District

institute: Shanghai Jiao Tong University

data_processing:
All RNA-Seq data were trimmed and aligned to the mm9 reference genome using Hisat2 (version 4.8.2)(Pertea et al., 2016) with the default parameters.
Gene expression as FPKM was calculated by Cufflinks (version 2.2.1)(Trapnell et al., 2012) using the RefSeq database from the UCSC genome browser.
Genome_build: mm9
Supplementary_files_format_and_content: Microsoft Office Excel (xls) file include RPKM values for each Sample

source_name: FGSC

growth_protocol: FGSCs were cultured on mitotically inactivated STO (SIM mouse embryo-derived thioguanine- and ouabain-resistant) cell feeders in minimum essential medium alpha (MEMa; Invitrogen) supplemented with 10% fetal bovine serum (FBS) (Life Technologies), 10 ng/mL mouse leukemia inhibitory factor (Santa Cruz Biotechnology), 20 ng/mL mouse epidermal growth factor (EGF) (PeproTech), 10 ng/mL basic fibroblast growth factor (bFGF) (PeproTech), 10 ng/mL mouse glial cell line-derived neurotrophic factor (GDNF) (PeproTech), 1mM non-essential amino acids (NEAA) (Life Technologies), 2 mM L-glutamine (Sigma), 30 mg/mL pyruvate (Amresco) and 50 mM -mercaptoethanol (Biotech).The primary NSCs was seeded onto poly-l-ornithine (Sigma-Aldrich) and laminin (Invitrogen) coated dishes, cultured as monocultures. Neural basal medium with 20ng/ml EGF (PeproTech), 20ng/ml bFGF(PeproTech), 20ng/ml Hepairn (Sigma-Aldrich) and 2% B27 (Invitrogen) was used as NSC proliferation medium.

extract_protocol:
Total RNA was extracted from 1–2×106 cells using Trizol Reagent.
The RNA quality was assessed using an Agilent Bioanalyzer 2100. RNA-Seq libraries were prepared using the KAPA Stranded mRNA-Seq kit, following the manufacturer’s instructions.

tag: passages


title: RNA-Seq shCTCF_Rep1


title: RNA-Seq control_Rep3


title: RNA-Seq control_Rep2


title: Smooth muscle cell - D128_Proliferative

description: Proliferative.tsv


title: Smooth muscle cell - D127_Proliferative

description: Proliferative.tsv


title: Smooth muscle cell - D126_Quiescent

description: Quiescent.tsv


title: Smooth muscle cell - D126_Proliferative

description: Proliferative.tsv


title: Smooth muscle cell - D125_Quiescent

description: Quiescent.tsv


title: Smooth muscle cell - D125_Proliferative

description: Proliferative.tsv


title: input_8dpp_Ythdc2KO_homo_DJ132

description: total RNA

value: Testis

value: Postnatal day 8


title: Smooth muscle cell - D124_Quiescent

description: Quiescent.tsv

value: ascending aorta

value: Quiescent


title: Smooth muscle cell - D132_Proliferative

description: Proliferative.tsv


title: Smooth muscle cell - D123_Proliferative

description: Proliferative.tsv


title: Smooth muscle cell - D123_Quiescent

description: Quiescent.tsv


title: Smooth muscle cell - D124_Proliferative

description: Proliferative.tsv


title: Smooth muscle cell - D121_Proliferative

description: Proliferative.tsv


title: Smooth muscle cell - D120_Quiescent

description: Quiescent.tsv


title: Smooth muscle cell - D122_Proliferative

description: Proliferative.tsv


title: Smooth muscle cell - D121_Quiescent

description: Quiescent.tsv


title: Smooth muscle cell - D119_Quiescent

description: Quiescent.tsv


title: D8_WT_2

value: pregnant day 9


title: Smooth muscle cell - D120_Proliferative

description: Proliferative.tsv


title: Smooth muscle cell - D119_Proliferative

description: Proliferative.tsv


title: Smooth muscle cell - D118_Quiescent

description: Quiescent.tsv


title: RNA-Seq shCTCF_Rep3


title: Smooth muscle cell - D118_Proliferative

description: Proliferative.tsv


title: Smooth muscle cell - D127_Quiescent

description: Quiescent.tsv


title: Smooth muscle cell - D117_Quiescent

description: Quiescent.tsv


title: NHV_Rep03

city: Wien

first: Andreas

middle: B

last: Diendorfer

address: Leberstraße 20

country: Austria

institute: TAmiRNA GmbH

data_processing:
fastQC (v0.11.8) quality control
cutadapt (v2.3) adapter trimming and filtering
bowtie (v1.2.2) genome alignment
miRDeep2 (v2.0.1.2) miRNA quantification
edgeR (v3.28) differential expression
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: miRNA raw reads and RPM (based on total library size and total amount of mapped miRNA reads)

source_name: Plasma

extract_protocol:
Maxwell RSC miRNA Tissue kit (Promega, AS1460); miRNeasy Mini kit  (Qiagen,Cat. 217004)
NEXTFLEX Small RNA-Seq kit v3 for Illumina platforms (Cat. NOVA-5132-06, PerkinElmer), QIAseq miRNA Library kit (Cat. 331502, Qiagen), CleanTag small RNA library prep kit (Cat. 040L-3206-24, TriLink Biotechnologies) and RealSeq-Biofluids NGS library preparation kit for miRNAs and small RNAs for total RNA samples from biofluids (Cat. 600-00012-SOM, RealSeq Biosciences, protocol 20181220_RealSeq-BF_CL)
small RNA sequencing with various library preparation kits focusing on miRNAs

value: Plasma

tag: protocol

value: RealSeq

tag: disease

value: NHV

value: No

tag: operator

value: Operator 1


title: NHV_Rep01


title: NHV_Rep02


title: Smooth muscle cell - D117_Proliferative

description: Proliferative.tsv

value: Proliferative


title: Op03_Rep03

value: Operator 3


title: Op03_Rep02


title: Smooth muscle cell - D116_Quiescent

description: Quiescent.tsv


title: Op03_Rep01


title: RNA-Seq control_Rep1


title: Op02_Rep03

value: Operator 2


title: Smooth muscle cell - D116_Proliferative

description: Proliferative.tsv


title: Smooth muscle cell - D115_Quiescent

description: Quiescent.tsv


title: Smooth muscle cell - D115_Proliferative

description: Proliferative.tsv


title: Op02_Rep02


title: Smooth muscle cell - D114_Quiescent

description: Quiescent.tsv


title: Op02_Rep01


title: Op01_Rep03


title: Smooth muscle cell - D114_Proliferative

description: Proliferative.tsv


title: Op01_Rep02


title: Smooth muscle cell - D113_Quiescent

description: Quiescent.tsv


title: Smooth muscle cell - D112_Quiescent

description: Quiescent.tsv


title: Smooth muscle cell - D112_Proliferative

description: Proliferative.tsv


title: 80amol_Rep03

value: Yes


title: Smooth muscle cell - D113_Proliferative

description: Proliferative.tsv


title: 80amol_Rep01


title: 5amol_Rep03


title: Op01_Rep01


title: Smooth muscle cell - D111_Proliferative

description: Proliferative.tsv


title: Smooth muscle cell - D109_Proliferative

description: Proliferative.tsv


title: Smooth muscle cell - D110_Proliferative

description: Proliferative.tsv


title: 5amol_Rep02


title: Smooth muscle cell - D109_Quiescent

description: Quiescent.tsv


title: 20amol_Rep02


title: 20amol_Rep01


title: 5amol_Rep01


title: Smooth muscle cell - D108_Proliferative

description: Proliferative.tsv


title: 20amol_Rep03


title: APAP1NHV5_Rep02

value: APAP:NHV 1:5 ratio


title: Smooth muscle cell - D107_Quiescent

description: Quiescent.tsv


title: APAP1NHV5_Rep01


title: Smooth muscle cell - D106_Proliferative

description: Proliferative.tsv


title: APAP1NHV5_Rep03


title: APAP1NHV1_Rep03


title: Smooth muscle cell - D106_Quiescent

description: Quiescent.tsv


title: 80amol_Rep02


title: Smooth muscle cell - D104_Quiescent

description: Quiescent.tsv


title: APAP1NHV1_Rep02

value: APAP:NHV 1:1 ratio


title: Smooth muscle cell - D104_Proliferative

description: Proliferative.tsv


title: Smooth muscle cell - D105_Proliferative

description: Proliferative.tsv


title: Smooth muscle cell - D111_Quiescent

description: Quiescent.tsv


title: Smooth muscle cell - D105_Quiescent

description: Quiescent.tsv


title: APAP1NHV10_Rep02

value: APAP:NHV 10:1 ratio


title: Smooth muscle cell - D103_Quiescent

description: Quiescent.tsv


title: APAP1NHV10_Rep01


title: Smooth muscle cell - D110_Quiescent

description: Quiescent.tsv


title: APAP1NHV1_Rep01


title: Smooth muscle cell - D103_Proliferative

description: Proliferative.tsv


title: APAP1NHV10_Rep03


title: APAP_Rep03


title: APAP_Rep02

value: APAP


title: Smooth muscle cell - D102_Quiescent

description: Quiescent.tsv


title: Smooth muscle cell - D101_Quiescent

description: Quiescent.tsv


title: Smooth muscle cell - D101_Proliferative

description: Proliferative.tsv


title: Nextflex_plasma_Rep06

value: NEXTFLEX


title: Nextflex_plasma_Rep05


title: Smooth muscle cell - D100_Proliferative

description: Proliferative.tsv

value: ascending aorta


title: Nextflex_plasma_Rep03


title: Smooth muscle cell - D99_Quiescent

description: Quiescent.tsv

value: Quiescent


title: Nextflex_plasma_Rep02


title: Smooth muscle cell - D99_Proliferative

description: Proliferative.tsv


title: Nextflex_plasma_Rep04


title: Nextflex_plasma_Rep01


title: Smooth muscle cell - D100_Quiescent

description: Quiescent.tsv


title: Smooth muscle cell - D98_Quiescent

description: Quiescent.tsv


title: CleanTag_plasma_Rep06

value: CleanTag


title: CleanTag_plasma_Rep05

value: Plasma


title: Smooth muscle cell - D98_Proliferative

description: Proliferative.tsv


title: Smooth muscle cell - D97_Quiescent

description: Quiescent.tsv


title: Smooth muscle cell - D97_Proliferative

description: Proliferative.tsv


title: CleanTag_plasma_Rep04


title: CleanTag_plasma_Rep03


title: CleanTag_plasma_Rep01


title: CleanTag_plasma_Rep02


title: Smooth muscle cell - D102_Proliferative

description: Proliferative.tsv


title: Smooth muscle cell - D95_Quiescent

description: Quiescent.tsv


title: APAP_Rep01

value: RealSeq


title: Smooth muscle cell - D95_Proliferative

description: Proliferative.tsv


title: Smooth muscle cell - D94_Quiescent

description: Quiescent.tsv


title: RealSeq_plasma_Rep05

value: NHV


title: RealSeq_plasma_Rep04

value: No


title: Smooth muscle cell - D94_Proliferative

description: Proliferative.tsv


title: RealSeq_plasma_Rep06

value: Operator 1


title: RealSeq_plasma_Rep03


title: Smooth muscle cell - D93_Quiescent

description: Quiescent.tsv


title: Smooth muscle cell - D92_Quiescent

description: Quiescent.tsv


title: Smooth muscle cell - D92_Proliferative

description: Proliferative.tsv

value: Proliferative


title: Smooth muscle cell - D91_Quiescent

description: Quiescent.tsv


title: Qiaseq_plasma_Rep06

value: Qiaseq


title: Qiaseq_plasma_Rep05


title: RealSeq_plasma_Rep02


title: Smooth muscle cell - D90_Quiescent

description: Quiescent.tsv


title: Qiaseq_plasma_Rep03


title: Smooth muscle cell - D96_Quiescent

description: Quiescent.tsv