title: TPC_1_NC3

city: zhengzhou

first: xinguang

last: qiu

address: Erqi District, Zhengzhou City, Henan Province

institute: First Affiliated Hospital of Zhengzhou University

description: Papillary thyroid cancer empty vector stable transfer cell line

data_processing:
We use the RPKM (Reads per Kilobase per Million reads) value as a measure of all gene expression (Mortazavi A. et al. Nature Methods 2008). rpkm=total exon reads/((mapped reads( millions)*exon length(KB)). The RPKM method can eliminate the effect of gene length and sequencing volume differences on the calculated expression, and the calculated binding amounts can be directly used to compare the binding differences between different samples.
Assembly: mm9
Supplementary files format and content: read counts; RPKM

source_name: Papillary thyroid cancer cells

growth_protocol: TPC-1-Lv-FTO and TPC-1-NC were raised in 1640 medium, 10% FBS, 37 degree incubator.

extract_protocol:
Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
DNA digestion was carried out after RNA extraction by DNaseI. RNA quality was determined by examining A260/A280 with NanodropTM OneCspectrophotometer (Thermo Fisher Scientific Inc).
Qualified RNAs were finally quantified by Qubit3.0 with QubitTM RNA Broad Range Assay kit (Life Technologies, Q10210).
2 μg total RNAs were used for stranded RNA sequencing library preparation using KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction.
The kit eliminates duplication bias in PCR and sequencing steps, by using unique molecular identifier (UMI) of 8 random bases to label the pre-amplified cDNA molecules.
The library products corresponding to 200-500 bps were enriched, quantified and finally sequenced on Novaseq 6000 sequencer (Illumina) with PE150 model.

treatment_protocol: Total RNAs were extracted from TPC-1_OE/TPC-1-NC using TRIzol Reagent (Invitrogen, cat. NO 15596026）following the methods by Chomczynski et al

value: TPC-1 empty carrier


title: TPC_1_OE1

status: Public on May 06 2022

type: SRA

country: China

description: Thyroid papillary carcinoma overexpressing FTO stably transfected cell line

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: genotype

value: FTO overexpression

tag: treatment


title: TPC_1_OE3


title: RNA-seq_HCC1954_rep1

city: Daejeon

first: Taemook

last: Kim

address: 291 Daehak-ro, Yuseong-gu

department: Biological sciences

country: South Korea

institute: Korea Advanced Institute of Science and Technology

data_processing:
(RNA-seq) The sequenced short reads were aligned to the human reference genome (hg19) using STAR.
The aligned read was used to generate read count and fragment per kilobase of transcript per million (FPKM) of genes using Cufflinks (Cuffnorm and Cuffdiff).
Differentially expressed genes (DEG) between normal (HMEC and normal tissue) and breast cancer (cell or tissue) was classified by statistically significant criteria (q-value<0.01, abs(log2FC) > 1) using Cuffdiff.
Gene ontology (GO) analysis of DEGs was performed using a ConsensusPathDB-human (KEGG pathway and gene ontology).
Gene expression and DEG were visualized by heatmap and boxplot using the R package (pheatmap and ggplot2). The vocano plot and venn diagram was drawn using a R package (ggplot2)
Genome_build: hg19
Supplementary_files_format_and_content: diff.txt.gz

molecule: polyA RNA

source_name: Her2+ cell

growth_protocol:
All cell lines, which is a normal cell and breast cancer cell, used in this study were purchased from ATCC. Human mammary epithelial cell (HMEC, PCS-600-010, ATCC) was cultured in mammary epithelial cell basal medium (PCS-600-030, ATCC) supplemented with mammary epithelial cell growth kit (PCS-600-040) as ATCC suggested. T47D (HTB-133) was cultured in RPMI-1640 (ATCC, 30-2001) supplemented with 10% FBS (ATCC, 30-2020) and 0.2 units/ml of human insulin (Life Technologies, 12585-014). BT549 (HTB-122) was cultured in RPMI-1640 supplemented with 10% FBS and 0.023 units/ml of human insulin. HCC1954, HCC70, and ZR-75-30 were cultured in RPMI-1640 supplemented with only 10% FBS. All cell lines were grown in the humidified incubator at 37°C containing 5% CO2.
The frozen fresh tumor samples were collected from resected breast tumors from patients at the Seoul National University Hospital (SNUH) in South Korea with informed consent and institutional IRB approval. The frozen tissues provided are as follows: Contralateral breast normal tissue and triple negative breast cancer tissue. These frozen samples were snap-frozen in liquid nitrogen and stored at -80°C.

extract_protocol:
(RNA-seq) Total RNAs were purified using TRIzol reagent (Invitrogen, cat # 15596-026) according to the manufacturer’s protocol. mRNA isolation were performed using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB; E7490L)
(RNA-seq) The RNA-seq libraries were generated using a NEBNext Ultra II Directional RNA Library Prep Kit (NEB; E7760S).

tag: tissue/cell type

value: Her2+ cell


title: TPC_1_NC2


title: RNA-seq_HMEC_rep2

source_name: human mammary epithelial cell

value: human mammary epithelial cell


title: TPC_1_NC_Input

data_processing:
library strategy: meRIP-seq
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.
The exomePeak (Version 3.8) software was used for peak calling.
The m6A peaks were annotated using bedtools (Version 2.25.0) .
The deepTools (version 2.4.1) was used for peak distribution analysis.
The differentially m6A peaks were identified by a python script，using fisher test.
Assembly: mm9
Supplementary files format and content: peak text files

extract_protocol: NOT PROVIDED; REQUESTED

tag: cell type

value: Papillary thyroid cancer cells


title: atac.no.crush.rep3

city: Los Angeles

first: Yuyan

last: Cheng

state: CA

address: 695 Charles E Young Dr S Rm 2305

department: Neurology

country: USA

institute: UCLA

description: atac.3dpc.rep3.macs2_peaks.narrowPeak_rmBlk

library_source: genomic

data_processing:
For ATAC-seq, Raw sequencing fastq files were assessed for quality, adapter content and duplication rates with FastQC, trimmed using trim-galore and aligned with bowtie2.The reference genome was mouse GRCm38 vM11. Samtools was used to calculate the read statistics, and Picard Tools was used to remove duplicate.
MACS2 was used to call peaks on each sample. Peaks from each sample were merged to a set of union peaks across all conditions using bedtools merge. The consensus peaks were further annotated to the transcriptional start site of genes in a distance of +-2 kb from the gene start using ChIPseeker. Gencode vM24 was used for annotations.
We obtained the number of reads for consensus peaks (hereafter referred to as peaks) across samples using featureCounts from the Subread package, and the GC content using bedtools nuc.
We then calculated normalization factors for each peak accounting for GC content, peak width, and total number of unique non-mitochondrial fragments sequenced using conditional quantile normalization from cqn package. To obtain differential accessible peak-regions (DAR) comparing injured vs uninjured RGCs, we used a negative binomial regression with normalization based on the size factors from cqn and implemented in DEseq2 with default parameters (fitType=“parametric”,test=“Wald”). Normalized peak-count matrix with batch effects regressed out was used for subsequent analysis.
mm10
peak files in bed format for each sample

molecule: genomic DNA

organism: Mus musculus

source_name: Retinal Ganglion Cells

extract_protocol:
Samples were dissociated in papain, followed by FACS sorting. For ATAC-seq, 50,000 - 100,000 sorted RGCs were lysed in 100 µL ice-cold Resuspension Buffer (RSB, 10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, pH=7.4) with 0.1% NP40, 0.1% Tween- 20, and 0.01% Digitonin. Cell lysis were washed with 1 ml of cold ATAC-RSB containing 0.1% Tween-20 but NO NP40 or digitonin, and centrifuged at 4 °C for 10 minutes at 500 x g. Pelleted nuclei were resuspended gently in 50 µL transposition mix (25 ul 2x TD buffer, 2.5 ul transposase (100nM final), 16.5 ul PBS, 0.5 ul 1% digitonin, 0.5 ul 10% Tween-20, 5 ul H2O) and incubated for 30 minutes at 37 °C. DNA was cleaned using Zymo DNA Clean and Concentrator-5 Kit.
Purified DNA was PCR amplified 5 cycles in a 50 µL reaction with Illumina Nextera adaptors using NEBNext High Fidelity 2x Master Mix. To determine the number of additional cycles to amplify the libraries, a side qPCR reaction was performed using 5 µL (10%) of the pre-amplified PCR. We used the Ct value of the qPCR at ¼ maximum fluorescence as the number of additional cycles. Final PCR products were cleaned using Zymo DNA Clean and Concentrator-5 Kit, and quantified by the KAPA Library Quantification kit prior to pooling and sequencing.

tag: strain

value: No Crush (Day0)


title: TPC_1_NC_IP


title: atac.no.crush.rep1

description: atac.3dpc.rep1.macs2_peaks.narrowPeak_rmBlk


title: p38_dn_unirradiated_rep3

type: RNA

city: New York

first: Constantinos

last: Broustas

state: NY

address: 630 168th Street

department: Center for Radiological Research

institute: Columbia University

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k v.2 array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 12.0.2 (Agilent) using default parameters (protocol GE1_1200_Jun14 and Grid: 026655_D_F_20140728) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: blood

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was purified following the PAXgene RNA kit recommendations with on-column DNase I treatment

treatment_protocol: Blood was collected by cardiac puncture at the time of euthanasia 24 h post-irradiation. Each sample  was added to a 15 ml centrifuge tube that contained of PAXgene Blood RNA stabilization and lysis solution and mixed thoroughly

tag: Sex

value: male

value: unirradiated


title: p38_dn_unirradiated_rep2


title: ChIP-seq_H3K27ac_BT549_rep2

data_processing:
(ChIP-seq) The ChIP-seq data were aligned to the human reference genome (hg19) using bowtie2.
CTCF and H3K27ac peaks were called using Macs2 with option (p < 0.001).
Super enhancer and enhancer was identified using Homer (findPeaks) with options (-style superhistone and -typical) from H3K27ac ChIP-seq data.
BigWig was generated by normalizing to total mapped read each sample. Briefly, bedGraph was generated using a Macs2 (pileup) and normalized by total mapped reads. The replicate sample was calculated as an average normalized bedGraph. Finally, normalized bedGraph was converted to bigWig using a bedGraphToBigWig.
The CTCF enrichment around the HMEC CTCF peak at the HMEC TAD boundaries was used meta value calculated using bwtool with meta-option (up:meta:down, 1:1:1). The enrichment difference of CTCF or H3K27ac between HMEC and BT549 cells was calculated as log2 (BT549/HMEC) value, respectively.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

source_name: Triple negative breast cancer B cell

growth_protocol: All cell lines, which is a normal cell and breast cancer cell, used in this study were purchased from ATCC. Human mammary epithelial cell (HMEC, PCS-600-010, ATCC) was cultured in mammary epithelial cell basal medium (PCS-600-030, ATCC) supplemented with mammary epithelial cell growth kit (PCS-600-040) as ATCC suggested. T47D (HTB-133) was cultured in RPMI-1640 (ATCC, 30-2001) supplemented with 10% FBS (ATCC, 30-2020) and 0.2 units/ml of human insulin (Life Technologies, 12585-014). BT549 (HTB-122) was cultured in RPMI-1640 supplemented with 10% FBS and 0.023 units/ml of human insulin. HCC1954, HCC70, and ZR-75-30 were cultured in RPMI-1640 supplemented with only 10% FBS. All cell lines were grown in the humidified incubator at 37°C containing 5% CO2.

extract_protocol:
(ChIP-seq) The cells were washed twice with PBS and incubated with 1% formaldehyde for 10 min at RT. The crosslinking was quenched with 125 mM glycine for 5min at RT, and the cells were harvested with cold PBS and suspended in SDS lysis buffer (50mM Tris-HCl, pH 8.0, 1% SDS, 10mM EDTA). Following the suspended chromatin was sheared using a ultrasonicator (Covaris S220) and incubated overnight with the relevant antibodies against anti-CTCF (Millipore; 07-729), anti-H3K27ac (Abcam; ab4729) and Protein A, G sepharose (GE Healthcare; 17-1279-03 and 17-0618-05) at 4°C with agitation. The Immune complex was washed in the order of low-salt wash buffer (20mM Tris-HCl, pH8.0, 150mM NaCl, 0.1% SDS, 1% Triton X-100, 2mM EDTA), high-salt wash buffer (20mM Tris-HCl, pH 8.0, 250mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1mM EDTA), and LiCl wash buffer, and finally, washed twice with TE buffer. Following the washed immune complexes were eluted with elution buffer (1% SDS, 0.1M NaHCO3). Finally the immune complexes were eluted with elution buffer (1% SDS, 0.1M NaHCO3) and de-crosslinked overnight at 68°C. The immunoprecipitated DNA was treated with proteinase K and RNase A and phenol-chloroform-isoamyl alcohol precipitation.
(ChIP-seq) The ChIP-seq libraries were prepared using a Accel-NGS 2S Plus DNA Library Kit (SWIFT; 21024)

value: Triple negative breast cancer B

tag: chip antibody

value: anti-H3K27ac (ab4729,Abcam)


title: p38_dn_unirradiated_rep1


title: ChIP-seq_H3K27ac_BT549_rep1


title: atac.3dpc.rep6

description: atac.1dpc.rep3.macs2_peaks.narrowPeak_rmBlk

value: Crush (Day 3)


title: p38_dki_irradiated_rep5

value: irradiated


title: TPC_1_OE_Input


title: p38_dki_irradiated_rep3


title: TPC_1_OE_IP


title: RNA-seq_HMEC_rep1


title: atac.3dpc.rep5

description: atac.1dpc.rep2.macs2_peaks.narrowPeak_rmBlk


title: atac.no.crush.rep2

description: atac.3dpc.rep2.macs2_peaks.narrowPeak_rmBlk


title: scRNAseq day 16

city: Albany

first: Janet

middle: L

last: Paluh

address: CNSE, Nanofab East, 257 Fuller Road

department: Nanobioscience

institute: SUNY Polytechnic Institute

description: EMLO to EMLOC protocol

data_processing:
Illumina RTA 2.2.68 Basecaller
Cellranger 6 mkoutput with Bcl2Fastq 2.20.0.422
Cellranger 6 Count against GRCh38 genome to produce count matrix
Seurat 4.0 used for marker gene analysis and visualization
Genome_build: GRCh38
Supplementary_files_format_and_content: H5 Matrix Files

source_name: Human iPSC  line H3.1.1

growth_protocol: hiPSC EMLO protocol modified for multilineage neurogenesis with cardiogenesis

extract_protocol:
10X CellPlex 3' Capture
TruSeq Stranded RNA (illumina)

value: Hispanic Latino self designation

tag: tissue

value: hiPSC derived

tag: developmental stage

value: Day 16


title: ChIP-seq_H3K27ac_HCC70_rep1

source_name: Triple negative breast cancer A cell

value: Triple negative breast cancer A


title: p38_dki_irradiated_rep4


title: atac.3dpc.rep3

description: atac.no.crush.rep6.macs2_peaks.narrowPeak_rmBlk


title: atac.3dpc.rep4

description: atac.1dpc.rep1.macs2_peaks.narrowPeak_rmBlk


title: scRNAseq day 7

description: EMLO to EMLOC protocol

value: Day 7


title: p38_dki_irradiated_rep2


title: p38_dki_irradiated_rep1


title: RNA-seq_Normal_Tissue5

source_name: Contralateral breast tissue, patient N5

value: Contralateral breast tissue, patient N5


title: ChIP-seq_H3K27ac_HCC1954_rep1

value: Her2 positive


title: atac.3dpc.rep1

description: atac.no.crush.rep4.macs2_peaks.narrowPeak_rmBlk


title: RNA-seq_Normal_Tissue3

source_name: Contralateral breast tissue, patient N3

value: Contralateral breast tissue, patient N3


title: atac.3dpc.rep2

description: atac.no.crush.rep5.macs2_peaks.narrowPeak_rmBlk


title: p38_dki_unirradiated_rep5


title: p38_dki_unirradiated_rep3


title: ChIP-seq_H3K27ac_HCC1954_rep2


title: ChIP-seq_H3K27ac_ZR7530_rep2

source_name: Luminal B cell

value: Luminal B


title: RNA-seq_Normal_Tissue4

source_name: Contralateral breast tissue, patient N4

value: Contralateral breast tissue, patient N4


title: atac.1dpc.rep3

description: atac.no.crush.rep3.macs2_peaks.narrowPeak_rmBlk

value: Crush (Day 1)


title: ChIP-seq_H3K27ac_T47D_rep2

source_name: Luminal A cell

value: Luminal A


title: ChIP-seq_H3K27ac_ZR7530_rep1


title: p38_dki_unirradiated_rep1

value: male

value: unirradiated


title: p38_dki_unirradiated_rep4


title: DN003-HUETH-con-3-LDC11434

city: Sapporoshi kitaku

first: Daigo

last: Nakazawa

state: Hokkaido

address: kita15 nishi7

country: Japan

institute: Hokkaido University

data_processing:
Sequencing was performed on a NovaSeq 6000 platform in a 2 × 150 bp paired-end configuration with over 20 million reads per sample.
Raw sequencing reads with low-quality and adapter sequences were removed using cutadapt v 2.1
The trimmed reads were mapped to hg38 (Ensembl version 93) and quantified using STAR aligner v 2.5.1
Assembly: hg38 (Ensembl version 93)
Supplementary files format and content: text files include raw, tpm , FPKM values for each Sample

source_name: vessel

growth_protocol: HK2 (human) tubular cells (1 × 105 cells/mL) were grown in an epithelial basal medium using a supplement kit (Thermo Fisher Scientific, Waltham, MA, USA). HUEhT cells (immortalized human umbilical vein endothelial cell line established by the electroporation of pIRES-hTERT-hygr) were cultured in HuMedia-EG2 (Kurabo, Osaka, Japan) at 1 × 105 cells/mL concentration

extract_protocol:
total RNA was isolated from each cell using ISOGEN II kit (Nippon Gene, Tokyo, Japan) according to the manufacturer’s instructions, The rRNAs were depleted using the NEBNext rRNA Depletion Kit
sequencing libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina

treatment_protocol: SARS-CoV-2 solutions or mock

value: vessel

tag: cell line

value: HUEhT

value: WT

value: Mock


title: ChIP-seq_H3K27ac_HMEC_rep1

value: Primary Mammary Epithelial Cell

value: anti-H3K27ac (ab4729,Abcam)


title: DN004-HUETH-cov-10-3-1-LDC11427

value: SARS-CoV-2 solution


title: ChIP-seq_H3K27ac_HMEC_rep2


title: RNA-seq_Normal_Tissue1

source_name: Contralateral breast tissue, patient N1

value: Contralateral breast tissue, patient N1


title: ChIP-seq_H3K27ac_T47D_rep1


title: atac.1dpc.rep1

description: atac.no.crush.rep1.macs2_peaks.narrowPeak_rmBlk


title: DN013-HUETH-con-1-LDC11437


title: repro_5d (scRNA-seq)

city: Lyon

first: Fabrice

last: Lavial

address: 28 rue Laennec

country: France

institute: CRCL

data_processing:
Bcl2 files were transormed to fastq files with cellranger mkfastq  v 5.0.1.
Alignment, filtering and quantification were done with cellranger count v 5.0.1.
Genome_build: mm10
Supplementary_files_format_and_content: Outputs from cellranger count: barcodes, features and matrix files.

source_name: mouse embryonic fibroblasts

growth_protocol: MEF were generated from E13.5 Bcl11b-tdTomato mice embryos and cultivated in DMEM medium supplemented with 10% foetal bovine serum (FBS), 100U/ml penicillin / streptomycin (PS), 1mM sodium pyruvate, 2mM L-glutamine, 0.1mM Non Essential Amino Acids (NEAA) and 0.1mM b-mercaptoethanol. iPS cells were grown in DMEM containing 15% KnockOut™ Serum Replacement, 1,000 U/ml leukemia inhibitory factor, 100U/ml PS, 1mM sodium pyruvate, 2mM L-glutamine, 0.1mM NEAA and 0.1mM b-mercaptoethanol. Transformed cells were cultivated in the same medium than MEF.

extract_protocol:
Cell suspension was mixed with master mix and loaded with Single Cell 3′ Gel Beads and Partitioning Oil into a Single Cell G Chip. RNA transcripts from single cells were uniquely barcoded and reverse-transcribed within droplets. cDNA molecules were pooled and the cDNA pool then go through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products are then purified and enriched with PCR to create the final cDNA library.
10x Genomics Chromium 3' v3.1 Single Cell Gene Expression Kit protocol was followed according to manufacturer instructions.
scRNAseq

treatment_protocol: MEF are infected by OSKM retroviruses to induce Repro or by K-Ras G12V, shp53 lentiviruses combined with cMyc retroviral infection to induce Transfo.

value: mouse embryonic fibroblasts

value: mouse embryonic fibroblasts after 5 days of Repro

tag: treatment time

value: 5 days


title: DN008-HK2-con-2-LDC11435

source_name: kidney

value: kidney

value: HK-2 cell


title: repro_10d (scRNA-seq)

value: mouse embryonic fibroblasts after 10 days of Repro

value: 10 days


title: atac.1dpc.rep2

description: atac.no.crush.rep2.macs2_peaks.narrowPeak_rmBlk

value: Crush (Day 1)


title: p38_dki_unirradiated_rep2

value: male

value: unirradiated


title: ChIP-seq_CTCF_BT549_rep2

value: Triple negative breast cancer B

value: anti-CTCF (07-729, Millipore)


title: ChIP-seq_CTCF_HCC70_rep2

value: Triple negative breast cancer A


title: ChIP-seq_CTCF_BT549_rep1


title: Hi-C_Normal_Tissue5

data_processing:
(Hi-C) Hi-C data were analyzed according to the HiC-Pro protocol.
Raw paired-end data were separately aligned to the human reference genome (hg19) and filter out artifacts (self-ligation, singleton, dangling end, and dumped pairs).
The extracted valid-paired reads were used to build a contact matrix for each resolution. (10, 20, 40, 100 and 500kb) and to normalize with iterative correction and eigenvector (ICE) method.
The GENOVA was used to draw the figure such as contact map, relative contact probability (RCP), cis-interaction within each chromosome, and trans-interaction between chromosomes.
The scatter plot, density plot, Venn diagram, and boxplot associated with a contact at peaks were drawn using an R package.
Genome_build: hg19
Supplementary_files_format_and_content: hic

extract_protocol:
(Hi-C) The in situ Hi-C experiments for cells and tissues was performed according to the Arima-HiC protocol (Arima Genomics, Inc.; Cat #A160259).
(Hi-C) The Hi-C library was generated using the Arima-HiC kit (Arima Genomics, Inc.; Cat #A510008)

value: Contralateral breast tissue, patient N5


title: transfo_10d (scRNA-seq)

value: mouse embryonic fibroblasts after 10 days of Transfo


title: DN006-HUETH-cov-10-3-3-LDC11429

value: vessel

value: HUEhT

value: WT

value: SARS-CoV-2 solution


title: DN014-HK2-con-1-LDC11438

value: Mock


title: RNA-seq_T47D_rep2

value: Luminal A cell


title: TC_ctrl (scRNA-seq)

value: mouse embryonic fibroblasts

value: transformed cells derived from MEF expressing K-RasG12V + cMyc + shp53


title: Hi-C_Normal_Tissue3

value: Contralateral breast tissue, patient N3


title: RNA-seq_Normal_Tissue2

source_name: Contralateral breast tissue, patient N2

value: Contralateral breast tissue, patient N2


title: DN009-HK2-con-3-LDC11436

value: kidney

value: HK-2 cell


title: DN012-HK2-cov-10-3-3-LDC11432


title: TC_Atoh8_KD (scRNA-seq)

value: Atoh8 downregulation


title: iPS (scRNA-seq)

value: induced pluripotent stem cells derived from MEF OSKM doxycycline-inducible


title: ChIP-seq_CTCF_HCC1954_rep2

source_name: Her2+ cell

value: Her2 positive

value: anti-CTCF (07-729, Millipore)


title: Hi-C_Normal_Tissue2


title: ChIP-seq_CTCF_HCC1954_rep1


title: DN011-HK2-cov-10-3-2-LDC11431


title: rna-2dpc-rep3

description: rawEx.tsv.gz

data_processing:
For RNA-seq, raw sequenced reads were mapped to the reference genome Mus musculus (mm10) refSeq (refFlat) using STAR with default parameter.
Data quality was assessed on base-quality calls, nucleotide composition of sequences, insert sizes, per cent of uniquely aligned reads and transcript coverage using custom scripts and Picard Tools.
Total counts of read fragments aligned to candidate gene regions were derived using the HTSeq program with mouse mm10 refSeq (refFlat table) as a reference.
Differential expression analysis was conducted with the Bioconductor package edgeR.
mm10

extract_protocol:
Samples were dissociated in papain, followed by FACS sorting. For RNA-seq, RNA from 5,000 – 10,000 FACS-sorted RGCs were isolated with RNeasy Micro Kit (Qiagen), and RNA-seq libraries were prepared with SMART-Seq v4 Ultra Low Input RNA Kit (Clontech), following manufacturers’ protocols.
The cDNA was fragmented to 300 base pairs (bp) using the Covaris M220 (Covaris), and then the manufacturer’s instructions were followed for end repair, adaptor ligation, and library amplification. The libraries were quantified by the Qubit dsDNA HS Assay Kit (Molecular Probes); Library size distribution and molar concentration of cDNA molecules in each library were determined by the Agilent High Sensitivity DNA Assay on an Agilent 2200 TapeStation system.

value: Crush (Day 2)


title: Hi-C_Normal_Tissue4

value: Contralateral breast tissue, patient N4


title: ChIP-seq_CTCF_ZR7530_rep2

value: Luminal B


title: DN010-HK2-cov-10-3-1-LDC11430

value: WT


title: Hi-C_HCC70_rep2

value: Triple negative breast cancer A


title: ChIP-seq_CTCF_ZR7530_rep1


title: Hi-C_BT549_rep2

value: Triple negative breast cancer B


title: ChIP-seq_CTCF_HCC70_rep1


title: MEF (scRNA-seq)

value: control mouse embryonic fibroblasts


title: transfo_5d (scRNA-seq)

value: mouse embryonic fibroblasts

value: mouse embryonic fibroblasts after 5 days of Transfo

value: 5 days


title: unaffected [11885X6]

city: Salt Lake City

first: Robert

middle: B

last: Weiss

state: UT

department: Human Genetics

institute: University of Utah

data_processing:
Single-end and Paired-end FASTQ reads were preprocessed using Trimmomatic for adaptor removal and with the quality filtering/clipping MAXINFO parameter set to 50:0.2 (Bolger, Lohse, & Usadel, 2014; DOI: 10.1093/bioinformatics/btu170) .
Trimmed reads were mapped by the STAR RNA-seq aligner (version 2.7.2b; Dobin et al., 2013; DOI: 10.1093/bioinformatics/bts635) to the GRCh37/hg19 reference genome with splice junction annotations built using the basic 2-pass mapping strategy with known junctions from the GENCODE comprehensive gene annotation GTF file (Release 31lift37, https://www.gencodegenes.org) and novel junctions detected in the first pass mapping.  Sorted bam alignments files were filtered for secondary alignments and retained only uniquely mapped reads.
The featureCounts program (version 1.6.5) was used to summarize the gene level expression values as integer number (Liao et al., 2014; DOI: 10.1093/bioinformatics/btt656).
Coverage analysis used the BEDTools genomecov function with the UCSC bedGraphToBigWig utility.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: tab-delimited text file includes raw counts for each sample extracted by featureCounts
Supplementary_files_format_and_content: bigWig coverage files from bam alignment files for each sample

source_name: Skeletal muscle

extract_protocol:
Frozen muscle biopsies (~ 4 milligrams) were cut on a cryostat (20 microns) and homogenized with a 26-gauge needle in 400 microliters of 20 mM Tris*Cl pH 7.4, 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, and 1% Triton X-100.  RNA was extracted using TRIzol® and precipitated with isopropanol according to the manufacturer’s instruction (Life Technologies).
Total RNA (~1 microgram) was depleted of human cytoplasmic and mitochondrial rRNA using tiling oligodeoxynucleotides and the RNase H digestion method (Adiconis et al., 2013; DOI: 10.1038/nmeth.2483).  Illumina TruSeq Stranded Total RNA library kits were used to prepare indexed libraries.

tag: presenting symptoms (age at onset)

tag: clinical diagnosis

value: unaffected, 9 yrs

tag: dystrophin mutation (hgvs_genomic_grch37 of cdna)

value: no mutation

value: Skeletal muscle


title: DN005-HUETH-cov-10-3-2-LDC11428

value: vessel

value: HUEhT

value: SARS-CoV-2 solution


title: ChIP-seq_CTCF_T47D_rep2

value: Luminal A

value: anti-CTCF (07-729, Millipore)


title: Type1A_Intron7 [15357X4]

value: Abnormal gait, frequent falls, difficulty climbing stairs, thigh pain (2y)

value: DMD


title: Type1A_Intron38 [16244X3]

description: 16244X3_190808_D00550_0569_ACDY98ANXX_S32_L004

value: Gross motor delay (10m)


title: Type1C_Intron43 [14857X12]

description: 14857X12_180124_D00294_0371_ACC69YANXX_1

value: mild proximal weakness, calf hypertrophy, CK 10,000s

value: BMD


title: ChIP-seq_CTCF_T47D_rep1


title: MJ_PIP_48h_rep2

city: Athens

first: Chung-Jui

last: Tsai

state: GA

address: 120 Green Street

department: Department of Genetics

institute: The University of Georgia

description: gene expression data from combination elicitor and C4H inhibitor treatment

hyb_protocol: Affymetrix

scan_protocol: Affymetrix

data_processing: Data were analyzed using Microarray Suite v.5.0 (MAS 5.0) using Affymetrix default analysis settings.  Global scaling was used for normalization.

label: biotin

organism: Populus tremuloides

source_name: cell culture, methyl jasmonate & PIP in DMSO

label_protocol: Affymetrix

growth_protocol: Growth and maintenance medium for P. tremuloides cell cultures was WPM with 3% sucrose, and 2.2 mg/L 2,4-D.  Cell cultures were maintained in the dark and subcultured every 11 d by transfering 5 mL of culture to 30 mL of fresh medium.  Experiment was initiated 5 days post-subculture, during which time cultures were in the log phase of growth.

extract_protocol: CTAB protocol

treatment_protocol: PIP dissolved in DMSO was added to all flasks at experiment initiation, yielding an initial concentration of 117 mM of the C4H inhibitor, followed by a second addition yielding 58 mM 12 h after initiation, for a total exposure of 175 mM for the following 36 h.  MJ treatment consisted of addition of methyl jasmonate in DMSO to flasks 6 h after experiment initiation, yielding a final concentration of 0.29 mM of the elicitor.  Cells were harvested 48 h after initiation by rinsing in water, vacuum filtration, and flash freezing in liquid nitrogen for storage at -80 C prior to total RNA extraction.

value: clone L4

value: heterotrophic liquid cell culture

value: methyl jasmonate & PIP in DMSO


title: ChIP-seq_CTCF_HMEC_rep1

source_name: human mammary epithelial cell

value: Primary Mammary Epithelial Cell


title: Type1B_Intron22 [14857X11]

description: 14857X11_180124_D00294_0371_ACC69YANXX_1

value: Hyper CK / BMD


title: Hi-C_HCC1954_rep2

value: Her2 positive


title: ChIP-seq_CTCF_HMEC_rep2


title: Type2_Intron1 [13707X5]

value: lower limb weakness, abnormal gait, elevated CK (5y)

value: Skeletal muscle


title: Hi-C_ZR7530_rep2

value: Luminal B


title: WT-3

city: Beijing

first: Zhi

last: Hu

address: No.20, Nanxin Village, Xiangshan, Haidian District, Beijing

institute: Institute of Botany, Chinese Academy of Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
To ensure that the Reads are of high enough quality, the low quality reads with connectors are removed from the raw reads to obtain the clean reads. The clean reads were then aligned to the Oryza sativa Nipponbare reference genome using HISAT2
The number of Mapped Reads and the length of transcripts in the sample were normalized. Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated as a measure of transcript or gene expression level.
Genome_build: IRGSP-1.0 and RGAP 7
Supplementary_files_format_and_content: Matrix table with raw gene counts and FPKM value for every gene and every sample

organism: Oryza sativa

source_name: Leaf

growth_protocol: WT and osatg5-1 were growth on a faddy field under natural long-day conditions.  The mature leaves were frozen in liquid nitrogen before mRNA extraction for sequencing at the tillering stage.

extract_protocol:
RNA was extracted by PureLink RNA Mini Kit (Cat no. 12183018A. Invitrogen). RNA-seq libraries were constructed using the illumina TruSeq Stranded mRNA LT kit (ref no15032612) following manufacterers' instructions.
Using mRNA as template, the first cDNA strand was synthesized with six-base random hexamers, and then the second cDNA strand was synthesized. cDNA was purified using AMPure XP beads. Finally, the cDNA library was enriched by PCR

tag: development stage

value: at the tillering stage

value: mature leaf

value: WT


title: osatg5-1-1


title: Hi-C_HMEC_rep2


title: Type1A_Intron26 [11183X8]

value: not reported


title: osatg5-1-2


title: Type1A_Intron44 [11689X23]

description: 11689X23_150720_D00550_0275_AC7GAGANXX_3

value: incidental finding of elevated AST


title: PIP_48h_rep2

description: gene expression data from C4H inhibitor treatment

source_name: cell culture, PIP in DMSO

value: PIP in DMSO


title: osatg5-1-3


title: PIP_48h_rep1


title: Hi-C_T47D_rep2

value: Luminal A


title: WT-2


title: Type1A_Intron47 [11689X20]

description: 11689X20_150720_D00550_0275_AC7GAGANXX_3

value: pain in legs (3.5y)

value: BMD


title: AOPP_48h_rep2

description: gene expression data from PAL inhibitor treatment

source_name: cell culture, AOPP in DMSO

treatment_protocol: MJ treatment consisted of addition of 4.6 mM methyl jasmonate dissolved in DMSO to flasks 6 h after experiment initiation.  AOPP treatment consisted of addition of 200 mM of alpha-aminooxy-beta-phenylpropionic acid dissolved in DMSO to flasks at experiment initiation.  DMSO was also added to controls as a sham treatment.  Cells were harvested 48 h after initiation by rinsing in water, vacuum filtration, and flash freezing in liquid nitrogen for storage at -80 C prior to total RNA extraction.

value: clone L4

value: heterotrophic liquid cell culture

value: AOPP in DMSO


title: MJ_AOPP_48h_rep1

description: gene expression data from combination elicitor and PAL inhibitor treatment

source_name: cell culture, methyl jasmonate & AOPP in DMSO

value: methyl jasmonate & AOPP in DMSO


title: WT-1


title: MJ_48h_rep1

description: gene expression data from elicitor treatment

source_name: cell culture, methyl jasmonate in DMSO

value: methyl jasmonate in DMSO


title: Control_48h_rep2

description: gene expression data from experimental control

source_name: cell culture, DMSO control

value: DMSO


title: Control_48h_rep1


title: MJ_48h_rep2


title: Type3_Intron60 [10869X3]

value: Abnormal gait, frequent falls, difficulty climbing stairs, thigh pain (2y)

value: DMD

value: Skeletal muscle


title: DN002-HUETH-con-2-LDC11433

value: vessel

value: HUEhT

value: Mock


title: MJ_PIP_48h_rep1

value: methyl jasmonate & PIP in DMSO


title: Type1C_Intron61 [11015X12]

description: 11015X12_140919_D00294_0133_AC4P3VANXX_1

value: muscle pain after play (4y)

value: Hyper CK / BMD


title: AOPP_48h_rep1


title: GSC23pn_PDPNPos_CD133Neg

status: Public on May 05 2022

first: Aram

middle: S

last: Modrek

address: 460 E 26th Street

department: Radiation Oncology

institute: New York University School of Medicine

description: Sorted GSCs for CD133 and PDPN

hyb_protocol: per Affymetrix protocols.

scan_protocol: per Affymetrix protocols.

source_name: PDPN/CD133 sort

label_protocol: per Affymetrix protocols.

growth_protocol: Gloma Stem Cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM)-12 (1:1) media with 1x B27 (Life Technologies), 20 ng/mL bFGF (Sigma), 20 ng/mL EGF (Sigma), and 1% penicillin streptomycin solution (Cellgro)

extract_protocol: Total RNA was isolated from FACs sorted PDPN+ and PDPN- subpopulations using the MasterPure Complete DNA/RNA Purification kit (Epicentre)

treatment_protocol: All samples were grown as described (no treatments).

value: Glioma Stem Cells

tag: pdpn status

value: Positive

tag: cd133 status

value: Negative


title: GSC20pp_PDPNPos_CD133Pos

description: Sorted GSCs for CD133 and PDPN


title: GSC23nn_PDPNNeg_CD133Neg

description: Sorted GSCs for CD133 and PDPN


title: GSC13np_PDPNNeg_CD133Pos

description: Sorted GSCs for CD133 and PDPN


title: GSC23np_PDPNNeg_CD133Pos

description: Sorted GSCs for CD133 and PDPN


title: GSC11pp_PDPNPos_CD133Pos

description: Sorted GSCs for CD133 and PDPN


title: GSC11pn_PDPNPos_CD133Neg

description: Sorted GSCs for CD133 and PDPN


title: GSC20pn_PDPNPos_CD133Neg

description: Sorted GSCs for CD133 and PDPN


title: TPAC_P009_01_K459_log2 Signal

city: Munich

first: Rouzanna

last: Istvánffy

address: Ismaningerstr. 22

department: Department of Surgery

country: Germany

institute: Klinikum rechts der Isar

description: P009_01_K459_log2 Signal

hyb_protocol: 3.8 μg of fragmented and labeled sense-strand cDNA were hybridized to Affymetrix GeneChip Mouse Gene 1.0 ST microarrays for 16 h at 45°C and 60 rpm in an Affymetrix GeneChip hybridization oven 640.

scan_protocol: GeneChips were washed and stained in an Affymetrix GeneChip Fluidics Station 450, and the fluorescent signals were measured with an Affymetrix GeneChip Scanner 3000 7G System. Fluidics and scan functions were controlled by the Applied Biosystems GeneChip Command Console v4.1.3 software.

data_processing: log2 gene level RMA signal intensity, generated by the Affymetrix GeneChip Expression Console v1.4 software.

source_name: Pancreas

label_protocol: The Ambion WT Expression Kit Protocol was used for the preparation of biotinylated sense-strand cDNA from 300ng of total RNA, followed by fragmentation and labeling according to the Affymetrix GeneChip WT Terminal Labeling and Hybridization User Manual.

growth_protocol: Pancreas derived tumors were choped in small pieces and incubated for 10 minutes at 37°C in digestion buffer (HBSS, HEPES and Liberase Blenzyme). After digestion cell suspension was filtered through 100µm filters and centrifuged. Cells were  cultured in DMEM supplemented with pen/strep and 10% FSC.

extract_protocol: Total RNA from cancer cells was isolated with the RNEasy Plus Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instruction.

treatment_protocol: no treatment was applied

tag: genotype

value: pancreatic tumor cells


title: GSC11nn_PDPNNeg_CD133Neg

description: Sorted GSCs for CD133 and PDPN


title: TPC_P009_03_TPC18645_log2 Signal

description: P009_03_TPC18645_log2 Signal

value: Ela-TGFa;Ptg1a+/CRE; Trp53fl/fl


title: KPC 5_A955_02_410704_log2 Signal

description: A955_02_410704_log2 Signal

value: LSL-KrasG12D;Ptg1a+/CRE; Trp53fl/fl


title: MJ_AOPP_48h_rep2

value: clone L4

value: heterotrophic liquid cell culture

tag: treatment

value: methyl jasmonate & AOPP in DMSO


title: GSC20np_PDPNNeg_CD133Pos

description: Sorted GSCs for CD133 and PDPN


title: GSC11np_PDPNNeg_CD133Pos

description: Sorted GSCs for CD133 and PDPN


title: GSC23pp_PDPNPos_CD133Pos

description: Sorted GSCs for CD133 and PDPN


title: TPAC_P009_02_TCPA18654_log2 Signal

description: P009_02_TCPA18654_log2 Signal


title: TPC_P009_04_TPC20223_log2 Signal

description: P009_04_TPC20223_log2 Signal


title: KPC 1_P004_01_K1654_log2 Signal

description: P004_01_K1654_log2 Signal


title: KPC 3_A796_04_3039_P7_10Pr_FLS_

description: A796_04_3039_P7_10Pr_FLS_RNA_12_7_12_log2 Signal


title: KC 7_A796_02_9907_P9_10Pr_FLS_

description: A796_02_9907_P9_10Pr_FLS_subb_11_7_12_log2 Signal


title: KC 3_P009_07_20057_log2 Signal

description: P009_07_20057_log2 Signal


title: KPC 4_A955_01_1048_log2 Signal

description: A955_01_1048_log2 Signal


title: KPC 2_A796_03_3042_P4_10Pr_FLS_

description: A796_03_3042_P4_10Pr_FLS_subb_RNA_13_7_12_log2 Signal


title: KC 6_A796_01_78_P5_10Pr_FLS_

description: A796_01_78_P5_10Pr_FLS_RNA12+12_log2 Signal


title: KC 5_P009_09_K78_log2 Signal

description: P009_09_K78_log2 Signal


title: ChIP-seq_H3K27ac_HCC70_rep2

source_name: Triple negative breast cancer A cell

value: Triple negative breast cancer A

value: anti-H3K27ac (ab4729,Abcam)


title: KC 4_P009_08_20076_log2 Signal

description: P009_08_20076_log2 Signal


title: GSC13pp_PDPNPos_CD133Pos

description: Sorted GSCs for CD133 and PDPN


title: KC 1_P009_05_K225_log2 Signal

description: P009_05_K225_log2 Signal


title: preCFU-E wt rep 1

city: Copenhagen

first: Bo

last: Porse

address: Ole Maaløes Vej 5, 4

department: Finsen Laboratory and BRIC

country: Denmark

institute: University of Copenhagen

data_processing:
Salmon 0.12.0 was used to quantify expression of transcripts from RNA-seq experiments using mm10/GRCm38_94 Ensembl transcriptome (salmon quant -l IU --seqBias --gcBias --numBootstraps 30)
Genome_build: GRCm38.p6 (Ensembl release 94)
Supplementary_files_format_and_content: Tab-delimited text file including estimated number of reads mapping to each transcript and relative abundance of transcript in TPM.

source_name: Bone marrow

extract_protocol:
Indicated populations were FACS sorted and total RNA was isolated using the RNeasy micro kit (Qiagen) according to manufacturers protocol.
RNA was subjected to double-stranded cDNA synthesis by help of the Ovation RNA-Seq System V2 (NuGEN). Sequencing libraries were prepared using the Ovation Ultralow System V2 (NuGEN).

value: preCFU-Es (Lin- Sca-1- c-kit+ CD41- FcgRII/III - CD150+ CD105+)

value: Ptbp1 fl/fl


title: preMegE KO rep 3

value: preMegEs (Lin- Sca-1- c-kit+ CD41- FcgRII/III - CD150+ CD105-)

value: Ptbp1 KO


title: mESC_ATAC_WT_rep2

city: Chicago

first: Chuan

last: He

state: IL

address: 929 E 57th Street

department: Chemistry

institute: University of Chicago

data_processing:
Sequencing reads were trimmed of low quality nucleotides by trim_galore.
High-quality reads were then mapped to mm9 reference genome by bowtie2 with uniquely mapped reads retained for the following analyses.
Reads mapped to chrM were removed before normalization.
Normalization were performed by Deeptools with duplication removed.
Peak calling was performed with macs2.
Assembly: mm9
Supplementary files format and content: peaks

source_name: mESC

growth_protocol: mESCs were maintained in DMEM (Invitrogen) supplemented with 15% FBS, 1% nucleosides (100×),1 mM L-glutamine,1% nonessential amino acid, 0.1 mM 2-mercaptoethanol, 1,000 U/ml LIF, 3 μM CHIR99021 and 1 μM PD0325901 at 37 °C in 5% CO2.

extract_protocol:
Cells were harvested and proceeded to the transposition reaction.
ATAC-seq was performed by using Illumina Nextera DNA Flex Library Prep Kit following the manufacturer's protocols.

value: mESC

value: wild type


title: preMegE wt rep 1


title: preCFU-E wt rep 3


title: preMegE wt rep 2


title: preMegE KO rep 1


title: preCFU-E KO rep 1


title: preCFU-E KO rep 2


title: preMegE wt rep 3


title: KC 2_P009_06_K223_log2 Signal

description: P009_06_K223_log2 Signal


title: HSC KO rep 2


title: preMegE KO rep 2


title: HSC KO rep 3


title: mESC_ATAC_FtoKO_rep1

value: Fto Knockout


title: preCFU-E wt rep 2


title: 76: BMDMs CPEB4 WT RIP LPS Infected Lane 8

city: Barcelona

first: Oscar

last: Reina Garcia

state: Barcelona

address: C/Baldiri Reixac 10

department: Biostatistics and Bioinformatics

country: Spain

institute: IRB Barcelona

description: 76 rip lps Lane 8

data_processing:
Libraries were sequenced by Illumina 100bp single-end and FastQ files for Input and IP samples were aligned against the mouse reference genome mm10 with Bowtie2 version 2.2.2 in local mode accepting 1 mismatch in the read seed and using default options.
Alignments were sorted and indexed with sambamba v0.5.1. Putative over-amplification artifacts (duplicated reads) were assessed and removed with the same software.
A preliminary peak calling process was performed for duplicate filtered sequences with the MACS 1.4.2 software using default options to assess overall enrichment in the IP sequenced samples against their respective Input controls. The identified peaks were annotated against the mouse reference genome mm10 annotation using the ChIPpeakAnno package version 2.16.
Additionally, log2RPKM quantification for mm10 UCSC 3’UTR genomic regions (Biomart ENSEMBL archive february 2014) in all samples was obtained using custom R scripts, and potentially enriched 3’UTRs between IP and Input in CPEB4 wild type and Cpeb4KO were identified using the enrichedRegions function from the htSeqTools package using default options and reporting Benjamini-Yekutielli adjusted pvalues.
Then, for each analyzed 3’UTR genomic region, the maximum peak score for MACS overlapping peaks was retrieved (MaxScore). 3’UTR regions without any overlapping MACS reported peak were given a MaxScore value of 0. Finally, CPEB4 associated mRNAs were defined as those with either (I) pvBY<0,02 and log2RPKMFC>0,5; (II) pv<0,02 and log2RPKMFC>1,2 or (III) MaxScore>500 and log2RPKMFC>0,5. High-confident CPEB4 targets were defined as those with pvBY<0,05 and MaxScore>500.
Genome_build: mm10
Supplementary_files_format_and_content: htSeqTools enrichedRegions results at 3'UTR level and overlapping MACS peak calling information.
Supplementary_files_format_and_content: ChIPpeakAnno MACS annotated peak calling results.

source_name: Bone Marrow Derived Macrophages (BMDMs)

growth_protocol: BMDMs were isolated from the femurs of adult mice as previously described (Celada et al. 1996). Bone marrow cells were differentiated for 7 days on bacteria-grade plastic dishes (Nirco, Ref. 140298) in DMEM supplemented with 20% (vol/vol) FBS, penicillin (100 units/ml), streptomycin (100 mg/ml), L-glutamine (5mg/ml) and 20% L-cell conditioned medium as a source of M-CSF; changing its media on day 5 when BMDMs were plated for the experiment. On day 7, media was changed to DMEM containing 10% FBS, penicillin (100 units/ml), streptomycin (100 mg/ml), L-glutamine (5mg/ml).

extract_protocol:
RNA was extracted by phenol-chlorofom following manufacturers instructions.
RNA depletion treatment were applied to the Input samples using (NEBNext rRNA depletion kit catalog number# E6310) following the manufacturer's intructions. Library generation were performed with NEBNext Ultra II RNA Library Prep Kit (New England Biolabs, catalog number# E7770) following manufacturer´s instructions and 7 cycles of amplification.

treatment_protocol: BMDMs were left untreated or stimulated with LPS for 9 h (10 ng/ml, E. coli 0111:B4, Santa Cruz SC-3535)

value: Bone Marrow Derived Macrophages (BMDMs)

tag: rip antibody

tag: flowcell lane

value: Lane 8

value: CPEB4 WT


title: mESC_ATAC_FtoKO_rep2

tag: cell type


title: 76: BMDMs CPEB4 WT RIP LPS Infected Lane 7

description: 76 rip lps Lane 7

tag: strain

value: Lane 7


title: HSC wt rep 3


title: HSC wt rep 2


title: preCFU-E KO rep 3


title: HSC KO rep 1


title: 73: BMDMs CPEB4 KO RIP Untreated Lane 7

description: 73 rip un Lane 7

value: CPEB4 KO


title: 76: BMDMs CPEB4 WT Input Untreated Lane 7

description: 76 input un Lane 7


title: 76: BMDMs CPEB4 WT Input LPS Infected Lane 7

description: 76 input lps Lane 7


title: 73: BMDMs CPEB4 KO Input LPS Infected Lane 7

description: 73 input lps Lane 7


title: 73: BMDMs CPEB4 KO RIP Untreated Lane 8

description: 73 rip un Lane 8


title: HSC wt rep 1


title: mESC_mRNA_m6A_WT_rep2_Input

data_processing:
library strategy: MeRIP-seq
Base-calling was performed using CASAVA.
sequencing data were sent to trimmomatic to remove low quality bases and adaptor sequence contaminants under default parameters except for “–length 50”
Remaining reads were then aligned to the mouse transcriptome annotation based on mm10 assembly using hisat2 aligner (v2.1.0), default parameters were used.
Peaks were called for each pair of samples by MACS2. Then peaks with at least 5 reads in Input files and more reads in IP files than responsed Input files were kept.
Genome_build: mm10
Supplementary_files_format_and_content: txt; m6A peaks

growth_protocol: Cells were maintained in DMEM (Invitrogen) supplemented with 15% FBS, 1% nucleosides (100×),1 mM L-glutamine,1% nonessential amino acid, 0.1 mM 2-mercaptoethanol, 1,000 U/ml LIF, 3 μM CHIR99021 and 1 μM PD0325901 37 °C in 5% CO2.

extract_protocol:
Total RNA was isolated from chromatin-associated fraction of mESCs. Non-ribosome RNA was further enriched from total RNA by using RiboMinus transcriptome isolation kit (Invitrogen). 1 μL 1:1000 diluted m6A spike-in from EpiMark N6-Methyladenosine Enrichment Kit (NEB #E1610S) was added to 1 μg non-ribosome RNA, followed by fragmentation according to previously published protocols. m6A-IP was performed using EpiMark N6-Methyladenosine Enrichment Kit following the manufacturer’s protocols.
polyA RNA was purified with the Dynabeads mRNA Purification Kit from mESCs, followed by fragmentation according to previously published protocols. m6A-IP was performed using EpiMark N6-Methyladenosine Enrichment Kit following the manufacturer’s protocols.
Library preparation was performed by using SMARTer Stranded Total RNA-Seq Kit v2 (Takara) according to the manufacturer’s protocols.
Truseq stranded mRNA library prep according to the manufacturer’s protocols.

tag: antibody


title: 73: BMDMs CPEB4 KO Input Untreated Lane 8

description: 73 input un Lane 8


title: mESC_ATAC_WT_rep1


title: 76: BMDMs CPEB4 WT RIP Untreated Lane 8

description: 76 rip un Lane 8


title: 76: BMDMs CPEB4 WT Input LPS Infected Lane 8

description: 76 input lps Lane 8


title: 76: BMDMs CPEB4 WT RIP Untreated Lane 7

description: 76 rip un Lane 7


title: 73: BMDMs CPEB4 KO Input LPS Infected Lane 8

description: 73 input lps Lane 8


title: 73: BMDMs CPEB4 KO Input Untreated Lane 7

description: 73 input un Lane 7


title: 73: BMDMs CPEB4 KO RIP LPS Infected Lane 7

description: 73 rip lps Lane 7


title: fadu-bs-wt1 [bs03-wt1]

city: Heidelberg

first: Sylvain

last: Delaunay

address: Im Neuenheimer Feld 280

department: Tumor BIology

institute: German Cancer Research Center (DKFZ)

description:
BSseq FaDu rep1
Delaunay_MT_TM.meth_Kerats_FaDu.txt

data_processing:
Raw sequencing fastq files were trimmed with ‘TrimGalore !’
Reads were aligned to the GRCh38 (hg38) reference genome using Bismark
mtRNA genomic coordinates for the GRCh38 reference genome were obtained from the ENSEMBL database
Original targeted sequencing reads and their multiple sequence alignments on mtRNAs were extracted from sorted Bismark alignment (bam) files using the R packages RSamtools and GenomicAlignments
Assembly: hg38
Supplementary files format and content: Table Delaunay_MT_TM.meth_Kerats_FaDu.txt is a tab delimited text file which contains the calculated total number of reads to the mt-tRNA methionine and the number of Cytosine in position 34 of the targeted tRNA.
Supplementary files format and content: Table Delaunay_UntargetedfCABseq_20nt_meth.table_MitoGenome.txt is tab delimited text and contains the calculated methylation levels of Cs and coverage on the mitochondrial genome (fragments >20nt)

source_name: FaDu cell line

growth_protocol: NHEK cells were maintained in KSFM medium with antibiotics, FaDu cells were maintained in EMEM madium supplement with fetal bovin serum albumin (FBS) 10% with antibiotics, in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was extracted with Trizol kit, according to manufacturers' protocol. tRNA were isolated using Mirvana kit.
for the untargeted samples, the library was created with the Il TruSeq Small RNA kit. For the targeted apporach, the NEBNext Ultra II DNA library prep kit was used.

value: FaDu cell line

value: Pharynx squamous cell carcinoma

value: WT

tag: sample type

value: BSseq


title: fadu-bs-wt2 [bs03-wt2]

description:
BSseq FaDu rep2
Delaunay_MT_TM.meth_Kerats_FaDu.txt


title: mESC_mRNA_m6A_WT_rep2_IP

value: anti-m6A from EpiMark® N6-Methyladenosine Enrichment Kit


title: fadu-fcabs-wt1 [fcabs03-wt1]

description:
fCABseq FaDu rep1
Delaunay_MT_TM.meth_Kerats_FaDu.txt

value: fCABseq


title: mESC_mRNA_m6A_WT_rep1_Input


title: fadu-fcabs-wt2 [fcabs03-wt2]

description:
fCABseq FaDu rep2
Delaunay_MT_TM.meth_Kerats_FaDu.txt


title: mESC_mRNA_m6A_FTOko_rep2_Input


title: fadu-fcabs-wt3 [fcabs03-wt3]

description:
fCABseq FaDu rep3
Delaunay_MT_TM.meth_Kerats_FaDu.txt


title: 73: BMDMs CPEB4 KO RIP LPS Infected Lane 8

description: 73 rip lps Lane 8


title: nhek-fcabs-wt1 [fcabs03-wt1]

description:
fCABseq NHEK rep1
Delaunay_MT_TM.meth_Kerats_FaDu.txt

source_name: NHEK

value: NHEK

value: Keratinocyte


title: mESC_mRNA_m6A_WT_rep1_IP


title: nhek-bs-wt3 [bs03-wt3]

description:
BSseq NHEK rep3
Delaunay_MT_TM.meth_Kerats_FaDu.txt


title: mESC_mRNA_m6A_FTOko_rep1_IP


title: mESC_mRNA_m6A_FTOko_rep1_Input


title: mESC_mRNA_m6A_FTOko_rep2_IP


title: 76: BMDMs CPEB4 WT Input Untreated Lane 8

description: 76 input un Lane 8


title: nhek-fcabs-wt3 [fcabs03-wt3]

description:
fCABseq NHEK rep3
Delaunay_MT_TM.meth_Kerats_FaDu.txt


title: nhek-bs-wt2 [bs03-wt2]

description:
BSseq NHEK rep2
Delaunay_MT_TM.meth_Kerats_FaDu.txt


title: nhek-bs-wt1 [bs03-wt1]

description:
BSseq NHEK rep1
Delaunay_MT_TM.meth_Kerats_FaDu.txt


title: fadu-bs-wt3 [bs03-wt3]

description:
BSseq FaDu rep3
Delaunay_MT_TM.meth_Kerats_FaDu.txt


title: nhek-fcabs-wt2 [fcabs03-wt2]

description:
fCABseq NHEK rep2
Delaunay_MT_TM.meth_Kerats_FaDu.txt


title: B3 [6_S47]

city: Minneapolis

first: Mark

middle: C

last: Herzberg

state: MN

address: 515 Delaware St., SE

institute: University of Minnesota

description: Overnight Biofilms

data_processing:
Raw sequence that passed CASAV 1.8P/F filter were assessed by fastqc (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Read mapping was performed via Tophat (v2.0.13) using the mouse (mm10 as a reference.
Counts were quantified via Feature counts (Subread Package).
Differentially expressed genes were identified using the edgeR (negative binomial) feature in CLCGWB (Qiagen, Redwood city, CA) using raw read counts.
Assembly: Streptococcus gordonii (CH1) NC_009785.1

organism: Streptococcus gordonii

source_name: Bacteria

growth_protocol: 37°C overnight at 5% CO2

extract_protocol:
Zymo Direct-zol RNA extraction kit was used
RNA libraries were prepared for sequencing using Illumina Truseq protocols

treatment_protocol: Biofilms were grown on surfaces coated with either MUC5B or LDP

value: Wild Type

tag: tissue

value: Biofilm

value: LDP static


title: D2 [11_S52]

description: Overnight Biofilms

value: LDP with shear


title: C2 [8_S49]

description: Overnight Biofilms

value: MUC5B with shear


title: D1 [10_S51]

description: Overnight Biofilms


title: D3 [12_S53]

description: Overnight Biofilms


title: C1 [7_S48]

description: Overnight Biofilms


title: B2 [5_S46]

description: Overnight Biofilms


title: C3 [9_S50]

description: Overnight Biofilms


title: A2 [2_S43]

description: Overnight Biofilms

value: MUC5B static


title: B1 [4_S45]

description: Overnight Biofilms


title: normal adjacent tissues_138

city: Changsha

first: Lin

last: Qi

address: 139 Renmin Road

institute: The Second Xiangya Hospital, Central South University

data_processing:
Base calling performed by Guppy software in MinKNOW2.2 package
Full-length sequences  were obtained from the original sequences which have been filtered the low-quality (length less than 500bp, Qscore less than 6) reads and ribosomal RNA sequences.
Full-length sequences were aligned with the reference genome by minmap2 software. After clustering the alignment information, the consistent sequences were obtained by pinfish software.
Gffcompare is used to align transcripts obtained by full-length sequencing to known transcripts of the genome, so novel genes and transcripts can be obtained to supplement genome annotation.
Astalavista is used to obtain the alternative splicing types of each sample. TAPIS pipeline was used to further analyze full-length non-chimeric sequence (FLNC) to identify APA. The transcripts above 500bp were screened from the novel transcripts, and MISA software was used for SSR analysis.
Astalavista is used to obtain the alternative splicing types of each sample. TAPIS pipeline was used to further analyze full-length non-chimeric sequence (FLNC) to identify APA. The transcripts above 500bp were screened from the novel transcripts, and MISA software was used for SSR analysis.
Assembly: Full-length sequences were aligned with the reference genome by minmap2 software.
Supplementary files format and content: tab-delimited text files include CPM values for each Sample

growth_protocol: Patients with soft-tissue sarcoma were included in this study.

extract_protocol:
RNA was extracted and the purity, concentration and integrity of RNA samples were detected by advanced equipment to ensure that qualified samples can be used for transcriptome sequencing.
1) primer annealing, reverse transcription to get cDNA, add switch oligo; 2) synthesis of complementary chains; 3) DNA damage repair and end repair, magnetic beads purification.

treatment_protocol: Appropriate surgical operations were performed based on the characteristics of STS. Tumor and normal adjacent tissues were excised and  properly stored.

tag: age

tag: gender

value: Male

tag: site

value: Lower-limb

value: Surgery

value: normal


title: Vv_Yeast_12h_rep2

city: Lincoln

first: Christopher

last: Winefield

state: Canterbury

address: Ellesmere Junction Road/Springs Road

country: New Zealand

institute: Lincoln University

description:
Illumina Hiseq 2500
Vv_Illumina_htseqcount_Gene_counts.txt
Vv_Illumina_htseqcount_Gene_FPKM.txt
Vv_Illumina_htseqcount_TE_counts.txt
Vv_Illumina_bedtools_TE_counts.txt
Vv_Illumina_bedtools_TE_average_read_depth.txt
Vv_Illumina_TEFingerprint_TE_dangler_counts.txt

data_processing:
For short-read sequencing:
Illumina Casava v1.8.2 used for basecalling.
Sequenced reads were trimmed for adaptor sequence following removal of low-quality sequence and tRNA and rRNA reads, then mapped to V. vinifera 12X PN40024 reference genome using HISAT2 v2.1.0 with parameters --rna-strandness RF --dta -k 100.
Raw read counts for genes were calculated using htseq-count v0.10.0 with parameters -f bam -t exon -i transcript_id -s reverse -m intersection-nonempty.
Gene FPKM was calculated by dividing gene's raw read counts per kb gene transcript length with per million mapped reads.
For TEFingerprint analysis, sequenced reads were trimmed for adaptor sequence following removal of low-quality sequence and tRNA and rRNA reads, then mapped to TE sequences extraced from all annotated TE loci using bwa mem (with default setting).
Read counts for TE loci were calculated by htseq-count v0.10.0 (-f bam -t exon -i transcript_id -s reverse -m intersection-nonempty), bedtools v2.27.0 (bedtools coverage), and TEFingerprint v0.1.4 (tef preprocess --exclude-tails and then tef compare -m 11 -e 600 -q 30 -t 8).
Average read depth of each TE locus was calculated by dividing the sum of read bases overlapping with a TE locus (obtained from bedtools intersect v2.27.0) with the read-covered bases of the TE locus (obtained from bedtools coverage v2.27.0).
Read counts for TE families were calculated by TEtranscripts with parameters --mode multi --stranded reverse.
TE family FPKM was calculated by dividing TE familiy's read counts per kb TE length with per million mapped reads.
For long-read sequencing:
Oxford Nanopore Technology Guppy v3.1.5 used for basecalling.
The resulting fastq files were processed by Pychopper2 (v2.0.1) to capture full-length reads and remove adapter sequences.
The full-length reads were mapped to the 12X PN40024 V. vinifera reference genome using minimap2 v2.17 with the option -ax splice for long-read splice alignment. For TE loci analysis, the minimap2 parameters -N 100  -ax splice  were used instead. For TE family analysis, reads were mapped to V. vinifera canonical TE sequences (Repbase) with the option -ax splice.
Gene TPM was calculated using FLAIR pipeline (v1.4).
Read counts for TE loci and TE families were calculated by bedtools v2.27.0 (bedtools coverage).
TE family TPM was calculated by dividing read counts of TE families with per million mapped reads.
Genome_build: 12X PN40024
Supplementary_files_format_and_content: Tab-delimited table with raw counts for every gene and every Illumina RNA-seq library.
Supplementary_files_format_and_content: Tab-delimited table with FPKM values for every genes and every Illumina RNA-seq library.
Supplementary_files_format_and_content: Tab-delimited table with raw count values (htseq-count) for every TE loci and every Illumina RNA-seq library.
Supplementary_files_format_and_content: Tab-delimited table with raw count values (bedtools) for every TE loci and every Illumina RNA-seq library.
Supplementary_files_format_and_content: Tab-delimited table with TE's average read depth of mapped region for every TE loci and every Illumina RNA-seq library.
Supplementary_files_format_and_content: Tab-delimited table for raw count values (TEFingerprint) for every TE loci and every Illumina RNA-seq library.
Supplementary_files_format_and_content: Tab-delimited text files include gene TPM values for each ONT cDNA-seq library.
Supplementary_files_format_and_content: Tab-delimited text files include TE loci read count values (bedtools) for each ONT cDNA-seq library.

organism: Vitis vinifera

source_name: Embryogenic callus

growth_protocol: Embryogenic callus (EC) cultures were established from Vitis vinifera cv Pinor noir clone UCD5 and maintained in C1P medium which contains half strength MS medium, half strength MS micro elements, 0.1 % (w/v) casein hydrolysate, 3 % (w/v) sucrose, 0.5 % (w/v) gelrite, 250 μg myo-inositol, 5 μg nicotinic acid, 5 μg pyridoxine-HCl, 5 μg thiamine-HCl, 5 μg Ca-pantothenoate, 50 μg D-biotin, 1 μM BAP and 5 μM 2,4-D.

extract_protocol:
For short-read RNA-seq, total RNA of harvested embryogenic callus were isolated according to the manufacturer’s instructions of Spectrum Plant Total RNA Kit (Sigma). Each purified RNA sample was treated with DNase I following the TURBO DNA-free kit protocol (Ambion) to remove contaminating genomic DNA. For long-read sequencing, Total RNA was extracted and separated using NORGEN Plant microRNA purification kit (Norgen Biotek) according to the manufacturer’s instruction. Genomic DNA contamination was removed with the standard protocol of the TURBO DNA-free kit (Thermo Fisher).
For short-read RNA-seq, RNA libraries were prepared using standard Illumina protocols. For long-read cDNA-seq, the libraries were prepared following the protocol of Oxford Nanopore cDNA-PCR kit (SQK-PCS109).

treatment_protocol: For mock treatment, the embryogenic callus cultures were subjected to vigorous shaking in hormone-free C1P liquid medium to break the lumps of callus apart. For the yeast treatment, the embryogenic callus cultures were firstly subjected to mock treatment and then exposed to live H. uvarum cultures. For both mock and yeast treatments, samples were harvested at 1, 3, 6, and 12 hours. A common untreated 0 hour time point  for mock and the biotic treatment was taken prior to any treatment.

tag: clone

value: Pinot noir UCD5

value: embryogenic callus

tag: time-point

value: wild type

value: yeast


title: A1 [1_S42]

description: Overnight Biofilms


title: Vv_Yeast_12h_rep3


title: A3 [3_S44]

description: Overnight Biofilms


title: Vv_Yeast_12h_rep1


title: Vv_Yeast_06h_rep3


title: Vv_Yeast_06h_rep2


title: Vv_Yeast_06h_rep1


title: Vv_Yeast_03h_rep1


title: Vv_Yeast_03h_rep3


title: normal adjacent tissues_135

value: Female

value: Upper-limb


title: Vv_Yeast_03h_rep2


title: normal adjacent tissues_134


title: Vv_Yeast_01h_rep3


title: soft-tissue sarcoma_100

value: sarcoma


title: Vv_Yeast_01h_rep2


title: normal adjacent tissues_100


title: Vv_Mock_12h_rep3

value: mock


title: Vv_Yeast_01h_rep1


title: Vv_Mock_06h_rep2


title: Vv_Mock_12h_rep1


title: Vv_Mock_03h_rep3


title: soft-tissue sarcoma_138


title: Vv_Mock_12h_rep2


title: Vv_Mock_03h_rep1


title: Vv_Mock_06h_rep3


title: nonBPD cord blood of sample 4009

city: Research Triangle Park

first: Xuting

last: Wang

state: NC

address: 111 TW Alexander Dr

institute: NIEHS/NIH

description: nonBPD cord blood sample

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with Illumina GenomeStudio

source_name: nonBPD cord blood

label_protocol: Total RNA isolated from cord blood of individuals was amplified, labeled, and fragmented according to the manufacturer’s protocol (NuGEN Technologies, Inc., Redwood City, CA)

extract_protocol: Umbilical cord blood samples were collected at birth in PAXgene reagent (Qiagen Inc., Valencia, CA) and snap frozen at -80°C. Samples were processed with PAXgene Blood miRNA Kit (PreAnalytix/Qiagen). The isopropanol precipitants were added into the PAXgene RNA spin columns and processed for DNase treatment followed by RNA extraction procedures as indicated in the manufacturer’s brochure.

tag: disease status

value: nonBPD

value: Umbilical cord blood


title: nonBPD cord blood of sample 1031

description: nonBPD cord blood sample


title: Vv_Mock_01h_rep2


title: nonBPD cord blood of sample 2023

description: nonBPD cord blood sample


title: nonBPD cord blood of sample 3010-1

description: nonBPD cord blood sample


title: Vv_Mock_01h_rep3


title: nonBPD cord blood of sample 1010

description: nonBPD cord blood sample


title: nonBPD cord blood of sample 3010-2

description: nonBPD cord blood sample


title: nonBPD cord blood of sample 1001

description: nonBPD cord blood sample


title: nonBPD cord blood of sample 4015

description: nonBPD cord blood sample


title: nonBPD cord blood of sample 4002

description: nonBPD cord blood sample


title: soft-tissue sarcoma_135


title: Vv_Mock_06h_rep1


title: Vv_Mock_01h_rep1


title: Vv_00h_rep3

value: time zero

value: control (untreated)


title: nonBPD cord blood of sample 4010

description: nonBPD cord blood sample


title: nonBPD cord blood of sample 4011

description: nonBPD cord blood sample


title: Vv_Mock_03h_rep2


title: Vv_00h_rep2


title: nonBPD cord blood of sample 3008

description: nonBPD cord blood sample


title: Vv_00h_rep1


title: GSC20nn_PDPNNeg_CD133Neg

description: Sorted GSCs for CD133 and PDPN

value: Glioma Stem Cells

tag: pdpn status

value: Negative


title: nonBPD cord blood of sample 3002

description: nonBPD cord blood sample


title: nonBPD cord blood of sample 3011

description: nonBPD cord blood sample


title: nonBPD cord blood of sample 1028

description: nonBPD cord blood sample


title: nonBPD cord blood of sample 2005

description: nonBPD cord blood sample


title: nonBPD cord blood of sample 3001

description: nonBPD cord blood sample


title: BPD cord blood of sample 3013

description: BPD cord blood sample

source_name: BPD cord blood

value: BPD


title: BPD cord blood of sample 1013

description: BPD cord blood sample


title: BPD cord blood of sample 2017

description: BPD cord blood sample


title: BPD cord blood of sample 2002

description: BPD cord blood sample


title: BPD cord blood of sample 1012

description: BPD cord blood sample


title: Patient 1, post-infusion

city: Houston

first: David

last: Hong

state: Texas

address: Room FC8.3050, 1400 Holcombe Blvd.

department: Department of Investigational Cancer Therapeutics

institute: University of Texas M.D. Anderson Cancer Center

description: 100 ng of total RNA was hybridyzed with the NanoString nCounter panel of probes

hyb_protocol: 65°C for 16-24 hours. Details are in user manual for nCounter Gene Expression CodeSet RNA hybridization protocol (Nanostring)

scan_protocol: nCounter® FLEX Analysis System (following the manufacturer's protocol)

data_processing: Raw counts were exported using nSolver® Analysis Software (Nanostring) and analysed using custom R scripts (R v3.6.3). Background gene count levels were determined for each sample using mean plus two standard deviations of the included negative control counts. For data normalization, background-subtracted counts were then scaled using geometric means of 27 housekeeping genes (AGK, AMMECR1L, CNOT10, CNOT4, COG7, DDX50, DHX16, DNAJC14, EDC3, EIF2B4, ERCC3, FCF1, HDAC3, MRPS5, MTMR14, NOL7, NUBP1, PRPF38A, SAP130, SF3A3, TLK2, TMUB2, TRIM39, USP39, ZC3H14, ZNF143, ZNF346), with the expected value set to 444.

label: 6x fluorescent marker barcode

source_name: Synovial sarcoma cancer

label_protocol: Detailed in user manual for nCounter Gene Expression CodeSet RNA hybridization protocol (Nanostring)

extract_protocol: Tumor tissue was macro-dissected from 4 μm sections of FFPE tissues and total RNA was extracted using the High Pure RNA FFPE Micro Kit (Roche), following the manufacturer’s protocol.

tag: individual

value: Patient 1

tag: disease state

value: Synovial sarcoma cancer

tag: timepoint

value: On-treatment


title: Patient 4, post-infusion

source_name: Ovarian cancer

value: Patient 4

value: Ovarian cancer


title: Patient 2, pre-infusion

value: Patient 2

value: Baseline


title: Patient 4, pre-infusion


title: Patient 2, post-infusion

value: At completion


title: Patient 3, post-infusion

value: Patient 3


title: Patient 1, pre-infusion


title: 1255 microoxic 2

city: Granada

first: Socorro

last: Mesa

address: C/Profesor Albareda 1

department: Soil and Plant Microbiology

institute: CSIC

description: B. diazoefficiens C183D FixK2 encoding strain grown microoxically

hyb_protocol: Hybridisation, washing, staining, and scanning were done according to the Affymetrix manual using a gene chip fluidics station 450 (Affymetrix) and a gene chip scanner 3000 (Affymetrix). For hybridization of individual gene chips, 1.8 µg of labeled cDNA  were used.

scan_protocol: Standard Affymetrix procedures

data_processing: Signal intensities were detected and analyzed with MAS5 statistical algorithm (http://www.affymetrix.com).

organism: Bradyrhizobium diazoefficiens

source_name: B. diazoefficiens C183D FixK2 encoding strain grown under microoxic conditions

label_protocol: The fragmented cDNA was end-labeled with biotin-ddUTP using terminal dexoynucleotidyl transferase (Promega) in combination with the gene chip labeling reagent (Affymetrix). The reaction was incubated for 75 min at 37°C and stopped by the addition of 2 µl of 0.5 M EDTA.

growth_protocol: B. diazoefficiens cells were grown in PSY medium (Regensburger and Hennecke 1983; Mesa et al., 2018) to mid-exponential phase (OD600 of 0.45-0.55) under microoxic conditions (0.5% O2).

extract_protocol: RNA was extracted as described by Hauser et al. (2007) and Pessi et al. (2007)

treatment_protocol: No treatment was applied

tag: genotype

tag: growth condition

value: microoxic

tag: medium

value: PSY


title: 1255 microoxic 3


title: 110spc4 microoxic 2

description: B. diazoefficiens wild type grown microoxically

source_name: B. diazoefficiens wild type grown under microoxic conditions


title: 110spc4 microoxic 3


title: BPD cord blood of sample 1007

description: BPD cord blood sample

value: Umbilical cord blood


title: atm-1, 70 Gy, 2

city: Yangzhou

first: Mingnan

last: Qu

state: Jiangsu

address: Pazhou Dadao Rd, 17-19

institute: Yangzhou Univerisity

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to Oryza MSU7.0 database using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: Oryza MSU7.0 database
Supplementary files format and content: Excel files include RPKM values for each Sample

source_name: leaves

growth_protocol: All the plant materials used in our report were grown in paddy fields under ambient (normal) conditions.

extract_protocol:
the total RNA was isolated from the leaf tissue using the RNA extraction kit (Huayueyang, China).
The RNA-Seq library construction was performed using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB, Ispawich, USA) following the manufacturer’s instructions.

treatment_protocol:
Seedlings were cultivated in glass test tubes using 0.5× Murashige and Skoog (½ MS) solid medium, at 26 °C under a photoperiod of 13h/11h (light/dark). The 14 d cultivated seedlings received a γ-ray irradiation from a 60Co source at the dose rate of 1 Gy min-1
Seedlings were cultivated in glass test tubes using 0.5× Murashige and Skoog (½ MS) solid medium, at 26 °C under a photoperiod of 13h/11h (light/dark). The 14 d cultivated seedlings treated by cold (4°C) for 24 h

tag: cell type

value: leaves

value: atm-1 mutant

tag: treatment

value: Irradiation 70 Gy

tag: time

value: 6 h after treatment


title: 110spc4 microoxic 1


title: ATM, 70 Gy, 3

value: WT (ATM)


title: atr, 70 Gy

value: atr mutant


title: atm-1, 70 Gy, 1


title: ATM, 4°C

description: cold.xlsx

value: cold  4°C

value: 24 h treatment


title: atm-1, 4°C

description: cold.xlsx


title: ATM, 70 Gy, 2


title: atm-1, 70 Gy, 3


title: ATM, 70 Gy, 1


title: TOP6A3-OE1 atm, 40Gy

value: TOP6A3-OE1 atm-2 (overexpression mutation)

value: Irradiation 40 Gy


title: ku70, 40Gy, 2

value: ku70 mutant


title: TOP6A3-OE1, 40Gy


title: DJ, 40Gy, 1

value: WT (DJ)


title: atr, Control

value: Control


title: top6a3, Control, 1

value: top6a3 mutant


title: atm-1, Control, 3


title: 1255 microoxic 1

value: microoxic


title: atm-1, Control, 2


title: top6a3, Control, 3


title: ku70, 40Gy, 1


title: TOP6A3, Control

value: WT (TOP6A3)


title: atm-1, Control, 1


title: ATM, Control, 3


title: DJ, Control, 1


title: ATM, Control, 2


title: ku70, Control, 1


title: top6a3, Control, 2


title: DJ, Control, 2


title: ku70, Control, 2


title: Non-muscle invasive bladder cancer 33-recur-2 [D378R086]

city: Singapore

first: Tuan Zea

last: Tan

address: 14 Medical Drive, #11-01, Singapore

department: Cancer Science Institute Singapore

country: Singapore

institute: National University of Singapore

description:
D378R086
recurrent 33

data_processing:
bcl2fastq 2.17.1.14 were used for basecalling.
Sequenced reads were mapped to hg38 using STAR v2.4.2a with default parameters settings.
Counts Per Kilobase per Megabase of library size (CPM) were computed using RSEM v1.2.25 and Gencode v35 annotation.
Assembly: hg38
Supplementary files format and content: CPM_table.txt: Tab-delimited text file includes CPM values for every gene of Sample.

source_name: FFPE

extract_protocol:
RNA from the FFPE sections were extracted using QIAGEN RNeasy FFPE kit.
RNA libraries were prepared for sequencing using QUANTSEQ 3’mRNA-Seq Library Prep (REV) LEXOGEN kit & standard Illumina protocol.

tag: tissue

value: Bladder

value: Recurrent tumor

tag: case


title: ATM, Control, 1

value: leaves


title: ER8PEAR2, uninduced, biological rep2

city: Toyonaka

first: Tatsuo

last: Kakimoto

state: Osaka

address: 1-1 Machikaneyama

department: Graduate School of Science

institute: Osaka University

description: 68-hours-old plants were mock-treated for 16 hours

hyb_protocol: Hybridization, washing, and staining procedures were run on Fluidics Station 450 (Affymetrix) with GeneChip Hybridization, Wash, and Stain Kit (Affymetrix)

scan_protocol: GeneChips were scanned with GeneChip Scanner 3000 7G.

data_processing: Transcriptional Analysis Console 4.0 (Thermofisher) was used for data analysis. RMA algorithm was used for normalization.

organism: Arabidopsis thaliana

source_name: root samples of ER8PEAR2, uninduced

label_protocol: GeneChip WT Terminal Labeling Kit was used.

growth_protocol: Plants were grown on GM plates under continuous light at 23 C.

extract_protocol: Entire roots were sampled in a tube cooled with liquid nitrogen. RNA was purified by using RNAeasy micro.

treatment_protocol: 68-hours-old plants were moved onto plates without or with 10 µM estriol and incubated for 16 hours.

value: mock

value: root


title: ER8PEAR2, uninduced, biological rep1


title: Non-muscle invasive bladder cancer 17-recur [D378R074]

description:
D378R074
recurrent 17


title: Non-muscle invasive bladder cancer 6-recur-2 [D378R088]

description:
D378R088
recurrent 6


title: Non-muscle invasive bladder cancer 25-post [D378R087]

description:
D378R087
post-treatment 25

value: Post-treatment


title: ER8PEAR2, induced, biological rep2

description: 68-hours-old plants were treated with 10 µM estriol for 16 hours

source_name: root samples of ER8PEAR2, induced

value: 10 µM estriol for 16 hrs


title: ER8Dof2.2, induced, biological rep1

source_name: root samples of ER8Dof2.2, induced


title: fetal lung tissue, Sample97

city: Aurora

first: Sunita

last: Sharma

address: 13199 East Montview Blvd

department: Medicine-Pulmonary Sciences & Critical Care

institute: University of Colorado Hospital

data_processing:
Trimming for low-quality base calls and adpator sequeiencs was completed using cutadapt v.2.7. FastQC v0.11.8 was applied to each trimmed .fastq file to assess adaptor removal. Then reads were mapped to counts of known miRNAs using miR-MaGiC with reference to the Homo sapiens miRbase v22.1 database with collapsed functional groups (repo verision 7147b7a).
Samples passing quality-control (≥1x10^5 mapped reads, having available phenotypic information, and being within the 7 - 17 week pseudoglandular period) and autosomal miRNAs passing pre-filtering criteria (non-zero counts in at least 25% of samples; passes DESeq2 independent filtering algorithm;and not mapped to X or Y chromosome) were tested for differences by sex.
Using RUV-Seq v1.22.0, we also obtained four RUVr factors representing unmeasured miRNA expression heterogeneity for inclusion in regression models.
Assembly: Homo sapiens miRBase database v22.1
Supplementary files format and content: Matrix table with raw miRNA counts for every miRNA and every sample

source_name: fetal lung tissue

extract_protocol:
Total RNA was extracted from 30mg of homogenized prenatal lung tissue with the miRNeasy Mini Kit per manufacturer instructions.
Samples were block-randomized by age, sex, and smoke exposure status to four batches of miRNA library preparation (Small RNA Sequencing Kit v3 for Illumina Platforms; Bio Scientific) and sequencing (HiSeq2500; Illumina; San Diego, CA, USA).

tag: age (days post coitum)

tag: age orthogonal polynomial linear term

tag: age orthogonal polynomial quadratic term

tag: Sex

value: male

tag: smokebinary

value: <7.5 ng cotinine/g placenta

tag: run


title: fetal lung tissue, Sample98

value: female


title: fetal lung tissue, Sample95


title: Non-muscle invasive bladder cancer 26-recur [D378R078]

description:
D378R078
recurrent 26


title: Non-muscle invasive bladder cancer 19-recur [D378R060]

description:
D378R060
recurrent 19


title: Non-muscle invasive bladder cancer 30-recur [D378R062]

description:
D378R062
recurrent 30


title: ER8Dof1.1, induced, biological rep2

source_name: root samples of ER8Dof1.1, induced


title: ER8Dof1.1, uninduced, biological rep2

source_name: root samples of ER8Dof1.1, uninduced


title: ER8Dof2.2, uninduced, biological rep2

source_name: root samples of ER8Dof2.2, uninduced


title: fetal lung tissue, Sample99


title: ER8Dof1.1, induced, biological rep1


title: Non-muscle invasive bladder cancer 28-post [D378R043]

description:
D378R043
post-treatment 28


title: Non-muscle invasive bladder cancer 30 [D378R032]

description:
D378R032
Primary tumor 30

value: Primary tumor


title: ER8Dof1.1, uninduced, biological rep1


title: ER8Dof2.2, induced, biological rep2


title: fetal lung tissue, Sample90

value: >=7.5 ng cotinine/g placenta


title: fetal lung tissue, Sample96


title: Non-muscle invasive bladder cancer 31 [D378R017]

description:
D378R017
Primary tumor 31


title: Non-muscle invasive bladder cancer 19 [D378R019]

description:
D378R019
Primary tumor 19


title: Non-muscle invasive bladder cancer 17 [D378R016]

description:
D378R016
Primary tumor 17


title: fetal lung tissue, Sample89


title: fetal lung tissue, Sample9


title: fetal lung tissue, Sample92


title: fetal lung tissue, Sample94


title: ER8Dof2.2, uninduced, biological rep1


title: Non-muscle invasive bladder cancer 28 [D378R027]

description:
D378R027
Primary tumor 28


title: fetal lung tissue, Sample86


title: fetal lung tissue, Sample93


title: soft-tissue sarcoma_134

tag: age

tag: gender

value: Female

tag: site

value: Upper-limb

value: Surgery

tag: sample type

value: sarcoma


title: Non-muscle invasive bladder cancer 18-recur [D378R073]

description:
D378R073
recurrent 18

tag: disease state


title: Patient sample 341A

city: Los Angeles

first: Matthew

middle: A

last: Fischer

address: 650 Charles Young Dr

department: Anesthesiology and Perioperative Medicine

institute: University of California, Los Angeles

data_processing:
BSBolt (PMID 33966074) was used to align to human reference genome hg38.
We removed from analysis CpGs with less than 10x coverage. Additionally, CpGs were removed from the cohort if they were located at SNPs with minor allele frequency greater than 1% in humans (dbSNP build 150 common SNPs: http://hgdownload.cse.ucsc.edu/goldenpath/hg38/database/snp150Common.txt.gz) or not present in at least 50% of the cohort after filtering for coverage.
Genome_build: hg38
Supplementary_files_format_and_content: Each patient's methylation call file contains the chromosome and base pair location of each CpG and each CpG's coverage and percent methylation data.

source_name: Whole blood

extract_protocol:
Genomic DNA was isolated (PureLink Genomic DNA Kit, K1820-01) from whole blood (separately we biobanked buffy coat containing leukocytes and platelets at -80ºC), subjected to enzymatic digestion with MspI (NEB, R0106S) and bisulfite converted (EpiTect Fast. DNA Bisulfite Kit, Qiagen, 59824).
Samples underwent library preparation involving unique adaptor ligation and were subsequently pooled to be individually sequenced together. Single stranded DNA was then isolated and hybridized with 120 bp biotinylated DNA probes from Integrated DNA Technologies (Coralville, IA). Following probe pull down with streptavidin magnetic coated beads, the pooled samples underwent bisulfite conversion, PCR amplification and sequencing on NovaSeq 6000 instrunments.
Bisulfite-seq (targeted)

value: Male

tag: paroxysmal atrial fibrillation

value: No

tag: diabetes mellitus

value: Yes

tag: hypertension

tag: congestive heart failure

tag: pulmonary vein isolation

tag: maze procedure

tag: combined surgery

tag: cardiopulmonary bypass time

tag: body mass index

tag: current smoker

tag: asian

tag: black

tag: hispanic

tag: post-operative atrial fibrillation


title: Patient sample 339A

tag: Sex

tag: age


title: fetal lung tissue, Sample84

tag: age (days post coitum)

tag: age orthogonal polynomial linear term

tag: age orthogonal polynomial quadratic term

tag: smokebinary

tag: run


title: Patient sample 337A

tag: paroxysmal atrial fibrillation

tag: diabetes mellitus

tag: hypertension

tag: congestive heart failure

tag: pulmonary vein isolation


title: fetal lung tissue, Sample88


title: fetal lung tissue, Sample91


title: fetal lung tissue, Sample80


title: fetal lung tissue, Sample87


title: Patient sample 329A

tag: maze procedure

tag: combined surgery

tag: cardiopulmonary bypass time

tag: body mass index

tag: current smoker


title: fetal lung tissue, Sample8

tag: Sex


title: Non-muscle invasive bladder cancer 18 [D378R029]

description:
D378R029
Primary tumor 18

tag: tissue

value: Bladder

tag: disease state

tag: case


title: Patient sample 330A

tag: age

tag: asian

tag: black

tag: hispanic

tag: post-operative atrial fibrillation


title: Non-muscle invasive bladder cancer 14 [D378R023]

description:
D378R023
Primary tumor 14


title: fetal lung tissue, Sample79

tag: age (days post coitum)

tag: age orthogonal polynomial linear term

tag: age orthogonal polynomial quadratic term

tag: smokebinary

tag: run


title: Patient sample 326A

tag: paroxysmal atrial fibrillation

tag: diabetes mellitus

tag: hypertension

tag: congestive heart failure

tag: pulmonary vein isolation

tag: maze procedure

tag: combined surgery

tag: cardiopulmonary bypass time


title: fetal lung tissue, Sample83

tag: Sex


title: fetal lung tissue, Sample85


title: Patient sample 334A

tag: age

tag: body mass index

tag: current smoker

tag: asian

tag: black


title: Non-muscle invasive bladder cancer 6 [D378R011]

description:
D378R011
Primary tumor 6

tag: tissue

tag: disease state

tag: case


title: fetal lung tissue, Sample81

tag: age (days post coitum)

tag: age orthogonal polynomial linear term

tag: age orthogonal polynomial quadratic term

tag: smokebinary

tag: run


title: fetal lung tissue, Sample74


title: Patient sample 340A

tag: paroxysmal atrial fibrillation

tag: diabetes mellitus

tag: hypertension

tag: congestive heart failure

tag: pulmonary vein isolation

tag: maze procedure

tag: hispanic

tag: post-operative atrial fibrillation


title: fetal lung tissue, Sample77

tag: Sex


title: Patient sample 311A

tag: age

tag: combined surgery

tag: cardiopulmonary bypass time

tag: body mass index

tag: current smoker

tag: asian

tag: black


title: fetal lung tissue, Sample82

tag: age (days post coitum)

tag: age orthogonal polynomial linear term

tag: age orthogonal polynomial quadratic term

tag: smokebinary

tag: run


title: Patient sample 338A

tag: paroxysmal atrial fibrillation

tag: diabetes mellitus

tag: hypertension

tag: congestive heart failure

tag: pulmonary vein isolation


title: Patient sample 310A

tag: Sex

tag: age

tag: maze procedure

tag: hispanic

tag: post-operative atrial fibrillation


title: Patient sample 327A

tag: combined surgery

tag: cardiopulmonary bypass time

tag: body mass index

tag: current smoker

tag: asian


title: Patient sample 306A

tag: black


title: Patient sample 325A


title: fetal lung tissue, Sample69

tag: age (days post coitum)

tag: age orthogonal polynomial linear term

tag: age orthogonal polynomial quadratic term

tag: smokebinary

tag: run


title: fetal lung tissue, Sample7


title: Patient sample 305A

tag: paroxysmal atrial fibrillation

tag: diabetes mellitus

tag: hypertension

tag: congestive heart failure

tag: pulmonary vein isolation


title: Patient sample 328A

tag: Sex

tag: age

tag: maze procedure

tag: hispanic

tag: post-operative atrial fibrillation


title: Patient sample 304A

tag: combined surgery

tag: cardiopulmonary bypass time

tag: body mass index

tag: current smoker

tag: asian


title: fetal lung tissue, Sample75

tag: age (days post coitum)

tag: age orthogonal polynomial linear term

tag: age orthogonal polynomial quadratic term

tag: smokebinary


title: Patient sample 333A

tag: paroxysmal atrial fibrillation

tag: diabetes mellitus

tag: hypertension

tag: black


title: fetal lung tissue, Sample73

tag: Sex

tag: run


title: Patient sample 324A

tag: age

tag: congestive heart failure

tag: pulmonary vein isolation

tag: maze procedure

tag: hispanic


title: Patient sample 309A

tag: combined surgery

tag: cardiopulmonary bypass time

tag: body mass index

tag: current smoker

tag: post-operative atrial fibrillation


title: fetal lung tissue, Sample71

tag: age (days post coitum)

tag: age orthogonal polynomial linear term

tag: age orthogonal polynomial quadratic term

tag: smokebinary


title: fetal lung tissue, Sample72


title: Patient sample 308A

tag: paroxysmal atrial fibrillation

tag: diabetes mellitus

tag: hypertension

tag: asian

tag: black


title: Patient sample 303A

tag: Sex

tag: age

tag: congestive heart failure

tag: pulmonary vein isolation


title: fetal lung tissue, Sample70

tag: run


title: fetal lung tissue, Sample76


title: fetal lung tissue, Sample64


title: Patient sample 300A

tag: maze procedure

tag: combined surgery

tag: cardiopulmonary bypass time

tag: body mass index

tag: hispanic


title: fetal lung tissue, Sample62

tag: age (days post coitum)

tag: age orthogonal polynomial linear term

tag: age orthogonal polynomial quadratic term


title: Patient sample 312A

tag: paroxysmal atrial fibrillation

tag: diabetes mellitus

tag: current smoker

tag: post-operative atrial fibrillation


title: fetal lung tissue, Sample78

tag: Sex

tag: smokebinary


title: fetal lung tissue, Sample68


title: fetal lung tissue, Sample67


title: DJ, 40Gy, 2

tag: cell type

value: leaves

tag: genotype

value: WT (DJ)

tag: treatment

value: Irradiation 40 Gy

tag: time

value: 6 h after treatment


title: fetal lung tissue, Sample65

tag: run


title: fetal lung tissue, Sample63


title: fetal lung tissue, Sample66

value: male


title: Patient sample 301A

tag: age

tag: hypertension

tag: congestive heart failure

tag: pulmonary vein isolation

tag: maze procedure

tag: combined surgery

tag: cardiopulmonary bypass time

tag: asian

tag: black


title: Patient sample 302A

tag: paroxysmal atrial fibrillation

tag: diabetes mellitus

tag: body mass index

tag: current smoker

tag: hispanic

tag: post-operative atrial fibrillation


title: fetal lung tissue, Sample57

tag: age (days post coitum)

tag: age orthogonal polynomial linear term

tag: age orthogonal polynomial quadratic term

tag: Sex

tag: smokebinary


title: fetal lung tissue, Sample61

value: <7.5 ng cotinine/g placenta

tag: run


title: Patient sample 299A

tag: age

tag: hypertension

tag: congestive heart failure

tag: pulmonary vein isolation

tag: maze procedure


title: fetal lung tissue, Sample56

value: female


title: Patient sample 289A

tag: paroxysmal atrial fibrillation

tag: combined surgery

tag: cardiopulmonary bypass time

tag: asian

tag: black


title: fetal lung tissue, Sample60


title: fetal lung tissue, Sample6


title: Patient sample 295A

tag: diabetes mellitus

tag: body mass index

tag: current smoker

tag: hispanic

tag: post-operative atrial fibrillation


title: Patient sample 293A

tag: Sex


title: fetal lung tissue, Sample58

tag: age (days post coitum)

tag: age orthogonal polynomial linear term

tag: age orthogonal polynomial quadratic term

tag: smokebinary

tag: run


title: Patient sample 288A

tag: age

tag: hypertension

tag: congestive heart failure

tag: pulmonary vein isolation

tag: maze procedure


title: fetal lung tissue, Sample59


title: Patient sample 292A

tag: paroxysmal atrial fibrillation

tag: combined surgery

tag: cardiopulmonary bypass time

tag: asian

tag: black


title: Patient sample 287A

tag: diabetes mellitus

tag: body mass index

tag: current smoker

tag: hispanic

tag: post-operative atrial fibrillation


title: Patient sample 290A

tag: Sex


title: Patient sample 298A


title: Patient sample 291A


title: fetal lung tissue, Sample55

tag: age (days post coitum)

tag: age orthogonal polynomial linear term

tag: age orthogonal polynomial quadratic term

tag: smokebinary

tag: run


title: fetal lung tissue, Sample52


title: Patient sample 286A

tag: age

tag: hypertension

tag: congestive heart failure

tag: pulmonary vein isolation

tag: maze procedure


title: Patient sample 285A

tag: paroxysmal atrial fibrillation

tag: combined surgery

tag: cardiopulmonary bypass time

tag: asian

tag: black


title: fetal lung tissue, Sample53


title: Patient sample 284A

tag: diabetes mellitus

tag: body mass index

tag: current smoker

tag: hispanic

tag: post-operative atrial fibrillation


title: fetal lung tissue, Sample54

tag: age (days post coitum)

tag: age orthogonal polynomial linear term

tag: age orthogonal polynomial quadratic term

tag: Sex

tag: smokebinary


title: fetal lung tissue, Sample51

tag: run


title: Patient sample 283A

tag: age

tag: hypertension

tag: congestive heart failure

tag: pulmonary vein isolation

tag: maze procedure


title: Patient sample 281A

tag: paroxysmal atrial fibrillation

tag: combined surgery

tag: cardiopulmonary bypass time

tag: asian

tag: black


title: fetal lung tissue, Sample5


title: Patient sample 282A

tag: diabetes mellitus

tag: body mass index

tag: current smoker

tag: hispanic

tag: post-operative atrial fibrillation


title: fetal lung tissue, Sample49

tag: age (days post coitum)

tag: age orthogonal polynomial linear term

tag: age orthogonal polynomial quadratic term

tag: Sex

tag: smokebinary


title: Patient sample 280A

tag: age

tag: hypertension

tag: congestive heart failure

tag: pulmonary vein isolation


title: fetal lung tissue, Sample46

tag: run


title: fetal lung tissue, Sample45


title: Patient sample 277A

tag: paroxysmal atrial fibrillation

tag: maze procedure

tag: combined surgery

tag: cardiopulmonary bypass time

tag: asian


title: Patient sample 278A

tag: diabetes mellitus

tag: body mass index

tag: current smoker

tag: black

tag: hispanic


title: fetal lung tissue, Sample42

tag: age (days post coitum)

tag: age orthogonal polynomial linear term

tag: age orthogonal polynomial quadratic term

tag: Sex


title: ER8PEAR2, induced, biological rep1

tag: genotype

tag: treatment

value: 10 µM estriol for 16 hrs

tag: tissue

value: root


title: fetal lung tissue, Sample44

tag: smokebinary

value: >=7.5 ng cotinine/g placenta

tag: run


title: Patient sample 274A

tag: age

tag: paroxysmal atrial fibrillation

tag: hypertension

tag: congestive heart failure

tag: pulmonary vein isolation

tag: maze procedure

tag: combined surgery

tag: post-operative atrial fibrillation


title: fetal lung tissue, Sample50

tag: age (days post coitum)


title: fetal lung tissue, Sample47

tag: age orthogonal polynomial linear term


title: fetal lung tissue, Sample41

tag: age orthogonal polynomial quadratic term


title: fetal lung tissue, Sample43

tag: Sex


title: Patient sample 276A

value: Female

tag: diabetes mellitus

tag: cardiopulmonary bypass time

tag: body mass index

tag: current smoker

tag: asian

tag: black

tag: hispanic


title: Patient sample 273A

tag: age

tag: paroxysmal atrial fibrillation

tag: hypertension


title: Patient sample 272A

tag: congestive heart failure

tag: pulmonary vein isolation

tag: maze procedure


title: fetal lung tissue, Sample39

tag: age (days post coitum)

tag: smokebinary

tag: run


title: Patient sample 267A

tag: Sex

tag: combined surgery

tag: post-operative atrial fibrillation


title: Patient sample 270A

tag: diabetes mellitus

tag: cardiopulmonary bypass time

tag: body mass index


title: fetal lung tissue, Sample4

tag: age orthogonal polynomial linear term

tag: age orthogonal polynomial quadratic term


title: Patient sample 279A

tag: age

tag: current smoker

tag: asian

tag: black

tag: hispanic


title: Patient sample 265A

tag: paroxysmal atrial fibrillation

tag: hypertension

tag: congestive heart failure

tag: pulmonary vein isolation

tag: maze procedure


title: Patient sample 264A

tag: Sex

tag: combined surgery


title: fetal lung tissue, Sample34

tag: age (days post coitum)

tag: smokebinary

tag: run


title: fetal lung tissue, Sample48

tag: age orthogonal polynomial linear term


title: Patient sample 269A

tag: diabetes mellitus

tag: cardiopulmonary bypass time

tag: body mass index

tag: post-operative atrial fibrillation


title: fetal lung tissue, Sample31

tag: age orthogonal polynomial quadratic term


title: Patient sample 263A

tag: age

tag: current smoker

tag: asian

tag: black

tag: hispanic


title: Patient sample 261A

tag: paroxysmal atrial fibrillation

tag: hypertension

tag: congestive heart failure

tag: pulmonary vein isolation

tag: maze procedure


title: Patient sample 262A

tag: Sex

tag: combined surgery


title: fetal lung tissue, Sample38

tag: age (days post coitum)

tag: age orthogonal polynomial linear term

tag: smokebinary

tag: run


title: fetal lung tissue, Sample30

tag: age orthogonal polynomial quadratic term


title: Patient sample 275A

tag: age

tag: diabetes mellitus

tag: cardiopulmonary bypass time

tag: body mass index

tag: post-operative atrial fibrillation


title: fetal lung tissue, Sample37


title: Patient sample 268A

tag: paroxysmal atrial fibrillation

tag: current smoker

tag: asian

tag: black

tag: hispanic


title: fetal lung tissue, Sample36

tag: Sex


title: fetal lung tissue, Sample33


title: Patient sample 271A

tag: hypertension

tag: congestive heart failure

tag: pulmonary vein isolation

tag: maze procedure

tag: combined surgery


title: fetal lung tissue, Sample298

tag: age (days post coitum)

tag: age orthogonal polynomial linear term

tag: age orthogonal polynomial quadratic term

tag: smokebinary

tag: run


title: Patient sample 258A

tag: age

tag: diabetes mellitus

tag: cardiopulmonary bypass time

tag: body mass index

tag: post-operative atrial fibrillation


title: fetal lung tissue, Sample35


title: fetal lung tissue, Sample297


title: fetal lung tissue, Sample32


title: fetal lung tissue, Sample3


title: Patient sample 260A

tag: paroxysmal atrial fibrillation

tag: current smoker

tag: asian

tag: black

tag: hispanic


title: fetal lung tissue, Sample294

tag: Sex


title: Patient sample 259A

tag: hypertension

tag: congestive heart failure

tag: pulmonary vein isolation

tag: maze procedure

tag: combined surgery


title: Patient sample 255A


title: fetal lung tissue, Sample291

tag: age (days post coitum)

tag: age orthogonal polynomial linear term

tag: age orthogonal polynomial quadratic term

tag: smokebinary

tag: run


title: Patient sample 257A

tag: age

tag: diabetes mellitus

tag: cardiopulmonary bypass time

tag: body mass index

tag: post-operative atrial fibrillation


title: fetal lung tissue, Sample296


title: Patient sample 250A

tag: paroxysmal atrial fibrillation

tag: current smoker

tag: asian

tag: black

tag: hispanic


title: fetal lung tissue, Sample290

tag: Sex


title: Patient sample 266A

tag: hypertension

tag: congestive heart failure

tag: pulmonary vein isolation

tag: maze procedure

tag: combined surgery


title: Patient sample 256A


title: fetal lung tissue, Sample289

tag: age (days post coitum)

tag: age orthogonal polynomial linear term

tag: age orthogonal polynomial quadratic term

tag: smokebinary

tag: run