title: exbD rep2

first: Saixiang

last: Feng

address: South China Agricultural University, No. 483, Wushan Road, Tianhe District

institute: South China Agricultural University

data_processing:
Data quality. Control The quality information of raw data in FASTQ format was calculated and then the raw data was filtered using Cutadapt(v1.15) software, clean data was obtained by removing reads containing adapter, reads containing ploy-N and low quality reads. All the subsequent analysis was based on high quality clean data.
Data mapping analysis. The reference genome and gene annotation files were downloaded from genome website. Reference genome index was built by Bowtie2(v2.2.6) and the filtered reads were mapping to the reference genome using Bowtie2 (http://bowtie-bio.sourceforge.net/index.shtml).
Expression level analysis. The gene read count value was counted using HTSeq(v0.9.1) as the original expression level of the gene. In order to make the gene expression levels of different genes and different samples comparable, FPKM(fragments per kilobaseof exon per million fragments mapped) is used to normalize the expression.
Differential expression analysis DESeq(v1.30.0) was conducted to analyze the differential expressed mRNA, transcripts with |log2FoldChange|>1 and P-value
Cluster analysis. Cluster analysis was used to determine the expression pattern of differentially expressed mRNA under different experimental conditions, mRNA with high correlation between samples was classified into one class. Therefore, unknown biological links between mRNA can be found by clustering gene expression levels. R language Pheatmap (v1.0.8) software package was used to perform bidirectional cluster analysis on all mRNA and samples, Euclidean method was used to calculate the distance and the hierarchical clustering longest distance method was used to accomplish the clustering.
Assembly: ASM694v2
Supplementary files format and content: Excel files include RPKM values for each Sample

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: bacterial cell

extract_protocol:
Total RNA was isolated using the Trizol Reagent (Invitrogen Life Technologies), after which the concentration, quality and integrity were determined using a NanoDrop spectrophotometer (Thermo Scientific)
Zymo-Seq RiboFree Total RNA Library Kit was used to remove rRNA from total RNA. Random oligonucleotides and SuperScript III were used to synthesize the first strand cDNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities and the enzymes were removed. After adenylation of the 3′ ends of the DNA fragments, Illumina PE adapter oligonucleotides were ligated to prepare for hybridization. To select cDNA fragments of the preferred 400-500 bp in length, the library fragments were purified using the AMPure XP system (Beckman Coulter, Beverly, CA, USA). DNA fragments with ligated adaptor molecules on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. Products were purified (AMPure XP system) and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system (Agilent).

value: bacterial cell

value: exbD


title: exbB rep3

status: Public on Sep 29 2022

type: SRA

city: Guangzhou

state: Guangdong

country: China

library_source: transcriptomic

molecule: total RNA

tag: cell type

tag: genotype

value: exbB

tag: treatment


title: exbD rep1


title: exbD rep3


title: MDA-MB-468 cells, Control 2

city: Southampton

first: Yihua

last: Wang

address: University Road

country: United Kingdom

institute: University of Southampton

data_processing:
Quality control of RNA-seq raw paired data was performed using FastQC  and MultiQC.
Trim Galore was used to trim adapters, reads with low quality (<30) and short length (<50 bp).
RNA-seq reads were mapped to Homo_sapiens.GRCh38.100 using Hisat2 with default codes.
Sam files were transformed into bam files using samtools.
The read counts of each genes were summarized using featureCounts.
Assembly: Homo_sapiens.GRCh38.100
Supplementary files format and content: tab-delimited text files include raw count values for each Sample

organism: Homo sapiens

growth_protocol: Cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) (Gibco® by Life Technology) with 10% FBS and 1% (v/v) penicillin/streptomycin, and were kept at 37 °C and 5% CO2.

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen) according to manufacturer’s instructions and quantified using a Nanodrop Spectophotometer 2000c (Thermo Fisher Scientific). A total amount of 3 μg RNA per sample was used as input material for library construction.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, Ipswich, Massachusetts, USA) following manufacturer’s instruction. Libraries were pooled in equimolar and sequenced using the paired-end strategy (2 × 150) on the Illumina NovaSeq 6000 platform following the standard protocols (Novogene, UK).

treatment_protocol: MDA-MB-468 cells were treated with Limonium Sinense Water extract (LSW) for 48 hours at 500 μg/mL

tag: cell line

value: breast cancer cells

value: WT


title: cell transfected siJunB-848, biological rep2

type: RNA

city: Valencia

first: Rosa

last: Farràs

state: Valencia

address: Eduardo Primo Yúfera, 12

country: Spain

institute: Centro de Investigación Príncipe Felipe

description:
Gene expression data from JUNB depleted exponentially growing U2OS cells
JB3_s9

hyb_protocol: Hybridization was performed in the  Affymetrix Human Gene 2.0 ST Array.

scan_protocol: Scan was performed according to Affymetrix instructions (user manual P/N 702731 Rev. 3).

data_processing:
Data were processed with Partek Suite and differentially expressed genes detected with the LIMMA package.
Significantly differentially expressed genes were selected based on a false discovery rate (FDR) threshold of less than 0.05.
Log2 probe set signal intensities after RMA normalization were generated.

label: biotin

source_name: exponentially growing U2OS cells

label_protocol: Label protocol were prepared according to the standard Affymetrix protocol. See manufacturer's web site

growth_protocol: U2OS-derived UTA6 cells were seeded at subconfluence in DMEM medium supplemented with 10% foetal bovine serum and penicillin/streptomycin (100µg/ml each) in a humidified 5% CO2 atmosphere at 37°C.

extract_protocol: Total RNA was extracted 48 h post-transfection using High Pure RNA Isolation kit (Roche). Triplicate RNA samples for each conditions were quality checked (RIN>9) with Eukaryotic Total RNA Nano Kit on Bioanalyser 2100 (Agilent) and then analysed on GeneChip Human Transcriptome Array 2.0 (Affymetrix)

treatment_protocol: cells were transfected with siRNAs at a final concentration of 8 nM using Interferine (Polyplus) according to manufacturer’s instructions

value: U2OS-derived UTA6 cells

value: osteosarcoma cell

value: JUNB depletion


title: exbB rep2


title: MDA-MB-468 cells, Control 1


title: MDA-MB-468 cells, LSW 1

value: LSW, 500 microg/mL, 48 hours


title: MDA-MB-468 cells, LSW 3


title: cell transfected siJunB-792, biological rep3

description:
Gene expression data from JUNB depleted exponentially growing U2OS cells
JB1_s10


title: ATACseq DIDO3 MUT rep2

city: Madrid

first: Tirso

last: Pons

state: Madrid

address: C/ Darwin 3

department: Inmunology and Oncology

institute: Centro Nacional de Biotecnologia

library_source: genomic

data_processing:
Sequenced reads were mapped to mm10 whole genome using BWA-MEM 0.7.15 with parameters mem -M -t 4 mm10bwaidx file_1.fastq file_2.fastq
The sequences aligned in blacklisted regions  (sites.google.com/site/anshulkundaje/projects/blacklists) were removed with the Intersect tool from BEDTools before calculating accessible regions of chromatin using the MACS2 program
For the calculation of the differential accessibility of chromatin, the accessible and equivalent regions were analyzed with HOMER
The allocation of genes, promoters, UTRs, introns and exons to the accessible regions was carried out with the ChIPseeker program
StringTie was used for assembling RNA-seq alignments into potential transcripts, and also getting count and normalize reads with parameters -e -v -p 32 -G knownGene_UCSC_mm10.gtf
Differentially expressed genes were defined with edgeR
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include ChIPseeker annotations of the accessible regions determined with HOMER and MACS2 for each sample
Supplementary_files_format_and_content: tab-delimited text files include cov, FPKM, and TPM values for each sample

molecule: genomic DNA

organism: Mus musculus

source_name: mouse hematopoietic precursors

extract_protocol:
The tagged DNA was purified with the DNA Clean® ConcentratorTM5 Kit (ZYMO Research).
DNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The LSK cell samples obtained by sorting were processed with the DNA Library Prep Kit (Illumina). The samples were pre-amplified with the Nextera®Index kit (Illumina) and the Nextera®DNA Library kit Preparation (Illumina), incorporating index sequences at the ends. DNA from the PCR reaction was purified using the DNA Clean® ConcentratorTM5 Kit. For the quantification of tagged DNA, the 1x dsDNA HS Assay kit (QubitTM) was used. The samples were then enriched in DNA sizes between 200 and 600 bp (corresponding to between 1 and 3 nucleosomes using AMPure XP magnetic beads (Beckman-Coulter), following the manufacturer's guidelines. To analyze the size distribution DNA analysis was performed by electropherogram (Agilent 2100 Bioanalyzer). For sequencing of tagged DNA, a mixture of libraries with a balanced proportion of 2 samples of LSK-wt cells and 2 samples of LSK-Dido1dE16 cells was used, each sample with ca. 100,000 pmol/l of tagged DNA fragments. Once the samples were sequenced, the fragment size distribution was determined to have maxima corresponding to lengths of two nucleosomes (~ 350 bp), one nucleosome (~ 180 bp), and less than one nucleosome, the latter corresponding to what was expected from naked DNA.

tag: strain

tag: tissue

value: hematopoietic precursors

value: DIDO3_exon16 mutant


title: cell transfected siCT, biological rep3

description:
Gene expression data from JUNB depleted exponentially growing U2OS cells
CT_s10

value: siCT

value: control


title: ATACseq DIDO3 MUT rep1


title: ATACseq DIDO3 WT rep2

value: wild type


title: WT rep3


title: WT rep2


title: TonB rep1

value: tonB


title: exbB rep1


title: ATACseq DIDO3 WT rep1


title: TonB rep3


title: TonB rep2


title: cell transfected siJunB-848, biological rep1

description:
Gene expression data from JUNB depleted exponentially growing U2OS cells
JB3_s8


title: WT rep1


title: 2nd restim TBBz rep2

status: Public on Sep 28 2022

city: Daejeon

first: YoungHo

last: Lee

address: 48, Yuseong-daero 1184beon-gil, Yuseong-gu

country: South Korea

institute: Curocell

data_processing:
RNA-seq analysis carried out via Galaxy platform (https://usegalaxy.org/).
The FASTQ data was mapped to the reference genome hg19 using HISAT2 v2.1.0.
The number of reads per annotated gene was then computed from the mapped reads using featurecounts v1.6.4.
The R package limma with voom method v3.38.3 was used to both normalized all dataset and analyzed differential expression between all groups.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited file containing normalized counts

source_name: Healthy donor-derived T cells

growth_protocol: CD19-specific CAR+ΔLNGFR+ T cells are sorted by LNGFR microbeads (Miltenyi), and cultured for 6 days.

extract_protocol:
Total RNA of isolated CAR T cells was isolated using NucleoSpin RNA XS kit (MACHEREY-NAGEL, Germany). The RNA quality was determined with the Agilent 4200 Tapestation (RIN value > 9).
RNA sequencing libraries were constructed using Illumina Truseq Stranded mRNA LP kit. Briefly, mRNA was purified by oligo-dT beads and fragmented through an enzymatic reaction. After fragmentation, cDNA was generated through reverse transcription. The cDNA libraries were constructed and followed by 100 bp paired-end mode on DNBSEQ-400 platform. External RNA controls consortium (ERCC) RNA spike-in mixes (Thermo Fisher, 4456740) were included for quality assurance. The quality of all paired-end reads was analyzed using FastQC software, and the per base sequence quality of all sample was above Q30.

treatment_protocol: 6 days after ΔLNGFR+ cell isolation, CAR T cells were co-cultured with γ-irradiated Nalm-6-PD-L1-CD80 for 6 day. Subsequently, CAR T cells were restimulated under the same condition. 1st or 2nd restimulated CAR-T cells were collected at 48 hr after each stimulation, followed by magnetic selection of ΔLNGFR+ T cells. .

value: CD3+CAR+ T cells

value: CAR expressing T cell with TIGIT downregulation


title: 2nd restim PTBBz rep1

value: CAR expressing T cell with PD-1/TIGIT downregulation


title: cell transfected siJunB-792, biological rep1

description:
Gene expression data from JUNB depleted exponentially growing U2OS cells
JB1_s8


title: 2nd restim PBBz rep2

value: CAR expressing T cell with PD-1 downregulation


title: 2nd restim PTBBz rep2


title: 2nd restim PBBz rep1


title: dESFs co-cultured with BeWo rep 2

city: Farmington

first: Yasir

last: Suhail

state: Connecticut

address: 263 Farmington Avenue

department: BME

country: USA

institute: UCHC

data_processing:
Alignment to Transcriptome: Hisat2
Feature Counting: featurecounts
Genome_build: GRCh38
Supplementary_files_format_and_content: *.counts.txt: Tab-delimited text files include read counts.

molecule: polyA RNA

source_name: Decidualized Endometrial Stromal Fibroblasts

extract_protocol: RNA was extracted.

tag: co-culture condition

value: BeWo


title: cell transfected siJunB-848, biological rep3

description:
Gene expression data from JUNB depleted exponentially growing U2OS cells
JB3_s10


title: 2nd restim GBBz rep2

value: CAR expressing T cell with GFP downregulation


title: 2nd restim GBBz rep1


title: 1st restim GBBz rep2


title: dESFs co-cultured with BeWo rep 3

value: Decidualized Endometrial Stromal Fibroblasts


title: 1st restim GBBz rep1


title: BeWo cells co-cultured with dESFs rep 2

source_name: BeWo Placental Trophoblasts

value: BeWo Placental Trophoblasts

value: dESFs


title: dESFs co-cultured with BeWo rep 1


title: BeWo cells co-cultured with dESFs rep 1


title: BeWo cells co-cultured with dESFs rep 3


title: 2nd restim TBBz rep1


title: dESFs co-cultured with HTR8 rep 3


title: dESFs co-cultured with HTR8 rep 2


title: cell transfected siJunB-792, biological rep2

description:
Gene expression data from JUNB depleted exponentially growing U2OS cells
JB1_s9

value: U2OS-derived UTA6 cells

value: osteosarcoma cell

value: JUNB depletion


title: dESFs co-cultured with HTR8 rep 1


title: HTR8 co-cultured with dESFs rep 2

source_name: HTR8 Placental Trophoblasts

value: HTR8 Placental Trophoblasts


title: HTR8 co-cultured with dESFs rep 3


title: HTR8 co-cultured with dESFs rep 1


title: Decidualized ESFs in HTR8 conditioned medium rep 3

value: HTR8 conditioned medium


title: cell transfected siCT, biological rep1

description:
Gene expression data from JUNB depleted exponentially growing U2OS cells
CT_s8

value: osteosarcoma cell line

value: siCT

value: control


title: Decidualized ESFs in HTR8 conditioned medium rep 2


title: Decidualized ESFs (dESFs) rep 2


title: Decidualized ESFs in HTR8 conditioned medium rep 1


title: untreated HTR8 rep 2


title: untreated HTR8 rep 3


title: untreated BeWo rep 2


title: Decidualized ESFs (dESFs) rep 3


title: untreated BeWo rep 1


title: untreated HTR8 rep 1


title: untreated ESFs rep 1

source_name: Endometrial Stromal Fibroblasts

value: Endometrial Stromal Fibroblasts


title: RNA_CKO_Rep3

first: Yuyu

last: Chen

address: Zhongshan II road, 74th

institute: Sun Yat-sen University

data_processing:
Cutadapt (v2.5) was used to trim adapters and filter for sequences.
The 150 bp paired-end reads were mapped to the reference genome by using hisat2
The reads mapped the genome were calculated using featureCounts (v1.6.3).

source_name: mice growth plate chondrocytes

extract_protocol:
Total RNA was isolated from samples using TRIzol reagent.
VAHTSTM Stranded mRNA-seq Library Prep Kit for Illumina v2 was used for library construction.

tag: genotype/variation

value: CKO

tag: tag

value: chondrocytes


title: untreated ESFs rep 3


title: untreated BeWo rep 3


title: untreated ESFs rep 2


title: RNA_CKO_Rep2


title: RNA_CKO_Rep1


title: RNA_WT_Rep3

value: WT


title: Decidualized ESFs (dESFs) rep 1


title: RNA_WT_Rep2


title: NDM4

city: guangzhou

first: Meng

last: Ren

address: 107 Yanjiang West Road

department: endocrinology department

institute: Sun Yat-sen Memorial Hospital, Sun Yat-sen University

description: full thickness skin of 8-week old sham-treated SD male rat replicate4

hyb_protocol: Array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology). 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing:
the scanned images were analysed using Agilent Feature Extraction software (v11.0.0.1).
Normalization of signal Raw signal intensities were normalized in quantile method by GeneSpring GX v11.5.1, and low intensity LncRNAs were filtered intensity using Agligent GeneSpring GX v12.1 software

organism: Rattus norvegicus

label_protocol: Sample labeling were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology). Briefly, total RNA from each sample was linearly amplified and labeled with Cy3-UTP. The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Total RNA was extracted from the cells using TRIzol reagent (AGbio, China) following the manufacturer’s instructions.RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol:
4-week old Sprague-Dawley (SD) male rats were sham-treated with Sodium citrate solution were housed for 4 weeks before being anesthetized, and full-thickness skin tissue was harvested for microarray analysis.
Four-week-old male Sprague Dawley (SD) rats (weighing 250-300 g) were purchased from the Laboratory Animal Center of Sun Yat-sen University. the animals were i.p. injected with 60 mg/kg streptozotocin (STZ) to induce diabetes and allowed to manifest hyperglycemia for 4 weeks before inflicting a cutaneous wound.

value: Sprague-Dawley (SD)

value: full thickness skin

value: sham-treated


title: NDM1

description: full thickness skin of 8-week old sham-treated SD male rat replicate1


title: RNA_WT_Rep1


title: DM3

description: full thickness skin of 8-week old STZ induced SD male rat replicate3

treatment_protocol:
4-week old Sprague-Dawley (SD) male rats were intraperitoneally (i.p.) injected with 60 mg/kg streptozotocin  to induce diabetes and were housed for 4 weeks before being anesthetized, and full-thickness skin tissue was harvested for microarray analysis.
Four-week-old male Sprague Dawley (SD) rats (weighing 250-300 g) were purchased from the Laboratory Animal Center of Sun Yat-sen University. the animals were i.p. injected with 60 mg/kg streptozotocin (STZ) to induce diabetes and allowed to manifest hyperglycemia for 4 weeks before inflicting a cutaneous wound.


title: Day0_siBrd4_rep2

city: Singapore

first: Pierre-alexis

last: Goy

state: Singapore

address: 60 Biopolis Street

country: Singapore

institute: Genome Institute of Singapore (GIS-ASTAR)

data_processing:
RNA-seq reads were mapped to the mm9 mouse genome assembly using STAR version 2.4.2a with the following parameters : --sjdbOverhang 99 --outSAMstrandField intronMotif --outSAMtype BAM Unsorted --outFilterMultimapNmax 40 --twopassMode Basic
Bam files were sorted with samtools sort and indexed with samtools index.
Differential expression was performed using Cuffdiff 2.2.1
Genome_build: mm9
Supplementary_files_format_and_content: Expression levels (FPKM) table from Cuffdiff

source_name: Cell line (C2C12)

growth_protocol: C2C12 cells were cultured in DMEM medium supplemented with 20% FBS

extract_protocol:
RNA was isolated using RNeasy MinElute Cleanup Kit (Qiagen, Cat# 74204) and subsequently treated with TURBO™ DNase  (Cat#: 2239)
For RNA-Seq library preparation we followed the Illumina TruSeq RNA Sample Preparation Kit v2 manual.

treatment_protocol: C2C12 cells were transfected with 100nM siRNA in a 6 well plate using 4ul of RNAiMAX (Invitrogen) following manufacturer protocol

value: Myoblast


title: Day1_scm_rep2


title: Day1_scm_rep3


title: Day1_scm_rep1


title: Day1_siBrd4_rep3


title: Day0_scm_rep3


title: Day1_siBrd4_rep1


title: Day1_siBrd4_rep2


title: Day0_scm_rep2


title: Day0_siBrd4_rep1


title: Day0_siBrd4_rep3


title: DM2

description: full thickness skin of 8-week old STZ induced SD male rat replicate2

value: intraperitoneally (i.p.) injected with 60 mg/kg streptozotocin


title: Day0_scm_rep1


title: DM4

description: full thickness skin of 8-week old STZ induced SD male rat replicate4


title: cell transfected siCT, biological rep2

description:
Gene expression data from JUNB depleted exponentially growing U2OS cells
CT_s9

value: U2OS-derived UTA6 cells


title: DM1

description: full thickness skin of 8-week old STZ induced SD male rat replicate1


title: ref6c 24h imbibed seeds seeds_rep2

city: Beijing

first: Jie

last: Pan

address: No.1 West Beichen Road,Chaoyang District

institute: Institute of Genetics and Developmental Biology

data_processing:
Adapter trimming was performed and low-quality reads were filtered with fastp version 0.20.1
Reads were mapped to the Arabidopsis genome (TAIR10) using Hisat2 version 2.1.10
Transcripts per million (TPM) values were generated using R
Differential gene expression analysis was performed using DESeq2 version 1.26.0
Genes displayed a more than two-fold expression change and had a padj value<0.05 were considered as differentially expressed
Genome_build: TAIR10
Supplementary_files_format_and_content: *.txt: TPM values for all samples

organism: Arabidopsis thaliana

source_name: ref6c 24h imbibed seeds

growth_protocol: After-ripened ref6-1;REF6-HA seeds (seeds harvested and stored at room temperature for at least three months) were sown on 1/2 MS medium,and subsequently subjected for germination in long days at ~22°C,and collected at different imbibition time points

extract_protocol:
Total RNA was extracted using Minibest plant RNA extraction kit (Takara)
Library was prepared with BGISEQ-500 RNA-Seq Library kit according to the manufacture’s instruction

value: seeds

tag: time

tag: ecotype

value: Col


title: ref6c 24h imbibed seeds seeds_rep3


title: NDM3

description: full thickness skin of 8-week old sham-treated SD male rat replicate3


title: ref6c 48h imbibed seeds seeds_rep2

source_name: ref6c 48h imbibed seeds


title: NDM2

description: full thickness skin of 8-week old sham-treated SD male rat replicate2


title: ref6c 0h imbibed seeds_rep2

source_name: ref6c 0h imbibed seeds


title: ref6c 6h imbibed seeds seeds_rep3

source_name: ref6c 6h imbibed seeds


title: Col 24h imbibed seeds seeds_rep3

source_name: Col 24h imbibed seeds

value: wild type


title: ref6c 24h imbibed seeds seeds_rep1


title: ref6c 6h imbibed seeds seeds_rep2


title: ref6c 48h imbibed seeds seeds_rep3


title: Col 48h imbibed seeds seeds_rep3

source_name: Col 48h imbibed seeds


title: Col 48h imbibed seeds seeds_rep1


title: Col 48h imbibed seeds seeds_rep2


title: Col 24h imbibed seeds seeds_rep1


title: ref6c 0h imbibed seeds_rep1


title: Col 6h imbibed seeds seeds_rep3

source_name: Col 6h imbibed seeds


title: ref6c 0h imbibed seeds_rep3


title: Col 6h imbibed seeds seeds_rep2


title: Col 6h imbibed seeds seeds_rep1


title: ref6c 48h imbibed seeds seeds_rep1


title: 20180928-1-ZYQ

city: Fuzhou

first: Jinyan

address: No.7 Wusi Road

institute: Fufian Academy of Medical Sciences

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human lncRNA Arrays (4x44K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: Data was extracted using Agilent Feature Extraction software.A series of data processing including quantile normalization were performed using the R software package. The lncRNAs that at least 7 out of 14 samples have flags in P or M (defined by GeneSpring software) were retained for further differential analyses. Differentially expressed lncRNAs and mRNA with statistical significance between the two groups were identified through Volcano Plot filtering.

source_name: Peripheral Blood

label_protocol: Total RNA from each sample was amplified and transcribed into fluorescent cRNA utilizing ramdom primer according to Arraystar Super RNA Labeling protocol (Arraystar, Inc.)

extract_protocol: The plasma was separated and total RNA from plasma was isolated using TRIzol LS Reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions.

treatment_protocol: The venous blood of HCM patients and healthy controls was collected into BD Vacutainer Venous Blood Collection Tubes containing ethylenediaminetetraacetic acid (EDTA), respectively.

value: plasma

tag: diagnosis

value: Normal control


title: Col 0h imbibed seeds_rep3

source_name: Col 0h imbibed seeds


title: Col 0h imbibed seeds_rep2


title: Col 0h imbibed seeds_rep1


title: Col 24h imbibed seeds seeds_rep2


title: OsEMF2b_H3K27me3_ChIP_Rep2

city: Wuhan

first: yue

last: li

address: Shizishan Street

institute: HUAZHONG Agriculture University

data_processing:
Raw reads were filtered for adapter and low quality reads by Trimmomatic
Clean reads mapped to the reference genome with bwa mem
The reads with mapping quality lower 30 and duplication were filtered by samtools
MACS2 were used to call the peak
Assembly: Download the genome from http://rice.hzau.edu.cn/
Supplementary files format and content: bogWig file by deepTools bamCoverage

organism: Oryza sativa Japonica Group

source_name: seedling

extract_protocol:
Rice tissues were crosslinked with 1% formaldehyde and quenched with 0.2 M glycine.
0.5 to 1g of the sample was ground into a fine powder in liquid nitrogen, the chromatin was fragmented into 200-600 bp by ultrasound processing using Bioruptor (Diagenode). The lysates were incubated at 4 °C for 1 to 6 h and rotated to form antibody-bead complexes. After reverse cross-linking of DNA and protein, ChIP-DNA was extracted using phenol: chloroform: isoamyl alcohol (P3803; Sigma-Aldrich). ChIP-DNA libraries were prepared by Illumina® (New England BioLabs, E7645) using the NEBNext® Ultra™ II DNA Library Preparation Kit. AMPure XP beads (Beckman, A63881) were used to select 250-650 bp library fragments.

tag: cultivar

value: Dongjin

value: seedling

tag: chip antibody

value: H3K27me3 antibodies (Abclonal, A2363)


title: OsEMF2b_H3K27me3_ChIP_Rep1


title: 20180926-4-LBL

value: Human with familial hypertrophic cardiomyopathy

value: MYBPC3 gene mutations


title: CQH


title: 20180930-1-TXZ


title: OsEMF2b_H3K27me3_ChIA_Rep1

data_processing:
Raw ChIA-PET data were analysed using the ChIA-PET pipeline
PETs were  used for further classification as self-ligation,inter-ligation, and other PETs
Assembly: Download the genome from http://rice.hzau.edu.cn/
Supplementary files format and content: cluster.bedpe file was filtered with false discovery (FDR) > 0.05

extract_protocol:
Rice tissues were dual cross-linked with 1% formaldehyde (SIGMA, F8775) for 10 min and 1.5 mM ethylene glycol bis (succinimidylsuccinate) (Thermo Fisher Scientific, 21565) for 30 min at 25 ℃, after which glycine was added to a final concentration of 0.2 M to stop the cross-linking reaction.
pl-DNA was end-repaired, A-tailed, and proximity ligated using a single biotinylated bridge-linker (Forward strand: 5′-[5Phos]CGCGATATC/iBIOdT/TATCTGACT-3′, Reverse strand: 5′-[5Phos]GTCAGATAAGATATCGCGT-3′). Proximity ligated protein-DNA complexes were eluted and reverse cross-linked (similar to that in eChIP-Seq). Tn5 transposase (VAHTS， TD501) was used to prepare ChIA-PET libraries according to the operation manual, and the libraries were sequenced (paired end 150 bp) using an Illumina HiSeq X-Ten (AnnoRoad Company, Beijing, China).


title: DJ_H3K27me3_ChIA_Rep1


title: ref6c 6h imbibed seeds seeds_rep1


title: OsEMF2b_H3K27me3_ChIA_Rep2


title: 20180926-3-SXS


title: DJ_H3K27me3_ChIP_Rep2


title: DJ_H3K27me3_ChIA_Rep2


title: MLF


title: Δpfk2_c_2D_1

city: Tianjin

first: Yongli

last: Zhang

address: 32 West 7th Avenue, Tianjin Airport Economic Area

institute: Chinese Academy of Sciences

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence with NGSQCToolkit (v2.3).
Clear reads were mapped to Myceliophthora thermophila ATCC 42464 genome using Tophat (version 2.0.8b) with parameters -i 10 -g 1 --segment-length 24 --b2-very-sensitive --no-convert-bam --library-type fr-unstranded.
The counts of reads uniquely mapped to only one gene for each gene were calculated by HTseq-count( v0.5.4p2).
Assembly: Myceliophthora thermophila ATCC 42464(https://genome.jgi.doe.gov/Spoth2/Spoth2.home.html)
Supplementary files format and content: tab-delimited text files including Reads count for each sample.

organism: Thermothelomyces thermophilus ATCC 42464

source_name: Myceliophthora thermophila ATCC 42464

growth_protocol: The experiments were performed in 100 mL medium inoculated with 2.5×105 spores per milliliter in 250 mL Erlenmeyer flask shaken at 150 rpm. The minimal medium (per liter) contained 75 g glucose, 8 g yeast extract, 0.15 g KH2PO4, 0.15 g K2HPO4, 0.15 g MgSO4·7H2O, 0.1 g CaCl2·2H2O, 1 mL biotin (0.1 g/L), and 1 mL trace elements (Vogel’s salts). The culture was incubated at  45 °C.

extract_protocol:
Mycelia for RNA isolation were harvested at exponential growth phase (2 days and 4 days). After filtration, the collected mycelia were washed twice and immediately frozen in liquid nitrogen. The samples stored at -80 °C until RNA extraction. About 100mg frozen samples were quickly ground into powder in liquid nitrogen in the mortar. Total RNA was extracted from the powder using RNeasy mini kit (Qiagen) according to the manufacturer's instruction.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: mycelia

tag: timepoint

value: 2 days

value: pfk2-c ko


title: Δpfk2_a_4D_2

value: 4 days

value: pfk2-a ko


title: Δpfk2_abc_4D_2

value: pfk2-a/b/c ko


title: Δpfk2_c_4D_2


title: DJ_H3K27me3_ChIP_Rep1


title: Δpfk2_b_2D_2

value: pfk2-b ko


title: Δpfk2_abc_2D_1


title: Δpfk2_b_2D_1


title: Δpfk2_abc_2D_2


title: Δpfk2_abc_4D_1


title: Δpfk2_c_4D_1


title: WT_2D_2

value: WT


title: WT_4D_2


title: WT_4D_1


title: Δpfk2_a_4D_1


title: Δpfk2_a_2D_2


title: Δpfk2_c_2D_2


title: Δpfk2_a_2D_1


title: WT_2D_1


title: control_1_input

first: Xiao-ning

last: Gao

state: Beijing

address: 28 Fuxing Road

department: Department of Hematology

institute: Chinese PLA General Hospital

data_processing:
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter.
Then sequence quality of IP and Input samples were also verified using fastp.
We used HISAT2 (http://daehwankimlab.github.io/hisat2) to map reads to the reference genomeHomo sapiens (Version: v101). Mapped reads of IP and input libraries were provided for R package exomePeak (https://bioconductor.org/packages/exomePeak), which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software (http://www.igv.org). MEME (http://meme-suite.org) and HOMER (http://homer.ucsd.edu/homer/motif) were used for de novo and known motif finding followed by localization of the motif with respect to peak summit.
Called peaks were annotated by intersection with gene architecture using R package ChIPseeker (https://bioconductor.org/packages/ChIPseeker).
Library strategy: MeRIP-Seq

source_name: Homo sapiens

growth_protocol: Kasumi-1 cells were maintained in RPMI 1640 medium supplemented with 50 µg/ml streptomycin, 50 IU/ml penicillin and 10% fetal calf serum.

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure.
The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel. Poly (A) RNA is purified from 50μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 86℃ 7min. Then the cleaved RNA fragments were incubated for 2h at 4℃ with m6A-specific antibody (No. 202003, Synaptic Systems, Germany) in IP buffer (50 mM Tris-HCl, 750 mM NaCl and 0.5% Igepal CA-630). Then the IP RNA was reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

treatment_protocol: Kasumi-1 cells were seeded into 6-well plates overnight before transfection and the medium was changed approximately 12 to 16 hours after transfection. Forty-eight hours after shRNA transfection, cells were selected with puromycin (2 microgram per milliliter) for at least 24 hours before further investigations.

value: Homo sapiens

value: Kasumi-1 cell line

value: acute myeloblastic leukemia cell

value: stably transfected with scramble control shRNA

tag: rip antibody

value: none (input)


title: control_3_input


title: shWTAP_2_input

value: stably transfected with WTAP shRNA


title: control_3_IP


title: shWTAP_3_input


title: control_2_IP


title: control_1_IP


title: shWTAP_3_IP


title: shWTAP_2_IP


title: shWTAP_1_input


title: control_2_input


title: shWTAP_1_IP


title: HUVECs, miR-210-3p OE2

city: Shanghai

first: Han

last: Tang

address: No. 130, Dong’an Road, Xuhui district

department: Orthopedic Surgery

institute: Zhongshan Hospital, Fudan University, Shanghai, China

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 GrCM38/mm10 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: mm10
Supplementary files format and content: tab-delimited files include FPKM values for each Sample

source_name: HUVECs

growth_protocol: HUVECs were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 and 1% O2 at 37C

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany).
The library construction and sequencing were performed by Sinotech Genomics Co., Ltd (Shanghai, China).

treatment_protocol: The miR-210-3p mimic was synthesized by Ribobio (Guangzhou, China) and transfected into HUVECs using Lipo3000 (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's protocol.

value: HUVECs

value: human umbilical vein endothelial cells

value: miR-210-3p overexpression

value: 1% oxygen concentration

value: Day 3


title: HUVECs, Control3


title: HUVECs, miR-210-3p OE1


title: HUVECs, Control1


title: HUVECs, Control2


title: HUVECs, miR-210-3p OE3


title: Input

first: Shenglin

last: Huang

address: 270 Dongan

institute: Fudan University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using Bowtie2. Only uniquely mapping reads with at most two mismatches were retained.
Peaks were called uing MACS v1.4 with the significance cut-off p-value <=0.001
Assembly: hg38
Supplementary files format and content: narrowPeak (except for Input sample)

extract_protocol:
Chromatin and associated protein in live cells were cross-linked with formaldehyde, and then trimmed using sonication and micrococcal nuclease to generate DNA fragments. The antibodies of interest were used to immunoprecipitate the DNA-protein complex and then extracted DNA fragments.
ChIP-Seq library was prepared by KAPA kapa hyper prep kit

value: breast cancer cell line


title: HiPSC-CMs - Baseline - DIAPH1-2

city: New York

first: Raveena

last: Vakil

state: NY

address: 435 E 30th St

department: Diabetes Research Program

institute: NYU Langone Health

data_processing:
Trimmed low quality bases and removed adapter contamination with Trimmomatic 0.36 with parameters ILLUMINACLIP:adapters.fa:2:30:10:1:true TRAILING:5 SLIDINGWINDOW:4:15 MINLEN:35
Aligned reads to the human hg19 genome build using STAR 2.7.3a including parameters --outFilterMismatchNoverLmax 0.2 --outFilterMultimapNmax 1 --outFilterType BySJout --outSAMstrandField intronMotif --outSAMattributes NH HI AS nM NM MD XS --outSAMmapqUnique 60 --twopassMode Basic --quantMode GeneCounts --outSAMtype BAM Unsorted --outStd BAM_Unsorted
Sorted BAM files with samtools sort 1.9
Counted reads per gene (GENCODE 34lift37) using featureCounts function in subread 1.6.3 with parameter -p for paired-end
Normalized read counts by library size as log2(counts per million) with TMM normalization using edgeR 3.26.8
Assembly: hg19
Supplementary files format and content: Tab-delimited text files with raw read pair counts and log2(CPM) TMM-normalized read pair counts per gene (rows) per sample (columns)

source_name: HiPSC-CMs

growth_protocol: Human iPSCs were differentiated into functional cardiomyocytes characterized by beating phenotype and double positive for adult cardiomyocyte marker TNNI3 and TNT2 detected by flow cytometry. See methods section for more details

extract_protocol:
High quality RNA samples devoid of genomic DNA from shScr and shDIAPH1 silenced HiPSC-CMs was obtained using RNeasy Plus Mini Kit (QIAGEN, cat#74134). cDNA synthesis was performed using qScript™ cDNA SuperMix (Quanta BioSciences, Inc. cat # 95048). Before proceeding to RNAseq, samples were analyzed using Bioanalyzer High Sensitivity RNA Analysis. All samples used had a minimum RNA Integrity number (RIN) value of 9.5 or above.
Raw 52-bp paired-end Illumina read data were processed following standard quality control practices to remove low-quality reads and adapter sequence contamination. Remaining high-quality trimmed read pairs were aligned to the human genome (hg19) using STAR 2.7.3a, and read pair counts per gene were summed with the featureCounts function in subread 1.6.3 using the GENCODE 34lift37 annotation release to obtain a gene expression matrix9-11. Technical replicates across two Illumina sequencing batches were summed.

treatment_protocol: Silencing of gene was achieved using short hairpin Lentiviral particles for scrambled control or DIAPH1 silencing. Cells were exposed 30mins hypoxia at 0.1% oxygen and 1 hour reoxygenation (H/R) at 21% oxygen which was achieved using BioSpherix hypoxia chamber.

value: HiPSC-CMs

value: Cardiomyocytes

value: DIAPH1 knockdown

value: Baseline


title: HiPSC-CMs - Hypoxia/Reoxygenation  - H-R-DIAPH1-2

value: DIAPH1 knockdown & hypoxia

value: Hypoxia/Reoxygenation


title: HiPSC-CMs - Hypoxia/Reoxygenation  - H-R-Scr4

value: Scramble & hypoxia


title: HiPSC-CMs - Baseline - DIAPH1-1


title: HiPSC-CMs - Baseline - DIAPH1-4


title: HiPSC-CMs - Hypoxia/Reoxygenation  - H-R-DIAPH1-4


title: HiPSC-CMs - Hypoxia/Reoxygenation  - H-R-DIAPH1-3


title: H3K4me3

value: Cell signaling technology #9751


title: HiPSC-CMs - Hypoxia/Reoxygenation  - H-R-DIAPH1-1


title: HiPSC-CMs - Hypoxia/Reoxygenation  - H-R-Scr3


title: HiPSC-CMs - Baseline - DIAPH1-3


title: H3K27ac

value: Active motif #39133


title: HiPSC-CMs - Baseline - Scr4

value: Scramble


title: HiPSC-CMs - Hypoxia/Reoxygenation  - H-R-Scr1


title: HiPSC-CMs - Baseline - Scr3


title: HiPSC-CMs - Baseline - Scr1


title: HiPSC-CMs - Baseline - Scr2


title: HiPSC-CMs - Hypoxia/Reoxygenation  - H-R-Scr2


title: H3K4me1_GFP_C11orf53

city: Chicago

first: Lu

state: Illinois

address: 303 E. Superior Street Simpson Querrey 7-414

department: Biochemistry and Molecular Genetics

institute: Northwestern University

description: Cells transduced with lentivirus expressing GFP-tagged C11orf53

data_processing:
Basecalls were performed using bcl2fastq v2.17 for NextSeq output.
Both ChIP-seq and RNA-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to UCSC hg19 using Bowtie version 0.12.9.  Only uniquely mapping reads with at most two mismatches were retained.
RNA-seq reads were aligned to UCSC hg19 using Tophat version 2.0.9.  Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
To create RNA-seq coverage plots, the mapped RNA-seq reads were split according to strand, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Assembly: hg19
Supplementary files format and content: bigWig files were generated using the genomicRanges R package.  Score represents the normalized coverage of RNA or DNA fragments at a given genomic coordinate.

growth_protocol: Cells were maintained with either DMEM (Gibco, Gaithersburg, MD) or ATCC-formulated RPMI-1640 medium  containing 10% FBS (Sigma)

extract_protocol:
RNA was extracted using QIAGEN RNeasy kit. DNA after ChIP protocol was isolated using QIAGEN PCR purification kit. For ATAC-seq, frozen cells were thawed and washed once with PBS and then resuspended in 500 uL of cold ATAC lysis buffer. The cell number was assessed by Cellometer Auto 2000 (Nexcelom Bioscience). 50K to 100K nuclei were then centrifuge (pre-chilled) at 500 g for 10 min. Supernatant was then removed and the nuclei were resuspended in 50 uL of tagmentated DNA by pipetting up and down six times. The reactions were incubated at 37 °C for 30 min in a thermomixer shaking at 1,000 rpm, and then cleaned up by the MiniElute reaction clean up kit (Qiagen).
ChIP-seq: ChIP-sequencing libraries were prepared using KAPA HyperPrep Kit (Kapa Biosystems) following manufacturer’s recommendation. In brief, 500ng of input DNA sheared by Covaris LE220 ultrasonicator or 10 ng of immunoprecipitated DNA was end-repaired and 3'-dA tailed. Adapter was then ligated to the DNA, and ligated product was PCR amplified and cleaned up using SPRIselect Reagent (Beckman Coulter). for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250- 450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit. RNA-sequencing  libraries were prepared using the Illumina TruSeq Stranded Total RNA Preparation Kit with  Ribo-Depletion. Input RNA quality was validated using the Agilent RNA 6000 Nano Kit. 200ng-1 µg  of total RNA was used as starting material. Libraries were validated using the Agilent DNA  1000 Kit
RNA-seq: Paramagnetic beads coupled with oligo d(T) are combined with total RNA to isolate poly(A)+ transcripts based on NEBNext® Poly(A) mRNA Magnetic Isolation Module manual. Prior to first strand synthesis, samples are randomly primed (5´ d(N6) 3´ [N=A,C,G,T]) and fragmented based on manufacturer’s recommendation (NEBNext® Ultra™ II RNA Nondirectional Library Prep Kit for Illumina®). The first strand is synthesized with the Protoscript II Reverse Transcriptase with an longer extension period (40 minutes for 42◦C). All remaining steps for library construction were used according to the NEBNext® Ultra™ II RNA Nondirectional Library Prep Kit for Illumina®. Illumina 8-nt dual-indices were used. Samples were pooled and sequencing on a HiSeq with a read length configuration of 150 PE.
ATAC-seq: Tagmentated DNA was amplified with barcode primers. Library quality and quantity were assessed with Qubit 2.0 DNA HS Assay (ThermoFisher, Massachusetts, USA), Tapestation High Sensitivity D1000 Assay (Agilent Technologies, California, USA), and QuantStudio® 5 System (Applied Biosystems, California, USA). Equimolar pooling of libraries was performed based on QC values and sequenced on an Illumina® HiSeq (Illumina, California, USA) with a read length configuration of 150 PE for 50M PE reads (25M in each direction) per sample.

treatment_protocol: no treatment

value: Kidney cell line

tag: passages

value: Low passages (6-10)

value: anti-H3K4me1 (CST #5326)

value: GFP-C11orf53 overexpressing cells


title: sgPOU2F3-1_Rep2

description: cells transduced with POU2F3 specific sgRNA #1

data_processing:
Basecalls were performed using bcl2fastq v2.17 for NextSeq output.
Both ChIP-seq and RNA-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to UCSC hg19 using Bowtie version 0.12.9.  Only uniquely mapping reads with at most two mismatches were retained.
RNA-seq reads were aligned to UCSC hg19 using Tophat version 2.0.9.  Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
To create RNA-seq coverage plots, the mapped RNA-seq reads were split according to strand, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated using the genomicRanges R package.  Score represents the normalized coverage of RNA or DNA fragments at a given genomic coordinate.

tag: cell type

value: small cell lung cancer

value: POU2F3 depleted cells


title: sgPOU2F3-1_Rep1

tag: genotype


title: JQ1_Rep1

description: cells treated with JQ1 (1 mM)

value: normal cells


title: sgC11orf53-1_Rep1

description: cells transduced with C11orf53 specific sgRNA #1

value: C11orf53 depleted cells


title: sgC11orf53-2_Rep2

description: cells transduced with C11orf53 specific sgRNA #2


title: H3K4me1_GFP

description: Cells transduced with lentivirus expressing GFP

value: GFP overexpressing cells


title: DMSO_Rep2

description: cells treated with DMSO


title: sgC11orf53-2_Rep1


title: DMSO_Rep1

description: cells treated with DMSO


title: sgC11orf53-1_Rep2


title: sgPOU2F3-2_Rep2

description: cells transduced with POU2F3 specific sgRNA #2


title: sgPOU2F3-2_Rep1


title: H3K4me1_H211

description: normal cells


title: H3K27ac_H211

description: normal cells

value: anti-H3K27ac (CST #8173)


title: POU2F3_H211

description: normal cells

value: anti-POU2F3 (CST #36135)


title: C11orf53_Halo_POU2F3

description: Cells transduced with lentivirus expressing GFP-tagged C11orf53 and Halo-tagged POU2F3

value: anti-C11orf53-Ab2 (home made)

value: GFP-C11orf53 and Halo-POU2F3 overexpressing cells


title: H3K27ac_GFP


title: C11orf53_H211

description: normal cells


title: H3K27ac_GFP_C11orf53


title: C11orf53_Halo

description: Cells transduced with lentivirus expressing GFP-tagged C11orf53 and Halo-tag

value: GFP-C11orf53 and Halo overexpressing cells


title: sgNONT_Rep2

description: cells transduced with non-targeting shRNA


title: sgNONT_Rep1


title: genomic DNA from ischemic stroke patients 2 [HM]

type: genomic

city: Zhengzhou

first: Yang

last: Liu

state: Henan

address: No.100 science avenue

department: Medical Genetics

institute: Zhengzhou University

description: ischemic stroke patients

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 850k Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: genomestudio software; Unmethylated and methylated signal intensities

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from blood samples using Tiangen DNeasy Kit according to standard instructions

tag: gender

value: Female

tag: sample type

value: blood

tag: disease state

value: ischemic stroke patient


title: ATAC_sgC11orf53-2

tag: strain


title: ATAC_sgC11orf53-1


title: H3K4me1_sgNONT


title: Input_sgNONT


title: Input_sgC11orf53-1


title: H3K27Ac_sgC11orf53-2

value: anti-H3K27Ac (CST #8173)


title: genomic DNA from healthy people 3 [ZSS]

description: normal people

source_name: genomic DNA from healthy people

value: healthy control


title: Input_sgC11orf53-2

value: Low passages (6-10)


title: H3K4me1_sgC11orf53-2

value: anti-H3K4me1 (CST #5326)


title: H3K4me1_sgC11orf53-1

value: small cell lung cancer


title: H526_Input

description: normal cells


title: H3K27Ac_sgC11orf53-1


title: ATAC_sgNONT


title: H526_C11orf53-Ab2

description: normal cells


title: H3K27Ac_sgNONT


title: H526_H3K4me1

description: normal cells


title: genomic DNA from ischemic stroke patients 1 [RWH]

description: ischemic stroke patients

value: Male


title: H526_POU2F3

description: normal cells

value: normal cells


title: genomic DNA from ischemic stroke patients 3 [ZM]

description: ischemic stroke patients


title: A999

city: Leicester

first: Shu

last: Ye

state: Leicestershire

address: British Heart Foundation Cardiovascular Research Centre, Department of Cardiovascular Sciences, University of Leicester, Glenfield General Hospital

institute: University of Leicester

data_processing:
Illumina Casava1.7 software used for basecalling.
Read quality was checked with FastQC. Adapters were trimmed with BBMap.
Reads were mapped with STAR v2.7.1a
SAMtools v1.9 was used for processing aligned reads.
Rsubread was used to obtain raw read counts
Genome_build: GRCh38
Supplementary_files_format_and_content: Table and individual files of raw gene counts in all samples

source_name: Vascular Smooth Muscle Cells

extract_protocol:
Total RNA was extracted from an aliquot of passage-3 VSMCs stored with the use of the Biobasic EZ-10 DNAaway RNA miniprep kit (Biobasic), according to the manufacturer’s protocol with additional wash steps to ensure complete removal of residual salts from the samples
A strand specific library with rRNA removal was prepared from total RNA of each of the 1,499 VSMC samples, and 150bp paired-end sequencing at 30 million read depth was performed.

tag: source tissue

value: Umbilical cord artery

value: Vascular Smooth Muscle Cells


title: H526_H3K27me3

last: Wang

description: normal cells


title: H526_H3K27Ac

description: normal cells


title: H526_C11orf53-Ab1

description: normal cells

value: anti-C11orf53-Ab1 (home made)


title: H526_H3K4me3

description: normal cells

value: anti-H3K4me3 (CST #9751)


title: A998


title: A994


title: A995


title: A984


title: A981


title: A993


title: genomic DNA from healthy people 2 [YXG]

description: normal people


title: A992


title: A985


title: A983


title: A980


title: A989


title: A982


title: A987


title: A986


title: A991


title: A978


title: genomic DNA from healthy people 1 [ZXJ]

description: normal people


title: A973


title: A977


title: A974


title: A976


title: A975


title: A972


title: A988


title: A971


title: A968


title: A969


title: A967


title: A979


title: A966


title: A965


title: A963


title: A959


title: A964


title: A958


title: A954


title: A970


title: A953


title: A957


title: A961


title: A949


title: A952


title: A950


title: A951


title: A955


title: A948


title: A947


title: A962


title: A944


title: A945


title: A942


title: A941


title: A956


title: A960


title: JQ1_Rep2

description: cells treated with JQ1 (1 mM)


title: A939


title: A931


title: A938


title: A946


title: A928


title: A930


title: A933


title: A936


title: A943


title: A940


title: A921


title: A925


title: A922


title: A920


title: A923


title: A924


title: A919


title: A937


title: A918


title: A914


title: A935


title: A916


title: A917


title: A913


title: A932


title: A934


title: A927


title: A929


title: A926


title: A912


title: A909


title: A903


title: A910


title: A906


title: A902


title: A908


title: A904


title: A907


title: A901


title: A899


title: A896


title: A897


title: A900


title: A893


title: A891


title: A892


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title: A1541


title: A1509


title: A1508


title: A1540


title: A1531


title: A1533


title: A1530


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title: A1502


title: A1535


title: A1495


title: A1494


title: A1511


title: A1521


title: A1493


title: A1518


title: P. aeruginosa - ∆algR rep-2

city: Hong Kong

first: Xin

last: DENG

address: 1/F, Block 1, To Yuen Building, City University of Hong Kong, 31 To Yuen Street, Kowloon Tong

department: Department of Biomedical Sciences

country: Hong Kong

institute: City University of Hong Kong

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to P. aeruginosa and P. syringae whole genome using bowtie2
The Deeptools was used to visulized the RNA desinty
Genome_build: P. syringae 1448A
Genome_build: P. aeruginosa PAO1
Supplementary_files_format_and_content: Bigwig files for RNA density for each strand

organism: Pseudomonas aeruginosa

extract_protocol:
The LM-seq procedure was done following a previous study with slight modification (Hou et al., 2015). In brief, the overnight culture was transferred to a fresh medium (1:100). Until the OD600 reached 0.6, the strain was pelleted and washed before RNA extraction using bacteria total RNA isolation kit (Sangon Biotech).
RNA libraries were prepared for sequencing using LM-seq protocols

value: {delta}algR


title: A1492


title: A1490


title: A1507


title: A1488


title: A1505


title: A1520


title: A1506


title: A1487


title: A1504


title: A1503


title: A1500


title: A1486


title: A1485


title: A1510


title: A1491


title: A1498


title: A1483


title: A1482


title: A1480


title: A1496


title: P. aeruginosa - WT rep-2

value: wild type


title: P. aeruginosa - ∆algR rep-1


title: A1473


title: A1471


title: A1489


title: A1467


title: A1464


title: A1463


title: A1477


title: A1461


title: A1462


title: AjapCNR, replicate 1, scRNAseq

city: Qingdao

first: Yingqiu

last: Zheng

address: Yushan Road 5

institute: Ocean university of China

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Assembly: CNGBdb Accession Number: CNP0002776 (https://db.cngb.org/)
Supplementary files format and content: Tab-separated values files and matrix files

organism: Apostichopus japonicus

source_name: circumoral nerve ring

extract_protocol:
Fresh CNR tissue was incubated with 2 mg/ml Papain in HE-Ca solution at 37 °C for 20 min and rinsed with Hibernate E®/B27®/GlutaMAX™ (HEB) medium. The single-cell suspension was filtered through a 40 µm cell strainer.  Cell concentration and viability were determined with a Countess® II automated cell counter and 0.4% trypan blue staining. The cell suspension at a concentration of ~1000 cells/µL and cell viability > 90% was ready for scRNA-seq.
Cellular suspensions were loaded on a 10X Genomics GemCode Single-cell instrument that generates single-cell Gel Bead-In-EMlusion (GEMs). Libraries were prepared using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1. Every single cell was coated with unique primers containing (i) an Illumina® R1 sequence (read 1 sequencing primer), (ii) a 16 nt 10x Barcode, (iii) a 10 nt Unique Molecular Identifier (UMI), and (iv) a poly-dT primer sequence. Then, Reversed transcription to cDNA and made an amplification in a Veriti rapid thermal cycler (Applied Biosystems, Foster City, CA, USA).

tag: tissue

value: circumoral nerve ring


title: A1457


title: A1479


title: A1458


title: A1460


title: A1481


title: A1455


title: A1474


title: A1475


title: A1468


title: A1456


title: A1453


title: A1470


title: A1476


title: A1478


title: P. aeruginosa - WT rep-1


title: A1452


title: A1465


title: A1484


title: A1466


title: A1450


title: A1472


title: A1469


title: A1447


title: A1446


title: A1454


title: A1459


title: A1445


title: A1451


title: A1443


title: A1448


title: A1449


title: A1442


title: A1439


title: A1441


title: A1438


title: A1437


title: A1436


title: liver tissue, OE(KO) I/R, 2

first: Sanyang

address: No. 1, Jianshe Road, Erqi District

institute: The First Affiliated Hospital of Zhengzhou University

data_processing:
Raw reads of fastq format were firstly processed using fastp.
The low quality reads were removed to obtain the clean reads.
The clean reads were mapped toGRCm39 using HISAT2.
FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count.
PCA analysis were performed using R(v 3.2.0) to evaluate the biological duplication of samples.Differential expression analysis was performed using the DESeq2. P value < 0.05 and foldchange > 2 or foldchange < 0.5 was set as the threshold for significantly differential expression gene (DEGs).
Assembly: GRCm39
Supplementary files format and content: Excel file includes FPKM values for each Sample

source_name: liver

growth_protocol: Male C57 BL/6 mice and MIF knock out (KO) mice (C57 BL/6 background as previously described)(16) aged 8-10 weeks (25 ± 2 g) were housed in a specific pathogen-free (SPF) facility under a controlled environment with 12-h light/dark photocycle (temperature, 23 ± 2 ℃). Food and water were available ad libitum throughout the study period. Animals received human care in adherence with the “Guide for the Care and Use of Laboratory Animals” prepared by the National Academy of Sciences and published by the National Institutes of Health (NIH; publication 86-23 revised in 1985).

extract_protocol:
Total RNA was isolated using mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol. 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

treatment_protocol: Partial (70%) liver warm ischemia mouse model was established as previously described(1). Briefly, mice were first anesthetized by pentobarbital sodium (60 mg/kg; Sigma) and subjected to midline laparotomy. A microvascular clip was used to clamp the left and middle portal vein and hepatic artery branches to interrupt the blood supply of the liver. After 1 h of ischemia, the clamp was removed for reperfusion. After 6 h reperfusion, the animals were sacrificed to collect liver and serum samples for further analysis. The residual blood was discharged by portal vein injection of normal saline.

value: liver

value: MIF-KO

tag: treatment

value: liver I/R treatment


title: A1440


title: liver tissue, N3(WT) I/R

value: WT

tag: time


title: liver tissue, N1(WT) I/R


title: 6_6_IMISol_1_day

city: Mainz

first: Matthias

last: Klein

address: Langenbeckstrasse 1

department: Inst. for Immunology

country: Germany

institute: University Medical Center Mainz

data_processing:
Sequence reads were trimmed for adapter sequences and further processed using the software CLC Genomics workbench (v12.0 with CLC's default settings for RNA-Seq analysis). Reads were aligned to GRCm38 genome. Expression value unit is RPKM.
Genome_build: GRCm38
Supplementary_files_format_and_content: "Expression value"      "TPM"   "RPKM"

source_name: Murine ear skin

extract_protocol:
Total RNA was isolated using RNeasy plus micro kit (Qiagen). Quantity of total RNA was assessed with the Qubit 2.0 and quality was checked using a RNA 6000 Nano chip on Agilent's bioanalyzer.
Barcoded mRNA seq libraries were prepared from 250 ng total RNA using a NEBNext® Poly(A) mRNA Magnetic Isolation Module and NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® according to the manual (with a final amplification of 12 cycles) . Concentration was determined using Invitrogen’s Qubit HS assay and fragment size was analyzed on Agilent’s 2100 Bioanalyzer on a HS DNA chip.

treatment_protocol:
25mg dithranol-vaseline (1/16%) or IMI-Sol (containing 5% imiquimod), topically applied on murine ear skin for 24 hours
Murine ears were treated topically with either 25mg dithranol-vaseline (1/16 %) or 50mg IMI-Sol (containing 5 % imiquimod). 24 hours after the treatment mice were sacrificed and RNA was extracted from dithranol or IMI-Sol treated murine ear skin.

value: Wildtype

tag: agent

value: IMI-Sol


title: liver tissue, OE(KO) I/R, 1


title: liver tissue, N2(WT) I/R


title: A1433


title: liver tissue, OE(KO) I/R, 3


title: A1430


title: 4_4_IMISol_1_day


title: DN thymocytes Toxf/fPdcd1Cre rep3

city: Nanjing

first: qifeng

last: he

state: JIANGSU

address: zhongshan Road

department: general surgery

institute: nanjing university

data_processing:
to get high quality clean reads, reads were further filtered by fastp (version 0.18.0). The parameters were as follows:
1) removing reads containing adapters;
2) removing reads containing more than 10% of unknown nucleotides (N);
3) removing low quality reads containing more than 50% of low quality (Q-value≤20) bases.
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2. 2.4 with “-rna-strandness RF” and other parameters set as a default.
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach. For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using StringTie software.
Genome_build: Ensembl_release100
Supplementary_files_format_and_content: tab-delimited text files include fpkm,count values and symbol of genes for each Sample

source_name: Thymus

extract_protocol:
Thymi were obtained and prepared for FACS sorting, and the pellets of sorted DN2 thymocytes were frozen on dry ice. RNA was extracted using Trizol reagent. The NEBNext Ultra RNA Library Prep Kit for Illumina (NEB #7530) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: age


title: A1431


title: A1428


title: A1429


title: A1434


title: DN thymocytes Toxf/f rep3

value: Toxf/f


title: DN thymocytes Toxf/fPdcd1Cre rep1


title: 2_2_Anthralin_1_day

value: dithranol-vaseline


title: 1_1_Anthralin_1_day


title: A1432


title: DN thymocytes Toxf/fPdcd1Cre rep2


title: DN thymocytes Toxf/f rep1


title: DN thymocytes Toxf/f rep2


title: A1425


title: A1424


title: A1426


title: A1421


title: 3_3_Anthralin_1_day


title: A1422


title: A1427


title: db_m-3

city: Kyoto

first: Tetsuro

last: Kusaba

state: Kyoto

address: 465 Kajii-cho, Kamigyo-ku

department: Department of Nephrology

country: Japan

institute: Graduate School of Medical Science, Kyoto Prefectural University of Medicine

data_processing:
Sequenced reads were mapped to the mouse reference genome sequences (mm10) using TopHat v 2.0.13 in combination with Bowtie2 ver. 2.2.3 and SAMtools ver. 0.1.19. The fragments per kilobase of exon per million mapped fragments (FPKMs) was calculated using Cufflinks version 2.2.1.
Genome_build: mm10
Supplementary_files_format_and_content: fpkm

source_name: Kidney

extract_protocol:
Total RNA was isolated from the kidneys using TRIzol (Life Technologies, Inc., Carlsbad, CA) and Direct-zol RNA MiniPrep (Zymo Research Corporation., Irvine, CA) according to the manufacturer's protocol.
The Library preparation was performed using a TruSeq stranded mRNA sample prep kit (Illumina, San Diego, CA) according to the manufacturer's instructions.
Sequencing was performed on an Illumina HiSeq 2500 platform in a 101 bp single-end mode.

tag: surgery

value: db/m

value: Kidney


title: db_db-3

value: db/db


title: 5_5_IMISol_1_day


title: db_m-1


title: db_m-2


title: db_db-1


title: A1416

value: Umbilical cord artery

value: Vascular Smooth Muscle Cells


title: A1414


title: SJG17-AG-AG_plate3_ADT

city: NIJMEGEN

first: Dyah

last: Karjosukarso

address: Geert Grooteplein Zuid 28

country: Netherlands

institute: Radboud University

data_processing:
The sequence data were demultiplexed using bcl2fastq software (Illumina). RNA sequence data were processed using CELseq2 pipeline (Hashimshony et al., 2016) which includes demultiplexing based on cell barcodes, mapping to GRCh38 using Bowtie2 and UMI counting by HTseq. Antibody-derived tags (ADT) sequence data were subjected to CITE-seq -Count pipeline (Roelli, bbimber, Flynn, santiagorevale, & Gui, 2019) with the following settings (--max-error 1 --bc_collapsing_dist 1 --umi_collapsing_dist 1).
Assembly: hg38
Supplementary files format and content: tab separated count files

extract_protocol:
The RAID staining was performed as previously described (Gerlach et al., 2019). Briefly, cultured cells were dissociated, followed by fixation with 2.5 mM DSP and 2.5 mM SPDP in sodium phosphate buffered saline (pH 8.4) for 45 minutes at RT. The fixation was quenched by adding 100 mM Tris-HCl pH 7.5 and 150 mM NaCl for 10 minutes. Subsequently, the cells were blocked and permeabilized for 30 min at RT in a mix of 0.5x PFBB (protein free blocking buffer, Thermo Fisher Scientific) in PBS supplemented with 10 µg/ml tRNA (Roche), 0.5 U/µl RNAsin Plus (Promega) and 0.1% Triton X-100. The panel of ssDNA-labelled antibodies was mixed with 2 U/µl RNAsin Plus (Promega) and 0.1% Triton X-100 in PBS:PFBB (1:1) and used to stain the cells. The staining was performed overnight at 4°C on a rotating mixer. To remove unbound antibodies, the cells were washed four times after the staining with a wash-buffer (10% PFBB and 0.05% Triton X-100 in PBS). Subsequently, the cells were washed two more times in 10% PFBB in PBS, followed by single cell sorting (BD FACS Aria) into 384-well plates containing CEL-seq2 primers.
The library preparation is based on the previously published protocol (Gerlach et al., 2019), with some adaptations. ERCC spike-in (1:100,000 dilution, Thermo Fisher Scientific) was added to the reverse crosslinking mix. The transcriptome and antibody barcodes were separated by performing a double bead-purification after first strand synthesis and pooling. The RNAs were selected using a 0.6x Ampure XP bead ratio (Beckman Coulter) purification, while the antibody barcodes were selected through 2.0x Ampure XP bead ratio purification. The RNAs were subsequently subjected to second strand synthesis and in vitro transcription as previously described (Gerlach et al., 2019). The antibody barcode part was first linearly amplified using FWD pre-amplification primer (5’ CACGACGCTCTTCCGATCT 3’) for 10 cycles followed by addition of T7 primer (5’ GCCGGTAATACGACTCACTATAGGG 3’) for 2 cycles to generate dsDNA. The dsDNA generated was then subjected to in vitro transcription using Megascript T7 transcription kit (Thermo Fisher Scientific). The amplified RNA from the transcriptome part and antibody barcode part was subjected to reverse transcription primed with random octamer with FWD handle (5’ CACGACGCTCTTCCGATCTNNNNNNNN 3’) and FWD pre-amplification primer (5’ CACGACGCTCTTCCGATCT 3’), respectively. Subsequently, the cDNA was amplified followed by Illumina sequencing index addition as previously described (Gerlach et al., 2019). The sequencing was performed with Illumina Nextseq 500.

tag: cell line

value: HNSCC


title: db_db-2


title: A1419


title: A1420


title: SJG17_AG-DMSO_plate3_ADT

value: AG1478 + DMSO


title: A1413


title: A1410


title: A1409


title: db_db_dap-2

value: db/db + Dapa


title: SJG17_AG-DMSO_plate1_ADT


title: A1407


title: db_db_dap-1


title: A1406


title: A1417


title: db_db_dap-3


title: A1404


title: SJG17-AG-AG_plate2_ADT


title: SJG17_NT-DMSO_plate2_ADT

value: no treatment + DMSO


title: A1402


title: SJG17_NT-DMSO_plate1_ADT


title: A1412


title: A1418


title: SJG17-AG-AG_plate1_ADT


title: A1415


title: A1408


title: A1397


title: SJG17_AG-DMSO_plate2_ADT


title: A1398


title: SJG17_NT-AG_plate2_ADT

value: no treatment + AG1478


title: SJG17_NT-AG_plate1_ADT


title: SJG17_NT-AG_plate3_ADT


title: A1405


title: SJG17_NT-DMSO_plate3_ADT


title: SJG17-AG-AG_plate3_mRNA


title: A1401


title: SJG17-AG-AG_plate2_mRNA


title: A1399


title: SJG17-AG-AG_plate1_mRNA


title: SJG17_AG-DMSO_plate3_mRNA


title: A1391


title: A1400


title: SJG17_AG-DMSO_plate2_mRNA


title: A1395


title: A1393


title: SJG17_AG-DMSO_plate1_mRNA


title: SJG17_NT-AG_plate3_mRNA


title: SJG26-AG-AG_plate2_ADT


title: SJG17_NT-DMSO_plate1_mRNA


title: A1392


title: SJG17_NT-DMSO_plate2_mRNA


title: SJG17_NT-DMSO_plate3_mRNA


title: A1386


title: A1385


title: SJG17_NT-AG_plate1_mRNA


title: SJG26_AG-DMSO_plate3_ADT


title: A1396


title: A1383


title: A1387


title: SJG17_NT-AG_plate2_mRNA


title: A1390


title: SJG26-AG-AG_plate1_ADT


title: A1382


title: SJG26_AG-DMSO_plate1_ADT


title: A1389


title: SJG26_AG-DMSO_plate2_ADT


title: A1379


title: A1435


title: SJG26_NT-AG_plate1_ADT


title: A1380


title: SJG26_NT-AG_plate3_ADT


title: A1378


title: SJG26_NT-AG_plate2_ADT


title: A1377


title: A1376


title: SJG26_NT-DMSO_plate2_ADT


title: SJG26_NT-DMSO_plate3_ADT


title: A1388


title: A1375


title: A1374


title: SJG26-AG-AG_plate3_mRNA


title: SJG26-AG-AG_plate2_mRNA


title: A1371


title: A1373


title: A1444


title: SJG26_AG-DMSO_plate2_mRNA


title: SJG26_NT-DMSO_plate1_ADT


title: SJG26_AG-DMSO_plate3_mRNA


title: A1370


title: A1365


title: A1364


title: A1366


title: SJG26_AG-DMSO_plate1_mRNA


title: A1368


title: SJG26_NT-AG_plate3_mRNA


title: SJG26_NT-DMSO_plate1_mRNA


title: SJG26_NT-DMSO_plate2_mRNA


title: A1361


title: SJG26-AG-AG_plate1_mRNA


title: A1363


title: A1369


title: A1381


title: SJG26_NT-AG_plate2_mRNA


title: SJG17_RAG_plate1_ADT

value: Radiation + AG1478


title: SJG26_NT-AG_plate1_mRNA


title: A1372


title: SJG17_R_plate3_ADT

value: Radiation


title: A1359


title: SJG26_NT-DMSO_plate3_mRNA


title: A1362


title: A1360


title: SJG17_RAG_plate3_ADT


title: SJG17_AG_plate1_ADT


title: SJG17_NT_plate1_ADT

value: no treatment


title: A1353


title: SJG17_NT_plate2_ADT


title: SJG17_R_plate2_ADT


title: A1351


title: SJG17_RAG_plate2_ADT


title: A1356


title: SJG17_RAG_plate3_mRNA


title: A1367


title: SJG17_NT_plate3_ADT


title: SJG17_RAG_plate1_mRNA


title: SJG17_AG_plate2_ADT


title: A1350


title: SJG17_R_plate1_ADT


title: A1358


title: A1354


title: A1355


title: A1357


title: A1346


title: SJG17_R_plate3_mRNA


title: A1347


title: A1345


title: SJG17_R_plate2_mRNA


title: A1348


title: A1352


title: A1349


title: A1344


title: SJG17_RAG_plate2_mRNA


title: A1338


title: SJG17_AG_plate2_mRNA


title: SJG26_RAG_plate2_ADT


title: SJG17_R_plate1_mRNA


title: SJG17_NT_plate3_mRNA


title: SJG17_AG_plate1_mRNA


title: A1343


title: SJG26_R_plate3_ADT


title: A1342


title: SJG26_R_plate1_ADT


title: SJG26_AG_plate3_ADT


title: SJG17_NT_plate2_mRNA


title: A1335


title: SJG26_RAG_plate3_ADT


title: SJG26_AG_plate1_ADT


title: A1339


title: A1333


title: SJG26_AG_plate2_ADT


title: A1340


title: A1337


title: A1331


title: SJG26_R_plate2_ADT


title: SJG26_NT_plate1_ADT


title: A1334


title: A1332


title: SJG17_NT_plate1_mRNA


title: SJG26_RAG_plate3_mRNA


title: A1329


title: SJG26_RAG_plate2_mRNA


title: SJG26_RAG_plate1_ADT


title: SJG26_NT_plate2_ADT


title: A1330


title: A1336


title: SJG26_RAG_plate1_mRNA


title: A1326


title: A1423


title: SJG26_R_plate2_mRNA


title: A1323


title: SJG26_R_plate1_mRNA


title: SJG26_AG_plate3_mRNA


title: SJG26_NT_plate3_ADT


title: A1327


title: A1328


title: SJG26_R_plate3_mRNA


title: A1324


title: A1325


title: A1320


title: A1322


title: SJG26_NT_plate2_mRNA


title: A1341


title: SJG26_AG_plate1_mRNA


title: A1319


title: SJG26_NT_plate3_mRNA


title: A1317


title: A1318


title: SJG17_RAG_rep1

data_processing:
The obtained bulk RNA sequencing data were demultiplexed with bcl2fastq software (Illumina) and mapped to GRCh38 using STAR version 2.7.9a (Dobin et al., 2013).
The obtained count tables were further analysed using DEseq2 (version 1.30.1) (Love, Huber, & Anders, 2014).
Assembly: hg38
Supplementary files format and content: tab delimited file of counts

source_name: HSNCC

extract_protocol:
The RNA isolation was performed using Quick-RNA Miniprep kit (Zymo Research), following manufacturer’s instructions.
Sequencing libraries were prepared using KAPA RNA Hyperprep kith with Riboerase (Roche) without alteration to the provided manual. The libraries were sequenced on Illumina Nextseq 500.

value: HSNCC


title: A1316


title: A1315


title: SJG17_R_rep1

value: radiation


title: SJG17_R_rep2


title: SJG26_AG_plate2_mRNA


title: A1313


title: A1321


title: A1311


title: A1312


title: SJG17_AG_rep2


title: A1310


title: A1314


title: SJG26_NT_plate1_mRNA


title: A1308


title: SJG17_AG_rep1


title: SJG17_RAG_rep2


title: SJG17_NT_rep2

value: NT


title: SJG17_NT_rep1


title: SJG26_RAG_rep2


title: SJG26_RAG_rep1


title: A1307


title: SJG26_R_rep1


title: SJG26_R_rep2


title: SJG26_AG_rep2


title: A1306


title: SJG26_NT_rep2


title: A1303


title: A1302


title: A1309


title: POI patient with Turner syndrome Turner_7

city: Incheon

first: meesup

last: Yoon

address: 155,Gaebeol-ro, yenosu-gu

institute: Gachon university

description: Exosomal RNA

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hsa (miRBase) using Bowtie2
Read count extraction using bedtools.
Assembly: has
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: POI patient with Turner syndrome

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). Exosomal RNA was isolated using TRIzol LS reagent (Ambion). Total RNA was extracted from 200㎕ serum/plasma using miRNeasy Serum/Plasma Kit (Quaigen). Total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using NEBNext Multiplex SmallRNA Library Prep Kit (New England BioLabs) standard protocols.

value: urine


title: SJG26_AG_rep1


title: SJG26_NT_rep1


title: POI patient with Turner syndrome Turner_6

description: Exosomal RNA


title: A1301


title: A1299


title: A1297


title: A1305


title: POI patient with Turner syndrome Turner_5

description: Exosomal RNA


title: A1296


title: POI patient with Turner syndrome Turner_3

description: Exosomal RNA


title: A1298


title: POI patient with Turner syndrome Turner_1

description: Exosomal RNA


title: POI patient with Turner syndrome Turner_4

description: Exosomal RNA


title: A1294


title: A1293


title: POI patient without Turner syndrome POI_6

description: Exosomal RNA

source_name: POI patient without Turner syndrome


title: A1304


title: POI patient without Turner syndrome POI_4

description: Exosomal RNA


title: POI patient without Turner syndrome POI_5

description: Exosomal RNA


title: A1300


title: POI patient without Turner syndrome POI_7

description: Exosomal RNA


title: A1295


title: normal individual N_6

description: Exosomal RNA

source_name: normal individual


title: POI patient with Turner syndrome Turner_2

description: Exosomal RNA


title: POI patient without Turner syndrome POI_3

description: Exosomal RNA


title: POI patient without Turner syndrome POI_2

description: Exosomal RNA


title: A1287


title: A1281


title: A1292


title: A1289


title: normal individual N_2

description: Exosomal RNA


title: A1279


title: A1280


title: A1288


title: A1284


title: siRNAaRNF4_7d_of_osteogenesis_4

city: Haifa

first: Amir

last: Orian

address: Efron 1

country: Israel

institute: technion

data_processing:
Quality control for total RNA was performed using TapeStation (Agilent). The RINe value of all samples was in the range of 8.0-9.8, indicates that all samples have a good quality
Quality control was assessed using Fastqc (v0.11.5), reads were trimmed for adapters, low quality 3` and minimum length of 20 using CUTADAPT (v1.12).
80 bp single-end reads were aligned to human reference genome (Homo_sapiens.GRCh38.dna.primary_assembly.fa downloaded from ENSEMBL) and annotation file (Homo_sapiens.GRCh38.92.gtf downloaded from ENSEMBL) using STAR aligner (v2.6.0a).
The number of reads per gene was counted using Htseq (v0.9.1).
A statistical analysis was preformed using DESeq2 R package (version 1.18.1) (Genome Biology 2014 15:550). The number of reads per gene was extracted into Count.xls and NormalizedCounts.xls files for raw counts and normalized counts, respectively
Assembly: Homo_sapiens.GRCh38

source_name: mesenchymal stem cells

growth_protocol: hBMSCs were cultured in Minimum Essential Medium-Alpha (αMEM) supplemented with 10% Fetal Bovine Serum (FBS), 2mM L-glutamine and Pen-Strep (both 100U/ml)

extract_protocol:
RNA was extracted with Rneasy Mini Kit (Qiagene)
12 RNAseq libraries (NEBNext UltraII Directional RNA Library Prep Kit for Illumina, cat no. E7760) were produced according to manufacture protocol using 800 ng total RNA. mRNAs pull-up was performed using Magnetic Isolation Module (NEB, cat no. E7490). All 12 libraries were mixed into a single tube with equal molarity. The RNAseq data was generated on Illumina NextSeq500, 75 cycles, high-output mode (Illumina, cat no. FC-404-2005).

treatment_protocol: hBMSCs were cultured in the osteogenic induction conditions (culture medium supplemented with 100ug/ml ascorbic acid-magnesium and 10-8M dexamethasone, 10mM sodium β-glycerophosphate).

value: mesenchymal stem cells

value: KD RNF4 day 7

value: Osteogenic Differentiation


title: scrambled_7d_of_osteogenesis_4

value: WT day 7


title: A1285

value: Umbilical cord artery

value: Vascular Smooth Muscle Cells


title: A1291


title: A1278


title: A1277


title: A1286


title: scrambled_untreated_4

value: WT day 0


title: A1275


title: A1282


title: A1274


title: scrambled_untreated_2


title: normal individual N_3

description: Exosomal RNA


title: normal individual N_5

description: Exosomal RNA


title: A1273


title: A1276


title: normal individual N_4

description: Exosomal RNA


title: A1272


title: siRNAaRNF4_untreated_4

value: KD RNF4 day 0


title: A1271


title: A1270


title: siRNAaRNF4_7d_of_osteogenesis_1


title: A1269


title: A1283