title: A_CTRL_3

value: vehicle


title: HTLV-1c-infected and Uninfected cells

status: Public on Dec 31 2025

type: SRA

city: Melbourne

first: James

middle: Patrick

last: Cooney

state: Victoria

address: 1G, Royal Parade, Parkville

country: Australia

institute: The Walter and Eliza Hall Institute

library_source: transcriptomic

data_processing:
Read alignment and count summarization were performed using CellRanger v3.1.0 using the Illumina BCL files as input.
Genome_build: GRCh38
Supplementary_files_format_and_content: The 'raw' data are that provided by CellRanger whereas the 'demultiplexed' and ‘filtered’ data are what was used for downstream analyses. Only the demultiplexed gene expression data have sample metadata (coldata.csv.gz)
Supplementary_files_format_and_content: matrix.csv.gz: Count matrix
Supplementary_files_format_and_content: barcodes.tsv.gz: Barcode data
Supplementary_files_format_and_content: features.tsv.gz: Feature data
Supplementary_files_format_and_content: coldata.csv.gz: Sample metadata
Supplementary_files_format_and_content: filtered_contig_annotations.csv.gz: CellRanger's filtered VDJ contig annotations

molecule: total RNA

organism: Homo sapiens

source_name: CD4+ T cell

extract_protocol:
Cells were isolated by FACS from bulk splenocytes. Single cell gel beads in emulsion (GEM) were generated in a 10X Chromium Controller (10X Genomics). cDNA from single cells were prepared as per 10X Genomics Chromium single cell 5' library preperation insturctions.
RNA libraries (GEX, VDJ, hashtag) were prepared following 10X Genomics Chromium single cell 5' library preperation insturctions
scRNA-seq

treatment_protocol: Cells were either mock-infected (PBS) or HTLV-1c-infected

tag: cell type

value: CD4+ memory T cell

tag: disease state

value: HTLV-1c-infected and Uninfected cells


title: hepa1-6-vector-2

city: Shanghai

first: guangchuan

last: Wang

state: Shanghai

address: 320 Yue Yang Road

country: China

institute: Chinese Academy of Sciences

data_processing:
HISAT2
Assembly: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file include RPKM values for each sample

organism: Mus musculus

source_name: cell

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

tag: tissue

value: cell

tag: cell line

value: Liver cancer cell

tag: genotype

value: WT

tag: treatment

value: Normal culture


title: A_SP-D_1

city: Odense M

first: Kim

last: Ravnskjaer

state: CA

address: Campusvej 55

department: Department of Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

data_processing:
Initial filtering for high-quality reads was perfomed using CutAdapt. STAR (v. 2.7.0a) was used for alligning reads to the hg38 genome, and featureCounts (v.2.0.0)  for read annotation using the GRCh38 gtf file.
Assembly: hg38
Supplementary files format and content: raw count matrix

molecule: polyA RNA

source_name: lung

growth_protocol: Non-small lung cancer cell line A549 was obtained from the ATCC (Middlesex, UK). All cells were cultured in RPMI-1640 medium, supplemented with 10% fetal bovine serum (FBS, 0010, ScienCell) and 1% penicillin-streptomycin (P/S, 0503, ScienCell).

extract_protocol:
Whole-cell RNA was extracted according to the manufacturer’s instructions by Trizol reagent (Ambion, Austin, TX). The Qubit 3.0 Fluorometer (Thermo Fisher Scientific) was used for RNA quantity measurement and RNA quality was measured by the Fragment Analyzer 5200 (Agilent, Santa Clara, CA).
According to the manufacture's protocol, libraries were constructed using the NEBNext Ultra RNA Library Prep Kit for Illumina and paired-end sequencing.

treatment_protocol: A549 cells were treated with recombinant human SP-D protein (10µg/ml) or vehicle for 48h. Vehicle treatment is the same volume of buffer used for elution of SP-D after purification.

value: lung

value: adenocarcinomic human alveolar basal epithelial cells

value: rhSP-D


title: MDA-MB-231 Control (Replicate 1 and 2 compilated)

city: Lille

first: Kekely

middle: Boanerges

last: Klouyovo

address: Bd du Professeur Jules Leclercq

country: France

institute: CANTHER UMR9020 CNRS U1277 Inserm

description:
Library name: Control_MDA_MB_231_(n=2)
IMPORTANT NOTE : The raw data files are no longer available. The processed data files provided in this submission are used twice in the metadata table because each processed data file represents a comparison between two conditions: Control vs H19 Overexpression. The files named “(n=2)” represent compiled replicates, while individual replicates are also included separately. Each comparison corresponds to a single processed data file.

data_processing:
1. Quality control of raw reads using FastQC.
2. Adapter trimming and filtering of low-quality reads using Trimmomatic.
3. Alignment of filtered reads to the reference genome (hg38/ GRC38, UCSC) using HISAT2.
4. Quantification of gene expression using FeatureCounts.
5. Differential expression analysis performed with DESeq2.
Assembly: hg38/ GRC38,UCSC
Supplementary files format and content: Processed data files are provided as .tsv files containing gene expression data (FPKM combined, Differentially Expressed Genes (DEGs), and Top Expressed Genes). Each file is named according to the comparison being made (e.g., Control vs H19 Overexpression) with replicate information included when applicable.

source_name: Breast

growth_protocol: MDA-MB-231 cells were maintained routinely in Roswell Park Memorial Institute medium GlutaMAX supplement (RPMI 1640 + GlutaMAX, Gibco®, #1870036) containing 10% fetal bovine serum (FBS) and 1% ZellShield (Gibco®, #13-0050). MCF-7 cells were maintained in Dulbecco’s Modified Eagle’s Medium low glucose (DMEM + GlutaMAX, Gibco®, #21885025) containing 10% FBS and 1% ZellShield.

extract_protocol:
RNA extraction was performed using Trizol/Chloroform protocol, and the RNA Integrity Number (RIN) was assessed with Bioanalyzer 2100 (Agilent Technologies).
Strand-specific cDNA library preparation was performed using the following steps: - Purification of poly-A containing mRNA molecules from total RNA. - mRNA fragmentation - Random primed cDNA synthesis (strand-specific) - Adapter ligation and adapter-specific PCR amplification

treatment_protocol: Cells were transfected with H19 plasmid (H19 overexpression) or emply plasmid (control) using Lipofectamine 2000 according to the manufacturer's instructions (Invitrogen, Thermo Fisher Scientific).

value: Breast

value: mesenchymal breast cancer cell

value: mock (control)

value: Transfected with emply plasmid

tag: batch


title: MDA-MB-231 Overexpressing H19 (Replicate 1 and 2 compilated)

description:
Library name: H19_MDA_MB_231_(n=2)
IMPORTANT NOTE : The raw data files are no longer available. The processed data files provided in this submission are used twice in the metadata table because each processed data file represents a comparison between two conditions: Control vs H19 Overexpression. The files named “(n=2)” represent compiled replicates, while individual replicates are also included separately. Each comparison corresponds to a single processed data file.

value: H19 overexpressed

value: Transfected with H19 plasmid


title: hepa1-6-vector-1


title: 6day_PCBP2_KD_b2

city: Fort Collins

first: Carol

middle: J

last: Wilusz

state: Colorado

address: 1682 Campus Delivery

department: Microbiology, Immunology and Patholgy

country: USA

institute: Colorado State University

data_processing:
Quality of sequence reads was assessed via FastQC v0.11.5.  Reads were trimmed of adaptor sequences and filtered for low-complexity or low-quality reads via Trimmomatic v0.32.  rRNA reads were filtered out using Bowtie2 v2.3.4.3 (Langmead and Salzberg, 2012) and a reference fasta file of mature 5S, 18S and 28S rRNA named mature_rRNA.fasta. Filtered reads were mapped to the hg19 genome using TopHat2 v2.0.12 (Kim et al., 2013) under default parameters.  The output .bam alignment files were converted to .bam.tdf format using igv-tools and read distributions were viewed on IGV v2.3.91.  RNA-seq alignment files in .sam format were utilized to calculate read counts associated with each transcript using HTSeq v0.11.1 (Anders et al., 2015), Samtools v1.9 (Li et al., 2009) and the hg19 genome feature file obtained from GENCODE (hg19, Ensembl 74).  The HTseq function htseq-count was used with the following options: --stranded=no --minaqual=20.  Raw counts generated by this analysis can be found in the documents 2day_raw_counts.txt and 6day_raw_counts.txt. Raw count data was filtered for detectable genes (> 30 total counts across all samples of a specified treatment), imported into R and analyzed using DESeq2 v1.22.1 (Love et al., 2014) under default parameters.  Results of the DESeq2 analysis can be found in the document 2day_DESeq_results.xlsx and 6day_DESeq_results.xlsx.
Genome_build: hg19
Supplementary_files_format_and_content: .tdf files: IGV-ready alignment files for individual samples.  *_HTseq_raw_counts.txt file: Tab-delimited text files of raw read counts generated by HTseq.   *_DESeq_results.xlsx: Excel files of DESeq2 results. hg19_gene_annotations.gtf.gz:  Gene annotation file used for calculating raw read counts with HTSeq. mature_rRNA.fasta.gz: Fasta file containing the mature rRNA sequences used for rRNA filtering.

source_name: induced pluripotent stem cell

growth_protocol: iPSCs (System Biosciences, #SC101A-iPSC, Lot #110415-01) were cultured on Matrigel (Corning #354277) in mTeSR1 media (STEMCELL Technologies, #85850) at 37°C in 5% CO2. Plates were coated with MatriGel in accordance with manufacturer protocols, MatriGel was diluted in DMEM/F12 (+ L-glutamine, + 15 mM HEPES, - phenol red; Gibco, #11039-021).

extract_protocol:
Total RNA extractions were performed in accordance with recommended protocols (Invitrogen, #15596026).
Libraries were constructed from 500 ng of total RNA using the SMARTer™ PCR cDNA Synthesis Kit (Clontech, #634926) and Advantage 2 PCR kit (Clontech, #639207) followed by Tn5-mediated tagmentation.

treatment_protocol: For 2 day knockdown, cells were grown for five days after passage before being transfected with an siRNA targeting PCBP2 or a negative scrambled control using Stemfect RNA Transfection kit (Stemgent, #00-0069). Transfection was repeated 24 hours later and cells were collected 24 hours after the second transfection. For 6 day knockdown samples, cells were grown for one day after passage before being transfected using the same protocol. Cells were transfected daily for five days and collected 24 hours after the last transfection. Cells were harvested in TRIzol Reagent (Invitrogen, #15596026) and stored at -80°C.

value: Fibroblast-derived stem cell

value: KD

tag: duration


title: SUM159-R cells treated with Enzastaurin

data_processing:
Gene expression was defined by FPKM value (fragments per kilobase of exon per million fragments mapped) using RSEM software. Bioinformatics analysis was performed using Omicsmart, a dynamic and interactive online platform for data analysis (https://www.omicsmart.com). A log2 (fold change) >2 and a false discovery rate (FDR) < 0.01 were used as cut-off thresholds.
Assembly: hg38
Supplementary files format and content: FPKM

growth_protocol: SUM159 and its resistant derives were cultured in Ham’s F-12 Nutrient Mix medium with L-Glutamine (Gibco®) and supplemented with 5% FBS, 10mM HEPES (Gibco®), 5ng/ml Insulin, 1μg/ml hydrocortisone and 5000U/mL penicillin/streptomycin.The resistant cell lines were maintained in 150nM Paclitaxel

extract_protocol:
Total RNA was extracted using a mini-RNA isolation kit (cat. no.74106; Qiagen, Germany) and transcribed to cDNA with random primers.
The cDNA was ligated to Illumina sequencing adaptors and sequenced on the Illumina NovaSeq6000 by Gene Denovo Biotechnology Co. (Guangzhou, China).

treatment_protocol: Paclitaxel, 500nM,24h; Enzastaurin,2.5uM,24h; or dual compounds

value: paclitaxel-resistant TNBCs

value: Enzastaurin


title: A_CTRL_2

value: vehicle


title: MCF-7 Overexpressing H19 (Replicate 1 and 2 compilated)

description:
Library name: H19_MCF7_(n=2)
IMPORTANT NOTE : The raw data files are no longer available. The processed data files provided in this submission are used twice in the metadata table because each processed data file represents a comparison between two conditions: Control vs H19 Overexpression. The files named “(n=2)” represent compiled replicates, while individual replicates are also included separately. Each comparison corresponds to a single processed data file.

value: epithelial breast cancer cell


title: 6day_PCBP2_KD_b1


title: A_CTRL_1


title: MCF-7 Control (Replicate 1 and 2 compilated)

description:
Library name: Control_MCF7_(n=2)
IMPORTANT NOTE : The raw data files are no longer available. The processed data files provided in this submission are used twice in the metadata table because each processed data file represents a comparison between two conditions: Control vs H19 Overexpression. The files named “(n=2)” represent compiled replicates, while individual replicates are also included separately. Each comparison corresponds to a single processed data file.


title: Human chorionic trophoblasts，Experiment3

city: Chongqing

first: MIngrui

last: LI

address: No.1, Medical College Road

institute: Chongqing Medical University

data_processing:
such as Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.  Specific steps：2_methods_med
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes TPM values for each sample

extract_protocol: Following the washing of the HTR8/SVneo cells with PBS (Beyotime), the cells were trypsinized and digested. Subsequently, 1ml of TRIzol (TaKaRa) was added to the cells in each group and sent to the company (Novogene, Beijing, China) for sequencing

value: interference and overexpression of HMGB1


title: 1.65nM NIH3T3

first: Wen

last: Xiao

address: 320 Yueyang Road

department: Institute of Biochemistry and Cell Biology

institute: Shanghai Institutes for Biological Sciences, CAS

description: Testing the accuracy of the quantitative standard curve

data_processing:
Raw data (read1) were pre-processed using the FASTX Toolkit (v0.0.14). The first 70 bp of each read were retained, and low-quality sequences were filtered out (-q 20, -p 90). After quality filtering, adapter sequences were trimmed, requiring a minimum 10-nucleotide match at the 3' end. Reads without detected adapter or shorter than 32 bp were discarded. Only reads with "CGA" at positions 4-6 were retained, corresponding to the 5' random adapter. UMI extraction was performed with UMI_tools (v0.5.1) using the following parameters: extract --extract-method regex --bc-pattern="^(?P<umi_1>.{3})(?P<cell_1>.{3})(?P<umi_2>.{4})([A,T,C,G]{5,100})(?P<umi_3>.{4})$". Processed reads were aligned to the target genome using Bowtie (v1.2.1.1) with parameters --best -v 0. Duplicate reads were removed with UMI_tools using the following parameters: dedup --edit-distance-threshold 1 --soft-clip-threshold 0 --method adjacency. Unaligned reads were mapped to the spike-in reference sequences using Bowtie with parameters --best -v 1 --norc and de-duplicated in the same manner. Remaining unmapped reads were aligned to the isomiR reference library with the same parameters and de-duplicated. Molecules aligned to the genome were merged with isomiR molecules for downstream analysis. Molecules were annotated based on the following priority: mature miRNA > isomiR > tRNA > rRNA > snoRNA > snRNA > scRNA > scaRNA > YRNA > lncRNA > mRNA > piRNA > novel miRNA. Mature miRNA, isomiR, piRNA, and novel miRNA were annotated based on exact sequence and length matches, while other small RNA categories were aligned to known sequences using Bowtie with parameters -k=100 -v=0 -norc. Reads that aligned to the genome but lacked known annotations were classified as "others". The expression of molecules in each library was normalized using the standard curve generated from the external spike-ins.
Assembly: human:hg38;  mouse:mm10; crab-eating monkey:macFas5
Supplementary files format and content: tab-delimited text files include absolute quantification of miRNA expression for each Sample

extract_protocol:
1 ml of Trizol reagent (Invitrogen) was added to lyse the cells completely. Subsequently, 200 µl of trichloromethane was added and mixed thoroughly. The solution was then centrifuged at 12,000 rpm for 15 min at 4°C. The upper aqueous phase (450 µl) was transferred into a new 1.5 ml EP tube, followed by the addition of 900 µl of absolute ethanol. The solution was mixed by inversion, left to stand at -30°C for 30 min, and then centrifuged again at 12,000 rpm for 15 min at 4°C, until a distinct precipitate formed at the bottom of the tube. After removing the supernatant, the pellet was washed twice with 80% ethanol, air-dried for 2-3 min at room temperature, and dissolved in DEPC-treated water. RNA concentration was measured using a Nanodrop spectrophotometer, and the sample was diluted to a concentration of 100 ng/µl.
100 ng RNA with 0.05 µl of 20 nM EM or RM spike-in control oligos was ligated to a 0.55 µM 3' randomized adapter using 25 U/µl T4 RNA ligase 2 truncated KQ (NEB) in 0.83X T4 RNA ligase reaction buffer (NEB), supplemented with 20% PEG 8000 (NEB) at 25°C overnight. The ligated RNA was then annealed with 1.28 µM RTP. To remove the 3’ adapter-RTP byproduct, 3.33 U/µl 5’ deadenylase (NEB) and 0.2 U/µl lambda exonuclease (NEB) were added, followed by incubation at 30°C for 1 h and 37°C for 2 h, respectively. Subsequently, the product was ligated to a 5’ randomized adapter using 0.4 U/µl of T4 RNA ligase 1 (NEB) in 0.74X T4 RNA ligase reaction buffer, supplemented with 0.7 mM ATP and 17.3% PEG 8000 (NEB) at 25°C for 1 h. Reverse transcription was carried out using 5 U/µl of ProtoScriptII reverse transcriptase (NEB) in 1X ProtoScriptII RT reaction buffer (NEB), containing 0.5 mM dNTPs (Promega) and 10 mM DTT (NEB), at 50°C for 1 h. The resulting cDNA was then amplified using 0.02 U/µl of KOD-Plus-Neo (TOYOBO) in 1X PCR Buffer for KOD-Plus-Neo (TOYOBO), along with 0.5 µM primers, 1.5 mM MgSO4 (TOYOBO), and 0.2 mM dNTPs (TOYOBO). After PCR amplification, the cDNA was gel-purified on a 6% polyacrylamide gel to remove adapter dimers and sequenced using the Illumina NovaSeq platform.

tag: libtype

value: qMap-seq


title: 6day_Control_b2

value: Control


title: MDA-MB-231 Overexpressing H19 Replicate n°2

description:
Library name: H19_MDA_MB_231_Replicate2
IMPORTANT NOTE : The raw data files are no longer available. The processed data files provided in this submission are used twice in the metadata table because each processed data file represents a comparison between two conditions: Control vs H19 Overexpression. The files named “(n=2)” represent compiled replicates, while individual replicates are also included separately. Each comparison corresponds to a single processed data file.


title: 6day_Control_b1


title: day3, lenti_EV, Meg01-WT#3

city: Amsterdam

first: Emile

last: van den Akker

address: Plesmanlaan 125

country: Netherlands

institute: Sanquin Research Amsterdam

description:
Library name: sample 2
WT_3
I24-1085-14

data_processing:
In the trimming, Illumina adapter and poly-A sequences were removed from the reads
The trimmed reads were then aligned using HISAT2 (Kim et al, 2019)
After the HISAT2 alignment, SAMTools (Li et al, 2009) was used to sort and merge the alignments from multiple flow cells.
Quantification was performed using HT-seq count (Anders et al, 2015) after first sorting the alignments on readname using SAMTools.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: hematopoietic

extract_protocol:
RNA was isolated using TRIzol RNA isolation reagents (ThermoFisher Scientific)
RNA-Seq library was prepared for analysis according to the Illumina TruSeq stranded mRNA protocol (www.illumina.com).

value: hematopoietic

value: leukemic

value: WT


title: Human chorionic trophoblasts，Experiment2


title: 1.65nM Mouse2-breast

source_name: breast

value: breast


title: non4N-mouse-testis-2

description: Testing piRNA ligation efficiency

source_name: testis

value: testis

value: Salt-seq


title: SUM159-R cells treated with Paclitaxel

value: Paclitaxel


title: 2day_PCBP2_KD_b3


title: MDA-MB-231 Overexpressing H19 Replicate n°1

description:
Library name: H19_MDA_MB_231_Replicate1
IMPORTANT NOTE : The raw data files are no longer available. The processed data files provided in this submission are used twice in the metadata table because each processed data file represents a comparison between two conditions: Control vs H19 Overexpression. The files named “(n=2)” represent compiled replicates, while individual replicates are also included separately. Each comparison corresponds to a single processed data file.

value: Breast

value: mesenchymal breast cancer cell

value: H19 overexpressed

value: Transfected with H19 plasmid


title: Human chorionic trophoblasts，Experiment1


title: day3, lenti_ETV6-WT, Meg01-WT#2

description:
Library name: sample 4
WT_WT_1
I24-1085-07


title: non4N-mouse-testis-1

description: Testing piRNA ligation efficiency


title: Human chorionic trophoblasts，control3


title: qMap-mouse-testis-2

description: Testing piRNA ligation efficiency


title: MDA-MB-231 Control Replicate n°2

description:
Library name: Control_MDA_MB_231_Replicate2
IMPORTANT NOTE : The raw data files are no longer available. The processed data files provided in this submission are used twice in the metadata table because each processed data file represents a comparison between two conditions: Control vs H19 Overexpression. The files named “(n=2)” represent compiled replicates, while individual replicates are also included separately. Each comparison corresponds to a single processed data file.

value: mock (control)

value: Transfected with emply plasmid


title: 2day_PCBP2_KD_b1

value: Fibroblast-derived stem cell

value: KD


title: 2day_PCBP2_KD_b2


title: MDA-MB-231 Control Replicate n°1

description:
Library name: Control_MDA_MB_231_Replicate1
IMPORTANT NOTE : The raw data files are no longer available. The processed data files provided in this submission are used twice in the metadata table because each processed data file represents a comparison between two conditions: Control vs H19 Overexpression. The files named “(n=2)” represent compiled replicates, while individual replicates are also included separately. Each comparison corresponds to a single processed data file.


title: Human chorionic trophoblasts，control2


title: qMap-mouse-testis-1

description: Testing piRNA ligation efficiency

value: qMap-seq


title: Human chorionic trophoblasts，control1


title: 2day_Control_b2

value: Control


title: MCF-7 Overexpressing H19 Replicate n°2

description:
Library name: H19_MCF7_Replicate2
IMPORTANT NOTE : The raw data files are no longer available. The processed data files provided in this submission are used twice in the metadata table because each processed data file represents a comparison between two conditions: Control vs H19 Overexpression. The files named “(n=2)” represent compiled replicates, while individual replicates are also included separately. Each comparison corresponds to a single processed data file.

value: epithelial breast cancer cell


title: Mouse-thymus-5

description: 20 tissues sample from mice

source_name: thymus

value: thymus


title: LMSCs-PMSCs-GFHA,rep3

city: Chang chun

first: huixin

last: Lv

address: 1500 Tsinghua Road

institute: School and Hospital of Stomatology, Jilin University

data_processing:
Fastp software was used to process raw reads in fastq format, and clean reads were obtained after removing low-quality reads for subsequent data analysis.
The clean reads were mapped to the reference genome using HISAT2.
Fragments Per Kilobase of exon model per Million fragments mapped (FPKM) of each gene was calculated.
The read counts of each gene were obtained through HTSeq-count.
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: human maxillary sinus membrane

growth_protocol: Mesenchymal stem cells were maintained in MEM α supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
RNA was harvested using RNAiso reagent (TAKARA, USA). RNA purity and quantification were evaluated using the NanoDrop2000 Spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
The transcriptome libraries were constructed using VAHTS Universal V5 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

treatment_protocol:
Osteogenic differentiation was induced by treatment of hLMSCs and hPMSCs with Osteogenic Differentiation Kits (Oricell).
The cells were cultured with the microspheres in normal complete medium (NCM) on the first day. For osteogenic induction, the medium was replaced by differentiation induction medium on the next day. The renewing time of the medium was 3 days.

value: human maxillary sinus membrane

value: mesenchymal stem cells

value: osteogenic differentiation，Fibrinogen-GelMA microspheres，and co-culture with PMSCs loaded Fibrinogen-GelMA microspheres using transwells


title: Mouse-thymus-4

description: 20 tissues sample from mice


title: LMSCs-PMSCs-GFHA,rep2


title: Human melanocyte, UV-irradiated, 1

city: Suwon

first: Jin Cheol

last: Kim

address: 206, World cup-ro, Yeongtong-gu

country: South Korea

institute: Ajou University School of Medicine

description: Library name: Sample1

library_source: transcriptomic single cell

data_processing:
Single cell gene expression data was analyzed using Cell Ranger v6.1.2 (10x Genomics; https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger). Briefly, raw BCL files from Illumina sequencing instrument were demultiplexed to generate FASTQ files using ‘cellranger mkfastq’. Then, these raw FASTQ files were analyzed using ‘cellranger count’. The ‘cellranger count’ step includes mapping to the human reference genome (GRCh38-2020-A), measuring gene expression with unique molecular identifier (UMI) and cell barcode, determining cell clusters, and conducting differential gene expression analysis.
Assembly: hg19
Supplementary files format and content: tav and mtx files contating cell barcodes and gene count  matrix

source_name: Primary normal human melanocytes (HEMn-MP, Gibco, C1025C)

extract_protocol:
Chromium Single Cell 3' Protocol of 10x genomics to profile 3' digital gene expression of 500-10,000 individual cells per sample.
Libraries were prepared using the Chromium controller according to the 10x chromium Next GEM Single Cell 3’ v3.1 protocol(CG000315). Briefly, the cell suspensions were diluted in nuclease-free water to achieve a targeted cell count of 10,000. Cell suspension was mixed with master mix and loaded with Single Cell 3’V3.1 Gel Beads and Partitioning Oil into a chromium Next GEM chip G. 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. The purified libraries were quantified using qPCR according to the qPCR Quantification Protocol Guide(KAPA) and qualified using the Agilent Technologies 4200 TapeStation(Agilent technologies). And then the libraries were sequenced using HiSeq X Ten(Illumina) according to the read length in the user guide.

value: Melanocyte

value: Ultraviolet (UV)


title: MCF-7 Control Replicate n°1

description:
Library name: Control_MCF7_Replicate1
IMPORTANT NOTE : The raw data files are no longer available. The processed data files provided in this submission are used twice in the metadata table because each processed data file represents a comparison between two conditions: Control vs H19 Overexpression. The files named “(n=2)” represent compiled replicates, while individual replicates are also included separately. Each comparison corresponds to a single processed data file.

value: Breast


title: Mouse-thymus-3

description: 20 tissues sample from mice


title: LMSCs-PMSCs-GFHA,rep1


title: Mouse-thymus-1

description: 20 tissues sample from mice


title: MCF-7 Control Replicate n°2

description:
Library name: Control_MCF7_Replicate2
IMPORTANT NOTE : The raw data files are no longer available. The processed data files provided in this submission are used twice in the metadata table because each processed data file represents a comparison between two conditions: Control vs H19 Overexpression. The files named “(n=2)” represent compiled replicates, while individual replicates are also included separately. Each comparison corresponds to a single processed data file.


title: NK-NC-3

first: Ziwei

last: Tang

address: 393 Huaxia Middle Road, Pudong New Area

institute: ShanghaiTech University

description:
Library name: sample12
the processed data file is a matrix containing multiple samples, in which the columns for this sample are NK-NC-1, NK-NC-2 and NK-NC-3.

data_processing:
CLC Genomics Workbench
mapped to human reference genome sequence (GRCh38) in the GenBank followed by further gene profiling analyses. Reads number of each gene was normalized to sample volume, and evaluated as transcripts per million (TPM).
Assembly: hg38
Supplementary files format and content: comma-separated values file containing a matrix includes total counts, RPKM, TPM and CPM for all samples

source_name: isolated from PBMC

growth_protocol: PBNK cells were maintained in RPMI-1640 supplemented with 10% fetal bovine serum (FBS) and 20 nM natural cytokine (IL-2 or IL-15) or antibody (scDb-2d) in humidified atmosphere with 5% CO2 at 37 ℃.

extract_protocol:
TRIrizol reagent was used to purify the total RNA of isolated cells according to the manufacturer’s instruction.
RNA-seq

treatment_protocol: Different stimulus treatments were used in different groups, with 20 nM  IL-2 or 20 nM IL-15 or 20 nM antibody (scDb-2d).

value: isolated from PBMC

value: nature killer cells

value: WT

value: PBNK were proliferated with irradiated (100 Gy) wild type K562 cells without natural cytokine or antibody .


title: LMSCs-GFHA,rep3


title: NK-NC-1

description:
Library name: sample10
the processed data file is a matrix containing multiple samples, in which the columns for this sample are NK-NC-1, NK-NC-2 and NK-NC-3.


title: LMSCs-GFHA,rep2


title: Mouse-testis-2

description: 20 tissues sample from mice

value: testis


title: Mouse-testis-4

description: 20 tissues sample from mice


title: HCT116, Ab: P-T-loop CDK11 Ab2, experiment2

city: München

first: Caroline

last: Friedel

address: Amalienstr. 17

department: Institut für Informatik

country: Germany

institute: Ludwig-Maximilians-Universität München

description: Library name: HCT116_P-CDK11Ab2_exp2

library_source: genomic

data_processing:
Raw sequencing reads were aligned to the human genome (GRCh38) using BWA and resulting sam output was converted to bam using samtools.
Sequence reads with an alignment score <20 reads were discarded.
Duplicates were removed with samtools rmdup
Resulting bam files were converted into bedgraph format using the genomecov command of bedtools.
Assembly: GRCh38
Supplementary files format and content: bedGraph, read coverage per genome position

molecule: genomic DNA

extract_protocol:
ChIP was performed using the following antibodies for each biological technical replicate: 40 30 ul of P CDK11 (Ab 2 or Ab 3), 5 μg of SF3B1 (MBL, MB-D221-3). in tTwo technical replicates that were pooled together to obtain one biological replicate. In brief, 20 µl of Dynabeads protein G (Thermo Fisher Scientific, 10009D) per immunoprecipitation were pre-blocked with 0.2 mg ml−1 BSA (Thermo Fisher Scientific, AM2616) for 4 hours, washed 3× with RIPA buffer, followed by incubation with the specific antibody at 4 °C for at least 4 hours. HCT116 cells (70 % confluency) were treated with 50 nM SY 351 for 2 h. Cells were cross-linked with 1 % formaldehyde for 10 min, and the reaction was quenched with glycine (final concentration 125 mM) for 5 min. Cells were washed 2× with ice-cold PBS, scraped and split to several tubes so that there was about 20 µl packed cell pellet per tube. Each 20 µl packed cell pellet was lysed in 650 µl of RIPA buffer and sonicated 20× 7 s (amplitude 0.85) using a 5/64 probe (QSonica Q55A). Supernatant (13000 g/4 °C/10 min) was pooled and pre-cleared by incubating with Dynabeads protein G (Thermo Fisher Scientific, 10009D) at 4 °C for 2‒4 hours. Pre-cleared extracts were split into two technical replicates (900 µl each) and incubated overnight with antibody (P CDK11, SF3B1)-bound Dynabeads protein G. Beads were sequentially washed once with low-salt buffer (20 mM Tris-Cl, (pH 8), 150 mM NaCl, 2 mM EDTA, 1% Triton X 100, 0.1% SDS), once with high-salt buffer (20 mM Tris-Cl, (pH 8), 500 mM NaCl, 2 mM EDTA, 1% Triton X 100, 0.1% SDS), once with LiCl buffer (20 mM Tris-Cl, (pH 8), 250 mM LiCl, 2 mM EDTA, 1% NP 40, 1% sodium deoxycholate) and 2× with TE buffer (10 mM Tris Cl, (pH 8), 1 mM EDTA). Immunoprecipitated complexes were eluted 2× 15 min with 250 µl of elution buffer (1% SDS, 0.1 M NaHCO3). NaCl was added to final concentration of 0.2 M and samples were incubated at 65 °C for at least 4 hours to reverse cross-linking. Tris, pH 7.8, proteinase K (Sigma-Aldrich, P5568) and GlycoBlue (Thermo Fisher Scientific, AM9516) were added to final concentration of 30 mM, 0.04 mg/ml and 0.06 mg/ml, respectively, and incubated at 42 °C for 2 hours. After phenol–chloroform extraction (Sigma-Aldrich, P3803), immunoprecipitated DNA was dissolved in 17 µl of water and technical replicates were pooled.
ChIP–seq libraries were generated using KAPA Biosystems Hyper Prep Kit (Roche, KK8502) and NEBNext Multiplex Oligos for Illumina (New England Biolabs, E7335S, E7500S).

treatment_protocol: Indicated samples were treated with DMSO or 50nM SY-351 for 2 hours.


title: NK-J9H4-3

description:
Library name: sample9
the processed data file is a matrix containing multiple samples, in which the columns for this sample are NK-J9H4-1, NK-J9H4-2 and NK-J9H4-3.

value: PBNK were proliferated with irradiated (100 Gy) wild type K562 cells adding 20 nM scDb-2 (aslo termed J9H4).


title: LMSCs-GFHA,rep1


title: HCT116, Ab: none, experiment2

description: Library name: HCT116_noAb_exp2


title: iZ013 hMSC after adipogenesis trial 3

city: Irvine

first: Brittanie Yukimtiao

middle: Arcenal

last: Yukimtiao

address: Ring Rd

department: Department of Dev & Cell

institute: University of California, Irvine

description: Library name: A315

data_processing:
1. quality control: FastQC
2. trimming: Trimmomatic
3. aligning: STAR Aligner
Assembly: GRCh38
Supplementary files format and content: BAM

source_name: Bone Marrow MSCs

extract_protocol:
Total RNAs extracted using Zymo MiniPrep (#2052)
SMARTER mRNA-seq Library prep kit

value: Bone Marrow MSCs

value: MSC

value: 14 day adipogenesis


title: 2day_Control_b1

value: Fibroblast-derived stem cell

value: Control


title: NK-J9H4-1

description:
Library name: sample7
the processed data file is a matrix containing multiple samples, in which the columns for this sample are NK-J9H4-1, NK-J9H4-2 and NK-J9H4-3.


title: Mouse-stomach-4

description: 20 tissues sample from mice

source_name: stomach

value: stomach

value: qMap-seq


title: iZ013 hMSC after adipogenesis trial 2

description: Library name: A314


title: MCF-7 Overexpressing H19 Replicate n°1

description:
Library name: H19_MCF7_Replicate1
IMPORTANT NOTE : The raw data files are no longer available. The processed data files provided in this submission are used twice in the metadata table because each processed data file represents a comparison between two conditions: Control vs H19 Overexpression. The files named “(n=2)” represent compiled replicates, while individual replicates are also included separately. Each comparison corresponds to a single processed data file.

value: epithelial breast cancer cell

value: H19 overexpressed

value: Transfected with H19 plasmid


title: PMSCs-GFHA,rep2

value: human maxillary sinus membrane

value: mesenchymal stem cells


title: Mouse-stomach-2

description: 20 tissues sample from mice


title: NK-IL15-3

description:
Library name: sample6
the processed data file is a matrix containing multiple samples, in which the columns for this sample are NK-IL15-1, NK-IL15-2 and NK-IL15-3.

value: isolated from PBMC

value: nature killer cells

value: PBNK were proliferated with irradiated (100 Gy) wild type K562 cells adding 20 nM IL-15.


title: iZ013 hMSC after adipogenesis trial 1

description: Library name: A313

value: WT


title: Mouse-stomach-1

description: 20 tissues sample from mice


title: PMSCs-GFHA,rep1


title: NK-NC-2

description:
Library name: sample11
the processed data file is a matrix containing multiple samples, in which the columns for this sample are NK-NC-1, NK-NC-2 and NK-NC-3.

value: PBNK were proliferated with irradiated (100 Gy) wild type K562 cells without natural cytokine or antibody .


title: PMSCs-G,rep3


title: NK-IL15-2

description:
Library name: sample5
the processed data file is a matrix containing multiple samples, in which the columns for this sample are NK-IL15-1, NK-IL15-2 and NK-IL15-3.


title: Z013 hMSC after adipogenesis trial 3

description: Library name: A312

value: Bone Marrow MSCs


title: PMSCs-GFHA,rep3


title: Mouse-spleen-4

description: 20 tissues sample from mice

source_name: spleen

value: spleen


title: NK-IL15-1

description:
Library name: sample4
the processed data file is a matrix containing multiple samples, in which the columns for this sample are NK-IL15-1, NK-IL15-2 and NK-IL15-3.


title: HCT116, Ab: P-T-loop CDK11 Ab3, experiment2

description: Library name: HCT116_P-CDK11Ab3_exp2


title: NK-J9H4-2

description:
Library name: sample8
the processed data file is a matrix containing multiple samples, in which the columns for this sample are NK-J9H4-1, NK-J9H4-2 and NK-J9H4-3.

value: PBNK were proliferated with irradiated (100 Gy) wild type K562 cells adding 20 nM scDb-2 (aslo termed J9H4).


title: Mouse-spleen-3

description: 20 tissues sample from mice


title: PMSCs-G,rep2


title: Z013 hMSC after adipogenesis trial 2

description: Library name: A311

value: MSC

value: 14 day adipogenesis


title: NK-IL2-3

description:
Library name: sample3
the processed data file is a matrix containing multiple samples, in which the columns for this sample are NK-IL2-1, NK-IL2-2 and NK-IL2-3.

value: PBNK were proliferated with irradiated (100 Gy) wild type K562 cells adding 20 nM IL-2.


title: Z013 hMSC after adipogenesis trial 1

description: Library name: A310


title: NK-IL2-2

description:
Library name: sample2
the processed data file is a matrix containing multiple samples, in which the columns for this sample are NK-IL2-1, NK-IL2-2 and NK-IL2-3.


title: PMSCs-G,rep1


title: Mouse-stomach-3

description: 20 tissues sample from mice

value: stomach

value: qMap-seq


title: iZ013 hMSC before adipogenesis test 3

description: Library name: A309

value: untreated


title: Mouse-spleen-1

description: 20 tissues sample from mice


title: HIBEpiC cells, OE rep3

city: Changsha

first: Yidi

last: Guan

state: 湖南省

address: No.87 Xiangya road

institute: Xiangya hospital of central south university

data_processing:
The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition. Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quali
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5). We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
FeatureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene
Assembly: hg38
Supplementary files format and content: tab-delimited exel file includes raw counts for each Sample

source_name: human biliary tissues

extract_protocol:
RNA was harvest using Trizol reagent (Invitrogen), total RNA was used for the construction of sequencing libraries.
Briefly, mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained.

value: human biliary tissues

value: HIBEpiC

value: human biliary

value: PPDPF overexpressed


title: HIBEpiC cells, OE rep2


title: iZ013 hMSC before adipogenesis test 2

description: Library name: A308


title: HIBEpiC cells, OE rep1


title: CAKI_1SH3_3

city: wuhan

first: xuan

last: hu

state: hubei

address: Donghu Road 169, Wuhan, Hubei, China

institute: wuhan university

data_processing:
CLC Genoics Workbench v11.0.1
Assembly: mm10
Supplementary files format and content: FPKM, read count, normalized read count

source_name: kidney

extract_protocol:
Before collecting the samples, ensure that the cell condition is good and free from microbial contamination. During sample collection, wash the cells twice with PBS, then add 1 mL of Trizol to the cell pellet of each group, and gently pipette to ensure complete cell lysis
The impact of RNA sequencing library construction protocols on transcriptomic profiling of ccRCC after TAF1D knockdown

value: kidney

value: clear cell renal cell carcinomacells

value: TAF1D knockdown


title: Mouse-skin-5

description: 20 tissues sample from mice

source_name: skin

value: skin


title: HIBEpiC cells, CV rep3

value: control vector


title: CAKI_1SH3_1


title: Z013 hMSC before adipogenesis trial 3

description: Library name: A306

value: Bone Marrow MSCs

value: WT


title: HIBEpiC cells, CV rep2


title: Mouse-skin-4

description: 20 tissues sample from mice


title: Mouse-skin-3

description: 20 tissues sample from mice


title: CAKI_1SH1_3


title: Z013 hMSC before adipogenesis trial 2

description: Library name: A305

value: MSC


title: Z013 hMSC before adipogenesis trial 1

description: Library name: A304


title: Mouse-spleen-2

description: 20 tissues sample from mice

value: spleen


title: Mouse-rectum-4

description: 20 tissues sample from mice

source_name: rectum

value: rectum


title: Mouse-rectum-3

description: 20 tissues sample from mice


title: HBx_ChIP

city: beijing

first: yanjun

last: wang

address: Xitoutiao,8#,Youanmenwai Street,Fengtai District, Beijing, 100069, China

institute: Beijing Institute of Hepatology, Beijing You An Hospital, Capital Medical University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Clean reads were mapped to the reference genome using Bowtie2 software. And reads from organelle, mapping quality smaller then 30, PCR duplicated reads all removed. Those high quality mapping reads were subjected to further peak calling.
Macs2 was used to call peaks with qvalue < 0.05.
Peaks were annotated by ChIPseeker package.
Assembly: hg38
Supplementary files format and content: bw

source_name: cell line

extract_protocol:
Briefly, cells were harvested and crosslinker with 1% formaldehyde for 10 min at room temperature. After sonication, immunoprecipitation was performed with anti His-Tag. The immunoprecipitated complex was washed, and DNA was extracted and purified by Universal DNA Purification Kit (TIANGEN, #DP214).
The ChIP-Seq library was prepared using original Ultra II DNA Library Kits (NEB, #E7645) according to the manufacturer’s instructions. For ChIP-seq, extracted DNA was ligated to specific adaptors followed by deep sequencing in the Illumina Novaseq 6000 using 150bp paired-end.

value: cell line

value: Human enbryonic kidney

tag: chip antibody

value: His-Tag (D3I1O) XP® Rabbit mAb #12698


title: CAKI_1SH1_2


title: P12

city: Guangzhou

first: Hong

last: Zeng

state: Hunan

address: 87 Xiangya Street

department: Reproductive medicine center

institute: Xiangya Hospital Central South University

description:
Library name: P12
Displaced WOI

data_processing:
The raw sequencing reads were filtered to exclude low-quality reads and alternative alignment with RNA_x0002_SeQC [41]. Qualified reads were mapped to the human reference genome (Ensembl primary assembly, version GRCh37) by using STAR
Assembly: GRCh37
Supplementary files format and content: raw counts for each sample

source_name: endometrium

extract_protocol:
Total RNA extraction was performed using the RNe_x0002_asy Micro Kit (74004; Qiagen, Germantown, MD, USA)
RNA reverse transcription was conducted using the MALBAC® Platinum Single Cell RNA Amplifica_x0002_tion Kit (KT110700796; Yikon Genomics, Suzhou, Jiangsu, China). 1 µl purified cDNA was reasonably diluted for detec_x0002_tion on the Agilent 2100 Bioanalyzer High Sensitivity DNA Chip (Agilent Technologies, Santa Clara, CA, USA). Library construction was accomplished using a gene sequencing and library preparation kit (XY045; Yikon Genomics, Suzhou, Jiangsu, China) according to the instruction manual. After purifcation, the libraries were quantifed using the Qubit dsDNA HS Assay Kit (Q32584; Invitrogen). Based on the results of Qubit quantitation, 10 ng of the library was taken for each sam_x0002_ple and mixed in equal proportion

value: endometrium

tag: group

value: Displaced WOI


title: HIBEpiC cells, CV rep1

value: human biliary tissues

value: HIBEpiC

value: human biliary


title: WI-38, co-culture with H1975-vec clones, scRNAseq

city: Miaoli County

first: Shihmiao

last: Li

address: 35, Keyan Road, Zhunan Town

country: Taiwan

institute: National Health Research Institutes

description:
BD Rhapsody
Sample 1: Co-culture with H1975-vec clone
Sample 2: Co-culture with H1975-OEN clone
Sample 3: Co-culture with PC9-Cas9
Sample 4: Co-culture with PC9-NKO

data_processing:
Sequence quality, library quality, alignment categories, reads and molecules, as well as putative cells were made by using the Rhapsody Sequence Analysis Pipeline (Pipeline Version: 1.11.1)
1292 fibroblasts_raw counts_condition.rds was output by Seurat packages.
Assembly: GRCh38
Supplementary files format and content: 1292 fibroblasts_raw counts_condition.rds

source_name: Lung

growth_protocol: Lung fibroblast cell line WI-38 was cultured in MEM medium supplemented with 10% fetal bovine serum (FBS). Lung adenocarcinoma cell lines H1975 and PC9 were cultured in RPMI 1640 medium supplemented with 10% FBS.

extract_protocol:
Isolating cell from co-cultured cell mixture by trypsinizing.
Library was performed according to the manufactor's instructions (mRNA Targeted Library Preparation Protocol, BD RhapsodyTM System).

treatment_protocol: Lung fibroblast cell line WI-38 was cultured in 10-cm dish for 24 hours. Each of lung cancer cell line H1975 or PC9 (and their stable transfectant cells with overexpressed or knock down NMU) was added to dish of fibroblast with ratio of 1:3 of numbers of lung cancer cell to that of fibroblast cell and co-cultured for 72 hours.

value: Lung

value: Fibroblast

value: hESC-derived lung cells and lung-macrophage co-cultured cells


title: P11

description:
Library name: P11
Displaced WOI


title: CAKI_1SH1_1

value: kidney

value: clear cell renal cell carcinomacells

value: TAF1D knockdown


title: Mouse-rectum-2

description: 20 tissues sample from mice

value: qMap-seq


title: CAKI_1NC3

value: WT


title: Mouse-skin-6

description: 20 tissues sample from mice

value: skin


title: HCMEC, DNR+MSC-EVs, rep2

city: Jinan

first: Shule

last: Zhang

address: 107 Wenhua Xilu

institute: Qilu Hospital of Shandong University

data_processing:
Raw reads were processed using Trimmomatic. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to reference genome using hisat 2.
FPKM value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq-count.
Assembly: GRCH38.104

extract_protocol:
Total RNA was extracted using using Trizol reagent following the manufacturer's protocol.
The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer's instructions.

value: cell line

value: HCMEC

tag: phenotype

value: DNR-damaged + MSC-EVs


title: P10

description:
Library name: P10
WOI

value: endometrium

value: WOI


title: iZ013 hMSC before adipogenesis test 1

description: Library name: A307

value: Bone Marrow MSCs

value: MSC

value: untreated


title: CAKI_1SH3_2


title: CAKI_1NC2


title: Mouse-rectum-1

description: 20 tissues sample from mice

value: rectum


title: HCMEC, DNR+MSC-EVs, rep1


title: P09

description:
Library name: P09
Displaced WOI

value: Displaced WOI


title: CAKI_1NC1


title: Mouse-pancreas-4

description: 20 tissues sample from mice

source_name: pancreas

value: pancreas


title: shRRM2-3

city: Wuhan

first: Haixin

last: Yu

state: Hubei Province

address: 1277, Jiefang Avenue

institute: Wuhan union hospital

data_processing:
Basecalls performed using Rsubread v2.12.3
Sequencing read quality was inspected using fastp v0.23.4. Adapter removal and read trimming were performed. Sequencing reads were trimmed from the end (base quality less than Q20) and filtered by length (less than 25).
Paired-end reads were aligned to the hg38. FeatureCounts (Rsubread) was used to count the reads numbers mapped to each gene. And then FPKM/TPM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file includes gene ids, sample names, and read-counts values for each Sample.

extract_protocol:
RNA was harvested using Trizol reagent (Life Technologies). Illumina NEB Ultra directional RNA library Prep Kit was used with 1 ug of total RNA for the construction sequencing libraries.
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: human pancreatic cancer cells


title: HCMEC, DNR, rep2

value: DNR-damaged


title: HCMEC, DNR, rep1


title: P08

description:
Library name: P08
WOI


title: P07

description:
Library name: P07
WOI


title: Mouse-pancreas-2

city: Shanghai

description: 20 tissues sample from mice


title: Mouse-pancreas-1

description: 20 tissues sample from mice


title: HCMEC, Blank, rep1

value: blank


title: HCMEC, Blank, rep2


title: P06

description:
Library name: P06
WOI


title: P05

description:
Library name: P05
WOI


title: Mouse-ovary-3

description: 20 tissues sample from mice

source_name: ovary

value: ovary

value: qMap-seq


title: NC-3

value: WT

value: shControl


title: Mouse-ovary-1

description: 20 tissues sample from mice


title: shRRM2-1


title: NK-IL2-1

description:
Library name: sample1
the processed data file is a matrix containing multiple samples, in which the columns for this sample are NK-IL2-1, NK-IL2-2 and NK-IL2-3.

value: isolated from PBMC

value: nature killer cells

value: PBNK were proliferated with irradiated (100 Gy) wild type K562 cells adding 20 nM IL-2.


title: Mouse-muscle-4

description: 20 tissues sample from mice

source_name: muscle

value: muscle


title: P04

description:
Library name: P04
WOI

value: endometrium

value: WOI


title: P03

description:
Library name: P03
Displaced WOI


title: NC-2


title: P02

description:
Library name: P02
Displaced WOI


title: Mouse-muscle-3

description: 20 tissues sample from mice


title: Mouse-pancreas-3

description: 20 tissues sample from mice


title: SC8_12, Spatial Transcriptomics

city: Xiamen

first: Jing

last: Wang

state: Fujian

address: 668 Jimei Road

department: School of Medicine and School of Biomedical Sciences

institute: Huaqiao University

data_processing:
We use in-house script to perform basic statistics of raw data, and evaluate the data quality and GC content along the sequencing cycles.
Raw FASTQ files and histology images were processed by sample with the Space Ranger (version spaceranger-1.2.0, 10X Genomics) software with default parameters.
The filtered gene-spots matrix and the fiducial-aligned low-resolution image was used for down-streaming data analyses (Seurat).
Assembly: GRCh38
Supplementary files format and content: gzip files and raw count matrix files
Library strategy: Spatial Transcriptomics

source_name: spinal cord

extract_protocol: The Visium Spatial Gene Expression Slide & Reagent kit (10X Genomics) was used to construct sequencing libraries according to the Visium Spatial Gene Expression User Guide (CG000239, 10X Genomics). A 10um frozen tissue section was placed on one of the Visium gene expression slide capture areas in a slide. After tissue Hematoxylin and Eosin (H&E) staining, bright-field images were acquired as described in the Spatial Transcriptomics procedure. Tissue permeabilization was performed for a optimal minutes, as established in the TO procedure. Then reverse transcription experiment was conducted and sequencing libraries were prepared following the manufacturer’s protocol.

treatment_protocol: Fresh tissues were concurrently frozen and embedded in optical cutting tissue (OCT) compound in liquid nitrogen.

value: neuron

value: spinal cord

tag: time


title: shRRM2-2


title: F1-8-DIC

first: Chuang

last: Yuan

address: Xiangya Road #87

institute: Central South University

description: DIC

data_processing:
Sequence reads were trimmed for adaptor sequence/low quality sequence using fastp (v 0.19.5)
Trimmed sequence reads were mapped to GRCh38/hg38 using hisat2 (2.2.1.0) software.
Read count extraction and normalization were performed using htseq-count (v 0.9.1)
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: Leukocytes

extract_protocol:
Total RNA was extracted using the RNA Isolation Kit (Ambion-1561)  following the manufacturer’s protocol.
The libraries were constructed using TruSeq Stranded Total RNA with Ribo-Zero Gold according to the manufacturer’s instructions

tag: disease

value: sepsis with overt DIC

value: Leukocytes

value: No Treatment


title: Mouse-muscle-2

description: 20 tissues sample from mice


title: HepG2 cells, siRNA2-treated HepG2, HepG2_24h_siRNA2

city: Chengdu City

first: Ruiping

last: Huai

state: Sichuan Province

address: Jiulidi Campus, Southwest Jiaotong University, No. 111, North 1st Section of Second Ring Road, Jinniu District

institute: Southwest Jiaotong university

data_processing:
SOAP
The high-quality clean reads were mapped to human reference genome by SOAP (allowing no more than one mismatch) for the analysis of their expression and distribution on the genome.
Blast was used to align the reads to miRBase database in order to identify the known miRNAs
Supplementary files format and content: txt files include miRNAs reads

source_name: liver

growth_protocol: HepG2 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for small RNA-seq were prepared using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (NEB, USA) following manufacturer's protocols.

treatment_protocol: The HepG2 cells were treated with two different siRNAs in a time-dependent manner (0, 24, 36 and 48h) to down-regulate the expression of TEAD1.

value: liver

value: Hepatocellular carcinoma cells

value: TEAD1 knockdown

value: siRNA2-treated 24h


title: NC-1

value: human pancreatic cancer cells

value: WT


title: HepG2 cells, siRNA2-treated HepG2, HepG2_36h_siRNA2

value: siRNA2-treated 36h


title: Mouse-muscle-1

first: Wen

last: Xiao

address: 320 Yueyang Road

institute: Shanghai Institutes for Biological Sciences, CAS

description: 20 tissues sample from mice

data_processing:
Raw data (read1) were pre-processed using the FASTX Toolkit (v0.0.14). The first 70 bp of each read were retained, and low-quality sequences were filtered out (-q 20, -p 90). After quality filtering, adapter sequences were trimmed, requiring a minimum 10-nucleotide match at the 3' end. Reads without detected adapter or shorter than 32 bp were discarded. Only reads with "CGA" at positions 4-6 were retained, corresponding to the 5' random adapter. UMI extraction was performed with UMI_tools (v0.5.1) using the following parameters: extract --extract-method regex --bc-pattern="^(?P<umi_1>.{3})(?P<cell_1>.{3})(?P<umi_2>.{4})([A,T,C,G]{5,100})(?P<umi_3>.{4})$". Processed reads were aligned to the target genome using Bowtie (v1.2.1.1) with parameters --best -v 0. Duplicate reads were removed with UMI_tools using the following parameters: dedup --edit-distance-threshold 1 --soft-clip-threshold 0 --method adjacency. Unaligned reads were mapped to the spike-in reference sequences using Bowtie with parameters --best -v 1 --norc and de-duplicated in the same manner. Remaining unmapped reads were aligned to the isomiR reference library with the same parameters and de-duplicated. Molecules aligned to the genome were merged with isomiR molecules for downstream analysis. Molecules were annotated based on the following priority: mature miRNA > isomiR > tRNA > rRNA > snoRNA > snRNA > scRNA > scaRNA > YRNA > lncRNA > mRNA > piRNA > novel miRNA. Mature miRNA, isomiR, piRNA, and novel miRNA were annotated based on exact sequence and length matches, while other small RNA categories were aligned to known sequences using Bowtie with parameters -k=100 -v=0 -norc. Reads that aligned to the genome but lacked known annotations were classified as "others". The expression of molecules in each library was normalized using the standard curve generated from the external spike-ins.
Assembly: human:hg38;  mouse:mm10; crab-eating monkey:macFas5
Supplementary files format and content: tab-delimited text files include absolute quantification of miRNA expression for each Sample

extract_protocol:
1 ml of Trizol reagent (Invitrogen) was added to lyse the cells completely. Subsequently, 200 µl of trichloromethane was added and mixed thoroughly. The solution was then centrifuged at 12,000 rpm for 15 min at 4°C. The upper aqueous phase (450 µl) was transferred into a new 1.5 ml EP tube, followed by the addition of 900 µl of absolute ethanol. The solution was mixed by inversion, left to stand at -30°C for 30 min, and then centrifuged again at 12,000 rpm for 15 min at 4°C, until a distinct precipitate formed at the bottom of the tube. After removing the supernatant, the pellet was washed twice with 80% ethanol, air-dried for 2-3 min at room temperature, and dissolved in DEPC-treated water. RNA concentration was measured using a Nanodrop spectrophotometer, and the sample was diluted to a concentration of 100 ng/µl.
100 ng RNA with 0.05 µl of 20 nM EM or RM spike-in control oligos was ligated to a 0.55 µM 3' randomized adapter using 25 U/µl T4 RNA ligase 2 truncated KQ (NEB) in 0.83X T4 RNA ligase reaction buffer (NEB), supplemented with 20% PEG 8000 (NEB) at 25°C overnight. The ligated RNA was then annealed with 1.28 µM RTP. To remove the 3’ adapter-RTP byproduct, 3.33 U/µl 5’ deadenylase (NEB) and 0.2 U/µl lambda exonuclease (NEB) were added, followed by incubation at 30°C for 1 h and 37°C for 2 h, respectively. Subsequently, the product was ligated to a 5’ randomized adapter using 0.4 U/µl of T4 RNA ligase 1 (NEB) in 0.74X T4 RNA ligase reaction buffer, supplemented with 0.7 mM ATP and 17.3% PEG 8000 (NEB) at 25°C for 1 h. Reverse transcription was carried out using 5 U/µl of ProtoScriptII reverse transcriptase (NEB) in 1X ProtoScriptII RT reaction buffer (NEB), containing 0.5 mM dNTPs (Promega) and 10 mM DTT (NEB), at 50°C for 1 h. The resulting cDNA was then amplified using 0.02 U/µl of KOD-Plus-Neo (TOYOBO) in 1X PCR Buffer for KOD-Plus-Neo (TOYOBO), along with 0.5 µM primers, 1.5 mM MgSO4 (TOYOBO), and 0.2 mM dNTPs (TOYOBO). After PCR amplification, the cDNA was gel-purified on a 6% polyacrylamide gel to remove adapter dimers and sequenced using the Illumina NovaSeq platform.

value: qMap-seq


title: A549-ACE2, N277A, 24hpi, rep3

city: Taipei

first: Hsin-Ping

last: Chiu

address: No.1 Jen Ai road section 1

department: Microbiology

institute: National Taiwan University

data_processing:
The reference genome was generated by concatenating the hg38 human and rSARS-CoV-2-Venus genomes, which was used for aligning fastq reads using STAR (v2.7.11a). Transcript abundances were then quantified using salmon (v1.10.2) and scaled by transcript length and library size using the R package ‘tximport’ (v1.26.1).
Assembly: hg38 and rSARS-CoV-2-Venus
Supplementary files format and content: The processed data file includes normalized gene counts (shown by TPM values) for each sample.

growth_protocol: A549-ACE2 cells were maintained in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin at 37 °C with 5% CO2.

extract_protocol:
Total RNA was extracted and on-column DNase I treated using Direct-zol RNA Miniprep kit.
100ng of total RNA was applied to generate RNA sequecing library. Briefly, mRNAs were enriched with Oligo d(T) beads and the RNA library was prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions.

value: human lung carcinoma cell


title: P01

description:
Library name: P01
WOI


title: HepG2 cells, siRNA1-treated HepG2, HepG2_48h_siRNA1

value: siRNA1-treated 48h


title: F1-6-DIC

description: DIC


title: SC10, Spatial Transcriptomics


title: F1-5-DIC

description: DIC


title: Mouse-lung-5

description: 20 tissues sample from mice

source_name: lung

value: lung


title: A549-ACE2, N277A, 24hpi, rep2


title: Mouse-lung-6

description: 20 tissues sample from mice


title: A549-ACE2, H234A, 24hpi, rep3


title: HepG2 cells, siRNA2-treated HepG2, HepG2_48h_siRNA2

value: siRNA2-treated 48h


title: F3-10-NonDIC

description: Non-DIC

value: sepsis without overt DIC


title: A549-ACE2, N277A, 24hpi, rep1


title: HepG2 cells, siRNA1-treated HepG2, HepG2_36h_siRNA1

value: siRNA1-treated 36h


title: HepG2 cells, siRNA1-treated HepG2, HepG2_24h_siRNA1

value: siRNA1-treated 24h


title: Mouse-lung-4

description: 20 tissues sample from mice


title: A549-ACE2, WT, 24hpi, rep3


title: A549-ACE2, H234A, 24hpi, rep2


title: Mouse-liver-2

description: 20 tissues sample from mice


title: Mouse-liver-4

description: 20 tissues sample from mice


title: MRC5,sh,input

city: Tianjin

first: Jian

address: Huanhu West Road, Hexi District

institute: Tianjin Medical University Cancer Institute and Hospital

data_processing:
Reads were aligned on the GRCh37 (hg19) human genome assembly using Bowtie 2 (version 2.3.4.2) , with paired-end option fragment length for valid paired-end alignments set from 10 to 700, and otherwise default options.
Peak predictions for FOXN3 occupancy were performed with the model-based analysis for ChIP-seq MACS2 (version v2.1.1.20160309.0) , with the following parameters: -f BAMPE, --bw 300, -m and -p set to default values and --bdg.
The samples were analyzed against the control, rabbit IgG sample. Read density was visualized with the UCSC genome browser, and heatmap profiles of FOXN3 occupancy were represented using deepTools (version 2.0.1)
Assembly: hg19
Supplementary files format and content: bedGraph, narrowPeak (except for Input sample)
Library strategy: CUT&RUN

extract_protocol:
Cells were washed and incubated for 5 min at room temperature with 10 μL of concanavalin A-coated beads. Cells bound to beads were permeabilized with digitonin buffer and incubated with an anti-FOXN3 antibody (Cat No. AP19255B, Abgent, USA) at 4°C overnight. The cells were incubated with 50 μL pAG-MNase at 4°C for 1 h. Next, pAG-MNase was activated with 3 μL of precooled CaCl2, and digestion was performed for 30 min at 4°C. The reaction was stopped with 150 μL of stop buffer for 10 min at 37°C. Release of the DNA fragments was achieved by incubating samples with 3 μL 10% SDS and 2 μL proteinase K at 65°C for 2 h.
Barcoded CUT&RUN-seq libraries were constructed using the NEBNext Ultra II DNA Library Prep kit (Cat No. E7645, Biolabs, USA) following the manufacturer’s instructions

value: Human embryonic lung fibroblasts


title: Human VDR siRNA transfected cells with 2 nM of 1,25(OH)2VitaminD3 treatment well 3

city: RTP

first: Franco

last: Demayo

state: NC

address: 111 TW Alexander Drive

institute: NIEHS

data_processing:
Filter reads of Qual score <20
Map the reads to reference genome (hg 38) using HISAT2
Remove duplicated reads by Picard
Only keep paired mapped reads
Assembly: hg38
Supplementary files format and content: RPKM was caculated for each gene in each sample by Partek Suite Version 7.0

source_name: Immortalized endometrial stromal cells (T-HESC)

growth_protocol: The cells were cultured and distributed into a 6-well plate in DMEM/F12 containing 10% v/v fetal bovine serum, 100 units/mL penicillin, and 100 ug/mL streptomycin.

extract_protocol:
Total RNA was extracted by TRIzol and cleaned up using the Qiagen RNAeasy Kit
RNA libraries were prepared by the Illumina Tru-Seq mRNA kit

treatment_protocol: The cells were transfected with each siRNA in OPTI-MEM medium for 48 hr and the medium was replaced with either vehicle or 2 nM of 1,25(OH)2D3 for 24 hr in OPTI-MEM containing 2% v/v charcoal-stripped fetal bovine serum.

value: endometrial stromal cells

value: 2 nM of 1,25(OH)2VitaminD3

tag: sirna

value: Human VDR siRNA


title: Human VDR siRNA transfected cells with vehicle (0.001% EtOH) treatment well 3

value: vehicle (0.001% EtOH)


title: Mouse-liver-1

description: 20 tissues sample from mice

value: liver


title: B3-8-NonDIC

description: Non-DIC

value: Leukocytes

value: No Treatment


title: HepG2 cells, untreated HepG2, HepG2_0h

value: Hepatocellular carcinoma cells

value: WT

value: untreated


title: A549-ACE2, H234A, 24hpi, rep1

value: human lung carcinoma cell


title: MRC5,scr,igG


title: MRC5,sh,igG


title: Mouse-lung-1

description: 20 tissues sample from mice

value: lung

value: qMap-seq


title: Human VDR siRNA transfected cells with vehicle (0.001% EtOH) treatment well 2


title: A549-ACE2, WT, 24hpi, rep2


title: B4-1-NonDIC

description: Non-DIC

value: sepsis without overt DIC


title: Human VDR siRNA transfected cells with 2 nM of 1,25(OH)2VitaminD3 treatment well 2


title: Human VDR siRNA transfected cells with 2 nM of 1,25(OH)2VitaminD3 treatment well 1


title: MRC5,sh,IP

value: FOXN3(Abgent, #AP19255B)


title: Mouse-leukocyte-6

description: 20 tissues sample from mice

source_name: leukocyte

value: leukocyte


title: MRC5,scr,input

value: Human embryonic lung fibroblasts


title: MRC5,scr,IP


title: A549-ACE2, mock, 24hpi, rep3


title: Human VDR siRNA transfected cells with vehicle (0.001% EtOH) treatment well 1

value: endometrial stromal cells


title: A549-ACE2, mock, 24hpi, rep2


title: Mouse-leukocyte-5

description: 20 tissues sample from mice


title: Mouse-liver-3

description: 20 tissues sample from mice


title: A549-ACE2, WT, 24hpi, rep1


title: Non-targeting pooled siRNA transfected cells with 2 nM of 1,25(OH)2VitaminD3 treatment well 3

value: 2 nM of 1,25(OH)2VitaminD3

value: Non-targeting pooled siRNA


title: A549-ACE2, mock, 24hpi, rep1


title: Mouse-leukocyte-4

description: 20 tissues sample from mice


title: mid-Hep from f-Hep P1 rep1

city: Beijing

first: Jie

last: Hao

state: 北京

address: Beijing

institute: Tsinghua University

data_processing:
RNA-seq reads were trimmed using Trimmomatic to remove detected adapters.
Trimmed sequence reads were mapped to hg19 using hisat2 with default parameters.
The number of reads mapped to each gene was counted with StringTie
Assembly: hg19
Supplementary files format and content: tab-delimited text files include gene expression counts for each sample

source_name: hESC (H9)

extract_protocol:
Total RNA was isolated by Trizol (Invitrogen) following the manufacturer’s instructions.
RNA-seq libraries were constructed with NEBNext® UltraTM RNA Library Prep Kit for Illumina (NEB, E7530L)

treatment_protocol: mid-Heps rep1 were differentiated by culturing f-Hep P1 in 6C medium for 15days, and 6C medium was changed every other day.

value: hESC (H9)

value: Pluripotent stem cells derived hepatocytes


title: A549-ACE2, N277A, 8hpi, rep3


title: Non-targeting pooled siRNA transfected cells with 2 nM of 1,25(OH)2VitaminD3 treatment well 1


title: 6C-S rep2

treatment_protocol: 6C-S rep2 were differentiated by culturing f-Hep P1 in 5C (withdrawing S) medium for 15days, and the medium was changed every other day.

value: Pluripotent stem cells derived cells


title: Non-targeting pooled siRNA transfected cells with 2 nM of 1,25(OH)2VitaminD3 treatment well 2


title: Mouse-leukocyte-1

description: 20 tissues sample from mice


title: 6C-S rep1

treatment_protocol: 6C-S rep1 were differentiated by culturing f-Hep P1 in 5C (withdrawing S) medium for 15days, and the medium was changed every other day.


title: A549-ACE2, N277A, 8hpi, rep1


title: Mouse-kidney-3

description: 20 tissues sample from mice

value: kidney


title: Mouse-kidney-2

description: 20 tissues sample from mice


title: 6C-A rep2

treatment_protocol: 6C-A rep2 were differentiated by culturing f-Hep P1 in 5C (withdrawing A) medium for 15days, and the medium was changed every other day.


title: Non-targeting pooled siRNA transfected cells with vehicle (0.001% EtOH) treatment well 1

value: vehicle (0.001% EtOH)


title: 6C-A rep1

treatment_protocol: 6C-A rep1 were differentiated by culturing f-Hep P1 in 5C (withdrawing A) medium for 15days, and the medium was changed every other day.


title: Non-targeting pooled siRNA transfected cells with vehicle (0.001% EtOH) treatment well 2


title: A549-ACE2, H234A, 8hpi, rep2


title: Mouse-kidney-4

description: 20 tissues sample from mice


title: Non-targeting pooled siRNA transfected cells with vehicle (0.001% EtOH) treatment well 3


title: HDAC7_3

city: Badalona

first: Maribel

last: Parra

state: Barcelona

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

department: Lymphocyte Development and Disease

country: Spain

institute: Josep Carreras Leukaemia Research Institute

data_processing:
Quality control of the samples was performed with the FASTQC tool
Paired-end reads were aligned to the human reference genome (GRCh38) using STAR (version 2.7.0a).
A count table file indicating the number of reads per gene in each sample was generated using HTSeq (version 0.10.0).
Genes with no or very low expression were filtered out and differentially expressed genes were identified using DESeq2.
Assembly: Genome Reference Consortium Human Build 38 (GRCh38).
Supplementary files format and content: Text file include normalized count values obtained using DESeq2

growth_protocol: Cells were extracted from subcutaneously injected mice and disgregated to obtain a single cell suspension of the tumor.

extract_protocol:
Total RNA was extracted with Quiagen RNA extraction kit.
Standard library was performed in all samples.
Paired-end mode with 100bp read length. 30 milion paired-end reads were generated per each sample

treatment_protocol: All injected mice received doxycicline in the drinking water.

value: DLBCL

value: doxycicline


title: A549-ACE2, H234A, 8hpi, rep3

value: human lung carcinoma cell


title: Mouse-kidney-1

description: 20 tissues sample from mice


title: 6C-P rep2

treatment_protocol: 6C-P rep2 were differentiated by culturing f-Hep P1 in 5C (withdrawing P) medium for 15days, and the medium was changed every other day.H57


title: A549-ACE2, H234A, 8hpi, rep1


title: HDAC7_2


title: 6C-P rep1

treatment_protocol: 6C-P rep1 were differentiated by culturing f-Hep P1 in 5C (withdrawing P) medium for 15days, and the medium was changed every other day.


title: mid-Hep from f-Hep P1 rep2

treatment_protocol: mid-Heps rep2 were differentiated by culturing f-Hep P1 in 6C medium for 15days, and 6C medium was changed every other day.


title: A549-ACE2, WT, 8hpi, rep3


title: HDAC7_1


title: A549-ACE2, N277A, 8hpi, rep2


title: Empty_2


title: Mouse-heart-2

description: 20 tissues sample from mice

source_name: heart

value: heart


title: 6C-C rep2

treatment_protocol: 6C-C rep2 were differentiated by culturing f-Hep P1 in 5C (withdrawing C) medium for 15days, and the medium was changed every other day.


title: 6C-C rep1

treatment_protocol: 6C-C rep1 were differentiated by culturing f-Hep P1 in 5C (withdrawing C) medium for 15days, and the medium was changed every other day.


title: Empty_1


title: A549-ACE2, WT, 8hpi, rep2


title: A549-ACE2, WT, 8hpi, rep1


title: Mouse-heart-3

description: 20 tissues sample from mice

value: qMap-seq


title: Mouse-erythrocyte-4

description: 20 tissues sample from mice

source_name: erythrocyte

value: erythrocyte


title: BLEODMY03 (dihydromyricetin)

first: Yu

last: Sun

address: 320 Yueyang Rd, Life Sciences Building A #1508

department: Shanghai Institute of Nutrition and Health

institute: Chinese Academy of Sciences

description: PE150 high throughout data

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 bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Human prostate tissue

growth_protocol: Normal human prostate stromal cells (PSC27) were routinely cultured in stromal complete media supplemented with 10% FBS, until a total number of approximately 1,000,000 was reached in each flask and subject to treatment by the chemotherapeutic agent bleomycin (BLEO) or BLEO combined with the phytochemical drug DMY.

extract_protocol:
Cells were lysed for RNA preparation using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 2 μg of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: To induce senescence, bleomycin (BLEO) was added to the media at 50 μg/ml, and cells were treated for 12 h before media change. Seven days later, to suppress the senescence-associated secretory phenotype (SASP) by a specific mechanism, the medicinal agent DMY was applied to the media at 100 µM.

value: Normal human primary prostate stromal cells

tag: passage

tag: name


title: A549-ACE2, mock, 8hpi, rep2

tag: cell type


title: A549-ACE2, mock, 8hpi, rep3


title: 6C-D rep1

treatment_protocol: 6C-D rep1 were differentiated by culturing f-Hep P1 in 5C (withdrawing D) medium for 15days, and the medium was changed every other day.


title: BLEODMY02 (dihydromyricetin)

description: PE150 high throughout data


title: 6C-M rep2

treatment_protocol: 6C-M rep2 were differentiated by culturing f-Hep P1 in 5C (withdrawing M) medium for 15days, and the medium was changed every other day.


title: A549-ACE2, mock, 8hpi, rep1


title: Mouse-heart-4

description: 20 tissues sample from mice


title: Mouse-erythrocyte-3

description: 20 tissues sample from mice


title: 6C-M rep1

treatment_protocol: 6C-M rep1 were differentiated by culturing f-Hep P1 in 5C (withdrawing M) medium for 15days, and the medium was changed every other day.


title: HUVEC_replicate_3

city: New York

first: Andrew

middle: A

last: Sproul

state: NY

address: 650 West 168th Street

institute: Columbia Univeristy

data_processing:
Illumina bcl2fastq 2.17 software
Possible adapter sequences and mucleotides rewmoed by using Trimmomatic v.0.36
Trimmed reads were mapped to Homo sapiens reference genome with STAR aligner v.2.5.2b
Hit counts were calculated by using featureCounts from the Subread package v.1.5.2
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: tab-delimited files contain raw counts for each sample
Supplementary files format and content: comma-seperated values contain FPKM values for each sample

source_name: Umbilical Cord

extract_protocol:
RNAs were harvested using QIAGEN mini RNA easy kit. 2 ul RNA was used for construction of RNA sequence
RNA libraries built woth NEBNext Ultra II RNA Library Prep Kit.

value: Umbilical Cord

value: HUVEC


title: Mouse-erythrocyte-1

description: 20 tissues sample from mice


title: f-Hep P1 rep2

treatment_protocol: To guarantee consistency of different samples for mechanism analysis, f-Heps were passaged and f-Heps P1 were employed.  f-Heps were dissociated with ACCUTASE (STEMCELL Technologies), and split at a ratio of 1:3 into the dish coated with Matrigel. Passaged cells were firstly cultured with hepatocyte plating medium (HPM) for 24h~48h. HPM was prepared with HCM medium (without EGF, Lonza) supplemented with 10μM Y-27632 (Selleck), 20ng/ml human HGF, 20ng/ml human OSM, 0.1μM Dex, 0.5μM A83-01, and 0.1μM Compound E. Then cells were cultured with hepatocyte differentiated medium (HDM) for 7days~10days, and the medium was changed every two days.


title: BLEO03 (dihydromyricetin)

description: PE150 high throughout data


title: HUVEC_replicate_2


title: Mouse-heart-1

description: 20 tissues sample from mice


title: 6C-D rep2

treatment_protocol: 6C-D rep2 were differentiated by culturing f-Hep P1 in 5C (withdrawing D) medium for 15days, and the medium was changed every other day.


title: Mouse-colon-4

description: 20 tissues sample from mice

source_name: colon

value: colon


title: HUVEC_replicate_1


title: f-Hep P1 rep1


title: Mouse-colon-3

description: 20 tissues sample from mice


title: a-Hep D40-2

treatment_protocol: a-Heps were differentiated by culturing mid-Hep in 4C medium for 40days, and 4C medium was changed every three days.


title: HBMEC_replicate_3

source_name: Brain

value: Brain

value: HBMEC


title: Mouse-colon-2

description: 20 tissues sample from mice


title: Mouse-colon-1

description: 20 tissues sample from mice


title: a-Hep D20-2

treatment_protocol: a-Heps were differentiated by culturing mid-Hep in 4C medium for 20days, and 4C medium was changed every three days.

value: hESC (H9)


title: a-Hep D40-1

value: Pluripotent stem cells derived hepatocytes


title: Mouse-erythrocyte-2

description: 20 tissues sample from mice


title: BLEODMY01 (dihydromyricetin)

description: PE150 high throughout data


title: CTRL02 (dihydromyricetin)

description: PE150 high throughout data


title: CTRL01 (dihydromyricetin)

description: PE150 high throughout data


title: a-Hep D20-1


title: BLEO02 (dihydromyricetin)

description: PE150 high throughout data


title: Mouse-breast-6

description: 20 tissues sample from mice

source_name: breast

value: breast


title: HBMEC_replicate_1


title: RAD03  (genotoxic chemotherapy and ionizing radiation)

description:
RAD03
PE150 high throughout data

source_name: Primary normal human prostate

growth_protocol: Normal human prostate stromal cells (PSC27) were routinely cultured in stromal complete media supplemented with 10% FBS, until a total number of approximately 1,000,000 was reached in each flask and subject to treatment by the chemotherapeutic agent bleomycin (BLEO) or exposure to 10 Gy ionizing radiation.

treatment_protocol: To induce senescence, bleomycin (BLEO) was added to the media at 50 μg/ml, and cells were treated for 12 h before media change. Alternatively, cells were exposed to ionizing radiation at 10 Gy. Each case, cellular senescence was allowed to develop for 7-10 days after treatment.

value: Normal human stromal cells


title: Mouse-breast-5

description: 20 tissues sample from mice


title: a-Hep D10-2

treatment_protocol: a-Heps were differentiated by culturing mid-Hep in 4C medium for 10days, and 4C medium was changed every three days.


title: Mouse-breast-3

description: 20 tissues sample from mice


title: pEC_replicate_4

value: pEC


title: RAD02  (genotoxic chemotherapy and ionizing radiation)

description:
RAD02
PE150 high throughout data


title: pEC_replicate_3


title: a-Hep D10-1


title: BLEO01 (dihydromyricetin)

description: PE150 high throughout data


title: Mouse-brain-4

description: 20 tissues sample from mice

source_name: brain

value: brain


title: PHH-3

source_name: Human liver

value: Human liver

value: primary human hepatocytes


title: CTRL03 (dihydromyricetin)

description: PE150 high throughout data


title: RAD01  (genotoxic chemotherapy and ionizing radiation)

description:
RAD01
PE150 high throughout data


title: BLEO03  (genotoxic chemotherapy and ionizing radiation)

description:
BLEO03
PE150 high throughout data


title: HBMEC_replicate_2


title: Mouse-brain-3

description: 20 tissues sample from mice


title: rBMEC_replicate_5

value: rBMEC


title: pEC_replicate_5


title: BLEO02  (genotoxic chemotherapy and ionizing radiation)

description:
BLEO02
PE150 high throughout data


title: Mouse-brain-2

description: 20 tissues sample from mice

value: qMap-seq


title: rBMEC_replicate_4


title: PHH-1


title: PHH-2


title: a-Hep-3(a-Hep D60-3)

treatment_protocol: a-Heps were differentiated by culturing mid-Hep in 4C medium for 60days, and 4C medium was changed every three days.


title: pEC_replicate_2


title: Mouse-brain-1

description: 20 tissues sample from mice


title: BLEO01  (genotoxic chemotherapy and ionizing radiation)

description:
BLEO01
PE150 high throughout data


title: a-Hep-2(a-Hep D60-2)


title: Mouse-blood-4

description: 20 tissues sample from mice

source_name: blood

value: blood


title: CTRL03  (genotoxic chemotherapy and ionizing radiation)

description:
CTRL03
PE150 high throughout data


title: Mouse-blood-3

description: 20 tissues sample from mice


title: rBMEC_replicate_3


title: CTRL02  (genotoxic chemotherapy and ionizing radiation)

description:
CTRL02
PE150 high throughout data


title: CTRL01  (genotoxic chemotherapy and ionizing radiation)

description:
CTRL01
PE150 high throughout data


title: mid-Hep-2

treatment_protocol: mid-Heps were differentiated by culturing f-Hep in 6C medium for 15days, and 6C medium was changed every other day.


title: HUVBR03

description: D.annot

source_name: Primary human umbilical vein

growth_protocol: Normal human umbilical vein-derived stromal cells (HUVEC) were routinely cultured in stromal complete media supplemented with 10% FBS, until a total number of approximately 1,000,000 was reached in each flask and subject to treatment by the chemotherapeutic agent bleomycin (BLEO) and/or ginkgo boliba extract (GBE) or rattan tea extract (RTE).

extract_protocol:
Cells were lysed for RNA preparation using Trizol reagent. 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.

treatment_protocol: To induce senescence, bleomycin (BLEO) was added to the media at 50 μg/ml, and cells were treated for 12 h before media change. To suppress the senescence-associated secretory phenotype (SASP) by a specific mechanism, medicinal agents ginkgo boliba extract (GBE) and rattan tea extract (RTE) were applied to the media at 900 µM, individually.

value: Normal human primary umbilical vein cells

value: rattan tea extract


title: a-Hep-1(a-Hep D60-1)


title: Mouse-blood-1

description: 20 tissues sample from mice


title: mid-Hep-3


title: Mouse-blood-2

description: 20 tissues sample from mice


title: pEC_replicate_1


title: rBMEC_replicate_1


title: HUVBR02

description: D.annot

value: HUVEC


title: Mouse-adipose-4

description: 20 tissues sample from mice

source_name: adipose

value: adipose


title: Mouse-adipose-3

description: 20 tissues sample from mice


title: mid-Hep-1


title: SKMEL-103 cells-BAY-850 treated, replicate 2

city: Birmimgham

first: Romi

last: Gupta

state: Alabama

address: 720, 20th street south

institute: University of Alabama at Birmingham

data_processing:
The reads were first mapped to the latest UCSC transcript set using Bowtie2 version 2.1.0 and the gene expression level was estimated using RSEM v1.2.15.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw count values for each Sample

source_name: SKMEL-103 cell line

growth_protocol: Cells were grown in DMEM medium or RPMI medium with 10% Fetal bovine serum and Penicilline and Streptomycin at  37 C under 5% CO2 condition.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen) as per the instruction from the manufacture and then purified using RNAeasy mini columns (Qiagen) as per the manufactures instructions.
mRNA is purified from approximately 500ng of total RNA with oligo-dT beads and sheared by incubation at 94C.  Following first-strand synthesis with random primers, second strand synthesis is performed with dUMP for generating strand-specific sequencing libraries.  The cDNA library is then end-repaired, and A-tailed, adapters are ligated and second-strand digestion is performed by Uricil-DNA-Glycosylase. Indexed libraries that meet appropriate cut-offs for both are quantified by qRT-PCR using a commercially available kit (KAPA Biosystems) and insert size distribution determined with the LabChip GX or Agilent Bioanalyzer. Samples with a yield of ≥0.5 ng/ul are used for sequencing.

value: SKMEL-103 cell line


title: f-Hep-2

treatment_protocol: human pluripotent stem cells (hPSCs) were maintained in matrigel-coated plates with mTeSR (Stem Cells). For mesendoderm differentiation, hPSCs were cultured in RPMI1640 (Gibco) supplemented with 100ng/ml Activin A (R&D), 3μM CHIR-99021 (Selleck), 1% GlutamaxTM (Gibco) and 1% penicillin/streptomycin (Gibco) for one day. For endoderm differentiation, mesendoderm cells were cultured in RPMI 1640 supplemented with 0.2% FBS (Gibco), 100ng/ml Activin A, 1% GlutamaxTM and 1% penicillin/ streptomycin for 1 days, and then cultured in RPMI1640 supplemented with 2% FBS (Gibco), 100ng/ml Activin A, 1% GlutamaxTM and 1% penicillin/ streptomycin for another day. For hepatoblast differentiation, endoderm cells were induced in DMEM (Gibco) supplemented with 20ng/ml bFGF (Invitrogen), 20ng/ml human BMP4 (R&D), 0.5μM A83-01 (Tocris Bioscience), 0.1μM Dex (Invitrogen), 0.05% BSA (Invitrogen), 2% B27 (Gibco) and 1%P/S for 4 days, and the medium was changed every other day. For f-Hep differentiation, hepatoblasts were further cultured in hepatocyte differentiated medium (HDM) for 10 days. HDM medium was prepared with HCM (without EGF, Lonza) with 20ng/ml human HGF (R&D), 20ng/ml human OSM (R&D), 0.1μM Dex (Sigma-Aldrich), 0.5μM A83-01(Tocris Bioscience) and 0.1μM Compound E (Tocris Bioscience), and the medium was changed every other day.


title: SKMEL-103 cells-BAY-850 treated, replicate 3


title: HUVBG03

description: C.annot

value: ginkgo boliba extract


title: HUVBR01

description: D.annot


title: f-Hep-3

value: hESC (H9)


title: Mouse-adipose-1

description: 20 tissues sample from mice


title: f-Hep-1

value: Pluripotent stem cells derived hepatocytes


title: SKMEL-103 cells-DMSO treated, replicate 3

value: DMSO


title: Mouse-ESC-4

description: 24 commonly used cell lines samples

value: ESC


title: HUVBG02

description: C.annot


title: SKMEL-103 cells-BAY-850 treated, replicate 1


title: HUVBG01

description: C.annot


title: rBMEC_replicate_2


title: PHH-2 ATAC-seq

data_processing:
ATAC-seq adapter sequence were identified and trimmed with cutadapt tool.
ATAC-seq reads were aligned to human hg19 reference genome using BWA-MEM with default parameters. Fragments were identified as read pairs with mapping quality >10 and non-mitochondrial reads.
PCR duplicates were removed with sambamba (v0.8.0). The start and end of the fragments were adjusted (+4 for +strand and −5 for −strand) to account for the Tn5 transposase enzyme occupied region.
ATAC peak calling was performed using MACS with a p-value threshold of 0.01, and with other settings as --nomodel --shift -75 --extsize 150 --SPMR.
ATAC bigWig files were generated using the bamCoverage tools. Score represents the normalized coverage of DNA fragments at a given genomic coordinate.
Assembly: hg19
Supplementary files format and content: bigWig, bed

source_name: liver

extract_protocol:
f-Heps, mid-Heps, and a-Heps were dissociated with Accutase, and collected in HCM medium. Frozen PHHs purchased from Celsis IVT (Lot: ONO) were recovered according to the manufacturer’s instructions.
ATAC libraries were prepared using Omni-ATAC protocol as previously described, and TruePrep® DNA Library Prep Kit V2 for Illumina (Vazyme, China) was employed. Briefly, 50,000 cells were washed with cold PBS once and lysed with 50 μl cold ATAC-Resuspension Buffer (RSB) (10 mM pH 7.4 Tris-HCl, 10 mM NaCl, and 3 mM MgCl) containing 0.1% NP40 and 0.1% Tween-20. After incubation on ice for 3 minutes, 1 ml of cold ATAC-RSB containing 0.1% Tween-20 (without NP40) was added to the cell lysate and mixed by inverting 3 times. The nuclei were collected by centrifuging at 500 g for 10 minutes at 4 °C. For the transposition reaction, nuclei were incubated with Tn5 Transposition mix (10 μl 5 × TTBL buffer, 3 μl TTE Mix V50 transposase, 16.5 μl PBS, 0.5 μl 10% Tween-20 and 20 μl H2O) at 37 °C for 30  minutes. Next, the stop buffer was directly added to end the reaction, and  PCR was performed to amplify the library for 12 cycles. Then the libraries were purified with 1.2 × AMPure beads (Beckman), and sequenced using an Illumina Novaseq 6000.

treatment_protocol: Frozen PHH purchased from Celsis IVT (Lot: ONO) were defrosted according to manufacturer’s instructions  and collected in HCM medium.

value: liver

value: primary human hepatocyte

value: primary cell


title: rBMEC_replicate_6


title: SKMEL-103 cells-DMSO treated, replicate 2


title: HUVB03

description: B.annot

value: bleomycin


title: SKMEL-103 cells-DMSO treated, replicate 1


title: PHH-1 ATAC-seq


title: Mouse-ESC-3

description: 24 commonly used cell lines samples


title: Mouse-ESC-2

description: 24 commonly used cell lines samples


title: HUVB02

description: B.annot


title: A375 cells-BAY-850 treated, replicate 3

source_name: A375 cell line

value: A375 cell line


title: Mouse-ESC-1

description: 24 commonly used cell lines samples

value: qMap-seq


title: a-Hep-2 ATAC-seq

source_name: hESC (H9)


title: HUVB01

description: B.annot


title: Mouse-adipose-2

description: 20 tissues sample from mice


title: A375 cells-BAY-850 treated, replicate 2


title: Mouse-3T3-4

description: 24 commonly used cell lines samples


title: a-Hep-1 ATAC-seq


title: A375 cells-BAY-850 treated, replicate 1


title: mid-Hep-2 ATAC-seq


title: HUV02

description: A.annot


title: Mouse-3T3-3

description: 24 commonly used cell lines samples


title: Mouse-3T3-2

description: 24 commonly used cell lines samples


title: A375 cells-DMSO treated, replicate 2


title: HUV03

description: A.annot


title: A375 cells-DMSO treated, replicate 3


title: HUV01

description: A.annot


title: mid-Hep-1 ATAC-seq


title: Sample 9 (C03)

description:
PE150 high throughout data
C.gene.count.matrix.annot
Sample 9 (C03)

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 mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: BLEO/CCE 03

growth_protocol: Normal human prostate-derived stromal cells (PSC27) were routinely cultured in stromal complete media supplemented with 10% FBS, until a total number of approximately 1,000,000 was reached in each flask and subject to treatment by the chemotherapeutic agent bleomycin (BLEO) and/or cocoa extract (CCE).

treatment_protocol: To induce senescence, bleomycin (BLEO) was added to the media at 50 μg/ml, and cells were treated for 12 h before media change. To suppress the senescence-associated secretory phenotype (SASP) by a specific mechanism, the medicinal agent cocao extract (CCE) was applied to the media at 200 µM, individually.

value: Normal human prostate derived primary stromal cells


title: Mouse-3T3-1

description: 24 commonly used cell lines samples


title: A375 cells-DMSO treated, replicate 1


title: f-Hep-1 ATAC-seq


title: Mouse-3T3_L1-4

description: 24 commonly used cell lines samples


title: Sample 8 (C02)

description:
PE150 high throughout data
C.gene.count.matrix.annot
Sample 8 (C02)

source_name: BLEO/CCE 02


title: Sample 7 (C01)

description:
PE150 high throughout data
C.gene.count.matrix.annot
Sample 7 (C01)

source_name: BLEO/CCE 01