title: X_106_blood

value: male


title: 115_hglBM3

status: Public on Oct 15 2021

type: SRA

city: Rochester

first: Stephan

last: Emmrich

state: NY

address: 213 Hutchison Hall, River Campus

country: USA

institute: University of Rochester

library_source: transcriptomic

data_processing:
library strategy: single-cell CITE-Seq
Cellranger 3.1.0 was used to generate count matrices from either an ENSEMBL94 mouse reference ("mmuBM") or FRAMA naked mole-rat BM transcriptome assembly ("hglBM")
RNA features were uniquefied using data.table by sum-up each duplicate
ADT features from each sample were concatenated
Annotation of features, molecules/cells and samples was indexed against the feature matrices
Supplementary_files_format_and_content: R workspace containing RNA count matrix, ADT count matrix and cell annotation

molecule: total RNA

organism: Heterocephalus glaber

source_name: hematopoietic system

growth_protocol: Naked mole-rat or Mouse primary bone marrow cells from healthy specimen

extract_protocol:
Cells were DAPI-sorted as viable unfractionated marrow tissue
Chromium Single-Cell 3′ Library & Gel Bead Kit v3 (10X Genomics)

treatment_protocol: Cells were processed for TotalSeq™ CITE reagents according to the manufacturers instructions (BioLegend), using both human and mouse Fc blocking reagents (BioLegend)

tag: strain

value: Naked mole-rat

tag: tissue

value: bone marrow

tag: age

value: 11 years

tag: genotype

value: wildtype

tag: molecule subtype

value: 3' mRNA UMI


title: Young 2

city: Raleigh

first: Raquel

last: Maeso-Diaz

state: United States

address: 3901 Sue Lane

institute: Duke University

description: Young 2

data_processing:
Trim_galore trim off adapter and low quality reads
STAR aligning the reads (STAR/2.5.0c-fasrc01)
Samtools index sorted bam files
Picard remove duplicates
HTSeq quantify Gene Expression Data
Genome_build: mm10_STAR_genome_idx
Supplementary_files_format_and_content: BAM counts
Supplementary_files_format_and_content: File Counts Young and Old: Young Hepatocytes (Young 1, Young 2, Young 3), Young Regenerating Hepatocytes (YoungPH1, YoungPH2, YoungPH3), Old Hepatocytes (Old1 , Old2, Old3), Old Regenerating Hepatocytes (OldPH1, OldPH2, OldPH3)
Supplementary_files_format_and_content: File Counts Smo+ and Smo- : Smo + Hepaotcytes (Luci), Smo + Regenerating Hepatocytes (LuciPH), Smo - Hepatocytes (Cre 1, Cre2), Smo - Regenerating Hepatocytes (CrePH1, CrePH2)

organism: Mus musculus

source_name: Hepatocytes

growth_protocol: To obtain primary hepatocytes, livers were perfused with collagenase as described.  Hepatocyte preparations were evaluated by light microscopy to assure that viability and purity were at least 95%. Freshly isolated hepatocytes were immediately processed to obtain RNA.

extract_protocol:
Global transcriptome profiling of was performed by RNA-seq using freshly isolated hepatocytes from young and old wild type mice or Smo-floxed mice before and at 48 h after PH (n=3wild type mice/group/time point), n=1 Smo-flox-Luci mice/time point and n=2 Smo-flox-Cre mice/time point). Total RNA was extracted using RNeasy mini kit (Qiagen, Hilden, Germany) following the manufacturer’s instructions.
mRNA library preparation (poly A enrichment)

treatment_protocol: C57BL/6J 3-month-old wild-type (Young) mice were obtained from Jackson Laboratories (Bar Harbor, ME). C57BL/6J 24-month-old wild-type (Old) mice were obtained from the NIA Aged Rodent Colonies (https://www.nia.nih.gov/research/dab/agedrodent-colonies-handbook). Adult male, C57BL/6J wild-type (WT) mice (Jackson Laboratory, Bar Harbor, ME) and adult male Smoothened (Smo) tm2Amc/J (Smo-flox) mice on a C57Bl6/J background were purchased from the Jackson Laboratory (Bar Harbor, ME) and studied at 2-3 months of age. All mice were housed in a barrier facility on 12 h:12 h light cycle with free access to water and standard chow diet (Rodent diet 20, 5033; Picolab, St. Louis, MO). Male Smo flox/flox mice were injected by tail vein with 5 × 1011 genome-equivalents of AAV8-TBG-Luc (control; Smo (+); n = 50 mice) or AAV8-TBG-Cre (Smo (-); n = 50 mice) to selectively delete the Smoothened (Smo) gene in hepatocytes. Viruses were obtained from the University of Pennsylvania Viral Vector Core.   70% partial hepatectomy (PH) (10, 16) was performed on young and old wild type mice and young Smo-floxed mice without or with Smo deletion (n=50 mice/group). Smo-floxed mice underwent PH 7 days after viral injection based on pilot studies showing reproducibly efficient deletion of floxed Smo alleles by this time point.

value: 3 months-old

tag: aav8-luci or cre

value: No

tag: quiescent or regenerating

value: Quiescent


title: OX_379_CBM-PV-CD42b

city: London

first: Tiago

last: Cunha Luis

address: South Kensington, Sir. Alexander Fleming Building

department: Department of Life Sciences

country: United Kingdom

institute: Imperial College London

description:
Central bone marrow perivascular cells
counts.txt
OX_379

data_processing:
Reads were trimmed with trimgalore settings  --stringency 3 --nextera
Reads were aligned to the mm10 genome reference with tophat version 2.0.10 and the refSeq annotation
Reads were sorted and indexed with samtools
Reads were filtered with samtools options -b F 0xF00
Reads were counted and assigned to mm10  transcripts in R with packages Rsamtools and GenomicAlignments
Genome_build: mm10
Supplementary_files_format_and_content: csv, raw counts

extract_protocol:
Cells were FACS sorted directly into lysis buffer
Clonetech/SmartSeq kits; Libraries were sequenced on a HiSeq2500 or a HighSeq4000 sequecing machine.

treatment_protocol: Platelet depletion by injecting anti-CD42b antibody. Controls received an IgG Isotype control antibody

tag: background strain

tag: cell markers

value: CD45- Ter119- CD31- LepR+

tag: cell type

value: Central bone marrow perivascular cells

tag: treatment

value: GPIba/CD42b Antibody


title: Old 1

description: Old 1

value: 24 months-old


title: X_31_pleural effusion

city: Beijing

first: Mingming

last: Shao

state: State...

address: 8 Gongren Tiyuchang Nanlu

country: China

institute: Beijing Chao-Yang Hospital

data_processing:
The data alignment to the reference genome with Cell Ranger using "mkfastq" and "count" commands and default parameters.
Used Seurat to create data objects from the matrix outputs.
Genes with an expression ratio of > 0.1% and cells with 200 to 6,000 detected genes were selected.
Genome_build: GRCh38.93
Supplementary_files_format_and_content: Matrix table with gene counts

organism: Homo sapiens

source_name: Human_pleural effusion

extract_protocol:
Pleural fluid samples from each subject were collected in heparin-treated tubes within 24 hours after hospitalization, using standard thoracentesis techniques. Approximately 5 mL of venous blood were drawn simultaneously. The pleural effusion specimens were immediately immersed in ice and were then centrifuged at 1,200 rpm for 5 min. The cell-free supernatants of PE and sera were frozen at -80°C immediately after centrifugation. Mononuclear cells from pleural ﬂuid and blood were isolated by Ficoll-Hypaque gradient centrifugation within 1 hour and were resuspended in PBS.
Single-cell libraries were constructed using the Single Cell 5′ Library & Gel Bead Kit, Single Cell V(D)J Enrichment Kit, Human T Cell, or Single Cell V(D)J Enrichment Kit, Human B Cell. According to the cDNA synthesis and Chromium Single Cell A Chip Kits, cell suspensions were loaded on a Chromium Controller to generate single-cell gel beads in the emulsion. The cDNA libraries were constructed using Single Cell 5′ Library Construction Kit and i7 Multiplex Kit.

tag: diagnosis

value: lung adenocarcinoma

tag: Sex

value: female

value: pleural effusion


title: 116_hglBM4

value: 3 years


title: 113_hglBM1


title: X_103_pleural effusion

value: male


title: X_52_pleural effusion


title: OX_375_CBM-PV-CD42b

description:
Central bone marrow perivascular cells
counts.txt
OX_375


title: Rgnavus_Preg_rep2

status: Public on Oct 14 2021

city: Bellinzona

first: Andrea

last: Alimonti

address: Via vela 6

department: Molecular Oncology

country: Switzerland

institute: Institute of oncology research

data_processing:
Samples were processed starting from stranded, single ended 75bp-long sequencing reads
Fastq files were generated using BaseSpace tool (Illumina, San Diego, CA, USA). Ruminococcus Gnavus ATCC 29149 genome assembly ASM16947v1 was retrieved from EnsemblBacteria (https://bacteria.ensembl.org) along with the respective gene annotations.
Genome indexes and the subsequent sequencing read alignment were performed using bwa-mem.
Genome_build: genome assembly ASM16947v1
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Mediterraneibacter gnavus

source_name: bacteria culture

growth_protocol: R. gnavus was cultured in anaerobic condition in TSB medium.

extract_protocol:
Bacterial cultures were then stabilized with RNAprotect Bacteria Reagent, then enzymatic lysis (15mg/ml lysozyme) and proteinaseK digestion were performed following manufacturers’ guidelines. RNA was then extracted using RNeasy Mini Kit and on-column DNase treatment was performed following manufacturers’ guidelines.
RNA integrity was checked by agarose gel electrophoresis. Illumina Stranded Total RNA with Ribo Zero Plus  was employed with IDT® for Illumina® RNA UD Indexes Set A,  for cDNA synthesis and addition of barcode sequences. Sequencing of the libraries was performed using the NextSeq 500 with the NextSeq 500/550 High Output Kit v2 (75 cycles; Illumina).

treatment_protocol: Exponentially growing culture of R.gnavus were inoculated with vehicle (EtOH) or pregnenolone for 1h.

value: Pregnenolone

value: Ruminococcus Gnavus ATCC 29149


title: Young 1

description: Young 1


title: X_52_blood

value: blood


title: Rgnavus_Preg_rep1


title: 2-hg

city: Hangzhou

first: Jing

last: Zhao

address: Yuhang Road 866

institute: Zhejiang University

data_processing:
All bulk RNA-seq reads were trimmed using Trimmomatic software with the following parameters “ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36” (Version 0.36) and were further quality-filtered using fastq_quality_trimmer command in FASTX Toolkit (Version 0.0.13) with the minimum quality score 20 and minimum percent of 80% bases that has a quality score larger than this cutoff value.
The high-quality reads were mapped to the mm10 genome by HISAT2, a fast and sensitive spliced alignment program for mapping RNA-seq reads, with -dta paramenter; PCR duplicate reads were removed using Picard tools
The expression levels of genes and repeat sequences were independently calculated by StringTie (Version v1.3.4d) with -e -B -G parameters using Release M18 (GRCm38.p6) gene annotations downloaded from GENCODE data portal and annotated repeats (RepeatMasker) downloaded from the UCSC genome browser, respectively.
Differential expression analysis of genes in different samples was performed by DESeq2 using the reads count matrix produced from a python script “prepDE.py” provided in StringTie website (http://ccb.jhu.edu/software/stringtie/).

source_name: mouse embryo

growth_protocol: Zygotes were harvested from oviduct and culture in KSOM

extract_protocol:
The embryo were treated 0.2% Triton X-100
Sequencing libraries were constructed from 1 ng of pre-amplified cDNA using DNA library preparation kit

treatment_protocol: 2PN were treatment with 0.15 mM  α-KG or 0.3 mM 2-HG


title: akg

value: alpha-kg


title: NC_2hg

value: Negative control_2hg


title: NC_akg

value: Negative control_akg


title: KD2_rep2

first: Chen

last: Dong

address: Haidian District

department: Institute for Immunology and School of Medicine

institute: Tsinghua University

data_processing:
Clean reads were aligned to mm10 by bowtie2 with default parameters
Uniquely mapping reads were summarized by featureCounts(from Subread package)
RPKM (Reads Per Kilobase of exon model per Million mapped reads) were calculated using edgeR TMM normalization
Differentially expressed genes were identified by at least 1.5fold change and fdr adjusted p-value 0.05 using Deseq2
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include gene symbol and gene expression (or read count) for each sample

source_name: Tfh-like cell

growth_protocol: wild type or Mapk1-KO naïve CD4+ T cells were activated and cultured under IL-6 plus anti-IL2/IL-4/IFN-γ/TGFβ

extract_protocol: The total RNA was extracted with Trizol (Life Technologies) according to manufacturer’s instructions

treatment_protocol: PMA/ionomycin treatment or viral infection when specified

value: pMKO.1-sh-Zfp831 transfected

value: Spleen+Lymph nodes

value: Tfh-like cell

value: 3 days in vitro


title: EV_rep2

value: empty vector transfected


title: EV_rep1


title: KD2_rep1


title: Mapk1_WT_rep2

value: wild type


title: 114_hglBM2

value: Naked mole-rat

value: bone marrow

value: 11 years

value: wildtype

value: 3' mRNA UMI


title: PI

value: PMA/ionomycin


title: Mapk1_KO_rep2


title: 3+28


title: Rgnavus_Veh_rep1

value: Vehicle (Ethanol)

value: Ruminococcus Gnavus ATCC 29149


title: Rgnavus_Veh_rep2


title: Rgnavus_Veh_rep4


title: Rgnavus_Veh_rep3


title: Rgnavus_Veh_rep5


title: Brain, RFPpos4

city: Groningen

first: Emma

last: Gerrits

email: e.gerrits@rug.nl, e.gerrits@umcg.nl

state: Groningen

address: Antonius Deusinglaan 1

department: BSCS

country: Netherlands

institute: UMCG

description: countmtx.csv

data_processing:
Bulk: Lexogen Quantseq 2.3.1. FWD UMI pipeline on the BlueBee Genomics platform (1.10.18); Single-cell: Cell ranger v3.0.0 with default settings.
Genome_build: mm10
Supplementary_files_format_and_content: Raw count files

source_name: Brain

extract_protocol:
RNA isolation: All Prep DNA/RNA micro kit (Qiagen).
3' Quantseq FWD from Lexogen. 3' Single-cell RNA sequencing protocol v3 from 10x Genomics

tag: protocol

value: Bulk RNAseq

tag: mouse #

tag: age (weeks)

tag: gender

value: M

value: C57BL/6 background

value: brain

value: RFPpos cells


title: Mapk1_WT_rep1

value: Spleen+Lymph nodes

value: Tfh-like cell


title: Mapk1_KO_rep1

value: 3 days in vitro


title: Differentiated erythroid cells - Phase II Day 14 - Replicate 2

city: Vellore

first: Shaji

middle: R

last: Velayudhan

state: Tamil Nadu

address: Centre for Stem Cell Research, Christian Medical College, Bagayam

country: India

institute: Christian Medical College

description:
Phase II Day 14- R2
Early stage erythroid progenitor cells from day 14 of phase II of the culture
Small RNA-seq

data_processing:
The bioinformatics analysis to estimate the differential expression of miRNAs was performed with The UEA small RNA Workbench (http://srna-workbench.cmp.uea.ac.uk/) using default settings allowing 1 mismatch during the alignments with the small RNA sequence lengths ranging from 16 to 26 nucleotides.
The reads were aligned with miRBase version 22.1 (https://www.mirbase.org/ftp.shtml), and normalization of the miRNA reads and differential expression were calculated using DESeq using default parameters.
Human genome hg19 reference fasta files were indexed using bowtie tool version 0.12.9.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Processed_files_RVS_raw_reads_GEO.txt: Tab-delimited text file includes DESeq normalized counts.

source_name: Cultured erythroid cells

growth_protocol: CD34+ HSPCs were isolated from mobilized peripheral blood of a healthy individual using a positive magnetic bead-based selection kit (StemCell Technologies, Vancouver, BC, Canada). Phase I of the culture, 5 X 10^6 purified CD34+ cells were seeded in a serum-free HSPC expansion medium composed of StemSpan SFEM-II (Stem Cell Technologies, Vancouver, Canada) supplemented with 100 U/ml penicillin,100 µg/ml streptomycin (Thermo Fisher Scientific, Inc., Grand Island, NY, USA), 2mM L-glutamine (Thermo Fisher Scientific, Inc., Grand Island, NY, USA), 100ng/ml recombinant human stem cell factor (rh SCF), 100ng/ml recombinant human fms related tyrosine kinase 3-ligand (rh Flt3-L), 20ng/ml recombinant human interleukin-6 (rh IL-6), 50ng/ml recombinant human interleukin-3 (rh IL-3) and 100ng/ml recombinant human thrombopoietin (rh TPO). After expanding the cells for 5 days in phase I of the culture, the cells were transferred to phase II of the culture in Stem Span SFEM-II medium containing 50ng/ml rh SCF, 40ng/ml recombinant human insulin growth factor-1 (rh IGF1),10ng/ml IL-3 and 3U/ml recombinant human erythropoietin (rh Epo). All cytokines were purchased from Peprotech Inc., Rocky Hill, NJ, USA. The cell density was maintained at 0.5 X 10^6 cells/ml throughout the culture, and the medium was changed every alternate day.

extract_protocol:
Total RNA was extracted using Total RNA Purification Kit (Norgen Biotek Corp).
Small RNA libraries were prepared NEBNext Multiplex Small RNA Library Preparation Kit (New England Biolabs, Ipswich, MA, USA) as per the manufacturer’s protocols. The products were checked for fragment size distribution (140-160bp) on TapeStation (Agilent Technologies) using High Sensitivity D1000 DNA ScreenTapes (Agilent Technologies) followed by size selection (140-160bp) on 4% E-Gel EX Agarose Gel (Thermo Fisher Scientific, Rockford, IL, USA). Prepared libraries were quantified using Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific). The obtained libraries were pooled and diluted to a final optimal loading concentration before cluster amplification on the Illumina flow cell (Illumina Inc., San Diego, CA, USA). Once the cluster generation was completed, the cluster flow cell was loaded on Illumina HiSeq 2500 instrument to generate 20 million 50bp paired-end reads.

treatment_protocol: No treatment was performed.

value: Differentiated late stage erythroid cells

tag: time point

value: Day 14 of phase II of the culture


title: Brain, RFPpos3

description: countmtx.csv

tag: strain

tag: tissue


title: Brain, SC_total_viable

value: Single-cell RNAseq

value: F

value: total viable population cells


title: Brain, RFPpos2

description: countmtx.csv

tag: genotype


title: Differentiated erythroid cells - Phase II Day 14 - Replicate 3

description:
Phase II Day 14- R3
Early stage erythroid progenitor cells from day 14 of phase II of the culture
Small RNA-seq


title: Brain, SC_RFP_pos


title: Brain, RFPpos5

description: countmtx.csv


title: Differentiated erythroid cells - Phase II Day 9 - Replicate 3

description:
Phase II Day 9- R3
Early stage erythroid progenitor cells from day 9 of phase II of the culture
Small RNA-seq

value: Differentiated early stage erythroid cells

value: Day 9 of phase II of the culture


title: Differentiated erythroid cells - Phase II Day 14 - Replicate 1

description:
Phase II Day 14- R1
Early stage erythroid progenitor cells from day 14 of phase II of the culture
Small RNA-seq


title: Differentiated erythroid cells - Phase II Day 11 - Replicate 2

description:
Phase II Day 11- R2
Early stage erythroid progenitor cells from day 11 of phase II of the culture
Small RNA-seq

value: Differentiated intermediate stage erythroid cells

value: Day 11 of phase II of the culture


title: Brain, RFPpos1

description: countmtx.csv

value: Bulk RNAseq


title: Differentiated erythroid cells - Phase II Day 11 - Replicate 1

description:
Phase II Day 11- R1
Early stage erythroid progenitor cells from day 11 of phase II of the culture
Small RNA-seq


title: Brain, RFPneg1

description: countmtx.csv

value: M

value: RFPneg cells


title: Colon mesenchyme-1

city: New Haven

first: Jun

state: CT

address: 300 George Street

department: Pathology/Immunology

institute: Yale University

data_processing:
Drop-seq_tools-1.0 was used to perform alignment and generation of gene expression matrix
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene in every single cell

source_name: Colon mesenchyme

growth_protocol: Standard mouse housing conditions, freshly isolated cells

extract_protocol:
Epithelial depletion with EDTA and DTT. Mesenchymal cell isolation with Collagenase XI and Dispase
Drop-seq protocol

treatment_protocol: No treatment of mice. No treatement of cells.

tag: age

value: 10 weeks

value: middle and distal colon

value: Mesenchymal cell


title: Differentiated erythroid cells - Phase II Day 9 - Replicate 1

description:
Phase II Day 9- R1
Early stage erythroid progenitor cells from day 9 of phase II of the culture
Small RNA-seq


title: Brain, RFPneg4

description: countmtx.csv

value: C57BL/6 background

value: brain


title: Cultured CD34+ cells - Phase I Day 3 - Replicate 3

description:
Phase I Day 3 -R3
Expanded CD34+ HSPCs from day 3 of phase I of the culture
Small RNA-seq

source_name: Cultured CD34+ cells

value: Undifferentiated HSPCs

value: Day 3 of phase I of the culture


title: Brain, RFPneg5

description: countmtx.csv


title: SMN Day 32

city: Albany

first: Janet

middle: L

last: Paluh

address: CNSE, Nanofab East, 257 Fuller Road

department: Nanobioscience

institute: SUNY Polytechnic Institute

description:
NMP differentiation protocol
SMN_NS_32_S6

data_processing:
Illumina RTA 2.2.68 Basecaller
Hisat2 Alignments 2-2.1.0 to UCSC HG38
FeatureCounts v1.6.2 Quantiication
DESeq Differential Expression
Genome_build: hg38
Supplementary_files_format_and_content: CSV File with quantifications

source_name: Human iPSC  line F3.5.2 passage  20

growth_protocol: hiPSC in 2D grown in mTeSR Plus medium were induced to Neuromesodermal Progenitors (NMPs) and neurons as described in text and 2D colonies dissociated

extract_protocol: TruSeq Stranded RNA (illumina)

value: African-American self designation

value: hiPSC derived

value: Spinal Motor Neurons

tag: developmental stage

value: Day 32


title: Differentiated erythroid cells - Phase II Day 11 - Replicate 3

description:
Phase II Day 11- R3
Early stage erythroid progenitor cells from day 11 of phase II of the culture
Small RNA-seq


title: Differentiated erythroid cells - Phase II Day 9 - Replicate 2

description:
Phase II Day 9- R2
Early stage erythroid progenitor cells from day 9 of phase II of the culture
Small RNA-seq

value: Differentiated early stage erythroid cells

value: Day 9 of phase II of the culture


title: Brain, RFPneg3

description: countmtx.csv


title: SMN Day 37

description:
NMP differentiation protocol
SMN_NS_37_S7

source_name: Human iPSC  line F3.5.2 passage 20

value: Day 37


title: Cultured CD34+ cells - Phase I Day 3 - Replicate 2

description:
Phase I Day 3 -R2
Expanded CD34+ HSPCs from day 3 of phase I of the culture
Small RNA-seq


title: Cultured CD34+ cells - Phase I Day 3 - Replicate 1

description:
Phase I Day 3 -R1
Expanded CD34+ HSPCs from day 3 of phase I of the culture
Small RNA-seq


title: NMP Day 25

description:
NMP differentiation protocol
SMN_25_S4

value: Motor Neuron Progenitors

value: Day 25


title: scNSC Rosettes  Day 10

description:
NMP differentiation protocol
NSC_Rosette_1_S1

value: scNSC Rosettes

value: Day 10


title: Brain, RFPneg2

description: countmtx.csv

value: Bulk RNAseq

value: M

value: RFPneg cells


title: iPSC-/- PP1 1 [TBX3 KO D8]

city: Philadelphia

first: Paul

last: Gadue

state: PA

address: 3501 Civic Center Blvd Room 5012

institute: Children's Hospital of Philadelphia

data_processing:
Reads were trimmed using cutadapt and quality scores were assessed using FastQC
Reads were aligned to the Homo sapiens genome build hg19 using STAR
Individual sample reads were quantified using HTseq and normalized via Relative Log Expression (RLE) using DESeq2 R library
Read Distribution percentages, violin plots, identity heatmaps, and sample MDS plots were generated as part of the QC step using RSeQC
DEseq2 was also used to calculate fold changes and p-values and perform optional covariate correction
Clustering of genes for the final heatmap of differentially expressed genes was done using the PAM (Partitioning Around Medoids) method using the fpc R library
Hypergeometric distribution was used to analyze the enrichment of pathways, gene ontology, domain structure, and other ontologies.
Differentially expressed genes passed a threshold of +/- 1.5 fold change and have an adjusted p-value < 0.05
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file (.txt) including raw read counts for each sample
Supplementary_files_format_and_content: tab-delimited text file (.txt) including normalized read counts for each sample

source_name: Pluripotent-stem cell derived pancreatic progenitor 1 cells (day 8)

growth_protocol: Wildtype and TBX3 knockout iPS cells were differentiated to gut tube (day 6) and pancreatic progenitor 1 (day 8) stages folowing a pancreatic differentiation protocol

extract_protocol:
RNA was extracted using the PureLink RNA Micro Kit (Invitrogen) following the manufacturer's protocol
RNA libraries were prepared for sequencing following protocols from the TruSeq Stranded mRNA Library Prep Kit High Throughput kit (Illumina)

value: Pancreatic progenitor 1 (Day 8)

tag: differentiation protocol

value: Pancreatic differentation protocol


title: iPSC-/- PP1 3 [TBX3 KO D8]


title: SMN Day 42

description:
NMP differentiation protocol
SMN_NS_42_S8

value: Day 42


title: GES-1 cells, CDCA Treatment, Input

city: Shanghai

first: Ben

last: Yue

address: 160 Pujian Road

institute: Renji Hospital, School of Medicine, Shanghai Jiao Tong University

data_processing:
Low-quality and adaptor bases were trimed by Trimmomatictools (version:0.36)
clean reads undergone rRNA deleting through RNAcentralt to get effective reads.
Genomic alignment was using Tophat (2.0.13) to get uniquely mapping reads.
MACS2 (2.1.0.) was employed to perform m6A peak calling.
Differential methylation was determined by Pyicoenrich (2.0.7).
Genome_build: hg19
Supplementary_files_format_and_content: xls, m6A peaks

source_name: Human Gastric Epithelial Cells

growth_protocol: Cultured in RPMI-1640 medium

extract_protocol:
RNA was immunoprecipitated by m6A antibody.
100ng RNA was used for library building following NEBNext Ultra RNA Library Prep Kit protocol for Illumina (NEB, USA).  rRNA-removal RNA.
Final library product sequenced on Illumina platform, pair end reads for 150bp.

treatment_protocol: GES-1 cells treated with CDCA (100 μM for 48 h)

tag: cell line

value: Gastric Epithelial Cell line GES-1

value: CDCA Treatment

tag: rip antibody


title: scNSC Rosettes + chABC Day 10

description:
NMP differentiation protocol
NSC_Rosette_2_S2

value: African-American self designation

value: hiPSC derived

tag: cell type

value: scNSC Rosettes + chABC


title: GES-1 cells, Control, MeRIP

tag: treatment

value: No Treatment

value: m6A antibody


title: GES-1 cells, CDCA Treatment , MeRIP


title: iPSC+/+ PP1 3 [WT D8]

value: Wildtype


title: SMN Day 28

description:
NMP differentiation protocol
SMN_28_S5

value: Spinal Motor Neurons

value: Day 29


title: iPSC+/+ PP1 2 [WT D8]


title: iPSC+/+ PP1 1 [WT D8]


title: iPSC-/- GT 3 [TBX3 KO D6]

source_name: Pluripotent-stem cell derived gut tube cells (day 6)

value: Gut tube (Day 6)


title: iPSC+/+ GT 2 [WT D6]


title: GES-1 cells, Control, Input


title: iPSC+/+ GT 1 [WT D6]


title: iPSC-/- GT 2 [TBX3 KO D6]


title: PB_T2D+MI

city: wuhan

first: han

middle: shao

last: qing

address: whu

institute: school

description:
clinical samples
PB_T2D_MI

data_processing:
Library strategy: SLIM-m6A-seq/RNA-seq/m6A-seq
According to the principle of library construction, the raw data is split by custom scripts.
Adapter seqeucnes were trimmed by using trim galore.
fastuniq is used to remove PCR duplication. Then use seqtk trimfq remove random sequences added in library construction.
Clean reads were mapped to genome by using STAR; with parameter "--outFilterMultimapNmax 20 --outFilterMismatchNmax 10". Only the proper pair and uniquely mapped alignments was persisted for the downstream pipelines.
Aligned reads were used for peak calling and enriched regions comparing by exomePeak.
HOMER was used for peak annotation and detection of the sequence motif.
Genome_build: hg38 and mm10

molecule: polyA RNA

source_name: human peripheral blood

growth_protocol: HEK293T (ATCC) cells were cultured in T25 cell culture flask using DMEM (Dulbecco's modified Eagle's medium, high glucose, Gibco) supplemented with 10% fetal bovine serum (FBS, Gibco), and 1% penicillin/streptomycin (Beijing Dingguo changsheng Biotechnology Co.,Ltd, GA3502).

extract_protocol:
Total RNA was isolated from cell lines, peripheral blood or Murine heart tissue with TRIzol (Invitrogen) according to the manufacture’s protocol. The mRNA was isolated by subjecting total RNA to oligo(dT) enrichment using Dynabeads Oligo(dT)25 (NEB)
for No.1-SING &No. 1-SING-IP: Fragmented mRNAs from Hek293T cells were first treated with T4 PNK. Then the samples were ligated with 3'-linker (5'- rApp-NNNNNNTGGAATTCTCGGGTGCCAAGG-SpC3 -3', Italic N represents for 6-nt random sequences). Extra 3'-linker were removed by 5′-deadenylase and RecJf digestion. The reaction mixtures were subsequently purified. 1/50 of the purified sample was retained as input control while the remaining sample was applied to m6A antibody immunoprecipitation (IP). The input control sample and the IP sample were reverse transcripted using RT primer (5'-ACACGACGCTCTTCCGATCT-3') to obtain cDNA samples. The cDNA samples were then ligated with 5'-adaptor (5'-Phos-NNNNNNNNNNAGATCGGAAGAGCACACGTCTG-SpC3-3'), followed by determination of PCR cycle number by RT-qPCR. Finally, library PCR amplification was performed using the NEB primers and the products were purified by magnetic beads or agarose gel electrophoresis.
for samples other than No.1-SING &No. 1-SING-IP: Fragmented mRNAs from different samples were first treated with T4 PNK. Then the samples were ligated with pre-adenylated 3'-linkerLs (5'-NNNNNNNNNNNNAGATCGGAAGAGCGTCGTG-3', Bold N represnts for designed 6-nt barcode sequences, Italic N represents for 6-nt random sequences). Extra 3'-linkerLs were removed by 5′-deadenylase and RecJf digestion. The reaction mixtures were subsequently pooled together and purified. 1/50 of the purified sample was retained as input control while the remaining sample was applied to m6A antibody immunoprecipitation (IP). The input control sample and the IP sample were reverse transcripted using RT primer (5'-ACACGACGCTCTTCCGATCT-3') to obtain cDNA samples. The cDNA samples were then ligated with 5'-adaptor (5'-Phos-NNNNNNNNNNAGATCGGAAGAGCACACGTCTG-SpC3-3'),followed by determination of PCR cycle number by RT-qPCR. Finally, library PCR amplification was performed using the NEB primers and the products were purified by magnetic beads or agarose gel electrophoresis.

value: Human Blood

value: Type 2 diabetic myocardial infarction


title: Input ESRRB-piPSCs

city: Yangling

first: Shuai

last: YU

address: No.22 Xinong Road,

institute: Northwest A&F University

library_source: genomic

data_processing:
sequenced on Illumina HiSeq2500 PE150 by SEQHEALTH Technology Corporation
The clean reads were mapped to pig genome Ssc11.1 (NCBI) using STRA software
Annotation and visualization of ChIP peak coverage over the chromosomes were conducted using the ChIPseeker package in R (version 1.18.0)
Genome_build: pig genome Ssc11.1 (NCBI)
Supplementary_files_format_and_content: The CHIP-seq data of ESRRB in piPSCs contain the peaks and the motif

molecule: genomic DNA

organism: Sus scrofa

source_name: ESRRB-piPSCs

growth_protocol: The ESRRB piPSCs constructed followed by Ma et al were used in this study (Ma et al., 2018; Zhu et al., 2021a). The piPSCs were grown on feeder cells (mouse embryonic fibroblasts (MEFs) treated by mitomycin-C) and maintained in the standard medium as shown as follows (was named as LBCS medium): DMEM (Hyclone, USA) supplemented with 15% FBS (VISTECH, VIS59216269, New Zealand), 0.1 mM NEAA (Gibco, USA), 1 mM L-glutaMAX (Gibco), 0.1 mM β-mercaptoethanol (Sigma Aldrich, USA), 100 units/mL penicillin, 100 μg/mL streptomycin, 10 ng/mL LIF (Sino Biological, China), 10 ng/mL bFGF (Sino Biological), 3 µM CHIR99021 (MCE, USA), 2 µM SB431542 (Selleck, China) and 4 μg/mL doxycycline (DOX, Sigma Aldrich).

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ESRRB piPSCs were crosslinking with formaldehyde and chromatin was sonicated to 200-1000 bp, and then the sonicated chromatin was immunoprecipitated with the antibody FLAG. The DNA fragments were agarose electrophoresis quantified using Qubit 2.0 and sequenced on Illumina HiSeq2500 PE150 by SEQHEALTH Technology Corporation (China).

treatment_protocol: untreated

value: ESRRB-piPSCs

tag: chip antibody

value: untreated


title: PB_T2D+MI_IP

description:
clinical samples
PB_T2D_MI_IP


title: Flag  ESRRB-piPSCs

value: Flag


title: iPSC+/+ GT 3 [WT D6]

value: Pancreatic differentation protocol


title: iPSC-/- GT 1 [TBX3 KO D6]


title: NMP Day 19

description:
NMP differentiation protocol
SMN_19_S3

value: Motor Neuron Progenitors

value: Day 19


title: iPSC-/- PP1 2 [TBX3 KO D8]

value: Pancreatic progenitor 1 (Day 8)


title: PB_T2D_IP

description:
clinical samples
PB_T2D_IP

value: Type 2 diabetes


title: PB_T2D

description:
clinical samples
PB_T2D


title: PBMCs pool of samples 7-14 run 1

city: Munich

first: Binder

last: Elisabeth

address: Kraepelinstr. 2+10

country: Germany

institute: Max-Planck-Institute Psychiatry

data_processing:
Pre-processing of sequencing results to generate count matrices was performed using the 10x genomics Cell Ranger pipeline with default settings(v2.0.0 and v2.1.1)
Doublets were detected using Demuxlet (v1.0) and Scrublet (v0.1)
Basic filtering of cells was performed using Scanpy (v1.4)
Genome_build: GRCh37
Supplementary_files_format_and_content: QC filtered cell ranger output consists of gene by barcode (cell) count matrices in sparse matrix market format (mtx) and corresponding row and column annotation in *genes.tsv and *barcode.tsv files. In addition we added csv formated files with cell annotations for each run

source_name: peripheral blood mononuclear cells

growth_protocol: Perinuclear blood cells (PBMCs) were isolated and cryopreserved in RPMI 1640 medium (Sigma-Aldrich) supplemented with 10% Dimethyl Sulfoxide at a concentration of roughly 1M cells per ml.

extract_protocol:
Cell pools were concentrated and resuspended in PBS supplemented with 0.04 % bovine serum albumin, and loaded on the Chromium microfluidic system (10X Genomics) aiming for 8000 cells per run and followed by single-cell sequencing library preparation according to the manufacturer’s standard protocol.
Single-cell libraries were created using the standard protocol from 10X Genomics: Chromium Single Cell 3′library and gel bead kit v2 ( #120237)
Pooling was performed on groups of 7 individuals or 14 individulals. Sequencing was performed  with a targeted depth of  approximately 50,000 reads per cell on the HiSeq4000 (Illumina) with 150 bp paired-end  sequencing of read2

treatment_protocol: For single-cell experiments, 14 cell vials from different individuals (7 male and 7 female) were snap-thawed in a 37oC water bath and serially diluted in RPMI 1640 medium (Sigma-Aldrich) supplemented with 10% Fetal Bovine Serum (Sigma-Aldrich) medium. Cells were counted and equal cell numbers per individual were pooled in two pools of 7 individuals each.

value: peripheral blood mononuclear cells


title: PBMCs pool of samples 1-14 run 2


title: Method_SING

value: Cell


title: PBMCs pool of samples 1-14 run 1


title: PBMCs pool of samples 1-14 run overloaded with 25k cells


title: Method_SING_IP


title: WT-D12-Hep-2-resub [ATAC-seq]

data_processing:
Reads were trimmed using cutadapt and quality scores were assessed using FastQC
Reads were aligned to the Homo sapiens genome build hg19 using bowtie2
Per-sample quality assessment plots were generated with HOMER and Mosaics.
Peaks were called using MACS2. Peak overlaps and differential accessibility were calculated using the DiffBind R library
Differential accessibility was calculated at gene promoter sites
Read distribution percentages, identity heatmaps, and FRiP plots were generated as part of the QC step using ChIPQC R library and HOMER
HOMER was also used to generate known and de novo motifs and perform functional enrichment analysis of pathways, gene ontology, domain structure and other ontologies
Differentially expressed genes passed a threshold of +/- 1.5 fold change and have a p-value < 0.05
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files for each samples containing peak information

source_name: Pluripotent-stem cell hepatoblasts (day 12)

extract_protocol:
Cells were lysed and nuclei were treated with Tn5 enzyme (Illumina, Cat. #20034197) for 30 minutes at 37°C. DNA was purified with Minelute PCR Purification Kit (Qiagen, Cat. #28004) to produce tagmented DNA samples.
Tagmented DNA was barcoded with Nextera Index Kit v2 (Illumina, Cat. #FC-131-2001) and libraries were made for sequencing following standard protocols from Illumina

value: Hepatoblast (day 12)

value: liver differentation protocol


title: AGS-EBV-2

city: Guangzhou

first: Jingyue

last: Zhang

address: No. 600 Tianhe Road, Guangzhou 510630, China

institute: Department of Pathology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China

data_processing:
Illumina Casava1.9 software used for basecalling.
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. TMM (trimmed mean of M-values) was used to normalize the gene expression. Differentially expressed (DE) genes were identified using the edgeR program.
Genes showing altered expression with p < 0.05 and more than 1.5-fold changes were considered differentially expressed.
Genome_build: CXCL8
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: gastric cancer cell

growth_protocol: All the cells were cultured at a humidified incubator with 5% CO2 at 37°C.

extract_protocol:
Total RNA was extracted from cultured cells using TRIzol reagent (Invitrogen). RNA quality was evaluated using a bioanalyzer.
RNA-seq libraries were prepared using a NEBNext Ultra II Directional RNA Library Prep kit according to the manufacturer’s instructions.

treatment_protocol: EBV-infected cells (AGS-EBV ) were obtained by co-culture AGS with Akata-EBV-GFP using the cell-to-cell infection method.

tag: infection

value: EBV

value: gastric cancer cell

value: AGS


title: PBMCs pool of samples 1-14 run 3


title: Method_MIX


title: Method_MIX_IP


title: AGS-3

value: control


title: iPSC-/- Hep 3 [TBX3 KO D12 hepatoblast 3]

growth_protocol: Wildtype and TBX3 knockout iPS cells were differentiated to hepatoblast (day 12) folowing a hepatocyte differentiation protocol

extract_protocol:
RNA was extracted using the PureLink RNA Micro Kit (Invitrogen) following the manufacturer's protocol
RNA libraries were prepared for sequencing following protocols from the TruSeq RNA Library Prep Kit v2, Set A/B (Illumina)


title: AGS-EBV-3


title: WT-D12-Hep-1-resub [ATAC-seq]

value: Wildtype


title: AGS-EBV-1


title: TBX3-KO-D12-Hep-2-resub [ATAC-seq]


title: TBX3-KO-D12-Hep-1-resub [ATAC-seq]


title: PBMCs pool of samples 1-7 run 1


title: LGALS1_input_2

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

data_processing:
Illumina bcl2fastq software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 12 --microexon-search --no-coverage-search --report-secondary-alignments. Uniquely mapped reads were remained. One more reads with the same start and end position, only one is considered.
After reads were aligned onto the genome, we analysed the unique reads binding regions of LGALS1 on genome using “ABLIRC” strategy.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include peak information for each group.

source_name: HeLa cell

growth_protocol: HeLa cells were first lysed in ice-cold lysis buffer (10 mM HEPES, pH 7.0, 100 mM KCl, 5 mM MgCl2, 0.5% NP-40, 10 mM DTT) with 200 U/ml RNase inhibitor (Promega) and a protease inhibitor (Roche) on ice for 5 min

extract_protocol:
The beads were washed 6 times with lysis buffer and then divided into two groups, one for RNA isolation from LGALS1-RNA complexes and another for the western blotting assay for LGALS1 immunoprecipitation.The LGALS1-bound RNAs were isolated from the immunoprecipitate of monoclonal Flag antibody (Sigma), followed by the preparation of the Illumina Truseq pair-end libraries.
The reverse transcription was performed with RT primers harboring 3′ adaptor sequence and random hexamer. The generated cDNAs were PCR-amplified and the 200–500 bp products were purified

treatment_protocol: The supernatant was pre-cleared with 100 μl of DynaBeads protein G (Life Technologies) at 4 °C for 30 min. The pre-cleared supernatant was incubated with DynaBeads protein G conjugated with monoclonal Flag antibody (Sigma) or Input at 4℃ for 30 min.

tag: antibody

value: input


title: LGALS1_IP_2


title: LGALS1_IP_1


title: iPSC-/- Hep 1 [TBX3 KO D12 hepatoblast 1]


title: iPSC+/+ Hep 3 [WT D12 hepatoblast 3]


title: iPSC+/+ Hep 2 [WT D12 hepatoblast 2]


title: iPSC+/+ Hep 1 [WT D12 hepatoblast 1]


title: iPSC-/- Hep 2 [TBX3 KO D12 hepatoblast 2]


title: LGALS1_input_1


title: BRCM-82 tissue bulk RNA

first: Shengshou

last: Hu

address: No.167 North Lish Road

institute: Fuwai Hospital

data_processing:
scRNA-seq sequencing reads were aligned to human genome reference build hg38 with cellranger 3.0
bulk RNA-seq sequencing reads were aligned to human genome reference build hg38,  transcript per million (TPM) were calculated with RSEM software.
Genome_build: hg38
Supplementary_files_format_and_content: scRNA-seq expression matrix were uploaded as zipped file. In each zipped file, it contains barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz. T cell receptor sequencing had additional clonotype file and metrics_summary.csv files.

source_name: Myocardium

growth_protocol: ACKR1+ endothelial cells derived from human explanted hearts were sorted by FACS and cultured in 0.1% gelatin-coated dishes with an endothelial cell medium complete kit (Sciencell, 1001).

extract_protocol:
cell pellete was collected and RNA was extracted using an RNeasy Mini kit (QIAGEN, 74104) by following the manufacturer’s protocol.
Libraries were prepared with an NEBNext Poly(A) mRNA Magnetic Isolation Module kit (NEB) and an NEBNext Ultra RNA Library Prep Kit for Illumina Paired-end Multiplexed Sequencing Library (NEB).

treatment_protocol: Human CXCL8 protein (R&D, 208-I-050) was added to stimulate ACKR1+ ECs at a final concentration of 8 ng/ml. Seventy-two hours after stimulation, the cells were harvested and washed twice with PBS.

value: whole cells

value: heart

tag: tissue type

value: left ventricle, normal heart

tag: other

value: bulk RNAseq (total mRNA)


title: HCT116 EV2 rep4

city: SIngapore

first: Giulia

last: Rancati

address: Biomedical Grove

department: SRIS

country: Singapore

institute: A*STAR

data_processing:
FastQC for quality control of raw sequencing data
STAR read alignment to reference genome (GRCh38)
RSEM for calculation of FPKM (fragments per kilobase of transcript per million)
t-test and multiple testing correction (q-value) for differential expression
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with FPKM for every gene in each sample

source_name: HCT116 cell line

growth_protocol: Cells cultured in 10cm culture dishes at 37 ˚C and 5% CO2; 4X10^6 collected at ~70% of confluence

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (Qiagen) and processed as per manufacturer’s instructions
Illumina TrueSeq HT Kit

value: HCT116 cell line

value: ctrl_Cas9 transfected without gRNA


title: HCT116 WT rep4


title: BRCM-78 tissue bulk RNA

value: left ventricle, heart failure


title: HCT116 EV1 rep4

value: wild-type


title: AGS-2


title: BRCM-71 tissue bulk RNA


title: HAP1 C6 rep4

source_name: HAP1 cell line

value: HAP1 cell line

value: NUP58 mutated


title: BRCM-70 tissue bulk RNA


title: HAP1 C5 rep4


title: BRCM-69 tissue bulk RNA


title: HAP1 C1 rep4


title: BRCM-67 tissue bulk RNA


title: BRCM-66 tissue bulk RNA


title: HAP1 C2 rep4


title: BRCM-65 tissue bulk RNA


title: HAP1 EV rep4


title: HCT116 EV2 rep3


title: HCT116 EV1 rep3


title: BRCM-62 tissue bulk RNA


title: BRCM-60 tissue bulk RNA


title: AGS-1


title: HCT116 Clone rep3


title: BRCM-73 tissue bulk RNA


title: HAP1 C6 rep3


title: HAP1 C5 rep3


title: SAL_SAL_L9_2

city: Palo Alto

first: Nathalie

last: Khoury

state: CA California

address: 3801 Miranda Avenue Blvd. 100 VAPA D3-111 - Neurology

institute: Stanford University

data_processing:
Trimmed sequences were aligned using STAR (v2.5.3a) using the mm10
GeneCounts function and differential expression analysis was performed using the RStudio v1.2.5033 DESeq2 package v2.36 51 using built-in algorithms

source_name: Hippocampus

extract_protocol:
RNeasy Qiagen RNA isolation from homogenized tissue.
RNA was converted into cDNA using a SMART-seq® v4 Ultra Low Input Kit for Sequencing. cDNA was then fragmented, normalized, and pooled using a Nextera XT library preparation kit

value: RP

value: Whole HC


title: BRCM-68 tissue bulk RNA


title: BRCM-57 tissue bulk RNA


title: HAP1 C3 rep4


title: HAP1 C4 rep4


title: HAP1 WT rep4


title: SAL_SAL_L1_2


title: BRCM-55 tissue bulk RNA


title: HCT116 Clone rep4


title: SAL_SAL_L9_1


title: BRCM-58 tissue bulk RNA


title: HAP1 C3 rep3


title: SAL_SAL_L5_2


title: BRCM-53 tissue bulk RNA


title: HAP1 C2 rep3


title: HAP1 C4 rep3


title: SAL_SAL_L13_1


title: SAL_SAL_L1_1


title: SAL_SAL_L5_1


title: BRCM-64 tissue bulk RNA


title: BRCM-61 tissue bulk RNA


title: HAP1 C1 rep3


title: SAL_SAL_L13_2


title: BRCM-51 tissue bulk RNA


title: BRCM-52 tissue bulk RNA


title: BRCM-56 tissue bulk RNA


title: BRCM-50 tissue bulk RNA


title: LPS_SAL_L2_2


title: LPS_SAL_L6_2


title: HAP1 EV rep3


title: BRCM-49 tissue bulk RNA


title: HCT116 EV2 rep2


title: LPS_SAL_L2_1


title: BRCM-48 tissue bulk RNA


title: LPS_SAL_L14_2


title: BRCM-47 tissue bulk RNA


title: BRCM-46 tissue bulk RNA


title: HCT116 WT rep2


title: BRCM-45 tissue bulk RNA


title: HCT116 Clone rep2


title: LPS_SAL_L6_1


title: HAP1 C5 rep2


title: HAP1 WT rep3


title: BRCM-43 tissue bulk RNA


title: LPS_SAL_L10_2


title: HCT116 EV1 rep2


title: LPS_SAL_L14_1


title: BRCM-44 tissue bulk RNA


title: HAP1 C6 rep2


title: LPS_RP_L8_1


title: LPS_RP_L8_2


title: LPS_SAL_L10_1


title: E10.0-post01

type: RNA

city: Sapporo

first: Tatsuya

last: Sato

state: Hokkaido

address: South-1, West-17, Chuo-ku

department: Department of Cellular Physiology and Signal Transduction

country: Japan

institute: Sapporo Medical University School of Medicine

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent GE hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to SurePrint G3 Rat GE 8x60K Microarray (Agilent, G4853A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid 028279_D_F_20110906) to obtain background subtracted and spatially detrended Processed Signal intensities. The 75th percentile shift normalization and the baseline transformation (to median of all samples) were performed using Agilent GeneSpring GX 13.1.1.

organism: Rattus norvegicus

source_name: heart primordium, from rat(E10 post-heartbeat)

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 10 ng Total RNA using Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted from the embryonic heart primordium using an RNeasy micro Kit (Qiagen). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: heart primordium, post-heartbeat

value: embryo

tag: embryonic day

value: Wister rat


title: E10.0-post03


title: E10.0-post02


title: E10.0-pre02

source_name: heart primordium, from rat(E10 pre-heartbeat)

value: heart primordium, pre-heartbeat


title: E10.0-pre01


title: Control 2

city: Montreal

first: Andrew

last: Bateman

state: Quebec

address: 1001 boul. Décarie

department: Medicine

country: Canada

institute: McGill University

description: vector only control

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Quantile normalization with Background Subtraction

label: biotin

source_name: NSC-34 Cells

label_protocol: Biotinylated cRNA were prepared for Illumina arrays

growth_protocol: NSC-34/shPGRN, NSC-34/hPGRN or control constructs were cultured in T75 flasks.They were sub-cultured in 4 replicates. NSC-34 cells (200000) from each of 12 flasks were plated in T25 flasks with serum.

extract_protocol: 24 hours later cells were lysed in Trizol and total RNA was extracted. The RNA concentration was determined using a NanoDrop chip.

treatment_protocol: After 24 hours the media containing 10% serum was removed and replaced with media containing 5% serum. After a further 24 hours the media was changed of one containing 1% serum.

value: Motor neuron like


title: Control 3

description: vector only control


title: BRCM-42 tissue bulk RNA

city: Beijing

value: whole cells


title: HAP1 C4 rep2


title: Control 4

description: vector only control


title: BRCM-41 tissue bulk RNA

value: heart


title: HAP1 C3 rep2


title: Control 1

description: vector only control


title: LPS_RP_L16_2


title: HAP1 C2 rep2


title: HAP1 C1 rep2


title: BRCM-38 tissue bulk RNA


title: LPS_RP_L4_2


title: LPS_RP_L4_1


title: hPGRN 3

description: overexpression(hPGRN)


title: BRCM-40 tissue bulk RNA


title: hPGRN 1

description: overexpression(hPGRN)


title: BRCM-39 tissue bulk RNA


title: LPS_RP_L16_1


title: BRCM-36 tissue bulk RNA


title: HCT116 EV2 rep1


title: BRCM-35 tissue bulk RNA


title: HAP1 EV rep2


title: HCT116 EV1 rep1


title: E10.0-pre03


title: HCT116 Clone rep1


title: shPGRN 4

description: Knockdown(shPGRN)


title: BRCM-34 tissue bulk RNA


title: shPGRN 3

description: Knockdown(shPGRN)


title: hPGRN 4

description: overexpression(hPGRN)


title: HAP1 WT rep2


title: hPGRN 2

description: overexpression(hPGRN)


title: BRCM-37 tissue bulk RNA


title: LPS_RP_L12_1


title: LPS_CP_L7_2


title: LPS_CP_L7_1


title: LPS_RP_L12_2


title: CLP2-Day31

city: Washington

first: Weiqun

last: Peng

state: DC

address: 1918 F Street, NW , DC

institute: The George Washington University

data_processing:
The sequencing quality of RNA-Seq libraries were assessed by FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
RNA-Seq libraries were mapped to mouse genome using Tophat (v2.1.0, Trapnell et al., Bioinformatics). UCSC genes for mouse mm10 from iGenome(http://support.illumina.com/sequencing/sequencing_software/igenome.html) were used for gene annotation.
Mapped reads were then processed by Cuffdiff (v2.2.1, Trapnell et al., Nature biotechnology) to estimate expression levels of all genes and identify differentially expressed genes (FC=1.5, FDR = 0.1, FPKM>1.0). The expression level of a gene is expressed as a gene-level Fragments Per Kilobase of transcripts per Million mapped reads (FPKM) value.
Genome_build: mm9

source_name: memory CD8 T cells

extract_protocol:
Memory P14 CD8 T cells were sort-purified from the spleen and total RNA was extracted using standard Qiagen RNease columns
RNA libraries were prepared for sequencing using stardard Illumina protocol

tag: sample type

value: splenocytes

tag: markers

value: CD11a hi, CD8a lo, Thy1.1+


title: LPS_CP_L15_2

tag: strain


title: HAP1 C5 rep1

tag: genotype


title: HAP1 C4 rep1


title: BRCM-32 tissue bulk RNA

tag: tissue

value: bulk RNAseq (total mRNA)


title: Sham3-Day31


title: shPGRN 2

description: Knockdown(shPGRN)


title: shPGRN 1

description: Knockdown (shPGRN)


title: LPS_CP_L11_2


title: BRCM-31 tissue bulk RNA


title: HAP1 C3 rep1


title: BRCM-33 tissue bulk RNA


title: LPS_CP_L3_1


title: HAP1 C6 rep1


title: CLP3-Day1


title: HCT116 WT rep1

value: HCT116 cell line


title: Sham2-Day31


title: Sham1-Day31


title: CLP1-Day31


title: BRCM-30 tissue bulk RNA

value: left ventricle, heart failure


title: LPS_CP_L15_1


title: HAP1 EV rep1

value: ctrl_Cas9 transfected without gRNA


title: HC_RP6


title: BRCM-29 tissue bulk RNA


title: HC_RP5


title: Sham2-Day1


title: HAP1 C2 rep1

value: HAP1 cell line


title: Sham3-Day1


title: LPS_CP_L11_1


title: BRCM-28 tissue bulk RNA


title: HAP1 C1 rep1

value: NUP58 mutated


title: CLP2-Day1


title: HC_RP8

value: RP


title: HC_RP7

value: Whole HC


title: CLP1-Day1


title: BRCM-27 tissue bulk RNA


title: HC_RP3


title: small RNA data of DCL3 H909A rep2 in dcl234

city: Los Angeles

first: Zhenhui

last: Zhong

address: 610 Charles E Young Dr East

department: Department of Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

description:
small RNA data of DCL3 H909A rep2
m4-3_sRNAseq

data_processing:
Small reads adaptors were removed with TrimGalore (v0.4.2, https://github.com/FelixKrueger/TrimGalore) and mapped to Arabidopsis thaliana reference genome TAIR10 using Bowtie2 (v2.1.0) allowing only uniquely mapping reads with 0 mismatches (Langmead and Salzberg, 2012). sRNA reads that mapped to chloroplast, mitochondrial DNA, tRNA, rRNA, small nucleolar RNAs (snoRNAs), and small nuclear RNAs (snRNAs) have been removed using bedtools (v2.26.0) (Quinlan and Hall, 2010).
Genome_build: TAIR10
Supplementary_files_format_and_content: bigWig

organism: Arabidopsis thaliana

source_name: Arabidopsis floral tissue

growth_protocol: Arabidopsis plants of the Columbia-0 (Col-0) ecotype were used in this study. All plants were grown under green house condition (16 h light/8 h dark, 22C). Floral tissues were collected from 5-6 week plants

extract_protocol:
Floral tissues from 5-6 week old seedlings were used for RNA extraction with Zymo Direct-zol RNA MiniPrep kit (Zymo Research) following manufacturer’s instructions.
Floral tissues of two independent T1 plants of each genotype were used to characterize the abundance of 24 nt siRNA. Total RNA was extracted using the Direct-zol RNA Miniprep kit (Zymo) according to the manufacturer’s instructions. Two micrograms of total RNA was mixed with equal volume of the 2x RNA loading dye (NEB), denatured at 65◦C for 10 min and immediately chilled on ice. Denatured total RNA was separated on 15% TBE urea gel (Invitrogen) and small RNAs from 15-30 nts were excised. The excised gel pieces were forced through gel breaker tubes (IST engineering inc) by centrifuging at 20,000 g for 3 min. small RNA was then eluted with nuclease free water by incubation at 70◦C for 10 min and precipitated with EtOH. Small RNA libraries were made using NEBNext® Small RNA Library Prep Set for Illumina® (Multiplex Compatible) (NEB) according to the manufacturer’s instructions.

value: floral tissue

tag: developmental stage

value: 7-8 weeks


title: BRCM-21 tissue bulk RNA


title: P14_CLP3

data_processing:
The sequencing quality of ATAC-Seq libraries were assessed by FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Bowtie2 (v2.2.5, Langmead et al., Nature Methods) was used to align the sequencing reads to the mouse genome. UCSC genes for mouse mm9 from iGenome (http://support.illumina.com/sequencing/sequencing_software/igenome.html) were used for gene annotation.
For ATAC-Seq libraries, MACS2 (v2.1.1, Zhang et al., Genome Biol) was used for peaks calling. We used the criteria of a P value of < 1E-5, 4 fold enrichment  as identified Tcf1 binding peaks.
Genome_build: mm9

extract_protocol:
Memory P14 CD8 T cells  were sort-purified from the spleen, treated with TN5 transposase to generate tagged DNA fragments. TN5-tagged DNA fragements were purified, PCR amplified to build ATAC-seq libraries
DNA libraries were prepared for sequencing using stardard Illumina protocol

value: CLP

tag: cell phenotype


title: HC_RP2


title: P14_CLP1


title: BRCM-25 tissue bulk RNA


title: HC_RP4


title: BRCM-18 tissue bulk RNA


title: small RNA data of DCL3 D1133A/E1136A/E1015A/D1019A rep2 in dcl234

description:
small RNA data of DCL3 D1133A/E1136A/E1015A/D1019A rep2
DCL3m2-13_sRNAseq


title: Sham1-Day1


title: BRCM-24 tissue bulk RNA


title: HAP1 WT rep1

tag: cell line

value: wild-type


title: small RNA data of DCL3 H909A rep1 in dcl234

description:
small RNA data of DCL3 H909A rep1
m4-1_sRNAseq


title: hdLEC_TLA_DLL4_rep3

city: Chicago

first: Jan

middle: K

last: Kitajewski

state: IL

address: 909 S. Wolcott Ave. MC 901

department: Dept. of Physiology and Biophysics

institute: University of Illinois at Chicago

data_processing:
Alignment of fastq files: fastq files were aligned to human (ENSEMBL/GRCh38) using STAR (version 2.5.0a)
Bam files generation : Aligned files were convered to Sam and Bam format using Samtools (version 1.4.1)
Assignment and Raw counts generation: Raw counts were extracted from the Bam files using FeatureCounts (version 1.5.2)
Differential Gene Expression analysis: Normalized read counts and analysis to generate a list of differentially expressed genes was done using DESeq2 (version 1.18.1)
Gene Ontology/Pathway analysis: Panther Db
Genome_build: Human Genome (ENSEMBL/GRCh38)
Supplementary_files_format_and_content: Raw count files (.txt) were generated using FeatureCounts (v1.5.2) ; Normalized count files (.csv) were generated by DESeq2 (version 1.18.1)

source_name: Human Dermal Lymphatic Endothelial Cells

growth_protocol: Neonatal human dermal lymphatic endothelial cells (HdLECs)  were cultured on fibronectin-coated plates in EGM2-MV2 (Lonza; complete medium) supplemented with 10 ng/mL VEGF-C (R&D).

extract_protocol:
RNA was isolated from lysates (RLT+beta-mercaptoethanol) using RNEasy Mini Kit (Qiagen), as per the manufacturer's recommendation.
RNA libraries were prepared using standard protocols recommended by Illumina at NovogeneCorp.

treatment_protocol: Cells were detached by trypsinization and seeded on Fc (Control) or DLL4 coated plates for 6h from the time of seeding.

value: Primary Cells


title: P14_CLP2


title: small RNA data of DCL3 K695A/K957A/K903A rep2 in dcl234

description:
small RNA data of DCL3 K695A/K957A/K903A rep2
m3-2_sRNAseq


title: small RNA data of DCL3 K695A/K957A/K903A rep1 in dcl234

description:
small RNA data of DCL3 K695A/K957A/K903A rep1
m3-1_sRNAseq


title: HC_RP1


title: hdLEC_TLA_DLL4_rep2

value: Human Dermal Lymphatic Endothelial Cells


title: BRCM-14 tissue bulk RNA

value: whole cells

value: heart

value: left ventricle, normal heart


title: BRCM-19 tissue bulk RNA

value: bulk RNAseq (total mRNA)


title: BRCM-20 tissue bulk RNA


title: small RNA data of DCL3-deletion 1450-1570 rep1 in dcl234

description:
small RNA data of DCL3-deletion 1450-1570 rep1
DCL3-del-4-44_sRNAseq


title: BRCM-13 tissue bulk RNA


title: small RNA data of DCL3 D1133A/E1136A/E1015A/D1019A rep1 in dcl234

description:
small RNA data of DCL3 D1133A/E1136A/E1015A/D1019A rep1
DCL3m2-12_sRNAseq


title: P14_Sham2

value: control

value: splenocytes

value: CD11a hi, CD8a lo, Thy1.1+


title: HC_CP7

value: CP


title: BRCM-17 tissue bulk RNA

value: left ventricle, heart failure


title: HC_CP8


title: small RNA data of DCL3 deletion 1356-1570 rep2 in dcl234

description:
small RNA data of DCL3 deletion 1356-1570 rep2
DCL3-del-3-40_sRNAseq


title: BRCM-23 tissue bulk RNA


title: P14_Sham1


title: small RNA data of DCL3 D1316A/E1319A/E1224A/D1228A rep2 in dcl234

description:
small RNA data of DCL3 D1316A/E1319A/E1224A/D1228A rep2
DCL3m1-8_sRNAseq


title: HC_CP5


title: HC_CP6


title: BRCM-16 tissue bulk RNA


title: NK_neg_neg_NYBC259_run2_8

city: Ithaca

first: Colleen

last: Lau

state: New York

address: 930 Campus Road

department: Microbiology & Immunology

institute: Cornell University

data_processing:
BCL files were converted to fastq using bcl2fastq2 (v2.17.1.14, v2.18.0,  or v2.20.0.422).
RNA-seq reads were trimmed for quality and adaptors using Trimmomatic (v.0.38).
Transcript quantification was performed by salmon (v0.13.1) using arguments '-l IU --gcBias --validateMappings --rangeFactorizationBins 4 --useVBOpt --numBootstraps 30' and tximport (v0.10.1) using the UCSC Known Gene transcript assembly.
Please note that some biological samples were sequenced twice (designated as 'run1' and 'run2').
Genome_build: hg38
Supplementary_files_format_and_content: Text files are raw estimated gene-level counts (1 count = 1 read pair) as quantified by salmon (v0.13.1) and imported by tximport (v1.10.1). Also provided are gene IDs (Entrez and Ensembl), gene names, gene descriptions, and chromosome.

source_name: peripheral blood NK cells

extract_protocol:
RNA was isolated from sorted cell populations using TRIzol (Invitrogen).
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 0.27-2.0ng total RNA with RNA integrity numbers ranging from 3.3 to 10 underwent amplification using the SMART-Seq v4 Ultra Low Input RNA Kit (Clonetech catalog # 63488), with 12 cycles of amplification. Subsequently, 5.7-7.0ng of amplified cDNA was used to prepare libraries with the KAPA Hyper Prep Kit (Kapa Biosystems KK8504) using 8 cycles of PCR. Samples were barcoded and run on a NovaSeq 6000 in a PE50 run, using the NovaSeq 6000 S1 or S2 Reagent Kit (100 Cycles) (Illumina).  An average of 71 million paired reads were generated per sample and the percent of mRNA bases per sample ranged from 29% to 65%.

tag: celltype

value: NK

value: neg

tag: donor

tag: run

tag: sampleID


title: small RNA data of DCL3 deletion 865-895 rep1 in dcl234

description:
samll RNA data of DCL3 deletion 865-895 rep1
DCL3-del-2-1_sRNAseq

value: floral tissue


title: small RNA data of DCL3 deletion 865-895 rep2 in dcl234

description:
samll RNA data of DCL3 deletion 865-895 rep2
DCL3-del-2-2_sRNAseq

value: 7-8 weeks


title: HC_CP4

tag: treatment

tag: cell type

value: Whole HC


title: HC_CP3


title: experimental group_input

city: chongqing

first: xiaofang

last: luo

address: 1 Youyi Road, Yuzhong District

institute: The First Affiliated Hospital of Chongqing Medical University

data_processing:
Base calling were performed with lllumina CASAVA pipeline
Raw data (raw reads) of fastq format were firstly processed using fastp (version 0.19.11)  Raw data (raw reads) of fastq format were firstly processed using fastp (version 0.19.11)  Raw data (raw reads) of fastq format were firstly processed using fastp (version 0.19.11)
Reference genome and gene model annotation files were downloaded from genome website directly.
Peak finding algorithm to indentify regions of lP enrichment over background used the MACS2 version 2.1.0
Different peak analysis was based on the fold enrichment of peaks of different experiments.
Genome_build: ftp://ftp.ensembl.org/pub/release-94/fasta/mus_musculus/dna/
Supplementary_files_format_and_content: tab-delimited text files include fold-enrichment values for each sample

growth_protocol: The 3T3-L1 was routinely cultured in growth media which consisted of Dulbecco’s Modified Eagle Medium, High Glucose (DMEM high glucose, Gibco, USA), 10% neonatal bovine serum (Gibco, USA) and 1% PS

extract_protocol:
3T3-L1 preadipocytes and PPARγ-OE HTR8-Exos treated 3T3-L1 preadipocytes (4th day of differentiation process) were fixed in 37% formaldehyde, pelleted and resuspended in lysis buffer. The cell nucleus was then pelleted, enzymolysised, sonicated and centrifuged to remove insoluble material. The supernatants were collected, and protein G magnetic beads (Bio-Rad, USA) labeled with anti-PPARγ antibody (cell signaling technology, CST, USA) or Profinity IMAC Resin (Bio-Rad, USA) were added prior to incubation at 4°C overnight. The binding chromatin was collected, eluted and de-crosslinked at 65°C overnight. The DNA was then purified using spin-column, quantified by Qubit 3.0 Fluorometer (Life Technologies, USA) and checked by agarose gel electrophoresis for integrity. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (PE-401-3001, Illumina, USA) according to the manufacturer’s instructions.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.

value: preadipocytes

tag: chip antibody

value: none (input)

value: PPARgamma-OE HTR8-Exos treated


title: small RNA data of DCL3-WT-3 in dcl234

description:
small RNA data of DCL3-WT-3 in dcl234
DCL3-WT-3_sRNAseq


title: NK_neg_neg_NYBC281_run2_74

description: Sample_HD-281NK-NKG2AC-DN_IGO_08801_D_74_run2


title: hdLEC_TLA_Control_rep3

tag: tissue type

value: Primary Cells

value: Human Dermal Lymphatic Endothelial Cells


title: HC_CP2


title: hdLEC_TLA_DLL4_rep1


title: BRCM-15 tissue bulk RNA

value: whole cells

value: heart

tag: other


title: BRCM-10 tissue bulk RNA

value: bulk RNAseq (total mRNA)


title: small RNA data of DCL3 D1316A/E1319A/E1224A/D1228A rep1 in dcl234

description:
small RNA data of DCL3 D1316A/E1319A/E1224A/D1228A rep1
DCL3m1-10_sRNAseq


title: small RNA data of DCL3-deletion 1450-1570 rep2 in dcl234

description:
small RNA data of DCL3-deletion 1450-1570 rep2
DCL3-del-4-45_sRNAseq


title: HC_CP1


title: Isotype Control rep1

first: hongchuan

last: liu

state: Shanghai

address: NO.826 Zhangheng Road

department: School of Pharmacy

institute: Fudan University

data_processing:
Illumina Casava1.8 software used for basecalling.
The raw paired end reads were trimmed and quality controlled by Fastp (https://github.com/OpenGene/fastp )with parameters -q 20 --length_required 30 -5 20 -3 20 -W 4 -M 20 -n 0.
Then clean reads were separately aligned to reference genome with orientation mode using hisat software.
the expression level of each transcript was calculated according to the Transcripts Per Kilobase of exon model per Million mapped reads (TPM) method. RSEM (http://deweylab.biostat.wisc.edu/rsem/) was used to quantify gene abundances.
Genome_build: GRCm39 (Mus musculus Ensembl Release 103)
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

source_name: MC38 tumor

extract_protocol:
Total RNA was extracted from the mouse tissue using TRIzol® Reagent according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined by 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample (OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >10μg) was used to construct sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: age

value: about 8 weeks

tag: location

value: School of Pharmacy,Fudan University

value: Isotype Control


title: hdLEC_TLA_Control_rep1


title: BRCM-9 tissue bulk RNA

value: left ventricle, heart failure


title: experimental group_IP

treatment_protocol: 3T3-L1 preadipocytes (4th day of differentiation process) were fixed in 37% formaldehyde, pelleted and resuspended in lysis buffer

value: anti-PPARgamma antibody (cell signaling technology, CST, USA)


title: Isotype Control rep3


title: CD8_neg_neg_NYBC245_run2_36

value: neg


title: BRCM-1 tissue bulk RNA


title: IL-21-αHSA rep1


title: BRCM-7 tissue bulk RNA


title: control group_IP

value: untreated


title: CD8_neg_neg_NYBC245_run1_36


title: NK_neg_neg_NYBC259_run1_8

value: NK


title: BRCM-8 tissue bulk RNA


title: small RNA data of DCL3-WT-1 in dcl234

description:
small RNA data of DCL3-WT-1 in dcl234
DCL3-WT-1_sRNAseq

value: floral tissue

value: 7-8 weeks

tag: strain


title: hdLEC_TLA_Control_rep2


title: small RNA data of DCL3 deletion 1356-1570 rep1 in dcl234

description:
small RNA data of DCL3 deletion 1356-1570 rep1
DCL3-del-3-39_sRNAseq


title: control group_input

value: preadipocytes

value: none (input)


title: BRCM-6 tissue bulk RNA


title: BRCM-4 tissue bulk RNA


title: small RNA data of dcl234_rep2

description:
small RNA data of dcl234_rep2
dcl234_sRNAseq_rep2


title: BRCM-5 tissue bulk RNA


title: NK_neg_neg_NYBC265_run2_64

description: Sample_HD-265NK-NKG2AC-DN_IGO_08801_D_64_run2


title: BRCM-3 tissue bulk RNA


title: small RNA data of dcl234_rep1

description:
small RNA data of dcl234_rep1
dcl234_sRNAseq_rep1


title: NK_neg_neg_NYBC230_run2_54

description: Sample_HD-230NK-NKG2AC-DN_IGO_08801_D_54_run2


title: NK_neg_neg_NYBC230_run1_54

description: Sample_HD-230NK-NKG2AC-DN_IGO_08801_D_54_run1


title: CD8_neg_neg_NYBC234_run1_32


title: small RNA data of Col_rep2

description:
small RNA data of Col_rep2
Col_sRNAseq_rep2


title: MYCN KD2

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

institute: Genotypic Technology

description: Gene expression analysis in MYCN knockdown cells

hyb_protocol: Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Agilent Technologies, Part Number 5188-5327)

scan_protocol: Scanned using Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D).

data_processing: Data extraction from Images was done using Feature Extraction software  and Normalization of the data was done in GeneSpring GX  : 75th percentile shift  method and gene based analysis was performed

source_name: Y79 cells transduced with lentiviruses containing MYCN shRNA construct-2

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). The total RNA were reverse transcribed at 40°C using oligo dT primer tagged to a T7 polymerase promoter and converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

growth_protocol: Y79 retinoblastoma cells were cultured  in RPMI-1640 medium supplemented with 10% fetal bovine serum and 1% (v/v) antibiotics mixture (Penicillin/Streptomycin/Amphotericin-B) and maintained in a humidified CO2 incubator supplied with  5% CO2 at 37 ºC .

extract_protocol: RNA was extracted using TRIzol method as per manufacturer’s protocol

treatment_protocol: Y79 cells were transduced with lentiviral particles containing either scrambled shRNA or MYCN shRNA constructs in the presence of polybrene (4µg/ml). The next day, virus containing media was replenished with fresh RPMI-1640 media. Transduced cells were selected in medium containing 3µg/ml puromycin. Knockdown  efficiency was confirmed by immunoblotting.

tag: genotype

value: MYCN KD2


title: RM-42 scRNA-seq

source_name: primary human-derived cells

value: CD3+ cells

tag: tissue

value: blood

value: 5' scRNA-seq


title: Isotype Control rep2

city: Shanghai


title: anti-mTIGIT rep3

value: anti-mTIGIT


title: anti-mTIGIT rep2

value: about 8 weeks


title: BRCM-2 tissue bulk RNA

value: whole cells

value: heart

value: bulk RNAseq (total mRNA)


title: Combination rep1

value: School of Pharmacy,Fudan University

value: Combination


title: small RNA data of Col_rep1

description:
small RNA data of Col_rep1
Col_sRNAseq_rep1

tag: developmental stage


title: CD8_neg_neg_NYBC230_run2_58

description: Sample_HD-230T-NKG2AC-DN_IGO_08801_D_58_run2

value: neg


title: IL-21-αHSA rep2


title: Combination rep2


title: RM-46 scRNA-seq


title: RM-44 scRNA-seq

value: left ventricle from ischemic cardiomyopathy patient


title: RM-40 scRNA-seq

value: left ventricle from dilated cardiomyopathy patient


title: RM-37 scRNA-seq


title: CD8_neg_neg_NYBC234_run2_32


title: CD8_neg_neg_NYBC265_run2_68

description: Sample_HD-265T-NKG2AC-DN_IGO_08801_D_68_run2


title: H1975 cells treated with osimertinib and pemetrexed

city: Tokyo

first: Natsuki

last: Takano

address: 1-1-5, Sendagi, Bunkyo-ku

institute: Nippon Medical School

hyb_protocol: 0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a Agilent fragmentation buffer and was hybridized at 65°C for 17 hr using Gene Expression Hybridization Kit.

scan_protocol: Microarray slides were scanned at 3 μm resolution using an Agilent SureScan (G4900DA).

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

source_name: Lung adenocarcinoma cell line

label_protocol: Agilent one-color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling protocol

growth_protocol: These cell lines were cultured in RPMI-1640 (FUJIFILM, Osaka, Japan) containing 10% fetal bovine serum (FBS; Biowest, Nuaille, France) and 1% penicillin and streptomycin (FUJIFILM) at 37°C in a 5% CO2 incubator.

extract_protocol: RNA was prepared using the miRNeasy micro kit (QIAGEN) following the manufacturer's recommendations. RNA quantity and quality were determined using NanoDrop One spectrophotometer (Thermo Fisher Scientific, Inc.) and Agilent 2100 Bioanalyzer (Agilent Technologies, Inc.), as recommended.

treatment_protocol: PC-9 and H1975 cells were incubated for 24 hours with osimertinib or pemetrexed or a combination of both at doses equivalent to their IC50 values.

value: osimertinib and pemetrexed


title: CD8_neg_pos_NYBC245_run1_35

value: pos


title: H1975 cells treated with osimertinib

value: osimertinib


title: SCRAMBLED CONTROL

description: Gene expression analysis in scrambled control cells

source_name: Y79 cells transduced with lentiviruses containing scrambled shRNA

value: SCRAMBLED CONTROL


title: anti-mTIGIT rep1


title: MYCN KD1

source_name: Y79 cells transduced with lentiviruses containing MYCN shRNA construct-1

value: MYCN KD1


title: CD8_neg_neg_NYBC281_run2_78

description: Sample_HD-281T-NKG2AC-DN_IGO_08801_D_78_run2


title: H1975 cells treated with pemetrexed

value: pemetrexed


title: RM-39 TCR-seq

data_processing:
Library strategy: TCR-seq
scRNA-seq sequencing reads were aligned to human genome reference build hg38 with cellranger 3.0
bulk RNA-seq sequencing reads were aligned to human genome reference build hg38,  transcript per million (TPM) were calculated with RSEM software.
Genome_build: hg38
Supplementary_files_format_and_content: scRNA-seq expression matrix were uploaded as zipped file. In each zipped file, it contains barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz. T cell receptor sequencing had additional clonotype file and metrics_summary.csv files.

value: CD3+ cells

value: blood

value: TCR--seq


title: Muscle_LFCR_12

city: Nakhonratchasima

first: Chotima

last: Poompramun

state: Nakhon Ratchasima

address: School of Animal Technology and Innovation, Institute of Agricultural Technology, Suranaree University of Technology

country: Thailand

institute: Suranaree University of Technoogy

hyb_protocol: Transcriptome profiling was performed using a Custom Gene Expression 8x60K Gallus gallus array (Agilent). A total of 21 samples were analysed, For each sample, 600 ng of Cy3-labeled cRNA (specific activity > 6.0 pmol Cy3/µg of cRNA) were fragmented at 60°C for 30 min in a reaction volume of 25 µl containing 25x Agilent Fragmentation buffer and 10x Agilent Blocking Agilent following the manufacturer’s instructions. Subsequently, 25 µl of 2x Agilent Hybridization Buffer were added to fragmentation mixture and hybridized to the SuperPrint G3 Custom GE 8 x 60K (Agilent Technology, design ID: G4102A) for 17 h at 65°C in rotating Agilent hybridization oven (Agilent Technologies).

scan_protocol: The slides were scanned on Agilent G2565CA Scanner System using one color scan setting for 8x60k array slide with a resolution of 3μm and a dynamic range of 20 bits.

data_processing:
The scaned images were analyzed with the Feature Extraction Software v10.7.3.1 (Agilent Technologies), using the GE2_107_Sep09 protocol to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
The fluorescence signal of expressed probes were log2 transformed and then normalized by median of each array.

organism: Gallus gallus

source_name: Thigh muscle

label_protocol: Cyanine-3 (Cy3) labeled cRNA were prepared using 200 ng of total RNA using the One-Color Low Input Quick Amp labeling kit (Agilent Technologies, Santa Clara, CA, USA) following the recommended protocol.

growth_protocol: Individual cages size 63 cm x 125 cm x 63 cm with floor covered with rice hull, were used to raise chicken individually, at Suranaree University of Technology (SUT), document ID is U1-02631-2559

extract_protocol: Total RNA from thigh muscles were extracted by TRIzol reagents (Invitrogen, San Diego, CA). Briefly, after mixing with TRIzol, thigh muscle sample was transferred into the 1.5 ml microtube with chloroform and incubated for 5 min. Samples were centrifugated at 7500 rpm (Thermo Fisher Scientific, Langenselbold, Germany) at 4°C for 10 min. Pellet was precipitated using Isopropanol and washed with 75% ethanol. Pellet was dried at 25°C for 5 min. RNA pellet was re-suspended in 20 µl Nuclease-free water. Quality of total RNA was assessed using a NanoDrop ND-1000 spectophotometer (Thermo Fisher Scientific, Walthman, MA, USA). 260/280 and 260/230 ratios of all samples were above 2.0. RNA integrity Number (RIN) was assessed using RNA 6000 Nano chips (Agilent Technologies, Santa Clara, CA, USA). RIN for all samples were above 8.0.

value: Thigh muscle

tag: genetic line

value: Korat chicken

tag: gender

value: male

value: 10 weeks

tag: trait

value: low FCR


title: CD8_neg_pos_NYBC234_run2_31

tag: celltype

value: neg

tag: donor


title: ICM-3-Bld scRNA-seq

value: CD45+ cells

value: 3' scRNA-seq


title: RM-38 TCR-seq

value: heart

value: left ventricle from dilated cardiomyopathy patient


title: CD8_neg_neg_NYBC230_run1_58

description: Sample_HD-230T-NKG2AC-DN_IGO_08801_D_58_run1

tag: run

tag: sampleID


title: IL-21-αHSA rep3

value: about 8 weeks

value: School of Pharmacy,Fudan University

tag: treatment


title: ICM-3-RVN scRNA-seq

tag: cell type

value: CD45- cells

value: left ventricle, non-infarcted myocardium


title: CD8_neg_pos_NYBC234_run1_31

value: pos


title: ICM-3-RVP scRNA-seq

tag: tissue type


title: CD8_neg_pos_NYBC281_run2_77

description: Sample_HD-281T-NKG2C-SP_IGO_08801_D_77_run2


title: CD8_neg_pos_NYBC245_run2_35


title: CD8_neg_pos_NYBC281_run1_77

description: Sample_HD-281T-NKG2C-SP_IGO_08801_D_77_run1


title: Combination rep3

value: Combination


title: SMCC-sibcat1

city: Pittsburgh

first: Shuchang

last: Liu

address: 203 Lothrop Street

institute: University of Pittsburgh

description: CTNNB1 silencing model

data_processing:
Low-quality reads and adapter sequences were filtered out by tool Trimmomatic (version 0.38)
Reads were aligned to mouse reference genome mm10 by HISAT2 aligner (version 2.1.0)
Gene counts were quantified by htseq-count (version 0.11.2)
Genome_build: mm10
Supplementary_files_format_and_content: wig files were generated using Python

source_name: cell line

growth_protocol: SMCC were cultured in EMEM (with Glutamine) at 37 degreen 5% CO2

extract_protocol:
SMCC RNA was harvested using Trizol reagent and Qiagen Rneasy kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: SMCC were transfected with either eGFP or S45Y plasmid with Lipofectamine™ 3000 Transfection Reagent for 48h, or with either siCTL or si-bcatenin with Lipofectamine™ RNAiMAX Transfection Reagent for 24h

tag: model

value: CTNNB1 silencing model

tag: cell line

value: small mice cholangiocyte cell line (SMCC)

tag: transfection

value: si-bcatenin


title: ICM-2-Bld scRNA-seq

data_processing:
scRNA-seq sequencing reads were aligned to human genome reference build hg38 with cellranger 3.0
bulk RNA-seq sequencing reads were aligned to human genome reference build hg38,  transcript per million (TPM) were calculated with RSEM software.
Genome_build: hg38
Supplementary_files_format_and_content: scRNA-seq expression matrix were uploaded as zipped file. In each zipped file, it contains barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz. T cell receptor sequencing had additional clonotype file and metrics_summary.csv files.

value: blood

tag: other


title: SMCC-siCTl3

description: CTNNB1 silencing control

value: CTNNB1 silencing control

value: siCTL


title: Muscle_LFCR_09

department: School of Animal Technology and Innovation

value: Thigh muscle

value: Korat chicken

value: male

tag: age

value: 10 weeks

value: low FCR


title: Muscle_LFCR_10

tag: tissue


title: PC-9 cells negative control

value: negative control


title: Muscle_HFCR_12

value: high FCR


title: Muscle_HFCR_09


title: ICM-2-RVN scRNA-seq

value: CD45- cells

value: heart

value: 3' scRNA-seq


title: RM-36 scRNA-seq

value: CD3+ cells

value: left ventricle from dilated cardiomyopathy patient

value: 5' scRNA-seq


title: H1975 cells negative control


title: SMCC-sibcat2

description: CTNNB1 silencing model

value: CTNNB1 silencing model

value: small mice cholangiocyte cell line (SMCC)

value: si-bcatenin


title: ICM-2-RVP scRNA-seq

value: CD45+ cells

value: left ventricle, non-infarcted myocardium


title: CD8_neg_pos_NYBC230_run1_57

description: Sample_HD-230T-NKG2C-SP_IGO_08801_D_57_run1

value: neg

value: pos


title: PC-9 cells treated with osimertinib

value: osimertinib


title: SMCC-sibcat3

description: CTNNB1 silencing model


title: Muscle_HFCR_11

value: Thigh muscle

value: Korat chicken

value: male

value: 10 weeks


title: Muscle_LFCR_11

value: low FCR


title: SMCC-siCTl1

description: CTNNB1 silencing control

value: CTNNB1 silencing control

value: siCTL


title: PC-9 cells treated with pemetrexed

value: pemetrexed


title: ICM-3-LVN scRNA-seq

value: CD45- cells

value: heart

value: left ventricle, infarcted myocardium

value: 3' scRNA-seq


title: Muscle_HFCR_10

value: high FCR


title: Muscle_LFCR_08


title: ICM-3-LVP scRNA-seq

value: CD45+ cells


title: CD8_neg_pos_NYBC265_run2_67

description: Sample_HD-265T-NKG2C-SP_IGO_08801_D_67_run2

value: neg


title: Muscle_LFCR_07


title: E2F1 siRNA 0.1nM R1881 3 [R20-024; SBS20-016]

city: BUFFALO

first: Eduardo

last: Cortes

state: NY

address: ELM AND CARLTON STREETS

department: Biostatistics and Bioinformatics

institute: ROSWELL PARK CANCER INSTITUTE

data_processing:
Basecalls performed using CASAVA version 1.8.2
Sequenced reads were mapped to GRCh38 reference GENCODE annotation (p7) using tophat 2.0.13
TopHat aligned BAMs were merged using MergeSamFiles from Picard v1.97
Reads counts are obtained using featureCounts from SubRead (v1.6.4)
Genome_build: hg38
Supplementary_files_format_and_content: raw counts

source_name: LNCaP_E2F1 siRNA_0.1nM R1881

growth_protocol: LNCaP prostate cancer cells were seeded in  androgen-deprived media (9% charcoal-stripped serum), next day cells were transfected with siRNA SmartPools targeting E2F1, or E2F2 or a non-targeting siRNA SmartPool using Lipofectamine 2000.

extract_protocol:
Cells were harvested 48h after treatment, RNA was isolated using Trizol and purified using RNAeasy columns.
RNA Libraries are prepared using the Illumina NextSeqTruSeq RNA Exome protocol and kit reagents.

treatment_protocol: 48h post transfection, cells were treated with 0.1nM of synthetic androgen R1881 or vehicle.

value: LNCaP

value: prostate cancer cells

tag: genotype/varaition

value: E2F1 siRNA


title: SMCC-eGFP3

description: CTNNB1 activation control

value: CTNNB1 activation control

value: small mice cholangiocyte cell line (SMCC)

value: eGFP


title: Muscle_LFCR_06

value: Thigh muscle

tag: genetic line

value: Korat chicken

value: male

value: 10 weeks

value: low FCR


title: CD8_neg_pos_NYBC230_run2_57

description: Sample_HD-230T-NKG2C-SP_IGO_08801_D_57_run2

value: pos


title: PC-9 cells treated with osimertinib and pemetrexed

value: osimertinib and pemetrexed


title: SMCC-siCTl2

description: CTNNB1 silencing control

value: CTNNB1 silencing control

value: siCTL


title: E2F2 siRNA 0.1nM R1881 3 [R20-030; SBS20-018]

source_name: LNCaP_E2F2 siRNA_0.1nM R1881

value: E2F2 siRNA


title: control siRNA vehicle 3 [R20-015; SBS20-013]

source_name: LNCaP_control siRNA_ETOH

value: control siRNA

value: ETOH


title: SMCC-eGFP1

description: CTNNB1 activation control


title: E2F2 siRNA vehicle 3 [R20-027; SBS20-017]

source_name: LNCaP_E2F2 siRNA_ETOH

value: LNCaP

value: prostate cancer cells


title: SMCC-S45Y3

description: CTNNB1 activation model

value: CTNNB1 activation model


title: Muscle_HFCR_07

tag: gender

value: high FCR


title: ICM-1-MIP scRNA-seq

extract_protocol:
cell pellete was collected and RNA was extracted using an RNeasy Mini kit (QIAGEN, 74104) by following the manufacturer’s protocol.
Libraries were prepared with an NEBNext Poly(A) mRNA Magnetic Isolation Module kit (NEB) and an NEBNext Ultra RNA Library Prep Kit for Illumina Paired-end Multiplexed Sequencing Library (NEB).

value: CD45+ cells

value: heart

value: left ventricle, infarcted myocardium

value: 3' scRNA-seq


title: SMCC-S45Y2

description: CTNNB1 activation model

value: small mice cholangiocyte cell line (SMCC)


title: E2F1 siRNA 0.1nM R1881 2 [R20-023; SBS20-010]

value: E2F1 siRNA


title: ICM-2-LVN scRNA-seq

value: CD45- cells


title: Muscle_HFCR_08

value: Thigh muscle

value: Korat chicken

value: male

value: 10 weeks

tag: trait


title: ICM-2-LVP scRNA-seq


title: SMCC-S45Y1

description: CTNNB1 activation model


title: E2F1 siRNA vehicle 3 [R20-021; SBS20-015]

source_name: LNCaP_E2F1 siRNA_ETOH


title: ICM-1-NMIP scRNA-seq

value: left ventricle, non-infarcted myocardium


title: control siRNA 0.1nM R1881 3 [R20-018; SBS20-014]

source_name: LNCaP_control siRNA_0.1nM R1881

value: control siRNA


title: ICM-1-Bld scRNA-seq

value: blood


title: SMCC-eGFP2

description: CTNNB1 activation control

value: CTNNB1 activation control

value: eGFP


title: Muscle_LFCR_05

value: low FCR


title: Muscle_HFCR_06

value: high FCR


title: DCM-3-LVP scRNA-seq

value: CD45+ cells

value: heart

value: left ventricle


title: control siRNA vehicle 2 [R20-014; SBS20-007]

value: LNCaP

value: prostate cancer cells

value: ETOH


title: Muscle_HFCR_03

value: Thigh muscle


title: ICM-1-MIN scRNA-seq

value: CD45- cells

value: left ventricle, infarcted myocardium

value: 3' scRNA-seq


title: E2F2 siRNA vehicle 2 [R20-026; SBS20-011]

value: E2F2 siRNA


title: DCM-2-Bld scRNA-seq


title: Muscle_LFCR_04

value: Korat chicken

value: male

value: 10 weeks


title: DCM-3-Bld scRNA-seq

value: blood


title: DCM-3-RVN scRNA-seq

value: right ventricle


title: DCM-2-RVN scRNA-seq


title: Muscle_LFCR_02

value: low FCR


title: E2F2 siRNA 0.1nM R1881 2 [R20-029; SBS20-012]


title: Muscle_HFCR_01

value: high FCR


title: DCM-3-RVP scRNA-seq

value: CD45+ cells

value: heart


title: Muscle_LFCR_03


title: Muscle_HFCR_04


title: Muscle_LFCR_01


title: PF543_6hr_rep2

city: Darlinghurst

first: Hui-Ming

last: Lin

state: NSW

address: 384 Victoria Street

country: Australia

institute: Garvan Institute of Medical Research

description: Gene expression data from C42B cells after 6 hour treatment with drug(s) or vehicle control

hyb_protocol: Following fragmentation, 2.3 ug of cRNA were hybridized on Clariom S arrays for 17 hr at 45C and 60 rpm as per Affymetrix Hybridisation Protocol. Arrays were washed and stained in the Affymetrix GeneChip Fluidics Station 450 ( Fluidics protocol FS450_0007).

scan_protocol: Arrays were scanned using the Affymetrix GCS3000 scanner, and Affymetrix GeneChip Command Console (AGCC) Scan Control software (version 4.0.0.1567).

data_processing: The data were analysed with Transcriptome Analysis Console software (version 4.02) with RMA as the normalisation method.

source_name: C42B cells treated with 15uM PF-543 for 6 hours

label_protocol: Biotinylated cRNA were prepared from 100 ng total RNA with GeneChip WT PLUS Reagent Kit P/N (GeneChip WT Plus Reagent Kit Manual Target Preparation for GeneChip Whole Transcript (WT) Expression Arrays P/N 703174 Rev.2

growth_protocol: C42B cell were cultured in RPMI media with 10% fetal bovine serum at a seeding density of 140000 cells in 2ml per well of 6-well plates.

extract_protocol: Total RNA was extracted with the Qiagen RNAeasy mini kit according to the manufacturer's instructions.

treatment_protocol: After 3 days of culture, drug(s) or DMSO vehicle control were added to each well. After 6 hours of treatment, cells were lysed with lysis buffer from the RNA extraction kit (Qiagen RNAeasy mini kit) and the lysates were frozen at minus 70C. Total RNA extraction was completed on another day.

tag: disease

value: human prostate cancer


title: DCM-3-LVN scRNA-seq

first: Shengshou

last: Hu

address: No.167 North Lish Road

institute: Fuwai Hospital

value: left ventricle


title: PF543_6hr_rep3


title: DCM-2-LVN scRNA-seq


title: E2F1 siRNA vehicle 2 [R20-020; SBS20-009]

value: LNCaP

value: prostate cancer cells

value: E2F1 siRNA

value: ETOH


title: Muscle_HFCR_05

value: Thigh muscle


title: control siRNA 0.1nM R1881 2 [R20-017; SBS20-008]

value: control siRNA


title: PF543_6hr_rep1


title: RNA-seq analysis of CON-piPSCs 1

city: Yangling

first: Shuai

last: YU

address: No.22 Xinong Road,

institute: Northwest A&F University

data_processing:
Clean reads were aligned to pig genome Ssc11.1, and the expression level was normalized as RPKM with gene annotation file.
Differential expression genes and functional enrichment for Gene Ontology (GO) and KEGG were plotted by http://www.bioinformatics.com.cn, an online platform for data analysis and visualization
Genome_build: pig genome Ssc11.1 (NCBI)
Supplementary_files_format_and_content: The RNA-seq of ESRRB-piPSCs and CON-piPSCs contains the differential expression genes

source_name: piPSCs

extract_protocol:
Total RNA of the RNA samples was isolated from cell pellets by Trizol reagent (TaKaRa) and RNA-seq library was generated according to the manufacturer’s recommendations.
Paired-end 150 bp sequencing was performed on DNBSEQ (Illumina) at BGI Technology Corporation (China).

value: CON-piPSCs


title: enzalutamide-PF543_6hr_rep2

source_name: C42B cells treated with 10uM enzalutamide and 15uM PF-543 for 6 hours


title: enzalutamide-PF543_6hr_rep3


title: RNA-seq analysis of ESRRB-piPSCs 2

value: ESRRB-piPSCs


title: Muscle_HFCR_02

value: Korat chicken

value: male

value: 10 weeks


title: ACKR1-IL8ICM2 cell bulk RNAseq

value: ACKR1+ endothelial cells

value: left ventricle, infarcted myocardium, stimulated with CXCL8

value: bulk RNAseq (polyA enriched mRNA)


title: E2F2 siRNA 0.1nM R1881 1 [R20-028; SBS20-006]

value: E2F2 siRNA


title: RNA-seq analysis of ESRRB-piPSCs 1


title: E2F2 siRNA vehicle 1 [R20-025; SBS20-005]


title: N-1-RVP scRNA-seq

value: CD45+ cells

value: heart

value: right ventricle

value: 3' scRNA-seq


title: ACKR1-IL8ICM1 cell bulk RNAseq


title: DMSO_6hr_rep3

source_name: C42B cells treated with 0.125% DMSO vehicle control for 6 hours

value: human prostate cancer


title: MM_IP

city: wuhan

first: han

last: qing

address: whu

institute: school

data_processing:
Library strategy: SLIM-m6A-seq/RNA-seq/m6A-seq
According to the principle of library construction, the raw data is split by custom scripts.
Adapter seqeucnes were trimmed by using trim galore.
fastuniq is used to remove PCR duplication. Then use seqtk trimfq remove random sequences added in library construction.
Clean reads were mapped to genome by using STAR; with parameter "--outFilterMultimapNmax 20 --outFilterMismatchNmax 10". Only the proper pair and uniquely mapped alignments was persisted for the downstream pipelines.
Aligned reads were used for peak calling and enriched regions comparing by exomePeak.
HOMER was used for peak annotation and detection of the sequence motif.
Genome_build: hg38 and mm10

source_name: murine model heart tissue

growth_protocol: HEK293T (ATCC) cells were cultured in T25 cell culture flask using DMEM (Dulbecco's modified Eagle's medium, high glucose, Gibco) supplemented with 10% fetal bovine serum (FBS, Gibco), and 1% penicillin/streptomycin (Beijing Dingguo changsheng Biotechnology Co.,Ltd, GA3502).

extract_protocol:
Total RNA was isolated from cell lines, peripheral blood or Murine heart tissue with TRIzol (Invitrogen) according to the manufacture’s protocol. The mRNA was isolated by subjecting total RNA to oligo(dT) enrichment using Dynabeads Oligo(dT)25 (NEB)
for No.1-SING &No. 1-SING-IP: Fragmented mRNAs from Hek293T cells were first treated with T4 PNK. Then the samples were ligated with 3'-linker (5'- rApp-NNNNNNTGGAATTCTCGGGTGCCAAGG-SpC3 -3', Italic N represents for 6-nt random sequences). Extra 3'-linker were removed by 5′-deadenylase and RecJf digestion. The reaction mixtures were subsequently purified. 1/50 of the purified sample was retained as input control while the remaining sample was applied to m6A antibody immunoprecipitation (IP). The input control sample and the IP sample were reverse transcripted using RT primer (5'-ACACGACGCTCTTCCGATCT-3') to obtain cDNA samples. The cDNA samples were then ligated with 5'-adaptor (5'-Phos-NNNNNNNNNNAGATCGGAAGAGCACACGTCTG-SpC3-3'), followed by determination of PCR cycle number by RT-qPCR. Finally, library PCR amplification was performed using the NEB primers and the products were purified by magnetic beads or agarose gel electrophoresis.
for samples other than No.1-SING &No. 1-SING-IP: Fragmented mRNAs from different samples were first treated with T4 PNK. Then the samples were ligated with pre-adenylated 3'-linkerLs (5'-NNNNNNNNNNNNAGATCGGAAGAGCGTCGTG-3', Bold N represnts for designed 6-nt barcode sequences, Italic N represents for 6-nt random sequences). Extra 3'-linkerLs were removed by 5′-deadenylase and RecJf digestion. The reaction mixtures were subsequently pooled together and purified. 1/50 of the purified sample was retained as input control while the remaining sample was applied to m6A antibody immunoprecipitation (IP). The input control sample and the IP sample were reverse transcripted using RT primer (5'-ACACGACGCTCTTCCGATCT-3') to obtain cDNA samples. The cDNA samples were then ligated with 5'-adaptor (5'-Phos-NNNNNNNNNNAGATCGGAAGAGCACACGTCTG-SpC3-3'),followed by determination of PCR cycle number by RT-qPCR. Finally, library PCR amplification was performed using the NEB primers and the products were purified by magnetic beads or agarose gel electrophoresis.

value: Murine Heart

value: Murine （Type 2 diabetes/Type 3 diabetic myocardial infarction/healthy control）


title: enzalutamide-PF543_6hr_rep1


title: ACKRR1-NCICM2 cell bulk RNAseq

source_name: primary human-derived cells

value: left ventricle, infarcted myocardium


title: control siRNA 0.1nM R1881 1 [R20-016; SBS20-002]

value: LNCaP

value: prostate cancer cells

value: control siRNA


title: DCM-2-RVP scRNA-seq


title: N-1-LVN scRNA-seq

value: CD45- cells

value: left ventricle


title: DCM-2-LVP scRNA-seq


title: enzalutamide-ABC294640_6hr_rep3

source_name: C42B cells treated with 10uM enzalutamide and 15uM ABC294640 for 6 hours


title: N-1-LVP scRNA-seq


title: enzalutamide-ABC294640_6hr_rep1


title: ACKRR1-NCICM1 cell bulk RNAseq

value: ACKR1+ endothelial cells


title: RNA-seq analysis of CON-piPSCs 2

value: CON-piPSCs


title: enzalutamide-ABC294640_6hr_rep2