title: HUES8, HNF6-KO_PP_Rep3 (ATAC-seq)

city: Aachen

first: Ivan

last: Costa

address: Pauwelsstraße 19

institute: Unikilink RWTH Aachen

description: [Diff-peaks_*.bed]  Differential peak regions of HNF6-Knockout in PP stage

data_processing:
Reads were trimmed with skewer and aligned with Bowtie2 to the human hg19 genome. Only properly mapped pairs were further considered and duplicates were removed.
We used MACS2 with FDR of 5% to find condition specific peaks using corresponding input DNA and replicates.
We used THOR to detect regions with differential peaks between consecutive differentiation steps in wild type cells (ESC vs DE, DE vs. GTE, GTE vs. PE and PE vs. PP) and to compare WT and HNF6 KO condition for each day (p-value < 10-5).
We combined all differential peaks in WT condition and quantified  the number of reads per peak, which were first normalized by library size and then by removing the mean and scaling to unit variance, and performed clustering with K-medoids using pearson correlation as similarity metric.
R (Spearman correlation) and RGT-THOR (defualt parameter)
Genome_build: hg19
Supplementary_files_format_and_content: Clusters on wild-type(Con_Clusters), and Wild-type versus Knock-out differential peaks on each stages (Diff-peaks)

source_name: embryonic stem cells, HUES8

value: embryonic stem cells

tag: Stage

value: pancreatic progenitors


title: Male_B6_H3K27ac_Repl3_G162_M3

status: Public on Oct 27 2021

type: SRA

city: Boston

first: David

middle: J.

last: Waxman

state: MA

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

country: USA

institute: Boston University

description: ChIP-seq Library

library_source: genomic

data_processing:
READ MAPPING: ChIP-seq reads were aligned using Bowtie2 (Langmead et al 2009, Genome Biology) with default settings. Reads were filtered so that only uniquely-aligned reads were used for downstream analysis.
PEAK CALLING: Peaks were called using Macs2 (Zhang et al 2008, Genome Biology) with default parameters without filtering for PCR duplicates. Peaks were filtered to remove blacklisted regions (www.sites.google.com/site/anshulkundaje/projects/blacklists) and also regions called as peaks that contain only PCR duplicated reads.
Genome_build: mm9
Supplementary_files_format_and_content: Replicate merged peak lists for H3K27ac ChIP-seq, merged by strain and sex. Samples were combined at the fastq level and processed through a standard ChIP-seq pipeline as described. Columns are in BED6+4 format from MACS2 narrowPeak defaults. Specifically, columns 1-3 represent genomic coordinates of the indicated peak; column 4 is the peak name (unique identifier); column 5 is an integer score for display calculated as -10*log10(qvalue); column 6 indicates the strand; column 7 indicates the fold-change over background; column 8 indicates -(log10pvalue); column 9 indicates -log10(qvalue); and column 10 indicates the summit position relative to the 5' end of the peak.

molecule: genomic DNA

organism: Mus musculus

source_name: Liver

growth_protocol: Male and female C57BL/6J and CAST/EiJ mice, 8-9 weeks of age, were purchased from Jackson Labs.

extract_protocol:
Liver was dounce homogenized, passed through a 70 micron filter, and then crosslinked with 1% formaldehyde for 10 minutes. Samples were sonicated with a Bioruptor Pico (Diagenode, cat#:B01060010) until the majority of DNA fragments were between 100-400bp (25 cycles total, 30 sec ON 30 sec OFF). Chromatin was quantified and 15 ug of chromatinized DNA was incubated with anti-H3K27ac antibody (Abcam, cat#:ab4729).
Samples were prepared for sequencing with NEBNext Ultra II DNA Library Prep Kit for Illumina according to the manufacturer's directions for low input samples (New England Biolabs, #E7645). All samples were subjected to double-sided SPRI size selection prior to PCR amplification (Agencourt AMPure XP; Beckman Coulter: A63882). Samples were barcoded using New England Biolabs NEBNext Multiplex Oligos for Illumina (#E7335) with 8 rounds of PCR per the manufacturer's instructions.

tag: strain

value: C57BL/6J (Jackson Labs, cat#:000664)

tag: chip antibody

value: Abcam anti H3K27ac (cat# Ab4729)

tag: Sex

value: Male

tag: age

value: 8 weeks


title: AS1066-t

city: New York

first: Jens

last: Hansen

state: NY

address: 1425 Madison Ave

department: Department of Pharmacological Sciences

institute: Icahn School of Medicine at Mount Sinai

library_source: transcriptomic

data_processing:
Random removal of reads from each fastq-file to ensure that all samples that are subjected to the same comparison have the same final read counts (e.g. all mouse samples have the same read counts before alignment)
Alignment to the reference genome using Tophat 2.0.8
Identification of differentially expressed genes using Cufflinks 1.3.0
Genome_build: h19 and mm9

molecule: total RNA

organism: Homo sapiens

source_name: Thoracic aortic wall

extract_protocol: none provided by the submitter

tag: tissue

value: control thoracic aortic tissue


title: Male_B6_H3K27ac_Repl4_G162_M4

description: ChIP-seq Library


title: Male_B6_H3K27ac_Repl2_G162_M2

description: ChIP-seq Library


title: HUES8, HNF6-KO_PP_Rep2 (ATAC-seq)

country: Germany

growth_protocol: HUES8 control and HNF6 KO hESC were subjected to in vitro pancreatic differentiation.

extract_protocol:
Single cells were harvested at definitve endoderm (DE), gut tube  (GT), pancreatic endoderm (PE) and pancreatic progenitor (PP) stage. Cells were directly lysed in tagmentation buffer (Nextera DNA Library Preparation Kit, Illumina) followed by DNA extraction.
Nextera DNA Library Preparation Kit, Illumina

tag: cell line

tag: cell type

tag: genotype


title: HUES8, HNF6-KO_PE_Rep3 (ATAC-seq)

description: [Diff-peaks_*.bed]  Differential peak regions of HNF6-Knockout in PE stage

value: pancreatic endoderm


title: HUES8, HNF6-KO_PP_Rep1 (ATAC-seq)


title: HUES8, HNF6-KO_PE_Rep2 (ATAC-seq)


title: RVSMC transfected with NGGap and treated with AngII 3hr, biological rep3

type: RNA

city: Duarte

first: Rama

last: Natarajan

state: California

address: 1500 E Duarte Rd

department: Department of Diabetes Complications and Metabolism

institute: Beckman Research Institute, City of Hope

description: Gene expression data from RVSMC transfected with negative control GapmeR (100nM) for 48hours and treated with Angiotensin II (100 nM) for 3 hours

hyb_protocol: The chips were hybridized in Affymetrix Hybridization Oven 640 and washed using Affymetrix Fluidics Station 450 according to manufacturer's protocols.

scan_protocol: The chips were scanned by Affymetrix scanner 3000 7G using manufacturer's default settings

data_processing: Raw Affymetrix intensity measurements of all probe sets were background-corrected, normalized, and summarized into gene level expression measurements using RMA method implemented in Partek Genomic Suite V6.6.

label: biotin

organism: Rattus norvegicus

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 200 ng total RNA.

growth_protocol: Rat vascular smooth muscle cells (RVSMCs) were isolated from thoracic aortas of male Sprague-Dawley rats by enzymatic digestion and cultured in M199 medium supplemented with 10% FBS and antibiotics.

extract_protocol: Total RNA was isolated using RNeasy reagent (Qiagen) following manufacturer's instructions.

treatment_protocol: Cells were transfected with either negative control GapmeR (NCGap) or rat Alivec Gapmer (AlivecGap) for 48 hours, and then treated with either 100 nM of Angiotensin II or equivalent volume of 1x PBS for 3 hours.

value: rat vascular smooth muscle cells

tag: treatment


title: PIM3_KO

city: Birmingham

first: Elizabeth

last: Beierle

state: AL

address: 1670 University Blvd

institute: University of Alabama at Birmingham

description: FPKMvalues.xlsx

data_processing:
Illumina bcl2fastq version 2.18.0.12 was used for basecalling
STAR version 2.7.3a was used to align the short sequences using parameters --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outSAMattributes All
Transcript abundances were calculated using Cufflinks version 2.2.1 using parameters --library-type fr-firststrand -G -L
Cuffmerge, Cuffquant and Cuffidff were then used to merge, quantify and perform differential expression using default parameters
Genome_build: Gencode GRCh38 p13 Release 32
Supplementary_files_format_and_content: tab-delimited file containing FPKM values for each gene in each sample

source_name: Hepatoblastoma

growth_protocol: Both cell lines were maintained in Dulbecco’s Modified Eagle’s Medium supplemented with 10 % fetal bovine serum (HyClone, GE Healthcare Life Sciences, Logan, UT), 1 µg/mL penicillin/streptomycin (Gibco, Carlsbad, CA), and 2 mmol/L L-glutamine (Thermo Fisher Scientific, Waltham, MA). Cells were maintained in culture under standard conditions at 37 °C and 5 % CO2.

extract_protocol:
Total cellular RNA was extracted using the RNeasy kit (Qiagen) according to the manufacturer's protocol.
The quality of the total RNA was assessed using the Agilent 2100 Bioanalyzer followed by 2 rounds of poly A+ selection and conversion to cDNA. The NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® library generation kit (New England Biolabs) was used per the manufacturer’s instructions. The libraries were quantitated using qPCR in a Roche LightCycler 480 with the Kapa Biosystems kit for library quantitation (Kapa Biosystems, Woburn, MA). Subsequently, sequencing was performed on the Illumina NextSeq500 using the latest versions of the sequencing reagents and flow cells with single-end 75 bp reads.

treatment_protocol: No treatment was involved

value: Hepatoblastoma cells

value: Untreated

value: HuH6 cell line


title: HuH6_WT

description: FPKMvalues.xlsx


title: Mammospheres_experiment #2

city: Ioannina

first: Angeliki

last: Magklara

address: Panepistimioupoli Ioanninon

department: Department of Medicine/Department of Biomedical Research (Ioannina) Foundation for Research & Technology-Hellas

country: Greece

institute: University of Ioannina/nstitute of Molecular Biology & Biotechnology

description: Mammospheres enriched in breast cancer stem cells

data_processing:
Quality Control was performed for the fastq raw data files using the “FASTQC” software
FastQ files were aligned to the human genome (hg19) using HISAT2
Counts were defined using HTSeq htseq-count command with the “intersection non empty” option . The count files were used as input for DESeq2
Normalization was performed with the estimate size factor function followed by Differentially Expressed Genes Analysis.
Genome_build: human genome (hg19)
Supplementary_files_format_and_content: Text files include reads per gene for each sample (#1, #2, #3, #4)
Supplementary_files_format_and_content: Text file for the comparison of mammospheres vs. adherent monolayer cells with the following information: Gene name; baseMean; log2foldChange; lfcSE; stat; pvalue; padj.

source_name: Breast cancer cells

growth_protocol: MCF-7 human breast cancer cell line was cultured in Dulbecco’s modified Eagle’s medium (DMEM, high glucose) supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin in a humidi-fied atmosphere of 5% CO2 at 37oC. Cells were routinely passaged every 2 or 3 days and tested for mycoplasma. For 1st generation mammopshere formation, MCF-7 cells at an early passage were resuspended in mammosphere medium (DMEM/F12 supplemented with B27, EGF (20 ng/mL), and FGF (20 ng/mL) and were cultured for 7 days. 1st generation mammospheres were dissociated and replated in mammosphere forming conditions. Four days upon replating, spheres were collected by centrifugation (800 RPM, 3 minutes, RT). Only mammospheres with a diameter over 50 µm were counted. The mammopshere formation efficiency (MFE) was calculated based on the following formula: (number of mammospheres per well/number of cells seeded per well) × 100.

extract_protocol:
For total RNA extraction the RNeasy Kit (Qiagen) was used. Total RNA concentration and purity was measured with NanoDropTM 2000.
RNA-sequencing libraries were prepared with the illumina TruSeq RNA v2 kit using 1 μg of total RNA. The libraries were checked with the Agilent bioanalyzer (DNA1000 chip), quantitated with the qubit HS spectrophotometric method and pooled in equimolar amounts for sequencing. Approximately 25 million, 75 bp long, single-end reads were generated for each sample on an Illumina NextSeq500 sequenc-er.

value: Breast cancer cells

tag: phenotype

value: 2nd generation mammospheres


title: RVSMC transfected with NGGap and treated with AngII 3hr, biological rep2

value: transfected with negative control GapmeR (100nM) for 48hours and treated with Angiotensin II (100 nM) for 3 hours


title: Adherent monolayer cells_experiment #2

description: Parental cells

value: Adherent monolayer cells


title: M5-3

city: Guangzhou

first: hongling

last: guan

address: tianhe

country: China

institute: South China Agricultural University

description: stage 5 of male flower

data_processing:
The filtered high-quality reads were assembled and mapped to litchi genome using HISAT2 (version 2.0.4) and StringTie.
Quantification of gene expression levels were estimated by FRPKM (fragments per kilobase of transcript per million fragments mapped)
Genome_build: In the process of publication, no number has been assigned yet
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Litchi chinensis

source_name: flower

extract_protocol:
Total RNA was extracted by a column RNA Extraction kit (Tiandz, Beijing, China) according to the manufacturer’s instructions, and digested by DNase to remove possible DNA contamination.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. The library preparations were sequenced on an Illumina platform and paired-end reads were generated.

tag: developmental stage

value: stage 5

tag: gender

value: male


title: M5-2

description: stage 5 of male flower


title: RVSMC transfected with AlivecGap, biological rep3

description: Gene expression data from RVSMC transfecated with Alivec GapmeR (100nM) for 48hours

source_name: RVSMC transfected with AlivecGap


title: HUES8, HNF6-KO_PE_Rep1 (ATAC-seq)

value: embryonic stem cells


title: RVSMC transfected with NGGap and treated with AngII 3hr, biological rep1


title: HUES8, HNF6-KO_GT_Rep3 (ATAC-seq)

description: [Diff-peaks_*.bed]  Differential peak regions of HNF6-Knockout in GT stage

value: primitive gut tube


title: M5-1

description: stage 5 of male flower


title: Male_B6_H3K27ac_Repl1_G162_M1

description: ChIP-seq Library

value: C57BL/6J (Jackson Labs, cat#:000664)

value: Abcam anti H3K27ac (cat# Ab4729)


title: THP-1 cells, Runx1_fRIP-seq

city: Bonston

first: Bon

middle: Quy

last: Trinh

address: 330 Brookline Ave

department: Medicine

institute: Beth Israel Deaconess Medical Center

data_processing:
fRIP-seq samples were demutliplexed. Reads were deduplicated by Clumpify from the BBtools suite, sourceforge.net/projects/bbmap/) with the parameters “dedupe spany addcount”. Adaptor quality trimming and filtering was performed by BBDuck from the BBtools suite with the parameters “ktrim=l hdist=2”. Low quality reads/bases were removed by Trimmomatic (Bolger et al., 2014) with the parameters “LEADING:28 SLIDINGWINDOW:4:26 TRAILING:28 MINLEN:20”.
The processed reads were then aligned to Human genome build 38 (hg38) by STAR aligner (Dobin et al., 2013) with the parameters “--outFilterScoreMinOverLread 0.05 --outFilterMatchNminOverLread 0.05 --outFilterMultimapNmax 30 --outSAMprimaryFlag AllBestScore”.
Peak calling was performed using HOMER (v4.10) (Heinz et al., 2010). Threshold: ten fold over local region
Genome_build: hg38
Supplementary_files_format_and_content: wig files were generated using bamCoverage (part of the deepTools suite (Ramirez et al., 2016) with default parameters.

source_name: THP-1 cells

growth_protocol: THP-1 cells were obtained from American Type Culture Collection (ATCC). The cells were cultured in RPMI-1640 supplemented with 10% (vol/vol) fetal bovine serum (FBS; Cellgro), 1% penicillin-streptomycin, and 2-mercaptoethanol to a final concentration of 0.05 mM.

extract_protocol:
fRIP was performed following a protocol reported by Hendrickson et al (Hendrickson et al., 2016) with modifications. Briefly, cells were crosslinked in 0.1% formaldehyde at room temperature for 10 minutes. The crosslinking reaction was quenched for 5 min at room temperature with 0.125 M glycine. Crosslinked cells were washed with ice-cold PBS. Cell pellet was lysed in RIPA lysis buffer (50 mM Tris (pH 8), 150 mM KCl, 0.1 % SDS, 1 % Triton-X, 5 mM EDTA, 0.5 % sodium deoxycholate, 0.5 mM DTT) supplemented with protease inhibitor cocktail (Thermo Scientific) and 100 U/ml RNaseOUT™ (Invitrogen). After sonication, cell lysate was pre-cleared by incubating with Dynabeads® Protein G (Invitrogen). Beads were then captured and removed using a magnet.  Pre-cleared lysate was incubated with anti-Runx1 antibody or IgG at 4°C for 2 h before adding 50 μl of Dynabeads® Protein G to capture antibodies. After washing, beads were kept at -200C or preceded to incubation with reverse-crosslinking buffer (3× PBS (without Mg or Ca), 6 % N-lauroyl sarcosine, 30 mM EDTA, 15 mM DTT) supplemented with Proteinase K (Ambion) and RNaseOUT together with input sample. Captured RNAs were extracted by Trizol reagent. Extracted RNA was treated with DNAse from RNase-Free DNase Set (QIAGEN) then ribosomal RNA was removed using the Ribo-Zero™ Magnetic Gold Kit (Epicentre). RNA quality was determined using the RNA 6000 Pico Kit on a Bioanalyzer (Agilent).
cDNA libraries were constructed with the Truseq stranded total RNA library prep kit (Illumina) according to manufacturer’s protocol. The libraries were pooled together and subjected to pair-end sequencing on a Nextseq500 (Illumina) to achieve 2×40 bp reads.

value: Runx1 (Abcam ab35962)


title: RVSMC transfected with AlivecGap, biological rep2

value: transfecated with Alivec GapmeR (100nM) for 48hours


title: HUES8, HNF6-KO_GT_Rep2 (ATAC-seq)


title: THP-1 cells, Input_fRIP-seq


title: HUES8, HNF6-KO_GT_Rep1 (ATAC-seq)


title: M4-3

description: stage 4 of male flower

value: stage 4


title: Divergent leukemia sub-clones derived from U-937 cells (MBU-7)

type: genomic

city: Badalona

first: Mar

last: Mallo

address: Ctra de Can Ruti, s/n, camí de les escoles. Edifici IMPPC

country: Spain

institute: Josep Carreras Leukaemia Research Institute

description: Hybridized to CytoScan 750K

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using ThermoFisher fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
The array image was acquired using ThermoFihser GeneChip® Operating Software. Copy number and SNP study was performed with the Chromosome Analysis Suite (ThermoFisher, versión 4.2).
Copy number and SNP data (CYCHP file)

label: Biotin

source_name: Cell line

label_protocol: As per manufacturer (ThermoFisher)

growth_protocol: All cell lines were cultured in RPMI 1640 (ThermoFisher Scientific) supplemented with 10%, 1% Pen/Strep, and 1% L-glutamine at 37ºC in 5% CO2. All cell lines were routinely analyzed for the presence of mycoplasma

extract_protocol: Genomic DNA was extracted from collected cells using PureLink Genomic DNA Mini Kit (ThermoFisher Scientific)

value: U-937 derived cell line MBU-7

tag: disease state

value: leukemia


title: HUES8, HNF6-KO_DE_Rep3 (ATAC-seq)

description: [Diff-peaks_*.bed]  Differential peak regions of HNF6-Knockout in DE stage

value: definitive endoderm


title: RVSMC transfected with NGGap, biological rep3

description: Gene expression data from RVSMC transfected with negative control GapmeR (100nM) for 48hours

source_name: RVSMC transfected with NGGap

value: rat vascular smooth muscle cells


title: Divergent leukemia sub-clones derived from U-937 cells (MBU-8)

description: Hybridized to CytoScan 750K


title: RVSMC transfected with NGGap, biological rep1

value: transfected with negative control GapmeR (100nM) for 48hours


title: HUES8, HNF6-KO_DE_Rep1 (ATAC-seq)


title: M4-1

description: stage 4 of male flower


title: SNc FACS sorted dopaminergic neurons that do not express Sox6 (mCherry+) [1211]

city: Chicago

first: Rajeshwar

last: Awatramani

state: Illinois

address: 320 E Searle

department: Neurology

institute: Northwestern University

data_processing:
Illumina NextSeq500 NGS Sequencer was used to sequence the libraries with the production of single-end, 75 bp reads.
The quality of reads, in FASTQ format, was evaluated using FastQC.
Reads were trimmed to remove Illumina adapters from the 3’ ends using cutadapt.
Trimmed reads were aligned to the Mus musculus genome (mm10) using STAR.
Read counts for each gene were calculated using htseq-count in conjunction with a gene annotation file for mm10 obtained from Ensembl.
Normalization and differential expression were calculated using DESeq2.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: NN_RNAseq_DESeq2-CompleteTesults-with-normalized.csv: Matrix table with raw gene counts and normalized using DESeq2 for every gene and every sample.

source_name: SNc dopaminergic neurons expressing mCherry

extract_protocol:
Cell dissociation was performed. Samples were processed with the Papain Dissociation System (Worthington Biochem #LK003150) following the manufacturer’s recommendations. However, we substituted the provided EBSS solution with ACSF buffer (200 mM Sucrose, 2.6 mM KCl, 10 mM MgCl2, 0.5 mM CaCl2, 26 mM NaHCO3, 1.27 mM NaH2PO4 and 10 mM Dextrose; equilibrated with 5% CO2/95% O2; pH 7.3). Total RNA was prepared according to Ambion mirVana miRNA isolation kit (Life Technology, AM1561).
The Illumina TruSeq Stranded mRNA Library Preparation Kit was used to prepare sequencing libraries of high-quality RNA samples (RIN > 7).

value: Sox6-FSF-Cre, Th-2A-Flpo, RC-Frepe

value: Adult

value: SNc dopaminergic neurons


title: SNc FACS sorted dopaminergic neurons that do not express Sox6 (mCherry+) [825]


title: M3-3

description: stage 3 of male flower

value: stage 3


title: M4-2

description: stage 4 of male flower

value: male


title: HUES8, HNF6-KO_DE_Rep2 (ATAC-seq)

value: embryonic stem cells


title: M3-1

description: stage 3 of male flower


title: SNc FACS sorted dopaminergic neurons expressing Sox6 (GFP+) [103]

source_name: SNc dopaminergic neurons expressing GFP


title: HUES8, HNF6-KO_ESC_Rep3 (ATAC-seq)

description: [Diff-peaks_*.bed]  Differential peak regions of HNF6-Knockout in ESC stage

value: undifferentiated


title: SNc FACS sorted dopaminergic neurons expressing Sox6 (GFP+) [825]


title: M3-2

description: stage 3 of male flower


title: M2-2

description: stage 2 of male flower

value: stage 2


title: dP2_NPIP-1

city: Buenos Aires

first: Florencia

last: Bannoud

address: Av Rivadavia 1971

country: Argentina

institute: Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)

description: Roots with high anthocyanin concentration in the outer phloem

data_processing:
Quality Control FastQC
Reads Filtration with Trimmomatic version 0.32 with adapter trimming and using a sliding window length ≥ 50 and Phred quality score ≥ 28
Reads for each gene available from the V1.0 gene annotation of the carrot genome  were mapped and quantified with RSEM , using Bowtie2 as aligner
Supplementary_files_format_and_content: Matrix table with the effective length, expected count, TPM and FPKM for each gene ID

organism: Daucus carota

source_name: Dark purple carrot roots

growth_protocol: Plants were grown on the field

extract_protocol:
Total RNA was extracted using the TRIzol® Plus RNA Purification Kit (Life Technologies, Carlsbad, CA) following the manufacturer’s protocol. DNA was removed with the ‘DNA free-kit’ provided with the RNA purification kit. RNA quantification was done in a Nanodrop One Spectrophotometer, and quality control was done in an Agilent 2100 Bioanalyzer RNA NanoChip.
RNA libraries were prepared for sequencing using standard Illumina protocols  at the University of Wisconsin Biotechnology Center

value: Inner phloem

tag: anthocyanin concentration

value: high


title: WT LP_75b45

city: Baton Rouge

first: Thomas

middle: W

last: Gettys

state: LA

address: 6400 Perkins Road

department: Nutrient Sensing and Adipocyte Signaling

institute: Pennington Biomedical Research Center

data_processing:
Lexogen Quantseq pipeline V1.8.8 on the Bluebee platform, quality control, mapping, and read count tables
Annotation and preparation for analysis, 3.5.2(2018-12-2), Rstudio V1.2.1511 and biomaRt V2.38.0
DESeq2  V1.22.2 differential gene expression
JMP Genomics V9 quality control, principal components, ANOVA, hierarchical clustering
Genome_build: mouse- GRCm38.84
Supplementary_files_format_and_content: raw counts and DESeq2 normalized counts

source_name: WT LP_kidney

growth_protocol: WT and FGF21 KO mice began the experimental diets (NP and LP) at 3 month of age and were remained on thses diets until 22 month of age.

extract_protocol:
Flash frozen kidney (cortex) was dissected and a small piece was placed in Trizol.  After homogenization, BCP was added, samples were vortexed vigorously, and then spun. The aqueous phase was combined with an equal volume of ethanol and the sample was processed through a Qiagen RNeasy column according to the manufacturer's instructions. mRNA was stored at -80°C and samples were diluted to 200ng/µl for RNAseq.
Lexogen Quant-Seq; indexed and pooled samples, 50bp forward read

treatment_protocol: Casein was the protein source for both normal protein (NP, 20% casein) and low protein diet (LP, 5% casein).  All mice were fed ad libitum.

tag: strain background

tag: genotype/variation

value: wild type

value: 22 months

tag: dietary protein level

value: Low protein (5%)

value: kidney


title: HUES8, HNF6-KO_ESC_Rep2 (ATAC-seq)

tag: Stage


title: SNc FACS sorted dopaminergic neurons expressing Sox6 (GFP+) [1211]

tag: strain


title: M2-3

description: stage 2 of male flower


title: WT LP_75b42

tag: Sex


title: WT LP_75b46

tag: age


title: dP2_NPIP-3

tag: tissue


title: M2-1

description: stage 2 of male flower


title: dP2_NPIP-2


title: dP2_POP-2

value: Outer phloem


title: dP2_POP-3


title: HUES8, Con_PE_Rep3 (ATAC-seq)

description:
[Diff-peaks_*.bed]  Differential peak regions of Control in PE stage
[Con_Cluster-*.bed]  Cluster #1 - #9 regions of wild-type peaks

tag: cell line

value: pancreatic endoderm


title: HUES8, Con_PP_Rep2 (ATAC-seq)

description:
[Diff-peaks_*.bed]  Differential peak regions of Control in PP stage
[Con_Cluster-*.bed]  Cluster #1 - #9 regions of wild-type peaks

tag: cell type

value: pancreatic progenitors


title: SNc FACS sorted dopaminergic neurons that do not express Sox6 (mCherry+) [103]

tag: genotype

value: Sox6-FSF-Cre, Th-2A-Flpo, RC-Frepe


title: HUES8, Con_PP_Rep3 (ATAC-seq)


title: WT LP_75b39


title: M1-2

description: stage 1 of male flower

value: stage 1


title: RVSMC transfected with NGGap, biological rep2

value: rat vascular smooth muscle cells

tag: treatment

value: transfected with negative control GapmeR (100nM) for 48hours


title: HUES8, Con_PE_Rep2 (ATAC-seq)


title: pP_NPIP-3

description: Roots with low anthocyanin concentration in the outer phloem

source_name: Pale purple carrot roots

value: low


title: HUES8, Con_PP_Rep1 (ATAC-seq)

value: embryonic stem cells


title: M1-1

description: stage 1 of male flower

value: male


title: HUES8, HNF6-KO_ESC_Rep1 (ATAC-seq)

value: undifferentiated


title: M1-3

description: stage 1 of male flower


title: F5-1

description: stage 5 of female flower

value: stage 5

value: female


title: WT LP_75b40

value: wild type


title: WT NP_75b32

source_name: WT NP_kidney

value: 22 months

value: Normal protein (20%)


title: F5-3

description: stage 5 of female flower


title: dP2_POP-1

value: high


title: HUES8, Con_DE_Rep3 (ATAC-seq)

description:
[Diff-peaks_*.bed]  Differential peak regions of Control in DE stage
[Con_Cluster-*.bed]  Cluster #1 - #9 regions of wild-type peaks

value: definitive endoderm


title: F4-2

description: stage 4 of female flower

value: stage 4


title: HUES8, Con_PE_Rep1 (ATAC-seq)

value: pancreatic endoderm


title: WT NP_75b29

value: kidney


title: HUES8, Con_GT_Rep3 (ATAC-seq)

description:
[Diff-peaks_*.bed]  Differential peak regions of Control in GT stage
[Con_Cluster-*.bed]  Cluster #1 - #9 regions of wild-type peaks

value: primitive gut tube


title: pP_NPIP-2

value: Inner phloem


title: F5-2

description: stage 5 of female flower


title: WT NP_75b34


title: F3-3

description: stage 3 of female flower

value: stage 3


title: dP1_NPIP-3


title: HUES8, Con_DE_Rep1 (ATAC-seq)


title: F4-3

description: stage 4 of female flower


title: WT LP_75b37

value: Low protein (5%)


title: pP_NPIP-1

value: low


title: HUES8, Con_GT_Rep2 (ATAC-seq)

value: embryonic stem cells


title: HUES8, Con_ESC_Rep3 (ATAC-seq)

description:
[Diff-peaks_*.bed]  Differential peak regions of Control in ESC stage
[Con_Cluster-*.bed]  Cluster #1 - #9 regions of wild-type peaks

value: undifferentiated


title: WT NP_75b31

value: male


title: HUES8, Con_GT_Rep1 (ATAC-seq)


title: FGF21 KO LP_75B20

source_name: FGF21 KO LP_kidney

value: FGF21 KO


title: F4-1

description: stage 4 of female flower

value: female


title: HUES8, Con_ESC_Rep2 (ATAC-seq)

source_name: embryonic stem cells, HUES8

value: wild type


title: pP_POP-2

value: Outer phloem


title: dP1_NPIP-1

value: high


title: HUES8, Con_DE_Rep2 (ATAC-seq)

value: definitive endoderm


title: WT NP_75b28

value: 22 months

value: Normal protein (20%)


title: pP_POP-1


title: F2-2

description: stage 2 of female flower

value: stage 2


title: dP1_POP-2


title: pP_POP-3


title: F3-2

description: stage 3 of female flower


title: F3-1

description: stage 3 of female flower


title: dP1_NPIP-2


title: CyT49, Input_D05 (ChIP-seq)

description: used as control for correction of CG bias and size of open chromatin regions.

data_processing:
HiSeq 4000 System (Illumina®) with single-end reads of 50bp
Reads were trimmed with skewer and aligned with Bowtie2(2.3.4.1) to the human hg19 genome.
MACS2(2.1.1.20160309) peakcalling between “TF” and “Input”. P-value under 1-e8.  condition specific peaks using corresponding input DNA.
Input_D10 and Input_D05 corresponds to input DNA sequences of Day 5 and Day 10 of our cultures. These sequences are given as controls (for correction of CG bias and size of open chromatin regions) together with ChIP-seq data of the corresponding day for peak calling algorithms
Genome_build: hg19
Supplementary_files_format_and_content: We provide predicted peaks (bed files) and genomic signals (bw files) from all ChIP libraries.

source_name: cell line

growth_protocol: CyT49 hESC were subjected to pancreatic differentiation according to Wang et al. (Cell Stem Cell, 2015; DOI:https://doi.org/10.1016/j.stem.2015.02.013). Of note, in this protocol NKX6.1-positive cultures at day 10 are labeled pancreatic endoderm. For consistent labeling we refer to pancreatic progenitors instead.

extract_protocol:
Cells were harvested at day 5 (corresponding to gut tube endoderm (GTE)) or day 10 (coressponding to NKX6.1-positive pancreatic progenitors  (PP). ChIP-IT High-Sensitivity kit (Active Motif) was used for chromatin isolation followed by immunoprecipitation with Monoclonal Rat Nkx6.1 raised in Mouse - Antibody RES310 (http://www.betacell.org/pdf/betacell-resource-310.pdf)
KAPA DNA Library Preparation Kits for Illumina® (Kapa Biosystems)

value: hESC

value: GTE stage

tag: chip antibody


title: F1-3

description: stage 1of female flower

tag: developmental stage

value: stage 1


title: FGF21 KO NP_75B10

source_name: FGF21 KO NP_kidney

value: kidney


title: CyT49, Input_D10 (ChIP-seq)

value: PE stage


title: FGF21 KO LP_75B19

value: Low protein (5%)


title: F2-3

description: stage 2 of female flower

tag: gender


title: HUES8, Con_ESC_Rep1 (ATAC-seq)

value: embryonic stem cells

value: undifferentiated


title: F1-2

description: stage 1of female flower


title: dP1_POP-3


title: FGF21 KO LP_75B23

value: FGF21 KO

value: male


title: CyT49, HNF6_D10 (ChIP-seq)


title: F1-1

description: stage 1 of female flower

value: female


title: FGF21 KO LP_75B17


title: CyT49, GATA6_D10 (ChIP-seq)


title: FGF21 KO LP_75B15


title: FGF21 KO NP_75B07


title: F2-1

description: stage 2 of female flower


title: dP1_POP-1

value: Outer phloem


title: CyT49, HNF_D05 (ChIP-seq)


title: FGF21 KO NP_75B05


title: Normal5

city: Xi′an

first: Xiaoxia

last: Dai

state: Shaanxi

address: No.76 Yanta West Road, Xi′an, Shaanxi 710061, China

institute: Xi′an Jiaotong University

data_processing:
RNA degradation and contamination, especially DNA contamination, was monitored on 1.5% agarose gels.RNA concentration and purity was mesured using a NanoDrop spectrophotometer
Clean data were obtained by filtering and discarding raw data containing adapter, low-quality data from raw data and reads accounting for more than 5% of N bases.Q30, GC-content and sequence duplication level of the clean data were calculated
Then transcriptome was assembled using the String Tie (V1.3.1) and clean reads mapped to human specific genomic GRCH38 through HISAT2 software (V2.0.4).
Differential expression analysis between two groups were performed using the DESeq R package (V1.10.1).
The databases of Gene Ontology (GO, http://www.geneontology.org/) and Kyoto Encyclopedia of Genes and Genomes (KEGG, http://www.genome.jp/kegg/) was employed to annotate gene biological function and explore the signaling pathways between the KBD group and control group. GO enrichment analysis was implemented by the Cluster Profiler
Genome_build: hg38
Supplementary_files_format_and_content: LncRNA_count expression

source_name: peripheral blood

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, Carlsbad, CA, USA).The purity and concentration of RNA were measured using a NanoDrop spectrophotometer (Thermo Scientific, USA). Samples with OD A260/A280 > 1.8 were qualified for subsequent experiments
Library preparations were sequenced on the Illumina Hiseq2500 platform

tag: diagnosis

value: Healthy person

value: peripheral blood


title: TEB_50µg/L_Male_rep3

city: Le Havre

first: Caroline

last: Arcanjo

address: 25, rue Philippe Lebon

country: France

institute: UMR-I02 SEBIO

data_processing:
Quality selection (Phred score > 30) and adapter trimming using Trimmomatic. Adapter sequence was removed from all samples. Reads with a length less than 36bp were removed
Reads alignment was performed with STAR, gene count information were collected from BAM files with FeatureCounts
Differential analysis was performed using DESeq2 and EdgeR
Genome_build: Eaff_2.0
Supplementary_files_format_and_content: Matrix table with gene counts for every gene and every sample

organism: Eurytemora affinis

source_name: entire adults

growth_protocol: Copepods were kept under optimal conditions (i.e. 15°C, 15 psu, 18h/6h light-dark cycle) in laboratory prior to exposure

extract_protocol:
Total RNA extraction was performed with ZR Tissue & Insect RNA Microprep kit (Zymo Research) following instructions
from 200 ng of total RNA was using the Universal Plus mRNA-Seq Library Preparation with NuQuant kit (NuGen Tecan Genomics)

treatment_protocol: Tebufenozide 0,5 µg/L and 50 µg/L or non-contaminated controls

value: entire adults

value: Male

value: 50 ug/L tebufenozide


title: FGF21 KO LP_75B13

value: 22 months


title: Normal4


title: TEB_50µg/L_Female_rep3

value: Female


title: TEB_50µg/L_Female_rep2


title: FGF21 KO NP_75B08

value: Normal protein (20%)


title: Normal3


title: m-carpel3

source_name: flower

value: carpel


title: m-stamen3

value: stamen


title: m-carpel2


title: m-stamen2


title: FGF21 KO NP_75B03

value: kidney


title: Normal1


title: TEB_50µg/L_Male_rep2


title: RVSMC transfected with AlivecGap, biological rep1

source_name: RVSMC transfected with AlivecGap

value: rat vascular smooth muscle cells

value: transfecated with Alivec GapmeR (100nM) for 48hours


title: TEB_0,5µg/L_Female_rep3

value: 0.5 ug/L tebufenozide


title: m-stamen1

value: male


title: Normal2


title: TEB_50µg/L_Female_rep1


title: KSL0608-Se-treated rep4

city: Shanghai

first: Donglei

last: Shi

address: meilong road 130

institute: Science and technology of east China 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 fragments per Transcripts Per Million reads (TPM) method. RSEM (http://deweylab.biostat.wisc.edu/rsem/) was used to quantify gene abundances.
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample.

source_name: mice

extract_protocol:
Total RNA was extracted from the sample 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

value: liver

tag: condition


title: TEB_0,5µg/L_Female_rep1


title: KSL0608-Se-treated rep2


title: F-carpel3

value: female


title: KSL0608-Se-treated rep3


title: THP-1 cells, IgG_fRIP-seq

source_name: THP-1 cells

value: IgG  ((Abcam ab171870)


title: F-carpel2


title: TEB_0,5µg/L_Male_rep2


title: TEB_0,5µg/L_Female_rep2


title: m-carpel1


title: KBD5

value: Kaschin-Beck disease patient

value: peripheral blood


title: KBD4


title: KSL0608-Se-treated rep1


title: F-carpel1


title: TEB_50µg/L_Male_rep1

value: entire adults

value: Male


title: FGF21 KO NP_75B02

tag: strain background

value: FGF21 KO

value: 22 months


title: aged control rep3

description: doxo

value: aged


title: TEB_0,5µg/L_Male_rep1


title: F-stamen2


title: KBD1


title: KBD3


title: F-stamen3


title: Control_Female_rep1

value: Female

value: Control


title: Control_Female_rep3


title: TEB_0,5µg/L_Male_rep3


title: F-stamen1

value: stamen


title: aged control rep4

description: doxo


title: aged control rep2

description: doxo


title: WT NP_75b35

tag: genotype/variation

value: wild type

value: Normal protein (20%)

value: kidney


title: young control rep3

description: control

value: young


title: aged control rep1

description: doxo

value: liver


title: M-carpel2

value: carpel

value: male


title: WTC11-3 replicate 3

city: Yokohama

first: Harshita

last: Sharma

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

country: Japan

institute: RIKEN IMS

description: Biorep#3: p39 harvested on February 17, 2020: ENCODE BioSample Accession # ENCBS476NOC

data_processing:
bcl2fastq v2.20.0.422 was used for basecalling and demultiplexing samples
Sequenced reads were trimmed for adapter sequences using fastx_clipper  and trimmed to average quality score of 33 with fastx_trimmer (FASTX toolkit v0.0.13.2)
Sequences containing Ns were removed using an in-house program, and any sequences matching to rRNA were removed using rRNAdust v1.06
Reads were mapped to hg38 whole genome using STAR v2.5.0a with parameters --alignIntronMin 20 --alignIntronMax 1000000 --outFilterMultimapNmax 20
Files were filtered based on mapq score threshold of 10. Single base resolution CTSS files were generated from filtered bam files using an in-house program that corrects for additional Gs at the start of reads.
CTSS were clustered into peaks using paraclu with a minimum value of 10, and paraclu-cut.sh with default parameters. CTSS files were intersected with these clusters to generate count files.
Genome_build: hg38
Supplementary_files_format_and_content: Single nucleotide resolution CTSS bed file, column 5 contains counts found at each position
Supplementary_files_format_and_content: Bed file containing counts for each of the peaks (column 7)

extract_protocol:
Modified from  Low Quantity Single Strand CAGE (LQ-ssCAGE) Maps Regulatory Enhancers and Promoters, 2021, Methods in moleclar biology, DOI: 10.1007/978-1-0716-1597-3_4
RNA-seq (single strand CAGE) for Illumina HiSeq2500 Rapid; Single-Read; 150base, 2 lanes for 6 samples

value: iPSC


title: WTC11-3 replicate 2

description: Biorep#3: p39 harvested on February 17, 2020: ENCODE BioSample Accession # ENCBS475NOC


title: WTC11-1 replicate 3

description: Biorep#1: p37 harvested on February 7, 2020: ENCODE BioSample Accession #ENCBS944CBA


title: M-carpel1


title: Control_Male_rep2


title: young control rep2

description: control


title: Control_Female_rep2


title: M-carpel3


title: young control rep4

description: control


title: KBD2

value: Kaschin-Beck disease patient

value: peripheral blood


title: Control_Male_rep1

value: entire adults

value: Male


title: M-stamen3


title: WTC11-1 replicate 1


title: Control_Male_rep3


title: WTC11-1 replicate 2


title: WTC11-3 replicate 1

description: Biorep#3: p39 harvested on February 17, 2020: ENCODE BioSample Accession # ENCBS474NOC


title: M-stamen1


title: Brain organoids  - vertical mixing rep3

city: Kyoto

first: Akira

last: Watanabe

state: Kyoto

address: Rm504, Miyako Bldg, 233, Isa-cho, kamigyo-ku

institute: CyberomiX Inc

data_processing:
Cell-specific FASTQ files were generated by deconvolution of UMIs and cell barcodes using bcl2fastq 2.20.0.422 (Illumina)
Alignment to the human reference genome GRCh38 and UMI counting were conducted by Cell Ranger v3.1.0 pipeline (10×Genomics)
Uniform manifold approximation and projection (UMAP) implemented in the Seurat package v3.2.3 was conducted using 1st to 10th principal components after filtering out the cells with a high number of detected genes (>= 9,000) and RNA molecules (>= 60,000), and with a high percentage of mitochondrial genes (> 60 %)
Genome_build: GRCh38
Supplementary_files_format_and_content: barcodes.tsv, features.tsv, matrix.mtx

source_name: Cells in brain organoids

growth_protocol: Human iPSCs were maintained on a recombinant fragment of laminin-511 (iMatrix-511TM, Nippi, Tokyo, Japan) by using StemFit AK02N medium (Ajinomoto, Tokyo, Japan).

extract_protocol:
cDNA was synsthesized directly from cells.
Dissociated cells were resuspended in PBS containing 1% BSA, immediately followed by a library preparation targeting single cells using the Chromium Single Cell 3’ Reagent Kit v3 (10×Genomics) and Chromium Controller (10×Genomics) according to the manufacturer’s instructions.

treatment_protocol: For orbirtal mixing, iPSCs were transferred into an embryoid body (EB) formation medium (EB medium) consisting of DMEM/F12 with 20% Knockout Serum replacement, 3% Fetal bovine serum (FBS), 1% Glutamax, 1% non-essential amino acids mix (NEAA), 1% penicillin / streptomycin, 4 ng/ml basic FGF and 50 µM Y-27632. Dissociated 9,000 alive iPSCs in EB medium were disseminated into single wells of U-bottom 96-well plates (ultra-low attachment type, NunclonTM SpheraTM microplates, 96U-Well Plate). The U-bottom 96-well plates were centrifuged at 200g for 3 minutes to make iPSCs aggregate quickly at the bottom of the well, and were kept in the incubator under a condition of 5% CO2 at 37oC. We defined the day of dissemination as Day 0. On Day 4, we replaced the medium with EB formation medium without basic FGF or Y-27632. On Day 6, we replaced the medium with neural induction medium consisting of DMEM/F12 with 1% N2 supplement, 1% GlutaMAX, 1% NEAA, 1 μg/ml heparin, and 1% penicillin / streptomycin. On Day 11, the outside of EBs became brighter and showed smooth edges. This appearance indicates that EBs contained radial organization. EBs were transferred into cold droplets of MatrigelTM on a sheet of Parafilm with small 3-mm dimples in a 10-cm petri dish and were incubated for 20 minutes in an incubator at 37oC to allow Matrigel polymerization. After the polymerization step, the EB-Matrigel droplets were removed from the Parafilm sheet and transferred into Neuroepithelial expansion medium, which consisted of a 1 : 1 mixture of DMEM/F12 and Neurobasal medium with 0.5% N2 supplement, 1% B-27 supplement without vitamin A, 1% GlutaMAX, 0.5% NEAA, insulin 2.5 μg/ml, 1% penicillin / streptomycin, and 0.1% Amphotericin B. On Day 15, 16 EB-Matrigel droplets were transferred into a 6-cm dish with 6 ml of Differentiation medium which consisting of 1 : 1 mixture of DMEM/F12 and Neurobasal medium with 0.5% N2 supplement, 1% B-27 supplement without AO, 1% GlutaMAX, 0.5% NEAA, insulin 2.5 μg/ml, 1% penicillin / streptomycin, and 0.1% Amphotericin B. All 6-cm dishes were horizontally rotated on an orbital shaker, equipped inside the incubator, at a rotating speed of 60 rpm42. The culture medium was refreshed every 3 to 4 days.  From Day 40, EB-Matrigel droplets were cultured in differentiation medium with additional 1% Matrigel. From Day 70, EB-Matrigel droplets were cultured in differentiation medium with additional 2% Matrigel (growth factor reduced type) and 2% B27 supplement without AO.  For vertical mixing, iPSCs were cultured up to 80% confluence (typically 10 days after passage). iPSC colonies were dissociated into single cells after 4 minutes of incubation in 0.5 x Tryple Select / 0.25mM EDTA in a 37oC incubator, and suspended in StemFit AK02N with 50 µM of Y-27632 for number counting and viability determination.   Dissociated 1 x 104 cells in 250 ml of StemFit AK02N plus 50 µM of Y-27632 were disseminated into a single-use bottle specialized for suspension culture under continuous vertical mixing of the HiD 4x4 system at a setting of 60 mm/second speed and 15-mm stroke with continuous air flow of 30 ml/sec. After 7 days of cultivation in StemFit AK02N medium, disseminated iPSCs formed spheres of homogeneous size (approximately 100 – 150 μm diameter), and the medium was refreshed with EB formation medium as described above. We defined the day of medium refreshment as Day 0. On Day 6, we replaced the medium with Neural induction medium, as described above. On Day 17, we replaced the medium with Neuroepithelial expansion medium, as described above. On Day 25, we replaced the medium with Differentiation medium, also as described above. Sphere cultivation in the vertical mixing system was continued up to Day 90, with weekly medium change under tight regulation of pH 6.5-7.5, O2 concentration 20%, and temperature 32 – 34˚C.

value: human iPS cell-derived neural cells

value: vertical mixing


title: Adherent monolayer cells_experiment #1

description: Parental cells

source_name: Breast cancer cells

value: Breast cancer cells

tag: phenotype

value: Adherent monolayer cells


title: CD4+Foxp3+ Treg ApoE-/- rep3

city: Philadelphia

first: Ying

last: Shao

state: Pennsylvania

address: 3500 N Broad St, MERB1083A

institute: Temple University

data_processing:
FASTQC were used to check the quality of sequencing data. kallisto v0.44.0 and Rstudio were used to quantify abundances of transcripts.
Sequenced reads were mapped to Mus_musculus.GRCm38.cdna.all.fa using kallisto with parameters quant -i transcripts.idx -o output -b 100 reads_1.fastq.gz.gz reads_2.fastq.gz.gz
Data were filtered using [rowSums(Txi_gene$counts)>=10,] as cutoff (done after DEG calculation).
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include gene counts values for each Sample ...

source_name: spleen

extract_protocol:
Spleen singlet cell suspension were made, stained with anti-mouse CD4 antibody, then CD4+GFP+ cells were purified by Aria Cell Sorter directly into TRIzol, and RNA was harvested using miRNeasy Mini kit.
Total RNA libraries were prepared by using Pico Input SMARTer Stranded Total RNA-Seq Kit (Takara). In short, 250 pg -10 ng total RNA from each sample was reverse-transcribed via random priming and reverse transcriptase. Full-length cDNA was obtained with SMART (Switching Mechanism At 5' end of RNA Template) technology. The template-switching reaction was used to keep the strand orientation of the RNA. The ribosomal cDNA was hybridized to mammalian-specific R-Probes and then cleaved by ZapR. Libraries containing Illumina adapter with TruSeq HT indexes were subsequently pooled and loaded to the Hiseq 2500. Single end reads at 75 bp with 30 million reads per sample were generated for bioinformatic analysis.

value: ApoE-/-

value: 12 weeks high fat diet


title: CD4+Foxp3+ Treg ApoE-/- rep4


title: M-stamen2

value: stamen


title: young control rep1

description: control


title: Mammospheres_experiment #1

description: Mammospheres enriched in breast cancer stem cells

value: 2nd generation mammospheres


title: PBMC

first: Qing

last: Min

address: 138 Yi Xue Yuan Road

department: Immunology

institute: Fudan University

data_processing:
Raw sequences were filtered for PCR errors to generate clean data.
Sequenced reads were trimmed for adaptor sequence, and aligned for V, D and J gene usage, composition, length of CDR3 by using Smith-Waterman algorithm and compared with  IMGT/GENE-DB database (http://www.imgt.org)
Genome_build: IMGT/GENE-DB database (http://www.imgt.org)
Supplementary_files_format_and_content: CSV file include CDR3 amino acid and nucleotide sequences, V gene, J gene and constant region for each CDR3 sequence

source_name: Peripheral blood mononuclear cells

extract_protocol:
Total RNA was extracted from bone marrow mononuclear cells and peripheral blood mononuclear cells and digested with DNase I (TIANGEN Biotech) to remove contaminating genomic DNA.
Equal amount of total RNA extracted from the patient BM and peripheral blood was used as template to perform dimer-avoided-multiplex PCR according to the manufacturer’s protocol (iRepertoire Inc.). PCR products were purified and sequenced (Illumina Nova6000).
RNA seq (iRepertoire)

tag: disease

value: primary immnodeficieny


title: CD4+Foxp3+ Treg ApoE-/- rep1

tag: strain


title: Brain organoids  - vertical mixing rep1


title: Brain organoids  - vertical mixing rep2


title: PT13: Monocytes_19

city: Bethesda

first: Shouguo

last: Gao

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: National Institutes of Health

data_processing:
The raw data was processed with cellranger
Paired-end reads were mapped to the hg19 genome with cellranger for gene-level read counts
Genome_build: hg19

source_name: Human peripheral blood

extract_protocol: Libraries were generted using Genomics Chromium Single Cell ‘3 Solution Kit V2 from 10XGenomics.

value: Human peripheral blood

tag: Sex

value: 36 years

tag: subject

tag: markers

tag: disease state

value: deficiency of adenosine deaminase 2


title: PT14: Monocytes_20

tag: tissue

tag: age

value: 10 years


title: CD4+Foxp3+ Treg ApoE-/- rep2

tag: treatment


title: BM

source_name: Bone marrow mononuclear cells


title: PT11: Monocytes_17

value: Female

value: 5 years


title: Brain organoids  - orbital mixing rep1

tag: cell type

tag: cell line

value: orbital mixing


title: Brain organoids  - orbital mixing rep3


title: CD4+Foxp3+ Treg WT rep3

value: wildtype


title: Brain organoids  - orbital mixing rep2

value: human iPS cell-derived neural cells


title: CM2020_16, SiOn, donor_38

city: Jena

first: Philipp

last: Koch

address: Beutenbergstraße 11

department: Core Facility Life Science Computing

institute: Leibniz Institute on Aging - Fritz Lipmann Institute

data_processing:
Reads were extracted in FastQ format using Illumina’s bcl2FastQ v2.20.0.422
The reads were aligned to the human reference genome (GRCh38 with the Ensembl genome annotation release 101) using STAR 2.7.6a (parameters: --alignIntronMax 100000, --outSJfilterReads Unique, --outSAMmultNmax 1, --outFilterMismatchNoverLmax 0.04) (PMID: 23104886).
For each gene, all reads that map uniquely to one genomic position were counted with FeatureCounts 1.6.5 (multi-mapping or multi-overlapping reads were discarded, stranded mode was set to “–s 2”) (PMID: 24227677).
DEG Analysis:
Differentially expressed genes (DEGs) were determined with R 4.0.1 using the package DESeq2 1.28.1. Only genes that have at least 1 read count in any of the analyzed samples of a particular comparison were subjected to DESeq2. HSCs cultured either on 2D PS, 3D PDMS or 3D SiOn for 14 days were compared to their initial state at day 0. In addition, the 14-days groups were compared with each other in a pairwise fashion: 3D PDMS versus 2D PS, 3D SiOn versus 2D PS and 3D PDMS versus 3D SiOn. In all 6 comparisons, the status 'donor' was considered as a co-factor. For each gene in each comparison, the p-value was calculated using the Wald significance test. Resulting p-values were adjusted for multiple testing using the Benjamini & Hochberg correction. The log2 fold change (L2FC) values were shrunk with the DESeq2 function lfcShrink(type="apeglm") to control for variance of L2FC estimates for genes with low read counts. Genes with an adjusted p<0.05 were considered differentially expressed.
Genome_build: GRCh38
Supplementary_files_format_and_content: csv file containing read counts per gene over all samples; DESeq2 results tables

growth_protocol: HSCs were analyzed at day 0 before in vitro culture and after 14 days in vitro (DIV) culture on 2D polystyrene (PS), 3D Polydimethylsiloxane (PDMS) and silicon oxide-coated 3D PDMS (3D SiOn) within an optimized HSC growth medium (refer to PMID: 32569325)

extract_protocol:
RNA was isolated from HSCs using the RNeasy Mini Kit (Qiagen) following the manufacturer’s instructions.
Preparation of libraries was done using NEBNext Ultra II directional library preparation kit including depletion of rRNA using NEBNext rRNA Depletion Kit (Human/Mouse/Rat) and NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs)  (all New England Biolabs) according the manufacturer‘s description.

treatment_protocol: No additional treatments were applied

tag: subject id

value: female

value: mobilized peripheral blood

value: Hematopoietic stem cells

value: SiOn


title: CM2020_15, PDMS, donor_38

value: PDMS


title: CM2020_14, PS, donor_38

value: PS


title: PT12: Monocytes_18

value: Male


title: CD4+Foxp3+ Treg WT rep2

value: 12 weeks high fat diet


title: KDM4A.G2.rep2

city: Boston

first: Fei

last: Ji

address: 185 Cambridge St

institute: Massachusetts General Hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to reference genome hg19 using STAR
Transcript abundance was calculated using Htseq
Genome_build: hg19
Supplementary_files_format_and_content: abundance measurements

source_name: RPE KDM4A 2

extract_protocol:
RNA was purified using the Qiagen miRNeasy kit including a DNAse treatment.
Total RNA sequencing libraries were prepped using the TruSeq Stranded Total RNA Sample Preparation with Ribo-Zero kit (Illumina).

treatment_protocol: Cells were incubated with Hoechst 33342 (ThermoFisher Scientific H3570) at 1/1000 directly into the media for 1h at 37 degrees. Cells were then trypsinized and resuspended in media containing Hoechst at 1/1000. Cells were sorted with a BD FACS Fusion using the laser BV421-A into Qiazol, based on DNA content.

value: Retinal Pigmented Epithelial

tag: cell cycle phase

tag: genotype

value: KDM4A overexpression


title: PT9: Monocytes_15

value: Human peripheral blood

value: 24 years

value: deficiency of adenosine deaminase 2


title: PT10: Monocytes_16

value: 8  years


title: CM2020_12, SiOn, donor_37


title: spinal cord without TSCI rep3 (miRNA)

city: Jinan

first: Bin

last: Ning

address: Jiefang Road #105

institute: Shandong University

description: small RNA

data_processing:
Subsequently, unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Genome_build: mm10
Supplementary_files_format_and_content: excel,expression profiles

source_name: spinal cord

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
Approximately 5 µg of total RNA were used to prepare nine small RNA librariesaccording to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq 2500  following the vendor’s recommended protocol. Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.

treatment_protocol: Briefly, 48 adult male C57BL/6 mice were randomly divided into the SCI (n=8)×3 and sham (n=8)×3 groups. Mice in the SCI group underwent  T8–10 vertebral laminectomy to expose the spinal cord after anesthesia was induced with 3% pentobarbital. Then, moderate SCI was induced using a modified Allen’s weight-drop apparatus, subsequently, the muscles and skin were sutured layer by layer. Mice in the sham group underwent the same laminectomy but without SCI.

value: spinal cord

value: post natal 8 weeks

value: laminectomy without TSCI


title: CM2020_13, Day0, donor_38

value: female


title: KDM4A.LS.rep2

value: late S


title: PT8: Monocytes_14

value: 57 years


title: spinal cord without TSCI rep1 (miRNA)

description: small RNA


title: spinal cord without TSCI rep2 (miRNA)

description: small RNA


title: KDM4A.G1.rep2


title: PT7: Monocytes_13

value: 55 years


title: CM2020_10, PS, donor_37

value: mobilized peripheral blood

value: Hematopoietic stem cells


title: CM2020_11, PDMS, donor_37

value: PDMS


title: KDM4A.ES.rep2

value: early S


title: spinal cord with TSCI rep3 (miRNA)

description: small RNA

value: traumatic spinal cord injury


title: Control.G2.rep2

source_name: RPE Control 2

value: Retinal Pigmented Epithelial

value: Control


title: Control.LS.rep2


title: PT6: Monocytes_12

value: Human peripheral blood

value: Female

value: 25 years


title: CM2020_9, Day0, donor_37


title: CM2020_8, SiOn, donor_25

value: male

value: SiOn


title: spinal cord with TSCI rep1 (miRNA)

description: small RNA

value: spinal cord

value: post natal 8 weeks


title: PT5: Monocytes_11

value: Male

value: 21 years

value: deficiency of adenosine deaminase 2


title: CD4+Foxp3+ Treg WT rep1

value: wildtype

value: 12 weeks high fat diet


title: PT4: Monocytes_10

value: 36 years


title: PT3: Monocytes_9

value: 16 years


title: spinal cord with TSCI rep2 (miRNA)

description: small RNA

value: traumatic spinal cord injury


title: 2D_Pref_HAd2_Diff17_d17

city: Solna

first: Joanne

last: Shen

state: Stockholm

address: Solnavägen 9 (Biomedicum)

department: Department of Physiology and Pharmacology

country: Sweden

institute: Karolinska Institutet

data_processing:
Base-call processing and conversion to fastq files performed with Illumina bcl2fastq software
Sequenced reads aligned to hg38 genome with STAR
Normalized counts generated with DESeq2 software
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts and normalized counts (DESeq2)

molecule: polyA RNA

source_name: Differentiated stromal vascular fraction-derived preadipocyte 2D culture

growth_protocol: Applies to all but mature adipocyte samples: Human primary SVF cells were seeded in culture flasks containing DMEM/F-12 GlutaMAX (10% FBS, 1% penicillin-streptomycin). After 48 h, the medium was changed and cells were grown to ≈70% confluence. Subsequently, cells were trypsinized, seeded into 96-well round bottom ultra-low attachment microplates (Corning) with 5000 cells per well and centrifuged at 150 g for 2 min. Four days after spheroid seeding, cultures were changed to serum-free differentiation medium. After 17 days of differentiation, medium was changed to serum-free maintenance medium without differentiation additives. For supplementation with free fatty acids (FFAs), 160 µM oleic acid and 160 µM palmitic acid were added to the medium. For 2D or monolayer culture, instead of seeding and differentiation in ULA plates, preadipocytes were cultured and differentiated in monolayers.

extract_protocol:
RNA was isolated using QIAzol Lysis Reagent and RNA Clean & Concentrator columns (Zymo Research) or using ZR-Duet DNA/RNA MiniPrep columns (Zymo Research).
RNA libraries were constructed using the NEBNext Ultra II Directional RNA Library Prep Kit

value: preadipocyte 2D culture

value: Differentiation medium

tag: duration of differentiation (days)

tag: timepoint during differentiation

tag: donor (from table 1 in manuscript)


title: Control.G1.rep2

value: Retinal Pigmented Epithelial

value: Control


title: CM2020_7, PDMS, donor_25

value: mobilized peripheral blood

value: Hematopoietic stem cells

value: PDMS


title: 2019_63_HAd2

source_name: Mature adipocytes

value: Mature adipocytes

value: Not applicable


title: KDM4A.G2.rep1

source_name: RPE KDM4A 1

value: KDM4A overexpression


title: HAd10_MatAd


title: PT1: Monocytes_7

value: Human peripheral blood

value: Male

value: 22 years


title: Control.ES.rep2

value: early S


title: PT2: Monocytes_8

value: Female

value: 30 years

value: deficiency of adenosine deaminase 2


title: HD6: Monocytes_6

value: 56 years

value: healthy


title: CM2020_5, Day0, donor_25

value: male


title: CM2020_4, SiOn, donor_6

value: SiOn


title: KDM4A.LS.rep1

value: Retinal Pigmented Epithelial

value: late S


title: HAd8_MatAd


title: HAd7_MatAd


title: CM2020_3, PDMS, donor_6

value: mobilized peripheral blood

value: Hematopoietic stem cells

value: PDMS


title: HD5: Monocytes_5

value: 38 years


title: KDM4A.ES.rep1

value: KDM4A overexpression


title: KDM4A.G1.rep1


title: HD4: Monocytes_4

value: Human peripheral blood

value: Male

value: 37 years


title: HAd6_MatAd

value: Mature adipocytes

value: Not applicable


title: CM2020_6, PS, donor_25

value: PS


title: Control.G2.rep1

source_name: RPE Control 1

value: Control


title: HAd4_MatAd


title: CM2020_1, Day0, donor_6


title: HD3: Monocytes_3

value: Female

value: 22 years

value: healthy


title: Control.LS.rep1

value: Retinal Pigmented Epithelial


title: day14 NK cells-rep4

city: Seongnam-si

first: Daun

last: Jung

state: Gyeonggi-do

address: Bundang-gu, 삼평동 689

department: Department of Pathology

country: South Korea

institute: CHA Bundang Medical Center

data_processing:
We preprocessed the raw reads from the sequencer to remove low quality and adapter sequence before analysis and aligned the processed reads to the Homo sapiens (hg19) using HISAT v2.1.0 (KIM et al, 2015).
And then, transcript assembly of known transcripts was processed by StringTie v1.3.4d (Pertea, Mihaela, et al., 2015, 2016).
Base on the result of that, expression abundance of transcript and gene were calculated as read count or FPKM value (Fragments Per Kilobase of exon per Million fragments mapped) per sample.
The expression profiles are used to do additional analysis such as DEG (Differentially Expressed Genes).
Genome_build: The reference genome sequence of Homo sapiens (hg19) and annotation data were downloaded from the NCBI.
Supplementary_files_format_and_content: The sheet contains FPKM values of genes for 6 samples, 3 from day 0 and 3 from day 14. The fold change was calculated between day 0 and day 14. The statistical significances were calculated using ANOVA.

source_name: primary natural killer cells

growth_protocol: Isolated PBMCs were seeded on γ-globulin (Greencross, Yongin, Korea) and anti-NKp46 (R&D systems, Minneapolis, MN, USA) coated flask at a density of 2x106 cells/ml and cultured in Alys505NK EX serum free medium (CSTI, Sendai, Japan) supplemented with 1000 IU/ml recombinant human IL-2 (Novartis, Basel, Switzerland), 50 ng/ml recombinant human IL-18 (R&D system, Minneapolis, MN, USA) and 5% heat-inactivated autologous plasma. Fresh culture medium was added every 1 to 3 days depending on the cell density (2x106 cells/ml). The cells were transferred to culture bag (NIPRO, OSAKA, Japan) at 6 days, and cultured in a 5% CO2 incubator at 37°C for 14 days.

extract_protocol:
In order to construct cDNA libraries with the TruSeq Stranded mRNA LT Sample Prep Kit, total RNA was used. The protocol consisted of polyA-selected RNA extraction, RNA fragmentation, random hexamer primed reverse transcription and 100nt paired-end sequencing by Illumina NovaSeq 6000.
A library was independently prepared with 1ug of total RNA for each sample by Illumina TruSeq Stranded mRNA Sample Prep Kit (Illumina, Inc., San Diego, CA, USA, #RS-122-2101). The first step in the workflow involves purifying the poly‐A containing mRNA molecules using poly‐T‐attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using SuperScript II reverse transcriptase (Invitrogen, #18064014) and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I, RNase H and dUTP. These cDNA fragments then go through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products are then purified and enriched with PCR to create the final cDNA library.
The libraries were quantified using KAPA Library Quantificatoin kits for Illumina Sequecing platforms according to the qPCR Quantification Protocol Guide (KAPA BIOSYSTEMS, #KK4854) and qualified using the TapeStation D1000 ScreenTape (Agilent Technologies, # 5067-5582). Indexed libraries were then submitted to an Illumina NovaSeq (Illumina, Inc., San Diego, CA, USA), and the paired-end (2×100 bp) sequencing was performed by the Macrogen Incorporated.

value: blood

value: primary natural killer cells

tag: culture day


title: HAd10_Diff17_d17_2D

value: preadipocyte 2D culture

value: Differentiation medium


title: HD2: Monocytes_2

value: 26 years


title: Control.ES.rep1

value: early S


title: day14 NK cells-rep3


title: Control.G1.rep1


title: HAd9_DiffFFA17_d17

source_name: Differentiated stromal vascular fraction-derived preadipocyte spheroids

value: preadipocyte spheroids

value: Differentiation medium with FFAs


title: HAd8_DiffFFA17_d17


title: HNF6-trunc_PP_Rep6

city: Aachen

first: Ivan

last: Costa

address: Pauwelsstraße 19

institute: Unikilink RWTH Aachen

data_processing:
HiSeq 3000/4000 System (Illumina®) with single-end reads of 50bp
Reads were aligned with STAR aligner (Dobin, 2013; Version 2.5.2b) on  human genome hg38 and using Ensembl Transcriptome Annotation e87 as  transcriptome reference.
DESeq2 (version 1.22.1) was used for  normalization and differential expression analysis (Love, 2014). Only  genes with at least 10 reads, an adjusted p-value < 0.05 and abs(FC) >  1.5 were considered
SAMtools and deepTools were used for further processing
Genome_build: hg38
Supplementary_files_format_and_content: We provide bigwig, VST(Variance Stabilizing Transformation) model count and FPKM(Fragments Per Kilobase Million)

extract_protocol:
Cells were harvested at definitve endoderm (DE), pancreatic endoderm (PE) and pancreatic progenitor (PP) stage. Total RNA from ESC-derived pancreatic cells was isolated using GeneJET RNA Purification Kit (Thermo Fisher Scientific) according to manufacturer’s instructions.
After quality check with samples reaching RNA integrity values RIN>8, up to 1µg of total RNA was used for poly-A enrichment and subsequent library preparation with the TrueSeq stranded mRNA Kit from Illumina (HUES8 n=6)

value: embryonic stem cells, HUES8

tag: Stage

value: pancreatic progenitors


title: day14 NK cells-rep2


title: day14 NK cells-rep1


title: CM2020_2, PS, donor_6

tag: Sex

value: male

value: mobilized peripheral blood

value: Hematopoietic stem cells


title: day0 PBMC-rep4

source_name: PBMC

value: PBMC


title: PP_Rep3

data_processing:
HiSeq 2500 System (Illumina®) with single-end reads of 50bp
Reads were aligned with STAR aligner (Dobin, 2013; Version 2.5.2b) on  human genome hg38 and using Ensembl Transcriptome Annotation e87 as  transcriptome reference.
DESeq2 (version 1.22.1) was used for  normalization and differential expression analysis (Love, 2014). Only  genes with at least 10 reads, an adjusted p-value < 0.05 and abs(FC) >  1.5 were considered
SAMtools and deepTools were used for further processing
Genome_build: hg38
Supplementary_files_format_and_content: We provide bigwig files.

growth_protocol: MEL1 hESC were subjected to in vitro pancreatic differentiation.

extract_protocol:
Cells were harvested at definitve endoderm (DE), pancreatic endoderm (PE) and pancreatic progenitor (PP) stage. Total RNA from ESC-derived pancreatic cells was isolated using GeneJET RNA Purification Kit (Thermo Fisher Scientific) according to manufacturer’s instructions.
After quality check with samples reaching RNA integrity values RIN>8, up to 1µg of total RNA was used for poly-A enrichment and subsequent library preparation with the TrueSeq stranded mRNA Kit from Illumina (Mel1 n=4)

value: embryonic stem cells, Mel1

value: wild type


title: HAd8_Diff17_d17


title: HNF6-trunc_PP_Rep5


title: HNF6-trunc_PP_Rep4


title: day0 PBMC-rep3


title: HAd9_Diff17_d17


title: HAd7_DiffFFA_d17


title: PP_Rep2


title: HNF6-trunc_PP_Rep3


title: HD1: Monocytes_1

value: Human peripheral blood

value: Male

value: 23 years

tag: subject

value: healthy


title: PP_Rep1


title: HAd7_Diff17_d17

value: Differentiation medium


title: HNF6-trunc_PP_Rep2


title: day0 PBMC-rep2

value: blood


title: day0 PBMC-rep1


title: PE_Rep4

value: pancreatic endoderm


title: HNF6-trunc_PE_Rep6


title: PE_Rep3


title: PP_Rep4


title: HAd6_DiffFFA_d42

value: preadipocyte spheroids


title: HAd6_DiffFFA_d17

value: Differentiation medium with FFAs


title: day14 NK(CD3-CD56+) cells-rep3

growth_protocol: Isolated pNK cells were seeded on γ-globulin (Greencross, Yongin, Korea) and anti-NKp46 (R&D systems, Minneapolis, MN, USA) coated flask at a density of 2x106 cells/ml and cultured in Alys505NK EX serum free medium (CSTI, Sendai, Japan) supplemented with 1000 IU/ml recombinant human IL-2 (Novartis, Basel, Switzerland), 50 ng/ml recombinant human IL-18 (R&D system, Minneapolis, MN, USA) and 5% heat-inactivated autologous plasma. Fresh culture medium was added every 1 to 3 days depending on the cell density (2x106 cells/ml). The cells were transferred to culture bag (NIPRO, OSAKA, Japan) at 6 days, and cultured in a 5% CO2 incubator at 37°C for 14 days.

value: sorted NK(CD3-CD56+) cells


title: HNF6-trunc_PP_Rep1

value: embryonic stem cells, HUES8

value: pancreatic progenitors


title: HNF6-trunc_PE_Rep5


title: day14 NK(CD3-CD56+) cells-rep1


title: PE_Rep1


title: day0 NK(CD3-CD56+) cells-rep3


title: day14 NK(CD3-CD56+) cells-rep2


title: PE_Rep2


title: HAd6_Diff10_d17


title: HNF6-trunc_PE_Rep4


title: DE_Rep4

value: definitive endoderm


title: HAd6_Diff17_d17


title: HNF6-trunc_PE_Rep3


title: HAd4_Diff10_d14


title: DE_Rep3


title: day0 NK(CD3-CD56+) cells-rep2


title: day0 NK(CD3-CD56+) cells-rep1


title: HAd6_Diff17_d42


title: DE_Rep2


title: HNF6-trunc_PE_Rep2


title: HNF6-trunc_PE_Rep1


title: HAd4_Diff17_d14


title: DE_Rep1


title: H1299 shEphexin1_3

city: Gwangju

first: Jeeho

last: Kim

address: 309, Pilmun-daero, Dong-gu, Gwangju, Republic of Korea

department: medical school

institute: chosun university

data_processing:
bcl2fastq2 v2.20 used for basecalling.
Using bowtie to align RNA-seq data to reference genome(Human hg19) and get histogram for insert size
Using Tophat v2.0.13 to mapping the read to reference(hg19) and generate bam files.
Fragments Per Kilobase of transcript per Million(FPKM) was calculated from mapped reads using cufflinks v2.2.1.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: FPKM

growth_protocol: NCI-H1299 cells were cultured in RPMI-1640 medium (Invitrogen). Culture media were supplemented with 10% heat-inactivated fetal bovine serum (FBS) and 1% penicillin/streptomycin. Cells were maintained in 5% CO2-humidified atmosphere at 37C.

extract_protocol:
total RNA extraction using the TRIzol
Truseq stranded totalRNA Library Prep Kit

treatment_protocol: pSilencer2.1-U6-neo control shRNA or pSilencer2.1-U6-neo Ephexin1 shRNA

value: Lung cancer cells

tag: genotype/variation


title: ESC_Rep4

value: undifferentiated


title: H1299 shEphexin1_2


title: HAd4_Diff17_d10


title: HNF6-trunc_DE_Rep6

growth_protocol: HUES8 control and HNF6 KO hESC were subjected to in vitro pancreatic differentiation.


title: HAd10_PrAd_3D

source_name: Stromal vascular fraction-derived preadipocyte spheroids

value: Not applicable


title: HNF6-trunc_DE_Rep5


title: H1299 shEphexin1_1


title: ESC_Rep3

value: embryonic stem cells, Mel1

value: wild type


title: H1299 shControl_2

value: shControl


title: HNF6-trunc_DE_Rep4


title: ESC_Rep1


title: HNF6-trunc_DE_Rep1


title: HNF6-trunc_DE_Rep3


title: HAd6_PrAd


title: H1299 shControl_1


title: HNF6-trunc_ESC_Rep6


title: HAd7_PrAd


title: H1299 shControl_3


title: HNF6-trunc_ESC_Rep5


title: sepsis #1/input

city: Lodz

first: Przemyslaw

last: Lewkowicz

address: Pomorska 251/A4

department: Immunogenetics

country: Poland

institute: Medical University of Lodz

description: sepsis #1/input

data_processing:
Basecalls performed using CASAVA version 1.4
Quality of the raw sequence reads was checked using the FASTQC software (version: 0.11.8).
All reads were subjected to the adapter and quality filtering (minimum quality (-q 25), minimum length (-m 15)) using the Cutadapt tool (version: 1.18) in NextSeq reads mode
Trimmed reads were aligned to the reference genome (GRCh38) using the Bowtie2 (version: 2.2.9) in the single-end mode.
Duplicated reads were located and tagged using the Picard MarkDuplicates tool (version: 2.18.4). Reads with low mapping quality score (MAPQ <10) were removed from downstream analysis with the Samtools software (version: 1.6).
Protein binding sites identification in the previously prepared BAM files was performed with the MACS2 (Model-based Analysis of ChIP-seq) software (version: 2.1.0) in narrow peak mode (Feng, 2012). Subsequently, identified peaks were annotated using annotatePeaks.pl from Homer software (version: 4.11.1, hg38 annotation library). Additionally, a functional enrichment analysis for various categories (e.g. gene function, biological pathways, domain structure, etc.) was executed (Schaefer, 2009). To find enriched motifs in ChIPseq peaks the findMotifsGenome.pl program from Homer software (version: 4.11.1) was used.
Genome_build: hg38
Supplementary_files_format_and_content: peak text files

source_name: highly purified peripheral blood neutrophils

growth_protocol: The first step of investigations was performed on neutrophils isolated from the healthy volunteers under different stimuli, that mimic natural process of their preactivation, activation or resolving inflammation.  2x106 of healthy neutrophils were incubated in vitro without stimulation, and in the presence of 100ng/mL ultrapure LPS from E. coli, 10ng/mL TNF-alfa or 10mg/mL IL-10 in RPMI 1640 for 5 h (5% CO2, 37oC, humid atmosphere). The validation of obtained results from in vitro model was performed by comparison to clinical status as follows: NMOSD (as neutrophils preactivated by TNF-alfa); Sepsis (as LPS-exposed neutrophils); Periodontitis (as IL-10-exposed neutrophils).  Neutrophils were purified by negative selection by microbeads, which allowed the removal of DCs, B cells, monocytes, macrophages, activated T cells, and activated NK cells (MACSxpress Whole Blood Neutrophil Isolation Kit; cat. 130-104-434). Residual erythrocytes were lysed with the use of 2mL ammonium chloride Lysing Reagent (BD cat. 555899) for 5 minutes. For DNA isolation, samples of isolated neutrophils were frozen and kept at -80C.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody
Double-stranded DNA was generated from single-stranded fraction of ChIPed DNA using NEBNext® Ultra™ II Non-Directional RNA Second Strand Synthesis Module (E6111S,New England Biolabs). Reaction was carried out in the presence of random primers from NEBNext® RNA First Strand Synthesis Module (E7525, New England Biolabs). Libraries for sequencing were prepared using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (E7645L, New England Biolabs). Single-end sequencing with read length of 75 bases (SE75) was performed with NextSeq550 (Illumina) in order to obtain at least 20 million of reads per sample that could be mapped to human genome

treatment_protocol: Cells were cultured in T75 Nunc flasks in RPMI medium for 5h. ChIP was carried out in neutrophils according to the manual of Magna ChIP™ A/G Chromatin Immunoprecipitation Kit (Merck Millipore, cat.17-1010). Cells were fixed with 1%  formaldehyde in RPMI solution for 10 min. at RT, which was quenched with 10x glycine in 5-minute incubation at RT to stop the fixatioan. After washing with cold PBS, cells were treated sequentially with 1x Protease Inhibitor Cocktail II, Lysis Buffer with Protease Inhibitor Cocktail II, and Protease Inhibitor Cocktail II with Nuclear Lysis Buffer. Supernatant was removed and the cell pellet was resuspended in Nuclear Lysis Buffer. Sonication (10 cycles; 30sec. “ON” 30sec. “OFF”) was done using Bioruptor® Pico Sonicator (Diagenode, Belgium). The obtained chromatin was spun at a minimum of 10,000 x g at 4°C for 10 minutes to remove insoluble material. Each immunoprecipitation required the addition of Dilution Buffer and Protease Inhibitor Cocktail II. 25 μL of the diluted chromatin as ‘Input’ was saved at 4°C for further proceeding. Chromatin immunoprecipitation was performed with the use of the set of antibodies: Normal mouse IgG (negative control), anti-RNA Polymerase II (clone CTD4H8) as positive control and anti-trimethyl-Histone H3 (Lys4) (MC315, Merck Millipore, cat. 04-745) mAbs. Both antibodies were recommended for the use in ChIP-Seq technique (Egelhofer 2011). Immunoprecipitation reactions were incubated overnight at 4°C with rotation. DNA was eluted and purified using spin columns. The DNA concentrations of obtained samples were measured by Qubit 4 Fluorometer (ThermoFisher Scientific).

tag: disease state

value: sepsis patient

tag: chip antibody

value: 2x106  freshly isolated neutrophils   (without stimulation)


title: sepsis #2

description: sepsis #2

value: highly purified peripheral blood neutrophils

value: anti-trimethyl-Histone H3 (Lys4) (MC315, Merck Millipore, cat. 04-745


title: NMOSD #3

description: NMOSD #3

value: NMOSD patient


title: sepsis #1

description: sepsis #1


title: HNF6-trunc_ESC_Rep4

tag: tissue


title: NMOSD #2

description: NMOSD #2

tag: treatment


title: HNF6-trunc_DE_Rep2


title: HNF6-trunc_ESC_Rep3


title: NMOSD #1/input

description: NMOSD #1/input

tag: cell type


title: NMOSD #1

description: NMOSD #1


title: HNF6-trunc_ESC_Rep2


title: input-control

city: La Jolla

first: Sam

last: Van de Velde

state: CA

address: 10010 North Torrey Pines Road

department: PBL

institute: Salk Institute

data_processing:
Reads were aligned to the mm10 mouse genome assembly using STAR
Aligned reads were further processed using Homer: sam files were converted to Homer tag directories and subsequently binding peaks were identified.
Multiwig hubs were made using Homer
Genome_build: mm10
Supplementary_files_format_and_content: peak file

source_name: 3T3L1 adipocytes

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were constructed using the NEBNext ChIP-Seq Library Kit (E6240) according to the manufacturer's instructions

treatment_protocol: Cells were treated for 1 hour

tag: cell line

value: adipocyte

value: no IP

value: no treatment


title: periodontitis #2

description: periodontitis #2

value: periodontitis patient


title: 3T3L1-H3AcK27-FSKTNFa

value: Histone H3 Acetyl K27 (Abcam ab4729)

value: 10 uM forskolin+TNFa 1 hour


title: 3T3L1-H3AcK27-TNFa

value: TNFa 1 hour


title: HNF6-KO_PDX1-NKX6.1-pos_Rep6

value: embryonic stem cells, HUES8

value: pancreatic progenitors, sorted PDX1+/NKX6.1+


title: HNF6-KO_PDX1-NKX6.1-pos_Rep5


title: HAd4_PrAd

value: preadipocyte spheroids

value: Not applicable


title: ESC_Rep2

value: embryonic stem cells, Mel1

value: wild type

value: undifferentiated


title: 3T3L1-H3AcK27-FSK

value: 10 uM forskolin 1 hour


title: periodontitis #1

description: periodontitis #1

value: highly purified peripheral blood neutrophils

value: anti-trimethyl-Histone H3 (Lys4) (MC315, Merck Millipore, cat. 04-745

value: 2x106  freshly isolated neutrophils   (without stimulation)


title: 3T3L1-H3AcK27-control

value: adipocyte


title: HC-3

value: healthy volunteer


title: HEK293_ATG7-/-_#2_APH300nM_72hours

city: Nagasaki city

first: Tsuyoshi

last: Kawabata

state: Nagasaki

address: 1-12-4 Sakamoto

department: Atomic Bomb Disease Institute

institute: Nagasaki University

description: 300nM APH 72hours/2 weeks recovery

hyb_protocol: 0.60 μg of Cy3 dye labeled cRNA were fragmented and hybridized at 65 ℃ for 17 hours onto Agilent SurePrint G3 Human GE v3 8x60K Microarray.

scan_protocol: the microarrays were scanned using Agilent SureScan Microarray Scanner (G4900DA).

data_processing: Intensity values of each scanned feature were quantified using Agilent feature extraction software version 12.1.1.1, which performs background subtractions. We only used features which were flagged as no errors (Detected flags) and excluded features which were not positive, not significant, not uniform, not above background, saturated, and population outliers (Not Detected and Compromised flags). Normalization was performed using Agilent GeneSpring software version 14.9.1 (per chip : normalization to 75 percentile shift).

label_protocol: cDNA template were combined with 5x Transcription Buffer, 0.1 M DTT, NTP mix, T7 RNA polymerase and Cyanine3-CTP. Labeled cRNAs were purified using QIAGEN’s RNeasy mini spin columns. The cRNA quantity and Cyanine-3 (Cy3) dye incorporation were determined using NanoDrop One spectrophotometer and Agilent 2100 Bioanalyzer.

extract_protocol: RNA was prepared using the PureLink® RNA Mini kit (ThermoFisher) following the manufacturer's recommendations.

treatment_protocol: HEK293 cells were cultured with/without 300nM aphidicolin for 72 hours, followed by 2 weeks culture without aphidicolin.

value: HEK293 cells


title: HEK293_ATG7+/+_APH300nM_72hours

description: 300nM APH 72hours/2 weeks recovery


title: HEK293_ATG7-/-_#1_NT

description: NT


title: HC-2


title: HEK293_ATG7+/+_NT

description: NT


title: HNF6-KO_PDX1-NKX6.1-pos_Rep3


title: HNF6-KO_PDX1-NKX6.1-pos_Rep1


title: HNF6-trunc_ESC_Rep1


title: 3T3L1-p65-TNFa

value: p65 (D14E12 - Cell Signaling 8242)


title: 3T3L1-p65-FSKTNFa

value: 10 uM forskolin+TNFa 1 hour


title: HC-1


title: HNF6-KO_PDX1-NKX6.1-pos_Rep4


title: HEK293_ATG7-/-_#2_NT

description: NT


title: HNF6-KO_PP_Rep6

value: pancreatic progenitors


title: HNF6-KO_PDX1-NKX6.1-pos_Rep2

value: embryonic stem cells, HUES8


title: HC-1/input


title: periodontitis #1/input

description: periodontitis #1/input

value: periodontitis patient


title: 3T3L1-p65-FSK


title: 3T3L1-p65-control

value: no treatment


title: HNF6-KO_PP_Rep3


title: 3T3L1-CRTC2-FSKTNFa

value: CRTC2 (6865 - in house)


title: 4-TNF

value: 2x106 neutrophils were incubated with 10ng/mL TNFalfa in RPMI 1640 for 5 h (5%CO2, 20C, humid atmosphere)


title: HNF6-KO_PP_Rep4


title: HNF6-KO_PP_Rep2


title: 4-IL10

value: 2x106 neutrophils were incubated with 10 ug/mL of IL-10 in RPMI 1640 for 5 h (5%CO2, 20C, humid atmosphere)


title: HNF6-KO_PP_Rep1


title: 4-ns

value: 2x106 neutrophils were incubated without stimulation in RPMI 1640 for 5 h (5%CO2, 20C, humid atmosphere)


title: HNF6-KO_PP_Rep5


title: HNF6-KO_PE_Rep5

value: pancreatic endoderm


title: 3-LPS

value: highly purified peripheral blood neutrophils

value: 2x106 neutrophils were incubated with 100ng/mL LPS in RPMI 1640 for 5 h (5%CO2, 20C, humid atmosphere)


title: spinal cord without TSCI rep2

data_processing:
Illumina Casava1.8 software used for basecalling.
Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20) were removed.
We aligned reads of samples to the reference genome using Hisat2 package.
The mapped reads of each sample were assembled using StringTie, all transcriptomes were merged to reconstruct a comprehensive transcriptome.
Unmapped reads were still mapped to genome using tophat-fusion. CIRCExplorer2 and CIRI were used to  identified circRNAs.
Genome_build: Mus_musculus Ensembl release-90
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer’s procedure. The total RNA quantity and purity were analysis of Aglient 2100 Bioanalyzer and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
Approximately 5 ug of total RNA was used to deplete ribosomal RNA according to the manuscript of the Ribo-Zero™ Magnetic Gold Kit (Illumina, San Diego, USA).Then the left RNA was fragmented into pieces using divalent cations under elevated temperature. The cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the TruSeq Stranded Total RNA Library Prep Kit (Illumina, San Diego, USA).

tag: strain

value: spinal cord

tag: age

value: post natal 8 weeks

value: laminectomy without TSCI


title: spinal cord without TSCI rep3


title: 3T3L1-CRTC2-control

value: adipocyte


title: HNF6-KO_PE_Rep6

tag: genotype


title: 3-TNF

value: healthy volunteer

value: anti-trimethyl-Histone H3 (Lys4) (MC315, Merck Millipore, cat. 04-745


title: 3-ns/input


title: 4-LPS


title: 3-ns


title: HNF6-KO_PE_Rep4


title: HNF6-KO_PE_Rep2


title: 3-IL10


title: spinal cord with TSCI rep3

value: traumatic spinal cord injury


title: 4-ns/input


title: 3T3L1-CRTC2-TNFa

value: TNFa 1 hour


title: spinal cord with TSCI rep2


title: HEK293_ATG7-/-_#1_APH300nM_72hours

description: 300nM APH 72hours/2 weeks recovery

value: HEK293 cells


title: spinal cord without TSCI rep1


title: HNF6-KO_PE_Rep3

value: embryonic stem cells, HUES8


title: HNF6-KO_DE_Rep6

value: definitive endoderm


title: 3T3L1-CRTC2-FSK

value: CRTC2 (6865 - in house)

value: 10 uM forskolin 1 hour


title: KO_Male_Untreated

city: Irvine

first: Lupe

last: Gutierrez

address: 825 Health Sciences Rd D288

institute: University of California, Irvine

description: untreated.normalized.csv

data_processing:
FASTQ files were trimmed using Trimmomatic version 0.35 (Bolger, et al. 2014) and aligned to the mm10 genome and counted using STAR version 2.5.2a (Dobin, et al. 2013). Differential expression analysis was performed using DESeq2 version 1.24.0 (Love, et al. 2014) on R version 3.6.1.
Genome_build: mm10
Supplementary_files_format_and_content: untreated.normalized.csv, treated.normalized.csv

source_name: Mouse back skin

growth_protocol: All mouse lines were maintained and bred following the procedures that conform with and have been approved by the UC Irvine Institutional Animal Care and Use Committee (IACUC).

extract_protocol:
Back skin was collected, and epidermis separated from dermis following incubation in a 1:1 dilution of dispase (Stem Cell Technologies, 07913) in Epilife media (Cascade Biologics, M-EPICF-500) at 37 °C for 1 hour. The epidermis was then lysed in TRIzol (ThermoFisher, 15596018), followed by chloroform extraction and RNA purification from the aqueous phase using ZYMO RESEARCH Quick-RNA MiniPrep per manufacturer’s protocol.
For RNA-seq, RNA was quantified using the NanoDrop ND-1000 spectrophotometer (ThermoFisher) and quality checked using the Agilent Bioanalyzer 2100 (Agilent). Library construction was performed according to the Illumina TruSeq® Stranded mRNA Sample Preparation Guide. One µg of total RNA was used and mRNA was enriched using oligo dT magnetic beads. The enriched mRNA was chemically fragmented for three minutes, followed by reverse transcription to make cDNA. The resulting cDNA was cleaned using AMPure XP beads, end repaired, and the 3’ ends were adenylated. Illumina barcoded adapters were ligated on the ends and the adapter-ligated fragments were enriched by nine cycles of PCR. The resulting libraries were validated by qPCR and sized by Agilent Bioanalyzer DNA high sensitivity chip. The barcoded cDNA libraries were multiplexed on the Illumina HiSeq 4000 platform to yield 100-bp paired end reads

value: M

value: back skin


title: 2-ns/input

value: highly purified peripheral blood neutrophils

value: 2x106 neutrophils were incubated without stimulation in RPMI 1640 for 5 h (5%CO2, 20C, humid atmosphere)


title: HNF6-KO_DE_Rep4


title: 2-IL10

value: 2x106 neutrophils were incubated with 10 ug/mL of IL-10 in RPMI 1640 for 5 h (5%CO2, 20C, humid atmosphere)


title: HNF6-KO_DE_Rep2


title: Control_Female_Treated

description: treated.normalized.csv

value: F

value: IMQ


title: Control_Male_Treated

description: treated.normalized.csv


title: 2-ns


title: 2-TNF

value: 2x106 neutrophils were incubated with 10ng/mL TNFalfa in RPMI 1640 for 5 h (5%CO2, 20C, humid atmosphere)


title: HNF6-KO_DE_Rep1


title: 1-LPS

value: healthy volunteer

value: 2x106 neutrophils were incubated with 100ng/mL LPS in RPMI 1640 for 5 h (5%CO2, 20C, humid atmosphere)


title: 1-IL10

value: anti-trimethyl-Histone H3 (Lys4) (MC315, Merck Millipore, cat. 04-745


title: HNF6-KO_DE_Rep5


title: 2-LPS


title: HNF6-KO_PE_Rep1

value: pancreatic endoderm


title: KO_Male_Treated

description: treated.normalized.csv


title: 1-TNF


title: HNF6-KO_ESC_Rep5

value: undifferentiated


title: Control_Female_Untreated

description: untreated.normalized.csv


title: Control_Male_Untreated

description: untreated.normalized.csv


title: HNF6-KO_DE_Rep3

value: embryonic stem cells, HUES8


title: KO_Female_Untreated

description: untreated.normalized.csv


title: 1-ns


title: KO_Female_Treated

description: treated.normalized.csv


title: HNF6-KO_ESC_Rep4


title: 1-ns/input


title: P30MTnt3

city: New York

first: Jens

last: Hansen

address: 1425 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Random removal of reads from each fastq-file to ensure that all samples that are subjected to the same comparison have the same final read counts (e.g. all mouse samples have the same read counts before alignment)
Alignment to the reference genome using Tophat 2.0.8
Identification of differentially expressed genes using Cufflinks 1.3.0
Genome_build: h19 and mm9

source_name: Thoracic aortic wall

extract_protocol: none provided by the submitter

value: thoracic aortic tissue from Marfan mouse

value: P60 (day after birth)


title: HNF6-KO_ESC_Rep6


title: P30MTnt1


title: P30WTnt4

value: thoracic aortic tissue from WT mouse


title: P30MTnt4


title: HNF6-KO_ESC_Rep1


title: Vehicle control 3

first: Christine

last: Becker

address: 1470 Madison Avenue

description: phHSC-AZ-Vehicle-72h---Ex3_GGAGCGTC_GCACGGAC_HLVTNBGX9_R1_001

data_processing:
RNASeq raw data were processed using FAST QC software (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Data were aligned with STAR aligner via a computational pipeline implemented in NextFlow (Di Tommaso et al.,  2017)
After alignment and summarization with featureCounts, data was normalized.
Supplementary_files_format_and_content: Tab delimited text files

source_name: primary human hepatic stellate cells

growth_protocol: 200,000 Primary human hepatic stellate cells (phHSCs) per well were plated in 6-well plates.

extract_protocol:
Cells were harvested and total RNA was extracted using RNeasy Mini Kit. The purity of RNA (RNA integrity number or RIN) was assessed using 2100 Bioanalyzer instrument (Agilent, CA).
To prepare sequencing libraries from mRNA we used TruSeq Stranded mRNA library prep kit (Illumina, CA).   Sequencing was performed on NextSeq Hi (Illumnina, CA) sequencing instrument with setting at following output: R1=100; index=8; R2=100.

treatment_protocol: After overnight serum starvation the cells were treated with either vehicle or 30 nM of AZD3355 in DMEM with 0.1% BSA for 72 hours.

value: Vehicle control

tag: timepoint

value: primary human hepatic stellate cells


title: HNF6-KO_ESC_Rep3


title: P30MTnt2


title: AZD3355 30nM 72h 1

description: phHSC-AZD3355-30nM-72h---Ex1_ATATGGAT_TAATACAG_HLVTNBGX9_R1_001


title: AZD3355 30nM 72h 3

description: phHSC-AZD3355-30nM-72h---Ex3_ATGGCATG_GGTACCTT_HLVTNBGX9_R1_001


title: Con_PDX1-NKX6.1-pos_Rep4

value: wild type

value: pancreatic progenitors, sorted PDX1+/NKX6.1+


title: AZD3355 30nM 72h 2

description: phHSC-AZD3355-30nM-72h---Ex2_AAGATACT_ATGTAAGT_HLVTNBGX9_R1_001


title: condM_rep2_time6

city: Mannheim

first: Johanna

middle: Daniela

last: Schott

address: Franz-Volhard-Straße 6

department: Mannheim Institute for Innate Immunoscience

institute: Heidelberg University

data_processing:
Reads were mapped with STAR v2.5.3a (Dobin et al., Bioinformatics 2012) to a common reference of the human genome (hg38) and the ERCC92 RNA Spike-In Mix, providing the basic set of Gencode V27 as downloaded from the UCSC Genome Browser wgEncodeGencodeBasic27 table as transcript annotations, allowing up to 2 mismatches and chimeric read detection with a minimum of 10 nt per segment  (--chimSegmentMin 10).
Read counts were summarized at the gene level with the featureCounts function of the subread package v1.6.3 (Liao et al., Bioinformatics 2014), requiring that a read is completely contained within an exon to be counted.
For normalization, read counts were divided by the sum of all reads assigned to ERCC92 spike-in sequences in the corresponding sample.
Linear regression was performed on log-transformed read counts. Half-lives were calculated from the slope of the regression line with the equation: ln(2) / -slope. Only genes with a positive half-life and a coefficient of determination  R2 of >0.5 in all conditions were used for subsequent analyses.
Genome_build: hg38
Supplementary_files_format_and_content: csv file containing raw read counts per gene, expression values after normalization to spike-in RNA reads, half-lives in hours and the coefficient of determination (R2) of the linear regression used for determination of half-lives

source_name: HeLa RNF219 KO + RNF219-mut

growth_protocol: HeLa cells were cultured in Dulbecco's modified Eagle's medium (DMEM, Gibco) supplemented with 10% (v/v) fetal bovine serum (FBS, Sigma), 2 mM L-Glutamine, 100 U/ml penicillin and 0.1 mg/ml streptomycin (all PAN Biotech) at 37°C in a humidified atmosphere with 5% CO2. Every two to three days, cells were carefully detached by scraping in warm 1x PBS and diluted 1:10. On the day before experiments, cells were seeded at a density of 0.26 x 105 cells/cm2.

extract_protocol:
RNA was extracted with the GeneMatrix universal RNA purification kit (Roboklon). 2 µl of 1:100 diluted ERCC RNA Spike-In Mix (Thermo Scientific) was added per µg total RNA.
After depletion of rRNA using the Ribo-Zero Gold Kit (Illumina), sequencing libraries were prepared with the NEBNext Ultra II Directional RNA Library Prep Kit (NEB) and sequenced on a NextSeq550 system (Illumina) with 75 bases single end.

treatment_protocol: Transcription was inhibited by adding 5 µg/ml Actinomycin D (ApplicChem, A1489,0005) for 0, 2, 4 and 6 hours.

value: HeLa

value: RNF219 KO + RNF219-mut

value: ActD, 6h


title: Con_PDX1-NKX6.1-pos_Rep2


title: Con_PDX1-NKX6.1-pos_Rep5


title: P30WTnt2


title: P30WTnt3


title: condM_rep2_time2

value: ActD, 2h


title: condM_rep2_time0

value: untreated


title: Con_PP_Rep6

value: pancreatic progenitors