title: Ioc4-dPWWP Flag-IP Replicate 3

description: Biological Replicate 3 of 3. ChIP enrichment of FLAG-IP over Input in the YMS264 IOC4dPWWP-3xFLAG strain.


title: Ioc4-dPWWP Flag-IP Replicate 1

status: Public on Jan 24 2022

type: genomic

city: Martinsried-Planegg

first: Michaela

middle: M

last: Smolle

address: Grosshaderner Street 9

department: Physiological Chemistry

country: Germany

institute: University of Munich

description: Biological Replicate 1 of 3. ChIP enrichment of FLAG-IP over Input in the YMS264 IOC4dPWWP-3xFLAG strain.

hyb_protocol: The hybridization mixture (Oligo CGH/Chip-on-chip hybridization kit, Agilent) was prepared according to manufacturer’s instructions with the addition of 20 ug of T7 blocking oligo (ttt ttt ttt ttt tt cac gcg tct ccc), and hybridized overnight at 65°C. Microarrays were washed using the Oligo aCCH/Chip-on-chip Wash buffers (Agilent) according to  manufacturer’s instructions.

scan_protocol: Scanned on Agilent Technologies Scanner G2505C US45102919 Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1).

data_processing: Data processed in R (version 2.13.0) using Bioconductor: MEDIAN normalization.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: IP DNA FLAG antibody

label_protocol: Briefly, up to 50 ng of IP or input DNA was treated with 2.5 U CIP enzyme (NEB) for 1 hour at 37°C, followed by phenol:chloroform extraction and ethanol precipitation. The CIP-treated template was incubated with 20 U TdT (NEB) for 20 minutes at 37C for T-tailing the ends, and the product isolated with the MinElute Reaction Cleanup Kit (Qiagen). An anchored T7 promoter-(dA)18 oligo was added by annealing and filling with 5 U Exo- Klenow (NEB) for 4 hours at 37°C, followed by phenol:chloroform extraction and ethanol precipitation. In vitro transcription was performed at 37°C overnight using the Ampliscribe T7 transcription kit (Epicentre Biotechnologies). RNAs purified using the RNeasy Mini Kit (Qiagen) and quantified on a Nanodrop 2000 Spectrophotometer (Thermo Scientific). For the second round amplification, 100 ng of RNA was reverse transcribed using Superscript III reverse transcriptase (Invitrogen) and purified with the MinElute Reaction Cleanup Kit (Qiagen). The T7 promoter primer was added to the product through a Klenow filling reaction as described above, followed by in vitro transcription with amino allyl-UTP (Ambion) instead of UTP. Final reaction cleanup was performed with the RNeasy Mini Kit (Qiagen). For the labeling reactions, 8 ug of amino allyl-incorporated RNA in a 5 uL volume of 0.1 M Carbonate Buffer, pH 8.7, was mixed with 5 uL (0.01 nmol) Cy3 or Cy5 dye (GE Healthcare) in DMSO (Sigma) and incubated at room temperature for 2 hours. Reactions were quenched with 5 uL 4 M hydroxylamine at room temperature for 15 minutes, purified by RNeasy MinElute Cleanup Kit (Qiagen), and the dye incorporation measured using the Nanodrop 2000 (Thermo Scientific). 4ug of input and IP were combined and fragmented (Fragmentation Reagent Kit, Ambion) according to manufacturer’s instructions.

growth_protocol: These strains were grown in YPD to an OD of 1.0. Cells were cross-linked and processed for the ChIP assay. The cell lysates were used to immunoprecipitate 3xFLAG tagged wildtype and mutant Ioc4 (2 ul αFLAG per IP).

extract_protocol: Lysates were prepared by bead beating in FA lysis buffer (50mM HEPES pH7.5, 1mM EDTA, 1% Triton X-100, 0.1%sodium deoxycholate and 150mM NaCl). The ChIP lysates were used to immunoprecipitate FLAG-tagged Ioc4. The immune complexes were pulled down with 50 ul of Protein G Dynabeads (Invitrogen) per IP and washed with FA lysis buffer, FA lysis buffer with 1M NaCl, FA lysis buffer with 0.5M NaCl, TEL buffer (0.25M LiCl, 1%NP-40, 1% sodium deoxycholate, 1mM EDTA, 10mM TrisHCL, pH8.1), and twice with TE. The Immune complexes were eluted with Elution buffer (1%SDS in TE with 250mM NaCl). The eluates were RNase A treated and Proteinase K was added to remove the bound proteins. Crosslinkss were reversed by incubating at 65°C overnight. Samples werte phenol:chloroform treated and ethanol precipitated. Input samples were treated the same way from the RNase A step.

tag: strain

tag: sample type

value: ChIP IP

source_name: Input DNA

value: ChIP Input


title: HLKMNBBXX_15771312_S34_L003

type: SRA

city: Bethesda

first: David

last: McGaughey

state: MD

address: 10 Center Dr

department: NEI

country: USA

institute: NIH

library_source: transcriptomic

data_processing:
Macaca_mulatta.Mmul_8.0.1.90.gtf.gz used as reference for Salmon index build
Quantified with Salmon 0.13
Imported into R with tximport (lengthScaledTPM)
HCOP annotation information used to align gene names with ensembl ID
TPM values scaled for library size with edgeR calcNormFactors
Genome_build: Macaca_mulatta.Mmul_8.0.1.90.gtf.gz
Supplementary_files_format_and_content: TSV

molecule: total RNA

organism: Macaca mulatta

extract_protocol: Two-millimeter punch biopsies were removed from macular/foveal, perimacular, temporal, and nasal regions of the retina.  Following the biopsy, the tissues were separated into layers of neural retina and RPE/choroid using microdissection techniques. otal RNA was isolated from fresh tissues using the PicoPure™ RNA Isolation Kit (Applied Biosystems, Waltham, Massachusetts, USA) following mortar and pestle tissue homogenization.  Extracted RNA samples were checked for quality using the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) and only samples with RIN value > 6.5 were used (Range 1 – 10).

treatment_protocol: Postmorterm rhesus

tag: tissue

value: Retina

tag: location

value: Nasal

tag: eye (od/os)

tag: macaque number


title: MRC5VA_HS120min_TTchem-seq_rep1

city: London

first: Richard

middle: James

last: Mitter

state: LONDON

address: 1 Midland Road

department: Bioinformatics & Biostatistics

country: United Kingdom

institute: The Francis Crick Institute

description:
TTchem-seq
Nascent RNA

data_processing:
cutadapt v1.18 was used to trim Illumina adapter sequence from all reads using the following settings: -a AGATCGGAAGAGC -e 0.1 -q 10 -m 25 -O 1
Trimmed reads were aligned against human genome version GRCh38 using STAR v2.5.2a with Ensembl release 86 transcript annotations.
Genome_build: GRCh38
Supplementary_files_format_and_content: Read depth coverage in bigWig format. Data are unscaled and represent reads mapping to both strands.

organism: Homo sapiens

source_name: MRC5-VA cell line

growth_protocol: DMEM (Thermo Fisher Scientific, 11965118) supplemented with 10% v/v FBS (Clontech, 631106), 100 U/ml penicillin, 100 μg/ml streptomycin.

extract_protocol:
RNA was extracted by TRIzol (Thermo Fisher Scientific, 15596026) according to the manufacturer’s instructions. As a control for equal sample preparation, we spiked-in S. cerevisiae (strain BY4741, MATa, his3D1, leu2D0, met15D0, ura3D0) 4-thiouracil (4TU)-labelled RNA. S. cerevisiae were grown in YPD medium overnight, diluted to an OD600 of 0.1, and grown to mid-log phase (OD600 of 0.8) and labelled with 5 mM 4TU (Sigma-Aldrich, 440736) for 6 min. Total RNA was extracted using the PureLink RNA Mini kit (Thermo Fisher Scientific, 12183020) following the enzymatic protocol. For purification of 4SU labelled RNA, 100 μg mammalian 4SU labelled RNA was spiked-in 1/100 of 4TU-labelled S. cerevisiae RNA. The 101 μg RNA was fragmented by addition of 20 μL 1 M NaOH to fragment RNA and left on ice for 20 min. Fragmentation was stopped by addition of 80 μL 1 M Tris pH 6.8 and cleaned up twice with Micro Bio-Spin™ P-30 Gel Columns (BioRad, 7326223) according to the manufacturer’s instructions. Biotinylation of 4SU-residues were carried out in a total volume of 250 μl, containing 10 mM Tris-HCl [pH 7.4], 1 mM EDTA and 5mg MTSEA biotin-XX linker (Biotium, BT90066) for 30 min at room temperature in the dark. RNA was then purified by phenol:chloroform extraction, denatured by 10 min incubation at 65°C and added to 200 μL μMACS Streptavidin MicroBeads (Miltenyi, 130-074-101). RNA was incubated with beads for 15 min at room temperature and beads applied to a μColumn in the magnetic field of a μMACS magnetic separator. Beads were washed twice with pull-out wash buffer (100 mM Tris-HCl, pH 7.4, 10 mM EDTA, 1 M NaCl and 0.1% Tween20). 4SU-RNA was eluted twice by addition of 100 mM DTT and RNA cleaned up using the RNeasy MinElute kit (Qiagen, 74204).
Libraries were prepared using the KAPA RNA HyperPrep kit (Roche) using 5 min 65°C fragmentation incubation to anneal primers but to prevent further fragmentation of the samples.

treatment_protocol: Nascent RNA labelling by addition of 1 mM 4-thiourdine to cell media for 15 min prior to harvest.

tag: cell line

tag: treatment

value: 120min Heat Shock, 15 min 4-thiouridine pulse


title: HLKMNBBXX_15771304_S26_L003


title: HLKMNBBXX_15771304_S26_L002


title: HLKJ7BBXX_15771292_S2_L001

value: RPE-Choroid


title: HLKJ7BBXX_15771313_S23_L002


title: HLKMNBBXX_15771304_S26_L004


title: WT Ioc4 Flag-IP Replicate 3

description: Biological Replicate 3 of 3. ChIP enrichment of FLAG-IP over Input in the YMS079 IOC4-3xFLAG strain.


title: MRC5VA_ctrl_TTchem-seq_rep1

description:
TTchem-seq
Nascent RNA

value: Control, 15 min 4-thiouridine pulse


title: HLKJ7BBXX_15771313_S23_L001


title: HLKMNBBXX_15771313_S35_L004


title: HLKMNBBXX_15771313_S35_L002


title: RNAseq_PreME_r1

city: Cambridge

first: Walfred

last: Tang

address: Tennis Court Road

department: Gurdon Institute

institute: University of Cambridge

data_processing:
The sequencing quality of libraries were checked by FastQC (v0.11.5). The low-quality reads and adaptor sequences were removed by Trim Galore (v0.4.1) using the default parameters.
The pre-processed reads were mapped to the human reference genome (UCSC GRCh38/hg38) using STAR (2.7.1a) (parameters: ‘--outFilterMismatchNoverLmax 0.05 --outFilterMultimapNmax 50 --outMultimapperOrder Random’) guided by the Gencode Human Release 30 comprehensive gene annotation.
Raw read counts per gene were extracted by the featureCounts function of the Subread package (1.6.2) using the default parameters. Normalized read counts and differentially expressed genes (absolute(log2(fold change)) > 2 and adjusted p-value < 0.05) were obtained using DEseq2 (1.26.0) in R (3.6.2) / Bioconductor (3.10.1).
Genome_build: hg38
Supplementary_files_format_and_content: Excel table with mRNA expression level [log2(normalised counts +1)] for all genes and differential expression [log2(fold change) and adjusted p-values] for selected contrast pairs

source_name: Pre-mesendoderm cells

extract_protocol:
cells were sorted directly into extraction buffer of PicoPure RNA Isolation Kit (Applied Biosystems) and RNA was extracted according to manufacturer’s protocol with on-column DNase I treatment (Qiagen 79254). Total RNA (5 ng) was then reverse transcribed and amplified into cDNA using Ovation RNA-Seq System V2 (Nugen).
Amplified cDNA was sonicated into 250 bp by Covaris E220 Focused-ultrasonicators. Subsequently, RNA-seq library was generated with 500 ng of fragmented cDNA using Ovation Rapid DR Multiplex System (Nugen). Libraries were subjected to single-end 50 bp sequencing on HiSeq 4000 sequencing system (Illumina)

tag: cell source

value: hESC-derived

tag: cell type

value: Pre-mesendoderm cells


title: RNAseq_PreME_r2


title: HLKMNBBXX_15771313_S35_L003


title: WT Ioc4 Flag-IP Replicate 1

description: Biological Replicate 1 of 3. ChIP enrichment of FLAG-IP over Input in the YMS079 IOC4-3xFLAG strain.


title: WT Ioc4 Flag-IP Replicate 2

description: Biological Replicate 2 of 3. ChIP enrichment of FLAG-IP over Input in the YMS079 IOC4-3xFLAG strain.


title: HLKJ7BBXX_15771293_S3_L001


title: RNAseq_ME_r2

source_name: Mesendoderm cells

value: Mesendoderm cells


title: SH-SY5Y_Hypoxia_3

type: RNA

city: Moscow

first: Sergey

last: Nikulin

address: 7, Vavilova st.

department: Faculty of Biology and Biotechnology

country: Russia

institute: HSE University

description: SH-SY5Y cells incubated for 2h under hypoxic conditions and then incubated for 5h under normal conditions

hyb_protocol: Hybridization was carried out with GeneChip™ Hybridization, Wash, and Stain Kit (Thermo Fisher Scientific) according to the manufacturer's recommendations.

scan_protocol: Gene-Chip Scanner 3000 7G system (Affymetrix).

data_processing:
CEL-files were jointly processed in Transcriptome Analysis Console 4.0.0.25 (Thermo Fisher Scientific) with summation method Gene + Exon - SST-RMA (Analysis Version 1) and empirical Bayes method.
HTA-2_0.r3.pgf
HTA-2_0.r3.Psrs.mps

label: biotin

source_name: SH-SY5Y, 2h preliminary hypoxia, 5h

label_protocol: Labelling was carried out with GeneChip™ WT PLUS Reagent Kit (Thermo Fisher Scientific) according to the manufacturer's recommendations using 500 ng total RNA as starting material.

growth_protocol: The human neuroblastoma SH-SY5Y cell line was grown on DMEM/F12 (Paneco) containing 10% FBS (Gibco). The cells were incubated in cell culture incubator (37 °C, 5% CO2).

extract_protocol: RNA was extracted from cell lysates using the miRNeasy Micro Kit (Qiagen) as recommended by the manufacturer.

treatment_protocol: The cells were plated in 6-well plates (TPP) at a cell/well density of 500000 the day before the drug treatment. The drugs - 2 uM oxyquinoline(s), 30 uM (roxadustat), and 0.5 mM DMOG - were added to the cells in triplicate, the cells were incubated for 5 h. The control wells contained 4 uL DMSO. The hypoxic conditions were created by incubation in 1% O2, 5% CO2, and 94% N2 atmosphere for 2 h (the medium was incubated under the same conditions for 16 h before addition to the cells). After 2 h hypoxia, the cells were returned to the original incubation conditions in a СО2 incubator and kept for another 5 h.

tag: origin

value: Cell line

value: Hypoxia


title: HLKMNBBXX_15771293_S15_L002


title: RNAseq_ME_r1


title: HLKMNBBXX_15771293_S15_L004


title: HLKJ7BBXX_15771293_S3_L002


title: SH-SY5Y_Hypoxia_2


title: SH-SY5Y_Hypoxia_1


title: RNAseq_hPGCLC_d4_r2

source_name: Human primordial germ cell-like cells (day4)


title: RNAseq_hPGCLC_d4_r1

value: Human primordial germ cell-like cells (day4)


title: HLKJ7BBXX_15771306_S16_L001

value: Perimacular


title: HLKMNBBXX_15771306_S28_L003


title: HLKMNBBXX_15771306_S28_L002


title: HLKJ7BBXX_15771306_S16_L002


title: RNAseq_hPGCLC_d2_r2

source_name: Human primordial germ cell-like cells (day2)


title: SH-SY5Y_Roxadustat_2

description: SH-SY5Y cells treated with 30 uM of Roxadustat for 5h

source_name: SH-SY5Y, 30 uM Roxadustat, 5h

value: Roxadustat


title: HLKJ7BBXX_15771307_S17_L001


title: SH-SY5Y_Roxadustat_1


title: SH-SY5Y_DMOG_3

description: SH-SY5Y cells treated with 0.5 mM of DMOG for 5h

source_name: SH-SY5Y, 0.5 mM DMOG, 5h

value: DMOG


title: HLKMNBBXX_15771293_S15_L003


title: RNAseq_hPGCLC_d2_r1

value: Human primordial germ cell-like cells (day2)


title: HLKMNBBXX_15771307_S29_L002


title: RNAseq_hESC_r2

source_name: Human embyronic stem cells

value: Human embyronic stem cells


title: HLKJ7BBXX_15771307_S17_L002


title: HLKMNBBXX_15771306_S28_L004


title: HLKJ7BBXX_15771300_S10_L002


title: RNAseq_hDE_d2_r2

source_name: Definitive endoderm cells

value: Definitive endoderm cells


title: HLKMNBBXX_15771300_S22_L003


title: HLKMNBBXX_15771307_S29_L003

value: Retina


title: RNAseq_hESC_r1


title: HLKMNBBXX_15771307_S29_L004


title: SH-SY5Y_Roxadustat_3


title: SH-SY5Y_DMOG_2


title: SH-SY5Y_DMOG_1


title: SH-SY5Y_Control_3

description: SH-SY5Y cells control (DMSO) cells

source_name: SH-SY5Y, Control DMSO, 5h

value: Control


title: SH-SY5Y_Control_2

description: SH-SY5Y cells control (DMSO) cells


title: HLKMNBBXX_15771300_S22_L004


title: SH-SY5Y_Control_1

description: SH-SY5Y cells control (DMSO) cells


title: HLKJ7BBXX_15771300_S10_L001


title: RNAseq_hDE_d2_r1


title: HLKMNBBXX_15771300_S22_L002


title: HLKMNBBXX_15771299_S21_L004


title: SH-SY5Y_4896-3249_3

description: SH-SY5Y cells treated with 2 uM of the compound 4896-3249 for 5h


title: HLKJ7BBXX_15771299_S9_L002


title: RNAseq_SOX17_OE_r2

data_processing:
The sequencing quality of libraries were checked by FastQC (v0.11.5). The low-quality reads and adaptor sequences were removed by Trim Galore (v0.4.1) using the default parameters.
The pre-processed reads were mapped to the human reference genome (UCSC GRCh38/hg38) using STAR (2.7.1a) (parameters: ‘--outFilterMismatchNoverLmax 0.05 --outFilterMultimapNmax 50 --outMultimapperOrder Random’) guided by the Gencode Human Release 30 comprehensive gene annotation.
To account for the directional reads, raw read counts per gene were extracted by featureCounts with the parameter ‘-s 2’. To exclude exogenous SOX17 and PRDM1 transcripts originated from the transgenes, only reads overlapping the 5’ and 3’ untranslated regions (UTRs) of SOX17 and PRDM1 transcript isoforms were counted. This allowed for monitoring the endogenous expression levels of SOX17 and PRDM1 in response to ectopic SOX17 and PRDM1. Normalization of read counts per gene and differential expression analysis (overexpression vs. control absolute(log2(fold change)) > 1 and adjusted p-value < 0.05) were performed using DEseq2.
Genome_build: hg38
Supplementary_files_format_and_content: Excel table with mRNA expression level [log2(normalised counts +1)] for all genes and differential expression [log2(fold change) and adjusted p-values] for selected contrast pairs

source_name: 12 hour PreME aggregate (SOX17 overexpression)

extract_protocol:
Cells were sorted directly into extraction buffer of PicoPure RNA Isolation Kit (Applied Biosystems) and RNA was extracted according to manufacturer’s protocol with on-column DNase I treatment (Qiagen 79254).
RNA-seq libraries were generated by the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, E7760S) and the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490) according to manufacturer’s protocol. Quantified and validated libraries were subjected to single-end sequencing on HiSeq 4000 sequencing system (Illumina).

treatment_protocol: PreME were induced from NANOS3–tdTomato hESCs bearing Dex-inducible SOX17 and Dox-inducible PRDM1 transgenes (WT + iSOX17 + iPRDM1). PreME aggregates were treated with vehicle (water), 100 μM dexamethasone (Sigma) or 0.5 μg/ ml doxycycline (Sigma) in the absence of cytokines. Aggregate were harvested for total RNA extraction 12 hours after transgene induction.

value: 100 μM dexamethasone (Sigma)

tag: genotype

value: SOX17 overexpression

value: PreME aggregates


title: HLKMNBBXX_15771298_S20_L002

value: RPE-Choroid


title: HLKMNBBXX_15771299_S21_L003


title: HLKJ7BBXX_15771299_S9_L001


title: HLKMNBBXX_15771299_S21_L002


title: RNAseq_SOX17_OE_r1

value: NANOS3–tdTomato hESCs bearing Dex-inducible SOX17 and Dox-inducible PRDM1 transgenes


title: RNAseq_PRDM1_OE_r1

source_name: 12 hour PreME aggregate (PRDM1 overexpression)

value: 0.5 μg/ ml doxycycline (Sigma)

value: PRDM1 overexpression


title: HLKJ7BBXX_15771298_S8_L001


title: RNAseq_PRDM1_OE_r2


title: HLKJ7BBXX_15771298_S8_L002


title: HLKMNBBXX_15771298_S20_L004


title: RNAseq_CTL_r1

source_name: 12 hour PreME aggregate (control)

value: vehicle (water)

value: control


title: HLKJ7BBXX_15771303_S13_L002

value: Perimacular


title: RNAseq_CTL_r2


title: HLKMNBBXX_15771303_S25_L004


title: SH-SY5Y_4896-3249_1

value: Cell line


title: HLKJ7BBXX_15771303_S13_L001


title: HLKMNBBXX_15771303_S25_L003


title: SH-SY5Y_5704-0720_3

description: SH-SY5Y cells treated with 2 uM of the compound 5704-0720 for 5h


title: HLKMNBBXX_15771303_S25_L002


title: SH-SY5Y_4896-3249_2


title: Maternal LT-GE 1_RRBS

city: Columbia

first: Yuanyuan

middle: R

last: Li

state: MO

address: University of Missouri School of Medicine, One Hospital Dr., Medical Sciences Building, NW508, Medical Sciences Building, NW508, Medical Sciences Building, M659

department: Ob&Gyn

institute: University of Missouri

library_source: genomic

data_processing:
RNA_Seq_step 1: Approximately 25- to 30-million sequencing reads were generated for each mRNA preparation. Quality control assessments were performed on RNA-Seq raw files by FASTQC.
RNA_Seq_step 2: Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to UCSC Genome Browser mouse GRCm38/mm10 reference sequence using RNA-STAR.
RNA_Seq__step 3: Readings were quantified and normalized by the fraction of reads assigned to each gene relative to the total number of reads to uniformly compare gene expression.
RNA_Seq_step 4: The number of fragments in each gene annotated in the RefSeq database was calculated using htseq-count from the HTSeq package. The DESeq platformwas utilized to evaluate DEGs by estimation of fold change and dispersion of sequence.
RRBS_step 1: Bisulfite-converted DNA libraries were produced and amplified, and single-end reads were sequenced on an Illumina HiSeq-2500 following library quality control.
RRBS_step 2: Quality control of RRBS raw reads was assessed by FastQC. Adaptor trimming and removal of trimmed reads shorter than 20 bp at the end of sequences were used by Trim Galore
RRBS_step 3: Bismark aligner was used to map trimmed bisulfite reads to UCSC Genome Browser mouse GRCm38/mm10 reference sequence.
RRBS_step 4: Post alignment and Bismark supplementary methylation extractor script that operates on Bismark result files were used to extract the methylation call for every single methylation locus analysis. Reads were filtered based on coverage, with a cutoff of at least three reads per site, and normalized for coverage before analysis.
RRBS_step 5: Statistical tests were conducted at each CpG site to determine differentially methylated loci (DML) followed by differentially methylated regions (DMRs). Because of our high average CpG coverage in a relatively small window size, we performed smoothing to quantify DMRs on a set of specified thresholds like minimum difference in the methylation levels between the groups of samples including minimum number CpG sites required (3 CpGs) and minimum length (30 bps) required for DMR determination.
Genome_build: UCSC Genome Browser mouse GRCm38/mm10 reference sequence
Supplementary_files_format_and_content: Statistical analysis summary of normalized abundance measurements for Differentially expressed gene (DEGs), Differentially methylated loci (DML), Differentially methylated regions (DMRs) and Integrative analysis by R (version 3.6.1).

organism: Mus musculus

source_name: Mammary tumor

extract_protocol:
RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Genomic DNAs were extracted from the mammary tumors of mice offspring using DNeasy Blood and Tissue Kit (Qiagen). Quality control was performed with Agilent Bioanalyser.
RNA libraries or bisulfite-converted DNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Dams were treated with either control or 250mg/kg GE diets from 4 weeks of age in mothers until weaning, all offspring remained control diet throughout the experiment.

value: Mammary tumor

value: FVB

tag: age

value: ~25 weeks

value: SV40 Tag transgenic mice

value: Maternal LT-GE


title: SOX17_hPGCLC_r1

data_processing:
ChIP-seq dataset of HA-SOX17 and myc-PRDM1 consisted of single-end and paired-end libraries. For consistency, only read 1 of pair-end libraries was used for analysis. Raw single-end reads of different libraries were trimmed to 50 bp by Cutadapt (1.15). Subsequently, reads were quality- and adaptor-trimmed by Trim Galore using default parameters.
The trimmed ChIP-seq and input reads were aligned to the human reference genome (UCSC hg38) by the bwa aln command of the Burrows–Wheeler Aligner (v0.7.17-r1188).
Samtools view was used to remove unmapped and low-mapping quality reads (options: ‘view -F 4 -q 20’). Duplicated reads were removed by samtools rmdup. Reads mapped to non-canonical hg38 contigs and mitochondrial DNA (chrM) were removed by samtools view. Finally, reads mapped to hg38 blacklisted regions were eliminated using bedtools subtract.
For peak calling, ‘cleaned’ ChIP-seq and input libraries were subsampled using samtools view so that each library contains approximately the same number of reads. This was followed by peak calling on the individual downsampled libraries and the merged downsampled libraries of the two replicates using macs2 callpeak against the corresponding inputs (options: ‘-g 3e9 –keep-dup all’).
Genome_build: hg38
Supplementary_files_format_and_content: Peaks of each biological replicates and pooled replicates in macs2 narrowPeak format

source_name: Human primordial germ cell-like cells

extract_protocol:
The whole day 2 embryoid bodies with hPGCLCs and day 2 DE cells (around 1.5-1.7 million cells) were collected for chromatin immunoprecipitation using the SimpleChIP Enzymatic Chromatin IP Kit (Magnetic Beads) (Cell Signaling Technology, 9003). Briefly, The cell pellets were washed twice with cold PBS containing 0.1% BSA and then fixed with paraformaldehyde. Following chromatin digestion with Micrococcal Nuclease, 2% volume of nuclei lysate was removed and stored at -80 °C as input control while the rest of the lysate was subjected to immunoprecipitation with anti-HA (Cell Signaling Technology, 3724) or anti-Myc (Cell Signaling Technology, 2276) antibody.
After elution of chromatin, reversal of cross-links and DNA purification, the ChIP and input DNA were prepared for sequencing using the KAPA HyperPrep Kit following the manufacturer’s instructions. Quantified and validated libraries were subjected to single-end or paired-end sequencing on HiSeq 4000 sequencing system (Illumina).

treatment_protocol: For HA-SOX17 and myc-PRDM1 ChIP-seq, PreME cells were induced from NANOS3–tdTomato hESCs bearing Dex-inducible SOX17 and Dox-inducible PRDM1 transgenes (WT + iSOX17 + iPRDM1). Subsequently, hPGCLCs were induced by hPGCLC induction medium in the presence of 100 μM dexamethasone (Sigma) (iSOX17) or 0.5 μg/ ml doxycycline (Sigma) (iPRDM1). For HA-SOX17 ChIP-seq in DE, ME cells were induced from the same hESC line, followed by DE induction in DE medium supplemented with 100 μM dexamethasone (iSOX17).

value: Human primordial germ cell-like cells

tag: chip antibody

value: HA (Cell Signaling Technology,3724)


title: Maternal LT-GE 2_RRBS


title: Maternal LT-GE 4_RRBS


title: Maternal LT-GE 3_RRBS


title: SOX17_hPGCLC_r3


title: SH-SY5Y_5704-0720_2


title: HLKMNBBXX_15771298_S20_L003


title: SH-SY5Y_5704-0720_1


title: Control 2_RRBS

value: Control


title: HLKMNBBXX_15771310_S32_L002


title: SOX17_hDE_r1

source_name: Definitive endoderm

value: Definitive endoderm


title: HLKJ7BBXX_15771310_S20_L001

value: RPE-Choroid


title: HLKMNBBXX_15771310_S32_L004


title: Control 1_RRBS


title: HLKMNBBXX_15771310_S32_L003


title: HLKJ7BBXX_15771310_S20_L002


title: HLKMNBBXX_15771301_S23_L003

value: Retina


title: Control 3_RRBS


title: HLKMNBBXX_15771301_S23_L004


title: HLKJ7BBXX_15771301_S11_L002


title: PRDM1_hPGCLC_r2

value: NANOS3–tdTomato hESCs bearing Dex-inducible SOX17 and Dox-inducible PRDM1 transgenes

value: Myc (Cell Signaling Technology, 2276)


title: HLKMNBBXX_15771301_S23_L002


title: Male_Rep3 [MeD-seq]

city: Rotterdam

first: Beatrice

last: Tan

address: Dr. Molewaterplein 40

department: Developmental Biology

country: Netherlands

institute: Erasmus MC

data_processing:
Library strategy: MeD-seq
Raw fastq files were subjected to Illumina adaptor trimming and reads were filtered based on LpnPI restriction site occurrence between 13-17 bp from either 5’ or 3’ end of the read. Reads that passed the filter were mapped to mm10 using bowtie2.
For each LpnPI site in mm10, the number of overlapping reads were counted. A bam file with all reads overlapping an LpnPI site was normalized using deepTools bamCoverage v3.5.0 with CPM as normalization method and a bin size of 1.
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig with normalized MeD-seq tracks

source_name: NSCs

growth_protocol: mNSCs were grown on gelatin-laminin-coated 6 well dishes in EuroMed-N (EuroClone), N2 supplement (Invitrogen), human insulin (final concentration 20 µg mL-1, Roche), BSA (final concentration 50 µg mL-1, Gibco), L-Glut (100x; Gibco), murine EGF (final concentration 10 ng mL-1, Peprotech), human bFGF (final concentration 10 ng mL-1, Peprotech), penicillin/streptomycin.

extract_protocol:
DNA was extracted using the QIAamp DNA micro kit following manufacter's instructions.
DNA samples were digested by LpnPI (New England Biolabs, Ipswich, MA, USA), resulting in snippets of 32 bp around a fully-methylated recognition site that contains a CpG. These short DNA fragments were further processed using a ThruPlex DNA–seq 96D kit (cat#R400407, Rubicon Genomics Ann Arbor, MI, USA) and a Pippin system. Stem-loop adapters were blunt-end ligated to repaired input DNA and amplified to include dual indexed barcodes using a high-fidelity polymerase to generate an indexed Illumina NGS library. The amplified end product was purified on a Pippin HT system with 3% agarose gel cassettes (Sage Science, Beverly, MA, USA). Multiplexed samples were sequenced on Illumina HiSeq2500 systems for single read of 50 bp according to the manufacturer’s instructions.

treatment_protocol: Xist knockdown was performed following manufacturer’s instructions for the Mouse Neural Stem Cell Nucleofector Kit (Lonza). NSCs were collected and resuspended in Nucleofector solution, supplement and 15 µL Xist ASO 10 µM (XIST-ANAND_1, cat. 339511 LG00116620-DDA: TCTTGGTTACTAACAG (Carrette 2018); Qiagen). Cells were nucleofected with a Lonza Nucleofector™, program A-033. Cells were then put back into culture and treated with 10 µM  5-Aza or its vehicle for 3 days. Cells were then FACS sorted according to Tomato fluorescence into three populations: Low-, Medium-, High-Tomato.

value: C57BL_6NJ x Cast/Ei

value: NSCs

value: WT

value: Untreated

tag: gender

value: Male


title: Male_Rep2 [MeD-seq]


title: PRDM1_hPGCLC_r1


title: HLKJ7BBXX_15771301_S11_L001

value: Perimacular


title: Input_hPGCLC_d2


title: HLKJ7BBXX_15771309_S19_L001

value: Fovea


title: Input_hDE


title: Input_PreME_r1

data_processing:
Paired-end ChIP-seq reads were quality- and adaptor-trimmed by Trim Galore (v0.4.1) using default parameters.
Trimmed reads were mapped to the human reference genome (UCSC GRCh38/hg38) by Bowtie 2 (v2.3.4.1) with options ‘--local -X 2000 --no-mixed --no-discordant’, hence retaining properly paired reads with a maximum fragment length of 2000 bp.
Unmapped reads, non-primary reads, supplementary alignment and QC-failed reads were removed using samtools view with option ‘-F 2828’. Duplicated reads were marked and removed by the MarkDuplicates function in Picard Tools (Broad Institute). Subsequently, fragments mapped to hg38 blacklisted regions (http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/hg38-human/hg38.blacklist.bed.gz), non-canonical hg38 contigs and mitochondrial DNA (chrM) were removed.
Prior to peak calling, libraries were subsampled using Picard DownSampleSam so that each library contains approximately the same number of paired-end reads.
Peaks were called following the Encode replicated peak calling guidelines (https://www.encodeproject.org/pipelines/ENCPL272XAE/) with modifications to accommodate for paired-end libraries. To obtain high resolution of peaks, narrow peak call was used for all marks. Histone peaks were called using the input reads as background. Peaks were initially called for each biological replicate (downsampled to similar read depth), for the pooled replicates, and for the pooled pseudoreplicates of each biological replicate using MACS2 with a relaxed p-value threshold of 0.05 (options: ‘-g 3e9 --keep-dup all -p 0.05’). Each pseudoreplicate consists of half the reads of each biological replicate, chosen at random without replacement. Narrow peaks from the pooled replicate set were retained if they overlapped peaks from both biological replicates or peaks from both pooled pseudoreplicates. The thresholds of overlap were set at 30% by peak length for histone peaks. This peak calling strategy allows for the retention of marginal peaks in one replicate to be rescued by a strong biological replicate. To obtain a final high confidence peak set, the reproducible peaks were further filtered using the MACS2 q-value (false discovery rate <0.001).
Genome_build: hg38
Supplementary_files_format_and_content: Reproducible peaks of the two biological replicates in macs2 narrowPeak format

source_name: Pre-mesendoderm cells

extract_protocol:
Cells were thawed on ice, incubated with 2 µl of 1 % Triton X-100, 1 % Sodium deoxycholate and digested with Micrococcal Nuclease (MNase) (NEB). MNase activity was blocked by addition of 11 µl 100 mM EDTA and cell lysate was incubated for 1 h in 400 µl of IP buffer at 4 °C followed by 2 h incubation in the presence of 5 µl blocked protein A/G beads (blocking buffer: 100 µg/ml yeast tRNA, 0.1 % BSA in IP buffer). After the removal of the protein A/G beads, the pre-cleared cell lysate was added to the antibody bead complex (antibody was incubated with 5 µl blocked protein A/G beads for 3 h on 4 °C) overnight at 4 °C. Unbound chromatin was removed, and beads were sequentially washed for 4 min for 1.) two times with low salt wash buffer, 2.) two times with high salt buffer, and 3.) two times with LiCl wash buffer (20 mM Tris-HCl pH 8.0, 2 mM EDTA, 250 mM LiCl, 1 % NP-40, 1 % Sodium deoxycholate). To elute the bound DNA, beads were incubated in Proteinase K digestion buffer (20 mM HEPES pH 8.0, 1 mM EDTA, 0.5 % SDS, 1 mg/ml RNase, 0.4 mg/ml Proteinase K) for 15 min at 55 °C and 1 h at 65 °C. The DNA was purified from the eluate through AMPure XP beads following the manufacturer’s instructions and eluted in 20 µl EB buffer (MinElute Reaction Cleanup Kit; Qiagen).
ULI-NChIP-seq libraries were generated by the KAPA Hyper Prep Kit (KAPA Biosystems) according to manufacturer’s protocol. To minimize adaptor dimer formation, the NEBNext Adaptor and NEBNext Index PCR Primers from the NEBNext® Multiplex Oligos for Illumina (Index Primers Set 1) (NEB, E7335S) were used. After library amplification, libraries were purified by AMPure XP beads with double-sided size selection. The libraries were subjected to paired-end sequencing on HiSeq 4000 sequencing system (Illumina)

value: hESC-derived

value: Pre-mesendoderm cells


title: SOX17_hDE_r2


title: HLKMNBBXX_15771309_S31_L003


title: Male_Rep1 [MeD-seq]


title: HLKMNBBXX_15771309_S31_L004


title: HLKJ7BBXX_15771309_S19_L002


title: HLKMNBBXX_15771297_S19_L002


title: HLKMNBBXX_15771309_S31_L002


title: HLKMNBBXX_15771297_S19_L004


title: HLKJ7BBXX_15771297_S7_L002


title: HLKJ7BBXX_15771297_S7_L001


title: Input_hPGCLC_d4_r1

value: Human primordial germ cell-like cells


title: HLKMNBBXX_15771297_S19_L003


title: HighTomato_Rep1 [MeD-seq]

value: Xist-/+ Mecp2+/NLucTom

value: Female


title: HighTomato_Rep2 [MeD-seq]


title: Control_Rep2 [MeD-seq]


title: Control_Rep3 [MeD-seq]


title: Input_ME_r1

source_name: Mesendoderm cells

value: Mesendoderm cells


title: HLKMNBBXX_15771314_S36_L004

value: RPE-Choroid


title: Input_hESC_r1

value: Human embyronic stem cells


title: Input_hPGC_r2

source_name: Human primodridal germ cells

value: Week7-9 human embyro

value: Human primodridal germ cells


title: HLKMNBBXX_15771314_S36_L002


title: HLKMNBBXX_15771314_S36_L003


title: Control_Rep1 [MeD-seq]

value: C57BL_6NJ x Cast/Ei


title: HLKJ7BBXX_15771314_S24_L002


title: Input_DE_r1

value: Definitive endoderm cells


title: HLKJ7BBXX_15771314_S24_L001


title: HighTomato_Rep3 [MeD-seq]

value: NSCs


title: HighTomato_Rep3 [RNA-seq]

data_processing:
The SNPs in the C57BL_6NJ and Cast/Ei lines were downloaded from the Sanger institute (v.5 SNP142). These were used as input for SNPsplit v0.3.4, to construct an N-masked reference genome based on mm10 in which all SNPs between C57BL_6NJ and Cast/Ei were masked. Reads were first mapped to a reference genome file containing the C57BL genome, Cast/Ei genome and the NanoLuciferase sequence using the default settings of hisat2 v2.2.1. Reads that mapped to the Nanoluciferase sequence without mismatches were removed from the fastq files, after which the remaining reads were remapped to the N-masked reference genome. SNPsplit was then used to assign the reads to either the C57BL_6NJ or Cast/Ei bam file based on the best alignment or to an unassigned bam file if mapping to a region without allele-specific SNPs. The allele-specific and unassigned bam files were sorted using samtools v1.10.
The number of mapped reads per gene were counted for both alleles separately using HTSeq v0.12.4 (--nonunique=none -m intersection-nonempty) based on the gene annotation from ensembl v98. For each sample, the number of reads that mapped perfectly to the Nanoluciferase sequence was added to the Mecp2 gene count of the Cast/Ei allele. Moreover, reads from the allele-specific and unassigned bam files overlapping each gene were counted as composite (total) read counts. The gene counts for 129/Sv, Cast/Ei and composite reads were merged into a tab-delimited text file.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include raw counts for each gene based on the C57BL6, Cast/Ei and composite reads

extract_protocol:
RNA was extracted using the ReliaPrep RNA miniprep protocol of Promega following manufacturer's instructions.
cDNA libraries from RNA samples were prepared using the Smart-seq2 method and subsequently sequenced on an Illumina HiSeq2500 sequencer.

value: 5-AZA + Xist KD


title: H3K4me3_PreME_r2


title: HLKMNBBXX_15771302_S24_L002

value: Retina


title: H3K4me3_PreME_r1


title: HLKMNBBXX_15771302_S24_L004


title: HLKMNBBXX_15771302_S24_L003


title: HighTomato_Rep1 [RNA-seq]


title: HLKJ7BBXX_15771302_S12_L002


title: H3K4me3_ME_r2


title: HLKJ7BBXX_15771294_S4_L002


title: HLKJ7BBXX_15771294_S4_L001


title: HLKMNBBXX_15771294_S16_L002


title: HLKMNBBXX_15771294_S16_L003


title: MediumTomato_Rep2 [RNA-seq]


title: H3K4me3_hPGCLC_d4_r1

description: H3K4me3_hPGCLC_d4_pool_final_q3.narrowPeak


title: HLKMNBBXX_15771305_S27_L003


title: MediumTomato_Rep1 [RNA-seq]


title: LowTomato_Rep3 [RNA-seq]


title: HLKJ7BBXX_15771305_S15_L002


title: H3K4me3_hPGC_r2

description: H3K4me3_hPGC_wk8_M_pool_final_q3.narrowPeak


title: HLKJ7BBXX_15771305_S15_L001


title: HLKMNBBXX_15771305_S27_L004


title: HighTomato_Rep2 [RNA-seq]


title: H3K4me3_hESC_r2


title: HLKJ7BBXX_15771296_S6_L002


title: HLKMNBBXX_15771305_S27_L002


title: H3K4me3_hPGC_r1


title: LowTomato_Rep1 [RNA-seq]


title: HLKJ7BBXX_15771302_S12_L001


title: HLKJ7BBXX_15771296_S6_L001


title: LowTomato_Rep2 [RNA-seq]


title: HLKMNBBXX_15771296_S18_L004


title: Control_Rep3 [RNA-seq]

value: Untreated


title: MediumTomato_Rep3 [RNA-seq]


title: H3K4me3_ME_r1


title: HLKMNBBXX_15771296_S18_L003

value: Fovea


title: H3K4me3_hESC_r1

value: hESC-derived


title: H3K4me3_hPGCLC_d4_r2


title: HLKMNBBXX_15771296_S18_L002


title: HLKJ7BBXX_15771295_S5_L002


title: Control_Rep1 [RNA-seq]


title: HLKJ7BBXX_15771295_S5_L001


title: H3K4me3_DE_r1


title: HLKMNBBXX_15771295_S17_L003


title: Zdbf2-KO_10dpp_rep2

city: paris

first: teissandier

last: aurelie

address: 26 rue d'Ulm

country: France

institute: institut curie

description: Whole hypothalamus RNA from Zdbf2-KO at 10dpp

data_processing:
Adapters sequences were trimmed using TrimGalore v0.6.2 (https://github.com/FelixKrueger/TrimGalore).
Paired-end reads were mapped using STAR_2.6.1a (citation) allowing 4% of mismatches. Gencode vM13 annotation was used to quantify gene expression using quantification mode from STAR. Normalization and differential gene expression was performed using EdgeR R package (v3.22.3) (citation). Genes were called as differentially expression if the fold discovery rate (FDR) is lower than 10%.
Genome_build: mm10
Supplementary_files_format_and_content: File text with gene count

source_name: 10dpp hypothalamus

extract_protocol:
Whole hypothalamus RNA was extracted using Trizol, Dnase-treated using QIAGEN Rnase-Free Dnase Set, and quality-controlled for integrity using Tapstation.
RNA-seq libraries were prepared from 500ng of DNase-treated RNA with the TruSeq Stranded mRNA Library Prep Kit (Illumina). Sequencing was performed in 100pb paired-end reads using Novaseq 6000 (for 3dpp samples) and HiSeq2500 (for 10dpp samples).

tag: genetic background

value: C57BL/6J background

value: male

value: Heterozygous mutant (paternal transmission)


title: HLKMNBBXX_15771295_S17_L004


title: Zdbf2-KO_10dpp_rep1


title: DC_rep2

city: Potsdam

first: Heinrich

last: Bente

address: Am Muehlenberg 1

institute: Max Planck Institute of Molecular Plant Physiology

description: prepared from totalRNA

data_processing:
fastq-file generation and demultipexing was done by sequencing facility
Adapter were trimmed using flexbar  (Version 3.5.0; options: -ap ON)
Corresponding forwards and reverse reads were combined using fastq-join (Version 1.3.1; option: -v ' ')
Reads were size-selected to the length of 18-26 nt using cutadapt (v1.9.1 ; options: -m 18 -M 26)
Reads were aligned to the Arabidopsis thaliana genome (TAIR10) and the CaMV genomic sequence using Bowtie2 (2.3.5.1 ; options: -k 500 -no-unal)
Genome_build: TAIR10; CaMV genomic sequence
Supplementary_files_format_and_content: For each sample two tab-delimited text files including distinct sequences and reads count values. One file for the sequences matching to CaMV, one file for the sequences against the TAIR10 genome.

organism: Arabidopsis thaliana

source_name: rosette

growth_protocol: plants were grown in walk in chambers in short day conditions (120 mE, 10h light / 14h dark cycle) at 22°C and 65% relative humidity

extract_protocol:
total RNA extraction with Trizol
NEBnext E7300 followed by size selection on PAGE gel

treatment_protocol: Arabidopsis plants were infected with CaMV 18 days after germination. The first true leaves were infiltrated with Agrobacterium tumefaciens strain C58C1 carrying CaMV strain CM1841 (OD 0.15) .

tag: ecotype background

value: CaMV (CM184I) infected

tag: plant age

value: 39 days

tag: days past infection


title: H3K4me1_ME_r2

value: Mesendoderm cells


title: LRC_rep2

description: prepared from totalRNA


title: Control_10dpp_rep1

description: Whole hypothalamus RNA from WT at 10dpp

value: Wild-type


title: DRC_rep2

description: prepared from totalRNA


title: RM_rep2

description: prepared from totalRNA

value: uninfected


title: H3K4me1_ME_r1


title: WM_rep2

description: prepared from totalRNA

value: wildtype


title: WC_rep2

description: prepared from totalRNA


title: Control_Rep2 [RNA-seq]

tag: strain

value: C57BL_6NJ x Cast/Ei

value: Xist-/+ Mecp2+/NLucTom


title: HLKMNBBXX_15771295_S17_L002

tag: tissue

tag: location


title: DRC_rep1

description: prepared from totalRNA


title: AOV_MSC_NMvOM_2wks_scRNAseq_InDrops

city: BOSTON

first: Julius

middle: L.

last: Decano

state: Massachusetts

address: 3 BLACKFAN CIRCLE. CENTER FOR LIFE SCIENCES, 17TH FLOOR

department: Medicine

institute: Brigham and Women's Hospital

description:
pool of six scRNAseq samples
20180524_pool_JD5590-2of2_S1_R1_001.fastq.gz: This is the entire gene transcript sequenced, post-demultiplexing.  It was demultiplexed using bcbio pipeline (see article). bcbio_R1 = R1 = 100 or 86 or 64 bp transcript read
20180524_pool_JD5590-2of2_S1_R2_001.fastq.gz: This is the cell barcodes, also a demultiplexed file. bcbio_R2 = I1 = 8 bp part 1 of cell barcode
20180524_pool_JD5590-2of2_S1_R3_001.fastq.gz: This is the sample index barcodes, post demultiplexing. bcbio_R3 = I2 = 8 bp sample (library) barcode
20180524_pool_JD5590-2of2_S1_R4_001.fastq.gz: This is part 2 of the single cell barcodes, post demultiplexing and transcript UMI. bcbio_R4 = R2 = 14 bp = 8 bp part 2 of cell barcode + 6 bp of transcript UMI

data_processing:
Post sequencing, raw FASTQ data files underwent bioinformatics processing via bcbio/bcbio nextgen-seq, a python toolkit (https://github.com/bcbio/bcbio-nextgen) and algorithm pipeline.
cell x gene matrix analysis used SeqGeq (BD Biosciences), Excel (Microsoft) and plotly desktop software (Plotly.com)
data visualization by plotly (Plotly.com) and Power BI (Microsoft)
Genome_build: Homo sapiens GRCh38.92

source_name: pool of six scRNAseq samples

growth_protocol: VICs are propagted using 20% FBS in DMEM; MSCs are propagated using ATCC Cat#PCS-500-030 (basal medium) supplemented with ATCC Cat# PCS-500-040 (supplements)

extract_protocol:
VICs are extracted from diseased valves immediately after surgery. Endothelial layer is scraped off, then valve is minced into 1 cubic millimeter pieces then digested in 40 mL of 1mg/mL collagenase IA (Sigma) with gentle agitation in 37C CO2 incubator for 2 hours. Single cell suspension are then harvested and filtered through 100 um cell strainer, then resuspended then either cultured immendiately (MIX) or FACS-sorted (PUR) prior to culturing
The cDNA library was prepared using the CEL-Seq/ MARS protocol with quality control analysis done with Agilent Bioanalyzer.
samples are indexed (indexes: TATGCAGT, AGGCTTAG, AGAGGATA, ATAGAGAG, CTCCTTAC, and TACTCCTT), library construction is followed as per 10x Genomics protocol

treatment_protocol: OM- exposure to osteogenic media (see article) for 2 weeks; NM - 10% FBS in DMEM with Pen-Strep

tag: media stimulation

value: pooled:see sample metadata file

tag: facs sorted prior to media stimulation


title: H3K4me3_DE_r2

value: Definitive endoderm cells


title: H3K4me1_hPGCLC_d4_r1

description: H3K4me1_hPGCLC_d4_pool_final_q3.narrowPeak

value: Human primordial germ cell-like cells


title: HLKMNBBXX_15771294_S16_L004

value: RPE-Choroid

tag: eye (od/os)

tag: macaque number


title: H3K4me1_PreME_r2

tag: cell source

tag: cell type

value: Pre-mesendoderm cells


title: H3K4me1_hPGC_r2

description: H3K4me1_hPGC_wk8_M_pool_final_q3.narrowPeak

value: Week7-9 human embyro

value: Human primodridal germ cells


title: 08I-BRCA1-N5-1year

city: Los Angeles

first: Michael

last: Workman

state: CA

address: 8700 Beverly Blvd., AHSP Suite 8405

institute: Cedars-Sinai Medical Center

description:
Batch 1
NY-017_S17

data_processing:
Demultiplexing and conversion of raw sequencing data to FASTQ was performed with Illumina bcl2fastq software
FastQC was used to assess sequence quality and reads were aligned to human GRCh38.p13 (GENCODE version 32) genome assembly using Salmon (v1.1.0)
Transcript abundance estimates were quantified with Salmon (v1.1.0) and summarized to gene-level counts with tximport in R
Genome_build: Human GRCh38.p13 (GENCODE version 32)
Supplementary_files_format_and_content: Transcript abundance estimates were quantified with Salmon (v1.1.0) and summarized to gene-level counts with tximport in R

molecule: polyA RNA

source_name: iPSC-derived fallopian tube

growth_protocol: Human iPSC-derived fallopian tube were differentiated following the protocol of Yucer et al., Stem Cell Reports (2017)

extract_protocol:
Total RNA was extracted using a Trizol reagent and then purified on-column DNAse digestion, according to the manufacturer’s instructions
RNA libraries were generated using SMART-Seq v4 Ultra Low Input RNA Kit (Takara) and prepared for sequencing using standard Illumina protocols

treatment_protocol: No treatment

tag: genotype

tag: background

value: Ovarian cancer

tag: Sex

value: Female


title: RC_rep1

description: prepared from totalRNA

tag: treatment

value: CaMV (CM184I) infected


title: LC_rep1

description: prepared from totalRNA

value: 39 days


title: DC_rep1

description: prepared from totalRNA


title: H3K4me1_PreME_r1

value: hESC-derived

tag: chip antibody


title: 70I-BRCA1-N1-1year

description:
Batch 1
NY-016_S16


title: LRC_rep1

description: prepared from totalRNA

tag: ecotype background


title: LC_rep2

description: prepared from totalRNA

tag: plant age


title: Control_10dpp_rep2

description: Whole hypothalamus RNA from WT at 10dpp

tag: genetic background

value: C57BL/6J background

tag: gender

value: male

value: Wild-type


title: H3K4me1_hPGC_r1


title: RM_rep1

description: prepared from totalRNA

value: uninfected

tag: days past infection


title: H3K4me1_hESC_r2

source_name: Human embyronic stem cells

value: Human embyronic stem cells


title: WC_rep1

description: prepared from totalRNA

value: wildtype


title: RC_rep2

description: prepared from totalRNA


title: WM_rep1

description: prepared from totalRNA


title: RNA_Activin_19hpf_2

city: Sevilla

first: Juan

middle: J.

last: Tena

address: Univ. Pablo Olavide, Ctra. Utrera km1

country: Spain

institute: CABD/CSIC

data_processing:
Alignment with HISAT2
Filtering of duplicated and not valid reads
Read count per gene with featureCounts
Differential gene expression analysis with EdgeR
Genome_build: Amphioxus Bl71nemr (Genomic sequencing data was submitted to ENA under the master PRJEB13665 accession)
Supplementary_files_format_and_content: Tabular format, differential expressed genes

organism: Branchiostoma lanceolatum

source_name: ecodermal explants

extract_protocol:
total RNA was extracted from frozen explants by using the QIAGEN RNeasy Plus Micro Kit
polyA-selected standard Illumina libraries

tag: developmental timing

value: 19 hpf

value: Activin (50 ng mL-1, human recombinant protein, R&D)


title: H3K4me1_hPGCLC_d4_r2

value: Human primordial germ cell-like cells


title: RNA_Activin_19hpf_1


title: 01MEC-CTR-N4-1year

description:
Batch 1
NY-014_S14

value: Healthy Control


title: 80I-CTR-TN3-1year

description:
Batch 1
NY-015_S15


title: 79I-BRCA1-N2-1year

description:
Batch 1
NY-018_S18


title: H3K4me1_hESC_r1


title: RNA_Activin_11hpf_2

value: 11 hpf


title: 87I-CTR-N3-1year

description:
Batch 1
NY-013_S13


title: RNA_Activin_11hpf_1


title: H3K4me1_DE_r2

source_name: Definitive endoderm cells

value: Definitive endoderm cells


title: RNA_Ctrl_19hpf_2

value: Control


title: RNA_Ctrl_19hpf_1


title: H3K4me1_DE_r1


title: RNA_Ctrl_11hpf_2


title: H3K27me3_PreME_r2

value: Pre-mesendoderm cells

value: H3K27me3 (Cell signaling, 9733, lot 8)


title: ATAC_Activin_19hpf_2

data_processing:
Alignment with BWA
Filtering of duplicated and not valid reads
Differential accessibility analysis, PCA and clustering with DESeq2
Genome_build: Amphioxus Bl71nemr (Genomic sequencing data was submitted to ENA under the master PRJEB13665 accession)
Supplementary_files_format_and_content: BED format, differentially accesible ATACseq peaks

extract_protocol:
Embryos were centrifugated at 13000 rpm for 1 min, and then seawater wasa carefully removed. Cells were lysed by gently pipetting in cold lysis buffer
Assay for Transposase-Accessible Chromatin with high throughput sequencing (ATAC-Seq) experiments were performed as described in Buenrostro et al., 2015. Curr. Protoc. Mol. Biol. 109, 21.29.1-9. doi:10.1002/0471142727.mb2129s109


title: ATAC_Activin_19hpf_1


title: 70I-BRCA1-N1-4month

description:
Batch 1
NY-007_S7

value: Ovarian cancer

value: Female


title: H3K27me3_PreME_r1

value: hESC-derived


title: ATAC_Activin_11hpf_2


title: ATAC_Activin_11hpf_1


title: ATAC_Ctrl_19hpf_2


title: H3K27me3_ME_r1

value: Mesendoderm cells


title: 87I-CTR-N3-4month

description:
Batch 1
NY-001_S1


title: 80I-CTR-TN3-4month

description:
Batch 1
NY-005_S5


title: 01MEC-CTR-N4-4month

description:
Batch 1
NY-003_S3


title: ATAC_Ctrl_11hpf_2


title: ATAC_Ctrl_11hpf_1


title: K27AC_Dex1hr_GBS4eKO_ChIPseq [GBS4eKO_Dex_K27ac.rep1.1]

city: Research Triangle Park

first: Jackson

middle: Andrew

last: Hoffman

state: North Carolina

address: 111 TW Alexander Dr, Building 101 Room C432

department: DIR

institute: NIEHS

data_processing:
Adapter sequences were trimmed from ChIP-seq reads using Cutadapt (Martin, 2011) and low quality reads were removed from analysis using Sickle (Joshi NA et al., 2011). Alignment was performed with Bowtie2 (Langmead and Salzberg, 2012). Aligned reads were sorted and processed with Samtools (Li et al., 2009) and de-duplicated using Picard Tools (http://broadinstitute.github.io/picard). Peaks were called using MACS2 (Zhang et al., 2008) and Homer (Heinz et al., 2010) using a false discovery rate cutoff of 0.001, and regions of high depth or with high signal in untreated or input samples were used to filter out false positive peak calls. Peak overlaps and distance analyses were performed using Bedtools (Quinlan and Hall, 2010). Coverage files and heatmaps were generated using Deeptools (Ramírez et al., 2016).
For 4C-seq, data was processed using Pipe4C (Krijger et al., 2020) and run via Rscript for R version 3.6.1 with the following parameters: trimLength=0, mismatchMax=0, and minAmountReads=10. Data QC involved reviewing output reports to verify that the overall alignment rate was typically >85% and resulted in at least 1 million reads aligned to the fragment index. Results were visualized using ggplot2 (Wickham, 2016).
Genome_build: hg19
Supplementary_files_format_and_content: bw

growth_protocol: Cells were cultured in modified Eagle medium (MEM) containing 10% fetal bovine serum, 1X Penicillin/Streptomycin (Sigma P0781), 1% HEPES (Sigma H0887), 1X Glutamax (Gibco 35050), and 250 ug/ml G418 (Gibco 10131).

extract_protocol:
For ChIPseq, cells were fixed in PBS with 1% methanol-free formaldehyde (Thermoscientific 28906) at 37C for 10 min and quenched with glycine. Cell pellets were resuspended in MNase swelling buffer (25 mM HEPES pH 7.9, 1.5 mM MgCl2, 10 mM KCl, 0.1% NP-40, 5 mM Sodium Butyrate, 0.5 mM PMSF, and protease inhibitor cocktail (PIC) (ThermoFisher Scientific, 78429)) for enzymatic fragmentation or into hypotonic buffer (10 mM HEPES-NaOH pH 7.9, 10 mM KCl, 1.5 mM MgCl2, 340 mM sucrose, 10% glycerol, 0.1% Triton X-100, 5 mM Sodium Butyrate, 0.5 mM PMSF, and PIC) for mechanical sonication. Cells were incubated on ice for 10 min then subjected to Dounce homogenization using 20-strokes (Duran Wheaton Kimble, 357542). For enzymatic fragmentation with MNase, nuclei were sedimented through digestion buffer (15mM Hepes pH 7.9, 60mM KCl, 15mM NaCl, 0.32M Sucrose, 5 mM Sodium Butyrate, 0.5 mM PMSF, and PIC) by centrifugation for 7 min at 930g (4C). Nuclei pellets were fully resuspended in digestion buffer containing 3.3 mM CaCl2 and digested with MNase (0.7U/1x10^6 cells, Worthington, cat#) at 37C for 15min. MNase fragmentation was stopped by addition of 10 mM EGTA and incubation for 5 min on ice. Digested nuclei were lysed in LB3 buffer (10 mM Tris-HCl pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-deoxycholate, 0.5% N- Lauroylsarcosine, 1% Triton X-100, 5 mM Sodium Butyrate, 0.5 mM PMSF, and PIC) using 5-passages through a 25g ( 0.508 mm x 1.6 cm) needle and brief sonication using 4 cycles (30 sec on/off, power high, 4C) with a Bioruptor sonicator (source). MNase digested chromatin lysate was recovered after 15 min centrifugation at 13,000g (4C).  For mechanical sonication, nuclei pellets were resuspended in Shearing buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 0.5 mM PMSF, 5 mM Sodium Butyrate, 0.1% SDS, and PIC) and chromatin was fragmented by sonication using the Covaris S220 (Peak Power, 175; Duty Factor, 10; Cycles/Burst, 200; Total Time, 600 sec). Sonicated chromatin was recovered by centrifugation at 20,000g (4C) for 10 min.
4C-seq was performed according to the published protocol (Krijger et al., 2020). Briefly, batches of 5-10 million cells were fixed in 2% Formaldehyde solution and flash frozen in liquid nitrogen. A single pellet of 5-10 million cells was used for each 4C replicate. Chromatin was first digested with NlaIII, ligated with T4 DNA Ligase to generate the 3C template, and purified with NucleoMag PCR beads. The purified 3C template was subsequently digested with DpnII, ligated with T4 DNA Ligase to generate the 4C template, and again purified with NucleoMag PCR beads.
ChIP-seq libraries were generated using the ACCEL-NGS® 2S PLUS DNA library kit according to manufacturer’s protocol and sequenced on the Illumina NextSeq platform.
4C-seq libraries were generated by two-step PCR using Expand Long Template PCR kit. The first step PCR reaction used reading and non-reading primers to amplify 4C fragments and was purified with a 0.8X AMPure XP purification. The second step PCR reaction added sequencing adapters and indexes and was purified using Qiagen PCR purification kits. Libraries were sequenced on an Illumina MiSeq with a target of 1-2 million single-end, 100bp reads per library.

treatment_protocol: For Dexamethasone treatments, cells were initially cultured for 24 hours in reduced-serum, hormone-stripped media (Phenol-red free MEM (Gibco 51200) with 5% Charcoal/Dextran treated FBS (R&D Systems S11650), 1X Penicillin/Streptomycin (Sigma P0781), 1% HEPES (Sigma H0887), 1X Glutamax (Gibco 35050), and 250 ug/ml G418 (Gibco 10131)). Subsequently, Dexamethasone (Sigma D4902) was added to the media at 100 nM for all treatments timepoints and 9.5 x 10-4% ethanol was used as vehicle control.

tag: cell line/type

value: A1-2 GBS4eKO breast cancer cells

value: 1hr Dex

tag: antibody

value: Abcam ab4729


title: H3K27me3_hPGCLC_d4_r2

description: H3K27me3_hPGCLC_d4_pool_final_q3.narrowPeak


title: H3K27me3_hPGCLC_d4_r1


title: 79I-BRCA1-N2-4month

description:
Batch 1
NY-011_S11


title: H3K27me3_hPGC_r2

description: H3K27me3_hPGC_wk7_M_pool_final_q3.narrowPeak

value: Week7-9 human embyro

value: Human primodridal germ cells


title: K27AC_EtOH_GBS4eKO_ChIPseq [GBS4eKO_EtOH_K27ac.rep1.1]

value: EtOH


title: 08I-BRCA1-N5-4month

description:
Batch 1
NY-009_S9


title: mock-2-A

city: New York

first: Shuibing

last: Chen

state: NY

address: A 827B, 1300 York Ave

department: Surgery

institute: Weill Cornell Medical College

data_processing:
Illumina bcl2fastq2 v2.20 was used for basecalling.
Sequenced reads were trimmed for low-quality bases and for adapter sequences using cutadapt; then mapped to the human GRCh38 reference genome plus SARS-CoV-2 genome using HISAT2 (version=2.2.1), for hamster samples, the reference genome is Mesocricetus_auratus.MesAur1.0.
Transcript abundances was estimated in Fragments Per Kilobase of exon per Million mapped reads (FPKM) or normalized counts by using edgeR package(version=3.36.0).
Raw reads counts were extracted using featureCounts (Subread package version=2.0.1).
Genome_build: GRCh38, MesAur1.0
Supplementary_files_format_and_content: Excel file storing counts and FPKM values(or normalized counts) per gene per sample

organism: Mesocricetus auratus

source_name: hamster heart

growth_protocol: For the differentiation of pacemaker cells, hPSCs were cultured between P20-P40 and seeded at a density of 3x10^5 cells/well of a 6-well plate and grown for 48 hr to 90% confluence in a humidified incubator with 5% CO2 at 37℃. On day 0, the medium was replaced with RPMI 1640 supplemented with B27 without insulin and 6 µM CHIR99021. On day 1, the medium was changed to RPMI 1640 supplemented with B27 without insulin for 48 hr. Day 3, medium was refreshed to RPMI 1640 supplemented with B27 without insulin and 5 µM SB431542+5 µM SU5402+0.1 µM Cucurbitacin+1 µM RA+5 µM XAV939+2.5 ng/ml BMP4 for another 48 hr. On day 5, the medium was changed back to RPMI-B27 without insulin and 3 µM CHIR99021 for 48 hr, and then switched to RPMI 1640 plus normal B27. From that day on, fresh RPMI 1640-B27 was changed every two days;

extract_protocol:
Total RNA was extracted in TRIzol (Invitrogen) and DNase I treated using Directzol RNA Miniprep kit (Zymo Research) according to the manufacturer’s instructions.
RNAseq libraries of polyadenylated RNA were prepared using the TruSeq RNA Library Prep Kit v2 (Illumina) or TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer’s instructions.

treatment_protocol: To analyze the gene expression of pacemaker cells infected with SARSCOV2 and treated with drugs using RNA-seq, we seeded pacemaker cells on the matrigel-coated 24 well plates and after 48 hr, we changed the medium with fresh prepared medium suppmented with drugs. Then infected with SARS-CoV-2 (MOI=0.1). 24 hpi, pacemaker cells were collected to extract total RNA. For hamster sample infected with virus, cardiac tissues were collected after infection then for total RNA.

tag: tissue

value: hamster heart

tag: infection

value: Uninfected

value: untreated


title: mock-1-A


title: in-3-A

value: SARS-CoV-2 infected hamster


title: RNA_Ctrl_11hpf_1

value: 11 hpf

value: Control


title: mock-3-A


title: H3K27me3_hPGC_r1

tag: cell source

value: H3K27me3 (Cell signaling, 9733, lot 8)


title: in-1-A


title: K27AC_EtOH_GBS3eKO_ChIPseq [GBS3eKO_EtOH_K27ac.rep1.1]

value: A1-2 GBS3eKO breast cancer cells


title: K27AC_Dex1hr_GBS3eKO_ChIPseq [GBS3eKO_Dex_K27ac.rep1.1]


title: Site 4 Donor 9 Multiome (ATAC)

city: Somerville

first: Daniel

middle: B

last: Burkhardt

state: MA

address: 101 South Street, 6th Floor

institute: Cellarity

description: 10X Genomics Chromium Single Cell Multiome ATAC + Gene Expression (ATAC library component)

data_processing:
For CITE data, BAM files were generated using Cell Ranger 6.1.0 following the manufacturers recommendation. For Multiome data, BAM files for each modality were created using Cell Ranger ARC 2.0 following the manufacturers recommendations.
Genome_build: Human reference, GRCh38 (GENCODE v32/Ensembl 98)
Supplementary_files_format_and_content: anndata (annotated data matrix) object saved in h5ad-file format

source_name: Frozen Bone Marrow Mononuclear Cells

extract_protocol:
Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Kits User Guide OR Chromium Single Cell 3' Reagent Kits User Guide (v3 Chemistry) with Feature Barcoding
Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Kits User Guide OR Chromium Single Cell 3' Reagent Kits User Guide (v3 Chemistry) with Feature Barcoding

tag: cell type

value: Primary Bone Marrow Mononuclear Cells

tag: disease state

value: Healthy

tag: vendor

value: AllCells (California)

tag: donor id

tag: vendor lot number

tag: donor age

tag: donor bmi

tag: donor blood type

value: O+

tag: donor race

value: Other Race

tag: donor ethnicity

value: HISPANIC OR LATINO

tag: donor sex

value: Male

tag: donor smoker

value: Nonsmoker


title: Site 4 Donor 8 Multiome (ATAC)

value: A+

value: Black or African American

value: NOT HISPANIC OR LATINO


title: Site 4 Donor 1 Multiome (ATAC)

value: B-

value: White


title: H3K27me3_ME_r2

value: hESC-derived

value: Mesendoderm cells

tag: chip antibody


title: K27AC_Dex1hr_GBS2eKO_ChIPseq [GBS2eKO_Dex_K27ac.rep1.1]

tag: cell line/type

value: A1-2 GBS2eKO breast cancer cells

tag: treatment

value: 1hr Dex

tag: antibody

value: Abcam ab4729


title: Site 3 Donor 7 Multiome (ATAC)

value: Primary Bone Marrow Mononuclear Cells

value: Healthy

value: Asian

value: Female


title: Site 3 Donor 6 Multiome (ATAC)

value: AllCells (California)

value: Other Race

value: HISPANIC OR LATINO


title: H3K27me3_hESC_r2

tag: cell source

value: Human embyronic stem cells

value: H3K27me3 (Cell signaling, 9733, lot 8)


title: ATAC_Ctrl_19hpf_1

tag: developmental timing

value: 19 hpf

value: Control


title: K27AC_EtOH_GBS2eKO_ChIPseq [GBS2eKO_EtOH_K27ac.rep1.1]

value: EtOH


title: Site 3 Donor 3 Multiome (ATAC)

tag: cell type

tag: disease state

value: O+

value: NOT HISPANIC OR LATINO

value: Male

value: Smoker


title: H3K27me3_hESC_r1

value: hESC-derived


title: H3K27me3_DE_r2

value: Definitive endoderm cells


title: K27AC_Dex1hr_GBS1eKO_ChIPseq [GBS1eKO_Dex_K27ac.rep1.1]

value: A1-2 GBS1eKO breast cancer cells

value: 1hr Dex

value: Abcam ab4729


title: Site 3 Donor 10 Multiome (ATAC)

value: Primary Bone Marrow Mononuclear Cells

value: Healthy

tag: vendor

value: AllCells (California)

tag: donor id

value: Female


title: H3K27me3_DE_r1

value: H3K27me3 (Cell signaling, 9733, lot 8)


title: Site 2 Donor 5 Multiome (ATAC)

tag: vendor lot number

tag: donor age

value: White

value: HISPANIC OR LATINO


title: Site 2 Donor 4 Multiome (ATAC)

tag: donor bmi

tag: donor blood type

value: Nonsmoker


title: in-2-A

tag: tissue

value: hamster heart

tag: infection

value: SARS-CoV-2 infected hamster

value: untreated


title: H3K27ac_PreME_r2

value: Pre-mesendoderm cells


title: K27AC_EtOH_GBS1eKO_ChIPseq [GBS1eKO_EtOH_K27ac.rep1.1]

value: EtOH


title: Site 2 Donor 1 Multiome (ATAC)

value: B-

tag: donor race

tag: donor ethnicity

tag: donor sex

value: Male

tag: donor smoker


title: Site 1 Donor 3 Multiome (ATAC)

value: O+

value: Asian

value: NOT HISPANIC OR LATINO

value: Smoker


title: Site 1 Donor 2 Multiome (ATAC)

value: Primary Bone Marrow Mononuclear Cells

value: Healthy

value: AllCells (California)

value: B+


title: K27AC_Dex1hr_A12_ChIPseq [A12_Dex_K27ac.rep1.1]

tag: cell line/type

value: A1-2 breast cancer cells

tag: treatment

value: 1hr Dex

tag: antibody

value: Abcam ab4729


title: H3K27ac_PreME_r1

tag: cell source

value: hESC-derived

tag: cell type

tag: chip antibody


title: K27AC_EtOH_A12_ChIPseq [A12_EtOH_K27ac.rep2.1]


title: Site 4 Donor 9 Multiome (GEX)

description: 10X Genomics Chromium Single Cell Multiome ATAC + Gene Expression (GEX library component)

tag: disease state

tag: vendor

tag: donor id

value: Other Race

value: HISPANIC OR LATINO

value: Nonsmoker


title: Site 1 Donor 1 Multiome (ATAC)

tag: vendor lot number

tag: donor age

tag: donor bmi

value: B-

value: White


title: H3K27ac_ME_r2

value: Mesendoderm cells


title: K27AC_EtOH_A12_ChIPseq [A12_EtOH_K27ac.rep1.1]

value: EtOH


title: H3K27ac_ME_r1


title: Site 3 Donor 6 Multiome (GEX)

tag: donor blood type

value: A+

value: Female


title: Site 4 Donor 1 Multiome (GEX)

value: Primary Bone Marrow Mononuclear Cells

tag: donor race

value: Male


title: RNAPII_Dex1hr_ChIPseq [Dex1hr_POL2.1]

value: Active Motif 102660


title: Site 3 Donor 3 Multiome (GEX)

value: Healthy

value: AllCells (California)

value: O+

value: Asian

tag: donor ethnicity

value: NOT HISPANIC OR LATINO

value: Smoker


title: Site 3 Donor 7 Multiome (GEX)

tag: donor sex


title: Site 2 Donor 5 Multiome (GEX)

value: HISPANIC OR LATINO

tag: donor smoker


title: H3K27ac_hPGCLC_d4_r2

description: H3K27ac_hPGCLC_d4_pool_final_q3.narrowPeak

value: hESC-derived

value: Human primordial germ cell-like cells


title: RNAPII_EtOH_ChIPseq [EtOH_POL2.1]

tag: cell line/type

value: A1-2 breast cancer cells


title: Site 3 Donor 10 Multiome (GEX)

value: Other Race


title: Site 2 Donor 4 Multiome (GEX)

value: White

value: Nonsmoker


title: H3K27ac_hPGCLC_d4_r1


title: Site 1 Donor 3 Multiome (GEX)


title: GR_Dex4hr_ChIPseq [GR_4HR.1]

tag: treatment

value: 4hr Dex

value: Novus MBP2-42221


title: H3K27ac_hPGC_r2

description: H3K27ac_hPGC_wk8_M_pool_final_q3.narrowPeak

value: Week7-9 human embyro

value: Human primodridal germ cells


title: Site 1 Donor 2 Multiome (GEX)

value: Primary Bone Marrow Mononuclear Cells

value: Healthy

value: B+

value: Female


title: Site 1 Donor 1 Multiome (GEX)

value: AllCells (California)

value: B-

value: Male


title: Site 2 Donor 1 Multiome (GEX)

value: HISPANIC OR LATINO


title: Site 4 Donor 9 Cite (GEX & ADT)

description: 10X Genomics 3' Single Cell Gene Expression with Feature Barcoding via BioLegend TotalSeq™-B Human Universal Cocktail, V1.0

value: O+


title: GR_Dex2hr_ChIPseq [GR_2HR.1]

value: A1-2 breast cancer cells

value: 2hr Dex

tag: antibody


title: H3K27ac_hPGC_r1

tag: cell source


title: Site 4 Donor 1 Cite (GEX & ADT)

tag: cell type

value: White


title: H3K27ac_hESC_r2

value: hESC-derived

value: Human embyronic stem cells

tag: chip antibody


title: GR_Dex1hr_ChIPseq [GR_1HR.1]

value: 1hr Dex

value: Novus MBP2-42221


title: Site 4 Donor 8 Multiome (GEX)

tag: disease state

value: A+

value: Black or African American

value: NOT HISPANIC OR LATINO

value: Nonsmoker


title: H3K27ac_hESC_r1


title: Site 3 Donor 7 Cite (GEX & ADT)

value: Primary Bone Marrow Mononuclear Cells

value: Healthy

tag: vendor

value: Asian

value: Female


title: Site 3 Donor 6 Cite (GEX & ADT)

value: AllCells (California)

tag: donor id

value: Other Race

value: HISPANIC OR LATINO


title: Site 2 Donor 5 Cite (GEX & ADT)

tag: vendor lot number

value: O+

value: Smoker


title: GR_Dex15min_ChIPseq [GR_15MIN.1]

value: A1-2 breast cancer cells

value: 15min Dex


title: H3K27ac_DE_r1

value: hESC-derived

value: Definitive endoderm cells


title: H3K27ac_DE_r2


title: GR_EtOH_ChIPseq [GR_0.1]

value: EtOH

value: Novus MBP2-42221


title: GR_Dex8hr_ChIPseq [GR_8HR.1]

value: 8hr Dex


title: Site 2 Donor 4 Cite (GEX & ADT)

tag: donor age

value: White

value: NOT HISPANIC OR LATINO

value: Male

value: Nonsmoker


title: ATAC_PreME_r2

data_processing:
Paired-end ATAC-seq reads were quality- and adaptor-trimmed by Trim Galore (v0.4.1) using default parameters.
Trimmed reads were mapped to the human reference genome (UCSC GRCh38/hg38) by Bowtie 2 (v2.3.4.1) with options ‘--local -X 2000 --no-mixed --no-discordant’, hence retaining properly paired reads with a maximum fragment length of 2000 bp.
Unmapped reads, non-primary reads, supplementary alignment and QC-failed reads were removed using samtools view with option ‘-F 2828’. Duplicated reads were marked and removed by the MarkDuplicates function in Picard Tools (Broad Institute). Subsequently, fragments mapped to hg38 blacklisted regions (http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/hg38-human/hg38.blacklist.bed.gz), non-canonical hg38 contigs and mitochondrial DNA (chrM) were removed. To adjust the read start sites to represent the center of the transposon binding event, all reads aligning to the positive strand were offset by +4 bp, and all reads aligning to the negative strand were offset -5 bp.
Prior to peak calling, paired-end reads with fragment size < 120 bp were extracted using deepTools alignmentSieve. These reads were considered nucleosome-free and were used to determine open chromatin regions. Subsequently, libraries were subsampled using Picard DownSampleSam so that each library contains approximately the same number of paired-end reads.
Peaks were called following the Encode replicated peak calling guidelines (https://www.encodeproject.org/pipelines/ENCPL272XAE/) with modifications to accommodate for paired-end libraries. To obtain high resolution of peaks, narrow peak call was used for all marks. Histone peaks were called using the input reads as background. Peaks were initially called for each biological replicate (downsampled to similar read depth), for the pooled replicates, and for the pooled pseudoreplicates of each biological replicate using MACS2 with a relaxed p-value threshold of 0.05 (options: ‘-g 3e9 --keep-dup all -p 0.05’). Each pseudoreplicate consists of half the reads of each biological replicate, chosen at random without replacement. Narrow peaks from the pooled replicate set were retained if they overlapped peaks from both biological replicates or peaks from both pooled pseudoreplicates. The thresholds of overlap were set at 20% for ATAC peaks. This peak calling strategy allows for the retention of marginal peaks in one replicate to be rescued by a strong biological replicate. To obtain a final high confidence peak set, the reproducible peaks were further filtered using the MACS2 q-value (false discovery rate <0.0001).
Genome_build: hg38
Supplementary_files_format_and_content: Reproducible peaks of the two biological replicates in macs2 narrowPeak format

extract_protocol:
Cells were sorted directly into Nuclei EZ Storage Buffer (Sigma, NUC-101) and stored at -80 °C. ATAC-seq libraries were prepared following the Omni-ATAC protocol described by Corces et al. (2017). Briefly, cells were washed in cold PBS and resuspended in cold ATAC-seq resuspension buffer (RSB; 10 mM Tris-HCl pH 7.4, 10 mM NaCl, and 3 mM MgCl2 in water). Cells were then lysed in 50 μl of RSB containing 0.1% NP40, 0.1% Tween-20, and 0.01% digitonin. After lysis, 1 ml of RSB containing 0.1% Tween-20 was added. Cell pellet was resuspended in 50 μl of transposition mix (25 μl 2x TD buffer, 2.5 μl TDE1 Tagment DNA Enzyme (Nextera DNA Library Prep Kit, FC-121-1031), 16.5 μl PBS, 0.5 μl 1% digitonin, 0.5 μl 10% Tween-20, and 5 μl water) by pipetting up and down six times. The 2X TD buffer was composed of 20 mM Tris-HCl pH 7.6, 10 mM MgCl2, 20% Dimethyl Formamide in water. Transposition reactions were incubated at 37 °C for 30 min in a thermomixer with shaking at 1,000 r.p.m. Reactions were cleaned up with MinElute Reaction Cleanup Kit (Qiagen).
Tagmented DNA was amplified using the KAPA HiFi HotStart Real-Time Library Amp Kit (Roche) with modified Nextera dual indexed primers as listed in Table 1. Amplified libraries were purified using Ampure XP beads (Beckman Coulter) with double-sided size selection (1st bead selection: 0.5x; 2nd bead selection: 1.2x) according to manufacturer’s protocol. Quantified and validated libraries (~ 150-1000 bp) were subjected to pair-end sequencing on HiSeq 4000 sequencing system (Illumina).

value: Pre-mesendoderm cells


title: Site 2 Donor 1 Cite (GEX & ADT)

value: Primary Bone Marrow Mononuclear Cells

value: Healthy

value: AllCells (California)

tag: donor bmi

value: B-


title: Site 1 Donor 3 Cite (GEX & ADT)

tag: donor blood type

value: O+

value: Asian

value: Smoker


title: Seq26@2@S11

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

data_processing:
Preprocessing: Low quality ends and adapter sequences were trimmed off from the Illumina reads with FastX 0.0.14 and Cutadapt 1.15 (HannonLab, 2010; Martin, 2011). Subsequently, small reads (length < 35 bp), polyA-reads (more than 90 % of the bases equal A), ambiguous reads (containing N), low-quality reads (more than 50 % of the bases < Q25) and artifact reads (all but three bases in the read equal one base type) were filtered using using FastX 0.0.14 and ShortRead 1.36.0 (Morgan et al, 2009). With Bowtie2 2.3.3.1 we identified and removed reads that align to phix_illumina (Langmead & Salzberg, 2012).
Mapping: The preprocessed reads were aligned with STAR aligner v2.5.2b to the reference genome of Homo sapiens (GRCh38) (AD et al, 2013).  Default STAR aligner parameter settings were used, except for ‘--outSAMprimaryFlag OneBestScore --twopassMode Basic --alignIntronMin 50 --alignIntronMax 500000 --outSAMtype BAM SortedByCoordinate’. Using Samtools 1.5, reads with a mapping quality smaller than 20 were removed from the alignments (Li et al, 2009).
Counting: The number of reads in the alignments that overlap with gene features were counted with featureCounts 1.5.3 (Liao et al, 2014). Following parameters were chosen: -Q 0 -s 2 -t exon -g gene_id. We removed genes for which all samples had less than 1 count-per-million. Raw counts were further corrected within samples for GC-content and between samples using full quantile normalization, as implemented in the EDASeq package from Bioconductor (Risso et al, 2011).
Genome_build: Homo sapiens (GRCh38)
Supplementary_files_format_and_content: Raw counts are in tab-delimited text file.
Supplementary_files_format_and_content: Statistical Table resulting from the EdgeR analysis in tab-delimited text file.

source_name: Tunica albuginea

extract_protocol:
RNA extraction: Tripure (Trizol reagents)
RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Only high quality RNA (RIN>7) was used for further processing. Per sample, an amount of 250ng of total RNA was used as input. Using the Illumina TruSeq® Stranded Total RNA Sample Prep Kit with Ribo-Zero Gold (protocol version “April 2013”) rRNA is depleted from the total RNA samples using Ribo-Zero ribosomal RNA reduction chemistry. Subsequently, RNA was purified and fragmented and converted into first strand cDNA in a reverse transcription reaction using random primers. Next, double-stranded cDNA was generated in a second strand cDNA synthesis reaction using DNA PolymeraseI and RNAse H. The cDNA fragments were extended with a single ‘A’ base to the 3’ ends of the blunt-ended cDNA fragments after which multiple indexing adapters were ligated introducing different barcodes for each sample. Finally an enrichment PCR was carried out to enrich those DNA fragments that have adapter molecules on both ends and to amplify the amount of DNA in the library. Sequence-libraries of each sample were equimolarly pooled and sequenced on a NextSeq500 flow-cell with a High Output 75bp kit (Single Read - 1.3pM Pool + 1.86% PhiX v3) at the VIB Nucleomics core (www.nucleomics.be).

tag: diagnosis

value: Control

tag: tissue

value: Tunica albuginea


title: ATAC_PreME_r1

value: hESC-derived


title: Site 1 Donor 2 Cite (GEX & ADT)

value: B+

tag: donor race

tag: donor ethnicity

tag: donor sex

value: Female


title: Site 1 Donor 1 Cite (GEX & ADT)

value: White

value: HISPANIC OR LATINO

tag: donor smoker


title: Site 4 Donor 8 Cite (GEX & ADT)

value: A+

value: Black or African American

value: NOT HISPANIC OR LATINO

value: Male


title: Seq24@2@S10


title: GR_Dex30min_ChIPseq [GR_30MIN.1]

tag: cell line/type

value: A1-2 breast cancer cells

tag: treatment

value: 30min Dex

tag: antibody

value: Novus MBP2-42221


title: ATAC_ME_r3

tag: cell source

tag: cell type

value: Mesendoderm cells


title: UM-UC-3-S1

city: Guangzhou

first: Ming

last: Huang

address: Yanjiang West Road

country: China

institute: Sun Yat-sen Memorial Hospital

data_processing:
Base-calling: Base-calling using bcl2fastq2 v2.19.1 with -r 4 -p 16 -w 4  --barcode-mismatches 0
Data filtering : Adaptor contamination was remove from reads (the number of bases contaminated by the adaptor in reads is greater than 5bp. For pair-end sequencing, if one end is contaminated by the adaptor, the Reads at both ends are removed)；Remove low-quality reads (Reads with more than 50% of the total bases are bases with a mass value of Q ≤ 19 . For pair-end sequencing, if one pair is low-quality reads, the both reads will be removed)；Remove the reads with N rate greater than 5%  (For pair-end sequencing, if one pair contains more than 5% N, the both reads will be removed)
Read alignment: Fastq reads were mapped to genome using hisat2 v2.1.0 with default parameters
transcript assemble: Reads count of echo gene was calculated using htseq-count v0.6.1 with -t exon -f bam -s no -a 10
Genome_build: hg19 (ftp://ftp.ensembl.org/pub/grch37/current/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.dna.toplevel.fa.gz)
Supplementary_files_format_and_content: Excel files include normalized values for each Sample

source_name: bladder cancer cell line UM-UC-3

growth_protocol: UM-UC-3 was cultured in DMEM (Gibco) supplemented with 10% FBS (Biological Industries) and 1% penicillin/streptomycin (Gibco). Cells were grown in a humidified atmosphere of 5% CO2 at 37°C.

extract_protocol:
Total RNA was extracted using Trizol reagent and was further purified using Qiagen RNeasy Mini Kit according to the manufactures’ instructions. The RNA quality was assessed by formaldehyde agarose gel electrophoresis and was quantitated spectrophotometrically.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 1 OD SiRNA was  diluted at a stocking solution of 125 μL in sterile DEPC-treated water, and cells were treated for 48h with 5 μL of SiRNA.

tag: cell line

value: bladder cancer cell line UM-UC-3

value: 0.04 OD Si-RNA-1


title: UM-UC-3-S2

value: 0.04 OD Si-RNA-2


title: ATAC_ME_r2


title: SAN0512

description: single cell RNA seq

data_processing:
The single cell library was sequenced with Illumina NovaSeq6000 platform.  Sequencing reads were aligned to human GRCh38 reference genome with Cell Ranger.
Genome_build: GRCh38
Supplementary_files_format_and_content: Cell Ranger output files (matrix.mtx, barcodes.tsv, genes.tsv)

source_name: human ES-derived pacemaker cell

extract_protocol:
This step was done by following the 10x Genomics single cell preparation protocol.
RNA libraries were prepared for sequencing using standard 10X Illumina single cell library preparation protocols

treatment_protocol: The Day30 sinoatrial nodal like pacemaker cells derived from our reporter cell line were sorted and the double positive and live cell population was filter out for the following single cell RNA seq library prepartion.

value: human ES-derived pacemaker cell

tag: age

tag: infection

value: Uninfected


title: UM-UC-3-NC

value: Negative control


title: Site 3 Donor 1 Cite (GEX & ADT)

value: Primary Bone Marrow Mononuclear Cells

tag: disease state

value: Healthy

tag: vendor

value: AllCells (California)

tag: donor id

tag: vendor lot number

tag: donor age

value: B-

value: Nonsmoker


title: ATAC_hPGCLC_d4_r2

source_name: Human primordial germ cell-like cells

value: hESC-derived

value: Human primordial germ cell-like cells


title: SAN-im-3

value: SARS-CoV-2 infected

value: Imatinib treated


title: SAN-im-2


title: s14@S6

tag: diagnosis

value: Control

tag: tissue

value: Tunica albuginea


title: Seq21@2@S8


title: s12@S5


title: SAN-im-1


title: SAN-de-1

value: Deferoxamine treated


title: ATAC_hPGCLC_d2_r1


title: ATAC_hPGCLC_d2_r2


title: SAN-de-3


title: SAN-de-2


title: ATAC_hPGCLC_d4_r1


title: s16@S7

value: Peyronie's disease


title: Seq27@S12


title: SAN-IN-5

value: DMSO treated


title: ATAC_hPGC_r2

description: ATAC_hPGC_wk7_M_pool_final_q4.narrowPeak

value: Week7-9 human embyro

value: Human primodridal germ cells


title: SAN-IN-2

value: human ES-derived pacemaker cell


title: Seq22@2@S9


title: SAN-IN-1


title: s7@S4


title: s1@S3


title: SAN-48M-3

value: Uninfected

value: untreated


title: IGF1-3

city: Jatai

first: Bruna

middle: Tereza Thomazini

last: Zanella

state: Goias

country: Brazil

institute: Federal University of Jatai (UFJ)

data_processing:
MicroRNAome was obtained in a single-end sequencing 50bp on an Illumina Hiseq 4000 following the manufacture's protocol
The quality was evaluated using the software FastQC (0.11.8)
Reads with more than 17 nucleotides in length were maintained using the software Trimmomatic
Bowtie2 aligner was used for the annotation and mapping steps based on the mature miRNA list of teleost fish available in miRBase version 22.1
Counts were normalized by the median of ratios method, with the counts divided by sample-specific size factors, using DESeq2 package in R environment. Only miRNA with counts mean >10 between samples were maintained.
Genome_build: A. burtoni (AstBur1.0),C. carpio, D. rerio (GRCz11), T. rubripes (FUGU5), G. morhua (GadMor_May2010), I. punctatus, M. zebra (M_zebra_UMD1), N. brichardi (NeoBri1.0), O. latipes (MEDAKA1), O. niloticus, P. nyererei (PunNye1.0), S. salar,T. nigroviridis (Tetraodon8).
Supplementary_files_format_and_content: Matrix table with normalized miRNA counts for every miRNA and every sample
Supplementary_files_format_and_content: Matrix table with raw miRNA counts for every miRNA and every sample

organism: Piaractus mesopotamicus

source_name: Muscle cells

growth_protocol: Cells were isolated from pacu fast-twitch muscle and growth in complete medium until the 8th day of cultivation

extract_protocol:
Total RNA was extracted using Trizol, following the manufactures instructions. Approximately 1 ug of total RNA were used to prepare small RNA library according to protocol of TruSeq Small RNA Sample Prep Kits
Small RNA library, size fractionaction

treatment_protocol:
CTR group cells were cultivated in nutrient restriction medium for 36 hours
AA group cells were cultivated in nutrient restriction medium for 12 hours followed by 24 hours of AA supplementation
IGF1 group cells were cultivated in nutrient restriction medium for 12 hours followed by 24 hours of IGF1 supplementation

value: Fast-twitch muscle

value: IGF1 treatment for 12 hours


title: ATAC_hESC_r2

value: Human embyronic stem cells


title: IGF1-2


title: Seq8@1@S2


title: SAN-48M-2


title: IGF1-1


title: ATAC_hPGC_r1


title: Seq4@S1


title: ATAC_hESC_r1

value: hESC-derived


title: SAN-48M-1


title: ATAC_DE_r2

value: Definitive endoderm cells


title: SAN-48I-3

value: SARS-CoV-2 infected


title: SAN-48I-2


title: ATAC_DE_r1


title: AA-3

value: AA treatment for 12 hours


title: SAN-48I-1


title: AA-1


title: 293TRex-Flp_Tet-induced_rep2

city: Daejeon

first: Kim

last: Hyoungmin

address: 291, Daehak-ro, Yuseong-gu, Daejeon, 34141, Rep. of KOREA

department: Department of Biological Sciences

country: South Korea

institute: Korea Advanced Institute of Science and Technology

description: Flp-In™, T-REx™

data_processing:
Sequencing reads were trimmed with Trimmomatic, aligned to hg38 with STAR, and quantified with featureCounts. Differentially-expressed genes analysis was performed by DESeq2.
Genome_build: hg38
Supplementary_files_format_and_content: Comma-separated differential expressed gene analysis file

growth_protocol: 293TREx is maintained in DMEM wtih 5% FBS and 1% penicillin/streptomycin.

extract_protocol:
RNA was extracted with Trizol.
Total RNA concentration was calculated by Quant-IT RiboGreen (Invitrogen, #R11490). To assess the integrity of the total RNA, samples are run on the TapeStation RNA screentape (Agilent, #5067-5576). Only high-quality RNA preparations, with RIN greater than 7.0, were used for RNA library construction.  A library was independently prepared with 0.5ug of total RNA for each sample by Illumina TruSeq Stranded Total RNA Library Prep Gold Kit (Illumina, Inc., San Diego, CA, USA, #20020599). The first step in the workflow involves removing the rRNA in the total RNA using Ribo-Zero rRNA Removal Kit (Human/Mouse/Rat Gold) (Illumina, Inc., San Diego, CA, USA). Following this step, the remaining 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 a Illumina NovaSeq (Illumina, Inc., San Diego, CA, USA), and the paired-end (2×100 bp) sequencing was performed by the Macrogen Incorporated.

treatment_protocol: For tetracylin induction, 1μM of tetracyclin was treated for 12hr, 37°C.

value: Flp-InTM, T-RExTM

value: Tetracylin-treated


title: murine preputial gland scRNA-seq

city: Vienna

first: Katharina

last: Klas

address: Medizinische Universität Wien Anna Spiegel Forschungsgebäude Lazarettgasse 14 1090 Wien, Austria Level 6, Lab 5

country: Austria

institute: Medical University of Vienna

description: Single-cell RNAseq data

data_processing:
Raw sequencing data were demultiplexed, aligned to a reference genome and counted using Cell Ranger (vcellranger-5.0.1; 10x Genomics).
Genome_build: mm10-2020-A
Supplementary_files_format_and_content: tsv files contain lists of genes and barcodes for each sample, mtx files count gene UMI counts for each sample

source_name: murine preputial gland

extract_protocol:
6mm tissue-biopsies were obtained from back skin, and preputial glands as a whole were dissociated using Miltenyi MACS whole skin dissociation kit
libraries were prepared using Chromium Next GEM Single Cell 3´GEM, Library & Gel Bead Kit v3.1, Chromium Nexxt GEM Chip G Single Cell Kit and Single Index Kit T Set A (all 19x Genomics, Pleasanton, CA, USA)

value: preputial gland

tag: strain

tag: Sex

value: male


title: Fetal alcohol exposed, 2 years replicate 5, discarded array

city: Montreal

first: Roberta

last: Palmour

state: Quebec

address: 1033 Pine West

department: Psychiatry

country: Canada

institute: McGill

description: miRNA expression data from the hippocampus of vervet green monkeys sacrificed at 2 years after birth

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneTitan at the McGill Genome Center

data_processing: The data were analyzed with FlexArray software and the Bioconductor package in R. These data were normalized using the Robust Multi-Array (RMA) normalization method. Probe sets have been trimmed for present/absent calls, annotation, and where multiple probe sets were available for a single miRNA only the probe set showing the highest mean expression value was selected

organism: Chlorocebus aethiops

source_name: Chlorocebus aethiops hippocampus sacrificed at 2 years after prenatal alcohol exposure

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: miRNeasy Qiazol extraction performed according to manufacturers specifications

treatment_protocol: Whole hippocampus was extracted and placed in a 1 ml sterile vial containing GITC

value: Sacrificed at 2 years

tag: ethanol exposure

value: Pre Natal Alcohol Exposure


title: CTR-3

tag: treatment

value: Nutrient restriction for 36 hours


title: Fetal alcohol exposed, 5 months replicate 2, discarded array

source_name: Chlorocebus aethiops hippocampus sacrificed at 5 months after prenatal alcohol exposure

value: Sacrificed at 5 months


title: murine back skin scRNA-seq

description: Single-cell RNAseq data

source_name: murine back skin

value: back skin


title: 293TRex-Flp_Tet-induced_rep1

description: Flp-In™, T-REx™


title: Fetal alcohol exposed, 5 months replicate 6


title: CTR-2


title: CTR-1


title: Fetal alcohol exposed, 5 months replicate 5


title: 293TRex-Flp_rep2

description: Flp-In™, T-REx™

value: Not treated


title: Fetal alcohol exposed, 5 months replicate 4


title: 293TRex-Flp_rep1

description: Flp-In™, T-REx™


title: CPSF3_depleted_HS_TTchem-seq_rep3

city: London

first: Richard

last: Mitter

address: 1 Midland Road

institute: The Francis Crick Institute

data_processing:
library strategy: TTchem-seq
cutadapt v1.18 was used to trim Illumina adapter sequence from all reads using the following settings: -a AGATCGGAAGAGC -e 0.1 -q 10 -m 25 -O 1
Trimmed reads were aligned against human genome version GRCh38 using STAR v2.5.2a with Ensembl release 86 transcript annotations.
Genome_build: GRCh38
Supplementary_files_format_and_content: Read depth coverage in bigWig format.  Data are unscaled and represent reads mapping to both strands.

extract_protocol:
RNA was extracted by TRIzol (Thermo Fisher Scientific, 15596026) accordingly to the manufacturer’s instructions. 100 μg RNA was fragmented by addition of 20 μL 1 M NaOH to fragment RNA and left on ice for 20 min. Fragmentation was stopped by addition of 80 μL 1 M Tris pH 6.8 and cleaned up twice with Micro Bio-Spin™ P-30 Gel Columns (BioRad, 7326223) according to the manufacturer’s instructions. Biotinylation of 4SU-residues were carried out in a total volume of 250 μl, containing 10 mM Tris-HCl [pH 7.4], 1 mM EDTA and 5mg MTSEA biotin-XX linker (Biotium, BT90066) for 30 min at room temperature in the dark. RNA was then purified by phenol:chloroform extraction, denatured by 10 min incubation at 65°C and added to 200 μL μMACS Streptavidin MicroBeads (Miltenyi, 130-074-101). RNA was incubated with beads for 15 min at room temperature and beads applied to a μColumn in the magnetic field of a μMACS magnetic separator. Beads were washed twice with pull-out wash buffer (100 mM Tris-HCl, pH 7.4, 10 mM EDTA, 1 M NaCl and 0.1% Tween20). 4SU-RNA was eluted twice by addition of 100 mM DTT and RNA cleaned up using the RNeasy MinElute kit (Qiagen, 74204).
Libraries were prepared using the KAPA RNA HyperPrep kit (Roche) using 5 min 65°C fragmentation incubation to anneal primers but to prevent further fragmentation of the samples.

treatment_protocol: Cells were exposed to different treatments: 120min Heat Shock; 120min 250nM dTAG7; 120min of Heat Shock and dTAG7 combined treatment. Nascent RNA was labelled by addition of 1 mM 4-thiourdine to cell media for 15 min prior to harvest

value: 120min dTAG7 and Heat Shock, 15 min 4-thiouridine pulse

tag: molecule subtype

value: Nascent RNA


title: IGF1-rep3

data_processing:
Transcriptome was obtained through the NovaSeq 6000 platform (Illumina, USA) with 150 base pairs, paired-end, and 6 GB data per sample
The quality of sequencing was evaluated using the software FastQC (0.11.8)
Adapters were removed and reads were filtered by quality, using a phred score >33, using the software Trimmomatic
Paired-end reads were de novo assembled using the Trinity software and contigs were blasted against A. mexicanus (Astyanax_mexicanus-2.0), D. rerio (GRcz11) and P. nattereri (Pygocentrus_nattereri-1.0.2) proteome using BLASTx (e-value cut-off 10−3)
Contigs were mapped using Bowtie2 aligner and differentially expressed genes were obtained using DESeq2 package in R enviroment
Counts were normalized by the median of ratios method, with the counts divided by sample-specific size factors, using DESeq2 package in R environment. Only genes with counts mean >10 between samples were maintained.
Genome_build: A. mexicanus (Astyanax_mexicanus-2.0), D. rerio (GRcz11) and P. nattereri (Pygocentrus_nattereri-1.0.2)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with normalized gene counts for every gene and every sample

extract_protocol:
Total RNA was extracted using Trizol, following the manufactures instructions. The material was prepared following Illumina’s TruSeq-stranded-mRNA sample preparation
Poly(A) RNA sequencing library using Illumina's protocol.

value: Fast-twitch muscle

value: IGF1 treatment for 12 hours


title: IGF1-rep2


title: 947 T-72 R2

city: Freiburg

first: Severin

last: Dicks

address: Breisacherstr. 153

department: Institute of Medical Bioinformatics and Systems Medicine

institute: University Freiburg Medical Center

data_processing:
Basecalling: bcl2fastq 2.20.0.422
Adapter trimming and low quality reads trimming: Trimmomatic 0.38; HEADCROP:3 TRAILING:10 SLIDINGWINDOW:4:15 MINLEN:18
Alignment and counting reads per gene: STAR 2.6.1b;
--outFilterType BySJout --outFilterMultimapNmax 10 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.05 i--alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMatchNmin 16 --quantMode GeneCounts TranscriptomeSAM --outSAMtype BAM SortedByCoordinate
Genome_build: mm10
Supplementary_files_format_and_content: table with raw gene counts for every gene

source_name: murine small intestinal TKA organoids

growth_protocol: TKA organoids were mechanically disrupted, seeded in 3 mg/ml Matrigel, and provided with Advanced DMEM/F12 supplemented with 1% (v/v) Penicillin/Streptomycin, 10 mM HEPES, 1 x GlutaMAX™ Supplement, 1 x N-2 Supplement, 1 x B-27™ Supplement, 1 mM n-acetyl-cysteine, 50 ng/mL EGF, and 100 ng/mL Noggin. Organoids were seeded 40 h prior to the onset of the experiments to allow re-development of a cystic shape.

extract_protocol:
Total RNA was isolated using the peqGOLD MicroSpin Total RNA Kit (Peqlab/VWR Life Science, 12-6831)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: TKA organoids were treated with 5 ng/ml human TGFβ1 for 6, 24, 48, and 72 h. For control, organoids were harvested at the onset of the experiment or after cultivation for 72 h in presence of solvent.

value: small intestinal TKA organoids

tag: organoid line

tag: genotype

value: Apcdelta/delta, KrasG12D, Trp53R172H, tgVillin-CreERT2

value: 72 h TGFBeta1


title: 947 C-72 R2

value: 72 h solvent


title: 947 T-48 R2

value: 48 h TGFBeta1


title: AA-2

value: AA treatment for 12 hours


title: Fetal alcohol exposed, 5 months replicate 3


title: 947 C-0 R2

value: 0 h solvent


title: IGF1-rep1


title: CPSF3_depleted_ctrl_TTchem-seq_rep3

value: ctrl, 120min dTAG7, 15 min 4-thiouridine pulse

tag: cell line


title: 947 T-24 R2

value: 24 h TGFBeta1


title: CPSF3_wt_HS_TTchem-seq_rep3

value: 120min Heat Shock, 15 min 4-thiouridine pulse


title: 947 T-6 R2

value: 6 h TGFBeta1


title: AA-rep3


title: Fetal alcohol exposed, 5 months replicate 2

tag: age

value: Sacrificed at 5 months

value: Pre Natal Alcohol Exposure


title: AA-rep2


title: Fetal alcohol exposed, 2 years replicate 6

value: Sacrificed at 2 years


title: CPSF3_wt_ctrl_TTchem-seq_rep3

value: ctrl, 15 min 4-thiouridine pulse

value: Nascent RNA


title: CPSF3_depleted_HS_TTchem-seq_rep2

value: 120min dTAG7 and Heat Shock, 15 min 4-thiouridine pulse


title: Fetal alcohol exposed, 2 years replicate 4


title: Fetal alcohol exposed, 2 years replicate 3


title: Fetal alcohol exposed, 2 years replicate 2


title: 947 C-0 R1

value: small intestinal TKA organoids


title: AA-rep1

value: Fast-twitch muscle


title: CPSF3_depleted_ctrl_TTchem-seq_rep2


title: 947 T-72 R1

value: Apcdelta/delta, KrasG12D, Trp53R172H, tgVillin-CreERT2

value: 72 h TGFBeta1


title: Fetal alcohol exposed, 2 years replicate 1


title: CTR-rep3

value: Nutrient restriction for 36 hours


title: 947 T-48 R1

value: 48 h TGFBeta1


title: CPSF3_wt_HS_TTchem-seq_rep2


title: CTR-rep2


title: 947 T-24 R1


title: CPSF3_wt_ctrl_TTchem-seq_rep2


title: CPSF3_depleted_HS_TTchem-seq_rep1


title: CTR-rep1


title: CPSF3_depleted_ctrl_TTchem-seq_rep1


title: 947 T-6 R1


title: 947 C-72 R1

value: 72 h solvent


title: Control 5 months, replicate 5

source_name: Chlorocebus aethiops hippocampus sacrificed at 5 months post sucrose exposure

value: Pre Natal sucrose exposure


title: Control 5 months, replicate 6


title: Control 5 months, replicate 4


title: 931 C-0 R2

value: 0 h solvent


title: CPSF3_wt_HS_TTchem-seq_rep1

value: 120min Heat Shock, 15 min 4-thiouridine pulse


title: Control 5 months, replicate 3


title: Control 5 months, replicate 2


title: 931 T-72 R2


title: CPSF3_wt_ctrl_TTchem-seq_rep1


title: Control 5 months, replicate 1


title: 931 T-48 R2