title: W2

data_processing:
RNA-Seq FASTQ files were generated using the Illumina CASAVA software
Sequencing results were first checked for quality control metrics using QuaCRS
reads were first aligned to the human reference genome GRCh37.p13 using STAR version 2.4.0
Cufflinks v2.2.1 was used to assemble transcripts from the STAR alignments
Cuffquant was used to quantify isoform counts using a GTF file generated by Cuffcompare
Cuffdiff utility was used to call differentially expressed genes, which were then compared and sorted using custom scripts written in Python
Additional processing of data was performed by using dChip software (Harvard University, Cambridge, MA)
Genome_build: GRCh37.p13

extract_protocol:
200 ng of total RNA was incubated with ribosomal RNA (rRNA) removal capture oligos followed by binding to magnetic beads for rRNA and mitochondrial RNA (mtRNA) subtraction. The ribo-depleted RNA was used to generate cDNA libraries
Total transcriptome libraries were generated using the Illumina TruSeq Stranded Total RNA Sample Prep Kit with Ribo-Zero Gold according to the manufacturer's instructions (Epicentre Biotechnologies). All samples were indexed with Illumina adapters followed by PCR amplification. Paired-end 50bp sequencing was performed with the Illumina HiSeq 2500 sequencer to ~40 million clusters per sample

treatment_protocol: RNA isolated from the UW human skin and chronic WE biopsies.

value: skin


title: Muscle biopsy_ID22_Baseline

status: Public on May 04 2022

type: SRA

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

library_source: transcriptomic

data_processing:
trimmed with trim_galore version 0.6.4. Parameters: --length 26 --phred33
Get raw counts with kallisto quant version 0.4.6.
TPM abundance estimates, generated with kallisto quant 0.4.6
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: TPM abundance estimates and raw counts generated with kallisto.

molecule: total RNA

organism: Homo sapiens

source_name: vastus lateralis muscle

extract_protocol:
Muscle biopsies were obtained from the VL of the right leg using a 5-mm Bergström needle with manual suction following local anesthesia (2% Xylocitin). The location of all incision sites was randomized, and all incisions were 2-3 cm apart at the mid-portion of the VL muscle. After collection of the muscle tissue, the material was cleaned if there was excess blood using blotting paper and frozen in liquid nitrogen. Subsequently, all samples were stored at -80°C for later analysis
RNA libraries were prepared for sequencing using standard BGISeq-500 protocols

tag: treatment

value: verum

tag: time


title: Muscle biopsy_ID20_24h

value: placebo


title: Muscle biopsy_ID22_1h


title: Muscle biopsy_ID21_4h


title: W1

city: Pittsburgh

first: Chandan

middle: K

last: Sen

state: Pennsylvania

address: 450 Technology Drive

department: Surgery

country: USA

institute: University of Pittsburgh

source_name: human chronic wound edge tissue

growth_protocol: Human tissue samples

tag: tissue


title: Sc_Skin1

data_processing:
BAM files were generated directly from raw Illumina BCL files using 10X Genomics Cellranger with default paramaters (cellranger)
Gene-barcode matrices were determined using 10X Genomics Cellranger  with default parameters (cellranger run)
Quality control, clustering and differential gene expression analysis were performed using Seurat v.3.1.0
Genome_build: hg:38
Supplementary_files_format_and_content: barcode files
Supplementary_files_format_and_content: gene names file
Supplementary_files_format_and_content: count matrix file

source_name: human unwounded skin tissue

extract_protocol:
The tissue was chopped into small pieces and subjected to enzymatic dissociation using whole skin dissociation kit (cat. no. 130-101-540) in MACS C Tubes (cat. no. 130-093-237) (Miltenyi Biotec Inc., San Diego, CA). The samples were incubated in a water bath at 37°C for approximately 3 hours. After incubation, the samples were diluted by adding 0.5 mL of cold cell culture medium in order to stop the enzymatic reaction. The C Tubes were then tightly closed and attached upside down onto the sleeve of the gentleMACS™ Octo dissociator and UW human skin dissociation program was performed. The cell suspension was subjected to a pre-Separation Filter, 70 µm, placed on a 15 mL tube in order to remove the debris. RBC were lysed using 10X RBC lysis buffer (cat. no. 420301, BioLegend, San Diego, CA).
The resulting cell suspension was utilized for single cell RNA sequencing using the 10x Genomics platform using Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1(10x Genomics, Inc.) and sequenced on an Illumina NovaSeq 6000 (Illumina, Inc).

treatment_protocol: Single-cell suspensions were generated from the UW human skin and chronic WE biopsies.

tag: gender

value: Male

tag: age (years)


title: Muscle biopsy_ID21_1h


title: Muscle biopsy_ID01_4h


title: Muscle biopsy_ID01_Baseline


title: Muscle biopsy_ID01_1h


title: D28M23Fe8

city: Baton Rouge

first: J. Michael

last: Salbaum

state: LA

address: 6400 Perkins Road

department: Regulation of Gene Expression

institute: Pennington Biomedical Research Center

data_processing:
base calling - Illumina
alignment - STAR
UMI - collapse_UMI_bam
gene counts - HTSEQ
Genome_build: Mouse mm10

organism: Mus musculus

source_name: NOD mouse strain

growth_protocol: Animals were housed in a 12 h dark/light cycle and fed a Chow diet (LabDiet 5001). The morning with presence of a vaginal plug being counted as 0.5 days.

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Quant Seq 3'mRNA-Seq Library Kit (FWD) for Illumina from Lexogen, UMI, 75bp cartridge v2.5, total of 4 runs on Nextseq, loaded 1.8pM per run

treatment_protocol: Embryos and their corresponding yolk sac tissue was dissected at 8.5 days of gestation and stored in Trizol at minus 80 deg Celsius.

tag: strain

value: NOD

tag: sex of the embryo

value: male

tag: somite number of the embryo

tag: glucose conc at euthanasia; mg/dl

value: embryo at E8.5, diabetic


title: Sc_Skin2

value: Female


title: W4


title: Muscle biopsy_ID21_24h


title: NS4


title: D28M23Ge8


title: D28M23De8

value: female


title: Muscle biopsy_ID20_Baseline


title: D28M23Dy8

value: yolk sac at E8.5, diabetic


title: NS2


title: Muscle biopsy_ID20_1h


title: D28M23By8


title: Muscle biopsy_ID19_4h


title: Muscle biopsy_ID01_24h


title: NS1


title: methyl_W2

library_source: genomic

data_processing:
DNA methylation values from MethylCap-seq data using PrEMeR-CG analysis
Differential methylation region (DMR) analysis was performed using mean vector test
Genome_build: hg:19

molecule: genomic DNA

extract_protocol:
1 µg DNA isolated from CW tissue or UW human skin was sonicated to generate 100-300 bp size fragments. This was followed by methylated DNA fragment enrichment using Diagenode AutoMethylCap kit following manufacturer’s protocol.
Illumina-compatible sequencing libraries were generated using the Kapa Hyper Prep kit. Single-end 50 bp sequencing was done using Illumina HiSeq 2500 to ~40 million clusters per sample
MethylCap-seq

treatment_protocol: DNA isolated from the UW human skin and chronic WE biopsies.


title: Muscle biopsy_ID20_4h


title: D28M23Be8


title: D28M02Ie8


title: Muscle biopsy_ID19_24h


title: Muscle biopsy_ID19_Baseline


title: methyl_W3


title: D28M02Iy8


title: Muscle biopsy_ID18_Baseline


title: methyl_W1


title: Muscle biopsy_ID18_4h


title: D28M02Gy8


title: Muscle biopsy_ID17_Baseline


title: Muscle biopsy_ID19_1h


title: D24M22Cy8


title: Muscle biopsy_ID18_24h


title: Muscle biopsy_ID16_24h


title: Muscle biopsy_ID17_4h


title: Muscle biopsy_ID18_1h


title: Muscle biopsy_ID17_1h


title: Muscle biopsy_ID15_24h


title: D28M02Ge8


title: methyl_NS2


title: D24M22Ce8


title: Muscle biopsy_ID16_1h


title: methyl_NS1


title: Muscle biopsy_ID16_4h


title: D24M15Jy8


title: Muscle biopsy_ID16_Baseline


title: CAGE HEP in vitro induced hepatocytes day28 rep1

city: Yokohama

first: Takahiro

last: Suzuki

state: Kanagawa

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

department: Center for Integrative Medical Sciences

country: Japan

institute: RIKEN

data_processing:
rDNA and low quality read filtering: MOIRAI pipeline (Hasegawa et al. 2014)
genome alignment: TopHat version 2.1.1
Count CAGE defined transcriptional start sites (CTSS): overlapping with FANTOM5 robust promoter set
Normalization: Tag Per Million
Genome_build: hg19
Supplementary_files_format_and_content: CTSS
Supplementary_files_format_and_content: TPM expression table text file

source_name: iPS cells (201B7)

growth_protocol: iPS cells (201B7) were mainteined in in Cellartis® DEF-CS™ Culture System (Takara Bio Inc., Shiga, Japan)

extract_protocol:
Total RNA was extracte using NucleoSpin® RNA ((Macherey-Nagel)
3 μg of total RNA from each sample were subjected to reverse transcription with random primers. The 5-end cap structure was biotinylated and captured with streptavidin-coated magnetic beads (Thermo Fisher). After ligation of 5′ and 3′ adaptors, second-strand cDNA was synthesized, followed by exonuclease I (New England BioLabs) digestion. The purified CAGE libraries were sequenced using single-end reads of 50 bp on the Illumina HiSeq 2500 (Illumina, USA).

treatment_protocol: in vitro hepatocyte differentiation was performed using  Cellartis® Hepatocyte Differentiation Kit (Takara Bio Inc.)

tag: differentiation day

value: day 28


title: Muscle biopsy_ID15_4h


title: CAGE HEP in vitro induced hepatocytes day28 rep2


title: CAGE HEP in vitro induced hepatocytes day28 rep3


title: Muscle biopsy_ID14_1h


title: CAGE HEP in vitro induced hepatocytes day21 rep2

value: day 21


title: differentiating CGNPs_007

city: Houston

first: Shinji

last: Maegawa

state: Texas

address: 7777 Knight Road

institute: University of Texas, MD Anderson Cancer Center

description:
WT_007_D
Batch_2

data_processing:
Quality control was performed using fastqc (v0.11.8).
Adaptors were trimmed using trimgalore (v0.6.4).
Fastq files were aligned to GRCm39 using star (v2.7.3a).
Raw counts were generated using featureCounts from subread (v1.6.3).
Genome_build: GRCm39
Supplementary_files_format_and_content: *_featureCounts_exon_level.txt: Tab-delimited count matrices.

source_name: mouse cerebellar granular progenitor cells (CGNPs)

growth_protocol: Cerebellar tissue from P8 pups were dissected and triturated to form single cell suspension. CGNPs were expanded for 10 days accompanied by trituration every 4 days, in Neurobasal medium supplemented with B27, Glutamax, Antibiotic/Antimycotic, Heparin and 20ug/ml of Epidermal growth factor (EGF), Fibroblast growth factor (FGF), and then for 4 days in the presence of 0.1ug/ml recombinant mouse sonic hedgehog (rmShh) (proliferation conditions). Differentiation of CGNPs was achieved by culturing them in the absence of EGF and FGF and with the addition of 20ug/ml of neural growth factor (NGF) after their initial cultivation in the presence of Shh ligand as above. Differentiated cells were collected with TrypLE.

extract_protocol:
The cells were flash frozen on liquid nitrogen, and RNA was harvested using Zymo pure Quick RNA mini prep Kit ( Catalog No. R1055). RNA quality/quantity of each sample was checked using RNA Nano assay using Bioanalyzer 2100 (Agilent Technologies - RNA RIN should be >8) and the RNA sample quantity was measured using Qubit 2.0 Fluorometer (Thermo Fisher Scientific). Using 1000 ng of RNA from each sample to start library prep using TruSeq Stranded Total RNA Gold (Illumina RS-122-2303).
Sequencing library preparations were performed by TruSeq Stranded Total RNA Sample Reference Guide (Illumina). RNA-seq library quality/quantity checking was done using Tape Station 2200 D1000 assay (Agilent Technologies) and QuantStudio 6 Flex Real time PCR System (Applied Biosystem). RNA-seq libraries were sequenced in Hiseq 3000 (Illumina) and the sequence type used was Paired End with 75 cycles.

tag: cell type

tag: condition

value: differentiating


title: Muscle biopsy_ID15_1h


title: CAGE HEP in vitro induced hepatocytes day21 rep1


title: Muscle biopsy_ID14_Baseline


title: Muscle biopsy_ID15_Baseline


title: Muscle biopsy_ID14_24h


title: D24M15Je8


title: Muscle biopsy_ID14_4h


title: Muscle biopsy_ID13_24h


title: D24M15Iy8


title: CAGE HEP in vitro induced hepatocytes day21 rep3


title: D24M15Hy8


title: differentiating CGNPs_006

description:
WT_006_D
Batch_2

value: cerebellar granular progenitor cells (CGNPs)


title: differentiating CGNPs_004

description:
WT_004_D
Batch_2


title: Muscle biopsy_ID13_4h


title: D24M15He8


title: differentiating CGNPs_005

description:
WT_005_D
Batch_2


title: CAGE HEP in vitro induced hepatocytes day14 rep3

value: day 14


title: differentiating CGNPs_008

description:
WT_008_D
Batch_1


title: D24M15Gy8d

description: duplicate, batch control


title: D24M15Gy8


title: CAGE HEP in vitro induced hepatocytes day7 rep2

value: day 7


title: D24M15Ge8d

description: duplicate, batch control


title: differentiating CGNPs_009

description:
WT_009_D
Batch_1


title: Muscle biopsy_ID12_24h


title: CAGE HEP in vitro induced hepatocytes day14 rep1


title: CAGE HEP in vitro induced hepatocytes day14 rep2


title: D24M15Fy8


title: CAGE HEP in vitro induced hepatocytes day7 rep3


title: Muscle biopsy_ID12_4h


title: CAGE HEP in vitro induced hepatocytes day7 rep1


title: proliferating CGNPs_007

description:
WT_007_P
Batch_2

value: proliferating


title: D24M15Fe8


title: Muscle biopsy_ID12_1h


title: CAGE HEP in vitro induced hepatocytes day0 rep3

value: day 0


title: Muscle biopsy_ID13_1h

value: verum


title: D24M15Ey8


title: D24M15Ie8


title: Muscle biopsy_ID13_Baseline


title: differentiating CGNPs_002

description:
WT_002_D
Batch_1


title: D24M15Ge8


title: CAGE HEP in vitro induced hepatocytes day0 rep2


title: Muscle biopsy_ID11_24h


title: CAGE HEP in vitro induced hepatocytes day0 rep1


title: proliferating CGNPs_004

description:
WT_004_P
Batch_2


title: Muscle biopsy_ID12_Baseline

value: placebo


title: D24M15Ee8


title: D24M15Dy8


title: proliferating CGNPs_009

description:
WT_009_P
Batch_1


title: Muscle biopsy_ID11_4h


title: D24M15De8


title: proliferating CGNPs_006

description:
WT_006_P
Batch_2


title: CAGE DE in vitro induced definitive endoderm 72h rep2

data_processing:
rDNA and low quality read filtering: MOIRAI pipeline (Hasegawa et al. 2014)
genome alignment: STAR(Ver 2.5.3a_modified)
Count CAGE defined transcriptional start sites (CTSS): overlapping with FANTOM5 robust promoter set
Normalization: Tag Per Million
Genome_build: hg19
Supplementary_files_format_and_content: CTSS
Supplementary_files_format_and_content: TPM expression table text file

treatment_protocol: in vitro definitive endoderm differentiation was performed using  Cellartis® Definitive Endoderm Differentiation Kit (Takara Bio Inc.)

tag: differentiation hour


title: CAGE DE in vitro induced definitive endoderm 72h rep3


title: D24M15Cy8


title: Muscle biopsy_ID11_1h


title: proliferating CGNPs_002

description:
WT_002_P
Batch_1


title: D24M15Ce8


title: proliferating CGNPs_005

description:
WT_005_P
Batch_2


title: CAGE DE in vitro induced definitive endoderm 72h rep1


title: Muscle biopsy_ID11_Baseline


title: CAGE DE in vitro induced definitive endoderm 66h rep3


title: CAGE DE in vitro induced definitive endoderm 66h rep2


title: Muscle biopsy_ID10_4h


title: proliferating CGNPs_008

description:
WT_008_P
Batch_1


title: Muscle biopsy_ID10_24h


title: D24M15Ay8


title: D24M15Ae8


title: D23M26Ay8


title: Epe1GFP_rep2

city: Edinburgh

first: Robin

last: Allshire

state: Scotland

address: Max Born Crescent

department: Institute of Cell Biology

country: United Kingdom

institute: University of Edinburgh

data_processing:
read QC and adapter trimming were done with FastQC, Cutadapt and Samtools
ChIPseq reads were alligned to the Spombe reference genome with bowtie2
RNAseq reads were mapped with Salmon
reads per genomic 1kb bin were counted wit Htseq-count for CHIPseq and reads per gene were counted with Salmon for RNAseq
BedGraphs were generated with deeptools
Genome_build: Schizosaccharomyces pombe GCF_000002945.1
Supplementary_files_format_and_content: BedGraph format, representing read coverage [ChIPseq]
Supplementary_files_format_and_content: tab-delimited text files include read counts for each genomic 1kb bin from Htseq-count [ChIPseq]
Supplementary_files_format_and_content: tab-delimited text files include read counts for each gene from Salmon [RNAseq]

organism: Schizosaccharomyces pombe

source_name: total RNA

extract_protocol:
Samples were prepared as previously described in Torres-Garcia, S. et al. Epigenetic gene silencing by heterochromatin primes fungal resistance. Nature 585, 453–458 (2020).
Libraries were prepared according to Illumina's instructions.

tag: extract

value: cell extract

tag: genotype


title: Epe1DNP150GFP_rep1


title: CAGE DE in vitro induced definitive endoderm 66h rep1


title: epe1D_rep1


title: Muscle biopsy_ID10_1h


title: Epe1DNP150GFP_rep4, input

source_name: chromatin IP


title: CAGE DE in vitro induced definitive endoderm 60h rep3


title: D23M26Ae8

value: NOD


title: Muscle biopsy_ID10_Baseline


title: D23M11Ay8

value: male


title: Epe1DNP150GFP_rep2


title: CAGE DE in vitro induced definitive endoderm 60h rep2


title: epe1D_rep2


title: CAGE DE in vitro induced definitive endoderm 60h rep1


title: RNAseq_mature_larvae_rep2

city: London

first: Yan

last: Liang

state: London

address: mile end road

department: SBBS

institute: Queen Mary Univerisity of London

data_processing:
RNA-seq: Sequencing adaptors were removed from raw reads by using trimomatic (version 0.39)
RNA-seq:the reads were mapped to the transcriptome by using Kallisto (0.46.2)
RNA-seq: the gene expression profile was normalized from 13 developmental stages by DESeq2 package (1.30.1) in R (version 3.6).
ATAC-seq: The adaptors of raw reads of each library were removed by using cutadaptor (version 2.5).
ATAC-seq: the reads were mapped to the genome by using NextGenMap (version 0.5.5) as paired-end reads (--paired). Duplications were removed by samtools (view -b -F 0x400 -f 0x2) (version 1.9). The mapped reads (bamfiles) were shifted by using deeptools (alignmentSieve ---ATACshift) (version 3.4.3).
ATAC-seq: MACS2 (version 2.2.7.1) were applied to each shifted bam file to call peaks (-f BAMPE; --min-length 100; --max-gap 75; -q 0.01).
Genome_build: PRJEB38497
Supplementary_files_format_and_content: RNA-seq:Owenia_annotation_v250920_filtered_mRNA.fasta is the filtered gene model we used for Kallisto mapping; ofu_RNAseq_gene_expression.txt is the output results from DESeq2 normalization; ATAC-seq: all the narrowPeak files are the output from MACS2 analysis.

organism: Owenia fusiformis

source_name: Mature larvae stage

growth_protocol: The Owenia fusiformis embryos, larvae and juvenile were reared in artificial sea water, and the larvae were fed with mix algae.

extract_protocol:
RNA-seq: All the fresh samples were snapped freezed by liquid nitrogen, then extracted using the Monarch total RNA Miniprep Kit; ATAC-seq:50,000 cells (~900 blastula, ~500 gastrula, ~300 elongation, ~150 mature larvae and ~40 competent larvae) were washed in 1 ml cold PBS and resuspended in 100  µl cold ATAC lysis buffer 1 (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% (v/v) IGEPAL, 0.1% (v/v) Tween-20, 0.01% (v/v) Digitonin) and used the pestle to homogenize the samples, then and incubated on ice for 3 minutes to lyse cells. The lysis reaction was stopped by adding 1 ml of cold ATAC wash buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% (v/v) Tween-20) and inverting the tube for 3 times to mix. The nuclei were pelleted by centrifugation at 500xg for 10 minutes at 4℃ in a fixed angle centrifuge.
RNA-seq: All the libraries were constructed by Oxford genomic center; ATAC-seq:  The supernatant was removed and the nuclei pellet was resuspended in transposition mix containing 5 µl of 10x TMg buffer (100 mM Tris-HCl pH 8.5, 50 mM MgCl2), 5 µl Dimethyl Formamide, 2.5 µl of 100 nM in-house made Tn5 enzyme, 16.5 µl PBS, 0.5 µl of 1% (v/v) digitonin, 0.5 µl of 10% (v/v) Tween-20, and 20 µl H2O. The transposition reaction was incubated at 37°C for 30 minutes in a thermomixer with 1000 rpm mixing. Transposed DNA was cleaned up using the NEB DNA Cleanup kit following manufacturer’s instructions. All 10 µl eluted DNA was subjected to 5 cycles of PCR amplification, and 5 µl of this pre-amplified library was used for qPCR to determine the PCR cycles, finally all the libraries were amplified in 7~12 cycles using the NEBNext High-Fidelity 2X PCR Master Mix.
RNA-seq and ATAC-seq

treatment_protocol: By adding few mud to stimulate the metaphomorphsis of competent larvae to  juvenile.

tag: developmental stage

value: Mature larvae stage

tag: developmental time points

value: 27 hpf

tag: morphology

value: larvae


title: D23M11Ae8

value: embryo at E8.5, diabetic


title: Epe1DNP150GFP_rep3, input


title: CAGE DE in vitro induced definitive endoderm 54h rep2


title: CAGE DE in vitro induced definitive endoderm 54h rep3


title: RNAseq_mature_larvae_rep1


title: Epe1DNP150GFP_rep2, input


title: LOW_INPUT_INIT10

city: wuhan

first: han

middle: shao

last: qing

address: whu

country: China

institute: school

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

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

extract_protocol:
Total RNA was isolated from cell lines, peripheral blood or Murine heart tissue with TRIzol (Invitrogen) according to the manufacture’s protocol. The mRNA was isolated by subjecting total RNA to oligo(dT) enrichment using Dynabeads Oligo(dT)25 (NEB)
Fragmented mRNAs from different samples were first treated with T4 PNK. Then the samples were ligated with pre-adenylated 3'-linkerLs (5'-NNNNNNNNNNNNAGATCGGAAGAGCGTCGTG-3', Bold N represnts for designed 6-nt barcode sequences, Italic N represents for 6-nt random sequences). Extra 3'-linkerLs were removed by 5′-deadenylase and RecJf digestion. The reaction mixtures were subsequently pooled together and purified. 1/50 of the purified sample was retained as input control while the remaining sample was applied to m6A antibody immunoprecipitation (IP). The input control sample and the IP sample were reverse transcripted using RT primer (5'-ACACGACGCTCTTCCGATCT-3') to obtain cDNA samples. The cDNA samples were then ligated with 5'-adaptor (5'-Phos-NNNNNNNNNNAGATCGGAAGAGCACACGTCTG-SpC3-3'),followed by determination of PCR cycle number by RT-qPCR. Finally, library PCR amplification was performed using the NEB primers and the products were purified by magnetic beads or agarose gel electrophoresis.

tag: cell line


title: RNAseq_early_larvae_rep2

source_name: Early larvae stage

value: Early larvae stage

value: 18 hpf


title: LOW_INPUT_INIT5_IP


title: RNAseq_early_larvae_rep1


title: LOW_INPUT_INIT5


title: CAGE DE in vitro induced definitive endoderm 48h rep3


title: Epe1DNP150GFP_rep1, input


title: RNAseq_elongation_rep1

source_name: Elongation stage

value: Elongation stage

value: 13 hpf

value: embryo


title: RNAseq_elongation_rep2


title: CAGE DE in vitro induced definitive endoderm 48h rep2


title: CAGE DE in vitro induced definitive endoderm 48h rep1


title: H3K9me_Epe1DNP150GFP_rep3

tag: antibody


title: LOW_INPUT_INIT10_IP


title: TGF-alpha_2

city: Xi'an

first: Yale

last: Liu

state: China (+86)

address: No.157, Xiwu Road, Xincheng District

department: Dermatology

institute: Xi'an Jiaotong University

data_processing:
Illumina Casava1.7 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Trimmed sequence reads were mapped to hg38 whole genome using hisat2 v 2.2.1.0 with parameters --rna-strandness rf --fr.
Assembly: hg38
Supplementary files format and content: tab-delimited xlsx file include FPKM values for each Sample

source_name: PHKs

growth_protocol: Primary human keratinocytes in RPMI1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
RNA was harvested using Trizol reagent. 1.0ug of total RNA was used for the construction of sequencing libraries.
Illumina TruSeq Stranded mRNA LT Sample Prep Kit (RS-122-2101) following manufacturer's protocols.

treatment_protocol: Some cells were stimulated with 100ng/mL TWEAK (R&D systems) for 48h, while some with 100ng/mL TGF-α (Peprotech) for 15min

value: PHKs

value: primary human keratinocytes

value: WT

tag: treatment

value: 100ng/mL TGF-alpha, 15min

tag: time

value: Day 0


title: TGF-alpha_3


title: TGF-alpha_1


title: H3K9me_Epe1DNP150GFP_rep1

value: cell extract


title: Epe1GFP_rep1


title: CAGE DE in vitro induced definitive endoderm 0h rep2

value: 0 h


title: CAGE DE in vitro induced definitive endoderm 0h rep3


title: RNAseq_gastrula_rep2

source_name: Gastrula stage

value: Gastrula stage

value: 9 hpf


title: RNAseq_gastrula_rep1


title: CAGE DE in vitro induced definitive endoderm 54h rep1


title: CAGE DE in vitro induced definitive endoderm 0h rep1


title: RNAseq_blastula_rep2

source_name: Blastula stage

value: Blastula stage

value: 5 hpf


title: Epe1GFP_rep4, input


title: TWEAK_3

value: 100ng/mL TWEAK, 48h

value: Day 2


title: H3K9me_Epe1DNP150GFP_rep4


title: Epe1GFP_rep3, input


title: in vitro induced definitive endoderm 72h rep2

data_processing:
genome alignment: bowtie2 version 2.1.0
Genome_build: hg19
Supplementary_files_format_and_content: Two replicate bam files were combined using samtools.
Supplementary_files_format_and_content: bigwig files were generated using bam2wig with wigtobigwig, following to removals of the mitochondrial genome and duplicated reads using removeChrom.py (Harvard ATAC-seq module) and samtools.

extract_protocol:
5 × 104 cells were stored at -80 °C in STEM CELLBANKER® (Takara Bio Inc.) until use. The cells were washed with PBS and nuclei were extracted.
OmniATAC-seq was performed as described previously in Corces et al., 2017


title: TWEAK_1


title: RNAseq_blastula_rep1


title: Epe1GFP_rep2, input


title: TWEAK_2


title: H3K9me_Epe1DNP150GFP_rep2


title: RNAseq_4h_rep2

source_name: 4h stage

value: 4h stage

value: 4 hpf


title: Epe1GFP_rep1, input


title: in vitro induced definitive endoderm 72h rep1


title: Ctrl_3

value: PBS


title: RNAseq_4h_rep1

value: embryo


title: Ctrl_2

value: PHKs


title: Ctrl_1

value: primary human keratinocytes


title: H3K9me_Epe1GFP_rep4


title: in vitro induced definitive endoderm 66h rep1


title: in vitro induced definitive endoderm 60h rep2


title: RNAseq_3h_rep1

source_name: 3h stage

value: 3h stage

value: 3 hpf


title: H3K9me_Epe1GFP_rep2


title: RNAseq_8cell_rep2

source_name: 8 cell

value: 8 cell


title: in vitro induced definitive endoderm 60h rep1


title: s201110N11

city: CHANG SHA

first: YONG

last: ZHONG

address: XIANGYA ROAD

institute: XIANGYA HOSPITAL

data_processing:
Basecalls performed using bcl2fastq V2.19.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Star 2.5.3a software was used for comparative analysis between sequencing data of single cell RNA and reference genome of Ensembl database
Quantify gene expression using read2 by featureCounts1.6.2 software
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: polyA RNA

source_name: kidney

extract_protocol:
A moderate amount of renal tissue was taken from the selected patients during renal puncture, and GEXSCOPE ® Single Cell RNA Library Kit Tissue was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: disease state

value: Acute kidney injury

tag: age

tag: proteinuria

value: normal urine


title: H3K9me_Epe1GFP_rep1

value: cell extract


title: in vitro induced definitive endoderm 54h rep2

value: 5h h


title: s200824n8

value: hypertensive nephropathy

value: proteinuria not conform to nephrotic syndrome


title: in vitro induced definitive endoderm 54h rep1


title: epe1D_rep3, input


title: epe1D_rep4, input


title: H3K9me_Epe1GFP_rep3


title: s201029N10


title: s200727N7

value: Normal tissue


title: RNAseq_4cell_rep1

source_name: 4 cell

value: 4 cell


title: in vitro induced definitive endoderm 66h rep2


title: epe1D_rep2, input


title: RNAseq_4cell_rep2


title: RNAseq_3h_rep2


title: epe1D_rep1, input


title: s200714N6


title: RNAseq_2cell_rep1

source_name: 2 cell

value: 2 cell


title: in vitro induced definitive endoderm 48h rep1


title: Human oocyte >40 -MII-Rep2

city: Hangzhou

first: Yunwen

last: Wu

state: Zhejiang

address: Yu Hang Tang Road

department: Life Sciences Institute

institute: Zhejiang University

description:
Aging-Human-FPKM.txt
D2-2

data_processing:
RNA-Seq was performed with biological replicates for all samples. Raw reads were trimmed to 50 bp and mapped to the human genome (hg19), mouse genome (mm9) and ERCC spike-in sequences with Tophat v2.1.1 respectively. Only uniquely mapped reads were subsequently assembled into transcripts guided by the reference annotation (UCSC gene models) with Cufflinks v2.2.1. Expression level of each gene was quantified with normalized FPKM (fragments per kilobase of exon per million mapped fragments) and was further normalized with the ERCC spike-in.
Genome_build: hg19, mm9
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values of all RNA-seq samples

source_name: Human MII

extract_protocol:
Oocytes were collected from indicated species (1 oocyte per sample for human and 10 oocytes per sample for mouse). Each sample was directly lysed with 4.2 ul lysis buffer (0.2% Triton X-100, RNase inhibitor, dNTPs, oligo-dT primers, and 1:1000 ERCC spike-in) and immediately used for cDNA synthesis using the Smart-seq2 method as described previously (Picelli et al, 2014).
Sequencing libraries were constructed from 500 pg of amplified cDNA using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD503) according to manufacturer’s instructions. Barcoded libraries were pooled and sequenced on the Illumina HiSeq X Ten platform with 150 bp paired-end reads

tag: tissue

value: oocyte


title: in vitro induced definitive endoderm 0h rep2

source_name: iPS cells (201B7)

value: 0 h


title: Human oocyte >40 -MII-Rep3

description:
Aging-Human-FPKM.txt
D2-3


title: RNAseq_8cell_rep1

value: embryo


title: RNAseq_1cell_rep2

source_name: 1 cell

value: 1 cell


title: H3K9me_epe1D_rep3


title: Human oocyte >40 -MII-Rep1

description:
Aging-Human-FPKM.txt
D2-1


title: in vitro induced definitive endoderm 0h rep1


title: in vitro induced definitive endoderm 48h rep2


title: Human oocyte >40 -GV-Rep3

description:
Aging-Human-FPKM.txt
D1-3

source_name: Human GV


title: RNAseq_2cell_rep2


title: H3K9me_epe1D_rep2

source_name: chromatin IP


title: H3K9me_epe1D_rep1


title: Human oocyte >40 -GV-Rep2

description:
Aging-Human-FPKM.txt
D1-2


title: RNAseq_oocyte_rep1

source_name: oocyte


title: pTUFA_ccpA_rep2

first: Sander

last: Granneman

address: Mayfield Road, Kings Buildings, Waddington building, room 3.06

department: Centre for Synthetic and Systems Biology

description: Total RNA of ccpA null mutant complemented with ccpA gene expressed from the pCN33 vector, second biological replicate.

data_processing:
Three experimental replicate datasets from the USA300 parental strain and USA300 DccpA processed using Flexbar to remove poor quality nucleotides (Phred score <23) and adapter sequences. The reads are then mapped to the USA300 genome using Novoalign (version 2.07). Reads that mapped to multiple features in the genome were randomly distributed over the features. To determine to which genes the reads mapped to, we generated a modified USA300 annotation file in the Gene Transfer Format (GTF). This file contains the start and end positions of each gene on the chromosome as well as what genomic features (i.e., sRNA, protein- coding, tRNA) it belongs to. To generate this file, we used the Rockhopper software on all our USA300 rRNA-depleted total RNA-seq data and a minimal GTF file obtained from ENSEMBL (without UTR information). The resulting GTF file contained information not only on the coding sequences, but also more complete 5’ and 3’ UTR coordinates. We then used pyReadCounters from the pyCRAC package (version 1.5.1) to count the total number of reads that map to each gene and genomic features. These tables with raw counts were subsequently used to perform a differential expression analyses using DESeq2.
The pyGTF2bedGraph script was used to convert the data to bedgraph files. The data in the bedgraph files has been normalised to 'read per million' (rpm).
Genome_build: USA300_FPR3757
Supplementary_files_format_and_content: text, bedgraph, fasta and GTF files

organism: Staphylococcus aureus

source_name: cells

growth_protocol: S. aureus cells were grown to saturation in TSB at 37 °C. Cells were then diluted in 20 ml fresh TSB supplemented with erytrhomicin to OD600 0.05 and then grown to an OD600 = 3. Subsequently, cells were harvested by centrifugation, and the cell pellets were snap frozen and stored at -80C.

extract_protocol:
Extraction of RNA from S. aureus was performed as previously described4. Briefly, cells were cultured to the desired optical density and rapidly harvested by centrifugation at 8,600 g for 5 min, 4°C. Cell pellets were incubated with 100 µl of guanidium thiocyanate (GTC)-Phenol mix (pH 5.4; 1:1 ratio) and lysed by vortexing the cells for 5 minutes with 100 µl of Zirconia beads (0.1 mm; Biospec products 11079101z). Subsequently, 550 µl of GTC was added and the mixture was vortexed for several minutes. After a 10-minute incubation at 65ºC for 10 minutes, the mixture was cooled on ice for 10 minutes. Phases were separated by adding 300 µl chloroform isoamylalcohol (24:1) and by adding 1/10th of a volume of 3 M NaAc (pH 5.2) followed by vigorous vortexing. After 5 minutes of centrifugation in an Eppendorf centrifuge (12,400 g), the RNA was purified from the upper phase via two additional rounds of phenol-chloroform extraction and precipitated with 3 volumes of 96% cold ethanol. Pellets were washed with 1ml of 70% cold ethanol, air dried and resuspended in DEPC-treated water.
RNA from three experimental replicates was extracted as described above and sequenced on an Illumina Novoseq6000 machine using the TruSeq library preparation protocol (Novogene).

tag: strain

value: USA300 LAC deltaccpA + pCN33:PtufA-ccpA-HTF

value: Grown to OD600 ~3.0 in TSB,  harversed by centrifugation and stored at -80ºC


title: pTUFA_ccpA_rep3

description: Total RNA of ccpA null mutant complemented with ccpA gene expressed from the pCN33 vector, third biological replicate.


title: Human oocyte >40 -GV-Rep1

description:
Aging-Human-FPKM.txt
D1-1


title: Human oocyte 36-39 -MII-Rep3

description:
Aging-Human-FPKM.txt
C2-3


title: pTUFA_ccpA_rep1

description: Total RNA of ccpA null mutant complemented with ccpA gene expressed from the pCN33 vector, first biological replicate.


title: ccpA_mut_rep3

description: Total RNA of ccpA null mutant, third biological replicate. Cells contained the empty pCN33 vector.

value: USA300 LAC deltaccpA + pCN33


title: PFA_Paraffin_TE_CA3_replicate1-4

city: Kyoto

first: Shinya

last: Oki

address: 53 Kawahara-cho, Shogoin

institute: Kyoto University

data_processing:
The barcodes and unique-molecular-identifiers in the reads were extracted using UMI-tools (version 1.0.0) with the command: umi_tools extract -I r1.fastq --read2-in=r2.fastq --bc-pattern=NNNNNNCCCCCC --read2-stdout.
The reads were mapped by the aligning software HISAT2 (version 2.1.0) to the reference genome (GRCm38).
Read counts per gene was performed with featureCounts (version 1.6.4) and UMI-tools with the command: umi_tools count --method=directional --per-gene --per-cell --gene-tag=XT.
The duplicates in unique molecular identifiers were discarded.
Using the resulting counts, differentially expressed genes (those with adjusted p-values < 0.1) were extracted by the R library DESeq2 (version 1.20.0).
Genome_build: GRCm38
Supplementary_files_format_and_content: count matrix:CSV

source_name: Hippocampal region

extract_protocol:
Lysis solution(0.1% Tween and 400 ug/ml of ProteinaseK in PBS) were loaded onto the specimens and incubated for 30 min at 55℃. cDNA;mRNA hybrids were purified with a Qiagen MinElute PCR Purification kit.
All subsequent steps are according to the CEL-seq2 method as follows: Second strand DNA is synthesized by nick translation method using RNase H, DNA polymerase I, and DNA ligase mix, by which only the cDNAs derived from the photo-irradiated region are filled-in to the 5' end of T7 promoter, thereby allowing the cDNAs to be linearly amplified as RNAs (aRNAs) by IVT reaction. The libraries are further reverse-transcribed, followed by paired-end sequencing on the Illumina platform.

treatment_protocol: Permeabilize the sections with HCl ; Drop 5% (vol/vol) Triton X-100 in PBS onto the section, and incubate at RT for 3 min.Then, Drop 0.1N HCl in Nuclease-free water onto the section, and incubate at RT for 5 min.  Permeabilize the sections with TE buffer ;  Immerse the sections in TE buffer (pH 8.0) preheated to 70°C in a polypropylene staining jar, and incubate in a hybridization oven for 1 hr.

tag: mice strain

value: ICR

tag: week old

value: 8 weeks

tag: Sex

value: male

tag: fix

tag: section type

value: Paraffin

tag: pre-treatment

value: TE buffer


title: PFA_Paraffin_TE_CA1_replicate1-4


title: H3K9me_epe1D_rep4

tag: extract

value: cell extract

tag: genotype


title: ccpA_mut_rep1

description: Total RNA of ccpA null mutant, first biological replicate. Cells contained the empty pCN33 vector.


title: Human oocyte 36-39 -MII-Rep2

description:
Aging-Human-FPKM.txt
C2-2


title: RNAseq_1cell_rep1

tag: developmental stage

tag: developmental time points

tag: morphology


title: Human oocyte 36-39 -MII-Rep1

description:
Aging-Human-FPKM.txt
C2-1


title: PFA_Paraffin_TE_DG_replicate1-4


title: PFA_Frozen_TE_DG_replicate1-4

value: Frozen


title: ccpA_mut_rep2

description: Total RNA of ccpA null mutant, second biological replicate. Cells contained the empty pCN33 vector.

tag: treatment


title: RNAseq_oocyte_rep2


title: Human oocyte 36-39 -GV-Rep3

description:
Aging-Human-FPKM.txt
C1-3


title: PFA_Frozen_TE_CA3_replicate1-4


title: Human oocyte 36-39 -GV-Rep2

description:
Aging-Human-FPKM.txt
C1-2


title: WT_rep2

description: Total RNA ofparental strain USA300, second biological replicate. Cells contained the empty pCN33 vector.

value: USA300 LAC pCN33


title: WT_rep1

description: Total RNA of parental strain USA300, first biological replicate. Cells contained the empty pCN33 vector.

value: Grown to OD600 ~3.0 in TSB + Erythromicin ,  harversed by centrifugation and stored at -80ºC


title: PFA_Frozen_TE_CA1_replicate1-4


title: None_Frozen_TE_DG_replicate1-4


title: None_Frozen_TE_CA3_replicate1-4


title: Human oocyte 36-39 -GV-Rep1

description:
Aging-Human-FPKM.txt
C1-1


title: RNAseq_TSB_LPM54_r3_T30

description: Ribosome-depleted total RNA extracted thirty minutes after shifting cells to LPM pH 5.4, third replicate

data_processing:
CLASH was performed on JKD6009 rnc::HTF in biological triplicates, with a single biological replicate for the wild type control. The cDNA libraries were sequenced on Illumina HiSeq 2500 machine. For USA300, four biological replicates of rnc::HTF were performed and two replicates of the untagged wild type. These were sequenced on a NovaSeq 6000. Raw sequencing reads in fastq files were processed using the CLASH data analysis pipeline developed by Sander Granneman, which uses tools from the pyCRAC package (version 1.5.0) (Webb et al., 2014). This PreProcessForHyb.py script first uses flexbar to trim the 3' adaptor sequence from the data and remove low quality nucleotides (Phred score <23). Subsequently, pyBarcodeFilter.py demultiplexes the data from the in-read barcode sequences found in the 5’ adapter. Using the random nucleotide information present in the 5’ adaptor sequences, the reads are then collapsed to remove potential PCR duplicates using pyFastqDuplicateRemover.py. For RNAseq, the CRAC_pipeline_PE.py script was used from the pyCRAC package. This firstly demultiplexes the data using pyBarcodeFilter.py and the in-read barcode sequences found in the L5 5’ adapters. Flexbar then trims the reads to remove 3’-adapter sequences and poor-quality nucleotides (Phred score <23). Using the random nucleotide information present in the L5 5’ adaptor sequences, the reads are then collapsed to remove potential PCR duplicates using pyFastqDuplicateRemover.py. The reads were then mapped to the JKD6008 and USA300 genomes using Novoalign (www.novocraft.com).
For mapping to the USA300 genome, we generated an annotation file in the Gene Transfer Format (GTF). This file contained the start and end positions of each gene on the chromosome as well as its encoded product (e.g. sRNA, protein- coding, tRNA). To generate this file, we used the Rockhopper software (Tjaden, 2015) on USA300 rRNA-depleted total RNA-seq data (Stuart McKellar and Ivayla Ivanova, unpublished) and a minimal GTF file obtained from ENSEMBL (without UTR information). The resulting GTF file contained information not only on the coding sequences, but also more complete 5’ and 3’ UTR coordinates. Overlapping features, such as sRNAs that overlap with UTRs of protein-coding genes, were removed from the GTF file. For USA300, we utilised already published genome annotations (Howden et al, 2010).
The hyb pipeline (Travis et al, 2014) was then used to detect RNA-RNA interactions. This uses bowtie2 and BLAST to map each half of the RNA-RNA interaction to the genome. Afterwards, a statistical analysis pipeline (Waters et al, 2017) was used to filter for statistical signifiance and intermolecular interactions were extracted, annotated and filtered for minimum folding energy cut-off using custom scripts. Finally, interactions involving only 'bona fide' sRNAs (Lui et al, 2018) were filtered from the data. To calculate enriched RNA structures, the MFE of structures were calculated using UNAFold and compared to a randomly shuffled control. The structures were converted into Vienna dot-bracket notation and double-stranded structures between 5 and 10 base-pairs were extracted.
Normalization and differential gene expression analysis on the RNAtag-Seq data were done with  DESeq2  package (Love et al., 2014).
Genome_build: NCBI:txid451515 (USA300), NCBI:txid546343 (JKD6009)
Supplementary_files_format_and_content: CLASH data: Supplementary Tables 3 and 4 are Excel tables describing the RNA-RNA complexes. The .hyb files give the unique, annotated output from hyb. For RNAseq, bedgraph files are provided which detail peaks that can be visualised by a genome browser, and the pyReadCounters.gtf output detailing the hit tables.

source_name: Staphylococcus aureus

growth_protocol: S. aureus cells expressing HTF-tagged RNase III (or an untagged, wild type control) were grown to saturation in TSB at 37 °C with shaking. Cells were then diluted into 500 mL of fresh TSB to an OD600 value of 0.05 and grown to an OD600 of 3. Subsequently, cells were harvested by vacuum filtration and shifted to an equivalent volume of stress media, either RPMI or LPM. As as control, cells were shifted back into their original TSB medium. For CLASH, samples were taken after 15 minutes of incubation in the stressful media. For RNAtag-Seq, samples were taken after 5, 10, 15 and 30 minutes.

extract_protocol:
For CLASH, the cells were washed off the filters using 25mL of cold phosphate buffer saline and pelleted by centrifugation. Cells were subsequently resuspended in 2 volumes of TN150-lysostaphin buffer (50 mM Tris pH 7.8, 150 mM NaCl, 100 µg/mL lysostaphin, 0.1% NP-40, 0.5% Triton X-100) and transferred to 5 mL screw-cap tubes (Eppendorf). Sixty µL of DNase RQ1 and 10 µL of SUPERase-In was added and the mixture was incubated at 37°C for 30 min to lyse the cells. Afterwards, 3 volumes/cell weight of zirconia beads (Thistle Scientific; 0.1 µm) were added and the mixture was vortexed vigorously 5 times for one minute with incubation on ice between each samples. Two volumes/cell weight of cold TN150 anti-peptidase (50 mM Tris pH 7.8, 150 mM NaCl, 1 Roche EDTA-free mini pellet, 0.1% NP-40, 0.5% Triton X-100 and 10 mM EDTA) was added before centrifugation for 30 minutes at 10000 g at 4°C. Subsequently, 75 µL of anti-FLAG® M2 Magnetic Beads (pre-washed with TN150 buffer) was added and incubated with the lysate for 2 hours at 4°C. The beads were then washed three times for five minutes with 2 mL of TN1000 buffer (50 mM Tris pH 7.8, 1M NaCl, 0.1% NP-40, 0.5% Triton X-100) and three times with 2 mL of TN150 buffer (50 mM Tris pH 7.8, 150 mM NaCl, 0.1% NP-40, 0.5% Triton X-100) for 5 minutes. Beads were subsequently resuspended in 250 µL of TN150 and 10 µL of homemade GST-TEV protease was added. The samples were rotated for 2 hours at room temperature. TN150 was added to a final volume of 600 µL and 550 µL of the TEV eluates were incubated with RNace-it™ (Agilent Technologies, 1 µL of 1:100 dilution) for exactly seven minutes at 20°C. Subsequently, 500 µL of the mixture was added to a tube with 0.4 g guanidium-HCl and vortexed vigorously to inactivate the RNases. Sodium chloride and imidazole (pH 8.0) were added to a final concentration of 300 mM and 10 mM respectively, and the mixture was transferred to 50 µL of Ni-NTA agarose beads (QIAGEN), pre-equilibrated with wash buffer I (300 mM NaCl, 10 mM imidazole, 6M GuHCl, 50 mM Tris-HCl pH 7.8, 0.1% NP40, 5 mM β- mercaptoethanol and 0.5% Triton X-100) and incubated at 4°C overnight on a rotator. The next day the beads were transferred to Pierce snap-cap columns (Thermo Scientific) and washed twice with 500 µL wash buffer I and three times with 500 µL 1x NP-PNK buffer (10 mM MgCl2, 50 mM Tris-HCl pH 7.8, 0.1% NP40, 5 mM βMe and 0.5% Triton X-100). For RNAtag-Seq, total RNA was extracted from the cells using standard guanidinium thiocyanate-phenol-chloroform extraction (Chomczynski et al, 1987).
For CLASH, the isolated RNA-RNA complexes had 3' and 5' Illumina adaptors ligated on their respective ends as described previously (McKellar et al, 2020; Granneman et al, 2009). For RNAtag-Seq, the total RNA samples were processed as described previously (Shishkin et al, 2015).

treatment_protocol: Following the shift, cells were UV cross-linked through 254 nm UV (1000 mJ/cm2) using a Vari-X-Linker (UVO3 (McKellar et al, 2020; van Nues et al, 2017). Afterwards, cells were harvested onto filters by vaccuum filtration, flash-frozen in liquid nitrogen and stored at -80°C until their processing.

value: USA300 rnc:HTF

tag: media

value: LPM 5.4

value: Sample harvested after shifting cells for 30min to LPM 5.4


title: Human oocyte 30-35 -MII-Rep3

description:
Aging-Human-FPKM.txt
B2-3

value: oocyte


title: Human oocyte 30-35 -MII-Rep2

description:
Aging-Human-FPKM.txt
B2-2


title: WT_rep3

description: Total RNA of parental strain USA300, third biological replicate. Cells contained the empty pCN33 vector.


title: Human oocyte 30-35 -MII-Rep1

description:
Aging-Human-FPKM.txt
B2-1


title: RNAseq_TSB_LPM54_r3_T15

description: Ribosome-depleted total RNA extracted fifteen minutes after shifting cells to LPM pH 5.4, third replicate

value: Sample harvested after shifting cells for 15min to LPM 5.4


title: RNAseq_TSB_LPM54_r3_T10

description: Ribosome-depleted total RNA extracted ten minutes after shifting cells to LPM pH 5.4, third replicate

value: Sample harvested after shifting cells for 10min to LPM 5.4


title: None_Frozen_HCl_DG_replicate1-4

value: HCl


title: None_Frozen_TE_CA1_replicate1-4


title: Human oocyte 30-35 -GV-Rep3

description:
Aging-Human-FPKM.txt
B1-3


title: None_Frozen_HCl_CA1_replicate1-4


title: Human oocyte 30-35 -GV-Rep2

description:
Aging-Human-FPKM.txt
B1-2


title: None_Frozen_HCl_CA3_replicate1-4


title: RNAseq_TSB_LPM54_r3_T5

description: Ribosome-depleted total RNA extracted five minutes after shifting cells to LPM pH 5.4, third replicate

value: Sample harvested after shifting cells for 5min to LPM 5.4


title: Human oocyte 30-35 -GV-Rep1

description:
Aging-Human-FPKM.txt
B1-1


title: RNAseq_TSB_LPM76_r3_T5

description: Ribosome-depleted total RNA extracted five minutes after shifting cells to LPM pH 7.6, third replicate

value: LPM 7.6

value: Sample harvested after shifting cells for 5min to LPM 7.6


title: RNAseq_TSB_LPM76_r3_T10

description: Ribosome-depleted total RNA extracted ten minutes after shifting cells to LPM pH 7.6, third replicate

value: Sample harvested after shifting cells for 10min to LPM 7.6


title: Human oocyte <30 -MII-Rep2

description:
Aging-Human-FPKM.txt
A2-2


title: RNAseq_TSB_LPM76_r3_T30

description: Ribosome-depleted total RNA extracted thirty minutes after shifting cells to LPM pH 7.6, third replicate

value: Sample harvested after shifting cells for 30min to LPM 7.6


title: Human oocyte <30 -MII-Rep3

description:
Aging-Human-FPKM.txt
A2-3


title: methyl_NS3

source_name: human unwounded skin tissue

value: skin


title: Human oocyte <30 -MII-Rep1

description:
Aging-Human-FPKM.txt
A2-1


title: RNAseq_TSB_r3_T0

description: Ribosome-depleted total RNA extracted before shifting cells to LPM media, third replicate

value: TSB

value: Sample harvested at OD600 = 3 after growth in TSB


title: Tumor-2 ADV-Ctrl

city: Nanjing

first: Shiqun

last: Wang

state: Jiangsu

address: 22 Hankou Road

institute: Nanjing university

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: Mus_musculus (GRCm39)
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: tumor

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Intracranial 14-day GL261CAR-bearing C57BL/6J mice were i.t. injected with 1 × 108 PFU AdVCtrl or 1 × 108 PFU AdVAPOA1. The tumor bulks were then collected 3 days after virus injection. Samples were stored at -80°C.

value: tumor

value: Injected with ADV-Ctrl


title: RNAseq_TSB_LPM54_r2_T30

description: Ribosome-depleted total RNA extracted thirty minutes after shifting cells to LPM pH 5.4, second replicate

value: USA300 rnc:HTF


title: Human oocyte <30 -GV-Rep3

description:
Aging-Human-FPKM.txt
A1-3


title: RNAseq_TSB_LPM76_r3_T15

description: Ribosome-depleted total RNA extracted fifteen minutes after shifting cells to LPM pH 7.6, third replicate

value: Sample harvested after shifting cells for 15min to LPM 7.6


title: EL1

city: Suita

first: Shotaro

last: Tatekawa

state: Osaka

address: 2-2(D10), Yamadaoka, Suita-city

department: Departments of Radiation Oncology,

institute: The University of Osaka Graduate School of Medicine

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The resulting raw reads were processed on a cellranger (10x Genomics). scRNAseq data processing was performed with the R v4.1 and Seurat v4.0.5 packages.
Assembly: GRCm38
Supplementary files format and content: F1938_EL_counts.txt
Supplementary files format and content: F1938_WTg_counts.txt

source_name: pancreas

extract_protocol:
ISOGEN (NIPPON GENE)
Single cell suspensions were processed with the 10x Genomics Chromium Controller according to the protocol described in the Chromium Single Cell 3' Reagent Kits User Guide Chromium Next GEM Single Cell 3' Kit v3.1 (Cat# PN-1000269), Chromium Next GEM Chip G Single Cell Kit (Cat# PN-1000127), and Dual Index Kit TT Set A (Cat# PN-1000215) were applied during processing. Following the manufacturer's recommendations, approximately 16,500 viable cells per sample were loaded into the Chromium controller to generate 10,000 single cell gel bead emulsions for library preparation and sequencing. Oil droplets of encapsulated single cells and barcoded beads (GEM) were then reverse transcribed on a Veriti Thermal Cycler (Thermo Fisher Scientific) to obtain cDNA tagged with cell barcodes and UMIs. The cDNA was then amplified and single-cell libraries were prepared according to the manufacturer's protocol. Quantification was performed using the Agilent Bioanalyzer High-Sensitivity DNA assay (Agilent, High-Sensitivity DNA Kit, Cat# 5067-4626). The amplified cDNA was then enzymatically fragmented, repaired at the ends, and polyA tagged. Amplified cDNA was cleaned/size-selected using SPRIselect magnetic beads (Beckman-Coulter, SPRIselect, Cat# B23317). Next, Illumina sequence adapters were ligated to the size-selected fragments and cleanup was performed using SPRIselect magnetic beads. Finally, sample indexes were selected, amplified, and double-sided size selection was performed using SPRIselect magnetic beads. Final library quality was assessed using the Agilent Bioanalyzer High-Sensitivity DNA assay.

value: pancreas

tag: cell line

value: primary

tag: cell type

value: epithelial cell

tag: age

value: 6 weeks


title: Tumor-1 ADV-Ctrl

tag: tissue


title: WTg

description: 10x Genomics

tag: strain

value: EL1-Luc/EL1-Tag x CAG-Mettl3


title: Human oocyte <30 -GV-Rep2

description:
Aging-Human-FPKM.txt
A1-2

value: oocyte


title: Tumor-3 ADV-APOA1

value: Injected with ADV-APOA1


title: Human oocyte <30 -GV-Rep1

description:
Aging-Human-FPKM.txt
A1-1


title: Tumor-2 ADV-APOA1


title: Tumor-3 ADV-Ctrl


title: MULTIseq Sample C

first: Dennis

last: Kostka

state: PA

department: Developmental Biology

data_processing:
Reads were processed using the Cell Ranger (version 3.1.0) count pipeline using the human reference genome GRCh38.p12, annotations from Ensembl (version 93) with the arguments --chemistry= SC3Pv3, --expect-cells=10,000 or 25,000, depending on the specific library. For MULTIseq fastq files, library_type was set to "Custom".
Sample demultiplexing was performed using the R package deMULTIplex (version 1.0.2) [https://github.com/chris-mcginnis-ucsf/MULTI-seq].
Quality control and filtering were performed using the R package scater [10.1093/bioinformatics/btw777] (v1.14.6). For each sample, cells with total library size >=2000, number of detected genes >=1000 and <= 8000, and <=30% percentage of mitochondrial reads were considered. Additionally doublets with the same MULTI-seq barcode were filtered using the scds R package [10.1093/bioinformatics/btz698] (v1.2.0) as described in Supplementary Note XYZ.1. Only genes with at least 1 count in at least five cells were considered and log-normalized counts were calculated using the deconvolution method of the scran R package [10.12688/f1000research.9501.2].
The sample metadata, barcodes, counts matrices, and log-normalized counts are additionally provided as processed data files.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: H5, mtx, txt and csv files.

source_name: MULTIseq pooled samples

growth_protocol: Two WTC lines (ACTN2-eGFP,Myl2-eGFP) and SCVI114 line were maintained in completely defined albumin-free E8 medium (DMEM/F12 with L-glutamine and HEPES, 64μg/ml L-Ascorbic Acid-2-phosphate, 20μg/ml insulin, 5μg/ml transferrin, 14ng/ml sodium selenite, 100ng/ml FGF2, 2ng/ml TGFb1) on Matrigel  coated tissue culture plates.

extract_protocol:
Cardiac cells from monolayer differentiation culture at day 15 and day 30 were dissociated with TrypLE and washed once with HBSS-/- (Ca2+/Mg2+ free). The cardiac organoids were sequencially incubated with 0.25% Trypsin/EDTA and a collagenase HBSS+/+ mixture before filtered through a 40 μm filter. The cells from each sample were stained with with a unique MULTI-seq barcode separately and pooled before library preparation.
The pooled cells were captured in 10X Chromium (10X Genomics, 120223) by following the single cell 3’ reagent kits v3 user guide. Briefly, cells were loaded into each chip well to be partitioned into gel beads in emulsion (GEMs) in the Chromium controller. We targeted for 25,000 cells in each chip well and profiled one well for the first batch experiment and two chip wells for the second experiment. The cells were then lysed and barcoded reverse transcribed in the GEMs. After breaking the GEMs and further cleanup and amplification, the cDNA was enzymatically fragmented and 3′ end fragments were selected for library preparation. After further processing including end repair, A-tailing, adaptor ligation, and PCR amplification, a string of sequences including sample index, UMI sequences, barcode sequences, and sequencing primer P5 and P7 were added to cDNA on both ends. The libraries were sequenced on Illumina HiSeq X platform.

treatment_protocol: Monolayer cardiac differentiation was carried out following a published protocol(Lian et al., 2015). The cardiac organoid differentiation procedure was adapted from a protocol described Previously (Branco et al., 2019).

tag: sample type

value: mixed pool

value: hiPSC derived cells

value: unsorted


title: RNAseq_TSB_LPM54_r2_T15

description: Ribosome-depleted total RNA extracted fifteen minutes after shifting cells to LPM pH 5.4, second replicate

value: LPM 5.4

value: Sample harvested after shifting cells for 15min to LPM 5.4


title: MULTIseq Sample B


title: RNAseq_TSB_LPM54_r2_T10

description: Ribosome-depleted total RNA extracted ten minutes after shifting cells to LPM pH 5.4, second replicate

value: Sample harvested after shifting cells for 10min to LPM 5.4


title: TAM-P-4 (CTRL)

source_name: sorted TAMs

treatment_protocol: C57 mice with 17-day intracranial GL261-Puro or GL261-APOA1 were sacrificed. Tumors were collected to obtain TAMs by anti-F4/80 MicroBeads (Miltenyi Biotec, 130-110-443). Samples were stored at -80°C.

value: sorted TAMs

value: TAMs sorted from intracranial GL261-Puro tumors


title: Tumor-1 ADV-APOA1

value: tumor


title: TAM-P-3 (CTRL)


title: RNAseq_TSB_LPM76_r2_T30

description: Ribosome-depleted total RNA extracted thirty minutes after shifting cells to LPM pH 7.6, second replicate

value: USA300 rnc:HTF

value: LPM 7.6

value: Sample harvested after shifting cells for 30min to LPM 7.6


title: MULTIseq Sample A

value: FACs-sorted


title: ChIPmentation HEP in vitro induced definitive endoderm 72h rep2

data_processing:
adapter trimming: skewer version 0.2.2
QC: PRINSEQ-lite version 0.20.4 with" -min_len 50 -trim_qual_right 20" options
genome alignment: bowtie2 version 2.1.0
Genome_build: hg19
Supplementary_files_format_and_content: Two replicate bam files were combined using samtools.
Supplementary_files_format_and_content: bigwig files were generated using bam2wig with wigtobigwig, following to removal of the mitochondrial genome and duplicated reads using removeChrom.py and samtools.
Supplementary_files_format_and_content: peakcalling were performed using MACS2 with cutoff p-value 1e-10.

extract_protocol:
The cells collected were fixed with 1% formaldehyde for 8 minutes at RT. The fixed cells were lysed in the lysis buffer.
Chromatin was sheared by sonication by using Picoruptor® (Diagenode) with the condition of 10 cycles. The shared chromatin from one million cells was subjected to following magnetic immunoprecipitation and tagmentation using SX-8G IP-STAR® Compact Automated System (Diagenode).The immunoprecipitated samples were stripped from the magnetic beads and subjected to the end repair and reverse cross-linking. The illumine sequence compatible sequencing libraries were amplified by nine cycles of PCR. The sequencing libraries were clean-up by AMPure XP beads (1:1.8 sample vol. to beads vol.; Beckman Coulter). The library size distribution was determined by Bioanalyzer (Agilent Technologies) library concentration. The libraries' concentration was quantified by GenNext NGS Library Quantification Kit (Toyobo Co., Ltd). The ChIPmeantaion libraries were sequenced using 150 bp paired-end reads on the HiSeq X (Illumina).

tag: differentiation hour


title: RNAseq_TSB_LPM54_r2_T5

description: Ribosome-depleted total RNA extracted five minutes after shifting cells to LPM pH 5.4, second replicate

value: Sample harvested after shifting cells for 5min to LPM 5.4


title: TAM-P-2 (CTRL)


title: ChIPmentation HEP in vitro induced definitive endoderm 72h rep1


title: RNAseq_TSB_LPM76_r2_T5

description: Ribosome-depleted total RNA extracted five minutes after shifting cells to LPM pH 7.6, second replicate

value: Sample harvested after shifting cells for 5min to LPM 7.6


title: RNAseq_TSB_LPM76_r2_T10

description: Ribosome-depleted total RNA extracted ten minutes after shifting cells to LPM pH 7.6, second replicate

value: Sample harvested after shifting cells for 10min to LPM 7.6


title: RNAseq_TSB_LPM76_r2_T15

description: Ribosome-depleted total RNA extracted fifteen minutes after shifting cells to LPM pH 7.6, second replicate

value: Sample harvested after shifting cells for 15min to LPM 7.6


title: RNAseq_TSB_r2_T0

description: Ribosome-depleted total RNA extracted before shifting cells to LPM media, second replicate

value: TSB

value: Sample harvested at OD600 = 3 after growth in TSB


title: TAM-P-1 (CTRL)


title: ChIPmentation HEP in vitro induced definitive endoderm 66h rep2


title: ChIPmentation HEP in vitro induced definitive endoderm 66h rep1


title: TAM-A-4 (APOA1)

value: TAMs sorted from intracranial GL261-APOA1 tumors


title: TAM-A-3 (APOA1)


title: RNAseq_TSB_LPM54_r1_T30

description: Ribosome-depleted total RNA extracted thirty minutes after shifting cells to LPM pH 5.4, first replicate

value: LPM 5.4

value: Sample harvested after shifting cells for 30min to LPM 5.4


title: ChIPmentation HEP in vitro induced definitive endoderm 60h rep2


title: RNAseq_TSB_LPM54_r1_T15

description: Ribosome-depleted total RNA extracted fifteen minutes after shifting cells to LPM pH 5.4, first replicate

value: Sample harvested after shifting cells for 15min to LPM 5.4


title: TAM-A-2 (APOA1)

value: sorted TAMs


title: ChIPmentation HEP in vitro induced definitive endoderm 60h rep1


title: TAM-A-1 (APOA1)


title: RNAseq_TSB_LPM54_r1_T10

description: Ribosome-depleted total RNA extracted ten minutes after shifting cells to LPM pH 5.4, first replicate

value: Sample harvested after shifting cells for 10min to LPM 5.4


title: RNAseq_TSB_LPM54_r1_T5

description: Ribosome-depleted total RNA extracted five minutes after shifting cells to LPM pH 5.4, first replicate


title: Kidneys, NICDwt3

city: CINCINNATI

first: Praneet

last: Chaturvedi

state: OH

address: 240 Albert Sabin Way

institute: Cincinnati Children's

data_processing:
Raw reads in fastq format were mapped against mm10 using CSBB-v3.0 (https://github.com/praneet1988/Computational-Suite-For-Bioinformaticians-and-Biologists).
CSBB-v3.0 uses RSEM with Bowtie2 (using default parameters) to map and quantify reads. Adapters and low quanlity reads were trimmed using bbduk as part of bioinformatics pipeline before mapping the reads.
Assembly: mm10
Supplementary files format and content: Gene TPM across samples in .txt
Supplementary files format and content: Gene Counts across samples in .txt

source_name: Kidney

extract_protocol:
Kidneys were isolated from e 15.5 mice and placed into ice cold PBS. RNA was extracted using the Invitrogen PureLink ™ RNA Mini Kit (Thermo Fisher Scientific, 12183025) following the manufacturer protocol.
Samples were sent to Novogene Corporation INC for library production and RNA sequencing.

value: embryo

value: Kidney

value: NICD wt


title: ChIPmentation HEP in vitro induced definitive endoderm 54h rep1


title: RNAseq_TSB_LPM76_r1_T30

description: Ribosome-depleted total RNA extracted thirty minutes after shifting cells to LPM pH 7.6, first replicate

value: USA300 rnc:HTF

value: LPM 7.6

value: Sample harvested after shifting cells for 30min to LPM 7.6


title: Kidneys, NICDwt2


title: ChIPmentation HEP in vitro induced definitive endoderm 48h rep2


title: Kidneys, NICDwt1


title: RNAseq_TSB_LPM76_r1_T15

description: Ribosome-depleted total RNA extracted fifteen minutes after shifting cells to LPM pH 7.6, first replicate


title: RNAseq_TSB_LPM76_r1_T10

description: Ribosome-depleted total RNA extracted ten minutes after shifting cells to LPM pH 7.6, first replicate


title: Kidneys, NICDmut2

description: Six2TGC/+, RosaN1ICD∆PEST (experiment, Cre line from Konbayashi et al 2008; activated Notch1 transgene from Murtaugh et al., 2003)

value: NICD mut

value: Activated Notch1∆PEST  in renal progenitors


title: ChIPmentation HEP in vitro induced definitive endoderm 48h rep1


title: RNAseq_TSB_LPM76_r1_T5

description: Ribosome-depleted total RNA extracted five minutes after shifting cells to LPM pH 7.6, first replicate

value: Sample harvested after shifting cells for 5min to LPM 7.6


title: Kidneys, NICDmut1


title: RNAseq_TSB_r1_T0

description: Ribosome-depleted total RNA extracted before shifting cells to LPM media, first replicate

value: TSB


title: Control (KC1-G36-H1806), genomic DNA

type: genomic

city: Daejeon

first: Su-Jin

last: Baek

address: 1672, Yuseong-daero

country: South Korea

institute: KOREA INSTITUTE of ORIENTAL MEDICINE

description: genomic DNA from control (KC1-G36-H1806)

hyb_protocol: Bisulfite-converted genomic DNA was used to hybridize the Illumina`s Infinium MethylationEPIC BeadChIP.

scan_protocol: Illumina iScan was used to scan the BeadChIP

data_processing: ChAMP

label: Cy5 and Cy3

source_name: PBMC

label_protocol: Standard Illumina protocol

extract_protocol: Genomic DNA  from PBMC were isolated using DNA MiniKit (Quagen) . DNA extractions were performed according to the manufactuer`s protocol

tag: Sex

value: Female

value: PBMC

tag: disease state

value: control


title: ChIPmentation HEP in vitro induced definitive endoderm 0h rep1

value: 0 h


title: Control (KC1-G36-H0826), genomic DNA

description: genomic DNA from control (KC1-G36-H0826)


title: Control (KC1-G36-H1549), genomic DNA

description: genomic DNA from control (KC1-G36-H1549)


title: ChIPmentation HEP in vitro induced definitive endoderm 54h rep2


title: Metabolic_syndrome (KC1-G36-H1297), genomic DNA

description: genomic DNA from Metabolic_syndrome (KC1-G36-H1297)


title: Metabolic_syndrome (KC1-G36-H0844), genomic DNA

description: genomic DNA from Metabolic_syndrome (KC1-G36-H0844)


title: RNAseq_TSB_RPMI_r2_T30

description: Ribosome-depleted total RNA extracted thirty minutes after shifting cells to RPMI, second replicate

value: RPMI

value: Sample harvested 30 minutes after shifting cells to RPMI


title: mouse embryonic stem cells repeat 1 [WGBS]

city: Beijing

first: Yiming

last: Sun

state: Beijing

address: NO.5, Yiheyuan Road, Haidian District

department: School of Life Sciences

institute: Peking University

data_processing:
The mouse reference genome mm10 and lambda genome were transformed into fully bisulfite-converted forward (C>T) and reverse (G>A conversion of the forward strand) versions using the script bismark_genome_preparation. Sequence reads were similarly transformed and mapped to prepared genomes using Bowtie2 with parameters set by Bismark.
The alignments to the same position in the genome from the Bismark mapping output were removed using the script deduplicate_bismark.
The methylation information of every single C were extracted using the script bismark_methylation_extractor with parameter ‘-p --no_overlap --ignore 5 --ignore_r2 5 --zero_based --CX --buffer_size 50%’. In this way we got the number of reads that supported methylation and the number of reads covering every CpG site, non-CpG sites were not considered in later analysis.
Assembly: mm10 (GRCm38)
Supplementary files format and content: BedGraph files containing CpG methylation counts for each site.

source_name: mouse embryonic stem cells

growth_protocol: Mouse TPS cells were cultured on feeder cells in CPEC condition. Mouse EPS cells were cultured on feeder cells in LCDM medium. Mouse ES cells were cultured on feeder cells in 2i+LIF condition.

extract_protocol:
Genomic DNAs were extracted using DNeasy Blood & Tissue Kits (QIAGEN, 69504). 100 ng genomic DNAs were fragmented into around 200 bp by Covaris. Then DNAs were bisulfite-converted using EZ DNA Methylation-GoldTM Kit (Zymo, D5005).
Bisulfite-converted DNA was captured using Accel-NGS Methyl-Seq DNA Library Kit (Swift Biosciences, 30024). Library samples were subjected to Illumina Nova-seq 6000 sequencing system.

value: embryonic stem cells


title: Metabolic_syndrome (KC1-G36-H1614), genomic DNA

description: genomic DNA from Metabolic_syndrome (KC1-G36-H1614)


title: mouse extended pluripotent stem cells 2# repeat 2 [WGBS]

value: extended pluripotent stem cells


title: RNAseq_TSB_RPMI_r2_T10

description: Ribosome-depleted total RNA extracted ten minutes after shifting cells to RPMI, second replicate

value: Sample harvested 10 minutes after shifting cells to RPMI


title: ChIPmentation HEP in vitro induced definitive endoderm 0h rep2


title: Blood (key metabolic tissues dataset)

first: Jiajin

address: Yuhangtang road

description: Blood

data_processing:
Sequences from NovaSeq 6000 system were  de-multiplexed and aligned using CellRanger version 3.1.0, available from 10x Genomics with default parameters.
Genome_build: Bos_taurus ensemblV99
Supplementary_files_format_and_content: Tab-delimited text files include barcodes, gene and count matrix for each Sample

organism: Bos taurus

source_name: Peripheral blood

extract_protocol:
The rumen, reticulum, omasum, abomasum, ileum, and rectum tissues isolated from lactating cows were stripped of the outer muscle layers, and then minced into 10×0.5mm2 pieces on ice with scissors. The tissues were incubated in a 37℃ water bath with 20 mM EDTA for 30 min, and then were rinsed with DPBS and chopped into 1 mm pieces. Tissue pieces were transferred to a 15 mL centrifuge tube, and re-suspended with 0.25% Trypsin-EDTA (Gibco). After incubated in a 37℃ water bath for 5 min, the centrifuge tube containing tissues was inserted into ice for 2min, and pre-chilled HBSS was added to stop the digestion. After centrifuged at 300 × g for 2 min at 4℃, the supernatant was discarded, and samples were washed twice with cold HBSS and then re-suspended with dissociation enzymes. Samples were treated with different enzymes for different durations (for rumen, reticulum, omasum, and abomasum tissues: 1.5mg/ml collagenase I, 1.5ml/ml collagenase IV,1.5mg/ml dispase, 100U/ml hyaluronidase, and 50U/ml DNase I for 30 min at 37℃; for ileum tissue:4.5ml Buffer X, 50μl enzyme P, 50μl buffer Y, 100μl enzyme D, and 20μl enzyme A of Multi Tissue Dissociation Kit 2 (Miltenyi biotec, Bergisch Gladbach, Germany); for rectum tissue: 1mg/ml collagenase/dispase for 41 min at  37℃). For salivary gland samples, the isolated tissues from parotid gland were transferred into cold 1×PBS, blood and fat were removed, and chopped into 0.5 mm pieces and then incubated with 1.5mg/ml collagenase II, 1.5mg/ml dispase, and 50U/ml DNase I for 20 min at 37℃. For liver samples, the isolated tissues were transferred into cold DPBS, minced into 1mm pieces, and then incubated with 1.5mg/ml collagenase I, 20U/ml papain, and 50U/ml DNase for 20 min at 37℃.For the mammary gland sample, the isolated tissues were were cut into 5 mm pieces and washed using 1 × PBS (with 5% FBS) after removing the adipose tissue. Subsequently, samples were bath with 20 mM EDTA (with 5% FBS) at 100 rpm for 20 min at 37°C, and then incubated with dissociation enzymes (Dataset S1). The mixture was passed through 70 μm and 30 μm SmartStrainers and transferred into a new EP tube, and centrifuged at 300 × g for 5 min at 25°C. After removing the supernatant, the cells were washed with 3 mL HBSS with 5% FBS and centrifuged at 300 g for 5 min at 25°C.For the peripheral blood sample, PBMC and neutrophil were enriched by Ficoll (HY2015, TBD) separation.
The single-cell RNA-seq library preparation was performed using the Chromium Single Cell 3' Reagent Kits v3.

tag: breed

value: Holstein dairy cows

value: Peripheral blood

value: Lactating


title: RNAseq_TSB_RPMI_r2_T15

description: Ribosome-depleted total RNA extracted fifteen minutes after shifting cells to RPMI, second replicate

value: Sample harvested 15 minutes after shifting cells to RPMI


title: MammaryGland_Lactating (key metabolic tissues dataset)

source_name: Mammary Gland

value: Mammary Gland


title: Metabolic_syndrome (KC1-G36-H1080), genomic DNA

description: genomic DNA from Metabolic_syndrome (KC1-G36-H1080)


title: Control (KC1-G36-H1099), genomic DNA

description: genomic DNA from control (KC1-G36-H1099)

value: Male


title: SalivaryGland_adult (key metabolic tissues dataset)

source_name: Salivary Gland

value: salivary gland


title: mouse embryonic stem cells repeat 2 [WGBS]


title: Liver_adult (key metabolic tissues dataset)

source_name: Liver

value: liver


title: Control (KC1-G36-H1176), genomic DNA

description: genomic DNA from control (KC1-G36-H1176)

value: Female


title: Control (KC1-G36-H1242), genomic DNA

description: genomic DNA from control (KC1-G36-H1242)

value: PBMC


title: mouse extended pluripotent stem cells 1# repeat 1 [WGBS]


title: Control (KC1-G36-H1740), genomic DNA

description: genomic DNA from control (KC1-G36-H1740)

value: control


title: RNAseq_TSB_RPMI_r1_T30

description: Ribosome-depleted total RNA extracted thirty minutes after shifting cells to RPMI, first replicate


title: mouse EPS cell derived mouse totipotent potential stem cells repeat 2 [WGBS]

value: totipotent potential stem cells


title: RNAseq_TSB_RPMI_r1_T15

description: Ribosome-depleted total RNA extracted fifteen minutes after shifting cells to RPMI, first replicate

value: RPMI


title: Metabolic_syndrome (KC1-G36-H0113), genomic DNA

description: genomic DNA from Metabolic_syndrome (KC1-G36-H0113)


title: Metabolic_syndrome (KC1-G36-H1873), genomic DNA

description: genomic DNA from Metabolic_syndrome (KC1-G36-H1873)


title: mouse extended pluripotent stem cells 2# repeat 1 [WGBS]


title: Metabolic_syndrome (KC1-G36-H0623), genomic DNA

description: genomic DNA from Metabolic_syndrome (KC1-G36-H0623)


title: Metabolic_syndrome (KC1-G36-H2002), genomic DNA

description: genomic DNA from Metabolic_syndrome (KC1-G36-H2002)


title: Ileum_adult (key metabolic tissues dataset)

source_name: Ileum

value: ileum


title: Control (KC1-G36-H0613), genomic DNA

description: genomic DNA from control (KC1-G36-H0613)


title: Metabolic_syndrome (KC1-G36-H0833), genomic DNA

description: genomic DNA from Metabolic_syndrome (KC1-G36-H0833)


title: Abomasum_adult (key metabolic tissues dataset)

source_name: Abomasum

value: abomasum


title: Metabolic_syndrome (KC1-G36-H0915), genomic DNA

description: genomic DNA from Metabolic_syndrome (KC1-G36-H0915)


title: mouse EPS cell derived mouse totipotent potential stem cells repeat 1 [WGBS]


title: RNAseq_TSB_RPMI_r2_T5

description: Ribosome-depleted total RNA extracted five minutes after shifting cells to RPMI, second replicate

value: Sample harvested 5 minutes after shifting cells to RPMI


title: RNAseq_TSB_RPMI_r1_T10

description: Ribosome-depleted total RNA extracted ten minutes after shifting cells to RPMI, first replicate

value: Sample harvested 10 minutes after shifting cells to RPMI


title: Omasum_adult (key metabolic tissues dataset)

source_name: Omasum

value: Holstein dairy cows

value: omasum


title: 2-cell mouse embryo derived mouse totipotent potential stem cells repeat 2 [WGBS]


title: RNAseq_TSB_RPMI_r1_T5

description: Ribosome-depleted total RNA extracted five minutes after shifting cells to RPMI, first replicate


title: Reticulum_adult (key metabolic tissues dataset)

source_name: Reticulum

value: reticulum

value: Lactating


title: Metabolic_syndrome (KC1-G36-H1870), genomic DNA

description: genomic DNA from Metabolic_syndrome (KC1-G36-H1870)


title: 2-cell mouse embryo derived mouse totipotent potential stem cells repeat 1 [WGBS]


title: RNAseq_TSB_RPMI_r2_T0

description: Ribosome-depleted total RNA extracted before shifting cells to RPMI, second replicate

source_name: Staphylococcus aureus

value: TSB

value: Sample harvested at OD600 = 3 after growth in TSB


title: CD235a+ Erythroid cells

city: Novosibirsk

first: Roman

middle: Yurievich

last: Perik-Zavodskii

state: Novosibirsk region

address: Yadrincevskaya 14

country: Russia

institute: "Research Institute of Fundamental and Clinical Immunology" (RIFCI)

data_processing:
BD Rhapsody pipeline V1.9
Link 1: https://www.bdbiosciences.com/content/dam/bdb/marketing-documents/BD_Single_Cell_Multiomics_Analysis_Setup_User_Guide.pdf
Link 2: https://www.bd.com/documents/guides/user-guides/GMX_BD-Rhapsody-genomics-informatics_UG_EN.pdf
Supplementary files format and content: Tab separated file with UMI counts for every gene and every cell, as well as Sample Tag Number.

source_name: multiplexed sample: Cord blood, Fetal liver, Thymus, Adult bone marrow

extract_protocol:
We extracted mononuclear cells from the fetal liver, the fetal thymus, the cord blood and the adult bone marrow, then performed positive magnetic separation of CD235a (Erythroid) cells using anti-CD235a-microbeads.
RNA libraries were prepared for sequencing using "mRNA Targeted, Sample Tag, and BDTM AbSeq Library Preparation with the BD RhapsodyTM Targeted mRNA and AbSeq Amplification Kit" protocol.

value: CD235a+ Erythroid cells

value: multiplexed sample:Cord blood, Fetal liver, Thymus, Adult bone marrow

value: multiplexed sample:week 18, week 20-22, 24 years old

tag: protocol

value: scRNA-Seq by BD Rhapsody


title: Control (KC1-G36-H0907), genomic DNA

description: genomic DNA from control (KC1-G36-H0907)

value: Male

value: PBMC

value: control


title: mouse extended pluripotent stem cells 1# repeat 2 [WGBS]

value: extended pluripotent stem cells


title: RNAseq_TSB_TSB_r2_T30

description: Ribosome-depleted total RNA extracted thirty minutes after shifting cells to TSB, second replicate

value: Sample harvested 30 minutes after shifting cells to their original TSB medium


title: HUCMSC4_P6_male

city: Hannover

first: Georg

last: Hansmann

address: Carl-Neuberg-Strasse 1

institute: Hannover Medical School

data_processing:
1.3 ml of denatured pool was sequenced on an Illumina NextSeq 550 sequencer using one High Output Flowcell for 75 cycles and 400 Million clusters (#20024906; Illumina).
The proprietary 10x Genomics CellRanger pipeline (v4.0.0) was used with default parameters except for the setting of expected cells (--expect-cells 1500).
CellRanger was used to align read data to the human reference genome provided by 10X Genomics (refdata-gex-GRCh38-2020-A) using the STAR aligner.
Assembly: GRCh38
Supplementary files format and content: CellRanger output

source_name: HUCMSC

growth_protocol: HUVECs were purchased from PromoCell (Heidelberg, Germany) subcultured till P3, according to manufacturer’s instructions (PromoCell Instruction Manual, Heidelberg, Germany). HUCMSCs were isolated from the human umbilical cord (Wharton’s jelly) following delivery of a full-term (38 weeks gestation) infant (here: younger sister, by cesarian section). The cells were cultivated by explant culture in MSC growth medium as reported previously (Otte et al. Tissue Eng Part C Methods. 2013;19:937-48.; PMID:23560527). Harvesting into subcultured passages was performed following treatment with accutase (Capricorn Scientific GmbH, Ebsdorfergrund, Germany) at 37°C for 3 min.

extract_protocol:
According to the Chromium NextGEM Single Cell 3ʹ Reagent Kits v3.1 User Guide (Manual Part Number CG000204 Rev B; 10x Genomics)
Library preparation for single cell mRNA-Seq analysis was performed according to the Chromium NextGEM Single Cell 3ʹ Reagent Kits v3.1 User Guide (Manual Part Number CG000204 Rev B; 10x Genomics). A twofold excess of cells was loaded to the 10x controller in the specified volume in order to reach a target number of 1500 cells per sample. Equal molar proportions of eight generated libraries were pooled accordingly, denatured with NaOH, and were finally diluted to 1.8pM according to the ‘Denature and Dilute Libraries Guide’ (Document # 15048776 v02; Illumina). 1.3 ml of denatured pool was sequenced on an Illumina NextSeq 550 sequencer using one High Output Flowcell for 75 cycles and 400 Million clusters (#20024906; Illumina).

tag: passage

value: HUCMSC

value: male


title: pLN_PBS_KG_2

city: Glasgow

first: John

middle: Joseph

last: Cole

address: University Avenue

institute: University of Glasgow

data_processing:
A high read quality (mean score above 28) in all samples was confirmed using FastQC.
To remove adapters, ensure proper read pairing and trim reads with low start or end read quality the package Trim-Galore! was used under default settings.
Next reads were aligned to the mm10 genome using Tophat2, with the flags: --b2-sensitive, --no-coverage-search, and version 87 of the mouse transcriptome.
FPKMs were generated using cufflinks under default settings. All samples had a concordant pair alignment rate above 75% and at least 20 million aligned concordant read pairs.
Differential expression was called using the bioconductor package DESeq2 with adjusted p < 0.05 and absolute log2fold >1 considered significant.
The data was visualised using Searchlight2 and R .
Genome_build: mm10, v87
Supplementary_files_format_and_content: Tab delimited read count file.

source_name: CD45+ leukocytes migrated from joint to Lymph Node

extract_protocol:
Ankle joints or ear pinnae were teased apart using forceps; excised LNs were passed through Nitex mesh (Cadisch Precision Meshes) and both tissues digested for 25 minutes at 37 °C with 2.64 mg/mL collagenase D (Roche). Joint tissue was then homogenized using the Miltenyi Tissue Dissociator and passed through a 70 μm cell strainer to obtain a single cell suspension. Joint and LN single cell suspensions were then washed in FACS buffer (PBS/ 2 % FCS/ 2mM EDTA) and stained for flow cytometry analysis. Cells stained for viability in PBS using Fixable Viability Dye (eFluor506; eBioscience) for 30 minutes at 4 °C. Cells were then washed in FACS buffer and subsequently incubated with FcR block for 10-15 minutes at 4 °C and then appropriate fluorochrome-conjugated antibodies (Supplemental Table 7) added and the cells stained for 30 minutes at 4 °C. Viable, single CD45+ Kaede Red+ cells were sorted using an Aria III (BD Biosciences).
RNA libraries were prepared for sequencing using standard Illumina protocols
Pair ended with a 100bp read length (Source Bioscience, Nottingham, UK).

treatment_protocol: CD4+ T cells from OT-II CD45.1 mice were polarized in vitro over 72 hours towards a Th1 phenotype in the presence of 1 μg/mL peptide OVA323-339 (pOVA) ((Sigma-Aldrich), 10 ng/mL rIL-12 and 2 μg/mL anti-IL-4 (Both R&D). Recipient mice received 3 x 106 in vitro polarized Vα2+Vβ5+ OT-II Th1 cells i.v. The following day, mice were immunization with 100 μg OVA (Worthingtons) in Complete Freuds Adjuvant (CFA) (Sigma Aldrich)in the scruff of the neck. Ten days later, mice were challenged in the footpad with PBS (Gibco) or 100 μg heat-aggregated ovalbumin (HAO), as previously described (10). Ear pinna inflammation was induced following the same protocol, except that the mice were challenged with either PBS or 100 μg HAO in the ear pinna.

value: Kaede

value: joint

value: steady state


title: mouse extended pluripotent stem cells [scATAC-seq]

description: EPS

library_source: genomic single cell

data_processing:
The single-cell ATAC-seq reads were mapped to mouse reference genome mm10 using Cell Ranger v3.1.0.
Assembly: mm10 (GRCm38)
Supplementary files format and content: Tar archives contain Cell Ranger ATAC output (fragments.tsv.gz, fragments.tsv.gz.tbi).

source_name: mouse extended pluripotent stem cells

extract_protocol:
Cells were washed and resuspended in 1X PBS (calcium and magnesium free) containing 10% FBS. Cell viability was determined by Count Star. The nuclei were isolated and washed according to the method provided by 10X Genomics: “Nuclei Isolation for Single Cell ATAC Sequencing (CG000169)”. Then the nucleus was resuspended by chilled Diluted Nuclei Buffer (10x Genomics; 2000153). The volume of Diluted Nuclei Buffer used to resuspend nuclei was based on the number of starting cells and the final target nuclei concentration. Countstar (Rigel S2) was used to count the nuclei. The nuclei were then immediately proceeded to construct single cell ATAC-seq libraries.
The nuclei were partitioned into nanoliter-scale GEMs by using Chromium Chip E Single Cell Kit (Product Code 1000156) and Chromium Single Cell ATAC Library & Gel Bead Kit (Product Code 1000110). A pool of ~750,000 10x Barcodes was sampled to separately and uniquely index the transposed DNA of each individual nucleus. Then the libraries were generated (performed by CapitalBio Technology, Beijing). The libraries were sequenced using an Illumina Novaseq sequencer with a sequencing depth of at least 25k read pairs per nucleus with pair-end 50 bp (PE50) reading strategy.


title: pLN_PBS_KG_1


title: HUCMSC3_P6_male


title: in vitro induced hepatocytes day7

city: Yokohama

first: Takahiro

last: Suzuki

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

institute: RIKEN

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

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

data_processing: GenomeStudio software v2010.3

source_name: iPS cells (201B7)

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified using NucleoSpin Tissue (Macherey-Nagel) according to standard instructions

tag: differentiation day

value: day 7


title: pLN_HAO_3

source_name: CD45+ leukocytes migrated from inflammed joint to Lymph Node

value: inflammed


title: RNAseq_TSB_TSB_r2_T15

description: Ribosome-depleted total RNA extracted fifteen minutes after shifting cells to TSB, second replicate

value: TSB

value: Sample harvested 15 minutes after shifting cells to their original TSB medium


title: mouse embryonic stem cells [scATAC-seq]

description: ES

value: embryonic stem cells


title: mouse EPS cell derived mouse totipotent potential stem cells [scATAC-seq]

description: EPS-TPS

value: totipotent potential stem cells


title: RNAseq_TSB_TSB_r2_T10

description: Ribosome-depleted total RNA extracted ten minutes after shifting cells to TSB, second replicate

value: Sample harvested 10 minutes after shifting cells to their original TSB medium


title: in vitro induced hepatocytes day28

value: day 28


title: RNAseq_TSB_TSB_r2_T5

description: Ribosome-depleted total RNA extracted five minutes after shifting cells to TSB, second replicate

value: Sample harvested 5 minutes after shifting cells to their original TSB medium


title: in vitro induced hepatocytes day21

value: day 21


title: HUCMSC2_P6_male


title: RNAseq_TSB_TSB_r2_T0

description: Ribosome-depleted total RNA extracted before shifting cells to TSB, second replicate

value: Sample harvested at OD600 = 3 after growth in TSB


title: in vitro induced definitive endoderm 72h

tag: differentiation time


title: pLN_HAO_1


title: Rectum_adult (key metabolic tissues dataset)

source_name: Rectum

value: Holstein dairy cows

value: rectum

tag: developmental stage

value: Lactating


title: mouse TPS cell derived blastoid [scRNA-seq]

description: TPS-blastoid

data_processing:
The clean single-cell RNA-seq reads were mapped to mouse reference genome mm10 using Cell Ranger v3.1.0.
Assembly: mm10 (GRCm38)
Supplementary files format and content: Tar archives contain Cell Ranger output (barcodes.tsv, features.tsv, matrix.mtx).

source_name: mouse TPS cell derived blastoid

extract_protocol:
Cells were washed and resuspended in 1X PBS (calcium and magnesium free) containing 10% FBS. Cell viability was determined by Count Star, and the density of living cells were adjusted  to 300-600 living cells per microliter. Cell suspension was loaded onto the Chromium single cell controller (10x Genomics). Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3.1 (10x Genomics, 1000075) and Chromium Single Cell B Chip Kit (10x Genomics, 1000074) were used to generate single-cell gel beads in the emulsion according to the manufacturer’s protocol. In short, single cells were suspended in PBS containing 0.04% BSA. About 6,000 cells were added to each channel, and the target cells were recovered (about 3,000 cells). Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs. Reverse transcription was performed on a S1000TM Touch Thermal Cycler (Bio Rad) at 53°C for 45 min, followed by 85°Cfor 5 min, and hold at 4°C. The cDNA was generated and then amplified, and quality assessed using an Agilent 4200(performed by CapitalBio Technology, Beijing).
Single-cell RNA-seq libraries were constructed using Single Cell 3’ Library and Gel Bead Kit V3.1 according to the manufacturer’s introduction. The libraries were finally sequenced using an IlluminaNovaseq6000 sequencer with a sequencing depth of at least 100,000 reads per cell with pair-end 150 bp (PE150) reading strategy (performed by CapitalBio Technology, Beijing).

value: blastoid


title: pLN_HAO_2

value: Kaede

value: joint

tag: treatment


title: HUCMSC1_P3_female

value: HUCMSC

value: female


title: 2-cell mouse embryo derived mouse totipotent potential stem cells [scATAC-seq]


title: in vitro induced hepatocytes day14

value: day 14


title: pLN_PBS_KG_3

value: steady state


title: in vitro induced definitive endoderm 66h


title: WD L-TBA_3

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

institute: MRC London Institute of Medical Sciences

data_processing:
Primary analysis RTA 1.17.21.3 and Secondary analysis CASAVA- 1.8.4
Sequencing was conducted on an Illumina HiSeq 2500 system with 50 base pair single-end reads
Sequencing reads were mapped to mm9 genome using Tophat 2.0.11
Gene based counting was performed using the Rsubread package.
Gene expression analysis was performed using the DESeq2 Bioconductor package (DESeq2_1.18.1 )
Genome_build: mm9
Supplementary_files_format_and_content: comma-delimited text file include raw counts for each Sample generated by  Rsubread.

growth_protocol: H-TBA and L-TBA mice were fed a Western diet for 30 weeks.

extract_protocol:
Livers were flash frozen. RNA was then extracted by Trizol Reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Liver

value: Western diet for 30 weeks

tag: group

value: L-TBA


title: HUVEC1_ P6_male

source_name: HUVEC

value: HUVEC

value: male


title: Naive_3

source_name: CD45+ leukocytes migrated from ear to Lymph Node

value: ear


title: HUVEC2_P6_male


title: RNAseq_TSB_RPMI_r1_T0

institute: University of Edinburgh

description: Ribosome-depleted total RNA extracted before shifting cells to RPMI, first replicate

tag: media

value: TSB

value: Sample harvested at OD600 = 3 after growth in TSB


title: RNAseq_TSB_TSB_r1_T15

description: Ribosome-depleted total RNA extracted fifteen minutes after shifting cells to TSB, first replicate

value: Sample harvested 15 minutes after shifting cells to their original TSB medium


title: mouse TPS cell derived teratomas 1# [scRNA-seq]

source_name: mouse TPS cell derived teratomas 1#

tag: cell type

value: teratoma


title: RNAseq_TSB_TSB_r1_T10

description: Ribosome-depleted total RNA extracted ten minutes after shifting cells to TSB, first replicate

value: Sample harvested 10 minutes after shifting cells to their original TSB medium


title: RNAseq_TSB_TSB_r1_T30

description: Ribosome-depleted total RNA extracted thirty minutes after shifting cells to TSB, first replicate

value: Sample harvested 30 minutes after shifting cells to their original TSB medium


title: WD L-TBA_2

source_name: Liver


title: LN_KR_2

source_name: CD45+ leukocytes migrated from inflammed ear to Lymph Node

value: Kaede

value: inflammed


title: mouse TPS cell derived teratomas 2# [scRNA-seq]

source_name: mouse TPS cell derived teratomas 2#


title: WD H-TBA_4

value: H-TBA


title: Naive_2


title: in vitro induced definitive endoderm 60h


title: Naive_1


title: LN_KR_3


title: mouse embryonic stem cells 2# [scRNA-seq]

source_name: mouse embryonic stem cells 2#

value: embryonic stem cells


title: USA300_CLASH_RNase_III_LPM54_r3.3

description:
RNA-RNA complexes immunoprecipitated via RNase III, LPM pH 5.4 medium, third replicate, technical replicate 3
Supplementary_Table_4.xlsx
Intermolecular_hybrids_LPM_shift_LPM5_data.txt

value: USA300 rnc:HTF

value: LPM 5.4

value: Sample harvested after shifting cells to LPM pH 5.4 for 15 minutes


title: mouse E17.5 chimeric placenta 1# [scRNA-seq]

source_name: mouse E17.5 chimeric placenta 1#

value: E17.5 placenta


title: mouse E17.5 chimeric placenta 2# [scRNA-seq]

source_name: mouse E17.5 chimeric placenta 2#


title: RNAseq_TSB_TSB_r1_T0

description: Ribosome-depleted total RNA extracted before shifting cells to TSB, first replicate

source_name: Staphylococcus aureus


title: LN_KR_1


title: RNAseq_TSB_TSB_r1_T5

description: Ribosome-depleted total RNA extracted five minutes after shifting cells to TSB, first replicate

value: Sample harvested 5 minutes after shifting cells to their original TSB medium


title: WD H-TBA_3

value: Liver

value: Western diet for 30 weeks


title: mouse extended pluripotent stem cells 1# [scRNA-seq]

value: extended pluripotent stem cells


title: USA300_CLASH_RNase_III_LPM54_r3.2

description:
RNA-RNA complexes immunoprecipitated via RNase III, LPM pH 5.4 medium, third replicate, technical replicate 2
Supplementary_Table_4.xlsx
Intermolecular_hybrids_LPM_shift_LPM5_data.txt


title: WD H-TBA_2


title: Joint_HAO_K_2

source_name: Inflammed joint non-migrated CD45+ leukocytes

value: joint


title: Joint_HAO_K_1


title: in vitro induced hepatocytes day0

value: day 0


title: WD H-TBA_1


title: mouse EPS cell derived mouse totipotent potential stem cells [scRNA-seq]

description: EPS-TPS

value: totipotent potential stem cells


title: USA300_CLASH_RNase_III_LPM76_r3.3

description:
RNA-RNA complexes immunoprecipitated via RNase III, LPM pH 7.6 medium, third replicate, technical replicate 3
Supplementary_Table_4.xlsx
Intermolecular_hybrids_LPM_shift_LPM7_data.txt

value: LPM 7.6

value: Sample harvested after shifting cells to LPM pH 7.6 for 15 minutes