title: COVID_33

description:
blood from COVID-19 patient
C33


title: NONCOVID_22

status: Public on May 31 2021

type: genomic

city: Madison

first: Andy

last: Madrid

state: Wisconsin

address: 600 Highland Ave

department: Neurological Surgery

country: USA

institute: University of Wiconsin - Madison

description:
blood from non-COVID-19 patient
NC22

hyb_protocol: hybridized to Illumina HumanMethylationEPIC arrays using standard Illumina instructions

scan_protocol: arrays were imaged using BeadArray Readerusing standard recommended settings

data_processing:
minfi
matrix_processed.csv = average beta
matrix_signal_intensities.csv = unmethylated and methylated signal intensities

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

label_protocol: standard illumina protocol

extract_protocol: genomic DNA from whole blood tissue was extracted using the GeneJET whole blood kit according to the manufacturer's recommendations

tag: Sex

value: M

tag: age

tag: race

value: AA

tag: death

tag: covid status

tag: tissue

value: blood


title: sRNA control_w1118 ovaries

type: SRA

city: Cambridge

first: Daniel

last: Gebert

state: Cambridgeshire

address: Downing Street

department: Department of Genetics

country: United Kingdom

institute: University of Cambridge

description:
Size-selected small RNA
4N adaptors at 5' and 3' ends

library_source: transcriptomic

data_processing:
Small RNA sequencing reads were quality-filtered and trimmed with Trim-Galore, applying standard settings.
For cross-sample normalization, trimmed reads were mapped to the complete set of mature miRNA sequences of D. melanogaster (miRBase; Kozomara and Griffiths-Jones, 2011) with bowtie (Langmead et al., 2009), reporting all best valid alignments without mismatches. In parallel, trimmed reads were mapped to the combined set of non-coding RNA, protein-coding, and pseudogene sequences (FlyBase) allowing two mismatches and retaining unmatched reads in the size range of 23-29 nt. Filtered reads were then mapped to the D. melanogaster genome (dm3) using bowtie and allowing either perfect unique matches or all best valid alignments without mismatches.
dm3
bedgraph files generated by bowtie, samtools, bedtools

molecule: total RNA

organism: Drosophila melanogaster

source_name: ovaries

extract_protocol:
Total RNA from dissected adult ovaries was isolated using Trizol reagent (Invitrogen) and quantified using Qubit (Invitrogen).
Small RNA-sequencing analysis was performed on 10 µg of total RNA using the NEBNext® Small RNA Library Prep Set for Illumina® and with an initial 2S rRNA depletion step as previously described (Li et al., 2009).
Libraries were multiplexed using the NEBNext® Multiplex Oligos for Illumina® and sequenced in single-end, 50-nt-long reads on an Illumina HiSeq 2500.

tag: strain

value: ovaries

value: adult

tag: genotype

value: control


title: sRNA w_38CD ovaries

description: Size-selected small RNA

value: w; 38C-delta


title: sRNA 20ApD_42ABD ovaries

description: Size-selected small RNA

value: 20A(p)-delta; 42AB-delta


title: ILC2

city: Braunschweig

first: Michael

last: Beckstette

state: Lower Saxony

address: Inhoffenstrase 7

department: Molecular Infection Biology

country: Germany

institute: Helmholtz Centre for Infection Research

library_source: genomic

data_processing:
Illumina RTA3 was used for basecalling.
All libraries have been assessed for sufficient sequencing quality and potential adapter contamination using programs FastQC (Babraham Bioinformatics; https://www.bioinformatics.babraham.ac.uk/projects/fastqc/), trim_galore and cutadapt. To avoid potential methylation bias due to insufficient end-repair reaction, from both reads (R1/R2) the first 10 bases at the 5' as well as the 3' end have been trimmed after adapter removal and trimming of low-quality ends with a Phred score below 20. Reads, which are shorter than 20 nucleotides after trimming have been discarded.
Quality controlled libraries have been mapped against the mouse reference genome (version: GRCm38, w/o gonosomes) using the bisulfite short read mapping software BSMAP. In order to accurately measure the methylation levels of cytosines inside CpG context genome-wide and obtain corresponding coverage information, methylation level calling has taken only properly paired unique read pair mappings (methratio.py parameters: --unique, --paired,--remove-duplicate) into account.
The reliable detection of DMRs even in the absence of replicates was performed with the software tool metilene. We considered for the detection process only CpG motifs with a coverage of at least five that are present in at least one sample. In addition, a DMR has to contain at least three CpG's with a distance between two CpGs of at most 200 nucleotides and a total length of the region of at least 300. Further on, to be classified as DMR, the difference in mean methylation (i.e., mean over all CpG's of a region) of a region between two compared samples/conditions has to be greater or equal 25 percent and the adjusted P-value from the 2D-KS test has to be at most 0.1
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: *,methout.txt: CSV formatted file with methylation values for all CpGs for each sample as generated by  BSMAp/methratio.py; *metilene_DMRs.csv.gz: Differentially methylated regions for each pairwise comparison (generated by metilene)

organism: Mus musculus

source_name: Innate lymphoid cells 2

extract_protocol:
Lymph nodes were removed and meshed through a sieve. Genomic DNA was prepared from ILC subpopulations sorted by FACS. Genomic DNA was converted by bisulfite and subjected to library preparation.
The bislufite converted DNA was fragmented by sonication and served as input for library preparation by using the Accel-NGS Methyl-Seq DNA Library Kit.

tag: cell type

value: Innate lymphoid cells

value: lymph node

tag: marker


title: NONCOVID_10

description:
blood from non-COVID-19 patient
NC10

value: W


title: ERT2-Cre_Pcgf6_Control_EB_rep1

city: Tsurumi-ku,Yokohama

first: Hiroki

last: Sugishita

state: Kanagawa

address: 1-7-22, Suehiro-cho

department: IMS

country: Japan

institute: RIKEN

data_processing:
Sequencing was performed with either 75 bp single-end read by NextSeq500 (run by Kazusa DNA Research Institute) or 50 bp single-end read by HiSeq1500 (run in RIKEN-IMS NGS facility).
The data were mapped onto UCSC-mm9 from illumina igenome and counted the reads on exon using STAR (version 2.5.2b: --outSAMtype BAM SortedByCoordinate), and the counted reads are normalized to TPM(Transcripts Per Million).
Each gene reads on exon were normalized by DESeq2 for fold change and p-value calculation.
Genome_build: mm9
Supplementary_files_format_and_content: tpm values

source_name: EB

growth_protocol: Embryonic stem cells (ESCs) were cultured with LIF (1U: Laboratory made), SU5402 (Altair corporation), PD184352 (Altair corporation) and CHIR99021 (Altair corporation) on MEF. For Embryoid Body (EB) formation, ESCs were cultured without LIF, SU5402, PD184352, CHIR99021 for 2 days on low attach culture dish. For epiblast stem cell (EpiSC) establishment, Embryoid Body (day2) are dispersed. And the cells were cultured on MEF with ActivinA (Peprotech), bFGF (Wako) and IWP-2 (Wako) on MEF in F12 medium (Gibco) 1%KSR (Gibco).

extract_protocol:
Total RNA was extracted using simplyRNA Tissue Kit (Promega).
Sequencing libraries were generated according to NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB) protocol.

tag: tamoxifen treatment

value: without 4-OHT

value: embryoid body

tag: replicate


title: RNAP2_ERT2-Cre_Pcgf1Control_Triptolide_rep1

description:
ERT2-Cre;Pcgf1f/f
SUZ12_ERT2-Cre_Pcgf1Control_Triptolide.bw

data_processing:
Sequencing was performed with 75 bp single-end read by NextSeq500 (run by Kazusa DNA Research Institute) or 50bp single-end read by HiSeq1500 (run in RIKEN-IMS NGS facility).
The data were mapped onto UCSC-mm9 from illumina igenome. Generated sam format file combine to bam format file using samtools view (version 1.3.1). Then, PCR duplicate and multiple aligned reads are removed.
For bigwig generation, bam format files were processed by deeptools bamCoverage. The data of CpG island and TSS are derived from UCSC mm9.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig

source_name: Triptolide

extract_protocol:
10^6-10^7 cells were cross-linking by 1% formaldehyde for 10 min at room temperature. Cross-linked cells were washed once with PBS, added swelling buffer (0.1% NP-40, 1 mM DTT in PBS) and chilled on ice for 10 minutes. After centrifuge, pellets were suspended with RIPA buffer (10 mM Tris-HCl pH8.0, 1mM EDTA, 140 mM NaCl, 1%Triton X-100, 0.1% SDS, 0.1% Sodium Deoxycholate), and then were sonicated by using a BioRuptor sonicator (Diagenode). After sonication, DNA concentration is measured with Qubit 1x dsDNA HS Assay Kit (Thermo, cat. Q33230). On the other hand, protein A/G beads were prepared as washed twice with beads blocking buffer and suspended with beads blocking buffer with approximately 5 µg of antibody and incubated at 4ºC for more than 2 hours. Then, antibody attached beads were washed twice with beads blocking buffer and the chromatin samples were added to those antibody-attached-beads. After overnight incubation at 4ºC, chromatin samples bound beads were washed with RIPA for 6 times, RIPA high salt buffer(10 mM Tris-HCl pH8.0, 1mM EDTA, 500 mM NaCl, 1%Triton X-100, 0.1% SDS, 0.1% Sodium Deoxycholate) twice, LiCl buffer (10 mM Tris-HCl pH8.0, 1 mM EDTA, 250 mM LiCl, 0.5% NP-40, 0.5% Sodium Deoxycholate) twice and TE twice. The chromatins were eluted with elution buffer (10 mM Tris-HCl pH8.0, 5 mM EDTA, 300 mM NaCl, 0.1 % SDS) overnight at 65ºC and treated with RNase for 30 min for 37°C and further incubation with Proteinase K for 1 hour at 37ºC. Then DNA samples were purified and used for further ChIP-qPCR or ChIP-seq.
ChIP-seq libraries were prepared by using NEBNext Ultra II FS DNA prep kit (NEB E7805) following manufacturer’s instruction.

value: embryonic stem cell

tag: antibody

value: RNAP2 (Abcam, #ab817)


title: NK

source_name: Natural killer cells


title: sRNA w_42ABD ovaries

description: Size-selected small RNA

value: w; 42AB-delta


title: sRNA w_38CD_42ABD ovaries

description: Size-selected small RNA

value: w; 38C-delta, 42AB-delta


title: COVID_20

description:
blood from COVID-19 patient
C20

value: M

value: O


title: ERT2-Cre_Pcgf6_Mutant_ES_rep1

source_name: ES

value: with 4-OHT


title: COVID_32

description:
blood from COVID-19 patient
C32

value: H

value: blood


title: SUZ12_ERT2-Cre_Pcgf1Mutant_Triptolide_rep2

description:
ERT2-Cre;Pcgf1∆/∆
SUZ12_ERT2-Cre_Pcgf1Mutant_Triptolide.bw

value: SUZ12 (Cell Signaling, #3737)


title: sRNA 20ApD ovaries

description: Size-selected small RNA

value: ovaries

value: adult


title: COVID_56

description:
blood from COVID-19 patient
C56

value: F


title: RNAP2_ERT2-Cre_Pcgf1Control_DMSO_rep1

description:
ERT2-Cre;Pcgf1f/f
SUZ12_ERT2-Cre_Pcgf1Control_DMSO.bw

source_name: DMSO


title: sRNA 20AD ovaries

description: Size-selected small RNA


title: COVID_68

description:
blood from COVID-19 patient
C68


title: ILC3

source_name: Innate lymphoid cells 3

value: Innate lymphoid cells

value: lymph node


title: ERT2-Cre_Pcgf2_Pcgf4_Control_EB_rep2

value: without 4-OHT


title: ERT2-Cre_Pcgf6_Mutant_EB_rep1

value: embryoid body


title: ERT2-Cre_Pcgf6_Control_ES_rep1

value: embryonic stem cell


title: sRNA w1118 ovaries

description: Size-selected small RNA

value: control


title: RNA het w_38CD_42ABD ovaries rep1

description: Poly(A)-selected RNA

data_processing:
RNA-seq data were mapped to the Drosophila melanogaster genome (dm3) and the FlyBase and Repbase transposon consensus database using the piPipes package (version 1.5.0; https://github.com/bowhan/piPipes), following the RNA-seq pipeline (Han et al., 2015).
Libraries were aligned to ribosomal RNA using Bowtie2 (Langmead and Salzberg, 2012), and non-rRNA-mapping reads were then mapped to the transcriptome and transposon consensus using Bowtie2.
dm3
bigwig files generated using the piPipes package

extract_protocol:
Total RNA from dissected adult ovaries was isolated using Trizol reagent (Invitrogen) and quantified using Qubit (Invitrogen). Contaminating DNA was removed using RQ1 DNAse as described by the manufacturer (Promega).
Poly(A)-selected RNA-sequencing (RNA-seq) analysis was performed on 2.5µg of total RNA using the NEBNext® Poly(A) mRNA Magnetic Isolation Module and the NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina®.
Libraries were multiplexed using the NEBNext® Multiplex Oligos for Illumina® and sequenced in single-end, 50-nt-long reads on an Illumina HiSeq 2500.

value: w; 38C-delta, 42AB-delta/+


title: ERT2-Cre_Pcgf2_Pcgf4_Mutant_EB_rep2


title: RNA het w_38CD_42ABD ovaries rep2

description: Poly(A)-selected RNA


title: RNA w_38CD_42ABD ovaries rep2

description: Poly(A)-selected RNA

value: w; 38C-delta, 42AB-delta


title: ERT2-Cre_Pcgf2_Pcgf4_Control_ES_rep2


title: COVID_43

description:
blood from COVID-19 patient
C43


title: RNA w_38CD_42ABD ovaries rep1

description: Poly(A)-selected RNA


title: COVID_19

description:
blood from COVID-19 patient
C19

value: M

value: W


title: SUZ12_ERT2-Cre_Pcgf1Control_DMSO_rep2


title: ERT2-Cre_Pcgf2_Pcgf4_Mutant_EB_rep1

value: with 4-OHT


title: SUZ12_ERT2-Cre_Pcgf1Mutant_Triptolide_rep1


title: COVID_07

description:
blood from COVID-19 patient
C7


title: ERT2-Cre_Pcgf2_Pcgf4_Mutant_ES_rep2


title: ERT2-Cre_Pcgf2_Pcgf4_Control_EB_rep1


title: NONCOVID_21

description:
blood from non-COVID-19 patient
NC21


title: SUZ12_ERT2-Cre_Pcgf1Control_Triptolide_rep1


title: SUZ12_ERT2-Cre_Pcgf1Mutant_DMSO_rep2

description:
ERT2-Cre;Pcgf1∆/∆
SUZ12_ERT2-Cre_Pcgf1Control_Triptolide.bw


title: ERT2-Cre_Pcgf2_Pcgf4_Mutant_ES_rep1


title: RNA het 20ApD_42ABD ovaries rep2

description: Poly(A)-selected RNA

value: 20A(p)-delta/+; 42AB-delta/+


title: RNA 20ApD_42ABD ovaries rep2

description: Poly(A)-selected RNA

value: 20A(p)-delta; 42AB-delta


title: COVID_67

description:
blood from COVID-19 patient
C67

value: blood


title: SUZ12_ERT2-Cre_Pcgf1Mutant_DMSO_rep1

description:
ERT2-Cre;Pcgf1∆/∆
SUZ12_ERT2-Cre_Pcgf1Mutant_DMSO.bw

value: SUZ12 (Cell Signaling, #3737)


title: RING1B_ERT2-Cre_Pcgf1Mutant_Triptolide_rep2

description:
ERT2-Cre;Pcgf1∆/∆
RING1B_ERT2-Cre_Pcgf1Mutant_Triptolide.bw

value: RING1B (Laboratory made)


title: ERT2-Cre_Pcgf2_Pcgf4_Control_ES_rep1


title: COVID_31

description:
blood from COVID-19 patient
C31

value: O


title: NONCOVID_09

description:
blood from non-COVID-19 patient
NC9

value: F


title: RING1B_ERT2-Cre_Pcgf1Control_Triptolide_rep2

description:
ERT2-Cre;Pcgf1f/f
RING1B_ERT2-Cre_Pcgf1Control_Triptolide.bw


title: SUZ12_ERT2-Cre_Pcgf1Control_Triptolide_rep2

description:
ERT2-Cre;Pcgf1f/f
SUZ12_ERT2-Cre_Pcgf1Mutant_DMSO.bw


title: COVID_55

description:
blood from COVID-19 patient
C55

value: AA


title: SUZ12_ERT2-Cre_Pcgf1Control_DMSO_rep1

value: without 4-OHT


title: COVID_42

description:
blood from COVID-19 patient
C42


title: RNA 20ApD_42ABD ovaries rep1

description: Poly(A)-selected RNA

value: ovaries

value: adult


title: ERT2-Cre_Pcgf3_Pcgf5_Control_EB_rep2

value: embryoid body


title: RING1B_ERT2-Cre_Pcgf1Mutant_DMSO_rep2

value: embryonic stem cell


title: RING1B_ERT2-Cre_Pcgf1Control_DMSO_rep2


title: RNA het 20ApD_38CD ovaries rep2

description: Poly(A)-selected RNA

value: 20A(p)-delta/+; 38C-delta/+


title: COVID_30

description:
blood from COVID-19 patient
C30

value: M


title: COVID_18

description:
blood from COVID-19 patient
C18

value: H


title: ERT2-Cre_Pcgf3_Pcgf5_Mutant_ES_rep2

value: with 4-OHT


title: RNA het 20ApD_38CD ovaries rep1

description: Poly(A)-selected RNA


title: RING1B_ERT2-Cre_Pcgf1Control_Triptolide_rep1


title: ERT2-Cre_Pcgf3_Pcgf5_Mutant_EB_rep1


title: RNA 20ApD_38CD ovaries rep1

description: Poly(A)-selected RNA

value: 20A(p)-delta; 38C-delta


title: RNA 20ApD_38CD ovaries rep2

description: Poly(A)-selected RNA


title: RNA het 20ApD_42ABD ovaries rep1

description: Poly(A)-selected RNA

value: 20A(p)-delta/+; 42AB-delta/+


title: RING1B_ERT2-Cre_Pcgf1Mutant_Triptolide_rep1


title: RING1B_ERT2-Cre_Pcgf1Mutant_DMSO_rep1

description:
ERT2-Cre;Pcgf1∆/∆
RING1B_ERT2-Cre_Pcgf1Mutant_DMSO.bw


title: ERT2-Cre_Pcgf3_Pcgf5_Control_ES_rep2


title: COVID_06

description:
blood from non-COVID-19 patient
C6

value: blood


title: ERT2-Cre_Pcgf3_Pcgf5_Control_EB_rep1


title: RING1B_ERT2-Cre_Pcgf1Control_DMSO_rep1

description:
ERT2-Cre;Pcgf1f/f
RING1B_ERT2-Cre_Pcgf1Control_DMSO.bw


title: RNA het triple mutant ovaries rep2

description: Poly(A)-selected RNA

value: 20A(p)-delta/+; 38C-delta, 42AB-delta/+


title: ERT2-Cre_Pcgf3_Pcgf5_Mutant_ES_rep1


title: NONCOVID_08

description:
blood from non-COVID-19 patient
NC8

value: W


title: ERT2-Cre_Pcgf3_Pcgf5_Mutant_EB_rep2


title: RNA triple mutant ovaries rep2

description: Poly(A)-selected RNA

value: 20A(p)-delta; 38C-delta, 42AB-delta


title: RNA het triple mutant ovaries rep1

description: Poly(A)-selected RNA


title: PCGF1_ERT2-Cre_EedMutant_EB_rep2

description:
ERT2-Cre;Eed∆/∆
PCGF1_ERT2-Cre_EedMutant_EB_rep2.bw

value: PCGF1 (Laboratory made)


title: PCGF1_ERT2-Cre_EedControl_EB_rep2

description:
ERT2-Cre;Eedf/f
PCGF1_ERT2-Cre_EedControl_EB_rep2.bw


title: COVID_53

description:
blood from COVID-19 patient
C53

value: F

value: O


title: PCGF1_ERT2-Cre_EedMutant_ES_rep2

description:
ERT2-Cre;Eed∆/∆
PCGF1_ERT2-Cre_EedMutant_ES_rep2.bw


title: NONCOVID_20

description:
blood from non-COVID-19 patient
NC20

value: AA


title: COVID_41

description:
blood from COVID-19 patient
C41


title: ERT2-Cre_Pcgf3_Pcgf5_Control_ES_rep1

value: without 4-OHT


title: H3K27me3_ERT2-Cre_Pcgf1Control_EB_rep2

data_processing:
Library strategy: CUT&Tag
Sequencing was performed with 50x2 bp pair-end reads by NovaSeq6000 (run in RIKEN-IMS NGS facility) or 75x2 bp pair-end read by NextSeq500 (run by Kazusa DNA Research Institute).
Paired-end fastq data were aligned to UCSC mm9-hg38 reference genome by Bowtie2 2.3.2 with default option. Generated sam format file combine to bam format file using samtools view (version 1.3.1).
Then, PCR duplicate and multiple aligned reads are removed. For bigwig generation, bam format files were processed by deeptools bamCoverage (version 2.5.0.1 : --scaleFactor).
Spike-in scaling factor is calculated by the ratio of each human mapped reads and total reads.
Genome_build: mm9

extract_protocol: CUT&Tag was performed as described in Kaya-Okur et al., (Kaya-Okur et al., 2019), with the minor changes. pAG-Tn5 was used insted of pA-Tn5. pAG-Tn5 was constructed from pAG-MNase (addgene #123461) and pA-Tn5 (addgene #124601) plasmid DNAs. pAG sequence was excised from the pAG-MNase plasmid by digestion with EcoRI-HindIII. The pAG fragment was integrated into the Tn5 vector in which pA sequence was removed. ESCs and EB from either Pcgf1-KO or Ring1a/b mutant were dissociated by Accumax (Innovative Cell Technologies. For each assay, 100,000 cells were used with 10,000 cells of HEK293T as spike-in control.

value: embryoid body


title: COVID_29

description:
blood from COVID-19 patient
C29


title: RNA w1118 ovaries rep2

description: Poly(A)-selected RNA

data_processing:
Paired-end reads were mapped to the D. melanogaster genome using BWA MEM (Li and Durbin, 2009).
The resulting SAM/BAM files were then filtered to retain only uniquely mapping reads using Samtools (Li et al., 2009) and the command line utility grep. A map quality filter with a threshold value of 60 was applied with Samtools.
Bigwig files were created with Bedtools (Quinlan and Hall, 2010) and the UCSC genome browser command-line tool bedGraphToBigWig.
Analysis of total genomic TE copy numbers was conducted by mapping paired-end reads to the complete set of D. melanogaster TE consensus sequences (FlyBase) using bowtie2 and limiting the number of distinct valid alignments to one per read (‘-k 1’). Read counts for each TE family were were multiplied by 150 nt paired-end read base pairs (300), divided by TE consensus sequence length and genomic read coverage.
dm3
bigwig files generated by BWA MEM, samtools, bedtools and bedGraphToBigWig

extract_protocol:
Genomic DNA was obtained from 20-40 female adult flies from w1118 and a triple mutant (20A(p)∆; 38C∆, 42AB∆) stock. DNA was extracted using the Quick-DNA Microprep Kit w/ Zymo-Spin™ (Zymo Research) and quantified using Qubit (Invitrogen).
Library preparation was performed on 0.25µg of genomic DNA using the Nextera DNA Flex Library Prep kit as described by the manufacturer (Illumina).
Libraries were multiplexed and sequenced in paired-end, 150-nt-long reads on an Illumina NovaSeq.

value: ovaries

value: adult

value: control


title: RNA w1118 ovaries rep1

description: Poly(A)-selected RNA


title: COVID_17

description:
blood from COVID-19 patient
C17

value: M


title: H3K27me3_ERT2-Cre_Pcgf1Mutant_EB_rep2

value: with 4-OHT


title: H3K27me3_ERT2-Cre_Pcgf1Control_ES_rep2

value: embryonic stem cell


title: PCGF1_ERT2-Cre_EedMutant_EB_rep1

description:
ERT2-Cre;Eed∆/∆
PCGF1_ERT2-Cre_EedMutant_EB_rep1.bw


title: PCGF1_ERT2-Cre_EedControl_ES_rep2

description:
ERT2-Cre;Eedf/f
PCGF1_ERT2-Cre_EedControl_ES_rep2.bw


title: H3K27me3_ERT2-Cre_Pcgf1Mutant_ES_rep2


title: COVID_05

description:
blood from COVID-19 patient
C5

value: H


title: RING1B_ERT2-Cre_Ring1aPM_Ring1bCPM_Mutant_EB_rep2

data_processing:
Sequencing was performed with 75 bp single-end read by NextSeq500 (run by Kazusa DNA Research Institute) or 50bp single-end read by HiSeq1500 (run in RIKEN-IMS NGS facility).
The data were mapped onto UCSC-mm9 from illumina igenome. Generated sam format file combine to bam format file using samtools view (version 1.3.1). Then, PCR duplicate and multiple aligned reads are removed.
For bigwig generation, bam format files were processed by deeptools bamCoverage. The data of CpG island and TSS are derived from UCSC mm9.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig

value: RING1B (Laboratory made)


title: NONCOVID_19

description:
blood from non-COVID-19 patient
NC19

value: blood


title: PCGF1_ERT2-Cre_EedControl_EB_rep1

description:
ERT2-Cre;Eedf/f
PCGF1_ERT2-Cre_EedControl_EB_rep1.bw


title: RNA triple mutant ovaries rep1

description: Poly(A)-selected RNA


title: NONCOVID_07

description:
blood from non-COVID-19 patient
NC7

value: W


title: Control3.Input

city: Chengdu

first: Wenchuan

last: Chen

state: Sichuan

address: renmin sothroad

country: China

institute: Sichuan university

data_processing:
Quality of paired-end reads were controlled by Q30.
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3). First, clean reads of input libraries were aligned to reference genome (UCSC HG19) by STAR software. were identified by DCC software using the STAR alignment results. After that, clean reads of all libraries were aligned to the reference genome by Hisat2 software (v2.0.4). Methylated sites on RNAs (peaks) were identified by MACS software. Differentially methylated sites were identified by diffReps. These peaks identified by both softwares overlapping with exons of mRNA, LncRNA and circRNA were figured out and choosed by home-made scripts. GO and Pathway enrichment analysis were performed by the differentially methylated protein coding genes, the associated genes of differentially methylated LncRNAs and the source genes of differentially methylated circRNAs separately.
Then circRNAs were identified by DCC software using the STAR alignment results. After that, clean reads of all libraries were aligned to the reference genome by Hisat2 software (v2.0.4).
Methylated sites on RNAs (peaks) were identified by MACS software. Differentially methylated sites were identified by diffReps. These peaks identified by both softwares overlapping with exons of mRNA, LncRNA and circRNA were figured out and choosed by home-made scripts.
Genome_build: HG19
Supplementary_files_format_and_content: peak bed files
Supplementary_files_format_and_content: Methylated sites of mRNA, LncRNA and circRNA were identified by MACS software.

source_name: umbilical cord mesenchymal stem cells

growth_protocol: HUCMSCs were cultured in 25 cm2 culture dish with complete medium, containing Dulbecco's minimum essential medium (DMEM; HyClone, USA), 10% fetal bovine serum (FBS; GIBCO, USA) and 1% penicillin/streptomycin. And the cell was incubated at 37 °C and 5 % CO2 in a humidified incubator.

extract_protocol:
RNA was harvested using Trizol reagent.
Briefly, m6A RNA immunoprecipitation was performed with the GenSeqTM m6A RNA IP Kit (GenSeq Inc., China) by following the manufacturer’s instructions. Both the input sample without immunoprecipitation and the m6A IP samples were used for RNA-seq library generation with NEBNext® Ultra II Directional RNA Library Prep Kit (New England Biolabs, Inc., USA).

treatment_protocol: Cells were cultured in osteogenic induction medium [complete DMEM medium, dexamethasone (0.1 mM), ascorbic acid (50 ug/ml) and β-glycerolphosphate (10 mM) (all from Sigma-Aldrich)] for 7days.

value: HUCMSCs

tag: treatment

value: cultured in complete medium

tag: rip antibody


title: COVID_66

description:
blood from COVID-19 patient
C66

value: F


title: PCGF1_ERT2-Cre_EedMutant_ES_rep1

description:
ERT2-Cre;Eed∆/∆
PCGF1_ERT2-Cre_EedMutant_ES_rep1.bw

value: PCGF1 (Laboratory made)


title: Control2.Input


title: RING1B_ERT2-Cre_Ring1aPM_Ring1bCPM_Control_EB_rep2


title: COVID_65

description:
blood from COVID-19 patient
C65

value: O


title: Control1.Input


title: Control2.IP

value: GenSeqTM m6A RNA IP Kit (GenSeq Inc., China)


title: Control3.IP


title: RING1B_ERT2-Cre_Pcgf6Mutant_EB_rep2

description:
ERT2-Cre;Pcgf6∆/∆
RING1B_ERT2-Cre_Pcgf6Mutant_EB.bw

value: embryoid body


title: COVID_52

description:
blood from COVID-19 patient
C52


title: Control1.IP


title: COVID_40

description:
blood from COVID-19 patient
C40


title: Induced3.Input

value: cultured in osteogenic induction medium


title: COVID_28

description:
blood from COVID-19 patient
C28


title: RING1B_ERT2-Cre_Pcgf6Mutant_ES_rep2

description:
ERT2-Cre;Pcgf6∆/∆
RING1B_ERT2-Cre_Pcgf6Mutant_ES.bw


title: RING1B_ERT2-Cre_Pcgf6Control_ES_rep2

description:
ERT2-Cre;Pcgf6f/f
RING1B_ERT2-Cre_Pcgf6Control_ES.bw

value: without 4-OHT


title: Induced3.IP


title: COVID_15

description:
blood from COVID-19 patient
C15

value: AA


title: Induced2.Input


title: PCGF1_ERT2-Cre_EedControl_ES_rep1

description:
ERT2-Cre;Eedf/f
PCGF1_ERT2-Cre_EedControl_ES_rep1.bw


title: NONCOVID_18

description:
blood from non-COVID-19 patient
NC18

value: M


title: Induced1.Input


title: RING1B_ERT2-Cre_Ring1aPM_Ring1bCPM_Mutant_ES_rep2

value: with 4-OHT


title: RING1B_ERT2-Cre_Pcgf6Control_EB_rep1

description:
ERT2-Cre;Pcgf6f/f
RING1B_ERT2-Cre_Pcgf6Control_EB.bw


title: RING1B_ERT2-Cre_Pcgf6Mutant_ES_rep1

value: embryonic stem cell


title: Induced2.IP


title: NONCOVID_06

description:
blood from non-COVID-19 patient
NC6


title: RING1B_ERT2-Cre_Ring1aPM_Ring1bCPM_Control_ES_rep2


title: KDM2B_ERT2-Cre_Pcgf1Control_EB_rep2

value: KDM2B (Laboratory made)


title: Induced1.IP


title: RING1B_ERT2-Cre_Ring1aPM_Ring1bCPM_Control_ES_rep1

value: RING1B (Laboratory made)


title: KDM2B_ERT2-Cre_Pcgf1Mutant_EB_rep2


title: RING1B_ERT2-Cre_Pcgf6Control_ES_rep1


title: RING1B_ERT2-Cre_Ring1aPM_Ring1bCPM_Mutant_EB_rep1


title: RING1B_ERT2-Cre_Pcgf6Control_EB_rep2


title: KDM2B_ERT2-Cre_Pcgf1Mutant_ES_rep2


title: COVID_64

description:
blood from COVID-19 patient
C64

value: blood


title: RING1B_ERT2-Cre_Ring1aPM_Ring1bCPM_Control_EB_rep1


title: COVID_51

description:
blood from COVID-19 patient
C51


title: COVID_03

description:
blood from COVID-19 patient
C3

value: W


title: RING1B_ERT2-Cre_Ring1aPM_Ring1bCPM_Mutant_ES_rep1


title: NP_3

city: Singapore

first: Vincent

last: Chow

address: 5 Science Drive 2, Blk MD4, Level 3

department: Microbiology & Immunology

country: Singapore

institute: National University of Singapore

data_processing:
quality of the raw data was first inspected using FASTQC.
5ʹ and 3ʹ adaptor sequences were trimmed using Trimmomatic version 0.39.
Processed reads were aligned against the GRCh38 Homo sapiens primary assembly (Ensembl release 102) using STAR version 2.7.6a with default parameters.
Reads mapping to the exons were quantified using featureCounts version 2.0.0.
Differential gene expression analysis was performed using the R package DESeq2 version 1.30.0, after filtering genes with zero counts in all samples.
Genome_build: GRCh38 Homo sapiens primary assembly (Ensembl release 102)
Supplementary_files_format_and_content: Comma-separated values (CSV) file includes Normalized Count of each sample, baseMean, log2FoldChange, lfcSE, stat, pvalue and padj.

source_name: Pro-monocytic cells

growth_protocol: Before transfection, 3.5 × 10^6 HL-CZ cells were seeded into T25 flasks containing RPMI medium supplemented with 15% fetal bovine serum (FBS), and incubated at 37°C in the presence of 5% CO2.

extract_protocol:
The transfected cells (1 million cells) were harvested after 24 hr for RNA isolation using the RNeasy kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: At 22 hr post-seeding, plasmid transfection was carried out. For each reaction, 7 µg of plasmid DNA was added to 14 µl of Lipofectamine 3000 (Life Technologies), and serum-free RPMI media was added to a final volume of 250 µl. After 5 min, 250 µl of mixture consisting of 14 µl of P3000 Enhancer reagent and serum-free RPMI were added to the diluted DNA. The DNA-lipid complex was further incubated for 30 min. After this, 500 µl of the DNA-lipid complex was added to the respective flask with HL-CZ cells.

value: Pro-monocytic cells

tag: cell line

value: HL-CZ


title: RING1B_ERT2-Cre_Pcgf6Mutant_EB_rep1


title: H3K27ac_Dox+_Mutant_ES_rep2


title: NP_2


title: KDM2B_ERT2-Cre_Pcgf1Mutant_EB_rep1


title: COVID_39

description:
blood from COVID-19 patient
C39

value: F


title: H3K27ac_Dox-_Control_ES_rep2


title: NSP16_5


title: KDM2B_ERT2-Cre_Pcgf1Mutant_ES_rep1


title: COVID_16

description:
blood from COVID-19 patient
C16


title: H3K27ac_Dox+_Control_ES_rep2


title: NP_1


title: NSP16_3


title: H2AK119ub_Dox-_Mutant_ES_rep2


title: COVID_27

description:
blood from COVID-19 patient
C27

value: H


title: KDM2B_ERT2-Cre_Pcgf1Control_EB_rep1


title: H2AK119ub_Dox+_Mutant_ES_rep2


title: H2Bub1-ChIP-P28-2

city: Indianapolis

first: Nathan

middle: J

last: VanDusen

state: IN

department: Pediatrics

institute: Indiana University School of Medicine

description:
ChIP-seq
H2Bub1_ChIP-seq.txt

data_processing:
Adapters were removed and reads trimmed by quality score.
Reads were aligned to the mouse genome by Bowtie2.
RPKM normalized bigwig files were generated using Deeptools.
Reads overlapping each gene body (first transcription start site to last transcription end site) were counted using Bedtools.
Counts for each gene were normalized for sequencing depth by DESeq2, and divided by gene body length.
Genome_build: mm10
Supplementary_files_format_and_content: H2Bub1_ChIP-seq.txt: tab delimited text, FPKM for each gene. Bigwig files: RPKM normalized genome browser file for each sample.

source_name: P28 ventricles

growth_protocol: In vivo maturation

extract_protocol:
Ventricles homogenized at P28
KAPA Hyper Prep Kit

value: P28 ventricles

value: WT

value: postnatal day 28

tag: sample type

value: H2Bub1 ChIP


title: H3K27ac_Dox-_Mutant_ES_rep2


title: COVID_04

description:
blood from COVID-19 patient
C4

tag: Sex


title: KDM2B_ERT2-Cre_Pcgf1Control_ES_rep1

value: without 4-OHT


title: NSP16_2


title: NSP15_2


title: H2AK119ub_Dox+_Control_ES_rep2


title: H2Bub1-ChIP-P28-1

description:
ChIP-seq
H2Bub1_ChIP-seq.txt

tag: age


title: NSP15_4


title: H3K27me3_Dox-_Mutant_ES_rep2


title: NSP15_1


title: H2AK119ub_Dox-_Control_ES_rep2


title: H2Bub1-Input-P28-2

description:
ChIP-seq
H2Bub1_ChIP-seq.txt

value: H2Bub1 Input


title: H2Bub1-ChIP-P1-2

description:
ChIP-seq
H2Bub1_ChIP-seq.txt

source_name: P1 ventricles

extract_protocol:
Ventricles homogenized at P1
KAPA Hyper Prep Kit

value: P1 ventricles

value: postnatal day 1


title: PCMVF_3

value: pCMV3-C-FLAG Negative Control Vector


title: H3K27me3_Dox+_Mutant_ES_rep2

value: with 4-OHT

value: embryonic stem cell


title: COVID_26

description:
blood from COVID-19 patient
C26

tag: race

value: blood


title: COVID_38

description:
blood from COVID-19 patient
C38

value: M

value: W

tag: death


title: KDM2B_ERT2-Cre_Pcgf1Control_ES_rep2

value: KDM2B (Laboratory made)


title: H2Bub1-Input-P1-2

description:
ChIP-seq
H2Bub1_ChIP-seq.txt


title: COVID_14

description:
blood from COVID-19 patient
C14

tag: covid status


title: PCMVF_1

value: Pro-monocytic cells

value: HL-CZ


title: S2_5


title: H3K27me3_Dox-_Control_ES_rep2


title: H3K27me3_Dox+_Control_ES_rep2


title: H3K27ac_Dox-_Mutant_ES_rep1


title: COVID_63

description:
blood from COVID-19 patient
C63

value: F

tag: tissue


title: H2Bub1-ChIP-P1-1

description:
ChIP-seq
H2Bub1_ChIP-seq.txt

value: WT


title: H2Bub1-Input-P1-1

description:
ChIP-seq
H2Bub1_ChIP-seq.txt


title: H3K27ac_Dox+_Mutant_ES_rep1


title: H2Bub1-Input-P28-1

description:
ChIP-seq
H2Bub1_ChIP-seq.txt

value: P28 ventricles

value: postnatal day 28


title: COVID_50

description:
blood from COVID-19 patient
C50

value: AA


title: S2_3


title: RNF20/40-KO-S10

description:
mRNA RNA-seq
RNF_RNA-seq

data_processing:
Adapters were removed and reads trimmed by quality score
Reads were aligned to the mouse transcriptome by Kallisto
Counts for individual transcripts were consolidated into gene level counts using TxImport, and analyzed for differential expression between control and RNF20/40 groups by DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: RNF_RNA-seq.txt: tab delimited text, DESeq2 comparison of gene expression between groups.

source_name: isolated adult CMs

extract_protocol:
Hearts were dissociated at P28. GFP+ CMs (Cre) or YFP+ CMs (RNF20/40 KO) were collected by FACS. RNA extraction by Trizol/Zymo RNA Clean and Concentrator.
Clontech SMARTseq v4 Ultra Low Input RNA-seq kit

value: isolated adult CMs

value: postnatal 4 weeks

value: KO (YFP+)


title: NONCOVID_16

description:
blood from non-COVID-19 patient
NC16


title: S2_1


title: NONCOVID_04

description:
blood from non-COVID-19 patient
NC4


title: RNF20/40-KO-S09

description:
mRNA RNA-seq
RNF_RNA-seq


title: H3K27ac_Dox-_Control_ES_rep1

value: without 4-OHT


title: COVID_62

description:
blood from COVID-19 patient
C62


title: RNF20/40-KO-S08

description:
mRNA RNA-seq
RNF_RNA-seq


title: H3K27ac_Dox+_Control_ES_rep1


title: RNF20/40-KO-S07

description:
mRNA RNA-seq
RNF_RNA-seq


title: S1_5


title: H2AK119ub_Dox-_Mutant_ES_rep1

value: with 4-OHT


title: S1_4


title: COVID_25

description:
blood from COVID-19 patient
C25

value: O


title: COVID_49

description:
blood from COVID-19 patient
C49

value: H

value: blood


title: H2AK119ub_Dox+_Control_ES_rep1

value: embryonic stem cell


title: H2AK119ub_Dox-_Control_ES_rep1


title: PCMV_5

value: pCMV3-untagged Negative Control Vector


title: H3K27me3_Dox-_Mutant_ES_rep1


title: PCMV_4

value: Pro-monocytic cells


title: H2AK119ub_Dox+_Mutant_ES_rep1


title: COVID_37

description:
blood from COVID-19 patient
C37

value: M


title: RNF20/40-KO-S06

description:
mRNA RNA-seq
RNF_RNA-seq


title: PCMV_3

value: HL-CZ


title: S1_3


title: RNF20/40-Control-S05

description:
mRNA RNA-seq
RNF_RNA-seq

value: Control (GFP+)

value: AAV-TnT-Cre


title: COVID_01

description:
blood from COVID-19 patient
C1

value: W


title: RNF20/40-Control-S04

description:
mRNA RNA-seq
RNF_RNA-seq


title: COVID_02

description:
blood from COVID-19 patient
C2


title: H3K27me3_Dox+_Mutant_ES_rep1


title: NONCOVID_17

description:
blood from non-COVID-19 patient
NC17

value: F


title: RNF20/40-Control-S03

description:
mRNA RNA-seq
RNF_RNA-seq

value: isolated adult CMs


title: NONCOVID_15

description:
blood from non-COVID-19 patient
NC15


title: NONCOVID_03

description:
blood from non-COVID-19 patient
NC3


title: H3K27me3_Dox-_Control_ES_rep1


title: RNF20/40-Control-S01

description:
mRNA RNA-seq
RNF_RNA-seq

value: postnatal 4 weeks


title: COVID_13

description:
blood from COVID-19 patient
C13

value: AA


title: Screen-S30-YFP

description:
gRNA amplicon-seq
screen_gRNA.txt
screen_gene.txt

data_processing:
Library strategy: CRISPR screen
Adapters and gRNA scaffold were trimmed, leaving only the 20bp gRNA.
Alignment to mm10 with Bowtie2.
Count aligned reads for each gRNA using Bedtools.
Genome_build: mm10
Supplementary_files_format_and_content: screen_gRNA.txt: tab delimited text files containing enrichement of each gRNA in YFP+ CMs, as calculated by DESeq2. screen_gene: tab delimited text files containing enrichment of gRNAs for each gene in YFP+ CMs, as calculated by MAGeCK.

extract_protocol:
Hearts were dissociated at P28. YFP+ cardiomyocytes were collected by FACS, or unsorted cardiomyocytes for input samples. RNA extraction by Trizol/Zymo RNA Clean and Concentrator.
gRNAs were specifically reverse transcribed, amplified, and sequenced

value: YFP(+)


title: H3K27me3_Dox+_Control_ES_rep1

value: without 4-OHT


title: EwS2 dual 1 GFP-positive

city: Torino

first: Paolo

last: Provero

address: Via Nizza 52

department: Molecular Biotechnology and Health Sciences

country: Italy

institute: University of Turin

data_processing:
Reads were aligned to the human genome (NCBI-hg38) using hisat2 with default parameters.
Gene-level counts for each sample were obtained with featureCounts against the hg38 RefSeq transcriptome.
Genome_build: hg38
Supplementary_files_format_and_content: csv file of raw counts for entrez gene ids

source_name: Ewing sarcoma organoid 2

growth_protocol: Primary EwS spheres were cultured in IMDM (Gibco, USA), supplemented with 20% KO serum (Gibco, USA), 10 ng/mL human recombinant EGF and bFGF (PROSPEC) and 1% Pen/Strep (Gibco, USA) in ultra-low

extract_protocol:
Total RNA was isolated using miRCURY™ RNA Isolation Kit – Cell & Plant (Exiqon) according to the manufacturer's recommendations. 100 ng of total RNA were used as input.
Flash Tag Biotin HSR RNA Labeling Kit (Thermo-Fischer) was used. Samples were end-labeled according to manufacturer’s guidelines.

treatment_protocol:
"Single" and "dual" refer to two different mir-145 reporters that we developed. In both cases green fluorescence reports mir-145 expression, but in the dual case we also use red fluorescence to monitor infection homogeneity.
Tumor bearing mice received 2 mg/ml of doxycycline (Sigma-Aldrich) and 5% Sucrose (Sigma-Aldrich) in drinking water starting 96 hr prior to sacrifice. The tumor tissue was dissociated using a tumor dissociation kit (Miltenyi Biotec) by gentleMACS™ dissociator (Miltenyi Biotec). Red blood cells were removed by RBC lysis buffer (Milytenyi Biotec) and human tumor cells were enriched by depletion of mouse cells using a mouse cell depletion kit (Miltenyi Biotec). Prior to sorting GFP+ and GFP- cell populations, dissociated tumor cells were treated with Calcein-AM (Thermofisher) live cell labeling dye and DAPI (BIOTIUM) to remove dead cells.

value: Ewing sarcoma organoid

tag: reporter

value: dual

tag: gfp status

value: positive


title: COVID_61

description:
blood from COVID-19 patient
C61

value: blood


title: Screen-S28-YFP

tag: genotype


title: COVID_48

description:
blood from COVID-19 patient
C48

value: H


title: Screen-S27-input

value: Control


title: EwS2 dual 1 GFP-negative

value: negative


title: Screen-S29-input


title: H2AK119ub1_CPM_Mutant_EB_rep2

value: with 4-OHT

tag: cell type

value: embryoid body


title: EwS1 single 2 GFP-positive

source_name: Ewing sarcoma organoid 1

value: single


title: EwS1 dual 2 GFP-positive


title: EwS1 single 2 GFP-negative


title: COVID_24

description:
blood from COVID-19 patient
C24

value: M


title: EwS1 dual 1 GFP-positive


title: H2AK119ub1_CPM_Control_EB_rep2

tag: tamoxifen treatment


title: H2AK119ub1_CPM_Mutant_ES_rep2

value: embryonic stem cell

tag: replicate


title: Screen-S26-YFP

value: isolated adult CMs


title: COVID_12

description:
blood from COVID-19 patient
C12


title: EwS1 dual 2 GFP-negative


title: RNF20/40-Control-S02

description:
mRNA RNA-seq
RNF_RNA-seq

value: postnatal 4 weeks

value: Control (GFP+)

value: AAV-TnT-Cre


title: H2AK119ub1_CPM_Control_ES_rep2

value: without 4-OHT

tag: antibody


title: Screen-S25-input

tag: treatment


title: H3K27me3_CPM_Mutant_EB_rep2


title: NONCOVID_26

description:
blood from non-COVID-19 patient
NC26

value: W


title: COVID_36

description:
blood from COVID-19 patient
C36


title: Screen-S24-YFP

value: YFP(+)


title: EwS2 single 2 GFP-positive

value: Ewing sarcoma organoid

value: positive


title: H3K27me3_CPM_Control_EB_rep2


title: EwS2 single 2 GFP-negative


title: NONCOVID_14

description:
blood from non-COVID-19 patient
NC14

value: F

value: blood


title: NONCOVID_02

description:
blood from non-COVID-19 patient
NC2

value: AA


title: Screen-S22-YFP


title: EwS2 single 1 GFP-positive


title: H3K27me3_CPM_Mutant_ES_rep2

value: with 4-OHT


title: EwS2 single 1 GFP-negative

value: negative


title: COVID_60

description:
blood from COVID-19 patient
C60


title: Screen-S23-input

value: Control


title: H2AK119ub1_CPM_Mutant_EB_rep1

value: embryoid body


title: H2AK119ub1_CPM_Control_EB_rep1


title: H2AK119ub1_CPM_Mutant_ES_rep1

value: embryonic stem cell


title: COVID_47

description:
blood from COVID-19 patient
C47

value: M


title: COVID_35

description:
blood from COVID-19 patient
C35

value: O


title: Screen-S19-input

value: isolated adult CMs

value: postnatal 4 weeks


title: Screen-S21-input


title: Screen-S20-YFP


title: SLC22A15_OE_B1

city: Columbus

first: Rajgopal

last: Govindarajan

state: Ohio

address: 496 west, 12th Ave

department: Division of Pharmaceutics and Pharmacology, College of Pharmacy

institute: The Ohio State 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, then mapped to mm9 whole genome using Rsubread
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a the edgeR workflow from Robinson  et al., Bioinformatics , 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include abundance values for each Sample

source_name: Pancreatic cancer cell line

growth_protocol: Vector, SLC22A10_OE, and SLC22A15_OE clones were grown in 90 mm cell culture grade Petri dishes. Culture medium used was Dulbeco's modified eagle medium (DMEM) with added 10% fetal bovine serum, antibiotics (penicilin and streptomycin), and puromycin (0.5 µg/ml) for selection of stable clones. Clones were passaged in each 2-3 days using 0.25% trypsin and after trypsinization, clones were incubated at 37 °C and 5% CO2 inside a humidified CO2 incubator. Experiments were performed within the 10th passage of the clones to avoid possibility of losing gene expression.

extract_protocol:
Total RNA was extracted from the above clones using E.Z.N.A Total RNA kit I (OMEGA bio-tek) following the manufacturer's protocol.
Strand-specific RNA-seq libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina following the manufacturer’s recommendations. In summary, total RNA quality was assessed using an RNA 6000 Nano kit on an Agilent 2100 Bioanalyzer (Agilent Biotechnologies), and the concentration was measured using a Qubit RNA HS assay kit (Life Technologies). A 500 ng aliquot of total RNA was depleted of rRNA using a Human/Mouse/Rat RNAse-H based Depletion kit from NEB (New England Biolabs, Ipswich, MA). Following rRNA removal, mRNA was fragmented and then used for first- and second-strand cDNA synthesis with random hexamer primers. Double-stranded cDNA fragments underwent end repair, poly (A) tailing and the ligation of two unique adapters (Integrated DNA Technologies, Coralville, IA). The adaptor-ligated cDNA was amplified by limited-cycle PCR. Library quality was analyzed with TapeStation High-Sensitivity D1000 ScreenTape (Agilent Biotechnologies) and quantified by KAPA qPCR (KAPA BioSystems). Libraries were pooled and sequenced at 2 × 150-bp read lengths on the Illumina HiSeq 4000 platform.

treatment_protocol: Vector, SLC22A10_OE, and SLC22A15_OE clones were prepared by transducing the PANC-1 cells with lentiviral plasmids pLV-EV (empty vector/control), pLV-SLC22A10, and pLV-SLC22A15 respectively and subsequent selection with puromycin (1 µg/ml) for two weeks.

value: Pancreas/duct

tag: disease

value: Epitheloid carcinoma

value: SLC22A15_OE clones


title: EwS1 single 1 GFP-negative

value: Ewing sarcoma organoid

value: single


title: EwS1 single 1 GFP-positive

value: positive


title: COVID_23

description:
blood from COVID-19 patient
C23

value: W

value: blood


title: H2AK119ub1_CPM_Control_ES_rep1

value: without 4-OHT


title: NONCOVID_05

description:
blood from non-COVID-19 patient
NC5

value: F


title: Screen-S18-YFP

value: YFP(+)


title: EwS1 dual 1 GFP-negative

value: dual

value: negative


title: H3K27me3_CPM_Control_ES_rep2

value: embryonic stem cell


title: COVID_11

description:
blood from COVID-19 patient
C11


title: SLC22A15_OE_A2

tag: cell line


title: NONCOVID_25

description:
blood from non-COVID-19 patient
NC25

value: M


title: Screen-S17-input

value: isolated adult CMs

tag: sample type

value: Control


title: Screen-S16-YFP

value: postnatal 4 weeks


title: SLC22A15_OE_A1

value: Pancreas/duct

value: Epitheloid carcinoma


title: SLC22A10_OE_B1

value: SLC22A10_OE clones


title: H3K27me3_CPM_Control_EB_rep1

value: embryoid body


title: H3K27me3_CPM_Mutant_ES_rep1

value: with 4-OHT


title: NONCOVID_01

description:
blood from non-COVID-19 patient
NC1

tag: Sex

value: W


title: NONCOVID_13

description:
blood from non-COVID-19 patient
NC13

tag: age

value: H

value: blood


title: Screen-S15-input


title: SLC22A10_OE_A2


title: Screen-S13-input


title: H2AK119ub_ERT2-Cre_Pcgf1Mutant_EB_rep2


title: H3K27me3_CPM_Control_ES_rep1

value: without 4-OHT


title: Screen-S14-YFP

value: YFP(+)


title: H2AK119ub_ERT2-Cre_Pcgf1Control_EB_rep2


title: Screen-S12-YFP


title: COVID_100

description:
blood from COVID-19 patient
C100

value: F

tag: race


title: COVID_76

description:
blood from COVID-19 patient
C76

value: AA

tag: death


title: COVID_88

description:
blood from COVID-19 patient
C88

tag: covid status


title: Vector_Control_A2

tag: tissue

value: Vector transduced clones


title: H2AK119ub_ERT2-Cre_Pcgf1Mutant_ES_rep2

value: embryonic stem cell


title: COVID_89

description:
blood from COVID-19 patient
C89


title: Screen-S11-input

value: isolated adult CMs


title: COVID_77

description:
blood from COVID-19 patient
C77


title: Screen-S10-YFP


title: H2AK119ub_ERT2-Cre_Pcgf1Control_ES_rep2


title: E24NocR2

first: Rodrigo

middle: Andres

last: Grandy

address: Cambridge Stem Cell Institute/ Anne McLaren Laboratory West Forvie Building, Robinson Way

department: Surgery

description: Mesendoderm 24h + Nocodazole

data_processing:
Base calling was done using illumina package RTA v2.7.7, and instrument control package called HCS v3.4.0.38.
Adaptors were clipped before alignment and then re-inserted
Alignment files were converted into BAM files. Reads were counted using Rsubread package, based on protocol: "Analyzing RNA-seq data with DESeq2". Michael I. Love, Simon Anders, and Wolfgang Huber. (http://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html)
Read counts were analyzed using DESeq2 based on protocole: "gene-level exploratory analysis and differential expression". Michael I. Love, Simon Anders, Vladislav Kim and Wolfgang Huber. (https://www.bioconductor.org/help/workflows/rnaseqGene/)
Genome_build: GRCh38_genecode
Supplementary_files_format_and_content: Read_counts_all_conditions.txt: Tab-delimited text file includes read counts per gene. DE_DESeq2_all_conditions.txt: Tab-delimited text file includes log2 fold change (log2FoldChange) and the adjustaed p-values (padj) for each convination of samples.

source_name: H9 cells

growth_protocol: H9 cells were grown in E8 medium containing penicillin (50 units/ml) and streptomycin (100 mg/ml)mycin, on plates coated with Vitronectin-XF (Stem Cells Technologies). Cells were incubated at 37ºC in atmosphere of 5% CO2

extract_protocol:
Total RNA was extracted using RNA extraction kit from Sigma, following manufaturer instructions.
RNA libraries were prepared for sequencing using Illumina TruSeq stranded mrNAseq kit; Ref N: 20020595

treatment_protocol: H9 cells were synchronized in their cell cycle by incubating them with nocodazole (100 ng/ml) for 16h. Then, nocodazole was withdrawn and cells induced to differentiated into mesendoderm for 24h (In CDM-PVA medium supplemented with Insulin (7ug/ml), Activin A (100 ng/ml), BMP (10 ng/ml), LY294002 (10 mM ), and CHIR99021 (3 mM). To block cells in their S phase during differentiation, we added Hydroxyurea (200 mM) at the start of the differentiation. To block the cells in their G2/M phases during differentiation, we added nocodazole 8h after the induction of the differentiation. In this way, we made sure that the cells were able to re-initiate the cell cycle and get blocked in the following G2/M phase. After 24h of differentiation, cells were collected for RNA extraction.

tag: type

value: embryonic stem cells

value: Mesendoderm 24h + Nocodazole

tag: biological replicate

value: Replicate 2


title: H2AK119ub_ERT2-Cre_Pcgf1Mutant_EB_rep1

tag: genotype


title: SLC22A10_OE_A1

value: Pancreas/duct

value: Epitheloid carcinoma


title: E24HUR2

description: Mesendoderm 24h + Hydroxyurea

value: Mesendoderm 24h + Hydroxyurea


title: H2AK119ub_ERT2-Cre_Pcgf1Control_EB_rep1

tag: cell type

value: embryoid body


title: COVID_99

description:
blood from COVID-19 patient
C99

data_processing:
minfi
matrix_processed.csv = average beta
matrix_signal_intensities.csv = unmethylated and methylated signal intensities

extract_protocol: genomic DNA from whole blood tissue was extracted using the GeneJET whole blood kit according to the manufacturer's recommendations

value: M

value: W


title: H3K27me3_CPM_Mutant_EB_rep1

tag: tamoxifen treatment

value: with 4-OHT


title: E24R2

description: Mesendoder 24h

value: Mesendoderm 24h


title: Screen-S08-YFP

value: postnatal 4 weeks

value: YFP(+)


title: UDR2

description: Undifferentiated

value: Undifferentiated


title: Screen-S09-input

value: Control


title: COVID_91

description:
blood from COVID-19 patient
C91

value: F

value: blood


title: Screen-S06-YFP

value: isolated adult CMs


title: Screen-S07-input


title: E24NocR1

description: Mesendoderm 24h + Nocodazole

value: embryonic stem cells

value: Mesendoderm 24h + Nocodazole

value: Replicate 1


title: H2AK119ub_ERT2-Cre_Pcgf1Control_ES_rep1

value: without 4-OHT

value: embryonic stem cell

tag: replicate


title: COVID_87

description:
blood from COVID-19 patient
C87


title: COVID_75

description:
blood from COVID-19 patient
C75

value: O


title: Screen-S05-input


title: Vector_Control_A1

value: Pancreas/duct

value: Epitheloid carcinoma

value: Vector transduced clones


title: Vector_Control_B1


title: COVID_102

description:
blood from COVID-19 patient
C102

value: M

value: W


title: E24HUR1

description: Mesendoderm 24h + Hydroxyurea

value: Mesendoderm 24h + Hydroxyurea


title: H3K27me3_ERT2-Cre_Pcgf1Control_EB_rep1

value: embryoid body

tag: antibody


title: H2AK119ub_ERT2-Cre_Pcgf1Mutant_ES_rep1

value: with 4-OHT


title: Screen-S04-YFP

value: postnatal 4 weeks

value: YFP(+)

tag: treatment


title: H3K27me3_ERT2-Cre_Pcgf1Mutant_ES_rep1


title: E24R1

description: Mesendoder 24h

value: Mesendoderm 24h


title: Screen-S03-input

value: isolated adult CMs

value: Control


title: Screen-S02-YFP


title: COVID_78

description:
blood from COVID-19 patient
C78

value: blood


title: H3K27me3_ERT2-Cre_Pcgf1Control_ES_rep1

value: without 4-OHT


title: COVID_101

description:
blood from COVID-19 patient
C101

value: H


title: PCMVF_4

value: Pro-monocytic cells

value: HL-CZ

value: pCMV3-C-FLAG Negative Control Vector


title: H3K27me3_ERT2-Cre_Pcgf1Mutant_EB_rep1


title: UDR1

description: Undifferentiated

value: embryonic stem cells

value: Undifferentiated

value: Replicate 1


title: RNA_E24_iKD-CDK1_+TET_R2

description: Mesendoderm 24h + TET

data_processing:
Base calling was done using illumina package RTA v2.7.7, and instrument control package called HCS v3.4.0.38.
Adaptors were clipped before alignment and then re-inserted
Alignment files were converted into BAM files. Reads were counted using Rsubread package, based on protocol: "Analyzing RNA-seq data with DESeq2". Michael I. Love, Simon Anders, and Wolfgang Huber. (http://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html)
Read counts were analyzed using DESeq2 based on protocole: "gene-level exploratory analysis and differential expression". Michael I. Love, Simon Anders, Vladislav Kim and Wolfgang Huber. (https://www.bioconductor.org/help/workflows/rnaseqGene/)
Genome_build: GRCh38.84
Supplementary_files_format_and_content: Read_counts_all_conditions.txt: Tab-delimited text file includes read counts per gene.

value: Mesendoderm 24h + TET

value: Replicate 2


title: COVID_98

description:
blood from COVID-19 patient
C98

value: M

value: W


title: Screen-S01-input

value: postnatal 4 weeks


title: RNA_E24_iKD-CDK1_woTET_R2

description: Mesendoderm 24h woTET

value: Mesendoderm 24h woTET


title: EB4

city: Vancouver

first: Kylynda

middle: C

last: Bauer

state: BC

address: #301 – 2185 East Mall

country: Canada

institute: Michael Smith Laboratories

data_processing:
Alignment: STAR (Mus musculus mm10 reference sequence)
gene counts were generated from bam files using htseq-count v.2.5
DESeq2: Prefilter remove low counts (sum less than 10 in samples in the smallest group, CON n=4)
DESeq2: DEGs (padj <0.05, FC > |1.5|
Genome_build: mm10 (GRCm38.94)

molecule: polyA RNA

source_name: cortical brain tissue

extract_protocol:
Cortical brain tissue was harvested and stored in RPMI media on ice before cell isolation and CD11b+ enrichment using Miltenyi Biotec murine kits
Standard Illumina protocols prepared by BRC-Seq (Sequencing core at the University of British Columbia, Vancouver, Canada)

treatment_protocol: After weaning, mice were fed a standard chow diet (CON), or an isocaloric low fat/protein diet (MAL) for one month, with a malnourished subset exposued to a mix of E. coli/Bacteroidales species (MAL-BG)

value: cortical brain tissue

tag: group

value: Malnourished_Microbes (MALBG)

tag: strain

value: CD11b+ cells


title: RNA_E24_RO8-24h_R2

description: Mesendoderm 24h + RO3306

value: Mesendoderm 24h + RO3306


title: adult1

city: New York

first: Maija

last: Slaidina

state: NY

address: 540 1st ave

department: Skirball Institute

institute: New York University School of Medicine

data_processing:
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
Additional cell-level demultiplexing and alignment was performed with 10x Cell Ranger software.
Genome_build: dm6
Supplementary_files_format_and_content: raw seq files and gene-barcode matrices.
Supplementary_files_format_and_content: Seurat_objects.RData: Seurat objects.

source_name: ovary

growth_protocol: Flies were raised on medium containing yeast, molasses and cornmeal, and kept at 25 oC. Adult females were fattened on yeast for 24-48 hours prior to dissections.

extract_protocol:
For each sample, 30-40 pairs of adult ovaries were dissected one by one in ice-cold DPBS, no calcium, no magnesium (Thermo Fisher Scientific #14190136). Abdomens were removed using forceps and parts of intestine and abdominal cuticle were removed. Using forceps and a dissection needle, we cut off the anterior tip of the ovary and transferred to a new well. Method A: For dissociation, anterior tips of ovaries were incubated in dissociation solution (0.5% Type I Collagenase (Thermo Fisher Scientific #17018029), 1% Trypsin 1:250 (Thermo Fisher Scientific #27250018) in DPBS) for 15 minutes with gentle rotation. The suspension was vigorously pipetted multiple times during the dissociation to enhance the dissociation efficiency. Enzymatic dissociation was stopped by adding Schneider cell culture media (Fisher # 21720-001) with 10% fetal bovine serum (Invitrogen #10082-147) (S-FBS). Starting from this step, all plastic materials – pipet tips, tubes, filters – were coated with S-FBS. Cell suspension was filtered through a custom-made ~40-micron cell strainer. The strainer was built by securing nylon mesh (Component Supply #U-CMN-40) in a cap of a 0.2 ml PCR tube and cutting the bottom of the tube and the cap (Slaidina et al. 2020). Upon filtering, dissociated cells were purified by fluorescence activated cell sorting (FACS) using a 100-micron nozzle on Sony SY3200 Cell Sorter. Cell suspension was centrifuged for 5 minutes at 250 rcf at RT, and resuspended in S-FBS.
10x Genomics Chromimum v2 kit

treatment_protocol: Samples 1, 2 were generated using the Method A and 10xGenomics kit v2. They were processed on two independent days.

value: w; His2AV:GFP/+

value: female

value: 2-3 days

value: anterior part of the ovary

tag: sample preparation protocol

value: protocol A


title: EB2


title: wild_type_7H9+B12_2

city: Lodz

first: Jakub

last: Pawełczyk

address: Lodowa 106

department: Mycobacterium Physiology and Genetics

country: Poland

institute: Institute of Medical Biology of the Polish Academy of Sciences

data_processing:
unzipping the .gz file with gunzip function with Ubuntu Linux command line
sequencing adapter removal with Cutadapt software with parameters set -a AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT -A TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -q 15
quality trimming was done with Sickle -pe script setting variable parameters as -t sanger -q 20 -l 20
mapping reads to the reference genome with Bowtie2 with default settings
sorting and indexing of the alignemnt files with Samtools
counting reads to features with HTSeq.count -t gene -i Locus -m intersection-nonempty
count matrix was build in excel by merging the HTSeq.count output files
Genome_build: NC_018143.2
Supplementary_files_format_and_content: Matrix_Pawelczyk.txt

organism: Mycobacterium tuberculosis H37Rv

source_name: Wild Type grown on 7H9 with OADC and Vit.B12

growth_protocol: The Mycobacterium tuberculosis H37Rv wild-type strain and derived ∆prpR mutant were maintained on Middlebrook 7H10 agar and 7H9 broth (Becton-Dickinson) supplemented with 10% OADC enrichment (Becton-Dickinson). For RNA sequencing, the Mtb wild-type and ∆prpR mutant were grown on defined carbon sources in minimal medium (0.5 g/liter asparagine, 1 g/liter KH2PO4, 2.5 g/liter Na2HPO4, 50 mg/liter ferric ammonium citrate, 0.5 g/liter MgSO4∙7H2O, 0.5 mg/liter CaCl2, and 0.1 mg/liter ZnSO4) containing either 0.1% glycerol (vol/vol) or 0.01% cholesterol (wt/vol). RNA sequencing data resulting from a comparison of the expression profile on glycerol vs cholesterol were also related to the results obtained for bacteria growing in standard 7H9/10% OADC medium. For the study on the influence of vitamin B12 on the Mtb transcriptome, bacteria were grown in 7H9/10% OADC medium with or without vitamin B12 (Sigma Aldrich) supplementation (10 μg/ml). Each bacterial culture was set in triplicate and grown to an optical density of OD600 0.6. Then, 100 ml of each culture was spun down and subjected directly to total RNA isolation.

extract_protocol:
RNA was isolated using TRIzol LS reagent (Invitrogen). Cells were lysed by bead beating with the MP FastPrep system (MP Biomedicals) using lysing matrix B. DNA contamination of the RNA samples was removed by DNase I turbo (Invitrogen) digestion according to the manufacturer’s protocol. The quantity and integrity of the DNase I-treated RNA was assessed using an Agilent 2100 BioAnalyzer according to the manufacturer's instructions (Agilent RNA 6000 Nano Kit).
RNA samples were purified using AMPure XP magnetic beads (Becton Dickinson) with a 2.2:1 bead-to-RNA ratio. Two micrograms of the purified total RNA was used per library. The ribosomal RNA was removed with the Ribo-Zero Bacteria rRNA Removal Kit (Illumina) according to the manufacturer’s protocol. The Illumina-compatible RNA/cDNA sequencing libraries were prepared with the use of KAPA Stranded RNA-Seq kit (Roche) according to the detailed instructions provided by the manufacturer.

tag: genotype/variation

value: wild-type

tag: growth medium/treatment

value: 7H9/10% OADC  medium supplemented with vitamin B12 (10 μg/ml)

tag: growth phase

value: grown to mid-exponential phase


title: COVID_74

description:
blood from COVID-19 patient
C74

tag: Sex

value: F

tag: age

tag: race

tag: death

value: blood


title: wild_type_7H9+B12_3


title: COVID_90

description:
blood from COVID-19 patient
C90

value: W

tag: covid status

tag: tissue


title: RNA_E24_R2

description: Mesendoderm 24h

tag: type

value: embryonic stem cells

value: Mesendoderm 24h

tag: biological replicate

value: Replicate 2


title: EB1

value: cortical brain tissue

value: Malnourished_Microbes (MALBG)

tag: cell type


title: wild_type_7H9+B12_1


title: COVID_103

description:
blood from COVID-19 patient
C103

value: M


title: RNA_UD_R2

description: Undifferentiated

value: Undifferentiated


title: COVID_79

description:
blood from COVID-19 patient
C79

value: H


title: EA4

value: CD11b+ cells


title: ∆prpR_7H9_3

source_name: Mutant PrpR grown on 7H9 with OADC

value: PrpR (Rv1129) mutant

value: 7H9/10% OADC  medium


title: RNA_E24_iKD-CDK1_+TET_R1

description: Mesendoderm 24h + TET

value: Mesendoderm 24h + TET

value: Replicate 1


title: ∆prpR_7H9_2

value: grown to mid-exponential phase


title: EA3


title: EA2


title: COVID_86

description:
blood from COVID-19 patient
C86

value: F


title: COVID_80

description:
blood from COVID-19 patient
C80

value: blood


title: COVID_92

description:
blood from COVID-19 patient
C92

value: W


title: ∆prpR_7H9_1


title: RNA_E24_RO8-24h_R1

description: Mesendoderm 24h + RO3306

value: embryonic stem cells

value: Mesendoderm 24h + RO3306


title: RNA_E24_iKD-CDK1_woTET_R1

description: Mesendoderm 24h woTET

value: Mesendoderm 24h woTET


title: RNA_E24_R1

description: Mesendoderm 24h

value: Mesendoderm 24h


title: EA1

value: cortical brain tissue

value: Malnourished_Microbes (MALBG)


title: ∆prpR_CHOL_2

source_name: Mutant PrpR grown on cholesterol

value: minimal medium with 0.01% cholesterol (wt/vol)


title: COVID_81

description:
blood from COVID-19 patient
C81

value: M

value: AA


title: COVID_97

description:
blood from COVID-19 patient
C97


title: COVID_85

description:
blood from COVID-19 patient
C85

value: H


title: RNA_UD_R1

description: Undifferentiated

value: Undifferentiated


title: ∆prpR_CHOL_1

value: PrpR (Rv1129) mutant


title: MALA3

value: Malnourished (MAL)

value: CD11b+ cells


title: COVID_73

description:
blood from COVID-19 patient
C73


title: ∆prpR_GLC_3

source_name: Mutant PrpR grown on glycerol

value: minimal medium with 0.1% glicerol (vol/vol)

value: grown to mid-exponential phase


title: 7mG_E24TET_R2

description:
RNA-IP-seq
Mesendoderm 24h + TET

data_processing:
Base calling was done using illumina package RTA v2.7.7, and instrument control package called HCS v3.4.0.38.
Adaptors were clipped before alignment and then re-inserted
Alignment files were converted into BAM files by the sequencing facility. To calculate differential enrichments we used the exomePeak r package from bioconductor. Because exomepeak package only accepts single-end files, pair-end bam files were converted back to fasq files and then only one of the ends was re-mapped using hisat2. This new bam files were used for the calculation of differential enrichments.
Genome_build: GRCh38.84
Supplementary_files_format_and_content: All bigWig files were generated using the function bamCompare from the Deeptools software for Histone marks vs Input, with a bin size = 10, normalized using RPKM method, and an effective genome size of 2913022398

extract_protocol: Libraries were prepared for sequencing using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina; Ref N: E7645S

treatment_protocol: H9 cells were synchronized in their cell cycle by incubating them with nocodazole (100 ng/ml) for 16h. Then, nocodazole was withdrawn and cells induced to differentiated into mesendoderm for 24h (In CDM-PVA medium supplemented with Insulin (7ug/ml), Activin A (100 ng/ml), BMP (10 ng/ml), LY294002 (10 mM ), and CHIR99021 (3 mM). To block cells in their S phase during differentiation, we added Hydroxyurea (200 mM) at the start of the differentiation. To block the cells in their G2/M phases during differentiation, we added nocodazole 8h after the induction of the differentiation. In this way, we made sure that the cells were able to re-initiate the cell cycle and get blocked in the following G2/M phase. After 24h of differentiation, cells were collected and processed for ChIP-seq library preparation.

value: Mesendoderm 24h + TET

value: Replicate 2


title: MALA4


title: 7mG_E24woTET_R2

description:
RNA-IP-seq
Mesendoderm 24h without TET

value: embryonic stem cells

value: Mesendoderm 24h without TET


title: COVID_93

description:
blood from COVID-19 patient
C93

value: F

value: W

value: blood


title: MALA2

value: cortical brain tissue


title: ∆prpR_GLC_2


title: 7mG_E24RO_R2

description:
RNA-IP-seq
Mesendoderm 24h + RO3306

value: Mesendoderm 24h + RO3306


title: MALA1


title: ∆prpR_CHOL_3

value: minimal medium with 0.01% cholesterol (wt/vol)


title: ∆prpR_GLC_1


title: CONB3

value: Control (CON)


title: 7mG_E24_R2

description:
RNA-IP-seq
Mesendoderm 24h

value: Mesendoderm 24h


title: Input_E24TET_R2

description:
RNA-IP-seq
Mesendoderm 24h + TET


title: wild_type_7H9_3

source_name: Wild Type grown on 7H9 with OADC

value: wild-type

value: 7H9/10% OADC  medium


title: MALB4

value: Malnourished (MAL)

value: CD11b+ cells


title: COVID_95

description:
blood from COVID-19 patient
C95

value: M

value: O


title: CONB2


title: COVID_83

description:
blood from COVID-19 patient
C83


title: wild_type_7H9_2

value: grown to mid-exponential phase


title: Input_E24woTET_R2

description:
RNA-IP-seq
Mesendoderm 24h without TET

value: embryonic stem cells

value: Replicate 2


title: wild_type_7H9_1


title: Input_E24_R2

description:
RNA-IP-seq
Mesendoderm 24h


title: COVID_96

description:
blood from COVID-19 patient
C96


title: COVID_84

description:
blood from COVID-19 patient
C84

value: F


title: wild_type_CHOL_3

source_name: Wild Type grown on cholesterol


title: wild_type_CHOL_2


title: COVID_72

description:
blood from COVID-19 patient
C72

value: H


title: wild_type_CHOL_1


title: COVID_82

description:
blood from COVID-19 patient
C82

value: W

value: blood


title: CONB1

value: cortical brain tissue


title: p53-knockout, SLC7A11 siRNA, experiment-2

type: RNA

city: Bedford Park

first: George

last: Mayne

state: SA

address: Room 3D213, Dept of Surgery, Flinders Medical Center

country: Australia

institute: Flinders University of South Australia

description:
Test
SLC7A11 siRNA expt-2

data_processing:
Fluorescence data was exported to comma delimited text files and then analysed using R statistical software (version 3.4.3), and Microsoft Excel for Mac (version 16). The cycle threshold (Ct) value for each PCR assay was determined using the qpcR package v1.4 in R (https://cran.r-project.org/web/packages/qpcR/index.html). The relative levels of the miRNAs were determined using the formula 2^(40-Ct), and were normalized using the geometric means of the relative levels of selected House Keeping Genes (HKGs).  The HKGs used in this study are included in a file on the series record named "Selected HKGs for p53-KO manuscript .xlsx".
normalized_data includes House Keeping Gene normalised miRNA relative levels

label: FAM

source_name: JH-EsoAd1 cell line derived from a patient with Barrett-associated adenocarcinoma, which has a missense c797G>A mutation in TP53 resulting in an amino acid change of G266E

label_protocol: For cell line experiments, high throughput QuantStudio™ 12K Flex OpenArray® PCR custom made plates were used for miRNA profiling. These arrays were comprised of a panel of 112 miRNA probes (miRBase version 22 miRNA names, seed sequences, and miRBase accession numbers are in Supplementary file 2) that were selected based upon their abundance in OAC patient samples from our previous study on serum small extracellular vesicle associated miRNAs [94]. For each sample, 3.35 μl of RNA was reverse transcribed using a matching Custom OpenArray® miRNA RT pool (Life Technologies cat # A25630) and the TaqMan® microRNA Reverse Transcription Kit (Life Technologies cat # 4366596). cDNA Pre-amplifications were carried out with a matching Custom OpenArray® PreAmp pool (Life Technologies cat # 4485255) and TaqMan PreAmp Master Mix (Life Technologies cat # 4488593) on 7.5 μl complementary DNA (cDNA)/sample for each pool. The pre-amplified products (4 μl per sample) were diluted at the recommended 1:40 dilution with 156 μl of RNase-free ultra pure water before mixing with TaqMan OpenArray Real-Time PCR Master Mix (Life Technologies cat # 4462164) and loading onto a 384-well TaqMan OpenArray loading plate. PCR runs were performed using a QuantStudio™ 12K Flex Real-Time PCR System.

growth_protocol: All cell lines were cultured using (phenol red free) RPMI 1640 medium  supplemented with 10 % fetal bovine serum (FBS) , 50 U/ml penicillin , 50 µg/ml streptomycin , and 100 µg/ml normocin.

extract_protocol: Total RNA isolation from untreated cell samples at time of treatment, including DNase digestion, was performed using the miRNeasy Mini Kit (Qiagen, #217004, Chadstone, Australia) and RNase-free DNase Set (Qiagen, #79254, Chadstone, Australia) as instructed by the manufacturer.

treatment_protocol:
The samples were collected from co-cultured cells prior to their counterparts being treated with drugs or irradiation.
SLC7A11 transfections: media was changed 24 h prior to transfection to antibiotic-free charcoal-stripped FCS. Cells were then transfected using Lipofectamine 2000 (Invitrogen, cat #11668019, Scoresby, Australia) in a pooled setting as described above. After harvesting of the cells, 2.04x 106 cells were placed in T25 flasks which resulted in 30-50% confluency after 6 h. Cells were transiently transfected with SLC7A11 siRNA (ON-TARGETplus Human SLC7A11 (23657) siRNA-SMARTpool, Dharmacon / Horizon, cat #L-007612-01-0010, Cambridge, UK) or control siRNA (ON-TARGETplus Non-targeting Pool, Dharmacon / Horizon, cat #D-001810-10-05, Cambridge, UK) to inhibit expression of SLC7A11 or not, respectively. The final siRNA concentration was 100 nM.

tag: cell line

tag: genotype

value: p53 KO with SLC7A11 siRNA


title: COVID_94

description:
blood from COVID-19 patient
C94


title: wild_type_GLC_2

source_name: Wild Type grown on glycerol

value: minimal medium with 0.1% glicerol (vol/vol)


title: p53-knockout, SLC7A11 siRNA, experiment-1

description:
Test
SLC7A11 siRNA expt-1


title: 7mG_E24_R1

description:
RNA-IP-seq
Mesendoderm 24h

tag: treatment

value: Mesendoderm 24h

value: Replicate 1


title: wild_type_GLC_1

value: wild-type


title: Input_E24TET_R1

description:
RNA-IP-seq
Mesendoderm 24h + TET

value: Mesendoderm 24h + TET


title: Input_E24woTET_R1

description:
RNA-IP-seq
Mesendoderm 24h without TET

value: Mesendoderm 24h without TET


title: Input_E24RO_R2

description:
RNA-IP-seq
Mesendoderm 24h + RO3306

value: Mesendoderm 24h + RO3306


title: p53-knockout, non-binding control, SLC7A11experiment-1

description:
Control
SLC7A11 non-binding control expt-1

value: p53 KO with control siRNA


title: 7mG_E24TET_R1

description:
RNA-IP-seq
Mesendoderm 24h + TET


title: 7mG_E24woTET_R1

description:
RNA-IP-seq
Mesendoderm 24h without TET


title: CONA3

tag: group

value: Control (CON)

tag: strain

value: CD11b+ cells


title: Input_E24_R1

description:
RNA-IP-seq
Mesendoderm 24h

value: embryonic stem cells


title: parental polyclonal cell line, p53-knockout, experiment-2

description:
Control
Parental polyclonal  expt-2

value: p53 KO


title: H3K27Ac_E24NocR2

description: Mesendoderm 24h + Nocodazole

data_processing:
Base calling was done using illumina package RTA v2.7.7, and instrument control package called HCS v3.4.0.38.
Adaptors were clipped before alignment and then re-inserted
Alignment files were converted into BAM files.
Genome_build: GRCh38_genecode
Supplementary_files_format_and_content: All bigWig files were generated using the function bamCompare from the Deeptools software for Histone marks vs Input, with a bin size = 10, normalized using RPKM method, and an effective genome size of 2913022398

extract_protocol:
Lysates were sonicated and histone-DNA complexes were pull-down with antibody.
Libraries were prepared for sequencing using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina; Ref N: E7645S

value: Mesendoderm 24h + Nocodazole

value: Replicate 2


title: clone of parental cell line, mutant-p53, experiment-2

description:
Control
Parental clonal  expt-2

value: parental (mutant-p53)


title: clone of parental cell line, mutant-p53, experiment-3

description:
Control
Parental clonal  expt-3


title: H3K27Ac_E24HUR2

description: Mesendoderm 24h + Hydroxyurea

value: Mesendoderm 24h + Hydroxyurea


title: wild_type_GLC_3

tag: genotype/variation

value: grown to mid-exponential phase


title: H3K27Ac_E24R2

description: Mesendoder 24h


title: H3K27Ac_UDR2

description: Undifferentiated

value: Undifferentiated


title: 7mG_E24RO_R1

description:
RNA-IP-seq
Mesendoderm 24h + RO3306


title: H3K4me1_E24HUR2

description: Mesendoderm 24h + Hydroxyurea


title: Cas-9 only clonal cell line, mutant-p53, experiment-3

description:
Control
Dox non-induced  expt-3


title: H3K4me1_E24NocR2

description: Mesendoderm 24h + Nocodazole


title: Cas-9 only clonal cell line, mutant-p53, experiment-2

description:
Control
Dox non-induced  expt-2


title: Cas-9 only clonal cell line, mutant-p53, experiment-1

description:
Control
Dox non-induced  expt-1


title: parental polyclonal cell line, p53-knockout, experiment-3

description:
Control
Parental polyclonal  expt-3


title: A549/DDP cells miRNA-seq 2

city: Monroe

last: Mattheolabakis

state: LA

address: 1800 Bienville Dr., University of Louisiana at Monroe, room 380

institute: University of Louisiana at Monroe

data_processing:
Raw data (UMIs) were extracted and uploaded to Partek Flow for additional analysis. Differential expression was done with Gene Specific Analysis (GSA)
Reference genome hg38 was downloaded from NCBI website, and paired-end cleaned read of samples were mapped using Spliced Transcripts Alignment to a Reference (STAR) software

source_name: lung adenocarcinoma

extract_protocol:
Zymo Research
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: lonog term incubation of Samples 3 and 4 with 20 μM of CDDP (short periods of 50 μM)

value: lung

value: adenocarcinoma

value: A549-cisplatin resistant


title: Input_E24RO_R1

description:
RNA-IP-seq
Mesendoderm 24h + RO3306

value: Replicate 1


title: clonal cell line-7, p53-knockout, experiment-2

description:
Test
Clone 7  expt-2


title: Input_E24NocR2

description: Mesendoderm 24h + Nocodazole


title: H3K4me1_UDR2

description: Undifferentiated


title: A549 cells miRNA-seq 1

value: A549 parental


title: parental polyclonal cell line, p53-knockout, experiment-1

description:
Control
Parental polyclonal  expt-1


title: H3K4me1_E24R2

description: Mesendoder 24h

value: Mesendoderm 24h


title: Input_E24R2

description: Mesendoder 24h

value: Mesendoder 24h


title: clone of parental cell line, mutant-p53, experiment-1

description:
Control
Parental clonal  expt-1


title: A549/DDP cells mRNA-seq 2


title: clonal cell line-7, p53-knockout, experiment-1

description:
Test
Clone 7  expt-1


title: Input_UDR2

description: Undifferentiated


title: clonal cell line-14, p53-knockout, experiment-2

description:
Test
Clone 14  expt-2


title: A549/DDP cells mRNA-seq 1


title: A549 cells mRNA-seq 2


title: clonal cell line-14, p53-knockout, experiment-1

description:
Test
Clone 14  expt-1


title: clonal cell line-1, p53-knockout, experiment-2

description:
Test
Clone 1  expt-2


title: clonal cell line-1, p53-knockout, experiment-3

description:
Test
Clone 1  expt-3


title: H3K27Ac_E24HUR1

description: Mesendoderm 24h + Hydroxyurea


title: H3K27Ac_E24NocR1

description: Mesendoderm 24h + Nocodazole


title: A549 cells mRNA-seq 1


title: clonal cell line-7, p53-knockout, experiment-3

description:
Test
Clone 7  expt-3


title: clonal cell line-1, p53-knockout, experiment-1

description:
Test
Clone 1  expt-1


title: SUDS3 RNAi knockdown replicate 3

city: Kansas City

first: Gaye

middle: L

last: Hattem

state: Missouri

address: 1000 E. 50th Street

department: Proteomics

institute: Stowers Institute

data_processing:
Sequenced reads were trimmed for adaptor sequence with Trimmomatic version 0.36
Reads were mapped to genome using Hisat2 version 2.1.0
Read counts were calculated with htseq-count
Genome_build: GRCh38
Supplementary_files_format_and_content: Read count .csv file and TPM .csv file

source_name: HEK293T cells with SUDS3 RNAi knockdown

growth_protocol: HEK293T cells were cultured in DMEM + 10 % FBS + GlutaMAX™ Supplement at 37 °C and 5 % CO2.

extract_protocol:
HEK293T total RNA was isolated using TRIzol™ Reagent. Isolates were DNAseI treated, then extracted with TRIzol™ Reagent a second time.
Illumina TruSeq RNA library prep kit
poly-A stranded RNA-Seq

treatment_protocol: HEK293T cells were transfected with Ambion Silencer™ Select siRNAs targeting SUDS3 (siRNA i.d.  s34740), PHF12 (siRNA i.d. s33518), or Silencer™ Select Negative Control No. 2 at final concentrations of 10 nM with Lipofectamine™ RNAiMAX Transfection Reagent for 36 h.


title: clonal cell line-14, p53-knockout, experiment-3

description:
Test
Clone 14  expt-3


title: A549/DDP cells miRNA-seq 1


title: SUDS3 RNAi knockdown replicate 2


title: H3K4me1_E24NocR1

description: Mesendoderm 24h + Nocodazole


title: H3K27Ac_UDR1

description: Undifferentiated


title: Input_E24HUR2

description: Mesendoderm 24h + Hydroxyurea


title: H3K4me1_E24HUR1

description: Mesendoderm 24h + Hydroxyurea


title: PHF12 RNAi knockdown replicate 3

source_name: HEK293T cells with PHF12 RNAi knockdown


title: PHF12 RNAi knockdown replicate 1


title: H3K4me1_E24R1

description: Mesendoder 24h


title: A549 cells miRNA-seq 2


title: Input_E24HUR1

description: Mesendoderm 24h + Hydroxyurea


title: H3K27Ac_E24R1

description: Mesendoder 24h


title: Control replicate 3 (PHF12/SUDS3 control)

source_name: HEK293T cells


title: Control replicate 2 (PHF12/SUDS3 control)


title: Input_E24R1

description: Mesendoder 24h


title: Control replicate 1 (PHF12/SUDS3 control)


title: KMR19

city: Leuven

first: Maurilio

last: Sampaolesi

address: Herestraat 49, ON4 - box 804

department: Department of Development and Regeneration

country: Belgium

institute: KU Leuven

data_processing:
50 bp single-end reads were generated. An average of 20 million reads were obtained from all samples. Quality control of raw reads was performed with the FastQC v0.11.5. The adapters were filtered with ea-utils v1.2.2.18. The splice-aware alignment was performed with TopHat v2.0.13 against the mouse genome mm10. The number of allowed mismatches was 2. Reads that mapped to more than one site to the reference genome were discarded.  The minimal score of alignment quality to be included in count analysis was 10. Resulting SAM and BAM alignment files were handled with Samtools v0.1.19.24. Quantification of reads per gene was performed with HT-Seq count v0.5.3p3.
Count-based differential expression analysis was done with R-based (The R Foundation for Statistical Computing, Vienna, Austria) Bioconductor package DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: csv file containing matrix with read counts normalized by the library size for all samples

source_name: Rhabdomyosarcoma GEMM

extract_protocol:
RNA was isolated using Total RNA isolation kit and post isolation DNAase (Thermo Fisher Scientific)- 2µg were processed
Library preparation was performed with the Illumina TruSeq Stranded mRNA Sample Preparation Kit, according to the manufacturers protocol. Denaturation of RNA was performed at 65oC in a thermocycler and cooled down to 4oC. Samples were indexed to allow for multiplexing. Sequencing libraries were quantified using the Qubit fluorometer (Thermo Fisher Scientific, Massachusetts, USA). Library quality and size range was assessed using the Bioanalyzer (Agilent Technologies) with the DNA 1000 kit (Agilent Technologies, California, USA) according to the manufacturer’s instructions. Libraries were diluted to a final concentration of 2nM and sequenced on Illumina HiSeq4000 sequencing system, according to the manufacturer’s recommendations.

value: MyoD-Cre x p53 R/+ x KRasG12D

tag: disease state

value: rhabdomyosarcoma


title: Blastocyst replicate 2 nuclear transfer

city: Munich

first: Alexander

last: Graf

address: Feodor-Lynen-Str. 25

department: Gene Center Munich

institute: Ludwig-Maximilians-Universität München

description: non ribosomal RNA

data_processing:
Reads were converted to Fastq using the CASAVA (v.1.6) base caller from Illumina.
Illumina adapters where clipped from each read using a custom script.
The first five bases were removed with a custom script from each read due to random priming effects
Poly-A tails were removed from the 3’-/5’-end of each read with a seed length of 10 nt. Reads with length <25nt after clipping were filtered out.
Reads were filtered from the 3′ and 5′ end with a quality cutoff of 20, and reads shorter than 30 were discarded
Reads were mapped against the reference genome (BosTau7) using Tophat2 (v.2.0.10) with default settings and the gene annotation obtained from Illumina’s iGenomes Project (UCSC: bosTau7).
Transcript abundance was counted using htseq-count (v. 0.6.1) with no strand specificity (-s no), union mode (-m union) and GFF attribute ‘gene’ (-i gene). The used gene annotation was obtained from Illumina’s iGenome Project (UCSC: bosTau7).
Genome_build: BosTau7
Supplementary_files_format_and_content: Tab-delimited text file containing the raw read counts per gene from HTSeq-count

organism: Bos taurus

source_name: nuclear transfer embryo

extract_protocol:
Pools of 10 oocytes or embryos were chosen after visual inspection for each biological replicate to minimize variance caused by a single specimen. IVF and SCNT embryos were cultured in vitro under identical conditions (protocol IVF1; (Hiendleder S, et al. (2006) Tissue-specific effects of in vitro fertilization procedures on genomic cytosine methylation levels in overgrown and normal sized bovine fetuses. Biology of reproduction 75(1):17-23.)) to the blastocyst stage (day 7). The following cell stages were collected: GV and MII oocytes (one set used as reference for both IVF and SCNT embryos) and embryos at the four-cell, eight-cell, 16-cell, and blastocyst stage (both embryo types). Pools of 10 oocytes or embryos per stage were frozen and stored at ‑80 °C until analysis.
Frozen pools of 10 oocytes or embryos were thawed and lysed in 10 µL of lysis buffer (Prelude kit, NuGEN). The Ovation RNAseq v2 kit (NuGEN) was used for cDNA generation and single primer isothermal amplification (SPIA). The amplified cDNA was bead-purified (AmpureXP, Beckman-Coulter) and fragmented by sonication (Bioruptor, Diagenode; 25 cycles 30 seconds on/30 seconds off), and Illumina-compatible sequencing libraries were constructed from 500 ng of fragmented cDNA by ligation of adapters with sample-specific barcodes. The libraries were amplified (KAPA hifi polymerase, eight cycles, 95 °C 80 seconds, 55 °C 30 seconds, 72 °C 60 seconds) and quantified on a Bioanalyzer 2100 (Agilent) before being pooled at 10 nM concentration for multiplexed sequencing. Three biological replicates of each stage were sequenced on an Illumina GAIIx (single-read, mean coverage of 20 × 10e6 reads, 80-base read length).

tag: embryo type

value: NT embryo

tag: developmental stage

value: Blastocyst


title: Blastocyst replicate 1 nuclear transfer

description: non ribosomal RNA


title: KMR46

value: MyoD-Cre x p53 F/+ x KRasG12D


title: SUDS3 RNAi knockdown replicate 1


title: SK_PB6_F6

city: Ithaca

first: Charles

middle: G.

last: Danko

address: Hungerford Hill Rd.

department: Baker Institute for Animal Health, College of Veterinary Medicine

institute: Cornell University

description:
nascent RNA
mouse ID 6
SK_PB6_F6_dedup_R1.B6.bowtie.gz
SK_PB6_F6_dedup_R1.CAST.bowtie.gz
SK_PB6_F5F6_R1.B6.specific.5prime.1bp.map2ref_plus.bw
SK_PB6_F5F6_R1.B6.specific.5prime.1bp.map2ref_minus.bw
SK_PB6_F5F6_R1.CAST.specific.5prime.1bp.map2ref_plus.bw
SK_PB6_F5F6_R1.CAST.specific.5prime.1bp.map2ref_minus.bw
SK_PB6_F5F6_R1.identical.5prime.1bp.map2ref_plus.bw
SK_PB6_F5F6_R1.identical.5prime.1bp.map2ref_minus.bw
SK_PB6_F5F6_R1.B6.specific.3prime.1bp.map2ref_plus.bw
SK_PB6_F5F6_R1.B6.specific.3prime.1bp.map2ref_minus.bw
SK_PB6_F5F6_R1.CAST.specific.3prime.1bp.map2ref_plus.bw
SK_PB6_F5F6_R1.CAST.specific.3prime.1bp.map2ref_minus.bw
SK_PB6_F5F6_R1.identical.3prime.1bp.map2ref_plus.bw
SK_PB6_F5F6_R1.identical.3prime.1bp.map2ref_minus.bw

data_processing:
Library strategy: ChRO-Seq
For ChRO-seq reads, adaptor sequences were trimmed with the cutadapt 1.16. PCR duplicates were removed using unique molecular identifiers (UMIs) in the sequencing data with prinseq-lite.pl. The reads were seperated with a custom J-barcode. The processed reads were then aligned with bowtie to to the diploid genome as input for AlleleDB.
The first base of nascent RNA in B6-specific, CAST-specific, or identical reads without SNPs was liftover to ref genome (mm10), and shown as bigwig files
Genome_build: mm10
Supplementary_files_format_and_content: ChRO-seq data are provided in standard bigWig file formats.

source_name: Skeletal muscle

extract_protocol: ChRO-seq library preparation: ChRO-seq libraries were prepared following a recent protocol (Mahat et al., 2016). We prepared some libraries to achieve single nucleotide resolution for the Pol II active site. In these cases, the chromatin pellet was incubated with 2x run-on buffer (10 mM Tris-HCl, pH 8.0, 5 mM MgCl2,1 mM DTT, 300 uM KCl, 20 uM  Biotin-11-ATP (Perkin Elmer, NEL544001EA), 200 uM Biotin-11-CTP (Perkin Elmer, NEL542001EA), 20 uM Biotin-11-GTP (Perkin Elmer, NEL545001EA), 200 uM Biotin-11-UTP (Perkin Elmer, NEL543001EA)) for 5 minutes at 37 C. In some libraries we modified the run-on buffer to extend the length of reads for more accurate allelic mapping at the expense of single nucleotide resolution for the Pol II active site. In these cases, the run-on reaction was performed using a different ribonucleotide composition in the nuclear run-on buffer (10 mM Tris-HCl, pH 8.0, 5 mM MgCl2,1 mM DTT, 300 mM KCl, 200 μ M  ATP (New England Biolabs (NEB), N0450S), 200 μ M  UTP, 0.4 μ M CTP, 20 μ  M Biotin-11-CTP (Perkin Elmer, NEL542001EA), 200 μ  M GTP (NEB, N0450S)).The run-on reaction was stopped by adding Trizol LS (Life Technologies, 10296-010) and RNA was pelleted with the addition of GlycoBlue (Ambion, AM9515) to visualize the RNA. RNA pellet was resuspended in diethylpyrocarbonate (DEPC)-treated water. RNA was heat denatured at 65 C for 40 s to remove secondary structure. RNA was fragmented using base hydrolysis (0.2N NaOH on ice for 4 min). RNA was purified using streptavidin beads (NEB, S1421S) and removed from beads using Trizol (Life Technologies, 15596-026). We ligated a 3′ adapter ligation using T4 RNA Ligase 1 (NEB, M0204L). We performed a second bead binding followed by a 5′ decapping with RppH (NEB, M0356S). RNA was phosphorylated on the 5’ end using T4 polynucleotide kinase (NEB, M0201L) then ligated onto a 5’ adapter. A third bead binding was then performed. The RNA was then reverse transcribed using Superscript III Reverse Transcriptase (Life Technologies, 18080-044) and amplified using Q5 High-Fidelity DNA Polymerase (NEB, M0491L) to generate the ChRO-seq libraries. Libraries were sequenced using an Illumina HiSeq by Novogene.

value: Castaneus x C57BL/6 F1 hybrid

value: Skeletal muscle

tag: age

value: post natal day 24

tag: gender

value: female


title: Blastocyst replicate 3 nuclear transfer

description: non ribosomal RNA


title: PHF12 RNAi knockdown replicate 2


title: Sixteen-cell replicate 2 nuclear transfer

description: non ribosomal RNA

value: Sixteen-cell


title: Sixteen-cell replicate 1 nuclear transfer

description: non ribosomal RNA


title: H3K4me1_UDR1

city: Cambridge

institute: University of Cambridge

description: Undifferentiated

source_name: H9 cells

value: embryonic stem cells

value: Undifferentiated


title: Sixteen-cell replicate 3 nuclear transfer

description: non ribosomal RNA


title: Input_E24NocR1

description: Mesendoderm 24h + Nocodazole

value: Mesendoderm 24h + Nocodazole


title: SK_PB6_F5

description:
nascent RNA
mouse ID 5
SK_PB6_F5_dedup_R1.B6.bowtie.gz
SK_PB6_F5_dedup_R1.CAST.bowtie.gz
SK_PB6_F5F6_R1.B6.specific.5prime.1bp.map2ref_plus.bw
SK_PB6_F5F6_R1.B6.specific.5prime.1bp.map2ref_minus.bw
SK_PB6_F5F6_R1.CAST.specific.5prime.1bp.map2ref_plus.bw
SK_PB6_F5F6_R1.CAST.specific.5prime.1bp.map2ref_minus.bw
SK_PB6_F5F6_R1.identical.5prime.1bp.map2ref_plus.bw
SK_PB6_F5F6_R1.identical.5prime.1bp.map2ref_minus.bw
SK_PB6_F5F6_R1.B6.specific.3prime.1bp.map2ref_plus.bw
SK_PB6_F5F6_R1.B6.specific.3prime.1bp.map2ref_minus.bw
SK_PB6_F5F6_R1.CAST.specific.3prime.1bp.map2ref_plus.bw
SK_PB6_F5F6_R1.CAST.specific.3prime.1bp.map2ref_minus.bw
SK_PB6_F5F6_R1.identical.3prime.1bp.map2ref_plus.bw
SK_PB6_F5F6_R1.identical.3prime.1bp.map2ref_minus.bw


title: KD_PB6_F6

description:
nascent RNA
mouse ID 6
KD_PB6_F6_dedup_R1.B6.bowtie.gz
KD_PB6_F6_dedup_R1.CAST.bowtie.gz
KD_PB6_F5F6_R1.B6.specific.5prime.1bp.map2ref_plus.bw
KD_PB6_F5F6_R1.B6.specific.5prime.1bp.map2ref_minus.bw
KD_PB6_F5F6_R1.CAST.specific.5prime.1bp.map2ref_plus.bw
KD_PB6_F5F6_R1.CAST.specific.5prime.1bp.map2ref_minus.bw
KD_PB6_F5F6_R1.identical.5prime.1bp.map2ref_plus.bw
KD_PB6_F5F6_R1.identical.5prime.1bp.map2ref_minus.bw
KD_PB6_F5F6_R1.B6.specific.3prime.1bp.map2ref_plus.bw
KD_PB6_F5F6_R1.B6.specific.3prime.1bp.map2ref_minus.bw
KD_PB6_F5F6_R1.CAST.specific.3prime.1bp.map2ref_plus.bw
KD_PB6_F5F6_R1.CAST.specific.3prime.1bp.map2ref_minus.bw
KD_PB6_F5F6_R1.identical.3prime.1bp.map2ref_plus.bw
KD_PB6_F5F6_R1.identical.3prime.1bp.map2ref_minus.bw

source_name: Kidney

value: Kidney


title: Eight-cell replicate 1 nuclear transfer

description: non ribosomal RNA

value: Eight-cell


title: Four-cell replicate 3 nuclear transfer

description: non ribosomal RNA

value: Four-cell


title: KD_PB6_F5

description:
nascent RNA
mouse ID 5
KD_PB6_F5_dedup_R1.B6.bowtie.gz
KD_PB6_F5_dedup_R1.CAST.bowtie.gz
KD_PB6_F5F6_R1.B6.specific.5prime.1bp.map2ref_plus.bw
KD_PB6_F5F6_R1.B6.specific.5prime.1bp.map2ref_minus.bw
KD_PB6_F5F6_R1.CAST.specific.5prime.1bp.map2ref_plus.bw
KD_PB6_F5F6_R1.CAST.specific.5prime.1bp.map2ref_minus.bw
KD_PB6_F5F6_R1.identical.5prime.1bp.map2ref_plus.bw
KD_PB6_F5F6_R1.identical.5prime.1bp.map2ref_minus.bw
KD_PB6_F5F6_R1.B6.specific.3prime.1bp.map2ref_plus.bw
KD_PB6_F5F6_R1.B6.specific.3prime.1bp.map2ref_minus.bw
KD_PB6_F5F6_R1.CAST.specific.3prime.1bp.map2ref_plus.bw
KD_PB6_F5F6_R1.CAST.specific.3prime.1bp.map2ref_minus.bw
KD_PB6_F5F6_R1.identical.3prime.1bp.map2ref_plus.bw
KD_PB6_F5F6_R1.identical.3prime.1bp.map2ref_minus.bw


title: HT_PB6_F6

description:
nascent RNA
mouse ID 6
HT_PB6_F6_dedup_R1.B6.bowtie.gz
HT_PB6_F6_dedup_R1.CAST.bowtie.gz
HT_PB6_F5F6_R1.B6.specific.5prime.1bp.map2ref_plus.bw
HT_PB6_F5F6_R1.B6.specific.5prime.1bp.map2ref_minus.bw
HT_PB6_F5F6_R1.CAST.specific.5prime.1bp.map2ref_plus.bw
HT_PB6_F5F6_R1.CAST.specific.5prime.1bp.map2ref_minus.bw
HT_PB6_F5F6_R1.identical.5prime.1bp.map2ref_plus.bw
HT_PB6_F5F6_R1.identical.5prime.1bp.map2ref_minus.bw
HT_PB6_F5F6_R1.B6.specific.3prime.1bp.map2ref_plus.bw
HT_PB6_F5F6_R1.B6.specific.3prime.1bp.map2ref_minus.bw
HT_PB6_F5F6_R1.CAST.specific.3prime.1bp.map2ref_plus.bw
HT_PB6_F5F6_R1.CAST.specific.3prime.1bp.map2ref_minus.bw
HT_PB6_F5F6_R1.identical.3prime.1bp.map2ref_plus.bw
HT_PB6_F5F6_R1.identical.3prime.1bp.map2ref_minus.bw

source_name: Heart

value: Heart


title: Input_UDR1

description: Undifferentiated

value: Replicate 1


title: Four-cell replicate 2 nuclear transfer

description: non ribosomal RNA


title: Four-cell replicate 1 nuclear transfer

description: non ribosomal RNA


title: HT_PB6_F5

description:
nascent RNA
mouse ID 5
HT_PB6_F5_dedup_R1.B6.bowtie.gz
HT_PB6_F5_dedup_R1.CAST.bowtie.gz
HT_PB6_F5F6_R1.B6.specific.5prime.1bp.map2ref_plus.bw
HT_PB6_F5F6_R1.B6.specific.5prime.1bp.map2ref_minus.bw
HT_PB6_F5F6_R1.CAST.specific.5prime.1bp.map2ref_plus.bw
HT_PB6_F5F6_R1.CAST.specific.5prime.1bp.map2ref_minus.bw
HT_PB6_F5F6_R1.identical.5prime.1bp.map2ref_plus.bw
HT_PB6_F5F6_R1.identical.5prime.1bp.map2ref_minus.bw
HT_PB6_F5F6_R1.B6.specific.3prime.1bp.map2ref_plus.bw
HT_PB6_F5F6_R1.B6.specific.3prime.1bp.map2ref_minus.bw
HT_PB6_F5F6_R1.CAST.specific.3prime.1bp.map2ref_plus.bw
HT_PB6_F5F6_R1.CAST.specific.3prime.1bp.map2ref_minus.bw
HT_PB6_F5F6_R1.identical.3prime.1bp.map2ref_plus.bw
HT_PB6_F5F6_R1.identical.3prime.1bp.map2ref_minus.bw


title: KD_PB6_E

description:
nascent RNA
pooled sample E
KD_PB6_all_R1.B6.bowtie.gz
KD_PB6_all_R1.CAST.bowtie.gz
KD_PB6_all_R1.B6.specific.5prime.1bp.map2ref_plus.bw
KD_PB6_all_R1.B6.specific.5prime.1bp.map2ref_minus.bw
KD_PB6_all_R1.CAST.specific.5prime.1bp.map2ref_plus.bw
KD_PB6_all_R1.CAST.specific.5prime.1bp.map2ref_minus.bw
KD_PB6_all_R1.identical.5prime.1bp.map2ref_plus.bw
KD_PB6_all_R1.identical.5prime.1bp.map2ref_minus.bw

value: male


title: KD_PB6_B

description:
nascent RNA
pooled sample B
KD_PB6_all_R1.B6.bowtie.gz
KD_PB6_all_R1.CAST.bowtie.gz
KD_PB6_all_R1.B6.specific.5prime.1bp.map2ref_plus.bw
KD_PB6_all_R1.B6.specific.5prime.1bp.map2ref_minus.bw
KD_PB6_all_R1.CAST.specific.5prime.1bp.map2ref_plus.bw
KD_PB6_all_R1.CAST.specific.5prime.1bp.map2ref_minus.bw
KD_PB6_all_R1.identical.5prime.1bp.map2ref_plus.bw
KD_PB6_all_R1.identical.5prime.1bp.map2ref_minus.bw

value: post natal day 25


title: KD_PB6_C

description:
nascent RNA
pooled sample C
KD_PB6_all_R1.B6.bowtie.gz
KD_PB6_all_R1.CAST.bowtie.gz
KD_PB6_all_R1.B6.specific.5prime.1bp.map2ref_plus.bw
KD_PB6_all_R1.B6.specific.5prime.1bp.map2ref_minus.bw
KD_PB6_all_R1.CAST.specific.5prime.1bp.map2ref_plus.bw
KD_PB6_all_R1.CAST.specific.5prime.1bp.map2ref_minus.bw
KD_PB6_all_R1.identical.5prime.1bp.map2ref_plus.bw
KD_PB6_all_R1.identical.5prime.1bp.map2ref_minus.bw


title: Eight-cell replicate 3 nuclear transfer

description: non ribosomal RNA

value: NT embryo


title: KD_PB6_D

description:
nascent RNA
pooled sample D
KD_PB6_all_R1.B6.bowtie.gz
KD_PB6_all_R1.CAST.bowtie.gz
KD_PB6_all_R1.B6.specific.5prime.1bp.map2ref_plus.bw
KD_PB6_all_R1.B6.specific.5prime.1bp.map2ref_minus.bw
KD_PB6_all_R1.CAST.specific.5prime.1bp.map2ref_plus.bw
KD_PB6_all_R1.CAST.specific.5prime.1bp.map2ref_minus.bw
KD_PB6_all_R1.identical.5prime.1bp.map2ref_plus.bw
KD_PB6_all_R1.identical.5prime.1bp.map2ref_minus.bw


title: KD_MB6_G

description:
nascent RNA
pooled sample G
KD_MB6_all_R1.B6.bowtie.gz
KD_MB6_all_R1.CAST.bowtie.gz
KD_MB6_all_R1.B6.specific.5prime.1bp.map2ref_plus.bw
KD_MB6_all_R1.B6.specific.5prime.1bp.map2ref_minus.bw
KD_MB6_all_R1.CAST.specific.5prime.1bp.map2ref_plus.bw
KD_MB6_all_R1.CAST.specific.5prime.1bp.map2ref_minus.bw
KD_MB6_all_R1.identical.5prime.1bp.map2ref_plus.bw
KD_MB6_all_R1.identical.5prime.1bp.map2ref_minus.bw

value: C57BL/6 x Castaneus F1 hybrid


title: KD_MB6_A

description:
nascent RNA
pooled sample A
KD_MB6_all_R1.B6.bowtie.gz
KD_MB6_all_R1.CAST.bowtie.gz
KD_MB6_all_R1.B6.specific.5prime.1bp.map2ref_plus.bw
KD_MB6_all_R1.B6.specific.5prime.1bp.map2ref_minus.bw
KD_MB6_all_R1.CAST.specific.5prime.1bp.map2ref_plus.bw
KD_MB6_all_R1.CAST.specific.5prime.1bp.map2ref_minus.bw
KD_MB6_all_R1.identical.5prime.1bp.map2ref_plus.bw
KD_MB6_all_R1.identical.5prime.1bp.map2ref_minus.bw

value: post natal day 23


title: Eight-cell replicate 2 nuclear transfer

description: non ribosomal RNA


title: ST_PB6_D

description:
nascent RNA
pooled sample D
ST_PB6_all_R1.B6.bowtie.gz
ST_PB6_all_R1.CAST.bowtie.gz
ST_PB6_all_R1.B6.specific.5prime.1bp.map2ref_plus.bw
ST_PB6_all_R1.B6.specific.5prime.1bp.map2ref_minus.bw
ST_PB6_all_R1.CAST.specific.5prime.1bp.map2ref_plus.bw
ST_PB6_all_R1.CAST.specific.5prime.1bp.map2ref_minus.bw
ST_PB6_all_R1.identical.5prime.1bp.map2ref_plus.bw
ST_PB6_all_R1.identical.5prime.1bp.map2ref_minus.bw

source_name: Stomach

value: Castaneus x C57BL/6 F1 hybrid

value: Stomach


title: ST_PB6_E

description:
nascent RNA
pooled sample E
ST_PB6_all_R1.B6.bowtie.gz
ST_PB6_all_R1.CAST.bowtie.gz
ST_PB6_all_R1.B6.specific.5prime.1bp.map2ref_plus.bw
ST_PB6_all_R1.B6.specific.5prime.1bp.map2ref_minus.bw
ST_PB6_all_R1.CAST.specific.5prime.1bp.map2ref_plus.bw
ST_PB6_all_R1.CAST.specific.5prime.1bp.map2ref_minus.bw
ST_PB6_all_R1.identical.5prime.1bp.map2ref_plus.bw
ST_PB6_all_R1.identical.5prime.1bp.map2ref_minus.bw

value: post natal day 24


title: ST_PB6_C

description:
nascent RNA
pooled sample C
ST_PB6_all_R1.B6.bowtie.gz
ST_PB6_all_R1.CAST.bowtie.gz
ST_PB6_all_R1.B6.specific.5prime.1bp.map2ref_plus.bw
ST_PB6_all_R1.B6.specific.5prime.1bp.map2ref_minus.bw
ST_PB6_all_R1.CAST.specific.5prime.1bp.map2ref_plus.bw
ST_PB6_all_R1.CAST.specific.5prime.1bp.map2ref_minus.bw
ST_PB6_all_R1.identical.5prime.1bp.map2ref_plus.bw
ST_PB6_all_R1.identical.5prime.1bp.map2ref_minus.bw