title: Yap shRNA knock-down vector 3

city: Melbourne

first: Mark

middle: D

last: Ziemann

state: VIC

address: 85 Commercial Rd

department: Bioinformatics Working Group

country: Australia

institute: Burnet Institute

description:
kevinwatt_YapKD_gnames_cnt.tsv
YAP3

data_processing:
HiSeq Control Software (HCS) v2.2.68 and Real Time Analysis (RTA) v1.18.66.3. The bcl2fastq 2.20.0.422 pipeline was used to generate the sequence data.
Reads underwent 3’ trimming to remove bases with quality less than Phred 20 and a final length shorter than 20 nt using Fastx-Toolkit.
Reads were mapped with to the Ensembl mouse genome (GRCm38 with version 85 gene annotations) using STAR2.5.2b
Feature counts (v1.5.1) was used to quantify reads mapped to gene exons with mapping quality ≥10 and otherwise default settings.
Genome_build: GRCm38
Supplementary_files_format_and_content: Expression count matrix

source_name: tibialis anterior muscles

growth_protocol: All animal experiments were performed in accordance with guidelines from the Alfred Medical Research and Education Precinct (AMREP) Animal Ethics Committee and the National Health and Medical Research Council of Australia. All rodents were housed in a temperature-controlled environment, with a 12-h light/dark cycle and access to chow (Specialty Feeds, Perth, WA, Australia) and water ad libitum.

extract_protocol:
7 days after injection, muscles were excised, and total RNA was extracted from harvested muscles using TRIzol (Life Technologies, Victoria, Australia) as per manufacturer’s protocols
cDNA libraries were constructed from polyA+ purified mRNA samples by the Australian Genome Research Facility (AGRF, Melbourne) using Illumina TruSeq reagents as per the manufacturer’s protocol.

treatment_protocol:
Vector generation: DNA sequences that encode mouse Yap2L and Yap shRNA were synthesised by Genscript, Piscataway, USA and sub-cloned into AAV6:CMV-MCS-SV40pA or AAV6:CMV-eGFP-MCS-SV40pA plasmids respectively as previously described (Watt et al., 2015). Empty vector (AAV6:CMV-MCS-SV40pA; called AAV6:empty vector hereafter), or shRNA targeting LacZ (AAV6:LacZ shRNA) were used as controls. Recombinant adeno- associated viral vectors were generated by co-transfection of 10 μg of plasmids containing cDNA constructs with 20 μg of pDGM6 packaging plasmid into HEK293 cells (seeded 16 hr prior at a density of 3.2-3.8 x10 6 cells) using the calcium phosphate precipitate method to generate type-6 pseudotyped viral vectors. After 72 hours, cells and culture medium were collected and homogenised, before homogenates were clarified using a 0.22 μm filter (EMD Millipore). Vectors were purified by affinity chromatography using a HiTrap heparin column (GE Healthcare), ultra-centrifuged overnight and resuspended in sterile Ringer’s solution. Vector concentration was determined using a customised quantitative PCR reaction (Applied Biosystems).
We performed intramusculus injections to the contralateral tibialis anterior (TA) muscles of 8 week old male C57BL/6 mice with AAV6:Yap-shRNA or AAV6:LacZ-shRNA vectors and performed RNA-sequencing after 7 days.  Control TA muscle was paired with the treated TA muscle in n=3 animals.

tag: gender

value: male

tag: vector

value: Yap knockdown

value: tibialis anterior muscles


title: BAP1-KO-clone2-H3K4me1

status: Public on Jun 27 2021

type: SRA

city: Milan

first: Federico

last: Rossi

address: Via Adamello 16

country: Italy

institute: Istituto Europeo Oncologia

library_source: genomic

data_processing:
Alignment; bowtie v1.2.2; --chunkmbs 1024 -m 1 --best -S --no-unal -q -I 10 -X 1000
Peak calling; MACS2 v2.1.1 narrow mode; –format BAMPE –keep-dup all -m 3 30 pvalue 1e-10
mm10
bed file format; narrow peaks called with MACS2 having a -log10 p-value higher than 10

molecule: genomic DNA

organism: Mus musculus

source_name: mESC

growth_protocol: mESCs were grown on 0.1% gelatin-coated dishes in 2i/LIF-containing GMEM medium (Euroclone) supplemented with 20% fetal calf serum (Euroclone), 2 mM glutamine (Gibco), 100 U/ml penicillin, 0.1 mg/ml streptomycin (Gibco), 0.1 mM non-essential amino acids (Gibco), 1 mM sodium pyruvate (Gibco), 50 µM ß-mercaptoethanol phosphate buffered saline (PBS; Gibco), 1000 U/ml leukemia inhibitory factor (LIF; produced in-house), and GSK3β and MEK 1/2 inhibitors (ABCR GmbH) to a final concentration of 3 mM and 1 mM, respectively.

extract_protocol:
ChIP experiments were performed according to standard protocols as described previously (Ferrari et al., 2014)
DNA libraries were prepared with 2–10 ng of DNA using an in-house protocol (Blecher-Gonen et al., 2013) by the IEO genomic facility

treatment_protocol: Indicated cells were treated for 48 hours with 500nM dTAG-13 (TOCRIS), or DMSO as vehicle, in order to degrade dTAG-BAP1. To generate stable KO cell lines, 10ug pX458 2.0 plasmid pairs (Addgene) encoding Cas9 and sgRNAs were transfected using Lipofectamine 2000 (Invitrogen), according to manufacturer’s instruction. Sorting of GFP positive cells was carried out 48 hours after transfection and 1000 cells were seeded onto a 15-cm dish. Clones were isolated 10-14 days later and grown further before screening for knockout by Western blot. For rescue clone generation, mESCs were transfected with 10ug pCAG vectors encoding 2xFlag-HA-tagged BAP1 wild-type or BAP1 C91S using Lipofectamine 2000 (ThermoFisher Scientific), according to manufacturer’s instructions. 24 hours post-transfection puromycin selection (1µg/ml) was added for a further 24 hours. Cells were then split to clonal density (~1:40) onto a 15cm plate. Clones were isolated 10-14 days later and grown further before screening for rescue allele expression by Western blot.

tag: chip antibody

tag: sample type


title: Female XO genotype subject 164 thoracic aorta

city: Lexington

first: Eric

middle: M

last: Blalock

state: KY

address: 800 Rose St.

department: Molecular and Biomedical Pharmacology

country: USA

institute: University of Kentucky

library_source: transcriptomic

data_processing:
Illumina Casava (v 1.8) was used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using STAR (v 2.6.1) in Partek Flow (v 8.0)
Counts were normalized to abundance measures with the TMM algorithm in WebMev
Genes annotated as protein-coding that had at least two samples with TMM measures > 1.5 were retained for statisitcal analysis
Statistical analysis was done using LIMMA in WebMev to perform pairwise comparison among groups to generate p-values, q-values, and log 2 fold-changes
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with TMM abundance measures for every gene and every sample annotated to mm10

molecule: polyA RNA

source_name: thoracic aorta

extract_protocol:
RNA was extracted from the thoracic aorta (defined as the segment extending from the aortic root to the diaphragm) and abdominal aorta (defined as the segment extending from the diaphragm to the iliac bifurcation) using a Maxwell Rapid Sample Concentrator (RSC) simply RNA Tissue kit (REF#AS1340, Promega, Madison, WI).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Female C57BL/6J Ldlr-/- mice at 14-18 wks of age (n = 5 XX genotype, n =5 X0 genotype) were fed a Western (high fat- TD88137, Envigo) diet for 1 wk

tag: strain

tag: genetic deficiency

value: Ldlr-/-

tag: Sex

value: female

tag: genotype

value: XO

tag: rin


title: Yap shRNA knock-down vector 1

description:
kevinwatt_YapKD_gnames_cnt.tsv
YAP1

molecule: total RNA

tag: tissue


title: BAP1-KO-clone1-H3K4me1


title: SNI 2, input

city: Tian Jin

first: Xianhu

last: Zhou

address: NO.154,Anshan Road,Heping District

department: Department of Orthopedics

country: China

institute: Tianjin Medical University General Hospital

data_processing:
Paired-end reads were harvested from Illumina NovaSeq 6000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3).
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 were figured out and choosed by home-made scripts.
Differentially Expressed mRNAs was obtained through the expression profile of input sample
Genome_build: rn5
Supplementary_files_format_and_content: Number of raw junction read

organism: Rattus norvegicus

source_name: Sciatic Nerve

extract_protocol:
Total RNA from each sample was isolated using TRIzol reagent (Invitrogen) and then quantified using a NanoDrop ND-1000 instrument. The Arraystar Seq-StarTMpoly(A) mRNA Isolation Kit (Arraystar, MD, USA) was used to extract Poly(A) mRNA. The concentration, purity and integrity of extracted RNA .  Fragment mRNA into 100-nucleotide fragments, and then use agarose electrophoresis to determine the post-fragmentation size distribution. mRNA was divided into two samples: input and IP samples
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). The library quality was evaluated with BioAnalyzer 2100 system (Agilent Technologies, Inc., USA). Library sequencing was performed on an illumina NovaSeq 6000 instrument with 150bp paired-end reads.

value: Wistar

tag: weight

tag: protocol

value: SNI


title: WT-H3K4me1


title: SNI 2

tag: antibody


title: Empty vector control 2

description:
kevinwatt_YapKD_gnames_cnt.tsv
C2

value: control


title: LnCaP

city: Seattle

first: Michael

middle: Christoph

last: Haffner

state: WA

address: 1100 Fairview Avenue

department: Human Biology

institute: Fred Hutchinson Cancer Research Center

data_processing:
Colorspace alignment: BioScope v1.3 was used to carry out colorspace alignments using the whole transcriptome workflow in Bioscope using default parameters
Expression counts: Gene expression read counts were derived using HTSeq.count and the hg18 refseq gtf file
Normalized gene abundance measure: Gene expression read counts were normalized to library size and gene length to derive FPKM values for each gene and sample using a custom python script
Genome_build: hg18
Supplementary_files_format_and_content: text files with raw counts, and normalized FPKM values as described in Processed data files below

organism: Homo sapiens

source_name: prostate cancer cell line

growth_protocol: RPMI supplemented with 10% FBS

extract_protocol:
Rneasy, Qiagen
SOLID Total RNA-Seq kit, ABI following standard protocols

treatment_protocol: All cell lines were grown in their respective growth medium without any other treatment

tag: cell line

value: LnCaP

tag: cell type

value: castration sensitive

value: prostate cancer


title: BAP1-KO-clone2-H3K4me3


title: SNI 1, input


title: LnCaP-abl

growth_protocol: RPMI supplemented with 10% charcoal-stripped FBS and 1XB27

value: LnCaP-abl

value: castration resistant


title: Female XO genotype subject 165 abdominal aorta

source_name: abdominal aorta


title: Yap shRNA knock-down vector 2

description:
kevinwatt_YapKD_gnames_cnt.tsv
YAP2


title: BAP1-KO-clone1-H3K4me3


title: SNI 3


title: Empty vector control 1

description:
kevinwatt_YapKD_gnames_cnt.tsv
C1


title: SNI 1


title: ISTMES2-PAR-rep1

description: counts.tsv

data_processing:
For ChIP-seq data, paired-end DNA reads were processed through fastp to trim adapters and to remove low quality nucleotides at read ends (Chen et al., 2018). Quality-filtered DNA reads were aligned to the mouse reference genome mm10, or mm10 and fly reference genome (dm6) for histone ChIP-Rx using Bowtie v1.2.2 retaining only uniquely aligned reads (-m 1) and using the parameters -I 10, -X 1000 (Langmead et al., 2009). Reads mapped to both mm10 and dm6 were discarded. Peaks were identified using MACS2 v2.1.1 in narrow mode with parameters –format BAMPE –keep-dup all -m 3 30 and p-value 1e-10 (Zhang et al., 2008). Peaks were annotated using the R package ChIPpeakAnno v3.15 using for each peak the 5 kbp region around the center of the peak  (Zhu et al., 2010).
For RNA-seq, reads were aligned to the mouse reference genome mm10 using STAR v2.7 without allowing for multimapping. PCR duplicates were removed using samblaster (Faust and Hall, 2014). Mapped reads were assigned to genes using featureCounts (Liao et al., 2014) with unstranded read counting on exons and using the gene name as attribute type in the annotation. Genes were annotated as in Gencode M21 (GRCm38) downloaded from https://www.genecodegenes.org/mouse/. Differentially expressed genes were identified using the R package DESeq2 v1.24 using default parameters (Love et al., 2014). The fold change of lowly expressed genes was corrected using the lfcShrink function of the apeglm R package with the type option set to apeglm v1.6 (Zhu et al., 2019). The adjusted p-value was corrected by the independent hypothesis weighting (IHW) method as implemented in the R package IHW v1.12 (Ignatiadis et al., 2016). Genes were considered differentially expressed when presenting an absolute log2 fold change equal or greater than 1.5 and an adjusted p-value lower than 0.05.
For HiC data, DNA reads were filtered for low-quality bases and adapters using fastp (Chen et al., 2018). Filtered DNA reads were processed through the HiCpro pipeline to obtain contact matrices reporting the chromatin interactions at the genome-wide level (Servant et al., 2015). Using default settings, DNA reads were aligned to the mouse reference genome mm10 using bowtie2 in end-to-end mode, uniquely aligned DNA reads were assigned to the DpnII genomic restriction fragments, valid interactions were identified and used to generate interaction matrices. The HiCpro matrices containing all of the valid pairs were converted in hic format using the hicpro2juicebox function (Robinson et al., 2018), and in cool format using the hic2cool function (https://github.com/4dn-dcic/hic2cool). Contact matrices in cool format where corrected using the ICE algorithm as implemented in the hicCorrectMatrix function (Wolff et al., 2020). Plots of the interactions occurring at single locus or whole-chromosome level were obtained by HiCplotter (Akdemir and Chin, 2015). Hi-C was performed in duplicate with key findings being overserved in each before pooling replicates to make the final high-depth analyses.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bed (MACS2), counts (counts.tsv), differential expression (DESeq2), validpairs (HiCPro).

growth_protocol: mESCs (both E14 and TCF background) were grown on 0.1% gelatin-coated dishes in 2i/LIF-containing GMEM medium (Euroclone) supplemented with 20% fetal calf serum (Euroclone), 2 mM glutamine (Gibco), 100 U/ml penicillin, 0.1 mg/ml streptomycin (Gibco), 0.1 mM non-essential amino acids (Gibco), 1 mM sodium pyruvate (Gibco), 50 µM ß-mercaptoethanol phosphate buffered saline (PBS; Gibco), 1000 U/ml leukemia inhibitory factor (LIF; produced in-house), and GSK3β and MEK 1/2 inhibitors (ABCR GmbH) to a final concentration of 3 μM and 1 μM, respectively. For ATRA stimulation of ESCs, cells were washed twice with PBS 24 hours after seeding and media was replaced with ESC media lacking LIF, GSK3β and MEK1/2 inhibitors, and instead supplemented with 1μM ATRA for 24 hours.

extract_protocol:
ChIP-seq: DNA was purified with QIAquick PCR purification kit (Qiagen) according to manufacturer’s instructions.
DNA was purified with QIAquick PCR purification kit (Qiagen) according to manufacturer’s instructions. DNA libraries were prepared with 2–10 ng of DNA using an in-house protocol (Blecher-Gonen et al., 2013) by the IEO genomic facility and sequenced on an Illumina HiSeq 2000.
RNA-seq: RNA-seq was performed following SMART-seq2 protocol (Picelli et al., 2014)  with minor modifications. Briefly, poly-A containing mRNA molecules obtained from 1 μg of total RNA were copied into first-strand cDNA by reverse transcription and template-switching using oligo (dT) primers and an LNA-containing template-switching oligo (TSO). Resulting cDNA was pre-amplified with KAPA HotStart Taq enzyme (Kapa Biosystems) and then purified with Ampure beads (Agencourt AMPure XP- Beckman Coulter). One nanogram of pre-amplified cDNA was tagmented with in-house produced Tn5 transposase and further amplified with KAPA HotStart Taq enzyme. After purification with Ampure beads, the quality of the obtained library was assessed by Bioanalyzer (High Sensitivity DNA kit, Agilent Technologies), prior to sequencing. Each RNA-seq experiment was performed in triplicate.
Hi-C: In situ Hi-C was performed as described (Rao et al., 2014) with slight alterations to the protocol. 5x10^6 ESCs were crosslinked for 10 minutes in 1% formaldehyde before quenching in 125mM Glycine for 5 minutes. Cell pellets were washed twice in PBS before contact generation. Pellet was resuspended in 500uL Hi-C lysis buffer (10mM Tris-HCl pH8.0, 10mM NaCl, 0.2% NP40 and protease inhibitors) and incubated with rotation for 30 minutes at 4°C. Cells were pelleted and washed in 500uL Hi-C lysis buffer. Pellet was resuspended in 100uL 0.5% SDS and incubated for 10 minutes at 62°C. 285uL of H20 and 50uL of 10% Triton X-100 was added to quench the SDS at 37°C for 15 minutes. 50uL of 10xNEB DpnII buffer and 750U of DpnII were added (NEB R0453M) then incubated at 37°C overnight with shaking. Digestion was heat inactivated the next day for 20 minutes at 62°C. Biotin fill in was performed by addition of 52uL fill-in mix (0.288mM dCTP/dTTP/dGTP, 50U DNA Polymerase I, Large Klenow fragment (NEB M0210) and 0.288mM biotin-dATP (Thermo 19524016)). Fill-in reaction was incubated at 37°C for 1 hour with shaking. Ligation was performed by adding 150uL 10x NEB T4 DNA ligase buffer, 125uL 10% Triton X-100, 3uL 50mg/mL BSA and 8000U of T4 DNA ligase and H20 up to 1.5mL. Ligation was performed overnight at 25°C with shaking. Nuclei were pelleted before resuspending in IP buffer (33 mM Tris-HCl pH 8, 100 mM NaCl, 5 mM EDTA, 0.2% NaN3, 0.33% SDS, 1.66% Triton X-100) and sonicating to fragment size between 200-1000bp. 15uL of the sample was de-crosslinked overnight at 65°C with 85ul of decrosslinking buffer (0.1M NaHCO3, 1% SDS) before clean up using QiaQuick PCR clean up kit from Qiagen.
Library prep was performed as described (Mumbach et al., 2016). Streptavidin C-1 beads (Thermo 65001) were washed and resuspended in 2x biotin binding buffer (10mM Tris-HCl pH7.5, 1mM EDTA, 2M NaCl). 10ng of DNA was used for biotin capture, streptavidin C-1 beads were added and incubated for 15 minutes at room temperature with shaking. Beads were washed twice at 55°C for 2 minutes in Tween wash buffer (5mM Tris-HCl pH7.5, 0.5mM EDTA, 1M NaCl, 0.05% Tween). Beads were washed once in 1xTD buffer (20mM Tris-HCl pH7.5, 10mM MgCl2, 20% DMF) before being tagmented with in-house produced Tn5 transposase in TD buffer for 55°C for 10 minutes. TN5 was quenched in 50mM EDTA for 30 minutes at 55°C before washing twice in 50mM EDTA, twice in Tween wash buffer and once in 10mM Tris. PCR amplification was carried out on beads using KAPA HotStart Taq enzyme. After purification of PCR product with Ampure beads, the quality of the obtained library was assessed by Bioanalyzer (High Sensitivity DNA kit, Agilent Technologies), prior to sequencing.

treatment_protocol: To generate stable KO cell lines, 10ug pX458 2.0 plasmid pairs (Addgene) encoding Cas9 and sgRNAs (Table S3) were transfected using Lipofectamine 2000 (Invitrogen), according to manufacturer’s instruction. Sorting of GFP positive cells was carried out 48 hours after transfection and 1000 cells were seeded onto a 15-cm dish. Clones were isolated 10-14 days later and grown further before screening for knockout by Western blot. For rescue clone generation, mESCs were transfected with 10ug pCAG vectors encoding 2xFlag-HA-tagged BAP1 wild-type or BAP1 C91S using Lipofectamine 2000 (ThermoFisher Scientific), according to manufacturer’s instructions. 24 hours post-transfection puromycin selection (1µg/ml) was added for a further 24 hours. Cells were then split to clonal density (~1:40) onto a 15cm plate. Clones were isolated 10-14 days later and grown further before screening for rescue allele expression by Western blot.


title: WT-H3K4me3


title: ISTMES2-BAP1KO-C91S-rep2

description: counts.tsv


title: Empty vector control 3

description:
kevinwatt_YapKD_gnames_cnt.tsv
C3


title: Control 3

value: Control


title: BAP1-KO-clone2-H3K27ac


title: Control 2, input


title: ISTMES2-PAR-rep3

description: counts.tsv


title: WT-H3K27ac


title: BAP1-KO-clone1-H3K27ac


title: ISTMES2-BAP1KO-C91S-rep1

description: counts.tsv


title: BAP1-KO-clone2-H3K27me2


title: Control 1, input


title: Control 3, input


title: ISTMES2-BAP1KO-C91S-rep3

description: counts.tsv


title: Control 2


title: Control 1


title: ISTMES2-PAR-rep2

description: counts.tsv


title: control soleus replicate 1

type: RNA

city: Mikajima, Tokorozawa

first: akiko

last: onda

state: Saitama

department: graduate school of sport sciences

country: Japan

institute: waseda university

hyb_protocol: standard Affymetrix procedures

scan_protocol: AGCC

data_processing: the data were processed by RMA using AGCC/Expression Console.

label: biotin

source_name: control soleus

label_protocol: standard Affymetrix procedures

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

tag: age

value: 8 weeks

value: soleus


title: hindlimb suspension soleus replicate 2

source_name: hindlimb suspension soleus

value: male


title: control soleus replicate 2


title: HS + electroacupuncture soleus replicate 2

source_name: HS + electroacupuncture soleus


title: hindlimb suspension soleus replicate 1


title: HS + electroacupuncture soleus replicate 1


title: E. coli WT vs hdeA 2

city: Koganei

first: Kaneyoshi

last: Yamamoto

state: Tokyo

address: 3-7-2 Kajinocho

department: Frontier Bioscience

institute: Hosei University

hyb_protocol: Each 300 ng of Cy3- and Cy5-labeled cDNA were mixed and added to 1X Blocking Buffer (Agilent) and 1X HI-RPM GE Hybridization Buffer (Agilent). After precipitation of impurities, 40 µl of the labelled-cDNA mixture was applied to theDNA chip, and the hybridization was carried out at 65°C for 17 hr. The DNA chip was washed at room temperature with Agilent Gene Expression Wash Buffer 1 (Agilent) and at 37°C with Agilent Gene Expression Wash Buffer 2 (Agilent).

scan_protocol: Scanned on an Agilent G2565CA scanner.

data_processing:
Images were quantified using Agilent Feature Extraction Software (version 8.1).
Agilent Feature Extraction Software (v 8.1) was used for background subtraction.

organism: Escherichia coli BW25113

source_name: WT 2

label_protocol: 5 µg of total RNA were used for labeled cDNA preparation using FairPlay III Microarray Labeling kit (Agilent).

growth_protocol: E. coli strains were grown at 37°C in M9-Glycerol medium containing 0.2% casamino until a mid-log phase.

extract_protocol: Total RNA was extracted by a hot phenol method. Water-saturated phenol and ethanol precipitation were used, following the digestion with RNase-free DNase I (Takara Bio). Total RNA was dissolved in RNase-free water.

value: Wild type

value: hdeA-deficient


title: E. coli WT vs hdeD 2

value: hdeD-deficient


title: E. coli WT vs hdeA 1

source_name: WT 1


title: ISTMES2-BAP1KO-WT-rep1

description: counts.tsv


title: BAP1-KO-clone1-H3K27me2


title: FGF_RNA_rep3

city: Philadelphia

first: Peder

middle: J

last: Lund

state: PA

address: 3400 Civic Center Blvd, Smilow 9-176

institute: University of Pennsylvania

data_processing:
Paired-end sequencing data (38 and 37 cycles for read 1 and read 2 with 6 cycle index) was acquired on an Illumina NextSeq 500 instrument.  FASTQ generation was provided by BaseSpace (Illumina) with GenerateFASTQWorker (version 1.37.0) with bcl2fastq2.
FASTQ files were aligned to the mm10 genome using STAR (version 2.5.2a),  For ChIP-seq, alignment parameters were: --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --alignMatesGapMax 1000000).  For RNA-seq, alignment parameters were: --outFilterType BySJout --outFIlterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000.
Sam files were filtered for unique alignments (MAPQ = 255) before conversion to bam and then bed files.  For ChIP-seq data, read pairs were condensed into a single bed entry allowing for a maximum fragment length of 1000 bp.  Read pairs matching to different chromosomes were discarded.  Bed files were converted to bedgraphs and then bigwigs with normalization to total reads (RPM) and, where specified, to input samples by division.  Software tools included samtools (v1.1), Python (v3.6.3), and bedtools (2.15.0).  RNA-seq data was processed similarly except bed files were produced with the -split option to eliminate introns.  For track visualization, RNA-seq data was normalized to total read counts (RPM) and read pairs were left unpaired.
Peaks were called from the bed file of paired fragments using MACS2 (v2.2.6, parameters -f BEDPE -g mm -q 1e-2).  The corresponding input sample was specified as background.  Quantitative comparisons were performed on indexed bam files with DiffBind.  Peak annotation was obtained with ChIPseeker in R.  For RNA-seq data, read counts were obtained with HTSeq (v0.10.0, parameters -f sam -r name -s reverse -t exon -i gene_id --nonunique none --secondary-alignments ignore --supplementary alignments ignore) for analysis by DESEQ2 in R.
Genome_build: mm10
Supplementary_files_format_and_content: bw files were generated as described above.  Scores represent tag density normalized to sequencing depth (RPM) with additional normalization to input samples (by division with replacement by reciprocal when < 1) where indicated.  Xls files contain the output of peak calling by MACS2 as described above.  Csv files contain quantitative information on ChIP-seq data and RNA-seq data as analyzed by DiffBind and DESEQ2.  The fold-change indicates log2(FGF/FBS).

source_name: Y1 murine adrenocortical cell line

growth_protocol: Y1 cells were grown in DMEM media supplemented with 10% serum, 100 mg/L streptomycin, 25 mg/L ampicillin, 1.2 g/L sodium bicarbonate and kept at 37°C in a 5% CO2 incubator.

extract_protocol:
Frozen cells were thawed on ice and resuspended in PBS for aliquotting purposes.  Total RNA was extracted using QIAshredder devices and the Qiagen RNeasy mini kit according to the manufacturer's instructions.
mRNA isolation, cDNA synthesis, and library preparation were performed using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs) with the NEBNext Poly(A) mRNA magnetic isolation module according to the manufacturer's instructions.

treatment_protocol: After plating, cells were allowed to reach 30% confluence before serum-starvation for 48 hours.  Starved cells were then stimulated with fetal bovine serum (10%) or serum plus FGF-2 (10 ng/mL) and harvested after 5 hrs.  Cell pellets were stored at -80C until sample extraction.

value: Y1 murine adrenocortical cell line

tag: treatment

value: serum + FGF-2


title: ISTMES2-BAP1KO-WT-rep2

description: counts.tsv


title: E. coli WT vs hdeD 1


title: E. coli WT vs gadE 2

value: gadE-deficient


title: FGF_RNA_rep2


title: BAP1-KO-clone2-H3K27me3


title: BAP1-KO-clone1-H3K27me3


title: E. coli WT vs gadE 1


title: FGF_RNA_rep1


title: WT-H3K27me2


title: ISTMES2-PAR-INPUT

description: Input


title: ISTMES2-BAP1KO-WT-rep3

description: counts.tsv


title: WT-H3K27me3


title: activated CD4+CD62Lhi cells from miR-7 deficiency mice

city: Zunyi

first: Juan

middle: Juan

last: Zhao

state: Guizhou

address: 6 Xuefu west Road

department: Immunology

institute: Zunyi medical University

description: This sample is activated CD4+T cells for 48 hours in the presence of anti-CD3 and CD28 antibody plus IL-2 from the splenocytes miR-7deficiency mice in vitro. The cell is representative sample of three activated miR-7deficiency biological replicates used in this experiment.

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

source_name: activated CD4+CD62Lhi cells from miR-7deficiency mice

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Bacteroides fragilis NCTC 9343 was grown to mid-log phase (O.D.600nm 0.8) anerobically (80% N2, 10% CO2, 10% H2) at 37°C in basal media (Pantosti et al. Infect. Immun. 59(6):2075).

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration were determined by analysis with an Agilent 2100 bioanalyzer at the Harvard-Partners Center for Genetics and Genomics (Harvard Medical School, Cambridge, MA USA).

treatment_protocol: Bacteroides fragilis NCTC 9343 delta-ungD1 delta-ungD2 delta-PSH was grown to mid-log phase (O.D.600nm 0.8) anaerobically (80% N2, 10% CO2, 10% H2) at 37°C in basal media (Pantosti et al. Infect. Immun. 59(6):2075).

tag: genotype/variation

value: miR-7 deficiency

value: CD4+ T cells

value: Activated


title: ISTMES2-FLAGBAP1-INPUT

description: Input


title: ISTMES2-PAR-H3K27me3


title: FBS_RNA_rep3

value: serum


title: FBS_RNA_rep2


title: BAP1-KO-clone2-H2AK119ub1


title: WT-H2AK119ub1


title: FBS_RNA_rep1


title: Virus+RDV-24hpi-Rep2-VeroE6-Ribozero

city: Shenzhen

first: Yan

address: No. 1088,Xueyuandadao

department: BIology

institute: Southern University of Science and Technology

data_processing:
The raw data was quality controled with fastp, with parameters "-n 10 -q 35 -w 8 --detect_adapter_for_pe".
The sequenced reads of Vero-E6 cell lines were aligned to the ChlSab1.1 reference genomes respectively by using STAR 2.7.1a [35]. Reference genome was downloaded from htps://www.ensembl.org/info/data/ftp/index.html.
Unmapped reads were output as fastq files and then aligned to SARS-COV-2 genome, which was downloaded from https://www.ncbi.nlm.nih.gov/nuccore/MT123290.1?report=fasta, by STAR
Picard toolkit v2.22.6 (“Picard Toolkit.” 2019) with option “MarkDuplicates” to mark the duplicated reads in sorted bam file that mapped to virus genome, then we used samtools v1.9 with option “-F 1024” to remove the duplicated reads. Cigars are extracted from bam files and results are listed in the Processed files ended with .cigar_jumps_no_dup.txt.
Bedtools v2.28.0 [37] with option “genomecov -strand +/-” was used to calculate coverage of reads mapped to both sense and anti-sense strand genome for Ribozero sequencing. (Processed files ended with jumps.txt )
Genome_build: Chlorocebus sabaeus: htps://www.ensembl.org/info/data/ftp/index.html. SARS-CoV-2: https://www.ncbi.nlm.nih.gov/nuccore/MT123290.1?report=fasta
Supplementary_files_format_and_content: txt format. The processed files contain position of junciton sites on both strands and cigar of reads mapped to SARS-CoV-2 genome.
Supplementary_files_format_and_content: *unmapped.cigar_jumps_no_dup.txt: each line starts with a number recording the #[StartMappingPostion], followed by a capital 't' to separate it with the [cigars extracted from bam files, eg. 50M3000N100M].
Supplementary_files_format_and_content: *unmapped.jumps_no_dup.txt: the j5 junction site, j3 junction site and read counts seperated by a capital 't'.
Supplementary_files_format_and_content: *FKDL*.cigar_jumps.txt: the strand flag, mapping start position of paired reads and mapping results (cigar from the bam files) are seperated by a space. [header: strand, StartPos, cigar]
Supplementary_files_format_and_content: *FKDL*.jumps.txt: header: [j5-junction-site j3-junction-site Strand  ReadsCount]

organism:
Chlorocebus sabaeus
Severe acute respiratory syndrome coronavirus 2

source_name: Vero E6 cells

growth_protocol: Cells were grown in Dulbecco’s modified Eagle’s medium (DMEM, Gibco) supplemented with 10% fetal bovine serum (FBS, Gibco) at 37 °C in a humidified atmosphere of 5% CO2.

extract_protocol:
Cultured cells were washed once with PBS before adding TRIzol (Vazyme, Cat no. R401-01). Total RNA extracted according to the manufacturer’s instructions. RNA was eluted in 20 μl RNase-free water.
Purified total RNAs from non-infected and SARS-CoV-2-infected Vero cells were reverse transcribed using the RT SuperMix Reagent Kit with gDNA Eraser (Vazyme, Cat no. R223-01). Briefly, 1 μg total RNA was firstly digested with gDNA eraser to remove contaminated DNA and then the first-strand cDNA was synthesized in 20 μl reaction with Oligo (dT) or forward and reverse PCR primer for negative-strand and positive-strand specific reverse transcription, respectively. Finally, 2 μl ten times diluted cDNA was used as template for quantitative PCR. RT-qPCR was performed on CFX96 Real-time PCR system (Bio-Rad) with the SYBR Green Master Mix (Yeasen, Cat no. 11201ES03)

treatment_protocol: For virus infection, Vero E6 cells, with 90% confluency in 12-well plates, were inoculated with the SARS-CoV-2 virus at a MOI of 0.05. One hour after incubation at 37 °C, cells were washed three times with phosphate buffered saline (PBS) followed by 24-hours.Remdesivir (Cat. No. HY-104077) was purchased from MedChemExpress (Monmouth Junction, NJ). The SARS-CoV-2 strains used in this research were isolated from COVID-19 patients in Guangzhou (Accession numbers: MT123290 ), and passaged on Vero E6.  incubation in the fresh normal culture medium with or without Remdesivir at 10 uM of final concentration.

value: Vero E6

value: SARS-CoV-2 + Remdesivir

tag: time

tag: rna population

value: Ribozero RNA


title: naïve CD4+CD62Lhi cells from miR-7 deficiency mice

description: This sample is naïve CD4+T cells from the splenocytes miR-7deficiency mice. The CD4+T cells was isolated by immune-magnetic beads, the cell is representative sample of three miR-7deficiency biological replicates used in this experiment.

source_name: naïve CD4+CD62Lhi cells from miR-7deficiency mice

value: Naive


title: FGF_input_rep2

extract_protocol:
Frozen cells were thawed on ice, resuspended in PBS, and cross-linked with 1% formaldehyde for 5 mins at room temperature.  Cross-linking was quenched with 125 mM glycine for 5 mins at room temperature.  Cells were lysed as previously described (Lee et al, 2006), except that N-lauroylsarcosine was used at 0.1%,  and sonicated with a S220 Focused-ultrasonicator (Covaris) for 15 min. Sonicated lysates were supplemented with 1% Triton X-100 and then cleared by centrifugation at full speed in microcentrifuge for 10 min at 4°C. The supernatant was transferred to a new tube and the protein content was measured by Bradford assay. Extracts were incubated overnight at 4°C with 5 ug of anti-H3K27ac (Active Motif) pre-bound to protein G dynabeads (Thermo Scientific) that were pre-blocked with 0.5% BSA in PBS. Beads were washed and then incubated with elution buffer (50 mM Tris-HCl, pH 8.0, 10 mM EDTA, 1% SDS) for 30 min at 65°C. Crosslink reversal was performed by overnight incubation at 65°C. Samples were diluted with 1 volume of TE and then treated with RNaseA (0.2 mg/ml for 2 hrs at 37°C) and proteinase K (0.2 mg/ml for 2 hrs at 55°C) prior to DNA extraction with phenol:chloroform:isoamyl alcohol.
Library preparation was performed using the NEBNextUltra II DNA Library Prep Kit for Illumina (New England Biolabs).

tag: chip antibody


title: BAP1-KO-clone1-H2AK119ub1

tag: sample type


title: activated CD4+CD62Lhi cells from Wild type mice

description: This sample is activated CD4+T cells for 48 hours in the presence of anti-CD3 and CD28 antibody plus IL-2 from the splenocytes wild-type mice in vitro. The cell is representative sample of three activated wild-type biological replicates used in this experiment.


title: Virus+RDV-24hpi-Rep1-VeroE6-Ribozero


title: ISTMES2-FLAGBAP1-H3K27me3


title: Virus-24hpi-Rep2-VeroE6-Ribozero


title: ISTMES2-PAR-H2AK119Ub1


title: BAP1-KO-clone2-input.2

description: Low-depth sequenced genomic DNA input for the normalisation of  BAP1-KO-clone2-H3K27me2, BAP1-KO-clone2-H3K27ac, BAP1-KO-clone2-H3K4me3, BAP1-KO-clone2-H3K4me1

value: Input


title: FGF_input_rep1


title: ISTMES2-FLAGBAP1-H2AK119Ub1


title: FBS_input_rep2


title: BAP1-KO-clone1-input.2

description: Low-depth sequenced genomic DNA input for the normalisation of  BAP1-KO-clone1-H3K27me2, BAP1-KO-clone1-H3K27ac, BAP1-KO-clone1-H3K4me3, BAP1-KO-clone1-H3K4me1


title: Virus-24hpi-Rep1-VeroE6-Ribozero


title: Virus+RDV-24hpi-Rep3-VeroE6-PolyA

value: PolyA RNA


title: WT-input..2

description: Low-depth sequenced genomic DNA input for the normalisation of  WT-H3K27me2, WT-H3K27ac, WT-H3K4me3, WT-H3K4me1

value: WT-input


title: Virus+RDV-24hpi-Rep2-VeroE6-PolyA


title: IBUN13A Gly3

city: Bogotá D.C.

first: Ximena

middle: Carolina

last: Perez-Mancilla

country: Colombia

institute: Universidad Nacional de Colombia

data_processing:
Sequence trimming and filtering was performed using BBDuk2 using standard parameters and SILVA 16SrRNA database,  and quality evaluation was done using FastQC
To determine transcripts abundance, genome sequence of Clostridium sp. IBUN13A previously obtained (JZWG00000000) and Kallisto 0.46.0 were used.
Differential expression was determined using Bioconductor's DESeq2 , taking into account log2 ratio  ≥1,5 and adjusted p value equal or less than 0,1
Genome_build: Accesion no. JZWG00000000
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Clostridium sp. IBUN13A

source_name: IBUN13A grown on Glycerol

growth_protocol: Microorganism was grown on an industrial culture media containing 40 g/L of glyerol or 20 g/L of glucose, under anaerobic conditions at 35 +/- 2°C for 24 hours

extract_protocol:
Pellets from 40 mL culture vessels were collected and the procedures from TRIzol® Max™ Bacterial RNA Isolation Kit  and  RNeasy Protect Bacteria Mini Kit de Qiagen ® were followed
RNA libraries were prepared for sequencing using standard Illumina protocols for Illumina TruSeq stranded mRNA (microbe)

tag: strain

value: wild type

value: grown on Glycerol


title: FGF_H3K27ac_rep2

value: H3K27ac (ActiveMotif 39133)


title: BAP1-KO-clone2-input.1

description: Low-depth sequenced genomic DNA input for the normalisation of  BAP1-KO-clone2-H2AK119ub1 and BAP1-KO-clone2-H3K27me3


title: Virus+RDV-24hpi-Rep1-VeroE6-PolyA


title: FBS_input_rep1

value: Y1 murine adrenocortical cell line


title: FGF_H3K27ac_rep1

value: serum + FGF-2


title: BAP1-KO-clone1-input.1

description: Low-depth sequenced genomic DNA input for the normalisation of  BAP1-KO-clone1-H2AK119ub1 and BAP1-KO-clone1-H3K27me3


title: IBUN13A Gly1


title: IBUN13A Glu3

source_name: IBUN13A grown on Glucose

value: grown on Glucose


title: IBUN13A Gly2


title: FBS_H3K27ac_rep2


title: WT-input.1

description: Low-depth sequenced genomic DNA input for the normalisation of  WT-H2AK119ub1 and WT-H3K27me3


title: Virus-24hpi-Rep3-VeroE6-PolyA


title: FBS_H3K27ac_rep1


title: E14-input

description: High-depth sequenced genomic DNA input for peak calling


title: Virus-24hpi-Rep1-VeroE6-PolyA


title: Virus-24hpi-Rep2-VeroE6-PolyA


title: H_3

status: Public on Jun 26 2021

city: Chengdu

first: Liming

last: Chang

address: No.9 Section 4,Renmin Nan Road,Chengdu, Sichuan, P.R. China

department: Chengdu Institute of Biology

institute: Chinese Academy of Sciences

description:
Microhyla fissipes_Unigene.fasta
Microhyla fissipes_FPKM.xlsx

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;The total clean reads from all libraries were assembled using Trinity as a reference transcriptome.
The expression level of each unigene was expressed as fragments per kilobase of exon model per million mapped reads (FPKM).
Genome_build: de novo
Supplementary_files_format_and_content: XLSX file includes FPKM values for all Samples
Supplementary_files_format_and_content: fasta file includes the sequences of all unigenes

organism: Microhyla fissipes

source_name: Whole tissue

extract_protocol:
Total RNA of each sample was extracted and purified using Trizol (Invitrogen, Carlsbad, CA, USA) following the manufacturer’s instructions. After purified with poly-T oligo-attached magnetic beads, the mRNAs were fragmented.
First-strand cDNA was synthesized using random hexamer primers and M-MuLV Reverse Transcriptase (RNase H−). Second-strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. The remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of the 3′ ends of the DNA fragments, NEBNext Adaptors with a hairpin loop structure were ligated to prepare for hybridization. To preferentially select cDNA fragments of 150–200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then, 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR. Then, PCR was performed with a Phusion High-Fidelity DNA polymerase, universal PCR primers and Index (X) primer. Finally, PCR products were purified (AMPure XP system), and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using the TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina HiSeq 2500 platform by NovoGene (Beijing), and paired-end reads were generated.

treatment_protocol: Tadpoles were exposed in GBH of various concentrations

tag: developmental stage

value: Gosner stage 30

tag: collection sites

value: Shifang County, Sichuan Province, China (31.1097° N, 104.1533° E)

value: 90 mg/L GBH exposure


title: IBUN13A Glu2

tag: genotype


title: IBUN13A Glu1


title: naïve CD4+CD62Lhi cells from Wild type mice

description: This sample is naïve CD4+T cells from the splenocytes wild-type mice. The CD4+T cells was isolated by immune-magnetic beads, the cell is representative sample of three wild-type biological replicates used in this experiment.

value: Wild type

value: CD4+ T cells


title: L_2

value: 60 mg/L GBH exposure


title: H_1


title: H_2


title: L_3


title: L_1


title: C_3

value: 0 mg/L (control) GBH exposure


title: C_2


title: C_1


title: Mutant_RCNMV_Rep4

city: Ames

first: Wyatt

middle: Allen

last: Miller

state: IA

address: 2213 Pammel Dr

department: Plant Pathology & Microbiology

institute: Iowa State University

description: RNA-seq data

data_processing:
de-multiplexed sequenced data (fastq) files were obtained from Zymo Research . The quality of raw sequencing reads was assessed using FastQC. The eleven RNA-seq samples were trimmed for adapters and quality using Trim galore 0.4.5 (https://github.com/FelixKrueger/TrimGalore).
Reads were mapped to the N. benthamiana 1.0.1 genome (obtained from the Sol Genomics Network) using Hisat2 2.1, processed using Samtools 1.9, and counts were obtained using featureCounts in the Subread 1.6.
For analyzing RCNMV RNA abundance, the adapter trimmed reads were mapped to RCNMV RNA1 /RNA1-m1 (RNA1 with a six-base substitution of TGTAGC to ACGTTG from nt position 3462 to 3467) and RNA2 using bowtie2 with the “--sensitive-local” option.
To obtain alignment information individually for positive and negative strands of RCNMV RNAs, the alignment file was split according to their flag information using Samtools.  Subsequently, the Salmon tool was used to quantify the number of reads mapping to positive and negative strands of the RCNMV genome.
Genome_build: N. benthamiana 1.0.1 genome ( Sol Genomics Network)
Supplementary_files_format_and_content: excel sheets (.xlsx) consisting of raw fragment count data of N. benthamiana-mapped reads and raw read counts of RCNMV-mapped reads

organism: Nicotiana benthamiana

source_name: N. benthamiana leaves

growth_protocol: N. benthamiana plants were grown in a growth chamber with 16 h light at 24 ˚C and 8 h dark at 20 ˚C.  After inoculations, the growth conditions were changed to 16 h light at 20 ˚C and 8 h dark at 20 ˚C

extract_protocol:
At 15 day-post-inoculation, the 7th leaf was collected for each plant and pulverized in liquid nitrogen followed by addition of 1 ml TRIzol (Invitrogen).  Total RNA was extracted using Zymo Direct-zol miniprep columns (Zymo Research R2051) and quantified using Qubit RNA HS assay kit (Invitrogen Q32852).  Subsequently, 5 µg total RNA was treated with 1 µl Turbo DNase (Invitrogen AM2238) in a 50-µl reaction with 1x Turbo DNase buffer at 37 °C for 30 min followed by addition of 1 µl more Turbo DNase and incubation at 37 °C for additional 30 min, purification by Zymo RNA clean & concentrator −5 columns (Zymo Research R1016) and quantified using Qubit RNA HS assay kit (Invitrogen Q32852).  Total RNA integrity was verified using 1% agarose gel electrophoresis.
One µg DNAse-treated total RNA from 3 biological replicates of mock-inoculated and four biological replicates each of wt RCNMV- and RCNMV∆SR1f- inoculated N. benthamiana were used for library preparation using Zymo-seq RiboFree total RNA library prep kit (Zymo Research R3000S).  During the library preparation, the rRNA depletion was carried out for 45 min, and 10 cycles of library index PCR was performed using Zymo-Seq UDI primer set (Indexes 1-11, Zymo D3008).  Final libraries were quantified using Qubit dsDNA HS assay kit (Invitrogen Q32854), and the library quality was assessed using an Agilent bioanalyzer high sensitivity DNA assay kit.  Final libraries were sequenced using Zymo Research's services (www.zymoresearch.com/) on one high-output lane of Illumina Hiseq 1500 instrument with pair-ended 100 bp read length.

treatment_protocol: At the 4 leaf stage (2 true leaves and 2 false leaves), 1st and 2nd true leaves were mechanically inoculated with (i) 10 mM sodium phosphate (pH 6.8) buffer (Mock-inoculated), (ii) 1 µg RNA1 plus 1 µg RNA2 in 10 mM sodium phosphate (pH 6.8) buffer per leaf (wt RCNMV inoculated), (iii) 1 µg RNA1-m1 plus 1 µg RNA2 in 10 mM sodium phosphate (pH 6.8) buffer per leaf (RCNMV∆SR1f inoculated).  Five plants were inoculated for each condition.  Growth conditions were changed to 16 h light at 20 ˚C and 8 h dark at 20 ˚C.

tag: tissue

value: Non-inoculated systemic leaves

tag: inoculum/treatment

value: RCNMV RNA1-m1 plus wt RCNMV RNA2


title: Mock_Rep2

description: RNA-seq data

value: sodium phosphate buffer


title: Mock_Rep3

description: RNA-seq data


title: Mutant_RCNMV_Rep2

description: RNA-seq data


title: Mutant_RCNMV_Rep1

description: RNA-seq data


title: Mutant_RCNMV_Rep3

description: RNA-seq data


title: Mock_Rep1

description: RNA-seq data


title: wt_RCNMV_Rep3

description: RNA-seq data

value: wt RCNMV RNA1 plus wt RCNMV RNA2


title: wt_RCNMV_Rep2

description: RNA-seq data


title: wt_RCNMV_Rep1

description: RNA-seq data


title: M-A549-infection_plus_bem_lane2_20200605000

city: Iowa City

first: Wendy

last: Maury

state: Iowa

address: 51 Newton Rd, Bowen Science Building 3-615

department: Microbiology and Immunology

institute: University of Iowa

data_processing:
Paired-end sequencing reads were subject to alignment to suitable reference genomes: human GRCh38 (GCA_000001405.15 - A549 cells), green monkey (Chlsab1/GCA_000409795.2 - Vero E6 cells) and SARS-CoV-2 (MN985325 - both A549 and Vero E6 cells). Alignments to human and monkey genomes were performed using hisat2 v2.0.5, while to viral genome using bowtie2 v2.2.9. Aligned reads were counted using featureCounts from subread package v1.5.2. Counted reads were normalized in R, using DESeq2 v1.30.0 and subjected to statistical analysis. The statistical analysis included computation of median based fold changes, Student t-test p values and false discovery rate (multiple testing correction).
The only analysis we performed was alignment to the human genome and SARS-CoV-2 genome. In the VeroE6 samples nearly 80% of the reads aligned to the viral genome, making analysis of the human mRNA changes difficult.
Genome_build: GRCh38 (GCA_000001405.15 - A549 cells), green monkey (Chlsab1/GCA_000409795.2 - Vero E6 cells) and SARS-CoV-2 (MN985325 - both A549 and Vero E6 cells)
Supplementary_files_format_and_content: Processed data consists of % reads mapped to AGM/human genome and reads mapped to SARS-CoV-2 genomes. Summary gene counts are also provided for A549-ACE2 samples.

organism:
Homo sapiens
Severe acute respiratory syndrome coronavirus 2

source_name: A549 (ACE2 overexpressing)

extract_protocol:
Rneasy miniprep kit. Cells lysed in buffer RLT+betamercaptoethanol and homogenized with QIAshredder columns. RNA isolated accoring to protocol after DNAse digestion step with QIAgen kit. RNA integrity analyzed by Agilent Bioanalyzer.
Library prepared by University of Iowa Genomics Core using TruSeq Stranded mRNA kit protocol. Oligo-dT purification of polyA RNA, reverse transcription to cDNA, fragment purification, end polishing, followed by barcode ligation.

treatment_protocol: Liposome and inhibitors were prepared in DMEM + 10% fetal calf serum + 1% penicillin streptomycin at 1 micromolar (bemcentinib) or 50 micrmolar (PS or PC liposomes). SARS-CoV-2 was diluted and added to cells at MOI = 0.01 (VeroE6) or 0.5 (A549-ACE2). RNA was extracted 18 hours after infection (VeroE6) or 24 hours after infection (A549-ACE2)

value: A549 (ACE2 overexpressing)

tag: sars-cov-2 infected

value: TRUE

value: 1 micromolar bemcentinib


title: O-A549-infection_plus_bem_lane1_20200605000


title: P-A549-infection_plus_bem_lane1_20200605000


title: I-A549-infection_lane2_20200605000

value: Media


title: O-A549-infection_plus_bem_lane2_20200605000


title: P-A549-infection_plus_bem_lane2_20200605000


title: K-A549-infection_lane2_20200605000


title: L-A549-infection_lane2_20200605000


title: J-A549-infection_lane2_20200605000


title: J-A549-infection_lane1_20200605000


title: wt_RCNMV_Rep4

description: RNA-seq data


title: N-A549-infection_plus_bem_lane1_20200605000


title: K-A549-infection_lane1_20200605000


title: M-A549-infection_plus_bem_lane1_20200605000


title: L-A549-infection_lane1_20200605000


title: I-A549-infection_lane1_20200605000


title: TUH69-VEN+ARAC scRNA-seq

city: Toulouse

first: Jean-Emmanuel

last: Sarry

state: Occitanie

address: 2 Avenue Hubert Curien

country: France

institute: INSERM -CRCT

data_processing:
The output bcl2 file was converted to FASTQ format by using CellRanger v.3.0.2 (https:// www.10xgenomics.com/), and then loaded in an R session with the Seurat v.3.0 (https://satijalab.org/seurat/) toolkit package involving the normalization and variance stabilization package sctransform.
Cells were filtered based on number of expressed genes (Ctl : 300 < nFeatures < 5500, ARAC : 300 < nFeatures < 6000, VEN :  300 < nFeatures < 6500, ARAC+VEN : 100 < nFeatures < 3000).
Percentage of mitochondrial reads were: Ctl, AraC, VEN, 0.02 < percent.mito < 0.15;  AraC_VEN: 0.01 < percent.mito < 0.15.
Single-Cell Signature Explorer (https://sites-google-com.proxy.insermbiblio.inist.fr/site/fredsoftwares/products/single-cell-signature-explorer) was used for the visualization of gene and signatures in the UMAP.
Clustering was performed using with a resolution of 0.1.
Cluster markers were defined by Seurat package using Wilcoxon statistical test. Markers with adjusted p-value inferior to 0.05 were selected.
Geneset enrichment analysis for cluster markers were then performed using hypeR package using KEGG, Hallmark and GO databases. AUC score for genes signatures were performed using R package AUCell, a method that uses the Area Under the Curve to calculate whether a critical subset of the input gene set is enriched within the expressed genes for each cell.
A SCENIC analysis uses gene regulatory network inference, followed by a refinement step using cis-regulatory information, to generate a set of regulons (i.e. transcription factors and their target genes) in the scRNA-seq data.
The python implementation, pySCENIC (https://github.com/aertslab/pySCENIC, version 0.9.19), was run using a Nextflow pipeline (https://github.com/aertslab/SCENICprotocol, version 0.2.0) (in press, ref to come), which streamlined the main steps of GRN inference and refinement with pySCENIC, as well as the quantification of cellular activity.
For each regulon, SCENIC calculates an AUC score for each cell and then defines a binary activity (ON/OFF) by setting up an automatic threshold. SCENIC clustering and heatmap were based on matrix of binary regulon activity. Comparison of regulon activities between clusters were based on continuous AUC score and involved Mann-Whitney test and Benjamin-Hochberg correction for multiple tests.

source_name: VEN+ARAC

growth_protocol: Residual AML cells purifed from bone marrow of patient samples xenografted in 8 weeks NOD/LtSz-SCID/IL-2Rγchain null (NSG) mice.

extract_protocol:
Viable primary human AML cells (CD33+/CD45+/AnnexinV-) from mice bone marrow of PDX before treatment or following AraC, venetoclax treatment or venetoclax plus AraC doublet therapy were isolated using cell sorter cytometer.
To generate single-cell libraries the Chromium Single Cell 3' Reagent Kits (v3 Chemistry, 10x Genomics) was used and the sequencing-ready library was cleaned up prior to sequencing on a NextSeq550 instrument (Illumina).
The output bcl2 file was converted to FASTQ format by using CellRanger-3.0.2, and then loaded in an R session with the Seurat 3.0 toolkit package 8 involving the normalization and variance stabilization package sctransform 9.

treatment_protocol: The treatment consists in 5 days of AraC treatment (10 mg/kg for CLDXs and 30 mg/kg for PDXs) by intra-peritoneal injection, in association or not with 7 days of venetoclax treatment (100 mg/kg) by oral gavage.

tag: patient

value: Bone marrow

value: venetoclax plus cytarabine


title: N-A549-infection_plus_bem_lane2_20200605000

tag: cell line


title: TUH07-VEN+ARAC scRNA-seq

data_processing:
The output bcl2 file was converted to FASTQ format by using CellRanger v.3.0.2 (https:// www.10xgenomics.com/), and then loaded in an R session with the Seurat v.3.0 (https://satijalab.org/seurat/) toolkit package involving the normalization and variance stabilization package sctransform.
Cells were filtered based on number of expressed genes (Ctl : 300 < nFeatures < 5500, ARAC : 300 < nFeatures < 6000, VEN :  300 < nFeatures < 6500, ARAC+VEN : 100 < nFeatures < 3000).
Percentage of mitochondrial reads were: Ctl, VEN, AraC : 0.04 < percent.mito < 0.15 ; AraC+VEN : 0.01 < percent.mito < 0.1.
Single-Cell Signature Explorer (https://sites-google-com.proxy.insermbiblio.inist.fr/site/fredsoftwares/products/single-cell-signature-explorer) was used for the visualization of gene and signatures in the UMAP.
Clustering was performed using with a resolution of 0.1.
Cluster markers were defined by Seurat package using Wilcoxon statistical test. Markers with adjusted p-value inferior to 0.05 were selected.
Geneset enrichment analysis for cluster markers were then performed using hypeR package using KEGG, Hallmark and GO databases. AUC score for genes signatures were performed using R package AUCell, a method that uses the Area Under the Curve to calculate whether a critical subset of the input gene set is enriched within the expressed genes for each cell.
A SCENIC analysis uses gene regulatory network inference, followed by a refinement step using cis-regulatory information, to generate a set of regulons (i.e. transcription factors and their target genes) in the scRNA-seq data.
The python implementation, pySCENIC (https://github.com/aertslab/pySCENIC, version 0.9.19), was run using a Nextflow pipeline (https://github.com/aertslab/SCENICprotocol, version 0.2.0) (in press, ref to come), which streamlined the main steps of GRN inference and refinement with pySCENIC, as well as the quantification of cellular activity.
For each regulon, SCENIC calculates an AUC score for each cell and then defines a binary activity (ON/OFF) by setting up an automatic threshold. SCENIC clustering and heatmap were based on matrix of binary regulon activity. Comparison of regulon activities between clusters were based on continuous AUC score and involved Mann-Whitney test and Benjamin-Hochberg correction for multiple tests.

source_name: combo


title: TUH07-VEN scRNA-seq

value: venetoclax


title: TUH07-ARAC scRNA-seq

source_name: arac

value: cytarabine


title: TUH69-VEN scRNA-seq

source_name: VEN


title: treat3

city: shenzhen

first: feng

last: duan

address: Dongmen North Road, Luohu District

institute: Clinical Medical Research Center, Shenzhen People's Hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 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: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: spinal cord_injury

extract_protocol:
Take the intervertebral disc of mice, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

tag: sample group

value: spinal cord injury

value: spinal cord; intervertebral disc


title: TUH07-D0 scRNA-seq

source_name: ctl

tag: treatment


title: TUH69-D0 scRNA-seq


title: control1

source_name: spinal cord_control

value: control


title: control2


title: control3


title: TRAC-Seq_Mouse_Ctrl03_Alkb_Treated_Input

city: Guangzhou

first: Wanjie

last: Zhu

state: Guangdong

address: Zhongshan er road

institute: Sun Yat-sen University

data_processing:
For RNA-Seq data analysis, after adapter trimming and low quality sequence filtering (Q30), the clean reads were mapped to human reference genome (GRCh38) using Bowtie2. The raw counts of reads mapping to the gencode genes (v19) were computed by HTSeq with ‘union’ overlap mode. The raw counts were then normalized as fractions per kilo base per million mapped reads (FPKM) using edegR.
For TRAC-Seq, after adaptor trimming and quality filtering, the clean sequencing data were first mapped to the tRNA sequences using Bowtie2. Then read count for each tRNA was calculated using the method in (Cozen et al., 2015). The read counts of tRNA are normalized as reads per million (RPM) by the total number of small RNA reads that are matched to tRNAs in each sample.

source_name: liver tumor tissue

growth_protocol: HCC cell lines were  cultrued in DMEM medium. Cells were grown in a 5% CO2 cell culture incubator at 37℃. C57 mice were taken care in SPF-class laboratory animal housing.

extract_protocol:
Total RNA samples were isolated with Trizol following the manufacturer’s instructions. small RNAs (<200nt) were first purified using the mirVana miRNA Isolation Kit (Thermo Fisher Scientific).
Libraries were prepared according to Illumina's instructions accompanying the TrueSeq Stranded mRNA library preparation kit and the NEBNext Small RNA Library Prep Set.

treatment_protocol: Mettl1 gene knockdown was mediated by short hairpin RNA.

tag: cell type

value: wild type

value: small RNA-Seq


title: TRAC-Seq_Mouse_Ctrl03_Alkb_and_NaBH4_treated

value: small RNA-TRAC-Seq


title: TRAC-Seq_Mouse_Ctrl02_Alkb_Treated_Input


title: TRAC-Seq_Mouse_Ctrl01_Alkb_Treated_Input


title: TRAC-Seq_Mouse_Ctrl01_Alkb_and_NaBH4_treated


title: TRAC-Seq_Mouse_Ctrl02_Alkb_and_NaBH4_treated


title: LCC_Omen

city: Hong Kong

first: Mingo Ming Ho

last: YUNG

address: 21 Sassoon

department: O&G

country: Hong Kong

institute: HKU

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw data (raw reads) of fastq format were processed with fastp, an ultra-fast  FASTQ preprocessor with useful quality. Clean data (clean reads) were obtained after  quality control, adapter trimming, quality filtering and per-read quality cutting. All the  downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from  genome website directly. Paired-end clean reads were aligned to the reference genome  using HISAT2 v2.1.0 (hierarchical indexing for spliced alignment of transcripts), which  is a highly efficient system for aligning reads from RNA sequencing experiments.  HISAT2 uses an indexing scheme based on the Burrows-Wheeler transform and the  Ferragina-Manzini (FM) index, employing two types of indexes for alignment: a whole_x0002_genome FM index to anchor each alignment and numerous local FM indexes for very  rapid extensions of these alignments. HISAT2 is the fastest system currently available,   with equal or better accuracy than any other method. HISAT2 was run with the default  parameters.
Featurecount was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels (Trapnell, Cole, et al., 2010).
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq R package (1.18.1). DESeq provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with |log2(FoldChange)| > 1 and adjusted P_x0002_value
Genome_build: Homo sapiens reference genome (GRCh38)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample.

source_name: Clinical sample

extract_protocol:
RNeasy® PowerLyzer® Tissue & Cells Kit was used for the isolation of total RNA from ovarian tumor tissues according to the manufacturer's protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: CaOv tumor


title: WLH_T


title: WLH_Omen


title: MYY_Omen


title: LCC_T


title: LSP_T


title: LSP_Omen


title: treat1


title: treat2


title: TUH69-ARAC scRNA-seq

source_name: ARAC


title: CWC_Omen


title: CWC_T


title: TDRD3 KO MCF7 C3_rep1

city: Monrovia

first: Xiwei

last: Wu

state: CA

address: 655 HUNTINGTON DR.

institute: City of Hope

data_processing:
Basecalls performed using  using RTA workflow version 1.18.64
Sequenced reads were trimmed for adaptor sequence,  low-complexity or low-quality sequence using trimmomatic v0.39 and fastp v0.20.1, then mapped to hg19 whole genome using STAR v2.7.4a with parameters --twopassMode Basic --outSAMstrandField intronMotif
Raw counts of sequencing reads for genes were perfomred using featureCounts method in Rsubread V2.01.
Read counts normalization, Reads Per Kilobase of exon per Megabase of library size (RPKM), and detection of differentailly expressed genes were processed using edgeR v3.28.1.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files iraw counts of sequencing reads per gene for each Sample

source_name: breast cancer cell line

growth_protocol: MCF7 cells were grown in high glucose DMEM media supplemented with 10% Fetal Bovine Serum (FBS) and maintained at 37°C.

extract_protocol:
Total RNA from the cells were extreacted using Trizol reagent following the standard protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: TDRD3 knockout was carried out by CRISPR-cas9 using two different guide RNAs.

value: TDRD3 KO2a


title: TDRD3 KO MCF7 B1_rep1

value: TDRD3 KO1a


title: Control MCF7 cells_rep2

value: WT


title: TDRD3 KO MCF7 C3_rep2

value: TDRD3 KO2b


title: Control MCF7 cells_rep1


title: TRAC-Seq_SNU449_NC_Alkb_Treated_Input

source_name: hepatocellular carcinoma cell line


title: TRAC-Seq_SNU449_NC_Alkb_and_NaBH4_treated


title: TRAC-Seq_MHCC97H_shMETTL1-2_Alkb_and_NaBH4_treated

value: Mettl1 knockdown


title: TRAC-Seq_SNU449_OE-WT_Alkb_Treated_Input

value: Mettl1 overexpression


title: TDRD3 KO MCF7 B1_rep2

value: TDRD3 KO1b


title: TRAC-Seq_MHCC97H_shMETTL1-2_Alkb_Treated_Input


title: TRAC-Seq_MHCC97H_NC_Alkb_and_NaBH4_Treated


title: MYY_T


title: TRAC-Seq_MHCC97H_NC_Alkb_Treated_Input


title: Fc5T/Donor 054/Replicate 2 [Fc_54B]

city: Austin

first: Vishy

last: Iyer

state: TX

address: 2500 Speedway Dr. MBB 3.212

department: Molecular Biosciences

institute: University of Texas at Austin

data_processing:
Reads were trimmed using Cutadapt
Trimmed reads were aligned with Hisat
Reads were counted with feature counts
Genome_build: GRCh38
Supplementary_files_format_and_content: counts

source_name: Fc5T_Donor 054_human Naïve CD8+ T cells

growth_protocol: CellTrace-labelled naïve CD8+ T cells were activated with anti-CD3/anti-CD28 dynabeads (30uL per 1 million T cells) in complete medium with recombinant human IL-2 (10-20 ng/mL) and cultured for 5.5 days at 37°C, 5% CO2. At t= 60 hrs. post-activation, dynabeads were removed magnetically and fresh media (with IL2 and ICs)was added to replenish cultures.

extract_protocol:
Total RNA was extracted from InhT, StimT, and Fc5T samples (Qiagen); then, mRNA was isolated (poly-A capture) prior to library construction
Standard Illumina protocols were followed. Stranded libraries were created (dUTP Method; NEB NGS kit) for paired-end sequencing (PE75, NextSeq 500)

treatment_protocol: CellTrace Labelled naïve CD8+ T cells were pre-incubated with 50μg/mL WT IgG1-ICs or Fc5 IgG1-ICs for 2 hours prior to Dynabeads activation

value: Blood

value: Naive CD8+ T cells

tag: selection method

value: Magnetic Negative Selection

value: Activated with anti-CD3/anti-CD28 beads and IL-2 in the presence of Fc5 IgG1-ICs (non-sorted)


title: Fc5T/Donor 054/Replicate 1 [Fc_54A]


title: StimT/Donor 054/Replicate 1 [Stim_54A]

source_name: StimT_Donor 054_human Naïve CD8+ T cells

value: Activated with anti-CD3/anti-CD28 beads and IL-2 in the presence of WT IgG1-ICs (sorted for highly proliferative cells; CellTrace Violet Genereation 6+)


title: Fc5T/Donor 017/Replicate 2 [Fc_17B]

source_name: Fc5T_Donor 017_human Naïve CD8+ T cells


title: StimT/Donor 054/Replicate 2 [Stim_54B]


title: Fc5T/Donor 017/Replicate 1 [Fc_17A]


title: StimT/Donor 050/Replicate 1 [Stim_50A]

source_name: StimT_Donor 050_human Naïve CD8+ T cells


title: StimT/Donor 050/Replicate 2 [Stim_50B]


title: InhT/Donor 054/Replicate 1 [Inh_54A]

source_name: InhT_Donor 054_human Naïve CD8+ T cells

value: Activated with anti-CD3/anti-CD28 beads and IL-2 in the presence of WT IgG1-ICs (sorted for undivided cells; CellTrace Violet Genereation 1)


title: StimT/Donor 017/Replicate 2 [Stim_17C]

source_name: StimT_Donor 017_human Naïve CD8+ T cells


title: InhT/Donor 054/Replicate 2 [Inh_54B]


title: StimT/Donor 017/Replicate 1 [Stim_17B]


title: InhT/Donor 050/Replicate 2 [Inh_50B]

source_name: InhT_Donor 050_human Naïve CD8+ T cells


title: TRAC-Seq_SNU449_OE-WT_Alkb_and_NaBH4_treated


title: InhT/Donor 017/Replicate 2 [Inh_17C]

source_name: InhT_Donor 017_human Naïve CD8+ T cells


title: InhT/Donor 050/Replicate 1 [Inh_50A]


title: prime/boost3-mer/IVAX-1d83 (PB2) (mouse ID 7.2)

type: genomic

city: Irvine

first: David

middle: Huw

last: Davies

address: 812 Medical Plaza Drive, Med Surge II, Rm 376

department: Physiology & Biophysics

institute: UC Irvine

description:
SAMPLE 108
Fig. 2d

hyb_protocol: Mouse plasma samples were diluted 1:100 in protein array blocking buffer (GVS, Sanford, ME, USA) supplemented with 10 mg/ml E. coli lysate  (GenScript, Piscataway, NJ, USA) and 10g/ml of amino acid peptide HHHHHHHHHHGGGG (Biomatik, Wilmington, DE) to block any anti-polyhistidine antibodies, and pre-incubated at room temperature (RT) for 30 min. Concurrently, arrays were rehydrated in blocking buffer (without lysate) for 30 min prior to replacement of the blocking buffer with pre-incubated sera. Arrays were incubated overnight at 4°C with gentle agitation. After washing 6 times with Tris-buffered saline (TBS) containing 0.05% Tween 20 (T-TBS) at RT, arrays were incubated in biotinylated-SP-conjugated goat anti-mouse IgG (Jackson Immunoresearch, West Grove, PA) diluted 1:200 in blocking buffer for 2h at RT. Arrays were then washed 6 times with T-TBS, followed by incubation with streptavidin-conjugated Qdot-800 (ThermoFisher) diluted 1:250 in blocking buffer for 1h at RT. Arrays were washed three times each with T-TBS followed by TBS, dipped in distilled water, and air-dried by centrifugation at 500 × g for 10 min.

scan_protocol: Images were acquired using the ArrayCAM imaging system from Grace Bio-Labs (Bend, OR) with gain and exposure times of 50 and 400-1000ms, respectively.

data_processing: Spot and background intensities were measured using an annotated grid (.gal) file.  Signal intensities (SI) for each antigen on the array were first background corrected by subtracting sample-specific T-PBS buffer signals from purified protein spot signals. For statistical analysis, a floor of 10 was set for array signal intensities and the data transformed by Log2. Vaccine groups were compared using two-tailed Mann-Whitney test for unpaired data and the two-tailed Kruskal-Wallis test with Dunn’s multiple-comparisons using GraphPad Prism 6.7 (GraphPad, La Jolla, CA, USA). A P value of <0.05 was considered statistically significant. To determine antibody breadth, geometric means of Log2-transformed data for each antigen were determined for each vaccine group, and an antigen was scored seropositive if above a cutoff defined as the mean+2SD of the signals for an irrelevant protein on the array (NA) which was not used to immunize.

molecule: other

source_name: prime/boost3-mer/IVAX-1d83 (PB2) (mouseID B1)

tag: vaccine regimen

value: prime/boost

tag: vaccine

tag: time point

tag: mouse id

value: plasma


title: prime/boost3-mer/IVAX-1d83 (PB2) (mouse ID 7.6)

description:
SAMPLE 112
Fig. 2d

tag: sample type


title: prime/boost3-mer/IVAX-1d83 (PB2) (mouse ID 7.3)

description:
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Fig. 2d


title: prime/boost3-mer/IVAX-1d83 (PB2) (mouse ID 7.1)

description:
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Fig. 2d


title: prime/boost3-mer/IVAX-1d83 (PB2) (mouse ID 7.5)

description:
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Fig. 2d


title: prime/boost3-mer/IVAX-1d83 (PB2) (mouse ID 7.4)

description:
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Fig. 2d


title: prime/boost3-mer/IVAX-1d63 (PB1) (mouse ID 7.5)

description:
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Fig. 2d

source_name: prime/boost3-mer/IVAX-1d63 (PB1) (mouseID B1)


title: prime/boost3-mer/IVAX-1d63 (PB1) (mouse ID 7.4)

description:
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Fig. 2d


title: prime/boost3-mer/IVAX-1d63 (PB1) (mouse ID 7.2)

description:
SAMPLE 102
Fig. 2d


title: prime/boost3-mer/IVAX-1d63 (PB1) (mouse ID 7.3)

description:
SAMPLE 103
Fig. 2d


title: prime/boost3-mer/IVAX-1d44 (mouse ID 7.6)

description:
SAMPLE 100
Fig. 2d

source_name: prime/boost3-mer/IVAX-1d44 (mouseID B1)


title: prime/boost3-mer/IVAX-1d44 (mouse ID 7.5)

description:
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Fig. 2d


title: prime/boost3-mer/IVAX-1d28 (mouse ID 7.6)

description:
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Fig. 2d

source_name: prime/boost3-mer/IVAX-1d28 (mouseID B1)


title: prime/boost3-mer/IVAX-1d44 (mouse ID 7.4)

description:
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Fig. 2d


title: prime/boost3-mer/IVAX-1d44 (mouse ID 7.1)

description:
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Fig. 2d


title: prime/boost3-mer/IVAX-1d44 (mouse ID 7.2)

description:
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Fig. 2d


title: prime/boost3-mer/IVAX-1d44 (mouse ID 7.3)

description:
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Fig. 2d


title: prime/boost3-mer/IVAX-1d28 (mouse ID 7.3)

description:
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Fig. 2d


title: prime/boost3-mer/IVAX-1d28 (mouse ID 7.5)

description:
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Fig. 2d


title: prime/boost3-mer/IVAX-1d28 (mouse ID 7.4)

description:
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Fig. 2d


title: prime/boostH7/IVAX-1d56 (PB2) (mouse ID 6.5)

description:
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Fig. 3c

source_name: prime/boostH7/IVAX-1d56 (PB2) (mouseID B1)


title: prime/boost3-mer/IVAX-1d28 (mouse ID 7.2)

description:
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Fig. 2d


title: InhT/Donor 017/Replicate 1 [Inh_17B]


title: prime/boostH7/IVAX-1d56 (PB2) (mouse ID 6.3)

description:
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Fig. 3c


title: prime/boost3-mer/IVAX-1d28 (mouse ID 7.1)

description:
SAMPLE 89
Fig. 2d


title: prime/boostH7/IVAX-1d56 (PB2) (mouse ID 6.4)

description:
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Fig. 3c


title: prime/boost3-mer/IVAX-1d63 (PB1) (mouse ID 7.1)

description:
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Fig. 2d


title: prime/boost3-mer/IVAX-1d63 (PB1) (mouse ID 7.6)

description:
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Fig. 2d


title: prime/boostH7/IVAX-1d28 (PB1) (mouse ID 6.4)

description:
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Fig. 3c

source_name: prime/boostH7/IVAX-1d28 (PB1) (mouseID B1)


title: prime/boostH7/IVAX-1d28 (PB1) (mouse ID 6.5)

description:
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Fig. 3c


title: prime/boostH7/IVAX-1d56 (PB2) (mouse ID 6.1)

description:
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Fig. 3c


title: prime/boostH7/IVAX-1d28 (PB1) (mouse ID 6.2)

description:
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Fig. 3c


title: prime/boostH7/IVAX-1d28 (PB1) (mouse ID 6.3)

description:
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Fig. 3c


title: prime/boostH7/IVAX-1d28 (PB1) (mouse ID 6.1)

description:
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Fig. 3c


title: prime/boostH7/IVAX-1d56 (PB2) (mouse ID 6.2)

description:
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Fig. 3c


title: prime/boostH5/IVAX-1d56 (PB2) (mouse ID 5.1)

description:
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Fig. 3b

source_name: prime/boostH5/IVAX-1d56 (PB2) (mouseID B1)


title: prime/boostH7/IVAX-1d10 (mouse ID 6.4)

description:
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Fig. 3c

source_name: prime/boostH7/IVAX-1d10 (mouseID B1)


title: prime/boostH7/IVAX-1d10 (mouse ID 6.5)

description:
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Fig. 3c


title: prime/boostH7/IVAX-1d10 (mouse ID 6.1)

description:
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Fig. 3c


title: prime/boostH5/IVAX-1d10 (mouse ID 5.5)

description:
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Fig. 3b

source_name: prime/boostH5/IVAX-1d10 (mouseID B1)


title: prime/boostH7/IVAX-1d10 (mouse ID 6.3)

description:
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Fig. 3c


title: prime/boostH7/IVAX-1d10 (mouse ID 6.2)

description:
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Fig. 3c


title: prime/boostH5/IVAX-1d28 (PB1) (mouse ID 5.1)

description:
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Fig. 3b

source_name: prime/boostH5/IVAX-1d28 (PB1) (mouseID B1)


title: prime/boostH5/IVAX-1d56 (PB2) (mouse ID 5.5)

description:
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Fig. 3b


title: prime/boostH5/IVAX-1d28 (PB1) (mouse ID 5.4)

description:
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Fig. 3b


title: prime/boostH5/IVAX-1d28 (PB1) (mouse ID 5.5)

description:
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Fig. 3b


title: prime/boostH5/IVAX-1d56 (PB2) (mouse ID 5.4)

description:
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Fig. 3b


title: prime/boostH5/IVAX-1d10 (mouse ID 5.4)

description:
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Fig. 3b


title: prime/boostH5/IVAX-1d28 (PB1) (mouse ID 5.3)

description:
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Fig. 3b


title: prime/boostH5/IVAX-1d28 (PB1) (mouse ID 5.2)

description:
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Fig. 3b


title: prime/boostH5/IVAX-1d10 (mouse ID 5.3)

description:
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Fig. 3b


title: prime/boostH5/IVAX-1d56 (PB2) (mouse ID 5.2)

description:
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Fig. 3b


title: prime/boostH5/IVAX-1d56 (PB2) (mouse ID 5.3)

description:
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Fig. 3b


title: prime/boostH5/IVAX-1d10 (mouse ID 5.2)

description:
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Fig. 3b


title: prime/boostH1/IVAX-1d56 (PB2) (mouse ID 4.5)

description:
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Fig. 3a

source_name: prime/boostH1/IVAX-1d56 (PB2) (mouseID B1)


title: prime/boostH1/IVAX-1d56 (PB2) (mouse ID 4.4)

description:
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Fig. 3a


title: prime/boostH1/IVAX-1d56 (PB2) (mouse ID 4.3)

description:
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title: prime/boostH1/IVAX-1d28 (PB1) (mouse ID 4.5)

description:
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Fig. 3a

source_name: prime/boostH1/IVAX-1d28 (PB1) (mouseID B1)


title: prime/boostH1/IVAX-1d56 (PB2) (mouse ID 4.1)

description:
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Fig. 3a


title: prime/boostH5/IVAX-1d10 (mouse ID 5.1)

description:
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Fig. 3b


title: prime/boostH1/IVAX-1d28 (PB1) (mouse ID 4.3)

description:
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Fig. 3a


title: TE5-SREBF1-R1 4C

city: Los Angeles

first: Qian

last: Yang

address: 8700 Beverly Blvd

department: Department of Surgery

institute: CEDARS SINAI MEDICAL CENTER

data_processing:
Library strategy: 4C-seq
DNA Sequencing was performed in MiSeq platform using Illumina 150 bp pair-end kit. Two replicates were generated and sequencing results were analyzed by r3Cseq package
Genome_build: hg19
Supplementary_files_format_and_content: txt files representing 4C interaction list

source_name: Esophageal Squamous cell carcinomas cell line

extract_protocol: We performed Circularized chromosome conformation capture (4C) assays in TE5 cells using the SREBF1 promoter as bait to measure the direct contact between the super-enhancer and SREBF1 promoter. The viewpoint of SREBF1 promoter region was chr17:17738740-17740085 (hg19) with 4C primers: NEST-Forward-GCAACCAGCTGGGCTCAT, OUTER-Forward-GAAGCAACGGGCCTCCTAAT, NEST-Reverse-CTGCTGACCGACATCGAAGG and OUTER-Reverse-TTGCGAGGTTACTCACGGTC

value: Esophageal squamous cell carcinoma


title: TE5-SREBF1-R2 4C


title: prime/boostH1/IVAX-1d28 (PB1) (mouse ID 4.2)

description:
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Fig. 3a


title: prime/boostH1/IVAX-1d28 (PB1) (mouse ID 4.4)

description:
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Fig. 3a


title: prime/boostH1/IVAX-1d10 (mouse ID 4.5)

description:
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Fig. 3a

source_name: prime/boostH1/IVAX-1d10 (mouseID B1)


title: prime/boostH1/IVAX-1d10 (mouse ID 4.1)

description:
SAMPLE 44
Fig. 3a


title: prime/boostH1/IVAX-1d10 (mouse ID 4.3)

description:
SAMPLE 46
Fig. 3a


title: SPZ-4

city: Amsterdam

first: Robin

last: Struijk

address: Meibergdreef 9

department: Center for Reproductive Medicine

country: Netherlands

institute: Amsterdam UMC location AMC

description: Bisulfite converted amplicons

data_processing:
Paired-end sequencing reads (2 × 150bp) were trimmed using TrimGalore v0.6.5 .
Alignment of reads to an artificial genome containing both hg18 and hg19 sequences as reference using Bismark v0.22.3.
Reads were aligned specifically to the amplicon sequences (± 10,000bp) annotated prior to the experiment in order to reduce data noise.
Methylation values were extracted from the aligned reads and further processed using BiSeq v1.30.0 (Hebestreit et al., 2020).
For the comparison of amplicon methylation values between germ cell types, analysis-of-variance (ANOVA) was carried out.
Genome_build: hg19
Supplementary_files_format_and_content: RDS
Supplementary_files_format_and_content: meth_per_cpg

source_name: Spermatozoa

extract_protocol:
Genomic DNA was isolated from 2N/MAGEA4bright spermatogonia and 4N/MAGEAdim/neg spermatocytes using a QIAamp DNA Micro Kit (Qiagen, cat. no. 56304) according to manufacturer’s instructions. Genomic DNA from 1N round spermatids, sub1N elongating spermatids and PureSperm purified mature spermatozoa was extracted with a high salt DNA extraction method. Briefly, purified cells (either FACS or PureSperm for spermatids and sperm, respectively) were lysed  in sperm lysisbuffer (7.5mM NaCl/2.5mM EDTA/2.75mM NaOH/10% SDS in dH2O, pH = 8.0) supplemented with 2 mg/ml Proteinase K and 10mM DTT at 55°C overnight while shaking at 750 rpm. After incubation, 6M NaCl (1/3 volume) was added and vortexed vigorously for 5 minutes. The lysed cellular mixtures were then centrifuged and 0.1 ug/ml glycogen solution and 70% (v/v) isopropanol were added to the supernatant and incubated for one hour at -20°C and subsequently centrifuged. The pellet was washed in 70% (v/v) pure ethanol and allowed to dry at room temperature for 5-10 minutes or until translucent. Finally, the pelleted DNA was suspended in TE buffer and stored until further use. DNA concentration of all isolated samples was determined using a Quant-iT dsDNA HS Assay Kit on a Qubit fluorometer (Invitrogen). A total of 25 ng of genomic DNA per sample was subjected to bisulfite conversion using an EZ DNA Methylation Gold Bisulfite Kit (Zymo Research, cat. no. D5-005) according to manufacturer’s instructions and subsequently amplified using an EpiTect Whole Bisulfitome Kit (Qiagen, cat. no. 59203). After amplification, DNA concentrations were measured using the Qubit method described above, yielding 1.5 – 6.1 μg of high molecular amplified, bisulfite-converted DNA per sample. The amplified DNA was subsequently purified using Agencourt AMPure Beads XP (concentration 1.5×, Beckton Dickinson, cat. no. A63881) according to manufacturer’s protocol and eluted in 40 μl low-TE buffer.
To generate paired-end indexed MiSeq libraries, a two-step PCR based protocol was performed for 30 amplicons of established imprinted loci (Table S1) (Woodfine et al., 2011; Mulder et al., 2020). In the first round of PCR, amplicons were generated using the EpiTect MSP Kit (Qiagen, cat. no. 59305) of 20 ng amplified DNA and 4 μM forward/reverse primer oligonucleotides. The conditions of the thermocycler were as follows: 10 minutes at 95°C, followed by 40 cycles of 1 minute at 95°C, 1 minute at 56°C and 30 seconds at 72°C and a final extension step of 10 minutes at 72°C. Efficiency of the PCR reactions was evaluated for each amplicon by visualization of the products using agarose gel electrophoresis. Amplicon reactions were then pooled for each sample and subjected to AMPure Beads XP purification as described above. These pools were subsequently indexed with patient-specific dual TruSeq indices (Illumina, USA) in a second round of PCR as follows: 5 μl pooled amplicon PCR products and 0.5 μl forward/reverse specific tag primers (10μM) were added to 45 μl of High Fidelity Platinum PCR SuperMix (Invitrogen, USA) and amplified as follows: 1 minute at 95°C, 5 minutes at 72°C, followed by 8 cycles of 30 seconds at 95°C, 2 minutes at 62°C and 2 minutes at 72°C and a final extension step of 10 minutes at 72°C. After second round PCR, indexed libraries were evaluated using a High Sensitivity DNA chip on a Bioanalyzer instrument (Agilent) and a normal distribution of amplicon peaks was confirmed (data not shown). After DNA concentration measurements, individual libraries were combined into a single volume in equimolar fashion and sequenced on an Illumina MiSeq sequencer using the MiSeq Reagent Kit (v2, 500 cycles) at the Sequencing and Genotyping Facility, Amsterdam UMC Location VU.

value: Primary germ cell

value: Seminal fluid

tag: sorting-profile

value: PureSperm


title: ESPT-5

description: Bisulfite converted amplicons

source_name: Elongating spermatids

value: Testis


title: SPZ-2

description: Bisulfite converted amplicons


title: ESPT-4

description: Bisulfite converted amplicons


title: SPZ-3

description: Bisulfite converted amplicons


title: prime/boostH1/IVAX-1d10 (mouse ID 4.4)

description:
SAMPLE 47
Fig. 3a


title: ESPT-3

description: Bisulfite converted amplicons


title: prime/boostH1/IVAX-1d28 (PB1) (mouse ID 4.1)

description:
SAMPLE 49
Fig. 3a


title: SPZ-1

description: Bisulfite converted amplicons


title: prime/boostH1/IVAX-1d10 (mouse ID 4.2)

description:
SAMPLE 45
Fig. 3a


title: ESPT-2

description: Bisulfite converted amplicons


title: single doseH7/IVAX-1d42 (mouse ID 3.5)

description:
SAMPLE 43
Fig. 2c

source_name: single doseH7/IVAX-1d42 (mouseID B1)

value: single dose


title: SPZ-5

description: Bisulfite converted amplicons


title: RSPT-5

description: Bisulfite converted amplicons

source_name: Round spermatids


title: single doseH7/IVAX-1d42 (mouse ID 3.2)

description:
SAMPLE 40
Fig. 2c


title: single doseH7/IVAX-1d42 (mouse ID 3.3)

description:
SAMPLE 41
Fig. 2c


title: single doseH7/IVAX-1d42 (mouse ID 3.1)

description:
SAMPLE 39
Fig. 2c


title: prime/boostH1/IVAX-1d56 (PB2) (mouse ID 4.2)

description:
SAMPLE 55
Fig. 3a


title: RSPT-3

description: Bisulfite converted amplicons


title: RSPT-4

description: Bisulfite converted amplicons


title: single doseH7/IVAX-1d42 (mouse ID 3.4)

description:
SAMPLE 42
Fig. 2c


title: single doseH7/IVAX-1d28 (mouse ID 3.5)

description:
SAMPLE 38
Fig. 2c

source_name: single doseH7/IVAX-1d28 (mouseID B1)


title: RSPT-2

description: Bisulfite converted amplicons


title: RSPT-1

description: Bisulfite converted amplicons


title: SPC-4

description: Bisulfite converted amplicons

source_name: Spermatocytes

value: 4N, MAGEA4dim/–


title: SPC-5

description: Bisulfite converted amplicons


title: SPC-3

description: Bisulfite converted amplicons


title: SPC-1

description: Bisulfite converted amplicons


title: single doseH7/IVAX-1d28 (mouse ID 3.2)

description:
SAMPLE 35
Fig. 2c


title: ESPT-1

description: Bisulfite converted amplicons


title: single doseH7/IVAX-1d10 (mouse ID 3.4)

description:
SAMPLE 31
Fig. 2c

source_name: single doseH7/IVAX-1d10 (mouseID B1)


title: single doseH7/IVAX-1d10 (mouse ID 3.2)

description:
SAMPLE 29
Fig. 2c


title: single doseH7/IVAX-1d28 (mouse ID 3.1)

description:
SAMPLE 34
Fig. 2c


title: SPG-5

description: Bisulfite converted amplicons

source_name: Spermatogonia

value: 2N, MAGEA4bright


title: SPG-4

description: Bisulfite converted amplicons


title: SPG-3

description: Bisulfite converted amplicons


title: SPG-2

description: Bisulfite converted amplicons


title: SPC-2

description: Bisulfite converted amplicons


title: single doseH7/IVAX-1d28 (mouse ID 3.3)

description:
SAMPLE 36
Fig. 2c


title: single doseH5/IVAX-1d42 (mouse ID 2.4)

description:
SAMPLE 26
Fig. 2b

source_name: single doseH5/IVAX-1d42 (mouseID B1)


title: single doseH5/IVAX-1d42 (mouse ID 2.5)

description:
SAMPLE 27
Fig. 2b


title: single doseH7/IVAX-1d10 (mouse ID 3.6)

description:
SAMPLE 33
Fig. 2c


title: polyribosome associated mRNA-seq-MHCC97H_shMETTL1-2_repeat 3

description: FPKM_polyribosome associated mRNA-seq.txt

source_name: hepatocellular carcinoma cell line

value: Mettl1 knockdown

value: polyribosome associated mRNA-seq


title: single doseH7/IVAX-1d10 (mouse ID 3.3)

description:
SAMPLE 30
Fig. 2c


title: single doseH7/IVAX-1d10 (mouse ID 3.5)

description:
SAMPLE 32
Fig. 2c


title: polyribosome associated mRNA-seq-MHCC97H_shMETTL1-2_Input_repeat 3

value: RNA-Seq


title: polyribosome associated mRNA-seq-MHCC97H_shMETTL1-2_Input_repeat 2


title: polyribosome associated mRNA-seq-MHCC97H_shMETTL1-2_repeat 2


title: single doseH7/IVAX-1d28 (mouse ID 3.4)

description:
SAMPLE 37
Fig. 2c


title: single doseH5/IVAX-1d28 (mouse ID 2.5)

description:
SAMPLE 22
Fig. 2b

source_name: single doseH5/IVAX-1d28 (mouseID B1)


title: polyribosome associated mRNA-seq-MHCC97H_shMETTL1-2_Input_repeat 1


title: polyribosome associated mRNA-seq-MHCC97H_shMETTL1-2_repeat 1


title: single doseH7/IVAX-1d10 (mouse ID 3.1)

description:
SAMPLE 28
Fig. 2c


title: single doseH5/IVAX-1d28 (mouse ID 2.4)

description:
SAMPLE 21
Fig. 2b


title: SPG-1

description: Bisulfite converted amplicons


title: Bap1KO-C91S-RYBP-rep1

city: Milan

first: Federico

last: Rossi

address: Via Adamello 16

institute: Istituto Europeo Oncologia

data_processing:
For ChIP-seq data, paired-end DNA reads were processed through fastp to trim adapters and to remove low quality nucleotides at read ends (Chen et al., 2018). Quality-filtered DNA reads were aligned to the mouse reference genome mm10, or mm10 and fly reference genome (dm6) for histone ChIP-Rx using Bowtie v1.2.2 retaining only uniquely aligned reads (-m 1) and using the parameters -I 10, -X 1000 (Langmead et al., 2009). Reads mapped to both mm10 and dm6 were discarded. Peaks were identified using MACS2 v2.1.1 in narrow mode with parameters –format BAMPE –keep-dup all -m 3 30 and p-value 1e-10 (Zhang et al., 2008). Peaks were annotated using the R package ChIPpeakAnno v3.15 using for each peak the 5 kbp region around the center of the peak  (Zhu et al., 2010).
For RNA-seq, reads were aligned to the mouse reference genome mm10 using STAR v2.7 without allowing for multimapping. PCR duplicates were removed using samblaster (Faust and Hall, 2014). Mapped reads were assigned to genes using featureCounts (Liao et al., 2014) with unstranded read counting on exons and using the gene name as attribute type in the annotation. Genes were annotated as in Gencode M21 (GRCm38) downloaded from https://www.genecodegenes.org/mouse/. Differentially expressed genes were identified using the R package DESeq2 v1.24 using default parameters (Love et al., 2014). The fold change of lowly expressed genes was corrected using the lfcShrink function of the apeglm R package with the type option set to apeglm v1.6 (Zhu et al., 2019). The adjusted p-value was corrected by the independent hypothesis weighting (IHW) method as implemented in the R package IHW v1.12 (Ignatiadis et al., 2016). Genes were considered differentially expressed when presenting an absolute log2 fold change equal or greater than 1.5 and an adjusted p-value lower than 0.05.
For HiC data, DNA reads were filtered for low-quality bases and adapters using fastp (Chen et al., 2018). Filtered DNA reads were processed through the HiCpro pipeline to obtain contact matrices reporting the chromatin interactions at the genome-wide level (Servant et al., 2015). Using default settings, DNA reads were aligned to the mouse reference genome mm10 using bowtie2 in end-to-end mode, uniquely aligned DNA reads were assigned to the DpnII genomic restriction fragments, valid interactions were identified and used to generate interaction matrices. The HiCpro matrices containing all of the valid pairs were converted in hic format using the hicpro2juicebox function (Robinson et al., 2018), and in cool format using the hic2cool function (https://github.com/4dn-dcic/hic2cool). Contact matrices in cool format where corrected using the ICE algorithm as implemented in the hicCorrectMatrix function (Wolff et al., 2020). Plots of the interactions occurring at single locus or whole-chromosome level were obtained by HiCplotter (Akdemir and Chin, 2015). Hi-C was performed in duplicate with key findings being overserved in each before pooling replicates to make the final high-depth analyses.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bed (MACS2), counts (counts.tsv), differential expression (DESeq2), validpairs (HiCPro).

source_name: Mouse Embryonic Stem Cells

extract_protocol:
ChIP-seq: DNA was purified with QIAquick PCR purification kit (Qiagen) according to manufacturer’s instructions.
DNA was purified with QIAquick PCR purification kit (Qiagen) according to manufacturer’s instructions. DNA libraries were prepared with 2–10 ng of DNA using an in-house protocol (Blecher-Gonen et al., 2013) by the IEO genomic facility and sequenced on an Illumina HiSeq 2000.
RNA-seq: RNA-seq was performed following SMART-seq2 protocol (Picelli et al., 2014)  with minor modifications. Briefly, poly-A containing mRNA molecules obtained from 1 μg of total RNA were copied into first-strand cDNA by reverse transcription and template-switching using oligo (dT) primers and an LNA-containing template-switching oligo (TSO). Resulting cDNA was pre-amplified with KAPA HotStart Taq enzyme (Kapa Biosystems) and then purified with Ampure beads (Agencourt AMPure XP- Beckman Coulter). One nanogram of pre-amplified cDNA was tagmented with in-house produced Tn5 transposase and further amplified with KAPA HotStart Taq enzyme. After purification with Ampure beads, the quality of the obtained library was assessed by Bioanalyzer (High Sensitivity DNA kit, Agilent Technologies), prior to sequencing. Each RNA-seq experiment was performed in triplicate.
Hi-C: In situ Hi-C was performed as described (Rao et al., 2014) with slight alterations to the protocol. 5x10^6 ESCs were crosslinked for 10 minutes in 1% formaldehyde before quenching in 125mM Glycine for 5 minutes. Cell pellets were washed twice in PBS before contact generation. Pellet was resuspended in 500uL Hi-C lysis buffer (10mM Tris-HCl pH8.0, 10mM NaCl, 0.2% NP40 and protease inhibitors) and incubated with rotation for 30 minutes at 4°C. Cells were pelleted and washed in 500uL Hi-C lysis buffer. Pellet was resuspended in 100uL 0.5% SDS and incubated for 10 minutes at 62°C. 285uL of H20 and 50uL of 10% Triton X-100 was added to quench the SDS at 37°C for 15 minutes. 50uL of 10xNEB DpnII buffer and 750U of DpnII were added (NEB R0453M) then incubated at 37°C overnight with shaking. Digestion was heat inactivated the next day for 20 minutes at 62°C. Biotin fill in was performed by addition of 52uL fill-in mix (0.288mM dCTP/dTTP/dGTP, 50U DNA Polymerase I, Large Klenow fragment (NEB M0210) and 0.288mM biotin-dATP (Thermo 19524016)). Fill-in reaction was incubated at 37°C for 1 hour with shaking. Ligation was performed by adding 150uL 10x NEB T4 DNA ligase buffer, 125uL 10% Triton X-100, 3uL 50mg/mL BSA and 8000U of T4 DNA ligase and H20 up to 1.5mL. Ligation was performed overnight at 25°C with shaking. Nuclei were pelleted before resuspending in IP buffer (33 mM Tris-HCl pH 8, 100 mM NaCl, 5 mM EDTA, 0.2% NaN3, 0.33% SDS, 1.66% Triton X-100) and sonicating to fragment size between 200-1000bp. 15uL of the sample was de-crosslinked overnight at 65°C with 85ul of decrosslinking buffer (0.1M NaHCO3, 1% SDS) before clean up using QiaQuick PCR clean up kit from Qiagen.
Library prep was performed as described (Mumbach et al., 2016). Streptavidin C-1 beads (Thermo 65001) were washed and resuspended in 2x biotin binding buffer (10mM Tris-HCl pH7.5, 1mM EDTA, 2M NaCl). 10ng of DNA was used for biotin capture, streptavidin C-1 beads were added and incubated for 15 minutes at room temperature with shaking. Beads were washed twice at 55°C for 2 minutes in Tween wash buffer (5mM Tris-HCl pH7.5, 0.5mM EDTA, 1M NaCl, 0.05% Tween). Beads were washed once in 1xTD buffer (20mM Tris-HCl pH7.5, 10mM MgCl2, 20% DMF) before being tagmented with in-house produced Tn5 transposase in TD buffer for 55°C for 10 minutes. TN5 was quenched in 50mM EDTA for 30 minutes at 55°C before washing twice in 50mM EDTA, twice in Tween wash buffer and once in 10mM Tris. PCR amplification was carried out on beads using KAPA HotStart Taq enzyme. After purification of PCR product with Ampure beads, the quality of the obtained library was assessed by Bioanalyzer (High Sensitivity DNA kit, Agilent Technologies), prior to sequencing.

value: Mouse embryonic stem cells

tag: chip antibody

value: RYBP


title: single doseH5/IVAX-1d42 (mouse ID 2.1)

description:
SAMPLE 23
Fig. 2b


title: polyribosome associated mRNA-seq-MHCC97H_NC_repeat 3

value: wild type


title: polyribosome associated mRNA-seq-MHCC97H_NC_repeat 2


title: polyribosome associated mRNA-seq-MHCC97H_NC_repeat 1


title: single doseH5/IVAX-1d28 (mouse ID 2.3)

description:
SAMPLE 20
Fig. 2b


title: single doseH5/IVAX-1d28 (mouse ID 2.1)

description:
SAMPLE 18
Fig. 2b


title: single doseH5/IVAX-1d42 (mouse ID 2.3)

description:
SAMPLE 25
Fig. 2b


title: polyribosome associated mRNA-seq-MHCC97H_NC_Input_repeat 3


title: single doseH5/IVAX-1d42 (mouse ID 2.2)

description:
SAMPLE 24
Fig. 2b


title: polyribosome associated mRNA-seq-MHCC97H_NC_Input_repeat 2


title: PR20-PFI

city: Madrid

first: Oscar

last: Fernandez-Capetillo

address: MFA 3

department: Genomic Instability Group

country: Spain

institute: CNIO

description:
PR20.PFI
processed data files:
counts.txt
resTablePR20.PFI-v-C.txt

data_processing:
Image analysis, per-cycle basecalling and quality score assignment was performed with Illumina Real Time Analysis software. Conversion of Illumina BCL files to fastq file format was performed with the bcl2fastq software from Illumina.
RNA-seq reads were aligned to the GRCh38/hg38 using STAR (2.5.3) with --quantMode GeneCounts option  (Dobin A et al. Bioinformatics 29:15, 2013).
Differential gene expression (DGE) analysis was subsequently performed with DESeq2 (Love MI et al. Genome Biol 15:550, 2014)
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: "Counts.txt" tab-delimited text file contains the read counts for the six samples as counted by STAR and normalised with function counts() from DESeq2.
Supplementary_files_format_and_content: DESeq2 results are presented in "resTable*-v-C.txt" tab-delimited text files, where (*) denotes each treatment name being compared with the control (C) sample.

source_name: Hybrid cell line, with properties of motor neurons

growth_protocol: NSC34 cells were grown on gelatin at 37°C, 5% CO2, in high glucose DMEM (Invitrogen) supplemented with 15% fetal bovine serum (FBS), 1% glutamine and 1% Penicillin/Streptomycin

extract_protocol:
RNA was purified by using absolutely RNA kit from Agilent.
1 µg of total RNA samples with RIN above 9 were converted to sequencing libraries with "NEBNext Ultra II Directional RNA Library Prep Kit for Illumina" (NEB, Cat. No. E7760) by following manufacturer instructions.

treatment_protocol: Cells were treated with 5 µM of PR20 during 24 hours, 10 µM PFI or 10 µM of NaPhen  for 48 hours, or in combination (24 hours of 10 µM PFI or 10 µM of NaPhen follow by 24 hours of 5 µM of PR20).

value: NSC-34 is produced by fusion of motor neuron enriched, embryonic mouse spinal cord cells with mouse neuroblastoma

tag: genotype

value: WT


title: single doseH5/IVAX-1d10 (mouse ID 2.4)

description:
SAMPLE 16
Fig. 2b

source_name: single doseH5/IVAX-1d10 (mouseID B1)

value: plasma


title: single doseH5/IVAX-1d10 (mouse ID 2.3)

description:
SAMPLE 15
Fig. 2b


title: PR20-NaPhen

description:
PR20.NaPhen
processed data files:
counts.txt
resTablePR20.NaPhen-v-C.txt


title: polyribosome associated mRNA-seq-MHCC97H_NC_Input_repeat 1


title: PR20

description:
PR20
processed data files:
counts.txt
resTablePR20-v-C.txt


title: single doseH5/IVAX-1d10 (mouse ID 2.2)

description:
SAMPLE 14
Fig. 2b