title: H661_A485_R3

description: Library name: H661_A485_R3

data_processing:
Reads in fastq files were filtered (for quality (phred score > 20) and length (>20 bases)) and trimmed (Illumina adapters) using TrimGalore (v0.6.6) in single-end mode with the following flags (--phred33 --fastqc --quality 20 --length 20).
Filtered and trimmed reads were then aligned to the human genome (GRCh38.p13) using the STAR aligner (v2.7.5b) with the following flags (--outSAMattributes Standard --outSAMtype BAM SortedByCoordinate --outSAMunmapped Within). A STAR index was generated prior to alignment using gencode v36 gene annotations (--runMode genomeGenerate).
Coordinate sorted binary alignment files (BAM) were indexed and mapping statistics were generated using samtools (v1.9) (index/flagstat).
Read counts in indexed BAM files were then quantified at the gene level using the featureCounts utility from subread (v2.0.6) with default flags using gencode v36 gene annotations.
Raw counts were normalised by total library size and gene length (Transcripts Per Million) using R (v4.0.2).
Assembly: GRCh38 (GRCh38.p13)
Supplementary files format and content: A tab-delimited text file that includes raw gene count values for each sample.
Supplementary files format and content: A tab-delimited text file that includes TPM normalised gene count values for each sample.

growth_protocol: Non-small cell lung cancer cell lines NCI-H661 and NCI-H1299 were cultured in RPMI-1640 (Gibco), A427 and HuTu80 with EMEM (Gibco), DMS114 with Waymouth (Gibco) and Cov318 with DMEM (Gibco) growth medium, all supplemented with 10% heat-inactivated fetal bovine serum (FBS) and 1x penicillin/streptomycin at 37℃, 5% CO2. Cells were routinely passaged to maintain exponential growth, using Trypsin-Low EDTA (LE) Express (Gibco) to detach cells each time. Cells were regularly tested for mycoplasma contamination using the Mycoplasma PCR Detection Kit (abcam, #ab289834). NSCLC cell lines were also STR profiled to ensure authenticity. NCI-H661, NCI-H1299, A427, HuTu80, DMS114 and Cov318 were purchased from ATCC.

extract_protocol:
RNA extraction was performed on cell pellets collected from each cell line, using the Monarch Total RNA miniprep kit (NEB #T2010S) with DNAse I treatment according to the manufacturers instructions. RNA was quantified using the Qubit™ RNA High Sensitivity (HS) Assay Kit (Invitrogen) on a Qubit 3.0 flourometer.
Following RNA quantitation, 1 microgram of RNA was used as input for PolyA+ directional RNA-seq library preparation using the NEBNext Ultra II Directional RNA-seq Kit (#E7765, NEB) with the PolyA mRNA magnetic isolation module (#E7490, NEB) according to the manufacturers instructions. Following adaptor ligation, the final PCR used to incorportate multiplexing oligos for Illumina libraries using the NEBNext Multiplex Oligos for Illumina (Index Primers Set 1-4) was ran for a total of 8 cycles. Individual and pooled libraries were quantified and quality controlled using the dsDNA high sensitivity (HS) Qubit assay (Invitrogen) on the Qubit 3.0 fluorometer (Invitrogen) and D1000 High Sensitivity DNA kit (Agilent) on the TapeStation 2200 (Agilent).The pooled library was sequenced on an Illumina NextSeq 500 or NextSeq 2000 either as single-end 75bp or 100bp configurations respectively.

treatment_protocol: For NCI-H661 CRISPR knockouts, cells were electroporated using Neon™ Transfection System (ThermoFisher) with Cas9 RNP (loaded with a single guide RNA targeted to DPPA2 or DPPA4. Post electroporation, cells were seeded at low density (1 cell/well in a 384-well plate) to isolate monoclonal populations. After 3 weeks in single-cell dilution, populations were screened by PCR and edits identified by Sanger sequencing. Based on sequencing data, clones were selected for further genotype evaluation.Clones with an indel knockout on all alleles were expanded, cryopreserved, and tested for mycoplasma. For NCI-H661 inducible shRNA knockdowns miR30 based shRNAs were expressed using a tetracycline-inducible PiggyBac transposon system (pCLIIPi-iRFP-shRNA-pGK-mVenus), as previously described (Eckersley-Maslin et al. 2020). Established shRNA sequences against either; Renilla luciferase (non-targeting control) (#713), human DPPA2 (#760) or DPPA4 (#1993) were cloned by first annealing complementary oligo’s and ligating them into a digested pMSCV-miR30 backbone3 , followed by PCR, digestion and ligation into the pCLIIPi backbone. Stable cell lines were generated by transfecting NCI-H661 cells with the shRNA vectors along with PiggyBac transposase (pRM1024), waiting for 2 weeks, then sorting mVenus positive cells twice with expansion in between, collecting the top 50% of mVenus positive cells each time as a bulk population for further experiments. The mVenus DPPA4 shRNA construct underwent additional cloning to replace mVenus with tagBFP to allow for selection of cells containing both DPPA2 and DPPA4 inducible shRNA. To generate the double inducible knockdown line, stable shDPPA2 (mVenus+) cells were transfected with the shDPPA4 (tagBFP) vector and selected as above for both mVenus+/tagBFP+ cells. To induce shRNA expression, cells were treated with 2μg/ml doxycycline (Dox) for 7 days. For NCI-H661, A427, HuTu80, DMS114 and Cov318 siRNA knockdowns, 10uL Lipofectamine 2000 (ThermoFisher, #11668027) and 200pmol of non-targeted and DPPA2/4 targeted siRNA twice over 96 hours (first dose at day 0, second dose at day 2, collection on day 4) using SMARTpool siRNA (containing 4 siRNAs per pool) (Horizon/Dharmacon, Non-targeting; #D-001810-10-05, DPPA2; #L-018977-01-0005, DPPA4; #L-020766-01-0005). Lipofectamine 2000 and siRNA complexes were first formed with reduced-serum OptiMEM medium (Gibco) for 20 mins at room temperature, prior to addition to cells grown in complete medium. For the drug treatment experiment, NCI-H661 cells were treated with either a vehicle control (DMSO) or the p300/CBP inhibitor A-485 (10uM) for 24 hours.


title: H661_A485_R2

status: Public on Jan 20 2026

type: SRA

city: Melbourne

first: Janith

last: Seneviratne

state: VIC

address: Peter MacCallum Cancer Centre, 305 Grattan Street

country: Australia

institute: Peter MacCallum Cancer Centre

description: Library name: H661_A485_R2

library_source: transcriptomic

molecule: polyA RNA

organism: Homo sapiens

source_name: lung cancer

tag: tissue

value: lung cancer

tag: cell line

tag: cell type

value: lung large cell carcinoma

tag: genotype

value: Parental

tag: treatment

tag: batch


title: H661_A485_R1

description: Library name: H661_A485_R1


title: H661_CTRL_R2

description: Library name: H661_CTRL_R2

value: DMSO 1 day


title: H661_CTRL_R1

description: Library name: H661_CTRL_R1


title: H661-IgGIgG-R2

description: Library name: H661-IgGIgG-R2

library_source: genomic

data_processing:
Single-end reads in fastqs were trimmed and filtered for quality (phred33 score > 20) and length (>20bp) using TrimGalore (https://github.com/FelixKrueger/TrimGalore) v0.6.6 in single-end mode.
Trimmed and quality filtered reads were then aligned to the hg38 human genome GRCh38.p13 using bwa-mem (bwa v0.7.13) with default parameters. Alignments were then converted to the bam format and indexed using samtools v1.9. Duplicate alignments were marked with using MarkDuplicates (picard v2.6.0, https://broadinstitute.github.io/picard/) and re-indexed with samtools. bigWig files containing CPM/bp normalised coverage values for each sample were derived from duplicate marked bam files using bamCoverage (DeepTools v3.5.0) where reads were extended to 147bp.
The resultant BAM files were then input to EPIC2 (v0.0.52) (--bin-size 100 –gaps-allowed 1 –fragment-size 147 -- false-discovery-rate-cutoff 0.05) using matched NCI-H661 genomic inputs as the control.
Assembly: GRCh38.p13
Supplementary files format and content: Peak files output by EPIC2.
Supplementary files format and content: Bigwig files output by deepTools summarising read density across the genome with values as CPM/bp.

molecule: genomic DNA

growth_protocol: Non-small cell lung cancer cell line NCI-H661 was cultured in RPMI-1640 (Gibco) growth medium and supplemented with 10% heat-inactivated fetal bovine serum (FBS) and 1x penicillin/streptomycin at 37℃, 5% CO2. Cells were routinely passaged to maintain exponential growth, using Trypsin-Low EDTA (LE) Express (Gibco) to detach cells each time. Cells were regularly tested for mycoplasma contamination using the Mycoplasma PCR Detection Kit (abcam, #ab289834). This cell line was also STR profiled to ensure authenticity. NCI-H661 was purchased from ATCC.

extract_protocol:
For each reChIP 1x10^6 single-crosslinked NCI-H661 cells were used. Pellets of single-crosslinked NCI-H661 cells were washed twice with 1mL NP buffer (10mM Tris-HCl, 1M sorbitol, 50mM NaCl, 5mM MgCl2, 1mM CaCl2, 0.1% IGEPAL CA-630, 0.1% Tween-20 in H2O freshly supplemented 1x protease inhibitor tablet) on ice. Nuclei were pooled and resuspended in 800µL ChIP buffer (as for ChIP), then left to incubate on ice for at least 5 minutes. Chromatin was transfered to a milliTUBE AFA Snap Fibre sonication vial (Covaris, #520135) and sheared on a Covaris ME220 instrument for 20mins (4C, 75% power, 15% duty factor, 1000 cycles) and debris were pelleted at 12,000xg for 15 mins at 4°C. The supernatant containing chromatin was pre-cleared by adding 20µL washed Protein-A dynabeads resuspended in ChIP dilution buffer: 67mM Tris-HCl, 100mM NaCl, 5mM EDTA, 0.33% SDS, 1.67% Triton-X) and incubated at 4°C with rotation for at least 3 hours. 10µL of the pre-cleared chromatin was set aside as 5% input. For each reChIP, 200µL of pre-cleared chromatin (1x106 cells) was made up to 500µL in a dilution buffer to get a final concentration of 67mM Tris-HCl, 100mM NaCl, 5mM EDTA, 0.33% SDS, 1.67% Triton-X, 0.1μM PMSF, 1x protease inhibitors (reChIP buffer). 20µL Protein-A dynabeads were pre-incubated (as for ChIP) with either 0.5µg H3K4me3 (CST, #9751) or H2AK119ub (CST, #8240) antibodies or Rabbit IgG (Invitrogen, #02-6102), then resuspended in the 500µL diluted chromatin. The first immunoprecipitation was performed overnight at 4°C with rotation, antibody-chromatin complexes were then washed three times in 500µL low-salt buffer (as for ChIP), three times in 500µL high-salt buffer (as for ChIP), twice in 200µL LiCl buffer (as for ChIP) and twice in 500µL 10mM TrisCl pH7.5 on ice. Complexes were eluted in 100µL ChIP elution buffer (as for ChIP) supplemented with 0.1μM PMSF and 1x protease inhibitors for 37°C for 30 mins on a thermomixer at 300RPM, of which 10µL were put aside as a 10% single ChIP control. To dilute the SDS, the eluate volume was increased to 300µL with reChIP buffer and purified using Amicon Ultra-0.5ml 3kDa filter columns (Millipore, #UFC5003) according to the manufacturer’s instructions, with chromatin being additionally washed twice with 400µL ChIP dilution buffer. Purified chromatin was made up to 500µL in reChIP buffer for the second immunoprecipitation, which was performed using the alternate antibody or IgG control bead conjugates overnight at 4°C with rotation. Complexes were washed (as for ChIP) and resuspended in 100µL ChIP elution buffer. Samples were treated with 2µL RNase A and 2µL Proteinase K, then reversed crosslinked (as for ChIP). DNA was purified using the Monarch PCR & DNA Cleanup Kit (NEB) and eluted in 25µL H2O for qPCR and library preparation for sequencing.
reChIP libraries were prepared using the NEBNext UltraII DNA Library Preparation Kit (NEB) according to the manufacturer’s instruction. During library preparation the NEBNext Multiplex Oligos for Illumina (Index Primers Set 1-4) were used to enable library multiplexing. Individual and pooled libraries were quantified and quality controlled using the dsDNA high sensitivity (HS) Qubit assay (Invitrogen) on the Qubit 3.0 fluorometer (Invitrogen) and HSD1000 High Sensitivity DNA kit (Agilent) on the TapeStation 4150 (Agilent). Libraries were pooled and sequenced on the NextSeq2000 platform in a single-end configurations with 100bp read lengths.

treatment_protocol: No treatments were made.

tag: replicate

tag: antibody 1

value: Invitrogen #02-6102

tag: antibody 2

tag: target 1

value: IgG

tag: target 2


title: 7a134d098af2ecae;PLACEBO

city: New York

first: Stuart

last: Sealfon

state: NY

address: One Gustave L. Levy Place

department: Department of Neurology

country: USA

institute: Icahn School of Medicine at Mount Sinai

description: Library name: 7a134d098af2ecae

data_processing:
Reads from all samples were processed using the MoTrPAC RNA-Seq pipeline
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes counts for each sample

molecule: total RNA

source_name: Whole Blood

extract_protocol:
Human total RNA from blood (collected in PAXgene tubes, http://www.bdbiosciences.com/us/applications/blood-collection/cell-biomarker-preservation/paxgenereg-blood-rna-tube/p/762165) was extracted using the Agencourt RNAdvance blood kit (Beckman Coulter) on an automated Biomek Fxp workstation (Beckman Coulter).The purity of the RNA was assessed using a NanoDrop (Thermo Fisher Scientific) and quantified with the Quant-iT RiboGreen RNA Assay kit (Thermo Fisher Scientific). RNA integrity (RIN) was measured using the RNA Nano 6000 Assay kit on an Agilent Bioanalyzer 2100 system (Agilent Technologies) and the samples with RIN above 7.0 were processed to libraries.
The mRNA libraries were prepared using the Universal Plus mRNA-Seq Library preparation kit (NuGEN) on an automated Biomek i7 workstation (Beckman Coulter). In brief, mRNA was purified from 400 ng of total RNA using oligo-dT beads, and cDNA was synthesized according to NuGEN’s protocol. The AnyDeplete kit (NuGEN) was used to remove ribosomal RNA (rRNA) and globin transcripts before library amplification. The purified libraries were quantified with the Qubit dsDNA HS kit (Thermo Fisher Scientific), and their size and distribution were analyzed using a Bioanalyzer with the High Sensitivity DNA kit (Agilent). After library preparation, samples were pooled, and library integrity was verified by sequencing on an Illumina MiSeq. Deep sequencing was then conducted on a NovaSeq 6000 (Illumina, Inc., San Diego, CA), with an average depth of 30 million 100 bp paired-end reads per sample.

value: Whole Blood

value: PLACEBO


title: H661-IgGIgG-R1

description: Library name: H661-IgGIgG-R1


title: 7a840fd1725782ba;MVA-NP+M1

description: Library name: 7a840fd1725782ba


title: H661_CTRL_R3

description: Library name: H661_CTRL_R3


title: 79cec72cea5b808f;MVA-NP+M1

description: Library name: 79cec72cea5b808f


title: H661-SUZ12-R1

description:
Library name: H661-SUZ12-R1
parental H661

data_processing:
Single-end reads in fastqs were trimmed and filtered for quality (phred33 score > 20) and length (>20bp) using TrimGalore (https://github.com/FelixKrueger/TrimGalore) v0.6.6 in single-end mode.
Trimmed and quality filtered reads were then aligned to the hg38 human genome GRCh38.p13 using bwa-mem (bwa v0.7.13) with default parameters. Alignments were then converted to the bam format and indexed using samtools v1.9. Duplicate alignments were marked with using MarkDuplicates (picard v2.6.0, https://broadinstitute.github.io/picard/) and re-indexed with samtools. bigWig files containing CPM/bp normalised coverage values for each sample were derived from duplicate marked bam files using bamCoverage (DeepTools v3.5.0) where reads were extended to 147bp.
For all histone modifications and transcription factors, the resultant BAM files were input to EPIC2 (v0.0.52) (--bin-size 100 –gaps-allowed 1 –fragment-size 147 -- false-discovery-rate-cutoff 0.05) to call peaks using genomic inputs as the control. For DPPA2, DPPA4, SUZ12 ChIPs we also used MACS217  (v2.2.7.1) to call narrow peaks, using matched genomic inputs as the control (-B --nomodel --extsize 147 --SPMR -q 0.05).
Assembly: GRCh38.p13
Supplementary files format and content: Bigwig files output by deepTools summarising read density across the genome with values as CPM/bp.
Supplementary files format and content: Peak files produced by EPIC2.
Supplementary files format and content: Peak files produced by MACS2.

growth_protocol: The non-small cell lung cancer cell lines NCI-H661 and NCI-H1299 were cultured in RPMI-1640 (Gibco) growth medium and supplemented with 10% heat-inactivated fetal bovine serum (FBS) and 1x penicillin/streptomycin at 37℃, 5% CO2. Cells were routinely passaged to maintain exponential growth, using Trypsin-Low EDTA (LE) Express (Gibco) to detach cells each time. Cells were regularly tested for mycoplasma contamination using the Mycoplasma PCR Detection Kit (abcam, #ab289834). These cell lines was also STR profiled to ensure authenticity. NCI-H661 and NCI-H1299 were purchased from ATCC.

extract_protocol:
For DPPA2, DPPA4, KDM2A and SUZ12 ChIPs 4x10^6 NCI-H661 cells were utilised per ChIP and underwent double-crosslinking prior to chromatin isolation. All other ChIPs against histone modifications (H3K4me3, H3K4me1, H3K27ac, H3K27me3, H2AK119ub, H3K9me3, H3K36me3, H3K36me2) utilised 0.5x10^6 NCI-H661 or 1x10^6 NCI-H1299 cells per ChIP and underwent single-crosslinking. For double-crosslinking, cells were harvested, washed once with PBS, and resuspended in 10mL of PBS with 5mM EDTA on ice. A fresh stock of 0.24M disuccinimidyl glutarate (ThermoFisher #20593) was reconstituted in DMSO and added to the suspension of cells to reach a final concentration of 2mM, which were then incubated at room temperature whilst rocking for 45 mins to crosslink cells. Cells were pelleted at 3200xg for 5 mins and resuspended in 9.375mL of PBS with 5mM EDTA. Cells undergoing only single-crosslinking were resuspended in 9.375mL PBS at this point. 625uL of fresh 16% formaldehyde (methanol-free) (ThermoFisher, #28908) were added to each cell suspension to reach a final concentration of 1% and then incubated on a rocker for 12.5 mins at room temperature to crosslink cells. Crosslinkers were then quenched by supplementing cell suspensions with 1M ice-cold glycine to reach a final concentration of 125mM and rocked for a further 5 mins at room temperature. Crosslinked cells were then pelleted at 3200xg for 5mins at 4C, washed with 1mL ice-cold PBS with 5mM EDTA and protease inhibitors, and then immediately snap frozen with dry ice and stored at -80C until ChIPs were performed. Crosslinked cell pellets were washed with 1mL ice-cold NP buffer (10mM Tris-HCl, 1M sorbitol, 50mM NaCl, 5mM MgCl2, 1mM CaCl2, 0.1% IGEPAL CA-630, 0.1% Tween-20 in H2O freshly supplemented with 0.385μM beta-mercaptoethanol, 1.82mM spermidine, 1x protease inhibitor tablet) twice to isolate nuclei, with nuclei spun at 2000xg for 5 mins at 4C each time for pelleting. Nuclei were resuspended in 900uL ChIP buffer (20mM Tris-HCl, 2mM EDTA, 150mM NaCl, 0.6% SDS, 1% Triton-X in H2O freshly supplemented with 0.1μM PMSF, 1x protease inhibitor tablet), transferred to a milliTUBE AFA Snap Fibre sonication vial (Covaris, #520135) and left to incubate on ice for 1hr. Chromatin was then  sheared to ~200bp fragments using the ME220 sonicator (Covaris) (4C, 75% power, 15% duty factor, 1000 cycles) for either 30 mins (double-crosslinked) or 20 mins (single-crosslinked). Debris were pelleted at 12,000xg for 15 mins at 4C, and the supernatant containing sheared chromatin was transferred to a new tube. Sheared chromatin was regularly checked through gel electrophoresis to ensure predominantly mononucleosomal fragments. For double-crosslinked ChIPs Protein-G dynabeads were used, and for single-crosslinked ChIPs Protein-A dynabeads were used. 50uL of beads were washed twice in 1mL of low-salt wash buffer (20mM Tris-HCl, 2mM EDTA, 150mM NaCl, 0.1% SDS, 1% Triton-X in H2O) and resuspended in 100uL of low-salt buffer. To pre-clear chromatin, 20uL of washed beads were added to 180uL sheared chromatin and then incubated at 4C for 5 hours on a rotator, followed by transfer of the supernatant to a new tube. To conjugate antibodies to beads, 0.5-4μg of antibodies were diluted to 320uL with ChIP dilution buffer (100mM NaCl, 0.02% sodium azide, 100mM Tris-HCl, 5mM EDTA, 5% Triton-X in H2O supplemented with 1x protease inhibitor tablet) and were left to conjugate with 80uL of washed beads at 4C for 5 hours whilst rotating (IgG controls (0.5-4ug Mouse IgG (Invitrogen, #31903), 0.5-4ug Rabbit IgG (Invitrogen, #012-6102)) or antibodies (4ug DPPA2 (Sigma, #MAB4356), 4ug DPPA4 (abcepta, #AP1438a, abcepta, #AP21202c, abcam, #ab154642), 4ug KDM2A (Invitrogen, #PA5-40421), 1ug SUZ12 (CST, #3737), 0.5ug H3K4me3 (CST, #9751), 0.5ug H3K27me3 (CST, #9733), 0.5ug H2AK119ub (CST, #8240), 0.5ug H3K4me1 (CST, #5326T), 1ug H3K27ac (abcam, #ab4729), 1ug H3K9me3 (abcam, #ab8898), 0.5ug H3K36me2 (abcam, #ab9049), 0.5ug H3K36me3 (CST, #4909)). Antibody-bead conjugates were washed with 1mL of ChIP dilution buffer and subsequently resuspended with 180uL of pre-cleared chromatin and left to incubate overnight whilst rotating at 4C, 9uL of the remaining pre-cleared chromatin was set aside as an input control. Beads were then washed three times with 200uL low-salt wash buffer, three times with 200uL high-salt wash buffer (20mM Tris-HCl, 2mM EDTA, 500mM NaCl, 0.1% SDS, 1% Triton-X in H2O), two times with 200uL LiCl wash buffer (250mM LiCl, 1% sodium deoxycholate, 10mM Tris-HCl, 1mM EDTA, 1% IGEPAL CA-630) and once with 200uL 10mM Tris-HCl pH7.5. Beads as well as input controls were then resuspended/diluted in 50uL ChIP elution buffer (1% SDS, 0.1M NaHCO3 in H2O). Samples were subject to a RNAse A digest (5uL 20mg/mL NEB) for 1hr at 37C, then a Proteinase K digest (5uL 800U/mL NEB) for 1hr at 37C and crosslinks were reversed overnight by incubation at 65C on a thermomixer (1200RPM). DNA was then enriched from eluates using a 1.8X bead cleanup (SergiLabs) and eluted in 30uL H2O for downstream qPCR analyses and DNA library preparation.
ChIP libraries were prepared using the NEBNext UltraII DNA Library Preparation Kit (NEB) according to the manufacturer’s instruction. During library preparation the NEBNext Multiplex Oligos for Illumina (Index Primers Set 1-4) were used to enable library multiplexing. Individual and pooled libraries were quantified and quality controlled using the dsDNA high sensitivity (HS) Qubit assay (Invitrogen) on the Qubit 3.0 fluorometer (Invitrogen) and HSD1000 High Sensitivity DNA kit (Agilent) on the TapeStation 4150 (Agilent). Libraries were pooled and sequenced on the NextSeq2000 platform in a single-end configurations with 100bp read lengths.

treatment_protocol: No treatments were made to NCI-H661 cells. For inducible overexpression experiments in NCI-H1299 the pCLIIi vector backbones were cloned to replace the (iRFP-shRNA) fragment downstream of the tet-response element (TRE) with cDNA encoding human DPPA2 (ORF:NM_138815) or DPPA4 (ORF:NM_018189) with additional N-terminal Flag or V5 tags respectively (gene fragments synthesised by IDT). Stable cell lines were generated in the same way as  shRNA lines for the NCI-H1299 cell line (which does not express DPPA2/4). All cell sorting was undertaken on FACSAria Fusion flow cytometry instruments (BD). To induce cDNA expression, cells were treated with 2μg/ml doxycycline (Dox) for 7 days and knockdown or overexpression were confirmed by RT-qPCR or western blot analysis.

tag: target

tag: antibody


title: 79071bcbe6a9052d;PLACEBO

description: Library name: 79071bcbe6a9052d


title: 7d4ee9a32e518465;PLACEBO

description: Library name: 7d4ee9a32e518465


title: H661-KDM2A-R1

description:
Library name: H661-KDM2A-R1
parental H661

value: Invitrogen #PA5-40421


title: H661-Input-R2_S1

description:
Library name: H661-Input-R2_S1
parental H661

value: none (genomic input, single crosslinked)


title: 774ad352d03053a7;PLACEBO

description: Library name: 774ad352d03053a7


title: H661-Input2x-R1

description:
Library name: H661-Input2x-R1
parental H661

value: none (genomic input, double crosslinked)


title: 77259f27ce2a965c;MVA-NP+M1

description: Library name: 77259f27ce2a965c


title: H661-H3K9me3-R2

description:
Library name: H661-H3K9me3-R2
parental H661

value: abcam #ab8898


title: 7b2ded0042a5f4a5;MVA-NP+M1

description: Library name: 7b2ded0042a5f4a5


title: H661-H3K9me3-R1

description:
Library name: H661-H3K9me3-R1
parental H661


title: 76f3d786ff849d95;MVA-NP+M1

description: Library name: 76f3d786ff849d95


title: 78f31ee34290badd;MVA-NP+M1

description: Library name: 78f31ee34290badd


title: 7b0efc60f5f05e4c;MVA-NP+M1

description: Library name: 7b0efc60f5f05e4c


title: 76e272b5f48c5b1a;MVA-NP+M1

description: Library name: 76e272b5f48c5b1a


title: H661-H3K4me3-R1

description:
Library name: H661-H3K4me3-R1
parental H661


title: H661-H3K4me1-R2

description:
Library name: H661-H3K4me1-R2
parental H661


title: H661-H3K4me3-R2

description:
Library name: H661-H3K4me3-R2
parental H661


title: 76994626f3ab63b1;MVA-NP+M1

description: Library name: 76994626f3ab63b1


title: 75d7983c2087898c;PLACEBO

description: Library name: 75d7983c2087898c


title: 757693b588e9f3bd;MVA-NP+M1

description: Library name: 757693b588e9f3bd


title: H661-H3K4me1-R1

description:
Library name: H661-H3K4me1-R1
parental H661


title: 7527484fb8f22af8;PLACEBO

description: Library name: 7527484fb8f22af8


title: H661-H3K36me3-R1

description:
Library name: H661-H3K36me3-R1
parental H661


title: H661-H3K27me3-R2

description:
Library name: H661-H3K27me3-R2
parental H661


title: 756bd85d49b642b0;MVA-NP+M1

description: Library name: 756bd85d49b642b0


title: 7520e974d7413801;MVA-NP+M1

description: Library name: 7520e974d7413801


title: 7640727873a51dbf;MVA-NP+M1

description: Library name: 7640727873a51dbf


title: H661-H3K36me3-R2

description:
Library name: H661-H3K36me3-R2
parental H661


title: H661-H3K36me2-R1

description:
Library name: H661-H3K36me2-R1
parental H661

value: abcam #ab9049


title: 751175a4c566962a;PLACEBO

description: Library name: 751175a4c566962a


title: H661-H3K36me2-R2

description:
Library name: H661-H3K36me2-R2
parental H661


title: 744369adf5c919f2;PLACEBO

description: Library name: 744369adf5c919f2


title: 7599c7c8407f6e0a;MVA-NP+M1

description: Library name: 7599c7c8407f6e0a


title: H661-H3K27me3-R1

description:
Library name: H661-H3K27me3-R1
parental H661


title: 74943e1d0e11b398;MVA-NP+M1

description: Library name: 74943e1d0e11b398


title: 74b27f85b95f0fc8;MVA-NP+M1

description: Library name: 74b27f85b95f0fc8


title: 7412e346ed129456;MVA-NP+M1

description: Library name: 7412e346ed129456


title: H661-H3K27ac-R2

description:
Library name: H661-H3K27ac-R2
parental H661

value: abcam #ab4729


title: H661-H2AK119ub-R2

description:
Library name: H661-H2AK119ub-R2
parental H661


title: 740de61dde6bb9a0;MVA-NP+M1

description: Library name: 740de61dde6bb9a0


title: H661-H2AK119ub-R1

description:
Library name: H661-H2AK119ub-R1
parental H661


title: H661-H3K27ac-R1

description:
Library name: H661-H3K27ac-R1
parental H661


title: 733acc34de1928a1;MVA-NP+M1

description: Library name: 733acc34de1928a1


title: 733d22d063d31a60;PLACEBO

description: Library name: 733d22d063d31a60


title: H661-DPPA4n-R3

description:
Library name: H661-DPPA4n-R3
parental H661

value: DPPA4n (N-terminal)

value: abcepta #AP1438a


title: H661-DPPA4n-R2

description:
Library name: H661-DPPA4n-R2
parental H661


title: H661-DPPA2-R3

description:
Library name: H661-DPPA2-R3
parental H661

value: Sigma #MAB4356


title: 7310a2d45172cf2f;MVA-NP+M1

description: Library name: 7310a2d45172cf2f


title: H661-DPPA2-R1

description:
Library name: H661-DPPA2-R1
parental H661

value: lung cancer


title: 728d0f9a7c8ecb9a;MVA-NP+M1

description: Library name: 728d0f9a7c8ecb9a


title: H1299-DOVE-DOX-INP-R1

description:
Library name: H1299-DOVE-DOX-INP-R1
DPPA2 and DPPA4 stable inducible

value: lung adenocarcinoma

value: DPPA2 and DPPA4 stable inducible

value: 7 days doxycyline 2ug/mL

value: none (genomic input)


title: 72e4b3d92ce2d907;PLACEBO

description: Library name: 72e4b3d92ce2d907


title: H1299-DOVE-DOX-H3K9me3-R2

description:
Library name: H1299-DOVE-DOX-H3K9me3-R2
DPPA2 and DPPA4 stable inducible


title: 728c584c0a53a242;MVA-NP+M1

description: Library name: 728c584c0a53a242


title: 7235f332680abc2b;MVA-NP+M1

description: Library name: 7235f332680abc2b


title: 7233018aca2db412;PLACEBO

description: Library name: 7233018aca2db412


title: H1299-DOVE-DOX-H3K4me1-R1

description:
Library name: H1299-DOVE-DOX-H3K4me1-R1
DPPA2 and DPPA4 stable inducible


title: H1299-DOVE-DOX-H3K4me3-R1

description:
Library name: H1299-DOVE-DOX-H3K4me3-R1
DPPA2 and DPPA4 stable inducible


title: H1299-DOVE-DOX-H3K9me3-R1

description:
Library name: H1299-DOVE-DOX-H3K9me3-R1
DPPA2 and DPPA4 stable inducible


title: 717c59168fd9b2ac;PLACEBO

description: Library name: 717c59168fd9b2ac


title: 730673b004f3bb66;MVA-NP+M1

description: Library name: 730673b004f3bb66


title: 72284454de92cca0;PLACEBO

description: Library name: 72284454de92cca0


title: 716e83960c6f77d5;MVA-NP+M1

description: Library name: 716e83960c6f77d5


title: H1299-DOVE-DOX-H3K36me3-R1

description:
Library name: H1299-DOVE-DOX-H3K36me3-R1
DPPA2 and DPPA4 stable inducible


title: H1299-DOVE-DOX-H3K27me3-R2

description:
Library name: H1299-DOVE-DOX-H3K27me3-R2
DPPA2 and DPPA4 stable inducible


title: H1299-DOVE-DOX-H3K36me3-R2

description:
Library name: H1299-DOVE-DOX-H3K36me3-R2
DPPA2 and DPPA4 stable inducible


title: 730ee761872a7491;PLACEBO

description: Library name: 730ee761872a7491


title: 6f7fef5f0749e69b;MVA-NP+M1

description: Library name: 6f7fef5f0749e69b


title: H1299-DOVE-DOX-H3K27ac-R1

description:
Library name: H1299-DOVE-DOX-H3K27ac-R1
DPPA2 and DPPA4 stable inducible


title: H1299-DOVE-DOX-H3K4me1-R2

description:
Library name: H1299-DOVE-DOX-H3K4me1-R2
DPPA2 and DPPA4 stable inducible


title: 6e4c9ca14369527a;MVA-NP+M1

description: Library name: 6e4c9ca14369527a


title: 7167f5cb3adfbfd4;PLACEBO

description: Library name: 7167f5cb3adfbfd4


title: 6e7915e2a003b0d0;MVA-NP+M1

description: Library name: 6e7915e2a003b0d0


title: 6d842c4f35dc9ea7;MVA-NP+M1

description: Library name: 6d842c4f35dc9ea7


title: H1299-DOVE-DOX-H2AK119ub-R1

description:
Library name: H1299-DOVE-DOX-H2AK119ub-R1
DPPA2 and DPPA4 stable inducible


title: 6f5539fd6dc0fcf1;MVA-NP+M1

description: Library name: 6f5539fd6dc0fcf1


title: H1299-DOVE-CTRL-H3K9me3-R1

description:
Library name: H1299-DOVE-CTRL-H3K9me3-R1
DPPA2 and DPPA4 stable inducible

value: 7 days of H20


title: H1299-DOVE-DOX-H3K27ac-R2

description:
Library name: H1299-DOVE-DOX-H3K27ac-R2
DPPA2 and DPPA4 stable inducible


title: H1299-DOVE-DOX-H3K4me3-R2

description:
Library name: H1299-DOVE-DOX-H3K4me3-R2
DPPA2 and DPPA4 stable inducible


title: H1299-DOVE-CTRL-H3K9me3-R2

description:
Library name: H1299-DOVE-CTRL-H3K9me3-R2
DPPA2 and DPPA4 stable inducible


title: 6ca0affb569ba583;MVA-NP+M1

description: Library name: 6ca0affb569ba583

value: Whole Blood


title: H1299-DOVE-DOX-H2AK119ub-R2

description:
Library name: H1299-DOVE-DOX-H2AK119ub-R2
DPPA2 and DPPA4 stable inducible


title: 6be0c83bb16fa680;PLACEBO

description: Library name: 6be0c83bb16fa680

value: PLACEBO


title: H1299-DOVE-CTRL-H3K4me1-R2

description:
Library name: H1299-DOVE-CTRL-H3K4me1-R2
DPPA2 and DPPA4 stable inducible


title: H1299-DOVE-CTRL-INP-R1

description:
Library name: H1299-DOVE-CTRL-INP-R1
DPPA2 and DPPA4 stable inducible


title: 6bdd52d4da94435a;PLACEBO

description: Library name: 6bdd52d4da94435a


title: 6fb1d1ec6028671b;MVA-NP+M1

description: Library name: 6fb1d1ec6028671b


title: H1299-DOVE-CTRL-H3K4me3-R2

description:
Library name: H1299-DOVE-CTRL-H3K4me3-R2
DPPA2 and DPPA4 stable inducible


title: 69c337fb7aca2701;MVA-NP+M1

description: Library name: 69c337fb7aca2701


title: 6b4f477012c675b0;PLACEBO

description: Library name: 6b4f477012c675b0


title: H1299-DOVE-CTRL-H3K4me3-R1

description:
Library name: H1299-DOVE-CTRL-H3K4me3-R1
DPPA2 and DPPA4 stable inducible


title: 6cc00d39349dbccb;PLACEBO

description: Library name: 6cc00d39349dbccb


title: H1299-DOVE-CTRL-H3K36me3-R2

description:
Library name: H1299-DOVE-CTRL-H3K36me3-R2
DPPA2 and DPPA4 stable inducible


title: 69b5480d36d37f2f;MVA-NP+M1

description: Library name: 69b5480d36d37f2f


title: 69b31321096384fc;MVA-NP+M1

description: Library name: 69b31321096384fc


title: H1299-DOVE-CTRL-H3K36me3-R1

description:
Library name: H1299-DOVE-CTRL-H3K36me3-R1
DPPA2 and DPPA4 stable inducible


title: 68efdd1da9c3b447;PLACEBO

description: Library name: 68efdd1da9c3b447


title: H1299-DOVE-CTRL-H3K27me3-R1

description:
Library name: H1299-DOVE-CTRL-H3K27me3-R1
DPPA2 and DPPA4 stable inducible


title: 68daca88d1e6f363;MVA-NP+M1

description: Library name: 68daca88d1e6f363


title: H1299-DOVE-CTRL-H2AK119ub-R2

description:
Library name: H1299-DOVE-CTRL-H2AK119ub-R2
DPPA2 and DPPA4 stable inducible


title: H1299-DOVE-CTRL-H3K27me3-R2

description:
Library name: H1299-DOVE-CTRL-H3K27me3-R2
DPPA2 and DPPA4 stable inducible


title: H1299-DOVE-CTRL-H3K4me1-R1

description:
Library name: H1299-DOVE-CTRL-H3K4me1-R1
DPPA2 and DPPA4 stable inducible


title: 682fc86671ae9707;MVA-NP+M1

description: Library name: 682fc86671ae9707


title: 677443cd0ebef607;MVA-NP+M1

description: Library name: 677443cd0ebef607


title: H1299-DOVE-CTRL-H3K27ac-R1

description:
Library name: H1299-DOVE-CTRL-H3K27ac-R1
DPPA2 and DPPA4 stable inducible


title: 66e89b682b58b69e;MVA-NP+M1

description: Library name: 66e89b682b58b69e


title: H1299-DOVE-CTRL-H3K27ac-R2

description:
Library name: H1299-DOVE-CTRL-H3K27ac-R2
DPPA2 and DPPA4 stable inducible


title: H1299-DOVE-CTRL-H2AK119ub-R1

description:
Library name: H1299-DOVE-CTRL-H2AK119ub-R1
DPPA2 and DPPA4 stable inducible


title: 66ddd40ea97a1587;MVA-NP+M1

description: Library name: 66ddd40ea97a1587


title: 6678f42507c45242;MVA-NP+M1

description: Library name: 6678f42507c45242


title: 660f21f01c94a336;MVA-NP+M1

description: Library name: 660f21f01c94a336


title: shR-DOX-K4-R1

description:
Library name: shR-DOX-K4-R1
shREN inducible

data_processing:
Single-end reads in fastqs were trimmed and filtered for quality (phred33 score > 20) and length (>20bp) using TrimGalore (https://github.com/FelixKrueger/TrimGalore) v0.6.6 in single-end mode.
Trimmed and quality filtered reads were then aligned to the hg38 human genome GRCh38.p13 (and for spike-in ChIP were also aligned to the mm10 mouse genome GRCm38.p6 separately) using bwa-mem (bwa v0.7.13) with default parameters. Alignments were then converted to the bam format and indexed using samtools v1.9. Duplicate alignments were marked with using MarkDuplicates (picard v2.6.0, https://broadinstitute.github.io/picard/) and re-indexed with samtools. We used the xenofilteR (v1.6)12  R package to split human and mouse aligned reads. bigWig files containing CPM/bp normalised coverage values for each sample were derived from duplicate marked bam files containing only human reads using bamCoverage (DeepTools v3.5.0) where reads were extended to 147bp.
The resultant BAM files were then input to EPIC2 (v0.0.52) (--bin-size 100 –gaps-allowed 1 –fragment-size 147 -- false-discovery-rate-cutoff 0.05) using genomic inputs as the control.
Assembly: GRCh38.p13
Supplementary files format and content: Bigwig files output by deepTools summarising read density across the genome with values as CPM/bp.
Supplementary files format and content: Peak files produced by EPIC2.

growth_protocol: The non-small cell lung cancer cell line NCI-H661 was cultured in RPMI-1640 (Gibco) growth medium and supplemented with 10% heat-inactivated fetal bovine serum (FBS) and 1x penicillin/streptomycin at 37℃, 5% CO2. E14 mouse embryonic stem cells were cultured on feeder-free gelatinised plates at 37 ℃, 5% CO2 using standard serum/LIF conditions (high-glucose DMEM supplemented with 15% FBS, 1x GlutaMax, 1x penicillin/streptomycin, 0.1mM nonessential amino acids, 50mM beta-mercaptoethanol and LIF (made in house in HEK293 cells and titrated for optimal ESC growth)). Cells were routinely passaged to maintain exponential growth, using Trypsin-Low EDTA (LE) Express (Gibco) to detach cells each time. Cells were regularly tested for mycoplasma contamination using the Mycoplasma PCR Detection Kit (abcam, #ab289834). These cell lines was also STR profiled to ensure authenticity. NCI-H661  was purchased from ATCC, and E14 mouse embryonic stem cells were a gift from Wolf Reik’s laboratory.

extract_protocol:
0.5x106 NCI-H661 cells were utilised per ChIP and underwent single-crosslinking. Cells were pelleted at 3200xg for 5 mins and resuspended in 9.375mL of PBS with 5mM EDTA. 625uL of fresh 16% formaldehyde (methanol-free) (ThermoFisher, #28908) were added to each cell suspension to reach a final concentration of 1% and then incubated on a rocker for 12.5 mins at room temperature to crosslink cells. Crosslinkers were then quenched by supplementing cell suspensions with 1M ice-cold glycine to reach a final concentration of 125mM and rocked for a further 5 mins at room temperature. Crosslinked cells were then pelleted at 3200xg for 5mins at 4C, washed with 1mL ice-cold PBS with 5mM EDTA and protease inhibitors, and then immediately snap frozen with dry ice and stored at -80C until ChIPs were performed. 50,000 (10%) single-crosslinked E14 mouse ESCs (prepared in the same way above) were additionally spiked-in prior to each ChIP to act as exogenous normalisation references in case global changes to histone modifications were observed. Crosslinked cell pellets were washed with 1mL ice-cold NP buffer (10mM Tris-HCl, 1M sorbitol, 50mM NaCl, 5mM MgCl2, 1mM CaCl2, 0.1% IGEPAL CA-630, 0.1% Tween-20 in H2O freshly supplemented with 0.385μM beta-mercaptoethanol, 1.82mM spermidine, 1x protease inhibitor tablet) twice to isolate nuclei, with nuclei spun at 2000xg for 5 mins at 4C each time for pelleting. Nuclei were resuspended in 900uL ChIP buffer (20mM Tris-HCl, 2mM EDTA, 150mM NaCl, 0.6% SDS, 1% Triton-X in H2O freshly supplemented with 0.1μM PMSF, 1x protease inhibitor tablet), transferred to a milliTUBE AFA Snap Fibre sonication vial (Covaris, #520135) and left to incubate on ice for 1hr. Chromatin was then  sheared to ~200bp fragments using the ME220 sonicator (Covaris) (4C, 75% power, 15% duty factor, 1000 cycles) for 20 mins. Debris were pelleted at 12,000xg for 15 mins at 4C, and the supernatant containing sheared chromatin was transferred to a new tube. Sheared chromatin was regularly checked through gel electrophoresis to ensure predominantly mononucleosomal fragments. Protein-A dynabeads were used donwstream, wherein 50uL of beads were washed twice in 1mL of low-salt wash buffer (20mM Tris-HCl, 2mM EDTA, 150mM NaCl, 0.1% SDS, 1% Triton-X in H2O) and resuspended in 100uL of low-salt buffer. To pre-clear chromatin, 20uL of washed beads were added to 180uL sheared chromatin and then incubated at 4C for 5 hours on a rotator, followed by transfer of the supernatant to a new tube. To conjugate antibodies to beads, 0.5-1μg of antibodies were diluted to 320uL with ChIP dilution buffer (100mM NaCl, 0.02% sodium azide, 100mM Tris-HCl, 5mM EDTA, 5% Triton-X in H2O supplemented with 1x protease inhibitor tablet) and were left to conjugate with 80uL of washed beads at 4C for 5 hours whilst rotating (IgG controls (0.5ug Mouse IgG (Invitrogen, #31903), 0.5ug Rabbit IgG (Invitrogen, #012-6102)) or antibodies (0.5ug H3K4me3 (CST, #9751), 0.5ug H3K27me3 (CST, #9733), 0.5ug H2AK119ub (CST, #8240), 1ug H3K27ac (abcam, #ab4729)). Antibody-bead conjugates were washed with 1mL of ChIP dilution buffer and subsequently resuspended with 180uL of pre-cleared chromatin and left to incubate overnight whilst rotating at 4C, 9uL of the remaining pre-cleared chromatin was set aside as an input control. Beads were then washed three times with 200uL low-salt wash buffer, three times with 200uL high-salt wash buffer (20mM Tris-HCl, 2mM EDTA, 500mM NaCl, 0.1% SDS, 1% Triton-X in H2O), two times with 200uL LiCl wash buffer (250mM LiCl, 1% sodium deoxycholate, 10mM Tris-HCl, 1mM EDTA, 1% IGEPAL CA-630) and once with 200uL 10mM Tris-HCl pH7.5. Beads as well as input controls were then resuspended/diluted in 50uL ChIP elution buffer (1% SDS, 0.1M NaHCO3 in H2O). Samples were subject to a RNAse A digest (5uL 20mg/mL NEB) for 1hr at 37C, then a Proteinase K digest (5uL 800U/mL NEB) for 1hr at 37C and crosslinks were reversed overnight by incubation at 65C on a thermomixer (1200RPM). DNA was then enriched from eluates using a 1.8X bead cleanup (SergiLabs) and eluted in 30uL H2O for downstream qPCR analyses and DNA library preparation.
ChIP-Rx libraries were prepared using the NEBNext UltraII DNA Library Preparation Kit (NEB) according to the manufacturer’s instruction. During library preparation the NEBNext Multiplex Oligos for Illumina (Index Primers Set 1-4) were used to enable library multiplexing. Individual and pooled libraries were quantified and quality controlled using the dsDNA high sensitivity (HS) Qubit assay (Invitrogen) on the Qubit 3.0 fluorometer (Invitrogen) and HSD1000 High Sensitivity DNA kit (Agilent) on the TapeStation 4150 (Agilent). Libraries were pooled and sequenced on the NextSeq2000 platform in a single-end configurations with 100bp read lengths.

treatment_protocol: For inducible knockdown experiments, miR30 based shRNAs were expressed using a tetracycline-inducible PiggyBac transposon system (pCLIIPi-iRFP-shRNA-pGK-mVenus), as previously described (Eckersley-Maslin et al. 2020). Established shRNA sequences against either; Renilla luciferase (non-targeting control) (#713), human DPPA2 (#760) or DPPA4 (#1993) were cloned by first annealing complementary oligo’s and ligating them into a digested pMSCV-miR30 backbone, followed by PCR, digestion and ligation into the pCLIIPi backbone. Stable cell lines were generated by transfecting NCI-H661 cells with the shRNA vectors along with PiggyBac transposase (pRM1024), waiting for 2 weeks, then sorting mVenus positive cells twice with expansion in between, collecting the top 50% of mVenus positive cells each time as a bulk population for further experiments. The mVenus DPPA4 shRNA construct underwent additional cloning to replace mVenus with tagBFP to allow for selection of cells containing both DPPA2 and DPPA4 inducible shRNA. To generate the double inducible knockdown line, stable shDPPA2 (mVenus+) cells were transfected with the shDPPA4 (tagBFP) vector and selected as above for both mVenus+/tagBFP+ cells. All cell sorting was undertaken on FACSAria Fusion flow cytometry instruments (BD). To induce either shRNA expression, cells were treated with 2μg/ml doxycycline (Dox) for 7 days and knockdown or overexpression were confirmed by RT-qPCR or western blot analysis.

value: lung large cell carcinoma

value: shREN stable


title: 6605394e0c05ec82;PLACEBO

description: Library name: 6605394e0c05ec82


title: 67e14b21ec434fcb;MVA-NP+M1

description: Library name: 67e14b21ec434fcb


title: shR-DOX-K27-R3

description:
Library name: shR-DOX-K27-R3
shREN inducible


title: 6577aeda995deec4;PLACEBO

description: Library name: 6577aeda995deec4


title: shR-DOX-K119ub-R1

description:
Library name: shR-DOX-K119ub-R1
shREN inducible


title: shR-DOX-K27-R1

description:
Library name: shR-DOX-K27-R1
shREN inducible


title: 65275ad08707879f;MVA-NP+M1

description: Library name: 65275ad08707879f


title: shR-DOX-INP-R2

description:
Library name: shR-DOX-INP-R2
shREN inducible


title: 651797fc134b0f58;PLACEBO

description: Library name: 651797fc134b0f58


title: H1299-DOVE-DOX-H3K27me3-R1

description:
Library name: H1299-DOVE-DOX-H3K27me3-R1
DPPA2 and DPPA4 stable inducible


title: 648c95d9edcd93da;PLACEBO

description: Library name: 648c95d9edcd93da


title: 64b582e131c39c9e;MVA-NP+M1

description: Library name: 64b582e131c39c9e


title: shR-CTRL-K4-R2

description:
Library name: shR-CTRL-K4-R2
shREN inducible

value: 7 days H20


title: 63c0dc2eee730a0c;MVA-NP+M1

description: Library name: 63c0dc2eee730a0c


title: shR-CTRL-K119ub-R3

description:
Library name: shR-CTRL-K119ub-R3
shREN inducible


title: 640a04829235a5df;MVA-NP+M1

description: Library name: 640a04829235a5df


title: 63dc11767a3286de;MVA-NP+M1

description: Library name: 63dc11767a3286de


title: shR-CTRL-K27-R3

description:
Library name: shR-CTRL-K27-R3
shREN inducible


title: shR-CTRL-K4-R1

description:
Library name: shR-CTRL-K4-R1
shREN inducible


title: shR-CTRL-K27-R1

description:
Library name: shR-CTRL-K27-R1
shREN inducible


title: shR-DOX-K4-R2

description:
Library name: shR-DOX-K4-R2
shREN inducible


title: 633bc4c36a04037c;MVA-NP+M1

description: Library name: 633bc4c36a04037c


title: shR-CTRL-INP-R2

description:
Library name: shR-CTRL-INP-R2
shREN inducible


title: shR-CTRL-K119ub-R1

description:
Library name: shR-CTRL-K119ub-R1
shREN inducible


title: shR-DOX-K119ub-R3

description:
Library name: shR-DOX-K119ub-R3
shREN inducible


title: 62d031f166b1d5d1;MVA-NP+M1

description: Library name: 62d031f166b1d5d1


title: 627d17f2db639de8;MVA-NP+M1

description: Library name: 627d17f2db639de8


title: shDKD-DOX-K4-R2

description:
Library name: shDKD-DOX-K4-R2
double shDPPA2 and shDPPA4 inducible

value: shDPPA2 and shDPPA4 stable


title: 622cfeff0733ee40;MVA-NP+M1

description: Library name: 622cfeff0733ee40


title: shDKD-DOX-K27-R3

description:
Library name: shDKD-DOX-K27-R3
double shDPPA2 and shDPPA4 inducible


title: shDKD-DOX-K4-R1

description:
Library name: shDKD-DOX-K4-R1
double shDPPA2 and shDPPA4 inducible


title: 60ed9d4ef98e23a1;PLACEBO

description: Library name: 60ed9d4ef98e23a1


title: shDKD-DOX-K119ub-R1

description:
Library name: shDKD-DOX-K119ub-R1
double shDPPA2 and shDPPA4 inducible


title: 6075ddb81f27c669;PLACEBO

description: Library name: 6075ddb81f27c669


title: 622ad6ec2f10f9cd;MVA-NP+M1

description: Library name: 622ad6ec2f10f9cd


title: 620f14805d555acb;PLACEBO

description: Library name: 620f14805d555acb


title: shDKD-DOX-INP-R2

description:
Library name: shDKD-DOX-INP-R2
double shDPPA2 and shDPPA4 inducible


title: shDKD-CTRL-K4-R2

description:
Library name: shDKD-CTRL-K4-R2
double shDPPA2 and shDPPA4 inducible


title: shDKD-DOX-K27-R1

description:
Library name: shDKD-DOX-K27-R1
double shDPPA2 and shDPPA4 inducible


title: 60068a656930937b;PLACEBO

description: Library name: 60068a656930937b


title: 6059806c2a24c606;MVA-NP+M1

description: Library name: 6059806c2a24c606


title: shDKD-CTRL-K27-R3

description:
Library name: shDKD-CTRL-K27-R3
double shDPPA2 and shDPPA4 inducible


title: shDKD-CTRL-K4-R1

description:
Library name: shDKD-CTRL-K4-R1
double shDPPA2 and shDPPA4 inducible


title: 5fe2ef5c040233db;MVA-NP+M1

description: Library name: 5fe2ef5c040233db


title: 5feb6c7495b9791c;PLACEBO

description: Library name: 5feb6c7495b9791c


title: shDKD-CTRL-K119ub-R3

description:
Library name: shDKD-CTRL-K119ub-R3
double shDPPA2 and shDPPA4 inducible


title: 6275250419e3d5e2;PLACEBO

description: Library name: 6275250419e3d5e2


title: 5fd34a0db1184fab;MVA-NP+M1

description: Library name: 5fd34a0db1184fab


title: shDKD-CTRL-K119ub-R1

description:
Library name: shDKD-CTRL-K119ub-R1
double shDPPA2 and shDPPA4 inducible


title: shD4-DOX-K4-R1

description:
Library name: shD4-DOX-K4-R1
shDPPA4 inducible

value: shDPPA4 stable


title: 5fa2602b74c98454;PLACEBO

description: Library name: 5fa2602b74c98454


title: 5e0a09162099c877;PLACEBO

description: Library name: 5e0a09162099c877


title: shDKD-CTRL-K27-R1

description:
Library name: shDKD-CTRL-K27-R1
double shDPPA2 and shDPPA4 inducible


title: shD4-DOX-K4-R2

description:
Library name: shD4-DOX-K4-R2
shDPPA4 inducible


title: 5e0036991105eddb;MVA-NP+M1

description: Library name: 5e0036991105eddb


title: shDKD-DOX-K119ub-R3

description:
Library name: shDKD-DOX-K119ub-R3
double shDPPA2 and shDPPA4 inducible


title: 5d568f7137b3e4d2;MVA-NP+M1

description: Library name: 5d568f7137b3e4d2


title: shD4-DOX-K27-R3

description:
Library name: shD4-DOX-K27-R3
shDPPA4 inducible


title: 5cdec7df397bf313;MVA-NP+M1

description: Library name: 5cdec7df397bf313


title: shD4-DOX-K27-R1

description:
Library name: shD4-DOX-K27-R1
shDPPA4 inducible


title: shD4-DOX-K119ub-R3

description:
Library name: shD4-DOX-K119ub-R3
shDPPA4 inducible


title: 5c619ba8b637419e;MVA-NP+M1

description: Library name: 5c619ba8b637419e


title: shDKD-CTRL-INP-R2

description:
Library name: shDKD-CTRL-INP-R2
double shDPPA2 and shDPPA4 inducible


title: 5ba3100b8b7f44b8;MVA-NP+M1

description: Library name: 5ba3100b8b7f44b8


title: shD4-DOX-K119ub-R1

description:
Library name: shD4-DOX-K119ub-R1
shDPPA4 inducible


title: 5b95d0d913ad06cf;MVA-NP+M1

description: Library name: 5b95d0d913ad06cf


title: shD4-DOX-INP-R2

description:
Library name: shD4-DOX-INP-R2
shDPPA4 inducible


title: 5b22ef0b05e149fa;PLACEBO

description: Library name: 5b22ef0b05e149fa


title: 590a00687087d970;MVA-NP+M1

description: Library name: 590a00687087d970


title: 5f9f9e5ff94eaae7;MVA-NP+M1

description: Library name: 5f9f9e5ff94eaae7


title: 58f0b7d50173d993;MVA-NP+M1

description: Library name: 58f0b7d50173d993


title: 58f8019104736c2e;MVA-NP+M1

description: Library name: 58f8019104736c2e


title: shD4-CTRL-K119ub-R3

description:
Library name: shD4-CTRL-K119ub-R3
shDPPA4 inducible


title: shD4-CTRL-K27-R1

description:
Library name: shD4-CTRL-K27-R1
shDPPA4 inducible


title: 57e2b0d938795aae;MVA-NP+M1

description: Library name: 57e2b0d938795aae


title: shD4-CTRL-K4-R1

description:
Library name: shD4-CTRL-K4-R1
shDPPA4 inducible


title: shD4-CTRL-INP-R2

description:
Library name: shD4-CTRL-INP-R2
shDPPA4 inducible


title: shD4-CTRL-K27-R3

description:
Library name: shD4-CTRL-K27-R3
shDPPA4 inducible


title: 581e04165fef7ff2;MVA-NP+M1

description: Library name: 581e04165fef7ff2


title: shD4-CTRL-K119ub-R1

description:
Library name: shD4-CTRL-K119ub-R1
shDPPA4 inducible


title: 57a48e39c1d09ada;MVA-NP+M1

description: Library name: 57a48e39c1d09ada


title: 567cd524b00b7386;MVA-NP+M1

description: Library name: 567cd524b00b7386


title: shD2-DOX-K119ub-R3

description:
Library name: shD2-DOX-K119ub-R3
shDPPA2 inducible

value: shDPPA2 stable


title: shD2-DOX-K4-R2

description:
Library name: shD2-DOX-K4-R2
shDPPA2 inducible


title: 56750bd27866d800;PLACEBO

description: Library name: 56750bd27866d800


title: 577a64c7beac93c9;MVA-NP+M1

description: Library name: 577a64c7beac93c9


title: 5568362ad2aac422;PLACEBO

description: Library name: 5568362ad2aac422


title: 55a5cbcfe6439517;PLACEBO

description: Library name: 55a5cbcfe6439517


title: shD2-DOX-K27-R3

description:
Library name: shD2-DOX-K27-R3
shDPPA2 inducible


title: 5707aa9ca6993495;MVA-NP+M1

description: Library name: 5707aa9ca6993495


title: shD2-DOX-INP-R2

description:
Library name: shD2-DOX-INP-R2
shDPPA2 inducible


title: shD2-DOX-K27-R1

description:
Library name: shD2-DOX-K27-R1
shDPPA2 inducible


title: shD4-CTRL-K4-R2

description:
Library name: shD4-CTRL-K4-R2
shDPPA4 inducible


title: shD2-CTRL-K4-R2

description:
Library name: shD2-CTRL-K4-R2
shDPPA2 inducible


title: shD2-DOX-K4-R1

description:
Library name: shD2-DOX-K4-R1
shDPPA2 inducible


title: shD2-DOX-K119ub-R1

description:
Library name: shD2-DOX-K119ub-R1
shDPPA2 inducible


title: 5558686afcefec0e;MVA-NP+M1

description: Library name: 5558686afcefec0e


title: 54c789eb26be5dc8;PLACEBO

description: Library name: 54c789eb26be5dc8


title: 54f1208538b11665;PLACEBO

description: Library name: 54f1208538b11665


title: 554f216aa19ab07f;PLACEBO

description: Library name: 554f216aa19ab07f


title: shD2-CTRL-K119ub-R3

description:
Library name: shD2-CTRL-K119ub-R3
shDPPA2 inducible


title: shD2-CTRL-K4-R1

description:
Library name: shD2-CTRL-K4-R1
shDPPA2 inducible


title: shD2-CTRL-K27-R3

description:
Library name: shD2-CTRL-K27-R3
shDPPA2 inducible


title: 54263479bc6ab84b;PLACEBO

description: Library name: 54263479bc6ab84b


title: 53ff79f92cd5186a;PLACEBO

description: Library name: 53ff79f92cd5186a


title: shD2-CTRL-K27-R1

description:
Library name: shD2-CTRL-K27-R1
shDPPA2 inducible


title: shD2-CTRL-INP-R2

description:
Library name: shD2-CTRL-INP-R2
shDPPA2 inducible


title: 5347027177b83956;PLACEBO

description: Library name: 5347027177b83956


title: 52a3a5cfcece62e1;MVA-NP+M1

description: Library name: 52a3a5cfcece62e1


title: shD2-CTRL-K119ub-R1

description:
Library name: shD2-CTRL-K119ub-R1
shDPPA2 inducible


title: DMSO-K27ME3-R3

description:
Library name: DMSO-K27ME3-R3
parental H661

value: Parental

value: 1 day DMSO


title: DMSO-K27ME3-R4

description:
Library name: DMSO-K27ME3-R4
parental H661


title: DMSO-K27AC-R4

description:
Library name: DMSO-K27AC-R4
parental H661

value: abcam #ab4729


title: 528c2c01b58c1f4c;MVA-NP+M1

description: Library name: 528c2c01b58c1f4c


title: DMSO-K27ME3-R2

description:
Library name: DMSO-K27ME3-R2
parental H661

value: lung cancer


title: DMSO-K27AC-R2

description:
Library name: DMSO-K27AC-R2
parental H661


title: 538e231b5fa9b15a;MVA-NP+M1

description: Library name: 538e231b5fa9b15a


title: DMSO-INP-R1

description:
Library name: DMSO-INP-R1
parental H661


title: DMSO-SUZ12-R3

description:
Library name: DMSO-SUZ12-R3
parental H661


title: 527f232df65f45d0;PLACEBO

description: Library name: 527f232df65f45d0


title: 508e09293f799363;MVA-NP+M1

description: Library name: 508e09293f799363


title: 51f8e860bac3a6b2;PLACEBO

description: Library name: 51f8e860bac3a6b2


title: 51301d56d55bc4e9;PLACEBO

description: Library name: 51301d56d55bc4e9


title: A485-K27AC-R4

description:
Library name: A485-K27AC-R4
parental H661


title: A485-K119UB-R4

description:
Library name: A485-K119UB-R4
parental H661


title: 521db310eb89669a;MVA-NP+M1

description: Library name: 521db310eb89669a


title: A485-K27ME3-R4

description:
Library name: A485-K27ME3-R4
parental H661


title: 5088cf9caaab71a5;PLACEBO

description: Library name: 5088cf9caaab71a5


title: DMSO-K119UB-R4

description:
Library name: DMSO-K119UB-R4
parental H661


title: 511d3c2b8f49e244;PLACEBO

description: Library name: 511d3c2b8f49e244


title: 53d33f8a342d8ed6;MVA-NP+M1

description: Library name: 53d33f8a342d8ed6


title: DMSO-K119UB-R3

description:
Library name: DMSO-K119UB-R3
parental H661


title: 4d38f510f5910561;MVA-NP+M1

description: Library name: 4d38f510f5910561


title: A485-K27ME3-R3

description:
Library name: A485-K27ME3-R3
parental H661


title: H661-shDKD-DOX-RING1B-Rb-1

description:
Library name: H661-shDKD-DOX-RING1B-Rb-1
double shDPPA2 and shDPPA4 inducible

data_processing:
Paired-end reads in fastqs were trimmed and filtered for quality (phred33 score > 20) and length (>20bp) using TrimGalore (https://github.com/FelixKrueger/TrimGalore) v0.6.6 in paired-end mode (valid read pairs were only kept).
Trimmed and quality filtered reads were then aligned to the hg38 human genome GRCh38.p13 using bwa-mem (bwa v0.7.13) with default parameters. Alignments were then converted to the bam format and indexed using samtools v1.9. Duplicate alignments were marked with using MarkDuplicates (picard v2.6.0, https://broadinstitute.github.io/picard/) and re-indexed with samtools. bigWig files containing CPM/bp normalised coverage values for each sample were derived from duplicate marked bam files using bamCoverage (DeepTools v3.5.0) where reads were not extended (relying instead on the true fragment length determined by read-pairs).
The resultant BAM files were then input to EPIC2 (v0.0.52) (--bin-size 100 –gaps-allowed 1 –fragment-size 147 -- false-discovery-rate-cutoff 0.05) using species matched isotype controls (IgG) as the control. BAM files were also input to MACS2 (v2.27.1) for peak calling in paired-end mode with an FDR threshold of <0.05 (-f BAMPE -q 0.05) again using species matched isotype controls (IgG) as the control.
Assembly: GRCh38.p13
Supplementary files format and content: Bigwig files output by deepTools summarising read density across the genome with values as CPM/bp.
Supplementary files format and content: Peak files produced by MACS2.
Supplementary files format and content: Peak files produced by EPIC2.
Library strategy: CUT&Run

growth_protocol: Non-small cell lung cancer cell lines NCI-H661 and NCI-H1299 were cultured in RPMI-1640 (Gibco) growth medium and supplemented with 10% heat-inactivated fetal bovine serum (FBS) and 1x penicillin/streptomycin at 37℃, 5% CO2. Cells were routinely passaged to maintain exponential growth, using Trypsin-Low EDTA (LE) Express (Gibco) to detach cells each time. Cells were regularly tested for mycoplasma contamination using the Mycoplasma PCR Detection Kit (abcam, #ab289834). These cell lines was also STR profiled to ensure authenticity. NCI-H661 and NCI-H1299 were purchased from ATCC.

extract_protocol:
NCI-H661 or NCI-H1299 cells were harvested and counted after staining cells with 0.4% Trypan blue where 500,000 live cells were used per CUT&Run. Cells were washed with ice cold cell wash buffer (150mM NaCl, 20mM HEPES in H2O) and kept on ice. 11uL Concanavalin A beads (Epicypher) were washed twice with 100uL cold bead activation buffer (20mM HEPES, 50uL KCl, 1mM CaCl2, 1mM MnCl2 in H2O) and then resuspended in 11uL of the same buffer on ice. Cells were washed twice with NE buffer (20mM HEPES, 10mM KCl, 0.1% Triton X, 20% glycerol in H2O) to release nuclei with gentle pipetting and 300xg spins at 4C in between for 5 mins each. Nuclei were resuspended in 100uL of cold cell wash buffer and then incubated with 10uL of washed beads to allow for nuclei-bead adsorption for 10 mins at room temperature. Beads were then resuspended in 50uL of cold antibody buffer (20mM HEPES, 150mM NaCl, 0.5mM Spermidine, 0.05% digitonin, 2mM EDTA in H2O) followed by the addition of 1ug of IgG controls (Mouse IgG (Invitrogen, #31903), Rabbit IgG (Invitrogen, #012-6102)) or antibodies (DPPA2 (Sigma, #MAB4356), DPPA4 (abcepta, #AP1438a, abcepta, #AP21202c, abcam, #ab154642), V5-tag (Invitrogen #46-0705), Flag-tag (Merck #F1084 (monoclonal), Invitrogen #740001 (superclonal), RING1B (CST #5694), PCGF1 (Santa Cruz Biotechnology #sc515371), MTF2 (Proteintech #16208-1-AP), EP300 (Aviva Systems Biology (#OAAF01891), SOX2 (abcam #97959)) (or 0.5ug for the H3K4me3 (CST, #9751) positive control) and incubation overnight at 4C on a nutator. Bead complexes were then washed twice with 200uL cold antibody buffer (same as above, but without EDTA) and then resuspended in 50uL of the same buffer. 1.5uL of Protein-A/G-MNase (CST) was added to each bead suspension, pipette mixed and incubated at room temperature for 10 mins. Beads were washed two times with cold 250uL of antibody buffer and resuspended in 50uL of the same buffer. 1uL of 100mM CaCl2 was added to each bead suspension to activate the bound MNase followed by incubation at 4C for 1hr on a thermalcycler to facilitate chromatin digestion. 38uL of stop buffer (340mM NaCl, 20mM EDTA, 4mM EGTA, 50ug/mL RNase A, 50ug/mL glycogen in H2O) containing 250pg of E.coli normalisation spike-in DNA (CST) was added to each suspension to inhibit MNase, degrade RNA and release digested chromatin into the supernatant by incubation at 37C for 10 mins in a thermalcycler. The supernatant containing digested chromatin was transferred to a new tube and treated with 1uL 20mg/mL proteinase K for 1hr at 37C. DNA was purified using a 1.8X bead cleanup (SergiLabs) and eluted in 30uL of H20 for DNA library preparation.
CUT&Run libraries were prepared using the NEBNext UltraII DNA Library Preparation Kit (NEB) according to the manufacturer’s instruction. During library preparation the NEBNext Multiplex Oligos for Illumina (Index Primers Set 1-4) were used to enable library multiplexing. Individual and pooled libraries were quantified and quality controlled using the dsDNA high sensitivity (HS) Qubit assay (Invitrogen) on the Qubit 3.0 fluorometer (Invitrogen) and HSD1000 High Sensitivity DNA kit (Agilent) on the TapeStation 4150 (Agilent). Libraries were pooled and sequenced on the Illumina NextSeq2000 platform in a paired-end configurations with 100bp read lengths.

treatment_protocol: For inducible knockdown experiments, miR30 based shRNAs were expressed using a tetracycline-inducible PiggyBac transposon system (pCLIIPi-iRFP-shRNA-pGK-mVenus), as previously described (Eckersley-Maslin et al. 2020). Established shRNA sequences against either; Renilla luciferase (non-targeting control) (#713), human DPPA2 (#760) or DPPA4 (#1993) were cloned by first annealing complementary oligo’s and ligating them into a digested pMSCV-miR30 backbone, followed by PCR, digestion and ligation into the pCLIIPi backbone. Stable cell lines were generated by transfecting NCI-H661 cells with the shRNA vectors along with PiggyBac transposase (pRM1024), waiting for 2 weeks, then sorting mVenus positive cells twice with expansion in between, collecting the top 50% of mVenus positive cells each time as a bulk population for further experiments. The mVenus DPPA4 shRNA construct underwent additional cloning to replace mVenus with tagBFP to allow for selection of cells containing both DPPA2 and DPPA4 inducible shRNA. To generate the double inducible knockdown line, stable shDPPA2 (mVenus+) cells were transfected with the shDPPA4 (tagBFP) vector and selected as above for both mVenus+/tagBFP+ cells. For inducible overexpression experiments the above vector backbones were cloned to replace the (iRFP-shRNA) fragment downstream of the tet-response element (TRE) with cDNA encoding human DPPA2 (ORF:NM_138815) or DPPA4 (ORF:NM_018189) with additional N-terminal Flag or V5 tags respectively (gene fragments synthesised by IDT). Stable cell lines were generated in the same way as above for shRNA lines for the NCI-H1299 cell line (which does not express DPPA2/4). All cell sorting was undertaken on FACSAria Fusion flow cytometry instruments (BD). To induce either shRNA or cDNA expression, cells were treated with 2μg/ml doxycycline (Dox) for 7 days and knockdown or overexpression were confirmed by RT-qPCR or western blot analysis.


title: H661-shDKD-DOX-DPPA4n-Rb-1

description:
Library name: H661-shDKD-DOX-DPPA4n-Rb-1
double shDPPA2 and shDPPA4 inducible

value: DPPA4n (N-terminal)

value: abcepta #AP1438a


title: 50d9a6c2c54f485d;MVA-NP+M1

description: Library name: 50d9a6c2c54f485d


title: H661-shDKD-CTRL-RING1B-Rb-1

description:
Library name: H661-shDKD-CTRL-RING1B-Rb-1
double shDPPA2 and shDPPA4 inducible


title: A485-K119UB-R3

description:
Library name: A485-K119UB-R3
parental H661


title: 506d07dd05a5699d;MVA-NP+M1

description: Library name: 506d07dd05a5699d


title: A485-K27ME3-R2

description:
Library name: A485-K27ME3-R2
parental H661


title: H661-shDKD-CTRL-MTF2-Rb-1

description:
Library name: H661-shDKD-CTRL-MTF2-Rb-1
double shDPPA2 and shDPPA4 inducible

value: Proteintech #16208-1-AP


title: H661-shDKD-CTRL-IgG-Ms-1

description:
Library name: H661-shDKD-CTRL-IgG-Ms-1
double shDPPA2 and shDPPA4 inducible

value: IgG (mouse)

value: Invitrogen #31903


title: 4a9a115c207107c2;PLACEBO

description: Library name: 4a9a115c207107c2

value: Whole Blood


title: 4f9a19eaeb88225b;MVA-NP+M1

description: Library name: 4f9a19eaeb88225b


title: 4fc7ee5c14229275;MVA-NP+M1

description: Library name: 4fc7ee5c14229275


title: A485-K27AC-R2

description:
Library name: A485-K27AC-R2
parental H661


title: 4d3289c71a545779;MVA-NP+M1

description: Library name: 4d3289c71a545779


title: 4ec457616138f8d8;PLACEBO

description: Library name: 4ec457616138f8d8

value: PLACEBO


title: 4e5c6c0d88ff8c47;MVA-NP+M1

description: Library name: 4e5c6c0d88ff8c47


title: 4927219d3cb6b324;MVA-NP+M1

description: Library name: 4927219d3cb6b324


title: H661-shD4-DOX-DPPA4n-Rb-1

description:
Library name: H661-shD4-DOX-DPPA4n-Rb-1
shDPPA4 inducible

value: lung large cell carcinoma

value: 7 days doxycyline 2ug/mL


title: A485-INP-R1

description:
Library name: A485-INP-R1
parental H661

value: none (genomic input)


title: 4a461ce13807fc1b;MVA-NP+M1

description: Library name: 4a461ce13807fc1b


title: 4e185c2fc123ec66;MVA-NP+M1

description: Library name: 4e185c2fc123ec66


title: 4cb70b6ddda4f2bf;PLACEBO

description: Library name: 4cb70b6ddda4f2bf


title: H661-shDKD-CTRL-IgG-Rb-1

description:
Library name: H661-shDKD-CTRL-IgG-Rb-1
double shDPPA2 and shDPPA4 inducible

value: shDPPA2 and shDPPA4 stable

value: 7 days H20

value: IgG (rabbit)

value: Invitrogen #012-6102


title: H661-shD4-CTRL-MTF2-Rb-1

description:
Library name: H661-shD4-CTRL-MTF2-Rb-1
shDPPA4 inducible

value: shDPPA4 stable


title: 4bd9a273e7e89b39;MVA-NP+M1

description: Library name: 4bd9a273e7e89b39


title: H661-shD4-CTRL-IgG-Rb-1

description:
Library name: H661-shD4-CTRL-IgG-Rb-1
shDPPA4 inducible


title: H661-shDKD-CTRL-PCGF1-Ms-1

description:
Library name: H661-shDKD-CTRL-PCGF1-Ms-1
double shDPPA2 and shDPPA4 inducible

value: Santa Cruz Biotechnology #sc515371


title: 4a3c4b075404e601;PLACEBO

description: Library name: 4a3c4b075404e601


title: 462e2c115964bcb3;MVA-NP+M1

description: Library name: 462e2c115964bcb3


title: 46086f5ed59436fa;MVA-NP+M1

description: Library name: 46086f5ed59436fa


title: H661-shDKD-CTRL-DPPA4n-Rb-1

description:
Library name: H661-shDKD-CTRL-DPPA4n-Rb-1
double shDPPA2 and shDPPA4 inducible

value: lung cancer


title: H661-Asynch-Rb-IgG-1

description:
Library name: H661-Asynch-Rb-IgG-1
parental H661

value: Parental


title: 4ce20291de2c1eaa;PLACEBO

description: Library name: 4ce20291de2c1eaa


title: 44f0a4e857839541;MVA-NP+M1

description: Library name: 44f0a4e857839541


title: 489c75f532af9d68;MVA-NP+M1

description: Library name: 489c75f532af9d68


title: 45374d952bfc7f06;MVA-NP+M1

description: Library name: 45374d952bfc7f06


title: 445a11c25df00b08;MVA-NP+M1

description: Library name: 445a11c25df00b08


title: 481ed8f69f680d8e;MVA-NP+M1

description: Library name: 481ed8f69f680d8e


title: H661-shD4-CTRL-PCGF1-Ms-1

description:
Library name: H661-shD4-CTRL-PCGF1-Ms-1
shDPPA4 inducible


title: 484b2670c11217ba;MVA-NP+M1

description: Library name: 484b2670c11217ba


title: 485c51524a632484;MVA-NP+M1

description: Library name: 485c51524a632484


title: 4709c3d966a1794e;MVA-NP+M1

description: Library name: 4709c3d966a1794e


title: H661-shD4-DOX-RING1B-Rb-1

description:
Library name: H661-shD4-DOX-RING1B-Rb-1
shDPPA4 inducible


title: H661-shD4-CTRL-IgG-Ms-1

description:
Library name: H661-shD4-CTRL-IgG-Ms-1
shDPPA4 inducible


title: H661-Asynch-Rb-DPPA4-1

description:
Library name: H661-Asynch-Rb-DPPA4-1
parental H661

value: abcam #ab154642


title: H661-shDKD-CTRL-EP300-Rb-1

description:
Library name: H661-shDKD-CTRL-EP300-Rb-1
double shDPPA2 and shDPPA4 inducible

value: Aviva Systems Biology (#OAAF01891)


title: H661-shD4-CTRL-RING1B-Rb-1

description:
Library name: H661-shD4-CTRL-RING1B-Rb-1
shDPPA4 inducible


title: H661-Asynch-Rb-Sox2-1

description:
Library name: H661-Asynch-Rb-Sox2-1
parental H661


title: 4351264802abb4e6;PLACEBO

description: Library name: 4351264802abb4e6


title: H661-Asynch-Rb-DPPA4N-1

description:
Library name: H661-Asynch-Rb-DPPA4N-1
parental H661

value: DPPA4n (N-terminal)

value: abcepta #AP1438a


title: 46c9308d45c2860a;MVA-NP+M1

description: Library name: 46c9308d45c2860a

value: Whole Blood


title: H661-shD4-CTRL-EP300-Rb-1

description:
Library name: H661-shD4-CTRL-EP300-Rb-1
shDPPA4 inducible

value: Aviva Systems Biology #OAAF01891


title: H661-Asynch-Ms-DPPA2-1

description:
Library name: H661-Asynch-Ms-DPPA2-1
parental H661

value: lung large cell carcinoma

value: Sigma #MAB4356


title: 42f93f1b71e3afea;PLACEBO

description: Library name: 42f93f1b71e3afea

value: PLACEBO


title: 43e332769fd0a4df;MVA-NP+M1

description: Library name: 43e332769fd0a4df


title: H661-Asynch-Rb-H3K4me3-1

description:
Library name: H661-Asynch-Rb-H3K4me3-1
parental H661


title: H1299-DOX-V5-Ms-2

description:
Library name: H1299-DOX-V5-Ms-2
double inducible Flag-DPPA2 and V5-DPPA4 expression

value: lung adenocarcinoma

value: DPPA2 and DPPA4 stable

value: 7 days doxycyline 2ug/mL

value: Invitrogen #46-0705


title: 46031083b0014c25;MVA-NP+M1

description: Library name: 46031083b0014c25


title: H661-shD4-CTRL-DPPA4n-Rb-1

description:
Library name: H661-shD4-CTRL-DPPA4n-Rb-1
shDPPA4 inducible

value: shDPPA4 stable

value: 7 days H20


title: 4135a267861a1385;MVA-NP+M1

description: Library name: 4135a267861a1385


title: 433715e58746f070;MVA-NP+M1

description: Library name: 433715e58746f070


title: H661-Asynch-Rb-DPPA4C-1

description:
Library name: H661-Asynch-Rb-DPPA4C-1
parental H661

value: lung cancer

value: DPPA4c (Centre)

value: abcepta #AP21202c


title: 413a1eae476693d0;PLACEBO

description: Library name: 413a1eae476693d0


title: 413316170dff7b1d;MVA-NP+M1

description: Library name: 413316170dff7b1d


title: H1299-DOX-Flagmono-Ms-1

description:
Library name: H1299-DOX-Flagmono-Ms-1
double inducible Flag-DPPA2 and V5-DPPA4 expression

value: Flag (monoclonal)

value: Merck #F1084


title: H1299-DOX-Flagsuper-Rb-1

description:
Library name: H1299-DOX-Flagsuper-Rb-1
double inducible Flag-DPPA2 and V5-DPPA4 expression

value: Flag (superclonal)

value: Invitrogen #740001


title: 42da049421a36a94;MVA-NP+M1

description: Library name: 42da049421a36a94

value: Whole Blood


title: H661-Asynch-Ms-IgG-1

description:
Library name: H661-Asynch-Ms-IgG-1
parental H661

value: lung large cell carcinoma

value: Parental

value: IgG (mouse)

value: Invitrogen #31903


title: H1299-DOX-IgG-Rb-1

description:
Library name: H1299-DOX-IgG-Rb-1
double inducible Flag-DPPA2 and V5-DPPA4 expression

value: lung adenocarcinoma

value: DPPA2 and DPPA4 stable

value: IgG (rabbit)

value: Invitrogen #012-6102


title: 40d3d9c2b19e7990;PLACEBO

description: Library name: 40d3d9c2b19e7990

value: PLACEBO


title: 42d87ea6f5f348c8;PLACEBO

description: Library name: 42d87ea6f5f348c8


title: H1299-DOX-V5-Ms-1

description:
Library name: H1299-DOX-V5-Ms-1
double inducible Flag-DPPA2 and V5-DPPA4 expression

value: lung cancer

value: 7 days doxycyline 2ug/mL

value: Invitrogen #46-0705


title: 41839c3b81b367bd;PLACEBO

description: Library name: 41839c3b81b367bd


title: H1299-DOX-IgG-Ms-1

description:
Library name: H1299-DOX-IgG-Ms-1
double inducible Flag-DPPA2 and V5-DPPA4 expression


title: STB2-s96_S48_all_lanes_L001_control_minus3

city: Kilifi

first: Abdirahman

last: Abdi

state: Not US or Canada

address: Mombasa-Malindi Road

department: Bioscience

country: Kenya

institute: KEMRI-Wellcome Trust Research Programme

description:
Library name: STB2-s96_S48_all_lanes_L001
Plasma derived extracellular vesicle RNA

data_processing:
RNAseq reads were quantified using Salmon
EdgeR was used to normalize read counts for sequencing depth and gene length
Assembly: Homo Sapiens GRch38.104
Supplementary files format and content: supplementary file containing data in the units of counts per million (CPM)

source_name: Plasma

extract_protocol:
RNA was extracted using Isolate II RNA kit (Bioline) following Manufacturer’s instructions
Library preparation was performed using NEBNext Ultra II FS DNA Library Prep Kit following manufacturer’s instructions

value: Plasma


title: 3f476f7f6d9ee0fb;MVA-NP+M1

description: Library name: 3f476f7f6d9ee0fb


title: H1299-DOX-Flagmono-Ms-2

description:
Library name: H1299-DOX-Flagmono-Ms-2
double inducible Flag-DPPA2 and V5-DPPA4 expression

value: Flag (monoclonal)

value: Merck #F1084


title: 4167f80ae5470654;PLACEBO

description: Library name: 4167f80ae5470654


title: STB2-s94_S46_all_lanes_L001_case_minus3

description:
Library name: STB2-s94_S46_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: STB2-s93_S45_all_lanes_L001_control_minus3

description:
Library name: STB2-s93_S45_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: 4004e4e827e9acb8;PLACEBO

description: Library name: 4004e4e827e9acb8


title: 3d4234dbec2f3dbb;MVA-NP+M1

description: Library name: 3d4234dbec2f3dbb


title: 3f83d41b3919dd48;PLACEBO

description: Library name: 3f83d41b3919dd48


title: H1299-DOX-DPPA4-Rb-2

description:
Library name: H1299-DOX-DPPA4-Rb-2
double inducible Flag-DPPA2 and V5-DPPA4 expression

value: abcam #ab154642


title: STB2-s92_S44_all_lanes_L001_control_minus3

description:
Library name: STB2-s92_S44_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: 3f4cef323ccf514d;MVA-NP+M1

description: Library name: 3f4cef323ccf514d

value: Whole Blood


title: 3c34f0493df568b7;MVA-NP+M1

description: Library name: 3c34f0493df568b7


title: STB2-s95_S47_all_lanes_L001_control_minus3

description:
Library name: STB2-s95_S47_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: 3d282cc11f9b00c4;MVA-NP+M1

description: Library name: 3d282cc11f9b00c4


title: 3c06c775146ebb07;PLACEBO

description: Library name: 3c06c775146ebb07


title: 3e7c7b37ca7580b5;PLACEBO

description: Library name: 3e7c7b37ca7580b5


title: 3e330b36ca95de6f;MVA-NP+M1

description: Library name: 3e330b36ca95de6f


title: STB2-s91_S43_all_lanes_L001_case_minus3

description:
Library name: STB2-s91_S43_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: 3b4d3c17e8f1f6f1;PLACEBO

description: Library name: 3b4d3c17e8f1f6f1


title: 3bf44f4146d5bbfb;PLACEBO

description: Library name: 3bf44f4146d5bbfb


title: STB2-s89_S41_all_lanes_L001_control_minus3

description:
Library name: STB2-s89_S41_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: STB2-s90_S42_all_lanes_L001_control_minus3

description:
Library name: STB2-s90_S42_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: 3c252885468c21f0;MVA-NP+M1

description: Library name: 3c252885468c21f0


title: STB2-s87_S39_all_lanes_L001_control_minus3

description:
Library name: STB2-s87_S39_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: 3a8bbdc4748493fa;PLACEBO

description: Library name: 3a8bbdc4748493fa


title: 397ef27a9522ced5;PLACEBO

description: Library name: 397ef27a9522ced5


title: STB2-s86_S38_all_lanes_L001_control_minus3

description:
Library name: STB2-s86_S38_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: 39060ae20834684b;PLACEBO

description: Library name: 39060ae20834684b


title: 3b34ebc7a7cd2d2f;MVA-NP+M1

description: Library name: 3b34ebc7a7cd2d2f


title: STB2-s80_S32_all_lanes_L001_control_minus3

description:
Library name: STB2-s80_S32_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: STB2-s83_S35_all_lanes_L001_control_minus3

description:
Library name: STB2-s83_S35_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: 38013b901b4b7b2a;PLACEBO

description: Library name: 38013b901b4b7b2a


title: STB2-s79_S31_all_lanes_L001_case_minus3

description:
Library name: STB2-s79_S31_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: STB2-s84_S36_all_lanes_L001_control_minus3

description:
Library name: STB2-s84_S36_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: H1299-DOX-Flagsuper-Rb-2

description:
Library name: H1299-DOX-Flagsuper-Rb-2
double inducible Flag-DPPA2 and V5-DPPA4 expression

value: Flag (superclonal)

value: Invitrogen #740001


title: STB2-s82_S34_all_lanes_L001_case_minus3

description:
Library name: STB2-s82_S34_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: STB2-s81_S33_all_lanes_L001_control_minus3

description:
Library name: STB2-s81_S33_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: STB2-s85_S37_all_lanes_L001_case_minus3

description:
Library name: STB2-s85_S37_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: STB2-s88_S40_all_lanes_L001_case_minus3

description:
Library name: STB2-s88_S40_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: STB2-s78_S30_all_lanes_L001_control_minus3

description:
Library name: STB2-s78_S30_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: 394d434be88cce4d;PLACEBO

description: Library name: 394d434be88cce4d


title: 37df0fb38da42319;MVA-NP+M1

description: Library name: 37df0fb38da42319


title: STB2-s74_S26_all_lanes_L001_control_minus3

description:
Library name: STB2-s74_S26_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: 37f23b58770e0061;PLACEBO

description: Library name: 37f23b58770e0061


title: 36a6f0666b2da01e;PLACEBO

description: Library name: 36a6f0666b2da01e


title: 37e829811bb2b53d;MVA-NP+M1

description: Library name: 37e829811bb2b53d


title: STB2-s77_S29_all_lanes_L001_control_minus3

description:
Library name: STB2-s77_S29_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: STB2-s75_S27_all_lanes_L001_control_minus3

description:
Library name: STB2-s75_S27_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: STB2-s73_S25_all_lanes_L001_case_minus3

description:
Library name: STB2-s73_S25_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: STB2-s76_S28_all_lanes_L001_case_minus3

description:
Library name: STB2-s76_S28_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: 3606e79767226930;MVA-NP+M1

description: Library name: 3606e79767226930


title: STB2-s71_S23_all_lanes_L001_control_minus3

description:
Library name: STB2-s71_S23_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: 378090ea4b6d6f5a;PLACEBO

description: Library name: 378090ea4b6d6f5a


title: 3568890a7fadbfb1;MVA-NP+M1

description: Library name: 3568890a7fadbfb1


title: 355625e819011739;MVA-NP+M1

description: Library name: 355625e819011739


title: 369f60b632d7e19b;PLACEBO

description: Library name: 369f60b632d7e19b


title: STB2-s72_S24_all_lanes_L001_control_minus3

description:
Library name: STB2-s72_S24_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: 34efc600aef17d90;PLACEBO

description: Library name: 34efc600aef17d90


title: STB2-s67_S19_all_lanes_L001_case_minus3

description:
Library name: STB2-s67_S19_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: 3543af64b75023ac;MVA-NP+M1

description: Library name: 3543af64b75023ac


title: 3731c44d0739e58f;MVA-NP+M1

description: Library name: 3731c44d0739e58f


title: 36059071cc6dd364;PLACEBO

description: Library name: 36059071cc6dd364


title: STB2-s70_S22_all_lanes_L001_case_minus3

description:
Library name: STB2-s70_S22_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: STB2-s64_S16_all_lanes_L001_case_minus3

description:
Library name: STB2-s64_S16_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: STB2-s62_S14_all_lanes_L001_control_minus3

description:
Library name: STB2-s62_S14_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: 3584e15db691d6d8;PLACEBO

description: Library name: 3584e15db691d6d8


title: 345296be0aad8bd6;PLACEBO

description: Library name: 345296be0aad8bd6


title: 34cce57b27b0bad9;MVA-NP+M1

description: Library name: 34cce57b27b0bad9


title: STB2-s68_S20_all_lanes_L001_control_minus3

description:
Library name: STB2-s68_S20_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: 343082b871c26c62;MVA-NP+M1

description: Library name: 343082b871c26c62


title: STB2-s61_S13_all_lanes_L001_case_minus3

description:
Library name: STB2-s61_S13_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: STB2-s63_S15_all_lanes_L001_control_minus3

description:
Library name: STB2-s63_S15_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: STB2-s65_S17_all_lanes_L001_control_minus3

description:
Library name: STB2-s65_S17_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: STB2-s60_S12_all_lanes_L001_control_minus3

description:
Library name: STB2-s60_S12_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: STB2-s58_S10_all_lanes_L001_case_minus3

description:
Library name: STB2-s58_S10_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: STB2-s66_S18_all_lanes_L001_control_minus3

description:
Library name: STB2-s66_S18_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: STB2-s59_S11_all_lanes_L001_control_minus3

description:
Library name: STB2-s59_S11_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: 33c45b39ab4a4b59;PLACEBO

description: Library name: 33c45b39ab4a4b59


title: 3426c78a9d682337;PLACEBO

description: Library name: 3426c78a9d682337


title: 34d67b40f8ca71b6;PLACEBO

description: Library name: 34d67b40f8ca71b6


title: 335a599bd5462939;MVA-NP+M1

description: Library name: 335a599bd5462939


title: 343d19d63737e430;MVA-NP+M1

description: Library name: 343d19d63737e430


title: STB2-s55_S7_all_lanes_L001_case_minus3

description:
Library name: STB2-s55_S7_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: STB2-s53_S5_all_lanes_L001_control_minus3

description:
Library name: STB2-s53_S5_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: 33452e9cc1a48471;PLACEBO

description: Library name: 33452e9cc1a48471


title: STB2-s56_S8_all_lanes_L001_control_minus3

description:
Library name: STB2-s56_S8_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: 33961509711945a5;MVA-NP+M1

description: Library name: 33961509711945a5


title: 32d364d5adabfe0a;PLACEBO

description: Library name: 32d364d5adabfe0a


title: 342bf10d41153ff5;MVA-NP+M1

description: Library name: 342bf10d41153ff5


title: STB2-s54_S6_all_lanes_L001_control_minus3

description:
Library name: STB2-s54_S6_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: STB2-s51_S3_all_lanes_L001_control_minus3

description:
Library name: STB2-s51_S3_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: STB2-s57_S9_all_lanes_L001_control_minus3

description:
Library name: STB2-s57_S9_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: 32d461d428ca3337;PLACEBO

description: Library name: 32d461d428ca3337


title: STB2-s50_S2_all_lanes_L001_control_minus3

description:
Library name: STB2-s50_S2_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: 32fab72cdddd1651;MVA-NP+M1

description: Library name: 32fab72cdddd1651


title: 325bd0af7133a8c2;PLACEBO

description: Library name: 325bd0af7133a8c2


title: STB2-s49_S1_all_lanes_L001_case_minus3

description:
Library name: STB2-s49_S1_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: 321bcf5efc7e0665;MVA-NP+M1

description: Library name: 321bcf5efc7e0665


title: 31df292ea8eef1fe;MVA-NP+M1

description: Library name: 31df292ea8eef1fe


title: 32192989d75c8030;MVA-NP+M1

description: Library name: 32192989d75c8030


title: 30b500ed6f152b22;PLACEBO

description: Library name: 30b500ed6f152b22


title: STB2-NC_S49_all_lanes_L001_water_minus3

description:
Library name: STB2-NC_S49_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: STB1-s9_S9_all_lanes_L001_control_minus3

description:
Library name: STB1-s9_S9_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: STB2-NTC_S50_all_lanes_L001_water_minus3

description:
Library name: STB2-NTC_S50_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: STB1-s6_S6_all_lanes_L001_control_minus3

description:
Library name: STB1-s6_S6_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: 2fddedd44c5b85a7;MVA-NP+M1

description: Library name: 2fddedd44c5b85a7


title: STB2-s69_S21_all_lanes_L001_control_minus3

description:
Library name: STB2-s69_S21_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: 2ea6bffe4fcdb5ba;PLACEBO

description: Library name: 2ea6bffe4fcdb5ba


title: 2ea3a26abfeeeda0;MVA-NP+M1

description: Library name: 2ea3a26abfeeeda0


title: STB1-s8_S8_all_lanes_L001_control_minus3

description:
Library name: STB1-s8_S8_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: STB1-s5_S5_all_lanes_L001_control_minus3

description:
Library name: STB1-s5_S5_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: 2d8e6b40bf850464;PLACEBO

description: Library name: 2d8e6b40bf850464


title: STB2-s52_S4_all_lanes_L001_case_minus3

description:
Library name: STB2-s52_S4_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: 2c038c2292b63e65;PLACEBO

description: Library name: 2c038c2292b63e65


title: STB1-s7_S7_all_lanes_L001_case_minus3

description:
Library name: STB1-s7_S7_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: STB1-s47_S47_all_lanes_L001_control_minus3

description:
Library name: STB1-s47_S47_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: STB1-s48_S48_all_lanes_L001_control_minus3

description:
Library name: STB1-s48_S48_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: STB1-s46_S46_all_lanes_L001_case_minus3

description:
Library name: STB1-s46_S46_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: 2c0f0b6d48082846;MVA-NP+M1

description: Library name: 2c0f0b6d48082846


title: 2c921d52a30aea09;MVA-NP+M1

description: Library name: 2c921d52a30aea09


title: 2cc7a451f3ba2973;MVA-NP+M1

description: Library name: 2cc7a451f3ba2973


title: STB1-s45_S45_all_lanes_L001_control_minus3

description:
Library name: STB1-s45_S45_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: STB1-s44_S44_all_lanes_L001_control_minus3

description:
Library name: STB1-s44_S44_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: STB1-s42_S42_all_lanes_L001_control_minus3

description:
Library name: STB1-s42_S42_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: STB1-s43_S43_all_lanes_L001_case_minus3

description:
Library name: STB1-s43_S43_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: 2d59255ba1b58b55;PLACEBO

description: Library name: 2d59255ba1b58b55


title: 2bd98575ce5bee18;PLACEBO

description: Library name: 2bd98575ce5bee18


title: 2bd5d9aaa2b99568;MVA-NP+M1

description: Library name: 2bd5d9aaa2b99568


title: 2bc96f1896bdf5d7;MVA-NP+M1

description: Library name: 2bc96f1896bdf5d7


title: STB1-s40_S40_all_lanes_L001_case_minus3

description:
Library name: STB1-s40_S40_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: STB1-s4_S4_all_lanes_L001_case_minus3

description:
Library name: STB1-s4_S4_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: STB1-s41_S41_all_lanes_L001_control_minus3

description:
Library name: STB1-s41_S41_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: 2ba4a71d70f501fa;MVA-NP+M1

description: Library name: 2ba4a71d70f501fa


title: 2baf1c1f241296f8;PLACEBO

description: Library name: 2baf1c1f241296f8


title: 2ba47274630c9772;PLACEBO

description: Library name: 2ba47274630c9772


title: 2b75a93b0e5cc52a;MVA-NP+M1

description: Library name: 2b75a93b0e5cc52a


title: STB1-s35_S35_all_lanes_L001_control_minus3

description:
Library name: STB1-s35_S35_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: STB1-s34_S34_all_lanes_L001_case_minus3

description:
Library name: STB1-s34_S34_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: 2b9c2d22c5700a1b;MVA-NP+M1

description: Library name: 2b9c2d22c5700a1b


title: STB1-s32_S32_all_lanes_L001_control_minus3

description:
Library name: STB1-s32_S32_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: 2836774855a4d5b6;PLACEBO

description: Library name: 2836774855a4d5b6


title: STB1-s39_S39_all_lanes_L001_control_minus3

description:
Library name: STB1-s39_S39_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: STB1-s38_S38_all_lanes_L001_control_minus3

description:
Library name: STB1-s38_S38_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: STB1-s33_S33_all_lanes_L001_control_minus3

description:
Library name: STB1-s33_S33_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: STB1-s37_S37_all_lanes_L001_case_minus3

description:
Library name: STB1-s37_S37_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: 27de4a9fdf59ee16;MVA-NP+M1

description: Library name: 27de4a9fdf59ee16


title: 28a70c1cf53827fd;PLACEBO

description: Library name: 28a70c1cf53827fd


title: STB1-s31_S31_all_lanes_L001_case_minus3

description:
Library name: STB1-s31_S31_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: 2855665dfae5a7e7;MVA-NP+M1

description: Library name: 2855665dfae5a7e7


title: 2764bb09fc610271;MVA-NP+M1

description: Library name: 2764bb09fc610271


title: STB1-s36_S36_all_lanes_L001_control_minus3

description:
Library name: STB1-s36_S36_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: 26f6e1afc227c083;PLACEBO

description: Library name: 26f6e1afc227c083


title: 279ae9500691394b;MVA-NP+M1

description: Library name: 279ae9500691394b


title: 29a7843522e7f01a;PLACEBO

description: Library name: 29a7843522e7f01a


title: STB1-s27_S27_all_lanes_L001_control_minus3

description:
Library name: STB1-s27_S27_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: STB1-s3_S3_all_lanes_L001_control_minus3

description:
Library name: STB1-s3_S3_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: 26de84e680c262de;PLACEBO

description: Library name: 26de84e680c262de


title: 2642da09b487697c;MVA-NP+M1

description: Library name: 2642da09b487697c


title: STB1-s29_S29_all_lanes_L001_control_minus3

description:
Library name: STB1-s29_S29_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: STB1-s28_S28_all_lanes_L001_case_minus3

description:
Library name: STB1-s28_S28_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: STB1-s26_S26_all_lanes_L001_control_minus3

description:
Library name: STB1-s26_S26_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: 260ad1ffc22e4e90;PLACEBO

description: Library name: 260ad1ffc22e4e90


title: 2beb7e78da2587cf;PLACEBO

description: Library name: 2beb7e78da2587cf


title: 2618884727624ebf;PLACEBO

description: Library name: 2618884727624ebf


title: STB1-s24_S24_all_lanes_L001_control_minus3

description:
Library name: STB1-s24_S24_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: STB1-s25_S25_all_lanes_L001_case_minus3

description:
Library name: STB1-s25_S25_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: STB1-s30_S30_all_lanes_L001_control_minus3

description:
Library name: STB1-s30_S30_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: 25b26c5db9f708d7;PLACEBO

description: Library name: 25b26c5db9f708d7


title: STB1-s23_S23_all_lanes_L001_control_minus3

description:
Library name: STB1-s23_S23_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: 25b5e960432c3292;MVA-NP+M1

description: Library name: 25b5e960432c3292


title: 25a81bcff2288603;MVA-NP+M1

description: Library name: 25a81bcff2288603


title: 268a1f5ccee1c971;PLACEBO

description: Library name: 268a1f5ccee1c971


title: STB1-s2_S2_all_lanes_L001_control_minus3

description:
Library name: STB1-s2_S2_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: 257c4d30fded8649;PLACEBO

description: Library name: 257c4d30fded8649


title: 2503667bfe5dcc26;MVA-NP+M1

description: Library name: 2503667bfe5dcc26


title: STB1-s20_S20_all_lanes_L001_control_minus3

description:
Library name: STB1-s20_S20_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: STB1-s18_S18_all_lanes_L001_control_minus3

description:
Library name: STB1-s18_S18_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: 24530cd84c76f5f0;PLACEBO

description: Library name: 24530cd84c76f5f0


title: 24f7099d10de2a52;MVA-NP+M1

description: Library name: 24f7099d10de2a52


title: STB1-s22_S22_all_lanes_L001_case_minus3

description:
Library name: STB1-s22_S22_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: STB1-s19_S19_all_lanes_L001_case_minus3

description:
Library name: STB1-s19_S19_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: 24287773d1617320;PLACEBO

description: Library name: 24287773d1617320


title: 215ad8232acf9ece;MVA-NP+M1

description: Library name: 215ad8232acf9ece


title: 2348c001ab8809c4;PLACEBO

description: Library name: 2348c001ab8809c4


title: STB1-s17_S17_all_lanes_L001_control_minus3

description:
Library name: STB1-s17_S17_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: STB1-s15_S15_all_lanes_L001_control_minus3

description:
Library name: STB1-s15_S15_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: 1ffc6eee9e90f3d1;MVA-NP+M1

description: Library name: 1ffc6eee9e90f3d1


title: 1fce6da016a18f8a;MVA-NP+M1

description: Library name: 1fce6da016a18f8a


title: 22a0026f0eeb1819;MVA-NP+M1

description: Library name: 22a0026f0eeb1819


title: 226c10803ad242bd;MVA-NP+M1

description: Library name: 226c10803ad242bd


title: STB1-s12_S12_all_lanes_L001_control_minus3

description:
Library name: STB1-s12_S12_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: STB1-s1_S1_all_lanes_L001_case_minus3

description:
Library name: STB1-s1_S1_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: STB1-s11_S11_all_lanes_L001_control_minus3

description:
Library name: STB1-s11_S11_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: 1f9dd3d1cd24059b;MVA-NP+M1

description: Library name: 1f9dd3d1cd24059b


title: 215165177cb16018;MVA-NP+M1

description: Library name: 215165177cb16018


title: STB1-s14_S14_all_lanes_L001_control_minus3

description:
Library name: STB1-s14_S14_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: STB1-s21_S21_all_lanes_L001_control_minus3

description:
Library name: STB1-s21_S21_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: STB1-s10_S10_all_lanes_L001_case_minus3

description:
Library name: STB1-s10_S10_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: STB1-s16_S16_all_lanes_L001_case_minus3

description:
Library name: STB1-s16_S16_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: 214dfbb84cb115ee;PLACEBO

description: Library name: 214dfbb84cb115ee


title: s9_S9_ME_L001_control_minus6

description:
Library name: s9_S9_ME_L001
Plasma derived extracellular vesicle RNA


title: s8_S8_ME_L001_case_minus6

description:
Library name: s8_S8_ME_L001
Plasma derived extracellular vesicle RNA


title: STB1-NTC_S50_all_lanes_L001_water_minus3

description:
Library name: STB1-NTC_S50_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: s7_S7_ME_L001_control_minus6

description:
Library name: s7_S7_ME_L001
Plasma derived extracellular vesicle RNA


title: 1edd46e0781ec276;PLACEBO

description: Library name: 1edd46e0781ec276


title: 1f0637f17b95ea4f;MVA-NP+M1

description: Library name: 1f0637f17b95ea4f


title: STB1-NC_S49_all_lanes_L001_water_minus3

description:
Library name: STB1-NC_S49_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: 1f635daefc3eaa72;MVA-NP+M1

description: Library name: 1f635daefc3eaa72


title: 1e848d74f3302d1f;PLACEBO

description: Library name: 1e848d74f3302d1f


title: 1ee617d4712de10e;MVA-NP+M1

description: Library name: 1ee617d4712de10e


title: s5_S5_ME_L001_case_minus6

description:
Library name: s5_S5_ME_L001
Plasma derived extracellular vesicle RNA


title: s6_S6_ME_L001_control_minus6

description:
Library name: s6_S6_ME_L001
Plasma derived extracellular vesicle RNA


title: STB1-s13_S13_all_lanes_L001_case_minus3

description:
Library name: STB1-s13_S13_all_lanes_L001
Plasma derived extracellular vesicle RNA


title: s45_S45_ME_L001_water_minus6

description:
Library name: s45_S45_ME_L001
Plasma derived extracellular vesicle RNA


title: s46_S46_ME_L001_water_minus6

description:
Library name: s46_S46_ME_L001
Plasma derived extracellular vesicle RNA


title: 1c930c0ef6b3c02d;PLACEBO

description: Library name: 1c930c0ef6b3c02d


title: 1d20b6bf9dd671dd;PLACEBO

description: Library name: 1d20b6bf9dd671dd


title: 1e19b10ad55f9fe5;MVA-NP+M1

description: Library name: 1e19b10ad55f9fe5


title: s44_S44_ME_L001_water_minus6

description:
Library name: s44_S44_ME_L001
Plasma derived extracellular vesicle RNA


title: 1ce0aea9e307a57b;PLACEBO

description: Library name: 1ce0aea9e307a57b


title: 1c65d7742cd18d1f;MVA-NP+M1

description: Library name: 1c65d7742cd18d1f


title: s41_S41_ME_L001_case_minus6

description:
Library name: s41_S41_ME_L001
Plasma derived extracellular vesicle RNA


title: s40_S40_ME_L001_case_minus3

description:
Library name: s40_S40_ME_L001
Plasma derived extracellular vesicle RNA


title: 1c5c69a13a7faf70;MVA-NP+M1

description: Library name: 1c5c69a13a7faf70


title: s4_S4_ME_L001_control_minus6

description:
Library name: s4_S4_ME_L001
Plasma derived extracellular vesicle RNA


title: 1ecd5e1ce379bb74;MVA-NP+M1

description: Library name: 1ecd5e1ce379bb74


title: 1c1c0ed85cbccfc0;PLACEBO

description: Library name: 1c1c0ed85cbccfc0


title: 1c2b583be6187d85;MVA-NP+M1

description: Library name: 1c2b583be6187d85


title: s39_S39_ME_L001_controls_minus6

description:
Library name: s39_S39_ME_L001
Plasma derived extracellular vesicle RNA


title: 1beefc8d46b3a99f;MVA-NP+M1

description: Library name: 1beefc8d46b3a99f


title: 1be9148ede02cc7a;PLACEBO

description: Library name: 1be9148ede02cc7a


title: s38_S38_ME_L001_case_minus3

description:
Library name: s38_S38_ME_L001
Plasma derived extracellular vesicle RNA


title: s35_S35_ME_L001_control_minus6

description:
Library name: s35_S35_ME_L001
Plasma derived extracellular vesicle RNA


title: s36_S36_ME_L001_case_minus3

description:
Library name: s36_S36_ME_L001
Plasma derived extracellular vesicle RNA


title: 1c00381bc65e10b9;MVA-NP+M1

description: Library name: 1c00381bc65e10b9


title: s37_S37_ME_L001_control_minus3

description:
Library name: s37_S37_ME_L001
Plasma derived extracellular vesicle RNA


title: 1920acbca01a523b;MVA-NP+M1

description: Library name: 1920acbca01a523b


title: 1a036cb73118b922;MVA-NP+M1

description: Library name: 1a036cb73118b922


title: 1af9cc9ba171e659;MVA-NP+M1

description: Library name: 1af9cc9ba171e659


title: s34_S34_ME_L001_control_minus6

description:
Library name: s34_S34_ME_L001
Plasma derived extracellular vesicle RNA


title: s42_S42_ME_L001_case_minus6

description:
Library name: s42_S42_ME_L001
Plasma derived extracellular vesicle RNA


title: 1866110ec630ef78;MVA-NP+M1

description: Library name: 1866110ec630ef78


title: s33_S33_ME_L001_control_minus6

description:
Library name: s33_S33_ME_L001
Plasma derived extracellular vesicle RNA


title: 1808f4627cb80d91;MVA-NP+M1

description: Library name: 1808f4627cb80d91


title: s43_S43_ME_L001_control_minus6

description:
Library name: s43_S43_ME_L001
Plasma derived extracellular vesicle RNA


title: s32_S32_ME_L001_control_minus6

description:
Library name: s32_S32_ME_L001
Plasma derived extracellular vesicle RNA


title: s31_S31_ME_L001_control_minus6

description:
Library name: s31_S31_ME_L001
Plasma derived extracellular vesicle RNA


title: 17e3aae7ccf6422d;PLACEBO

description: Library name: 17e3aae7ccf6422d


title: s30_S30_ME_L001_control_minus6

description:
Library name: s30_S30_ME_L001
Plasma derived extracellular vesicle RNA


title: 16a8b158f35bb602;PLACEBO

description: Library name: 16a8b158f35bb602


title: s3_S3_ME_L001_control_minus6

description:
Library name: s3_S3_ME_L001
Plasma derived extracellular vesicle RNA


title: s29_S29_ME_L001_control_minus6

description:
Library name: s29_S29_ME_L001
Plasma derived extracellular vesicle RNA


title: s28_S28_ME_L001_control_minus6

description:
Library name: s28_S28_ME_L001
Plasma derived extracellular vesicle RNA


title: 16826ca6fcdb3192;MVA-NP+M1

description: Library name: 16826ca6fcdb3192