title: P75 | 005 | TUMOUR

tag: bestresponse

tag: pathway

value: Nivolumab

value: N

value: Female

value: Previous

value: TUMOUR


title: SC8_4 - SHAM_NPHS2-rtTA_1 (E410)

status: Public on Aug 02 2024

type: SRA

city: Stony Brook

first: Bismark

last: Owusu Frimpong

state: NY

address: 100 Nicolls Rd

country: USA

institute: Stony Brook University

description: Cellbarcode/UMI: R1:28;i7 index: 8

library_source: transcriptomic

data_processing:
Illumina software used for basecalling.
CellRanger used for raw processing
Seurat R-package used for further analysis
Genome_build: mm10
Supplementary_files_format_and_content: A xlsx spreadsheet containing normalized expression of genes based on cluster and group

molecule: nuclear RNA

organism: Mus musculus

source_name: Kidney Cortex

extract_protocol:
Kidneys were perfused with HBSS and stored in RNALater at -80C. A 2 mm3 section of tissue was rinsed briefly with PBS and minced before adding 1 mL of lysis buffer containing 20 mM Tris-HCl (pH 8), 320 mM sucrose, 5 mM CaCl2, 3 mM MgAc2,  0.1 mM EDTA, and 0.1% TritonX-100. The tissue was initially dissociated by pipetting up and down ~10X with a p-1000 tip and then being passed through a 25G syringe ~10X. The tissue was incubated on ice for 10 minutes and then passed through a 30 µm CellTrics filter. Nuclei were pelleted by centrifugation (5 min, 500g, 4°C) and washed with PBS after removal of supernatant. Nuclei were pelleted again and resuspended in 1 mL of PBS containing 0.04% BSA and RNAse inhibitor (0.2u/µL) before counting by hemocytometer.  Nuclei were then diluted and prepared using the 10X Chromium System according to the manufacturer’s instructions (10X Genomics).
RNA libraries were prepared for sequencing using standard 10X Genomics and Illumina protocols

tag: genotype

tag: strain

value: FVB/N

tag: treatment

value: sham

tag: preparation

value: Single nuclei

tag: sample index

value: TACCACCACTAAGTTTGGGTCAAGACTGTGGC


title: 0d dermis Cthrc1-/-  rep2

city: Beijing

first: Sha

last: Huang

address: 51 Fu Cheng Road

country: China

institute: PLA General Hospital

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. And then by removing sequence-dependent bias and amplification noise using UMI-tools.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: Mus_musculus.GRCm38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

molecule: total RNA

source_name: dermis

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters, which including custom Unique Molecular Identifiers for minimizing sequence-dependent bias and amplification noise according to (Shiroguchi et al. 2012). Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

tag: tissue

value: dermis

tag: age

value: 6 weeks


title: P75 | 002 | TME

type: protein

city: Brisbane

first: Habib

last: Sadeghirad

state: Queensland

address: 37 Kent St, Woolloongabba, 37 Kent St, Woolloongabba

country: Australia

institute: The University of Queensland

hyb_protocol: DSP eluates were hybridised as per manufacturers instructions in nCounter Readout User Manual.

scan_protocol: Hybridised samples were loaded into Nanostring prep station and processed as per DSP Slide Prep User Manual. N counter was performed with default parameters, and counts from Ncounter uploaded back to DSP instrument

data_processing: Counts were aligned and ERCC corrected automatically on the DSP instrument. This QC data was exported for analysis.

molecule: protein

organism: Homo sapiens

source_name: HNSCC

label_protocol: DSP experiments were performed as per manufacturers DSP Slide Prep User Manual

extract_protocol: Clinical FFPE samples on individual slides were obtained with appropriate ethics approval

value: HNSCC

value: PR

value: TRUE

tag: mortality

tag: Sex

tag: smokingstatus

tag: pfs

value: 42 mos

tag: countofloweprgene

tag: percentofloweprgene

tag: foi

tag: responsesintumour

value: TME

tag: responsesintme


title: P75 | 004 | TME

tag: bestresponse

tag: pathway


title: P75 | 003 | TUMOUR


title: SC8_3 - STZ_hKLF6PODTA_1 (E403)

description: Cellbarcode/UMI: R1:28;i7 index: 8

tag: genotype

tag: strain

value: stz induced

value: GTTCCTCAAGGTACGCTAAGTATGCCCAGGAT


title: PBMCs, healthy control, clinically healthy, healthy control 5

city: Wien

first: Andreas

middle: B

last: Diendorfer

address: Leberstraße 20

country: Austria

institute: TAmiRNA GmbH

description: 2 - HC-V

data_processing:
quality evaluation with fastQC v0.11.8 and multiQC v1.7
adapter trimmed and quality filtered  using bbduk from the bbmap package v38.69(filtered minimum length of 17nt and phred quality of 30)
alignment steps were performed with STAR v2.7 mapped against the genomic reference GRCh38.p13 provided by Ensembl
indexing with samtools v1.9, assignment of features to the mapped reads was done with htseq-count v0.13
differential expression analysis with edgeR v3.30
Assembly: GRCh38.p13
Supplementary files format and content: Microsoft Excel file .xlsx includes the raw counts for each sample
Supplementary files format and content: Microsoft Excel file .xlsx includes the edgeR normalized counts and statistics for each gene and sample

source_name: peripheral blood

growth_protocol: PBMCs were isolated from peripheral blood samples and directly used for total RNA isolation

extract_protocol:
Total RNA was isolated using Monarch® Total RNA Miniprep Kit (New England Biolabs Inc., Massachusetts, USA).
mRNA Library Prep with Quantseq mRNA Library Prep Kit FWD UDI

treatment_protocol: no treatment

value: peripheral blood

tag: cell type

value: peripheral blood mononuclear cells

value: healthy control


title: PBMCs, healthy control, clinically healthy, healthy control 3

description: 3 - HC-III


title: PBMCs, TTD1, ERCC2 deficiency, patient 2

description: 5 - TTD-II


title: PBMCs, TTD1, ERCC2 deficiency, patient 3

description: 6 - TTD-III


title: SC8_2 - STZ_NPHS2-rtTA_1 (E393)

description: Cellbarcode/UMI: R1:28;i7 index: 8

tag: treatment

tag: preparation

tag: sample index

value: ACCGTATGGATTAGATCTGACTGATGACGCCC


title: PBMCs, TTD1, ERCC2 deficiency, patient 1

description: 6 - TTD

tag: tissue


title: 0d dermis Cthrc1-/-  rep1

tag: age


title: P72_Baseline

type: RNA

city: Madrid

first: Enrique

last: Perez Navarro

state: Madrid

address: Av. de Córdoba

department: Oncology Department

country: Spain

institute: Hospital 12 de Octubre

description: Gene expression data from whole blood samples from patients with mCRPC at Pre-treatment stage with enzalutamide

hyb_protocol: Complementary DNA (cDNA) was synthesized from 100 ng of each RNA sample using the WT PLUS Reagent Kit (Thermo Scientific, Newark, DE, USA) following the standard protocol. This cDNA was then amplified, fragmented, and labelled with biotin for hybridization.

scan_protocol: The hybridized array was scanned using the GeneChip Scanner 3000 (Affymetrix, Thermo Scientific, Newark, DE, USA).

data_processing: Gene microarray analyses were derived after a quality control, background correction, normalization, logarithmic conversion and remove batch effects processing using Transcriptome Analysis Console (TAC) Software (version 4.0.1, Thermo)

label: biotin

source_name: Patient with mCRPC at Pre-treatment stage

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

extract_protocol: Whole-blood samples collected in PAXgene RNA tubes were subjected to isolation and purification following the manufacturer’s prescribed protocol

treatment_protocol: The PREMIERE trial constituted a cohort of 98 mCRPC patients, all of whom had not received prior chemotherapy treatments   . These participants were recruited across 17 established hospitals within Spain. The selection criteria for patient inclusion incorporated individuals with histologically verified prostate adenocarcinoma, documented metastases, and tumour progression, alongside a serum testosterone level equal to or below 50 ng per decilitre, despite the continuation of androgen-deprivation therapy.

tag: Stage

value: Pre-treatment

value: Whole blood


title: P75 | 003 | TME

value: Nivolumab

tag: mortality

value: N

tag: Sex

value: Female

tag: smokingstatus

value: Previous

tag: pfs


title: PBMCs, healthy control, clinically healthy, healthy control 4

description: 1 - HC-IV


title: PBMCs, healthy control, clinically healthy, healthy control 1

description: 1 - HC-I


title: SC8_1 - SHAM_hKLF6PODTA_1 (F351)

description: Cellbarcode/UMI: R1:28;i7 index: 8

value: FVB/N

value: sham

value: Single nuclei

value: CGTTAATCGCCACGCTTTACTCAGAAGGGTGA


title: PBMCs, healthy control, clinically healthy, healthy control 2

description: 2 - HC-II


title: P53 | 006 | Tumour

value: HNSCC

value: SD

value: TRUE

value: Y

value: Current

value: 12 mos

tag: countofloweprgene

tag: percentofloweprgene

tag: foi

tag: responsesintumour

value: TUMOUR


title: P75 | 001 | TUMOUR

tag: bestresponse

value: PR

tag: pathway

value: 42 mos

tag: responsesintme


title: PRRSV Male Saline A9

city: Urbana

first: Sandra

last: Rodriguez Zas

state: IL

address: 1207 W. Gregory Dr.

institute: University of Illinois

description:
PRRSV Male Saline A9
P_M_c_9

data_processing:
Quality-scores line in fastq files processed with Casava1.8 use an ASCII offset of 33
Sequences were trimmed for adaptor seuqences and masked for low-complexity and low-quality
150 nt paired-end reads were assembled into transcript isoforms and mapped to the pig genome (assembly 11.1) using Kallisto v0.43 (Bray et al., 2016)
Assembly: Sus scrofa genome (version 11.1)
Supplementary files format and content: cvs format,  transcripts per million (TPM) values for each sample, one column per sample

organism: Sus scrofa

source_name: Hypothalamus

extract_protocol:
RNA was extracted from all samples using standards protocols. TRIzol reagent (Life Technologies, Grand Island, New York) was used to isolate total RNA and the QIAGEN RNeasy kit (Qiagen, Valencia, California) was use for purification
The RNAseq libraries were prepared with Illumina's 'TruSeq Stranded mRNAseq Sample Prep kit' (Illumina). Read 1 aligns to the antisense strand and read 2 aligns to the sense strand. The libraries were quantitated by qPCR and sequenced on 4 lanes first and 5 lanes later for 101 cycles from one end of the fragments on a HiSeq 4000 with a HiSeq 4000 sequencing kit version 1. Fastq files were generated and demultiplexed with with the bcl2fastq v2.17.1.14 Conversion Software (Illumina).

value: Hypothalamus

tag: sampleID

tag: mia

value: PRRSV

value: Male

tag: weaning

value: Saline


title: PRRSV Male Saline A8

description:
PRRSV Male Saline A8
P_M_c_8

tag: tissue


title: P53 | 005 | Tumour

value: Nivolumab

tag: age

value: Female


title: SYT13_Het_2

city: Blaubeuren

first: Alberto

last: Catanese

address: Albert-Einstein-Allee 11

country: Germany

institute: Ulm University, Anatomy and Cell Biology

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data
HISAT2 was used to map the clean reads to the reference genome
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. Afterwards, the  FPKM of each gene was calculated based on the length of the gene and reads count mapped to this specific gene
Assembly: hg38 (homo sapiens)
Supplementary files format and content: Excel file with raw counts for each sample

source_name: hiPSC

growth_protocol: HiPSCs were cultured in mTeSR1-Plus. At 80% of confluence, were detached to create EmbryoBodies, which were cultured in suspension for 8 days. Afterwards, EmbryoBodies were dissociated, plated onto Matrigel-coated plates and cultured for further 5 weeks to induce the differentiation of spinal motor neurons. Details regarding the differentiation protocol can be found in the following article PMCID: PMC8261490

extract_protocol:
RNAeasy Kit (Qiagen)
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library

tag: cell line

value: hiPSC

tag: cell type

value: Motor neurons

tag: genotype

value: Het KO


title: P53 | 005 | TME

value: HNSCC

value: SD

tag: mortality

tag: Sex

tag: smokingstatus

value: TME


title: P53 | 004 | Tumour

value: TRUE

value: Y

value: Current

tag: pfs

tag: countofloweprgene

tag: percentofloweprgene


title: PRRSV Male Saline A7

description:
PRRSV Male Saline A7
P_M_c_7


title: PRRSV Male Saline A6

description:
PRRSV Male Saline A6
P_M_c_6


title: P53 | 003 | Tumour

tag: bestresponse

value: 12 mos

tag: foi

tag: responsesintumour

value: TUMOUR


title: P68_Baseline

tag: Stage

value: Pre-treatment

value: Whole blood


title: P53 | 004 | TME

tag: pathway

tag: responsesintme


title: P69_Baseline

tag: tissue


title: P70_Baseline


title: P53 | 003 | TME

tag: age


title: SYT13_WT_3

tag: cell line

value: WT


title: P67_Baseline


title: P71_Baseline


title: P64_Baseline


title: P65_Baseline


title: P66_Baseline


title: P61_Baseline


title: P62_Baseline


title: PRRSV Male Saline A5

description:
PRRSV Male Saline A5
P_M_c_5

value: Hypothalamus

tag: sampleID

tag: mia

value: PRRSV

value: Male

tag: weaning

value: Saline


title: SYT13_Het_3

value: hiPSC

tag: cell type

value: Motor neurons

tag: genotype


title: P60_Baseline


title: SYT13_WT_2


title: SYT13_Het_1

value: Het KO


title: SYT13_WT_1


title: PRRSV Male Saline A2

description:
PRRSV Male Saline A2
P_M_c_2

tag: Sex


title: PRRSV Male Saline A4

description:
PRRSV Male Saline A4
P_M_c_4


title: P53 | 002 | Tumour

value: HNSCC

value: SD

value: Nivolumab

tag: mortality

value: Female

tag: smokingstatus

tag: pfs

tag: countofloweprgene


title: P53 | 001 | Tumour

tag: bestresponse

value: TRUE

value: Y

value: Current

tag: percentofloweprgene

tag: foi

tag: responsesintumour


title: RT- snATAC-seq

city: Stockholm

first: Ning

last: Xu Landén

address: K2 Medicin, Solna, K2 Derm o Ven Xu Landén N

country: Sweden

institute: Karolinska Institutet

library_source: genomic

data_processing:
The single cell multiome data was mapped with CellRanger-ARC (v2.0.2) to a manually built human reference genome GRCh38 with annotation file GENCODE version 44.
The single cell multiome data was processed using Seurat (v5.0.1) and Signac (v1.12.0) packages. Peaks within each dataset were identified using the MACS2 package.
The scDblFinder (v1.15.3) was further performed on each sample to detect potential doublets. Data normalization and scaling were performed using the SCTransform package.
Assembly: GRCh38
Supplementary files format and content: zip file: the hdf5 files contain the count matrix generated by CellRanger ARC for each sample.
Supplementary files format and content: zip file: the fragments.tsv.gz and fragments.tsv.gz.tbi files contain unique ATAC-seq fragments captured by the assay and related information about the fragments.

molecule: genomic DNA

source_name: Skin

extract_protocol:
Single-cell isolation used Whole Skin Dissociation Kit – human (MACS CAT. 130-101-540). The nulcei extraction followed the protocol from 10X Genomics.
The library preparation is followed by 10X Genomics Single Cell Multiome ATAC + Gene Expression protocol, and the samples were sequenced by Illumina NovaSeq X 300 (2x150bp) at the National Genomics Infrastructure at SciLifeLab Stockholm.
Single Cell Multiome ATAC + Gene Expression

tag: tissue

value: Skin

tag: gender

tag: treatment

value: Non-irradiated


title: RT+ snATAC-seq

tag: age

value: Radiotherapy


title: PRRSV Male Saline A3

description:
PRRSV Male Saline A3
P_M_c_3

value: Hypothalamus

tag: sampleID

tag: mia


title: PRRSV Male Saline A11

description:
PRRSV Male Saline A11
P_M_c_11

value: PRRSV

tag: weaning


title: P53 | 001 | TME

tag: pathway

value: 12 mos

value: TME

tag: responsesintme


title: P59_Baseline

tag: Stage

value: Pre-treatment

value: Whole blood


title: P53 | 002 | TME

tag: mortality

tag: Sex

tag: smokingstatus


title: P58_Baseline


title: P56_Baseline


title: RT+ snRNA-seq

library_source: transcriptomic single cell


title: RT- snRNA-seq


title: PRRSV Male Saline A10

description:
PRRSV Male Saline A10
P_M_c_10

value: Male

value: Saline


title: P55_Baseline


title: PRRSV Female Saline A6

description:
PRRSV Female Saline A6
P_F_c_6


title: P22 | 006 | TME

value: HNSCC

tag: bestresponse

value: SD

value: N

value: Previous

tag: pfs

value: 6 mos

tag: countofloweprgene


title: Bulk RNA-seq RS6_RT-

description: RNA-seq (donor fibroblast)

data_processing:
RNA-seq: Raw reads of mRNA sequencing were first trimmed for adaptors and low-quality bases using Trimmomatic v0.36 software. Clean reads were aligned to the human reference genome (GRCh38.p12), coupled with the comprehensive gene annotation file (GENCODEv31) using STAR v2.7.1a. Gene expression was then quantified by counting unique mapped fragments to exons using featureCount function from the Subread package. Raw counts for each gene were normalized to fragments per kilobase of transcript, per million mapped reads (FPKM)-like values.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include gene FPKM values for each Sample
Supplementary files format and content: Matrix table with raw read counts for every gene and every sample

source_name: skin

extract_protocol:
Total RNA was extracted from fibroblasts using miRNeasy mini kit (Qiagen, Hilden, Germany) and RNA integrity was examined using the Agilent RNA 6000 Nano Kit and 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA, USA).
The RNA-seq library preparation and sequencing were performed by Illumina NovaSeq 6000 SP-300 or DNBSEQ-G400 (2x150 bp).

value: skin

tag: cell type

value: Dermal fibroblast

value: Female


title: PRRSV Male Saline A1

description:
PRRSV Male Saline A1
P_M_c_1

tag: tissue


title: Bulk RNA-seq RS6_RT+

description: RNA-seq (donor fibroblast)

value: Radiotherapy


title: PRRSV Female Saline A5

description:
PRRSV Female Saline A5
P_F_c_5

value: Hypothalamus


title: P54_Baseline


title: P22 | 005 | TUMOUR

value: TRUE

tag: percentofloweprgene

tag: foi

tag: responsesintumour

value: TUMOUR


title: P53_Baseline


title: PRRSV Female Saline A4

description:
PRRSV Female Saline A4
P_F_c_4

tag: sampleID

tag: age

value: PRRSV


title: Bulk RNA-seq RS4_RT-

description: RNA-seq (donor fibroblast)

tag: treatment

value: Non-irradiated


title: P22 | 005 | TME

tag: pathway

value: TME


title: P52_Baseline

value: Pre-treatment

value: Whole blood


title: Bulk RNA-seq RS4_RT+

description: RNA-seq (donor fibroblast)


title: P22 | 006 | TUMOUR

value: HNSCC

value: Male

tag: responsesintme


title: PRRSV Female Saline A3

description:
PRRSV Female Saline A3
P_F_c_3

tag: mia

tag: weaning

value: Saline


title: Bulk RNA-seq RS3_RT+

description: RNA-seq (donor fibroblast)

tag: Sex


title: P51_Baseline

tag: Stage


title: P22 | 004 | TME

tag: bestresponse

value: SD

tag: mortality

value: N

tag: smokingstatus

value: Previous


title: P22 | 004 | TUMOUR

tag: pfs

value: 6 mos

tag: countofloweprgene


title: PRRSV Female Saline A1

description:
PRRSV Female Saline A1
P_F_c_1

tag: tissue

value: Female


title: PRRSV Female Saline A2

description:
PRRSV Female Saline A2
P_F_c_2


title: P22 | 003 | TME

tag: percentofloweprgene

tag: foi


title: P48_Baseline


title: P22 | 003 | TUMOUR

tag: responsesintumour


title: Bulk RNA-seq RS2_RT-

description: RNA-seq (donor fibroblast)

value: skin

tag: cell type

value: Dermal fibroblast

tag: age


title: Bulk RNA-seq RS2_RT+

description: RNA-seq (donor fibroblast)

tag: treatment

value: Radiotherapy


title: P50_Baseline


title: P22 | 002 | TUMOUR

value: TRUE

tag: pathway

tag: responsesintme

value: TUMOUR


title: PRRSV Male Metabolic A8

description:
PRRSV Male Metabolic A8
P_M_f_8

value: Hypothalamus

tag: sampleID

tag: mia

value: PRRSV

tag: weaning

value: Metabolic


title: PRRSV Male Metabolic A7

description:
PRRSV Male Metabolic A7
P_M_f_7

tag: Sex


title: Bulk RNA-seq RS1_RT+

description: RNA-seq (donor fibroblast)


title: P46_Baseline

tag: Stage

value: Pre-treatment

value: Whole blood


title: PRRSV Male Metabolic A9

description:
PRRSV Male Metabolic A9
P_M_f_9

value: Male


title: P22 | 002 | TME

value: HNSCC

tag: bestresponse

tag: mortality

tag: smokingstatus

value: TME


title: P45_Baseline

tag: tissue


title: P22 | 001 | TUMOUR

value: SD

value: N

tag: pfs

tag: countofloweprgene

tag: percentofloweprgene


title: P44_Baseline


title: PRRSV Male Metabolic A6

description:
PRRSV Male Metabolic A6
P_M_f_6


title: Bulk ATAC-seq IR_D7_2

description: ATAC-seq (in vitro irradiation)

data_processing:
ATAC-seq: Raw data were processed using Trimmomatic v0.36 by removing reads of low qualities and with a length of less than 30 nucleotides. The PCR duplicated reads were excluded using Picard (v2.20.4) tools after mapping to GRCh38 human reference genome using Bowtie2 (v2.3.5.1). The uniquely mapped reads were shifted and converted into bigwig format with a 200-bp extension size for IGV visualization using the deepTools. Peaks were called on each sample individually using MACS2/3 (v2.2.6/v3.0.0b1) with the default parameter except for using-f BAMPE option. Peaks overlapping with the repetitive regions in ENCODE blacklist downloaded from UCSC Table Browser were filtered out using BEDTools suite.
Assembly: GRCh38, GRCm39
Supplementary files format and content: Files contains the peaks of ATAC-seq.

extract_protocol:
ATAC-seq was performed as described in Corces, M., et al. Nat Methods (2017). Briefly, after washing with cold PBS, fibroblasts were treated with lysis buffer to extract nuclei. The isolated nuclei were incubated for 30 minutes at 37°C in a 50 µl Tn5 transposase reaction mix (Illumina FC-121-1031). The transposed chromatin was purified with Zymo DNA Clean & Concentrator (Zymo Research).
The ATAC-seq library preparation and sequencing were performed by Illumina NovaSeq 6000 SP-300 or NovaSeq X 10B-300 (2x150 bp) at the National Genomics Infrastructure at SciLifeLab Stockholm.

tag: cell type

value: Irradiated (8 Gy)


title: P43_Baseline


title: Bulk ATAC-seq IR_D7_1

description: ATAC-seq (in vitro irradiation)

tag: age


title: Bulk RNA-seq RS3_RT-

description: RNA-seq (donor fibroblast)

value: Female

tag: treatment

value: Non-irradiated


title: P41_Baseline


title: P06 | 002 | TME

value: PR

tag: pathway

value: Nivolumab

value: Y

value: Previous

value: 33 mos

tag: foi

tag: responsesintumour


title: PRRSV Male Metabolic A4

description:
PRRSV Male Metabolic A4
P_M_f_4

value: Hypothalamus

tag: sampleID

tag: mia

value: PRRSV


title: Bulk ATAC-seq Ctr_D7_2

description: ATAC-seq (in vitro irradiation)

value: skin

value: Dermal fibroblast

tag: Sex

value: Non-irradiated (0 Gy)


title: PRRSV Male Metabolic A3

description:
PRRSV Male Metabolic A3
P_M_f_3

value: Male

tag: weaning

value: Metabolic


title: P39_Baseline

tag: Stage

value: Pre-treatment

value: Whole blood


title: P49_Baseline


title: Bulk RNA-seq RS1_RT-

description: RNA-seq (donor fibroblast)


title: Bulk ATAC-seq IR_D1_1

description: ATAC-seq (in vitro irradiation)

value: Irradiated (8 Gy)


title: Bulk ATAC-seq IR_D1_2

description: ATAC-seq (in vitro irradiation)


title: P06 | 004 | TME

value: HNSCC

tag: bestresponse

value: TRUE

tag: mortality

value: TME

tag: responsesintme


title: P36_Baseline

tag: tissue


title: PRRSV Male Metabolic A1

description:
PRRSV Male Metabolic A1
P_M_f_1


title: P22 | 001 | TME

value: SD

value: N

tag: smokingstatus

tag: pfs

value: 6 mos

tag: countofloweprgene


title: Bulk ATAC-seq Ctr_D1_2

description: ATAC-seq (in vitro irradiation)

tag: cell type

tag: age


title: PRRSV Male Metabolic A5

description:
PRRSV Male Metabolic A5
P_M_f_5


title: P40_Baseline


title: P06 | 003 | TME

value: PR

tag: pathway

value: Nivolumab

value: Y

value: Previous

value: 33 mos

tag: percentofloweprgene


title: PRRSV Female Metabolic A6

description:
PRRSV Female Metabolic A6
P_F_f_6

value: Hypothalamus

value: PRRSV

value: Female


title: P06 | 003 | TUMOUR

value: Male

tag: foi

tag: responsesintumour

value: TUMOUR


title: PRRSV Female Metabolic A5

description:
PRRSV Female Metabolic A5
P_F_f_5

tag: sampleID

tag: mia

value: Metabolic


title: PRRSV Female Metabolic A4

description:
PRRSV Female Metabolic A4
P_F_f_4

tag: Sex

tag: weaning


title: Bulk ATAC-seq Ctr_D7_1

description: ATAC-seq (in vitro irradiation)

value: skin

value: Dermal fibroblast

tag: treatment

value: Non-irradiated (0 Gy)


title: Bulk ATAC-seq RS26_RT+

description: ATAC-seq (donor fibroblast)

value: Radiotherapy


title: P06 | 005 | TME

value: HNSCC

tag: bestresponse

value: TRUE

tag: mortality

value: TME


title: PRRSV Male Metabolic A2

description:
PRRSV Male Metabolic A2
P_M_f_2

tag: tissue


title: P06 | 004 | TUMOUR

value: PR

value: Nivolumab

tag: smokingstatus

tag: responsesintme


title: P06 | 002 | TUMOUR

value: Y

value: Previous

tag: pfs

tag: countofloweprgene


title: P32_Baseline

tag: Stage

value: Pre-treatment

value: Whole blood


title: P37_Baseline


title: P06 | 005 | TUMOUR

tag: pathway

tag: age

value: 33 mos


title: P33_Baseline


title: PRRSV Female Metabolic A3

description:
PRRSV Female Metabolic A3
P_F_f_3

value: Hypothalamus

value: PRRSV

value: Female


title: Bulk ATAC-seq RS26_RT-

description: ATAC-seq (donor fibroblast)

value: skin

tag: cell type

value: Non-irradiated


title: PRRSV Female Metabolic A1

description:
PRRSV Female Metabolic A1
P_F_f_1

value: Metabolic


title: PRRSV Female Metabolic A2

description:
PRRSV Female Metabolic A2
P_F_f_2


title: Bulk ATAC-seq RS17_RT+

description: ATAC-seq (donor fibroblast)

value: Dermal fibroblast

value: Radiotherapy


title: Bulk ATAC-seq Ctr_D1_1

description: ATAC-seq (in vitro irradiation)

value: Non-irradiated (0 Gy)


title: P31_Baseline


title: PRRSV Male Immune A9

description:
PRRSV Male Immune A9
P_M_i_9

value: Male

value: Immune


title: P06 | 006 | TME

value: HNSCC

value: PR

value: TRUE

value: Nivolumab

tag: percentofloweprgene

tag: foi

tag: responsesintumour

value: TME


title: Bulk ATAC-seq RS17_RT-

description: ATAC-seq (donor fibroblast)

tag: Sex


title: P06 | 001 | TME

value: Y

value: Previous

value: 33 mos


title: Bulk ATAC-seq RS6_RT+

description: ATAC-seq (donor fibroblast)

value: Female


title: PRRSV Male Immune A8

description:
PRRSV Male Immune A8
P_M_i_8

value: Hypothalamus

tag: sampleID

tag: mia

value: PRRSV

tag: weaning


title: P29_Baseline

value: Pre-treatment

value: Whole blood


title: P06 | 006 | TUMOUR

tag: bestresponse

tag: mortality

value: TUMOUR


title: PRRSV Male Immune A7

description:
PRRSV Male Immune A7
P_M_i_7

tag: tissue


title: P28_Baseline


title: P30_Baseline


title: Bulk ATAC-seq RS6_RT-

description: ATAC-seq (donor fibroblast)

value: skin

value: Dermal fibroblast

tag: treatment

value: Non-irradiated


title: PRRSV Male Immune A6

description:
PRRSV Male Immune A6
P_M_i_6

value: Male

value: Immune


title: Bulk ATAC-seq RS5_RT+

description: ATAC-seq (donor fibroblast)

value: Radiotherapy


title: P27_Baseline


title: PRRSV Male Immune A5

description:
PRRSV Male Immune A5
P_M_i_5


title: Bulk ATAC-seq RS4_RT+

description: ATAC-seq (donor fibroblast)


title: Bulk ATAC-seq RS5_RT-

description: ATAC-seq (donor fibroblast)


title: P08 | 004 | TME

value: HNSCC

value: SD

value: TRUE

value: Nivolumab

tag: smokingstatus

value: Never

tag: pfs

value: 7 mos

tag: responsesintme


title: P26_Baseline

tag: Stage


title: PRRSV Male Immune A4

description:
PRRSV Male Immune A4
P_M_i_4

value: Hypothalamus

tag: age


title: P08 | 004 | TUMOUR

tag: pathway

value: Y

tag: countofloweprgene


title: Bulk ATAC-seq RS4_RT-

description: ATAC-seq (donor fibroblast)

tag: cell type

value: Female


title: P25_Baseline

value: Pre-treatment

value: Whole blood


title: P24_Baseline


title: P08 | 002 | TME

tag: percentofloweprgene

tag: foi

tag: responsesintumour

value: TME


title: PRRSV Male Immune A3

description:
PRRSV Male Immune A3
P_M_i_3

tag: sampleID

tag: mia

value: PRRSV

tag: Sex


title: Bulk ATAC-seq RS3_RT+

description: ATAC-seq (donor fibroblast)

value: skin

value: Dermal fibroblast


title: P08 | 008 | TME

tag: bestresponse

tag: mortality

value: Male


title: PRRSV Male Immune A2

description:
PRRSV Male Immune A2
P_M_i_2

tag: tissue

tag: weaning

value: Immune


title: P22_Baseline


title: Bulk ATAC-seq RS3_RT-

description: ATAC-seq (donor fibroblast)

tag: treatment

value: Non-irradiated


title: P34_Baseline


title: P18_Baseline


title: P08 | 010 | TME

value: HNSCC

value: SD

tag: smokingstatus

tag: pfs

tag: responsesintme


title: P17_Baseline

tag: Stage


title: P08 | 001 | TUMOUR

value: TRUE

tag: pathway

value: Nivolumab

tag: age

tag: countofloweprgene

value: TUMOUR


title: Bulk ATAC-seq RS2_RT+

description: ATAC-seq (donor fibroblast)

tag: cell type

value: Radiotherapy


title: PRRSV Female Immune A9

description:
PRRSV Female Immune A9
P_F_i_9

value: Hypothalamus


title: Bulk ATAC-seq RS2_RT-

description: ATAC-seq (donor fibroblast)

value: Female


title: P08 | 001 | TME

value: Y

value: Never

value: 7 mos

tag: percentofloweprgene

tag: foi

tag: responsesintumour


title: PRRSV Female Immune A8

description:
PRRSV Female Immune A8
P_F_i_8

tag: sampleID

tag: mia

value: PRRSV

tag: Sex


title: NCI-H1299 Sh1-3

city: Nanjing

first: Shan

last: Gao

address: No. 2 Sipailou, Xuanwu District

institute: Southeast University

data_processing:
Raw FASTQ files were trimmed by Trim_galore v0.6.6
Trimmed FASTQ files were aligned to hg38 genome by STAR v2.7.0d
FeatureCounts v2.0.1 was used to calculate the reads count of genes.
DESeq2 1.30.1 was used to perform differential analysis
Assembly: hg38
Supplementary files format and content: counts.csv, csv format, containing the raw counts.

growth_protocol: NCI-H1299 cell lines were maintained in RPMI1640 medium (Gibco) supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidfied atmosphere with 5%CO2 at 37℃.

extract_protocol:
Total RNA isolated using RNAiso Plus (Takara).
RNA libraries for RNA-seq were prepared using Tru-seq Library Prep Kit following manufacturer's protocols

tag: cell line

value: lung adenocarcinoma

tag: genotype

value: FuHsi-konock down


title: P67 | 001 | TME

tag: tissue

tag: bestresponse

value: PR

tag: mortality

value: N

value: Male

value: Previous

value: 15 mos

value: TME


title: PRRSV Female Immune A7

description:
PRRSV Female Immune A7
P_F_i_7

tag: weaning

value: Immune


title: P67 | 002 | TME

value: HNSCC

value: TRUE

value: Nivolumab

tag: smokingstatus

tag: pfs

tag: responsesintme


title: P08 | 010 | TUMOUR

value: SD

tag: pathway

tag: age

tag: countofloweprgene

value: TUMOUR


title: P35_Baseline

tag: Stage

value: Pre-treatment

value: Whole blood


title: NCI-H1299 Sh1-1

tag: cell type


title: PRRSV Male Immune A1

description:
PRRSV Male Immune A1
P_M_i_1

value: Hypothalamus

tag: sampleID

value: PRRSV


title: PRRSV Female Immune A5

description:
PRRSV Female Immune A5
P_F_i_5

tag: mia

value: Female


title: P67 | 003 | TME

value: PR

tag: Sex

tag: percentofloweprgene

tag: foi

tag: responsesintumour


title: NCI-H1299 Puro-3

tag: cell line

value: lung adenocarcinoma

tag: genotype

value: WT


title: PRRSV Female Immune A4

description:
PRRSV Female Immune A4
P_F_i_4

tag: tissue

tag: weaning


title: P67 | 003 | TUMOUR

tag: bestresponse

tag: mortality

value: N

value: Male

tag: smokingstatus

value: Previous

tag: pfs


title: NCI-H1299 Puro-2


title: P16_Baseline


title: P15_Baseline


title: PRRSV Female Immune A3

description:
PRRSV Female Immune A3
P_F_i_3

tag: age

value: Immune


title: NCI-H1299 Sh1-2

value: FuHsi-konock down


title: P67 | 004 | TME

value: HNSCC

value: TRUE

tag: pathway

value: 15 mos

tag: countofloweprgene

value: TME

tag: responsesintme


title: P14_Baseline

tag: Stage

value: Pre-treatment


title: P13_Baseline

value: Whole blood


title: NCI-H1299 Puro-1

tag: cell type


title: PRRSV Female Immune A2

description:
PRRSV Female Immune A2
P_F_i_2

value: Hypothalamus

tag: sampleID

tag: mia

tag: Sex


title: PRRSV Female Immune A6

description:
PRRSV Female Immune A6
P_F_i_6

value: PRRSV


title: P9_Baseline


title: P67 | 002 | TUMOUR

value: Nivolumab

tag: percentofloweprgene

tag: foi

tag: responsesintumour

value: TUMOUR


title: P7_Baseline

tag: tissue


title: P10_Baseline


title: P67 | 004 | TUMOUR

tag: bestresponse

value: PR


title: K-562 cells, 711 48h, biol rep 3

city: Seoul

first: Marc

last: Diederich

address: Gwanak-ro, Gwanak-gu, 1

department: College of Pharmacy

country: South Korea

institute: Seoul National University

description:
Strand-specific cDNA library
711_48h_biol_rep_3

data_processing:
Raw fastq files were trimmed with cutadapt with default settings.
Salmon was employed for quantifying transcript and gene expression levels.
The tximeta R package was employed to import the transcript quantification data.
Differential expression analysis was performed using the DESeq2 R package.
Assembly: GRCh38
Supplementary files format and content: Normalized counts from DESeq2

molecule: polyA RNA

source_name: Blood

growth_protocol: K-562 cells were cultured  at 37 °C in a humid atmosphere and 5% CO2 in RPMI1640 medium supplemented with 10% heat-inactivated fetal bovin serum and  1% (v/v) antibiotics (streptomycin and penicillin) and antimycotic

extract_protocol:
Total RNA extraction, quantification and quality control were performed by Eurofins Genomics (Ebersberg, Germany)
RNA library construction was performed by Eurofins Genomics (Ebersberg, Germany); Strand-specific cDNA library

treatment_protocol: K-562 cells in exponential growth phase were treated with 5 µM Si-711 for 0, 8, 24 and 48 h

value: Blood

tag: cell line

value: lymphoblast, Chronic Myeloid Leukemia

tag: treatment

value: SIRT1/SIRT2 inhibitor


title: PRRSV Female Immune A1

description:
PRRSV Female Immune A1
P_F_i_1

value: Female

tag: weaning


title: K-562 cells, 711 48h, biol rep 2

description:
Strand-specific cDNA library
711_48h_biol_rep_2


title: Control Male Saline A9

description:
Control Male Saline A9
C_M_c_9

tag: age

value: Control

value: Male

value: Saline


title: P5_Baseline


title: P67 | 005 | TME

value: HNSCC

value: TRUE

tag: pathway

tag: mortality

value: N

tag: smokingstatus

value: Previous

tag: pfs


title: P67 | 005 | TUMOUR

value: 15 mos

tag: countofloweprgene

tag: responsesintme


title: K-562 cells, 711 48h, biol rep 1

description:
Strand-specific cDNA library
711_48h_biol_rep_1

tag: cell type


title: Control Male Saline A8

description:
Control Male Saline A8
C_M_c_8

value: Hypothalamus

tag: sampleID

tag: mia

tag: Sex


title: K-562 cells, 711 24h, biol rep 3

description:
Strand-specific cDNA library
711_24h_biol_rep_3


title: P67 | 006 | TME

tag: percentofloweprgene

tag: foi

tag: responsesintumour

value: TME


title: P6_Baseline

tag: Stage

value: Pre-treatment

tag: tissue

value: Whole blood


title: P4_Baseline


title: P3_Baseline


title: Control Male Saline A7

description:
Control Male Saline A7
C_M_c_7

tag: weaning


title: K-562 cells, 711 24h, biol rep 2

description:
Strand-specific cDNA library
711_24h_biol_rep_2

tag: cell line

tag: treatment


title: Rseq-1_S1_merged_L001_CC

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: Plasma derived extracellular vesicle RNA

data_processing:
RNAseq reads were quantified using Kallisto
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

value: not applicable

tag: genotype

value: CC


title: P67 | 006 | TUMOUR

tag: bestresponse

value: PR

tag: pathway

value: Nivolumab

tag: mortality

tag: age

tag: smokingstatus

value: TUMOUR


title: K-562 cells, 711 24h, biol rep 1

description:
Strand-specific cDNA library
711_24h_biol_rep_1

value: Blood

tag: cell type

value: lymphoblast, Chronic Myeloid Leukemia

value: SIRT1/SIRT2 inhibitor


title: Control Male Saline A6

description:
Control Male Saline A6
C_M_c_6

tag: sampleID

tag: mia

value: Control

value: Male

value: Saline


title: P2_Baseline


title: Rseq-4_S4_merged_L001_CC


title: P1_Baseline

description: Gene expression data from whole blood sample from patient with mCRPC at Pre-treatment stage with enzalutamide


title: K-562 cells, 711 8h, biol rep 3

description:
Strand-specific cDNA library
711_8h_biol_rep_3


title: Control Male Saline A4

description:
Control Male Saline A4
C_M_c_4

tag: Sex


title: P72 | 006 | Tumour

value: HNSCC

value: PD

value: TRUE

tag: pfs

tag: countofloweprgene

tag: percentofloweprgene

tag: foi

tag: responsesintme


title: Rseq-7_S7_merged_L001_CC

tag: tissue

tag: cell line


title: Rseq-6_S6_merged_L001_CC

tag: genotype

tag: treatment


title: K-562 cells, 711 8h, biol rep 2

description:
Strand-specific cDNA library
711_8h_biol_rep_2


title: Control Male Saline A5

description:
Control Male Saline A5
C_M_c_5

value: Hypothalamus

tag: weaning


title: Control Male Saline A3

description:
Control Male Saline A3
C_M_c_3


title: Rseq-5_S5_merged_L001_CC


title: K-562 cells, 711 8h, biol rep 1

description:
Strand-specific cDNA library
711_8h_biol_rep_1


title: P72 | 006 | TME

tag: bestresponse

tag: pathway

tag: mortality

tag: responsesintumour

value: TME


title: Rseq-9_S9_merged_L001_CC

value: Plasma

tag: cell type


title: P72 | 004 | Tumour

tag: age

tag: smokingstatus


title: K-562 cells, untreated, biol rep 3

description:
Strand-specific cDNA library
711_0h_biol_rep_3

value: Untreated


title: P67 | 001 | TUMOUR

value: N

tag: Sex

value: Previous

tag: pfs

value: 15 mos


title: Rseq-10_S10_merged_L001_CC

value: not applicable

value: CC


title: K-562 cells, untreated, biol rep 2

description:
Strand-specific cDNA library
711_0h_biol_rep_2

value: Blood

value: lymphoblast, Chronic Myeloid Leukemia


title: Control Male Saline A12

description:
Control Male Saline A12
C_M_c_12

tag: sampleID

tag: mia

value: Control


title: Control Male Saline A11

description:
Control Male Saline A11
C_M_c_11

value: Male


title: P72 | 004 | TME

tag: countofloweprgene

tag: percentofloweprgene

tag: foi

tag: responsesintme


title: Rseq-3_S3_merged_L001_CC

tag: tissue

tag: cell line

tag: genotype

tag: treatment


title: Control Male Saline A10

description:
Control Male Saline A10
C_M_c_10

tag: weaning

value: Saline


title: P72 | 003 | Tumour

value: HNSCC

tag: bestresponse

tag: pathway

tag: mortality

tag: responsesintumour

value: TUMOUR


title: Rseq-41_S41_merged_L001_CM-R⁻

tag: cell type

value: CM-R⁺


title: K-562 cells, untreated, biol rep 1

description:
Strand-specific cDNA library
711_0h_biol_rep_1


title: Rseq-35_S35_merged_L001_CM-R⁻


title: P72 | 003 | TME

value: PD

value: TRUE

tag: age

tag: Sex

tag: smokingstatus

tag: pfs


title: Control Male Saline A1

description:
Control Male Saline A1
C_M_c_1

value: Hypothalamus

tag: sampleID

tag: mia


title: Control Female Saline A9

description:
Control Female Saline A9
C_F_c_9

value: Female


title: lymphocytes, GFP+, Donor 206F (miRNA)

city: Montreal

first: Eric

middle: A

last: Cohen

state: Quebec

address: 110 Ave des Pins Ouest

country: Canada

institute: IRCM

data_processing:
Reads were aligned to the reference genome version GRCh38 using STAR version 2.5.1b
Raw counts for each feature from GRCh38 ENSEMBL v98 annotation file were extracted using FeatureCounts v1.6.0
DESeq2 version  1.24.0  was used to normalize gene readcounts and compute differential expression between conditions
GRCh38
Assembly: Matrix table with normalized gene counts for every miRNA and every sample

source_name: Human primary CD4+ T-cells

extract_protocol:
Total RNA was isolated from sorted cell populations using Rneasy kit from QIAGEN
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: individual

value: Human primary CD4+ T-cells

value: Infected/GFP+


title: Rseq-32_S32_merged_L001_CM-R⁻

tag: tissue

value: Plasma


title: P72 | 005 | TME

tag: countofloweprgene

tag: percentofloweprgene

tag: foi

value: TME

tag: responsesintme


title: P72 | 002 | Tumour

tag: bestresponse


title: P72 | 001 | TME

tag: pathway


title: Control Male Saline A2

description:
Control Male Saline A2
C_M_c_2

tag: weaning


title: Control Female Saline A8

description:
Control Female Saline A8
C_F_c_8


title: lymphocytes, uninfected, Donor 173M (miRNA)

tag: treatment

value: Uninfected


title: Rseq-34_S34_merged_L001_CM-R⁺

tag: cell line

value: not applicable

tag: cell type

tag: genotype


title: Control Female Saline A7

description:
Control Female Saline A7
C_F_c_7

tag: age

tag: Sex


title: lymphocytes, GFP+, Donor 173M (miRNA)


title: P72 | 001 | Tumour

tag: mortality

tag: smokingstatus

tag: pfs

tag: responsesintumour


title: Rseq-37_S37_merged_L001_CM-R⁺

tag: tissue


title: lymphocytes, uninfected, Donor 206F (miRNA)

tag: individual


title: Rseq-11_S11_merged_L001_CM-R⁺

value: CM-R⁻


title: P72 | 005 | Tumour

tag: countofloweprgene

tag: percentofloweprgene

tag: foi


title: Control Female Saline A6

description:
Control Female Saline A6
C_F_c_6

tag: sampleID

tag: mia

value: Control


title: Control Female Saline A5

description:
Control Female Saline A5
C_F_c_5

tag: weaning


title: lymphocytes, GFP-, Donor 173M (miRNA)

tag: treatment

value: Infected/GFP-


title: lymphocytes, uninfected, Donor 146M (miRNA)

tag: cell type


title: Rseq-23_S23_merged_L001_CM-R⁻

tag: cell line

tag: genotype


title: Rseq-21_S21_merged_L001_CM-R⁻


title: Control Female Saline A4

description:
Control Female Saline A4
C_F_c_4

tag: age

tag: Sex

value: Saline


title: P05 | 010 | TME

value: HNSCC

tag: bestresponse

tag: pathway

value: Nivolumab

tag: mortality

value: Y

value: Male

tag: smokingstatus

value: Previous

value: 2 mos

tag: responsesintme


title: lymphocytes, GFP-, Donor 206F (miRNA)

tag: individual


title: lymphocytes, GFP+, Donor 146M (miRNA)


title: Control Female Saline A3

description:
Control Female Saline A3
C_F_c_3

tag: tissue

value: Hypothalamus

value: Female


title: P72 | 002 | TME

value: PD

value: TRUE

tag: pfs

tag: countofloweprgene

tag: percentofloweprgene

tag: foi

tag: responsesintumour


title: lymphocytes, GFP-, Donor 146M (miRNA)

tag: cell type

value: Human primary CD4+ T-cells

tag: treatment


title: Rseq-47_S47_merged_L001_CM-R⁻

value: Plasma

tag: cell line

tag: genotype

value: CM-R⁺


title: Rseq-40_S40_merged_L001_CM-R⁺

value: not applicable


title: Control Female Saline A2

description:
Control Female Saline A2
C_F_c_2

tag: sampleID

tag: age

tag: mia

value: Control

tag: Sex

tag: weaning


title: lymphocytes, uninfected, Donor 206F (mRNA)

data_processing:
Reads were aligned to the reference genome version GRCh38 using STAR version 2.5.1b
Raw counts for each feature from GRCh38 ENSEMBL v98 annotation file were extracted using FeatureCounts v1.6.0
DESeq2 version  1.24.0  was used to normalize gene readcounts and compute differential expression between conditions
GRCh38
Assembly: Matrix table with normalized gene counts for every gene and every sample

value: Uninfected


title: Rseq-26_S26_merged_L001_CM-R⁺

value: CM-R⁻


title: P05 | 008 | Tumour

value: HNSCC

tag: bestresponse

tag: pathway

tag: mortality

tag: smokingstatus

tag: responsesintme

value: TUMOUR


title: lymphocytes, GFP+, Donor 206F (mRNA)

tag: individual

value: Infected/GFP+


title: Control Female Saline A1

description:
Control Female Saline A1
C_F_c_1

tag: tissue

value: Saline


title: Control Male Metabolic A9

description:
Control Male Metabolic A9
C_M_f_9

value: Male

value: Metabolic


title: lymphocytes, GFP-, Donor 206F (mRNA)

value: Infected/GFP-


title: Rseq-39_S39_merged_L001_CM-R⁺


title: P05 | 009 | TME

value: Nivolumab

value: Y

value: Previous

tag: pfs

value: 2 mos

tag: countofloweprgene

tag: percentofloweprgene

tag: foi

tag: responsesintumour

value: TME


title: P05 | 004 | TME

value: PD

value: TRUE


title: P08 | 002 | TUMOUR

value: SD

value: Never

value: 7 mos


title: Rseq-27_S27_merged_L001_CM-R⁻

value: Plasma

tag: cell line

value: not applicable

tag: cell type

tag: genotype

tag: treatment

value: CM-R⁺


title: P06 | 001 | TUMOUR

value: HNSCC

value: PR

tag: age

tag: Sex

value: 33 mos

value: TUMOUR


title: lymphocytes, uninfected, Donor 173M (mRNA)

value: Human primary CD4+ T-cells

value: Uninfected


title: Control Male Metabolic A7

description:
Control Male Metabolic A7
C_M_f_7

value: Hypothalamus

tag: sampleID

tag: mia

value: Control

value: Male

tag: weaning

value: Metabolic


title: Rseq-14_S14_merged_L001_CM-R⁺


title: P05 | 003 | Tumour

tag: bestresponse

value: PD

value: TRUE

tag: pathway

value: Nivolumab

tag: mortality

value: Y

tag: smokingstatus

value: Previous

value: 2 mos

tag: responsesintme


title: P05 | 010 | Tumour

tag: tissue

tag: pfs

tag: countofloweprgene

tag: percentofloweprgene


title: P05 | 009 | Tumour

tag: foi

tag: responsesintumour


title: P05 | 002 | Tumour


title: lymphocytes, GFP+, Donor 173M (mRNA)

tag: individual

tag: cell type

tag: treatment

value: Infected/GFP+


title: Control Male Metabolic A6

description:
Control Male Metabolic A6
C_M_f_6

tag: sampleID

tag: age

tag: Sex


title: Rseq-17_S17_merged_L001_CM-R⁺

value: Plasma

tag: cell line

value: not applicable

tag: genotype

value: CM-R⁺


title: P05 | 005 | TME

value: HNSCC

tag: bestresponse

tag: pathway

tag: mortality

value: TME


title: lymphocytes, GFP-, Donor 173M (mRNA)

value: Human primary CD4+ T-cells

value: Infected/GFP-


title: Control Male Metabolic A5

description:
Control Male Metabolic A5
C_M_f_5

tag: tissue

value: Hypothalamus

tag: mia

value: Control

tag: weaning


title: Rseq-24_S24_merged_L001_CM-R⁺


title: lymphocytes, uninfected, Donor 146M (mRNA)

value: Uninfected


title: P99 | 001 | Tumour

value: PD

value: Male

tag: smokingstatus

value: Current

tag: pfs

value: 3 mos

tag: countofloweprgene

tag: percentofloweprgene

tag: responsesintme

value: TUMOUR


title: P99 | 002 | TME

value: TRUE

value: Nivolumab

value: Y

tag: foi

tag: responsesintumour


title: Rseq-42_S42_merged_L001_CM-R⁺

value: Plasma

value: not applicable

tag: cell type

tag: treatment


title: Control Male Metabolic A8

description:
Control Male Metabolic A8
C_M_f_8

tag: sampleID

tag: age

tag: Sex

value: Metabolic


title: Control Male Metabolic A3

description:
Control Male Metabolic A3
C_M_f_3


title: lymphocytes, GFP+, Donor 146M (mRNA)

tag: individual

value: Infected/GFP+


title: Rseq-13_S13_merged_L001_CM-R⁻

tag: cell line

tag: genotype

value: CM-R⁺


title: lymphocytes, GFP-, Donor 146M (mRNA)

value: Human primary CD4+ T-cells

value: Infected/GFP-


title: ileum_cdp5, scBCR-seq

city: Saint Louis

first: Khai

last: Nguyen

state: MO

address: 425 South Euclid Ave, 8107, 8th floor BJCIH,

department: Pathology & Immunology

institute: Washington University in St. Louis

description: counts.txt.gz

data_processing:
Sample demultiplexing, barcode processing, and single-cell counting was performed using Cell Ranger suite. The Seurat R package (v4.0.4) was used for downstream analyses. Broad quality control was performed with cutoffs of < 15% mitochondrial content, > 200 and < 6000 unique features. Doublet removal was performed using DoubletFinder (v2.0.3). Samples from different batches were integrated using Seurat’s FindIntegrationAnchors and reciprocal principal component analysis (rPCA), and regressed on percentage of mitochondrial genes. Counts were normalized using SCTransform.
Assembly: GRch38
Supplementary files format and content: scRNA-seq:  count.txt (aggregated scRNA-seq matrix) and metadata.txt.  In count.txt, sample column "1" corresponds to metadata.txt 1st sample row (AAACCTGAGACCCACC-1_1), sample column "2" corresponds to metadata.txt 2nd sample row (AAACCTGAGATATGGT-1_1), and so on.
Supplementary files format and content: scTCR-seq:  filtered_contig_annotations_vdj_t.csv
Supplementary files format and content: scBCR-seq:  filtered_contig_annotations_vdj_b.csv
Library strategy: scBCR-seq

source_name: ileum

extract_protocol:
Live nucleated cells were sort-purified from mucosal cell suspensions as 7AAD-, MHC-I+ singlets.
Sorted cells were sequenced using 10X Genomics platform with chemistry version 2 at the Genome Technology Access Center at Washington University

tag: tissue

value: ileum

tag: condition

value: cdp


title: Rseq-19_S19_merged_L001_CM-R⁺


title: Control Male Metabolic A2

description:
Control Male Metabolic A2
C_M_f_2

value: Hypothalamus

tag: mia

value: Control

tag: weaning


title: P99 | 002 | Tumour

value: HNSCC

tag: bestresponse

value: PD

tag: pathway

tag: mortality

value: Male

tag: smokingstatus

value: Current

tag: pfs

tag: countofloweprgene


title: Control Male Metabolic A1

description:
Control Male Metabolic A1
C_M_f_1


title: Rseq-31_S31_merged_L001_CM-R⁻

tag: cell type

tag: treatment


title: pouch_cdp5, scBCR-seq

description: counts.txt.gz

source_name: pouch

value: pouch


title: ileum_cdp4, scBCR-seq

description: counts.txt.gz


title: RSeq-2_S2_merged_L001_CM-R⁻

value: CM-R⁻


title: P99 | 003 | Tumour

value: TRUE

value: Nivolumab

value: Y

tag: age

value: 3 mos

tag: percentofloweprgene

tag: foi

tag: responsesintumour

tag: responsesintme

value: TUMOUR


title: P99 | 003 | TME

tag: tissue

tag: Sex

value: TME


title: Control Female Metabolic A9

description:
Control Female Metabolic A9
C_F_f_9

tag: sampleID

tag: mia

value: Female

value: Metabolic


title: pouch_cdp4, scBCR-seq

description: counts.txt.gz

tag: condition

value: cdp


title: Rseq-22_S22_merged_L001_CM-R⁻

value: Plasma

tag: cell line

value: not applicable

tag: genotype

value: CM-R⁺


title: Control Female Metabolic A7

description:
Control Female Metabolic A7
C_F_f_7

value: Hypothalamus

value: Control

tag: weaning


title: P99 | 004 | Tumour

value: HNSCC

tag: bestresponse

value: PD

tag: pathway

tag: mortality

value: Male

tag: smokingstatus

value: Current

tag: pfs


title: Rseq-16_S16_merged_L001_CM-R⁻

tag: cell type

tag: treatment


title: ileum_cdp3, scBCR-seq

description: counts.txt.gz

value: ileum


title: P99 | 004 | TME

value: TRUE

value: Nivolumab

value: Y

tag: age

tag: countofloweprgene

tag: percentofloweprgene

tag: foi

tag: responsesintumour


title: P99 | 005 | TME

tag: tissue

tag: Sex

value: 3 mos

value: TME

tag: responsesintme


title: Control Male Metabolic A4

description:
Control Male Metabolic A4
C_M_f_4

tag: sampleID

tag: mia

value: Metabolic


title: Control Female Metabolic A6

description:
Control Female Metabolic A6
C_F_f_6

value: Female

tag: weaning


title: pouch_cdp3, scBCR-seq

description: counts.txt.gz

value: pouch

tag: condition

value: cdp


title: Rseq-45_S45_merged_L001_CM-R⁻

value: Plasma

tag: cell line

value: not applicable

tag: genotype

value: CM-R⁺


title: Control Female Metabolic A5

description:
Control Female Metabolic A5
C_F_f_5

value: Hypothalamus

value: Control


title: P99 | 005 | Tumour

value: HNSCC

tag: bestresponse

value: PD

tag: pathway

tag: mortality

value: Male

tag: smokingstatus

tag: pfs

value: TUMOUR


title: P99 | 006 | TME

value: TRUE

value: Nivolumab

tag: age

value: Current

tag: countofloweprgene

tag: percentofloweprgene


title: Rseq-30_S30_merged_L001_CM-R⁻

tag: tissue

tag: cell type

tag: treatment

value: CM-R⁻


title: Rseq-15_S15_merged_L001_CM-R⁻


title: Rseq-43_S43_merged_L001_CM-R⁻


title: Control Female Metabolic A4

description:
Control Female Metabolic A4
C_F_f_4

tag: sampleID

tag: Sex

value: Metabolic


title: pouch_cdp1, scBCR-seq

description: counts.txt.gz


title: Control Female Metabolic A8

description:
Control Female Metabolic A8
C_F_f_8

tag: mia

value: Female

tag: weaning


title: P99 | 006 | Tumour

value: Y

value: 3 mos

tag: foi

tag: responsesintumour

tag: responsesintme


title: Control Female Metabolic A2

description:
Control Female Metabolic A2
C_F_f_2


title: pouch_ctrl5, scBCR-seq

description: counts.txt.gz

value: pouch

tag: condition

value: ctrl


title: ileum_ctrl5, scBCR-seq

description: counts.txt.gz

value: ileum


title: Control Female Metabolic A3

description:
Control Female Metabolic A3
C_F_f_3

value: Hypothalamus


title: Control Female Metabolic A10

description:
Control Female Metabolic A10
C_F_f_10

value: Control


title: ileum_ctrl4, scBCR-seq

description: counts.txt.gz


title: Rseq-33_S33_merged_L001_CM-R⁻

value: Plasma

tag: cell line

value: not applicable

tag: genotype


title: Rseq-29_S29_merged_L001_CM-R⁻


title: P11 | 005 | Tumour

value: HNSCC

tag: bestresponse

value: PR

tag: pathway

value: Epacadostat+Pembrolizumab

tag: mortality

value: Male

tag: smokingstatus

value: Previous

tag: pfs

value: 14 mos


title: P11 | 005 | TME

tag: tissue

value: TRUE

tag: age

tag: countofloweprgene

tag: percentofloweprgene

value: TME


title: Control Female Metabolic A1

description:
Control Female Metabolic A1
C_F_f_1

tag: sampleID

tag: mia

tag: Sex

value: Female

value: Metabolic


title: P99 | 001 | TME

value: PD

value: Nivolumab

value: Y

value: Current

value: 3 mos

tag: foi

tag: responsesintumour


title: Control Male Immune A9

description:
Control Male Immune A9
C_M_i_9

value: Hypothalamus

value: Control

tag: weaning

value: Immune


title: pouch_ctrl4, scBCR-seq

description: counts.txt.gz

value: pouch

tag: condition

value: ctrl


title: ileum_cdp1, scBCR-seq

description: counts.txt.gz

value: ileum

value: cdp


title: P11 | 004 | Tumour

value: HNSCC

value: PR

value: Epacadostat+Pembrolizumab

value: Male

value: Previous

value: 14 mos

tag: responsesintme

value: TUMOUR


title: P11 | 004 | TME

tag: bestresponse

value: TRUE

value: Y

value: TME


title: Rseq-46_S46_merged_L001_CM-R⁻

value: Plasma

tag: cell line

value: not applicable

tag: cell type

tag: genotype

tag: treatment

value: CM-R⁻


title: ileum_ctrl3, scBCR-seq

description: counts.txt.gz

tag: tissue


title: Rseq-20_S20_merged_L001_CM-R⁻


title: Control Male Immune A8

description:
Control Male Immune A8
C_M_i_8

value: Hypothalamus

tag: age

value: Control

value: Immune


title: Rseq-28_S28_merged_L001_CM-R⁻


title: Rseq-18_S18_merged_L001_CM-R⁻


title: Control Male Immune A7

description:
Control Male Immune A7
C_M_i_7


title: ileum_ctrl2, scBCR-seq

description: counts.txt.gz

value: ileum

value: ctrl


title: Rseq-36_S36_merged_L001_CM-R⁻


title: Control Male Immune A6

description:
Control Male Immune A6
C_M_i_6


title: pouch_ctrl2, scBCR-seq

description: counts.txt.gz

value: pouch


title: ileum_ctrl1, scBCR-seq

description: counts.txt.gz


title: P11 | 003 | Tumour

value: HNSCC

value: PR

tag: pathway

value: Epacadostat+Pembrolizumab

tag: mortality

tag: smokingstatus

tag: pfs

tag: countofloweprgene


title: Control Male Immune A5

description:
Control Male Immune A5
C_M_i_5

tag: sampleID

tag: mia

tag: Sex

value: Male


title: P11 | 003 | TME

value: Previous

value: 14 mos

tag: percentofloweprgene

tag: foi

tag: responsesintumour


title: ileum_cdp6, scTCR-seq

description: counts.txt.gz

data_processing:
Sample demultiplexing, barcode processing, and single-cell counting was performed using Cell Ranger suite. The Seurat R package (v4.0.4) was used for downstream analyses. Broad quality control was performed with cutoffs of < 15% mitochondrial content, > 200 and < 6000 unique features. Doublet removal was performed using DoubletFinder (v2.0.3). Samples from different batches were integrated using Seurat’s FindIntegrationAnchors and reciprocal principal component analysis (rPCA), and regressed on percentage of mitochondrial genes. Counts were normalized using SCTransform.
Assembly: GRch38
Supplementary files format and content: scRNA-seq:  count.txt (aggregated scRNA-seq matrix) and metadata.txt.  In count.txt, sample column "1" corresponds to metadata.txt 1st sample row (AAACCTGAGACCCACC-1_1), sample column "2" corresponds to metadata.txt 2nd sample row (AAACCTGAGATATGGT-1_1), and so on.
Supplementary files format and content: scTCR-seq:  filtered_contig_annotations_vdj_t.csv
Supplementary files format and content: scBCR-seq:  filtered_contig_annotations_vdj_b.csv
Library strategy: scTCR-seq

tag: condition

value: cdp


title: Control Male Immune A4

description:
Control Male Immune A4
C_M_i_4

tag: weaning


title: P11 | 002 | Tumour

tag: bestresponse

value: TRUE

value: Y

tag: responsesintme

value: TUMOUR


title: P11 | 001 | Tumour

tag: tissue


title: Rseq-44_S44_merged_L001_CM-R⁻

value: Plasma

tag: cell line

value: not applicable

tag: cell type

tag: genotype

tag: treatment

value: CM-R⁻


title: P11 | 002 | TME

tag: pathway

tag: mortality

tag: age

tag: smokingstatus

tag: pfs

value: TME


title: pouch_cdp6, scTCR-seq

description: counts.txt.gz


title: Rseq-12_S12_merged_L001_CM-R⁻


title: Control Male Immune A2

description:
Control Male Immune A2
C_M_i_2

value: Hypothalamus

tag: sampleID

tag: mia

value: Control

tag: Sex

value: Immune


title: Rseq-38_S38_merged_L001_CM-R⁻


title: P11 | 001 | TME

value: HNSCC

tag: countofloweprgene

tag: percentofloweprgene

tag: foi

tag: responsesintumour


title: ileum_cdp5, scTCR-seq

description: counts.txt.gz

tag: tissue

value: ileum

tag: condition


title: P11 | 006 | Tumour

tag: bestresponse

value: PR

value: Epacadostat+Pembrolizumab

tag: responsesintme


title: pouch_ctrl3, scBCR-seq

description: counts.txt.gz

value: pouch

value: ctrl


title: pouch_cdp5, scTCR-seq

description: counts.txt.gz

value: cdp


title: CTRLsiKDM3B_Input_CTCF_exp1_rep2

city: Boston

first: Kashish

last: Chetal

state: MA

address: 55 Fruit St

department: Molecular biology

institute: MGH

description: Control input CTCF experiment 1 replicate 2

data_processing:
Sequencing reads were aligned against the hg19 reference genome using BWA (PMID:20080505). Alignmentswere filtered for uniquely mapped readsand duplicateswere removed.
ChIP over Input ratio coverage tracks weregenerated using deepTools (PMID:27079975).
Peaks were called using HOMER(PMID:20513432) with defaultparameters.

source_name: RPE

extract_protocol:
Cells were fixed with 1% formaldehyde for 13 minutes. After quenching and cell lysis, chromatin was sonicated using a Q800R3 sonicator (QSonica).
ChIP-seq libraries were prepared using the Illumina TruSeq ChIP Library Preparation Kit Set A and B with associated index barcode adapters. 1 ng or 30µL of DNA was used as starting material for input and ip samples. Libraries were amplified using 14 cycles on the thermocycler. Post amplification libraries were cleaned up using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity D1000 DNA Kit.

tag: antibody

value: CTCF

tag: cell line

value: RPE

tag: cell type

value: Retinal pigment epithelial

tag: treatment

value: siRNA Knockdown


title: Control Male Immune A1

description:
Control Male Immune A1
C_M_i_1

tag: age

value: Male

tag: weaning


title: Control Male Immune A10

description:
Control Male Immune A10
C_M_i_10

tag: sampleID


title: ileum_cdp4, scTCR-seq

description: counts.txt.gz


title: P86 | 001 | Tumour

value: PD

value: TRUE

tag: pathway

value: Nivolumab

tag: mortality

value: Y

tag: smokingstatus

value: Previous

tag: pfs

value: 1 mos

value: TUMOUR


title: Rseq-25_S25_merged_L001_CM-R⁻

value: Plasma

value: not applicable

tag: genotype

value: CM-R⁻


title: pouch_cdp4, scTCR-seq

description: counts.txt.gz

value: pouch


title: siCTRL_2_CTCF_exp1_rep2

description: Control siKDM3B CTCF experiment 1 replicate 2


title: pouch_cdp3, scTCR-seq

description: counts.txt.gz

value: cdp


title: ileum_cdp3, scTCR-seq

description: counts.txt.gz

value: ileum


title: Control Female Immune A7

description:
Control Female Immune A7
C_F_i_7

value: Hypothalamus

tag: mia

value: Control

tag: Sex

value: Female

value: Immune


title: CTRLsiKDM3B_Input_CTCF_exp1_rep1

description: Control input CTCF experiment 1 replicate 1

value: CTCF

value: RPE

value: Retinal pigment epithelial

value: siRNA Knockdown


title: Control Female Immune A8

description:
Control Female Immune A8
C_F_i_8

tag: tissue


title: siCTRL_1_CTCF_exp1_rep1

description: Control siKDM3B CTCF experiment 1 replicate 1


title: P86 | 003 | TME

value: HNSCC

tag: bestresponse

value: PD

value: TRUE

value: Nivolumab

value: Y

value: Male

value: Previous

tag: countofloweprgene

tag: percentofloweprgene

tag: foi

tag: responsesintumour

value: TME


title: P86 | 002 | Tumour

value: 1 mos

tag: responsesintme

value: TUMOUR


title: Control Female Immune A9

description:
Control Female Immune A9
C_F_i_9

value: Hypothalamus

tag: age

value: Control


title: ileum_cdp2, scTCR-seq

description: counts.txt.gz

value: ileum

tag: condition

value: cdp


title: pouch_cdp2, scTCR-seq

description: counts.txt.gz

value: pouch


title: Control Male Immune A3

description:
Control Male Immune A3
C_M_i_3

tag: sampleID

tag: weaning

value: Immune


title: siKDM3B_58_CTCF_exp1_rep2

description: siKDM3B (#58) CTCF experiment 1 replicate 2

tag: antibody

value: CTCF

tag: cell line

value: RPE

tag: cell type

value: Retinal pigment epithelial

tag: treatment

value: siRNA Knockdown


title: Control Female Immune A5

description:
Control Female Immune A5
C_F_i_5

tag: mia

value: Female


title: Rseq-48_S48_merged_L001_CM-R⁻

value: Plasma

value: not applicable

tag: genotype

value: CM-R⁻


title: P11 | 006 | TME

tag: tissue

value: HNSCC

value: PR

value: TRUE

tag: pathway

value: Epacadostat+Pembrolizumab

tag: mortality

value: Y

tag: Sex

value: Male

tag: smokingstatus

value: Previous

tag: pfs

value: 14 mos

value: TME


title: P86 | 003 | Tumour

tag: bestresponse

value: PD

value: Nivolumab

value: 1 mos

tag: countofloweprgene

tag: percentofloweprgene

tag: foi

tag: responsesintumour

tag: responsesintme

value: TUMOUR


title: ileum_cdp1, scTCR-seq

description: counts.txt.gz

value: ileum

tag: condition

value: cdp


title: P86 | 002 | TME

tag: age


title: Control Female Immune A3

description:
Control Female Immune A3
C_F_i_3

value: Hypothalamus

tag: sampleID

value: Control

value: Female

tag: weaning

value: Immune


title: P86 | 004 | TME

value: HNSCC

value: TRUE


title: pouch_cdp1, scTCR-seq

description: counts.txt.gz

value: pouch


title: Control Female Immune A4

description:
Control Female Immune A4
C_F_i_4

tag: mia


title: siKDM3B_57_CTCF_exp1_rep1

description: siKDM3B (#57) CTCF experiment 1 replicate 1

tag: antibody

value: CTCF

tag: cell line

value: RPE

tag: cell type

value: Retinal pigment epithelial

tag: treatment

value: siRNA Knockdown


title: P86 | 005 | TME

tag: tissue

value: PD

tag: pathway

tag: mortality

value: Y

tag: Sex

value: Male

tag: smokingstatus

value: Previous

value: TME


title: P86 | 004 | Tumour

tag: bestresponse

value: Nivolumab

tag: pfs

value: 1 mos

tag: countofloweprgene

tag: percentofloweprgene

tag: foi

value: TUMOUR


title: CTRLsiKDM3B_Input_exp1_rep2

description: Control siKDM3B input experiment 1 replicate 2

value: Input


title: siKDM3B_58_Input_CTCF_exp1_rep2

description: siKDM3B (#58) input CTCF  experiment 1 replicate 2


title: Control Female Immune A12

description:
Control Female Immune A12
C_F_i_12

value: Hypothalamus

tag: sampleID

tag: age

value: Control

value: Female

value: Immune


title: ileum_ctrl5, scTCR-seq

description: counts.txt.gz

value: ileum

tag: condition

value: ctrl


title: pouch_ctrl5, scTCR-seq

description: counts.txt.gz

value: pouch


title: Control Female Immune A11

description:
Control Female Immune A11
C_F_i_11

tag: mia

tag: weaning


title: ileum_ctrl4, scTCR-seq

description: counts.txt.gz


title: P86 | 006 | TME

value: HNSCC

value: TRUE

tag: responsesintumour

tag: responsesintme


title: P86 | 005 | Tumour

tag: tissue

value: PD

value: Y


title: CTRLsiKDM3B_Input_exp1_rep1

description: Control siKDM3B input experiment 1 replicate 1

tag: antibody

tag: cell line

value: RPE

tag: cell type

value: Retinal pigment epithelial

tag: treatment

value: siRNA Knockdown


title: pouch_ctrl4, scTCR-seq

description: counts.txt.gz


title: Control Female Immune A10

description:
Control Female Immune A10
C_F_i_10

tag: Sex


title: P86 | 006 | Tumour

tag: bestresponse

tag: pathway

value: Nivolumab

tag: mortality

value: Male

tag: smokingstatus

value: Previous

tag: pfs

value: 1 mos


title: Control Female Immune A1

description:
Control Female Immune A1
C_F_i_1

value: Hypothalamus

tag: sampleID

tag: age

value: Control


title: P86 | 001 | TME

tag: countofloweprgene

tag: percentofloweprgene

tag: foi

value: TME


title: siKDM3B_57_Input_CTCF_exp1_rep1

description: siKDM3B (#57) input CTCF  experiment 1 replicate 1

value: Input


title: ileum_ctrl3, scTCR-seq

description: counts.txt.gz

value: ileum

tag: condition

value: ctrl


title: CTRLsiKDM3B_H3K9me2_exp1_rep1

description: Control siKDM3B H3K9me2 experiment 1 replicate 1


title: Control Female Immune A2

description:
Control Female Immune A2
C_F_i_2

tag: tissue

tag: mia

value: Female

tag: weaning

value: Immune


title: Msn2_3_24h

city: Kunming City, Yunnan Province

first: Liu

last: Qianqian

address: No.2 Cuihu North Road, Wuhua District

institute: Yunnan University

description: original provided organism name: Arthrobotrys oligospora

data_processing:
The data from high-throughput sequencing were analyzed using the OmicShare tools, a free online platform for data analysis (www.majorbio.com).
Assembly: https://www.ncbi.nlm.nih.gov/assembly/GCF_000225545.1
Supplementary files format and content: Expression analysis table include TPM values for each sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Orbilia oligospora

source_name: Fungal hyphae cells

growth_protocol: The WT and ΔAomsn2 strains were cultured in a PDA medium for 7 days. Afterward, 200 C. elegans cells were added to each plate for 24 hours.

extract_protocol:
After collecting the samples, RNA was extracted with the AxyPrep Multisource RNA Miniprep Kit (Axygen, Jiangsu, China)
The libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Mycelium was collected and washed three times with 0.1 mphosphate buffer saline (PBS) (pH 6.8-7.2).

value: Fungal hyphae

tag: genotype

value: 24 hours of contact with C. elegans cells


title: P61 | 001 | TME

data_processing: Counts were aligned and ERCC corrected automatically on the DSP instrument. This QC data was exported for analysis.

value: HNSCC

value: CR

value: TRUE

value: Pembrolizumab

value: N

value: 78 mos

tag: responsesintumour

tag: responsesintme


title: CTRLsiKDM3B_H3K9me2_exp1_rep2

description: Control siKDM3B H3K9me2 experiment 1 replicate 2

tag: antibody

tag: cell line

value: RPE

tag: cell type

value: Retinal pigment epithelial

tag: treatment

value: siRNA Knockdown


title: CTRLsiKDM3B_H3K9me1_exp1_rep1

description: Control siKDM3B H3K9me1 experiment 1 replicate 1


title: pouch_ctrl3, scTCR-seq

description: counts.txt.gz

value: pouch


title: ileum_ctrl2, scTCR-seq

description: counts.txt.gz


title: Control Female Immune A6

description:
Control Female Immune A6
C_F_i_6

value: Hypothalamus

value: Control

tag: Sex


title: siKDM3B_57_Input_exp1_rep2

description: siKDM3B (#57) input experiment 1 replicate 2

value: Input


title: Msn2_2_24h


title: Msn2_1_24h


title: pouch_ctrl1, scTCR-seq

description: counts.txt.gz

value: ctrl


title: ileum_cdp6, scRNA-seq

description:
counts.txt.gz
metadata.txt

data_processing:
Sample demultiplexing, barcode processing, and single-cell counting was performed using Cell Ranger suite. The Seurat R package (v4.0.4) was used for downstream analyses. Broad quality control was performed with cutoffs of < 15% mitochondrial content, > 200 and < 6000 unique features. Doublet removal was performed using DoubletFinder (v2.0.3). Samples from different batches were integrated using Seurat’s FindIntegrationAnchors and reciprocal principal component analysis (rPCA), and regressed on percentage of mitochondrial genes. Counts were normalized using SCTransform.
Assembly: GRch38
Supplementary files format and content: scRNA-seq:  count.txt (aggregated scRNA-seq matrix) and metadata.txt.  In count.txt, sample column "1" corresponds to metadata.txt 1st sample row (AAACCTGAGACCCACC-1_1), sample column "2" corresponds to metadata.txt 2nd sample row (AAACCTGAGATATGGT-1_1), and so on.
Supplementary files format and content: scTCR-seq:  filtered_contig_annotations_vdj_t.csv
Supplementary files format and content: scBCR-seq:  filtered_contig_annotations_vdj_b.csv

value: ileum

value: cdp


title: P61 | 002 | TME

tag: bestresponse

tag: pathway

tag: mortality

value: Male

tag: smokingstatus

value: Previous

tag: pfs

value: TME


title: CTRLsiKDM3B_H3K9me1_exp1_rep2

description: Control siKDM3B H3K9me1 experiment 1 replicate 2


title: Msn2_2_0h

value: Fungal hyphae

value: no contact with C. elegans cells


title: P61 | 002 | Tumour

value: HNSCC

value: CR

value: TRUE

value: Pembrolizumab

value: N

tag: age

tag: countofloweprgene

tag: percentofloweprgene

tag: foi

value: TUMOUR


title: P61 | 003 | TME

tag: tissue

value: 78 mos


title: Msn2_3_0h

tag: genotype


title: siKDM3B_57_H3K9me1_exp1_rep2

description: siKDM3B (#57) H3K9me1 experiment 1 replicate 2

value: RPE

value: Retinal pigment epithelial

value: siRNA Knockdown


title: siKDM3B_57_H3K9me2_exp1_rep2

description: siKDM3B (#57) H3K9me2 experiment 1 replicate 2


title: siKDM3B_58_Input_exp1_rep1

description: siKDM3B (#58) input experiment 1 replicate 1

value: Input


title: pouch_cdp6, scRNA-seq

description:
counts.txt.gz
metadata.txt

value: pouch

tag: condition

value: cdp


title: Msn2_1_0h


title: P61 | 003 | Tumour

value: Male

value: Previous

tag: responsesintumour

tag: responsesintme


title: P61 | 004 | TME

value: TME


title: P61 | 004 | Tumour


title: siKDM3B_58_H3K9me2_exp1_rep1

description: siKDM3B (#58) H3K9me2 experiment 1 replicate 1

tag: antibody

tag: cell line

tag: cell type


title: ileum_cdp5, scRNA-seq

description:
counts.txt.gz
metadata.txt

value: ileum


title: pouch_cdp5, scRNA-seq

description:
counts.txt.gz
metadata.txt


title: siKDM3B_58_H3K9me1_exp1_rep1

description: siKDM3B (#58) H3K9me1 experiment 1 replicate 1

tag: treatment


title: AO_3_24h

value: Fungal hyphae

value: WT

value: 24 hours of contact with C. elegans cells


title: siKDM3B_58_H3K9me1_rep2

description: siKDM3B (#58) H3K9me1 replicate 2

data_processing:
Sequencing reads were aligned against the hg19 reference genome using BWA (PMID: 20080505). Alignments were filtered for uniquely mapped reads and duplicates were removed.
ChIP over Input ratio coverage tracks were generated using deepTools (PMID: 27079975).
Peaks were called using HOMER (PMID: 20513432) with default parameters.


title: AO_2_24h


title: P61 | 005 | Tumour

value: HNSCC

tag: bestresponse

value: CR

value: TRUE

tag: pathway

value: Pembrolizumab

tag: Sex


title: AO_1_24h


title: P61 | 005 | TME

tag: mortality

value: N

tag: smokingstatus

tag: pfs

value: 78 mos


title: P61 | 006 | TME

tag: age

tag: countofloweprgene

tag: percentofloweprgene


title: siKDM3B_58_siG9A_70_H3K9me1_rep2

description: siKDM3b (#58) siG9A (#70) H3K9me1 replicate 1

value: RPE

value: Retinal pigment epithelial

value: siRNA Knockdown


title: siKDM3B_58_siG9A_70_Input_rep2

description: siKDM3b (#58) siG9A (#70) input replicate 1


title: pouch_cdp3, scRNA-seq

description:
counts.txt.gz
metadata.txt

tag: tissue

value: pouch

value: cdp


title: AO_2_0h

tag: genotype

value: no contact with C. elegans cells


title: AO_1_0h


title: siKDM3B_43_H3K9me1_rep1

description: siKDM3B (#43) H3K9me1 replicate 1


title: siKDM3B_43_Input_rep1

description: siKDM3B (#43) input replicate 1


title: ileum_cdp3, scRNA-seq

description:
counts.txt.gz
metadata.txt

tag: condition


title: Bulk ATAC-seq IR dermal cell D7-3

description: ATAC-seq

value: skin

value: Dermal cells

value: Male

value: Irradiated


title: P61 | 006 | Tumour

value: Previous

tag: foi

tag: responsesintumour

tag: responsesintme

value: TUMOUR


title: Bulk ATAC-seq IR dermal cell D7-2

description: ATAC-seq

tag: cell type


title: P61 | 001 | Tumour

value: HNSCC

value: CR


title: pouch_cdp2, scRNA-seq

description:
counts.txt.gz
metadata.txt


title: ileum_cdp4, scRNA-seq

description:
counts.txt.gz
metadata.txt

value: ileum


title: siKDM3B_43_siG9A_69_H3K9me1_rep1

description: siKDM3b (#43) siG9A (#69) H3K9me1 replicate 1

tag: cell line

tag: antibody

tag: treatment


title: P33 | 002 | TME

tag: bestresponse

value: PD

value: TRUE

tag: pathway

value: Nivolumab

value: Y

tag: Sex

value: 2 mos

value: TME


title: ileum_cdp1, scRNA-seq

description:
counts.txt.gz
metadata.txt

value: cdp


title: siKDM3B_58_Input_rep1

description: siKDM3B (#58) input replicate 2

value: RPE

value: Retinal pigment epithelial

value: siRNA Knockdown


title: P33 | 001 | TUMOUR

tag: mortality

value: Male

tag: smokingstatus

tag: pfs


title: pouch_cdp4, scRNA-seq

description:
counts.txt.gz
metadata.txt

value: pouch


title: P33 | 002 | TUMOUR

tag: age

value: Previous

tag: countofloweprgene

tag: percentofloweprgene


title: pouch_cdp1, scRNA-seq

description:
counts.txt.gz
metadata.txt

tag: tissue

tag: condition


title: P33 | 003 | TUMOUR

tag: foi

tag: responsesintumour

value: TUMOUR


title: Bulk ATAC-seq IR dermal cell D7-1

description: ATAC-seq

value: skin

tag: cell type

value: Dermal cells

value: Irradiated


title: AO_3_0h

value: Fungal hyphae

tag: genotype

value: WT

value: no contact with C. elegans cells


title: Bulk ATAC-seq Ctr dermal cell 3

description: ATAC-seq

value: Non-irradiated


title: ileum_cdp2, scRNA-seq

description:
counts.txt.gz
metadata.txt

value: ileum


title: P33 | 004 | TME

value: HNSCC

value: PD

value: TRUE

value: Nivolumab

value: Y

value: 2 mos

value: TME

tag: responsesintme


title: siKDM3B_58_H3K9me3_rep2

description: siKDM3B (#58) H3K9me3 replicate 2

tag: cell line

value: RPE

value: Retinal pigment epithelial

tag: antibody

tag: treatment

value: siRNA Knockdown


title: ileum_ctrl5, scRNA-seq

description:
counts.txt.gz
metadata.txt

value: ctrl


title: Bulk ATAC-seq Ctr dermal cell 1

description: ATAC-seq

value: skin

value: Dermal cells

tag: Sex

value: Male


title: siKDM3B_58_H3K9ME2_rep2

description: siKDM3B (#58) H3K9me2 replicate 2


title: pouch_ctrl5, scRNA-seq

description:
counts.txt.gz
metadata.txt

value: pouch


title: Bulk ATAC-seq Ctr dermal cell 2

description: ATAC-seq

value: Non-irradiated


title: P33 | 005 | TUMOUR

tag: bestresponse

tag: pathway

tag: mortality

value: Previous

value: TUMOUR


title: siKDM3B_58_siG9A_70_H3K9ME3_rep2

description: siKDM3b (#58) siG9A (#70) H3K9me3 replicate 1


title: pouch_ctrl4, scRNA-seq

description:
counts.txt.gz
metadata.txt


title: ileum_ctrl4, scRNA-seq

description:
counts.txt.gz
metadata.txt

value: ileum


title: Bulk ATAC-seq IR dermal fibroblasts D1-3

description: ATAC-seq

value: Dermal fibroblast

tag: age

value: Irradiated


title: P33 | 004 | TUMOUR

value: HNSCC

value: PD

value: TRUE

value: Nivolumab

value: Y

tag: smokingstatus

tag: pfs

tag: countofloweprgene


title: siKDM3B_58_siG9A_70_H3K9ME2_rep2

description: siKDM3b (#58) siG9A (#70) H3K9me2 replicate 1

value: RPE

value: Retinal pigment epithelial

value: siRNA Knockdown


title: P33 | 006 | TME

tag: tissue

value: 2 mos

tag: percentofloweprgene

value: TME


title: siKDM3B_43_siG9A_69_Input_rep1

description: siKDM3b (#43) siG9A (#69) input replicate 1


title: ileum_ctrl3, scRNA-seq

description:
counts.txt.gz
metadata.txt

tag: condition

value: ctrl


title: siKDM3B_43_H3K9me3_rep1

description: siKDM3B (#43) H3K9me3 replicate 1

tag: cell type


title: Bulk ATAC-seq IR dermal fibroblasts D1-2

description: ATAC-seq

value: skin

value: Male


title: Bulk ATAC-seq IR dermal fibroblasts D1-1

description: ATAC-seq


title: siKDM3B_43_H3K9ME2_rep1

description: siKDM3B (#43) H3K9me2 replicate 1


title: P33 | 006 | TUMOUR

value: Previous

tag: foi

tag: responsesintumour

value: TUMOUR


title: P33 | 001 | TME

tag: responsesintme


title: ileum_ctrl2, scRNA-seq

description:
counts.txt.gz
metadata.txt

value: ileum


title: pouch_ctrl3, scRNA-seq

description:
counts.txt.gz
metadata.txt

value: pouch


title: Bulk ATAC-seq Ctr dermal fibroblasts 1

description: ATAC-seq

value: Dermal fibroblast

value: Non-irradiated


title: Bulk ATAC-seq Ctr dermal fibroblasts 2

description: ATAC-seq


title: P28 | 005 | TME

value: HNSCC

value: PD

value: TRUE

value: 3 mos


title: P28 | 006 | TUMOUR

value: Nivolumab

value: Y


title: siKDM3B_43_siG9A_69_H3K9ME2_rep1

description: siKDM3b (#43) siG9A (#69) H3K9me2 replicate 1

tag: cell line

value: RPE

value: Retinal pigment epithelial

tag: antibody

value: siRNA Knockdown


title: pouch_ctrl2, scRNA-seq

description:
counts.txt.gz
metadata.txt

value: ctrl


title: siG9A_70_H3K9me1_rep2

description: siG9A (#70) H3K9me1 replicate 2

tag: treatment


title: ΔvanAB Hfq:3xFLAG pBVMCS6-EV 15´Vanillate Plus R3

city: Würzburg

first: Manuel

last: Velasco Gomariz

address: Josef-Schneider-Straße 2/D15

institute: Helmholtz Institute for RNA-based Infection Research (HIRI)

data_processing:
Pipeline for RNAseq analysis CLC Genomics Workbench 22.0.2
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomics Workbench 22.0.2 (parameter-Quality limit: 0.05)
Trimmed sequence reads were mapped to NC_011916.1 using CLC Genomics Workbench 22.0.2 (parameters-mismatch cost:2 insertion cost:3 deletion cost:3 lenght fraction: 0.8 similarity fraction: 0.8 strand specific:rev)
Read count extraction and normalization were performed using CLC genomic workbench
Assembly: NCBI Reference Sequence: NC_011916.1
Supplementary files format and content: xlsx file including TPM from each sample

organism: Caulobacter vibrioides

growth_protocol: Growth in PYE-Medium, 200 rpm shaking, 30 °C until OD 0.4

extract_protocol:
UV-crosslinking, mechanic cell lysis with glass beads, pull-down with streptavidin beads & DNA-antisense oligo to AbnZ/scrambled. RNA extraction with Trizol, following DNase treatment/Pci extraction
RNA libraries for RNAseq were prepared using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® following manufacturer´s protocol

treatment_protocol: 500 µM Vanillate, 15´

tag: strain

tag: genotype

value: {delta}vanAB Hfq:3xFLAG pBVMCS6-AbnZ

value: 500 uM Vanilalte


title: siG9A_69_H3K9me1_rep1

description: siG9A (#69) H3K9me1 replicate 1


title: pouch_ctrl1, scRNA-seq

description:
counts.txt.gz
metadata.txt


title: ΔvanAB Hfq:3xFLAG pBVMCS6-EV 15´Vanillate Plus R1


title: ΔvanAB Hfq:3xFLAG pBVMCS6-EV 15´Vanillate Plus R2


title: siKDM3B_43_siG9A_69_H3K9ME3_rep1

description: siKDM3b (#43) siG9A (#69) H3K9me3 replicate 1


title: ΔvanAB Hfq:3xFLAG pBVMCS6-AbnZ 15´Vanillate Minus R2


title: siG9A_70_Input_rep2

description: siG9A (#70) input replicate 2


title: SW480 cells, shRBM39, rep3

city: shenyang

first: Yuxin

last: He

address: 77 Puhe Road, Shenbei New District

institute: China Medical University

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.
They were mapped to the reference genome using STAR software (version 2.5.3a) with default parameters.
Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKM was calculated.
Genes differentially expressed between groups were identified using the edgeR package (version 3.12.1).
Alternative splicing events were detected by using rMATS (version 3.2.5) with a FDR value cutoff of 0.05 and an absolute value of Δψ of 0.05.
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: All_reads_counts.txt and All_samples_rpkm.txt show raw counts and RPKM.
Supplementary files format and content: TargetAndJunction_event_records.txt file shows results after shRBM39 samples are compared to shCtrl samples (provided by sequencing company). Group1, Group2 and Group3 represent AS events resulting from three replicate comparisons of shRBM39 versus shCtrl samples.
Supplementary files format and content: ASEvent_summary.txt shows a statistical table of AS events from shRBM39 versus shCtrl samples.

source_name: Colorectal cancer

growth_protocol: SW480 colorectal cancer cells were maintained in 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
2 ug of total RNA was collected using Trizol (TaKaRa) for construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China)following manufacturer's protocols.

value: Colorectal cancer

value: Colorectal cancer cells

value: RBM39 knockdown


title: P28 | 003 | TME

extract_protocol: Clinical FFPE samples on individual slides were obtained with appropriate ethics approval

tag: bestresponse

tag: pathway

tag: mortality

tag: Sex

value: Male

value: Previous

value: TME


title: ΔvanAB Hfq:3xFLAG pBVMCS6-AbnZ 15´Vanillate Minus R3


title: ΔvanAB Hfq:3xFLAG pBVMCS6-AbnZ 15´Vanillate Minus R1


title: SW480 cells, shRBM39, rep1


title: CTRLsiKDM3B_H3K9me1_rep2

description: Control siKDM3B H3K9me1 replicate 2


title: SW480 cells, shRBM39, rep2


title: CTRLsiKDM3B_Input_rep2

description: Control siKDM3B input replicate 2


title: SW480 cells, shCtrl (control for shRBM39), rep3

value: WT


title: P28 | 004 | TUMOUR

value: HNSCC

value: PD

value: TRUE

tag: age

tag: smokingstatus

tag: pfs

tag: countofloweprgene

value: TUMOUR


title: P28 | 004 | TME

tag: tissue

value: Nivolumab

value: Y

value: 3 mos

tag: percentofloweprgene


title: P28 | 005 | TUMOUR

tag: foi

tag: responsesintumour


title: ileum_ctrl1, scRNA-seq

description:
counts.txt.gz
metadata.txt

value: ileum

tag: condition

value: ctrl


title: CTRLsiKDM3B_H3K9me1_rep1

description: Control siKDM3B H3K9me1 replicate 1

tag: cell line

value: RPE

tag: cell type

value: Retinal pigment epithelial

tag: antibody

value: siRNA Knockdown


title: SW480 cells, shCtrl (control for shRBM39), rep2

value: Colorectal cancer

value: Colorectal cancer cells

tag: genotype


title: P28 | 002 | TUMOUR

tag: bestresponse

value: Male

value: Previous

tag: responsesintme


title: P28 | 002 | TME

tag: pathway

tag: mortality

value: TME


title: P28 | 003 | TUMOUR

value: HNSCC

tag: age

tag: Sex


title: siG9A_69_Input_rep1

description: siG9A (#69) input replicate 1

tag: treatment


title: ΔvanAB pBVMCS6-AbnZ 15´Vanillate-R2

extract_protocol:
RNA extraction using the Hot Phenol methode, following DNase treatment/Pci extraction, rRNAdepletion and mRNA purification
RNA libraries for RNAseq were prepared using NEBNext® Small RNA Library Prep Set for Illumina® following manufacturer´s protocol

tag: strain

value: {delta}vanAB pBVMCS6-AbnZ

value: 500 uM Vanilalte


title: CTRLsiKDM3B_Input_rep1

description: Control siKDM3B input replicate 1


title: SW480 cells, shCtrl (control for shRBM39), rep1

tag: tissue

value: WT


title: P28 | 001 | TME

value: PD

value: TRUE

value: Nivolumab

tag: smokingstatus

tag: pfs

tag: countofloweprgene

tag: percentofloweprgene


title: ΔvanAB pBVMCS6-AbnZ 15´Vanillate-R1


title: siG9A_70_H3K9ME3_rep2

description: siG9A (#70) H3K9me3 replicate 2

tag: cell line


title: SW480 cells, shMORC2, rep2

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.
They were mapped to the reference genome using STAR software (version 2.5.3a) with default parameters.
Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKM was calculated.
Genes differentially expressed between groups were identified using the edgeR package (version 3.12.1).
Alternative splicing events were detected by using rMATS (version 3.2.5) with a FDR value cutoff of 0.05 and an absolute value of Δψ of 0.05.
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: All_reads_counts.txt and All_samples_rpkm.txt files show raw counts and RPKM
Supplementary files format and content: TargetAndJunction_event_records.txt file shows results after shMORC2 samples are compared to shCtrl samples (provided by sequencing company). Group1, Group2 and Group3 represent AS events resulting from three replicate comparisons of shMORC2 versus shCtrl samples.
Supplementary files format and content: ASEvent_summary.txt shows a statistical table of AS events from shMORC2 versus shCtrl samples.

tag: cell type

value: MORC2 knockdown


title: siG9A_70_H3K9ME2_rep2

description: siG9A (#70) H3K9me2 replicate 2

tag: antibody


title: SW480 cells, shMORC2, rep3

tag: genotype


title: Diabetic mouse infected-4

city: Livermore

first: Kunal

last: Poorey

state: CA

address: 7011 East Avenue MS9292

institute: Sandia National Labs

data_processing:
For bacterial sequence information, read abundance was quantified using the S. aureus USA300 FPR3757 reference genome (GenBank accession number NC_007793) and Kallist, a kmer-based pseudoalignment tool, with analysis and visualization using Degust (https://github.com/drpowell/degust). Degust uses Voom/Limma and generates an interactive website to analyze and explore the data. Differential expression was considered statistically significant by applying threshold cutoffs of a >1.5-fold change and a P value of <0.05 (adjusted for false discovery). Bacterial genes were categorized into orthologous groups, and pathways were interpreted using Genome2D.
Assembly: S. aureus USA300 FPR3757 reference genome (GenBank accession number NC_007793)
Supplementary files format and content: all genes.xls (differential expression results)

organism: Staphylococcus aureus

extract_protocol:
RNA was isolated from punch biopsy homogenates of 1-day-old infection sites using the Direct-zol RNA extraction kit (Zymo), after treatment for 5 min with 50 μg/ml of lysostaphin. Isolated RNA was further treated with DNase according to the manufacturer’s instructions (Ambion).
A quantitative PCR (qPCR) assay was performed on the captured cDNA samples to determine the correct number of cycles required to generate the final sequencing library as well as to assess the efficacy of normalization and enrichment (73). Typically, higher threshold cycle (CT) values indicate greater depletion of host transcripts. The final library was created by PCR amplifying the samples with the full-length sequencing adaptors and 6-mer ScriptSeq (Epicentre) barcodes. Following PCR, the samples were cleaned and size selected in a two-step cleanup using 0.75 volumes of AMPure XP beads followed by 0.15 volumes to achieve a final library with an average size of ∼330 bp. Libraries were combined with 12 samples each, in equal amounts, and concentrated using DNA Clean & Concentrator-5 (Zymo Research). Prior to sequencing, the final libraries were quantified using qPCR.
Combined libraries were sequenced on an Illumina NextSeq instrument using 75-cycle kits. Samples were loaded at 1.8 pM, and 75-base single-end reads were obtained.

tag: disease state

value: Diabetic

value: Skin

tag: host

value: mouse


title: ΔvanAB pBVMCS6-EV 15´Vanillate-R3

value: {delta}vanAB pBVMCS6-EV


title: Diabetic mouse infected-3


title: SW480 cells, shMORC2, rep1

value: Colorectal cancer


title: ΔvanAB pBVMCS6-EV 15´Vanillate-R2


title: siG9A_69_H3K9ME3_rep1

description: siG9A (#69) H3K9me3 replicate 1

value: RPE

value: Retinal pigment epithelial

value: siRNA Knockdown


title: siG9A_69_H3K9ME2_rep1

description: siG9A (#69) H3K9me2 replicate 1


title: ΔvanAB pBVMCS6-EV 15´Vanillate-R1


title: SW480 cells, shCtrl (control for shMORC2), rep3

value: Colorectal cancer cells


title: ΔvanAB pBVMCS6-AbnZ 15´Vanillate-R3


title: Diabetic mouse infected-2


title: Mitis_Mono_3

city: Columbus

first: Justin

middle: Ray

last: Kaspar

state: OH

address: 305 W 12th Ave

department: Biosciences

institute: The Ohio State University

data_processing:
Step 1: FASTQ Groomer
Step 2: FASTQ Quality Trimmer
Step 3: Cutadapt removing GATCGGAAGAGCACACGTCTGAACTCCAGTCAC
Step 4: Map with Bowtie for Illumina
Step 5: sort
Step 6: htseq-count (see our publication for details)
Assembly: NC_004350.2 for S. mutans UA159; CP079724.1 for S. oralis
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: excel workbook file includes Log2 fold changes and Log10 P values from Degust output, as well as gene descriptions and normalized read counts

organism: Streptococcus mitis

source_name: whole cell lysate

growth_protocol: Bacterial cells used for extraction of RNA were grown in TYG medium in the presence of 5% CO2 at 37°C without agitation, until they reached mid-exponential growth phase (OD600 nm ≈ 0.4)

extract_protocol:
Total RNA was extracted from bacterial cells using the RNeasy Mini kit (Qiagen), with chromosomal DNA removed using a DNase I kit (Qiagen). To remove 16S and 23S rRNAs, 10 µg of total RNA was treated using the MICROBExpressTM Bacterial mRNA Enrichment Kit
cDNA libraries were created from 100 ng enriched mRNA samples using the NEBNext Ultra Directional RNA Library Prep kit for Illumina and NEBNext multiplex Oligos for Illumina (New England Biolabs, Ipswich, MA) following instructions from the supplier.

treatment_protocol: Cells were harvested by centrifugation at 4°C for 5 min, treated with bacterial RNAprotect Bacteria Reagent (Qiagen), and immediately stored at -80°C.

value: whole cell lysate

value: planktonic bacterial culture

value: wild-type

value: TYG; growth to OD600 nm =  0.4


title: CTRLsiKDm3B_H3K9me3_rep2

description: Control siKDM3B H3K9me3 replicate 2


title: CTRLsiKDM3B_H3K9ME2_rep2

description: Control siKDM3B H3K9me2 replicate 2


title: Diabetic mouse infected-1


title: SW480 cells, shCtrl (control for shMORC2), rep2

value: WT


title: Mitis_Mono_2


title: SW480 cells, shCtrl (control for shMORC2), rep1


title: WT mouse infected-4

value: control


title: P28 | 001 | TUMOUR

city: Brisbane

first: Habib

last: Sadeghirad

address: 37 Kent St, Woolloongabba, 37 Kent St, Woolloongabba

institute: The University of Queensland

value: HNSCC

tag: bestresponse

value: PD

value: TRUE

tag: pathway

value: Nivolumab

value: Y

value: Male

value: Previous

value: 3 mos

tag: foi

tag: responsesintumour

tag: responsesintme

value: TUMOUR


title: SW480 cells, RBM39_IP, Abcam

data_processing:
Illumina PE library constructed (~ 300 bp) for sequencing.
Raw sequencing sequences (raw reads) were obtained for each sample, and raw data was assessed for quality using FastQC software.
Clean was performed on raw data using Trimmomatic software. Removal of adapter contamination at the 3 'end, at least 10 bp overlap (AGATCGGAAG), allows a 20% base error rate; removal of reads containing more N (N means that base information cannot be determined) (≥ 10%); and removal of low-quality sequences (bases with Q ≤ 10 account for more than 50% of the overall number of sequence bases, which we consider low-quality sequences).
Clean data were aligned to the reference genome to obtain comprehensive transcript information. Total Mapped Reads or Fragments locate to more than 70% of the reference genome, with Multiple Mapped Reads or Fragments accounting for no more than 10% of the total.
RRNA detection was performed on reads on different sample alignments, and the number of reads containing rRNA in each sample was counted as a proportion of reads on all alignments. Statistics of the distribution of sequencing sequences mapped to the reference genome were used to detect sources on the sequenced sequence genome.
RPKM (Reads per Kilobase per Million reads) values were used as a measure of expression for all genes. The entire genome is then cut into intervals of 200 nt in length, and the adjacent intervals merge as the final protein-binding region, that is, the final peak.
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: Txt file shows the ID and strength of RBM39 binding RNA

extract_protocol:
Cells were collected with PBS at 4 ° C, centrifuged at 4 ° C, 1000 g, and 5 min and the supernatant was discarded and placed in liquid nitrogen.
The enriched RNA was fragmented into short fragments using Fragmentation Buffer. Then a cDNA strand was synthesized using six-base random primers based on the fragment mRNA template, and then a two-strand cDNA was synthesized by adding buffer, dNTPs and DNA polymerase I. The eluted and purified double-stranded cDNA was then treated with terminal repair, base A and sequencing splice. The target size fragments were recovered by magnetic beads and amplified by PCR. Qubit 2.0 was used to quantify the libraries, and then different libraries were sequenced on Illumina sequencers according to the requirements of effective concentration and target on-machine data volume.

value: Colorectal cancer

tag: rip antibody


title: WT mouse infected-3

tag: tissue

value: Skin

value: mouse


title: Mitis_Mono_1

value: whole cell lysate

tag: strain

value: planktonic bacterial culture

tag: treatment


title: SMU_Mono_3

organism: Streptococcus mutans

value: wild-type

value: TYG; growth to OD600 nm =  0.4


title: P28 | 006 | TME

tag: mortality

tag: age

tag: Sex

tag: smokingstatus

tag: pfs

tag: countofloweprgene

value: TME


title: CTRLsiKDM3B_H3K9ME2_rep1

description: Control siKDM3B H3K9me2 replicate 1

tag: cell line

value: RPE

tag: cell type

value: Retinal pigment epithelial

tag: antibody

value: siRNA Knockdown


title: WT mouse infected-1

tag: disease state

value: control

tag: genotype

tag: host


title: WT mouse infected-2


title: SMU_Mono_2


title: SMU_Mono_1


title: SW480 cells, RBM39_Input