title: nos, 2-3h, rep3

city: Columbus

first: Mohammad

last: Marhabaie

state: OH

address: 700 Children's Dr

institute: Nationwide Children's Hospital

data_processing:
Adapter sequences were trimmed from paired-end 150-nucleotide raw reads followed by trimming low-quality bases from the 3’ end of reads based on a minimum Phred quality score of 15.
Reads of less than 60nt were removed, as were reads mapping to mtRNA, tRNA, and rRNA.
STAR (v2.5.3a) was used to map the reads to dmel_r6.22_FB2018_03.
Mapped reads were counted using RSEM (v1.3.0). The resulting outputs were analyzed in R (v4.2.1) using the edgeR package (v3.40.2) to find differentially expressed genes and transcripts.
Low abundance genes and transcripts were filtered out by setting min.count=30 and min.total.count=30 in filterByExpr function in the edgeR package, removing genes and transcripts with < ~2 counts per million mapped reads.
Assembly: dmel_r6.22_FB2018_03 (BDGP6.22.96)
Supplementary files format and content: tab-delimeted text files include raw counts for each sample
Supplementary files format and content: tab-delimeted text files include TPM values for each sample

organism: Drosophila melanogaster

source_name: embryos

growth_protocol: Fly stocks were maintained by standard methods and grown at 25°C. Embryos were collected on apple-juice agar plates smeared with yeast paste.

extract_protocol:
Total RNA was extracted from sorted embryos using TRIzol reagent (Thermo Fisher Scientific).
Samples were poly(A) selected and libraries were prepared using TruSeq Library Prep Kit (Illumina) following manufacturer's protocols.

value: embryos

value: nos


title: OSKM iPSC,Tsc1 KO,Day5,rep2

status: Public on Aug 13 2024

type: SRA

city: Guangzhou

first: shuhui

last: xu

address: 190 Kaiyuan Avenue, Huangpu District

country: China

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

library_source: transcriptomic

data_processing:
the libraries were sequenced on an MGISEQ-2000 sequencer in paired-end 100 mode.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

molecule: polyA RNA

organism: Mus musculus

source_name: OSKM D5

extract_protocol:
RNA from reprogramming day 5 and 10 were extracted from all experimental groups using a standard protocol. A total of 1 µg RNA per sample was utilized for library preparation at China National GeneBank (CNGB).
The sequencing libraries were generated using the MGIEasy RNA Library Prep Set (MGI, 1000006384) following the manufacturer's protocol

tag: cell type

value: OSKM D5

tag: genotype

value: Tsc1 KO

tag: treatment


title: DNA-seq - Patient 26

city: Rochester

first: Alexandre

last: Gaspar-Maia

state: MN

address: 200 First street SW

country: USA

institute: Mayo Clinic

library_source: genomic

data_processing:
library strategy: Target Capture Chip Assay for Bulk Sequencing
Bioinformatics analysis included quality assessment and alignment to the hg19 build reference genome using Novoalign, followed by GATK based single nucleotide and small insertion / deletion variant calling, structural variation discovery, and annotation. Somatic single nucleotide variations (SNVs) were genotyped using SomaticSniper, whereas insertions and deletions were called by GATK Somatic Indel Detector. Each variant in coding regions was functionally annotated by SnpEff, SAVANT, ClinVar, dbNSFP, OMIM, and the Human Gene Annotation Database to predict biological effects. Each variant was also annotated with allele frequency from the Exoma Aggregation Consortium. The total list of all variants was internally compared for internal duplicates indicative of false positives, and variants of concern are additionally hand annotated for identification using Alamut Software. Interpretation for relevant alterations included absence in international normal variant allele databases (GnomAD, ExAC), deleterious effect on protein function by multiple phenotype prediction models, somatic and functional annotation in literature, consequence of variant (nonsense, truncating, etc.) and location proximal to important domains.
Assembly: hg19
Supplementary files format and content: Supplementary file containing the variant calls for mutations associated with Clonal Hematopoiesis.

molecule: genomic DNA

organism: Homo sapiens

source_name: Peripheral blood mononuclear cells

extract_protocol:
Sample DNA was extracted from peripheral blood mononuclear cells isolated by gradient centrifugation and re-suspended in a concentration of 500 ng in 50µl of low TE buffer.
Paired-end indexed libraries were prepared using the Sureselect XT Low Input Library prep protocol on the Agilent Bravo liquid handler following the manufacturer’s protocol (NewEngland Biolabs, Ipswitch, MA, and Agilent Technologies, Ankeny, IA). Briefly, 200ng of target DNA was fragmented using the Covaris LE220 plus sonicator. The settings of duty factor 30%, peak incident power (PIP) 450, cycles per burst 200, time 180 seconds generated double-stranded DNA fragments with blunt or sticky ends with a fragment size mode of between 150-200bp. The ends were repaired using the Sureselect End-Repair-A-Tailing enzyme mix. Adapter ligated DNA fragments were size selected to enrich for 200 bp inserts (~320 bp total library size) using AMPURE XP bead purification. The size selected adapter-modified fragments were enriched, and specific indexes were added by 12 cycles of PCR using universal index primers. The concentration and size distribution of the libraries was determined on an Agilent Bioanalyzer DNA 1000 chip. The Custom Capture hybrid-target enrichment probes were designed using Agilent SureSelect design software (Agilent Technologies, Santa Clara, CA). The targeted gene panel was comprised of 62,962 single probes with size 1.805Mbp, and covered the coding regions, UTRs, and overlapping intron/exon regions for 205 genes described and / or enriched for CH mutations (see Appendix: Target Gene Panel). The custom capture was carried out using the Agilent Bravo liquid handler following Agilent’s SureSelect XT Low. Purified capture products were then amplified using the SureSelect Post-Capture primer mix for 14 cycles. Libraries were validated and quantified on the Agilent Bioanalyzer. Samples were sequenced by 150 paired end reads, 21 samples to a Flow Cell, on an Illumina NovaSeq 6000 SP with an expected depth of ≥1,000X coverage (Illumina, SanDiego, CA).

value: Peripheral blood mononuclear cells

tag: disease state_2


title: nos, 2-3h, rep2

tag: tissue

tag: developmental stage


title: OSKM iPSC,Tsc1 KO,Day5,rep1


title: DNA-seq - Patient 25

tag: disease state_1

value: Clonal Hematopoiesis


title: unphased_pool9_R2

city: Basel

first: Dirk

last: Schuebeler

address: Fabrikstrasse 24

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

data_processing:
Reads were trimmed to remove adapters using Trimmomatic version 0.32.
Reads were mapped using the Bioconductor package QuasR with default settings for bisulfite-converted templates.
Methylation of Cs in the GpC contexts was quantified using qMeth, excluding GCG and GCCG contexts and Cs with coverage <10. Such GpCs were defined as GCH.
Supplementary files format and content: Average methylation data are tab separated tables with three columns: position of the Cs in the GCH context, average methylation values, inserted constructs.
Supplementary files format and content: Single molecule data are tar.gz archives containing tab separated tables for each inserted construct. Each table is a matrix where each column is the position of the Cs in the GCH context, and each row is the binary methylation data for a single read.

extract_protocol:
DNA was extracted with Phenol/Chlroform, bisulfite converted and then PCR was performed. PCR was purified with SPRI beads and submitted to library preparation.
Libraries were prepared using the NEBNext ChIP-Seq Library Prep Master Mix Set following manufacturer instructions.

tag: cell line

value: embryonic stem cells


title: nos, 2-3h, rep1


title: OSKM iPSC,wildtype,Day5,rep2

value: Tsc1 WT


title: DNA-seq - Patient 24


title: unphased_pool8_R2


title: DNA-seq - Patient 23


title: w, 2-3h, rep3

value: w


title: unphased_pool8_R1


title: w, 2-3h, rep1


title: unphased_pool7_R2


title: DNA-seq - Patient 22


title: DNA-seq - Patient 21


title: unphased_pool7_R1


title: DNA-seq - Patient 20


title: unphased_pool6_R2


title: DNA-seq - Patient 19


title: unphased_pool9_R1


title: DNA-seq - Patient 18


title: nos, 0-1h, rep1


title: unphased_pool6_R1


title: unphased_pool5_R2


title: w, 0-1h, rep3


title: OSKM iPSC,wildtype,Day5,rep1


title: DNA-seq - Patient 17


title: unphased_pool5_R1


title: DNA-seq - Patient 16


title: UdRPCs UM51 72h JNK inhibition

type: RNA

city: Düsseldorf

first: Wasco

last: Wruck

address: Moorenstr. 5

country: Germany

institute: Universitätsklinikum Düsseldorf

description: replicate 1

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scanning protocol for Affymetrix Clariom S Assay Gene Expression Array

data_processing: The data were normalised using RMA normalisation from R/Bioconductor

label: biotin

molecule: total RNA

source_name: Urine-derived renal progenitor cell (UdRPC)

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

growth_protocol: UdRPCs were cultured in Proliferation Medium (PM) composed of 50% DMEM high Glucose and 50% Keratinocyte medium supplemented with 5% FCS, 0.5% NEAA, 0.25% Gtx and 0.5% Penicillin and Streptomycin at 37°C (Gibco, Carlsbad, United States) under hypoxic conditions. In order to study the role of JNK signalling in the maintenance of self-renewal of UdRPCs, the cells were seeded on plates coated with 0.2% gelatine and grown in PM for 24 hours. After this the medium was changed to PM supplemented with 10 µM AEG3482, a JNK inhibitor. Results were analysed after 72 h.

extract_protocol: The RNA was extracted using TRIzol reagent (Thermo Fisher Scientific) and the manufactural protocol. The quality of the RNA was checked with a NanodropTM spectrophotometer (Thermo Scientific).

treatment_protocol: ANG II (Sigma Aldrich, St. Louis, Missouri, United States) was diluted in the culture medium to a final concentration of 100 µM. Cells were incubated for 6h and 24h with ANGII and the conditioned medium was kept for secretome analyses.

value: 72h JNK inhibition


title: w, 0-1h, rep1


title: UdRPCs UM51 120h JNK inhibition

description: replicate 1

value: Urine-derived renal progenitor cell (UdRPC)

value: 120h JNK inhibition


title: pent1_10uM_ABA_rep3

city: Valencia

first: Pedro L

last: Rodriguez

address: CPI-UPV, C/ de l'Enginyer Fausto Elio, s/n, Algirós

country: Spain

institute: IBMCP (CSIC-UPV)

description:
Nben.pent1.ABA.3
all.counts.20-MM_pent1.txt

data_processing:
After quality analysis with FastQC and read cleaning and adaptor trimming with cutadapt, clean reads were mapped to reference genome Nicotiana benthamiana LAB360 using STAR. Read counts table produced by STAR was used to perform the differential expression analysis with DESeq2
Assembly: Nicotiana benthamiana Lab360
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Nicotiana benthamiana

source_name: whole seedlings

growth_protocol: N. benthamiana seedlings (10 d.a.g.) were transferred from plates to flash with liquid media during 10 days

extract_protocol:
RNA was harvested using E.Z.N.A.® Plant RNA Kit (Omega Biotek).
The library was constructed using the DNBSEQ Eukaryotic Strand-specific mRNA library kit (BGI Genomics, Shenzhen, China)

treatment_protocol: the medium was refreshed, and it was supplemented with either 0.1% DMSO (mock) or 10 μM ABA. Samples were collected after 3 hours of incubation

value: whole seedlings

value: 10uM ABA


title: unphased_pool4_R2


title: UdRPCs UM51 72h control

description: replicate 1

value: 72h control


title: UdRPCs UM51 120h control

description: replicate 1

value: 120h control


title: nos, 0-1h, rep3


title: nos, 0-1h, rep2


title: Nos, cycle9, rep3

value: cycle 9

value: Nos


title: UdRPCs UM51 24h JNK inhibition

description: replicate 1

value: 24h JNK inhibition


title: unphased_pool4_R1


title: pent1_10uM_ABA_rep1

description:
Nben.pent1.ABA.1
all.counts.20-MM_pent1.txt


title: pent1_10uM_ABA_rep2

description:
Nben.pent1.ABA.2
all.counts.20-MM_pent1.txt


title: DNA-seq - Patient 14


title: w, 2-3h, rep2

value: embryos


title: Nos, cycle9, rep2


title: unphased_pool3_R2


title: pent1_DMSO_rep3

description:
Nben.pent1.Mock.3
all.counts.20-MM_pent1.txt

value: 0.1% DMSO


title: DNA-seq - Patient 13

value: Peripheral blood mononuclear cells


title: unphased_pool3_R1


title: Nos, cycle9, rep1


title: w, 0-1h, rep2


title: unphased_pool2_R2


title: Upf1, cycle9, rep3


title: pent1_DMSO_rep2

description:
Nben.pent1.Mock.2
all.counts.20-MM_pent1.txt


title: Upf1, cycle9, rep2


title: UdRPCs UM51 24h control

description: replicate 1

value: 24h control


title: unphased_pool2_R1

value: embryonic stem cells


title: DNA-seq - Patient 10


title: Upf1, cycle9, rep1


title: WT_10uM_ABA_rep3

data_processing:
After quality analysis with FastQC and read cleaning and adaptor trimming with cutadapt, clean reads were mapped to reference genome Nicotiana benthamiana LAB360 (https://apollo.nbenth.com/annotator/loadLink?organism=3135830&loc=NbLab360C01:772823..793502&tracks=Annotation%20v103,TEs,Averaged%20expression%20across%20all%20tissues) using STAR. Read counts table produced by STAR was used to perform the differential expression analysis with DESeq2
Assembly: Nicotiana benthamiana LAB360 (https://apollo.nbenth.com/annotator/loadLink?organism=3135830&loc=NbLab360C01:772823..793502&tracks=Annotation%20v103,TEs,Averaged%20expression%20across%20all%20tissues)
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

value: WT


title: pent1_DMSO_rep1

description:
Nben.pent1.Mock.1
all.counts.20-MM_pent1.txt


title: unphased_pool1_R2


title: DNA-seq - Patient 48


title: DNA-seq - Patient 9

value: Clonal Hematopoiesis


title: WT_10uM_ABA_rep2


title: DNA-seq - Patient 11


title: unphased_pool1_R1


title: WT_10uM_ABA_rep1


title: MCF7, s4U, IAA, rep2

city: Wuhan

first: Ziang

last: Lu

address: Wuhan University, No.299, Bayi Road, Wuchang District

institute: Wuhan University

data_processing:
After trimming adapters, CUT&TAG raw reads were aligned to hg38 human genome using bowtie2 and duplicate reads were removed from unique mapping reads using Picard MarkDuplicates.
The clean reads were used to call peaks using MACS2. After removing peaks in blacklist, the high repeatability peaks between biological replicates were get using IDR.
After trimming adapters, AMUC-seq raw reads were alinged to human rRNA using bowtie2 to remove rRNA sequences.
Unmapped reads were mapped to hg38 human genome with STAR. Duplicate reads were removed from unique reads using Picard MarkDuplicates .
Mutation sites were collected and annotated with REDItools, and SNP sites were removed.
Mutation rate calculation and s4U labeled reads extraction were performed with custom script. Raw counts of s4U labeled mRNA and all mRNA were obtained using htseq. TPM expression matrix and fold change were calculated with custom script.
Assembly: hg38
Supplementary files format and content: bigwig, aligned reads or labeled reads in AMUC-seq
Supplementary files format and content: bed, IDR peak result
Library strategy: AMUC-seq

growth_protocol: All cells were cultured with Dulbecco’s modified Eagle’s medium (DMEM) (Gibco) containing 10% fetal bovine serum, 100 U/mL penicillin, and 100 μg/mL streptomycin (Gibco) in the presence of 5% CO2 at 37°C incubators.

extract_protocol:
Genomic DNA was extracted by EasyPure Genomic DNA Kit (TransGen Biotech). Total RNA was extracted by Invitrogen TRIzol (Thermofisher) . PolyA RNA was extracted by NEBNext® High Input Poly(A) mRNA Isolation Module.
CUT&TAG libraries were constructed with CUT&TAG kit (Vazyme, #TD903). AMUC-seq libraries were constructed with NEBNext Ultra II Directional RNA Library Prep Kit for Illumina.

treatment_protocol: 500μM s4U and 500μM IAA will be treated in corresponding samples.

tag: antibody

value: s4U and IAA treated


title: Upf1-Nos, cycle9, rep3


title: DNA-seq - Patient 7


title: WT_DMSO_rep3


title: DNA-seq - Patient 8


title: MCF7, s4U, IAA, rep1


title: DNA-seq - Patient 12


title: Upf1-Nos, cycle9, rep2


title: DNA-seq - Patient 6


title: WT_DMSO_rep2


title: Upf1-Nos, cycle9, rep1


title: MCF7, nos4U, IAA, rep2

value: nos4U and IAA treated


title: Upf1-NosL7, cycle9, rep3


title: WT_DMSO_rep1


title: Upf1-NosL7, cycle9, rep2


title: DNA-seq - Patient 4


title: MCF7, s4U, noIAA, rep2

value: s4U and noIAA treated


title: Upf1-NosL7, cycle9, rep1


title: TM-2

city: Beijing

first: ZHAOYANG

last: JIN

institute: Chinese Academy of Sciences

data_processing:
Data filtering The raw data obtained from sequencing were filtered by SOAPnuke (v1.5.6), which filtered out 1) reads containing junctions (junction contamination); 2) reads with unknown base N content greater than 5%; and 3) low-quality reads (reads with the proportion of bases with a quality value lower than 15 to the total number of bases in the reads greater than 20% are considered low-quality reads) to obtain clean data. reads), to obtain clean data. Data were subsequently analysed, mapped and mined using the Dr. Tom Multi-Organomics Data Mining System (https://biosys.bgi.com). Differential gene analysis The clean data were compared to the reference genome using HISAT2 (v2.1.0) software. Clean data was compared to the reference gene set using Bowtie2 (v2.3.4.3). Gene expression was quantified using RSEM (v1.3.1) software and clustered heatmap of gene expression in different samples was plotted using pheatmap (v1.0.8). Differential gene detection was performed using DESeq2 (v1.4.5) with Q value ≤ 0.05 or FDR ≤ 0.001.  KEGG and GO enrichment analysis To further explore gene functions associated with phenotypic changes in depth, we performed GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of differential genes using Phyper based on the hypergeometric test, with Qvalue ≤ 0.05 as the threshold, and satisfying this condition was defined as significant enrichment in candidate genes.
Assembly: GCF_000001405.39_GRCh38.p13
Supplementary files format and content: tab-delimited text file includes st_gene_id gene_id gene_symbol fpkm_CONTROL fpkm_TLS1 fpkm_TM1 fpkm_TLS2 fpkm_TM2 tpm_CONTROL tpm_TLS1 tpm_TM1 tpm_TLS2 tpm_TM2 read_count_CONTROL read_count_TLS1 read_count_TM1 read_count_TLS2 read_count_TM2 diffexp_log2fc_CONTROL-vs-TLS1 diffexp_possiondis_fdr_CONTROL-vs-TLS1 diffexp_possiondis_pvalue_CONTROL-vs-TLS1 diffexp_log2fc_CONTROL-vs-TM1 diffexp_possiondis_fdr_CONTROL-vs-TM1 diffexp_possiondis_pvalue_CONTROL-vs-TM1 gene_symbol gene_other_symbol gene_type gene_tran_num gene_tran_list gene_coding_capacity gene_known_novel gene_chr gene_start gene_end gene_strand gene_map_loc url_ncbi_gene_id url_hgnc_gene_id url_ensembl_gene_id url_genecard_gene_id url_mirbase_gene_id gene_kegg_k_id cr2cancer cellmarker cog eggnog genebank go_c go_f go_p interpro kegg_disease kegg_module kegg_pathway kegg_reaction msigdb_archived_c2_cgp msigdb_archived_c2_cp msigdb_archived_c2_cp_reactome msigdb_c1 msigdb_c2_cgp msigdb_c2_cp msigdb_c2_cp_biocarta msigdb_c2_cp_kegg msigdb_c2_cp_pid msigdb_c2_cp_reactome msigdb_c3_mir_mir_legacy msigdb_c3_mir_mirdb msigdb_c3_tft_gtrd msigdb_c3_tft_tft_legacy msigdb_c4_cgn msigdb_c4_cm msigdb_c6 msigdb_c7 msigdb_h pfam reactome tf tf_cofactors uniprot

extract_protocol:
Total cellular RNA was isolated using TRIZOL reagent (Invitrogen, Karlsruhe, Germany) following the manufacturer's instructions. The isolated RNA was then shipped to BGI for transcriptome sequencing and basic data analysis, preserved on dry ice.
RNA libraries for RNA-seq were prepared using Optimal Dual-mode mRNA Library Prep Kit (BGI-Shenzhen, China) following manufacturer's protocols.

value: Human hepatocellular carcinomas


title: TM-1


title: DNA-seq - Patient 5


title: MCF7, s4U, noIAA, rep1


title: w, cycle9, rep3

value: w


title: TLS-2


title: DNA-seq - Patient 2


title: TLS-1


title: DNA-seq - Patient 1


title: w, cycle9, rep2


title: MCF7, nos4U, noIAA, rep1

value: nos4U and noIAA treated


title: MCF7, nos4U, noIAA, rep2


title: CONTROL


title: M28ΔRD2 (3) for 60 mins

status: Public on Aug 12 2024

city: Reno

first: Paul

last: Sumby

state: NV

address: 1554 N. Virginia St.

department: Microbiology & Immunology

institute: University of Nevada

description: Processed file 60 mins.xls

data_processing:
CLC Genomics Workbench version 8 RNA-seq was used for basecalling and aligning the sequence reads to the MGAS6180 genome
Parameters for alignment were set up:  Similar fraction=0.8, Length fraction=0.8, Mismatch cost=2, Insertion cost=3.
Normalization was performed to overall sequencing depth using total mapped reads data.
Statistical significance was tested using Kal’s Z-test with a false-discovery rate correction.
Supplementary_files_format_and_content: Excel file containing columns for the gene name, gene border (left), gene border (right), normalized expression value for the WT strain, normalized expression value for the mutant strain, expression ratios, and Kal's Z-test with FDR correction value

organism: Streptococcus pyogenes

growth_protocol: GAS strains were grown in THY broth to the exponential phase of growth (an O.D.600 of 0.5).  GAS were then pelleted by centrifugation, resuspended in an equal volume of pre-warmed (37°C) human plasma, and incubated at 37°C.  Samples were taken for processing after 15 and 60 mins.

extract_protocol:
Total RNA was isolated and rRNAs were depleted using the RiboMinus Bacteria Transcriptome Isolation Kit (Invitrogen).
The rRNA depleted RNA was used to generate cDNA libraries using the ScriptSeq kit v2 (Epicentre).  Briefly, RNA was fragmented, cDNA was synthesized using random hexamers containing a 5′ tagging sequence, the RNA was hydrolyzed, and the cDNA was tagged at the 3′ end.  A limited number of PCR cycles (n=14) were used to amplify the libraries via the 5′ and 3′ tags (the libraries were barcoded by using different primers), and the libraries size-selected (170 to 300 bp).  The size-selected and barcoded libraries were run on an Illumina HiSeq flowcell.

tag: sample type

value: Derivative of MGAS6180 that lacks RD2

value: Plasma exposure for 60 mins


title: DNA-seq - Patient 3


title: w, cycle9, rep1

value: cycle 9


title: M28ΔRD2 (2) for 60 mins

description: Processed file 60 mins.xls


title: M28ΔRD2 (3) for 15 mins

description: Processed file 15 mins.xls

value: Plasma exposure for 15 mins


title: M28ΔRD2 (1) for 15 mins

description: Processed file 15 mins.xls


title: MGAS6180 (3) for 60 mins

description: Processed file 60 mins.xls

value: Parental M28 GAS isolate


title: M28ΔRD2 (2) for 15 mins

description: Processed file 15 mins.xls


title: MGAS6180 (1) for 60 mins

description: Processed file 60 mins.xls


title: MGAS6180 (1) for 15 mins

description: Processed file 15 mins.xls


title: Tfeb/3 SC-dKO 5DPI (400_2)

city: Newark

first: Haesun

last: Kim

address: 195 University Ave

institute: Rutgers University

data_processing:
The raw sequence files (fastq files) were aligned to the mouse genome (MM10) reference sequence using the default parameters and the alignment tool of the torrent suite browser software.
Aligned BAM files were uploaded into the StrandNGS bioinformatic software.
The genes and transcripts annotations that were used was retrieved from the Ensembl data base.
Quality control was assessed by the Strand NGS program, which determined the pre- and post-alignment quality of the reads for each sample.  The aligned reads were then filtered based on alignment score threshold (≥90), N’s allowed in the read (0 ≤), match count (=1) and reads that failed vendors QC were removed.
Normalization was performed using DEseq2 in R version 4.2.1 in R Studio.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes normalized counts from DEseq2 for each sample

source_name: sciatic nerve

extract_protocol:
Mice were euthanized with CO2 and intact and 5DPI sciatic nerves were collected with distal nerves cut to remove ~1mm from injury site. Nerves were placed into ice cold DEPC treated PBS with RNasin where the epineurium was removed from intact nerves and then nerves were snap frozen in liquid nitrogen. Nerves were then placed into a 2ml bead mill tube with 1ml Tri-Reagent. Nerves were homogenized in a Fisherbrand Bead Mill 24 homogenizer for 30sec at 5m/s for 2 cycles. Chloroform was added and mixed and the tubes were centrifuged. The aqueous phase was removed and mixed with 70% EtOH. The mixture was then centrifuged through the NucleoSpin RNA Mini Kit (Macherey-Nagel, Cat#: 740955.50) and RNA extraction was completed following the manufacturer instructions. RNA was dissolved in RNAse free water.
cDNA libraries were constructed using Ion Total RNA-Seq Kit v2 from ThermoFisher (Cat# 4479789) and manufacturers recommended protocol.

treatment_protocol: For 5DPI samples, sciatic nerve was cut adjacent to and distal from the sciatic notch using angled micro dissecting spring scissors. Nerves were collected 5 days later. For intact samples, contralateral intact sciatic nerves were collected at the same time as 5DPI samples.

value: sciatic nerve

value: transection


title: MCF7, nos4U, IAA, rep1


title: Tfeb/3 SC-dKO 5DPI (400_3)


title: Tfeb/3 SC-dKO Intact (200_4)

value: Intact


title: Tfeb/3 SC-dKO 5DPI (400_4)


title: Control 5DPI (300_4)


title: Tfeb/3 SC-dKO Intact (200_3)


title: Control 5DPI (300_1)


title: Control Intact (100_1)


title: Control Intact (100_2)


title: Control Intact (100_3)


title: Control 5DPI (300_2)


title: Tfeb/3 SC-dKO Intact (200_2)


title: M28ΔRD2 (1) for 60 mins

description: Processed file 60 mins.xls


title: MGAS6180 (3) for 15 mins

description: Processed file 15 mins.xls


title: MGAS6180 (2) for 60 mins

description: Processed file 60 mins.xls


title: MGAS6180 (2) for 15 mins

description: Processed file 15 mins.xls


title: DNA-seq - Patient 15

value: Peripheral blood mononuclear cells


title: soil_metaT_fire_94

city: Sevilla

first: Daniel

last: Revillini

address: Avenida Reina Mercedes 10

institute: IRNAS-CSIC

description: processed data file columns: sample = sample name; treat = prescribed burn or control (unburned); gap (open sand gap collection site); tsf = time since last fire; num_fires = historic number of fires; pair = paired samples yes or no; all next columns are individual KOs with description from KEGG database. For taxa file (daa25_normalized_all_TAXA), "taxa" column = refseq identified taxa at the Genus level. Columns = sample names

data_processing:
de-interleave files (formated from JGI) with reformat.sh in BBmap
SAMSA2 worflow: fastq files were cleaned to remove low-quality sequences and adaptor contamination using the program Trimmomatic (v0.36), where phred = 33, sliding window = 4:15, and minlen = 70. SortMeRNA (v2.1) was then used to retain only mRNA for annotation, and DIAMOND (v0.8.38) was used to match mRNA sequences against the NCBI-nr database (accessed May 19, 2022) with blastx (-k 25)
MEGAN6 Ultimate Edition (v6.24.16; Huson et al. 2016), was then used to aggregate all annotated reads (>154 million) to the RefSeq database for taxonomy, and the KEGG database for functional genes (KEGG orthologs, genes) from the MEGAN6 UE database mapping file
Read counts were extracted from MEGAN6 for taxa at the phyla level, and for all known functional genes at the KEGG orthologs
Assembly: NCBI-nr database (accessed May 19, 2022
Supplementary files format and content: .csv file with read counts of all KEGG orthologs per sample
Supplementary files format and content: .daa files were processed in MEGAN6 UE and read-to-count was used for all KEGG orthologs associated with samples that passed quality filtering

organism: soil metagenome

source_name: soil sample

growth_protocol: sampled from soil, flash frozen in liquid N, -80C before extraction

extract_protocol:
RNeasy PowerSoil Total RNA Kit (Qiagen, Carlsbad, CA, USA) and a slightly modified protocol. Briefly, we used ~4 g of homogenized soil, 2.25 mL PowerBead Solution, and 3.25 mL phenol/chloroform/isoamyl alcohol (25:24:1) for extractions. Wash and elution steps were performed in an Avanti JXN-26 High-Speed Centrifuge (Beckman Coulter Inc., Brea, CA, USA) at 4500 g, and final elution was performed with 75 μL elution buffer. RNA was quantified with a Qubit 4 fluorometer (Qiagen, Carlsbad, CA, USA) using the Qubit RNA HS Assay Kit.
Libraries were prepared using Qiagen FastSelect using a minimum of 100 ng RNA after ribo-depletion

treatment_protocol: Three soil trays from each gap were transferred to a single rosemary scrub site at ABS to undergo a prescribed burn, and were separated into three replicates (burn blocks) to ensure uniform fire coverage across each block. One tray from each site was placed outside of the burn area as the ‘control’ treatment soil. To determine fire coverage and intensity, we placed nine HOBO temperature data loggers randomly across each burn block (Supplementary Figure 1). The prescribed burn was carried out on May 8, 2019. Within 4 hours of prescribed fire, 50 mL of soil was collected from the top 5 cm of each tray, flash frozen in the field with liquid N, and then stored at -80℃ until RNA extractions were performed.

tag: condition

value: fire


title: soil_metaT_fire_93


title: soil_metaT_fire_97


title: soil_metaT_control_94

value: control


title: soil_metaT_control_99


title: soil_metaT_control_90


title: soil_metaT_fire_90


title: Whole Blood from BAB2805

type: genomic

city: Seattle

first: Jesse

last: Bengtsson

state: WA

address: 720 Broadway

institute: Pacific Northwest Research Institute

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed following the manufacturer’s protocol.

scan_protocol: Scanned on an Agilent G2600D scanner. Images were quantified using Agilent Feature Extraction Software (version 12.1.1.1)

data_processing: Agilent Feature Extraction Software (version 12.1.1.1) was used for background subtraction and normalization.

source_name: Whole Blood from Male BAB2805

label_protocol: 1.2 ug of genomic patient and reference DNA were digested with AluI (5 U) and RsaI (5 U) (Promega, R6281 and R6371) for 2 hr at 37°C, 65°C for 20 minutes. Labeling reactions were performed according to the manufacturer’s instructions (BioPrime Array CGH Genomic Labeling Module,Invitrogen Corporation, #18095-012; Perkin-Elmer Las Inc. Cyanine Smart Pack dCTP,

extract_protocol: DNA was isolated from either peripheral blood or LCLs with a Puregene kit (Gentra Systems), following the manufacturer’s protocol

value: Patient BAB2805

tag: Sex

value: Male

value: Whole Blood

source_name: Male LCL GM10928

value: Reference Sample


title: Whole Blood from BAB12574

source_name: Whole Blood from Male BAB12574

value: Patient BAB12574

source_name: Male LCL GM10921


title: Whole Blood from BAB15785

source_name: Whole Blood from Male BAB15785

value: Patient BAB15785

source_name: Male LCL GM10915


title: Whole Blood from BAB15672

source_name: Whole Blood from Male BAB15672

value: Patient BAB15672

source_name: Male LCL GM10926


title: Whole Blood from BAB3212

source_name: Whole Blood from Male BAB3212

value: Patient BAB3212

source_name: Male LCL GM10918


title: Whole Blood from BAB15793

source_name: Whole Blood from Male BAB15793

value: Patient BAB15793

source_name: Male LCL GM10912


title: Whole Blood from BAB12077

source_name: Whole Blood from Male BAB12077

value: Patient BAB12077

source_name: Male LCL GM10920


title: Whole Blood from BAB15760

source_name: Whole Blood from Male BAB15760

value: Patient BAB15760

source_name: Male LCL GM10917


title: Whole Blood from BAB15646

source_name: Whole Blood from Male BAB15646

value: Patient BAB15646

source_name: Male LCL GM10906


title: soil_metaT_fire_9

source_name: soil sample


title: soil_metaT_fire_89


title: LCL from BAB13110 LCL

source_name: LCL from Male BAB13110 LCL

value: Patient BAB13110LCL

value: LCL

source_name: Male LCL GM10924


title: Whole Blood from BAB15691

source_name: Whole Blood from Male BAB15691

value: Patient BAB15691

source_name: Male LCL GM10913


title: Whole Blood from BAB15790

source_name: Whole Blood from Male BAB15790

value: Patient BAB15790

source_name: Male LCL GM10914


title: Whole Blood from BAB15617

source_name: Whole Blood from Male BAB15617

value: Patient BAB15617

source_name: Male LCL GM10905


title: LCL from BAB14298 LCL

source_name: LCL from Male BAB14298 LCL

value: Patient BAB14298LCL

source_name: Male LCL GM10925


title: Whole Blood from BAB14764

source_name: Whole Blood from Male BAB14764

value: Patient BAB14764

value: Male

source_name: Male LCL GM10904


title: Whole Blood from BAB15677

source_name: Whole Blood from Male BAB15677

value: Patient BAB15677

value: Whole Blood

source_name: Male LCL GM10907

value: Reference Sample


title: Whole Blood from BAB2727

source_name: Whole Blood from Male BAB2727

value: Patient BAB2727

source_name: Male LCL GM10927


title: Whole Blood from BAB11979

source_name: Whole Blood from Male BAB11979

value: Patient BAB11979

source_name: Male LCL GM10919


title: soil_metaT_fire_8

source_name: soil sample

value: fire


title: Whole Blood from BAB3039

source_name: Whole Blood from Male BAB3039

value: Patient BAB3039

source_name: Male LCL GM10902


title: Whole Blood from BAB15787

source_name: Whole Blood from Male BAB15787

value: Patient BAB15787

source_name: Male LCL GM10911


title: soil_metaT_fire_70N


title: Whole Blood from BAB15795

source_name: Whole Blood from Male BAB15795

value: Patient BAB15795

source_name: Male LCL GM10916


title: soil_metaT_control_5E

value: control


title: soil_metaT_fire_59


title: Whole Blood from BAB15679

source_name: Whole Blood from Male BAB15679

value: Patient BAB15679

source_name: Male LCL GM10908


title: Whole Blood from BAB2977

source_name: Whole Blood from Male BAB2977

value: Patient BAB2977

source_name: Male LCL GM10903


title: soil_metaT_control_65E


title: Whole Blood from BAB15599

source_name: Whole Blood from Male BAB15599

value: Patient BAB15599

source_name: Male LCL GM10900


title: Whole Blood from BAB15596

source_name: Whole Blood from Male BAB15596

value: Patient BAB15596

source_name: Male LCL GM10899


title: soil_metaT_control_46W


title: soil_metaT_fire_49W


title: soil_metaT_control_45S


title: Whole Blood from BAB15589

source_name: Whole Blood from Male BAB15589

value: Patient BAB15589

source_name: Male LCL GM10898


title: soil_metaT_fire_43

source_name: soil sample


title: Whole Blood from BAB15387

source_name: Whole Blood from Male BAB15387

value: Patient BAB15387

source_name: Male LCL GM10894


title: Whole Blood from BAB15382

source_name: Whole Blood from Male BAB15382

value: Patient BAB15382

value: Male

source_name: Male LCL GM10893


title: Whole Blood from BAB15386

source_name: Whole Blood from Male BAB15386

value: Patient BAB15386

value: Whole Blood

source_name: Male LCL GM10889


title: soil_metaT_fire_40


title: soil_metaT_control_37


title: soil_metaT_control_35N


title: soil_metaT_control_31


title: soil_metaT_control_9


title: soil_metaT_fire_28


title: Whole Blood from BAB15381

source_name: Whole Blood from Male BAB15381

value: Patient BAB15381

source_name: Male LCL GM10886

value: Reference Sample


title: Whole Blood from BAB15403

source_name: Whole Blood from Male BAB15403

value: Patient BAB15403

source_name: Male LCL GM10890


title: Whole Blood from BAB3251

source_name: Whole Blood from Male BAB3251

value: Patient BAB3251

source_name: Male LCL GM10883


title: soil_metaT_control_28


title: soil_metaT_control_40


title: Whole Blood from BAB15383

source_name: Whole Blood from Male BAB15383

value: Patient BAB15383

source_name: Male LCL GM10887


title: Whole Blood from BAB15385

source_name: Whole Blood from Male BAB15385

value: Patient BAB15385

source_name: Male LCL GM10888


title: Whole Blood from BAB15243

source_name: Whole Blood from Male BAB15243

value: Patient BAB15243

source_name: Male LCL GM10879


title: Whole Blood from BAB15345

source_name: Whole Blood from Male BAB15345

value: Patient BAB15345

source_name: Male LCL GM10882


title: Whole Blood from BAB15364

source_name: Whole Blood from Male BAB15364

value: Patient BAB15364

source_name: Male LCL GM10885


title: soil_metaT_fire_31

source_name: soil sample

value: fire


title: soil_metaT_control_24N

value: control


title: soil_metaT_fire_24N


title: Whole Blood from BAB15343

source_name: Whole Blood from Male BAB15343

value: Patient BAB15343

source_name: Male LCL GM10881


title: soil_metaT_control_23


title: Whole Blood from BAB14951

source_name: Whole Blood from Male BAB14951

value: Patient BAB14951

source_name: Male LCL GM10878


title: soil_metaT_control_22E


title: Whole Blood from BAB15291

source_name: Whole Blood from Male BAB15291

value: Patient BAB15291

source_name: Male LCL GM10880


title: soil_metaT_control_20


title: Whole Blood from BAB14606

source_name: Whole Blood from Male BAB14606

value: Patient BAB14606

value: Male

source_name: Male LCL GM10875


title: Whole Blood from BAB15407

source_name: Whole Blood from Male BAB15407

value: Patient BAB15407

value: Whole Blood

source_name: Male LCL GM10892


title: Whole Blood from BAB15404

source_name: Whole Blood from Male BAB15404

value: Patient BAB15404

source_name: Male LCL GM10891

value: Reference Sample


title: soil_metaT_fire_19E


title: soil_metaT_control_59


title: Whole Blood from BAB14623

source_name: Whole Blood from Male BAB14623

value: Patient BAB14623

source_name: Male LCL GM10874


title: soil_metaT_fire_15


title: soil_metaT_control_43


title: Whole Blood from BAB14716

source_name: Whole Blood from Male BAB14716

value: Patient BAB14716

source_name: Male LCL GM10877


title: Whole Blood from BAB14617

source_name: Whole Blood from Male BAB14617

value: Patient BAB14617

source_name: Male LCL GM10873


title: soil_metaT_control_13

source_name: soil sample


title: mESC_H3K27me3_ViCAR_3

city: Cambridge

first: Somdutta

last: Dhir

address: Robinson Way

department: CRUK-CI

country: United Kingdom

institute: University of Cambridge

description:
mESC_H3K27me3_ViCAR_05_01kb.interactions_FitHiC_Q0.01.bed
mESC_H3K27me3_ViCAR.05_01kb.interactions_FitHiC_Q0.01_WashU.bed.gz
mESC_H3K27me3_ViCAR.05_01kb.interactions_FitHiC_Q0.01_WashU.bed.gz.tbi

library_source: other

data_processing:
reads were aligned to hg38(human) /mm10(mouse) reference genome using bwa mem with flags -SP5M
Pairtools pipeline was used to generate pairs and bam files and identify unique valid interactions
FitHiChIPwas used with CovBias for normalization, and q value thresholds of q<0.01
Assembly: hg38, mm10
Supplementary files format and content: Bed, WashU.bed,BigWigs

molecule: other

source_name: E14 ES cells

growth_protocol: K562 cells were cultured in RPMI1640 (Glutamine plus, Life Technologies) with 10% of fetal bovine serum (Life Technologies) at 37°C with 5% CO2. GM12878 cells were cultured in RPMI1640 (Glutamine plus, Life Technologies) with 10% of fetal bovine serum (Life Technologies) at 37°C with 5% CO2. E14 mESC cells were cultured in serum/LIF medium, containing 10% fetal bovine serum and 1,000 U/mL LIF.

extract_protocol: HiCAR was performed with 100,000 K562 cells, crosslinked with 1% formaldehyde.ViCAR was performed on beads using 15 µL MyOneT1 beads per sample. For 4 samples, 60 µL MyOneT1 beads were washed 3x with 500 µL PBS pH6.8 and resuspended in 60 µL PBS pH 6.8 with 0.01% Tween-20. 30 µL biotin-Conjugated con A solution (2.3mg/ml, Sigma Aldrich C2272) were added to the bead suspension, and binding performed at room temperature (RT) for 30mins with rotation (400rpm). After 30 min, supernatant was removed on a magnet, and beads were washed once with 60 µL PBS pH 6.8 with 0.01% Tween-20, and twice with 1mL binding buffer (20 mM HEPES pH 7.5, 10 mM KCl, 1mM CaCl2 and 1mM MnCl2). After the last wash, beads were resuspended in 60µL binding buffer. 200,000-500,000 cells per sample were fixed in 1 mL 1% formaldehyde (Thermo Fisher Scientific, 28906) in PBS for 10 min at RT with rotation. Formaldehyde was quenched by addition of Glycine to a final concentration of 0.2M, and samples were incubated at RT for 10min. Cells were spun for 4 min at 1300xg at 4°C, supernatant was removed, cells resuspended in 1 mL PBS, and then pelleted again by spinning at 4 min at 1300xg at 4°C. To prepare nuclei, cells were resuspended in 1 mL NE1 buffer (20 mM HEPES pH7.5, 10 mM KCl, 0.5 mM spermidine (S0266-5G), 0.1% Triton X-100, 20% glycerol, plus 1 Roche Complete Protease Inhibitor EDTA-Free tablet), and incubated on ice for 10 min. Nuclei were pelleted by spinning for 4 min at 1300xg at 4°C, supernatant was removed, and cells were washed in 1 mL PBS. Nuclei were pelleted again by spinning for 4 min at 1300xg at 4°C, supernatant was removed, and nuclei were resuspended in 150 µL wash buffer (20 mM HEPES pH7.5, 150 mM KCl, 0.5 mM spermidine, plus 1 Roche Complete Protease Inhibitor EDTA-free tablet). 15µL conA-MyOneT1 beads (prepared above) were added, and samples incubated for 10 min at RT, with rotation at 800rpm. Beads were immobilized on a magnet, supernatant removed, and samples washed twice in 100 µL antibody buffer (2 mM EDTA, 1% BSA (Sigma-Aldrich A8577), 0.05% digitonin (EMD Milipore 300410), 20 mM HEPES pH7.5, 150 mM KCl, 0.5 mM spermidine plus 1 Roche Complete Protease Inhibitor EDTA-free tablet). After the second wash, beads were resuspended in 100 µL antibody buffer, and blocked for 1 h, at RT with rotation at 800rpm. After 1 h, primary antibodies were added. For the following antibodies, 2 µL antibody were added to 100 µL sample: anti- anti-H3K27me3 (Cell Signalling 9733), H3K4me3 (Abcam ab8580), anti-H3K4me1 (Thermo 710795). For BG4, 4 µL 1.3 µM antibody prepared in-house1 were added to 100 µL sample. Primary antibody incubation was performed at 4°C overnight, with rotation at 600 rpm. The next day, supernatant was removed on a magnet, and beads washed twice with 100 µL dig-wash buffer (0.05% digitonin, 20 mM HEPES pH7.5, 150 mM KCl, 0.5 mM spermidine plus 1 Roche Complete Protease Inhibitor EDTA-free tablet). For BG4 samples, 4 µL anti-FLAG antibody (Cell Signaling 2368) in 100 µL dig-wash buffer was added to beads with incubation for 1h at RT, shaking at 800 rpm. BG4 samples were then washed 3x in 100 µL dig-wash buffer. Next, for all samples, 1 µL anti-Rabbit IgG antibody in 100 µL dig-wash buffer was added (Antibodies-Online ABIN101961), and samples were rotated at 800rpm at RT for 1h. pA-Tn5 was prepared in-house and loaded with ME-rev and BfaI-truseqR1-pmeI-nextera. Samples were washed 3x in dig-wash buffer, resuspended in 50 µL of a 1:250 dilution of pA-Tn5 in dig-300 buffer (0.01% digitonin, 20 mM HEPES pH7.5, 300 mM KCl, 0.5 mM spermidine plus 1 Roche Complete Protease Inhibitor EDTA-free tablet). Tagmentation was performed for 1 h at 37°C, shaking at 800rpm. Nuclei were washed twice in 200 µL TAPS wash buffer (10 mM TAPS, 0.2 mM EDTA) on a magnet, then washed twice in 300 µL 0.075% BSA in PBS. Beads were resuspended in nuclei in 50µL solution containing 32.5 µL nuclease-free water, 5 µL 10x NEBuffer r3.1(NEB B6003S) and 12.5µL 2% SDS and incubated at 62°C for 10 min without rotation. 139 µL solution containing 100 µL nuclease-free water, 14 µL 10x NEBuffer3.1, 25 µL 10% Triton X-100 and incubated 37°C for 15 min, shaking at 800 rpm. Supernatant was removed on a magnet and resuspended in 300 µL 1.1X NEBuffer r3.1. Next, supernatant was removed on a magnet and resuspended in 101 µL solution containing: 90 µL 1.1X NEBuffer r3.1, 10µL CviQI (NEB, R0639L), 1µL splint oligo. Samples were incubated for 3h at 25°C, with rotation at 800 rpm. After 3h, 374 µL solution containing 283.6µL nuclease-free water, 40µL 10% Triton X-100, 2.4 µL 20 mg/mL BSA (NEB B9000S), 48 µL 10X T4 ligation Buffer was added. 6 µL T4 DNA ligase were then added, samples were mixed by pipetting, and in situ ligation was performed overnight at 16°C with interval shaking. The next day, beads were captured on a magnet and supernatant was removed. Beads were resuspended in 100µL solution containing 0.5mg/mL Proteinase K, 0.5% SDS and 10mM Tris-HCl buffer pH 8.0. Samples were mix by vortexing and incubated for 1 hr at 55 ºC, then for 2 h at 68 ºC, shaking at 800rpm. DNA was purified using DNA Clean & Concentrator-5 (Zymo D4013): sample and beads were added to 500 µL binding buffer, transferred to a spin column, washed twice following manufacturer’s instructions, and DNA was eluted in 20 µL elution buffer.

value: E14 ES cells

value: Embryonic stem cells


title: mESC_H3K27me3_ViCAR_4


title: Whole Blood from BAB11934

source_name: Whole Blood from Male BAB11934

value: Patient BAB11934

source_name: Male LCL GM10872


title: Whole Blood from BAB14598

source_name: Whole Blood from Male BAB14598

value: Patient BAB14598

source_name: Male LCL GM10871


title: Whole Blood from BAB14390

source_name: Whole Blood from Male BAB14390

value: Patient BAB14390

source_name: Male LCL GM10868


title: soil_metaT_control_89

value: control


title: Whole Blood from BAB14380

source_name: Whole Blood from Male BAB14380

value: Patient BAB14380

source_name: Male LCL GM10867


title: mESC_H3K27me3_ViCAR_1


title: soil_metaT_fire_13

value: fire


title: Whole Blood from BAB14369

source_name: Whole Blood from Male BAB14369

value: Patient BAB14369

source_name: Male LCL GM10866


title: mESC_H3K27me3_ViCAR_2


title: FMT CZA + PD-1_T990

city: DIJON

first: François

last: Ghiringhelli

address: 1 rue du Professeur Marion

country: France

institute: UMR INSERM 1231

description:
T-990
TPM_tumor.csv

data_processing:
Pseudo alignment and quantification were performed using kallisto 0.45
Assembly: GRCm38
Supplementary files format and content: semicolon-delimited csv file including TPM values for CD8 and Tumor cells, respectively

source_name: Tumor bulk

growth_protocol: MCA-205 fibrosarcoma cells, class I MHC H-2b syngeneic cell lines for C57BL/6 mice were used for this study. MCA-205 were cultured in RPMI+FBS10% medium. All cultures were checked for Mycoplasma using PlasmoTest Mycoplasma Detection Kit (InvivoGen). 2 weeks after FMT with HV stools treated with CZA or CZA+DAV132 for 6 days, C57Bl6 mice were implanted subcutaneously with 0.8 × 10^6 MCA-205 cells. When tumors reached 25 to 35 mm2 in size, mice were treated four times intraperitoneally every three days with αPD-1 mAb (250 μg/mouse; clone RMP1-14, Bio X Cell) or isotype control (clone 2A3, Bio X Cell). The mice were sacrificed 2 days after the last treatment and the tumor were harvested and snap frozen for a tumor bulk RNAseq analysis. A duplicat of this experiemnst was performed with the same setting and using the same FMT samples, the tumor were also haversed at the sacrifice and the CD8+ T cells were cell sorted and immediately snap frozen for a specific analysis of the gene expression of this cell population.

extract_protocol:
Total RNA was extracted from cells by using Monarch Total RNA Miniorep Kit according to the manufacturer's instructions.
300 ng of total RNA were ribodepleted with the Ribocop rRNA depletion kit. Then, libraries were prepared thanks to NEBNext Ultra II Directional RNA library prep kit for Illumina according to manufacturer's instructions.

value: Tumor

value: Tumor bulk

value: WT

value: FMT HV CZA + anti-PD-1


title: FMT CZA + PD-1_T989

description:
T-989
TPM_tumor.csv

treatment_protocol: 2 weeks after FMT with HV stools treated with CZA or CZA+DAV132 for 6 days, C57Bl6 mice were implanted subcutaneously with 0.8 × 10^6 MCA-205 cells. When tumors reached 25 to 35 mm2 in size, mice were treated four times intraperitoneally every three days with αPD-1 mAb (250 μg/mouse; clone RMP1-14, Bio X Cell) or isotype control (clone 2A3, Bio X Cell).


title: FMT CZA + PD-1_T988

description:
T-988
TPM_tumor.csv


title: FMT CZA + ISO_T987

description:
T-987
TPM_tumor.csv

value: FMT HV CZA + Isotype control


title: Whole Blood from BAB14525

source_name: Whole Blood from Male BAB14525

value: Patient BAB14525

value: Male

value: Whole Blood

source_name: Male LCL GM10865

value: Reference Sample


title: Whole Blood from BAB14413

source_name: Whole Blood from Male BAB14413

value: Patient BAB14413

source_name: Male LCL GM10863


title: Whole Blood from BAB14395

source_name: Whole Blood from Male BAB14395

value: Patient BAB14395

source_name: Male LCL GM10862


title: Whole Blood from BAB14417

source_name: Whole Blood from Male BAB14417

value: Patient BAB14417

source_name: Male LCL GM10864


title: Whole Blood from BAB14383

source_name: Whole Blood from Male BAB14383

value: Patient BAB14383

source_name: Male LCL GM10861


title: FMT CZA + ISO_T986

description:
T-986
TPM_tumor.csv


title: FMT CZA + ISO_T991

description:
T-991
TPM_tumor.csv


title: FMT CZA + ISO_T985

description:
T-985
TPM_tumor.csv


title: LCL from BAB2627

source_name: LCL from Male BAB2627

value: Patient BAB2627LCL

value: LCL

source_name: Male LCL GM10855


title: Tonsil

city: Stanford

first: Menglan

last: Xiang

state: CA

address: 450 Serra Mall

institute: Stanford University

library_source: transcriptomic single cell

data_processing:
Reads were mapped to the GRCh38 reference genome using Cell Ranger. Hashtag demultiplexing was performed using the HTODemux function of the “Seurat” package. Per cell normalization of raw count data was performed using the NormalizeData function of “Seurat” or the deconvolution method implemented in the computeSumFactors function from the “scran” package. Gene imputation was performed on log-normalized count data using the original implementation of the MAGIC (Markov Affinity-based Graph Imputation of Cells) algorithm with optimized parameters (t = 2, k = 9, ka = 3) (https://github.com/kbrulois/magicBatch).
Assembly: GRCh38
Supplementary files format and content: tsv and mtx files from Cell Ranger; csv files with cell type information

source_name: Tonsil

extract_protocol:
A human tonsil specimen obtained by surgical resection was mechanically processed and cells were preserved frozen. Cells were later thawed and stained with the following flow cytometry panel: anti human CD45RA-FITC (HI100), anti human HLA -PercpCy5.5 (L243), anti human TCRab-BUV737 (IP26) and anti human IgD-BUV395 (IA6-2) antibodies from BD: anti human CD69-PECy7 (FN50), anti human CD45RO-BV605 (UCHL1), anti human CD8-BV421 (SK1), anti human CD4-BV786 (SK3), anti human CD38-APCCy7 (HIT2) and anti human CD19-AF700 (HIB19) antibodies from Biolegend. Next, cells were FACS sorted as follows using an Aria lll sorter (BD) and the indicated number of cells from each subset were combined in preparation for one 5’ 10x genomics scRNAseq capture.   T cell sample: CD45RA+CD45RO+ CD4+ T Cells (50K), HLADR+CD38+/- CD4 T Cells (20K) and total TCRab+ CD4+ cells (10K).  B cell sample: TCRab- CD4- CD8- (20K), TCRab- CD4- CD8- IgD- (20K), TCRab- CD4- CD8- IgD- CD38+ (20K), TCRab- CD4- CD8- IgD- CD38+++ (15K).
Library was constructed using the 10x Genomics 5' v2 kit according to the manufacturer's instructions.

value: Tonsil

value: T and B cells


title: Whole Blood from BAB15586

source_name: Whole Blood from Male BAB15586

value: Patient BAB15586

source_name: Male LCL GM10897


title: Human_Lymphoma_DLBCL_Region2_10um pixel-size device

city: New Haven

first: Rong

last: Fan

state: Connecticut

address: 55 Prospect St.

department: Biomedical Engineering

institute: Yale University

data_processing:
*library strategy: Spatial Transcriptomics
To decode sequencing data, the FASTQ file Read 2 underwent processing, involving the extraction of unique molecular identifiers (UMIs) and spatial Barcode A and Barcode B. The Read 1 containing cDNA sequences was trimmed using Cutadapt V3.4 and then aligned to either the mouse GRCm38-mm10 or human GRCh38 reference genome using STAR V2.7.7a. Utilizing ST_Pipeline V1.7.6, spatial barcode sequences were demultiplexed based on the predefined coordinates of the microfluidic channels and ENSEMBL IDs were converted to gene names, generating the gene-by-pixel expression matrix for downstream analysis. Matrix entries corresponding to pixel positions devoid of tissues were excluded.
Assembly: GRCm38-mm10 or human GRCh38
Supplementary files format and content: Integrated Seurat .rds object

source_name: Lymph node

extract_protocol:
The spatially barcoded tissue was enclosed with a clean polydimethylsiloxane (PDMS) reservoir and securely clamped using acrylic chips. A 2X lysis buffer was prepared in advance, consisting of 20 mM Tris-HCl pH 8.0, 400 mM NaCl, 100 mM EDTA, and 4.4% SDS. For tissue digestion, 70 µL of the lysis mix (30 µL 1X DPBS, 30 µL 2X lysis buffer, 10 µL 20 µg/µL Proteinase K solution) was loaded into the PDMS reservoir, sealed with parafilm, and incubated in a humidified box at 55°C for 2 hours. After the reaction, the parafilm was removed, and all the liquid containing cDNA was collected into a 1.5mL DNA low-bind tube.
PCR amplification was executed to directly ligate sequencing primers, using a 100 µL system consisting of 50 µL 2X KAPA HiFi HotStart ReadyMix, ~42 µL solution from the rRNA removal step, 4 µL 10 µM P5 Primer, and 4 µL 10 µM P7 Primer. The resulting library underwent purification using SPRIselect beads at a 0.8X ratio, quality control checked using TapeStation, and was then sequenced on an Illumina NovaSeq 6000 Sequencing System with a paired-end 150bp read length.

value: Lymph node

tag: disease

value: Lymphoma

value: Patho-DBiT Protocol


title: FMT CZA + ISO_T983

description:
T-983
TPM_tumor.csv

source_name: Tumor bulk

value: Tumor

value: Tumor bulk

value: WT

value: FMT HV CZA + Isotype control


title: Human_Lymphoma_DLBCL_Region1_10um pixel-size device


title: Healthy_Donor_LymphNode_20um pixel-size device

value: Normal


title: Blood

source_name: Blood

extract_protocol:
Blood was collected by venipuncture from a healthy donor and PBMC were isolated with a ficoll gradient. T cells were isolated by negative magnetic selection using the total T cell isolation kit (STEMCELL technologies). T cells were then rested for 2 hours in RPMI-10 at 37C and subsequently used as input in a transwell-based chemotaxis assay using h4CysCXCL17 300nM as chemoattractant as described above. Migrated cells were recovered from 9 independent transwell wells and along with the corresponding input samples, were separately hash tagged and finally mixed together in preparation for a single 5’ 10x Genomics scRNAseq capture.
Library was constructed using the 10x Genomics 5' v3 kit according to the manufacturer's instructions.

value: Blood

value: T cells


title: Whole Blood from BAB14399

source_name: Whole Blood from Male BAB14399

value: Patient BAB14399

value: Female

value: Whole Blood

source_name: Female LCL GM12156

value: Reference Sample


title: FMT CZA + PD-1_T982

description:
T-982
TPM_tumor.csv

value: FMT HV CZA + anti-PD-1


title: Whole Blood from BAB6280

source_name: Whole Blood from Male BAB6280

value: Patient BAB6280

value: Male

source_name: Male LCL GM10857


title: FMT CZA + DAV132 + PD-1_T030

description:
T-030
TPM_tumor.csv

value: FMT HV CZA + DAV132 + anti-PD-1


title: Whole Blood from BAB14379

source_name: Whole Blood from Male BAB14379

value: Patient BAB14379

source_name: Male LCL GM10860


title: Whole Blood from BAB3053

source_name: Whole Blood from Male BAB3053

value: Patient BAB3053

source_name: Male LCL GM10854


title: FMT CZA + PD-1_T984

description:
T-984
TPM_tumor.csv

value: Tumor


title: FMT CZA + DAV132 + PD-1_T029

description:
T-029
TPM_tumor.csv

value: Tumor bulk


title: FMT CZA + DAV132 + PD-1_T026

description:
T-026
TPM_tumor.csv

value: WT


title: FMT CZA + DAV132 + ISOTYPE_T028

description:
T-028
TPM_tumor.csv

value: FMT HV CZA + DAV132 + Isotype control


title: Whole Blood from BAB2684

source_name: Whole Blood from Male BAB2684

value: Patient BAB2684

source_name: Male LCL GM10852


title: FMT CZA + DAV132 + PD-1_T023

description:
T-023
TPM_tumor.csv


title: Whole Blood from BAB13429

source_name: Whole Blood from Male BAB13429

value: Patient BAB13429

source_name: Male LCL GM10851


title: p53kd-15.18 replicate 2

city: Amsterdam

first: Dorine

last: Hintzen

address: Plesmanlaan 121

department: Cell Biology

country: Netherlands

institute: Netherlands Cancer Institute

data_processing:
The reads were sequenced using a stranded RNA protocol
The reads that are of low complexity or repetitive sequences are filtered
The reads are mapped to the transcriptome. Reads that do not map to the transcriptome are used for a whole genome mapping in the last step.
Samples are aligned with HiSat2. settings: --min-intronlen 20 --max-intronlen 500000 --rna-strandness F -k 5 --minins 0 --maxins 500 --fr --new-summary Steps performed: link, count, QCstrandness, eset
Read counts are determined.Count parameters Count library type stranded: true Icount (based on HTSeq-count) GTF version: Homo_sapiens.GRCh38.87.gtf mode -> union: If a read is mapped to a region with overlapping genes, this read will be dismissed. However, when stranded RNA sequencing has been performed, the read can be used there is an overlap of 2 genes which are in opposite direction.
Assembly: Homo sapiens GRCh38.102
Supplementary files format and content: tab-separated gene counts and gene annotation for all samples

source_name: RPE-1 (human non-transformed cell line)

extract_protocol:
polyA RNA
The library was prepared using TruSeq RNA sample prep kit according to the manufacturer’s protocol (Illumina). polyA+ stranded RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Clones were generated by blocking RPE-1 p53kd cells in Thymidine for 14 hours, after which they were released in medium containing a combination of an Mps1 inhibitor (NMS-P715) (480uM) and a CENP-E inhibitor (GSK923295) (50nM) for 8 hours to induce whole chromosome aneuploidies and segmental, then plated single cell to obtain aneuploid clones. Adapted clones were obtained by long-term culturing for months.

value: RPE-1 (human non-transformed cell line)

value: retinal pigment epithelial cell

value: P53KD aneuploid clone


title: p53kd-D3 replicate 2


title: p53kd-D3-adapted replicate 2


title: p53kd-15.16-adapted replicate 2


title: p53kd-15.18-adapted replicate 2


title: FMT CZA + DAV132 + PD-1_T021

description:
T-021
TPM_tumor.csv


title: FMT CZA + DAV132 + ISOTYPE_T022

description:
T-022
TPM_tumor.csv


title: p53kd-15.16 replicate 2


title: Human_Lymphoma_AITL_50um pixel-size device

value: Lymph node

value: Lymphoma

value: Patho-DBiT Protocol


title: p53kd-15.14 replicate 2


title: FMT CZA + DAV132 + anti-PD-1_CD8-20

description:
CD8-20
TPM_CD8.csv

source_name: CD8+ T cell sorted from tumor

value: Tumor Infiltrated CD8+ T cells


title: p53kd-15.14-adapted replicate 2


title: FMT CZA + DAV132 + anti-PD-1_CD8-18

description:
CD8-18
TPM_CD8.csv


title: p53kd-15.12 replicate 2


title: FMT CZA + DAV132 + anti-PD-1_CD8-19

description:
CD8-19
TPM_CD8.csv


title: FMT CZA + DAV132 + ISOTYPE_T027

description:
T-027
TPM_tumor.csv


title: FMT CZA + DAV132 + ISOTYPE_T024

description:
T-024
TPM_tumor.csv


title: FMT CZA + DAV132 + anti-PD-1_CD8-17

description:
CD8-17
TPM_CD8.csv


title: FMT CZA + DAV132 + anti-PD-1_CD8-16

description:
CD8-16
TPM_CD8.csv


title: p53kd-14.21 replicate 2


title: FMT CZA + DAV132 + ISO_CD8-15

description:
CD8-15
TPM_CD8.csv


title: p53kd-14.20-adapted replicate 2


title: FMT CZA + DAV132 + ISO_CD8-14

description:
CD8-14
TPM_CD8.csv


title: p53kd-14.20 replicate 2


title: FMT CZA + DAV132 + ISO_CD8-13

description:
CD8-13
TPM_CD8.csv


title: p53kd-14.17-adapted replicate 2


title: p53kd-14.16-adapted replicate 2


title: p53kd-14.17 replicate 2


title: FMT CZA + DAV132 + ISO_CD8-11

description:
CD8-11
TPM_CD8.csv


title: p53kd-14.16 replicate 2


title: FMT CZA + anti-PD-1_CD8-9

description:
CD8-9
TPM_CD8.csv

value: FMT HV CZA + anti-PD-1


title: FMT CZA + anti-PD-1_CD8-10

description:
CD8-10
TPM_CD8.csv


title: FMT CZA + anti-PD-1_CD8-7

description:
CD8-7
TPM_CD8.csv


title: p53kd-14.14 replicate 2


title: p53kd-14.14-adapted replicate 2


title: p53kd-15.12-adapted replicate 2


title: p53kd-14.10-adapted replicate 2


title: p53kd-14.10 replicate 2


title: p53kd-14.6-adapted replicate 2


title: p53kd-14.21-adapted replicate 2


title: FMT CZA + ISO_CD8-4

description:
CD8-4
TPM_CD8.csv

value: FMT HV CZA + Isotype control


title: p53kd-14.6 replicate 2


title: FMT CZA + ISO_CD8-5

description:
CD8-5
TPM_CD8.csv


title: p53kd-14.2-adapted replicate 2


title: p53kd-14.2 replicate 2


title: FMT CZA + ISO_CD8-3

description:
CD8-3
TPM_CD8.csv


title: FMT CZA + ISO_CD8-2

description:
CD8-2
TPM_CD8.csv


title: FMT CZA + DAV132 + ISO_CD8-12

description:
CD8-12
TPM_CD8.csv


title: p53kd-12.10-adapted replicate 2


title: Week4_barcode

city: New York

first: Joshua

middle: Seth

last: Schiffman

state: New York

address: 101 Avenue of the Americas

institute: New York Genome Center

description: Lineage barcodes

data_processing:
CellRanger multi was used to generate count matrices.
Cassiopeia  was used to generate lineage tables and phylogenies.
Assembly: hg38
Supplementary files format and content: CellRanger output files: wk4_no3_barcodes.tsv.gz, wk4_no4_barcodes.tsv.gz, wk4_no3_features.tsv.gz, wk4_no4_features.tsv.gz, wk4_no3_matrix.mtx.gz, wk4_no4_matrix.mtx.gz
Supplementary files format and content: Cassiopeia output files: wk4_no3_call_lineages.txt, wk4_no4_call_lineages.txt, and wk4_no3_trees.tar.gz, wk4_no4_trees.tar.gz, which contain phylogenies in Newick format.

source_name: Brain

growth_protocol: Patient-derived human GBM cells (MGG23) [Wakimoto et al., 2011] were grown in Neurobasal Medium (Thermo Fisher Scientific) supplemented with 1/2 x N2 and 1 x B27 (Thermo Fisher Scientific), 1% Penicillin/Streptomycin (Thermo Fisher Scientific), 1.5 x Glutamax (Thermo Fisher Scientific), 20 ng/mL of EGF and 20 ng/mL of FGF2 (Shenandoah Biotechnology).

extract_protocol:
GBM cells were dissociated with TrypLE (Thermo Fisher) and incubated with TotalSeq-B anti-human antibodies (BioLegend) according to manufacturer instructions. TotalSeq-B0253 and B0254 were used for the two replicates.
scRNAseq libraries were generated using the Chromium Next GEM Single Cell GEM, Library & Gel Bead Kit v3.1, Chromium Single Cell Feature Barcode Library Kit, Chromium Next GEM Chip G, and 10x Chromium Controller (10x Genomics) according to manufacturer instructions. The Cas9-edited Molecular Recorder barcodes were PCR amplified from single-cell cDNA libraries as previously described [Chan et al., 2019].

treatment_protocol: The Molecular Recorder cassette PCT62 [Chan et al., 2019] was introduced into MGG23 cells using piggyBac-mediated transposition (Systems Biosciences). Lineage tracing was initiated by infecting cells with lentivirus expressing Cas9-EGFP, followed by FACS sorting for EGFP-positive cells. Cells were subsequently grown in vitro for 4 weeks and lineage traced with the Molecular Recorder approach for two replicates.

value: Brain

value: GBM

tag: library type

value: mRNA


title: p53kd-12.10 replicate 2


title: FMT CZA + anti-PD-1_CD8-8

description:
CD8-8
TPM_CD8.csv

value: Tumor


title: FMT CZA + anti-PD-1_CD8-6

description:
CD8-6
TPM_CD8.csv

value: WT


title: Week4_surface

description: Multiplexing Capture

molecule: protein

value: CellHash


title: p53kd-parental-adapted-21 replicate 2


title: Week4_mRNA

description: Gene Expression


title: p53kd-parental-adapted-20 replicate 2


title: p53kd-parental replicate 2


title: p53kd-D3-adapted replicate 1


title: K562_RNAseq_G4_mutant_clone1_rep3

data_processing:
reads were aligned to hg38 reference genome using bwa mem with flags -SP5M
Pairtools pipeline was used to generate pairs and bam files and identify unique valid interactions
FitHiChIPwas used with CovBias for normalization, and q value thresholds of q<0.05 and q<0.01
Assembly: hg38
Supplementary files format and content: Bed, WashU.bed, BigWigs

growth_protocol: K-562 cells were cultured in RPMI1640 (Glutamine plus, Life Technologies) with 10% of fetal bovine serum (Life Technologies) at 37°C with 5% CO2

extract_protocol:
RNA from 1 × 106 cells was extracted with RNeasy Plus Mini Kit (Qiagen 74136) following manufacturer’s instructions.
500 ng RNA was used for library preparation with NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760S), following manufacturer’s instructions. Polyadenylated transcripts were enriched using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB E7490) as per the manufacturer’s protocol. Libraries were sequenced in paired-end mode on a NextSeq 2000 (60 bp paired-end).

value: lymphoblast cells


title: K562_RNAseq_G4_mutant_clone1_rep2


title: p53kd-15.18-adapted replicate 1


title: p53kd-15.18 replicate 1


title: p53kd-15.16-adapted replicate 1


title: K562_RNAseq_G4_mutant_clone2_rep4


title: K562_RNAseq_G4_mutant_clone2_rep3


title: K562_RNAseq_G4_mutant_clone1_rep1


title: K562_RNAseq_G4_mutant_clone2_rep2


title: p53kd-15.16 replicate 1


title: FMT CZA + ISO_CD8-1

description:
CD8-1
TPM_CD8.csv


title: p53kd-15.14-adapted replicate 1


title: p53kd-15.14 replicate 1


title: p53kd-15.12-adapted replicate 1


title: K562_RNAseq_WT_rep4


title: GM12878_H3K27ac_ViCAR_1

description:
GM12878_H3K27ac_ViCAR.05_01kb.interactions_FitHiC_Q0.05.bed
GM12878_H3K27ac_ViCAR.05_01kb.interactions_FitHiC_Q0.05_WashU.bed.gz
GM12878_H3K27ac_ViCAR.05_01kb.interactions_FitHiC_Q0.05_WashU.bed.gz.tbi


title: K562_RNAseq_WT_rep3


title: K562_RNAseq_WT_rep1


title: K562_RNAseq_WT_rep2


title: p53kd-15.12 replicate 1


title: GM12878_H3K27ac_ViCAR_2


title: p53kd-14.21-adapted replicate 1


title: p53kd-14.21 replicate 1


title: K562_G4_mutant_clone1_Pol2_5SP_CnT_rep7

extract_protocol:
CUT&Tag was performed as previously described3. 300,000 nuclei were lightly fixed in 1 mL 0.1% formaldehyde for 2min, followed by formaldehyde quenching by the addition of 60 µL1.25M Glycine. Cells were spun for 4 min at 500xg at 4°C, supernatant removed, cells resuspended in 1 mL PBS, and then pelleted again by spinning at 4 min at 1300xg at 4°C. To prepare nuclei, cells were resuspended in 1 mL NE1 buffer (20 mM HEPES pH7.5, 10 mM KCl, 0.5 mM spermidine (S0266-5G), 0.1% Triton X-100, 20% glycerol, plus 1 Roche Complete Protease Inhibitor EDTA-Free tablet), and incubated on ice for 10 min. Nuclei were pelleted by spinning for 4 min at 500xg at 4°C, supernatant removed, and cells washed in 1 mL PBS. Nuclei were pelleted again by spinning for 4 min at 1300xg at 4°C, supernatant removed, and nuclei resuspended in 150 µL wash buffer (20 mM HEPES pH7.5, 150 mM KCl, 0.5 mM spermidine, plus 1 Roche Complete Protease Inhibitor EDTA-free tablet). 15 µL conA-MyOneT1 beads (prepared above) were added, and samples incubated for 10 min at RT, with rotation at 800rpm. Beads were then immobilized on a magnet, supernatant removed, and samples washed twice in 100 µL antibody buffer (2 mM EDTA, 1% BSA (Sigma-Aldrich A8577), 0.05% digitonin (EMD Milipore 300410), 20 mM HEPES pH7.5, 150 mM KCl, 0.5 mM spermidine plus 1 Roche Complete Protease Inhibitor EDTA-free tablet). After the second wash, beads were resuspended in 100 µL antibody buffer, and blocked for 1 h, at RT with rotation at 800rpm. After 1 h, 1:50 anti-Ser5 phosphorylated Rpb1 antibody (Cell Signaling 13523) was added, with incubation performed at 4°C overnight with rotation at 600 rpm. The next day, supernatant was removed on a magnet, and beads washed twice with 100 µL dig-wash buffer (0.05% digitonin, 20 mM HEPES pH7.5, 150 mM KCl, 0.5 mM spermidine plus 1 Roche Complete Protease Inhibitor EDTA-free tablet). 1 µL anti-Rabbit IgG antibody in 100 µL dig-wash buffer were added (Antibodies-Online ABIN101961), and samples were rotated at 800rpm at RT for 1h. Samples were washed 3x in dig-wash buffer, resuspended in 50 µL of a 1:250 dilution of adapter-loaded pA-Tn5 in dig-300 buffer (0.01% digitonin, 20 mM HEPES pH7.5, 300 mM KCl, 0.5 mM spermidine plus 1 Roche Complete Protease Inhibitor EDTA-free tablet). Samples were then washed 3x in 100 µL dig-300 buffer, resuspended in 100 µL tagmentation buffer (dig-300 buffer with 10 mM MgCl2), and tagmentation was performed for 1 h at 37°C, shaking at 800rpm. Nuclei were washed twice in 200 µL TAPS wash buffer (10 mM TAPS, 0.2 mM EDTA) on a magnet, then incubated for 1h at 55°C, shaking at 800rpm, in 100 µL buffer containing 0.5mg/mL Proteinase K, 0.5% SDS, and10mM Tris-HCl pH 8.0.
A total of 9 PCR cycles was performed and libraries were sequenced in paired-end mode on a NextSeq 2000 (60 bp paired-end).


title: p53kd-14.17-adapted replicate 1


title: K562_G4_mutant_clone1_Pol2_5SP_CnT_rep5


title: p53kd-D3 replicate 1


title: K562_G4_mutant_clone1_Pol2_5SP_CnT_rep6


title: p53kd-14.20-adapted replicate 1


title: K562_G4_mutant_clone1_Pol2_5SP_CnT_rep4


title: K562_G4_mutant_clone1_Pol2_5SP_CnT_rep3


title: K562_RNAseq_G4_mutant_clone2_rep1


title: p53kd-14.16 replicate 1


title: p53kd-14.16-adapted replicate 1


title: K562_G4_mutant_clone1_Pol2_5SP_CnT_rep2


title: p53kd-14.14-adapted replicate 1


title: p53kd-14.17 replicate 1


title: p53kd-14.14 replicate 1


title: K562_G4_mutant_clone1_Pol2_5SP_CnT_rep1


title: K562_G4_mutant_clone2_Pol2_5SP_CnT_rep6


title: p53kd-14.10-adapted replicate 1


title: K562_G4_mutant_clone2_Pol2_5SP_CnT_rep5


title: K562_G4_mutant_clone2_Pol2_5SP_CnT_rep7


title: p53kd-14.6-adapted replicate 1


title: p53kd-14.10 replicate 1


title: K562_G4_mutant_clone2_Pol2_5SP_CnT_rep4


title: K562_G4_mutant_clone2_Pol2_5SP_CnT_rep3


title: p53kd-14.2-adapted replicate 1


title: K562_G4_mutant_clone2_Pol2_5SP_CnT_rep2


title: p53kd-14.6 replicate 1


title: K562_G4_mutant_clone2_Pol2_5SP_CnT_rep1


title: K562_WT_Pol2_5SP_CnT_rep7


title: p53kd-14.20 replicate 1


title: K562_WT_Pol2_5SP_CnT_rep6


title: K562_WT_Pol2_5SP_CnT_rep5


title: p53kd-12.10 replicate 1


title: p53kd-12.10-adapted replicate 1


title: p53kd-parental-adapted-21 replicate 1

value: near-diploid


title: p53kd-parental-adapted-20 replicate 1

value: RPE-1 (human non-transformed cell line)


title: p53kd-parental replicate 1

value: retinal pigment epithelial cell


title: K562_WT_Pol2_5SP_CnT_rep4


title: K562_WT_Pol2_5SP_CnT_rep2


title: K562_WT_Pol2_5SP_CnT_rep1


title: H1_H3K27me3_ViCAR_rep2

growth_protocol: H1 hESCs were cultured on Matrigel-coated (#354277, Corning) 6 well plates, in mTESR1 media (# 85850, StemCell Technologies) supplemented with 10 μM ROCK inhibitor Y-27632 for the first 24h (cat. # 1254, Tocris). Media was changed after 1 or 2 days. H1 cells were passaged using ReLeSR (#05872, StemCell Technologies). Cell cultures were routinely checked for mycoplasma infection.

extract_protocol:
ViCAR was performed on beads using 15 µL MyOneT1 beads per sample. For 4 samples, 60 µL MyOneT1 beads were washed 3x with 500 µL PBS pH6.8 and resuspended in 60 µL PBS pH 6.8 with 0.01% Tween-20. 30 µL biotin-Conjugated con A solution (2.3mg/ml, Sigma Aldrich C2272) were added to the bead suspension, and binding performed at room temperature (RT) for 30mins with rotation (400rpm). After 30 min, supernatant was removed on a magnet, and beads were washed once with 60 µL PBS pH 6.8 with 0.01% Tween-20, and twice with 1mL binding buffer (20 mM HEPES pH 7.5, 10 mM KCl, 1mM CaCl2 and 1mM MnCl2). After the last wash, beads were resuspended in 60µL binding buffer. 200,000-500,000 cells per sample were fixed in 1 mL 1% formaldehyde (Thermo Fisher Scientific, 28906) in PBS for 10 min at RT with rotation. Formaldehyde was quenched by addition of Glycine to a final concentration of 0.2M, and samples were incubated at RT for 10min. Cells were spun for 4 min at 1300xg at 4°C, supernatant was removed, cells resuspended in 1 mL PBS, and then pelleted again by spinning at 4 min at 1300xg at 4°C. To prepare nuclei, cells were resuspended in 1 mL NE1 buffer (20 mM HEPES pH7.5, 10 mM KCl, 0.5 mM spermidine (S0266-5G), 0.1% Triton X-100, 20% glycerol, plus 1 Roche Complete Protease Inhibitor EDTA-Free tablet), and incubated on ice for 10 min. Nuclei were pelleted by spinning for 4 min at 1300xg at 4°C, supernatant was removed, and cells were washed in 1 mL PBS. Nuclei were pelleted again by spinning for 4 min at 1300xg at 4°C, supernatant was removed, and nuclei were resuspended in 150 µL wash buffer (20 mM HEPES pH7.5, 150 mM KCl, 0.5 mM spermidine, plus 1 Roche Complete Protease Inhibitor EDTA-free tablet). 15µL conA-MyOneT1 beads (prepared above) were added, and samples incubated for 10 min at RT, with rotation at 800rpm. Beads were immobilized on a magnet, supernatant removed, and samples washed twice in 100 µL antibody buffer (2 mM EDTA, 1% BSA (Sigma-Aldrich A8577), 0.05% digitonin (EMD Milipore 300410), 20 mM HEPES pH7.5, 150 mM KCl, 0.5 mM spermidine plus 1 Roche Complete Protease Inhibitor EDTA-free tablet). After the second wash, beads were resuspended in 100 µL antibody buffer, and blocked for 1 h, at RT with rotation at 800rpm. After 1 h, primary antibodies were added. For the following antibodies, 2 µL antibody were added to 100 µL sample: anti- anti-H3K27me3 (Cell Signalling 9733), H3K4me3 (Abcam ab8580), anti-H3K4me1 (Thermo 710795). For BG4, 4 µL 1.3 µM antibody prepared in-house1 were added to 100 µL sample. Primary antibody incubation was performed at 4°C overnight, with rotation at 600 rpm. The next day, supernatant was removed on a magnet, and beads washed twice with 100 µL dig-wash buffer (0.05% digitonin, 20 mM HEPES pH7.5, 150 mM KCl, 0.5 mM spermidine plus 1 Roche Complete Protease Inhibitor EDTA-free tablet). For BG4 samples, 4 µL anti-FLAG antibody (Cell Signaling 2368) in 100 µL dig-wash buffer was added to beads with incubation for 1h at RT, shaking at 800 rpm. BG4 samples were then washed 3x in 100 µL dig-wash buffer. Next, for all samples, 1 µL anti-Rabbit IgG antibody in 100 µL dig-wash buffer was added (Antibodies-Online ABIN101961), and samples were rotated at 800rpm at RT for 1h. pA-Tn5 was prepared in-house and loaded with ME-rev and BfaI-truseqR1-pmeI-nextera. Samples were washed 3x in dig-wash buffer, resuspended in 50 µL of a 1:250 dilution of pA-Tn5 in dig-300 buffer (0.01% digitonin, 20 mM HEPES pH7.5, 300 mM KCl, 0.5 mM spermidine plus 1 Roche Complete Protease Inhibitor EDTA-free tablet). Tagmentation was performed for 1 h at 37°C, shaking at 800rpm. Nuclei were washed twice in 200 µL TAPS wash buffer (10 mM TAPS, 0.2 mM EDTA) on a magnet, then washed twice in 300 µL 0.075% BSA in PBS. Beads were resuspended in nuclei in 50µL solution containing 32.5 µL nuclease-free water, 5 µL 10x NEBuffer r3.1(NEB B6003S) and 12.5µL 2% SDS and incubated at 62°C for 10 min without rotation. 139 µL solution containing 100 µL nuclease-free water, 14 µL 10x NEBuffer3.1, 25 µL 10% Triton X-100 and incubated 37°C for 15 min, shaking at 800 rpm. Supernatant was removed on a magnet and resuspended in 300 µL 1.1X NEBuffer r3.1. Next, supernatant was removed on a magnet and resuspended in 101 µL solution containing: 90 µL 1.1X NEBuffer r3.1, 10µL CviQI (NEB, R0639L), 1µL splint oligo. Samples were incubated for 3h at 25°C, with rotation at 800 rpm. After 3h, 374 µL solution containing 283.6µL nuclease-free water, 40µL 10% Triton X-100, 2.4 µL 20 mg/mL BSA (NEB B9000S), 48 µL 10X T4 ligation Buffer was added. 6 µL T4 DNA ligase were then added, samples were mixed by pipetting, and in situ ligation was performed overnight at 16°C with interval shaking. The next day, beads were captured on a magnet and supernatant was removed. Beads were resuspended in 100µL solution containing 0.5mg/mL Proteinase K, 0.5% SDS and 10mM Tris-HCl buffer pH 8.0. Samples were mix by vortexing and incubated for 1 hr at 55 ºC, then for 2 h at 68 ºC, shaking at 800rpm. DNA was purified using DNA Clean & Concentrator-5 (Zymo D4013): sample and beads were added to 500 µL binding buffer, transferred to a spin column, washed twice following manufacturer’s instructions, and DNA was eluted in 20 µL elution buffer.
To fill-in: 31 µL solution containing 20.5 µL nuclease-free water, 5 µL 10x rCutSmart buffer (B6004S), 4 µL 10 mM dNTP, 1.5 µL T4 DNA polymerase (NEB M0203L) were added to the DNA, and samples were incubated at RT for 30 min, followed by 20 min at 75°C. To digest DNA, 1 µL NlaIII was added and samples were incubated at 37°C for 1 h. DNA was purified using 0.9X AMPure XP beads, eluting DNA in 80 µL 10 mM Tris-HCl (pH8.0). For circularization, DNA was diluted to 2 ng/µL in 938 µL nuclease-free water, then 50 µL 10x T4 ligation buffer and 6 µL T4 DNA ligase (NEB M0203L) were added. Samples were incubated at RT for 2 h. After ligation, DNA was purified using DNA Clean & Concentrator-5 (Zymo D4013), by combining 1 mL sample with 2 mL binding buffer, transferring 750 µL of the mix to the spin column 4 times, spinning between each transfer, washing following manufacturer’s instructions, and eluting in 20 µL. 2.3 µL 10x rCutSmart buffer and 1.8 µL PmeI (NEB R0560L) added to the DNA, and digestion performed at 37°C for 1 h. PCR reactions contained: 21 µL DNA, 2 µL i7 primer, 2 µL i5 primer and 25 µL NEBNext High-Fidelity 2X PCR Master Mix (M0541S), and the following PCR programme performed: step 1 72°C 4 min, step 2 98°C 30 s, step 3 98°C 10 s, step 4 59°C 30s, step 5 72°C 45s, step 6 72°C 5min, repeating steps 3-5 for a total of 12 cycles. PCR reactions were cleaned up using 1.3X AMPure XP beads, and libraries size-selected using 0.4X followed by 1.4X AMPure XP beads. Libraries were sequenced in paired end mode using the NextSeq 500 (36 bp paired-end) or NextSeq 2000 (60 bp paired-end) with 3 dark cycles for the first 3 bp of Read 1.

value: embryonic stem cells


title: K562_WT_Pol2_5SP_CnT_rep3


title: H1299-miR-29a-3p-1

city: Nanjing

first: Jie

last: Mei

state: Jiangsu

address: No. 101, Longmian Road

institute: Nanjing Medical University

data_processing:
Stringtie（version:1.3.0）
Assembly: GRCh38
Supplementary files format and content: csv file include FPKM values for each sample

source_name: lung

extract_protocol:
Total RNA was extracted using TRIZOL Reagent (Cat#15596-018, Life technologies, Carlsbad, CA,US) following the manufacturer’s instructions.
RNA library for RNA-seq were perpared using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina® following the manufacturer’s instructions.

value: lung

value: lung cancer cell


title: H1299-miR-29a-3p-2


title: H1_H3K27me3_ViCAR_rep1


title: H1299-control-1

value: Control


title: A549-miR-29a-3p-2


title: H1_BG4_ViCAR_rep1


title: p53kd-14.2 replicate 1

value: P53KD aneuploid clone


title: H1_BG4_ViCAR_rep2


title: K562_H3K4me3_ViCAR_rep2_tech2


title: A549-miR-29a-3p-1


title: K562_H3K4me3_ViCAR_rep1_tech2


title: K562_H3K4me3_ViCAR_rep2


title: A549-control-1


title: K562_H3K4me3_ViCAR_rep1


title: PBMCs, TCR, Day 7, CAR118

first: Isabella

last: Grabski

state: NY

data_processing:
Cellranger v5.0.0 for CITE-seq data, and Cellranger v6.1.2 for TCR data
Assembly: hg38
Supplementary files format and content: Gene expression, TCR sequences, and antibody abundance

source_name: PBMCs

extract_protocol:
Cryopreserved infusion product bag washings and peripheral blood mononuclear cells (PBMCs) were thawed in warmed RPMI with 10% fetal bovine serum. Cells were washed in 100ul cell staining buffer (biolegend) and resuspended in the Cite-Seq antibody cocktail for 30 minutes at 4 degrees Celcius according to manufacturer instructions. Following incubation, cells were washed three times in cell staining buffer and finally resuspended in 0.04% bovine serum albumin in PBS at a concentration of 1000 cells per microliter. 10,000 cells were loaded into the Chromium Next GEM Chip for each sample.
CITE-seq and scTCR-seq: Cryopreserved infusion products and PBMCs were thawed, stained with CITE-seq antibodies according to established protocols, and resuspended in 0.04% ultra pure bovine serum albumin (ThermoFisher) in PBS at 1000cells/μl before loading on a 10x Genomics Chromium instrument according to manufacturer instructions. scRNA-seq libraries were processed using the Chromium single cell 5’ library and GelBeadkitv2 with coupled scTCR-seq library generation (ChromiumsinglecellV(D)J enrichment kit [humanTcell](10xGenomics)), and sequenced (IlluminaNovaSeqS4platform). Amplified cDNA libraries and final sequencing libraries were assessed for quality control with a Bioanalyzer High Sensitivity DNA Kit (Agilent).

value: PBMCs

tag: time point

value: Day 7


title: PBMCs, RNA, Day 14, CAR118

value: Day 14


title: A549-control-2


title: K562_H3K4me1_ViCAR_rep3


title: K562_H3K4me1_ViCAR_rep2


title: PBMCs, RNA, Day 14, CAR142


title: PBMCs, TCR, Day 7, CAR142


title: PBMCs, TCR, Day 14, CAR142


title: K562_H3K4me1_ViCAR_rep1


title: PBMCs, RNA, Day 7, CAR118


title: G4_mutant_clone2_K562_BG4_ViCAR_rep1


title: G4_mutant_clone2_K562_BG4_ViCAR_rep2


title: H1299-control-2


title: G4_mutant_clone1_K562_BG4_ViCAR_rep1


title: G4_mutant_clone1_K562_BG4_ViCAR_rep2


title: Infusion product, TCR, CAR142

source_name: Infusion product

value: Infusion product


title: Human_Lymphoma_MALT_S100_20um pixel-size device

source_name: Lymph node

value: Lymph node

value: Lymphoma

value: Patho-DBiT Protocol


title: E. coli culture, MM3, rep4

city: Gent

first: Christian

last: Maueroeder

state: Flanders

address: Technologiepark-Zwijnaarde

department: IRC

country: Belgium

institute: VIB

data_processing:
Reads were filtered using filterbytile.sh from bbmap=39.01 (parameters- usekmers:f interleaved:f)
Tile filtered reads were trimmed using trim-galore=0.6.10 (parameters- illumina  stringency:5 length:75)
Trimmed reads were mapped to GCF_000017765.1 assembly using STAR=2.7.10 (alignIntronMax:1000000 outFilterMultimapNmax:5) after indexing (parameter- sjdbOverhang:149)
Features were counted using featureCounts=2.0.1 (parameters- t:"gene" F:"GTF")
Lowly expressed genes were then removed using filtByExp from edgeR=3.40.2 in R=4.2.3 (paramters- min.count:7), then collapsed using collapseReplicates function and normalized through DESeq2=1.38.3 just taking into account the design (~1 + treatment)
Assembly: GCF_000017765.1
Supplementary files format and content: Tab delimited files with normalized counts for each feature. Two additional columns with translations of the features names extracted from GTF file. And extra columns designating the p-values, padjusted values (FDR) and logfold change for each comparison (Doxo vs Control, Doxo vs Doxo + Death inhibited, Doxo+ Death Inhibited vs Control) calculated with DESeq in default options
Supplementary files format and content: Tab delimited files with raw counts for each feature after filtering low count features. Two additional columns with translations of the features names extracted from GTF file

organism: Escherichia coli

source_name: Media + 3 metabolites

growth_protocol: E. coli was grown aerobically at 37 degrees with 200rpm agitation

extract_protocol:
Bacterial RNA was extracted and DNA removed as described using the RiboPure RNA Purification Kit (Thermo Fisher)
An mRNA library was constructed following rRNA depletion using NEBNext Ultra RNA Library Prep Kit for Illumni (NEB)

treatment_protocol: DMEM media containing 10% heat-inactived FBS was supplemented with a 6 metabolite mixture (spermidine, FBP, DHAP, GMP, IMP and UDP-glucose) or a 3 metabolite mixture (spermidine, GMP, IMP). E. coli was grown to mid log growth phase aerobically at 37 degrees C.

value: Media + 3 metabolites

tag: strain

value: HS

value: partial apoptotic mix

tag: tumour stage

value: mid log growth phase


title: PBMCs, ADT, Day 14, CAR139


title: PBMCs, RNA, Day 14, CAR139


title: E. coli culture, MM3, rep2


title: PBMCs, ADT, Day 7, CAR139


title: E. coli culture, MM3, rep3


title: E. coli culture, MM6, rep4

source_name: Media + 6 metabolites

value: Media + 6 metabolites

value: complete apoptotic mix


title: PBMCs, RNA, Day 7, CAR139


title: PBMCs, ADT, Baseline, CAR139

value: Baseline


title: PBMCs, RNA, Day 7, CAR142


title: E. coli culture, MM6, rep3


title: Infusion product, ADT, CAR139


title: Infusion product, RNA, CAR139


title: E. coli culture, MM6, rep1


title: E. coli culture, control, rep2

source_name: Media

value: Media

value: media backbone

value: control


title: E. coli culture, control, rep4


title: PBMCs, RNA, Baseline, CAR139

value: PBMCs


title: Infusion product, RNA, CAR142


title: Infusion product, TCR, CAR139


title: PBMCs, TCR, Baseline, CAR139


title: PBMCs, ADT, Day 14, CAR141


title: PBMCs, TCR, Day 14, CAR141


title: E. coli culture, control, rep1


title: Doxo experiment, E. coli culture, Doxo + QVD, rep 4

data_processing:
Reads were filtered using filterbytile.sh from bbmap=39.01 (parameters- usekmers:f interleaved:f)
Tile filtered reads were trimmed using trim-galore=0.6.10 (parameters- illumina  stringency:5 length:75)
Trimmed reads were mapped to GCF_000017765.1 assembly using STAR=2.7.10 (alignIntronMax:1000000 outFilterMultimapNmax:5) after indexing (parameter- sjdbOverhang:149)
Features were counted using featureCounts=2.0.1 (parameters- t:"gene" F:"GTF")
Lowly expressed genes were then removed using filtByExp from edgeR=3.40.2 in R=4.2.3 (paramters- min.count:7), then collapsed using collapseReplicates function and normalized through DESeq2=1.38.3 just taking into account the design (~1 + treatment)
Assembly: GCF_000017765.1
Supplementary files format and content: Tab delimited files with normalized counts for each feature. Technical replicates were collapsed as explained above. Two additional columns with translations of the features names extracted from GTF file. And extra columns designating the p-values, padjusted values (FDR) and logfold change for each comparison (Doxo vs Control, Doxo vs Doxo + Death inhibited, Doxo+ Death Inhibited vs Control) calculated with DESeq in default options
Supplementary files format and content: Tab delimited files with raw counts for each feature after filtering low count features and collapsing replicates as explained above. Two additional columns with translations of the features names extracted from GTF file

source_name: DMEM + 10% FBS background

treatment_protocol: Murine CT26 cells were treated with 20ug/ml doxorubicin, with or without 30uM QVD treatment, for 24 hours to induce death. Cell free supernatants were collected and filtered before being used as growth medium for E. coli. E. coli was grown in these cell free supernatants until mid log growth phase.

value: DMEM + 10% FBS background

value: Doxorubicin-treated, death-inhibited

value: Caspase-inhibited supernatants

value: 20ug/ml doxorubicin + 30uM QVD


title: Doxo experiment, E. coli culture, Doxo + QVD, rep 3


title: PBMCs, RNA, Day 14, CAR141

value: Day 14


title: E. coli culture, MM3, rep1


title: PBMCs, ADT, Day 7, CAR141

value: Day 7


title: Doxo experiment, E. coli culture, Doxo + QVD, rep 2


title: PBMCs, TCR, Day 14, CAR139


title: PBMCs, TCR, Day 7, CAR141


title: PBMCs, RNA, Day 7, CAR141


title: E. coli culture, MM6, rep2


title: E. coli culture, control, rep3


title: Doxo experiment, E. coli culture, Doxo + QVD, rep 1


title: 12.silicosis.day56.3

first: Cole

last: Trapnell

address: 3720 15th Ave NE

institute: University of Washington

description:
sci RNA-seq
Silicosis Day 56, Replicate 3

data_processing:
Raw sequencing output from the original sequencing and re-sequencing of the same library was processed using a pair of Nextflow processing pipelines available at https://github.com/bbi-lab/bbi-dmux (handling sample demultiplexing) and https://github.com/bbi-lab/bbi-sci (handling assignments of reads to cells, filtering, alignment, and cell-by-gene matrix generation). Analysis was performed using Monocle 3 (v1.2.9). Cells were filtered for quality control based on the following thresholds: >100 unique molecular identifiers (UMIs), <10% mitochondrial RNA, and <0.2 Scrublet doublet score.
Assembly: GRCm38
Supplementary files format and content: Count Matrices (.mtx), Cell Metadata (.txt), Gene Metadata (.txt), Monocle3 cds object (RDS file)

source_name: Whole lung

extract_protocol:
Snap-frozen C57BL/6J mouse whole lung tissue (93 to 223 mg) was dissociated using a gentleMACS tissue dissociator. Nuclei suspension were snap-frozen in liquid nitrogen and stored in liquid nitrogen for single-cell combinatorial indexing RNA sequencing (sci RNA-seq) library preparation.
The sci-RNA-seq two-level workflow described by Cao, et al 2017 (10.1126/science.aam8940) was used.

value: Whole lung

value: 5 mg silica

value: Silicosis Day 56


title: PBMCs, ADT, Day 14, CAR138


title: Doxo experiment, E. coli culture, Doxo, rep 4

value: HS

value: Doxorubicin-induced apoptosis

value: Apoptotic supernatants

value: 20ug/ml doxorubicin


title: 4.silicosis.day56.1

description:
sci RNA-seq
Silicosis Day 56, Replicate 1


title: 8.silicosis.day56.2

description:
sci RNA-seq
Silicosis Day 56, Replicate 2


title: PBMCs, RNA, Day 14, CAR138


title: PBMCs, TCR, Day 14, CAR138


title: PBMCs, ADT, Baseline, CAR138

value: Baseline


title: PBMCs, ADT, Day 7, CAR138


title: 11.silicosis.day28.3

description:
sci RNA-seq
Silicosis Day 28, Replicate 3

value: Silicosis Day 28


title: PBMCs, TCR, Baseline, CAR138


title: Doxo experiment, E. coli culture, Doxo, rep 3


title: Doxo experiment, E. coli culture, Doxo, rep 2


title: PBMCs, TCR, Day 7, CAR138


title: Doxo experiment, E. coli culture, Doxo, rep 1


title: PBMCs, RNA, Day 7, CAR138


title: 7.silicisos.day28.2

description:
sci RNA-seq
Silicosis Day 28, Replicate 2


title: PBMCs, RNA, Baseline, CAR138


title: PBMCs, ADT, Day 14, CAR128


title: 3.silicosis.day28.1

description:
sci RNA-seq
Silicosis Day 28, Replicate 1


title: PBMCs, TCR, Day 14, CAR128


title: 10.silicosis.day07.3

description:
sci RNA-seq
Silicosis Day 7, Replicate 3

value: Silicosis Day 7


title: Doxo experiment, E. coli culture, control, rep 3

value: Media control

value: Media

value: control


title: PBMCs, ADT, Day 7, CAR128

value: PBMCs


title: Doxo experiment, E. coli culture, control, rep 4

value: DMEM + 10% FBS background


title: 6.silicosis.day07.2

description:
sci RNA-seq
Silicosis Day 7, Replicate 2


title: PBMCs, RNA, Day 14, CAR128

value: Day 14


title: PBMCs, RNA, Day 7, CAR128

value: Day 7


title: Doxo experiment, E. coli culture, control, rep 2


title: 2.silicosis.day07.1

description:
sci RNA-seq
Silicosis Day 7, Replicate 1

value: Whole lung


title: Infusion product, ADT, CAR128

value: Infusion product


title: Infusion product, TCR, CAR128


title: Doxo experiment, E. coli culture, control, rep 1


title: 9.silicosis.day00.3

description:
sci RNA-seq
Silicosis Day 0, Replicate 3

value: Silicosis Day 0


title: PBMCs, ADT, Baseline, CAR142


title: control, Pbx1 input , ChIP

city: Cleveland

first: Polyxeni

last: Philippidou

address: 2210 Circle Dr.

department: Neuroscience

institute: Case Western Reserve University

data_processing:
75-nucleotide sequence reads were mapped to the mm10 genome using Bowtie2 (v2.3.5.1) with flag “--local”.
Reads were then sorted and indexed with samtools (v1.10) and filtered for blacklist regions defined by ENCODE.
MACS2 was used to call narrowpeak with a flag “--nomodel --ext 220” against the input control. Macs2 peaks were further filtered using the adj P cutoff of e-7 and the signal value > 5.
Assembly: mm10
Supplementary files format and content: bigwig, bed(except for input)

source_name: cervical spinal cord

extract_protocol:
e12.5 cervical spinal cords from multiple embryos were microdissected in ice cold PBS and combined for Chromatin immunoprecipation.
Hoxa5, Pbx1, and input libraries were prepared by Active Motif and 75-nucleotide sequence reads were generated by Illumina sequencing (NextSeq 500)

value: cervical spinal cord

value: Wt

tag: chip antibody

value: IgG


title: Infusion product, RNA, CAR128


title: control, Pbx1 ab, ChIP

tag: genotype


title: PBMCs, TCR, Day 14, CAR137


title: PBMCs, ADT, Day 14, CAR137


title: 1.silicosis.day00.1

description:
sci RNA-seq
Silicosis Day 0, Replicate 1


title: PBMCs, RNA, Day 14, CAR137


title: 5.silicosis.day00.2

description:
sci RNA-seq
Silicosis Day 0, Replicate 2


title: PBMCs, ADT, Day 7, CAR137


title: KP3_STINGV154M

city: Madrid

first: Laura

last: Serrano-Ron

state: Madrid

address: Calle Emilio Ortuño 35 1B

department: Bioinformatics Unit

institute: CNIO

description: normalizedcounts_genes_STING_vs_emtpy.tsv

data_processing:
FASTQ files obtained from the RNA sequencing were processed using the cluster_RNAseq pipeline (https://github.com/cniobu/cluster_rnaseq).
Samples were subjected to quality control using FastQC (version 0.11.9) (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Subsequently, polyA tails and adapters were removed using BBDuk (BBMap version 38.90-3) (https://sourceforge.net/projects/bbmap/).
The resulting reads were aligned to the mouse reference genome (GRCm39) using STAR (version 2.7.10b)
genomic feature counts were obtained using htseq-count (version 0.12.4) and differential expression analysis was performed with DESeq2 (version 1.30.1)
Assembly: Mouse reference genome (GRCm39)
Supplementary files format and content: tab-separated values files include normalized counts for each sample. Two separated files are provided, each one including the samples concerning each comparison (IFN-beta expressing cells vs non-expressing cells or constitutively active STING expressing cells vs non-expressing cells).

source_name: KP3 cell line transduced with STING(V154M) tetracycline inducible vector, 48 hours post-doxycyclin

growth_protocol: DMEM + 10% of tetracycline-free FBS

extract_protocol:
Total RNA from established cells lines was isolated using the RNeasy Mini Kit (Qiagen 74104) following manufacturer’s recommendations. DNA digestion with RNase-Free DNase (Qiagen, 70254) was performed during isolation.
Sequencing libraries were prepared with the QuantSeq 3’ mRNA-Seq Library Prep Kit (FWD) for Illumina (Lexogen, 015)

treatment_protocol: 1 μg/ml doxycycline for 48 hours with daily replenishment of the media

tag: cell type

value: lung adenocarcinoma cell line

tag: treatment

value: 1 ug/ml doxycycline for 48 h


title: control, Hoxa5 input , ChIP

tag: tissue


title: KP3_IFN-Beta

description: normalizedcounts_genes_IFNB_vs_empty.tsv

source_name: KP3 cell line transduced with IFN-Beta tetracycline inducible vector, 48 hours post-doxycyclin


title: PBMCs, RNA, Day 7, CAR137


title: KP3_empty-2

description:
normalizedcounts_genes_IFNB_vs_empty.tsv
normalizedcounts_genes_STING_vs_emtpy.tsv

source_name: KP3 cell line transduced with empty tetracycline inducible vector, 48 hours post-doxycyclin


title: BLA, p56_3

city: Martinsried

first: Tobias

last: Straub

address: Großhadener Str. 9

department: Biomedical Center, Bioinformatics

institute: LMU Munich

description: 10x Genomics

data_processing:
We used cellranger (version 7.0.1) to extract fastq files and align the reads to the mouse genome (10x genomics reference build MM10 2020 A)
Assembly: mm10
Supplementary files format and content: cellranger filtered_feature_bc_matrix files

molecule: nuclear RNA

source_name: brain, amygdala tissue

extract_protocol:
Mice were deeply anesthetized by i.p. injections of 200 mg/kg Ketamine and 40 mg/kg Xylazine, and perfused with 10 mL ice-cold Sucrose-HEPES Cutting Buffer containing (in mM) 110 NaCl, 2.5 KCl, 10 HEPES, 7.5 MgCl2, and 25 glucose, 75 sucrose (~350 mOsm/kg), pH=7.4 2.All the solutions/reagents were kept on ice in the following procedures unless otherwise specified. The brain was extracted and cut (300 μm) on a vibratome (Leica VT1000S, Germany) in cutting buffer, and the slices were transferred into a  Dissociation Buffer  containing (in mM): 82 Na2SO4, 30 K2SO4, 10 HEPES, 10 glucose and 5 MgCl2, pH=7.4 2.BLA was microdissected under a microscope (Olympus SZX10) covering the anterior (Bregma −0.59) and posterior (Bregma −3.0) for adult BLA and the anterior (Bregma −0.8) and posterior (Bregma −2.8) for juvenile BLA. The protocol for single nucleus isolation was optimized from previous studies (Matson KJE, et al. Isolation of Adult Spinal Cord Nuclei for Massively Parallel Single-nucleus RNA Sequencing. J Vis Exp (2018).
Nanoliterscale Gel Beads-in-emulsion (GEMs) generation, barcoding, cDNA amplification, and library preparation were done using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 according to the manufacturer’s protocol.

value: brain, amygdala tissue

value: male

value: neuronal cell types


title: Infusion product, TCR, CAR137


title: BLA, p56_2

description: 10x Genomics


title: KP2_STINGV154M

source_name: KP2 cell line transduced with STING(V154M) tetracycline inducible vector, 48 hours post-doxycyclin


title: PBMCs, TCR, Day 7, CAR137


title: Infusion product, ADT, CAR137


title: Infusion product, RNA, CAR137


title: PBMCs, ADT, Day 14, CAR147


title: KP2_IFN-Beta

source_name: KP2 cell line transduced with IFN-Beta tetracycline inducible vector, 48 hours post-doxycyclin


title: PBMCs, RNA, Baseline, CAR142

value: Baseline


title: PBMCs, TCR, Day 14, CAR147


title: KP2_empty-2

source_name: KP2 cell line transduced with empty tetracycline inducible vector, 48 hours post-doxycyclin