title: hNPC, SMYD5, 37°C, replicate 2

description: NPC_rep1_rep2_37_SMYD5_merged_depthnorm.bw

data_processing:
We demultiplexed the fastq files and trimmed the raw Fastq reads in paired mode with TrimGalore (v.0.6.7)
Bowtie2 (v.2.4.4.) to align the reads to Hg38 and E. Coli reference genome, downloaded from UCSC
aligned Sam files were then converted to Bam files, indexed, and sorted via SAMtools (v.1.15) and BedGraphtoBigWig (v.4) from BEDTools (v.2.3)
SEACR (v.1.3) for peak calling after normalization with the normalization factor calculated as 1/(percent alignment to E. coli). We also used MACS3 callpeak function to call peaks on individual bam files for each replicate against merged IgG files for each condition, with the following settings: --broad --broad-cutoff 0.05 --outdir MASC3 (v.3.0.0) -B --keep-dup all --max-gap 20 --format BAMPE for H3K36me3. For H3K4me3 we used --broad --broad-cutoff 0.05 --outdir MASC3 -B --keep-dup all --max-gap 300 and --format BAMPE.  For the differential peak analysis we used DiffBind (v.3.9.6) where we used the default normalization and analyzing mode. ChIPseeker (v.1.35.3), TxDb.Hsapiens.UCSC.hg38.knownGene (v.3.4.6) and org.Hs.eg.db (v.3.8.2) were used for annotation, all in R.
We used DiffBind  (v.3.9.6) for the differential peak analysis, ChIPseeker (v.1.35.3), TxDb.Hsapiens.UCSC.hg38.knownGene (v.3.4.6) and org.Hs.eg.db (v.3.8.2) for annotation. We used  deepTools (v. 3.5.1) computeMatrix, plotProfile and bamCoverage (binSize 5, normalized using RPGC),  for making bigwig files for visualization in the UCSC Genome Browser as well as visualizing the Plot Profile of distinct modifications.  For further analysis and image creation we used deepTools (v.3.5.1.) as well as R.
Assembly: Hg38 and E. coli downloaded from UCSC
Supplementary files format and content: bedgraph file, normalized to e.coli, containing peaks for SEACR calling
Supplementary files format and content: bigwig file made from merged bam files, alignments, for replicate 1 and 2, normalized to genome size
Supplementary files format and content: bigwig file made from bam files, alignments, for each replicate, normalized to genome size
Supplementary files format and content: peak file made with MACS3 peakcall function
Library strategy: CUT&RUN

extract_protocol:
We followed the Epicypher CUTANA protocol (v.1.7) on 300.000 cells per sample. We permeabilized the cells with 0.01% digitonin (Sigma, D141). For normalization we spiked in E. Coli DNA (Epicypher, 23618-1401) at the final concentration of 0.2 ng per sample.
The library preparation was performed with TrueSeq-Chip Sample preparation Kit (Illumina, IP-202-9001). We also used a NextSeq 550 using the NextSeq 500/550 Mid Output Kit v2.5 (20024904) with 75 bp paired-end sequencing

value: neural progenitor cells


title: ICoVax_57_i30

status: Public on Jul 26 2024

type: SRA

city: Lausanne

first: Yannick

middle: D

last: Muller

state: Vaud

address: Rue du Bugnon 46

department: Center for Human Immunology and Vaccinology

country: Switzerland

institute: Lausanne University Hospital (CHUV)

library_source: transcriptomic

data_processing:
RNA-sequencing libraries were aligned to the human genome (GRCh38.96) using STAR (2.4.0j).
Only uniquely mapped reads were kept for downstream steps.
Gene expression quantification was performed with featureCounts for reads overlapping protein-coding genes.
Low-count genes were filtered out with the filtered.data() function from the NOISeq R package using the following parameters: method = 1, norm = FALSE, cv.cutoff = 100, cpm = 1.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file containing raw counts for each sample.

molecule: total RNA

organism: Homo sapiens

source_name: whole blood

extract_protocol:
Blood samples were collected in PAXgene Blood RNA Tube (BD Biosciences). RNA extraction was performed using the PAXgene Blood miRNA Kit (BD) on the QIAcube instrument (QIAGEN) following the manufacturer’s instructions.
RNA concentration and quality were assessed by using the Qubit instrument (Invitrogen) and the Agilent 2100 Bioanalyzer, respectively. The Stranded Total RNA Ribo-Zero Plus kit from Illumina was used for the library preparation with 100 ng of total RNA as input. Library molarity and quality were assessed with the Qubit and Tapestation using a DNA High sensitivity chip (Agilent Technologies). Libraries were pooled at 2 nM for clustering and sequenced on an Illumina HiSeq4000 sequencer for a minimum of 30 million single-end 100 reads per sample.

tag: tissue

value: whole blood

tag: condition

value: ICoVax


title: Whole blood, ID43_Day13

city: Canyon

first: Matthew

middle: Adam

last: Scott

state: TX

address: 3201 Russell Long Blvd

department: Large Animal Clinical Sciences

country: USA

institute: Texas A&M University

data_processing:
Illumina RTA v3 software was used for basecalling.
Read quality was assessed in FastQC v0.11.9
Read trimming was performed with Trimmomatic v0.39 with parameters for a 4-base pair sliding window and removing read segments below a minimum base quality score of 20, read length of less than 28 bases, leading and trailing basepairs below a quality score of 3, and removal of all Illumina adaptors.
Read mapping and indexing was performed with HISAT2 v2.1.1, using the bovine whole genome assembly ARS-UCD1.3; parameters -p 14 --dta -x GCF_002263795.2_ARS-UCD1.3
Read assembly and quantification was performed with StringTie v2.2.0 with parameters -p 14 -G GCF_002263795.2_ARS-UCD1.3_genomic.gff, followed by stringtie --merge -p 14 -G GCF_002263795.2_ARS-UCD1.3_genomic.gff -o mergefile.gtf, and stringtie -e -p 14 -G mergefile.gtf -o. A read count matrix was generated with prepDE3.py with parameters python prepDE3.py  -l 150 -i mergelist.txt. Differential expression analysis was performed with edgeR v3.36.0, glmmSeq v0.2.0, and EBSeq-HMM v1.32.0.
Assembly: GCF_002263795.2
Supplementary files format and content: Comma-delimited text file of raw gene counts for each sample

organism: Bos taurus

source_name: Whole blood

extract_protocol:
Total RNA was isolated from Tempus Blood Tubes with Tempus Spin RNA Isolation Kit per product instruction.
RNA libraries were prepared for sequencing using Illumina Stranded mRNA Prep kits, using standard Illumina protocols.

treatment_protocol: All  samples were collected in Tempus blood RNA tubes (Applied Biosystem). Samples were stored per product recommendation.

value: Whole blood

tag: time point

tag: treatment

value: INR

tag: pen

tag: individual id

tag: disease

value: Yes


title: hNPC, IgG, 37°C, replicate 2

city: Reykjavik

first: Hans

middle: Tomas

last: Bjornsson

state: Hofudborgarsvaedid

address: Sturlugata 8

department: Faculty of Medicine

country: Iceland

institute: University of Iceland

library_source: genomic

molecule: genomic DNA

growth_protocol: HEK293WT cells were  cultured in DMEM/F12 with GlutaMAX (Gibco, 10565018) with 10% filtered FBS (Gibco, 10270106) under 5% CO2. Cells were sub-cultured when they had reached 70-90% confluence and media was changed every other day. Human iPS cells (ATCC, ACS-1019)  were used to generate NPCs by neural induction of iPSCs using dual SMAD inhibition and embryoid body generation (StemCell Technologies; 08581, 05832, 05838)77, prior to experiments described here the NPCs were cultured in STEMdiff Neural Progenitor Medium (StemCell Technologies, 05833) on Matrigel (Corning, 354234).

treatment_protocol: Cells were exposed to 32°C for 6h or kept at 37°C. For siRNA knockdown we transfected the HEK293 cells with predesigned DsiRNA (IDT, hs.Ri.SMYD5.13.8) and Negative control using Lipofectamine 3000 (Thermo Fisher Scientific, L3000015) based on the manufacturer´s protocol. After 48 hours of transfection, the cells were placed in 32°C and 37°C for 6 hours post which they were harvested for CUT&RUN and RT-qPCR (for validation of the knockdown of SMYD5).

tag: cell line

tag: cell type

tag: genotype

tag: antibody

value: IgG


title: NPC, 37°C, replicate 3

data_processing:
Fastq files were pseudo-aligned to the GRCm39 mouse transcriptome, downloaded from NCBI, using Kallisto (v.0.48.0) with paired-end mode on and 100 bootstraps.
Kallisto output files were imported into R using the tximport package. Transcripts were assigned to genes using the TxDb.Mmusculus.UCSC.mm10.ensGene package (v.3.4.0) in R . Differential expression analysis was performed using the DESeq2 package (v.3.16) in R after discarding transcripts with less than 10 counts. Differentially expressed genes were defined as those with an adjusted p-value less than 0.1.
Assembly: mm39,  downloaded from NCBI
Supplementary files format and content: HDF5 binary file containing run info, abundance esimates, bootstrap estimates, and transcript length information length.
Supplementary files format and content: csv file containing result from DESeq such as; count and p-value and logfoldchange

organism: Mus musculus

source_name: Brain

growth_protocol: Mouse NPCs were isolated from the cortex of E17.5 C57BL6/NTac embryos. The protocol was adapted from Bernas et al, 2017105. Embryo cortices were manually dissected from brains and the tissue was dissociated in 1X TrypLE™ Select Enzyme (Thermo Fisher Scientific, A1217701) for 10 min, with manual dissociation using a 1000 µL pipette. The cell suspension was washed in Neurobasal medium (Thermo Fisher Scientific, 21103049) and filtered through a 70 µm cell strainer (Miltenyi Biotech, 130-110-916). Cells were washed twice in 5 mL Neurobasal medium (Gibco, 21103049) by centrifugation at 200 xg for 10 min. Cells were resuspended in 1 mL Neurobasal growth medium containing 1X B27 supplement (Thermo Fisher Scientific, 17504044), 1X Penicillin/Streptomycin (Thermo Fisher Scientific, 15140122), 1X Glutamax (Thermo Fisher Scientific, 35050038), 20ng/mL FGF-2 (Peprotech, 100-18B), 20 ng/mL EFG (Peprotech, AF-100-15), and 2 µg/mL Heparin (MP Biomedicals, 210193125). Cells were seeded onto 12-well plates, previously coated for 2 h at 37°C in 1:100 dilution of Matrigel (Corning, 354234). After passaging, NPCs were cultured in media described above on plates coated overnight in poly-D-lysine (Sigma, P7280), and then coated for 2 h in laminin (Sigma, L2020). Cells were either sub-cultured or media was changed every 2 days. Primary mouse NPC lines from 4 separate embryos were seeded 0.3 x 106 cells per well, in two batches, in a poly-D-lysine/laminin coated 6-well plate after 9 days in vitro.

extract_protocol:
Cells from both 37°C and 32°C conditions were harvested in tri-reagent and RNA was isolated using the Direct-zol RNA Microprep kit (Zymo Research, R2063).
RNAseq library construction and Illumina next generation sequencing was performed by Novogene on a PE150 flow cell, generating 30 million paired-end reads per sample.

treatment_protocol: Following 36 h of incubation at 37°C, one plate with 4 lines was incubated at 32°C for 6 h.

value: Brain

value: cortical mNPC

value: nouse neural progenitor cells

tag: strain


title: HEK293WT+Cas9, control, replicate 1

description:
80 cycles and 8 indexing cycles with PhiX spike in of 20%
CTRLvsLOW4Replicates.countsummary.txt/CTRLvsHIGH4Replicates.countsummary.txt
10_6_20_control_merge

data_processing:
Cat command to merge fastq files for samples 1-3
mageck count -l Human_GeCKOv2_Library_combine.csv
mageck test -k CTRLvsHIGH4Replicates.count.txt --sort-criteria pos --norm-method control --control *HIGH*nontargetingsgrna.txt --paired
Assembly: Reference sequence downloaded from Library site (addgene), named  "Human_GeCKOv2_Library_combine.csv"
Supplementary files format and content: text file, counts of sgRNA in library in all replicates of control and low/high sorted cells
Supplementary files format and content: text file, counts of sgRNA in library normalized to internal control count in all replicates of control and low/high sorted cells
Supplementary files format and content: text file, information on vaues e.g. P-value, RRA score and more for all genes in library
Supplementary files format and content: text file, information on vaues e.g. P-value, RRA score and more for all sgRNAs in library
Library strategy: CRISPR Screen

growth_protocol: HEK293WT cells were  cultured in DMEM/F12 with GlutaMAX (Gibco, 10565018) with 10% filtered FBS (Gibco, 10270106) under 5% CO2. Cells were sub-cultured when they had reached 70-90% confluence and media was changed every other day. We selected for stable sgRNAs with puromycin selection for 6 days and 8 hours and exposesd to 32°C the last 16h before FACS

extract_protocol:
genomic DNA extracted with DNA mediprep kit from Zymo Research.
Custom library amplification protocol ac. To Joung et al. Nat Protoc. 2017
sgRNA-sec, genome wide CRISPR-Cas9 library screening

treatment_protocol: 6 days and 6 h selection with puromycin before 16 hours exposure of 32°C

value: 16 h of 32degreeC


title: NPC, 32°C, replicate 2

value: 32degreeC 6h


title: Whole blood, ID50_Day13

value: No


title: Whole blood, ID42_Day13

value: COMBO


title: NPC, 37°C, replicate 2


title: ICoVax_37_i30


title: NPC, 37°C, replicate 1


title: Whole blood, ID41_Day13

value: AAC


title: hNPC, H4K20me3, 37°C, replicate 2

description: NPC_rep1_rep2_37_H4K20_merged_depthnorm.bw


title: CovUrt_8669

value: CovUrt


title: hNPC, H3K36me3, 37°C, replicate 2

description: NPC_rep1_rep2_37_H3K36_merged_depthnorm.bw


title: Whole blood, ID40_Day13


title: hNPC, H3K27me3, 37°C, replicate 2

description: NPC_rep1_rep2_37_H3K27_merged_depthnorm.bw


title: GC_Bcells_WT_434

city: New York

first: Riccardo

last: Dalla-Favera

state: NY

address: 1130 St Nicholas Avenue

institute: Columbia University

description: Mouse genotype is Mef2b+/+; Cγ1-Cretg/+. Mice are littermates obtained by crossing Mef2bP297L/+;Cγ1-Cretg/+ with Mef2bP297L/+;Cγ1-Cre+/+ mice.

data_processing:
Sequencing data were acquired through the default Illumina pipeline using Casava V1.8.
Reads were aligned to the mouse genome (UCSC mm10) using hisat2 with the following options: --threads 4 --add-chrname --ignore-quals -q -x mm10 -k 5.
Reads were mapped to exons using featureCounts to produce abundance tables.
Assembly: mm10
Supplementary files format and content: Tab delimited text file of read counts produced by featureCounts

source_name: Spleen

extract_protocol:
The RNAs were extracted by the Nucleospin RNA XS RNA Isolation Kit (Macherey-Nagel), according to the manufacturer’s instructions.
~200 ng RNA was used for library preparation by Azenta Life Sciences (South Plainfield, NJ, USA).

treatment_protocol: Mice were immunized with two sequential injections of sheep red blood cells (day 0, 1x 108 cells; day 5, 1x109 cells), and splenic tissue was collected cells at day 12.  GC B cells (B220+PNA+GL7+) were isolated by cytofluorimetric sorting.

value: Spleen

value: Germinal Center B cells

value: WT


title: GC_Bcells_P297L_HOMO_436

description: Mouse genotype is Mef2bP297L/P297L; Cγ1-Cretg/+. Mice are littermates obtained by crossing Mef2bP297L/+;Cγ1-Cretg/+ with Mef2bP297L/+;Cγ1-Cre+/+ mice.


title: hNPC, H3K9me3, 37°C, replicate 2

description: NPC_rep1_rep2_37_H3K9_merged_depthnorm.bw

value: neural progenitor cells


title: Whole blood, ID39_Day13

value: Whole blood


title: CovUrt_6398

value: whole blood


title: Whole blood, ID34_Day13


title: GC_Bcells_P297L_HOMO_426


title: Whole blood, ID31_Day13

value: Yes


title: hNPC, SMYD5, 6 h at 32°C, replicate 2

description: NPC_rep1_rep2_32_SMYD5_merged_depthnorm.bw

value: 6 h of 32degreeC


title: CovUrt_5818


title: hNPC, H3K4me3, 37°C, replicate 2

description: NPC_rep1_rep2_37_H3K4_merged_depthnorm.bw


title: GC_Bcells_P297L_HOMO_428


title: Whole blood, ID30_Day13

value: INR


title: GC_Bcells_WT_421


title: hNPC, IgG, 6 h at 32°C, replicate 2

value: IgG


title: CovUrt_5700


title: CovUrt_5326


title: hNPC, H4K20me3, 6 h at 32°C, replicate 2

description: NPC_rep1_rep2_32_H4K20_merged_depthnorm.bw


title: GC_Bcells_P297L_HET_390

description: Mouse genotype is Mef2bP297L/+; Cγ1-Cretg/+. Mice are littermates obtained by crossing Mef2bP297L/+;Cγ1-Cretg/+ with Mef2bP297L/+;Cγ1-Cre+/+ mice.


title: CovUrt_4673


title: Whole blood, ID29_Day13


title: Whole blood, ID27_Day13


title: GC_Bcells_WT_355


title: hNPC, H3K36me3, 6 h at 32°C, replicate 2

description: NPC_rep1_rep2_32_H3K36_merged_depthnorm.bw


title: GC_Bcells_WT_352


title: Whole blood, ID23_Day13


title: CovUrt_3796


title: hNPC, H3K27me3, 6 h at 32°C, replicate 2

description: NPC_rep1_rep2_32_H3K27_merged_depthnorm.bw


title: CovUrt_4589


title: GC_Bcells_P297L_HET_350


title: CovUrt_3769


title: hNPC, H3K9me3, 6 h at 32°C, replicate 2

description: NPC_rep1_rep2_32_H3K9_merged_depthnorm.bw


title: Whole blood, ID18_Day13


title: hNPC, H3K4me3, 6 h at 32°C, replicate 2

description: NPC_rep1_rep2_32_H3K4_merged_depthnorm.bw


title: Whole blood, ID17_Day13


title: GC_Bcells_P297L_HET_349


title: CovUrt_2884


title: CovUrt_2471


title: Whole blood, ID21_Day13


title: CovUrt_1644


title: hNPC, SMYD5, 37°C, replicate 1


title: Whole blood, ID10_Day13


title: Whole blood, ID16_Day13


title: hNPC, IgG, 37°C, replicate 1


title: CovUrt_1635


title: Whole blood, ID7_Day13


title: Whole blood, ID9_Day13


title: CovUrt_1631


title: SGBS Differentiated replicate 2

city: Philadelphia

middle: C

last: Pahl

state: PA

address: 3615 Civic Center Blvd

department: Center for Spatial and Functional Genomics

institute: Children's Hospital of Philadelphia

data_processing:
The fastq files of technical replicates were concatenated.  Paired-end reads from two replicates were pre-processed using the HICUP pipeline v0.7.4 , with bowtie as aligner and hg38 as the reference genome.
Significant promoter interactions at 1-DpnII fragment resolution were called using CHiCAGO (v1.1.8) [3] with default parameters except for binsize set to 2500. Significant interactions at 4-DpnII fragment resolution were also called using CHiCAGO with artificial.baitmap and .rmap files in which DpnII fragments were concatenated in silico into 4 consecutive fragments using default parameters except for removeAdjacent set to False. The significant interactions (CHiCAGO score > 5) from both 1-fragment and 4-fragment resolutions were exported in.ibed format.
Assembly: hg38
Supplementary files format and content: ibed (interaction bed files)

source_name: SGBS

growth_protocol: EndoC BH1 cells were expanded in DMEM low glucose (1g/mL), 2% Albumin Bovine Serum fraction V, 50uM 2 (beta)-mercaptoethanol, 10mM Nicotinamide, 5.5uM Transferrin, 6.7ng/mL sodium selenite, 100 U penicillin/100ug/mL streptomycin/0.25ug/mL amphotericin B (1x Gibco). Plates were coated with either Matrigel or MaxGel ECM (Sigma) and 2 ug/mL fibronectin according to manufacturer’s instructions: Cells were passaged when confluence was observed or otherwise passaged by two-thirds every two weeks. The other cell lines were maintained under standard conditions. HepG2 Cells (ATCC,  HB¬8065TM) were maintained in Eagle's Minimum Essential Medium  supplemented with 10% heat inactivated fetal bovine serum and 1X Antibiotic-Antimycotic at standard tissue culture conditions; 37C and 5% CO2.

extract_protocol:
For each library, 10^7 fixed cells were thawed at 37C, followed by centrifugation at RT for 5 mins at 1845 xg. The cell pellet was resuspended in 1 mL of dH2O supplemented with 5 uL 200X protease inhibitor cocktail, incubated on ice for 10 mins, then centrifuged. The cell pellet was resuspended to a total volume of 650 uL in dH2O. Samples underwent a pre-digestion incubation in a Thermomixer (BenchMark) with the addition of 0.3%SDS, 1x NEB DpnII restriction buffer, and dH2O for 1hr at 37ºC shaking at 1,000 rpm. A 1.7% solution of Triton X-100 was added to each tube and shaking was continued for another hour. After pre-digestion incubation, 10 ul of DpnII (NEB, 50 U/µL) was added to each sample tube only and continued shaking until the end of the day. An additional 10 µL of DpnII was added to each digestion reaction and digested overnight.  The next day, a further 10 µL DpnII was added and continue shaking for another 2-3 hours.  The samples were incubated at 1000 rpm in a MultiTherm for 20 min at 65°C to inactivate the DpnII, and cooled on ice for 20 additional minutes. Digested samples were ligated with 8 uL of T4 DNA ligase (HC ThermoFisher, 30 U/µL) and 1X ligase buffer at 1,000 rpm overnight at 16°C in a MultiTherm. The next day, an additional 2 µL of T4 DNA ligase was spiked in to each sample and incubated for another few hours. The ligated samples were then de-crosslinked overnight at 65°C with Proteinase K (20 mg/mL, Denville Scientific) along with pre-digestion and digestion control. The following morning, both controls and ligated samples were incubated for 30 min at 37°C with RNase A (Millipore), followed by phenol/chloroform extraction, ethanol precipitation at -20°C, the 3C libraries were centrifuged at 1000 xg for 45 min at 4°C to pellet the samples. The controls were centrifuged at 1845 xg. The pellets were resuspended in 70% ethanol and centrifuged as described above. The pellets of 3C libraries and controls were resuspended in 300uL and 20μL dH2O, respectively, and stored at −20°C. Sample concentrations were measured by Qubit. Digestion and ligation efficiencies were assessed by gel electrophoresis on a 0.9% agarose gel and also by quantitative PCR (SYBR green, Thermo Fisher). The HepG2 libraries were prepared following the Arima Promoter Capture HiC protocol, using two restriction enzymes (targeting ^GATC and G^ANTC as restriction sites).
For Promoter focused Capture C, isolated DNA from 3C libraries was quantified using a Qubit fluorometer (Life technologies), and 10 μg of each library was sheared in dH2O using a QSonica Q800R to an average fragment size of 350bp 26,28–31.  QSonica settings used were 60% amplitude, 30s on, 30s off, 2 min intervals, for a total of 5 intervals at 4 °C. After shearing, DNA was purified using AMPureXP beads (Agencourt). DNA size was assessed on a Bioanalyzer 2100 using a DNA 1000 Chip (Agilent) and DNA concentration was checked via Qubit. SureSelect XT library prep kits (Agilent) were used to repair DNA ends and for adaptor ligation following the manufacturer protocol. Excess adaptors were removed using AMPureXP beads. Size and concentration were checked by Bioanalyzer using a DNA 1000 Chip and by Qubit fluorometer before hybridization. One microgram of adaptor-ligated library was used as input for the SureSelect XT capture kit using manufacturer protocol and our custom-designed 41K promoter Capture-C library. The quantity and quality of the captured library was assessed by Bioanalyzer using a high sensitivity DNA Chip and by Qubit fluorometer. SureSelect XT libraries were then paired-end sequenced either the Illumina HiSeq 4000 or on Illumina NovaSeq 6000 platform (51 bp read length). EndoC-BH1, SGBS_undiff, and SGBS_diff libraries were generated in triplicate, while HepG2 were generated in duplicate.

treatment_protocol: SGBS differentiation began by washing cells with phosphate buffered saline (PBS) three times and changing to a serum- and albumin-free differentiation medium (DMEM/F12 supplemented with 2 μmol/l rosiglitazone, 25 nmol/l dexamethasone, 0.5 mmol/l methylisobuthylxantine, 0.1 μmol/l cortisol, 0.01 mg/ml transferrin, 0.2 nmol/l triiodotyronin, and 20 nmol/l human insulin). After 4 days, the differentiation medium was changed, and cells were further cultured in DMEM/F12 supplemented with 0.1 μmol/l cortisol, 0.01 mg/ml transferrin, 0.2 nmol/l triiodotyronin, and 20 nmol/l human insulin. Successful differentiation was assessed by the presence of lipid droplets.

value: SGBS

value: Adipocyte cell line


title: Whole blood, ID6_Day13


title: hNPC, H3K36me3, 37°C, replicate 1


title: SGBS Differentiated replicate 1


title: hNPC, H3K9me3, 37°C, replicate 1


title: RPE, DCA+FGF 48h, 3

city: Baltimore

first: Seth

last: Blackshaw

state: MD

address: 733 N Broadway

department: Neuroscience

institute: Johns Hopkins University

data_processing:
Each sample was sequenced across two lanes of HiSeq X Ten. Raw fastq files for each sample were merged from the two lanes at the beginning of the analysis.
Adapters and low-quality bases were removed with Trim Galore v 0.6.4_dev with the parameters --stringency 3 --paired --length 36
A genome index for the STAR alignment software v2.7.5b was generated with the parameters --runMode genomeGenerate --sjdbOverhang 149 --genomeSAindexNbases 13, and splice sites were incorporated from Ensembl release 106
Trimmed reads were aligned to chicken genome GRCg6a using the STAR alignment tool and parameters --quantMode GeneCounts TranscriptomeSAM --runThreadN 30 --limitBAMsortRAM 60000000000 --readFilesCommand zcat --genomeLoad LoadAndKeep --outSAMstrandField intronMotif --outSAMtype BAM SortedByCoordinate
Gene counts were generated with Stringtie v2.1.4 using the parameters --rf -e
Count normalization was performed using DESeq2 v1.34.0
Assembly: GRCg6a
Supplementary files format and content: Normalized_counts.tsv contains tab-separated values of normalized gene counts generated by DESeq2 with default parameters. Rows represent genes based on the Ensembl annotation and each column is a unique biological sample.

molecule: polyA RNA

organism: Gallus gallus

source_name: RPE

extract_protocol:
Explants were collected in 200 uL of DNA/RNA Shield buffer (Zymo Research, 1220-25). Total RNA was isolated using Quick-RNA Microprep Plus Kit Microprep (Zymo Research, R1051) following manufacturer’s instructions.
100ng of total intact RNA was used with the NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB, E7490S), and the enriched mRNA was prepped for sequencing with the NEBNext® Ultra™ II Directional RNA Library Prep with Sample Purification Beads (NEB, E7765S) per manufacturer’s instructions. A total of 13 PCR amplification cycles were used, and indexing was performed with single index oligos (NEB, 7710; NEB, 7730).

value: RPE

value: Dichloroacetate + FGF2


title: Whole blood, ID3_Day13

value: COMBO

value: No


title: hNPC, H3K4me3, 37°C, replicate 1


title: Whole blood, ID57_Day0


title: RPE, DCA+FGF 48h, 2


title: EndoC-BH1 replicate 3

value: Pancreatic Beta cell line


title: hNPC, H4K20me3, 37°C, replicate 1


title: EndoC-BH1 replicate 2


title: hNPC, SMYD5, 6 h at 32°C, replicate 1


title: RPE, DCA+FGF 48h, 1


title: EndoC-BH1 replicate 1


title: Whole blood, ID50_Day0


title: RPE, FGF 48h, 3


title: Whole blood, ID54_Day0


title: hNPC, H4K20me3, 6 h at 32°C, replicate 1


title: hNPC, H3K27me3, 37°C, replicate 1


title: Burned Larval Zebrafish, 48 hours post-burn

city: Madison

first: Huy

last: Dinh

state: WI

address: 1111 Highland Avenue

institute: University of Wisconsin-Madison

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 (Unwounded-4days, Burn-24 hours), v6.1.2 (Unwounded-3days, Unwounded-5days, Burn-6hours, Burn-48hours)
UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object (V4)
Assembly: GRCz11 (danRer11)
Supplementary files format and content: RNA count matrix

organism: Danio rerio

growth_protocol: Zebrafish embroys were collected from adult Tg(mpx:dendra,mpeg1.1:mCherry) fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator.

extract_protocol:
Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions.
Library construction was performed per 10x instructions with 3' v2 chemistry
Each prepared library was sequenced on the NovaSeq using dual index sequencing

treatment_protocol: Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer.

value: Macrophage

value: Neutrophil

value: Burn


title: Whole blood, ID49_Day0

value: AAC


title: hNPC, H3K36me3, 6 h at 32°C, replicate 1

value: neural progenitor cells


title: RPE, FGF 48h, 1


title: Burned Larval Zebrafish, 6 hours post-burn

description: 10x Genomics

value: Whole blood

value: WT


title: Burned Larval Zebrafish, 24 hours post-burn

description: 10x Genomics


title: RPE, DCA 48h, 3

value: Dichloroacetate


title: hNPC, H3K27me3, 6 h at 32°C, replicate 1

value: 6 h of 32degreeC


title: Whole blood, ID46_Day0


title: hNPC, H3K9me3, 6 h at 32°C, replicate 1


title: hNPC, IgG, 6 h at 32°C, replicate 1

value: IgG


title: Whole blood, ID43_Day0

value: INR

value: Yes


title: Whole blood, ID42_Day0


title: RPE, DCA 48h, 1

value: RPE


title: Unwounded Larval Zebrafish, 4 days post-fertilization

description: 10x Genomics

value: Unwounded


title: HEK293WT, IgG, 37°C, replicate 3


title: Unwounded Larval Zebrafish, 3 days post-fertilization

description: 10x Genomics


title: RPE, FGF 48h, 2


title: RPE, Control 48h, 2

value: Media


title: RPE, Control 48h, 3


title: Whole blood, ID41_Day0


title: HEK293WT, H3K36me3, 37°C, replicate 3

description: HEK293_rep1_rep2_rep3_37_H3K36_merged_depthnorm.bw


title: HEK293WT, IgG, 37°C, replicate 2


title: RPE, Control 48h, 1


title: Whole blood, ID39_Day0


title: Combinatorial_2_output3

city: Barcelona

first: Mireia

last: Seuma

state: Barcelona

address: Carrer de Baldiri Reixac, 10, 12

country: Spain

institute: Institute for Bioengineering of Catalonia

description: PCR DNA amplicon from plasmid library

library_source: other

data_processing:
FastQ files from paired-end sequencing of each Aß42 library before (‘input’) and after selection (‘output’) were processed using the DiMSum pipeline (https://github.com/lehner-lab/DiMSum)
Assembly: NA
Supplementary files format and content: Spreadsheet file with columns indicating aa_seq = amino acid sequence of variant, aa_seq_full = full amino acid sequence of AB42 containing the variant (ready to feed in MoCHI), dataset = dataset label (N_terminal_Ab42_double_mutants, C_terminal_Ab42_double_mutants, Combinatorial_1, Combinatorial_2), mean_count= Mean read counts of the input replicates, fitness= Merged fitness, sigma = Merged error over fitness, fAD_category = Associated pathogenicity (non-fAD, fAD).
Library strategy: DNA-seq

molecule: other

organism: Saccharomyces cerevisiae

source_name: single cell eukaryotic microorganism

growth_protocol: For each Aβ42 plasmid library, yeast cells were transformed in 3 biological replicas (1,2,3), with a minimum of 3, 2.2, 0.99 and 0.43 million transformants for each of the replicate of N_terminal_Ab42_double_mutants, C_terminal_Ab42_double_mutants, Combinatorial_1 and Combinatorial_2 libraries, respectively. Once the culture reached the exponential phase, cells were resuspended in 100-1000mL protein inducing medium (-URA, 20% glucose, 100uM Cu2SO4) at OD600=0.05. Selection was performed for each biological replica. After 24h, 25-50ml of cells were harvested for input pellets and a minimum of 75, 12, 230 and 1.5 million cells / replica (for N_terminal_Ab42_double_mutants, C_terminal_Ab42_double_mutants, Combinatorial_1 and Combinatorial_2 libraries, respectively) were plated on -URA-ADE selection medium plates (145cm2, Nunc, Thermo Scientific) and incubated for 6-7 days at 30C. The number of cells plated ensures a minimum coverage of 10 times each variant in the library. Finally, colonies were scraped off the plates and harvested for output pellets. Inputs and output pellets were stored at -20C and later treated for DNA extraction.

extract_protocol:
Input and output pellets (3 biological replicates each, 6 tubes in total) were resuspended in 2ml extraction buffer (2% Triton-X, 1% SDS, 100 mM NaCl, 10 mM Tris pH 8, 1 mM EDTA pH 8) and subjected to two cycles of freezing-thawing in an ethanol-dry ice bath and water bath at 62C for 10min each. 1.5ml of phenol:chloroform:isoamyl 25:24:1 was then added to the pellets and vortexed for 10min. The aqueous phase was recovered by means of 30min centrifugation at 3000 rpm. DNA was precipitated with 1:10 V NaOAc 3M and 2.2 V of 99% cold ethanol and incubated at -20C for 2h. After centrifugation, pellets were dried overnight at RT. The next day, pellets were resuspended in TE 1X buffer (10mM Tris pH8, 1mM EDTA pH8) and treated with 10ul RNase A (Thermo Scientific) for 1h at 37C. DNA was purified using a silica beads extraction kit (QIAEX II Gel Extraction Kit, Qiagen).
PCR amplification in two steps using Q5 High-Fidelity DNA Polymerase (NEB). In step 1, 50 (for Combinatorial_2) or 100 (for N_terminal_Ab42_double_mutants, C_terminal_Ab42_double_mutants and Combinatorial_1 libraries) million plasmids were amplified for 15 cycles using frame-shifted adaptor primers with a partial homology to standard Illumina sequencing primers. PCR products from the first step were used as templates in the second PCR step, where indexed Illumina primers were used for a 10 cycles amplification. The three input samples were pooled together equimolarly, and the same for the three output samples. The two final pools were purified from a 2% agarose gel using a silica beads extraction kit (QIAEX II Gel Extraction Kit, Qiagen).

value: single cell eukaryotic microorganism

value: [psi-pin-] (MATa ade1-14 his3 leu2-3,112 lys2 trp1 ura3-52)

value: protein expression


title: Whole blood, ID48_Day0

value: No


title: HEK293WT, H3K36me3, 37°C, replicate 2


title: Combinatorial_2_output1

description: PCR DNA amplicon from plasmid library


title: RPE, DCA+FGF 24h, 3

value: Dichloroacetate + FGF2


title: Whole blood, ID34_Day0

value: AAC


title: Combinatorial_2_output2

description: PCR DNA amplicon from plasmid library


title: Unwounded Larval Zebrafish, 5 days post-fertilization

description: 10x Genomics

value: Macrophage

value: Neutrophil


title: Combinatorial_2_input3

description: PCR DNA amplicon from plasmid library


title: RPE, DCA 48h, 2


title: RPE, DCA+FGF 24h, 2


title: HEK293WT, IgG, 37°C, replicate 1


title: hNPC, H3K4me3, 6 h at 32°C, replicate 1

value: neural progenitor cells


title: Whole blood, ID31_Day0

value: Whole blood


title: HEK293WT, H3K36me3, 37°C, replicate 1


title: Whole blood, ID30_Day0


title: Combinatorial_2_input2

description: PCR DNA amplicon from plasmid library


title: RPE, DCA+FGF 24h, 1


title: Whole blood, ID40_Day0


title: RPE, FGF 24h, 3


title: Combinatorial_2_input1

description: PCR DNA amplicon from plasmid library


title: Whole blood, ID29_Day0


title: HEK293WT, H3K36me3, 6 h at 32°C, replicate 3

description: HEK293_rep1_rep2_rep3_32_H3K36_merged_depthnorm.bw

value: 6 h of 32degreeC


title: RPE, FGF 24h, 2


title: Whole blood, ID27_Day0


title: Combinatorial_1_output2

description: PCR DNA amplicon from plasmid library


title: HEK293WT, IgG, 6 h at 32°C, replicate 2

value: IgG


title: Whole blood, ID23_Day0

value: INR


title: RPE, DCA 24h, 3

value: Dichloroacetate


title: RPE, FGF 24h, 1

value: RPE


title: Combinatorial_1_output1

description: PCR DNA amplicon from plasmid library


title: Whole blood, ID21_Day0

value: Yes


title: Combinatorial_1_input3

description: PCR DNA amplicon from plasmid library


title: HEK293WT, IgG, 6 h at 32°C, replicate 1


title: RPE, DCA 24h, 2


title: Whole blood, ID18_Day0

value: COMBO


title: Combinatorial_1_input2

description: PCR DNA amplicon from plasmid library

value: single cell eukaryotic microorganism


title: HEK293WT, H3K36me3, 6 h at 32°C, replicate 1


title: RPE, DCA 24h, 1


title: Whole blood, ID17_Day0


title: HEK293WT, IgG, 6 h at 32°C, replicate 3


title: GC2_SMARCA4

data_processing:
Sequencing data were acquired through the default Illumina pipeline using Casava V1.8.
Reads were aligned to the human genome (GENCODE grch38) using hisat2 with the following options: --no-mixed --no-discordant --phred33 --minins 10 --maxins 700 –add-chrname
BAM files were converted to bed using bedtools bamtobed using the -bedpe option and filtered for fragments < 1kb in size
Peaks were called using MACS 3 using callpeak --format BEDPE --keep-dup all -g hs and cut-off q < 0.00000001
Assembly: grch38
Supplementary files format and content: narrowPeak (except for IGG)
Library strategy: CUT&RUN

source_name: Tonsil

extract_protocol:
Human normal GC B cells were purified by magnetic cell separation from tonsils with anti-CD77-FITC antibody (BioLegend) conjugated with magnetic anti-FITC beads (Miltenyi Biotec) according to the manufacturer’s instructions (Miltenyi Biotec). Nuclei were freshly isolated from GC B cells using a nuclear extraction buffer (20 mM pH 7.9 HEPES, 10 mM KCl, 0.1% Triton X-100, 20% glycerol and 1 mM MnCl2). Cut&Run sample preparation was performed using the CUTANATM ChIC/CUT&RUN Kit version 3.1 (EpiCypher).
Library preparation was performed with 5 ng of CUT&RUN enriched DNA (or the total sample volume if DNA output was less than 5 ng) using the CUTANA™ CUT&RUN Library Prep Kit version 1.0 (EpiCypher) following the manufacturer’s instructions.

value: Tonsil

value: Germinal center B cells


title: Whole blood, ID16_Day0


title: Combinatorial_1_input1

description: PCR DNA amplicon from plasmid library

value: [psi-pin-] (MATa ade1-14 his3 leu2-3,112 lys2 trp1 ura3-52)

value: protein expression


title: RPE, Control 24h, 3

value: Media


title: HCT116 cells, MTHFD2-KO, TimeFinal, Rep3

first: Luca

last: Cozzuto

address: Carrer Dr. Aiguader 88

department: Bioinformatics facility

institute: Centre for genomic regulation (CRG)

data_processing:
Reads were aligned to hg38 genome using STAR.
Gene level counts were obtained with featureCounts from subread.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw count values for all samples

source_name: colon

growth_protocol: HCT116 were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was harvested using PureLink RNA mini kit (Thermo Fisher Scientific).
RNA libraries for RNA-seq were prepared using a poly-A selection method following manufacturer's protocols.

treatment_protocol: HCT116 knock-out cells were generated by CRISPR-Cas9, a single knock-out clone was isolated, and RNA samples were harvested right after knock-out generation (initial) or after two months in cell culture (final).

value: colon

tag: time

value: final


title: GC2_MEF2B


title: RPE, Control 24h, 2


title: Combinatorial_1_output3

description: PCR DNA amplicon from plasmid library


title: HCT116 cells, MTHFD2-KO, TimeFinal, Rep2


title: Whole blood, ID10_Day0

value: No


title: RPE, Control, 24h, 1


title: GC2_IgG


title: HEK293WT, H3K36me3, 6 h at 32°C, replicate 2


title: Whole blood, ID9_Day0

value: Whole blood

value: AAC


title: GC1_SMARCA4


title: HCT116 cells, MTHFD2-KO, TimeFinal, Rep1


title: Whole blood, ID7_Day0


title: HCT116 cells, MTHFD2-KO, Time0, Rep3

value: initial


title: RS2Z36 KO, heat stress, Replicate 3

city: Frankfurt am Main

first: Remus

middle: Richard Elrik

last: Rosenkranz

address: Max-von-Laue-Str. 9

country: Germany

institute: Goethe University Frankfurt

data_processing:
Raw reads were mapped against the tomato reference genome (S. lycopersicum cv. Heinz 1706, genome build 4.0; ITAG 4.0) in a splice-aware manner using Star (Galaxy version 2.7.8a) with default settings, except for the following changes: --genomeSAindexNbases 14, --sjdbGTFfile ITAG4.0_gene_models.gff, -- sjdbOverhang 149, --chimOutType don’t report, --outFilterType yes, --outFilterMultimapNmax 1, -- outFilterMismatchNmax 999, --outFilterMismatchNoverLmax 0.05.
Reads per gene were counted using htseq-count (Galaxy version 0.9.1) with the following settings: --mode union. –stranded no, --minaqual 10, --type gene, --idattr ID
Batch effects in the heat stress samples were identified by principal component analysis and consequently removed using ComBat-Seq. Read counts per gene (ITAG 4.0 annotation) are deposited as processed data.
Assembly: Tomato Genome version SL4.0
Supplementary files format and content: tab-delimited text files contain read counts for each sample

organism: Solanum lycopersicum

source_name: Leaf

extract_protocol:
Total RNA was isolated using TriZol (Invitrogen) followed by DirectZol (Zymo Research)
RNA libraries for RNA-seq were prepared using the NEBNext Ultra II non-directional RNA Library Kit with polyA selection

treatment_protocol: Excised leaves from six 6-week-old wild type and RS2Z KO mutant plants were exposed to 1 h 40 °C on wet tissue paper in sealed petri dishes in a water bath.

value: Leaf

value: RS2Z36 KO

value: heat stress


title: RS2Z36 KO, heat stress, Replicate 2


title: HCT116 cells, MTHFD2-KO, Time0, Rep2


title: Whole blood, ID6_Day0


title: GC1_IgG

value: IgG


title: RS2Z36 KO, heat stress, Replicate 1


title: CovUrt_853

value: whole blood

value: CovUrt


title: W8_donor5_SOX10 plus_iMicroglia_CSF-exposed

city: Milan

first: Edoardo

last: Pedrini

state: Lombardy

address: Via Olgettina 60

department: Division of Neuroscience

country: Italy

institute: Hospital San Raffaele

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Supplementary files format and content: normCount_allsample.tsv.gz Tab-separated values files and matrix files
Supplementary files format and content: metadata_allsample.tsv Tab-separated values files and matrix files

source_name: BS

extract_protocol:
For the enzymatic cellular dissociation, 30 organoids, for each experiment, were first washed in Hank’s balanced salt solution (HBSS) and, then, incubated with a freshly prepared dissociation solution (HBSS, papain and DNAase I) for 45 min at 37°C on an orbital shaker (90 rpm), and gently triturated using a P1000 pipette. Cells were incubated again for 15 min at 37°C on an orbital shaker (90 rpm) centrifuged and gently triturated using a P1000 pipette. After the single cell dissociation, the cell suspension was mixed (1:1) with 10 mg/mL ovomucoid protease inhibitor solution and centrifuged at 300g for 5 min. The pellet was resuspended in 1X PBS containing BSA (1:50). Cells were counted using trypan blue and a haemocytometer under bright field. A yield of 700–1,200 cells per μL per sample was targeted.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: BS

value: donor 05

tag: mg presence

value: yes

value: CSF

tag: doxy

value: pos


title: Whole blood, ID3_Day0

value: COMBO


title: HCT116 cells, MTHFD2-KO, Time0, Rep1

value: colon


title: RS2Z35 KO, heat stress, Replicate 3

value: RS2Z35 KO


title: W8_donor2_SOX10_plus_iMicroglia_CSF-exposed

description: 10x Genomics

value: donor 02


title: Ventral prostate organoid, T-ERG, WGS, replicate 2

city: Cambridge

first: Sofia

last: Hu

email: sofiahu@mit.edu, xsu@cpdr.org

state: MA

address: 500 Main Street

institute: MIT

data_processing:
Sequence reads were trimmed to 40 nucleotides, and the resultant reads were aligned to mm9 genome using BWA (0.7.12) backtrack algorithm. HMMcopy (0.1.1) was used to detect copy number alterations by estimating DNA copy number in 500-kb bins controlling for mappability and GC content (calculated by HMMcopy gcCounter).
Assembly: mm9
Supplementary files format and content: WGS_segments.txt

source_name: organoid

growth_protocol: A 4-month-old mouse carrying desired the genotype was euthanized, and aseptic surgical equipment was used to isolate the entire prostate. Anterior prostate, dorsolateral prostate and ventral prostate were separated under a dissection microscope. Each lope of a prostate was developed into organoid culture and organoids from ventral prostate were consistently used throughout this study. Mouse prostate organoids were developed and sub-cultured as described in Karthaus et al. Cell (2014) and Drost et al. Nat Protoc (2016). Organoids were sub-cultured every 6-7 days, depending on the specific experiments. To break the organoids down into single cells, they were incubated in TrypLE (Gibco) supplemented with 10µM Y-27632 for 20 minutes at 37oC at 1000rpm in the Eppendorf ThermoMixer F1.5. Cells were spun down and re-suspended in adMEM/F12 +/+/+ medium. The number of cells was determined using a Nexcelom cellometer after organoids were broken up into single cells. The desired number of cells were spun down to remove the AdMEM/F12 +/+/+ medium. Then, cells were resuspended in 100% Matrigel and seeded on a well plate in 30uL per Matrigel dome. 3000 single cells were seeded per 30uL Matrigel dome to develop into organoids throughout this study, unless otherwise noted.

extract_protocol:
DNA from 10,000 cells was extracted using QIAmp DNA Mini Kit (Qiagen).
Standard Nextera XT Illumina library preparation was applied. The libraries were sequenced with 40bp read length on an Illumina NextSeq500.

value: organoid

tag: biological replicate

tag: technical replicate

value: Ventral prostate


title: HCT116 cells, MTHFD2-WT, TimeFinal, Rep3

tag: tissue

value: final


title: W8_donor4_SOX10 plus_iMicroglia

description: 10x Genomics

value: donor 04

value: CTRL


title: Ventral prostate organoid, T-ERG, WGS, replicate 1


title: Ventral prostate organoid, control, WGS, replicate 2


title: RS2Z35 KO, heat stress, Replicate 1

value: Leaf

value: heat stress


title: RS2Z35 KO, heat stress, Replicate 2


title: W8_donor2_SOX10_plus_iMicroglia

description: 10x Genomics


title: HCT116 cells, MTHFD2-WT, TimeFinal, Rep1


title: W8_pool_Donor2Donor4Donor5_SOX10_no_doxy

description: 10x Genomics

value: pool

value: no

value: neg


title: GC1_MEF2B

value: Tonsil

value: Germinal center B cells


title: Ventral prostate organoid, control, WGS, replicate 1


title: Ventral prostate organoid, T-ERG, replicate 10

data_processing:
Quality control on each library was performed to assess coverage depth, enrichment for messenger RNA (exon/intron and exon/intergenic density ratios), fraction of rRNA reads and number of detected genes using bespoke scripts. The sequencing reads were mapped to the mm10 reference using star/2.5.3a. The negative strand sequences mapped to each gene were counted by rsem/1.3.0. Raw counts were normalized by DESeq2. GSEA/2.0.13 was then run projecting expression matrices to c2 cp MSigDB to identify enrichment patterns.
Assembly: mm10
Supplementary files format and content: RNAseq_ProstateOrganoids_log2FPKM.xlsx

extract_protocol:
Organoids from the same Matrigel dome were harvested for each RNA extraction using the RNeasy kit (Qiagen).
Library preparation for RNA sequencing was performed following the high-throughput protocol described in Mildrum et al. J Biomol Tech (2020) with the following modifications: RNA quantification and quality control (QC) were assessed individually using the AATI Fragment Analyzer. 5 replicates of RNA per each sample type were subjected to RNA-seq with QC. Following the template switching reaction, barcoded cDNA samples were pooled, treated with Exonuclease I and cleaned using RNA Ampure beads. Second strand synthesis and PCR amplification were performed using the Advantage 2 Polymerase Mix (Clontech) and the SINGV6 primer (IDT). 12 cycles of PCR were performed, followed by clean up using regular SPRI beads. Successful amplification of cDNA was confirmed using the Fragment Analyzer. Illumina libraries were then produced using standard Nextera tagmentation substituting P5NEXTPT5-bmc primer. Finally, libraries were cleaned using SPRI beads at 1X and quantified using the Fragment Analyzer and qPCR before being loaded for 40X40 paired-end sequencing using the Illumina NextSeq500.


title: RS2Z double KO, heat stress Replicate 2

value: RS2Z35 RS2Z36 KO


title: HCT116 cells, MTHFD2-WT, Time0, Rep3

value: initial


title: HCT116 cells, MTHFD2-WT, Time0, Rep2

value: colon


title: W8_donor3_SOX10_CSF-exposed

description: 10x Genomics

value: BS

value: donor 03

value: CSF

value: pos


title: HCT116 cells, MTHFD2-WT, Time0, Rep1


title: RS2Z double KO, heat stress Replicate 1


title: Ventral prostate organoid, T-ERG, replicate 9

value: organoid

value: Ventral prostate


title: Ventral prostate organoid, T-ERG, replicate 8


title: scAAV9-U6-mi405-Final Opt

city: Columbus

first: Scott

last: Harper

state: Ohio

address: Center for Gene Therapy, 575 Children’s Crossroads Room WC3740

institute: The Research Institute at Nationwide Children's Hospital

data_processing:
Library Prep & Sequencing
PacBio Subreads.bam
Lima Demultiplexing
CCS Reads Generation
Alignment to concatenated reference genome
Assembly: pbmm2
Supplementary files format and content: scAAV9-U6-mi405-FinalOpt_scAAV_mi405_FinalOpt_combined.alignment.csv: AAV9-C5 genomic DNA reads aligned to reference sequence.
Supplementary files format and content: scAAV9-U6-mi405-OG_scAAV_mi405_OG_combined.alignment.csv: AAV9-C1 genomic DNA reads aligned to reference sequence.

organism: synthetic construct

growth_protocol: AAV production performed by Andelyn Biosciences

extract_protocol:
Performed by Azenta Life Sciences Inc.
PacBio SMRT adapter library prep performed by Azenta Life Sciences Inc.


title: WT, heat stress Replicate 2

value: WT


title: W8_donor1_GIBCO

description: 10x Genomics

value: donor 01

value: CTRL


title: Ventral prostate organoid, T-ERG, replicate 7


title: W8_donor1_GIBCO_W8_CSF-exposed

description: 10x Genomics


title: WT, heat stress Replicate 1

value: Leaf

value: heat stress


title: Ventral prostate organoid, T-ERG, replicate 6


title: SKMCS_D60 scRNA-seq

city: Hangzhou

first: Xingnan

last: Huang

address: No.18 Shilongshan Road

country: China

institute: Westlake University

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
We mapped single-cell sequencing data to both human and mouse genome by using CellRanger 3.0.2  with setting ‘--localcores=10 --localmem=3 --mempercore=3 --maxjobs=10 --r1-length=26 --r2-length=151’.
We processed mapped data by using Seurat15. The count matrix was generated by using merge() function in Seurat and excluding low quality cells—cells with less than 200 genes and low quality genes—genes expressing less than 10 cells.
Genome_build: hg38, mm10

source_name: Skeletal muscle cells Day 60

growth_protocol: UiPSMs were digested into single cells using 0.25% Trypsin-EDTA (Gibco, 25200056) and sparsely passaged 7.5x104 onto new Matrigel-coated cell 24-well plate in UiPSMs maintain medium overnight. for subsequent myogenic differentiation, was initially induced via a modified approach including two stages. stage1 medium defined SM was conducted for 15 days, media was changed 2 days for this step; stage II medium defined DKHI was conducted until skeletal muscle fiber bundles are fully present, media was changed 3 days for this step. SM: DMEM/F12 supplemented with 15% KSR (Gibco, 10828028), 1% ITS(Gibco,41400045), 1% NEAA, 0.1µM ß-ME, 4ng/ml IGF-1 (Pepro Tech,250-19), 10ng/ml HGF (R & D systems,294-HG-250),3µM CHIR99021, 50ng/ml VC (Sigma-Aldrich,49752), 0.5ng/ml Dex(Target Mol, T0947L) and 2nM SB431542. DiKHI: DMEM supplemented with 15% KSR, 2% Horse serum (Gibco, 16050122), 1% NEAA, 0.1µM ß-ME, 4ng/ml IGF-1, and 10ng/ml HGF.

extract_protocol:
Cells suspensions (500-1000 cells per microliter) were loaded on a Chromium Single Cell Controller (10x Genomics) to obtain single-cell gel beads in emulsion (GEMs) by using Single Cell 3’ Library and Gel Bead Kit V2 (10x genomics, 120237). Captured cDNAs were lysed and the released RNA were barcoded through reverse transcription in singular GEMs (Zheng et al., 2017). Barcoded cDNAs were pooled and cleaned by DynaBeads® MyOne Silane Beads (Invitrogen, 37002D).
Single-cell RNA-seq libraries were prepared by Single Cell 3’ Library Gel Bead Kit V2 (10x Genomics, 120237) following the manufacturer’s instruction.

treatment_protocol: Preparing male MITRG mice of 4-6 weeks of age. The CTX (8µg/g, WHIGA, 9012-91-3) was injected into the anterior tibialis, after 24 hours treatment, urine cells were transplanted into the left side as negative control, and the skeletal muscle cells derived from UiPSM cells were transplanted to the right side to observe the activity in vivo. The UiPSM cells were labeled with lenti-luciference plasmid before the differentiation. The skeletal muscle cells derived from UiPSM at day60 and day30 with exogenous MYOD digested with the solution including equal volume of 0.25% Trypsin-EDTA and 0.01% collagenase IV (Gibco,17104019) for preparing of single cell suspension. The urine cells derived from UiPSM digested with 0.25% Trypsin-EDTA for preparing of single cell suspension. After centrifugation and pelleting, 1.5x106 cells were resuspended in a small volume(50~100µL) of cold DMEM/F12, counted, and diluted with an equal volume of cold Matrigel, yielding a cell suspension in a 1:1 mixture of DMEM-F12/Matrigel that was kept on ice until transplantation. Finally, the preparing cells were intramuscular injected into the anterior tibia.

value: Skeletal muscle cells Day 60

tag: method

value: scRNA-seq


title: HCT116 cells, MTHFD2-WT, TimeFinal, Rep2

value: final


title: RS2Z double KO, heat stress Replicate 3

value: RS2Z35 RS2Z36 KO


title: E25 Pantherophis guttatus dorsal skin single cells

city: Geneva

first: Athanasia

last: Tzika

address: Athanasia Tzika, LANE - Sciences III, 30 quai Ernest Ansermet, 1211 Genève 4, Switzerland

institute: University of Geneva

description: 10X Genomics Single Cell 3' v3 library

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using Cell Ranger software v7.0.0
Assembly: UNIGE_PanGut_3.0
Supplementary files format and content: h5ad file with count matrices, scores and clustering

organism: Pantherophis guttatus

source_name: Embryonic dorsal skin

extract_protocol:
Dorsal skin was extracted from one Pantherophis guttatus embryo at 25 days post-ovipositioning (E25). The dorsal skin was then processed according to the protocol detailed in “Dissociation of chick embryonic tissue for FACS and preparation of isolated cells for genome-wide downstream assays” by Williams et al., 2021. The resulting single cell suspension was frozen at -80°C and sent for library preparation followed by sequencing.
10X Genomics Single Cell 3' v3 performed by Single Cell Discoveries, subsequent sequencing was performed by Macrogen.

value: Embryonic dorsal skin

value: Skin-resident cells

value: Wild Type +/+


title: Ventral prostate organoid, T-ERG, replicate 5


title: RS2Z36 KO, control, Replicate 3

value: RS2Z36 KO

value: control


title: SKMCS_D30_(OE_MYOD) scRNA-seq

source_name: Skeletal muscle cells Day 30 (over-expression MYOD)


title: W8_donor3_SOX10

description: 10x Genomics

value: BS

value: donor 03

value: no

value: pos


title: RS2Z36 KO, control, Replicate 2


title: Ventral prostate organoid, T-ERG, replicate 4

value: organoid

value: Ventral prostate


title: 180 dph, replicate 2, scRNAseq

city: Haizhu district, Guangzhou

first: wang

last: tong

state: GD

address: School of Life Sciences，Sun Yat-Sen University East Campus

institute: School of Life Sciences, Sun Yat-Sen University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, genes.tsv, matrix.mtx)

organism: Epinephelus coioides

source_name: Gonad

extract_protocol:
A mixture of 30 gonads at 80 dph was dissociated for single-cell transcriptomics with two repetitions. With the development of the fish, 20 gonad tissue samples at 120 dph and 5 gonad tissue samples at 180 dph were mixed and dissociated for scRNA-seq, too. Briefly, gonadal samples were cut into pieces, then cleaned by 1×Hank's Balanced Salt Solution twice. Next, the samples were centrifuged at 1000×g for 3 min and incubated with 500 U/mL collagenase IV (diluted by DPBS buffer without calcium and magnesium ion) at 37 °C for 2 h. Then the samples were centrifuged at 1000×g for 3 min and followed by a filtration step through a 40 µm strainer (Corning, USA). The cell numbers of the suspensions were calculated by the blood counting chamber, then the cells were stained by 0.4% trypan blue to estimate cell viability. Next, the suspensions (cell viability >85%) were used for further single-cell RNA sequencing (scRNA-seq).
ScRNA-seq libraries were constructed by Chromium Next GEM Single Cell 3’Reagent Kits v3.1 (10X Genomics, USA). The prepared suspensions were used to generate single-cell Gel Beads-In-Emulsions (GEMs) by loading onto a 10X Genomics GemCode Single-cell. Upon dissolution of the Single Cell 3’ Gel Bead in a GEM, primers containing (i) an Illumina® R1 sequence (read 1 sequencing primer), (ii) a 16 nt 10x Barcode, (iii) a 10 nt Unique Molecular Identifier (UMI), and (iv) a poly-dT primer sequence are released and mixed with cell lysate and Master Mix. The GEMs were incubated to produce barcoded, full-length cDNA from poly adenylated mRNA. Then the cDNA was amplified by PCR to generate sufficient mass for library construction. R1 (read 1 primer sequence) was added to the molecules during GEM incubation. P5, P7, a sample index, and R2 (read 2 primer sequence) were added during library construction via end repair, A-tailing, adaptor ligation, and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification.  The Single Cell 3’ Protocol produced Illumina-ready sequencing libraries. A Single Cell 3’ Library comprised standard Illumina paired-end constructs which began and ended with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI were encoded in Read 1, while Read 2 was used to sequence the cDNA fragment. Sample index sequences were incorporated as the i7 index read. Read 1 and Read 2 were standard Illumina® sequencing primer sites used in paired-end sequencing.

value: Gonad

value: 180 dph


title: Ventral prostate organoid, T-ERG, replicate 3


title: RS2Z36 KO, control, Replicate 1

value: Leaf


title: NC(UC) scRNA-seq

source_name: Urine cells

value: Urine cells

value: scRNA-seq


title: UiPSM Day9-CHIR ATAC

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
Raw reads were trimmed with TrimGalore (v.0.6.4)
The data was mapped to human genome hg38 using bowtie22.
Low quality reads were filtered by SAMtools. Unique reads mapping to a single genomic location and strand were remained.  Mitochondrial sequences were removed using “grep –v ‘chrM’”.
Genome_build: hg38

source_name: UiPSM Day9-CHIR

growth_protocol: Specific culture media for each cell type

extract_protocol:
The precipitation were lysed within 50 µL lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.2% (v/v) IGEPAL CA-630) and centrifuged at 500 g for 5 min at 4℃, then fragmentated with 50µL transposition reaction mix of TruePrep DNA Library Prep Kit V2 for Illumina® (TD501, Vazyme) under an 37℃ incubation condition for 30min, purified using a MinElute Kit (QIAGEN).
The fragmented genome suspension was amplificated 8-13 cycles with 50µL amplification mix of TruePrep DNA Library Prep Kit V2 for Illumina® (TD501, Vazyme), and purified using a MinElute Kit (QIAGEN).amplification mix of TruePrep DNA Library Prep Kit V2 for Illumina® (TD501, Vazyme), and purified using a MinElute Kit (QIAGEN).

treatment_protocol: A total of 50,000 cells cleaned up with ice-cold DPBS for 5 minutes  and centrifuged at 500g for 5 minutes in 4℃.

value: UiPSM Day9


title: 180 dph, replicate 1, scRNAseq

description: 10x Genomics


title: RS2Z35 KO, control, Replicate 3

value: RS2Z35 KO


title: UiPSM Day6-CHIR ATAC

source_name: UiPSM Day6-CHIR

value: UiPSM Day6


title: WT, heat stress Replicate 3

value: WT

value: heat stress


title: UiPSM Day3-CHIR ATAC

source_name: UiPSM Day3-CHIR

value: UiPSM Day3


title: scAAV9-U6-mi405-OG

treatment_protocol: AAV production performed by Andelyn Biosciences


title: RS2Z35 KO, control, Replicate 2

value: control


title: 80 dph, replicate 2, scRNAseq

description: 10x Genomics

value: 80 dph


title: Ventral prostate organoid, T-ERG, replicate 1


title: Ventral prostate organoid, T-ERG, replicate 2


title: RS2Z35 KO, control, Replicate 1


title: Ventral prostate organoid, control, replicate 10


title: Ventral prostate organoid, control, replicate 9


title: 80 dph, replicate 1, scRNAseq

description: 10x Genomics


title: RS2Z double KO, control Replicate 3

value: RS2Z35 RS2Z36 KO


title: UiPSM Day9-EPZ ATAC

source_name: UiPSM Day9-EPZ


title: RS2Z double KO, control Replicate 2


title: RNA-MCF7-EMT-D12-w-GSK126-R2

city: Granada

first: Ivan

middle: Fernández

last: Rengel

address: Avenida de la Ilustración 114

institute: GENyO

data_processing:
Reads quality control performed with FastQC
STAR_v2.5.3a used for aligning sequences to reference genome hg19
featureCounts used to obtain gene expression values
BamCoverage 3.5.1 used to normalize with BPM method and to apply a smoothing of 10 bp.
Assembly: GRCh37.p13 (hg19)
Supplementary files format and content: Bigwig files containing Reads per Million (RPM) with a 10 bp smoothing

source_name: Breast adenocarcinoma

growth_protocol: Cells were cultured in 5% CO2 at 37 ºC  in DMEM High glucose media supplemented with 10% FBS heat inactivated, penicillin/streptomycin (Gibco), L-glutamine (Gibco) and 2-mercaptoethanol (Gibco).

extract_protocol:
Trizol extraction
DNBSEQ library construction protocol
Strand specific mRNA-seq libraries

treatment_protocol:
MCF-7 cells were grown in presence of a EZH2 inhibitor, 5uM of GSK126 or 2uM of EPZ-6438 for 12 days. The inhibitors were refreshed every two days as cells were split.  MCF-7, MDA-MB-231 and SKBR3 were plated at low density and cultured in presence or absence of GSK126 for 14 days. The inhibitor was refreshed every 5 days.
For the induction of EMT-MET, MCF-7 cells were treated during 6 days with TGF-B (10 ng/mL), EGF (50 ng/mL ) followed by additional 6 days upon removal of the cytokines from the media. Cells were mantained in the presence of 5uM GSK126 during the course of the experiment.  Cells were diluted 1:4 every 48h and GSK126 was refreshed every two days when the cells were diluted.

value: Breast adenocarcinoma

value: Cells treated during 6 days with TGF-B (10 ng/mL), EGF (50 ng/mL ) followed by additional 6 days upon removal of the cytokines from the media. Cells were mantained in the presence of 5uM GSK126 during the course of the experiment.


title: Ventral prostate organoid, control, replicate 8

value: organoid

value: Ventral prostate


title: UiPSM Day3-EPZ ATAC

source_name: UiPSM Day3-EPZ


title: RNA-MCF7-EMT-D12-w-GSK126-R1


title: RS2Z double KO, control Replicate 1


title: 120 dph, replicate 2, scRNAseq

description: 10x Genomics

value: Gonad

value: 120 dph


title: RNA-MCF7-EMT-D6-w-GSK126-R2

value: Cells treated with TGF-B (10 ng/mL), EGF (50 ng/mL)and GSK126 (5uM) for 6 days.


title: Ventral prostate organoid, control, replicate 7


title: UiPSM Day9 ATAC

source_name: UiPSM Day9


title: 120 dph, replicate 1, scRNAseq

description: 10x Genomics


title: UiPSM Day6 ATAC

source_name: UiPSM Day6


title: WT, control Replicate 3

value: Leaf


title: WT, control Replicate 2


title: Ventral prostate organoid, control, replicate 6


title: Ventral prostate organoid, control, replicate 5


title: RNA-MCF7-EMT-D12-R2

value: Cells treated during 6 days with TGF-B (10 ng/mL), EGF (50 ng/mL ) followed by additional 6 days upon removal of the cytokines from the media


title: Ventral prostate organoid, control, replicate 4


title: Urine Cell ATAC

source_name: Urine Cell

value: Urine Cell


title: RNA-MCF7-EMT-D12-R1


title: UiPSM Day3 ATAC

source_name: UiPSM Day3


title: S16_SLX-17131.NEBNext19

first: Adriana

last: Ordonez

state: Cambridgeshare

address: Keith Peters Building, Biomedical Campus, Hills Rd

department: Biochemistry

country: United Kingdom

institute: Cambridge Institute for medical Research

description:
pKLV_NEBNXT19_1776
Single Read, 50bp

data_processing:
A comprehensive quality control was performd by  using the Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) computational software. This involved quantification of Total HiSeq read counts, percentage of mapped reads to the CHO library, the number of sgRNA in the library, the number of sgRNA with zero read counts,  the GiniIndex of the read count distribution and the frequency distribution of sgRNA in each sample.
Generation of a total read counts table and normalized read count table using MAGECK software (Li et al., 2014)
Identification of positively and negatively selected sgRNA and generation of the corresponding gene list by comparing single samples using MAGeCK tool.
Assembly: Chinese Hamster Ovary (CHO) CRISPR library
Supplementary files format and content: text files and fastq data

organism: Cricetulus griseus

source_name: Chinese Ovary cells (CHO-K1)

growth_protocol: Approximately 2.1 × 108 dual UPR reporter (ATF6⍺/IRE1⍺, XC45-6S) CHO-K1 Cas9 stable cells were infected at a multiplicity of infection (MOI) of 0.3 to favour infection with a single viral particle per cell. Two days after infection, transduced cells were selected with 8 µg/ml puromycin for 14 days.

extract_protocol:
To prepare samples for deep sequencing, genomic DNA from enriched and sorted populations as well unsorted cells (to represent the entire library) was extracted from ~3.6× 107 and ~1-3× 106 and, respectively, by incubation in proteinase K solution [100 mM Tris-HCl pH 8.5, 5 mM EDTA, 200 mM NaCl, 0.25% (w/v) SDS, 0.2 mg/ml Proteinase K] overnight at 50°C.
Integrated sgRNA sequences were amplified by nested PCR and the adaptors for Illumina sequencing (HiSeq4000) were introduced at the final amplification round. After quantification the products were subjected to NGS sequencing using custom primer and the illumina indexing primer with single-end reads of 50 bp on a hiseq 4000. The sequences were processed and guide counts, gene rankings and statistics were generated using MAGECK software (Li et al., 2014).

treatment_protocol: Ttransduced cells were split in two subpopulations, one treated with 2-deoxy-D-glucose (2DG) to induce ER stress and the other untreated. Approximately 6.6 × 107 Mab2C1-stained cells were subjected to FACS. In the screen performed in the presence of ER stress < 2% of cells that had a XBP1s::mCherry+/BiP::sfGFP– phenotype were selected for analysis. For the screen performed in basal conditions < 2% of total sorted cells that had a XBP1s::mCherry-/BiP::sfGFP+ phenotype were selected for analysis. Rounds of enrichment were carried on by sorting, cellular recovering/expansion and sorting. Equal number of transduced cells, untreated or 2DG treated, were passed without sorting as a control group in each round of sorting.

value: Chinese Ovary cells (CHO-K1)

value: Infected_Untreated (UT)_Sorted (S)_Round 2 (R2)_Bright GFP (B)_x2


title: UiPSM Day6-EPZ ATAC

source_name: UiPSM Day6-EPZ

value: UiPSM Day6


title: SKM_D30 (OE MYOD)

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
Raw reads were trimmed with TrimGalore (v.0.6.4)
Reads were aligned to  hg38 ensembl v101 transcriptome using rsem (v1.3.1) and bowtie2 (v2.4.1) (—bowtie2—bowtie2-sensitivity-level very_sensitive— no-bam-output—estimate-rspd).
The gene expression level was calculated by using  RSEM
The gene expression was normalized using EDAseq on a basis of GC-content. RNA-seq data was expressed in units of GC-normalized tag counts.
Genome_build: hg38
Supplementary_files_format_and_content: *csv file includes expected count for all samples, *txt files include RSEM output with expected count, TPM, FPKM

source_name: induced skeletal muscle Day 30 (OE MYOD)

extract_protocol:
Purified total RNA was capture with magnetic bead with oligo-polyA, interrupt and reverse-transcribed into cDNA using the VAHTSTM mRNA-seq V3 Library Prep Kit for Illumina (NR611, Vazyme), purified using VAHTS DNA Clean Beads (N411, Vazyme).
cDNAs ligated adapters and amplified libraries using the amplification mix (NR611, Vazyme). Finally, sequencing the cDNAs library to obtain 150bp paired-end reads.

treatment_protocol: Extracted RNA using phenolic chloroform after pretreatment with Trizol


title: RNA-MCF7-EMT-D6-R2

value: WT

value: Cells treated with TGF-B (10 ng/mL) and EGF (50 ng/mL) for 6 days


title: S15_SLX-17131.NEBNext18

description:
pKLV_NEBNXT16_1774
Single Read, 50bp

value: Infected_Untreated (UT)_Sorted (S)_Round 2 (R2)_Bright GFP (B)


title: Ventral prostate organoid, control, replicate 2

source_name: organoid


title: SKM_D15 (OE MYOD)

source_name: induced skeletal muscle Day 15 (OE MYOD)


title: RNA-MCF7-EMT-D6-R1


title: S14_SLX-17131.NEBNext16

description:
pKLV_NEBNXT09_1767
Single Read, 50bp

value: Infected_Untreated (UT)_Sorted (S)_Round 1 (R1)_Bright GFP (B)_x2


title: Ventral prostate organoid, control, replicate 1


title: RNA-SKBR3-GSK126

value: Breast adenocarcinoma

value: Cells plated at low density and  treated with EZH2 inhibitor GSK126 5uM for 14 days


title: SKM_D60

source_name: induced skeletal muscle Day 60

value: induced skeletal muscle Day 60


title: RNA-MCF7-EMT-D6-w-GSK126-R1


title: RNA-seq_P20_Spocd1-dSpin1_3

city: Edinburgh

first: Madeleine

last: Heep

address: 5 Little France Drive

department: MRC Centre for Regenerative Medicine

institute: University of Edinburgh

data_processing:
Adapter sequence 'AGATCGGAAGAGC' was removed from FASTQ files using cutadapt version 1.18 and reads less than 50 nts were discarded using option '-m 50'
Trimmed and filtered reads were mapped against consensus sequences of repetitive elements in Mus from RepBase 24.01 using bowtie2 2.4.2 with options '--qc-filter --no-unal'
The number of reads mapping to each consensus sequence were counted from column 2 of the SAM file using a custom Perl script
Assembly: mm10, RepBase 24.01
Supplementary files format and content: The processed data file is a tab-delimited text file containing RepBase 24.01 identifier, length, and counts in each sample of identified repetitive element transcripts

source_name: testis

extract_protocol:
RNA was extracted from one testis with Qiagen Rneasy Mini kit (Qiagen) with additional on-column Dnase treatment. rRNA depletion with NEBrRNA depletion kit v2.
Libraries were prepared with NEBNext Ultra II dDirectional RNA Library Prep Kit for Illumina (8 PCR cycles for amplification)

value: testis

value: mixed B6CBAF1/Crl; C57BL/6N

tag: developmental stage

value: Spocd1 dSpin/dSpin


title: SKM_D30

source_name: induced skeletal muscle Day 30

value: induced skeletal muscle Day 30


title: S12_SLX-17131.NEBNext14

description:
pKLV_NEBNXT13_1771
Single Read, 50bp

tag: treatment


title: S13_SLX-17131.NEBNext15

description:
pKLV_NEBNXT15_1773
Single Read, 50bp

value: Infected_Untreated (UT)_Sorted (S)_Round 1 (R1)_Bright GFP (B)


title: WT, control Replicate 1

source_name: Leaf

value: Leaf

value: control


title: S11_SLX-17131.NEBNext13

description:
pKLV_NEBNXT12_1770
Single Read, 50bp

value: Chinese Ovary cells (CHO-K1)

value: Infected_Untreated (UT)_Unsorted (US)


title: RNA-MDA-MB-231-GSK126


title: RNA-seq_P20_Spocd1-dSpin1_1


title: RNA-seq_P20_Spocd1-dSpin1_2


title: RNA-MDA-MB-231-Untreated

value: Cells plated at low density


title: RNA-seq_P20_wild-type_control_3

value: WT


title: S10_SLX-17131.NEBNext12

description:
pKLV_NEBNXT18_1775
Single Read, 50bp

value: Infected_Treated (T) with 2DG_Sorted (S)_Round 3 (R3)_Dull GFP_Right


title: Osteoblast

source_name: induced Osteoblast

value: induced Osteoblast


title: PDAC-003

city: Shanghai

first: Christopher

last: Heeschen

address: South Chongqing Road 227

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
10X Cell Ranger 5.0 pipeline was used for basecalling, demultiplexing, alignment and UMI quantification
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with UMI counts for every gene and every cell

source_name: PDAC patient-derived xenograph cell culture

extract_protocol: Libraries were prepared according to the 10x Chromium Single Cell 3ʹ Reagent Kits v3 with Feature Barcode technology for Cell Surface Protein protocol (CG000185).

treatment_protocol: CTRL, MCM and ETO were applied to PDAC-003; CTRL and MCM were applied to PDAC-002 and PDAC-021

value: PDAC patient-derived xenograph

value: ETO, MCM, CTRL treated, separately


title: Chondroblast

source_name: induced Chondroblast

value: induced Chondroblast


title: RNA-seq_P20_wild-type_control_2


title: S9_SLX-17131.NEBNext10

description:
pKLV_NEBNXT14_1772
Single Read, 50bp

value: Infected_Treated (T) with 2DG_Sorted (S)_Round 3 (R3)_Dull GFP_Up


title: Ventral prostate organoid, control, replicate 3

value: organoid

value: Ventral prostate


title: PDAC-002/PDAC-021

value: MCM, CTRL treated, separately


title: RNA-MCF7-Untreated

source_name: Breast adenocarcinoma

value: Breast adenocarcinoma


title: S8_SLX-17131.NEBNext09

description:
pKLV_NEBNXT10_1768
Single Read, 50bp

value: Infected_Treated (T) with 2DG_Sorted (S)_Round 3 (R3)_Dull GFP_Left


title: RNA-seq_P20_wild-type_control_1

value: testis

value: mixed B6CBAF1/Crl; C57BL/6N


title: WT_UiPSM_RNA-seq

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
Raw reads were trimmed with TrimGalore (v.0.6.4)
Reads were aligned to  hg38 ensembl v101 transcriptome using rsem (v1.3.1) and bowtie2 (v2.4.1) (—bowtie2—bowtie2-sensitivity-level very_sensitive— no-bam-output—estimate-rspd).
The gene expression level was calculated by using  RSEM
The gene expression was normalized using EDAseq on a basis of GC-content. RNA-seq data was expressed in units of GC-normalized tag counts.
Genome_build: hg38

source_name: UiPSM

tag: genotype/variation


title: RNA-SKBR3-Untreated


title: S7_SLX-17131.NEBNext07

description:
pKLV_NEBNXT06_1764
Single Read, 50bp

value: Chinese Ovary cells (CHO-K1)

value: Infected_Treated (T) with 2DG_Sorted (S)_Round 2 (R2)_Dull GFP (D)


title: breastmilk_donor5_scRNAseq

city: Utrecht

first: Elise

middle: S.

last: Saager

address: Lundlaan 6

department: Centre for Translational Immunology

country: Netherlands

institute: University Medical Centre Utrecht

data_processing:
files contain UMI-corrected counts data without further processing
Assembly: human reference genome GRCh38
Supplementary files format and content: mapped UMI-corrected counts

source_name: breastmilk

extract_protocol:
cells were sorted into 384-wells plates (Biorad) with 5 μl of vapor-lock (QIAGEN) containing 100-200 nl of RT primers, dNTPs and synthetic mRNA Spike-Ins. Plates were immediately spun down after sorting and frozen to −80°C. Cells were prepared for SORT-seq as previously described.
Illumina sequencing libraries were prepared with the TruSeq small RNA primers (Illumina) and sequenced paired-end at 75 basepair read length with 75.000 reads per cell on a NextSeq500 platform (Illumina). Sequencing reads were mapped against the reference human genome (GRCh38) with BWA

treatment_protocol: immune cell fraction was isolated from breastmilk and stained for FACS sorting, after which CD3+ live cells were sorted using FACS Aria III

value: breastmilk

value: CD3+ T cells

value: sorted from fresh untreated breastmilk


title: RNA-MCF7-EPZ6438-D12-R1

value: WT

value: Cells treated with EZH2 inhibitor EPZ-6438 2uM for 12 days


title: S6_SLX-17131.NEBNext06

description:
pKLV_NEBNXT07_1765
Single Read, 50bp

value: Infected_Treated (T) with 2DG_Sorted (S)_Round 2 (R2)__Dull GFP (D)_x3


title: breastmilk_donor6_scRNAseq


title: WT_H3K27ac_ChIP-seq

growth_protocol: UiPSM and CDX2-/- UiPSM cultured with a defined medium(DM),Advanced DMEM/F12 supplemented with 5nM A8301,10ng/ml bFGF, 5ng/ml EGF and 3uM CHIR99021

extract_protocol:
Tagmentation was performed for 1 hr in Dig-300 buffer and then fragmentated with 300µL tagmentation buffer incubated for 1 hr at TM. Extracted nucleic acid with phenolic chloroform and dissolved in 1xTE solution.
The nucleic acid samples suspension was amplificated 15-20 cycles with 50µL amplification mix (TAE, TAB and P5, P7 primer) (TD901, Vazyme), and purified using VAHTS DNA Clean Beads (N411, Vazyme)

treatment_protocol: CUT&Tag-direct was performed as described (Kaya-Okur et al., 2020). Libraries were prepared according to HyperactiveTM In-Situ ChIP Library Prep Kit for Illumina (TD901, Vazyme) Briefly, collected 100,000 cells profiled nuclei thawed, mixed with activated Concanavalin A beads, magnetized and resuspended in Wash buffer. After successive incubations with primary antibody (TM for 1–2 hr or 4℃ through the night) with Antibody Buffer and secondary antibody (0.5–1 hr) in Dig-wash buffer, the beads were washed and resuspended in pG-Tn5 at 12.5 nM in Dig-300 buffer for 1 hr at room temperature in low-retention PCR tubes.

tag: genotype/variations

value: UiPSM


title: S5_SLX-17131.NEBNext05

description:
pKLV_NEBNXT05_1763
Single Read, 50bp

value: Infected_Treated (T) with 2DG_Sorted (S)_Round 2 (R2)_Dull GFP (D)_x2


title: CDX2 -/-_H3K27ac_ChIP-seq

value: CDX2-/- UiPSM


title: RNA-MCF7-EPZ6438-D0-R2

value: Untreated


title: RNA-MCF7-EPZ6438-D0-R1


title: breastmilk_donor1_scRNAseq


title: RNA-MCF7-GSK126

value: Cells plated at low density and  treated with EZH2 inhibitor GSK126 5uM for 14 days


title: S3_SLX-17131.NEBNext03

description:
pKLV_NEBNXT02_1760
Single Read, 50bp

value: Infected_Treated (T) with 2DG_Sorted (S)_Round 1 (R1)_Dull GFP (B)


title: RNA-MCF7-GSK126-D12-R2

value: Breast adenocarcinoma

value: Cells treated with EZH2 inhibitor GSK126 5uM for 12 days


title: CDX2 -/-_CDX2_ChIP-seq


title: WT_CDX2_ChIP-seq


title: breastmilk_donor2_scRNAseq


title: breastmilk_donor3_scRNAseq


title: RNA-MCF7-EPZ6438-D12-R2


title: S1_SLX-17131.NEBNext01

description:
pKLV_NEBNXT01_1759
Single Read, 50bp

value: Infected_Treated (T) with 2DG_Unsorted (US)


title: S2_SLX-17131.NEBNext02

description:
pKLV_NEBNXT04_1762
Single Read, 50bp

value: Chinese Ovary cells (CHO-K1)

value: Infected_Treated (T) with 2DG_Unsorted (US)_x2


title: RNA-MCF7-D0-R2


title: RNA-MCF7-GSK126-D12-R1


title: breastmilk_donor4_scRNAseq

value: breastmilk


title: WT_ATAC-seq

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
Raw reads were trimmed with TrimGalore (v.0.6.4)
The data was mapped to human genome hg38 using bowtie22.
Low quality reads were filtered by SAMtools. Unique reads mapping to a single genomic location and strand were remained.  Mitochondrial sequences were removed using “grep –v ‘chrM’”.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig


title: CDX2 -/-_ATAC-seq


title: RNA-MCF7-D0-R1


title: CDX2 -/-_UiPSM_RNA-seq


title: S4_SLX-17131.NEBNext04

description:
pKLV_NEBNXT03_1761
Single Read, 50bp

value: Infected_Treated (T) with 2DG_Sorted (S)_Round 2 (R1)_Dull GFP (D)


title: breastmilk_donor7_scRNAseq

value: CD3+ T cells

value: sorted from fresh untreated breastmilk


title: 6D-4W-4-Co

status: Public on Jul 25 2024

city: Syracuse

first: Joel

last: Wilmore

address: 766 Irving Ave

department: Microbiology and Immunology

institute: SUNY Upstate Medical University

data_processing:
basecalling: Illumina basespace pipeline
pseudoalignment: Kallisto (param: -b 150  -l 300 -s 30 -t 16)
differential expression: Voom (normalization), and limma linear fit and Bayesian statistics for differential expression
all data display and additional statistics: R statistical environment
Assembly: mm10
Supplementary files format and content: Bfrag_RNAseq.normExp.txt: tab-delimited text. normalized expression (log2 TPM) for all samples and transcripts condensed to official gene symbol
Supplementary files format and content: Bfrag_RNAseq.rawTPM.txt: tab-delimited text. raw TPM for all samples and transcripts condensed to official gene symbol

source_name: mice treated with B. fragilis 6 times

growth_protocol: Mice were housed in sterile cages to maintain their microbiome as present when the mice were received from Jackson Labs.

extract_protocol:
RNA was extracted by dounce homoginization of the tissue followed by the standard Trizol RNA extraction protocol.
NEB Next Ultra II (DIrectional) with Poly A Selection

treatment_protocol: Mice were treated with 1x10^8 CFU of B. fragilis by oral gavage either 1 time (1D), 6 doses every 3rd day for 15 days (6D), or left naïve as a control (Ctrl). The mice were then euthanized at 2 or 4 weeks post treatment (2W or 4W).

value: colon


title: 6D-4W-3-Co


title: 6D-4W-2-Co


title: 1D-4W-4-Co

source_name: mice treated with B. fragilis 1 time


title: 1D-4W-3-Co


title: 6D-4W-1-Co


title: 1D-2W-4-Co


title: 1D-4W-1-Co


title: 1D-4W-2-Co


title: 1D-2W-3-Co


title: 1D-2W-2-Co


title: Ctrl-4-Co

source_name: control mice


title: 1D-2W-1-Co


title: Ctrl-3-Co


title: Ctrl-2-Co


title: Ctrl-1-Co


title: 6D-4W-2-Si

value: small intestine


title: 1D-4W-3-Si


title: 1D-4W-4-Si


title: 1D-2W-4-Si


title: 1D-4W-1-Si


title: 1D-2W-2-Si


title: Ctrl-4-Si


title: 6D-4W-4-Si


title: 1D-2W-3-Si


title: 1D-2W-1-Si


title: 6D-4W-3-Si


title: Ctrl-3-Si


title: Ctrl-2-Si


title: Ctrl-1-Si


title: KR52

first: Loris

last: De Cecco

address: via Venezian 1

institute: IRCSS Istituto Nazionale Tumori

description: OTU genus read count

data_processing:
*library strategy: AmpliSeq
QIIME 2
Assembly: COBS, minHash and pp_sketch indices are available from: ftp.ebi.ac.uk/pub/databases/ENA2018-bacteria-661k
Supplementary files format and content: raw_count.txt

organism: Bacteria

source_name: faeces

extract_protocol:
microbial DNA extraction using QIAsymphony DSP Virus/Pathogen Midi Kit
16S metagenomics ION (ThermoFisher)

value: faeces

tag: cohort

value: validation

tag: age

tag: bmi

tag: smoke

value: Smoker

tag: diabetes

value: Diabetes

tag: psa at_diagnosis_(ng/ml)

tag: clinical stage_at_diagnosis

tag: tumour risk_class

value: intermediate

tag: primary gps_at_diagnosis

tag: secondary gps_at_diagnosis

tag: prostatectomy

value: No prostatectomy

tag: appendectomy

value: No appendectomy

tag: rt technique

value: VMAT

tag: rt intent

value: Radical

tag: dose to_the_prostate_ptv_(gy)

tag: lymph node_irradiation

tag: semil vesicle_irradiation

tag: fraction number

tag: dose/fraction

tag: acute gi_toxicity

tag: mb risk_class

tag: mean dose_to_the_rectum_(gy)

tag: probiotics use

value: No

tag: physical activity_status

value: sedentary

tag: molecule subtype

value: microbial DNA


title: KR54

description: OTU genus read count

tag: tissue

tag: cohort

tag: age

tag: bmi

tag: smoke

value: Non smoker

tag: diabetes

value: No diabetes

tag: psa at_diagnosis_(ng/ml)

tag: clinical stage_at_diagnosis

tag: tumour risk_class

tag: primary gps_at_diagnosis

tag: animal based_diet

tag: plant based_diet


title: KR53

description: OTU genus read count

tag: secondary gps_at_diagnosis

tag: prostatectomy

value: Prostatectomy

tag: appendectomy

tag: rt technique

tag: rt intent

value: Adjuvant

tag: dose to_the_prostate_ptv_(gy)

tag: lymph node_irradiation

tag: semil vesicle_irradiation

tag: fraction number

tag: dose/fraction

tag: acute gi_toxicity

tag: mb risk_class


title: KR51

description: OTU genus read count

tag: tissue

tag: cohort

tag: age

tag: bmi

tag: smoke

tag: diabetes

tag: psa at_diagnosis_(ng/ml)

tag: clinical stage_at_diagnosis

tag: mean dose_to_the_rectum_(gy)

tag: probiotics use

tag: physical activity_status

tag: molecule subtype


title: 6D-4W-1-Si

value: small intestine


title: KR50

description: OTU genus read count

value: faeces

tag: primary gps_at_diagnosis

tag: secondary gps_at_diagnosis

tag: prostatectomy

tag: appendectomy

tag: rt technique

tag: rt intent

tag: dose to_the_prostate_ptv_(gy)

tag: lymph node_irradiation

tag: semil vesicle_irradiation

tag: animal based_diet

tag: plant based_diet

value: active


title: KR48

description: OTU genus read count

tag: tissue

tag: cohort

value: validation

tag: age

tag: bmi

tag: smoke

tag: diabetes

tag: psa at_diagnosis_(ng/ml)

tag: tumour risk_class

value: low

tag: fraction number

tag: dose/fraction

tag: acute gi_toxicity

tag: mb risk_class

value: Yes


title: KR47

description: OTU genus read count

value: Diabetes

tag: clinical stage_at_diagnosis

tag: prostatectomy

value: No prostatectomy

tag: appendectomy

tag: rt technique

tag: rt intent

value: Salvage

tag: dose to_the_prostate_ptv_(gy)

tag: mean dose_to_the_rectum_(gy)

tag: probiotics use

tag: physical activity_status

tag: molecule subtype


title: KR49

description: OTU genus read count

tag: tissue

tag: cohort

tag: age

tag: bmi

tag: smoke

tag: diabetes

value: Appendectomy

value: VMAT

tag: lymph node_irradiation

tag: semil vesicle_irradiation

tag: animal based_diet

tag: plant based_diet


title: KR46

description: OTU genus read count

tag: psa at_diagnosis_(ng/ml)

tag: clinical stage_at_diagnosis

tag: tumour risk_class

value: intermediate

tag: primary gps_at_diagnosis

tag: secondary gps_at_diagnosis

tag: prostatectomy

tag: appendectomy

value: No appendectomy

tag: rt technique

value: Radical

tag: fraction number

tag: dose/fraction

tag: acute gi_toxicity

tag: mb risk_class

value: No


title: KR44

description: OTU genus read count

tag: tissue

tag: cohort

tag: age

tag: bmi

tag: smoke

value: Smoker

tag: diabetes

value: No diabetes

value: very high

tag: rt intent

tag: dose to_the_prostate_ptv_(gy)

tag: mean dose_to_the_rectum_(gy)

tag: probiotics use

tag: physical activity_status

value: sedentary

tag: molecule subtype

value: microbial DNA


title: KR45

description: OTU genus read count

value: faeces

value: validation

tag: psa at_diagnosis_(ng/ml)

tag: clinical stage_at_diagnosis

tag: tumour risk_class

tag: prostatectomy

tag: appendectomy

tag: rt technique

tag: lymph node_irradiation

tag: semil vesicle_irradiation

value: undeclared


title: KR41

description: OTU genus read count

tag: tissue

tag: cohort

tag: age

tag: bmi

value: Non smoker

tag: fraction number

tag: dose/fraction

tag: acute gi_toxicity

tag: mb risk_class


title: KR40

description: OTU genus read count

tag: smoke

tag: diabetes

value: oligometastatic

value: No prostatectomy

tag: rt intent

value: Oligometastatic

tag: dose to_the_prostate_ptv_(gy)

tag: mean dose_to_the_rectum_(gy)

tag: probiotics use

tag: molecule subtype


title: KR38

description: OTU genus read count

tag: psa at_diagnosis_(ng/ml)

tag: clinical stage_at_diagnosis

tag: tumour risk_class

value: high

tag: prostatectomy

tag: appendectomy

value: Appendectomy

tag: rt technique

value: VMAT

tag: lymph node_irradiation


title: KR37

description: OTU genus read count

tag: tissue

tag: cohort

tag: age

tag: bmi

value: Radical

tag: semil vesicle_irradiation

tag: fraction number

tag: dose/fraction

tag: animal based_diet

tag: plant based_diet

value: Yes

tag: physical activity_status

value: active


title: KR36

description: OTU genus read count

tag: smoke

tag: diabetes

value: No diabetes

tag: psa at_diagnosis_(ng/ml)

value: intermediate

value: No appendectomy

tag: rt intent

tag: dose to_the_prostate_ptv_(gy)

tag: acute gi_toxicity

tag: mb risk_class

tag: mean dose_to_the_rectum_(gy)

tag: probiotics use

value: No

tag: molecule subtype


title: KR34

description: OTU genus read count

tag: tissue

value: faeces

tag: cohort

tag: age

tag: bmi

tag: clinical stage_at_diagnosis

value: Tx

tag: tumour risk_class

tag: prostatectomy

value: Prostatectomy

tag: appendectomy

tag: rt technique

value: Salvage

tag: lymph node_irradiation

value: sedentary

value: microbial DNA


title: KR35

description: OTU genus read count

value: validation

tag: smoke

value: Non smoker

tag: diabetes

tag: psa at_diagnosis_(ng/ml)

tag: primary gps_at_diagnosis

tag: secondary gps_at_diagnosis

value: No prostatectomy

tag: rt intent

tag: semil vesicle_irradiation

tag: fraction number

tag: dose/fraction

tag: physical activity_status


title: KR33

description: OTU genus read count

tag: tissue

tag: cohort

tag: age

tag: bmi

value: VMAT

tag: dose to_the_prostate_ptv_(gy)

tag: acute gi_toxicity

tag: mb risk_class

tag: mean dose_to_the_rectum_(gy)

tag: probiotics use

tag: molecule subtype


title: KR32

description: OTU genus read count

tag: smoke

tag: diabetes

tag: psa at_diagnosis_(ng/ml)

tag: clinical stage_at_diagnosis

tag: tumour risk_class

tag: prostatectomy

tag: appendectomy

tag: rt technique

value: Radical

tag: lymph node_irradiation

tag: animal based_diet

tag: plant based_diet


title: KN90

description: OTU genus read count

tag: tissue

tag: cohort

tag: age

tag: bmi

value: Diabetes

value: high

tag: primary gps_at_diagnosis

tag: secondary gps_at_diagnosis

tag: rt intent

tag: dose to_the_prostate_ptv_(gy)

tag: semil vesicle_irradiation

tag: fraction number

tag: dose/fraction

value: Yes

tag: physical activity_status


title: KN88

description: OTU genus read count

tag: smoke

value: Smoker

tag: diabetes

value: No diabetes

tag: psa at_diagnosis_(ng/ml)

tag: prostatectomy

tag: appendectomy

tag: acute gi_toxicity

tag: mb risk_class

tag: mean dose_to_the_rectum_(gy)

tag: probiotics use

tag: molecule subtype


title: KN89

description: OTU genus read count

tag: tissue

tag: cohort

tag: age

tag: bmi

tag: clinical stage_at_diagnosis

tag: tumour risk_class

value: very high

value: No appendectomy

tag: rt technique

tag: lymph node_irradiation

value: No

tag: animal based_diet

tag: plant based_diet

value: active


title: KN53

description: OTU genus read count

value: faeces

tag: smoke

tag: diabetes

tag: psa at_diagnosis_(ng/ml)

tag: primary gps_at_diagnosis

tag: secondary gps_at_diagnosis

tag: prostatectomy

tag: rt intent

tag: dose to_the_prostate_ptv_(gy)

tag: semil vesicle_irradiation

tag: fraction number

tag: dose/fraction

tag: physical activity_status


title: KN52

description: OTU genus read count

tag: tissue

tag: cohort

tag: age

tag: bmi

tag: clinical stage_at_diagnosis

tag: tumour risk_class

value: low

tag: appendectomy

tag: acute gi_toxicity

tag: mb risk_class

tag: mean dose_to_the_rectum_(gy)

tag: probiotics use

value: sedentary

tag: molecule subtype


title: KG50

description: OTU genus read count

value: validation

tag: smoke

tag: diabetes

tag: psa at_diagnosis_(ng/ml)

tag: primary gps_at_diagnosis

tag: secondary gps_at_diagnosis

tag: prostatectomy

value: Appendectomy

tag: rt technique

tag: rt intent

tag: dose to_the_prostate_ptv_(gy)

tag: lymph node_irradiation

tag: animal based_diet

tag: plant based_diet

value: microbial DNA


title: KG47

description: OTU genus read count

tag: tissue

tag: cohort

tag: age

tag: bmi

tag: clinical stage_at_diagnosis

tag: tumour risk_class

value: intermediate

value: No prostatectomy

tag: appendectomy

value: VMAT

tag: semil vesicle_irradiation

tag: fraction number

tag: dose/fraction

tag: acute gi_toxicity

tag: physical activity_status


title: KN51

description: OTU genus read count

tag: smoke

value: Non smoker

tag: diabetes

tag: psa at_diagnosis_(ng/ml)

tag: primary gps_at_diagnosis

tag: secondary gps_at_diagnosis

tag: prostatectomy

tag: rt technique

tag: rt intent

value: Radical

tag: mb risk_class

tag: mean dose_to_the_rectum_(gy)

tag: probiotics use

tag: molecule subtype


title: KG49

description: OTU genus read count

tag: tissue

tag: cohort

tag: age

tag: bmi

tag: clinical stage_at_diagnosis

tag: tumour risk_class

value: high

tag: appendectomy

tag: dose to_the_prostate_ptv_(gy)

tag: lymph node_irradiation

tag: semil vesicle_irradiation

value: Yes

tag: animal based_diet

tag: plant based_diet


title: KG46

description: OTU genus read count

tag: smoke

value: Smoker

tag: diabetes

value: No diabetes

tag: psa at_diagnosis_(ng/ml)

tag: prostatectomy

value: Prostatectomy

tag: rt technique

tag: rt intent

value: Salvage

tag: fraction number

tag: dose/fraction

tag: acute gi_toxicity


title: KG45

description: OTU genus read count

tag: tissue

value: faeces

tag: cohort

tag: age

tag: bmi

tag: clinical stage_at_diagnosis

tag: mb risk_class

tag: mean dose_to_the_rectum_(gy)

tag: probiotics use

value: No

tag: physical activity_status

tag: molecule subtype


title: KG43

description: OTU genus read count

tag: smoke

tag: diabetes

tag: psa at_diagnosis_(ng/ml)

tag: tumour risk_class

tag: primary gps_at_diagnosis

tag: secondary gps_at_diagnosis

tag: appendectomy

value: No appendectomy

tag: dose to_the_prostate_ptv_(gy)

tag: lymph node_irradiation

tag: semil vesicle_irradiation

value: active


title: KG29

description: OTU genus read count

tag: tissue

tag: cohort

value: validation

tag: age

tag: bmi

tag: prostatectomy

tag: rt technique

tag: rt intent

tag: fraction number

tag: dose/fraction

tag: acute gi_toxicity


title: KG28

description: OTU genus read count

tag: smoke

tag: diabetes

value: Diabetes

tag: psa at_diagnosis_(ng/ml)

tag: clinical stage_at_diagnosis

tag: tumour risk_class

tag: mb risk_class

tag: mean dose_to_the_rectum_(gy)

tag: probiotics use

tag: physical activity_status

value: sedentary

tag: molecule subtype

value: microbial DNA


title: KG44

description: OTU genus read count

tag: tissue

tag: cohort

tag: age

tag: bmi

value: No prostatectomy

tag: appendectomy

value: VMAT

tag: dose to_the_prostate_ptv_(gy)

tag: lymph node_irradiation

tag: semil vesicle_irradiation


title: KG25

description: OTU genus read count

tag: smoke

value: Non smoker

tag: diabetes

tag: primary gps_at_diagnosis

tag: secondary gps_at_diagnosis

tag: prostatectomy

tag: rt technique

tag: rt intent

tag: fraction number

tag: dose/fraction

tag: acute gi_toxicity

tag: animal based_diet

tag: plant based_diet

value: undeclared


title: KG27

description: OTU genus read count

tag: tissue

tag: cohort

tag: age

tag: bmi

tag: psa at_diagnosis_(ng/ml)

tag: clinical stage_at_diagnosis

tag: tumour risk_class

value: high

value: Radical

tag: mb risk_class

tag: mean dose_to_the_rectum_(gy)

tag: probiotics use

tag: physical activity_status

tag: molecule subtype


title: KG23

description: OTU genus read count

tag: smoke

tag: diabetes

tag: primary gps_at_diagnosis

tag: secondary gps_at_diagnosis

tag: prostatectomy

tag: appendectomy

value: Appendectomy

tag: rt technique

tag: rt intent

tag: dose to_the_prostate_ptv_(gy)

tag: lymph node_irradiation

tag: semil vesicle_irradiation

tag: fraction number


title: KG24

description: OTU genus read count

tag: tissue

tag: cohort

tag: age

tag: bmi

value: Smoker

value: No diabetes

tag: psa at_diagnosis_(ng/ml)

tag: clinical stage_at_diagnosis

tag: tumour risk_class

value: intermediate

tag: dose/fraction

tag: acute gi_toxicity

tag: mb risk_class


title: KG20

description: OTU genus read count

value: faeces

tag: smoke

tag: diabetes

tag: primary gps_at_diagnosis

tag: secondary gps_at_diagnosis

tag: prostatectomy

tag: appendectomy

tag: mean dose_to_the_rectum_(gy)

tag: probiotics use

value: No

tag: physical activity_status

tag: molecule subtype


title: KG19

description: OTU genus read count

tag: tissue

tag: cohort

tag: age

tag: bmi

value: low

value: No appendectomy

tag: rt technique

tag: rt intent

tag: dose to_the_prostate_ptv_(gy)

tag: lymph node_irradiation

tag: semil vesicle_irradiation

tag: fraction number


title: KG22

description: OTU genus read count

value: validation

tag: smoke

tag: diabetes

tag: psa at_diagnosis_(ng/ml)

tag: clinical stage_at_diagnosis

tag: tumour risk_class

tag: primary gps_at_diagnosis

tag: secondary gps_at_diagnosis

tag: dose/fraction

tag: acute gi_toxicity

tag: mb risk_class

tag: animal based_diet

tag: plant based_diet


title: KG18

description: OTU genus read count

tag: tissue

tag: cohort

tag: age

tag: bmi

value: very low

tag: prostatectomy

tag: appendectomy

tag: rt technique

tag: rt intent

tag: mean dose_to_the_rectum_(gy)

tag: probiotics use

tag: physical activity_status

tag: molecule subtype


title: KR31

description: OTU genus read count

tag: smoke

tag: diabetes

tag: psa at_diagnosis_(ng/ml)

tag: clinical stage_at_diagnosis

tag: tumour risk_class

tag: dose to_the_prostate_ptv_(gy)

tag: lymph node_irradiation

tag: semil vesicle_irradiation

tag: fraction number

tag: dose/fraction

value: Yes

value: sedentary

value: microbial DNA


title: KG17

description: OTU genus read count

tag: tissue

tag: cohort

tag: age

tag: bmi

value: Non smoker

tag: primary gps_at_diagnosis

tag: secondary gps_at_diagnosis

tag: prostatectomy

value: Prostatectomy

tag: appendectomy

value: VMAT

value: Salvage

tag: acute gi_toxicity

tag: mb risk_class

value: active


title: JN39

description: OTU genus read count

tag: smoke

value: Smoker

tag: diabetes

value: Diabetes

tag: psa at_diagnosis_(ng/ml)

tag: clinical stage_at_diagnosis

value: high

tag: rt technique

tag: rt intent

tag: mean dose_to_the_rectum_(gy)

tag: probiotics use

tag: physical activity_status

tag: molecule subtype


title: JN38

description: OTU genus read count

tag: tissue

value: faeces

tag: cohort

tag: age

tag: bmi

value: No diabetes

tag: tumour risk_class

value: oligometastatic

value: No prostatectomy

value: Appendectomy

value: Oligometastatic

tag: dose to_the_prostate_ptv_(gy)

tag: lymph node_irradiation

tag: semil vesicle_irradiation

tag: fraction number

tag: dose/fraction

tag: animal based_diet

tag: plant based_diet

value: undeclared


title: JN37

description: OTU genus read count

value: validation

tag: smoke

tag: diabetes

tag: psa at_diagnosis_(ng/ml)

tag: clinical stage_at_diagnosis

value: very low

tag: prostatectomy

tag: appendectomy

value: No appendectomy

tag: rt technique

tag: rt intent

value: Radical

tag: acute gi_toxicity

tag: mb risk_class

value: No

value: Yes


title: KG48

description: OTU genus read count

tag: tissue

tag: cohort

tag: age

tag: bmi

tag: tumour risk_class

value: VMAT

tag: dose to_the_prostate_ptv_(gy)

tag: mean dose_to_the_rectum_(gy)

tag: probiotics use

tag: physical activity_status

value: sedentary

tag: molecule subtype

value: microbial DNA