title: SlyD-WT-3

value: SlyD WT

value: treated with H. pylori 26695


title: P10KOF_3_544

status: Public on Nov 26 2024

type: SRA

city: Worcester

first: Gregory

last: Pazour

state: MA

address: 373 Plantation St.

department: Program in Molecular Medicine

country: USA

institute: UMass Chan School of Medicine

description:
p10_kallisto_count_data_genes_expression_expected_count.csv
deseq2_p10WTKO_alldetected.csv

library_source: transcriptomic

data_processing:
DolphinNext RNA-seq Pipeline
Read quality was assessed using FastQC (v0.11.8)
Transcript abundance was estimated based on pseudoalignments using Kallisto (v0.46.0)
Differential gene expression analysis was performed in DEBrowser (v1.19.0) using DESeq2. Low count filtering by counts per million (cpm) >2 in 19/20 samples (Day 10) or >2 in 27/28 samples (Day 6)
Assembly: mm10
Supplementary files format and content: comma-separated text files include raw transcript abundances from kallisto pseudoalignment for each sample
Supplementary files format and content: comma-separated text files include gene expression normalized counts using median of ratios and differential expression analysis performed using DESeq2

molecule: total RNA

organism: Mus musculus

source_name: KO

growth_protocol: C5/BL6 background. Experimental "KO" were CAGG-CreER; Pkd2null/flox. Control "WT" were CAGG-CreER; Pkd2+/flox and Cre-negative; Pkd2null/flox.

extract_protocol:
RNA was harvested using Rneasy mini kit with on-column DNA digestion (Qiagen). RNA samples were submitted to BGI for library preparation.
RNA sequencing libraries were prepared by BGI according to manufacturer's protocols.

treatment_protocol:
All animals underwent intraperitoneal injection of tamoxifen in canola oil on postndatal day 2.
Mice were sacrificed and bilateral kidneys collected for RNA extraction at the designated time points.

tag: tissue

value: whole kidney

tag: postnatal age

value: Day 10

tag: genotype

value: CAGG-CreER; Pkd2null/flox

tag: strain

tag: Sex

value: F


title: SlyD-WT-2

city: Shenyang

first: Shuwen

last: Zheng

state: --- Select One ---

address: No.155 NanjingBei Street, Heping District

country: China

institute: the First Hospital of China Medical University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp (version 0.23.4) (parameter arsg: -l 39 --dont_eval_duplication  --qualified_quality_phred 20 --unqualified_percent_limit 8 --adapter_sequence  --adapter_sequence_r2  --fix_mgi_id)
Trimmed reads were mapped to GRCh38 using STAR software (version 2.5.3a) (parameters- --outSAMtype BAM SortedByCoordinate)
Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter -T 10 -d 30 -D 1000 -C -s 1 -t {exon} -g {geneid} --primary -O -a {gff_annotation_file}）
Assembly: GRCh38
Supplementary files format and content: Excel file includes RPKM values for each Sample

organism: Homo sapiens

source_name: AGS

growth_protocol: All H. pylori strains were cultured under microaerobic conditions at 37°C on brain-heart infusion plates supplemented with 10% defibrillated sheep blood.

extract_protocol:
RNA was harvested using TRIzol Reagent (Invitrogen, cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following manufacturer's protocols.

treatment_protocol: The AGS cells were treated with H. pylori 26695 and ΔSlyD for 24h at a multiplicity of infection (MOI) = 100, respectively.

tag: cell line

value: AGS

tag: cell type

value: gastric cancer cell

tag: treatment


title: Tumor_only, Cell_line_B, timepoint_1, EXP_9.6, rep_2

city: Vienna

first: CCRI

last: BiCU

address: Zimmermannpl. 10

department: Bioinformatics Core Unit

country: Austria

institute: St. Anna Children's Cancer Research Institute

data_processing:
Reads were mapped to a genome assembly using STAR (v2.7.10a).
Reads counting was performed with the help of Salmon (v1.8.0) or GenomicAlignments (v1.36.0)
Assembly: GRCm38/GRCh38
Supplementary files format and content: quant.sf files contain counted reads
Supplementary files format and content: tsv files contain counted reads performed by GenomicAlignments package

source_name: B

extract_protocol:
Extraction was done with the AllPrep DNA/RNA Mini Kit (Qiagen) and samples were treated with DNase I (Thermo Fisher Scientific) or the Monarch Total RNA Miniprep Kit (New England Biolabs)
QuantSeq 3‘ mRNA-Seq Library Prep Kit (FWD) for Illumina (Lexogen)

value: B

tag: time

value: Day 4

tag: time point

tag: genome assembly_used


title: Tumor_only, Cell_line_B, timepoint_1, EXP_9.6, rep_3


title: Tumor_only, Cell_line_C, timepoint_1, EXP_9.6, rep_1

source_name: C

value: C


title: Tumor_only, Cell_line_B, timepoint_1, EXP_9.6, rep_1


title: SlyD-WT-1


title: LY6A overexpressed, Experiment 2, Cell line K562, rep_3

value: LY6A OE2

value: LY6A overexpressed


title: P10KOF_2_578


title: Tumor_plus_NK, Cell_line_D, timepoint_2, EXP_9.5, rep_3

source_name: D

value: D


title: P06KOM_14_564

description:
p06_kallisto_count_data_genes_expression_expected_count.csv
deseq2_p06WTKO_alldetected.csv

value: Day 6

value: M


title: Tumor_only, Cell_line_A, timepoint_1, EXP_9.6, rep_1

source_name: A

value: A


title: P06KOM_13_558


title: Tumor_plus_NK, Cell_line_D, timepoint_2, EXP_9.5, rep_1


title: P10KOF_1_576


title: Tumor_only, Cell_line_A, timepoint_1, EXP_9.6, rep_3


title: Tumor_plus_NK, Cell_line_C, timepoint_2, EXP_9.5, rep_3


title: Tumor_plus_NK, Cell_line_D, timepoint_2, EXP_9.5, rep_2


title: LY6A overexpressed, Experiment 2, Cell line K562, rep_2


title: LY6A overexpressed, Experiment 1, Cell line K562, rep_3

value: LY6A OE1


title: P06KOM_11_568


title: Tumor_plus_NK, Cell_line_B, timepoint_2, EXP_9.5, rep_2


title: LY6A overexpressed, Experiment 2, Cell line K562, rep_1


title: LY6A overexpressed, Experiment 1, Cell line K562, rep_2


title: Tumor_plus_NK, Cell_line_B, timepoint_2, EXP_9.5, rep_1


title: P06KOM_12_581


title: Tumor_plus_NK, Cell_line_C, timepoint_2, EXP_9.5, rep_2


title: Tumor_plus_NK, Cell_line_B, timepoint_2, EXP_9.5, rep_3


title: Tumor_plus_NK, Cell_line_A, timepoint_2, EXP_9.5, rep_1


title: Tumor_plus_NK, Cell_line_A, timepoint_2, EXP_9.5, rep_3


title: P06KOM_10_591


title: P06KOM_8_563


title: LY6A Empty Vector - control, Experiment 2, Cell line K562, rep_3

value: LY6A EV2

value: LY6A Empty Vector - control


title: Tumor_only, Cell_line_A, timepoint_1, EXP_9.6, rep_2


title: LY6A overexpressed, Experiment 1, Cell line K562, rep_1


title: Tumor_plus_NK, Cell_line_A, timepoint_2, EXP_9.5, rep_2

value: Day 10


title: P06KOM_9_590

value: whole kidney

value: CAGG-CreER; Pkd2null/flox


title: Tumor_plus_NK, Cell_line_C, timepoint_2, EXP_9.5, rep_1


title: P06KOF_7_545

value: F


title: Tumor_plus_NK, Cell_line_D, timepoint_1, EXP_9.5, rep_2


title: LY6A Empty Vector - control, Experiment 2, Cell line K562, rep_2


title: 69

city: Moscow

first: Vasiliy

last: Akimov

email: VAkimov@cspfmba.ru, vasoakim@gmail.com

address: Pogodinskaya Street, 10, bld. 1

country: Russia

institute: Centre for Strategic Planning of FMBA of Russia

description:
Library name: 69
10x Genomics 3' v3

library_source: genomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger ATAC 1.2.0 pipeline (10x Genomics, Inc.)
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

molecule: genomic DNA

source_name: PBMC

extract_protocol:
The research materials were samples of nuclei isolated from PBMC cell suspensions. Nuclei were isolated using the following method: cells were pelleted and resuspended in 100 μl of lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1% Nonidet P40 Substitute, 0.01% Digitonin, 1% BSA, nuclease-free water), incubated for 5 min and added 1 ml of wash buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 1% BSA, nuclease-free water) , the nuclei were precipitated for 5 min at 500 rcf at a temperature of 4°C, then resuspended in the prepared Diluted Nuclei Buffer. Nuclear quality control was carried out using a Countess II FL counter and cell viability analyzer and an EVOS M7000 microscope.
For sample preparation of libraries, nuclei were used that met the requirements of the protocol. The sample of nuclei under study was added to the prepared Transposition Mix, 10 μl per sample. The volume of the sample was calculated based on the concentration of nuclei using the formula (10000*1.53)/n = x, where n is the concentration of nuclei in the sample, x is the required volume of the sample. The mixture was incubated for 60 min at 37°C. Next, 60 μl of the prepared Master Mix was added to the samples, mixed using an automatic dispenser 10 times and applied to the chip to generate an emulsion. Afterwards, gel particles and oil were applied to the chip. The loaded chip was processed at The Chromium Controller station. The resulting emulsion was amplified. After amplification, the emulsion was purified: 125 μl of Recovery Agent was added to each sample, the tubes with the mixture were carefully inverted 10 times, then briefly centrifuged and 130 μl of the lower pink phase was collected; This was followed by cleaning with magnetic Dynabeads MyOne SILANE and then cleaning with Beckman Coulter SPRIselect Reagent magnetic particles. After purifications, indexing PCR was performed. For it, we used Single Index Kit N Set A for one-way indexing. To 40 μl of sample, 57.5 μl of the prepared Sample Index PCR Mix and 2.5 μl of index were added. The number of cycles in the indexing PCR was set to 9. After indexing, the samples were subjected to double purification on magnetic particles and the quality of the resulting libraries was controlled using a Tape Station 4200 with a High Sensitivity D1000 kit, an Agilent Bioanalyzer 2100 with a High Sensitivity DNA chip kit, and a Qubit 4 fluorimeter. Ready-made libraries sequenced to a coverage of >250 million reads per sample.

value: PBMC

value: female

tag: age

tag: disease state

value: Mild/Moderate


title: LY6A Empty Vector - control, Experiment 2, Cell line K562, rep_1


title: DF_3

city: Bad Nauheim

first: Carsten

last: Kuenne

address: Ludwigstrasse 43

department: Bioinformatics

country: Germany

institute: Max Planck Institute for Heart and Lung Research

library_source: genomic

data_processing:
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data).
Reads were aligned versus human genome version hg38 (Ensembl release 104) with STAR 2.7.10a (Dobin et al., STAR: ultrafast universal RNA-seq aligner).
Alignments were filtered to remove: duplicates with Picard 2.25.5 (Picard: A set of tools (in Java) for working with next generation sequencing data in the BAM format), spliced, multi-mapping, ribosomal, or mitochondrial reads.
Peak calling was performed with Macs version 3.0.0a6 with FDR < 0.0001 (Zhang et al., Model-based Analysis of ChIP-Seq).
Peaks overlapping ENCODE blacklisted regions (known misassemblies, satellite repeats) were excluded.
Remaining peaks were unified to represent a common set of regions for all samples and counts were produced with featureCounts (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features).
The raw count matrix was normalized with DESeq2 version 1.30.1 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2).
Peaks were annotated with the promoter (TSS +- 5000 nt) of the nearest gene based on Ensembl release 104.
Assembly: hg38
Supplementary files format and content: The tab-delimited matrix shows DESeq normalized counts of unified peaks.

source_name: umbilical cord

extract_protocol:
In brief, 50,000 cells were centrifuged at 500g for 5 min at 4°C and washed with PBS.
The Cell pellet was resuspended in 50µl Lysis/Transposition reaction (12.5µl THS-TD-Buffer, 2.5µl Tn5, 5µl 0.1% Digitonin and 30µl water) and incubated at 37°C for 30min with occasional snap mixing. Following purification of the DNA fragments was done by MinElute PCR Purification Kit (Qiagen). Amplification of Library together with Indexing Primers was performed as described elsewhere (Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. (2013) Jason D Buenrostro, Paul G Giresi, Lisa C Zaba, Howard Y Chang & William J Greenleaf. Nature Methods. doi:10.1038/nmeth.2688). Libraries were mixed in equimolar ratios and sequenced (Illumina).

value: umbilical cord

value: HUAEC

value: Human Umbilical Artery Endothelial Cells

value: Healthy

tag: sirna

value: CTRL

tag: flow

value: Disturbed Flow


title: LY6A Empty Vector - control, Experiment 1, Cell line K562, rep_3

value: LY6A EV1


title: Tumor_plus_NK, Cell_line_D, timepoint_1, EXP_9.5, rep_3

value: D

value: Day 4


title: LY6A Empty Vector - control, Experiment 1, Cell line K562, rep_2

value: LY6A Empty Vector - control


title: DF_2


title: P06KOF_6_589

value: Day 6


title: Tumor_plus_NK, Cell_line_D, timepoint_1, EXP_9.5, rep_1


title: Tumor_plus_NK, Cell_line_C, timepoint_1, EXP_9.5, rep_3

value: C


title: DF_1


title: P06KOF_4_587

value: whole kidney

value: CAGG-CreER; Pkd2null/flox


title: LY6A Empty Vector - control, Experiment 1, Cell line K562, rep_1


title: Tumor_plus_NK, Cell_line_C, timepoint_1, EXP_9.5, rep_2


title: Tumor_plus_NK, Cell_line_C, timepoint_1, EXP_9.5, rep_1


title: Static_2

value: Static


title: 567

description:
Library name: 567
10x Genomics 3' v3

value: PBMC

value: female

value: Severe/Critical


title: KO_LY6E, clone 2, rep_2

value: Ly6a KO; clone 2


title: Static_3

value: umbilical cord

value: HUAEC

value: Human Umbilical Artery Endothelial Cells


title: P06KOF_3_585

value: F


title: KO_LY6E, clone 2, rep_1


title: P06KOF_2_571


title: Static_1

value: Healthy

value: CTRL


title: Tumor_plus_NK, Cell_line_B, timepoint_1, EXP_9.5, rep_3

value: B

value: Day 4


title: P06KOF_1_566

value: Day 6


title: P06KOF_5_588


title: Tumor_plus_NK, Cell_line_B, timepoint_1, EXP_9.5, rep_2


title: Tumor_plus_NK, Cell_line_B, timepoint_1, EXP_9.5, rep_1


title: P10WTM_10_561

source_name: WT

value: Day 10

value: Cre-negative; Pkd2null/flox

value: M


title: KO_LY6E, clone 1, rep_3

value: Ly6a KO; clone 1


title: SupT1 mock, DisomeSeq, cyclo, 0hpi, rep1

city: Würzburg

first: Neva

last: Caliskan

address: Josef-Schneider-Str. 2/D15

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

data_processing:
For PRICE analysis: (1) remove adapters cutadapt -a AGATCGGAAGAGCACACG -e 0.3 (2)  filter out short reads gedi -e FastqFilter -layout 2UI5U151 -min 18 (3) h.rRNA and mycoplasma removal  bowtie2 -un un --local -U (4) mapping reads STAR --runMode alignReads --alignIntronMax 1  --outSAMmode NoQS --outSAMtype BAM SortedByCoordinate --alignEndsType Extend5pOfRead1 --outSAMattributes nM MD NH (5) Convert BAM to CIT gedi -e BAM2CIT -umi (6) gedi -e CorrectCIT (7) deduplicate UMIs gedi -e DedupUMI (8) gedi -e MergeCIT (9) create report gedi -e Stats (10) P-site calling gedi -e Price
cutadapt 3.5, bowtie2 version 2.3.0, STAR version=2.7.10b, Gedi version 1.0.6, Price version 1.0.4
For differential gene expression analysis: (1) Count reads per genomic feature featureCounts -O (2) normalization and log2 fold change calculations by deltaTE/DTEG.R
featureCounts version 2.0.0, deltaTE (Chothani et al. 2019)
Assembly: GCF_000001405.36, AF324493
Supplementary files format and content: The PRICE codons BED files contain the genomic regions corresponding to predicted P-sites for each RiboSeq read. The "score" column equals to the read coverage at this position.
Supplementary files format and content: The countMatrix CSV files contain the read counts overlapping each genomic feature for every time point of infection for either cyclo RiboSeq or RNASeq.
Supplementary files format and content: The deltaTE text files contain the log2 fold changes (plus statistics) for each genomic feature, normalized by DESeq2 and calculated for each timepoint of infection against the 0h mock sample. This includes RiboSeq changes, RNASeq changes and  translation efficiency (TE) changes.
Supplementary files format and content: The DisomeSeq BED files contain the DisomeSeq reads that map to the HIV genome. The DisomeSeq text files contain the summed coverage per nucleotide for the HIV genome (column1: chromosome identifier; column2: genome position, column3: read coverage).
Supplementary files format and content: PRICE_report_harr_cyclo.tar contains quality control information for the RiboSeq PRICE pipeline, for both the cycloheximide and harringtonine treated samples. The index.html file allows interactive browsing through the different plots.
Supplementary files format and content: PRICE_report_disome.tar contains quality control information for the DisomeSeq PRICE pipeline. The index.html file allows interactive browsing through the different plots. Note that the p-site prediction is not valid for the DisomeSeq.
Supplementary files format and content: interactive_dTE_volcano_plots_DGE.tar contains interactive volcanoplots (translation efficiency) of the differential gene expression analysis with the deltaTE pipeline. Each infection timepoint was compared to the mock sample. Genes exceeding +/- 1 fold change and p_adj < 0.05 are colored based on consolidated gene ontology.
Supplementary files format and content: interactive_deltaTE_plots_DGE.tar contains interactive RiboSeq/RNASeq log2 fold change plots, of the differential gene expression analysis with the deltaTE pipeline. Each infection timepoint was compared to the mock sample. Only genes that are labelled as differentially expressed are plotted.
Library strategy: Ribo-seq

molecule: cytoplasmic RNA

growth_protocol: SupT1 cells (NIH HIV Reagent Program, Division of AIDS, NIAID, NIH: Sup-T1 Cells, ARP-100, contributed by Dr. Dharam Ablashi) were maintained in RPMI (Gibco) supplemented 10% FBS (Gibco), 1X L-Glutamine (Gibco), 100 μg/ml streptomycin and 100 U/ml penicillin. Cell lines were maintained at 37°C with 5% CO2.

extract_protocol:
Ribosome profiling samples were prepared as previously described (McGlincy and Ingolia., 2017) with modifications for suspension cell lines. Briefly, at each time point of infection, cells were treated with 100 μg/ml cycloheximide in DMSO at 37 °C for 5 min. For harringtonine treated samples, cells were treated with 2 μg/ml harringtonine in DMSO at 37 °C for 5 min, followed by cycloheximide treatment. Cells were immediately pelleted at 1000 RPM for 3 min at 4 °C, washed once with cold cycloheximide containing PBS and the cell pellet was snap-frozen in liquid nitrogen and stored at -80 °C, till further use. Cell pellet was thawed in the presence of ice-cold lysis buffer (20 mM Tris-Cl pH7.4, 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 100 μg/ml cycloheximide, 1% Triton-X, 25U/ml Turbo DNase ) and triturated 10 times through a 26G needle. The lysate was centrifuged at 17000g for 10 min at 4 °C and the supernatant was recovered. Cell lysates were subjected to RiboSeq and RNASeq.
RiboSeq libraries: RNase I footprinting of ribosomes, ribosome purification by ultracentrifugation through a sucrose cushion, RNA extraction, polyacrylamide gel size selection for footprint fragments, preadenylylated linker ligation, reverse transcription, first-strand cDNA circularization. RNASeq libraries from these samples were constructed using CORALL Total RNA-Seq Library Prep Kit (Lexogen), according to manufacturer’s instructions.

treatment_protocol: For ribosome, disome and polysome profiling experiments, SupT1 cells were either mock treated (with PBS) or infected with 50 µl of virus suspension per 40 million cells by spinoculation at 1500 g for 30 min at 37 °C, in presence of 8 µg/ml polybrene (Sigma). Cells were pelleted at 1000 RPM for 3 min at 37 °C, washed once with warm media, resuspended in 40 ml RPMI medium and incubated at 37 °C.

value: T-cell

value: cycloheximide


title: P10WTF_7_560

value: whole kidney

value: CAGG-CreER; Pkd2+/flox


title: P10WTM_9_550


title: WT_LY6E, clone 2, rep_3

value: WT; clone 2


title: Tumor_plus_NK, Cell_line_A, timepoint_1, EXP_9.5, rep_1

value: A


title: SupT1 mock, RiboSeq, harr, 0hpi, rep2

value: harringtonine


title: KO_LY6E,  clone 1, rep_1


title: KO_LY6E, clone 2, rep_3

value: Ly6a KO; clone 2


title: P10WTM_8_548


title: Tumor_only, Cell_line_D, timepoint_1, EXP_9.5, rep_3

value: D


title: SupT1 mock, RiboSeq, cyclo, 0hpi, rep2


title: SupT1 mock, RiboSeq, cyclo, 0hpi, rep1


title: SupT1 mock, DisomeSeq, cyclo, 0hpi, rep2


title: P10WTF_6_552

value: F


title: P10WTF_5_582


title: WT_LY6E, clone 2, rep_2


title: Tumor_plus_NK, Cell_line_A, timepoint_1, EXP_9.5, rep_3


title: WT_LY6E,  clone 1, rep_3

value: WT; clone 1


title: P10WTF_4_579


title: KO_LY6E, clone 1,  rep_2


title: WT_LY6E, clone 2, rep_1


title: Tumor_only, Cell_line_D, timepoint_1, EXP_9.5, rep_1

value: Day 4


title: SupT1 mock, RiboSeq, harr, 0hpi, rep1


title: Tumor_plus_NK, Cell_line_A, timepoint_1, EXP_9.5, rep_2


title: WT_LY6E, clone 1, rep_1


title: P10WTF_3_595


title: WT_LY6E,  clone 1, rep_2


title: Tumor_only, Cell_line_C, timepoint_1, EXP_9.5, rep_3

value: C


title: Tumor_only, Cell_line_C, timepoint_1, EXP_9.5, rep_1


title: K562 35Ab 500K

city: Pasadena

first: Isabel

last: Goronzy

state: CA

address: 1200 E California Blvd

department: Biology and Biological Engineering

institute: California Institute of Technology

description: NextSeq2000, NovaSeq6000

data_processing:
Adapters were trimmed from raw paired-end fastq files using Trim Galore! v0.6.2 and assessed with Fastqc v0.11.9. The split-and-pool barcodes of trimmed reads were identified from Read 2 with Barcode ID v1.2.0 (https://github.com/GuttmanLab/sprite2.0-pipeline) and the ligation efficiency is assessed. Reads with a DPM barcode or an antibody-identifying oligonucleotide sequence were split into two separate files. Subsequently, the DPM and antibody-identifying oligonucleotide sequences are trimmed using Cutadapt v2.5 from the 5’ end of Read 1.
DNA reads were aligned to mm10 or hg38 using Bowtie2 v2.3.5, filtering out unmapped reads and reads with a low MapQ score (samtools view -bq 20).  Reads intersecting ENCODE blacklisted regions were filtered out using Bedtools v2.29.0.
Antibody-identifying oligonucleotide reads and mapped DNA reads were merged to generate a cluster file for all downstream analysis. MultiQC v1.6 was used to aggregate all reports.
Each cluster in the cluster file was assigned to a single antibody based on the antibody-identifying oligonucleotide reads within the cluster (minimum reads > 2, minimum proportion > 0.8). All DNA reads corresponding to clusters assigned to the same antibody were collected into a single alignment file.
Bigwig files were generated from individual antibody DNA alignment files using deeptools v3.4.3
Assembly: mm10, hg38
Supplementary files format and content: Bigwig

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After cell lysis, chromatin was sonicated using a Branson needle-tip sonicator.
Prior to immunoprecipitation, Protein G beads were coupled with unique antibody identifying oligonucleotides and the corresponding antibodies. Protein-chromatin complexes were isolated from prepared chromatin with a heterogenous pool of these oligonucleotide-labeled, antibody-coupled Protein G beads.  After immunoprecipitation, DNA ends were repaired and dA-tailed to generate a protruding 3’ A. Split-and-pool barcoding was performed to associate IP'd DNA molecules with the antibody-identifying oligonucleotide on the same Protein G bead. Crosslinks were reversed, the DNA was isolated and the DNA was amplified 8-12 cycles using standard Illumina library prep (dual index). The PCR products were purified using SPRI beads and gel cut.

value: Human lymphoblastic cells

tag: chip antibody

value: See supplemental file


title: P10WTF_2_583

value: Day 10


title: Tumor_only, Cell_line_C, timepoint_1, EXP_9.5, rep_2


title: K562 10 Antibody Pool


title: P06WTM_13_572

value: Day 6

value: M


title: HCC,Cs+,4,T

city: Nanning

first: Min

last: Fang

state: None Selected

address: Guangxi Medical University Cancer Hospital 71, Hedi Road, Qingxiu District

department: Department of Clinical Laboratory

description: treatment(Cs+)

data_processing:
Illumina Novaseq platform
The clustering of the index-coded samples was performed on a cBot Cluster Generation System  using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer’s instructions. The library preparations weresequenced on Illumina Novaseq platform at Tianjin Novogene  Bioinformatic Technology Co., Ltd (Beijing, China) and 150 bp paired-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed using fastp (v 0.20.0). In this step, clean  data (cleanreads) were obtained by removing reads containing adapter, reads containing ploy-N  and low-quality reads (reads with a mass value of less than 15 bases more than 40% of the number  of bases of the reads and pruned reads shorter than 18bp) from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyseswere based on the clean data.
Reference genome and gene annotation files were downloaded from genome website directly.  Index of the reference genome was built using BWA(v 0.7.12) and clean reads were aligned to the  reference genome using BWA mem. Reads that were derived from mitochondrion DNA and chloroplast DNA were discarded. These reads were then filtered for high quality (MAPQ ≥ 13),we also removed reads that were not properly paired and with PCR duplicates. Only uniquely mapped(MAPQ ≥ 13) and de-duplicated reads were used for further analysis.
Assembly: Hg38
Supplementary files format and content: bw document

source_name: liver

growth_protocol: 1 ml of 1 XHB buffer was added into the tissue sample, after grinding and filtering, filtrate was centrifuged at 4 ℃ 500×g for 5 min, and then supernatant was discarded, density gradient  centrifugation for 10 min, nucleus suspension was obtained and counted with LUNA-FL. Taking 50000 nucleus , adding 1 ml washing buffer, mixing them well, ang then centrifuged 500 g  for 5 minutes, discarding supernatant, transposing finally.

extract_protocol: ATAC-seq was performed as previously reported . Briefly, nucleus was extracted from samples,  and the nucleus pellet was resuspended in the Tn5 transposase reaction mix.The transposition  reaction was incubated at 37 ℃ for 30 min. Equimolar Adapter1 and Adatper 2 were added after transposition, PCR was then performed to amplify the library(ATAC-seq_Novogene Kit). After the  PCR reaction, libraries were purified with the AMPure beads and library quality was assessed with Qubit.

value: liver


title: HCC,Cs+,4,P

institute: Guangxi Medical University Cancer Hospital

description: treatment(Cs+)


title: Tumor_only, Cell_line_B, timepoint_1, EXP_9.5, rep_2

value: B


title: Tumor_only, Cell_line_B, timepoint_1, EXP_9.5, rep_1


title: P10WTF_1_551

value: whole kidney

value: CAGG-CreER; Pkd2+/flox


title: Tumor_only, Cell_line_B, timepoint_1, EXP_9.5, rep_3


title: K562 35Ab 45M

description: NextSeq2000, NovaSeq6000


title: P06WTM_14_559


title: Tumor_only, Cell_line_D, timepoint_1, EXP_9.5, rep_2


title: HCC,Cs+,3,T

description: treatment(Cs+)


title: K562 50 Antibody Pool

description: NextSeq2000, NovaSeq6000


title: K562 52 Antibody Pool

description: NextSeq2000, NovaSeq6000


title: HCC,Cs+,3,P

description: treatment(Cs+)


title: HCC,Cs+,2,T

description: treatment(Cs+)


title: P06WTM_12_567


title: K562 35Ab 50K

description: NextSeq2000, NovaSeq6000


title: HCC,Cs+,2,P

description: treatment(Cs+)


title: 03_Lasor_50mj_mouse2

city: Suita

first: Kouichi

last: Hasegawa

state: Osaka

address: 6F Techno Alliance Bldg. 2-8 Yamadaoka

department: StemRIM Institute of Regeneration-Inducing Medicine

country: Japan

institute: Osaka University

data_processing:
Sequencing outputs were demultiplexed using bcl2fastq2 (https://jp.support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html)
Fastq files were aligned to Mus musculus GRCm38 reference using STAR aligner (2.7.6a; https://github.com/alexdobin/STAR)
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: Tar-archived STAR output directory (Solo.out).

source_name: skin

extract_protocol:
After euthanasia, part of dorsal skin were isolated and dissociated into single cells by the Liberase enzyme. To exclude dead cells,  cells were stained with SYTOX Blue Dead Cell Stain.
Cells were sorted into 384-well plates with barcoded oligo dT primer for each well (1 cell / well). After reverse transcription in each well, cDNA was pre-amplified using the Accel-NGS 1S Plus DNA Library Kit (Swift Biosciences, Ann Arbor, MI, USA). Purified cDNAs were tagmentationed with Amplicon Tagment enzyme (Illumina) and PCR for library construction was done by using NEBNext High-Fidelity 2× PCR Master Mix (NEB).

tag: model mouse

value: parabiosis (C57BL/6 mice joined to PDGFRα-Cre; ROSAtdTomato mice)

value: Live skin cells

value: post natal week 9

value: Lasor (50 mJ)


title: P06WTM_11_565

tag: tissue


title: Tumor_only, Cell_line_A, timepoint_1, EXP_9.5, rep_3

value: A


title: HCC,Cs+,1,P

description: treatment(Cs+)


title: Tumor_plus_NK, Cell_line_D, timepoint_1, EXP_9.4, rep_3

value: D


title: P06WTM_10_593

tag: postnatal age


title: Tumor_plus_NK, Cell_line_D, timepoint_1, EXP_9.4, rep_2

value: Day 4


title: Tumor_plus_NK, Cell_line_D, timepoint_1, EXP_9.4, rep_1


title: HCC,Cs+,1,T

description: treatment(Cs+)


title: P06WTM_9_574

tag: genotype


title: HCC,Cs-,4,P

description: control(Cs-)


title: 05_Lasor_50mj_mouse3

tag: strain


title: P06WTF_5_575

tag: Sex

value: F


title: P06WTM_8_569


title: Tumor_only, Cell_line_A, timepoint_1, EXP_9.5, rep_2

tag: cell line


title: mESC 67 Antibody Pool

description: NextSeq2000, NovaSeq6000

tag: cell type

value: Mouse embryonic stem cells


title: 01_control_0mj_mouse1

tag: treatment


title: P06WTF_7_557


title: Sample 32 hSPBTLR9isingle

type: RNA

city: Charleston

first: Martin

last: Kang

state: SC

address: 173 Ashley Avenue CR405D

department: Pediatrics

institute: Medical University of South Carolina

hyb_protocol: A total of 100 ng of RNA was hybridized to the Mouse Host Response Panel CodeSet (nCounter Pro MAX/Flex, NanoString). The Mouse Host Response Panel CodeSet includes 773 murine genes plus 12 internal reference genes involved in host susceptibility, the interferon pathway, the innate and adaptive immune response, and homeostasis. The samples were processed by the nCounter Prep Station and run by the Translational Science Laboratory in the Hollings Cancer Center at the Medical University of South Carolina

scan_protocol: The cartridge containing the probes and the bound RNA were scanned into the Digital Analyzer for image acquisition. The barcodes were counted and analyzed through the nCounter analysis software (nSolver 4.0).

data_processing: The recommended percentage for successful imaging in nCounter is 75% of 555 or 416 fields of view (FOV). In our samples, FOV ranged from 509 to 554 for an imaging quality control (QC) range of 92% to 99.8%. The binding density QC determines image saturation, and the acceptable range is 0.1 to 2.25. In our samples, binding density ranged from 0.44 to 1.51. The positive control linearity QC is an assessment of the efficacy of hybridization for six synthetic positive controls added to the hybridization reaction. The acceptable calculated R2 value is greater than 0.95. In our samples, the positive control linearity ranged from 0.99 to 1. The limit of detection QC examines the ability to detect the 0.5fM positive control probe. This count should be higher than two times the standard deviation above the mean of the negative control. In our samples the limit of detection QC ranged from 12.28 to 53.17. Normalization, fold changes and P-values were calculated based on criteria provided by Nanostring. ROSALIND® uses the nCounter protocol of dividing counts within a lane by the geometric mean of the normalizer probes from the same lane. Housekeeping probes for normalization were selected based on the geNorm algorithm as in the NormqPCR R library.

label: single molecule fluorescent barcodes through nucleotide hybridization

source_name: right lung

label_protocol: RNA samples isolated from lung tissue were adjusted to a concentration of 20 ng per µL for gene expression analyses (nCounter).

extract_protocol: For each lung tissue sample, approximately 30 mg of flash frozen murine lung tissue was placed in 600 µL of lysis buffer (PureLink RNA Mini Kit; Invitrogen, Carlsbad, CA) containing 1% of 2-mercaptoethanol (MP Biomedicals LLC, Santa Ana, CA). Each lung sample was mechanically homogenized on ice for 45 seconds at a speed of 25,000 rpm (maximum speed) using the Fisherbrand Homogenizer 850 (Version 2.1). RNA was extracted according to the manufacturer's instructions (PureLink RNA Mini Kit; Invitrogen), and all samples were stored at -80° C. RNA concentrations and absorbance were measured using a NanoDrop spectrophotometer (Thermo Fisher Scientific, Waltham, MA). In all samples in this study, the RNA concentrations ranged from 250 to 2000 ng per µL. The A260/A280 ratios (RNA purity) for all samples ranged from 2.09 - 2.17, and the A260/A230 ratios (nucleic acid purity) ranged from 1.3 - 2.4.

treatment_protocol: Lungs were flash frozen in liquid nitrogen.

value: AAV-hSPBTLR9i single

value: female

value: CCSP-rtTAtg/(teto)7Sftpb/Sftpb-/- generated on the FVB/N strain


title: HCC,Cs-,4,T

description: control(Cs-)


title: Sample 31 hSPBTLR9isingle


title: P06WTF_6_586

value: Day 6


title: Tumor_plus_NK, Cell_line_C, timepoint_1, EXP_9.4, rep_3

value: C

tag: time


title: Sample 33 hSPBTLR9isingle

value: male


title: Tumor_plus_NK, Cell_line_D, timepoint_2, EXP_9.4, rep_3

value: Day 10

tag: time point


title: HCC,Cs-,3,T

description: control(Cs-)

value: liver


title: P06WTF_4_570

value: whole kidney

value: CAGG-CreER; Pkd2+/flox


title: Tumor_only, Cell_line_A, timepoint_1, EXP_9.5, rep_1

tag: genome assembly_used


title: Tumor_plus_NK, Cell_line_C, timepoint_1, EXP_9.4, rep_2


title: HCC,Cs-,3,P

description: control(Cs-)


title: Sample 30 hSPBsingle

value: AAV-hSPB single


title: HCC,Cs-,1,T

description: control(Cs-)


title: Sample 27 1xPBS

value: 1x PBS


title: P06WTF_3_594


title: HCC,Cs-,2,T

description: control(Cs-)


title: Tumor_plus_NK, Cell_line_C, timepoint_1, EXP_9.4, rep_1


title: CAF, IL1A,rep3

city: Nanjing

first: Hongzhen

last: Li

state: Jiangsu

address: No. 321 Zhongshan Road, Nanjing, Jiangsu, 210008, China

institute: The Affiliated Hospital of Nanjing University Medical School

description: exp_CAF_cytokine treatment

data_processing:
Clean reads were aligned to the reference genome with HISAT2 in orientation mode, and FeatureCounts was used for read counting per gene.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: CAF

growth_protocol: Control and monoclonal cell lines selected after AGR2 knockout (Panc1 and Capan2 cells)  were maintained in DMEM supplemented with 10% FBS and antibiotics atmosphere with 5% CO2 at 37℃, and human PDAC derived CAFs were maintained in DMEM/F12 supplemented with 10% FBS and antibiotics atmosphere with 5% CO2 at 37℃

extract_protocol:
RNA was harvested using RNeasy Kit (QIAGEN, #74104) and RNA integrity was assessed using an Agilent Bioanalyzer 4150 (Agilent Technologies, CA, USA)
Paired-end libraries were prepared and sequenced on an BGISEQ-500, generating 150 bp paired-end reads.

treatment_protocol: CAFs were serum-free starved for 12 hours and treated with AGR2 (500ng/ml), TGFβ (4μg/ml) and IL1α (200ng/ml) for 24 hours.

value: CAF

value: cancer-associated fibroblasts

value: rIL1A treatment


title: Sample 29 hSPBsingle


title: Sample 26 1xPBS


title: CAF, IL1A,rep2

description: exp_CAF_cytokine treatment


title: HCC,Cs-,2,P

description: control(Cs-)


title: P06WTF_1_580

value: F


title: Sample 25 1xPBS


title: Tumor_plus_NK, Cell_line_D, timepoint_2, EXP_9.4, rep_2

value: D


title: P06WTF_2_584


title: Sample 28 hSPBsingle


title: HCC,Cs-,1,P

description: control(Cs-)


title: Tumor_plus_NK, Cell_line_C, timepoint_2, EXP_9.4, rep_3


title: Tumor_plus_NK, Cell_line_D, timepoint_2, EXP_9.4, rep_1


title: CAF, IL1A,rep1

description: exp_CAF_cytokine treatment


title: Tumor_plus_NK, Cell_line_C, timepoint_2, EXP_9.4, rep_2


title: mESC 165 Antibody Pool

description: NextSeq2000, NovaSeq6000

value: Mouse embryonic stem cells

value: See supplemental file


title: Sample 24 hSPBTLR9irepeat

value: AAV-hSPBTLR9i repeat

value: CCSP-rtTAtg/(teto)7Sftpb/Sftpb-/- generated on the FVB/N strain


title: CAF, TGFb,rep3

description: exp_CAF_cytokine treatment

value: rTGFb treatment


title: Tumor_plus_NK, Cell_line_C, timepoint_2, EXP_9.4, rep_1

value: C


title: Vc-D3-2 (ATAC-seq)

city: Guangzhou

first: Yage

last: Nie

address: No.74 Zhongshan Rd.2, Guangzhou

institute: Sun Yat-sen University

data_processing:
For ATAC-seq analysis, raw sequencing reads were mapped to human genome (hg19) by Bowtie2 (version 2.3.5). PCR duplicates were removed by Picard (version 1.124) and the mitochondrial DNA reads were removed by awk. ATAC-seq peaks were called using MACS2 (version 2.2.5). Peaks from the biological replicates were merged using SAMtools and Bedtools. The ATAC-seq data were visualized by using the WashU Epigenome Browser. Raw counts in peaks were normalized and the specific peaks were identified with a criterial of adjusted P-value<0.05, a log2 fold change>1 using the DESeq2.
Assembly: hg19
Supplementary files format and content: bw

source_name: hESC

extract_protocol:
ATAC-seq sequencing libraries were constructed using the TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD501) according to the manufacturer’s instruction.
Quality control of the libraries was performed using an Agilent 2100 Bioanalyzer and sequencing was performed using an Illumina NovaSeq 6000 Sequencer.

treatment_protocol: Activin-A (AA)-based DE differentiation was performed as previously reported1, 2. Briefly, undifferentiated hESCs cultured in E8 medium were dissociated into single cell suspension by Accutase (Stem Cells Technology, 7920) and reseeded onto Matrigel-coated 12-well plate at a density of 2×105 cells/per well in E8 medium containing 5 μM Rho kinase inhibitor Y-27632 (Selleck, S1049). When reached ~80-90% confluence, DE differentiation was initiated by switching to RPMI1640 medium containing B27 minus insulin supplement (ThermoFisher, 175004-44) and cultured for 3 days. 3 μM CHIR99021 (Selleck, S1263) and 100 ng ml-1 AA (R&D, 338-AC) were added from days 0-1 and days 0-3, respectively. For 4C-based DE differentiation, undifferentiated hESCs and hiPSCs were similarly dissociated, seeded onto Synthemax-coated plates, and grown to ~80-90% confluence. Cells were then cultured in DMEM/F12 medium (ThermoFisher, 11320033) supplemented with 71 μg ml-1 Vitamin C (Vc) (Sigma, A8960) and cultured for 3 days. 3 μM CHIR99021 and 0.1 μM LDN193189 (Selleck, S7507) were added from days 0-1 and days 2-3, respectively.

value: hESC

value: Vc


title: Vc-D2-2 (ATAC-seq)


title: Vc-D3-1 (ATAC-seq)


title: Tumor_only, Cell_line_D, timepoint_1, EXP_9.4, rep_3

value: Day 4


title: CAF, TGFb,rep2

description: exp_CAF_cytokine treatment


title: Sample 23 hSPBTLR9irepeat

value: male


title: Sample 22 hSPBTLR9irepeat

value: female


title: Vc-D2-1 (ATAC-seq)


title: CAF, TGFb,rep1

description: exp_CAF_cytokine treatment


title: Tumor_only, Cell_line_D, timepoint_1, EXP_9.4, rep_2


title: Tumor_only, Cell_line_D, timepoint_1, EXP_9.4, rep_1


title: CAF, AGR2,rep3

description: exp_CAF_cytokine treatment

value: rAGR2 treatment


title: Vc-D1-1 (ATAC-seq)


title: Sample 21 hSPBTLR9irepeat


title: Sample 20 hSPBrepeat

value: AAV-hSPB repeat


title: LDN-D3-2 (ATAC-seq)

value: LDN


title: Sample 19 hSPBrepeat


title: CAF, AGR2,rep2

description: exp_CAF_cytokine treatment

value: CAF

value: cancer-associated fibroblasts


title: CAF, AGR2,rep1

description: exp_CAF_cytokine treatment


title: LDN-D3-1 (ATAC-seq)


title: Tumor_only, Cell_line_C, timepoint_1, EXP_9.4, rep_2


title: Sample 18 hSPBrepeat


title: Tumor_only, Cell_line_C, timepoint_1, EXP_9.4, rep_1


title: LDN-D2-2 (ATAC-seq)


title: CAF, Control,rep2

description: exp_CAF_cytokine treatment

value: control


title: Sample 17 hSPBrepeat


title: Vc-D1-2 (ATAC-seq)


title: Sample 16 hSPBTLR9isingle

value: AAV-hSPBTLR9i single


title: CAF, Control,rep1

description: exp_CAF_cytokine treatment


title: Tissue explant #1 from vavP-Bcl2 mouse #2 cultured for 2 week

city: Lausanne

first: Divyanshu

last: Srivastava

address: SV, Station 19

country: Switzerland

institute: EPFL

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
Raw sequencing reads were aligned using 10xGenomcis Cellranger pipeline (cellranger-6.0.2).
Assembly: mm10
Supplementary files format and content: HDF5 format, contains gene counts for single cells

source_name: Spleen

growth_protocol: Tumor tissue biopsies were processed with a McIlwain Tissue Chopper and placed in inserts with permeable, membranous bottom containing a 1:1 solution of Vitrogel RGD High Concentration and RPMI1640 supplemented with 5% FBS, 1x normocin, 1x insulin/selenium/transferrin, and 1x sodium pyruvate. The insert was placed in a 12 well plate and left in a 5% CO2 incubator at 37ºC for 20 minutes for the matrix to gelify. Finally, RMPI1640 complete + 0.2 micrograms/ml hBAFF was added to each well.

extract_protocol:
Spleens and spleen-derived tissue explants were mechanically disaggreagted using 70mm strainers, erythrocytes were lysed using a Red Blood Cell Lysis buffer for 2 minutes at room temperature, and then cells were washed in PBS, resuspended in medium and processed for sequencing.
Samples were processed for sequencing using the SingleCell 3' Reagent Kit v3.1 and a 10x Chromium single cell controller following the manufacturer's instructions.

treatment_protocol: Tissue explants were grown for 1 or 2 weeks.

value: Spleen

tag: age

value: 43 weeks

value: vavP-Bcl2 in C57BL/6


title: Sample 15 hSPBTLR9isingle

value: CCSP-rtTAtg/(teto)7Sftpb/Sftpb-/- generated on the FVB/N strain


title: Vc-D3-3 (RNA-seq)

data_processing:
For RNA-seq analysis, sequence quality was assessed using FastQC and the raw RNA-seq reads were aligned to the human genome (hg19) by Hisat2 (version 2.1.0). Alignment files were sorted by SAMtools (version 1.9). HTSeq (version 0.11.2) was used to assign reads to genes and summarized as gene-level counts. DESeq2 package (version 1.30.1) in R was used to analyze gene differential expression by comparing transcriptomes of each sample using a criterial of adjusted P-value<0.05, a log2 fold change>1. The differential expression heatmap was produced using the R package pheatmap. Gene ontology enrichment analysis and KEGG enrichment analysis were performed using the R package clusterProfiler.
Assembly: hg19
Supplementary files format and content: txt file represents counts

extract_protocol:
Total RNA of cells was isolated using RNAzol.
Sequencing libraries were constructed using the VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina (Vazyme, NR605-1) according to the manufacturer’s instruction.

treatment_protocol: "Activin-A (AA)-based DE differentiation was performed as previously reported1, 2. Briefly, undifferentiated hESCs cultured in E8 medium were dissociated into single cell suspension by Accutase (Stem Cells Technology, 7920) and reseeded onto Matrigel-coated 12-well plate at a density of 2×105 cells/per well in E8 medium containing 5 μM Rho kinase inhibitor Y-27632 (Selleck, S1049). When reached ~80-90% confluence, DE differentiation was initiated by switching to RPMI1640 medium containing B27 minus insulin supplement (ThermoFisher, 175004-44) and cultured for 3 days. 3 μM CHIR99021 (Selleck, S1263) and 100 ng ml-1 AA (R&D, 338-AC) were added from days 0-1 and days 0-3, respectively. For 4C-based DE differentiation, undifferentiated hESCs and hiPSCs were similarly dissociated, seeded onto Synthemax-coated plates, and grown to ~80-90% confluence. Cells were then cultured in DMEM/F12 medium (ThermoFisher, 11320033) supplemented with 71 μg ml-1 Vitamin C (Vc) (Sigma, A8960) and cultured for 3 days. 3 μM CHIR99021 and 0.1 μM LDN193189 (Selleck, S7507) were added from days 0-1 and days 2-3, respectively. "Activin-A (AA)-based DE differentiation was performed as previously reported1, 2. Briefly, undifferentiated hESCs cultured in E8 medium were dissociated into single cell suspension by Accutase (Stem Cells Technology, 7920) and reseeded onto Matrigel-coated 12-well plate at a density of 2×105 cells/per well in E8 medium containing 5 μM Rho kinase inhibitor Y-27632 (Selleck, S1049). When reached ~80-90% confluence, DE differentiation was initiated by switching to RPMI1640 medium containing B27 minus insulin supplement (ThermoFisher, 175004-44) and cultured for 3 days. 3 μM CHIR99021 (Selleck, S1263) and 100 ng ml-1 AA (R&D, 338-AC) were added from days 0-1 and days 0-3, respectively. For 4C-based DE differentiation, undifferentiated hESCs and hiPSCs were similarly dissociated, seeded onto Synthemax-coated plates, and grown to ~80-90% confluence. Cells were then cultured in DMEM/F12 medium (ThermoFisher, 11320033) supplemented with 71 μg ml-1 Vitamin C (Vc) (Sigma, A8960) and cultured for 3 days. 3 μM CHIR99021 and 0.1 μM LDN193189 (Selleck, S7507) were added from days 0-1 and days 2-3, respectively.


title: Tissue explant #2 from vavP-Bcl2 mouse #2 cultured for 1 week

description: 10X Genomics


title: Capan2 cells, sgAGR2, rep3

value: pancreatic cancer cells

value: AGR2 knockout


title: Tumor_only, Cell_line_C, timepoint_1, EXP_9.4, rep_3

value: C


title: Vc-D3-2 (RNA-seq)

value: hESC

value: Vc


title: Tissue explant #1 from vavP-Bcl2 mouse #2 cultured for 1 week

description: 10X Genomics


title: Sample 14 hSPBTLR9isingle

value: female


title: Vc-D3-1 (RNA-seq)


title: CAF, Control,rep3

description: exp_CAF_cytokine treatment


title: Vc-D2-3 (RNA-seq)


title: Capan2 cells, sgAGR2, rep1


title: Capan2 cells, sgControl, rep3

value: WT


title: Tissue explant #2 from vavP-Bcl2 mouse #2 cultured for 2 week

description: 10X Genomics


title: Sample 11 hSPBsingle

value: AAV-hSPB single

value: male


title: Spleen of vavP-Bcl2 mouse #2

description: 10X Genomics


title: Tissue explant #1 from vavP-Bcl2 mouse #1 cultured for 1 week

description: 10X Genomics

value: 47 weeks


title: Vc-D2-1 (RNA-seq)


title: Sample 10 hSPBsingle


title: LDN-D2-1 (ATAC-seq)

value: LDN


title: Capan2 cells, sgControl, rep1


title: Spleen of vavP-Bcl2 mouse #1

description: 10X Genomics


title: Capan2 cells, sgControl, rep2


title: Sample 9 hSPBsingle


title: Panc1 cells, sgAGR2, rep3


title: Capan2 cells, sgAGR2, rep2


title: Vc-D2-2 (RNA-seq)


title: Vc-D1-3 (RNA-seq)


title: Sample 12 hSPBsingle


title: Panc1 cells, sgAGR2, rep2


title: Vc-D1-2 (RNA-seq)


title: Sample 8 NoTxOffDox

value: No Treatment - Off Doxycycline


title: Sample 13 hSPBTLR9isingle

value: AAV-hSPBTLR9i single


title: Vc-D1-1 (RNA-seq)


title: Tissue explant #2 from vavP-Bcl2 mouse #1 cultured for 1 week

description: 10X Genomics

value: Spleen


title: Panc1 cells, sgAGR2, rep1


title: CRISPR_screen.T10_rep3

city: Amsterdam

first: William

last: Faller

address: Plesmanlaan 121

department: Oncogenomics

country: Netherlands

institute: Netherlands Cancer Institute

data_processing:
Adapter trimming of sequencing data was performed with cutadapt. Fastq files contain these trimmed reads.
Quality control and drop-out analysis was performed with MAGECK-VISPR pipeline.
mm10
CRISPR_screen.MAGECK.all.count_normalized.txt file is a tab-seperated MAGECK-VISPR pipeline output summarizing the gRNA abundance in T0 and T10 timepoints. Columns include gRNA, Gene (target region), T0, and T10.

source_name: intestine

growth_protocol: Lentivirus was produced and Cas9 expressing organoids were transduced at 600-fold complexity of the library at a multiplicity of infection (MOI) of 0.3 for each of the three technical replicates. The precise working virus titre was determined in advance in a viral titration experiment on non-Cas9 expressing organoids in which survival was measured following puromycin selection. 60x106 cells were plated on a BME layer, infected with the determined viral volume and 24 hours after transduction their growth into organoids was promoted by overlaying them with BME. A day after this puromycin selection started (2 µg/ml) and after 48 hours selection of infected organoids was completed and T0 triplicates were collected. The replicates of the experimental arm were cultured for 10 days in ENR media supplemented with 10µM CHIR99021 (Cayman) and 1,5mM of VPA ( Biovision). On day 5 organoids were harshly disrupted by pipetting in order to potentiate their stem capacity. The surviving organoids were collected on day 10.

extract_protocol:
DNA of all time points and replicates  was extracted using the DNeasy Blood and Tissue kit (Qiagen).
sgRNA cassettes were amplified from the collected genomic DNA and Illumina sequencing adaptors and sample barcodes were introduced in two consecutive PCR reactions, first with primers PCR1 and then with PCR2 primers, using Phusion polymerase (2U/µl) (Thermo Fisher Scientific). PCR products were purified with a QIAquick PCR Purification kit (Qiagen), molarity was assessed  with the Agilent 2100.

value: intestine

value: organoid

value: stem cell enrichment


title: Sample 6 NoTxOffDox

value: CCSP-rtTAtg/(teto)7Sftpb/Sftpb-/- generated on the FVB/N strain


title: Sample 7 NoTxOffDox


title: LDN-D3-3 (RNA-seq)


title: CRISPR_screen.T10_rep2


title: Panc1 cells, sgControl, rep3

value: pancreatic cancer cells


title: LDN-D3-2 (RNA-seq)


title: Panc1 cells, sgControl, rep2


title: Sample 5 NoTxOffDox


title: CRISPR_screen.T10_rep1


title: Sample 4 NoTxOnDox

value: No Treatment - On Doxycycline


title: LDN-D3-1 (RNA-seq)

value: hESC


title: CRISPR_screen.T0_rep3


title: Panc1 cells, sgControl, rep1


title: Sample 3 NoTxOnDox


title: LDN-D2-3 (RNA-seq)


title: ZH-78-Hu-Lem-MP

city: Louisville

first: Huang-Ge

last: Zhang

state: KY

address: 505 S Hancock Street

department: James Graham Brown Cancer Center

institute: University of Louisville

description: 16s rRNA

data_processing:
3 μL of each library was pooled together into one tube.
The pooled library concentration was measured in ng/μL using the Qubit DNA HS assay.
Quality of the pooled library was checked using a Bioanalyzer. Size was measured at 636bp.
The pooled library was diluted to 10 nM using 10 mM Tris-HCl pH 8.5 0.1% Tween 20 buffer.
Sequencing was done on a Nano-300 cycle test chip (MS-103-1001) to confirm coverage of all libraries. Libraries with low reads were spiked in at higher concentrations to increase coverage. The re-pooled library was then ran on the MiSeq using an Illumina MiSeq Reagents kit v3 (600 cycles) (MS-102-3003) at 10 pM set at the below parameters according to kit instructions:
Supplementary files format and content: The 77 paired-end raw sequencing files (.fastq) representing two groups were generated in Genomics facility core, Univeristy of Louisville and downloaded from Illumina’s BaseSpace (https://basespace.illumina.com/) onto the KBRIN server for analysis using the script
Supplementary files format and content: The samples was further trimmed and analyzed using QIIME 2
Supplementary files format and content: The relative abundances of specific bacteria indicated in the file of 16s seq processing data Hu were generated by each toxonomic raw reads divided by whole reads on all samples
Library strategy: 16s rRNA sequencing

organism: feces metagenome

source_name: Faeces

extract_protocol:
Fecal DNA extract from 5 g feces of human using the QIAamp DNA Stool Mini Kit (Qiagen) according the instruction of manufactory.
QIAseq 16S/ITS 96-Index I (384) (Cat# 333825) and QIAseq 16S/ITS Screening Panel (24) (Cat# 333812)

treatment_protocol: No treatment

tag: source

value: Human uptake


title: CRISPR_screen.T0_rep2


title: LDN-D2-2 (RNA-seq)


title: Sample 2 NoTxOnDox

value: female


title: ZH-74-Hu-Lem-Exo

description: 16s rRNA


title: LDN-D2-1 (RNA-seq)


title: 5uM_VNC_7_7_30hrAPF_2

city: Rochester

first: Matthew

middle: D

last: Rand

state: NY

address: 601 Elmwood Ave Box EHSC

department: Environmental Medicine

institute: University of Rochester

description: Library name: 5uM_VNC_7_7_30hrAPF_2

data_processing:
Data Formatting bcl2fastq version 2.19.0
Data Cleaning FastP version 0.20.1 with parameters --length_required 35 --cut_front_window_size 1 --cut_front_mean_quality 13 --cut_front --cut_tail_window_size 1 --cut_tail_mean_quality 13 --cut_tail -y –r
Genome Alignment STAR_2.7.6a with parameters: "—twopass Mode Basic --runMode alignReads --outSAMtype BAM Unsorted – outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical –outReadsUnmapped Fastx
Read Quantification subread-2.0.1, featurecounts, -s 2 -t exon -g gene_name
Assembly: dm6
Supplementary files format and content: tab-delimited text file of gene counts

organism: Drosophila melanogaster

source_name: VNC

growth_protocol: Drosophila were maintained on Jazz-Mix food (Fisher Scientific AS153) at 25C, 70%humidity, 12hr/12hr light/dark cycle.

extract_protocol:
Pupa and adult flies were fixed in Methacarn (6:3:1 of methanol:chloroform:acetic acid) to preserve tissue integrity and nucleic acids prior to dissection.  Indirect flight muscles (IFMs) (inclusive of dorsal longitudinal muscles (DLMs) and dorsal ventral muscles (DVMs)) were microdissected separately from ventral nerve cord (VNC) (separated from central brain). A total of three replicates of n = 50 for each tissue/treatment/stage (n=150 total) were collected. Dissected tissues were immediately homogenized and preserved in TRIzol™ Reagent (Thermo-Fisher Scientific) and frozen at -80°C until processed for total RNA extraction.
RNA liibraries for RNA-Seq were prepared using TruSeq Stranded Total RNA Gold as per manufacturers protocol.

treatment_protocol: Larvae at the first instar stage (L1) were transferred to Jazz-Mix food containing 5µM (final conc.) methylmercury chloride or control food containing an equivalent amount of solvent (DMSO, 0.01 %) control  food. Animals were developed to the 30hr pupal stage or to the 15 day adult stage. Adult flies were trnasfered to MeHg-free Jazz-mix upon eclosion from the pupa case.

value: VNC

value: 5 µM MeHg


title: 5uM_VNC_7_7_30hrAPF_3

description: Library name: 5uM_VNC_7_7_30hrAPF_3


title: ZH-70-Hu-Alo-MP

description: 16s rRNA


title: Topas seeds at 20DAP, THT growth conditions, SCR, biological replicate 4

city: Brno

first: Helene

middle: S.

last: Robert

address: Kamenice 5

country: Czech Republic

institute: CEITEC Masaryk University

data_processing:
Quality check of raw paired-end fastq reads was carried out by FastQC (Andrews, 2010), and their origin was categorised using BioBloomTools v2.3.4 (Chu et al., 2014). The Illumina adapters and quality trimming of raw fastq reads were performed using Trimmomatic v0.39 (Bolger et al., 2014) with settings CROP:250 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:5 MINLEN:35.
Assembly: Trimmed RNA-Seq reads were mapped to the Brassica napus genome (genome build: Bra_napus_v2.0) with gene annotation (NCBI Brassica napus Annotation Release 101) using STAR v2.7.3a (Dobin et al., 2013) as splice-aware short read aligner and default parameters except outFilterMismatchNoverLmax 0.1 and twopassMode Basic. Quality control after alignment concerning the number and percentage of uniquely- and multi-mapped reads, rRNA contamination, mapped regions, read coverage distribution, strand specificity, gene biotypes, and PCR duplication was performed using RSeQC v4.0.0 (Wang et al., 2012), Picard toolkit v2.25.6 (Picard toolkit, 2018), Qualimap v.2.2.2 (Okonechnikov et al., 2016). All compatible results and statistics were processed by MultiQC v1.10.1 (Ewels et al., 2016).
Read count assignment was performed using featureCounts v2.0.3, the obtained raw counts were normalized and analyzed using DESeq2 v1.34.0. A cross-referencing between multiple databases was performed in order to complement the annotation file provided used.
Supplementary files format and content: tab-delimited text file including raw counts per sample
Supplementary files format and content: tab-delimited text file including DESeq2 normalized counts per sample

molecule: polyA RNA

organism: Brassica napus

source_name: seed

growth_protocol: Brassica napus spring cultivar Topas DH4079 was used for this study. Seeds were sterilised, germinated, and grown initially in the phytotron (21°C, 16/8 h long day period, 150 μmol/m2/s) until the emergence of the first flowering buds, as previously mentioned (Mácová et al., 2022).

extract_protocol:
Seeds collected at 14, 18, and 20DAP  in four biological replicates from three plants grown under TCT and THT conditions. RNA was extracted from 50 mg of ground tissue using a NucleoSpin RNA Plant and Fungi kit (Macherey-Nagel) following the manufacturer's protocol. The samples were treated with RNase-free rDNase (Macherey-Nagel) and repurified using the RNeasy MinElute Cleanup Kit (Qiagen).
RNA quantification and qualification. RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). Library preparation for Transcriptome sequencing. Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.
Clustering and sequencing (Novogene Experimental Department). The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.

treatment_protocol: Plants are then transferred to greenhouse chambers with control temperature treatment (TCT) and heat treatment (THT) conditions maintained under a long day regime (16 h light/8 h dark), LED lights with a light intensity of 150 μmol/m2/s, 35%–45% humidity, 18 °C during the night and 21 °C (TCT) and 32 °C (THT) during the day. Seeds used for the experiments are obtained from hand-pollinated flowers. The age of the seeds is counted from the day after pollination (DAP).

value: seed

tag: cultivar

value: Topas DH4079

value: WT

tag: phenotype

value: SCR

value: heat 32oC

value: 20 DAP


title: human macrophages stimulated by CCN3 (NOV) 1

city: Sapporo

first: Mohamad Alaa

last: Terkawi

state: Hokkaido

address: Kita-15, Nish-7, Kita-ku

department: Department of Orthopedic Surgery

institute: Hokkaido University

data_processing:
Data of 150 bp× 2 paired-end of 4-6G bases per sample (3 samples for each condition) was trimmed by fastp and mapped by alignment to the mouse hg38 reference genome using STAR. The reads were quantified using RSEM and the raw count data were subjected to Subio Platorm Plug-ins software (Tokyo, Japan)
Assembly: hg38
Supplementary files format and content: RPKM values for each Sample

source_name: Macrophage

growth_protocol: human monocytes were isolated from healthy blood donors using density gradient centrifugation and then isolated using the MACS Pan monocyte isolation kit. Monocytes were cultured for 6 days in the growth medium supplemented with 25 ng/mL of human recombinant macrophage colony-stimulating factor

extract_protocol:
human macrophage RNA was purified using TRIzol Reagent and RNA extraction kit (NucleoSpin®) according to the manufacturere's protocol
Libraries were generated from 1 µg of high-quality RNA using NEBNext Ultra II Directional RNA Library Prep Kit  .Data of 150 bp× 2 paired-end of 4-6G bases per sample (3 samples for each condition) was trimmed by fastp and mapped by alignment to the mouse mm10 reference genome using STAR. The reads were quantified using RSEM and the raw count data were subjected to Subio Platorm Plug-ins software .

treatment_protocol: human macrophage stimulated by CCN3 (100ng/mL) recombinant.

value: Macrophage


title: ZH-73-Hu-Lem-Exo

description: 16s rRNA


title: Topas seeds at 20DAP, THT growth conditions, SCR, biological replicate 3


title: 5uM_VNC_7_28_15day_4

description: Library name: 5uM_VNC_7_28_15day_4


title: ZH-77-Hu-Lem-MP

description: 16s rRNA


title: 5_uM_VNC_7_1_30hrAPF_1

description: Library name: 5_uM_VNC_7_1_30hrAPF_1


title: Topas seeds at 20DAP, THT growth conditions, SCR, biological replicate 2


title: FLS stimulated by CCN3 (NOV) 3

data_processing:
Data of 150 bp× 2 paired-end of 4-6G bases per sample (3 samples for each condition) was trimmed by fastp and mapped by alignment to the mouse hg38 reference genome using STAR. The reads were quantified using RSEM and the raw count data were subjected to Subio Platorm Plug-ins software (Tokyo, Japan)
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: FLS

growth_protocol: hFLS were cultured in α-modification minimum essential medium (α MEM) supplemented with 10% heat-inactivated fetal bovine serum, 1% penicillin/streptomycin, and 1% l-glutamine (growth medium) at 37°C in a humidified 5% CO2 atmosphere

extract_protocol:
hFLS RNA was purified using TRIzol Reagent and RNA extraction kit (NucleoSpin®) according to the manufacturere's protocol
Libraries were generated from 1 µg of high-quality RNA using NEBNext Ultra II Directional RNA Library Prep Kit  .Data of 150 bp× 2 paired-end of 4-6G bases per sample (3 samples for each condition) was trimmed by fastp and mapped by alignment to the mouse mm10 reference genome using STAR. The reads were quantified using RSEM and the raw count data were subjected to Subio Platorm Plug-ins software .

treatment_protocol: hFLS stimulated by CCN3 (100ng/mL) recombinant.

value: FLS


title: Topas seeds at 20DAP, THT growth conditions, SCR, biological replicate 1


title: 5uM_VNC_7_10_15day_3

description: Library name: 5uM_VNC_7_10_15day_3


title: FLS stimulated by CCN3 (NOV) 2


title: ZH-66-Hu-Alo-Exo

description: 16s rRNA


title: Methylation profiling of muscle

first: Xidong

last: Mu

address: No.1 Xingyu Road

institute: Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences

description: Methylation profiling of muscle of P. jordani

data_processing:
HiFi reads were aligned to the assembled genome using pbmm2 (version 1.13.1) (parameters --preset HIFI --sort -j 16 -J 16), generating a sorted BAM file, which was used as input for downstream analysis.
The site-level methylation modification proportions was determined using pb-CpG-tools (version 2.2.0-x86_64).
Assembly: JBGFUG000000000
Supplementary files format and content: txt file includes  site-level methylation information

organism: Ptychidio jordani

source_name: muscle

extract_protocol:
Genomic DNA was extracted using the DNeasy Blood and Tissue Kit (Qiagen, Germany) following the manufacturer’s instructions.
The PacBio HiFi library was prepared using the SMRTbell prep kit 3.0 (PacBio 102-182-700) following the manufacturer’s protocols. High-quality genomic DNA was sheared to 15-20 kb, end-repaired, A-tailed, and ligated to SMRTbell adapters. The prepared library was then loaded onto the PacBio Revio platform for sequencing.

value: muscle


title: 5uM_VNC_7_10_15day_1

description: Library name: 5uM_VNC_7_10_15day_1


title: CRISPR_screen.T0_rep1

value: intestine

value: organoid

value: stem cell enrichment


title: Topas seeds at 20DAP, THT growth conditions, no SCR, biological replicate 4

value: normal


title: human macrophages stimulated by CCN3 (NOV) 3

value: stimulated by CCN3 (100ng/mL) recombinant


title: Sample 1 NoTxOnDox

value: No Treatment - On Doxycycline

value: female

value: CCSP-rtTAtg/(teto)7Sftpb/Sftpb-/- generated on the FVB/N strain


title: FLS stimulated by CCN3 (NOV) 1


title: 5uM_IFM_7_7_30hrAPF_3

description: Library name: 5uM_IFM_7_7_30hrAPF_3

source_name: IFM

value: IFM

value: 5 µM MeHg


title: ZH-62-Hu-Gar-MP

description: 16s rRNA

value: Human uptake


title: human macrophages stimulated by CCN3 (NOV) 2


title: ZH-69-Hu-Alo-MP

description: 16s rRNA


title: ZH-61-Hu-Gar-MP

description: 16s rRNA


title: Topas seeds at 20DAP, THT growth conditions, no SCR, biological replicate 2

value: seed

value: Topas DH4079

value: WT


title: FLS not stimulated 2


title: 5uM_IFM_7_28_15day_4

description: Library name: 5uM_IFM_7_28_15day_4


title: FLS not stimulated 3


title: 5uM_IFM_7_7_30hrAPF_2

description: Library name: 5uM_IFM_7_7_30hrAPF_2


title: FLS not stimulated 1


title: Topas seeds at 18DAP, THT growth conditions, biological replicate 4

value: heat 32oC

value: 18 DAP


title: Chondrocyte stimulated by IL-1β +TGF-β-stimulated neutrophil derived Evs 3

data_processing:
Data of 150 bp× 2 paired-end of 4-6G bases per sample (3 samples for each condition) was trimmed by fastp and mapped by alignment to the hg38 reference genome using STAR. The reads were quantified using RSEM and the raw count data were subjected to Subio Platorm Plug-ins software .
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Human chondrocyte cell line C-28I2

growth_protocol: C-28I2 chondrocytes were seeded on 24-well plates with micromass, cultured in high glucose DMEM supplemented with 10% heat-inactivated FBS and penicillin/streptomycin  overnight, and then stimulated with DMEM+F12+1% ITS  for 24 hours.

extract_protocol:
Chondrocytes RNA was purified using TRIzol Reagent and RNA extraction kit (NucleoSpin®) according to the manufacturere's protocol
Libraries were generated from 1 µg of high-quality RNA using NEBNext Ultra II Directional RNA Library Prep Kit  .Data of 150 bp× 2 paired-end of 4-6G bases per sample (3 samples for each condition) was trimmed by fastp and mapped by alignment to hg38 reference genome using STAR. The reads were quantified using RSEM and the raw count data were subjected to Subio Platorm Plug-ins software.

treatment_protocol: Chondrocytes were stimulated with 20 ng/ml IL-1β or 24 h, washed 3 times with PBS , and co-cultured with or without  Evs

value: Human chondrocyte cell line C-28I2

value: IL-1Beta +TGF-Beta-stimulated neutrophil derived Evs


title: Topas seeds at 20DAP, THT growth conditions, no SCR, biological replicate 3

value: 20 DAP


title: 5_uM_IFM_7_1_30hrAPF_1

description: Library name: 5_uM_IFM_7_1_30hrAPF_1


title: 5uM_IFM_7_10_15day_3

description: Library name: 5uM_IFM_7_10_15day_3


title: ZH-54-Hu-Gin-MP

description: 16s rRNA


title: ZH-65-Hu-Alo-Exo

description: 16s rRNA


title: Topas seeds at 18DAP, THT growth conditions, biological replicate 3


title: 5uM_IFM_7_10_15day_1

description: Library name: 5uM_IFM_7_10_15day_1


title: ZH-57-Hu-Gar-Exo

description: 16s rRNA


title: Chondrocyte stimulated by IL-1β +TGF-β-stimulated neutrophil derived Evs 2


title: Topas seeds at 20DAP, THT growth conditions, no SCR, biological replicate 1


title: ZH-53-Hu-Gin-MP

description: 16s rRNA


title: Topas seeds at 18DAP, THT growth conditions, biological replicate 2


title: Chondrocyte stimulated by IL-1β +TGF-β-stimulated neutrophil derived Evs 1


title: ZH-50-Hu-Gin-Exo

description: 16s rRNA


title: Topas seeds at 18DAP, THT growth conditions, biological replicate 1


title: Chondrocyte stimulated by IL-1β +non-stimulated neutrophil derived Evs 3

value: IL-1Beta +non-stimulated neutrophil derived Evs


title: 0uM_VNC_7_7_30hrAPF_2

description: Library name: 0uM_VNC_7_7_30hrAPF_2

value: VNC

value: Control


title: ZH-49-Hu-Gin-Exo

description: 16s rRNA


title: ZH-58-Hu-Gar-Exo

description: 16s rRNA


title: Topas seeds at 14DAP, THT growth conditions, biological replicate 4

value: normal

value: 14 DAP


title: Chondrocyte stimulated by IL-1β +non-stimulated neutrophil derived Evs 2


title: ZH-32-B6-Lem-MP-SI-S-2

description: 16s rRNA

value: Mouse uptake


title: 0_uM_VNC_7_1_30hrAPF_1

description: Library name: 0_uM_VNC_7_1_30hrAPF_1


title: 0uM_VNC_7_10_15day_3

description: Library name: 0uM_VNC_7_10_15day_3


title: Topas seeds at 14DAP, THT growth conditions, biological replicate 3


title: Chondrocyte stimulated by IL-1β +non-stimulated neutrophil derived Evs 1


title: ZH-31-B6-Lem-MP-SI-S-1

description: 16s rRNA


title: Chondrocyte stimulated by IL-1β alone 2

value: IL-1Beta alone


title: 0uM_VNC_7_10_15day_2

description: Library name: 0uM_VNC_7_10_15day_2


title: Chondrocyte stimulated by IL-1β alone 3


title: ZH-29-B6-Lem-Exo-SI-S-1

description: 16s rRNA


title: ZH-30-B6-Lem-Exo-SI-S-2

description: 16s rRNA


title: 0uM_VNC_7_10_15day_1

description: Library name: 0uM_VNC_7_10_15day_1


title: Topas seeds at 20DAP, TCT growth conditions, biological replicate 4

value: control 21oC


title: 0uM_IFM_7_7_30hrAPF_3

description: Library name: 0uM_IFM_7_7_30hrAPF_3

value: IFM


title: Topas seeds at 20DAP, TCT growth conditions, biological replicate 3

value: seed


title: Control chondrocyte 3


title: ZH-28-B6-Lem-MP-LI-S-2

description: 16s rRNA


title: 0uM_IFM_7_7_30hrAPF_2

description: Library name: 0uM_IFM_7_7_30hrAPF_2


title: Chondrocyte stimulated by IL-1β alone 1


title: 0uM_VNC_7_7_30hrAPF_3

description: Library name: 0uM_VNC_7_7_30hrAPF_3


title: ZH-27-B6-Lem-MP-LI-S-1

description: 16s rRNA


title: Topas seeds at 14DAP, THT growth conditions, biological replicate 1

value: Topas DH4079


title: Control chondrocyte 2


title: Topas seeds at 20DAP, TCT growth conditions, biological replicate 2

value: WT


title: 0_uM_IFM_7_1_30hrAPF_1

description: Library name: 0_uM_IFM_7_1_30hrAPF_1


title: ZH-26-B6-Lem-Exo-LI-S-2

description: 16s rRNA


title: Topas seeds at 20DAP, TCT growth conditions, biological replicate 1


title: Control chondrocyte 1


title: ZH-25-B6-Lem-Exo-LI-S-1

description: 16s rRNA


title: Topas seeds at 14DAP, THT growth conditions, biological replicate 2

value: heat 32oC


title: 0uM_IFM_7_10_15day_3

description: Library name: 0uM_IFM_7_10_15day_3


title: 0uM_IFM_7_10_15day_2

description: Library name: 0uM_IFM_7_10_15day_2


title: Topas seeds at 18DAP, TCT growth conditions, biological replicate 4

value: 18 DAP


title: ZH-24-B6-Alo-MP-SI-S-2

description: 16s rRNA


title: GEX, PBMC, critical, Patient1, Day13

city: Bunkyo

first: Yoko

last: Tabe

state: Tokyo

address: 2 Chome-1-1 Hongo

department: Department of Clinical Laboratory Medicine

institute: Juntendo University

data_processing:
Cell Ranger v 6.1.2 (multi)
Quality control, mapping to human genome reference, and read count exctraction were performed using Cell Ranger multi
Assembly: hg38
Supplementary files format and content: Tab-delimited compressed text file includes barcode data for each Sample
Supplementary files format and content: Tab-delimited compressed text file includes feature data for each Sample
Supplementary files format and content: Tab-delimited compressed text file includes raw counts for each Sample
Library strategy: TCR-Seq

source_name: PBMC

extract_protocol:
PBMCs were isolated from blood samples from six COVID-19 inpatients admitted to Juntendo University Hospital in Tokyo, Japan, using BD Vacutainer CPT mononuclear cell preparation tubes containing sodium heparin. The isolated cells were washed with Dalbeccos' phosphate buffered saline (PBS), resuspended in 1 mL of CELLBANKER 1 Plus, and stored at -80°C until further use.
scRNA libraries were constructed with library-associated unique indexes, using the library construction kit (1000196), the Single Index Kit T Set A (1000213), and SI primer (2000095)

value: PBMC

value: Female


title: ZH-23-B6-Alo-MP-SI-S-1

description: 16s rRNA


title: Topas seeds at 18DAP, TCT growth conditions, biological replicate 2


title: 0uM_IFM_7_10_15day_1

description: Library name: 0uM_IFM_7_10_15day_1


title: GEX, PBMC, moderate, Patient1, Day3


title: Multiplexing set 7, Whole transcriptome analysis library (WTA), scRNAseq

city: Suwon

first: Karolina

middle: Hanna

last: Prazanowska

address: Worldcup-Ro 164

country: South Korea

institute: Ajou University School of Medicine

description: BD Rhapsody

data_processing:
FASTQ files were generated from Illumina basecall using bcl2fastq2 (v2.20.0). Obtained reads were processed following the BD Rhapsody WTA Analysis Pipeline (https://scomix.bd.com/hc/article_attachments/16954089124621).
Assembly: GRCh38
Supplementary files format and content: *.csv: Values are counts processed by BD Rhapsody Whole Transcriptome Analysis pipeline, which includes transformations like RSEC correction of UMIs.

source_name: Peripheral whole blood

extract_protocol:
Freshly collected peripheral whole blood samples were stored on EDTA tubes and processed directly on the same day. Red blood cell (RBC) lysis was conducted using 1xRBC lysis buffer in 1:3 ratio to the samples. Centrifugation and resuspension with 0.04% BSA/PBS were conducted twice to remove the lyzed RBCs. The cell pellets were resuspended to obtain 2x10^6`1x10^7 cell stock.
Library was constructed according to BD Rhapsody whole transcriptome analysis (WTA) and sample tag (ST) library preparation protocol. Samples were tagged with antibody-based sample tags and grouped for multiplexing (5 samples at a time, 30.000 cells per sample).

value: Peripheral whole blood

tag: samples (multiplexed)


title: PBMC, critical, Patient1, Day13

data_processing:
Cell Ranger v 6.1.2 (multi)
Quality control, mapping to human genome reference, and read count exctraction were performed using Cell Ranger multi
Assembly: hg38
Supplementary files format and content: Comma-delimited text files include clonotype information for each Sample
Supplementary files format and content: Comma-delimited text files include VDJ sequences and annotation for each barcode
Library strategy: TCR-Seq


title: Topas seeds at 18DAP, TCT growth conditions, biological replicate 1


title: ZH-22-B6-Alo-Exo-SI-S-2

description: 16s rRNA


title: Multiplexing set 6, Whole transcriptome analysis library (WTA), scRNAseq

description: BD Rhapsody


title: PBMC, moderate, Patient1, Day3


title: ZH-21-B6-Alo-Exo-SI-S-1

description: 16s rRNA


title: ZH-20-B6-Alo-MP-LI-S-2

description: 16s rRNA


title: Multiplexing set 7, Sample Tag library (ST), scRNAseq

description: BD Rhapsody


title: Multiplexing set 6, Sample Tag library (ST), scRNAseq

description: BD Rhapsody


title: ZH-19-B6-Alo-MP-LI-S-1

description: 16s rRNA


title: Topas seeds at 14DAP, TCT growth conditions, biological replicate 4


title: Topas seeds at 14DAP, TCT growth conditions, biological replicate 3


title: ZH-18-B6-Alo-Exo-LI-S-2

description: 16s rRNA


title: Topas seeds at 14DAP, TCT growth conditions, biological replicate 2


title: Multiplexing set 5, Sample Tag library (ST), scRNAseq

description: BD Rhapsody


title: Topas seeds at 14DAP, TCT growth conditions, biological replicate 1

description: TCT 14DAP_rep1


title: ZH-17-B6-Alo-Exo-LI-S-1

description: 16s rRNA


title: Topas seeds at 18DAP, TCT growth conditions, biological replicate 3


title: ZH-16-B6-Gar-MP-SI-S-2

description: 16s rRNA


title: Multiplexing set 4, Sample Tag library (ST), scRNAseq

description: BD Rhapsody


title: No nicotine, 24 HAI, replicate 7

city: Iași

first: Marius

last: Mihasan

state: Iași

address: Bulevardul Carol I, nr. 20 A

department: Biology

country: Romania

institute: Alexandru Ioan Cuza University of Iasi

description:
23_12_17_no_nic_T3_R7
nic_T3_R1, nic_T3_R2, nic_T3_R3, nic_T3_R4, nic_T3_R5 versus no_nic_T3_R1, no_nic_T3_R2, no_nic_T3_R3, no_nic_T3_R4, no_nic_T3_R5, no_nic_T3_R6, no_nic_T3_R7
stringtie.merged.gtf
counts_gene.txt
T3_deseq2.results.txt

data_processing:
Raw data files in fast5 format were basecalled using Guppy_6.5.7 with high accuracy (configuration file rna_r9.4.1_70bps_hac.cfg). Raw data files in fastq format contain the basecalled data, with a minimum Qscore = 7 per base.
Basecalled data was analyzed (quality checks to raw counts per gene) using the nf-core/nanoseq 3.1.0 pipeline (10.1038/s41587-020-0439-x) and the stringtie2 branch for transcript reconstruction. DESeq2 was used for differential gene expression analysis .
Assembly: Genome Build: ASM2191934v1 / NCBI_Assembly:GCA_021919345.1
Supplementary files format and content: stringtie.merged.gtf: for all samples, extended annotation that combines provided reference GTF with GTF file from each sample via StringTie2 Merge (takes as input a list of GTF/GFF files and merges/assembles these transcripts into a non-redundant set of transcripts; this mode is used in the differential analysis pipeline to generate a global, unified set of transcripts (isoforms) across multiple RNA-Seq samples).
Supplementary files format and content: counts_gene.txt: for all samples, gene expression estimates (raw counts) calculated by featureCounts.
Supplementary files format and content: deseq2.results.txt: a TXT file that contains differential gene expression results between samples found in the Description column, performed with DESeq2.

organism: Paenarthrobacter nicotinovorans

source_name: bacterial cell

growth_protocol: The strain was grown on citrate medium consisting of 0.2% Na-citrate, 34 mM Na2HPO4, 22 mM KH2PO4, 0.2% (NH4)2SO4, pH 7.0, 5% mineral solution (doi: 10.1515/bchm2.1961.323.1.236), 0.1 mg mL–1 biotin, and 35 μg mL–1 kanamycin.

extract_protocol:
Native RNA was extracted with the Promega SV Total RNA Isolation System (after 8.C., step 7 were added 8 µl of Proteinase K 20 mg/ml (Promega) and samples were incubated at 37⁰ C for 10 min before proceeding with 4.E, Steps 1–9).
Native RNA was polyadenylated using the Lucigen Poly(A) Polymerase Tailing Kit. Library preparation was performed with the Oxford Nanopore Technologies (ONT) Direct RNA sequencing kit (SQK-RNA002) and an adapted protocol for the MinION Flongle flowcells (https://www.protocols.io/view/flongle-directrna-library-preparation-kqdg35847v25/v1 ).

treatment_protocol: Cultures were grown without nicotine (no_nic samples) or supplemented with 0.3 mM nicotine (nic samples)

value: bacterial cell

value: control, no nicotine

value: 24 hours


title: No nicotine, 24 HAI, replicate 6

description:
23_12_07_no_nic_T3_R6
nic_T3_R1, nic_T3_R2, nic_T3_R3, nic_T3_R4, nic_T3_R5 versus no_nic_T3_R1, no_nic_T3_R2, no_nic_T3_R3, no_nic_T3_R4, no_nic_T3_R5, no_nic_T3_R6, no_nic_T3_R7
stringtie.merged.gtf
counts_gene.txt
T3_deseq2.results.txt


title: ZH-15-B6-Gar-MP-SI-S-1

description: 16s rRNA


title: No nicotine, 24 HAI, replicate 5

description:
23_11_01_no_nic_T3_R5
nic_T3_R1, nic_T3_R2, nic_T3_R3, nic_T3_R4, nic_T3_R5 versus no_nic_T3_R1, no_nic_T3_R2, no_nic_T3_R3, no_nic_T3_R4, no_nic_T3_R5, no_nic_T3_R6, no_nic_T3_R7
stringtie.merged.gtf
counts_gene.txt
T3_deseq2.results.txt


title: ZH-14-B6-Gar-Exo-SI-S-2

description: 16s rRNA


title: Multiplexing set 3, Whole transcriptome analysis library (WTA), scRNAseq

description: BD Rhapsody


title: Multiplexing set 3, Sample Tag library (ST), scRNAseq

description: BD Rhapsody


title: Multiplexing set 5, Whole transcriptome analysis library (WTA), scRNAseq

description: BD Rhapsody


title: ZH-12-B6-Gar-MP-LI-S-2

description: 16s rRNA


title: Multiplexing set 2, Whole transcriptome analysis and Sample Tag (ST) libraries, scRNAseq

description: BD Rhapsody


title: No nicotine, 10 HAI, replicate 6

description:
23_12_06_no_nic_T2_R6
nic_T2_R1, nic_T2_R2, nic_T2_R3, nic_T2_R4, nic_T2_R5 versus no_nic_T2_R1, no_nic_T2_R2, no_nic_T2_R3, no_nic_T2_R4, no_nic_T2_R6, no_nic_T2_R7
stringtie.merged.gtf
counts_gene.txt
T2_deseq2.results.txt

value: 10 hours


title: ZH-11-B6-Gar-MP-LI-S-1

description: 16s rRNA


title: Multiplexing set 1, Sample Tag library (ST), scRNAseq

description: BD Rhapsody


title: No nicotine, 10 HAI, replicate 5

description:
23_11_03_no_nic_T2_R5
nic_T2_R1, nic_T2_R2, nic_T2_R3, nic_T2_R4, nic_T2_R5 versus no_nic_T2_R1, no_nic_T2_R2, no_nic_T2_R3, no_nic_T2_R4, no_nic_T2_R6, no_nic_T2_R7
stringtie.merged.gtf
counts_gene.txt
NOT INCLUDED IN DIFFERENTIAL ANALYSIS BECAUSE THERE WAS ONLY 4% ALIGNMENT TO REFERENCE


title: Multiplexing set 1, Whole transcriptome analysis library (WTA), scRNAseq

description: BD Rhapsody


title: ZH-10-B6-Gar-Exo-LI-S-2

description: 16s rRNA


title: Multiplexing set 4, Whole transcriptome analysis library (WTA), scRNAseq

description: BD Rhapsody


title: ZH-09-B6-Gar-Exo-LI-S-1

description: 16s rRNA


title: No nicotine, 10 HAI, replicate 4

description:
23_04_02_no_nic_T2_R4
nic_T2_R1, nic_T2_R2, nic_T2_R3, nic_T2_R4, nic_T2_R5 versus no_nic_T2_R1, no_nic_T2_R2, no_nic_T2_R3, no_nic_T2_R4, no_nic_T2_R6, no_nic_T2_R7
stringtie.merged.gtf
counts_gene.txt
T2_deseq2.results.txt


title: ZH-08-B6-Gin-MP-SI-S-2

description: 16s rRNA


title: SPF Colon DSS D12 1

city: Cambridge

first: Ramnik

last: Xavier

address: 415 Main Street

institute: Broad Institute of MIT and Harvard

description: Fresh frozen spatial transcriptome sequencing

data_processing:
Raw sequencing BCL files were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files
Sequences were aligned to mm10 genome to generate gene expression counts using Space Ranger's default settings
Gene expression level of Refseq coding genes were quantified using Space Ranger's default settings
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg.gz: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg.gz: image of tissue and spots
Supplementary files format and content: scalefactors_json.json.gz: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png.gz: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png.gz: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv.gz: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

source_name: Colon

extract_protocol:
Fresh frozen intestinal tissue from  WT SPF, GF, and FMT mice and DSS treated WT mice was swiss rolled and OCT embedded, and 10um frozen sections were cut with cryostat.
Spatial transcriptome sequencing libraries were prepared with 10x Genomics Visium Spatial Gene Expression Slides & Reagent kit following the manufacturer's instruction.

value: Colon

value: intestinal tissue

value: SPF DSS


title: SPF Colon sham

value: SPF


title: RiboSeq_L22_PD_SCd_3

data_processing:
For the analysis of Riboseq data, adapters (-a AGATCGGAAGAGCACACGTCT -a CTGTAGGCACCATCAATATCTCGTATGCCGTCTTCTGCTTG) and (-g GTTCAGAGTTCTACAGTCCGACGATC) were removed with cutadapt version 1.18.
Transcript quantifications were done with salmon version 1.1.0 using Gencode vM21 annotation, for which UTRs were seperated from protein-coding transcripts.
mm10
"quant.sf" files are tab-seperated salmon outputs (includes transcript id, transcript length, effective length, TPM and raw_reads as columns).

growth_protocol: Small intestinal organoids were generated from intestinal crypts. They were cultured in BME (Amsbio) plugs in ENR media: Advanced Dulbecco’s modified Eagle’s media (DMEM)/F12 (Thermo Fisher Scientific), supplemented with 10mM  HEPES (ThermoFisher Scientific), 1x GlutaMAXTM (Thermo Fisher Scientific), 100 U/ml penicillin, 100µg/ml streptomycin (Thermo Fisher Scientific), 0,1% BSA (Sigma Aldrich), 1x B27 (Thermo Fisher Scientific) and 1x N2 (Thermo Fisher Scientific), together with 10% (v/v) Noggin conditioned media, 10% (v/v) R-spondin conditioned media and 50ng/ml EGF (Peprotech). All organoid lines were kept at 37oC in a humidified atmosphere with 5% CO2.

extract_protocol:
Briefly, intestinal organoids were generated from VillinCreERT2RPL22.HA mice, 150 plugs were used for each replicate. Translating ribosomes were stalled by treating cells with 100 μg/ml cycloheximide for 3–5 minutes at 37 °C and immediately incubating them on ice for the remainder of the experiment. After collecting the cells, pellets were washed twice with cold PBS supplemented with 100 µg/mL cycloheximide, resuspended in ice-cold lysis buffer (20 mM Tris HCl pH 7.4, 10 mM MgCl2, 150 mM KCl, 1% NP-40, 100 µg/mL cycloheximide and 1x EDTA-free proteinase inhibitor cocktail (Roche)) and incubated for 20 minutes on ice, followed by mechanical disruption with a 25G syringe. Lysates were then centrifuged at max speed for 20 minutes at 4 °C and the supernatants were collected. Lysates were precleared with Pierce™ Control Agarose Matrix (Thermo Fisher Scientific) for 20 minutes at 4°C, and immunoprecipitated with pre-washed AntiHA.11 Epitope Tag Affinity Matrix (BioLegend) for 4 hours at 4oC. Beads were washed twice with ice-cold lysis buffer and twice with ice-cold wash buffer (20 mM Tris HCl pH 7.4, 10 mM MgCl2, 350 mM KCl, 1% NP-40, 100 µg/mL cycloheximide and 1x EDTA-free protease inhibitor cocktail (Roche)). Tagged ribosomes were then eluted by incubating the beads with 200 µg/mL HA peptide (Thermo Fisher Scientific) for 15 minutes at 30oC with constant agitation. Digestion of non-protected RNA was performed with 10 µl of RNase I (Thermo Fisher Scientific) for 40 minutes at 25 °C and the reaction was stopped by adding 13 µl of SUPERASE (Thermo Fisher Scientific). Lastly, ribosome-protected fragments (RPFs) were purified using miRNeasy minikit (Qiagen), following manufacturer’s instructions.
Ribosome Protected Fragments ranging from 19 to 32 nucleotides were size-selected using a 10% TBE-Urea polyacrylamide gel. 3’ and 5’ ends were modified accordingly and the respective adapters were ligated with a T4 RNA ligase I (New England Biolabs). The final products were size-selected one last time and rRNA depletion was performed using custom-made biotinylated oligos together with MyOne Streptavidin C1 DynaBeads (Thermo Fisher Scientific). Purified RPFs were then used to synthesize cDNA with SuperScript III (Thermo Fisher Scientific), according to the manufacturer’s instructions, and using the RTP primer (Table yy). After purification with G50 columns (Merck), cDNA was amplified using Phusion High-Fidelity DNA Polymerase (Thermo Fisher Scientific), with primers containing different RP indexes to allow for sequencing. PCR products were purified with a QIAquick PCR purification kit (Qiagen) and size-selected one last time with an E-Gel SizeSelect II 2%, (Thermo Fisher Scientific).

treatment_protocol: Stem cell-depleted cultures (SCd) were obtained when culturing organoids in EN media (depleted of R-spondin) for 2 days.

value: intestine

value: organoid

value: stem cell depletion


title: No nicotine, 5 HAI, replicate 5

description:
23_11_02_no_nic_T1_R5
nic_T1_R1, nic_T1_R2, nic_T1_R3, nic_T1_R4, nic_T1_R5 versus no_nic_T1_R1, no_nic_T1_R2, no_nic_T1_R3, no_nic_T1_R4, no_nic_T1_R5, no_nic_T1_R6, no_nic_T1_R7
stringtie.merged.gtf
counts_gene.txt
T1_deseq2.results.txt

value: 5 hours


title: No nicotine, 24 HAI, replicate 4

description:
23_04_03_no_nic_T3_R4
nic_T3_R1, nic_T3_R2, nic_T3_R3, nic_T3_R4, nic_T3_R5 versus no_nic_T3_R1, no_nic_T3_R2, no_nic_T3_R3, no_nic_T3_R4, no_nic_T3_R5, no_nic_T3_R6, no_nic_T3_R7
stringtie.merged.gtf
counts_gene.txt
T3_deseq2.results.txt


title: ZH-06-B6-Gin-Exo-SI-S-2

description: 16s rRNA

value: Mouse uptake


title: ZH-13-B6-Gar-Exo-SI-S-1

description: 16s rRNA


title: RiboSeq_L22_PD_SCd_2


title: ZH-07-B6-Gin-MP-SI-S-1

description: 16s rRNA


title: No nicotine, 5 HAI, replicate 4

description:
23_04_01_no_nic_T1_R4
nic_T1_R1, nic_T1_R2, nic_T1_R3, nic_T1_R4, nic_T1_R5 versus no_nic_T1_R1, no_nic_T1_R2, no_nic_T1_R3, no_nic_T1_R4, no_nic_T1_R5, no_nic_T1_R6, no_nic_T1_R7
stringtie.merged.gtf
counts_gene.txt
T1_deseq2.results.txt


title: RiboSeq_L22_PD_SCd_1


title: Nicotine, 24 HAI, replicate 5

description:
23_12_14_nic_T3_R5
nic_T3_R1, nic_T3_R2, nic_T3_R3, nic_T3_R4, nic_T3_R5 versus no_nic_T3_R1, no_nic_T3_R2, no_nic_T3_R3, no_nic_T3_R4, no_nic_T3_R5, no_nic_T3_R6, no_nic_T3_R7
stringtie.merged.gtf
counts_gene.txt
T3_deseq2.results.txt

value: nicotine 0.3 mM


title: RNAseq_SCd_3

data_processing:
Transcript quantifications were done with salmon version 1.1.0 using Gencode vM21 annotation.
mm10
"quant.sf" files are tab-seperated salmon outputs (includes transcript id, transcript length, effective length, TPM and raw_reads as columns).

extract_protocol:
For RNA extraction, cells were collected on ice, washed in PBS and centrifuged at 1000rpm for 5 minutes at 4oC. Pellets were lysed with TRIzolTM Reagent (Thermo Fisher Scientific). RNA was isolated by chloroform extraction followed by centrifugation, isopropanol precipitation, washing in 75% ethanol and resuspension in nuclease-free water.
Libraries were generated with the TrueSeq Stranded mRNA kit (Illumina).


title: ZH-04-B6-Gin-MP-LI-S-2

description: 16s rRNA


title: ZH-03-B6-Gin-MP-LI-S-1

description: 16s rRNA


title: RNAseq_SCd_2


title: No nicotine, 10 HAI, replicate 7

description:
23_12_16_no_nic_T2_R7
nic_T2_R1, nic_T2_R2, nic_T2_R3, nic_T2_R4, nic_T2_R5 versus no_nic_T2_R1, no_nic_T2_R2, no_nic_T2_R3, no_nic_T2_R4, no_nic_T2_R6, no_nic_T2_R7
stringtie.merged.gtf
counts_gene.txt
T2_deseq2.results.txt


title: Nicotine, 5 HAI, replicate 5

description:
23_12_12_nic_T1_R5
nic_T1_R1, nic_T1_R2, nic_T1_R3, nic_T1_R4, nic_T1_R5 versus no_nic_T1_R1, no_nic_T1_R2, no_nic_T1_R3, no_nic_T1_R4, no_nic_T1_R5, no_nic_T1_R6, no_nic_T1_R7
stringtie.merged.gtf
counts_gene.txt
T1_deseq2.results.txt


title: No nicotine, 5 HAI, replicate 7

description:
23_12_15_no_nic_T1_R7
nic_T1_R1, nic_T1_R2, nic_T1_R3, nic_T1_R4, nic_T1_R5 versus no_nic_T1_R1, no_nic_T1_R2, no_nic_T1_R3, no_nic_T1_R4, no_nic_T1_R5, no_nic_T1_R6, no_nic_T1_R7
stringtie.merged.gtf
counts_gene.txt
T1_deseq2.results.txt


title: Nicotine, 10 HAI, replicate 5

description:
23_12_13_nic_T2_R5
nic_T2_R1, nic_T2_R2, nic_T2_R3, nic_T2_R4, nic_T2_R5 versus no_nic_T2_R1, no_nic_T2_R2, no_nic_T2_R3, no_nic_T2_R4, no_nic_T2_R6, no_nic_T2_R7
stringtie.merged.gtf
counts_gene.txt
T2_deseq2.results.txt


title: cut&tag, IGF1,rep3

data_processing:
Paired-end reads were aligned with Homo sapiens. GRCh38 genome using Bowtie2.
Peaks were called using MACS v2.2.6, and the bam files were converted to bigWiggle files using deeptools.
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

growth_protocol: Panc1 cells were maintained in DMEM supplemented with 10% FBS and antibiotics atmosphere with 5% CO2 at 37℃.

extract_protocol:
50000 control or IGF1-treated panc1 cells were submitted for Cut&Tag analysis. c-JUN antibody was used to purify DNA fragments that bind to cjun. libraries were constructed using Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme, Nanjing, China, #TD903) according to the manufacturer’s protocol.
Paired-end libraries were prepared and sequenced on an Illumina NovaSeq6000 platform

treatment_protocol: Panc1 cells were serum-free starved for 12 hours and treated with or without IGF1 for 12 hours.

value: pancreatic cancer cells

tag: antibody

value: c-JUN


title: ZH-02-B6-Gin-Exo-LI-S-2

description: 16s rRNA


title: ZH-01-B6-Gin-Exo-LI-S-1

description: 16s rRNA


title: ZH-36-B6

description: 16s rRNA

value: Mouse gut


title: cut&tag, IGF1,rep2


title: SupT1 infected, DisomeSeq, cyclo, 24hpi, rep1

city: Würzburg

first: Neva

last: Caliskan

address: Josef-Schneider-Str. 2/D15

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

data_processing:
For PRICE analysis: (1) remove adapters cutadapt -a AGATCGGAAGAGCACACG -e 0.3 (2)  filter out short reads gedi -e FastqFilter -layout 2UI5U151 -min 18 (3) h.rRNA and mycoplasma removal  bowtie2 -un un --local -U (4) mapping reads STAR --runMode alignReads --alignIntronMax 1  --outSAMmode NoQS --outSAMtype BAM SortedByCoordinate --alignEndsType Extend5pOfRead1 --outSAMattributes nM MD NH (5) Convert BAM to CIT gedi -e BAM2CIT -umi (6) gedi -e CorrectCIT (7) deduplicate UMIs gedi -e DedupUMI (8) gedi -e MergeCIT (9) create report gedi -e Stats (10) P-site calling gedi -e Price
cutadapt 3.5, bowtie2 version 2.3.0, STAR version=2.7.10b, Gedi version 1.0.6, Price version 1.0.4
For differential gene expression analysis: (1) Count reads per genomic feature featureCounts -O (2) normalization and log2 fold change calculations by deltaTE/DTEG.R
featureCounts version 2.0.0, deltaTE (Chothani et al. 2019)
Assembly: GCF_000001405.36, AF324493
Supplementary files format and content: The PRICE codons BED files contain the genomic regions corresponding to predicted P-sites for each RiboSeq read. The "score" column equals to the read coverage at this position.
Supplementary files format and content: The countMatrix CSV files contain the read counts overlapping each genomic feature for every time point of infection for either cyclo RiboSeq or RNASeq.
Supplementary files format and content: The deltaTE text files contain the log2 fold changes (plus statistics) for each genomic feature, normalized by DESeq2 and calculated for each timepoint of infection against the 0h mock sample. This includes RiboSeq changes, RNASeq changes and  translation efficiency (TE) changes.
Supplementary files format and content: The DisomeSeq BED files contain the DisomeSeq reads that map to the HIV genome. The DisomeSeq text files contain the summed coverage per nucleotide for the HIV genome (column1: chromosome identifier; column2: genome position, column3: read coverage).
Supplementary files format and content: PRICE_report_harr_cyclo.tar contains quality control information for the RiboSeq PRICE pipeline, for both the cycloheximide and harringtonine treated samples. The index.html file allows interactive browsing through the different plots.
Supplementary files format and content: PRICE_report_disome.tar contains quality control information for the DisomeSeq PRICE pipeline. The index.html file allows interactive browsing through the different plots. Note that the p-site prediction is not valid for the DisomeSeq.
Supplementary files format and content: interactive_dTE_volcano_plots_DGE.tar contains interactive volcanoplots (translation efficiency) of the differential gene expression analysis with the deltaTE pipeline. Each infection timepoint was compared to the mock sample. Genes exceeding +/- 1 fold change and p_adj < 0.05 are colored based on consolidated gene ontology.
Supplementary files format and content: interactive_deltaTE_plots_DGE.tar contains interactive RiboSeq/RNASeq log2 fold change plots, of the differential gene expression analysis with the deltaTE pipeline. Each infection timepoint was compared to the mock sample. Only genes that are labelled as differentially expressed are plotted.
Library strategy: Ribo-seq

organism:
Homo sapiens
Human immunodeficiency virus 1

extract_protocol:
Ribosome profiling samples were prepared as previously described (McGlincy and Ingolia., 2017) with modifications for suspension cell lines. Briefly, at each time point of infection, cells were treated with 100 μg/ml cycloheximide in DMSO at 37 °C for 5 min. For harringtonine treated samples, cells were treated with 2 μg/ml harringtonine in DMSO at 37 °C for 5 min, followed by cycloheximide treatment. Cells were immediately pelleted at 1000 RPM for 3 min at 4 °C, washed once with cold cycloheximide containing PBS and the cell pellet was snap-frozen in liquid nitrogen and stored at -80 °C, till further use. Cell pellet was thawed in the presence of ice-cold lysis buffer (20 mM Tris-Cl pH7.4, 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 100 μg/ml cycloheximide, 1% Triton-X, 25U/ml Turbo DNase ) and triturated 10 times through a 26G needle. The lysate was centrifuged at 17000g for 10 min at 4 °C and the supernatant was recovered. Cell lysates were subjected to RiboSeq and RNASeq.
RiboSeq libraries: RNase I footprinting of ribosomes, ribosome purification by ultracentrifugation through a sucrose cushion, RNA extraction, polyacrylamide gel size selection for footprint fragments, preadenylylated linker ligation, reverse transcription, first-strand cDNA circularization. RNASeq libraries from these samples were constructed using CORALL Total RNA-Seq Library Prep Kit (Lexogen), according to manufacturer’s instructions.

value: T-cell

value: cycloheximide


title: SupT1 infected, DisomeSeq, cyclo, 16hpi, rep2


title: No nicotine, 5 HAI, replicate 6

description:
23_12_05_no_nic_T1_R6
nic_T1_R1, nic_T1_R2, nic_T1_R3, nic_T1_R4, nic_T1_R5 versus no_nic_T1_R1, no_nic_T1_R2, no_nic_T1_R3, no_nic_T1_R4, no_nic_T1_R5, no_nic_T1_R6, no_nic_T1_R7
stringtie.merged.gtf
counts_gene.txt
T1_deseq2.results.txt

value: bacterial cell

value: control, no nicotine


title: cut&tag, IGF1,rep1


title: ZH-35-B6

description: 16s rRNA


title: ZH-34-B6

description: 16s rRNA


title: ZH-05-B6-Gin-Exo-SI-S-1

description: 16s rRNA


title: SupT1 infected, DisomeSeq, cyclo, 8hpi, rep2


title: SupT1 infected, DisomeSeq, cyclo, 16hpi, rep1


title: cut&tag, Control,rep2


title: SupT1 infected, DisomeSeq, cyclo, 8hpi, rep1


title: cut&tag, Control,rep3


title: ZH-33-B6

description: 16s rRNA