title: TM+CO rep1

first: Bin

last: Yan

address: 140Hanzhong Road

institute: Nanjing Medical University

data_processing:
First, we use FastQC performs basic statistics on the quality of the raw reads. Then, those read sequences produced by the Illumina pipeline in FASTQ format were preprocessed through Trimmomatic software which can be summarized as follows: (1) Remove low-quality reads: The reads that mean quality value less than 15 were removed. (2) Remove the reads that contain more than 6 N bases. (3) Remove adapters. Remove the reads that alignment with the adapter sequence. (4) Drop reads below the 50 bases long after trimming.
The remaining reads that passed all the filtering steps was counted as clean reads and all subsequent analyses were based on this. At last, we use FastQC performs basic statistics on the quality of the clean reads.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using BWA v0.7.12 (Burrows Wheeler Aligner) and clean reads were aligned to the reference genome using BWA mem v0.7.12.
All peak calling was performed with MACS2 using ‘macs2 -q 0.05 --call-summits --nomodel --shift -100 --extsize 200 --keep-dup all’. For simulations of peaks called per input read, aligned and de-duplicated BAM files were used without any additional filtering.
The position of peak summit around transcript start sites of genes can predict the interaction sites of protein and gene. PeakAnnotator was used to identify the nearest TSS of every peak and the distance distribution between peaks and TSS was shown. Besides, the distribution of peak summits on different function regions, such as 5’ UTR, CDS, 3’UTR, was performed.
Assembly: GRCm39
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

extract_protocol:
1x10^5 cells were harvested, counted and centrifuged for 5 min at 500g at room temperature. Cell activity was detected with LUNA-FLTM and counted. Cells are bound to Concanavalin A-coated magnetic beads, and the cell membrane is permeabilized by Digitonin. The enzyme pA-Tn5 Transposase precisely binds the DNA sequence near the target protein under the antibody guidance and results in factor-targeted tagmentation.
DNA sequence is tagmented, with adapters added at the same time at both ends, which can be enriched by PCR to form the sequencing-ready libraries. After the PCR reaction, libraries were purified with the AMPure beads and library quality was assessed on the Agilent Bioanalyzer 2100 system. The library preparations were sequenced on Illumina Novaseq platform and 150bp paired-end reads were generated.

value: Alveolar bone lysates from TM+CO models


title: TM rep2

status: Public on Apr 09 2025

type: SRA

city: Nanjing

country: China

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

source_name: BMDMs

tag: cell type

value: BMDMs

tag: treatment

value: Alveolar bone lysates from TM models


title: X813o

type: genomic

city: Copenhagen N

first: NNF CBMR

last: Single-Cell Omics Platform

address: Blegdamsvej 3B

department: Faculty of Health and Medical Sciences

country: Denmark

institute: University of Copenhagen

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol

data_processing: Raw data were transformed into methylation estimates (beta values) by normalization with the SeSAMe R package. Beta values were derived from the ratio of the fluorescence intensity of a methylated probe for a specific CpG to the total probe intensity (the sum of the signal from both the methylated and unmethylated probes plus a constant). These values fell in the range from zero to one, where zero indicated no methylation. A beta value was generated for each probe of the array for every animal and was supported by a detection p-value corresponding to the confidence in the normalized beta value.

label: Cy3 and Cy5

source_name: skeletal muscle

label_protocol: Standard Illumina protocol

extract_protocol: DNA from QUAD of young and old control and Nampt KO mice was isolated with the DNeasy Blood & Tissue Kit (Qiagen, Germany)

tag: tissue

value: skeletal muscle

tag: genotype

value: ko

tag: Sex

value: male


title: Sbj3_mAb12

type: protein

city: Siena

first: Viola

last: Viviani

address: Via Fiorentina, 1

country: Italy

institute: GSK

description:
FS00010035_Area2.txt
MENB NEXT GEN-001 (V114_01) 205285/ETR

hyb_protocol: Protein arrays were first blocked 60 min in Blocking Buffer (Block it, Arrayit). The array was then incubated 1h a room temperature (RT) with mAbs diluted 0,5 ug/ml for anti-human IgG-specific analysis. After two washing with 0.1% Tween in PBS buffer (TPBS), arrays were incubated with an AlexaFluor 647-conjugated IgG anti-human (1:800 – Jackson Immunoresearch) at RT for 1 h to detect interactions. Slides were washed again as before and washed once in PBS, then rinsed in sterile water and dried.

scan_protocol: Fluorescence signals were detected by using a InnoScan 710AL (Innopsys) and the 16-bit images were generated with Mapix software at 10 µm per pixel resolution.

data_processing: Images were processed using ImaGene 9.0 software (Biodiscovery Inc, CA, USA). Elaboration and analysis of image raw fluorescence Intensity (FI) data  was performed using in-house developed R scripts. For each protein the fluorescence intensity data of the replicates was subtracted by local background values surrounding each spot and averaged, hence resulting in a single data point per sample named Mean Fluorescence Intensity (MFI).

label: AlexaFluor 647-conjugated anti-human IgG secondary antibody

molecule: protein

organism: Homo sapiens

source_name: recombinant HumAbs

label_protocol: The secondary antibody used for arrays was from Jackson Immunoresearch, (872 W Baltimore Pike, West Grove, PA 19390 USA). It was conjugated to the Alexafluor dye (Alexa 647) by the company.

extract_protocol:
Protein extracted from samples.
Briefly: bacterial pellets were either resuspended in equilibration buffer (50?mM NaH2PO4 and 300?mM NaCl, pH 8.0) before mechanical lysis by sonication or resolubilized in B-PER Bacterial Protein Extraction Reagent (B-PER, Thermo Fisher, 1?g/10?ml) or Cell-Lytic Express (Sigma-Aldrich). The unbroken cells and bacterial debris were removed by centrifugation and proteins were purified from the supernatant by IMAC (immobilized metal-ion-affinity chromatography) purification using cobalt-based chelating columns (Hitrap TALON Crude; Merck) according to the manufacturer?s instructions. Columns were washed with equilibration buffer, and proteins bound to the resin were then eluted with imidazole gradient (from 0?mM to 250?mM imidazole) in equilibration buffer. Samples were dialyzed in PBS. The recombinant PorA and PorB proteins were instead purified from inclusion bodies. PorA bacterial pellets were dissolved in Guanidine 6?M, 50?mM Tris-HCl, pH 8.5, whereas PorB bacterial pellets were lysed in 8?M Urea, 50?mM Tris-HCl, pH 8,0. The solubilized inclusion bodies were concentrated in an Amicon concentrator, 10?kDa cutoff (Millipore). Then samples were diluted into a refolding buffer (200?mM CAPS, 400?mM NaCl, 50?mM Tris-HCl, 0.3% Lauryl-N,N-dimethylamine-N-Oxide [LDAO], pH 11). The mixtures were stirred ON at 4?°C and the pH was adjusted to 8.0 with 1?N HCl. The refolded porins were loaded onto an IMAC column (HisTrap HP, GE Healthcare), washed with PBS?+?0,1% LDAO (PBSL) and eluted with PBSL containing 300?mM imidazole. The samples were concentrated with Amicon (10?kDa cutoff) and then loaded onto an S-300 Sephacryl column (GE Healthcare) and the protein was eluted in 0,1% PBSL.

treatment_protocol: Recombinant expressed monoclonal antibodies in mammalian cells

tag: subclass

value: PBMC


title: RS4;11, 1:10000 DMSO, rep 3

city: Düsseldorf

first: Vera

middle: Helena

last: Jepsen

address: Moorenstraße 5

country: Germany

institute: University Hospital Düsseldorf

description:
Library name: Unknown_CF408-001T0021
G3

library_source: transcriptomic

data_processing:
Analysis of fastq files was performed by using the nf-core/rnaseq pipeline (https://nf-co.re/rnaseq/3.15.1/).
Assembly: hg38
Supplementary files format and content: text file includes TPM values for each sample

molecule: total RNA

growth_protocol: BCP-ALL cells were maintained at 37 °C and 5% CO2 in RPMI GlutaMAX (Thermo Fisher Scientific) with 20% fetal bovine serum (Biowest).

extract_protocol:
BCP-ALL cells were lysed using RLT buffer (Qiagen) and RNA was isolated with the RNeasy Mini kit with on-column DNA digestion (Qiagen).
RNA concentration was detected with Nanodrop2000 (Thermo Fisher Scientific) and the integrity was confirmed with Agient2100 (Perkin Elmer LabChip GX). VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina NR605 was used to construct the mRNA library in strict accordance with the protocol provided by Vazyme. Quality control, library preparation and sequencing were performed by Biomarker Technologies (BMK) GmbH (Münster, Germany).

treatment_protocol: 1 x 10^6 BCP-ALL cells were treated with 1 µM Quisinostat or a 1:10000 dilution of DMSO for 24 hours.

tag: cell line

value: B cell precursor leukemia

value: human hyperdiploid karyotype, KMT2A::AFF1 fusion gene

value: female


title: Total_RNA_WT_Rep4

city: Memphis

first: Paul

middle: A.

last: Northcott

address: 262 Danny Thomas Place

department: Developmental Neurobiology

country: USA

institute: St. Jude Children's Research Hospital

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence, cleaned reads were mapped to mm10 using STAR
Assembly: mm10
Supplementary files format and content: Tab-separated ReadsPerGene.out.tab

source_name: cerebellum

extract_protocol:
GNPs were isolated, and cell pellet snap frozen in liquid N2 (LN2). The 1.5 ml Eppendorf tubes containing the GNP pellet was placed in the mortar super cooled under LN2. 150 ml of 1X polysome lysis buffer- pH 7.5 (10 mM Tris-HCl pH 7.5, 100 mM KCl, 5 mM MgCl2, 0.5% (w/v) sodium deoxycholate, 1% (v/v) Nonidet-P40, 10 mM DTT, 100 µg/ml cycloheximide, 1 U/ml SUPERaseIn RNase Inhibitor, 1X protease inhibitor cocktail (EDTA-free) in RNAse-free deionized water). The frozen mix of cell pellet and lysis buffer was pulverized using a pre-chilled pestle. Eppendorf tubes were placed on ice to thaw and mixed with pipetting using a 200 ml tip. Samples were centrifuged at 2000×g for 5 min at 4°C to pellet nuclei and cell debris. Supernatant was transferred to a fresh tube and centrifuged at 12,000×g for 5 min at 4°C. 150 ml of the resulting supernatant was loaded onto the top of a 10-50% sucrose gradient in 4 ml Polypropylene ultracentrifuge tubes (Cat# 344062, Beckman Coulter, Inc) . The tubes were centrifuged in a SW60Ti rotor at 246,606×g (38,000 RPM) for 125 min with low acceleration and brakes off. All tubing was washed with RNase-free H2O at 3 ml/min using a clean ultracentrifuge tube. The BioComp™ Piston Gradient Fractionator was used to fractionate and record absorbance of the samples, setting the baseline absorbance by 60% sucrose. The first material to come out was free RNA and protein, followed by the 40S, 60S, 80S monosome, and increasing polysome peaks. Fractions were collected into microcentrifuge tubes as they exit the reader for use in downstream applications. Once the last of the sample was collected, several additional milliliters of 60% sucrose were flown through the tubing to clean it out and set the baseline again for next sample. RNA was extracted separately from monosomic, disomic and polysomic fractions using TRIzol™ Reagent (Life Technologies) and processed for RNA-sequencing.
RNA libraries for RNA-seq were prepared following manufacturer's protocols

value: cerebellum

tag: fraction

value: Total

value: GNP

value: WT


title: Sbj3_mAb3

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: RS4; 11, 1 µM Quisinostat, rep 3

description:
Library name: Unknown_CF408-001T0018
F3


title: 80S_MUT_Rep3

value: Elp1+/-16bp,  Elp1HET


title: TM rep1


title: Sbj3_mAb10

description:
FS00010034_Area3.txt
MENB NEXT GEN-001 (V114_01) 205285/ETR


title: X809o


title: TM+CO rep2


title: BLANK rep1

value: Alveolar bone lysates from BLANK models


title: X807o

value: wt


title: Polysome_MUT_Rep2

value: Polysome


title: Total_RNA_MUT_Rep3


title: Sbj2_mAb20

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: Di-trisome_MUT_Rep3

value: Di-trisome


title: Di-trisome_MUT_Rep2


title: Tumor, Cre+, scRNA seq, rep4

city: Beijing

first: Qianchen

last: Li

address: Beijing

institute: PKU

library_source: transcriptomic single cell

data_processing:
Raw reads were demultiplexed and mapped to the reference genome by 10X Genomics Cell Ranger pipeline (https://support.10xgenomics.com/single-cell-geneexpression/software/pipelines /latest/what-is-cell-ranger) using default parameters.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: tumor

extract_protocol:
Cells were captured in droplets at a targeted cell recovery of cells. After the reverse transcription step, emulsions were broken and Barcoded-cDNA was purified with Dynabeads, followed by PCR amplification.
Amplified cDNA was then used for 3’gene expression library construction. For gene expression library construction, 50 ng of amplified cDNA was fragmented and end-repaired, double-size selected with SPRIselect beads, and sequenced on an NovaSeq platform (Illumia) to generate 150 bp paired-end Reads

value: tumor

value: Cre+


title: Tumor, Cre-, scRNA seq, rep3

value: Cre-


title: X805o

value: skeletal muscle

value: ko

value: male


title: X803o


title: Polysome_MUT_Rep1


title: 80S_MUT_Rep2


title: Sbj2_mAb12

description: MENB NEXT GEN-001 (V114_01) 205285/ETR

value: PBMC


title: X811o


title: Tumor, Cre+, scRNA seq, rep2


title: Tumor, Cre-, scRNA seq, rep1


title: X791o


title: X789o


title: Di-trisome_MUT_Rep1


title: Sbj2_mAb11

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: Sbj2_mAb17

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: Sbj2_mAb5

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: X787y


title: Total_RNA_MUT_Rep1


title: 80S_MUT_Rep1


title: Sbj1_mAb15

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: X781y


title: 80S_WT_Rep5


title: Sbj2_mAb10

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: Patient 10 RLSS-177.RCC

type: RNA

city: Bangkok

first: Phu

middle: Nguyen Trong

last: Tran

address: 1873 Rama IV Rd, Pathum Wan

country: Thailand

institute: Faculty of Medicine, Chulalongkorn University

hyb_protocol: Standard Nanostring miRNA hybridization protocol (10 μL Reporter CodeSet, 10 μL hybridization buffer, a 5 μL aliquot  from the miRNA Sample Preparation Protocol, and 5 μL Capture ProbeSet)

scan_protocol: nSolverTM software (v4.0; NanoString)

data_processing: The raw count data were processed using the nSolverTM software (version 4.0; NanoString). Each miRNA's count data were adjusted by subtracting the geometric mean of the negative controls. Furthermore, normalization was conducted by using the average (geometric mean) of the positive controls and the geometric mean of the top 100 most highly expressed miRNAs.

label: Refer to the NanoString nCounter Assay System Manual

source_name: serum

label_protocol: Standard Nanostring miRNA protocols

extract_protocol: 200 μl of serum from patients underwent cell-free total RNA extraction using the miRNeasy Serum/Plasma Kit (Qiagen in Gaithersburg, MD, USA). 3  μl of each sample was used for nCounter Human v3 miRNA miRNA Expression Assays (NanoString Technologies, Seattle, USA). A subset of 12 serum samples (7 from the non-SPHS group and 5 from the SPHS group) was randomly chosen for analysis. All data were collected using the nCounter Digital Analyzer, with 280 fields of view per sample.

value: serum

tag: severity

value: NonSPHS

tag: age

value: Male


title: Patient  12 RLSS-345.RCC


title: X783y


title: Sbj1_mAb23

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: X779y


title: Polysome_WT_Rep5

value: cerebellum

value: GNP


title: Sbj1_mAb13

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: Sbj1_mAb21

description:
FS00010017_Area3.txt
MENB NEXT GEN-001 (V114_01) 205285/ETR


title: Di-trisome_WT_Rep5

value: WT


title: X777y


title: Polysome_WT_Rep4


title: Patient  8 RLSS-193.RCC

value: Female


title: X785y

value: wt


title: X777o


title: Sbj2_mAb7

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: Di-trisome_WT_Rep4


title: Patient 6 RLSS-171.RCC


title: Sbj1_mAb12

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: Patient  9 RLSS-202.RCC


title: X775y


title: 80S_WT_Rep4


title: Sbj1_mAb9

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: Patient 11 RLSS-185.RCC


title: Sbj3_mAb7

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: Sbj1_mAb14

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: Total_RNA_MUT_Rep4

value: Total

value: Elp1+/-16bp,  Elp1HET


title: X771y


title: Patient 4 RLSS-153.RCC

value: SPHS


title: Total_RNA_WT_Rep5


title: Sbj3_mAb3

description:
FS00010032_Area3.txt
MENB NEXT GEN-001 (V114_01) 205285/ETR


title: Patient 2 RLSS-138.RCC


title: X769y


title: Sbj1_mAb1

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: Patient 7 RLSS-176.RCC


title: Spt6 F249K, MNase, 37C, Rep2

city: Chapel Hill

first: Austin

middle: J

last: Hepperla

state: NC

address: 7018B Mary Ellen Jones Building

department: Genetics

institute: University of North Carolina at Chapel Hill

description: Library name: FK-HIV_MNase_rep2_R1.fastq.gz

data_processing:
RNA-seq were paired-end sequenced. Reads were filtered for adaptor contamination using cutadapt and filtered such that at least 90% of bases of each read had a quality score > 30. Reads were aligned to the reference genome (sacCer3) using STAR version 2.5.2b retaining only primary alignments. Reads overlapping blacklisted regions of the genome were then removed. Transcript abundance was then estimated using Salmon, and differentially expressed genes were detected using DESeq2 with the criteria of adjusted P values (adjP) < 0.05.
MNase-seq were paired-end sequenced. Reads were filtered for adapter contamination using cutadapt and filtered such that at least 90% of bases of each read had a quality score >20. Duplicated sequences were then capped at a maximum of 5 occurrences, and reads were aligned to the reference genome (sacCer3) using STAR version 2.5.2b retaining only primary alignments. Reads overlapping blacklisted regions of the genome were then removed. ChIP-seq reads were then extended in silico to a fragment size of 250 bp, while the center of the paired-end MNase-seq reads were denoted as the nucleosome dyad.
Assembly: sacCer3
Supplementary files format and content: Bigwig files contain the normalized signal across the genome, viewable in genome browsers.
Supplementary files format and content: RNA-seq raw counts files contain the raw read counts per gene, with all three replicates in separate columns.
Supplementary files format and content: MNase-seq nucleosome occupancy files contain the subsampled, calculated nucleosome occupancy scores for all samples. The replicates for each sample were merged first and subsampled so that the fewest number of reads for each fragment size was identified and used as the subsampling depth. Nucleosome dyad positions are calculated as previously described in Brogaard et al. 2012.

organism: Saccharomyces cerevisiae

source_name: budding yeast

growth_protocol: Wild-type (S288C), spt6-F249K, spn1-R263D, and spn1-F267E strains were engineered with a C-terminal 3X FLAG tag in the SPT6 gene using standard yeast manipulation protocols (Janke et al., 2004). The integrations were confirmed by PCR and immunoblotting. The spt6-F249K, spn1-R263D, and spn1-F267E temperature sensitive strains were grown in YPD to an OD600 of 0.6 at 30°C. An equal volume of YPD medium pre-warmed to 44°C was added, and the cultures were shifted to 37°C for an additional 120 minutes prior to harvesting for all experiments.

extract_protocol:
For both RNA-seq and ChIP-seq experiments, yeast strains were grown as described above and temperature shifts were performed. RNA extractions were prepared as described previously (Dronamraju et al., 2018). ChIPs were performed as described in Dronamraju et al. 2018, with minor modifications. In the current set of experiments, after the temperature shift and before cell lysis and sonication, yeast cells were mixed with 1% of S. pombe yeast cells. Following the spike-in of S. pombe, lysis and sonication and immunoprecipitation was performed with total RNAPII antibody as described previously (Dronamraju et al., 2018). MNase digestions were performed as described previously (Belsky et al., 2015).
RNA and ChIP libraries were performed as previously described (Dronamraju et al. 2018), with stranded libraries being made for the RNA-seq. MNase library preparations of the ideally digested samples (generating a nucleosomal ladder) were performed on bead-bound DNA as previously described (Gutierrez et al., 2019).

tag: strain

tag: temperature

value: 37° C

value: budding yeast


title: Sbj3_mAb9

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: X765o

value: skeletal muscle


title: Sbj3_mAb6

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: Sbj1_mAb10

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: X763y


title: 80S_WT_Rep3


title: Spn1 R263D, MNase, 37C, Rep3

description: Library name: RD-HIV_MNase_rep3_R1.fastq.gz


title: Di-trisome_WT_Rep2

value: Di-trisome


title: X761y

value: male


title: X775o


title: Total_RNA_WT_Rep3


title: X773o


title: Sbj1_mAb8

description: MENB NEXT GEN-001 (V114_01) 205285/ETR

value: PBMC


title: Patient  3 RLSS-222.RCC

value: serum


title: Sbj1_mAb2

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: Spt6 F249K, MNase, 37C, Rep1

description: Library name: FK-HIV_MNase_rep1_R1.fastq.gz


title: Polysome_WT_Rep3

value: Polysome


title: Sbj1_mAb24

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: Polysome_WT_Rep1


title: X757y

value: ko


title: Spn1 F267E, MNase, 37C, Rep3

description: Library name: FE-HIV_MNase_rep3_R1.fastq.gz


title: X767y


title: Spt6 F249K, MNase, 37C, Rep3

description: Library name: FK-HIV_MNase_rep3_R1.fastq.gz


title: Patient 1 CU018.RCC

value: Male


title: Polysome_WT_Rep2

value: cerebellum

value: GNP


title: Di-trisome_WT_Rep3

value: WT


title: Patient 5 RLSS-182.RCC


title: Di-trisome_WT_Rep1


title: Sbj3_mAb11

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: X755y


title: Sbj3_mAb4

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: Spn1 F267E, MNase, 37C, Rep2

description: Library name: FE-HIV_MNase_rep2_R1.fastq.gz


title: X759y

value: wt


title: 80S_WT_Rep2


title: Spn1 R263D, MNase, 37C, Rep2

description: Library name: RD-HIV_MNase_rep2_R1.fastq.gz


title: Sbj3_mAb16

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: BLANK rep2

value: BMDMs

value: Alveolar bone lysates from BLANK models


title: Sbj2_mAb14

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: Sbj3_mAb5

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: Spn1 R263D, MNase, 37C, Rep1

description: Library name: RD-HIV_MNase_rep1_R1.fastq.gz


title: Total_RNA_WT_Rep2

value: Total


title: WT, MNase, 37C, Rep3

description: Library name: WT-HIV_MNase_rep3_R1.fastq.gz

value: 37° C


title: Sbj1_mAb22

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: X517o


title: 80S_WT_Rep1


title: Spn1 F267E, MNase, 37C, Rep1

description: Library name: FE-HIV_MNase_rep1_R1.fastq.gz

value: budding yeast


title: X751y

value: skeletal muscle


title: WT, MNase, 37C, Rep1

description: Library name: WT-HIV_MNase_rep1_R1.fastq.gz


title: scRNA_Reference_e16.5_replicate1

city: Martinsried

first: Christian

last: Mayer

address: Am Klopferspitz 18

institute: Max Planck Institute for Biological Intelligence

description: 10x Genomics

data_processing:
Transcriptomic dataset:Sequencing reads in FASTQ files were aligned to a reference genome(mm10) and umi counts were calculated using 10x Genomics Cell ranger software.Data were read into R (version 3.6.0) as a count matrix and cells wer filtered using Seurat v3 with cut-offs for: max/min gene expression, max nCount_RNA, and percentage of total reads that aligned to the mitochondrial genome
Barcode dataset TrackerSeq: R2 FASTQ files were pre-processed using BBduk; the sequences to the left and right of the lineage barcodes were trimmed so that only the lineage barcode (BC) remained. Lineage barcodes shorter than 37 bp were discarded. Cell barcodes (Cell) were extracted from corresponding Seurat object of the dataset to generate a cell barcode whitelist. The extracted cell barcodes and UMIs were added to the read names of the lineage barcode FASTQ files. The resulting FASTQ files were processed by clonal_annotation.ipynb from LARRY (Klein lab), to output a sparse matrix in csv format, where rows were cells identified by individual cell barcodes and columns were lineage barcode, with 1 indicating its presence and 0 its absence. Only (Cell,UMI,BC) triples supported by at least 10 reads and (Cell,BC) pairs with at least 6 UMI were considered for further analyses. A CloneIDs were assigned to cell barcodes. The distance between the cell barcodes in the matrix could be determined by clustering the matrix using Jaccard similarity and average linkage, as demonstrated by Wagner et al. This could be accomplished by using the R function distance(method = ‘jaccard’) and hclust(method = ‘average’). The resulting dendrogram was cut at a height of 0.999 using cutree(hclust_avg, h = 0.999) to obtain the clonal groupings.
Assembly: mm10-2.1.0
Supplementary files format and content: Processed_Transcript: Rdata file with genes and counts
Supplementary files format and content: Processed_LBC TRACKERseq: Rdata file with columns for "CBC" and "Lineage-Barcode"

molecule: polyA RNA

source_name: ganglionic eminence, cortex, striatum

extract_protocol:
Embryonic tissue was collected in ice-cold Leibowitz medium  and papain dissociation was carried out (Wortington, #LK003150). Postnatal tissue was dissected in ice-cold bubbled ACSF and dissociatedwas carried out with the Miltenyi BioTech Neural Tissue Dissociation Kit (P) (#130-092-628)
Transcriptomic libraries were prepared for sequencing using standard Illumina protocols. Barcode libraries were prepared from PCR cDNA to amplify barcode regions with custumed primers with standard Illumina adapters.

value: ganglionic eminence, cortex, striatum

tag: developmental stage


title: Sbj2_mAb19

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: X511o.2

value: male


title: X511o


title: Sbj2_mAb4

description: MENB NEXT GEN-001 (V114_01) 205285/ETR

value: PBMC


title: WT, MNase, 37C, Rep2

description: Library name: WT-HIV_MNase_rep2_R1.fastq.gz


title: scRNA_FlashTag_e16.5+6h_replicate1

description: 10x Genomics

source_name: ganglionic eminence

value: ganglionic eminence

value: wild type

value: FlashTag labelling


title: scATAC_FlashTag_e16.5+6h_replicate2

description:
Sample 14
10x Genomics

library_source: genomic single cell

data_processing:
The sequenced data was processed using the Cell Ranger ATAC Software Suite (version 1.2.0). The reads were aligned to the mm10 reference genome
Fragment files was further processed and analyzed using ArchR pipeline. Peak calling was perfomed usig MACS2.
Assembly: mm10
Supplementary files format and content: ArchR output:Arrow files
Supplementary files format and content: ArchR output:Bigwig files

extract_protocol:
FACS-sorted cells were pelleted and resuspended in lysis buffer (10mM Tris-HCl, 10mM NaCl, 2mM MgCl2, 0.1% Tween-20, 0.1% Nonidet P40, 0.01% Digitonin, 1% BSA, and nuclease-free water) and incubated on ice for 3-5 minutes. To dilute the lysis, chilled wash buffer was added. Nuclei were then resuspended in Diluted Nuclei Buffer (10x Genomics). Nuclei concentrations were determined using Trypan Blue, pooled, and loaded into the 10x Genomics scATAC-seq (v1) transposition reaction.
The library preparation followed the manufacturer's 10x Genomics scATAC-seq (v1) protocol.


title: Sbj2_mAb15

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: scRNA_FlashTag_e12.5+6h_replicate1

description: 10x Genomics


title: X509o

value: ko


title: scRNA_Reference_e12.5_replicate1

description: 10x Genomics


title: Spt6 F249K, RNA, 37C, Rep3

description: Library name: A364A_Spt6_F249K_37C_RNA_Rep3_020320


title: Sbj2_mAb18

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: Spt6 F249K, RNA, 37C, Rep1

description: Library name: A364A_Spt6_F249K_37C_RNA_Rep1_020320


title: Sbj2_mAb16

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: Spn1 R263D, RNA, 37C, Rep3

description: Library name: A364A_Spn1_R263D_37C_RNA_Rep3_020320


title: Sbj3_mAb14

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: X507o


title: scATAC_FlashTag_e12.5+6h_replicate2

description:
Sample 12
10x Genomics


title: Spt6 F249K, RNA, 37C, Rep2

description: Library name: A364A_Spt6_F249K_37C_RNA_Rep2_020320


title: Spn1 R263D, RNA, 37C, Rep2

description: Library name: A364A_Spn1_R263D_37C_RNA_Rep2_020320


title: scATAC_FlashTag_e16.5+6h_replicate1

description:
Sample 13
10x Genomics


title: Sbj3_mAb8

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: Spn1 R263D, RNA, 37C, Rep1

description: Library name: A364A_Spn1_R263D_37C_RNA_Rep1_020320


title: X489o


title: X477y


title: X513o


title: X479y


title: Sbj2_mAb6

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: TLDR-Seq_mES-WT1_bc9

city: Copengagen

first: Albin

last: Sandelin

address: Ole Maaløes Vej 5

department: Department of Biology, Section for Computational and RNA Biology

data_processing:
Reads were basecalled with Guppy 6.4.2 using the parameter 'trim_strategy none'.
Reads  that passed the basecalling mean_qscore_template > 9 threshold  were demultiplexed with cutadapt v6.3.7
mESC  and HeLa-S3 demultiplexed reads were respectively mapped with minimap2 (2.24-r1122) to the Gencode v35 mouse transcriptome or to the Gencode v39 human transcriptome
Transcript quantification was then performed with Nanocount (v1.0.0)
Assembly: hg38 (HeLa-S3) and mm39 (mESC)
Supplementary files format and content: Processed data file are tab separated files containing 5 fields: transcript_name, raw, est_count, tpm, transcript_length

source_name: mESC

extract_protocol:
RNA was harvested using the TRIzol Plus RNA purification kit and Phasemaker tubes Complete system, DNaseI treated and purified using the Purelink RNA Mini kit. RNA quality is assessed on the RNA Bioanalyzer. 8ug of RNA was used as an input per sample for the TLDR-sequencing library prep
TLDR-seq library prep was carried out as as follows; Input RNA was dephosphorylated then quantified on the nanodrop. 5 ug of dephosphorylated RNA was used for 3'-end A1 adapter ligation with T4 RNA ligase 2 truncated KQ. Unligated A1 adapters were deadenylated and degraded. cDNA was synthesised using Induro reverse transcriptase, with partially reverse transcribed RNAs digested with RNaseONE. Samples are enriched for m7G capped RNA by cap trapping technology. The cDNA strand of the enriched capped RNA were ligated with barcoded 5'-linkers (A2_bc). The second strand cDNA was generated using LongAmp HotStart Taq 2x Master mix. For amplified samples, PCR amplification was carried out using LongAmp HotStart Taq 2x Master mix. Endprep/dA-tailing and nanopore adapter ligation was carried out using the SQK-LSK110 kit and sequenced on MinIOn flow cells (FLO-MIN106 - R9.4.1)

value: mESC


title: TLDR-Seq_mES-ZCCHC8_bc9


title: X471o


title: Spn1 F267E, RNA, 37C, Rep2

description: Library name: A364A_Spn1_F267E_37C_RNA_Rep2_020320


title: TLDR-Seq_mES-RBM7_bc9


title: Sbj1_mAb11

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: X467y


title: Sbj1_mAb18

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: X753y


title: Whole brain, Picrotoxin+Urolithin-A, 240 min,  rep2 [PU2]

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

country: India

institute: Theomics International Private Limited

data_processing:
nf-core rnaseq v3.12.
Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimgalore
Trimmed sequence reads were mapped to dm6 using STAR aligner
Read count extraction and normalization were performed using featureCounts
Assembly: dm6

organism: Drosophila melanogaster

source_name: Whole brain

extract_protocol:
Trizol Method
As per Illumina Recommended Protocol

value: Whole brain

value: Urolithin-A (22.8 µg/ml) + Picrotoxin (1mM)


title: Spn1 F267E, RNA, 37C, Rep1

description: Library name: A364A_Spn1_F267E_37C_RNA_Rep1_020320


title: Sbj1_mAb20

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: X465y


title: Sbj1_mAb19

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: Whole brain, Picrotoxin+Urolithin-A, 240 min, rep1 [PU1]


title: scATAC_FlashTag_e12.5+6h_replicate1

description:
Sample 11
10x Genomics


title: WT, RNA, 37C, Rep3

description: Library name: A364A_WT_37C_RNA_Rep3_020320

value: WT


title: X463y

value: wt


title: Whole brain, Urolithin-A, 240 min, rep2 [Uro2]

value: Urolithin-A (22.8 µg/ml)


title: X461o


title: Whole brain, Urolithin-A, 240 min, rep1 [Uro1]


title: WT, RNA, 37C, Rep2

description: Library name: A364A_WT_37C_RNA_Rep2_020320


title: WT, RNA, 37C, Rep1

description: Library name: A364A_WT_37C_RNA_Rep1_020320


title: Sbj1_mAb17

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: Sbj1_mAb3

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: X459y


title: Spt6 F249K, PolII ChIP, 37C, Rep3

description: Library name: A364A_Spt6_F249K_37C_PolII_ChIP_Rep3_020320_reprocessed

tag: antibody

value: RNA PolII


title: Spn1 F267E, RNA, 37C, Rep3

description: Library name: A364A_Spn1_F267E_37C_RNA_Rep3_020320

value: 37° C


title: Whole brain, Picrotoxin, 240 min, rep2 [PTX2]

value: Picrotoxin (1mM)


title: Whole brain, Picrotoxin, 240 min, rep1 [PTX1]


title: Sbj3_mAb15

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: Spt6 F249K, PolII ChIP, 37C, Rep2

description: Library name: A364A_Spt6_F249K_37C_PolII_ChIP_Rep2_020320_reprocessed

value: budding yeast


title: X457y

value: skeletal muscle


title: Whole brain, Control, 240 min, rep2 [SC2]

value: 0.5% DMSO


title: Spt6 F249K, PolII ChIP, 37C, Rep1

description: Library name: A364A_Spt6_F249K_37C_PolII_ChIP_Rep1_020320_reprocessed


title: X455y

value: male


title: Spn1 F267E, PolII ChIP, 37C, Rep3

description: Library name: A364A_Spn1_F267E_37C_PolII_ChIP_Rep3_020320_reprocessed


title: Sbj3_mAb13

description: MENB NEXT GEN-001 (V114_01) 205285/ETR

value: PBMC


title: Sd_39084_ONT_long_cDNA_flowers_expression

city: Heslington, York

first: Sara

last: Franco Ortega

address: Wentworth Way

department: Department of Biology

country: United Kingdom

institute: Centre for Novel Agricultural Products, University of York

description:
Library name: Sd_39084_ONT_long_cDNA_flowers
Solanum dulcamara ID 39084 obtained from seeds provided by the Royal Botanical Gardens Kew (UK). Seeds were surface-sterilised in 1% bleach and rinsed and then stratified during 10 days on wet tissue paper mianteined at 4C and darkness. After that, they were moved to soil (John Innes No2) and kept in a growth room of the University of York with an average temperature of 20C (2C) and 14h/10h light /dark. Root, stems, leaves, flowers and berries were collected from each plant simultaneously and stored at -80C until further processing. The plant material was ground using liquid nitrogen. The RNA was extracted using the E.Z.N.A.  Plant RNA Kit (VWR) including the treatment with DNase to remove residual DNA according to the manufacturers instruction. The quality of the RNA was assessed with Nanodrop, Qubit 4.0. using the Qubit RNA Broad Range and Agilent Technology 2100 Bioanalyzer (Agilent Technologies, CA, USA). Only samples with RIN >6 were used to prepare the cDNA libraries.

data_processing:
Minimap2 was used to map the cDNA long read from ONT to the S.dulcamara genome (BioProject PRJNA1014230) and create a bam file that was input in salmon
Salmon’s mapping-based mode was used to create an index from the reference genome, and then for quantification, using the bam files. Salmon output files were prepared for differential expression analysis using the R package TxImport, generating a table containing transcript abundance, counts, and length from the Salmon quantification files
Assembly: S.dulcamara genome (BioProject PRJNA1014230)
Supplementary files format and content: Salmon output (abundance, length and counts)

organism: Solanum dulcamara

source_name: Flowers

growth_protocol: Plant were grown in a growth room of the University of York (UK) with an average temperature of 20°C (±2°C) and 14h/10h light /dark for 3 months

extract_protocol:
We extracted mRNA-Seq from these 5 tissues by grounding using liquid nitrogen and extracting total RNA using the E.Z.N.A. ® Plant RNA Kit, which included DNase treatment to remove residual DNA according to the manufacturer’s instructions. The quality of the RNA was assessed with Nanodrop and Qubit 4.0. using the Qubit™ RNA Broad Range kit and the Agilent Technology 2100 Bioanalyzer
PromethION 9.4.1 cDNA libraries

value: Flowers


title: Spn1 F267E, PolII ChIP, 37C, Rep2

description: Library name: A364A_Spn1_F267E_37C_PolII_ChIP_Rep2_020320_reprocessed


title: Sd_39084_ONT_long_cDNA_berries_expression

description:
Library name: Sd_39084_ONT_long_cDNA_berries
Solanum dulcamara ID 39084 obtained from seeds provided by the Royal Botanical Gardens Kew (UK). Seeds were surface-sterilised in 1% bleach and rinsed and then stratified during 10 days on wet tissue paper mianteined at 4C and darkness. After that, they were moved to soil (John Innes No2) and kept in a growth room of the University of York with an average temperature of 20C (2C) and 14h/10h light /dark. Root, stems, leaves, flowers and berries were collected from each plant simultaneously and stored at -80C until further processing. The plant material was ground using liquid nitrogen. The RNA was extracted using the E.Z.N.A.  Plant RNA Kit (VWR) including the treatment with DNase to remove residual DNA according to the manufacturers instruction. The quality of the RNA was assessed with Nanodrop, Qubit 4.0. using the Qubit RNA Broad Range and Agilent Technology 2100 Bioanalyzer (Agilent Technologies, CA, USA). Only samples with RIN >6 were used to prepare the cDNA libraries.

source_name: Berries

value: Berries


title: Sbj3_mAb1

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: ΔmtDNA 3

first: David

last: Pla-Martín

address: Universitätsstr. 1 Building 22.03; 4th Floor

department: Institute of Biochemistry and Molecular Biology I

institute: Medical Faculty and University Clinics. Heinrich Heine University Düsseldorf

data_processing:
Assesing quality of raw data with Fastqc
Trimming of the Illumina's adapter and 3' poly(A) with Trimgalore-0.6.10 (--illumina --a2 {A}10)
Alignment into the Drosophila BDGP6.32 genome assembly from Ensembl with STAR (output BAM unsorted with just the highest scored alignment per read)
Evaluating the quality of the mapping with Qualimap-v2.2.1
Counting genes with RSEM-1.3.3 (--estimate-rspd --append-names --calc-ci)
Assembly: BDGP6.32
Supplementary files format and content: Gene-level results from RSEM in a tab delimited plain text file (.results) containing expected-counts, TPM and FPKM

source_name: L3 larval epidermis

growth_protocol: Flies were maintained at 25 °C under a 12:12 h light/dark cycle on standard fly food. All crosses were set up and maintained at 18°C under a 12:12 h light/dark cycle on standard fly food.

extract_protocol:
Each sample was obtained from the epidermis obtained from 5 larvae (L3).  RNA was isolated using Trizol and 2ug for each were used to construct the library
Libraries were prepared using TruSeq RNA sample preparation kit (Illumina) with 2ug of total RNA and  Poly A + selection. A total of 35-45 million reads per sample were obtained using paired-end 100 pb read length (Illumina NovaSeq 6000)

value: L3 larva

value: epidermis

value: w1118; UAS-mitoT4lig, UAS-mitoAflIII/+; A58-Gal4/+


title: ΔmtDNA 4


title: Sbj2_mAb8

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: Sbj2_mAb9

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: Sd_39084_ONT_long_cDNA_leaves_expression

description:
Library name: Sd_39084_ONT_long_cDNA_leaves
Solanum dulcamara ID 39084 obtained from seeds provided by the Royal Botanical Gardens Kew (UK). Seeds were surface-sterilised in 1% bleach and rinsed and then stratified during 10 days on wet tissue paper mianteined at 4C and darkness. After that, they were moved to soil (John Innes No2) and kept in a growth room of the University of York with an average temperature of 20C (2C) and 14h/10h light /dark. Root, stems, leaves, flowers and berries were collected from each plant simultaneously and stored at -80C until further processing. The plant material was ground using liquid nitrogen. The RNA was extracted using the E.Z.N.A.  Plant RNA Kit (VWR) including the treatment with DNase to remove residual DNA according to the manufacturers instruction. The quality of the RNA was assessed with Nanodrop, Qubit 4.0. using the Qubit RNA Broad Range and Agilent Technology 2100 Bioanalyzer (Agilent Technologies, CA, USA). Only samples with RIN >6 were used to prepare the cDNA libraries.

source_name: Leaves

value: Leaves


title: Spn1 R263D, PolII ChIP, 37C, Rep3

description: Library name: A364A_Spn1_R263D_37C_PolII_ChIP_Rep3_020320_reprocessed


title: Spn1 F267E, PolII ChIP, 37C, Rep1

description: Library name: A364A_Spn1_F267E_37C_PolII_ChIP_Rep1_020320_reprocessed


title: ΔmtDNA 2


title: Sd_39084_ONT_long_cDNA_stem_expression

description:
Library name: Sd_39084_ONT_long_cDNA_stem
Solanum dulcamara ID 39084 obtained from seeds provided by the Royal Botanical Gardens Kew (UK). Seeds were surface-sterilised in 1% bleach and rinsed and then stratified during 10 days on wet tissue paper mianteined at 4C and darkness. After that, they were moved to soil (John Innes No2) and kept in a growth room of the University of York with an average temperature of 20C (2C) and 14h/10h light /dark. Root, stems, leaves, flowers and berries were collected from each plant simultaneously and stored at -80C until further processing. The plant material was ground using liquid nitrogen. The RNA was extracted using the E.Z.N.A.  Plant RNA Kit (VWR) including the treatment with DNase to remove residual DNA according to the manufacturers instruction. The quality of the RNA was assessed with Nanodrop, Qubit 4.0. using the Qubit RNA Broad Range and Agilent Technology 2100 Bioanalyzer (Agilent Technologies, CA, USA). Only samples with RIN >6 were used to prepare the cDNA libraries.

source_name: Stem

value: Stem


title: Sd_39084_ONT_long_cDNA_roots_expression

description:
Library name: Sd_39084_ONT_long_cDNA_roots
Solanum dulcamara ID 39084 obtained from seeds provided by the Royal Botanical Gardens Kew (UK). Seeds were surface-sterilised in 1% bleach and rinsed and then stratified during 10 days on wet tissue paper mianteined at 4C and darkness. After that, they were moved to soil (John Innes No2) and kept in a growth room of the University of York with an average temperature of 20C (2C) and 14h/10h light /dark. Root, stems, leaves, flowers and berries were collected from each plant simultaneously and stored at -80C until further processing. The plant material was ground using liquid nitrogen. The RNA was extracted using the E.Z.N.A.  Plant RNA Kit (VWR) including the treatment with DNase to remove residual DNA according to the manufacturers instruction. The quality of the RNA was assessed with Nanodrop, Qubit 4.0. using the Qubit RNA Broad Range and Agilent Technology 2100 Bioanalyzer (Agilent Technologies, CA, USA). Only samples with RIN >6 were used to prepare the cDNA libraries.

source_name: Roots

value: Roots


title: Sbj2_mAb13

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: Sbj2_mAb3

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: Sbj2_mAb1

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: Spn1 R263D, PolII ChIP, 37C, Rep2

description: Library name: A364A_Spn1_R263D_37C_PolII_ChIP_Rep2_020320_reprocessed


title: Sbj1_mAb16

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: Control 4

value: w1118; UAS-mitoT4lig, UAS-mitoAflIII/+; +


title: Solanum dulcamara genome methylation

description: Methylation calling of the genome using

data_processing:
Base calling with guppy
Assembly with canu 2.1.1
Phased with purge haplotigs and polished with Pilon using Illumina data
f5c v1.2 to assess methylation, pore option set to r9
f5c v1.2 to assess methylation frequency
Assembly: NCBI accession number  JBBJLP000000000
Supplementary files format and content: TSV file with methylation calling
Supplementary files format and content: TSV file with methylation frequency
Library strategy: DNA-seq

extract_protocol:
gDNA extracted from high molecular weight gDNA extraction from plant leaves protocol, Oxford Nanopore Technologies [ONT], which utilised Carlson buffer and further purification using QIAGEN genomic-tip, see preprint Vaillancourt and Buell (2019) for details
the SQK-LSK109 ligation sequencing kit


title: Whole brain, Control, 240 min, rep1 [SC1]

value: Whole brain


title: Spn1 R263D, PolII ChIP, 37C, Rep1

description: Library name: A364A_Spn1_R263D_37C_PolII_ChIP_Rep1_020320_reprocessed

value: RNA PolII

value: 37° C


title: ΔmtDNA 1


title: Control 3


title: WT, PolII ChIP, 37C, Rep3

description: Library name: A364A_WT_37C_PolII_ChIP_Rep3_020320_reprocessed

value: WT

value: budding yeast


title: Fractionated spleen, Biological replicate 3

city: Auburn

first: Jason

last: Abernathy

state: AL

address: 990 Wire Road

institute: USDA-ARS

description: single-nuclei RNAseq, Chromium X Instrument (10x Genomics) and the Chromium Next GEM Single Cell 3’ GEM Kit v3.1 (10x Genomics)

data_processing:
Demultiplexing: Cell Ranger (v.5.0.0)`cellranger mkfastq`
Trimming, filtering, alignment: Cell Ranger (v.8.0.0) `cellranger count`
Assembly: CoCo_2.0, GCF_001660625.3
Supplementary files format and content: .h5, filtered feature-barcode matrices

organism: Ictalurus punctatus

source_name: spleen

extract_protocol:
Three channel catfish (~ 1 kg) were euthanized in a solution of buffered MS-222 for 10 min. The individual spleens were removed and placed into Petri dishes containing Leibovitz’s L-15 medium adjusted to catfish tonicity (cL-15) with PenStrep glutamine solution and 5% FBS.  The spleens were first processed through 70 µM and then 40 µM cell sieves into a 50 mL Falcon tube and cL-15 was added up to 10 mL. The splenic cell suspensions were washed 3 times in 10 mL cL-15 and centrifuged at 1200 RPM for 5 min. The final cell pellet was resuspended in 15 mL cL-15. Cells were counted, and cell viability was assessed. ~ 1.0x107 cells per sample were pelleted and resuspended in 1 mL of freezing medium (90% FBS, 10% DMSO) for another project. The remaining unfractionated cells were placed over a Ficoll density gradient and centrifuged at 1200 RPM for 15 minutes, no brake. The buffy coat was removed and washed one time and then stained with recombinant 9E1 mAb (anti-catfish IgM) and then labeled with a goat anti-mouse IgG FITC Ab. 1-3 x106 IgM+ cells were sorted using a Beckman Coulter CytoFLEX SRT cell sorter using lymphocyte and FITC gates. Sorted cell samples were pelleted and resuspended in 1 mL of freezing medium (90% FBS, 10% DMSO). All cell samples were placed into Mr. Frosty freezing containers at -80°C for 24 h. The cryogenic vials were then moved into a liquid nitrogen storage until be shipped to the sequencing vendor. Frozen cells were thawed in a water bath set to 28°C and added to 6 mL of cL-15. The cells were centrifuged at 1200 RPM for 5 minutes. The supernatant was removed, and the cells were resuspended with 1 mL of cl-15. Approximately 2.5 x 106 cells were transferred to new tubes, centrifuged at 600 RPM for 5 minutes at 4°C, and the supernatant was removed. The cells were lysed in 200 µl of lysis buffer and incubating for 1 minute on ice. The lysis buffer consisted of Tris-HCL at pH 7.4, NaCl, MgCl2.  The lysed cells were washed with 800 µl of buffer solution and centrifuged. The buffer contained BSA Solution, RNase Inhibitor, and 1x PBS. The nuclei were washed two times using 1 mL of buffer solution, pelleted and the supernatant was removed. Centrifugation was carried out at 1200 RPM for 10 minutes at 4°C. The nuclei concentration was diluted to the target concentration required for library preparation.
The single-nuclei RNA-seq libraries were prepared and constructed using the Chromium X Instrument (10x Genomics) and the Chromium Next GEM Single Cell 3’ GEM Kit v3.1 (10x Genomics) following the manufacturer’s protocol. The individual nuclei were partitioned to produce gel beads-in-emulsion (GEMs). The GEMs are generated by loading the nuclei in master mix, barcoded Single Cell 3’ v3.1 Gel Beads and partitioning oil onto Chromium Next GEM Chip G. The Gel Bead was dissolved to release the primers and incubated to produce barcoded full-length cDNA. The cDNA was cleaned to removed left over reagents using Dynabeads MyOne SILANE (ThermoFisher Scientific, Waltham, MA 2000048), then amplified via PCR. Optimal sized cDNA amplicons were selected using SPRIselect (Beckman Coulter, Brea, CA, B23318) and Illumina indexes and adapters were added via end repair, A-tailing, adaptor ligation, and PCR. Sample quality was checked using a TapeStation (Agilent, Santa Clara, CA) and TapeStation High Sensitivity D1000 ScreenTape (Agilent, Santa Clara, CA). cDNA samples were multiplex and sequenced using the Illumina NovaSeq X Plus sequencer (San Diego, CA).

value: spleen

value: adult

tag: weight

value: ~1 kg

value: Sorted for IgM+ cells


title: Fractionated spleen, Biological replicate 2


title: Control 2


title: Sbj1_mAb6

description: MENB NEXT GEN-001 (V114_01) 205285/ETR

value: PBMC


title: Fractionated spleen, Biological replicate 1


title: Sbj1_mAb7

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: Control 1

value: L3 larva


title: WT, PolII ChIP, 37C, Rep2

description: Library name: A364A_WT_37C_PolII_ChIP_Rep2_020320_reprocessed


title: WT, PolII ChIP, 37C, Rep1

description: Library name: A364A_WT_37C_PolII_ChIP_Rep1_020320_reprocessed


title: FunGeST MESO cell lines methylation, MPM_36 (MethylationEPIC)

status: Public on Apr 08 2025

city: Paris

first: Sandrine

last: Imbeaud

address: 15 rue de l'Ecole de Médecine

department: INSERM UMRS1138-EQUIPE 28, Sorbonne Université-Inserm-Université de Paris

country: France

institute: Centre de Recherche des Cordeliers

hyb_protocol: Methylation analysis was performed either on the Infinium HumanMethylation450 Beadchip (Illumina) or on the Infinium MethylationEPIC BeadChip Kit (Illumina), following the supplier’s recommendations. Briefly, samples were denatured, neutralised, and incubated in an Illumina hybridisation oven for 20-24 hours at 37°C to uniformly amplify genomic DNA and then enzymatically fragmented. Following the fragmentation step, the samples were hybridised to BeadChip and incubated at 48°C for 16-24 hours in an Illumina hybridisation oven. Finally, non-hybridised and non-specific hybridised DNA samples were washed from BeadChip, and labelled nucleotides were added to extend and stain the primers hybridised to the samples.

scan_protocol: The Illumina iScan system (with iScan Control Software) was used to scan Illumina HumanMethylation450 and MethylationEPIC BeadChips

data_processing:
Raw data were analysed using GenomeStudio software according to Illumina’s recommendations to generate result files with beta values.
Processed value definition: Average Beta

source_name: Pleural Mesothelioma

growth_protocol: Patient-derived PM cell lines were cultured in RPMI 1640 medium (Gibco Life Technologies) supplemented with 10% foetal bovine serum (Gibco Life Technologies) and 1% penicillin/streptomycin (Gibco Life Technologies), in a 37°C incubator with 5% CO2.

extract_protocol: Genomic DNA from cell pellets obtained from cultures of PM primary cell lines at low passages were extracted using the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen) according to the manufacturer’s protocol.

value: Pleural Mesothelioma

value: primary

value: male


title: FunGeST MESO cell lines methylation, MPM_85 (MethylationEPIC)


title: FunGeST MESO cell lines methylation, MPM_86 (MethylationEPIC)


title: Sbj1_mAb4

description: MENB NEXT GEN-001 (V114_01) 205285/ETR

source_name: recombinant HumAbs


title: FunGeST MESO cell lines methylation, MPM_88 (MethylationEPIC)


title: FunGeST MESO cell lines methylation, MPM_87 (MethylationEPIC)


title: FunGeST MESO cell lines methylation, MPM_82 (MethylationEPIC)

value: female


title: FunGeST MESO cell lines methylation, MPM_80 (MethylationEPIC)


title: FunGeST MESO cell lines methylation, MPM_60 (MethylationEPIC)


title: FunGeST MESO cell lines methylation, MPM_83 (MethylationEPIC)


title: FunGeST MESO cell lines methylation, MPM_58 (MethylationEPIC)


title: FunGeST MESO cell lines methylation, MPM_69 (MethylationEPIC)


title: FunGeST MESO cell lines methylation, MPM_68 (MethylationEPIC)


title: cancer, carbon ions, replicate 4

city: Chiba

first: Tatsuhiko

last: Imaoka

address: 4-9-1 Anagawa, Inage-ku

department: National Institute of Radiological Sciences

country: Japan

institute: National Institutes for Quantum and Radiological Science and Technology

description: Gene expression data from carbon-ion-induced rat mammary cancer

hyb_protocol: Labeled cRNA was placed in a hybridization mixture containing control biotinylated probes according to manufacturer’s instructions. GeneChip arrays were hybridized with labeled cRNA for 16 h at 45°C with constant rotation (60 rpm).

scan_protocol: The arrays were washed and then stained with streptavidin-phycoerythrin conjugate (Molecular Probes, Tokyo, Japan) in a Fluidics Station 450 (Affymetrix) and subsequently scanned with the GeneChip Scanner 3000 (Affymetrix).

data_processing: The scanned images were processed using Affymetrix GeneChip Analysis Suite software.

label: biotin

organism: Rattus norvegicus

source_name: mammary cancer of rat

label_protocol: Total RNA (8 µg) was used for the first-strand cDNA synthesis with a T7-(dT)24 primer (Proligo, Kyoto, Japan) and SuperScript III reverse transcriptase (Invitrogen Co., Carlsbad, CA, USA). Double-stranded cDNA was then synthesized with E. coli RNase, E. coli DNA polymerase and E. coli DNA ligase (Toyobo, Tokyo, Japan). Biotin-labeled fragmented cRNA was subsequently prepared with a BioArray HighYield RNA Transcript Labeling kit (Enzo, Farmingdale, NY, USA). Labeling was confirmed by formalin-containing agarose gel electrophoresis.

growth_protocol: 5-week-old female Sprague-Dawley rats were purchased, housed in autoclaved cages and maintained in a room with a controlled temperature (23 ± 1degreeC) and humidity (50 ± 5%) under a regular 12-h light, 12-h dark cycle. They were fed a standard laboratory animal diet) and sterilized water ad libitum.

extract_protocol: Total RNA was isolated by the acid guanidine phenol chloroform method (Isogen; Nippon Gene, Tokyo, Japan) and further purified with a silica-gel membrane (RNeasy Mini kit; Qiagen Inc., Valencia, CA, USA). The quality of all RNA samples was assessed by formalin-containing agarose gel electrophoresis.

treatment_protocol: At 7 weeks of age, the rats were given a single whole-body carbon-ion-irradiation (290 MeV/u, 6-cm SOBP, 0.5 Gy) from the HIMAC synchrotron. Rats were fed an AIN-76A diet containing 23.5% corn oil after 9 weeks of age.

value: cancer

tag: etiology

value: carbon ions, 290 MeV/u, 6-cm SOBP, 0.5 Gy

tag: background strain

value: Sprague-Dawley rats


title: FunGeST MESO cell lines methylation, MPM_71 (MethylationEPIC)

tag: cell type


title: FunGeST MESO cell lines methylation, MPM_77 (MethylationEPIC)


title: FunGeST MESO cell lines methylation, MPM_53 (MethylationEPIC)


title: FunGeST MESO cell lines methylation, MPM_57 (MethylationEPIC)


title: cancer, carbon ions, replicate 1


title: FunGeST MESO cell lines methylation, MPM_52 (MethylationEPIC)


title: FunGeST MESO cell lines methylation, MPM_45 (MethylationEPIC)


title: FunGeST MESO cell lines methylation, MPM_74 (MethylationEPIC)


title: FunGeST MESO cell lines methylation, MPM_38 (MethylationEPIC)


title: Sbj1_mAb5

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: cancer, carbon ions, replicate 2


title: FunGeST MESO cell lines methylation, MPM_73 (MethylationEPIC)


title: wswT3, biological replicate1

first: Qing

last: Wei

address: NO.1 Beichen West Road, Chaoyang District

institute: Institute of Microbiology, Chinese Academy of Sciences

description: Gene expression data from oxyR grown till exponential phase

data_processing:
The raw paired end reads were trimmed and quality controlled by Trimmomatic with default parameters.
Then clean reads were separately aligned to reference genome with orientation mode using Rockhopper software
To identify DEGs (differential expression genes) between two different samples, the expression level for each transcript was calculated using the fragments per kilobase of read per million mapped reads (RPKM) method. The method edgeR was used for differential expression analysis
Genome_build: Pseudomonas aeruginosa PAO1
Supplementary_files_format_and_content: differential expression analysis

organism: Pseudomonas aeruginosa

source_name: Exponential phase bacterial culture of oxyR mutant

growth_protocol: Bacterial cells were grown for 6 hr to reach exponential phase at 37C.

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
RNA-seq strand-specific libraries were prepared following TruSeq RNA sample preparation Kit from Illumina (San Diego, CA), using 5 μg of total RNA. Briefly, rRNA was removed by RiboZero rRNA removal kit (Epicenter), fragmented using fragmentation buffer. cDNA synthesis, end repair, A-base addition and ligation of the Illumina-indexed adaptors were performed according to Illumina’s protocol. Libraries were then size selected for cDNA target fragments of 200~300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase (NEB) for 15 PCR cycles.

treatment_protocol: Bacterial cells were collected and kept on ice to extract RNA.

value: oxyR

tag: medium

value: liquid LB

tag: growth phase

value: Exponential phase

value: mutant


title: wswT2, biological replicate2

description: Gene expression data from PAO1 grown till exponential phase

source_name: Exponential phase bacterial culture of PAO1

value: PAO1 strain in liquid LB medium

tag: genotype

value: wild type


title: wswT4, biological replicate2


title: RB837

city: Rochester

first: Cameron

last: Baker

state: NY

address: 601 Elmwood Ave

institute: University of Rochester

description: IgH amplicon library

data_processing:
RNA DEMULTIPLEXING - bcltofastq-2.19.0
RNA CLEANING - fastp 0.20.0, --in1 ../${SAMPLE}_R1.fastq.gz --out1 clt_${SAMPLE}_R1.fastq.gz --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 -w 8 -y -r -j ${SAMPLE}_fastp.json
RNA MAPPING - STAR_2.7.0f, --twopassMode Basic --runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM Unsorted --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical
RNA COUNTING - subread-1.6.4, featurecounts, -s 2 -t exon -g gene_name
RNA DIFFERENTIAL EXPRESSION - DESeq2_1.22.1
scRNA and scVDJ DEMULTIPLEXING - cellRanger 5.0.0 mkfastq --run=. --samplesheet=cellRanger.csv --output-dir ./cellRanger
scRNA COUNTING - cellRanger 5.0.0 count fastqs=./fastq_path --jobmode=slurm --maxjobs=100 --transcriptome=${REF} --project=${PROJECT} --id=Sample_${SAMPLEPREFIX} --sample=${SAMPLEPREFIX}
scVDJ COUNTING - cellRanger 5.0.0 vdj --fastqs=./fastq_path --jobmode=local --nopreflight --reference=${REF} --id=Sample_${SAMPLEPREFIX} --sample=${SAMPLEPREFIX} --localcores=20 --localmem=100
VDJ AMPLICON PROCESSING - Defining dominant L1 clones  L1 clones were defined by a common Jh identity and 6 identical upstream D-Jh junctional nucleotides (termed “6NJx”) comprising ≥5% of all IgH reads according to defined methods6. In their 2012 NGS analysis of IgH heterogeneity, Gawad et al. compared the extent of shared, consecutive intermediary non-Jh or Vh nucleotides (“NDN”) upstream of a common Jh among B-ALL clones to chronic lymphocytic leukemia (CLL), a malignancy of mature B cell lineage which would not be expected to demonstrate evolution by RAG-mediated Vh recombination6. They observed that only 0.03% of CLL clones with a common Jh shared >6 NDN bases with the index clone; they thus defined a threshold of 6 shared NDN nucleotides with a common Jh – or “6NJx” – as a marker of shared clonal lineage.   Because the 5% read threshold for defining clonality is arbitrarily defined, we assessed 2 end of induction (EOI) minimal residual disease (MRD)-negative samples as controls to ensure specificity. We observed that the presence of a 6NJx cluster at ≥5% read frequency was exclusively a feature of active disease specimens; 6NJx sequence clusters between this arbitrary 5% threshold and 1% were observed in some leukemia specimens, but not in MRD-negative control specimens7.  Defining L2 subclones  L2 subclones were defined as all sequences with an identical NDN sequence. NDN sequences include non-templated sequences on both sides of the D gene that arise during RAG-mediated recombination, including bases immediately downstream of the Vh alignment to the beginning of the Jh gene alignment, as determined by IgBlast8. Each novel NDN sequence was interpreted as an L2 subclone within its L1 grouping. For cases in which both the bone marrow (BM) and peripheral blood (PB) were analyzed, the greater L2 subclone proportion observed in either site was reported. To limit overcalling of L2 subclones due to sequencing errors, we allowed for 1 base difference in either length or sequence within NDN grouping.       L3 single nucleotide variation (SNV) analysis  SNV analysis with ultradeep NGS data is challenged by the high load of processing errors. Multiple steps were taken to minimize the effects of false base calls, including the merging of paired reads and replacement of base discrepancies with the base call of highest quality, and removal of all primers to eliminate base changes arising in primer preparation. Additional steps to minimize false SNVs are detailed below.   Defining L3 subclones  We defined a trimmed Vh sequence as the error-corrected and IgBlast-mapped DNA sequence beginning at the Vh gene start through 20 bp upstream of the Vh end. The number of L3 subclones was defined as the number of distinct, trimmed Vh sequences. Pairwise, global alignments were performed on each trimmed Vh and distance matrices were used to assess phylogenic relationships between L3 subclones. We compared the number of L3 subclones per L2 subclone between patients using Poisson mixed regression models, with random intercept for Patient ID, fixed and random effect for the number of L2 reads, and fixed effect for tissue site (PB vs. BM). Our software is available at github.com/amcdavid/igh-leukemia.  eUCR-based noise reduction  As an internal control, we incorporated a targeted amplicon of eUCR41 into each sample for use as a measure of processing and sequencing noise. Ultra-conserved regions have extremely low rates of biological mutations, thereby allowing these regions to be used as a measure of systematic error in the NGS pipeline (ranging from gDNA quality to initial PCR through final read sequencing)9. This error correction is used after mapping analysis by LoFreq10 to determine which SNV calls in amplicons of interest occur above the threshold for probable false calls.  Each biologically valid mutation call represents a mixture of true signal and false calls due to process errors. We use observed mutation calls and read depth in eUCR to generate a probable upper frequency boundary for false positives for each of the possible 12 transitions and transversions. Using the Clopper-Pearson confidence interval for binomial distribution11, we place upper bounds on the probability of a false positive observation based on eUCR SNV frequency, even for SNVs with 0 observations. Conversely, we likewise set lower bounds for each observed transition and transversion SNV for IgH amplicons, factoring in the read depth. From these data, we establish the set of SNV calls that occur above the false positive threshold, at p<0.0001, for each IgH of interest.   To collect the set of reads to evaluate for point mutations in L2 subclones, a multi-step process was used: Reads were mapped (SHRiMP212) and analyzed with LoFreq10 to establish an eUCR-based threshold for true SNVs.  Reads were then remapped and individually evaluated for putative SNV calls based on eUCR threshold, with SNV reverted to reference base at failure. Reads with more than 3 putative SNVs outside the eUCR determined set of true positive calls were eliminated from further analysis. To insure clonality via this mapping result, only reads with a CDR3 sequence identical to the reference of interest were taken to L3 analysis.   An important consideration involved the selection of IgH reference sequences for mapping, as the highly repetitive nature of IgH gene usages challenges mapping programs. To limit mapping errors, the following rules were applied to generate the mix of IgH reference sequences: 1. all single IgH sequences occurring at ≥1% total IgH; 2. The shortest representative of the L2s of interest, up to the top 3 if available; 3. Any other L1 IgH sequence that occurred at ≥10% of total reads in that L1 subset, up to a maximum of 15 sequences.
Assembly: GRCh38.p13 + Gencode-31 Annotation, 10X Genomics published transcriptome GRCh38-2020-A, 10X Genomics published VDJ reference refdata-cellranger-vdj-GRCh38-alts-ensembl-5.0.0
Supplementary files format and content: deSeq2_counts.txt contains the combined counts for all samples for use within DeSeq2 as well as the results of differential expression across the condition groups. RNA and VDJ files are output formats of 10X cellRanger workflow.

source_name: Bone marrow

extract_protocol: IgH AMPLICON SEQUENCING - Genomic DNA was isolated from frozen cell pellets and unsorted viably frozen samples (Wizard® Genomic DNA Purification; Promega™). DNA was quantified by absorbance at 260 nm (NanoDrop™, Thermo Fisher Scientific) and dsDNA binding of fluorescent dyes (Qubit™, Thermo Fisher Scientific). PCR amplification was performed using Q5 High Fidelity Polymerase (New England Biolabs, Inc., Ipswich, MA) using 500 ng genomic DNA as template divided across 4 amplicon reactions, representing approximately 80,000 mononuclear cells per specimen. Recombined IgH primers were specific to each joining (Jh) gene (J1-6) and family specific Framework 2 (FR2) variable (Vh) gene of the IgH locus (Supplemental Table 1). An ultraconserved region (eUCR41) found on Chr 11 was also amplified for use as an internal control for gDNA preparation damage, PCR, and NGS errors2. All amplicons were of similar size of approximately 250-300 nucleotides. Gene-specific primers were modified by the addition of NexteraXT sequences (Illumina Inc., San Diego, CA) at the 5’ primer end. Amplicons were size-selected and purified (SPRIselect; Beckman Coulter®) to maximize selection of 300 nt amplicons for NGS. Specimens were sequenced on an Illumina MiSeq System using 2x300 bp sequencing chemistry. BULK RNA SEQUENCING - Using viably frozen BM and/or PB, RNA was purified and total RNA concentration was determined with the NanopDrop 1000 spectrophotometer (NanoDrop, Wilmington, DE). RNA quality was assessed with the Agilent Bioanalyzer (Agilent, Santa Clara, CA). The TruSeq Stranded mRNA Sample Preparation Kit (Illumina, San Diego, CA) was used for next generation sequencing library construction per manufacturer protocol. mRNA was purified from 200ng total RNA with oligo-dT magnetic beads and fragmented. First-strand cDNA synthesis was performed with random hexamer priming followed by second-strand cDNA synthesis using dUTP incorporation for strand marking. End repair and 3’ adenylation was then performed on the double stranded cDNA. Illumina adaptors were ligated to both ends of the cDNA, purified by AMPURE XP bead cleanup and amplified with PCR primers specific to the adaptor sequences to generate cDNA amplicons of approximately 200-500bp in size. The amplified libraries were hybridized to the Illumina single end flow cell and amplified using the NovaSeq6000 DNA sequencer (Illumina, San Diego, CA). Single end reads of 100nt were generated for each sample. SINGLE CELL PREPARATION - Cellular suspensions were loaded on a Chromium Single-Cell Instrument (10x Genomics, Pleasanton, CA, USA) to generate single-cell Gel Bead-in-Emulsions (GEMs). Single-cell RNA-Seq libraries were prepared using the Chromium Single-Cell 5′ Library & Gel BeadKit (10x Genomics). The beads were dissolved and cells were lysed per manufacturer’s recommendations.GEM reverse transcription (GEM-RT) was performed to produce a barcoded, full-length cDNA from poly-adenylated mRNA.After incubation, GEMs were broken and the pooled post-GEM-RT reaction mixtures were recovered and cDNA was purified with silane magnetic beads (DynaBeads MyOne Silane Beads, ThermoFisher Scientific).The entire purified post GEM-RT product was amplified by PCR. This amplification reactiongenerated sufficient material to construct a B cell-enriched library and a 5’ gene expression library.The barcoded, full-length V(D)J segments were enriched by PCR with primers specific to the BCR constant regions using the Chromium Single Cell V(D)J Enrichment Kit, Human B cell (10x Genomics).For both B-cell enriched library and 5’ gene expression library, enzymatic fragmentation and size selection was used to optimize the cDNA amplicon size and indexed sequencing libraries were constructed by End Repair, A-tailing, Adaptor Ligation, and PCR. Final libraries contain the P5 and P7 priming sites used in Illumina bridge amplification.  The 5’ gene expression and B-cell libraries were sequenced following 10X Genomics read length guidelines on the NovaSeq6000 sequencer (Illumina). The sequencing run was demultiplexed and counted using 10x Genomics Cell Ranger 5.0.0 mkfastq and count, using the 10x Genomics provided human reference (refdata-gex-GRCh38-2020-A).Cellular suspensions were loaded on a Chromium Single-Cell Instrument (10x Genomics, Pleasanton, CA, USA) to generate single-cell Gel Bead-in-Emulsions (GEMs). Single-cell RNA-Seq libraries were prepared using the Chromium Single-Cell 5′ Library & Gel BeadKit (10x Genomics). The beads were dissolved and cells were lysed per manufacturer’s recommendations.GEM reverse transcription (GEM-RT) was performed to produce a barcoded, full-length cDNA from poly-adenylated mRNA.After incubation, GEMs were broken and the pooled post-GEM-RT reaction mixtures were recovered and cDNA was purified with silane magnetic beads (DynaBeads MyOne Silane Beads, ThermoFisher Scientific).The entire purified post GEM-RT product was amplified by PCR. This amplification reactiongenerated sufficient material to construct a B cell-enriched library and a 5’ gene expression library.The barcoded, full-length V(D)J segments were enriched by PCR with primers specific to the BCR constant regions using the Chromium Single Cell V(D)J Enrichment Kit, Human B cell (10x Genomics).For both B-cell enriched library and 5’ gene expression library, enzymatic fragmentation and size selection was used to optimize the cDNA amplicon size and indexed sequencing libraries were constructed by End Repair, A-tailing, Adaptor Ligation, and PCR. Final libraries contain the P5 and P7 priming sites used in Illumina bridge amplification.  The 5’ gene expression and B-cell libraries were sequenced following 10X Genomics read length guidelines on the NovaSeq6000 sequencer (Illumina). The sequencing run was demultiplexed and counted using 10x Genomics Cell Ranger 5.0.0 mkfastq and count, using the 10x Genomics provided human reference (refdata-gex-GRCh38-2020-A).

tag: patient id

tag: disease state

value: B cell acute lymphoblastic leukemia

tag: tissue

value: Bone marrow


title: wswT1, biological replicate1


title: RB838

description: IgH amplicon library

source_name: Peripheral blood

value: Peripheral blood


title: RB721

description: IgH amplicon library


title: RB695

description: IgH amplicon library


title: RB687

description: IgH amplicon library


title: RB688

description: IgH amplicon library


title: RB727

description: IgH amplicon library


title: RB707

description: IgH amplicon library


title: RB673

description: IgH amplicon library


title: FunGeST MESO cell lines methylation, MPM_78 (MethylationEPIC)

tag: cell line

tag: Sex


title: FunGeST MESO cell lines methylation, MPM_47 (MethylationEPIC)


title: cancer, carbon ions, replicate 3


title: RB672

description: IgH amplicon library


title: RB635

description: IgH amplicon library


title: RB662

description: IgH amplicon library


title: RB634

description: IgH amplicon library


title: FunGeST MESO cell lines methylation, MPM_70 (MethylationEPIC)


title: RB616

description: IgH amplicon library


title: RB615

description: IgH amplicon library


title: RB613

description: IgH amplicon library


title: RB612

description: IgH amplicon library


title: RB611

description: IgH amplicon library


title: RB610

description: IgH amplicon library


title: RB607

description: IgH amplicon library


title: RB609

description: IgH amplicon library


title: RB608

description: IgH amplicon library


title: RB606

description: IgH amplicon library


title: RB605

description: IgH amplicon library


title: RB603

description: IgH amplicon library


title: RB602

description: IgH amplicon library


title: RB600

description: IgH amplicon library


title: RB599

description: IgH amplicon library


title: RB598

description: IgH amplicon library


title: RB597

description: IgH amplicon library


title: RB647

description: IgH amplicon library


title: RB628

description: IgH amplicon library


title: RB596

description: IgH amplicon library


title: RB594

description: IgH amplicon library


title: RB627

description: IgH amplicon library


title: Liver, WHV infection, TLH, rep 3

city: Toronto

first: Zoe

middle: Alixandra

last: Clarke

state: Ontario

address: 27 King's College Cir

department: Molecular Genetics

country: Canada

institute: University of Toronto

data_processing:
Cell Ranger (v.5.0.0) followed by standard Seurat protocol using SCTransform normalisation and DropletQC filtering.
Assembly: Custom woodchuck genome and annotation. Available at https://doi.org/10.5281/zenodo.10855128.
Supplementary files format and content: Filtered data matrices from CellRanger outputs: gene expression matrices, feature lists, and barcode lists.
Supplementary files format and content: .RDS file of integrated Seurat objects

organism: Marmota monax

source_name: Liver

growth_protocol: scRNA-seq was performed on freshly isolated liver cells from woodchucks with a woodchuck hepatitis virus (WHV) infection; cells were never cultured.

extract_protocol:
Woodchuck livers were dissociated according to a previously described 2-step collagenase perfusion protocol https://doi.org/10.1038/s41467-018-06318-7.
Single-cell samples were sequenced with 10X Genomics SingleCell 3' v2 chemistry according to manufacturer's instructions.

value: Liver

tag: woodchuck type

value: Outbred

value: Liver cells

tag: sorting

value: Unsorted

tag: treatment

value: WHV infection


title: Liver, healthy, spatial, rep 2

data_processing:
Space Ranger (v1.2.2) followed by standard Seurat protocol using SCTransform normalisation.
Assembly: Custom woodchuck genome and annotation. Available at https://doi.org/10.5281/zenodo.10855128.
Supplementary files format and content: Filtered data matrices from CellRanger outputs: gene expression matrices, feature lists, and barcode lists.
Supplementary files format and content: .RDS and .Rdata files of integrated Seurat objects
Library strategy: Spatial transcriptomics

growth_protocol: Spatial transcriptomics data was fresh frozen.

extract_protocol:
Spatial transcriptomics was performed on 16-μM woodchuck liver tissue slices from fresh frozen OCT-embedded tissue of the L212 woodchuck following the protocol described in DOI: 10.1002/hep4.1854.
Samples were sequenced with 10X Genomics Spatial 3' v1 chemistry according to manufacturer's instructions.

value: Healthy


title: Liver, WHV infection, TLH, rep 2


title: Liver, healthy, TLH, rep 1

description: allIntegrated_cca_kanchor5_noBiopsyHeps_dropletQCFiltered.RDS

data_processing:
Cell Ranger (v.5.0.0) followed by standard Seurat protocol using SCTransform normalisation and DropletQC filtering.
Assembly: Custom woodchuck genome and annotation. Available at https://doi.org/10.5281/zenodo.10855128.
Supplementary files format and content: Filtered data matrices from CellRanger outputs: gene expression matrices, feature lists, and barcode lists.
Supplementary files format and content: .RDS and .Rdata files of integrated Seurat objects

growth_protocol: Healthy scRNA-seq was from freshly isolated liver cells and PBMCs, never cultured.

extract_protocol:
Woodchuck livers were dissociated according to a previously described 2-step collagenase perfusion protocol https://doi.org/10.1038/s41467-018-06318-7. For PBMCs, whole blood was collected in EDTA tubes. Plasma was collected from these tubes via 1000 x g spin for 10 minutes. Remaining blood was diluted using a 1:1 ratio of 1X PBS. This mixture was carefully layered on a Ficoll density gradient. Tubes containing layered blood were centrifuged at 400 x g for 20 minutes without brakes. The buffy coat layer was isolated using a Pasteur pipette and washed with 1X PBS.
Single-cell samples were sequenced with 10X Genomics SingleCell 3' v2 chemistry according to manufacturer's instructions.


title: PBMC, healthy, rep 2

description: integrated_PBMC_cca_kanchor5_scClustViz.RData

source_name: PBMC

value: PBMC

value: PBMCs


title: Liver, healthy, spatial, rep 1


title: RB595

description: IgH amplicon library


title: PBMC, healthy, rep 1


title: Liver, healthy, TLH, rep 2


title: RB601

description: IgH amplicon library


title: Mutant, loaded 3 hours + GSK205, sample2

city: Saint Louis

first: Farshid

last: Guilak

state: MO

address: 660 S Euclid Ave, Campus Box 8233

department: Dept of Orthopedics

institute: Washington University in St. Louis

description:
Library name: Sample77
h2_205_3hr_b

data_processing:
RNA-seq reads were  aligned and quantitated to the Ensembl release 101 primary assembly with an Illumina DRAGEN Bio-IT on-premise server running version 4.0.3-8.  software.
One sample was identified as an outlier and was excluded from the downstream analysis and submission to the GEO database.
Assembly: GRCh38.101
Supplementary files format and content: .txt file contains raw gene counts for each sample

source_name: Tissue-engineered cartilage

extract_protocol:
Total RNA was isolated using the Qiagen Total RNA Purification Plus Kit (Norgen Biotek, 48400) followed by a DNAse clean-up (Norgen 25720)
Library preparation was performed with 1 to 3ug of total RNA. Ribosomal RNA was removed by a hybridization method using Ribo-ZERO kits (Illumina-EpiCentre). mRNA was then fragmented in reverse transcriptase buffer and heating to 94 degrees for 8 minutes. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer's instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.

value: Tissue-engineered cartilage

value: hiPSC

value: COL6A3 Mutant

value: Loaded, 3 hours

tag: batch


title: Mutant, loaded 24 hours, sample1

description:
Library name: Sample82
h2_veh_24hr_b

value: Loaded, 24 hours


title: Mutant, loaded 3 hours + GSK205, sample6

description:
Library name: Sample81
h2_205_3hr_g


title: Mutant, loaded 24 hours, sample2

description:
Library name: Sample83
h2_veh_24hr_f


title: Mutant, loaded 3 hours + GSK205, sample3

description:
Library name: Sample78
h2_205_3hr_c


title: Mutant, loaded 3 hours + GSK205, sample4

description:
Library name: Sample79
h2_205_3hr_d


title: Mutant, loaded 3 hours, sample4

description:
Library name: Sample73
h2_veh_3hr_d


title: Mutant, loaded 3 hours + GSK205, sample1

description:
Library name: Sample76
h2_205_3hr_a


title: RB604

description: IgH amplicon library


title: Mutant, loaded 3 hours, sample5

description:
Library name: Sample74
h2_veh_3hr_f


title: Liver, WHV infection, TLH, rep 1


title: Mutant, loaded 3 hours, sample6

description:
Library name: Sample75
h2_veh_3hr_g


title: Mutant, loaded 3 hours, sample3

description:
Library name: Sample72
h2_veh_3hr_c


title: Mutant, loaded 3 hours, sample2

description:
Library name: Sample71
h2_veh_3hr_b


title: Mutant, loaded 3 hours, sample1

description:
Library name: Sample70
h2_veh_3hr_a


title: Mutant, loaded 0 hours + GSK205, sample4

description:
Library name: Sample67
h2_205_0hr_e

value: Loaded, 0 hours


title: Mutant, loaded 0 hours + GSK205, sample5

description:
Library name: Sample68
h2_205_0hr_f


title: Mutant, loaded 0 hours + GSK205, sample3

description:
Library name: Sample66
h2_205_0hr_c


title: Mutant, loaded 0 hours + GSK205, sample2

description:
Library name: Sample65
h2_205_0hr_b


title: Mutant, loaded 0 hours + GSK205, sample6

description:
Library name: Sample69
h2_205_0hr_g


title: Mutant, loaded 24 hours, sample3

description:
Library name: Sample84
h2_veh_24hr_g


title: Mutant, loaded 0 hours, sample6

description:
Library name: Sample63
h2_veh_0hr_f


title: Mutant, loaded 3 hours + GSK205, sample5

description:
Library name: Sample80
h2_205_3hr_f


title: Mutant, loaded 0 hours, sample4

description:
Library name: Sample61
h2_veh_0hr_d


title: Mutant, loaded 0 hours, sample3

description:
Library name: Sample60
h2_veh_0hr_c


title: Mutant, loaded 0 hours, sample5

description:
Library name: Sample62
h2_veh_0hr_e


title: Mutant, loaded 0 hours, sample1

description:
Library name: Sample58
h2_veh_0hr_a


title: Mutant, free-swelling + GSK205, sample6

description:
Library name: Sample57
h2_205_fs_g

value: Free-swelling


title: Mutant, free-swelling + GSK205, sample3

description:
Library name: Sample54
h2_205_fs_c


title: Mutant, free-swelling + GSK205, sample2

description:
Library name: Sample53
h2_205_fs_b


title: Mutant, free-swelling + GSK205, sample4

description:
Library name: Sample55
h2_205_fs_e


title: Mutant, free-swelling + GSK205, sample1

description:
Library name: Sample52
h2_205_fs_a


title: Mutant, free-swelling, sample6

description:
Library name: Sample51
h2_veh_fs_g


title: Mutant, free-swelling, sample5

description:
Library name: Sample50
h2_veh_fs_f


title: Mutant, free-swelling + GSK205, sample5

description:
Library name: Sample56
h2_205_fs_f


title: Mutant, free-swelling, sample4

description:
Library name: Sample49
h2_veh_fs_e


title: Mutant, free-swelling, sample3

description:
Library name: Sample48
h2_veh_fs_c


title: Mutant, free-swelling, sample1

description:
Library name: Sample46
h2_veh_fs_a


title: Wildtype, loaded 24 hours, sample3

description:
Library name: Sample44
rvr_veh_24hr_f

value: Wildtype


title: Wildtype, loaded 24 hours, sample4

description:
Library name: Sample45
rvr_veh_24hr_g


title: Wildtype, loaded 3 hours + GSK205, sample6

description:
Library name: Sample40
rvr_205_3hr_f


title: Wildtype, loaded 3 hours + GSK205, sample7

description:
Library name: Sample41
rvr_205_3hr_g


title: Mutant, loaded 0 hours + GSK205, sample1

description:
Library name: Sample64
h2_205_0hr_a


title: Wildtype, loaded 24 hours, sample2

description:
Library name: Sample43
rvr_veh_24hr_d


title: Wildtype, loaded 24 hours, sample1

description:
Library name: Sample42
rvr_veh_24hr_c


title: Wildtype, loaded 3 hours + GSK205, sample3

description:
Library name: Sample37
rvr_205_3hr_c


title: Wildtype, loaded 3 hours + GSK205, sample1

description:
Library name: Sample35
rvr_205_3hr_a


title: Wildtype, loaded 3 hours, sample7

description:
Library name: Sample34
rvr_veh_3hr_g


title: Wildtype, loaded 3 hours + GSK205, sample2

description:
Library name: Sample36
rvr_205_3hr_b


title: Mutant, loaded 0 hours, sample2

description:
Library name: Sample59
h2_veh_0hr_b


title: Wildtype, loaded 3 hours, sample5

description:
Library name: Sample32
rvr_veh_3hr_e


title: Wildtype, loaded 3 hours, sample6

description:
Library name: Sample33
rvr_veh_3hr_f


title: Wildtype, loaded 3 hours + GSK205, sample4

description:
Library name: Sample38
rvr_205_3hr_d


title: Wildtype, loaded 3 hours, sample4

description:
Library name: Sample31
rvr_veh_3hr_d


title: Wildtype, loaded 3 hours, sample3

description:
Library name: Sample30
rvr_veh_3hr_c


title: Wildtype, loaded 0 hours + GSK205, sample5

description:
Library name: Sample26
rvr_205_0hr_f


title: Wildtype, loaded 3 hours, sample1

description:
Library name: Sample28
rvr_veh_3hr_a


title: Wildtype, loaded 0 hours + GSK205, sample6

description:
Library name: Sample27
rvr_205_0hr_g


title: Wildtype, loaded 0 hours + GSK205, sample4

description:
Library name: Sample25
rvr_205_0hr_e


title: Wildtype, loaded 0 hours + GSK205, sample3

description:
Library name: Sample24
rvr_205_0hr_d


title: Wildtype, loaded 3 hours, sample2

description:
Library name: Sample29
rvr_veh_3hr_b


title: Wildtype, loaded 0 hours + GSK205, sample1

description:
Library name: Sample22
rvr_205_0hr_b


title: Wildtype, loaded 0 hours, sample6

description:
Library name: Sample20
rvr_veh_0hr_f


title: Wildtype, loaded 0 hours + GSK205, sample2

description:
Library name: Sample23
rvr_205_0hr_c


title: Wildtype, loaded 0 hours, sample7

description:
Library name: Sample21
rvr_veh_0hr_g


title: Mutant, free-swelling, sample2

description:
Library name: Sample47
h2_veh_fs_b


title: Wildtype, loaded 0 hours, sample5

description:
Library name: Sample19
rvr_veh_0hr_e


title: Wildtype, loaded 3 hours + GSK205, sample5

description:
Library name: Sample39
rvr_205_3hr_e


title: Wildtype, loaded 0 hours, sample2

description:
Library name: Sample16
rvr_veh_0hr_b


title: Wildtype, loaded 0 hours, sample3

description:
Library name: Sample17
rvr_veh_0hr_c


title: Wildtype, free-swelling +GSK205, sample7

description:
Library name: Sample14
rvr_205_fs_g


title: Wildtype, loaded 0 hours, sample1

description:
Library name: Sample15
rvr_veh_0hr_a


title: Wildtype, free-swelling +GSK205, sample5

description:
Library name: Sample12
rvr_205_fs_e


title: Wildtype, free-swelling +GSK205, sample6

description:
Library name: Sample13
rvr_205_fs_f


title: Wildtype, free-swelling +GSK205, sample4

description:
Library name: Sample11
rvr_205_fs_d


title: Wildtype, free-swelling, sample7

description:
Library name: Sample7
rvr_veh_fs_f


title: Wildtype, free-swelling +GSK205, sample2

description:
Library name: Sample9
rvr_205_fs_b


title: Wildtype, free-swelling +GSK205, sample3

description:
Library name: Sample10
rvr_205_fs_c


title: Wildtype, free-swelling, sample6

description:
Library name: Sample6
rvr_veh_fs_f


title: Wildtype, free-swelling, sample4

description:
Library name: Sample4
rvr_veh_fs_d


title: Wildtype, free-swelling, sample5

description:
Library name: Sample5
rvr_veh_fs_e


title: Wildtype, free-swelling +GSK205, sample1

description:
Library name: Sample8
rvr_205_fs_a


title: Wildtype, free-swelling, sample2

description:
Library name: Sample2
rvr_veh_fs_b


title: 786-O HA-VHL RB1 KO cells, Biol Rep 3

city: Ottawa

first: Mercy

last: Akuma

address: 451, Smyth road

department: Cellular and Molecular Medicine

institute: University of Ottawa

description:
Library name: Sample 9_VHLrecon_RB1KO
Column name in raw_counts_all_samples.xlsx: 786-O_VHL_RBKO_3

data_processing:
Raw sequencing data was processed using GenPipes with standard settings, which aligns reads to GRCh37 (hg19) with STAR 2-passes mode and counted to gene features using ‘htseq-count’ function from HTSeq. The raw count data was normalized and analyzed by DESeq2.
Assembly: GRCh37 (hg19).
Supplementary files format and content: xlsx files include raw counts for each sample.

source_name: kidney

growth_protocol: Each cell line was maintainedin RPMI supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Total RNA was extracted using Trizol reagent (15596026, Thermo Fisher Scientific). RNA was initially quality controlled by Qubit and Tapestation.
Libraries were prepared using the Truseq kit from Illumina using the manufacturer's protocol. All libraries were sequenced on 1 lane of NovaSeq S1 (PE100), to generate 50 million reads per condition.

value: kidney

value: clear cell renal cell carcinoma cells

value: HA-VHL reconstitution and RB1 knockout


title: 786-O RB1 KO cells, Biol Rep 3

description:
Library name: Sample 12_RB1KO
Column name in raw_counts_all_samples.xlsx: 786-O_RBKO_3

value: RB1 knockout


title: 786-O RB1 KO cells, Biol Rep 2

description:
Library name: Sample 11_RB1KO
Column name in raw_counts_all_samples.xlsx: 786-O_RBKO_2


title: 786-O HA-VHL RB1 KO cells, Biol Rep 2

description:
Library name: Sample 8_VHLrecon_RB1KO
Column name in raw_counts_all_samples.xlsx: 786-O_VHL_RBKO_2


title: 786-O wildtype cells, Biol Rep 3

description:
Library name: Sample 6_WT
Column name in raw_counts_all_samples.xlsx: 786-O_3

value: WT


title: Wildtype, loaded 0 hours, sample4

description:
Library name: Sample18
rvr_veh_0hr_d


title: 786-O wildtype cells, Biol Rep 1

description:
Library name: Sample 4_WT
Column name in raw_counts_all_samples.xlsx: 786-O_1


title: 786-O wildtype cells, Biol Rep 2

description:
Library name: Sample 5_WT
Column name in raw_counts_all_samples.xlsx: 786-O_2


title: 786-O HA-VHL cells, Biol Rep 2

description:
Library name: Sample 2_VHLrecon
Column name in raw_counts_all_samples.xlsx: 786-O_VHL_2

value: HA-VHL reconstitution


title: 786-O HA-VHL cells, Biol Rep 1

description:
Library name: Sample 1_VHLrecon
Column name in raw_counts_all_samples.xlsx: 786-O_VHL_1


title: 786-O HA-VHL cells, Biol Rep 3

description:
Library name: Sample 3_VHLrecon
Column name in raw_counts_all_samples.xlsx: 786-O_VHL_3


title: M-MDSC-TIE2+,pbmc of 3 differents melanoma patients before treatment initiation and pooled before sorting, replicat2

city: Besançon

first: Olivier

last: Adotévi

state: Franche-Comté

address: 8 rue du Dr JFX Girod

department: Oncology

institute: Université de Franche-Comté

description:
Library name: S12
M.MDSC_TIE.2_Ang2_S12

data_processing:
Quality of the sequences and potential contamination were assessed using FastQC (v. 0.11.9),  and MultiQC (v1.14).
Sequence reads were trimmed for adaptor sequence/low-quality using trimmomatic v0.39 (with parameters keepBothReads LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:33).
The trimmed sequences were mapped to the indexed human reference genome (GRCh38) using STAR v2.7.8a
read Counts were performed using the function featureCounts of Subread v2.0.3
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw count for all samples

source_name: PMBC

growth_protocol: Peripheral blood mononuclear cells (PBMC) were thawed in RPMI medium supplemented with 10% human serum and antibiotics. PBMC were counted and three different patients were pooled. M-MDSC TIE2- and TIE2+ were sorted using FACS (SONY) and then, cell pellets were formed and cryopreserved before RNA extraction.

extract_protocol:
RNA was extracted using Maxwell RNA blood kit (Promega)
Libraries were prepared using Illumina’s Stranded mRNA Prep Ligation kit following manufacturer’s instructions.

value: PMBC


title: MDA-MB-231 revertant cells, day 21

city: Solna

first: Roland

last: Nilsson

address: Akademiska Stråket 1

department: Dept. of Medicine, Solna

country: Sweden

institute: Karolinska Institutet

description: Library name: MDA231_D21

data_processing:
Mapping to the reference genome and generation of count matrices was perfomed by Novogene using the Cell Ranger software (10X Genomics).
Assembly: GRCh38
Supplementary files format and content: Cell Ranger counts matrix files are provided in .mtx format (compressed), with separate barcode and feature description files.

growth_protocol: MDA-MB-231 cells were maintained in custom-synthesized RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum (FBS) (catalog: 16140071, Gibco) dialyzed in SnakeSkin 3,500 molecular-weight cut-off dialysis tubing (88244, Thermo Fisher), and with 1% penicillin–streptomycin (PeSt; Gibco,15140148). Cells were maintained at 37 deg C and 5 % CO2.

extract_protocol:
Cells were collected and counted using a hand-held Coulter counter (Scepter 3, Merck Millipore). Cells were diluted to a target concentration of approximately [1000 cells/µL] for optimal loading onto the 10x Genomics Chromium Controller.
Single-cell suspensions were processed using the 10x Genomics Chromium Next GEM Single Cell 3’ Kit v3.1 (CG000315 REV E) according to the manufacturer’s protocol. Cells were loaded onto the Chromium Controller to generate Gel Bead-In Emulsions (GEMs) containing individual cells, barcoded primers, and enzymes necessary for reverse transcription (PN-1000123, 10x Genomics). GEM generation and barcoding efficiency were monitored during the process to ensure high-quality libraries. GEMs were lysed to release cellular RNA, followed by reverse transcription and amplification to generate full-length cDNA (PN-1000190, 10x Genomics). cDNA libraries were fragmented, end-repaired, A-tailed, and ligated to sequencing adapters. Library quality and concentration were assessed using the Agilent Bioanalyzer 2100 (catalog) and Qubit dsDNA HS Assay Kit (catalog), respectively. Libraries were sequencing-ready after achieving a target fragment size of approximately [~500 bp]. ]. Library sequencing was done by Novogene (www.novogene.com) on an Illumina [NovaSeq 6000/NextSeq] platform using paired-end reads with a read length of 150 bp.

treatment_protocol: Parental cells (D0) were maintained in RPMI-1640 medium containing 100uM methionine.  Revertant cells (D21) were cultured in RPMI-1640 medium lacking methionine but containing 100uM L-homocysteine (69453, Sigma-Aldrich) and 1.5uM vitamin B12 (cyanocobalamin, V6629, Sigma-Aldrich).

value: Breast cancer cell line

value: Homocysteine medium + 1.5uM B12


title: M-MDSC-TIE2-, pbmc of 3 differents melanoma patients before treatment initiation and pooled before sorting, replicat2

description:
Library name: S7
M.MDSC_S7


title: M-MDSC-TIE2+, pbmc of 3 differents melanoma patients before treatment initiation and pooled before sorting, replicat1

description:
Library name: S9
M.MDSC_TIE.2_Ang2_S9


title: Wildtype, free-swelling, sample3

description:
Library name: Sample3
rvr_veh_fs_c

value: Tissue-engineered cartilage


title: A549 cells+DOX,IL-33-C 1

city: Changchun

first: Chen

last: Shao

state: Jilin

address: 126 Xinmin ST

institute: Jilin University

data_processing:
RNA-sequencing reads were first trimmed to remove poly(A) and unqualified reads with Cutadapt(v2.7). For CUT&Tag, the bam file generated from uniquely mapped reads was used as input for peak calling with macs2 software, applying a cutoff q-value < 0.05. The peaks were annotated using in-house scripts. Peak analysis involved counting the annotation results and plotting the distribution using R.
Assembly: hg38
Supplementary files format and content: xls, expression matrix
Supplementary files format and content: bw, IL-33_F, bw, IL-33_C

extract_protocol:
A549 Cells infected with the virus were seeded at a density of 2 × 106 cells per 10 cm dish and incubated overnight. After drug treatment, TRIzol reagent was used for cell lysis according to the manufacturer’s instructions. Three independent biological replicates were used for each experiment. For CUT&Tag, cells infected with the virus were seeded at a density of 2 × 107 cells per 10 cm dish and incubated overnight. The cells were sent to Jingjie PTM BioLab Co., Inc. (Hangzhou, China) for CUT&Tag analysis.
The lysates were sent to Personalbio (Shanghai, China) for cDNA library construction and sequencing by Illumina NovaSeq 6000. RNA-sequencing reads were first trimmed to remove poly(A) and unqualified reads with Cutadapt(v2.7).Briefly, the CUT&Tag assay was performed using the NovoNGS CUT&Tag 4.0 High-Sensitivity Kit ( Illumina), according to the manufacturer’s protocol. Library quality was assessed on the Agilent 5400 system (Agilent, USA) and quantified by qPCR. Raw data in fastq format were processed using the Trimmomatic (RRID:SCR_011848) software. All downstream analyses were based on high-quality clean data.

value: lung cancer cells

value: IL-33-C overexpression

value: infected with lentivirus


title: A549 cells+DOX,IL-33-C 3


title: A549 cells+DOX,IL-33-C 2


title: A549 cells+DOX,IL-33-F 3

value: IL-33-F overexpression


title: M-MDSC-TIE2-, pbmc of 3 differents melanoma patients before treatment initiation and pooled before sorting, replicat1

description:
Library name: S6
M.MDSC_S6


title: A549 cells+DOX,IL-33-F 2


title: A549 cells+DOX,control 2

value: vector control


title: 786-O RB1 KO cells, Biol Rep 1

description:
Library name: Sample 10_RB1KO
Column name in raw_counts_all_samples.xlsx: 786-O_RBKO_1


title: Wildtype, free-swelling, sample1

description:
Library name: Sample1
rvr_veh_fs_a

value: hiPSC

value: Free-swelling


title: A549 cells+DOX,control 3


title: A549 cells+DOX,control 1


title: 786-O HA-VHL RB1 KO cells, Biol Rep 1

description:
Library name: Sample 7_VHLrecon_RB1KO
Column name in raw_counts_all_samples.xlsx: 786-O_VHL_RBKO_1

value: kidney


title: A549 cells,IL-33-C 2


title: A549 cells,IL-33-C 1


title: A549 cells,IL-33-F 3


title: A549 cells,IL-33-F 2


title: A549 cells,IL-33-F 1


title: A549 cells,lv-control 2


title: MDA-MB-231 parental cells, day 0

description: Library name: MDA231_D0

value: Control (methionine medium)


title: A549 cells,lv-control 1


title: A549 cells,lv-control 3