title: TDP-43 cKO scRNAseq rep2

city: Boston

first: Geoffrey

middle: M

last: Nelson

address: 45 Shattuck St

department: BCMP

institute: Harvard Medical School

description: 10x Genomics

data_processing:
Basecalling and demultiplexing of raw data was done with the mkfastq command of the software Cell Ranger 6.1.1 (10x Genomics)
Reads were mapped with 10x Genomics Cell Ranger 7.0.0 to the 2020-A version of the mm10 pre-built reference
Seurat v4.2.0 was used for downstream processing
The top 40 principal components were used for cell clustering which had a selected resolution parameter of 0.8
Differentially expressed genes in Spermatogonia across conditions were determined via a pseudobulk analysis, using the pairwise Wald test within DESeq2 v1.36.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
PND 24 (post-natal day 24) mice of TDP-43 cKO (N=3), Nelf-B cKO (N=2) and corresponding littermate/ non-littermate control (N=4) were used for single-cell RNA-seq. Testes were dissected and collected in 35 mm plate with ice cold DMEM (DMEM henceforth). Testes were decapsulated and the seminiferous tubules were minced thoroughly with micro squeeze scissors. The resulting minced tubules were collected in a 15 ml conical centrifuge tube with 10 ml DMEM and washed twice at 0.1 xg for 1 min in an Eppendorf swing bucket centrifuge (model 5702 R). After the final wash the pellet was suspended in 1 ml DMEM and digested with 250 µl of 1% collagenase and 10 µl of 1% DNase at 35.5°C for 20 min in a rotating shaker (100 rpm) until tubules were well separated. The enzymatic reactions were stopped by diluting the enzymes with excess amount of (12 ml) DMEM and washed twice at 0.1 xg for 1 min. After the final wash the pellet was suspended in 1 ml DMEM and put through a second enzymatic digestion with 1 mL of 0.25% trypsin, 350 µl of 1% hyaluronidase, 200 µl of 1% collagenase, and 10 µl of 1% DNase, at 35.5°C for 20 min in the rotating shaker. The enzymatic digestions were stopped by adding 12 ml of DMEM. The resulting single cell suspensions were filtered through 40 μm EZFlow nylon mesh (Foxx Life Sciences, Londonderry, NH) and the filtered samples were centrifuged at 0.3 xg for 5 min. The supernatant was discarded carefully, and single cells pellet was suspended in DMEM with 1-2% BSA. Finally, the cell suspensions were passed through Flowmi 40 μm cell strainer (SP Bel-Art, Wayne, NJ) to discard clumped cells and collected in 1.5 ml microfuge tubes. The tubes were stored on ice and proceeded for the 10X genomic facilities.
Single-cell 3’ cDNA libraries were prepared at the DNA Services laboratory of the Roy J. Carver Biotechnology Center at the University of Illinois at Urbana-Champaign. Single-cell suspensions were delivered to the facility and were counted and checked for viability >80% using the Nexcelom K2 brightfield/dual florescence cell counter (Nexcelom Biosciences, Lawrence MA) with AO/PI staining, then washed with PBS buffer containing 2.0% BSA, then recounted for library preparation. The target number of cells (5,000) from each population were converted into individually barcoded cDNA libraries with the Single-Cell 3’ NextGEM v3.1 Chromium kit from 10X Genomics (Pleasanton, CA) following the manufacturer’s protocols. Following ds-cDNA synthesis, individually-barcoded dual-index libraries compatible with the Illumina chemistry were constructed. The final libraries were quantitated on Qubit (Life Technologies, Grand Island, NY) and the average size determined on the AATI Fragment Analyzer (Agilent Technologies, Santa Clara, CA).  Libraries were pooled evenly and the final pool diluted to 5nM final concentration. The 5nM dilution was further quantitated by qPCR on a BioRad CFX Connect Real-Time System (Bio-Rad Laboratories, Inc. CA).

value: testis

value: germ and somatic

tag: developmental stage

value: post-natal day 24

value: TDP-43 cKO


title: HSCs, Mitol KO (1)

status: Public on Dec 18 2023

type: SRA

city: Kumamoto

first: Toshio

last: Suda

address: 2-2-1 Honjo, Chuo-ku

country: Japan

institute: Kumamoto University

description:
S9
raw_counts.csv

library_source: transcriptomic

data_processing:
mRNA profile generated by deep sequencing using Illumina Next-Seq 500
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm39 whole genome using Spliced Transcripts Alignment (STAR) pipeline (Dobin et al. Bioinformatics, 2013:29)
The generated BAM files were then merged using samtools and transcripts were counted using subread package.
Assembly: mm39
Supplementary files format and content: Tab-delimited csv file includes raw counts number for each Sample.

molecule: total RNA

organism: Mus musculus

source_name: Bone marrow

extract_protocol:
After 100 cells were sorted, first strand cDNA were synthesized followed by generating 2nd strand by minorly modified method that was previously reported (Hiyashi et al. Nature Communication, 2018: 9) .
Using Nextera XT DNA sample Prep Kit (Illumina Inc., San Diego, CA), libraries were prepared by minorly modified method that was previously reported (Hiyashi et al. Nature Communication, 2018: 9) .

tag: tissue

value: Bone marrow

tag: cell type

value: hematopoietic stem cells

tag: strain

tag: genotype

value: Mitol knockout

tag: age

value: 8-10 weeks


title: miRNA, rVSVΔG-ZEBOV-GP, D2 153_S57_L001

city: Göteborg

first: Björn

last: Andersson

address: Sahlgrenska akademin, Core Facilities, Box 413

department: Boinformatics and Data center

country: Sweden

institute: Univeristy of Gothenburg

description:
miRNA, rVSVΔG-ZEBOV-GP, D2
miRNA-seq

data_processing:
Adapters and indexes have been removed by using cutadapt v2.10.
Reads were aligned to GRCh38 by using bowtie2 v2.3.5.1.
Alignments were processed using samtools v1.9 to obtain a sorted bam-file which was used as input in HTSeq.count v0.13.0.
Counts were normalized by sequencing depth, dividing each sample with the column sums and multiplying them by 1 M. Baseline adjustment was performed individually by dividing the normalized data at each time point (day 1, 2, 3, and 7) by day 0 (e.g. day 1/day 0). All values were Log2-transfomed before further analyses. The R software v4.0.1 was used to perform normalization and baseline adjustment.
Assembly: GRCh38
Supplementary files format and content: txt file with normalized and log2 transformed counts

organism: Homo sapiens

source_name: serum-derived extracellular vesicles

extract_protocol:
extracellular vesicles (EV)-RNAs, including miRNAs, were isolated by using the PAXgene blood miRNA kit (PreAnalytiX). This kit guarantees the extraction of intracellular RNA and miRNA upon cell lysis and stabilization of intracellular RNA during whole blood collection in PAXgene blood RNA tubes (PreAnalytiX). The elutes were quantified with a Qubit fluorometer (ThermoFisher Scientific) by using the RNA Broad Range assay kit (ThermoFisher Scientific). RNA quality was assessed by using Agilent RNA (15nt) fragment analysis (Agilent).
Libraries were prepared using the NEBNextâ Multiplex Small RNA Library Prep Kit for Illumina (New England BioLabs) (Index Primers 1-48, #7560S). Their quality and yield were measured by Agilent HS NGS fragment analysis (Agilent). The final products have approximate size of 150 bp. The 1.1 nM libraries, derived from the WB RNAs, were sequenced using the NovaSeq 6000 sequencer with a 150 bp paired-end protocol. Between 9 and 41 million reads were obtained for each sample (average of 17 million reads per sample).

value: serum-derived extracellular vesicles

tag: treatment

value: rVSV-delta-G-ZEBOV-GP vaccine, dose 2x10^7

tag: time


title: miRNA, rVSVΔG-ZEBOV-GP, D3 154_S58_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D3
miRNA-seq


title: Old, Veh, 4

city: Madrid

first: Juan Ignacio

last: Jiménez-Loygorri

state: Madrid

address: Ramiro de Maeztu 9

department: Cellular and Molecular Biology

country: Spain

institute: Centro de Investigaciones Biológicas Margarita Salas

data_processing:
Resulting RNA-seq reads were processed and aligned using STAR at the Biostatistics and Bioinformatics Unit, IRB Barcelona.
Assembly: GRCm39
Supplementary files format and content: Normalized expression for each sample.

source_name: Neuroretina

growth_protocol: Animals were housed in an animal facility with food and water ad libitum and maintained in a 12h/12h light-dark cycle. Samples were collectec at 9am, one hour after light onset

extract_protocol:
Total RNA was extracted from a whole neuoretina using RNeasy Mini coupled to DNAse in-column treatment (Qiagen).
Total RNA extractions were quantified with a Nanodrop One (Thermo Fisher), and RNA integrity was assessed with the Bioanalyzer 2100 RNA Nano assay (Agilent). Libraries for RNA-seq were prepared at IRB Barcelona Functional Genomics Core Facility. Briefly, mRNA was isolated from 620 ng of total RNA using the kit NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs). The isolated mRNA was used to generate dual-indexed cDNA libraries using the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs). Ten cycles of PCR amplification were applied to all libraries. Sequencing-ready libraries were quantified using the Qubit dsDNA HS assay (Invitrogen) and quality controlled with the Bioanalyzer 2100 DNA HS assay (Agilent). An equimolar pool was prepared with the eighteen libraries for SE75 sequencing on a NextSeq550 (Illumina). Sequencing output was 513.7 million 75-nt single-end reads and a minimum of 26 million reads was obtained for all samples.

treatment_protocol: Animals were injected daily with UA or vehicle, dosage was adjusted to each animal according to their weight.

value: Neuroretina

value: WT

tag: Sex

value: F

value: Old

value: Veh


title: KOD

city: Bochum

first: Jacqueline

last: Reinhard

address: Universitätsstrasse 150

department: Cell Morphology and Molecular Neurobiology

country: Germany

institute: Ruhr University

data_processing:
FASTQ files were generated using bcl2fastq (Illumina).
To facilitate reproducible analyses, samples were processed using the publicly available nf-core/rnaseq pipeline version 3.5 implemented in Nextflow 21.10.6 using Docker 20.10.12 with the minimal command. In brief, lane-level reads were trimmed with Trim Galore 0.6.7 and aligned to the mouse genome (GRCm39) using STAR 2.7.9a. Gene-level and transcript-level quantification was done by Salmon v1.5.2.
Differential expression analyses were performed using custom scripts in R version 4.1.1 with the DESeq2 v.1.32.0 framework. Genes were considered differentially expressed if the adjusted p-value was < 0.05.
Assembly: GRCm39

source_name: retina

extract_protocol:
Mouse retinae were dissected from adult quadruple knockout and wildtype mice. Total RNA was extracted using the RNeasy Mini kit (Qiagen).  DNase treatment was made during the isolation procedure.
Sequencing libraries were generated from 450 ng of total RNA using the NEBNext Ultra II Directional Total RNA Library Prep Kit for Illumina as described by the manufacturer (NEB, Ipswich, MA, USA).

value: retina

value: Bcan, Ncan, Tnc and Tnr (quadruple) knockout


title: Old, Veh, 3


title: miRNA, rVSVΔG-ZEBOV-GP, D1 152_S56_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D1
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D0 151_S55_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D0
miRNA-seq


title: Old, Veh, 2

value: M


title: miRNA, rVSVΔG-ZEBOV-GP, D1 152_S56_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D1
miRNA-seq


title: HCC38

city: San Francisco

first: Sourav

last: Bandyopadhyay

state: California

address: 1450 3rd Street

department: Helen Diller Family Comprehensive Cancer Center

country: USA

institute: University of California, San Francisco

description: 10x genomics

data_processing:
Data were processed according to the 10x Cell Ranger v1.1.0 pipeline following the standard pipeline listed in the 10x software manual with default parameters.
Assembly: hg19
Supplementary files format and content: *_barcodes.tsv: Cell barcodes. *_genes.tsv: Genes. *_matrix.mtx: 10x gene barcode matrix

growth_protocol: Breast cancer cell lines were grown according to published guidelines except for SKBR3 cells which were cultured using RPMI media supplemented with 10% fetal bovine serum (FBS) and 1% pen/strep. All cell lines tested negative for mycoplasma contamination.

extract_protocol:
Breast cancer cell lines were thawed and carried according to published culture methods as described. Viably frozen PDX cell suspensions were thawed, washed and stained for fluorescence-activated cell sorting (FACS) using fluorescently labeled antibodies for human antigen CD298 (PE; 341704, BioLegend) and mouse antigens CD45 (APC; 559864, BD Pharmingen), CD31 (APC; 551262, BD Pharmingen) and Ter119 (APC; 557909, BD Pharmingen). Flow sorting was done using a BD FACSAria II cell sorter (Becton Dickinson) where contaminating hematopoietic and endothelial cells were excluded by gating out Lin+ (CD45, Ter119, CD31) cells. Dead populations from both PDX samples and cell lines were eliminated by excluding Sytox positive (SYTOX Blue Dead Cell Stain, S34857, Life Technologies) cells with cells showing at least 80% viability proceeded with for single-cell sequencing. Single-cell data for the HCC38 cell line was provided by 10x Genomics.
Sorted cells were washed in PBS with 0.04% BSA and resuspended at a concentration of ~1000 cells/µl. Single-cell RNA sequencing was performed at the IHG Genomics Core (UCSF) using the Chromium Single Cell 3ʹ Reagents Kit (CG00026 Rev B., 10x Genomics), and libraries were prepared following the manufacturer’s protocol. Libraries were then sequenced using the Illumina HiSeq2500 platform to achieve an average depth of 50,000 reads per cell.

treatment_protocol: HCI-002 PDX tissue was harvested and processed into single-cell suspensions following established protocols. Briefly, PDX tissue was mechanically chopped with scalpels and placed in culture medium DMEM/F12 with 5% FBS, 5 µg ml−1 insulin (UCSF Cell Culture Facility), 50 ng ml−1 gentamycin (UCSF Cell Culture Facility) and supplemented with 2 mg ml−1 collagenase-1 (Sigma). Sample was then digested for 45 min at 37 °C. The resulting suspensions were resuspended in 2 U µl−1 DNase (D4263-5VL, Sigma Aldrich) for 3 min at room temperature, washed and dissociated with 2 ml of 0.05% trypsin/EDTA (25-052-CI, Corning) for 10 min at 37 °C. Cell suspensions were then filtered through a 70 µm filter, and frozen in DMEM/F12 with 50% serum, 10% DMSO, and stored in liquid nitrogen prior to study.

tag: cell line

value: cell line


title: TDP-43 cKO scRNAseq rep1

state: MA

description: 10x Genomics

library_source: transcriptomic single cell

source_name: testis

value: testis

value: germ and somatic

value: post-natal day 24


title: Old, Veh, 5


title: KOB


title: TDP-43 cKO scRNAseq rep3

description: 10x Genomics

value: TDP-43 cKO


title: Control scRNAseq rep4

description: 10x Genomics

value: Control


title: miRNA, rVSVΔG-ZEBOV-GP, D0 151_S55_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D0
miRNA-seq


title: NELF-B cKO scRNAseq rep1

description: 10x Genomics

value: NELF-B cKO


title: NELF-B cKO scRNAseq rep2

description: 10x Genomics


title: miRNA, rVSVΔG-ZEBOV-GP, D7 150_S54_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D7
miRNA-seq

value: serum-derived extracellular vesicles


title: Control scRNAseq rep3

description: 10x Genomics


title: Control scRNAseq rep2

description: 10x Genomics


title: WTD

value: wildtype


title: WTC


title: KOC


title: WTB


title: Control scRNAseq rep1

description: 10x Genomics


title: Young, UA, 3

value: Neuroretina

value: Young

value: UA


title: Young, UA, 2

value: WT

value: F


title: Young, UA, 4


title: miRNA, rVSVΔG-ZEBOV-GP, D4 149_S53_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D4
miRNA-seq

value: rVSV-delta-G-ZEBOV-GP vaccine, dose 2x10^7


title: Old, Veh, 1

value: Old

value: Veh


title: WTA

value: retina


title: miRNA, rVSVΔG-ZEBOV-GP, D7 150_S54_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D7
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D4 149_S53_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D4
miRNA-seq


title: Young, UA, 1

value: M


title: Young, Veh, 3


title: Villin CreERT2 Pcgf6 KO crypts 15 days post TAM rep2

city: MILANO

first: Diego

last: Pasini

state: MI

address: Via Adamello 16

country: Italy

institute: European Institute of Oncology

description:
RNA-seq: Replicate 2 of intestinal crypts isolated from Pcgf6 cKO mice 15 days post administration of BNF
Villin_Pcgf6KO_7dTAM_rep2

data_processing:
Paired-end reads were aligned using STAR v2.7 to mm10 with default parameters plus  –outFilterMultimapNmax 1 to block reads multimapping
Gene counts were calculated using featureCounts (Liao et al., 2014) with parameters -s 0 -t exon -g gene_name using Gencode M21 (GRCm38) annotation downloaded from (https://www.gencodegenes.org/mouse/).
Differential expression analyses were performed using the R package DESeq2 v1.20 (Love et al., 2014) using default parameters
Log2FoldChanges were corrected using the apeglm (Zhu et al., 2019) package
adjusted P-values were corrected using the IHW (Ignatiadis et al., 2016) package
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM counts for each Sample

molecule: polyA RNA

source_name: small intestine

extract_protocol:
RNasy Plus KIT (Qiagen) on isolated crypts. 2ng of extracted RNA was used for NGS library construction
Smart-seq2  (Picelli et al., 2014)

value: small intestine

value: crypts

value: epithelial intestinal cells

tag: strain background

value: Pcgf6 KO

value: Day 15 from TAM administration


title: Villin CreERT2 Pcgf6 KO crypts 15 days post TAM rep1

description:
RNA-seq: Replicate 1 of intestinal crypts isolated from Villin Pcgf6 cKO mice 15 days post administration of BNF
Villin_Pcgf6KO_7dTAM_rep1


title: Young, Veh, 2


title: Young, Veh, 1


title: WT_CutRun_Diff_H3K4me3_rep1

city: Davis

first: Satoshi

last: Namekawa

state: CA

address: One Shields Avenue

institute: UC Davis

data_processing:
For CUT&RUN/Tag data processing, we basically followed the online tutorial posted by Henikoff Lab (https://protocols.io/view/cut-amp-tag-data-processing-and-analysis-tutorial-bjk2kkye.html).
Raw paired-end reads after trimming by Trim-galore (https://github.com/FelixKrueger/TrimGalore) (version 0.6.6) .
Trimmed reads were aligned mouse (GRCm38/mm10) genome using Bowtie2 (version 2.4.2) with options: --end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700. E. coli DNA carried along with bacterially-produced pAG-MNase protein brings along a fixed amount of E. coli DNA and can be used as spike-in DNA for CUT&RUN.  D. melanogaster DNA delivered by Drosophila S2 cells was used as spike-in DNA for CUT&Tag. For mapping E.coli or D. melanogaster spike-in fragments, we also use the --no-overlap --no-dovetail options to avoid cross-mapping. PCR duplicates were removed from low-cell-number data using the ‘MarkDuplicates’ command in Picard tools (version 2.23.8) (https://broadinstitute.github.io/picard/ ).
Biological replicates were pooled for the visualization and other analyses after validation of the reproducibility (Pearson correlation coefficient > 0.85). Spike-in normalization was implemented using the exogenous scaling factor computed from the E.coli or dm6 mapping files (the formula used for calculation of scale factors = 100,000 or 1,000,000 / spike-in reads).
For visualization using the Integrative Genomics Viewer55 (version 2.5.3), spike-in normalized genome coverage tracks were generated using the genomecov function of bedtools (version 2.29.2) with the ‘-bg -scale $scale_factor’ parameter.
SEACR (https://seacr.fredhutch.org/ ) was used for peak calling and HOMER (version 4.11) was used for peak annotation.
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&RUN

extract_protocol:
CUT&Tag libraries were prepared as previously described (a step-by-step protocol https://www.protocols.io/view/bench-top-cut-amp-tag-kqdg34qdpl25/v3 ). CUT&RUN libraries of PRC1ctrl, PRC1cKO, and WT spermatogonia were conducted as previously described (a step-by-step protocol https://www.protocols.io/view/cut-amp-run-targeted-in-situ-genome-wide-profiling-14egnr4ql5dy/v3 ).
CUT&Tag libraries were prepared using NEBNext HiFi 2x PCR Master mix (NEB, M0541L) according to the protocol (a step-by-step protocol https://www.protocols.io/view/bench-top-cut-amp-tag-kqdg34qdpl25/v3 ). CUT&RUN libraries were constructed using NEBNext® Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S).

value: testis

value: primary cells

value: Differentiating Spermatogonia

tag: chip antibody

tag: cell compartment

value: whole cell


title: miRNA, rVSVΔG-ZEBOV-GP, D3 148_S52_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D3
miRNA-seq

value: serum-derived extracellular vesicles


title: WT_CutRun_Diff_H3K4me3_rep2

value: WT


title: Villin CreERT2 Pcgf6 WT crypts 15 days post TAM rep2

description:
RNA-seq: Replicate 2 of intestinal crypts isolated from Villin WT mice 15 days post administration of BNF
Villin_Pcgf6WT_7dTAM_rep2


title: miRNA, rVSVΔG-ZEBOV-GP, D2 147_S51_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D2
miRNA-seq


title: WT_CutRun_Undiff_H3K4me3_rep2

value: Undifferentiated Spermatogonia


title: miRNA, rVSVΔG-ZEBOV-GP, D2 147_S51_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D2
miRNA-seq

value: rVSV-delta-G-ZEBOV-GP vaccine, dose 2x10^7


title: LH230119_FFPE_DX_1

first: Sara

last: Fernández

address: C/Arturo Soria 270

institute: MD Anderson Cancer Centre

library_source: genomic

data_processing:
Base calling software (Ion Reporter 5.18)
Filtered variants were reviewed and analyzed using the integrative genomics viewer (IgV)
Variants presents at germinal DNA were filetered out
Alamut visual Plus analysis version 1.6.1
Discard variants annotated as a single nucleotide polymorphism (SNP) or reported with a VAF greater than 1% in the genomeAD and single nucleotide polymorphism (dbSNP) databases
Variant analisys with databases such as ClinVar, Varsome, cBioportal, COSMIC (Catalogue Of Somatic Mutations in Cancer) and Ensembl, among others
Assembly: hg19
Supplementary files format and content: .xlsx files containing filtered and analized variants

molecule: genomic DNA

source_name: Diagnosic biopsy from cHL patient

extract_protocol:
For non-infiltrated bone marrow, and FFPE tissue the material was obtained by scraping de aPBirate slide based on phenol, sodium acetate andethanol protocol. For peripheral blood we used the DNeasy Blood & Tissue kit (Quiagen). For cell-free tumor cell DNA we used QiAamp circulating nucleic acid extraction kit (Quiagen).
The libraries were constructed following the protocol recommended by the Ion AmpliseqTM Library Preparation Kit (Thermo Fisher Scientific). We used a custom cHL-PBecific targeted panel.

value: Diagnosic biopsy from cHL patient


title: LH230119_FFPE_DX_2


title: Villin CreERT2 Pcgf6 WT crypts 15 days post TAM rep1

description:
RNA-seq: Replicate 1 of intestinal crypts isolated from Villin WT mice 15 days post administration of BNF
Villin_Pcgf6WT_7dTAM_rep1


title: WT_CutRun_Undiff_H3K4me3_rep1


title: LH230119_S_1.1

library_source: other

molecule: other

source_name: cell-free tumoral DNA

value: cell-free tumoral DNA


title: miRNA, rVSVΔG-ZEBOV-GP, D1 146_S50_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D1
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D3 148_S52_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D3
miRNA-seq


title: AhCre Pcgf6 KO crypts 15 days post BNF rep2

description:
RNA-seq: Replicate 2 of intestinal crypts isolated from AhCre Pcgf6 cKO mice 15 days post administration of BNF
AhCre_Pcgf6KO_7dBNF_rep2

value: Day 15 from BNF administration


title: AhCre Pcgf6 KO crypts 15 days post BNF rep1

description:
RNA-seq: Replicate 1 of intestinal crypts isolated from AhCre Pcgf6 cKO mice 15 days post administration of BNF
AhCre_Pcgf6KO_7dBNF_rep1


title: miRNA, rVSVΔG-ZEBOV-GP, D1 146_S50_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D1
miRNA-seq


title: Villin CreERT2 Pcgf6 WT crypts 15 days post TAM rep3

description:
RNA-seq: Replicate 3 of intestinal crypts isolated from Villin WT mice 15 days post administration of BNF
Villin_Pcgf6WT_7dTAM_rep3


title: 4T1 Myosin 1e WT Pool 2

city: SYRACUSE

first: Mira

last: Krendel

state: New York

address: 505 Irving Ave

institute: Upstate Medical University

data_processing:
RNA-seq data analysis pipeline
Sequence reads were trimmed for adaptor sequence and remove low-quality sequence/reads using Trimmomatic (v0.39)
Trimmed sequence reads were mapped to GENCODE GRCm38 release M24 Mouse reference genome by using STAR aligner (v2.7.3a)
Reads mapped to genes were summarized by the featureCounts program (57) in subread v1.6.4
Genes were filtered by CPM ≥ 1 in at least 2 samples, and data were normalized to effective library size by edgeR
Assembly: GENCODE GRCm38 release M24 Mouse reference genome
Supplementary files format and content: tab-delimited text files include normalized log2CPM values for each Sample

source_name: Breast; mammary gland

extract_protocol:
RNA was extracted using RNeasy Plus Mini kit (Qiagen). 100ng total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Stranded mRNA Library Prep (Illumina) following manufacturer's protocols.

value: Breast; mammary gland

value: Tumor Derived

value: Myosin 1e WT


title: KOA

value: retina

value: Bcan, Ncan, Tnc and Tnr (quadruple) knockout


title: AhCre Pcgf6 WT crypts 15 days post BNF rep2

description:
RNA-seq: Replicate 2 of intestinal crypts isolated from AhCre WT mice 15 days post administration of BNF
AhCre_Pcgf6WT_7dBNF_rep2

value: small intestine

value: crypts

value: epithelial intestinal cells


title: 4T1 Myosin 1e WT Pool 1


title: LH230119_S_1.1_A


title: miRNA, rVSVΔG-ZEBOV-GP, D0 145_S49_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D0
miRNA-seq


title: LH230119_S.0


title: AhCre Pcgf6 WT crypts 15 days post BNF rep1

description:
RNA-seq: Replicate 1 of intestinal crypts isolated from AhCre WT mice 15 days post administration of BNF
AhCre_Pcgf6WT_7dBNF_rep1


title: 4T1 Myosin 1e KO Pool 3

value: Myosin 1e KO


title: miRNA, placebo, D7 144_S48_L002

description:
miRNA, placebo, D7
miRNA-seq

value: placebo


title: WT ESC RING1B ChIP

description:
ChIP: PCGF6 IP of WT ESC chromatin
RING1B_ESC_WT

data_processing:
Paired-end reads were aligned to the mm10 mouse genome using bowtie v1.2.2 for ChIPseq analyses (Langmead et al., 2009) or to mm10 and dm6 genomes for ChIP-Rx with the alignment parameters: –m 1 –l 10 –X 1000
PCR duplicates were removed using samblaster (Faust and Hall, 2014)
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called using MACS2 v2.1.1 (Zhang et al., 2008) with the flags –BAMPE –m 10 30 –keep-dup all –p 1e-10
Calibrated quantification of ChIP-seq signal (ChIP-rx) was performed as described elsewhere (Orlando et al., 2014) including an additional normalization based on inputs sequencing
Assembly: mm10
Supplementary files format and content: narrowPeak (except for Input samples)

source_name: Embryonic Stem Cells

extract_protocol:
isolated crypts were fixed in 1% formaldehyde for 15 min. at room temperature followed by quenching with 2M Glycine for 10 min and sinicated at 500bp.
ChIP-seq libraries were prepared as described in (doi.org/10.1038/nprot.2013.023)

value: Embryonic Stem Cells

tag: molecule type

value: Chromatin (FA xlinked)


title: LH230118_FFPE_DX_2


title: 4T1 Myosin 1e KO Pool 2


title: miRNA, rVSVΔG-ZEBOV-GP, D0 145_S49_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D0
miRNA-seq

value: serum-derived extracellular vesicles


title: 4T1 Myosin 1e KO Pool 1


title: WT ESC PCGF6 ChIP

description:
ChIP: RING1B IP of WT ESC chromatin
PCGF6_ESC_WT

value: WT


title: 4T1 Myosin 1e WT Pool 3


title: miRNA, placebo, D7 144_S48_L001

description:
miRNA, placebo, D7
miRNA-seq


title: WT ESC reference Input

description:
ChIP: Input chromatin of WT ESC used as reference for peak calling
Input_ESC_WT

value: Input


title: LH230118_FFPE_DX_1

value: Diagnosic biopsy from cHL patient


title: Villin PCGF6 KO H2AK119ub1 ChIP with S2 spike

description:
ChIP-rx: H2AK119ub1 IP of Villin Pcgf6 KO crypt chromatin spiked with 5% S2 Drosophila  for normalization
H2AK119ub1_Villin_Pcgf6KO

value: Pcgf6 KO


title: miRNA, placebo, D4 143_S47_L001

description:
miRNA, placebo, D4
miRNA-seq


title: LH230118_S.0

value: cell-free tumoral DNA


title: miRNA, placebo, D4 143_S47_L002

description:
miRNA, placebo, D4
miRNA-seq


title: LH230118_PB_DNA NORMAL

source_name: germinal DNA from peripheral blood

value: germinal DNA from peripheral blood


title: Villin PCGF6 KO input with S2 spike

description:
ChIP-rx: Input chromatin of Villin Pcgf6 KO crypts spiked with 5% S2 Drosophila chromatin for normalization
InputS2_Villin_Pcgf6KO


title: LH230119_PB_DNA NORMAL


title: Villin WT input with S2 spike

description:
ChIP-rx: Input chromatin of Villin WT crypts spiked with 5% S2 Drosophila chromatin for normalization
InputS2_Villin_WT


title: C222201_FFPE_DX_2


title: Villin WT H2AK119ub1 ChIP with S2 spike

description:
ChIP-rx: H2AK119ub1 IP of Villin WT crypt chromatin spiked with 5% S2 Drosophila  for normalization
H2AK119ub1_Villin_WT


title: C222201_FFPE_DX_1


title: Villin PCGF6 KO RAD21 ChIP

description:
ChIP: RAD21 IP of Villin Pcgf6 KO crypt chromatin
RAD21_Villin_Pcgf6KO


title: Villin WT RAD21 ChIP

description:
ChIP: RAD21 IP of Villin WT crypt chromatin
RAD21_Villin_WT


title: C222201_S.0


title: C222201_PB_DNA NORMAL


title: miRNA, placebo, D1 140_S44_L002

description:
miRNA, placebo, D1
miRNA-seq


title: miRNA, placebo, D3 142_S46_L001

description:
miRNA, placebo, D3
miRNA-seq


title: miRNA, placebo, D2 141_S45_L002

description:
miRNA, placebo, D2
miRNA-seq


title: miRNA, placebo, D3 142_S46_L002

description:
miRNA, placebo, D3
miRNA-seq


title: miRNA, placebo, D2 141_S45_L001

description:
miRNA, placebo, D2
miRNA-seq


title: LH220016_FFPE_DX_2


title: LH220016_S_1.5


title: miRNA, placebo, D1 140_S44_L001

description:
miRNA, placebo, D1
miRNA-seq


title: Villin WT CTCF ChIP

description:
ChIP: CTCF IP of Villin WT crypt chromatin
CTCF_Villin_WT

value: anti-CTCF


title: Villin PCGF6 KO RING1B ChIP

description:
ChIP: RING1B IP of Villin Pcgf6 KO crypt chromatin
RING1B_Villin_Pcgf6KO


title: Villin PCGF6 KO CTCF ChIP

description:
ChIP: CTCF IP of Villin Pcgf6 KO crypt chromatin
CTCF_Villin_Pcgf6KO


title: C222201_S_1.4


title: Villin WT RING1B ChIP

description:
ChIP: RING1B IP of Villin WT crypt chromatin
RING1B_Villin_WT


title: miRNA, placebo, D0 139_S43_L002

description:
miRNA, placebo, D0
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D7 138_S42_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D7
miRNA-seq

value: rVSV-delta-G-ZEBOV-GP vaccine, dose 2x10^7


title: AhCre PCGF6 KO PCGF6 ChIP

description:
ChIP: PCGF6 IP of AhCre Pcgf6 KO crypt chromatin
PCGF6_AhCre_Pcgf6KO


title: AhCre WT PCGF6 ChIP

description:
ChIP: PCGF6 IP of AhCre WT crypt chromatin
PCGF6_AhCre_WT


title: LH220016_S_1.4


title: LH220016_FFPE_DX_1


title: miRNA, rVSVΔG-ZEBOV-GP, D7 138_S42_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D7
miRNA-seq


title: MODCs2015_12

type: RNA

city: Magdeburg

first: Constanze

last: Nossol

address: Leipziger Str. 44

department: Medical Faculty

institute: Otto-von-Guericke University

description: Gene expression data from cultered monocyte derived dendritic cells (MODC)

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 42C on Affymetrix GeneChip Porcine Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scanning using the GeneChip scanner 3000 were performed according to Affymetrix protocols

data_processing: Data were analysed with Affymetrix GCOS 1.1.1 software using global scaling to a target signal of 500 and BioConductor.

label: biotin

organism: Sus scrofa

source_name: monocyte derived dendritic cells (MODC)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 0.5 ug total RNA (Expression Analysis Technical Manual, 2009, Affymetrix).

extract_protocol: Total RNA was isolated using TRI Reagent (Sigma, Taufkirchen, Germany) according to the manufacturer’s protocol. After DNaseI treatment the RNA was cleaned up using the RNeasy Kit (Qiagen, Hilden, Germany).

treatment_protocol: Either a single or combined exposure to deoxynivalenol and lipopolysaccharide was applied to primary monocyte-derived cells

value: monocyte derived dendritic cells (MODC)

value: control

tag: duration of treatment


title: miRNA, placebo, D0 139_S43_L001

description:
miRNA, placebo, D0
miRNA-seq


title: AhCre PCGF6 KO RING1B ChIP

description:
ChIP: RING1B IP of AhCre Pcgf6 KO crypt chromatin
RING1B_AhCre_Pcgf6KO

value: small intestine

value: crypts


title: MODCs2015_13

value: deoxynivalenol


title: MODCs2015_10

value: deoxynivalenol, lipopolysaccharide


title: miRNA, rVSVΔG-ZEBOV-GP, D4 137_S41_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D4
miRNA-seq


title: AhCre WT RING1B ChIP

description:
ChIP: RING1B IP of AhCre WT crypt chromatin
RING1B_AhCre_WT

value: epithelial intestinal cells


title: LH220016_S_1.1


title: LH220016_S_1.3


title: miRNA, rVSVΔG-ZEBOV-GP, D4 137_S41_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D4
miRNA-seq


title: AhCre PCGF6 KO input with S2 spike

description:
ChIP-rx: Input chromatin of AhCre Pcgf6 KO crypts spiked with 5% S2 Drosophila chromatin for normalization
InputS2_AhCre_Pcgf6KO

value: Chromatin (FA xlinked)


title: LH220016_S.0


title: MODCs2015_06


title: LH220016_BM_DNA NORMAL

source_name: germinal DNA from bone marrow

value: germinal DNA from bone marrow


title: MODCs2015_14

value: lipopolysaccharide


title: MODCs2015_08


title: miRNA, rVSVΔG-ZEBOV-GP, D3 136_S40_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D3
miRNA-seq

value: serum-derived extracellular vesicles


title: miRNA, rVSVΔG-ZEBOV-GP, D3 136_S40_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D3
miRNA-seq


title: AhCre WT H2AK119ub1 ChIP with S2 spike

description:
ChIP-rx: H2AK119ub1 IP of AhCre WT crypt chromatin spiked with 5% S2 Drosophila  for normalization
H2AK119ub1_AhCre_WT

value: WT


title: miRNA, rVSVΔG-ZEBOV-GP, D2 135_S39_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D2
miRNA-seq


title: MODCs2015_15


title: AhCre WT input with S2 spike

description:
ChIP-rx: Input chromatin of AhCre WT crypts spiked with 5% S2 Drosophila chromatin for normalization
InputS2_AhCre_WT


title: LH220015_FFPE_DX_2

value: Diagnosic biopsy from cHL patient


title: LH220015_S_1.5

value: cell-free tumoral DNA


title: Nb-TraN selection, third round panning

city: Taipei

first: See-Yeun

last: Ting

address: 128 Academia Road, Section 2, Nankang

country: Taiwan

institute: Academia Sinica

data_processing:
The identification of nanobody sequences relied on detecting the presence of the 5' primer (CGGCAGCCTGCGCCT) and 3' primer (GGTGACCGTGAGCAGC) within the reads.
Reads sharing identical unique molecular identifier (UMI) sequences were grouped together, indicating their origin from the same original molecule.
This step enabled the removal of duplicate reads generated during library amplification, enhancing the precision of quantifying unique molecule diversity and abundance within the sample.
The determination of the variable region involved examining 25-base-pair segments surrounding conserved sequences.
Alignment of each conserved sequence with the nanobody was accomplished using the Smith-Waterman algorithm for local sequence alignment.
The variable region boundaries were established based on the alignments of conserved sequences at both ends.
Cases with more than 5 mismatches led to the identification of an absent variable region. Finally, all variable regions underwent clustering, and their frequencies were recorded for further analysis.
Assembly: None
Supplementary files format and content: Tab-delimited text file incluses raw count for each amplicon

organism: Escherichia coli

source_name: MG1655 delta-ompW

growth_protocol: E. coli MG1655 ∆ompW cells carrying nanobody library were cultured in LB broth with 50 μg/mL kanamycin at 37°C.

extract_protocol:
Plasmids were harvested using Maxi Plasmid DNA Kit (Geneaid). 10 ng of DNA were used for constructing sequencing library.
Libraries for Targeted amplicon sequencing (TAS) were prepared using  illumina IDT for Illumina DNA/RNA UD Indexes Set B following manufacturer’s protocol.

treatment_protocol: Cells were co-culture with the conjugative E. coli S17-1 strain at 37°C under 200 rpm shaking conditions for a 6-hour conjugation period. The induction of surface-displayed nanobodies or antigens was achieved through the addition of 500 ng/mL anhydrotetracycline. Subsequently, the S17-1 strain was eliminated using antibiotics.

value: MG1655 delta-ompW


title: MODCs2015_04


title: miRNA, rVSVΔG-ZEBOV-GP, D2 135_S39_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D2
miRNA-seq


title: MODCs2015_02


title: Nb-TraN selection, second round panning


title: miRNA, rVSVΔG-ZEBOV-GP, D1 134_S38_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D1
miRNA-seq


title: Nb-TraN selection, first round panning


title: Nb-TraN deep mutation scanning, input


title: LH220015_S_1.2


title: MODCs2015_11


title: LH220015_FFPE_DX_1


title: LH220015_S_1.1


title: Nb-TraN selection, before panning


title: MODCs2015_07


title: Round Spermatids PROseq rep3

first: Emily

last: Kaye

address: 45 Shattuck Street

description:
mm10_rs_proseq_n3spike_F.bw
mm10_rs_proseq_n3spike_R.bw

data_processing:
Read pairs were trimmed using cutadapt 1.14 to remove adapter sequences (-O 1 --match-read-wildcards -m 26)
The paired end reads were then mapped to a combined genome index, including both the spike (dm6) and primary (mm10) genomes, using bowtie2. Properly paired reads were retained. These read pairs were then separated based on the genome (i.e., spike-in vs primary) to which they mapped.
Reads mapping to the reference genome were then sorted, via samtools 1.3.1 (-n), and subsequently converted to bedGraph format using a custom script (bowtie2stdBedGraph.pl) that counts each read once at the exact 3’ end of the nascent RNA. Because R1 in PRO-seq reveals the position of the RNA 3’ end, the “+” and “-“ strands were swapped to generate bedGraphs representing 3’ end positions at single nucleotide resolution.
BedGraphs were normalized using the normalize_bedGraph custom script. For each library generated, we first divided the reads mapping to the spike genome (fly dm6)  by the primary genome (mm10). Next, we calculated the normalization factor by setting the lowest sample spike ratio to 1 and generated normalization factors based on that for each sample. Because the Round Spermatid cells are haploid, we added a genome copy number correction and divided the spike factors by 2.
Combined bedGraphs were generated by summing counts per nucleotide across replicates for each condition (bedgraphs2stdBedgraph). These were converted to bigwigs using UCSC tools.
Assembly: mm10
Supplementary files format and content: merged bigwigs of 3 normalized replicates, representing 3' ends of RNA
Library strategy: PRO-seq

molecule: nuclear RNA

extract_protocol:
Cells were washed in PBS, then permeabilized as in Reimer et al. 2021. Permeabilized cells were spiked with permeabilized S2 fly cells, then PRO-seq run-on reactions were performed using biotin-NTPs. Nascent RNA was extracted using a Total RNA Purification Kit following manufacturer instructions (Norgen Biotek Corp.).
Extracted RNA was chemically fragmented with magnesium chloride and heat, followed by bead purication and trizol extraction of nascent RNA. Purified RNA was then subjected to 3' adaptor ligation, bead purification, 5' decapping, and 5' hydroxyl repair, followed by 5' adaptor ligation. Libraries were prepared by on-bead reverse transcription and 9-10 cycle amplification of final PRO-seq libraries.

value: testis

value: Round Spermatids

value: wild type


title: Round Spermatids PROseq rep1


title: WT crypt reference Input

description:
ChIP: Input chromatin of WT crypts used as reference for peak calling
CryptSI_input

value: Input


title: MODCs2015_05

value: monocyte derived dendritic cells (MODC)


title: MODCs2015_03


title: Spermatocytes PROseq rep3

description:
mm10_sc_proseq_n3spike_F.bw
mm10_sc_proseq_n3spike_R.bw

value: Spermatocytes


title: MODCs2015_01

value: control


title: Round Spermatids PROseq rep2


title: miRNA, rVSVΔG-ZEBOV-GP, D7 132_S36_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D7
miRNA-seq

value: rVSV-delta-G-ZEBOV-GP vaccine, dose 2x10^7


title: LH220015_BM_DNA NORMAL


title: MODCs2015_09


title: miRNA, rVSVΔG-ZEBOV-GP, D0 133_S37_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D0
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D7 132_S36_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D7
miRNA-seq


title: C212118_FFPE_DX_1


title: miRNA, rVSVΔG-ZEBOV-GP, D0 133_S37_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D0
miRNA-seq


title: LH220015_S_1.4


title: Spermatocytes PROseq rep1


title: C212118_S.0


title: miRNA, rVSVΔG-ZEBOV-GP, D4 131_S35_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D4
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D4 131_S35_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D4
miRNA-seq


title: C212118_FFPE_DX_2


title: miRNA, rVSVΔG-ZEBOV-GP, D3 130_S34_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D3
miRNA-seq


title: Spermatogonia PROseq rep3

description:
mm10_sg_proseq_n3spike_F.bw
mm10_sg_proseq_n3spike_R.bw

value: Spermatogonia


title: miRNA, rVSVΔG-ZEBOV-GP, D3 130_S34_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D3
miRNA-seq


title: Spermatogonia PROseq rep1


title: C212118_S_1.3


title: LH200005_FFPE_DX_2


title: miRNA, rVSVΔG-ZEBOV-GP, D2 129_S33_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D2
miRNA-seq


title: LH200005_FFPE_DX_1


title: LH200005_S_2.4


title: ATAC_tumor

city: Nanjing

first: Yuchao

last: Jing

state: Jiangsu

address: 101 Longmian Ave Jiangning District

department: Immunology

country: China

institute: Nanjing Medical University

data_processing:
Raw paired-end sequenced reads were first cut adaptors and trimmed using trim_galore (v0.6.6) with “-q 20, --stringency 1, --length 20 and -e 0.1”.
Then, these cleaned fastq data were mapped using bowtie2 (v2.4.2) to the mm10 reference genome with “--end-to-end, --very-sensitive, --no-mixed, --no-discordant, --phred33, -I 10 and -X 700” model
Next, Picard was used for marking and removing duplication. Samtools (v1.11) was used for converting and sorting the sam files to sort bam files
Finally, Homer was used for peak calling. Differential peaks between Tumor treg and spleen treg were calculated by homer mergePeaks and homer getDifferentialPeaks. Differential peaks between WT and KO were calculated by homer.Peaks were annotated by annotatePeaks.pl with mm10 genome and gencodeVM25 gtf files.
Parallelly, deeptools was used for normalizing signals from sort bam files via bamCoverage.ComputeMatrix was used for calculating the overall signal distribution around the peak center called by homer using “reference-point” model with “-b 2000, -a 2000, --missingDataAsZero, --referencePoint center, --skipZeros, --blackListFileName mm10.blacklist.bed (discarding weird regions)”. Data were visualized using plotProfile and plotHeatmap in deeptools.
Assembly: mm10
Supplementary files format and content: bigwig
Supplementary files format and content: Tab-separated values peaks file

source_name: tumor

extract_protocol:
Tumor tissue was resected and digested with enzyme. Lymphocytes were purified using percoll. Treg cells were purified by magnetic-activated cell sorting (MACS) positive selection. Tumor infiltrated treg of the WT and jmjd1c tregcKO mice were isolated by Fluorescence-activated cell sorting (FACS) according to the presence or absence of fluorence signal. H3K9me2 modified genomic regions and Stat3 binding regions were harvested by anti-H3K9me2 antibody anti-Stat3 antibody and “TD903 Hyperactive® Universal CUT&Tag Assay Kit for Illumina”. Spleen treg cells were purified by magnetic-activated cell sorting (MACS) positive selection and isolated by Fluorescence-activated cell sorting (FACS) according to the presence or absence of fluorence signal.
Libraries were constructing using “TD903 Hyperactive® Universal CUT&Tag Assay Kit for Illumina” and “TD202 TruePrep® Index Kit V2 for Illumina®” from Vazyme Biotech Co., Ltd. ATACseq library was constructed in Active Motif. Inc.

value: tumor tissue

value: 8-12 weeks old

value: Treg cells


title: miRNA, rVSVΔG-ZEBOV-GP, D1 128_S32_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D1
miRNA-seq

value: serum-derived extracellular vesicles


title: LH200005_PB_DNA NORMAL

value: germinal DNA from peripheral blood


title: miRNA, rVSVΔG-ZEBOV-GP, D1 134_S38_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D1
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D2 129_S33_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D2
miRNA-seq


title: RNAseq_Undiff_win18446_PRC1cKO_rep2

data_processing:
Raw RNA-seq reads after trimming by Trim-galore (https://github.com/FelixKrueger/TrimGalore) (version 0.6.6) with the parameter ‘--paired’
Trimmed reads were aligned to the mouse (GRCm38/mm10) genome using HISAT2 (version 2.2.1) with default parameters. All unmapped reads, non-uniquely mapped reads and reads with low mapping quality (MAPQ < 30) were filtered out by samtools (version 1.9) with the parameter '-q 30'  before being subjected to downstream analyses.
Raw read counts for each gene were generated using the htseq-count function, part of the HTSeq package (version 1.6.0) based on the mouse gene annotation (gencode.vM24.annotation.gtf, GRCm38/mm10).
DESeq2 (version 1.28.1) was used for differential gene expression analyses
The TPM values of each gene were generated using RSEM (version 1.3.3).
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes TPM values for each Sample

extract_protocol:
Total RNA was extracted using the RNeasy Plus Micro Kit (QIAGEN, Cat # 74034) or RNeasy Plus Mini Kit (QIAGEN, Cat # 74134) according to the manufacturer's instructions.
RNA-seq libraries of PRC1ctrl and PRC1cKO Aundiff using the Smart-Seq2 method were prepared using NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina® (NEB, E6420S) according to the manufacturer’s instructions. Stranded RNA-seq libraries were prepared for (1) WT Aundiff and WT Adiff; (2) PRC1ctrl Aundiff and PRC1cKO Aundiff after Win18,446 treatment by the CCHMC DNA Sequencing and Genotyping Core (Cincinnati, Ohio, USA) using the Illumina TruSeq stranded mRNA kit after polyA enrichment.

treatment_protocol: For Win18,446 treatment experiments, 1-month-old male mice were injected subcutaneously with 40 μg/μl Win18,446 (N, N'-Octamethylenebis(2,2-dichloroacetamide), MP Biomedicals, 02158050), dissolved in 50 μl dimethyl sulfoxide (DMSO). After ~30 consecutive daily treatments, mice were euthanized 24h post-treatment for sampling. Collected testes were either fixed or dissociated for cell sorting.

value: primary cells

value: Undifferentiated Spermatogonia

value: C57BL/6 X FVB/NJ

value: Win18,446 inhibition


title: ATAC_spl

source_name: spleen

value: spleen tissue


title: LH200004_FFPE_DX_2

value: Diagnosic biopsy from cHL patient


title: RNAseq_Undiff_win18446_PRC1cKO_rep1

value: testis


title: LH200004_FFPE_DX_1


title: miRNA, rVSVΔG-ZEBOV-GP, D1 128_S32_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D1
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D0 127_S31_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D0
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D0 127_S31_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D0
miRNA-seq


title: RNAseq_Undiff_win18446_PRC1ctrl_rep2


title: LH200004_S_2.6

value: cell-free tumoral DNA


title: RNAseq_Undiff_win18446_PRC1ctrl_rep1


title: miRNA, rVSVΔG-ZEBOV-GP, D7 126_S30_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D7
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D7 126_S30_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D7
miRNA-seq


title: LH200004_S_2.5


title: LH200004_S_2.4


title: RNAseq_Undiff_PRC1cKO_rep2


title: RNAseq_Undiff_PRC1cKO_rep1


title: miRNA, rVSVΔG-ZEBOV-GP, D4 125_S29_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D4
miRNA-seq


title: RNAseq_Undiff_PRC1ctrl_rep1


title: LH200004_S_2.2


title: RNAseq_Undiff_PRC1ctrl_rep2


title: LH200004_S_2.0


title: LH200004_S_2.1


title: RNAseq_WT_Spg_Diff_rep2

value: Differentiating Spermatogonia

value: WT


title: RNAseq_WT_Spg_Diff_rep1


title: miRNA, rVSVΔG-ZEBOV-GP, D3 124_S28_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D3
miRNA-seq

value: rVSV-delta-G-ZEBOV-GP vaccine, dose 2x10^7


title: miRNA, rVSVΔG-ZEBOV-GP, D2 123_S27_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D2
miRNA-seq


title: LH200004_S.0


title: miRNA, rVSVΔG-ZEBOV-GP, D2 123_S27_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D2
miRNA-seq


title: LH210012_S_1.3


title: RNAseq_WT_Spg_Undiff_rep2


title: miRNA, rVSVΔG-ZEBOV-GP, D1 122_S26_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D1
miRNA-seq


title: RNAseq_WT_Spg_Undiff_rep1


title: LH200004_S_2.3


title: LH210012_S_1.4


title: PRC1cKO_win18446_CutRun_Undiff_H3K4me3_rep2

description: PRC1cKO_win18446_CutRun_Undiff_H3K4me3_scaled.bw

value: whole cell


title: miRNA, rVSVΔG-ZEBOV-GP, D1 122_S26_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D1
miRNA-seq


title: PRC1cKO_win18446_CutRun_Undiff_H3K4me3_rep1


title: Spermatogonia PROseq rep2

value: Spermatogonia

value: wild type


title: miRNA, rVSVΔG-ZEBOV-GP, D0 121_S25_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D0
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D0 121_S25_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D0
miRNA-seq


title: PRC1ctrl_win18446_CutRun_Undiff_H3K4me3_rep2

description: PRC1ctrl_win18446_CutRun_Undiff_H3K4me3_scaled.bw


title: miRNA, rVSVΔG-ZEBOV-GP, D7 120_S24_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D7
miRNA-seq


title: LH210012_PB_DNA NORMAL


title: PRC1cKO_win18446_CutRun_Undiff_H3K27me3_rep2

description: PRC1cKO_win18446_CutRun_Undiff_H3K27me3_scaled.bw


title: miRNA, rVSVΔG-ZEBOV-GP, D7 120_S24_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D7
miRNA-seq


title: LH210014_S_3.0


title: PRC1cKO_win18446_CutRun_Undiff_H3K27me3_rep1


title: miRNA, rVSVΔG-ZEBOV-GP, D4 119_S23_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D4
miRNA-seq


title: LH210014_BM_DNA NORMAL

value: germinal DNA from bone marrow


title: PRC1ctrl_win18446_CutRun_Undiff_H3K27me3_rep2

description: PRC1ctrl_win18446_CutRun_Undiff_H3K27me3_scaled.bw


title: LH210012_S_1.1


title: LH210013_FFPE_DX_2


title: miRNA, rVSVΔG-ZEBOV-GP, D4 125_S29_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D4
miRNA-seq

value: serum-derived extracellular vesicles


title: miRNA, rVSVΔG-ZEBOV-GP, D4 119_S23_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D4
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D3 124_S28_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D3
miRNA-seq


title: PRC1ctrl_win18446_CutRun_Undiff_H3K27me3_rep1


title: LH210013_FFPE_DX_1

source_name: Diagnosic biopsy from+D124 cHL patient

value: Diagnosic biopsy from+D124 cHL patient


title: PRC1cKO_CutRun_Undiff_H3K4me3_rep2

value: primary cells


title: LH210012_S.0


title: miRNA, rVSVΔG-ZEBOV-GP, D3 118_S22_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D3
miRNA-seq


title: LH210013_S_1.6


title: PRC1cKO_CutRun_Undiff_H3K4me3_rep1

value: Undifferentiated Spermatogonia


title: miRNA, rVSVΔG-ZEBOV-GP, D3 118_S22_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D3
miRNA-seq


title: PRC1ctrl_win18446_CutRun_Undiff_H3K4me3_rep1

value: C57BL/6 X FVB/NJ


title: LH210013_S_1.5


title: miRNA, rVSVΔG-ZEBOV-GP, D2 117_S21_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D2
miRNA-seq


title: PRC1ctrl_CutRun_Undiff_H3K4me3_rep2

description: PRC1ctrl_CutRun_Undiff_H3K4me3_scaled.bw


title: LH210014_FFPE_DX_2


title: miRNA, rVSVΔG-ZEBOV-GP, D2 117_S21_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D2
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D1 116_S20_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D1
miRNA-seq


title: PRC1ctrl_CutRun_Undiff_H3K4me3_rep1


title: LH210013_S_1.4


title: PRC1cKO_CutRun_Undiff_H3K27me3_rep2

description: PRC1cKO_CutRun_Undiff_H3K27me3_scaled.bw


title: miRNA, rVSVΔG-ZEBOV-GP, D1 116_S20_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D1
miRNA-seq


title: LH210013_FFPE_DNA NORMAL

source_name: germinal DNA

value: germinal DNA


title: PRC1cKO_CutRun_Undiff_H3K27me3_rep1


title: AhCre PCGF6 KO H2AK119ub1 ChIP with S2 spike

description:
ChIP-rx: H2AK119ub1 IP of AhCre Pcgf6 KO crypt chromatin spiked with 5% S2 Drosophila  for normalization
H2AK119ub1_AhCre_Pcgf6KO

value: small intestine

value: crypts

value: epithelial intestinal cells

value: Pcgf6 KO

value: Chromatin (FA xlinked)


title: miRNA, rVSVΔG-ZEBOV-GP, D0 115_S19_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D0
miRNA-seq

source_name: serum-derived extracellular vesicles


title: miRNA, rVSVΔG-ZEBOV-GP, D0 115_S19_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D0
miRNA-seq


title: PRC1ctrl_CutRun_Undiff_H3K27me3_rep2

description: PRC1ctrl_CutRun_Undiff_H3K27me3_scaled.bw

value: testis


title: LH190001_FFPE_DX_2

value: Diagnosic biopsy from cHL patient


title: LH190001_FFPE_DX_1


title: miRNA, rVSVΔG-ZEBOV-GP, D7 114_S18_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D7
miRNA-seq

value: rVSV-delta-G-ZEBOV-GP vaccine, dose 2x10^7


title: PRC1ctrl_CutRun_Undiff_H3K27me3_rep1

value: whole cell


title: KO-2

city: Noda

first: Daisuke

last: Kitamura

state: Chiba

address: Yamazaki 2669

institute: Tokyo University of Science

data_processing:
Data processing of RNA-seq was performed as described in Kato et al. (Kato et al., 2022 submitted).
In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or  fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by  Trimmomatic (v0.30).
Clean sequence reads were mapped to mouse reference genome sequence with Hisat2 (v2.0.1).
Transcripts per million (TPM) was calculated using StringTie (v2.1.2).
Assembly: GRCm39
Supplementary files format and content: Excel files include TPM values for each Sample

source_name: Primary marginal zone B cell

extract_protocol:
Two days after the immunization, donor B cells were magnetically enriched from pooled spleens of recipient mice using APC conjugated anti-CD45.1 (eBiosciences: Cat# 17-0453-82) and anti-APC MicroBeads (Miltenyi Biotec), with the MACS system (Miltenyi Biotec). After enrichment, cells were further stained with the respective Abs and CD45.1+ B220+ CD138- FSChi cells were sorted by using FACSAria III (BD Biosciences). Total RNA isolation was achieved using RNeasy Plus Micro Kit (QIAGEN).
cDNA libraries were prepared with TaKaRa SmartSeq Stranded kit (Takara) following manufacturer's protocols.

treatment_protocol: Marginal zone B cells purified from pooled spleens of CD45.1 B1-8flox/+, Dnase1l3+/+ or Dnase1l3-/-, mice (5–8 for each genotype) were transferred into 8 recipient mice (5 × 106 cells per mouse), which were immunized i.v. with NP- Ficoll on the following day.

value: Primary marginal zone B cell

value: female

value: Stimulation with NP-Ficoll

value: day 2 after stimulation


title: KO-1


title: LH190001_S_1.3

value: cell-free tumoral DNA


title: miRNA, rVSVΔG-ZEBOV-GP, D7 114_S18_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D7
miRNA-seq

value: serum-derived extracellular vesicles


title: LH190001_S_1.4


title: Nb-TraN deep mutation scanning, output

value: MG1655 delta-ompW


title: Sperm cell sRNA-Seq - VSL29

city: Orbassano

first: Giulio

last: Ferrero

state: TO

address: Regione Gonzole, 10

department: Dept. Clinical and Biological Sciences

institute: University of Turin

description: small RNA

data_processing:
Reads were trimmed from the adapter sequences using Cutadapt v1.10 by imposing a maximum error rate in terms of mismatches, insertions, and deletions equal to 0.15. Reads shorter than 14 nt were removed.
Trimmed reads were mapped against a miRNA reference based on miRBase v22 annotations using the small RNA-Seq module of Docker4Seq. The alignment was performed using BWA algorithm v0.7.127 with the default settings.
The results generated by the annotation and quantification methods were merged into a unique mature miRNA count matrix. In the case of mature miRNAs processed from different precursors but characterized by the same mature sequence, the read counts were summed.
The miRNA-unmapped reads were also aligned on other sncRNAs shorter than 80 nt from RNAcentral v22 using BWA. Annotations with identical sequences were merged into a single annotation. For Piwi-interacting RNAs (piRNAs), annotations belonging to the same cluster from piRNAclusterDB were joined into a single piRNA cluster annotation.
Assembly: hg38
Supplementary files format and content: Matrix tables with the raw mature miRNA and other sncRNA read counts for each sample

source_name: Sperm cells

extract_protocol:
Total RNA from semen samples was extracted using the Maxwell® RSC miRNA Tissue (Promega). Initially, 200ul of sperm samples were centrifuged for 15 minutes at 12,000x g at 4°C, discarded the supernatant and added at the pellet 200ul of Phosphate buffered saline (PBS), after centrifuge for 30 minutes at 5,000g at 4° C. At the end of the automated extraction, RNA samples were eluted in 50ul, following the manufacturer's instructions.
Small RNA-seq libraries were prepared using the NEBNext® Multiplex Small RNA Library Prep for Illumina® (New England Biolabs, Inc.) kit used to convert small RNA transcripts into barcoded cDNA libraries. For each library, 200 ng of RNA were processed as starting material. Each library was prepared with a unique indexed primer. Multiplex adapter ligations, reverse transcription primer hybridization, reverse transcription reaction and PCR amplification were performed according to the manufacturer's protocol. After PCR amplification, the cDNA constructs were purified with the QIAQuick® PCR Purification Kit (QIAGEN), following the modifications suggested by the NEBNext® Multiplex Small RNA Library Prep for Illumina® protocol. Final libraries were loaded on the Bioanalyzer® 2100 (Agilent Technologies) using the DNA High Sensitivity Kit (Agilent Technologies) according to the manufacturer's protocol. Libraries were pooled together (34-plex) and further purified with a gel size selection. A final Bioanalyzer® 2100 run with the High Sensitivity DNA Kit (Agilent Technologies) allowed the assessment of DNA libraries quality regarding size, purity, and concentration. The obtained libraries were subjected to the Illumina sequencing pipeline on Illumina NextSeq500 sequencers (75 cycles, Illumina Inc., USA).

value: Sperm cells

value: M

tag: residential area

value: VSL


title: miRNA, rVSVΔG-ZEBOV-GP, D4 113_S17_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D4
miRNA-seq


title: LH190001_S_1.2


title: Sperm cell sRNA-Seq - VSL27

description: small RNA


title: WT-1


title: Sperm cell sRNA-Seq - VSL19

description: small RNA


title: LH190001_PB_DNA NORMAL

value: germinal DNA from peripheral blood


title: miRNA, rVSVΔG-ZEBOV-GP, D3 112_S16_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D3
miRNA-seq


title: LH210013_S_1.3


title: Sperm cell sRNA-Seq - VSL18

description: small RNA


title: miRNA, rVSVΔG-ZEBOV-GP, D3 112_S16_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D3
miRNA-seq


title: C191819_S_2.0


title: Transgenic polysome sample 3

city: Seoul

first: Kihoon

last: Han

address: 73, Inchon-ro, Seongbuk-gu

department: Neuroscience

country: South Korea

institute: Korea University College of Medicine

data_processing:
Transcript abundance was estimated with Salmon(v1.1.0) in Quasi-mapping-based mode onto the Mus musculus genome (GRCm38) with GC bias correction (--gcBias).
Quantified gene-level abundance data was imported to R (v.3.6.2) with tximport package and differential gene expression analysis was carried out using R/Bioconductor DEseq2 (v1.26.0).
The normalized read counts were computed by dividing the raw read counts by size factors and fit to a negative binomial distribution.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file include normalized read count metrix calculated by using DESeq2.

source_name: Brain

extract_protocol:
RNA samples were prepared for sequencing using a TruSeq Stranded Total RNA LT Sample Prep Kit (Illumina) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Striatum

tag: genotype/variation

value: Shank3 TG

value: male

value: synaptosomal polysome RNA


title: Sperm cell sRNA-Seq - VSL17

description: small RNA


title: miRNA, rVSVΔG-ZEBOV-GP, D2 111_S15_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D2
miRNA-seq

data_processing:
Adapters and indexes have been removed by using cutadapt v2.10.
Reads were aligned to GRCh38 by using bowtie2 v2.3.5.1.
Alignments were processed using samtools v1.9 to obtain a sorted bam-file which was used as input in HTSeq.count v0.13.0.
Counts were normalized by sequencing depth, dividing each sample with the column sums and multiplying them by 1 M. Baseline adjustment was performed individually by dividing the normalized data at each time point (day 1, 2, 3, and 7) by day 0 (e.g. day 1/day 0). All values were Log2-transfomed before further analyses. The R software v4.0.1 was used to perform normalization and baseline adjustment.
Assembly: GRCh38
Supplementary files format and content: txt file with normalized and log2 transformed counts

extract_protocol:
extracellular vesicles (EV)-RNAs, including miRNAs, were isolated by using the PAXgene blood miRNA kit (PreAnalytiX). This kit guarantees the extraction of intracellular RNA and miRNA upon cell lysis and stabilization of intracellular RNA during whole blood collection in PAXgene blood RNA tubes (PreAnalytiX). The elutes were quantified with a Qubit fluorometer (ThermoFisher Scientific) by using the RNA Broad Range assay kit (ThermoFisher Scientific). RNA quality was assessed by using Agilent RNA (15nt) fragment analysis (Agilent).
Libraries were prepared using the NEBNextâ Multiplex Small RNA Library Prep Kit for Illumina (New England BioLabs) (Index Primers 1-48, #7560S). Their quality and yield were measured by Agilent HS NGS fragment analysis (Agilent). The final products have approximate size of 150 bp. The 1.1 nM libraries, derived from the WB RNAs, were sequenced using the NovaSeq 6000 sequencer with a 150 bp paired-end protocol. Between 9 and 41 million reads were obtained for each sample (average of 17 million reads per sample).

value: rVSV-delta-G-ZEBOV-GP vaccine, dose 2x10^7


title: Transgenic polysome sample 2


title: Transgenic polysome sample 1


title: C191819_FFPE_DX_2

value: Diagnosic biopsy from cHL patient


title: C191819_S_1.6


title: WT-2

value: Primary marginal zone B cell


title: Sperm cell sRNA-Seq - VSL16

description: small RNA


title: miRNA, rVSVΔG-ZEBOV-GP, D4 113_S17_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D4
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D2 111_S15_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D2
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D1 110_S14_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D1
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D1 110_S14_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D1
miRNA-seq


title: Wild-type polysome sample 3

value: wild type


title: C191819_BM_DNA NORMAL

value: germinal DNA from bone marrow


title: Sperm cell sRNA-Seq - VSL15

description: small RNA


title: Wild-type polysome sample 2


title: Wild-type polysome sample 1


title: Sperm cell sRNA-Seq - VSL12

description: small RNA


title: miRNA, rVSVΔG-ZEBOV-GP, D0 109_S13_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D0
miRNA-seq


title: Transgenic input sample 3

value: synaptosomal input RNA


title: LH200003_S_1.3

value: cell-free tumoral DNA


title: LH200003_FFPE_DX_1


title: miRNA, rVSVΔG-ZEBOV-GP, D0 109_S13_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D0
miRNA-seq

value: serum-derived extracellular vesicles


title: LH200003_S_1.1


title: C212118_FFPE_DNA NORMAL

value: germinal DNA


title: Sperm cell sRNA-Seq - VSL11

description: small RNA

value: Sperm cells


title: Sperm cell sRNA-Seq - VSL10

description: small RNA

value: M


title: LH200003_S.0


title: Sperm cell sRNA-Seq - VSL14

description: small RNA

value: VSL


title: Transgenic input sample 1


title: miRNA, rVSVΔG-ZEBOV-GP, D7 108_S12_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D7
miRNA-seq


title: Spermatocytes PROseq rep2

source_name: testis

value: testis

value: Spermatocytes


title: LH210011_FFPE_DX_B1

source_name: Diagnosic biopsy from cHL patient


title: Transgenic input sample 2

value: Striatum

value: Shank3 TG


title: miRNA, rVSVΔG-ZEBOV-GP, D7 108_S12_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D7
miRNA-seq


title: Wild-type input sample 3

value: male


title: Sperm cell sRNA-Seq - VSL02

description: small RNA


title: Wild-type input sample 2


title: Sperm cell sRNA-Seq - VSL01

description: small RNA


title: LH210011_FFPE_DX_A2


title: miRNA, rVSVΔG-ZEBOV-GP, D4 107_S11_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D4
miRNA-seq

value: rVSV-delta-G-ZEBOV-GP vaccine, dose 2x10^7


title: LH200003_FFPE_DX_2

value: Diagnosic biopsy from cHL patient


title: LH210011_FFPE_DX_A1


title: Wild-type input sample 1


title: miRNA, rVSVΔG-ZEBOV-GP, D3 106_S10_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D3
miRNA-seq


title: Sperm cell sRNA-Seq - VSL09

description: small RNA


title: Sperm cell sRNA-Seq - LF32

description: small RNA

value: LF


title: LH210011_S_1.2

source_name: cell-free tumoral DNA


title: LH210011_BM_DNA NORMAL


title: CD8+CD39+ HA-CAR-T cells, donor 3076

city: Stanford

first: Yiyun

last: Chen

address: 265 Campus Dr Room G2105

department: Stanford Cancer Institute

institute: Stanford University

description:
DN3076_CD8_CD39pos
TPM_CD39sortedCD4andCD8.csv

data_processing:
Reads mapping and counting were performed using STAR (version 2.7.6a) with GRCh38 as reference genome, HTSeq-count tools respectively.
Assembly: hg38
Supplementary files format and content: Data transcripts per million summarized to gene level. Each column in the table is a sample. Each row is a gene.

source_name: CAR T cells

extract_protocol:
Total mRNA was isolated using Qiagen RNEasy Plus mini-isolation kit.
Libraries and RNA-seq were performed by Novogene (Sacramento, CA) and 150 bp paired-end sequencing at a depth of 3×107 reads per sample was obtained using the Illumina NovaSeq6000 platform.

value: CAR T cells


title: miRNA, rVSVΔG-ZEBOV-GP, D4 107_S11_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D4
miRNA-seq


title: Sperm cell sRNA-Seq - LF31

description: small RNA


title: LH200002_FFPE_DX_1


title: LH200002_FFPE_DX_2


title: miRNA, rVSVΔG-ZEBOV-GP, D2 105_S9_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D2
miRNA-seq


title: Sperm cell sRNA-Seq - LF26

description: small RNA


title: CD8+CD39- HA-CAR-T cells, donor 3076

description:
DN3076_CD8_CD39neg
TPM_CD39sortedCD4andCD8.csv


title: Sperm cell sRNA-Seq - LF25

description: small RNA


title: miRNA, rVSVΔG-ZEBOV-GP, D1 104_S8_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D1
miRNA-seq


title: Sperm cell sRNA-Seq - LF24

description: small RNA


title: miRNA, rVSVΔG-ZEBOV-GP, D2 105_S9_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D2
miRNA-seq


title: CD8+CD39+ HA-CAR-T cells, donor 0351

description:
DN0351_CD8_CD39pos
TPM_CD39sortedCD4andCD8.csv


title: Sperm cell sRNA-Seq - LF33

description: small RNA


title: CD8+CD39- HA-CAR-T cells, donor 0490

description:
DN0490_CD8_CD39neg
TPM_CD39sortedCD4andCD8.csv


title: CD8+CD39- HA-CAR-T cells, donor 0351

description:
DN0351_CD8_CD39neg
TPM_CD39sortedCD4andCD8.csv


title: miRNA, rVSVΔG-ZEBOV-GP, D3 106_S10_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D3
miRNA-seq


title: LH200002_S_1.3


title: miRNA, rVSVΔG-ZEBOV-GP, D0 103_S7_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D0
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D1 104_S8_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D1
miRNA-seq


title: CD8+CD39+ HA-CAR-T cells, donor 0490

description:
DN0490_CD8_CD39pos
TPM_CD39sortedCD4andCD8.csv


title: CD4+CD39+ HA-CAR-T cells, donor 3076

description:
DN3076_CD4_CD39pos
TPM_CD39sortedCD4andCD8.csv


title: LH210010_FFPE_DX_1


title: LH210010_FFPE_DX_2


title: Sperm cell sRNA-Seq - LF22

description: small RNA


title: miRNA, rVSVΔG-ZEBOV-GP, D0 103_S7_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D0
miRNA-seq


title: CD4+CD39+ HA-CAR-T cells, donor 0490

description:
DN0490_CD4_CD39pos
TPM_CD39sortedCD4andCD8.csv


title: Sperm cell sRNA-Seq - LF20

description: small RNA


title: miRNA, placebo, D7 102_S6_L002

description:
miRNA, placebo, D7
miRNA-seq

value: placebo


title: BR210038_2


title: miRNA, placebo, D7 102_S6_L001

description:
miRNA, placebo, D7
miRNA-seq


title: CD4+CD39+ HA-CAR-T cells, donor 0351

description:
DN0351_CD4_CD39pos
TPM_CD39sortedCD4andCD8.csv


title: BR210038_1


title: Sperm cell sRNA-Seq - LF23

description: small RNA


title: CD4+CD39- HA-CAR-T cells, donor 3076

description:
DN3076_CD4_CD39neg
TPM_CD39sortedCD4andCD8.csv


title: miRNA, placebo, D4 101_S5_L002

description:
miRNA, placebo, D4
miRNA-seq


title: Sperm cell sRNA-Seq - LF18

description: small RNA


title: Sperm cell sRNA-Seq - LF17

description: small RNA


title: BR190012_1


title: Sperm cell sRNA-Seq - LF13

description: small RNA


title: BR190012_2


title: BR190010_2


title: miRNA, placebo, D4 101_S5_L001

description:
miRNA, placebo, D4
miRNA-seq


title: CD4+CD39- HA-CAR-T cells, donor 0351

description:
DN0351_CD4_CD39neg
TPM_CD39sortedCD4andCD8.csv


title: miRNA, placebo, D3 100_S4_L001

description:
miRNA, placebo, D3
miRNA-seq


title: miRNA, placebo, D3 100_S4_L002

description:
miRNA, placebo, D3
miRNA-seq


title: BR190010_1


title: TB-KSF50

city: Osakasayama City

first: Takashi

last: Kurosaki

address: 377-2 Ohno-higashi

institute: kindai university

description: Pancancer IO 360 panel

hyb_protocol: Hybridation was performed as per manufacturer's protocol.

scan_protocol: Scanned with nCounter SPRINT Profiler

data_processing: Data was normalised using the nSolver software, version 4.0.

label: Nanostring barcoding

source_name: advanced NSCLC

label_protocol: RNA were directly tagged with a capture probe and a reporter probe. This process was carried out according to the manufacturer's protocol.

extract_protocol: Tumor tissue was microdissected to avoid contamination from nontumor tissue before extraction of intratumoral RNA with the use of an AllPrep DNA/RNA FFPE Kit (Qiagen). The extracted RNA was measured with a NanoDrop system (Thermo Fisher Scientific) and an Agilent 2100 Bioanalyzer system (Agilent Technologies).

value: NSCLC tumor

tag: gender

value: Female

tag: smoking

value: never

tag: ecog ps

tag: pd-l1 tps

tag: histology

value: Adeno


title: LH210010_S.1.1A

tag: tissue


title: TB-KSF49

description: Pancancer IO 360 panel

tag: age

value: Sq


title: BR200032_2


title: Patient20, scRNA-seq

city: Houston

first: Hussein

last: Abbas

state: Texas

address: 1515 Holcombe Blvd

institute: The University of Texas at MD Anderson Cancer cent

data_processing:
Raw scRNA-seq data were demultiplexed and aligned and read count matrix was generated using the Cell Ranger Single Cell Software Suite provided by 10x Genomics. The Seurat v4 (version 4.2.1) R package77 was used to analyze the scRNA-seq data.
Genes detected in fewer than 3 cells and cells with fewer than 250 genes, or 500 transcripts were excluded from subsequent analysis. Cells with more than 10% of reads mapping to mitochondrial genes were removed as well.
Possible doublets were identified and removed
Batch effects were removed using the Harmony package
Assembly: GRCh38
Supplementary files format and content: Seurat object with expression matrix and metadata

source_name: Bone Marrow

extract_protocol:
Samples were freshly frozen with freezing medium containing 20% fetal calf serum (FCS) and 10% dimethyl sulfoxide (DMSO) in Dulbecco’s modified Eagle medium (DMEM) and stored in liquid nitrogen. All frozen BM samples were retrieved immediately before sample processing. To maximize the recovery of the cellular viability, samples were processed in batches according to a thawing protocol.
The 5’ gene expression libraries were prepared using a 10x Genomics Chromium Controller instrument and Chromium Single-Cell 5′ V5.1 reagent kits (10x Genomics).

value: Bone Marrow

tag: disease state

value: AML

tag: cell type

value: Hematopoietic

tag: treatment

value: Newly diagnosed


title: Sperm cell sRNA-Seq - LF19

description: small RNA

value: Sperm cells

tag: Sex

value: M


title: Patient19, scRNA-seq


title: BR200032_1


title: Sperm cell sRNA-Seq - LF03

description: small RNA


title: Patient18, scRNA-seq


title: TB-KSF45

description: Pancancer IO 360 panel

value: Male

value: current or former


title: Sperm cell sRNA-Seq - LF12

description: small RNA


title: Patient17, scRNA-seq


title: Sperm cell sRNA-Seq - LF02

description: small RNA


title: Patient16, scRNA-seq


title: BR200031_1

value: Diagnosic biopsy from cHL patient


title: BR200031_2


title: TB-KSF40

description: Pancancer IO 360 panel

value: NOS


title: TB-KSF41

description: Pancancer IO 360 panel


title: BR200030_2


title: HCT116 cells,T6, rep2

city: Pamplona

first: Maite

last: Huarte

state: Navarra

address: c/ Avd Pio XII, 55

institute: Centro de Investigación Médica Aplicada

data_processing:
Data were aligned to the genome assembly hg19 using STAR (Dobin et al., 2013) with default parameters.
Reads in each gene were counted with featureCounts (Liao et al., 2014) with default parameters
Assembly: hg19
Supplementary files format and content: one tab-delimited text matrix including raw counts values of each gene in each sample

extract_protocol:
RNA was isolated with TriZol according to the manufacturer’s instruction and RNAs were treated with DNAse I to remove contaminant DNA.
After quality and integrity check with RNA screen tape (Agilent Technologies), RNA was processed for library preparation with TruSeq Stranded Total RNA kit (Illumina), according to the manufacturer’s instructions

treatment_protocol: Cells were seeded at 60% confluency. The next day, they were treated with 2mM of Thymidinefor 16 hrs. Then, medium was removed, cells washed with PBS and fresh medium was added. After 9 hrs, 2mM thymidine were added again to the medium and incubated for an additional 14 hours. At this point, cells synchronized in G1/S were washed with PBS and one plate was collected at T=0 (cells in G1). Normal medium was added to the other plates and cells were collected at different time points and tested by propidium iodide staining to verify their cell cycle position.

tag: cell line

value: Thy synchronization - release, T6 (cells in G2)


title: HCT116 cells,T6, rep3


title: Sperm cell sRNA-Seq - LF11

description: small RNA

value: LF


title: TB-KSF35

description: Pancancer IO 360 panel

value: NSCLC tumor


title: BR200030_1


title: CD4+CD39- HA-CAR-T cells, donor 0490

description:
DN0490_CD4_CD39neg
TPM_CD39sortedCD4andCD8.csv

value: CAR T cells


title: Patient15, scRNA-seq


title: BR200021 _2


title: Patient14, scRNA-seq


title: TB-KSF26

description: Pancancer IO 360 panel

value: Female


title: HCT116 cells,T3, rep3

value: Thy synchronization - release, T3 (cells in late S)


title: BR200021 _1


title: Sperm cell sRNA-Seq - LF07

description: small RNA


title: Patient13, scRNA-seq


title: TB-KSF24

description: Pancancer IO 360 panel

value: Adeno


title: Patient12, scRNA-seq

value: Bone Marrow


title: Patient11, scRNA-seq

value: AML


title: HCT116 cells,T2, rep3

value: Thy synchronization - release, T2 (cells in mid S)


title: HCT116 cells,T3, rep1


title: TB-KSF34

description: Pancancer IO 360 panel


title: Patient9, scRNA-seq

value: Hematopoietic

value: Newly diagnosed


title: Patient10, scRNA-seq


title: BR200027_2


title: HCT116 cells,T6, rep1


title: BR200023_1


title: BR200026 _2


title: BR200027_1


title: TB-KSF16

description: Pancancer IO 360 panel

value: Sq


title: TB-KSF13

description: Pancancer IO 360 panel

value: Male


title: TB-KSF21

description: Pancancer IO 360 panel

value: current or former


title: HCT116 cells,T2, rep1


title: TB-KSF12

description: Pancancer IO 360 panel


title: HCT116 cells,T1, rep3

value: Thy synchronization - release, T1 (cells in early S)


title: Patient7, scRNA-seq


title: TB-KSF07

description: Pancancer IO 360 panel

value: never


title: HCT116 cells,T1, rep2


title: HCT116 cells,T3, rep2


title: Patient6, scRNA-seq


title: BR200029_1

value: Diagnosic biopsy from cHL patient


title: TB-KSF06

description: Pancancer IO 360 panel


title: Patient8, scRNA-seq


title: HCT116 cells,T2, rep2


title: HCT116 cells,T1, rep1


title: TB-KSF01

description: Pancancer IO 360 panel


title: TB-KSF14

description: Pancancer IO 360 panel

value: NOS


title: BR190020_2


title: HCT116 cells,T0, rep3

value: Thy synchronization, T0 (cells in G1)


title: Patient5, scRNA-seq


title: BR190019_2


title: BR190020_1


title: HCT116 cells,T0, rep1


title: BR200023_2


title: Patient2, scRNA-seq


title: TB-KCT29

description: Pancancer IO 360 panel

value: NSCLC tumor


title: BR190019_1


title: Patient4, scRNA-seq


title: BR190017_2


title: BR200029_2


title: BR190017_1


title: HCT116 cells, chromatin RNA, hydroxyurea treatment, rep2

data_processing:
Data were aligned to the genome assembly hg38 using STAR (Dobin et al., 2013) with default parameters.
Reads in each gene were counted with featureCounts (Liao et al., 2014) with default parameters
Assembly: hg38
Supplementary files format and content: one tab-delimited text matrix including raw counts values of each gene in each sample
Library strategy: ChrRNA-seq

extract_protocol:
1 x 10^7 HCT116 cells were harvested with trypsin after 8hrs of treatment with 1mM of HU, or PBS and washed with ice-cold PBS. One tenth aliquot of cells was put aside for total RNA isolation, the remaining was used for cell fractionation, according to[2]. All steps were performed in presence of protease inhibitors (Roche), phosphatase inhibitors (Roche) and RNAsin (Promega). Cells were resuspended in 200 µl of isotonic lysis buffer buffer (10mM Tris-Hcl pH7, 150 mM NaCl, 0.15% NP-40) for 5 min on ice and layered on a sucrose buffer (10mM Tris- HCl, 150 mM NaCl, 25% sucrose). Nuclei were centrifuged for 10 min at full speed to recover the supernatant as the cytoplasmic fraction. The nuclear pellet was washed (1 mM EDTA, 0.1% Triton-X100 in PBS), and resuspended in 200 µl glycerol buffer (20mM Tris-HCl pH8, 75mM NaCl, 0.5 mM EDTA, 505 glycerol, 0.85 mM DTT) and finally lysed with 200 µl of nuclear lysis buffer (20mM HEPES, 300mM NaCl, 1M urea, 0,2 mM EDTA, 1% NP-40, 1mM DTT). Lysed nuclei were centrifuged at full speed for 2 min to separate the soluble fraction (supernatant) from the chromatin associated fraction (pellet). RNA was isolated and DNAse I-treated with Maxwell RSC Simply RNA kit (Promega)
RNA was processed for library preparation with TruSeq Stranded Total RNA kit (Illumina), according to the manufacturer’s instructions

treatment_protocol: HCT116 cells were treated with 1mM HU or solvent in control cells for 8hrs

value: Hydroxyurea

tag: fraction

value: Chromatin RNA


title: TB-KCT19

description: Pancancer IO 360 panel

value: Female


title: TB-KCT21

description: Pancancer IO 360 panel


title: Patient1, scRNA-seq

value: Bone Marrow


title: HCT116 cells, chromatin RNA, hydroxyurea treatment, rep3


title: HCT116_ActD_4hr_3

city: Bethesda

first: Ashish

last: Lal

state: Maryland

address: 37 Convent Drive, Room 6134

department: NCI

institute: NIH

data_processing:
RTA 3.4.4. software used for basecalling.
Reads of the samples were trimmed for adapters and low-quality bases using Cutadapt
Reads were aligned with the reference genome (hg19) and the annotated transcripts using STAR 2.7
Gene expression was quantified using RSEM 1.3.1
Assembly: hg19
Supplementary files format and content: tab-delimited text files including output from RSEM for genes (expected counts, TPM and FPKM)

extract_protocol:
Samples had their RNA extracted with RNeasy Plus Mini Kit.
RNA libraries were prepared using Illumina® Stranded Total RNA

value: Colorectal cancer cell line

value: 5 ug/ml Actinomycin D treatment_ 4 hour


title: TB-KCT17

description: Pancancer IO 360 panel

value: Adeno


title: TB-KCT18

description: Pancancer IO 360 panel


title: TB-KCT12

description: Pancancer IO 360 panel


title: BR190016_2

city: Madrid

data_processing:
Base calling software (Ion Reporter 5.18)
Filtered variants were reviewed and analyzed using the integrative genomics viewer (IgV)
Variants presents at germinal DNA were filetered out
Alamut visual Plus analysis version 1.6.1
Discard variants annotated as a single nucleotide polymorphism (SNP) or reported with a VAF greater than 1% in the genomeAD and single nucleotide polymorphism (dbSNP) databases
Variant analisys with databases such as ClinVar, Varsome, cBioportal, COSMIC (Catalogue Of Somatic Mutations in Cancer) and Ensembl, among others
Assembly: hg19
Supplementary files format and content: .xlsx files containing filtered and analized variants

extract_protocol:
For non-infiltrated bone marrow, and FFPE tissue the material was obtained by scraping de aPBirate slide based on phenol, sodium acetate andethanol protocol. For peripheral blood we used the DNeasy Blood & Tissue kit (Quiagen). For cell-free tumor cell DNA we used QiAamp circulating nucleic acid extraction kit (Quiagen).
The libraries were constructed following the protocol recommended by the Ion AmpliseqTM Library Preparation Kit (Thermo Fisher Scientific). We used a custom cHL-PBecific targeted panel.


title: HCT116 cells, chromatin RNA, hydroxyurea treatment, rep1


title: HCT116 cells, chromatin RNA, untreated condition, rep3

value: No treatment


title: HCT116_ActD_4hr_2


title: HCT116 cells,T0, rep2


title: BR190016_1


title: HCT116 cells, chromatin RNA, untreated condition, rep2


title: Patient3, scRNA-seq

value: AML

value: Hematopoietic

value: Newly diagnosed


title: HCT116_ActD_4hr_1


title: HCT116_ActD_2hr_3

value: 5 ug/ml Actinomycin D treatment_ 2 hour


title: TB-KCT08

description: Pancancer IO 360 panel

value: Male

value: current or former


title: TB-KCT07

description: Pancancer IO 360 panel


title: BR190013_2

value: Diagnosic biopsy from cHL patient


title: HCT116 cells, total RNA, hydroxyurea treatment, rep3

data_processing:
Data were aligned to the genome assembly hg38 using STAR (Dobin et al., 2013) with default parameters.
Reads in each gene were counted with featureCounts (Liao et al., 2014) with default parameters
Assembly: hg38
Supplementary files format and content: one tab-delimited text matrix including raw counts values of each gene in each sample

value: Total RNA


title: TB-KCT06

description: Pancancer IO 360 panel

value: NSCLC tumor

value: NOS


title: HCT116 cells, total RNA, hydroxyurea treatment, rep2

value: Hydroxyurea


title: BR190014_2


title: HCT116_0hr_3

value: 5 ug/ml Actinomycin D treatment_ 0 hour


title: HCT116 cells, chromatin RNA, untreated condition, rep1

value: Chromatin RNA


title: HCT116 cells, total RNA, untreated condition, rep3


title: BR190014_1


title: BR190015_2


title: HCT116_ActD_2hr_1

value: Colorectal cancer cell line


title: HCT116_0hr_2


title: TB-KCT05

description: Pancancer IO 360 panel


title: HCT116_ActD_2hr_2


title: HCT116 cells, total RNA, hydroxyurea treatment, rep1


title: TB-KCP19

description: Pancancer IO 360 panel


title: TB-KCT10

description: Pancancer IO 360 panel

value: Sq


title: TB-KCP10

description: Pancancer IO 360 panel

value: Female

value: Adeno


title: HCT116_0hr_1


title: TB-KCP09

description: Pancancer IO 360 panel


title: LS180_ActD_4hr_2

value: 5 ug/ml Actinomycin D treatment_ 4 hour


title: BR190013_1


title: HCT116 cells, total RNA, untreated condition, rep1

value: No treatment


title: BR190005_2


title: BR190004_2


title: HCT116 cells, total RNA, untreated condition, rep2


title: LS180_ActD_4hr_3


title: BR190005_1


title: BR190004_1


title: LS180_ActD_2hr_3


title: X2532A_2


title: Sorted CD34+ cultured in condition X2B (14 days)

city: Ottawa

first: Nicolas

last: Pineault

state: Nicolas Pineault

address: 1800 Alta Vista Dr

country: Canada

institute: Canadian Blood Services

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3
Low UMI counts, doublets, and cells with relatively high mitochondrial DNA content were removed.
Cell cycle phase of each cell was predicted using the Cyclone method
Cell transcriptomes were normalized according to their pool and deconvolution normalization method in the scran R package in order to correct for differences in read depth and library size.
Normalized expression matrices were imported into Seurat (1.4.0.16) where PCA was performed using highly variable genes in the data. Run-tSNE was used to generate tSNE projections using the top principal components detected in the dataset.
Assembly: GRCm38
Supplementary files format and content: h5

source_name: Umbilical Cord Blood

extract_protocol: cDNA libraries were constructed using the 10X Genomics 3' GEX kit

value: Umbilical Cord Blood

value: Primary human cells

tag: genotype

value: WT

tag: time

value: Day 14


title: Fresh CD34+ cells

description: 10X Genomics

value: Male

value: Day 0

value: Non cultured


title: Sorted CD34+ cultured in condition C6 (14 days)

description: 10X Genomics


title: Sorted CD34+ cultured in condition X2A (14 days)

description: 10X Genomics


title: X2532A_1

value: Diagnosic biopsy from cHL patient


title: Fresh CD34+ cells (pooled from three donors), replicate 2

data_processing:
Files containing reads from two sequencing runs were concatenated.
Ran fastp to perform automatic adapter trimming and default sequence quality filtering (>60% of bases with Q≥15, and no more than 5 'N' basecalls)
Quantified transcripts from GENCODE v35 with salmon v1.4.0 using --gcBias flag and genomic decoys in index
Performed fold change analysis using DESeq2 as follows
Read transcript quantification data with tximport library and summarized to gene level quantification
Filtered to retain genes with at least 5 reads assigned in at least two samples
Constructed DESeqDataSet object with twelve samples (six conditions), using the model ~condition (treatment)
Calculated fold changes using the results() function, then ran lfcShrink() on the results using the apeglm method.
Assembly: GRCh38
Supplementary files format and content: Trancript quantiication (quant.sf) generated by Salmon
Supplementary files format and content: DESeq2 fold change results: Results from the DESeq2 lfcShrink() function comparing two condition, including results for all genes retained after filtering

extract_protocol:
RNA was isolated using miRNeasy Micro Kit (Qiagen, Hilden, Germany) including DNAse treatment
cDNA libraries were constructed using TruSeq mRNA stranded protocol (Illumina)


title: TB-KCP06

description: Pancancer IO 360 panel

value: NSCLC tumor

value: current or former


title: TB-KCP03

description: Pancancer IO 360 panel


title: TB-KCP04

description: Pancancer IO 360 panel


title: TB-KCP05

description: Pancancer IO 360 panel


title: Fresh CD34+ cells (pooled from three donors), replicate 1


title: BR190007_2


title: LS180_0hr_2

value: 5 ug/ml Actinomycin D treatment_ 0 hour


title: TB-KCP02

description: Pancancer IO 360 panel


title: TB-KC05

description: Pancancer IO 360 panel


title: TB-KCP01

description: Pancancer IO 360 panel


title: LS180_ActD_2hr_1

value: Colorectal cancer cell line

value: 5 ug/ml Actinomycin D treatment_ 2 hour


title: BR190008_2


title: TB-K35

description: Pancancer IO 360 panel


title: BR190006_1


title: CD34+ cells (pooled from three donors) cultured for 14 days in condition 'SM6', replicate 1


title: Cdes709-48hpi

city: Palaiseau

first: Adeline

last: SIMON

address: 22 place de l'agronomie

country: France

institute: INRAE

data_processing:
RNA-Seq paired reads were cleaned and trimmed using Trimmomatic
The tried reads were then mapped to the genome assembly of Colletotrichum destructivum CBS 520.97 genome using STAR.
A genome-guided transcript assembly was obtained from mappings with StingTie v1.3.4.
Assembled raw transcripts were then filtered based on the TPM distribution per transcript per library.
Assembly: Colletotrichum destructivum CBS 520.97 (CP137305-CP137317)
Supplementary files format and content: tab-delimited file with TPM counts

organism: Colletotrichum destructivum

source_name: fungal cell

growth_protocol: For PDB library, mycelium was grown for 3 days in potato dextrose liquid medium (PDB, Difco) at 25°C with shaking (150 rpm) and harvested by filtration. For infection libraries, seedlings of M. sativa (8 days old) were inoculated by placing a droplet (10 μl) of Cd709 spore suspension (7 x 105 spores/ml) onto the surface of each cotyledon and the plants were then incubated as described for M. truncatula. Discs of infected cotyledon tissue were harvested using a cork borer (4 mm diameter)

extract_protocol:
After grinding the tissues in liquid nitrogen, total RNA was extracted using the RNeasy plant mini kit (Qiagen).
TruSeq Paired-end Stranded mRNA Kit

tag: isolate

value: LARS 709

value: fungal cell

value: inoculated on Medicago sativa for 48h


title: BR190003_2


title: TB-K23

description: Pancancer IO 360 panel

value: never

value: NOS


title: CD34+ cells (pooled from three donors) cultured for 14 days in condition 'C6', replicate 1

value: Umbilical Cord Blood

value: Primary human cells


title: LS180_0hr_3


title: BR190008_1


title: TB-K16

description: Pancancer IO 360 panel


title: LS180_ActD_4hr_1

value: 5 ug/ml Actinomycin D treatment_ 4 hour


title: CD34+ cells (pooled from three donors) cultured for 14 days in condition 'SM6', replicate 2

value: WT

value: Male

value: Day 14


title: TB-KC03

description: Pancancer IO 360 panel


title: LS180_0hr_1


title: LS180_ActD_2hr_2


title: BAB12566 Proband

type: genomic

first: Christopher

last: Grochowski

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

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

scan_protocol: Scanned on an Agilent G2505C  scanner. Images were quantified using Agilent Feature Extraction Software (version 12.0)

data_processing: Agilent Feature Extraction Software (version 12.0) was used for background subtraction and normalization.

source_name: Whole Blood Extracted Genomic DNA

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

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

value: Female

tag: sample type

value: Reference Sample


title: CD34+ cells (pooled from three donors) cultured for 14 days in condition 'STFL', replicate 2

value: STFL (non SCAC)


title: BAB15789 Proband


title: BR190011_1

first: Sara

last: Fernández

address: C/Arturo Soria 270

value: Diagnosic biopsy from cHL patient


title: CD34+ cells (pooled from three donors) cultured for 14 days in condition 'STFL', replicate 1


title: Cdes709-72hpi

value: inoculated on Medicago sativa for 72h


title: BR190006_2


title: Cdes709-PDB

value: grown in vitro (in PDB)


title: TB-K18

description: Pancancer IO 360 panel

value: NSCLC tumor

tag: gender

value: current or former

value: Adeno


title: CD34+ cells (pooled from three donors) cultured for 14 days in condition 'C6', replicate 2


title: TB-K17

description: Pancancer IO 360 panel

tag: smoking

value: Sq


title: BR190007_1


title: BR190009_2


title: TB-K07

description: Pancancer IO 360 panel

tag: ecog ps


title: CD34+ cells (pooled from three donors) cultured for 14 days in condition 'X2B', replicate 2


title: RNASEH1_shRNA2_rep2

city: Shanghai

first: Li

last: Yang

address: 131 Dong-An Road

department: Institutes of Biological Sciences

institute: Fudan University

description: Ribominus RNA-seq

data_processing:
First filtered by using Trimmomatic v0.38; Next removed rRNA by bowtie v1.1.2.
Analyses by HISAT2, TopHat-Fusion v2.0.12, CLEAR and custom python script.
Genome_build: GRCh38/hg38 human reference genome with the GENCODE gene annotation (v28).
Supplementary_files_format_and_content: bw files include the read depths.
Supplementary_files_format_and_content: bb files include position of ciRNAs.

extract_protocol:
Total RNAs from cultured cells were extracted with Trizol Reagent (Life Technologies) according to the manufacturer’s protocol. RNAs were further treated with DNase I (Ambion, DNA-free kit) and cDNAs were reverse transcribed with PrimeScript II RTase (TAKARA) at 42 ℃ for 2hr, and then applied for qPCR analysis using the SYBR Green Realtime PCR Master Mix (TOYOBO).
For RNA-seq samples from PA1 cells treated with scramble or RNase H1 shRNAs, ribo minus RNA libraries were prepared using Illumina TruSeq Stranded Total RNA LT Sample Prep Kit according to the manufacturer’s protocol with slight modifications in the step for synthesizing first strand cDNA, which used PrimeScript enzyme mix (TAKARA) for reverse transcription at 42 ℃ for 2 hr. All libraries were size-selected with AmpureXP beads (Agencourt) and quantified using Agilent Bio analyzer 2100 and Qubit high-sensitivity dsDNA assay.

treatment_protocol: PA1 cells were cultured using standard protocols from ATCC. PA1 cells were maintained in MEMα supplemented with 10% FBS, 1% Glutamine and 0.1% penicillin/streptomycin. We maintained cell lines at 37 ℃ in a 5% CO2 cell culture incubator and tested all cell lines routinely for Mycoplasma contamination.

tag: shRNA


title: BAB14604 Proband


title: BR190003_1

institute: MD Anderson Cancer Centre


title: BR190009_1


title: TB-K15

description: Pancancer IO 360 panel

tag: pd-l1 tps

tag: histology

value: NOS


title: CD34+ cells (pooled from three donors) cultured for 14 days in condition 'X2B', replicate 1

tag: tissue

value: Umbilical Cord Blood


title: RNASEH1_shRNA2_rep1

description: Ribominus RNA-seq


title: TB-K13

description: Pancancer IO 360 panel

tag: age


title: RNASEH1_shRNA1_rep2

description: Ribominus RNA-seq


title: BR190011_2


title: BAB14686 Proband


title: CD34+ cells (pooled from three donors) cultured for 14 days in condition 'X2A', replicate 2

value: Primary human cells

tag: cell type


title: BAB14392 Proband


title: TB-K11

description: Pancancer IO 360 panel

value: never


title: RNASEH1_scramble_rep2

description: Ribominus RNA-seq

value: scramble


title: CD34+ cells (pooled from three donors) cultured for 14 days in condition 'X2A', replicate 1

value: WT

value: Male

tag: treatment


title: TB-K10

description: Pancancer IO 360 panel


title: RNASEH1_scramble_rep1

description: Ribominus RNA-seq


title: HIT-scISOseq Run2, scRNAseq

status: Public on Dec 17 2023

city: Guangzhou

first: Zhuoxing

last: Shi

state: GD

address: #7 Jinsui Road, Tianhe District

department: State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center

institute: Sun Yat-sen University

description: HIT-scISOseq

data_processing:
HIT-scISOseq analysis software kit scISA-Tools (https://github.com/shizhuoxing/scISA-Tools) for Full-Length Non-Concatemer (FLNC) reads identification, cell barcode and UMI extraction and correction.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and fasta files

source_name: preimplantation embryos

extract_protocol:
Tthe same amplification procedure as SCAN-seq，except for changing the reverse transcription primer with a 10x gel bead for each reaction for the embryonic samples.
Each pre-amplification product was purified by 0.6X Ampure XP beads (Beckman, Cat. A63882). The concentration was measured using Qubit™ dsDNA HS and BR Assay Kits (Invitrogen, Cat. Q32854). The PCR product from about 60 blastomeres which were confirmed of effective amplification were pooled together in proportion to the number of amplified cycles. We took 100ng of the pooled cDNA to build PacBio sequencing library following the protocol of HIT-scISOseq and sequenced for one cell with HiFi mode.

value: preimplantation embryos

tag: strain

value: DBA/2J x C57BL/6J


title: HIT-scISOseq Run4, scRNAseq

description: HIT-scISOseq