title: C.glabrata Pho4 binding levels at 2 uM

type: protein

city: Iowa City

first: Bin

last: He

email: emptyhb@gmail.com, bin-he@uiowa.edu

state: IA

address: 129 East Jefferson St., Biology Building 450

department: Biology

institute: the University of Iowa

hyb_protocol: Double-stranded microarrays were first pre-moistened in PBS / 0.01% Triton X-100 for 5 min and blocked with PBS / 2% (wt/vol) nonfat dried milk (Sigma) for 1 h. Microarrays were then washed once with PBS / 0.1% (vol/vol) Tween-20 for 5 min and once with PBS / 0.01% Triton X-100 for 2 min. Proteins were diluted to desired concentrations in a 175-μl protein binding reaction containing PBS / 2% (wt/vol) milk / 51.3 ng/μl salmon testes DNA (Sigma) / 0.2 μg/μl bovine serum albumin (New England Biolabs). Preincubated protein binding mixtures were applied to individual chambers of a four-chamber gasket cover slip in a steel hybridization chamber (Agilent), and the assembled microarrays were incubated for 1 h at room temperature. Microarrays were again washed once with PBS / 0.5% (vol/vol) Tween-20 for 3 min, and then once with PBS / 0.01% Triton X-100 for 2 min. Alexa-488-conjugated rabbit polyclonal antibody to GST (Invitrogen) was diluted to 50 μg/ml in PBS / 2% milk and applied to a single-chamber gasket cover slip (Agilent), and the assembled microarrays were again incubated for 1 h at 20°C. Finally, microarrays were washed twice with PBS / 0.05% (vol/vol) Tween-20 for 3 min each, and once in PBS for 2 min. After each hour-long incubation step, microarrays and cover slips were disassembled in a staining dish filled with 500 ml of the first wash solution. All washes were performed in Coplin jars on an orbital shaker at 125 r.p.m. Immediately following each series of washes, microarrays were rinsed in PBS (slowly removed over approximately 10 seconds) to ensure removal of detergent and uniform drying.

scan_protocol: Protein-bound microarrays were scanned to detect Alexa-488-conjugated antibody (488 nm ex, 522 nm em) using at least three different laser power settings to best capture a broad range of signal intensities and ensure signal intensities below saturation for all spots. Microarray TIF images were analyzed using GenePix Pro version 6.0 software (Molecular Devices), bad spots were manually flagged and removed, and data from multiple scans of the same slide were combined using masliner (MicroArray LINEar Regression) software.

data_processing: To correct for any possible non-uniformities in protein binding, we adjusted the fluorescence signals according to their positions on the microarray. We calculated the median normalized intensity of the 15 x 15 block centered on each spot and divided the spot's signal by the ratio of the median within the block to the median over the entire chamber. For each unique sequence represented on the array, we then calculated the median over replicate spots and then normalized the signal for direct comparison between experiments.

label: Alexa 488

molecule: protein

organism: Nakaseomyces glabratus

label_protocol: Proteins were tagged with N-terminal GST by cloning. Protein-bound arrays were incubated with Alexa-488-conjugated rabbit polyclonal antibody to GST (Invitrogen).

growth_protocol: Gateway-compatible clones containing the full-length genes for ScPho4 and CgPho4 were transferred into pDEST15. Cells were grown in LB broth to an OD600 of 0.8 and then expression was induced with 1mM IPTG at 30° for 3 hours. Pelleted cells were frozen, stored at -80 C, and thawed cells were lysed with lysozyme.

extract_protocol: GST-tagged protein was run on a GST column equilibrated with the lysis buffer and eluted with a gradient to buffer B (50mM Tris, 10mM glutathione, pH 8). GST-Pho4 fractions containing the protein were pooled and loaded onto a heparin column equilibrated with low salt buffer (25mM Na2HPO4 pH 7.4, 150mM NaCl, 0.5mM THP) and eluted with a gradient to high salt buffer (25mM sodium phosphate dibasic pH 7.4, 1.5M NaCl, 0.5mM THP). Fractions containing the protein were pooled and concentrated with a 30 kDa cutoff Amicon centrifugal filter (Sigma UFC9030) and loaded onto a Superdex 200 size exclusion column equilibrated with the storage buffer (25mM HEPES pH 7.4, 500mM NaCl, 0.5mM THP). Protein was run on an SDS-PAGE and pure fractions were pooled and concentrated. 10% glycerol was added before snap freezing and storage at −80°C.

tag: transcription factor

tag: tf concentration

value: 2 uM


title: Lung harvested from bat immediately after 1h heat shock followed by 4h recovery, replicate 3

status: Public on Apr 02 2025

type: SRA

city: Singapore

first: Leon Jia Wei

last: Tang

address: 21 Lower Kent Ridge Rd

country: Singapore

institute: National University of Singapore

description:
Es_Lg_R_3
es_counttable.csv

library_source: transcriptomic

data_processing:
STAR (version 2.7)
featureCounts
Assembly: GRCm39 for mice. Custom-in-house genome for bat (Chan et al, Unpublished)
Supplementary files format and content: comma separated

molecule: total RNA

organism: Eonycteris spelaea

source_name: Lung

extract_protocol:
TRIzol total RNA extraction
NEBNext Ultra Directional RNA Library Prep Kit for Illumina

tag: tissue

value: Lung


title: Lung harvested from bat immediately after 1h heat shock followed by 4h recovery, replicate 2

description:
Es_Lg_R_2
es_counttable.csv


title: Lung harvested from bat immediately after 1h heat shock followed by 4h recovery, replicate 1

description:
Es_Lg_R_1
es_counttable.csv


title: LNSCs after HTx_1

city: Baltimore

first: yang

last: song

state: MD

address: HSF-3, 3rd Floor; 670 W Baltimore St.

department: Department: Institute for Genome Sciences

country: USA

institute: University of Maryland in Baltimore

description: 10x Genomics

data_processing:
Reads were demultiplexed, aligned to the GRCm38 mm10 assembly reference genome, and filtered; and cell barcodes and UMIs were quantified using the Cell Ranger 6.1 with default parameters (https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome). 6.7 x 103 cells per sample were captured on the 10X Chromium chip.
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v4.0.2.
the samples are integrated together using Harmony (v1.2.0)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

organism: Mus musculus

source_name: Lymph node

extract_protocol:
LNs were harvested from C57BL/6 mice (8-12 weeks) and digested enzymatically. CD45- cells were purified with the CD45 negative selection beads and were stained with anti-mouse CD45 before sorting for viable CD45- cells.
About 1.0 x  10^4 LNSCs were run on the  the 10X Chromium Controller (10X Genomics) to partition single cells into nanoliter-scale droplets containing uniquely barcoded beads and processed for sequencing library preparation using the Chromium Single Cell 3’ Reagent Kit (v3 chemistry).
Generated cDNA libraries were sequenced on a NovaSeq 6000 sequencing system at the Institute for Genome Sciences in the University of Maryland, Baltimore.

value: Lymph node

tag: cell type

value: CD45 negative stromal cells

tag: strain

value: C57BL/6 mice

tag: age

value: 8-12 weeks old

tag: procedure and_treatment

value: day8 after heart transplantation without anti-CD40L


title: GT01017_0

type: RNA

city: Milano

first: Alessandra

last: Trojani

address: Piazza dell'Ospedale Maggiore, 3

country: Italy

institute: ASST Grande Ospedale Metropolitano Niguarda

description:
Gene expression data from BM CD34+/lin- cells
RNA extraction protocol: ONEDIRECT_1

hyb_protocol: cDNA wad hybridized to Affymetrix HTA 2.0 using the GeneChip platform (Affymetrix).

scan_protocol: Affymetrix GeneChip Scanner 3000 was used according to the manufacturer’s instructions to scan the signals.

data_processing: The data were normalized using the RMA method from the oligo package (version 1.42.0) from the Bioconductor repository (version 3.4). In this step, the measured signal intensities of the 6 million probes were summarized into probe sets specific for a given gene locus, realizing a one-to-one assignment of probe sets and genes. Data were first pre-processed using ComBat to adjust for batch effects and quantile normalization.

label: biotin

organism: Homo sapiens

label_protocol: cDNA was prepared starting from the previously extracted RNA (50 ng) using Ovation Pico WTA System V2 kit (NuGEN) and Encore Biotin Module Kit (NuGEN) following the manufacturer’s instructions. cDNA was prepared starting from 3 µl of the BM CD34+/lin- cells resuspended in Prelude direct Lysis module (NuGEN), using Ovation One Direct System kit followed by Encore Biotin Module Kit (NuGEN) adhering to the manufacturer’s instructions.

growth_protocol: The cells were resuspend in 50 µl of RNAlater (Thermo Fisher Scientific, Milano, Italy) and store at -20°C. Preserve the BM CD34+/lin- cells in 50 µl of RNAlater when the number of the cell count was equal to 10,000 or more and the cells were stored at -20°C. If the number of BM CD34+/lin- cells was less than 10,000, resuspend the cells in 10 µl of Prelude direct Lysis module (NuGEN, AC Leek, The Netherlands) and immediately after, store the cells at -80°C.

extract_protocol: RNA extraction was performed using MagMAX 96 Total RNA Isolation Kit (Thermo Fisher Scientific) according to the manufacturer’s instructions. Quality and yield of the extracted RNA were measured using Nanodrop (Thermo Fisher Scientific). We did not perform RNA extraction of the BM CD34+/lin- cells stored in Prelude direct Lysis module (NuGEN) because of the too low number of cells and perform the RNA processing starting from the cells.

treatment_protocol: The cells were not treated prior to the extraction of total RNA.

tag: disease state

value: Chronic Phase- Chronic Myeloid Leukemia (CP-CML)

value: CD34+/lin- cells

tag: timepoint

value: diagnosis

tag: treatment

value: nilotinib


title: S. cerevisiae Pho4 binding levels at 2 uM

organism: Saccharomyces cerevisiae


title: GTZ01019_12


title: ESCC179N

city: Shanghai

first: Zihan

last: Yu

address: 130 Dongan road, Xuhui district, shanghai

country: China

institute: Fudan University

data_processing:
Illumina bcf2fastq v2.20 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg38
Supplementary_files_format_and_content: mRNA_Expression_FPKM_Summary.txt

source_name: Esophageal Squamous Cell Cancer

extract_protocol:
RNAstormTM Kit (Cell Data cat. CD501) was used to extract FFPE RNA according the manufacturer's instructions.
Libraries were constructed by ribosomal RNA depletion methods. Ribosomal RNA were depleted using Ribo-off® rRNA Depletion Kit (H/M/R) (Vazyme #N406), and RNA libraries were constructed using VAHTS® Universal V8 RNA-seq Library Prep Kit for Illumina (Vazyme #NR605).

tag: idividual

value: ESCC

value: N


title: GR07003_0

description:
Gene expression data from BM CD34+/lin- cells
RNA extraction protocol: PICO


title: GN07008_12


title: ESCC189T

value: T


title: GD16001_0


title: GN07008_0


title: GD16001_12


title: ESCC178N


title: GR07003_12


title: ESCC176T


title: Muscle harvested from mice immediately after 1h heat shock followed by 4h recovery, replicate 3

description:
Mm_Mc_R_3
mm_counttable.csv

source_name: Muscle

value: Muscle


title: Lung harvested from bat immediately after 1h heat shock, replicate 1

description:
Es_Lg_Hs_1
es_counttable.csv


title: Lung harvested from Ctl bat, replicate 3

description:
Es_Lg_Ctl_3
es_counttable.csv


title: Lung harvested from bat immediately after 1h heat shock, replicate 2

description:
Es_Lg_Hs_2
es_counttable.csv


title: ESCC176N


title: Muscle harvested from mice immediately after 1h heat shock followed by 4h recovery, replicate 2

description:
Mm_Mc_R_2
mm_counttable.csv


title: GTZ01019_0


title: Muscle harvested from mice immediately after 1h heat shock followed by 4h recovery, replicate 1

description:
Mm_Mc_R_1
mm_counttable.csv


title: ESCC175T


title: Lung harvested from bat immediately after 1h heat shock, replicate 3

description:
Es_Lg_Hs_3
es_counttable.csv


title: GC18008_12


title: GC18008_0


title: Lung harvested from Ctl bat, replicate 2

description:
Es_Lg_Ctl_2
es_counttable.csv


title: ESCC175N


title: naïve LNSCs_1

description: 10x Genomics

value: naive


title: Muscle harvested from mice immediately after 1h heat shock, replicate 3

description:
Mm_Mc_Hs_3
mm_counttable.csv


title: ESCC173T


title: Lung harvested from Ctl bat, replicate 1

description:
Es_Lg_Ctl_1
es_counttable.csv


title: Muscle harvested from mice immediately after 1h heat shock, replicate 2

description:
Mm_Mc_Hs_2
mm_counttable.csv


title: GC10004_0

description:
Gene expression data from BM CD34+/lin- cells
RNA extraction protocol: ONEDIRECT_2


title: Blood harvested from bat immediately after 1h heat shock followed by 4h recovery, replicate 3

description:
Es_Bl_R_3
es_counttable.csv

source_name: Blood

value: Blood


title: GC05005_12


title: ESCC173N


title: Muscle harvested from mice immediately after 1h heat shock, replicate 1

description:
Mm_Mc_Hs_1
mm_counttable.csv


title: GC05005_0


title: Muscle harvested from Ctl mice, replicate 3

description:
Mm_Mc_Ctl_3
mm_counttable.csv


title: Blood harvested from bat immediately after 1h heat shock followed by 4h recovery, replicate 1

description:
Es_Bl_R_1
es_counttable.csv


title: Blood harvested from bat immediately after 1h heat shock followed by 4h recovery, replicate 2

description:
Es_Bl_R_2
es_counttable.csv


title: ESCC168N


title: Blood harvested from bat immediately after 1h heat shock, replicate 3

description:
Es_Bl_Hs_3
es_counttable.csv


title: ESCC163T


title: Muscle harvested from Ctl mice, replicate 1

description:
Mm_Mc_Ctl_1
mm_counttable.csv


title: Blood harvested from bat immediately after 1h heat shock, replicate 2

description:
Es_Bl_Hs_2
es_counttable.csv


title: GC05004_0


title: GC10004_12


title: naïve LNSCs_2

description: 10x Genomics


title: GC05004_12


title: Lung harvested from mice immediately after 1h heat shock followed by 4h recovery, replicate 2

description:
Mm_Lg_R_2
mm_counttable.csv


title: Blood harvested from Ctl bat, replicate 3

description:
Es_Bl_Ctl_3
es_counttable.csv


title: ESCC168T


title: GB01005_12


title: ESCC162N


title: FM10007_0


title: Lung harvested from mice immediately after 1h heat shock followed by 4h recovery, replicate 1

description:
Mm_Lg_R_1
mm_counttable.csv


title: ESCC158T


title: Muscle harvested from Ctl mice, replicate 2

description:
Mm_Mc_Ctl_2
mm_counttable.csv


title: Blood harvested from Ctl bat, replicate 1

description:
Es_Bl_Ctl_1
es_counttable.csv


title: Lung harvested from mice immediately after 1h heat shock, replicate 3

description:
Mm_Lg_Hs_3
mm_counttable.csv


title: FM10007_12


title: Blood harvested from Ctl bat, replicate 2

description:
Es_Bl_Ctl_2
es_counttable.csv


title: Lung harvested from mice immediately after 1h heat shock followed by 4h recovery, replicate 3

description:
Mm_Lg_R_3
mm_counttable.csv


title: 18-Enr-37C-rpt3

city: Würzburg

first: Laura

last: Jenniches

address: Josef-Schneider-Straße 2/D15

country: Germany

institute: Helmholtz Institute for RNA-based Infection Research

library_source: genomic

data_processing:
demultiplexed, filtered by transposon tag (up to 1 mismatch)
Adapter removal: BBDuk (BBMap v38.94)
Alignment/Quantification: Bio-TraDIS pipeline (v1.4.5)
Assembly: CP037923.1, CP037924.1
Supplementary files format and content: TraDIS_counts.csv: count table with all non-zero insertion sites, insertion sites are assigned to genes
Library strategy: Tn-Seq

molecule: genomic DNA

organism: Shigella flexneri

growth_protocol: The Shigella flexneri Tn5 Library #1 comprising 23 sub-libraries, cryopreserved at -80°C, were pooled together to generate a dense library containing ~130.000 mutants. 200µl of the pooled library, undergoing no further growth, were used to extract gDNA for TraDIS sequencing and used as Minimal Library reference. 13µl from the pooled library (~109 bacteria) was inoculated into 200ml of LB/50µg/ml Km and cultures were incubated at 30°C, 180rpm, for 16h. The following day, the ON culture was subculture 1:50 in 10 ml LB w/o antibiotics (~2x108 bacteria) at 37°C for 2h. Subsequently, 50µl aliquots of the subculture (~1.25x107 bacteria) were grown ON (12 h) in LB w/o antibiotics at either 30°C or 37°C, to mimic the growth enrichment step bacteria would undergo following infection experiments. Each passage was done in triplicate. 1.5ml culture fractions were collected at each step and used for gDNA extraction.

extract_protocol:
gDNA isolation was performed using the GenElute Bacterial gDNA kit (Sigma; NA2110-1KT).
TraDIS library (Barquist et al., 2016 Bioinformatics)

tag: genotype

value: pool of EZ-Tn5 transposase mutants

value: enriched ON at 37degreeC


title: Blood harvested from bat immediately after 1h heat shock, replicate 1

description:
Es_Bl_Hs_1
es_counttable.csv


title: ESCC158N


title: FG18004_0


title: ESCC155T


title: FG18004_12


title: Lung harvested from mice immediately after 1h heat shock, replicate 1

description:
Mm_Lg_Hs_1
mm_counttable.csv

value: Lung


title: ESCC162T


title: Lung harvested from mice immediately after 1h heat shock, replicate 2

description:
Mm_Lg_Hs_2
mm_counttable.csv


title: GB01005_0


title: Lung harvested from Ctl mice, replicate 3

description:
Mm_Lg_Ctl_3
mm_counttable.csv


title: ESCC155N


title: ESCC153T


title: FA06001_12


title: 16-Enr-37C-rpt1


title: Lung harvested from Ctl mice, replicate 1

description:
Mm_Lg_Ctl_1
mm_counttable.csv


title: ESCC153N


title: 15-Enr-30C-rpt3

value: enriched ON at 30degreeC


title: Blood harvested from mice immediately after 1h heat shock followed by 4h recovery, replicate 2

description:
Mm_Bl_R_2
mm_counttable.csv


title: ESCC151T


title: 13-Enr-30C-rpt1


title: ESCC151N


title: 14-Enr-30C-rpt2


title: 17-Enr-37C-rpt2


title: 12-Sub-37C-rpt3

value: subculture 1:50 in 10 ml LB


title: Blood harvested from mice immediately after 1h heat shock followed by 4h recovery, replicate 1

description:
Mm_Bl_R_1
mm_counttable.csv


title: Blood harvested from mice immediately after 1h heat shock, replicate 2

description:
Mm_Bl_Hs_2
mm_counttable.csv


title: ESCC150T


title: FF01007_12


title: FF01007_0


title: 11-Sub-37C-rpt2


title: DMG07001_12


title: FA06001_0


title: DO01018_12


title: DMG07001_0


title: DO01018_0


title: Lung harvested from Ctl mice, replicate 2

description:
Mm_Lg_Ctl_2
mm_counttable.csv


title: ESCC150N


title: Blood harvested from mice immediately after 1h heat shock, replicate 1

description:
Mm_Bl_Hs_1
mm_counttable.csv


title: 10-Sub-37C-rpt1


title: ESCC149T


title: Blood harvested from Ctl mice, replicate 3

description:
Mm_Bl_Ctl_3
mm_counttable.csv


title: 9-ON-37C-rpt3

value: incubated ON at 37degreeC


title: ESCC149N


title: Blood harvested from Ctl mice, replicate 1

description:
Mm_Bl_Ctl_1
mm_counttable.csv


title: Organoids, 48h IFNy

city: Berlin

first: Michael

last: Sigal

address: Augustenburger Platz 1

department: Dept. Hepatology and Gastroenterology

institute: Charité Universitätsmedizin

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Filtered matrices from CellRanger

molecule: polyA RNA

source_name: Colon epithelium

extract_protocol:
Libraries were constructed using Single Cell 3' Library & Gel Bead Kit v3 and the A Chip Kit (10x genomics) according to the manufacturer's instructions. Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM).
Library was performed according to the manufacter’s instructions (Single Cell 3' v3 Gene Expression protocol, 10x Genomics)

value: Colon epithelium

value: Epithelial cells

value: IFNy, 48h


title: 8-ON-37C-rpt2


title: 7-ON-37C-rpt1


title: Organoids, 24h IFNy

value: IFNy, 24h


title: ESCC147T


title: ESCC146T


title: 5-ON-30C-rpt2

value: incubated ON at 30degreeC


title: DF01016_12

value: Chronic Phase- Chronic Myeloid Leukemia (CP-CML)

value: CD34+/lin- cells

value: nilotinib


title: Organoids, untreated

value: untreated


title: DM01013_12


title: ESCC146N

value: ESCC

value: N


title: 6-ON-30C-rpt3

value: pool of EZ-Tn5 transposase mutants


title: 4-ON-30C-rpt1


title: ESCC145T

value: T


title: DM01013_0

value: diagnosis


title: TT2_Blastoid_D5_Rep2

city: Nanjing

first: Xi

last: Wang

address: Longmian Avenue 101, Jiangning District

institute: Nanjing Medical University

description: PlaB.cnt.matrix.tsv

data_processing:
The RNA-seq data were first subjected to adaptor trimming and low-quality read filtering with flexbar (version 2.5) with the following parameters: -u 6 -m 36 -ae RIGHT -at 2 -ao 2 -x 3 -y 1.
The trimmed paired-end reads were then aligned to the mouse reference genome (mm10) by STAR (version 2.7.10b) under the parameters: -outFilterMismatchNoverLmax 0.1 --alignIntronMin 20 --alignIntronMax 1000000 --alignSJoverhangMin 6 --alignSJDBoverhangMin 1 --outFilterType BySJout --outFilterIntronMotifs RemoveNoncanonicalUnannotated.
HTSeq (v0.13.5) was employed for gene expression quantification.
Assembly: mm10
Supplementary files format and content: Tab Separated Values (.tsv), raw read counts

growth_protocol: TT2 mESCs (CRL-1992, ATCC) were cultured on inactivated mouse embryonic fibroblast (MEF) feeder layers under 5% CO2 at 37℃.

extract_protocol:
2μl lysis buffer (0.2% TritonX-100 and 40 U/ml Recombinant RNase Inhibitor) was used to extract RNA from samples.
Poly(A)-tailed RNA molecules in cells were processed using the Smart-seq2 protocol.

treatment_protocol: The TT2 mESCs were first seeded for 48 hours, and then treated with 20 nM pladienolide (PlaB, Santa, sc-391691) for 6 hours.

tag: cell line

value: embryonic stem cell

value: PlaB

tag: treatment time

value: 6 h

tag: blastoid culture_time

value: 5 days


title: CS05001_12


title: 3-Min-rpt3

value: Minimal Library reference


title: TT2_Blastoid_D5_Rep1

description: PlaB.cnt.matrix.tsv


title: DF01016_0


title: ESCC147N


title: 2-Min-rpt2


title: CF01004_0


title: CS05001_0


title: CF01004_12


title: ESCC140T


title: 1-Min-rpt1


title: TT2_Blastoid_D4_Rep3

description: PlaB.cnt.matrix.tsv

value: 4 days


title: ESCC140N


title: ESCC135T


title: TT2_Blastoid_D4_Rep1

description: PlaB.cnt.matrix.tsv


title: 3_Fd_30C_S13

data_processing:
Adapters were removed with Cutadapt v4.1
Alignment/Quantification: STAR 2.6.0a (Dobin et al., 2013)
Assembly: CP037923.1, CP037924.1
Supplementary files format and content: read_counts.csv: count table with locus tags

growth_protocol: Shigella flexneri M90T wt and M90T ΔvirF strains were grown in LB broth at 30°C or 37°C to an OD 600 nm of ~0.7, in triplicate.

extract_protocol:
Total RNA was extracted with acidic phenol, DnaseI treated and ribosomal RNA were depleted.
An oligonucleotide adapter was ligated to the 3' end of the RNA molecules. First-strand cDNA synthesis was performed using M-MLV reverse transcriptase and the 3’ adapter as primer. 5' Illumina TruSeq sequencing adapter was ligated to the 3' end of the antisense cDNA. The resulting cDNA was PCR-amplified to about 10-20ng/μl using a high-fidelity DNA polymerase. The cDNA was purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics).

value: deltavirF

value: LB, 30C


title: CAM06002_0

value: Chronic Phase- Chronic Myeloid Leukemia (CP-CML)


title: ESCC135N


title: 1_Fd_30C_S11


title: ESCC132T


title: TT2_Blastoid_D3_Rep3

description: PlaB.cnt.matrix.tsv

value: 3 day


title: TT2_Blastoid_D3_Rep2

description: PlaB.cnt.matrix.tsv


title: 3_M90T_30C_S10


title: ESCC132N


title: TT2_Blastoid_D3_Rep1

description: PlaB.cnt.matrix.tsv


title: ESCC130T


title: TT2_Blastoid_D2_Rep3

description: PlaB.cnt.matrix.tsv

value: 2 days


title: BS18009_0

value: CD34+/lin- cells

value: nilotinib


title: BS11002_12


title: TT2_Blastoid_D4_Rep2

description: PlaB.cnt.matrix.tsv


title: CAM06002_12


title: BR18006_0


title: TT2_Blastoid_D2_Rep2

description: PlaB.cnt.matrix.tsv


title: 2_Fd_30C_S12


title: BR18006_12


title: ESCC128N

value: ESCC

value: N


title: 2_Fd_37C_S6

value: LB, 37C


title: 1_M90T_30C_S8


title: ESCC128T

value: T


title: BS11002_0

value: diagnosis


title: TT2_Blastoid_D2_Rep1

description: PlaB.cnt.matrix.tsv

value: embryonic stem cell

value: PlaB


title: 2_M90T_30C_S9


title: TT2_Blastoid_D1_Rep3

description: PlaB.cnt.matrix.tsv

value: 6 h

value: 1 day


title: BP07004_12


title: 1_Fd_37C_S5


title: ESCC130N


title: 3_Fd_37C_S7


title: TT2_Blastoid_D1_Rep2

description: PlaB.cnt.matrix.tsv


title: BS18009_12


title: ESCC163N


title: TT2_Blastoid_D1_Rep1

description: PlaB.cnt.matrix.tsv


title: 2_M90T_37C_S3


title: ESCC126T


title: 3_M90T_37C_S4


title: ESCC127T


title: ESCC126N


title: TT2_54h_PlaB_Rep1

description: Blastoid.cnt.matrix.tsv


title: 1_M90T_37C_S2


title: Lib43_OUTPUT

data_processing:
demultiplexed, filtered by transposon tag (up to 1 mismatch)
Adapter removal: BBDuk (BBMap v38.94)
Alignment/Quantification: Bio-TraDIS pipeline (v1.4.5) for each fastq file separately.
Assembly: CP037923.1, CP037924.1
Supplementary files format and content: shigella_infections_counts_neg_meta.csv.gz: count table with all non-zero insertion sites in the negative strand (summed over all fastq files), insertion sites are assigned to genes
Supplementary files format and content: shigella_infections_counts_pos_meta.csv.gz: count table with all non-zero insertion sites in the positive strand (summed over all fastq files), insertion sites are assigned to genes

growth_protocol: The Shigella flexneri Tn5 Library #2 comprising 43 sub-libraries were used to infect replicate wells containing ~800 basal-out enteroids at MOI 40 as described above. After infection, enteroids were lysed in 0.1% Na-deoxycholate by extensive pipetting. Intracellular bacterial populations were enriched ON at 30°C in 2ml LB. A diluted culture of the inoculum was also enriched and used as the input reference. A 1.5ml portion of the bacterial culture was used to extract genomic DNA.

extract_protocol:
gDNA isolation was performed using the GenElute Bacterial gDNA kit (Sigma; NA2110-1KT). 1.5ug of gDNA was cleaned with Ampure XP beads to remove EDTA. 500ng of cleaned gDNA was used as input for the sequencing library preprarations.
TraDIS library (Barquist et al., 2016 Bioinformatics)

value: pool of EZ-Tn5 transposase mutants

value: enriched intracellular bacteria


title: ESCC124N


title: Lib42_OUTPUT


title: ESCC121T


title: TT2_54h_Ctrl_Rep2

description: Blastoid.cnt.matrix.tsv


title: BP07004_0


title: TT2_54h_Ctrl_Rep1

description: Blastoid.cnt.matrix.tsv


title: Lib41_OUTPUT


title: ESCC121N


title: TT2_54h_PlaB_Rep2

description: Blastoid.cnt.matrix.tsv


title: Lib40_OUTPUT


title: ESCC116T


title: HF5: day 13 female embryos developed in heifers-Rep5

city: Bonn

first: Dessie Salilew

last: Wondim

address: Endenicher Allee 15

institute: University of Bonn

data_processing:
The raw sequence data (.bcl files) was converted into fastq files and de-multiplexed using Illumina's bcl2fastq software (version 2.17).
The quality of the raw data was evaluated using FastQC
Adapters, and non-informative sequence reads were removed using trim galore software (Babraham Bioinformatics).
Sequences were mapped to the bovine reference genome using bowtie2 by setting paired-end and end-to-end read alignment parameters.
Sequence Alignment Map (SAM) files were converted into the binary alignment map (BAM) files and sorted using the samtools command .
Quantification of read counts was done with the Seqmonk tool (version 1.48.0, Babraham Bioinformatics).
Assembly: Bos_taurus.ARS-UCD1.2
Supplementary files format and content: The final processed data is the text format consists of read counts.

organism: Bos taurus

source_name: Embryo

growth_protocol: Oocytes collected from the ovaries of the slaughterhouse were in vitro matured and in vitro fertilized with sex-sorted semen. On day 2, the male or female embryos were transferred to oestrous synchronized Holstein Frisian cows and heifers. At day 13 of the gestation period, embryos were recovered after slaughter in the nearby slaughterhouse.

extract_protocol:
Total RNA extraction from CM, CF, HM and HF sample group was done using AllPrep DNA/RNA/miRNA Universal Kit (Qiagen)
Illumina, RNA with PolyA selection. Libraries were clustered on one flowcell and loaded on the Illumina instrument (4000 or equivalent) following the manufacturer’s instructions and sequenced using a 2x150bp Paired End (PE) configuration.

treatment_protocol: Day 13 male and female embryos developed in cows and heifers were considered as a group. Accordingly, four groups were generated. Male embryos developed in cows (CM), female embryos developed in cows (CF) and male (HM) and female (HF)  embryos developed in heifers.

value: Embryo

value: Female

value: Female embryos developed in heifers


title: OsiCRY2-OX dark grown - II

city: Agra

first: Sushma

last: Mishra

state: Uttar Pradesh

address: Dayalbagh

department: Botany

country: India

institute: Dayalbagh Educational Institute, Agra, India

hyb_protocol: 15 µg of aRNA after fragmentation at 95 ºC for 35 min, was hybridized to the Affymetrix rice chips (GeneChip® Rice Genome Array) at 45 ºC for 16 h

scan_protocol: Gene chips were scanned using the Affymetrix GeneChip® Scanner 3000

data_processing:
The Affymetrix GeneChip Operating Software (GCOS) 1.2.1 was used for washing, scanning and preliminary data analysis to generate .CEL and .CHP files.
processed data file includes GC-RMA averages and statisical analysis.

organism: Oryza sativa Indica Group

source_name: 13.3 Dark

label_protocol: 500 ng of total RNA was used for first strand synthesis, followed by labelling with biotin  was used for first-strand synthesis Biotinylated cRNA were prepared according to the standard Affymetrix protocol

growth_protocol: The seeds were inoculated on Murashige and Skoog medium (pH 5.8)  in complete darkness in dark room for 7 days at 28 °C±2 ºC.

extract_protocol: Extraction of total RNA by RNeasy Plant Mini Kit to the manufacturer's instructions.

treatment_protocol: The seeds were surface sterilized with 70% ethanol and mercuric chloride, followed by rinsing in water and overnight imbibiton.

value: 7 day old seedling grown in dark

tag: cultivar

value: Pusa Sugandh 2

value: cryptochrome 2 overexpression (OsiCRY2)


title: ESCC127N

value: ESCC


title: Lib39_OUTPUT


title: HF4: day 13 female embryos developed in heifers-Rep4


title: BL02002_0

value: Chronic Phase- Chronic Myeloid Leukemia (CP-CML)

value: CD34+/lin- cells

value: nilotinib


title: BE07013_0

value: diagnosis


title: BABL07020_0


title: BABL07020_12


title: BE07013_12


title: AR01012_12


title: BL02002_12


title: AR01012_0


title: AP05006_0


title: HF3: day 13 female embryos developed in heifers-Rep3


title: Lib38_OUTPUT


title: AM05003_12


title: AP05006_12


title: WT dark grown - II

source_name: WT Dark

value: WT


title: HF2: day 13 female embryos developed in heifers-Rep2


title: HF1: day 13 female embryos developed in heifers-Rep1


title: WT dark grown - I


title: OsiCRY2-OX  dark grown - I


title: AM05003_0


title: Lib36_OUTPUT


title: HM5: day 13 male embryos developed in heifers-Rep5

value: Male

value: Male embryos developed in heifers


title: Drosophila_melanogaster_embryo_HyDrop_v2_beads_13

city: Leuven

first: Gert

last: Hulselmans

address: Herestraat 49 PO Box 602

department: Center for Brain and Disease Research

country: Belgium

institute: VIB

description:
Library name: FDM__eda215__240321_HyDropATAC_Dros_DGRP_Embryo_16-20AEL_Dechor_sampleAF3
re-sequenced on Illumina NovaSeqX

library_source: genomic single cell

data_processing:
In house generated data (prefix HYA and FDM):  Barcode reads (read 2) were trimmed to exclude the intersub-barcode PCR adapters MAWK
In house generated data (prefix HYA and FDM):  Barcode reads (read 2) were trimmed using trimgalore, corrected to a whitelist allowing 1 mismatch (in PUMATAC pipeline, nextflow version: nextflow-21.04.3), and appended to the fastq sequence identifier of the paired-end ATAC-seq reads (read 1 and read 3)
For all samples (mouse (in house generated and commercial), fly and barnyard cell lines): Reads were mapped to reference genomes using bwa-mem2 and fragemnet files were created with create_fragments_file by the (in PUMATAC pipeline, nextflow version: nextflow-21.04.3)
For mouse samples a data matrix (cistopic_obj) was generated using  pycistopic version 2.0a0. Cells passing the Otsu threshold in PUMATAC (nextflow version: nextflow-21.04.3) were included.
For Drosophila samples a data matrix (cistopic_obj) was generated using  pycistopic version 2.0a0. Cells passing  the trhshold of TSS_enrichment >2 and number of unique fragments > 800 in PUMATAC (nextflow version: nextflow-21.04.3) were included.
Assembly: For mouse samples: mm10, for hybrid samples in the barnyard: GRCh38_GRCm10 hybrid genome, for fly samples: dm6
Supplementary files format and content: For mouse and Drosophila samples: standard tab-separated fragments files, count matrix and metadata inforamtion for cell data (barcode) and region data in tsv format
Supplementary files format and content: For barnyard: standard tab separated fragment file

organism: Drosophila melanogaster

source_name: whole embryo

growth_protocol:
Barnyard cell culture: cultured in RPMI1640 (ThermoFisher 11875093) medium supplemented with 10% FBS (ThermoFisher 10270–106), 1% penicillin/streptomycin (Life Technologies 15140122), and 10 ug/mL insulin (Sigma Aldrich I9278) and passaged twice per week. Melanoma cell lines were derived by physical resection of primary cutaneous lesions. Mouse melanoma cells were cultured in DMEM (ThermoFisher 13345364) supplemented with 10% FBS and 1% penicillin/streptomycin and passaged once per week. All cell lines tested negative for mycoplasma prior to use.
Mouse: The mice were housed under standard housing conditions in a pathogen-free facility with a 14 hr light, 10 hr dark light cycle from 7 to 21 hr. Mice used in the study were 60 days old.
Drosophila: All flies were raised on a yeast-based medium and kept at 25 °C on a 12h/12h day/night light cycle. For embryo collection, flies were transferred to cages fixed to a plate with a normal yeast-based medium 24 hours before embryo collection. On the day of embryo collection, the plate was exchanged for a juice plate. The juice was prepped by adding 20 g agar and 22 g sucrose to 300 ml distilled water, boiling, and then mixing in 100 ml apple juice, 10 ml 95% ethanol, and 5 ml 100% glacial acetic acid. The flies laid eggs for four hours. Sixteen hours later, the embryos aged between 16 to 20 hours were collected from the juice plate with a small brush and transferred to a 70 µm nylon mesh filter.

extract_protocol:
Mouse: The nuclei were extracted from mouse cortex samples that were snap-frozen in liquid nitrogen and stored at -80 °C. We transferred ~1 cm3 of frozen mouse cortex to 500 μL of ice-cold homogenization buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 320 mM sucrose, 0.1 mM EDTA, 0.5% BSA, 0.1% IGEPAL CA-630, 1× complete protease inhibitor, and 1 mM DTT) in a Dounce Homogenizer. The tissue was left to thaw for 2 min before the tissue was homogenized with 10 strokes of the loose pestle and 5 strokes of the tight pestle. Before the end of a 5-minute incubation, the homogenate was filtered through a 70 μm cell strainer (Corning), and the homogenizer and strainer were washed with homogenization buffer to obtain a final volume of 1 mL. The filtrate was transferred to a 1.5 mL DNA LoBind tube (Eppendorf) and centrifuged at 500 xg for 5 minutes. The supernatant was discarded, and the pellet was topped up to 520 μL with wash buffer 1 (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 320 mM sucrose, 0.1 mM EDTA, 0.5% BSA, 1× complete protease inhibitor, and 1 mM DTT) and resuspended. Next, we added 520 μL gradient medium (50% Optiprep, 10 mM Tris-HCl pH 7.5, 1 mM CaCl2, 5 mM MgCl2, 75 mM sucrose, 1× complete protease inhibitor, and 1 mM DTT) and mixed the entire volume by gentle pipetting. In a 2 mL DNA LoBind tube we layered 790 μL Optiprep cushion (29% Optiprep, 31 mM Tris-HCl pH 8, 77.5 mM KCl, 15.5 mM MgCl2, 129.2 mM sucrose) at the bottom and 1040 μL of the sample on top, gently without disrupting the cushion. The tube was then centrifuged at 9000 xg for 20 minutes at 4 °C. After the centrifugation the debris on top was carefully removed with a 1 mL tip and the rest of the supernatant was also carefully removed until 50 μL was left in the tube. The pellet was gently resuspended before we mixed it with 50 μL 0.2× permeabilization buffer (20 mM Tris-HCl pH 7.5, 20 mM NaCl, 6 mM MgCl2, 0.2% Tween-20, 0.02% IGEPAL CA-630, 0.02% Digitonin, 2% BSA, and 2 mM DTT) and left the nuclei suspension for 2 minutes on ice before we stopped the permeabilization by mixing it with 1 mL of wash buffer 2 (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 1% BSA). The nuclei were pelleted by centrifugation at 500 xg for 5 minutes at 4 °C. The nuclei were resuspended in PBS with 0.04% BSA. For Drosophila, the nuclei were isolated by using an adapted protocol based on the nuclei isolation protocol for single-cell ATAC sequencing (10x Chromium CG000169-RevE).  Similar to mouse, for the barnyard, the cell lines were mixed to equal parts and a pellet of one million dissociated cells or fewer was incubated on ice in 200 μL of ATAC lysis buffer (1% BSA, 10 mM Tris-HCl pH 7.5, 10 mM NaCl, 0.1% Tween-20, 0.1% NP-40, 3 mM MgCl2, 70 μM Pitstop in DMSO, 0.01% digitonin) for 5 minutes. 1 mL of ATAC nuclei wash buffer (1% BSA, 10 mM Tris-HCl pH 7.5, 0.1% Tween-20, 10 mM NaCl, 3 mM MgCl2) was added and the nuclei were pelleted at 500 xg, 4 °C for 5 minutes. The resulting pellet was resuspended in 100 μL of ice-cold PBS and filtered with a 40 μm strainer (Flowmi).
Nuclei, resuspended in PBS (supplemented with 0.04% BSA), were tagmented for one hour at 37 °C in 15 μL ATAC reaction mix (10% DMF, 10 mM Tris-HCl pH 7.4, 5 mM MgCl2, 5 ng/µL Tn5, 70 µM Pitstop in DMSO, 0.1% Tween-20, 0,01% Digitonin). Tagmented nuclei were placed on ice and 95 µL of PCR mix (1.25× Phusion HF buffer, 15% Optiprep, 1.25 mM dNTPs, 75 mM DTT, 0.0625 U/µL Phusion HF polymerase, 0.0625 U/μL Deep Vent polymerase, 0.0125 U/μL ET SSB) was added. Next, 110 μL of nuclei mixed in PCR mix was co-encapsulated with 45 μL of HyDrop-ATACv2 beads in HFE-7500 Novac oil with EA-008 surfactant (RAN Biotech) using the Onyx microfluidics platform (Droplet Genomics). The resulting emulsion was split over two PCR tubes and was placed in a thermocycler with the following program: 72 °C – 15 mins, 98 °C – 3 mins, 12 cycles of 98 °C – 10 s; 55 °C – 30 s; 72 °C – 1 min; 72 °C – 5 mins, and finally the amplification products were cooled to 4 °C. To break the emulsion and remove excess oil, 125 μL of recovery agent (20% PFO in HFE) was added and the PCR tubes were inverted 10 times to mix before the oily phase was removed. Next, we added 180 μL GITC mix (5M GITC, 25 mM EDTA, 50 mM Tris-HCl pH 7.4), 10 μL Dynabeads, and 10 μL 2.4 M DTT to each of the aliquots, and mixed everything by pipetting up and down 10 times and incubating for 10 minutes. Dynabeads were pelleted on a magnet and washed twice with 80% ethanol. Elution was done in 50 μL of EB-DTT-Tween (24 mM DTT, 0.1% Tween-20 in EB (10 mM Tris-HCl pH 8.5)). Next, a 1.2× Ampure bead purification was performed according to manufacturer’s recommendations. Elution was done with 40 μL of EB-DTT (10 mM DTT in EB). The library was completed by amplifying the eluate in a total volume of 100 μL PCR mix (1× KAPA HiFi, 1 μM index i7 primer, 1 μM Universal P5 primer) with the following program: 95 °C – 3 mins, 12 cycles of 98 °C – 10 s; 63°C – 30 s; 72 °C – 1 min; 72 °C – 1 min, and finally a hold stage at 4 °C. The final libraries were subjected to 0.4×–1.2× doublesided Ampure purification and eluted in 20 μL elution buffer.

value: whole embryo

value: divers cells of whole Drosophila embryo

value: three DGRP fly lines (DGRP-639, DGRP-502, DGRP-409) mixed after collection for genetic diversity

tag: Sex

value: pooled male and female

value: 34 to 20h after egg laying, pooled samples

tag: batch


title: Lib35_OUTPUT

value: pool of EZ-Tn5 transposase mutants

value: enriched intracellular bacteria


title: Lib34_OUTPUT


title: Lib37_OUTPUT


title: Drosophila_melanogaster_embryo_HyDrop_v2_beads_11

description:
Library name: FDM__ad7491__240321_HyDropATAC_Dros_DGRP_Embryo_16-20AEL_Dechor_sampleAF6
re-sequenced on Illumina NovaSeqX

value: 32 to 20h after egg laying, pooled samples


title: HM3: day 13 male embryos developed in heifers-Rep3

value: Embryo


title: Lib33_OUTPUT


title: Drosophila_melanogaster_embryo_HyDrop_v2_beads_18

description:
Library name: FDM__0cd23d__240321_HyDropATAC_Dros_DGRP_Embryo_16-20AEL_Dechor_sampleAF4
re-sequenced on Illumina NovaSeqX

value: 29 to 20h after egg laying, pooled samples


title: ALC06005_0

value: Chronic Phase- Chronic Myeloid Leukemia (CP-CML)


title: ALC06005_12

value: CD34+/lin- cells


title: AG06006_12

value: nilotinib


title: HM2:day 13 male embryos developed in heifers-Rep2


title: Drosophila_melanogaster_embryo_10x_v2_beads_inhouse_5

description:
Library name: FDM__f83e74__240321_10xscATAC_Dros_DGRP_Embryo_16-20AEL_Dechor_sampleAF2
re-sequenced on Illumina NovaSeqX and NextSeq2000

value: 28 to 20h after egg laying, pooled samples


title: Lib32_OUTPUT


title: HM1: day 13 male embryos developed in heifers-Rep1


title: Lib30_OUTPUT


title: Lib29_OUTPUT


title: CF5: day 13 female embryos developed in cows-Rep5

value: Female

value: Female embryos developed in cows


title: Lib31_OUTPUT


title: Drosophila_melanogaster_embryo_10x_v2_beads_inhouse_2

description:
Library name: FDM__5260fa__240321_10xscATAC_Dros_DGRP_Embryo_16-20AEL_Dechor_sampleAF1
re-sequenced on Illumina NovaSeqX and NextSeq2000

value: 20 to 20h after egg laying, pooled samples


title: HM4: day 13 male embryos developed in heifers-Rep4

value: Male

value: Male embryos developed in heifers


title: CF3: day 13 female embryos developed in cows-Rep3


title: Lib28_OUTPUT


title: Drosophila_melanogaster_embryo_HyDrop_v2_beads_5

description:
Library name: FDM__15999e__240321_HyDropATAC_Dros_DGRP_Embryo_16-20AEL_Dechor_sampleAF5
re-sequenced on Illumina NovaSeqX

value: whole embryo

value: divers cells of whole Drosophila embryo

value: three DGRP fly lines (DGRP-639, DGRP-502, DGRP-409) mixed after collection for genetic diversity

value: 22 to 20h after egg laying, pooled samples


title: CF2: day 13 female embryos developed in cows-Rep2


title: ESCC145N

value: ESCC

value: N


title: TT2_Blastoid_D5_Rep3

description: PlaB.cnt.matrix.tsv

value: embryonic stem cell

value: PlaB

value: 6 h

value: 5 days


title: Lib27_OUTPUT

value: pool of EZ-Tn5 transposase mutants

value: enriched intracellular bacteria


title: HEK293 PHLPP2 KO #22, replicate 3

city: Wien

first: Luis

middle: Miguel

last: Cerron Alvan

address: Dr. Bohr Gasse 9

country: Austria

institute: Max Perutz Labs

description: Library name: KO22_Rep3

data_processing:
FASTQ files were processed using the Nextflow 24.10.1/5930/nf-core/rnaseq v3.17.0 pipeline. Quality control was conducted with fastQC (v0.12.1).
Transcript mapping to the hg38 human reference genome was performed using Salmon (v1.10.3) for pseudoalignment and STAR (v2.7.11b) as the aligner.
Assembly: human reference genome hg38
Supplementary files format and content: The TSV file containing raw counts, processed from FASTQ files using STAR and Salmon as part of the Nextflow 24.10.1/5930 workflow with the nf-core/rnaseq v3.17.0 pipeline.

growth_protocol: HEK293 cell lines (WT and PHLPP2 KO9 were cultured in DMEM high glucose (Sigma Aldrich) supplemented with 10 % FBS (Sigma Aldrich) and 1 % Penicillin/Streptomycin (Sigma Aldrich) at 37 °C and 5 % CO2.

extract_protocol:
RNA samples were extracted using the RNA isolation kit (RNAisomag) provided by the VBC Molecular Tools Shop and processed with the KingFisher Flex robot (Thermo Fisher Scientific).
Libraries were prepared using the Lexogen 3’ mRNA-Seq Library Prep Kit

value: human embryonic kidney cells

value: KO


title: CF4: day 13 female embryos developed in cows-Rep4

value: Embryo

value: Female

value: Female embryos developed in cows


title: CF1: day 13 female embryos developed in cows-Rep1


title: Lib26_OUTPUT


title: AF01011_12

value: Chronic Phase- Chronic Myeloid Leukemia (CP-CML)

value: CD34+/lin- cells

value: nilotinib


title: HEK293 wild type, RNA-Seq, replicate 3

description: Library name: WT_Rep3

value: wild type


title: AF01002_0

value: diagnosis


title: AE07007_0


title: AF01002_12


title: AG06006_0


title: AF01011_0


title: AE07007_12


title: CM5: day 13 male embryos developed in cows-Rep5

value: Male

value: Male embryos developed in cows


title: HEK293 PHLPP2 KO #22, replicate 2

description: Library name: KO22_Rep2


title: CM4: day 13 male embryos developed in cows-Rep4


title: Lib25_OUTPUT


title: AC06003_12


title: AD09001_0


title: CM3: day 13 male embryos developed in cows-Rep3


title: HEK293 PHLPP2 KO #22, replicate 1

description: Library name: KO22_Rep1


title: HEK293 wild type, RNA-Seq, replicate 1

description: Library name: WT_Rep1


title: UOK109 cells, TFE3 rescue, H3K27Ac, Rep3

first: Wanlu

last: Chen

address: 615 N. Wolfe Street

institute: Johns Hopkins University

data_processing:
Initial steps involved trimming raw fastq files using fastp.
Subsequently, reads were aligned to the hg38 genome assembly using bowtie2 v2.5.2.
Bigwigs were generated using bedtools.
Peak calling was performed against negative control using MACS2.
Assembly: hg38
Supplementary files format and content: bigwig, narrowPeak
Library strategy: CUT&RUN

source_name: UOK109 cells

growth_protocol: Cells were grown in Dulbecco's Modified Eagle's Medium (DMEM, 15-013-CV, Corning) supplemented with 10% v/v fetal bovine serum (FBS, 26140079, Gibco), 1% v/v Penicillin-Streptomycin (10,000 U/mL) (15140122, Thermo Fisher), 1% v/v GlutaMAX Supplement (35050061, Thermo Fisher), and 1% v/v Mem Non Essential Amino Acids Solution (100X) (11140050, Thermo Fisher). Cells were grown at 37°C with 5% CO2 in a humidified incubator.

extract_protocol:
We lightly fixed the cells with 0.4% w/v PFA for 1 min and quenched using 0.125 M glycine for 5 min. Cells were pelleted and washed once with PBS. Cell pellets were snap-frozen and stored in -80 ºC freezer until being processed.
CUT&RUN were performed with Epicypher’s CUTANA CUT&RUN kit v3 and library preparation kit v1.1 following the manufacturer’s instructions using a FLAG antibody (CST 14793, Cell Signaling) and H3K27Ac antibody (39034, Active Motif). No E. coli spike-in was used. Library quality and concentrations were assessed using the D1000 TapeStation system (Agilent). Libraries were sequenced for 25 cycles in 75-bp paired-end mode on Illumina Novaseq 6000 and data were analyzed as described.

treatment_protocol: Media was changed 6h before sample isolation.

value: UOK109 cells

value: Patient-derived cells harboring NONO::TFE3 fusion

value: TFE3 rescue

value: baseline culturing conditions

tag: cut&run antibody

value: H3K27Ac antibody (39034, Active Motif)

tag: i7 index_name*

tag: i7 index_sequence*

value: GAATTCGT

tag: i5 index_name*

tag: i5 index_sequence*

value: ACGTCCTG


title: Lib23_OUTPUT

tag: strain

value: pool of EZ-Tn5 transposase mutants

value: enriched intracellular bacteria


title: Lib24_OUTPUT


title: Lib22_OUTPUT


title: Lib21_OUTPUT


title: CM1: day 13 male embryos developed in cows-Rep1

tag: tissue

value: Embryo


title: BMC, miR-223 KO4

city: Guangzhou

first: DEWEI

last: YE

state: Guangdong

address: 280 Waihuan East Road, Guangzhou Higher Education Mega

institute: Guangdong Pharmaceutical University

data_processing:
A propriety Sub-pixel Registration algorithm developed by MGI was used for base call.
This project uses the filtering software SOAPnuke developed by BGI independently for filtering. The specific steps are as follows:  1) Remove the reads containing the adaptor(adaptor pollution);  2) Remove reads whose N content is greater than 5%;  3) Remove low-quality reads (we define reads with bases with a quality score less than 10 as the proportion of total bases in the reads that are greater than 20% as low-quality reads).  The filtered "Clean Reads" are saved in FASTQ format.
Bowtie2 was used to map the clean reads to the reference gene sequence (transcriptome), and then RSEM was used to calculate the gene expression level of each sample.
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: bone marrow cells

extract_protocol:
Total RNA was etracted using Trizol reagents (Thermo Fisher Scientific) and purified by Oligo(dT)-attached magnetic beads.
Samples of RNA-seq libraries were sequenced on the DNBSEQ platform.

tag: cell type

value: bone marrow cells

value: miR-223 KO

tag: age

value: 8 weeks old


title: Cardiac Organoid, D21_600um

city: New York

first: David

middle: William

last: McKellar

state: NY

address: 101 6th Ave

institute: New York Genome Center

description:
Library name: D21_600um
10X Genomics Chromium v3.1

data_processing:
Sequencing data were trimmed and quality-filtered using cutadapt (v4.1). Read 2 was trimmed by removing poly(A) and poly(G) sequences from the three-prime end, and removing template switch oligonucleotide sequence and its reverse complement from the five-prime end. After trimming, all reads shorter than 18bp were discarded. The remaining data were aligned and quantified using STARsolo (STAR v2.7.10a). The filtered count matrices (--soloCellFilter EmptyDrops_CR, --soloFeatures GeneFull) were used for downstream analysis. For preprocessing of all samples, SoupX (v1.5.2) with default settings was used to remove ambient RNA contamination71. Further quality control and preprocessing were performed individually for each sample using Scanpy (v1.9.1)72. First, cells with fewer than 500 detected features or fewer than 1,500 unique molecules were excluded. Genes detected in fewer than five cells were also removed. Cells with more than 20% of unique molecules mapping to the mitochondrial genome were also excluded. Doublet identification was performed using Scrublet (v0.2.3)73. Cells with a predicted doublet score greater than 0.4 were removed from Day 0 and Day 1 samples, while cells with a predicted doublet score greater than 0.2 were removed from all other samples. After filtering and doublet removal, a total of 96,401 cells were retained for subsequent analysis
Assembly: GRCh38p13
Supplementary files format and content: Market matrix (.mtx) along with cell barcodes and feature names are provided, as generated by STARsolo (GeneFull/filtered)

source_name: Cardiac Organoid

extract_protocol:
Cardioids were isolated by first scraping, aspirating, and discarding residual cells and tissue within the wells. Only beating cardioids (~ 15 – 25 cardioids) were collected from each well of 6-well plates. For timepoints prior to Day 6, samples were dissociated with Accutase and quenched with RPMI/B27 minus insulin medium, while samples from Day 6 onward were dissociated using cardiomyocyte dissociation medium (Stem Cell Technologies, cat. no. 05025) and quenched with RPMI/B27 complete medium. Cells were singularized by repeated pipetting and passing through a cell strainer.
Single-cell RNA sequencing libraries were prepared using the Chromium Single Cell 3′ reagent kit v3 (10x Genomics, PN-1000075) according to the manufacturer's protocol. Cells were diluted into the Chromium Single Cell A Chip to obtain approximately 6,000 single-cell transcriptomes. After preparation, libraries were sequenced on a NextSeq 500 (Illumina) with 75-cycle high-output kits (Index 1 = 8, Read 1 = 26, and Read 2 = 58).

value: Cardiac Organoid

value: hiPSC

value: WTC


title: CM2: day 13 male embryos developed in cows-Rep2

value: Male

tag: treatment

value: Male embryos developed in cows


title: UOK109 cells, NONOmut::TFE3 rescue, H3K27Ac, Rep3

value: UOK109 cells

value: Patient-derived cells harboring NONO::TFE3 fusion

tag: genotype

value: NONOmut::TFE3 rescue

value: TCAGAGCC


title: Cardiac Organoid, D21_200um

description:
Library name: D21_200um
10X Genomics Chromium v3.1

tag: cell line


title: HEK293 wild type, RNA-Seq, replicate 2

description: Library name: WT_Rep2

value: human embryonic kidney cells

value: wild type


title: Lib19_OUTPUT

value: pool of EZ-Tn5 transposase mutants


title: UOK109 cells, TFE3 rescue, H3K27Ac, Rep1

value: TFE3 rescue

value: baseline culturing conditions

value: H3K27Ac antibody (39034, Active Motif)

value: GAATTCGT

value: CTTCGCCT


title: Lib20_OUTPUT

value: enriched intracellular bacteria


title: UOK109 cells, NONOmut::TFE3 rescue, H3K27Ac, Rep2

value: AGGATAGG


title: BMC, miR-223 KO3

value: bone marrow cells

value: miR-223 KO

value: 8 weeks old


title: Cardiac Organoid, D21_1000um

description:
Library name: D21_1000um
10X Genomics Chromium v3.1

value: Cardiac Organoid

value: hiPSC

value: WTC


title: AD09001_12

tag: disease state

value: Chronic Phase- Chronic Myeloid Leukemia (CP-CML)

value: CD34+/lin- cells

tag: timepoint

value: nilotinib


title: BMC, miR-223 KO2


title: UOK109 cells, TFE3 rescue, H3K27Ac, Rep2

value: UOK109 cells

value: Patient-derived cells harboring NONO::TFE3 fusion

value: TAAGATTA


title: Cardiac Organoid, D12_600um

description:
Library name: D12_600um
10X Genomics Chromium v3.1


title: UOK109 cells, NONOmut::TFE3 rescue, H3K27Ac, Rep1

value: NONOmut::TFE3 rescue

value: baseline culturing conditions

value: H3K27Ac antibody (39034, Active Motif)

value: GCCTCTAT


title: Lib18_OUTPUT

value: pool of EZ-Tn5 transposase mutants

value: enriched intracellular bacteria


title: Lib17_OUTPUT


title: BMC, miR-223 KO1

value: bone marrow cells

value: miR-223 KO


title: Cardiac Organoid, D8_600um

description:
Library name: D8_600um
10X Genomics Chromium v3.1

value: Cardiac Organoid


title: AC06003_0

value: diagnosis


title: AB01009_12


title: BMC, WT4

value: WT

value: 8 weeks old


title: Lib16_OUTPUT


title: BMC, WT3


title: AB01009_0

value: Chronic Phase- Chronic Myeloid Leukemia (CP-CML)

value: CD34+/lin- cells


title: Lib14_OUTPUT


title: UOK109 cells, SFPQdeltaCCD::TFE3 rescue, H3K27Ac, Rep2

value: UOK109 cells

value: SFPQdeltaCCD::TFE3 rescue

value: ATTCAGAA

value: GTCAGTAC


title: UOK109 cells, SFPQdeltaCCD::TFE3 rescue, H3K27Ac, Rep1

value: Patient-derived cells harboring NONO::TFE3 fusion

value: baseline culturing conditions

value: ACGTCCTG


title: Cardiac Organoid, D4_1000um

description:
Library name: D4_1000um
10X Genomics Chromium v3.1

value: hiPSC

value: WTC


title: Cardiac Organoid, D4_600um

description:
Library name: D4_600um
10X Genomics Chromium v3.1


title: Lib15_OUTPUT

value: pool of EZ-Tn5 transposase mutants

value: enriched intracellular bacteria


title: UOK109 cells, SFPQ::TFE3 rescue, H3K27Ac, Rep2

value: SFPQ::TFE3 rescue

value: H3K27Ac antibody (39034, Active Motif)

value: CTTCGCCT


title: Lib13_OUTPUT


title: Lib12_OUTPUT


title: Cardiac Organoid, D6_600um

description:
Library name: D6_600um
10X Genomics Chromium v3.1

value: Cardiac Organoid


title: Cardiac Organoid, D1_600um

description:
Library name: D1_600um
10X Genomics Chromium v3.1


title: UOK109 cells, SFPQ::TFE3 rescue, H3K27Ac, Rep3

value: TAAGATTA


title: Cardiac Organoid, D4_200um

description:
Library name: D4_200um
10X Genomics Chromium v3.1


title: BMC, WT1

value: bone marrow cells

value: WT

value: 8 weeks old


title: UOK109 cells, SFPQ::TFE3 rescue, H3K27Ac, Rep1

value: UOK109 cells

value: ATTCAGAA

value: TCAGAGCC


title: HUDEP-2 cells, WT2

first: Xiuqin

last: Bao

address: No. 1838, Guangzhou avenue north, baiyun district, Guangzhou

institute: Southern Medical University

data_processing:
Sequenced reads were aligned to the UCSC hg19 (human) genome with HISAT2
The expression level of transcript or isoform was calculates using StringTie
Differential expression genes (DEGs) analysis was performed using DESeq2
Assembly: hg19
Supplementary files format and content: xls files include counts values for each Sample ...

source_name: BLOOD

extract_protocol:
HUDEP-2 cells were harvested and total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: BLOOD

value: Human umbilical cord blood-derived erythroid progenitor

value: differentiatioon


title: UOK109 cells, SFPQdeltaCCD::TFE3 rescue, H3K27Ac, Rep3

value: Patient-derived cells harboring NONO::TFE3 fusion

value: SFPQdeltaCCD::TFE3 rescue

value: baseline culturing conditions

value: GAATTCGT

value: AGGCTATA


title: HSSYII_MS67_WDR5_CR

city: Durham

first: Yao

state: North Carolina

address: Medical Science Res Bldg III, 3 Genome Court

institute: Duke University

description: Library name: HSSYII_MS67_WDR5_CR

data_processing:
Fastq files were mapped to the reference genome (hg38 and mm10) using bowtie2.3.5.
The non-primary alignment, PCR duplicates, or blacklist regions were removed from the aligned data by using Samtools (v1.9), Picard ‘MarkDuplicates’ function (v2.20.4), and bedtools (v2.28.0), respectively.
Peak calling was performed using MACS2 (macs2 callpeak -f BAMPE -g hs/mm –keep-dup 1).
Deeptools (v3.3.0) was used to generate bigwig files, heatmaps and averaged plotting of signals.
Assembly: hg38
Supplementary files format and content: bigWig
Supplementary files format and content: peak files
Library strategy: CUT&Run

source_name: Synovial Sarcoma

growth_protocol: The HSSY II human SS cells were freshly grown in the high-glucose DMEM base medium supplemented with 10% of FBS and 1% of antibiotics.

extract_protocol:
In brief, one million of HSSY II cells were used, and all sample groups were added with 50,000 of NIH-3T3 cells (wild type or stably trasduced with H2B-GFP)as the spike-in normalization control, was collected, washed and bound to ConA beads. Cell:bead sample was incubated with indicated antibodies overnight and then washed and treated with pAG-MNase, followed by adding 2mM of CaCl2 to activate pAG-MNase. Solubilized chromatin was then released using the CUT&RUN stop buffer.
DNA purification was carried out with the PCR cleanup kit (NEB, Monarch PCR & DNA Cleanup Kit, #T1030) followed by the PCR-based amplification using i5/i7 primers.
Libraries were prepared by NEBNext Ultra II kit (NEB, #E7645L) with 10ng CUT&RUN DNA as input.

treatment_protocol: Cells were treated with 2.5 uM of DMSO or MS67 for four days before collection.

value: Synovial Sarcoma

value: HSSY II

value: Treated with 2.5 uM of MS67 for 4 days


title: Lib11_OUTPUT

value: pool of EZ-Tn5 transposase mutants

value: enriched intracellular bacteria


title: HUDEP-2 cells, WT1

value: WT


title: UOK109 cells, NONOdeltaCCD::TFE3 rescue, H3K27Ac, Rep2

value: UOK109 cells

value: NONOdeltaCCD::TFE3 rescue

value: H3K27Ac antibody (39034, Active Motif)

value: GCCTCTAT


title: HUDEP-2 cells, BD1

value: BLOOD

value: Human umbilical cord blood-derived erythroid progenitor

value: insA


title: HSSYII_DMSO_WDR5_CR

description: Library name: HSSYII_DMSO_WDR5_CR

value: Treated with DMSO for 4 days as controls


title: UOK109 cells, NONOdeltaCCD::TFE3 rescue, H3K27Ac, Rep3

value: Patient-derived cells harboring NONO::TFE3 fusion

value: baseline culturing conditions

value: ATTCAGAA

value: AGGATAGG


title: BMC, WT2

value: bone marrow cells

value: 8 weeks old


title: HUDEP-2 cells, WT3

value: differentiatioon


title: Lib9_OUTPUT

value: pool of EZ-Tn5 transposase mutants

value: enriched intracellular bacteria


title: UOK109 cells, NONOdeltaCCD::TFE3 rescue, H3K27Ac, Rep1

value: UOK109 cells

value: AGGCTATA


title: Lib8_OUTPUT


title: HUDEP-2 cells, 4-18


title: UOK109 cells, NONO::TFE3 rescue, H3K27Ac, Rep3

value: NONO::TFE3 rescue

value: H3K27Ac antibody (39034, Active Motif)

value: GAGATTCC

value: GTCAGTAC


title: HUDEP-2 cells, 4-17

value: BLOOD

value: Human umbilical cord blood-derived erythroid progenitor

value: insA


title: UOK109 cells, NONO::TFE3 rescue, H3K27Ac, Rep2

value: Patient-derived cells harboring NONO::TFE3 fusion

value: baseline culturing conditions

value: ACGTCCTG


title: Cardiac Organoid, D0_600um

description:
Library name: D0_600um
10X Genomics Chromium v3.1

value: Cardiac Organoid

value: hiPSC

value: WTC


title: SA19897

city: Los Angeles

first: Alice

last: Mouton

state: CA

address: 610 Charles E. Young Dr. East

department: Ecology and Evolutionary Biology

institute: UCLA

description:
Library name: s26
150 bp

data_processing:
Raw sequences were processed using Trim Galore! 0.3.1 (https://github.com/FelixKrueger/TrimGalore) to remove Illumina adapters and sequences that did not meet the following quality thresholds: Q > 20, length > 25).
The alignment of the trimmed reads was performed on STAR 2.5.3 (Dobin et al. 2013) using the dog genome (Canis lupus familiaris: Ensembl release 95_31). We used HtSeq for read counts.
First, we checked for biological replicates and outliers. We filtered reads with low counts and remaining genes were normalized using TMM (trimmed mean of M-values) in the edgeR package (Robinson and Oshlack 2010) in R. Reads were then converted into log2 counts per million (logCPM) with voom in LIMMA (Law et al. 2014; Ritchie et al. 2015). We performed principal components analyses to identify technical factors from the dataset (Blighe and Lun 2020). We removed the batch effects using the removebatch command in LIMMA for visualization purposes. We explored the data to check for outliers and clustering of biological replicates using hierarchical clustering of the gene expression adjacency matrix with the R package WGCNA (Langfelder and Horvath 2008). After controlling for biological replicates and outliers, we checked for tissue-type heterogeneity on the samples using a web-based tool named SaVant (http://newpathways.mcdb.ucla.edu/savant-dev/) (Lopez et al. 2017)
RNAseq reads on 17 samples were filtered and processed as explained above. LIMMA (Law et al. 2016) and Deseq2 (Love et al. 2014) were used for our differential gene expressions analyses. Genes falling below FDR<0.05 in both methods were kept for Gene Ontology analyses in g:Profiler (Reimand et al. 2016). To ensure that the distribution of the false discovery rate satisfied the expectation for FDR under a null model, we ran 100 permutations of the original model where the significant variable was assigned randomly and compared the distribution of p-values under the null to the distribution of p-values under the true model.
Assembly: Canis lupus familiaris: Ensembl release 95_31
Supplementary files format and content: tab delimited txt including the raw counts for the individual after Htseq-counts
Supplementary files format and content: tab delimited txt including normalized counts corrected for batch effect after filtration

organism: Canis lupus familiaris

source_name: Olfactory epithelium

extract_protocol:
Total RNA was extracted from the epithelium tissues using the Invitrogen TRIzol® Plus RNA Purification Kit. Four samples were extracted in two separate batches.
cDNA libraries were constructed using the KAPA mRNA HyperPrep Kit with dual indices (Kapa Biosystems, Ltd). Individual libraries were then pooled in equimolar ratios and sequenced on two lanes of an Illumina Hiseq4000 (150bp paired-end). Sequencing was performed at Fulgent genetic (https://www.fulgentgenetics.com/).

value: Olfactory epithelium

tag: breed

tag: weight kg

tag: scent

tag: weight

tag: rin


title: HSSYII_MS67_SS18-SSX_CR

description: Library name: HSSYII_MS67_SS18-SSX_CR

value: Synovial Sarcoma

value: HSSY II

value: Treated with 2.5 uM of MS67 for 4 days


title: UOK109 cells, NONO::TFE3 rescue, H3K27Ac, Rep1

value: UOK109 cells

value: NONO::TFE3 rescue

tag: cut&run antibody

tag: i7 index_name*

tag: i7 index_sequence*

value: TAAGATTA


title: HSSYII_DMSO_SS18-SSX_CR

description: Library name: HSSYII_DMSO_SS18-SSX_CR

value: Treated with DMSO for 4 days as controls


title: Lib7_OUTPUT

tag: strain

value: pool of EZ-Tn5 transposase mutants

value: enriched intracellular bacteria


title: HSSYII_MS67N1_H2AK119ub1

description: Library name: HSSYII_MS67N1_H2AK119ub1

data_processing:
Fastq files were mapped to the reference genome (hg38 and mm10) using bowtie2.3.5.
The non-primary alignment, PCR duplicates, or blacklist regions were removed from the aligned data by using Samtools (v1.9), Picard ‘MarkDuplicates’ function (v2.20.4), and bedtools (v2.28.0), respectively.
Peak calling was performed using MACS2 (macs2 callpeak -f BAMPE -g hs/mm –keep-dup 1).
Deeptools (v3.3.0) was used to generate bigwig files, heatmaps and averaged plotting of signals.
Assembly: hg38
Supplementary files format and content: bigWig
Supplementary files format and content: peak files
Library strategy: CUT&Tag

growth_protocol: The human cancer cell lines (HSSY II, SYO1 and U2-OS) were grown in the high-glucose DMEM base medium supplemented with 10% of FBS and 1% of antibiotics.

extract_protocol:
CUT&Tag was performed with a commercial kit (EpiCypher CUTANA pAG-Tn5) based on the vendor’s specification. In brief, 100,000 of human cancer cells were used, and all sample groups were added with 5,000 of NIH-3T3 cells(wild type or stably trasduced with H2B-GFP) as the spike-in normalization control, followed by CUT&Tag using antibodies of either WDR5, H3K4me2, H3K4me3, SS18-SSX, H2AK119ub1 or BAF155, the library preparation and deep sequencing (using an Illumina NextSeq 500 machine).
DNA purification was carried out with the PCR cleanup kit (NEB, Monarch PCR & DNA Cleanup Kit, #T1030) followed by the PCR-based amplification using i5/i7 primers.

treatment_protocol: Parental cancer cells were treated with 2.5 uM of DMSO or MS67 (or with 2.5 uM of MS67N1 or MS67N2 in certain experiment) for four days before collection. Alternatively, cells were stably transduced with a previously reported shRNA targeting SSX (shSSX) or a scramble control (shSCR).

tag: tissue

value: Treated with 2.5 uM of MS67N1 for 4 days


title: SA19895

description:
Library name: s24
150 bp

tag: batch


title: Lib5_OUTPUT


title: UOK109 cells, NONO::TFE3-KO, H3K27Ac, Rep3

tag: cell type

value: Patient-derived cells harboring NONO::TFE3 fusion

value: NONO::TFE3 KO

value: H3K27Ac antibody (39034, Active Motif)

value: GAGATTCC

tag: i5 index_name*

tag: i5 index_sequence*

value: CTTCGCCT


title: Lib10_OUTPUT

tag: genotype

tag: treatment


title: SA19894

description:
Library name: s23
150 bp

value: Poodle

tag: age


title: HSSYII_MS67_H2AK119ub1

description: Library name: HSSYII_MS67_H2AK119ub1

tag: cell line


title: HSSYII_DMSO_H2AK119ub1

description: Library name: HSSYII_DMSO_H2AK119ub1


title: UOK109 cells, NONO::TFE3-KO, H3K27Ac, Rep1

value: baseline culturing conditions

value: AGGATAGG


title: Lib3_OUTPUT


title: SA19893

description:
Library name: s22
150 bp

value: Olfactory epithelium

tag: breed

tag: weight kg


title: HSSYII_MS67N2_H2AK119ub1

description: Library name: HSSYII_MS67N2_H2AK119ub1

value: Synovial Sarcoma

value: HSSY II

value: Treated with 2.5 uM of MS67N2 for 4 days


title: Lib2_OUTPUT


title: Lib6_OUTPUT


title: SA19889

description:
Library name: S18_rep1
150 bp

tag: scent

tag: weight


title: HSSYII_shSCR_WDR5

description: Library name: HSSYII_shSCR_WDR5

value: stably transduced with shScr, as negative Ctrl


title: UOK109 cells, NONO::TFE3-KO, Rabbit IgG CUT&RUN Negative Control Antibody

value: UOK109 cells

tag: cut&run antibody

value: CUTANA™ Rabbit IgG CUT&RUN Negative Control Antibody (13-0042k, EpiCypher)

value: AGGCTATA


title: UOK109 cells, TFE3 rescue, FLAG, Rep3

value: TFE3 rescue

value: FLAG antibody (CST 14793, Cell Signaling)

tag: i7 index_name*

value: CGCTCATT


title: HSSYII_shSSX_SS18-SSX

description: Library name: HSSYII_shSSX_SS18-SSX

value: stably transduced with shSS18-SSX


title: SA19887

description:
Library name: s16
150 bp

tag: rin


title: SA19885

description:
Library name: s14
150 bp

value: Dachshund


title: Lib42_INPUT

tag: strain

value: pool of EZ-Tn5 transposase mutants

value: enriched input


title: Lib43_INPUT


title: SA19892

description:
Library name: s21
150 bp

tag: tissue


title: UOK109 cells, TFE3 rescue, FLAG, Rep1

value: Patient-derived cells harboring NONO::TFE3 fusion

value: baseline culturing conditions

tag: i7 index_sequence*


title: UOK109 cells, TFE3 rescue, FLAG, Rep2

tag: cell type

value: TCAGAGCC


title: HSSYII_shSCR_SS18-SSX

description: Library name: HSSYII_shSCR_SS18-SSX

value: Synovial Sarcoma


title: HSSYII_shWdr5_RNA_R2

description: Library name: RNAseq28

data_processing:
For samples added with spike-in controls, the fastq files were mapped to both main reference genome and spike-in genome using STAR (v.2.7.11a). Then non-primary alignment and PCR duplicates alignments were removed respectively by Samtools (v.1.10) (-F 256) and Picard ‘MarkDuplicates’ function (v.2.18.2). The scale factor used for normalization was calculated by comparing the total number of spike-in alignment reads among different groups.
For differential gene expression, the raw read counts were used and followed by DESeq analysis.
Assembly: hg38
Supplementary files format and content: Log2 fold change of gene expression using Deseq analysis and filtered by q-val<0.05 and fold change>1.5

growth_protocol: HSSY II and SYO1 synovial sarcoma (SS) cells were grown in DMEM high glucose medium plus 10% of FBS and 1% of antibiotics.

extract_protocol:
RNA was prepared by using Qiagen RNeasy Mini Kit. 1 ug of total RNA for the construction of the pooled sequencing libraries.
Equal amount of ERCC RNA Spike-In Mix (Thermo, 4456740) was added into all samples as spike-in control before library preparation. NEBNext Ultra II RNA library Prep kit (NEB, #E7770) was used for library preparation.

treatment_protocol: Parental HSSY-II cells were stably transduced with a previously reported WDR5-targeting shRNA or a control (shScr). HSSY-II and SYO-1 cells were subject to a two-day or four-day treatment of either DMSO or 2.5 uM of MS67 or its non-PROTAC analogue (2.5 uM of MS67N1 or MS67N2).

value: HSSY II

value: stably transduced with WDR5-targeting shRNA


title: SA19882

description:
Library name: s11
150 bp

value: Olfactory epithelium

tag: batch


title: Lib4_OUTPUT

value: enriched intracellular bacteria


title: UOK109 cells, NONO::TFE3-KO, H3K27Ac, Rep2

value: UOK109 cells

value: NONO::TFE3 KO

value: H3K27Ac antibody (39034, Active Motif)

value: GAGATTCC

tag: i5 index_name*

tag: i5 index_sequence*


title: SA19881

description:
Library name: S10_rep1
150 bp

value: Beagle


title: HSSYII_shWdr5_RNA_R1

description: Library name: RNAseq27

tag: treatment


title: UOK109 cells, NONOmut::TFE3 rescue, FLAG, Rep3

tag: genotype

value: NONOmut::TFE3 rescue

value: FLAG antibody (CST 14793, Cell Signaling)

value: CGCTCATT

value: GCCTCTAT


title: UOK109 cells, NONOmut::TFE3 rescue, FLAG, Rep2

tag: cell line

value: Patient-derived cells harboring NONO::TFE3 fusion

value: AGGCTATA


title: HSSYII_shSSX_WDR5

description: Library name: HSSYII_shSSX_WDR5

value: stably transduced with shSS18-SSX


title: HSSYII_shScr_RNA_R2

description: Library name: RNAseq26

value: Synovial Sarcoma

value: stably transduced with scramble controls


title: SA19880

description:
Library name: S9
150 bp

tag: breed

tag: age


title: Lib1_OUTPUT

value: pool of EZ-Tn5 transposase mutants


title: Lib39_INPUT

value: enriched input


title: SA19879

description:
Library name: S8
150 bp

value: Olfactory epithelium

tag: weight kg

tag: scent


title: HSSYII_shScr_RNA_R1

description: Library name: RNAseq25

value: HSSY II


title: Lib38_INPUT


title: Brain, glioblastoma, rep6 (RNA-seq)

city: Debrecen

first: Zsuzsanna

last: Birkó

address: Egyetem tér 1.

department: Humangenetics

country: Hungary

institute: University of Debrecen

description:
Library name: Sample_10
G_rep6

data_processing:
Evaluation of mRNA expression data was perfomed by the iDEP.96 tool (http://bioinformatics.sdstate.edu/idep96;  In the preprocessing step mRNAs with low or missing expression values were filtered out (≥ CPM 1 in all libraries). Bioinformatics analysis included hierarchical clustering with heatmap, unconditional k-means clustering, PCA and MA plots applying the iDEP.96 web tool, as well. For differential expression analysis, the DESeq2 package of iDEP was used. Significantly deregulated miRNAs were identified after adjusting the cutoff values for fold change (FC) ≥ 2 and the false discovery rate (FDR) ≤ 0.05).
Assembly: Raw sequencing data (fastq) was aligned to human reference genome version GRCh38 using HISAT2 algorithm and BAM files were generated. Downstream analysis was performed using StrandNGS software (www.strand-ngs.com). BAM files were imported into the software, DESeq algorithm of the StrandNGS was used for normalization.
Supplementary files format and content: Processed data files are present in txt format containig information about normaized data of 6 control and glioblastoma patients.

source_name: Brain

extract_protocol:
Tissue samples were dissected on ice then disrupted and homogenized by MagNa Lyser instrument (Roche Ltd., Switzerland) for purification of total RNA (including small RNAs) using the miRNeasy Mini Kit (Qiagen, Hilden, Germany). Each step was performed according to the manufacturer's instructions. The amount of the tissue sample was 30 mg in each case. The quality of isolated RNA was analyzed by Nanodrop spectrophotometer (Thermo Scientific, Waltham, MA, USA).
The NEBNext® rRNA Depletion Kit (Human/Mouse/Rat) (New England BioLabs ) was used to remove rRNA species from total RNA . Then RNA-Seq libraries were generated from rRNA depleted samples using Ultra II RNA Sample Prep kit (New England BioLabs) according to the manufacturer’s protocol. Briefly, first strand cDNA was generated by random priming reverse transcription reaction, followed by second strand synthesis step and double stranded cDNA was generated. After repairing ends, A-tailing and adapter ligation steps adapter ligated fragments were amplified in enrichment PCR and finally sequencing libraries were generated. Sequencing run were executed on Illumina NextSeq 500 instrument using single-end 75 cycles sequencing.

value: Brain


title: UOK109 cells, SFPQdeltaCCD::TFE3 rescue, FLAG, Rep3

value: UOK109 cells

value: SFPQdeltaCCD::TFE3 rescue

value: baseline culturing conditions

tag: cut&run antibody

value: TCCGGAGA

value: ACGTCCTG


title: SA19878

description:
Library name: S7
150 bp

tag: weight


title: Lib37_INPUT


title: Lib36_INPUT


title: Lib41_INPUT


title: UOK109 cells, SFPQdeltaCCD::TFE3 rescue, FLAG, Rep1

value: FLAG antibody (CST 14793, Cell Signaling)

tag: i7 index_name*

value: CTTCGCCT


title: Brain, glioblastoma, rep3 (RNA-seq)

description:
Library name: Sample_8
G_rep3


title: SA19876

description:
Library name: S5
150 bp

tag: rin


title: SA19877

description:
Library name: S6_rep1
150 bp

tag: tissue


title: SA19875

description:
Library name: S4
150 bp

value: Pomeranian


title: Brain, glioblastoma, rep2 (RNA-seq)

description:
Library name: Sample_7
G_rep2


title: UOK109 cells, SFPQdeltaCCD::TFE3 rescue, FLAG, Rep2

value: Patient-derived cells harboring NONO::TFE3 fusion

tag: i7 index_sequence*

value: TAAGATTA


title: Brain, glioblastoma, rep4 (RNA-seq)

description:
Library name: Sample_9
G_rep4


title: Lib35_INPUT

tag: strain


title: UOK109 cells, SFPQ::TFE3 rescue, FLAG, Rep2

tag: cell type

value: SFPQ::TFE3 rescue

value: AGGATAGG


title: Lib40_INPUT

value: pool of EZ-Tn5 transposase mutants


title: UOK109 cells, SFPQ::TFE3 rescue, FLAG, Rep3

tag: i5 index_name*

value: TCAGAGCC


title: Brain, glioblastoma, rep1 (RNA-seq)

description:
Library name: Sample_6
G_rep1


title: Lib34_INPUT

value: enriched input


title: Lib33_INPUT


title: Brain, control, rep5 (RNA-seq)

description:
Library name: Sample_5
C_rep5


title: UOK109 cells, SFPQ::TFE3 rescue, FLAG, Rep1

tag: i5 index_sequence*

value: GCCTCTAT


title: Aged_sec

city: Jinan

first: Jing

last: Zhou

state: (optional)

address: #44 Wenhua Xi Road

institute: Shandong University

data_processing:
Single-stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single-stranded cyclized products are produced, while uncyclized linear DNA molecules are digested.
Single-stranded circle DNA molecules are replicated via rolling cycle amplification, and a DNA nanoball (DNB) which contain multiple copies of DNA is generated. Sufficient quality DNBs are then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS).
Assembly: combinatorial Probe-Anchor Synthesis (cPAS)
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes TPM values for each  Sample

source_name: Ovary

growth_protocol: GV-stage oocytes were collected by manual rupturing of antral ovarian follicles after 46–48 h with pipetting. The GV stage oocytes were incubated in M16 medium under 5% CO2, 5% O2, and 90% N2 at 37 °C for 16-18 h to obtain MⅡ stage oocytes.

extract_protocol:
1 Cell Lysis Delivered single-cell samples, which are stored in cell lysis buffer, are processed to cell lysis by PCR instrument.  2 cDNA Synthesis The reaction system is configured for reverse transcription. First-strand cDNA is synthesized with SMART-SeqII. The reaction system is configured for PCR amplification to process preamplification of cDNAs. 3 cDNA QC The corresponding quality control protocol will be selected for quality tests of the cDNAs.
1. Library Construction Qualified amplified cDNAs use transposon-based method for further library construction.  2. Library QC The corresponding library quality control protocol will be selected depending upon product requirements.

treatment_protocol: Oocytes were cultured in M16 medium with or without hUC-MSC-sec (1:1) and covered with mineral oil.

value: Ovary

value: ICR

value: Oocyte

value: MII stage

tag: treatment

value: hUC-MSC-sec


title: UOK109 cells, NONOmut::TFE3 rescue, FLAG, Rep1

value: UOK109 cells

tag: genotype

value: NONOmut::TFE3 rescue

value: baseline culturing conditions

value: TCCGGAGA

value: GTCAGTAC


title: Lib32_INPUT


title: Lib31_INPUT


title: Brain, control, rep4 (RNA-seq)

description:
Library name: Sample_4
C_rep4

value: Brain


title: UOK109 cells, NONOdeltaCCD::TFE3 rescue, FLAG, Rep2

tag: cell line

value: Patient-derived cells harboring NONO::TFE3 fusion

value: NONOdeltaCCD::TFE3 rescue

value: FLAG antibody (CST 14793, Cell Signaling)

value: ATTACTCG


title: Brain, control, rep3 (RNA-seq)

description:
Library name: Sample_3
c_rep3


title: UOK109 cells, NONOdeltaCCD::TFE3 rescue, FLAG, Rep3

value: AGGCTATA


title: Lib30_INPUT

value: pool of EZ-Tn5 transposase mutants

value: enriched input


title: Brain, control, rep2 (RNA-seq)

description:
Library name: Sample_2
C_rep2


title: Brain, control, rep1 (RNA-seq)

description:
Library name: Sample_1
C_rep1


title: UOK109 cells, NONOdeltaCCD::TFE3 rescue, FLAG, Rep1

value: ACGTCCTG


title: Lib29_INPUT


title: Young

value: Ovary

value: ICR

value: Oocyte


title: U2OS_parental_SS18-SSX

data_processing:
Fastq files were mapped to the reference genome (hg38) using bowtie2.3.5.
The non-primary alignment, PCR duplicates, or blacklist regions were removed from the aligned data by using Samtools (v1.9), Picard ‘MarkDuplicates’ function (v2.20.4), and bedtools (v2.28.0), respectively.
Peak calling was performed using MACS2 (macs2 callpeak -f BAMPE -g hs/mm –keep-dup 1).
Deeptools (v3.3.0) was used to generate bigwig files, heatmaps and averaged plotting of signals.
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

source_name: Osteosarcoma

growth_protocol: The human cancer cell lines (HSSY II, SYO1 and U2-OS) were grown in the high-glucose DMEM based medium supplemented with 10% of FBS and 1% of antibiotics.

extract_protocol:
CUT&Tag was performed with a commercial kit (EpiCypher CUTANA pAG-Tn5) based on the vendor’s specification. In brief, 100,000 of human cancer cells were used, and all sample groups were added with 5,000 of NIH-3T3 cells as the spike-in normalization control, followed by CUT&Tag using antibodies of either WDR5, H3K4me2, H3K4me3, SS18-SSX or BAF155, the library preparation and deep sequencing (using an Illumina NextSeq 500 machine).
DNA purification was carried out with the PCR cleanup kit (NEB, Monarch PCR & DNA Cleanup Kit, #T1030) followed by the PCR-based amplification using i5/i7 primers.

value: Osteosarcoma

value: parental


title: BMPC_IgG_P2_tom+_4

city: Erlangen

first: Hans-Martin

last: Jäck

address: Glückstrasse 6

department: Molecular Immunology

institute: Universitätsklinikum Erlangen

data_processing:
Removal of low-quality reads and adapter-trimming with TrimGalore (v0.6.6).
Mapping of reads to genome reference with STAR (v2.6.1d)
Quantification of aligned reads with Salmon (v1.4.0) and gene-level summarization
Assembly: GRCm38
Supplementary files format and content: Combined table with summarized gene-wise counts for each sample

source_name: bone marrow

extract_protocol:
Splenic plasma cells were FACS-purified (CD138+ TACI+) and sorted directly into beta-mercaptoethanol-containing RLT (Qiagen) Lysis buffer. Total RNA was isolated with the RNeasy Micro Kit (Qiagen).
Sequencing libraries were constructed with the Takara Clontech Smart-Seq v4 Plus kit according to manufacturers instructions and sequenced on Illumina Hiseq X instruments.

value: bone marrow

value: plasma cell (P2) CD138+ IgM- IgA- Blimp1-GFP+ CD19+ B220- BCMA:Tom+

value: immunization and boost s.c. (day70) with mRNA-1273 (Spikevax)


title: UOK109 cells, NONO::TFE3 rescue, FLAG, Rep2

city: Baltimore

value: UOK109 cells

value: NONO::TFE3 rescue

value: baseline culturing conditions

value: CTTCGCCT


title: UOK109 cells, NONO::TFE3 rescue, FLAG, Rep1

value: Patient-derived cells harboring NONO::TFE3 fusion

value: FLAG antibody (CST 14793, Cell Signaling)

value: ATTACTCG

value: TCAGAGCC


title: SYO1_parental_SS18-SSX2

value: Synovial Sarcoma


title: Lib28_INPUT

data_processing:
demultiplexed, filtered by transposon tag (up to 1 mismatch)
Adapter removal: BBDuk (BBMap v38.94)
Alignment/Quantification: Bio-TraDIS pipeline (v1.4.5) for each fastq file separately.
Assembly: CP037923.1, CP037924.1
Supplementary files format and content: shigella_infections_counts_neg_meta.csv.gz: count table with all non-zero insertion sites in the negative strand (summed over all fastq files), insertion sites are assigned to genes
Supplementary files format and content: shigella_infections_counts_pos_meta.csv.gz: count table with all non-zero insertion sites in the positive strand (summed over all fastq files), insertion sites are assigned to genes

extract_protocol:
gDNA isolation was performed using the GenElute Bacterial gDNA kit (Sigma; NA2110-1KT). 1.5ug of gDNA was cleaned with Ampure XP beads to remove EDTA. 500ng of cleaned gDNA was used as input for the sequencing library preprarations.
TraDIS library (Barquist et al., 2016 Bioinformatics)

value: pool of EZ-Tn5 transposase mutants

value: enriched input


title: Lib27_INPUT


title: BMPC_IgG_P2_tom-_4

value: plasma cell (P2) CD138+ IgM- IgA- Blimp1-GFP+ CD19+ B220- BCMA:Tom-


title: BMPC_IgG_P1_tom-_4

value: plasma cell (P1) CD138+ IgM- IgA- Blimp1-GFP+ CD19+ B220+ BCMA:Tom-


title: Lib26_INPUT


title: BMPC_IgG_P1_tom+_4

value: plasma cell (P1) CD138+ IgM- IgA- Blimp1-GFP+ CD19+ B220+ BCMA:Tom+


title: HSSYII_parental_SS18-SSX1

value: HSSYII

value: parental


title: BMPC_IgG_P2_tom+_3

value: bone marrow

value: plasma cell (P2) CD138+ IgM- IgA- Blimp1-GFP+ CD19+ B220- BCMA:Tom+

value: immunization and boost s.c. (day70) with mRNA-1273 (Spikevax)


title: UOK109 cells, NONO::TFE3-KO, FLAG, Rep3

value: UOK109 cells

value: NONO::TFE3 KO

value: baseline culturing conditions

value: AGGATAGG


title: Lib25_INPUT


title: Aged

value: Ovary

value: ICR

value: Oocyte

value: MII stage

value: hUC-MSC-sec


title: UOK109 cells, NONO::TFE3-KO, FLAG, Rep2

value: Patient-derived cells harboring NONO::TFE3 fusion

value: FLAG antibody (CST 14793, Cell Signaling)

value: ATTACTCG

value: GCCTCTAT


title: SA19873

description:
Library name: S2_rep1
150 bp

value: Olfactory epithelium

tag: breed

value: Dachsund

tag: batch


title: BMPC_IgG_P2_tom-_3

value: bone marrow

value: plasma cell (P2) CD138+ IgM- IgA- Blimp1-GFP+ CD19+ B220- BCMA:Tom-


title: SYO1_MS67_H3K4me3

value: Synovial Sarcoma

value: Treated with 2.5 uM of MS67 for 4 days


title: UOK109 cells, NONO::TFE3-KO, FLAG, Rep1

value: UOK109 cells

value: NONO::TFE3 KO

value: baseline culturing conditions

value: AGGCTATA


title: UOK109 cells, NONO::TFE3 rescue, FLAG, Rep3

value: NONO::TFE3 rescue

value: TAAGATTA


title: SYO1_DMSO_H3K4me3

value: Treated with DMSO for 4 days as controls


title: BMPC_IgG_P1_tom+_3

value: plasma cell (P1) CD138+ IgM- IgA- Blimp1-GFP+ CD19+ B220+ BCMA:Tom

value: immunization and boost s.c. (day70) with mRNA-1273 (Spikevax)


title: UOK109 cells, TFE3 rescue, Rep3

description: i7 Index Name: v2_Ad2.21_CGCGGACA

data_processing:
Initial steps involved trimming raw fastq files using fastp.
Subsequently, reads were aligned to the hg38 genome assembly using bowtie2 v2.5.2.
Duplicate reads in ATAC-seq data were removed using PICARD’s MarkDuplicates.
Bigwigs were generated using bedtools.
Peak calling was performed using MACS2.
Assembly: hg38
Supplementary files format and content: bigwig, narrowPeak

extract_protocol:
We used the Illumina Tagment DNA Enzyme and Buffer Kit (20034197, Illumina). We used 50,000 cells for each reaction. Upon transposition, we cleaned up the reaction using a Zymo DNA Clean and Concentrator-5 Kit (D4014, Zymo) according to the manufacturer’s protocol.
We amplified the eluted DNA using 2x NEBNext Q5 Hotstart HiFi PCR Master Mix (M0543L, NEB) for 11 cycles. We purified the amplified libraries using the Zymo DNA Clean and Concentrator-5 Kit.

value: Patient-derived cells harboring NONO::TFE3 fusion

value: TFE3 rescue


title: SYO1_MS67_H3K4me2


title: UOK109 cells, TFE3 rescue, Rep2

description: i7 Index Name: v2_Ad2.20_TTGACCCT


title: SYO1_DMSO_H3K4me2


title: Lib22_INPUT

value: pool of EZ-Tn5 transposase mutants

value: enriched input


title: UOK109 cells, TFE3 rescue, Rep1

description: i7 Index Name: v2_Ad2.19_TGGTCACA


title: Lib20_INPUT


title: UOK109 cells, NONOmut::TFE3 rescue, Rep3

description: i7 Index Name: v2_Ad2.18_TGGGTTTC

value: NONOmut::TFE3 rescue


title: Lib21_INPUT


title: SYO1_DMSO_WDR5


title: BMPC_IgG_P3_tom+_3

value: bone marrow

value: plasma cell (P3) CD138+ IgM- IgA- Blimp1-GFP+ CD19- B220- BCMA:Tom+


title: Lib19_INPUT


title: SYO1_MS67_WDR5

value: Synovial Sarcoma

value: Treated with 2.5 uM of MS67 for 4 days


title: BMPC_IgG_P3_tom-_3

value: plasma cell (P3) CD138+ IgM- IgA- Blimp1-GFP+ CD19- B220- BCMA:Tom-


title: UOK109 cells, NONOmut::TFE3 rescue, Rep2

description: i7 Index Name: v2_Ad2.17_GTGTGGTG

value: UOK109 cells

value: baseline culturing conditions


title: Lib24_INPUT


title: Lib18_INPUT


title: UOK109 cells, NONOmut::TFE3 rescue, Rep1

description: i7 Index Name: v2_Ad2.16_AGGTTGGG


title: BMPC_IgG_P3_tom+_2


title: HSSYII_DMSO_BAF155

value: HSSYII


title: Lib23_INPUT


title: UOK109 cells, SFPQΔCCD::TFE3 rescue, Rep3

description: i7 Index Name: v2_Ad2.15_TGCTGGGT

value: SFPQdeltaCCD::TFE3 rescue


title: HSSYII_MS67_SS18-SSX1


title: BMPC_IgG_P3_tom-_2


title: Lib17_INPUT


title: BMPC_IgG_P1_tom-_3

value: plasma cell (P1) CD138+ IgM- IgA- Blimp1-GFP+ CD19+ B220+ BCMA:Tom-


title: BMPC_IgG_P3_tom+_4


title: Lib16_INPUT


title: UOK109 cells, SFPQΔCCD::TFE3 rescue, Rep2

description: i7 Index Name: v2_Ad2.14_CCGTTTGT


title: Lib15_INPUT


title: BMPC_IgG_P3_tom-_4


title: BMPC_IgG_P3_tom+_1


title: HSSYII_MS67_H3K4me3


title: UOK109 cells, SFPQΔCCD::TFE3 rescue, Rep1

description: i7 Index Name: v2_Ad2.13_TGGATCTG


title: Lib14_INPUT


title: HSSYII_MS67_BAF155


title: BMPC_IgG_P3_tom-_1


title: Lib12_INPUT


title: UOK109 cells, SFPQ::TFE3 rescue, Rep3

description: i7 Index Name: v2_Ad2.12_GTAGAGGA

value: SFPQ::TFE3 rescue


title: UOK109 cells, SFPQ::TFE3 rescue, Rep2

description: i7 Index Name: v2_Ad2.11_AAGAGGCA


title: HSSYII_DMSO_H3K4me3

value: Treated with DMSO for 4 days as controls


title: gta-1_RNAi_rep3

city: Hangzhou

first: Xuanxuan

last: Guo

state: Zhejiang

address: No 600 Dunyu Road

institute: westlake university

data_processing:
Web-based RNA-Seq analysis platform of  WestLake University
Assembly: C.elegans WS274
Supplementary files format and content: text file inculdes raw counts for each sample
Supplementary files format and content: text file inculde RPKM values for each sample

organism: Caenorhabditis elegans

source_name: worm

extract_protocol:
RNA was harvested by TRIzol,1ug of total RNA was uesd for the construction of secquencing libraries.
RNA libraries for mRNA-seq were prepared using VAHTS Universal V8 RNA-seq Library Prep Kit following manfacturer's protocol.

value: worm

value: WT

value: gta-1 RNAi


title: gta-1_RNAi_rep2


title: Lib13_INPUT

first: Laura

address: Josef-Schneider-Straße 2/D15

institute: Helmholtz Institute for RNA-based Infection Research

value: pool of EZ-Tn5 transposase mutants

value: enriched input


title: UOK109 cells, SFPQ::TFE3 rescue, Rep1

description: i7 Index Name: v2_Ad2.10_CGAGGCTG

value: Patient-derived cells harboring NONO::TFE3 fusion


title: HSSYII_DMSO_H3K4me2

last: Yu


title: HSSYII_MS67_H3K4me2


title: UOK109 cells, NONOΔCCD::TFE3 rescue, Rep3

description: i7 Index Name: v2_Ad2.9_GCTACGCT

value: NONOdeltaCCD::TFE3 rescue


title: gta-1_RNAi_rep1


title: HSSYII_MS67_WDR5

value: Synovial Sarcoma


title: Lib11_INPUT

last: Jenniches


title: ech-4_RNAi_rep3

value: ech-4 RNAi


title: HSSYII_DMSO_SS18-SSX1


title: HSSYII_DMSO_WDR5


title: ech-4_RNAi_rep2


title: Lib9_INPUT


title: UOK109 cells, NONOΔCCD::TFE3 rescue, Rep1

description: i7 Index Name: v2_Ad2.7_CTCTCTAC


title: Lib7_INPUT


title: ech-4_RNAi_rep1


title: SYO1_MS67_D4_RNA_R2

data_processing:
For samples added with spike-in controls, the fastq files were mapped to both main reference genome and spike-in genome using STAR (v.2.7.11a). Then non-primary alignment and PCR duplicates alignments were removed respectively by Samtools (v.1.10) (-F 256) and Picard ‘MarkDuplicates’ function (v.2.18.2). The scale factor used for normalization was calculated by comparing the total number of spike-in alignment reads among different groups.
For differential gene expression, the raw read counts were used and followed by DESeq analysis.
Assembly: hg38
Supplementary files format and content: Log2 fold change of gene expression using Deseq analysis and filtered by q-val<0.05

growth_protocol: HSSY II and SYO1 synovial sarcoma cells were grown in DMEM high glucose medium plus 10% of FBS and 1% of antibiotics.

treatment_protocol: Cells were treated with 2.5 uM of DMSO or MS67 for two or four days before collection.

value: Treated by MS67 for 4 days


title: SYO1_MS67_D4_RNA_R1


title: SYO1_DMSO_D4_RNA_R1

value: Treated by DMSO for 4 days as controls


title: SYO1_DMSO_D4_RNA_R2

value: Treated by DMSO for4 days as controls


title: UOK109 cells, NONO::TFE3 rescue, Rep3

description: i7 Index Name: v2_Ad2.6_TAGGCATG

value: UOK109 cells

value: NONO::TFE3 rescue

value: baseline culturing conditions


title: cpt-1_RNAi_rep3

value: cpt-1 RNAi


title: SYO1_MS67N2_D2_RNA_R2

value: Treated by MS67N2 for 2 days


title: crtl2_RNAi_rep3

value: worm

value: control


title: UOK109 cells, NONOΔCCD::TFE3 rescue, Rep2

description: i7 Index Name: v2_Ad2.8_CAGAGAGG


title: Lib6_INPUT


title: cpt-1_RNAi_rep2

value: WT


title: Lib5_INPUT

value: pool of EZ-Tn5 transposase mutants


title: UOK109 cells, NONO::TFE3 rescue, Rep1

description: i7 Index Name: v2_Ad2.4_TCCTGAGC


title: UOK109 cells, NONO::TFE3-KO, Rep3

description: i7 Index Name: v2_Ad2.3_AGGCAGAA

value: NONO::TFE3 KO


title: UOK109 cells, NONO::TFE3 rescue, Rep2

description: i7 Index Name: v2_Ad2.5_GGACTCCT

value: Patient-derived cells harboring NONO::TFE3 fusion


title: Lib4_INPUT

value: enriched input


title: Lib10_INPUT


title: UOK109 cells, NONO::TFE3-KO, Rep2

description: i7 Index Name: v2_Ad2.2_CGTACTAG


title: cpt-1_RNAi_rep1


title: crtl2_RNAi_rep2


title: Lib3_INPUT


title: SYO1_MS67N1_D2_RNA_R2

value: Synovial Sarcoma

value: Treated by MS67N1 for 2 days


title: SYO1_MS67N2_D2_RNA_R1


title: Lib8_INPUT


title: SYO1_MS67N1_D2_RNA_R1


title: Lib1_INPUT


title: crtl2_RNAi_rep1