title: H3K4ME1_HSPC_STROKE_1

value: HSPC-enriched myeloid cells


title: H3K4ME1_HSPC_STROKE_2

status: Public on Jul 22 2024

type: SRA

city: Munich

first: Arthur

last: Liesz

address: Feodor-Lynen-Straße 17

department: Institute for Stroke and Dementia (ISD)

country: Germany

institute: LMU Hospital

library_source: genomic

data_processing:
*library strategy: CUT&tag
Libraries werepooled together andsequenced on anNovaseq 600 SP 300 flowcellusing paired-end sequencing(2*150).
CUT&Tag-seq datawas mapped using CUT&RUNTools 2.0
Differentially accessible peaks (3 groups - control, shared,stroke)wereidentified using csaw.8Motif enrichment analysis was performed usingmonaLisa.The plotting of the Cut&tagsignal at genomic features was performed using SeqPlots.
Assembly: mm10
Supplementary files format and content: bigwig

molecule: genomic DNA

organism: Mus musculus

source_name: bone marrow

extract_protocol:
Bone marrows (from femurs) were homogenized and filtered through 40 μm cell strainers to obtain single cell suspensions. BM monocytes(CD11b+Ly6C+Ly6G-)andthelineage-(CD3, CD4, CD8a, CD19,Ter119)and Ly6G)negative myeloid fraction of BM (HSPC-enriched population)weresorted using aFACS Aria II cell sorter (BD Biosciences, Inc.).
nuclei were extracted from 1·10^5 cells, washed twice and incubated with 10 μL of activated concanavalin A beads (ThermoFisher) for 10 min atRT. The beads were thenresuspended in cold antibody buffer containing primary antibodies(against H3K27ac, H3K4me1 or H3K4me3)and the mixture was incubated overnight at 4°C on anutator. Then, the beads were washed twice and resuspended in secondaryH+Lantibody(NovusBio)dilutedin 50 μL digitonin buffer, followed by incubation for 30 min atRTon a rotator. Samples were then incubated with 2.5 µL CUTANA pAG-Tn5 (EpiCypher) for 1 h at RT on a nutator. DNA was tagmented for 1 hat 37°C using tagmentation buffer and tagmented chromatin fragments were released for 1 h at 58°C. 13 ul of tagged DNA was used to prepare the library using NEBNext® High-Fidelity 2X PCR Master Mix(NEB)with CUT&Tag specific PCR cycling parameters. DNA was purified using AMPureXP Beads (Beckman Coulter). The quality of the CUT&Tag libraries was assessed using the Agilent 2100 Bioanalyzer System (Agilent).

treatment_protocol: Freshly isolated cells, as described below, from control mice and mice one month after experimental ischemic stroke

tag: tissue

value: bone marrow

tag: cell type

tag: disease state

value: stroke

tag: chip antibody

value: Histone H3K4me1 antibody (pAb), Active Motif, cat#39297


title: Tumor patient 7 (DDLPS_WD), scRNAseq

city: Paris

first: Fabien

last: Quinquis

address: 26 rue d'Ulm

country: France

institute: Institut Curie

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Alignment with cellranger (v3.0.0 to v6.0.0 according to sample), default options
Ambient RNA correction with SoupX v1.5.2
Doublet removal with DoubletFinder (v2.0.3), scDblFinder (v1.4.0) and scds (v1.6.0) in hybrid mode, default options, union of the three methods
Remove cells with more than 20% of reads mapping mitochondrial genes
Apply additional coverage based filters to remove low quality cells
Normalization and downstream analysis with Seurat v4.0.1
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text and MatrixMarket files containing raw counts generated by CellRanger and corresponding normalized counts generated by Seurat v3

molecule: total RNA

organism: Homo sapiens

extract_protocol:
Fresh tumor samples were cut in small pieces then dissociated 30 min at 37C in CO2-independent medium (Gibco) containing 150 mg/ml of Liberase TL (Roche) and DNase 1 (Sigma Aldrich). Dissociated cells were then filtered with a cell strainer and washed in PBS. Debris were removed by centrifugation (3,000 xg for 10 min at 4C), using the debris removal solution (Miltenyi Biotech). Cells were then resuspended in PBS, counted and adjusted at 10⁶ cells/ml. 6,000 cells were loaded on a 10X Chromium (10X Genomics) and libraries were prepared using a Single Cell 30 Reagent Kit (NextGem kit, 10X Genomics), according to the manufacturer’s protocol, targeting 3,000 recovered cells per cell type and sample. Libraries were sequenced on an Illumina NovaSeq 6000 sequencing platform.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

treatment_protocol:
NA
NA

tag: age at_diagnosis

tag: Sex

value: F

tag: location

value: retroperitoneum

tag: tumour size_(mm)

tag: tumour grade


title: Section_148-Sample_3

type: RNA

city: Albuquerque

first: Rajanikanth

last: Vadigepalli

state: PA

address: 1 University of New Mexico

country: USA

institute: University of New Mexico

description: RNA extracted from a single microdissected neuron

data_processing: Initial quality control included melt-curve analysis and removal of samples and genes with >30% failed reactions. Genes with >75% working reactions were used to generate a median expression level across all samples. Raw Ct values were normalized against this median expression level to obtain DCt values. DCt values were generated for each gene according to the following equation: DCt_gene = Ct_gene - (median sample Ct). The median across all samples within a gene was then used to calculate -DDCt from DCt values by use of the following equation: -DDCt_gene = -(DCt_gene - DCt_median_across_samples).

label: Evagreen

organism: Rattus norvegicus

source_name: Rat brainstem

label_protocol: The reverse transcriptase reaction was performed using SuperScript VILO Master Mix (Thermo Fisher Scientific, Waltham, MA). cDNA samples were processed for 22 cycles of specific target amplification of 96 genes using TaqMan PreAmp Master Mix as per the manufacturer’s protocol (Applied Biosystems, Foster City, CA, USA) followed by real-time PCR using Evagreen intercalated dye-based approach to detect the PCR-amplified product. Intron-spanning PCR primers were designed for every assay using Primer3 and BLAST. Real-time PCR reactions were performed using 96x96 BioMark Dynamic Arrays (Fluidigm, South San Francisco, CA, USA) of 81 samples and 173 genes enabling quantitative measurement of multiple mRNAs and samples under identical reaction conditions. Each run consisted of 30 amplification cycles (15 s at 95C, 5 s at 70C, 60 s at 60C). Two 96x96 BioMark Arrays were used to measure gene expression across all the 96 samples before QC. The same serial dilution sample set was included in each chip to verify reproducibility and test for technical variability. This 6-point dilution series also serves to detect any over-amplification that may lead to a bias in the data. Samples from each animal were run across the two chips to obtain data on 173 genes per sample. Each set of chip runs contained overlapping assays that served as technical replicates to evaluate chip-to-chip variability.

extract_protocol: Cell Lysates were directly processed for Reverse Transcription

tag: strain

value: Sprague Dawley

tag: age

value: 12 weeks

value: Male

tag: region

value: DMV

tag: connectivity

value: Non-FB

tag: position

value: Middle

tag: cluster

value: C

tag: side

value: Left


title: Section_148-Sample_1

value: E

value: Right


title: Tumor patient 7 (peritumoral_fat), scRNAseq

description: 10x Genomics


title: Tumor patient 10 (DDLPS_WD), scRNAseq

description: 10x Genomics


title: SKCO1, DMSO, 1

city: Boston

first: Amy

middle: E

last: Schade

state: MA

address: 77 Avenue Louis Pasteur

department: Medicine

institute: Brigham and Women's Hospital

description:
SK-CO1 cell line treated with DMSO, replicate 1
SKCO1_gene_count.xlsx
SKCO1_DMSO_1

library_source: transcriptomic

data_processing:
Raw reads were processed through fastp. Reads were aligned using Hisat2 v2.0.5. Data were then further processed using DESeq2.
Assembly: hg38
Supplementary files format and content: DESeq2 normalized counts are uploaded and processed using DESeq2 with count files as input.

molecule: polyA RNA

growth_protocol: Cells were cultured in growth medium supplemented with 10% FBS and 1% glutamine, and grown at 37 degree incubators with 5% CO2.

extract_protocol:
Total RNA was isolated after 16-24 hours of vehicle, single agent, or combination treatment using the RNeasy Plus Mini kit (Qiagen, #74136). Cells were scraped and collected in RLT plus buffer, homogenized using Qiagen QIAshredder, and gDNA was removed with gDNA eliminator columns.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads.  After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library.  After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library.

treatment_protocol: Cells were treated with the indicated agents for 16-24 hours before RNA collection. Cells were pretreated with DMSO or EZH2i (tazemetostat at 5uM) for 5 days, and then seeded into 6cm plates of 300,000 to 350,000 cells per plate. The following day, cells were treated with DMSO, MEKi (trametinib) or KRASi (MRTX1133) for LS513 cells, with and without EZH2i.

tag: cell line

value: Colorectal cancer

tag: treatment

value: DMSO


title: Tumor patient 7 (DDLPS_DD), scRNAseq

description: 10x Genomics

tag: tissue


title: Section_146-Sample_8

value: A


title: SW620, COMBO, 3

description:
SW620 cell line treated with a combination of trametinib and tazemetostat for 24 hours, with siControl, replicate 3
SW620_STAR_Gene_Counts.xlsx
SW620_COMBO_3

tag: cell type

value: COMBO


title: H3K4ME3_HSPC_STROKE_1

value: bone marrow

value: HSPC-enriched myeloid cells

tag: disease state

value: stroke

tag: chip antibody

value: Histone H3K4me3 antibody (pAb), ThermoFisher, cat#PA5-27029


title: Section_146-Sample_7

value: Sprague Dawley

value: 12 weeks

tag: Sex

value: FB


title: SW620, COMBO, 2

description:
SW620 cell line treated with a combination of trametinib and tazemetostat for 24 hours, with siControl, replicate 2
SW620_STAR_Gene_Counts.xlsx
SW620_COMBO_2


title: Tumor patient 6 (peritumoral_fat), scRNAseq

description: 10x Genomics

tag: age at_diagnosis

value: M

tag: location

value: retroperitoneum


title: SKCO1, DMSO, 2

description:
SK-CO1 cell line treated with DMSO, replicate 2
SKCO1_gene_count.xlsx
SKCO1_DMSO_2


title: Tumor patient 5 (WDLPS), scRNAseq

description: 10x Genomics

source_name: WDLPS

value: WDLPS

value: F

tag: tumour size_(mm)

tag: tumour grade


title: SKCO1, MEKi, 1

description:
SK-CO1 cell line treated with 2.5 nM trametinib (MEKi) after 16 hours, replicate 1
SKCO1_gene_count.xlsx
SKCO1_TRAM_1

value: MEKi


title: H3K4ME3_HSPC_STROKE_2


title: H3K4ME1_MONOCYTES_STROKE_1

value: monocytes

value: Histone H3K4me1 antibody (pAb), Active Motif, cat#39297


title: Section_146-Sample_6

tag: strain

tag: age

value: Male

value: Non-FB

value: Middle

value: B

value: Right


title: Tumor patient 6 (DDLPS_WD), scRNAseq

description: 10x Genomics


title: Section_148-Sample_2

tag: region

value: DMV

tag: connectivity

value: D


title: Section_146-Sample_5

value: Sprague Dawley

tag: position

tag: cluster


title: H3K4ME3_MONOCYTES_STROKE_2

value: bone marrow

value: stroke

value: Histone H3K4me3 antibody (pAb), ThermoFisher, cat#PA5-27029


title: SW620, COMBO, 1

description:
SW620 cell line treated with a combination of trametinib and tazemetostat for 24 hours,with siControl,  replicate 1
SW620_STAR_Gene_Counts.xlsx
SW620_COMBO_1

tag: cell line

value: Colorectal cancer

value: COMBO


title: H3K4ME3_MONOCYTES_STROKE_1


title: Section_146-Sample_3

value: 12 weeks

tag: side

value: Left


title: Tumor patient 4 (DDLPS_WD), scRNAseq

description: 10x Genomics

tag: tissue

value: M

value: spermatic cordon


title: Section_146-Sample_2

value: Male


title: SW620, EZH2i, 1

description:
SW620 cell line treated with 5 uM tazemetostat (EZH2i), with siControl, replicate 1
SW620_STAR_Gene_Counts.xlsx
SW620_EPZ_1

tag: cell type

tag: treatment


title: H3K27AC_HSPC_STROKE_2

value: HSPC-enriched myeloid cells

tag: disease state

tag: chip antibody

value: Histone H3K27ac antibody (pAb), ActiveMotif, cat#39134


title: Tumor patient 3 (WDLPS), scRNAseq

description: 10x Genomics

value: WDLPS

tag: age at_diagnosis

tag: Sex

value: retroperitoneum


title: H3K27AC_MONOCYTES_STROKE_2

value: monocytes


title: H3K27AC_MONOCYTES_STROKE_1


title: Section_139-Sample_9

value: FB

value: Middle

value: B


title: SW620, EZH2i, 2

description:
SW620 cell line treated with 5 uM tazemetostat (EZH2i), with siControl, replicate 2
SW620_STAR_Gene_Counts.xlsx
SW620_EPZ_2


title: Tumor patient 3 (peritumoral_fat), scRNAseq

description: 10x Genomics

tag: location

tag: tumour size_(mm)


title: SW620, MEKi, 3

description:
SW620 cell line treated with 50 nM trametinib (MEKi) after 24 hours,with siControl,  replicate 3
SW620_STAR_Gene_Counts.xlsx
SW620_TRAM_3

value: MEKi


title: Section_139-Sample_8

tag: strain

value: Sprague Dawley

value: H


title: Tumor patient 2 (DDLPS_sWD), scRNAseq

description: 10x Genomics

value: F

tag: tumour grade


title: Section_139-Sample_7

tag: age

value: 12 weeks

tag: region

value: Non-FB

value: C

value: Right


title: SW620, MEKi, 2

description:
SW620 cell line treated with 50 nM trametinib (MEKi) after 24 hours,with siControl,  replicate 2
SW620_STAR_Gene_Counts.xlsx
SW620_TRAM_2

value: Colorectal cancer


title: Tumor patient 4 (DDLPS_DD), scRNAseq

description: 10x Genomics

value: M

value: spermatic cordon


title: H3K4ME1_MONOCYTES_CONTROL_2

value: bone marrow

value: control

value: Histone H3K4me1 antibody (pAb), Active Motif, cat#39297


title: SW620, MEKi, 1

description:
SW620 cell line treated with 50 nM trametinib (MEKi) after 24 hours,with siControl,  replicate 1
SW620_STAR_Gene_Counts.xlsx
SW620_TRAM_1


title: H3K4ME1_HSPC_CONTROL_1

value: HSPC-enriched myeloid cells


title: H3K4ME1_MONOCYTES_CONTROL_1

value: monocytes


title: Tumor patient 2 (DDLPS_DD), scRNAseq

description: 10x Genomics

value: retroperitoneum


title: Section_139-Sample_5

value: Male

tag: connectivity

value: FB

tag: position

value: Middle


title: Tumor patient 1 (DDLPS_DD), scRNAseq

description: 10x Genomics

value: F


title: SW620, EZH2i, 3

description:
SW620 cell line treated with 5 uM tazemetostat (EZH2i), with siControl, replicate 3
SW620_STAR_Gene_Counts.xlsx
SW620_EPZ_3

tag: cell line


title: Section_139-Sample_10

value: Sprague Dawley

value: 12 weeks

tag: cluster

value: A

tag: side

value: Left


title: Tumor patient 1 (DDLPS_WD), scRNAseq

description: 10x Genomics

tag: tissue


title: H3K4ME3_HSPC_CONTROL_2

tag: cell type

value: Histone H3K4me3 antibody (pAb), ThermoFisher, cat#PA5-27029


title: Section_139-Sample_3

value: DMV

value: E

value: Right


title: SW620, DMSO, 3

description:
SW620 cell line treated with DMSO,with siControl,  replicate 3
SW620_STAR_Gene_Counts.xlsx
SW620_DMSO_3

value: Colorectal cancer

tag: treatment

value: DMSO


title: SW620, DMSO, 2

description:
SW620 cell line treated with DMSO,with siControl,  replicate 2
SW620_STAR_Gene_Counts.xlsx
SW620_DMSO_2


title: Tumor patient 42 (WDLPS), RNAseq

data_processing:
FastQC (v0.11.8 or v0.11.9 according to sample) and trimming with TrimGalore (v0.6.2) or Altropos according to sample, default options
STAR (v2.6.1a_08-27), Picard MarkDuplicates (v2.18.14) and Cufflinks (v2.2.1), default options
TPM-normalization of raw read counts generated by STAR (1)
log2-transformation of FPKM from Cufflinks with pseudo-count +2 and normalization between samples with limma in quantil mode (2)
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files containing raw counts generated by STAR and corresponding TPM-normalized or FPKM-normalized counts

extract_protocol:
Total RNAs were extracted using the Trizol reagent and dosed. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: WDLPS

value: limb


title: Tumor patient 43 (DDLPS_WD), RNAseq

value: retroperitoneum


title: Section_139-Sample_2

value: Male

value: Non-FB


title: Section_139-Sample_4

value: Middle


title: SW620, DMSO, 1

description:
SW620 cell line treated with DMSO, with siControl, replicate 1
SW620_STAR_Gene_Counts.xlsx
SW620_DMSO_1


title: H3K4ME3_HSPC_CONTROL_1

value: bone marrow

value: HSPC-enriched myeloid cells

tag: disease state

value: control

tag: chip antibody


title: Tumor patient 41 (DDLPS_WD), RNAseq

tag: age at_diagnosis

tag: Sex

value: F


title: Tumor patient 40 (DDLPS_DD), RNAseq

value: M

tag: location

tag: tumour size_(mm)


title: H3K4ME3_MONOCYTES_CONTROL_1

value: monocytes

value: Histone H3K4me3 antibody (pAb), ThermoFisher, cat#PA5-27029


title: LOVO, COMBO, 3

description:
LOVO cell line treated with a combination of trametinib and tazemetostat for 16 hours, replicate 3
LOVO_counts.xlsx
LOVO_COMBO_3

source_name: LOVO

value: LOVO

value: COMBO


title: Section_139-Sample_1

description: RNA extracted from a single microdissected neuron

tag: strain

value: Sprague Dawley

value: 12 weeks

value: DMV

value: FB

value: E

value: Right


title: Section_128-Sample_7

tag: age

value: Male

value: Caudal

value: D

value: Left


title: H3K27AC_HSPC_CONTROL_2

value: bone marrow

value: HSPC-enriched myeloid cells

value: control

value: Histone H3K27ac antibody (pAb), ActiveMotif, cat#39134


title: Section_128-Sample_8

tag: region

value: Non-FB


title: Tumor patient 38 (DDLPS_sWD), RNAseq

value: M

value: retroperitoneum

tag: tumour grade


title: LOVO, EZH2i, 3

description:
LOVO cell line treated with 5 uM tazemetostat (EZH2i), replicate 3
LOVO_counts.xlsx
LOVO_EPZ_3

value: LOVO

value: Colorectal cancer


title: LOVO, COMBO, 1

description:
LOVO cell line treated with a combination of trametinib and tazemetostat for 16 hours, replicate 1
LOVO_counts.xlsx
LOVO_COMBO_1

value: COMBO


title: Tumor patient 38 (DDLPS_DD), RNAseq


title: LOVO, EZH2i, 2

description:
LOVO cell line treated with 5 uM tazemetostat (EZH2i), replicate 2
LOVO_counts.xlsx
LOVO_EPZ_2


title: H3K27AC_HSPC_CONTROL_1


title: H3K4ME3_MONOCYTES_CONTROL_2

value: monocytes

value: Histone H3K4me3 antibody (pAb), ThermoFisher, cat#PA5-27029


title: LOVO, EZH2i, 1

description:
LOVO cell line treated with 5 uM tazemetostat (EZH2i), replicate 1
LOVO_counts.xlsx
LOVO_EPZ_1


title: Tumor patient 37 (DDLPS_WD), RNAseq

value: F


title: aP2-Cre;Aromatase_4

city: Toon

first: Yuuki

last: Imai

state: Ehime

address: Shituskawa

department: Proteo-Science Center

country: Japan

institute: Ehime University

data_processing:
RaNA-seq (Prieto C, and Barrios D. Bioinformatics. 2019, https://ranaseq.eu/)
In RaNA-seq, the FASTQ files are pre-processed (quality control, adapter trimming, quality filtering, per-read quality pruning etc.) with the Fastp tool (Chen et al., Bioinformatics. 2018), and expression quantification is performed with Salmon (Patro et al., Nat. Methods. 2017).
Trimmed seacence reads were mapped to GRCm38 using Salmon.
Assembly: GRCm38
Supplementary files format and content: tab-separated values file includes raw counts for each sample.

source_name: Epididymal adipose tiisue

extract_protocol:
RNA was harvested using Rneasy Mini Kit (Qiagen) with QIAzol lysis reagent (QIAGEN). Digestion of DNA was used Rnase-Free DNase set (QIAGEN).
BRB-seq (Alpern D et al. Genome Biol. 2019) was performed for preparing libraries with some following modifications. Oligo-dT based primer was used for single-stranded synthesis and Second Strand Synthesis Module (NEB, #E6111) was used for double-stranded cDNA synthesis. In-house MEDS-B Tn5 transposase (Picelli S et al., Genome Res. 2014, Sato et al., Open Biol. 2019) was used for tagmentation and amplified by 10 cycles of PCR using Phusion High-Fidelity DNA Polymerase (Thermo Scientific, #M0530). 51bp of insert read (Read2) were obtained on Illumina NovaSeq6000.

value: Epididymal adipose tiisue

tag: genotype

value: aP2-Cre;Aromatase flox/flox


title: H3K27AC_MONOCYTES_CONTROL_1


title: Tumor patient 36 (WDLPS), RNAseq

value: WDLPS

value: trunk


title: Section_128-Sample_5

value: Sprague Dawley

value: 12 weeks

value: Male

value: DMV

tag: connectivity

value: FB

tag: position

value: Caudal

value: C

value: Left


title: LOVO, MEKi, 3

description:
LOVO cell line treated with 50 nM trametinib (MEKi) after 16 hours, replicate 3
LOVO_counts.xlsx
LOVO_TRAM_3

tag: cell line

value: LOVO

value: Colorectal cancer

value: MEKi


title: Section_128-Sample_4

tag: cluster

value: B

tag: side

value: Right


title: LOVO, COMBO, 2

description:
LOVO cell line treated with a combination of trametinib and tazemetostat for 16 hours, replicate 2
LOVO_counts.xlsx
LOVO_COMBO_2

tag: cell type

tag: treatment

value: COMBO


title: H3K27AC_MONOCYTES_CONTROL_2

tag: tissue

value: bone marrow

value: monocytes

tag: disease state

value: control

tag: chip antibody

value: Histone H3K27ac antibody (pAb), ActiveMotif, cat#39134


title: Tumor patient 35 (peritumoral_fat), RNAseq

tag: age at_diagnosis

tag: Sex

value: M

tag: location

value: trunk


title: aP2-Cre;Aromatase_3

value: Epididymal adipose tiisue

value: aP2-Cre;Aromatase flox/flox


title: Tumor patient 34 (DDLPS_WD), RNAseq

value: F

value: retroperitoneum

tag: tumour size_(mm)


title: Section_128-Sample_3

tag: strain

value: Sprague Dawley

tag: age

value: 12 weeks

value: Male

tag: region

value: FB

value: Caudal

value: G


title: Section_128-Sample_2

value: DMV

tag: connectivity

value: Non-FB

value: D

value: Right


title: LOVO, MEKi, 2

description:
LOVO cell line treated with 50 nM trametinib (MEKi) after 16 hours, replicate 2
LOVO_counts.xlsx
LOVO_TRAM_2

value: LOVO

value: Colorectal cancer

value: MEKi


title: Tumor patient 33 (DDLPS_WD), RNAseq

value: M

value: trunk

tag: tumour grade


title: LOVO, MEKi, 1

description:
LOVO cell line treated with 50 nM trametinib (MEKi) after 16 hours, replicate 1
LOVO_counts.xlsx
LOVO_TRAM_1

tag: cell line


title: aP2-Cre;Aromatase_2

value: Epididymal adipose tiisue

tag: genotype

value: aP2-Cre;Aromatase flox/flox


title: Aromatase flox_4

value: Aromatase flox/flox


title: LOVO, DMSO, 3

description:
LOVO cell line treated with DMSO, replicate 3
LOVO_counts.xlsx
LOVO_DMSO_3

value: DMSO


title: Section_127-Sample_8

value: Sprague Dawley

value: 12 weeks

value: Male

tag: position

tag: cluster

tag: side


title: aP2-Cre;Aromatase_1

tag: tissue


title: Section_128-Sample_1

value: FB

value: Caudal

value: F


title: Aromatase flox_3


title: LOVO, DMSO, 2

description:
LOVO cell line treated with DMSO, replicate 2
LOVO_counts.xlsx
LOVO_DMSO_2

tag: cell type

tag: treatment


title: Tumor patient 31 (DDLPS_DD), RNAseq

tag: age at_diagnosis

value: retroperitoneum


title: Aromatase flox_1


title: LOVO, sgTLE4, COMBO, 3

description:
LOVO cell line transduced with lentivrus to express sgTLE4, and then treated with lentivrus to express a combination of trametinib and tazemetostat for 16 hours, replicate 3
LOVO_sgTLE4_COMBO_3

source_name: cell line

extract_protocol:
Total RNA was isolated after 16 hours of vehicle or Tazemetostat (5 uM) + Trametinib (50 nM) (Combo)  treatment using the RNeasy Plus Mini kit (Qiagen, #74136). Cells were scraped and collected in RLT plus buffer, homogenized using Qiagen QIAshredder, and gDNA was removed with gDNA eliminator columns.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads.  After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library.  After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library.

treatment_protocol: Colorectal cancer cell line, LOVO, were transduced with lentivirus to express Cas9 and sgControl or sgTLE4, and then treated with vehicle or tazemetostat (EZH2i) and trametinib (MEKi). Cells were pretreated with DMSO or EZH2i (tazemetostat at 5uM) for 5 days, and then seeded into 6cm plates of 300,000 to 350,000 cells per plate. The following day, cells were treated with DMSO, MEKi (50nM trametinib), with and without EZH2i.  Cells were collected 16 after combined treatment before onset of cell death.

value: cell line

value: COMBO


title: Tumor patient 30 (DDLPS_WD), RNAseq

tag: Sex


title: LOVO, DMSO, 1

description:
LOVO cell line treated with DMSO, replicate 1
LOVO_counts.xlsx
LOVO_DMSO_1

value: LOVO

value: Colorectal cancer


title: Section_127-Sample_6

value: Non-FB

value: C

value: Left


title: Aromatase flox_2

value: Epididymal adipose tiisue


title: Tumor patient 29 (DDLPS_DD), RNAseq

tag: location


title: Section_127-Sample_3

value: DMV


title: CoC

city: Providence

first: Geongoo

last: Han

address: 171 Meeting St.

institute: Brown University

data_processing:
Adapter and low-quality sequences were trimmed from the raw sequence reads using Trimmomatic v0.36
STAR v2.7.3a was used to align the trimmed sequences to the mm10 mouse genome and to estimate the number of reads per gene.
Gene count was normalized in DESeq2 v1.38.1
Assembly: mm10
Supplementary files format and content: tab-delimited text file raw counts for all samples
Supplementary files format and content: tab-delimited text file normalized counts by DESeq2 for all samples

source_name: CD8 T cells of Mus musculus

extract_protocol:
RNA was extracted from CD8 T cells using the RNeasy Plus Micro Kit (Qiagen)
The RNA library was prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina

value: CD8 T cells of Mus musculus

value: co-culture with vaginal epithelial organoid


title: Section_127-Sample_1

value: Sprague Dawley

value: 12 weeks

value: Right


title: LOVO, sgTLE4, COMBO, 2

description:
LOVO cell line transduced with lentivrus to express sgTLE4, and then treated with lentivrus to express a combination of trametinib and tazemetostat for 16 hours, replicate 2
LOVO_sgTLE4_COMBO_2


title: LOVO, sgTLE4, COMBO, 1

description:
LOVO cell line transduced with lentivrus to express sgTLE4, and then treated with lentivrus to express a combination of trametinib and tazemetostat for 16 hours, replicate 1
LOVO_sgTLE4_COMBO_1


title: CoB


title: Section_127-Sample_5

value: Male

value: FB

value: Caudal

value: A


title: LOVO, sgTLE4, DMSO, 3

description:
LOVO cell line transduced with lentivrus to express sgTLE4, and then treated with lentivrus to express DMSO, replicate 3
LOVO_sgTLE4_DMSO_3

value: cell line

value: DMSO


title: Tumor patient 28 (DDLPS_DD), RNAseq

value: M

value: spermatic cordon

tag: tumour size_(mm)


title: Section_127-Sample_7

tag: strain

value: B


title: CoA


title: Section_136-Sample_7

tag: age

value: Non-FB

value: Middle


title: Tumor patient 32 (lipoma), RNAseq

source_name: lipoma

value: lipoma

value: retroperitoneum


title: LOVO, sgTLE4, DMSO, 2

description:
LOVO cell line transduced with lentivrus to express sgTLE4, and then treated with lentivrus to express DMSO, replicate 2
LOVO_sgTLE4_DMSO_2

value: LOVO

value: Colorectal cancer


title: Section_136-Sample_8

description: RNA extracted from a single microdissected neuron

value: Sprague Dawley

value: 12 weeks

tag: region

value: H


title: LOVO, sgTLE4, DMSO, 1

description:
LOVO cell line transduced with lentivrus to express sgTLE4, and then treated with lentivrus to express DMSO, replicate 1
LOVO_sgTLE4_DMSO_1


title: CD8C

value: CD8 T cells of Mus musculus


title: Tumor patient 27 (DDLPS_WD), RNAseq

value: F


title: Section_136-Sample_6

value: Male

tag: connectivity

value: FB

value: Right


title: CD8B


title: Tumor patient 28 (DDLPS_WD), RNAseq

value: M

tag: tumour grade


title: Tumor patient 26 (DDLPS_DD), RNAseq


title: CD8A


title: LOVO, sgCTL, COMBO, 3

description:
LOVO cell line transduced with lentivrus to express sgControl, and then treated with lentivrus to express a combination of trametinib and tazemetostat for 16 hours, replicate 3
LOVO_sgCTL_COMBO_3

value: cell line

tag: cell line

value: sgControl

value: COMBO


title: Tumor patient 25 (DDLPS_WD), RNAseq


title: LOVO, sgCTL, COMBO, 2

description:
LOVO cell line transduced with lentivrus to express sgControl, and then treated with lentivrus to express a combination of trametinib and tazemetostat for 16 hours, replicate 2
LOVO_sgCTL_COMBO_2

tag: genotype


title: Section_136-Sample_3

value: DMV

value: Non-FB

tag: position

value: Middle

value: D

value: Left


title: Tumor patient 24 (lipoma), RNAseq

value: lipoma

value: retroperitoneum


title: Tumor patient 27 (DDLPS_DD), RNAseq


title: LOVO, sgCTL, COMBO, 1

description:
LOVO cell line transduced with lentivrus to express sgControl, and then treated with lentivrus to express a combination of trametinib and tazemetostat for 16 hours, replicate 1
LOVO_sgCTL_COMBO_1

value: LOVO

value: Colorectal cancer


title: Section_136-Sample_1

value: Sprague Dawley

value: 12 weeks

tag: cluster

value: F


title: PrP-/-;Mock, scRNAseq

city: Rijeka

first: Tihana

last: Lenac Rovis

address: B. Branchetta 20

department: Center for Proteomics

country: Croatia

institute: University of Rijeka Faculty of Medicine

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.1
Assembly: mm10
Supplementary files format and content: matrix files

source_name: Spleen

extract_protocol:
Splenic leukocytes were prepared using standard protocols including mechanical dissociation and brief erythrocytes lysis. To isolate lymphocytes from the brain, the tissue was mechanically dissociated. A 30% Percoll/brain homogenate suspension was underlaid with 70% Percoll in PBS and centrifuged (25’,1050g). Cells were counted and cryopreserved in fetal bovine serum (FBS) supplemented with 10% DMSO at -80°C. Gently thawed samples were stained with Fixable Viability Dye (FVD) and fluorochrome conjugated antibodies and live target populations were FACS sorted by MoFlo EQ Astrios (Beckman Coulter)  (CD8+ T cells: FVD-CD45.2+CD3+CD19-CD8+; NK cells: FVD-CD45.2+CD3-CD19-NK1.1+).
Library construction was performed according to manufacturer instructions in Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (Dual Index) guide. Briefly, gel bead-in-emulsion (GEM) was generated using Chromium Next GEM Chip G Single Cell Kit which was followed by GEM- reverse transcription incubation. Illumina TruSeq Read 1 (read 1 sequencing primer), and unique molecular identifier (UMI), poly(dT) sequence and 10x barcode were added through gel bead. Barcoded, full-length cDNA produced from poly-adenylated mRNA was purified using Dynabead, then the cDNA was amplified by PCR and again purified but with SPRIselect to select appropriate size of fragments. 3ʹ gene expression library construction included fragmentation, end repair, A-tailing and adaptor ligation with appropriate steps of SPRIselect of double-sided size selection and cleanup. In this step P5, P7, a sample index, and TruSeq Read 2 (read 2 primer sequence) were added to cDNA.

value: Spleen

value: CD8+T-cells and NK cells

value: PrP-/-

value: Not Exposed to MCMV


title: Tumor patient 26 (DDLPS_WD), RNAseq

value: M


title: PrP-/-;MCMV, scRNAseq 2

description: 10x Genomics

value: Exposed to MCMV


title: Section_136-Sample_5

value: Male

value: FB

value: H

tag: side

value: Right


title: LOVO, sgCTL, DMSO, 3

description:
LOVO cell line transduced with lentivrus to express sgControl, and then treated with lentivrus to express DMSO, replicate 3
LOVO_sgCTL_DMSO_3

tag: tissue

value: cell line

value: sgControl

value: DMSO


title: C57Bl6;Mock, scRNAseq

description: 10x Genomics

tag: cell type


title: Tumor patient 22 (Hibernoma), RNAseq

source_name: Hibernoma

value: Hibernoma

value: limb


title: Section_133-Sample_5

value: Sprague Dawley

value: 12 weeks

value: Non-FB

value: Middle

value: G

value: Left


title: C57Bl6;MCMV, scRNAseq

description: 10x Genomics

value: Spleen

value: CD8+T-cells and NK cells

tag: treatment


title: Tumor patient 21 (DDLPS_DD), RNAseq

tag: age at_diagnosis

value: M

value: trunk


title: Section_172-Sample_3

tag: Sex

value: Male

value: DMV

value: FB

value: Rostral

value: D


title: LOVO, sgCTL, DMSO, 2

description:
LOVO cell line transduced with lentivrus to express sgControl, and then treated with lentivrus to express DMSO, replicate 2
LOVO_sgCTL_DMSO_2

value: cell line

value: LOVO

value: Colorectal cancer

value: sgControl

value: DMSO


title: 3Pseq_UAS-PCF11-cbc_2_S8_R1_001

city: Stanford

first: Lorenzo

last: Gallicchio

state: california

address: Campus Drive W

department: developmental Biology

institute: Stanford University

description: Uploaded entire PolyA miner result folder

data_processing:
Reads that did not contain at least 10 consecutive As were filtered out using bbduk k=10 int=f hdist=0 and then adapters were trimmed also with bbduk k=13 ktrim=r useshortkmers=t mink=5 qtrim=t trimq=10 minlength=20 int=f.
Reads were mapped to the Drosophila melanogaster genome build dm6 using bowtie. Woth options -S -e 5000
Samtools was used to create indexed bam files: samtools view -S -b ${Input}.sam > ${Input}.bam ; samtools sort ${Input}.bam > ${Input}_Sorted_By_Coord.bam ; samtools index $Input
PolyAminer was run with the command: python3 PolyA_miner/PolyA-miner.py \
-mode bam \
-c1 CTRL1, CTRL2 \
-c2 OE-1,OE-2  \
-fasta Drosophila_melanogaster.BDGP6.28.dna.toplevel.fa\
-bed genes_bed.bed\
-pa bam_vs_Spermatocytes.bed \
-o output_folder_name \
-expNovel 0\
-novel_d 500\
-md 0\
-p 40\
-ip_d 40\
-ip_u 30\
-pa_m 5
Assembly: Ensembl annotation BDGP6.28
Supplementary files format and content: PolyA miner output of KDs vs Control
Supplementary files format and content: genes_bed.bed is a list of the drosophila genes in bed format
Supplementary files format and content: bam_vs_Spermatocytes.bed list of the proximal and distal siates of the ~500 genes identified from Berry et al. (2022)

organism: Drosophila melanogaster

source_name: Testes

growth_protocol: Crosses were maintained for 3 days at 25C, the adult flies removed and the progeny moved to 29C until dissection time.

extract_protocol:
total RNA was extracted using the kit: RNeasy Plus Mini Kit from QIAGEN
Libraries were prepared using Lexogen QuantSeq mRNA-Seq library Prep Kit for Illumina (FWD) (Catalog# 015)

treatment_protocol: 150 pairs of testes per sample were dissected in PBS in a glass cyclops dish in batches of 50 pairs. Testes were transferred to a 1.7 ml tube with PBS using forceps. PBS was removed and the sample snap-frozen in liquid nitrogen. Samples were kept at −80°C until the next step.

value: Testes


title: PrP-/-;MCMV, scRNAseq 1

description: 10x Genomics

value: PrP-/-

value: Exposed to MCMV


title: LOVO, B-catenin90, COMBO, 3

description:
LOVO cell line transduced with lentivrus to express B-catenin delta90 construct, and then treated with a combination of trametinib and tazemetostat for 16 hours, replicate 3
LOVO_B-catenin90_COMBO_3

treatment_protocol: Colorectal cancer cell line, LOVO, were transduced with lentivirus to ectopically express an empty vector or a constitutively active form of B-catenin, and then treated with vehicle, tazemetostat (EZH2i), and/or trametinib (MEKi). Cells were pretreated with DMSO or EZH2i (tazemetostat at 5uM) for 5 days, and then seeded into 6cm plates of 300,000 to 350,000 cells per plate. The following day, cells were treated with DMSO, MEKi (50nM trametinib), with and without EZH2i.  Cells were collected 16-24 hours after combined treatment before onset of cell death.

tag: condition

value: pLV B-catenin90

value: COMBO


title: LOVO, sgCTL, DMSO, 1

description:
LOVO cell line transduced with lentivrus to express sgControl, and then treated with lentivrus to express DMSO, replicate 1
LOVO_sgCTL_DMSO_1


title: LOVO, B-catenin90, COMBO, 2

description:
LOVO cell line transduced with lentivrus to express B-catenin delta90 construct, and then treated with a combination of trametinib and tazemetostat for 16 hours, replicate 2
LOVO_B-catenin90_COMBO_2


title: Tumor patient 20 (DDLPS_WD), RNAseq

value: M

tag: location

value: retroperitoneum

tag: tumour size_(mm)


title: Tumor patient 20 (DDLPS_DD), RNAseq


title: 3Pseq_UAS-PCF11-cbc_1_S7_R1_001


title: Tumor patient 23 (lipoma), RNAseq

value: lipoma

value: spermatic cordon


title: Section_187-Sample_1

tag: strain

value: Sprague Dawley

tag: age

value: 12 weeks

value: Male

value: DMV

value: FB

value: I

value: Left


title: LOVO, B-catenin90, COMBO, 1

description:
LOVO cell line transduced with lentivrus to express B-catenin delta90 construct, and then treated with a combination of trametinib and tazemetostat for 16 hours, replicate 1
LOVO_B-catenin90_COMBO_1

value: cell line

value: LOVO

value: Colorectal cancer


title: Section_134-Sample_2

tag: region

tag: connectivity

value: Non-FB

value: Middle

value: F

value: Right


title: 3Pseq_UAS-PCF11_2_S4_R1_001

value: Testes


title: Tumor patient 19 (lipoma), RNAseq

value: lipoma

value: M

value: limb

tag: tumour grade


title: Section_176-Sample_1

value: Sprague Dawley

value: 12 weeks

value: Rostral

value: G


title: Section_175-Sample_1

value: Male

value: DMV

value: FB


title: Tumor patient 21 (DDLPS_WD), RNAseq

value: trunk


title: Section_172-Sample_4

value: I

value: Left


title: Tumor patient 18 (DDLPS_DD), RNAseq

value: retroperitoneum


title: LOVO, B-catenin90, EZH2i, 3

description:
LOVO cell line transduced with lentivrus to express B-catenin delta90 construct, and then treated with 5 uM tazemetostat (EZH2i), replicate 3
LOVO_B-catenin90_EPZ_3

value: cell line

tag: cell line

value: LOVO

value: Colorectal cancer

value: pLV B-catenin90


title: Section_173-Sample_4

value: Non-FB

tag: position


title: Tumor patient 17 (DDLPS_DD), RNAseq

value: F


title: LOVO, B-catenin90, EZH2i, 2

description:
LOVO cell line transduced with lentivrus to express B-catenin delta90 construct, and then treated with 5 uM tazemetostat (EZH2i), replicate 2
LOVO_B-catenin90_EPZ_2


title: 3Pseq_UAS-cbc_2_S6_R1_001

value: Testes

tag: genotype


title: LOVO, B-catenin90, EZH2i, 1

description:
LOVO cell line transduced with lentivrus to express B-catenin delta90 construct, and then treated with 5 uM tazemetostat (EZH2i), replicate 1
LOVO_B-catenin90_EPZ_1


title: 3Pseq_UAS-cbc_1_S5_R1_001


title: LOVO, B-catenin90, MEKi, 3

description:
LOVO cell line transduced with lentivrus to express B-catenin delta90 construct, and then treated with 50 nM trametinib (MEKi) after 16 hours, replicate 3
LOVO_B-catenin90_TRAM_3

value: MEKi


title: Section_172-Sample_2

value: Sprague Dawley

value: 12 weeks

value: Rostral

tag: cluster

value: D

tag: side

value: Right


title: 3Pseq_bam_2_S2_R1_001

tag: tissue


title: Tumor patient 15 (DDLPS_WD), RNAseq


title: LOVO, B-catenin90, MEKi, 2

description:
LOVO cell line transduced with lentivrus to express B-catenin delta90 construct, and then treated with 50 nM trametinib (MEKi) after 16 hours, replicate 2
LOVO_B-catenin90_TRAM_2

tag: cell type

tag: treatment


title: Section_172-Sample_1

description: RNA extracted from a single microdissected neuron

tag: Sex

value: Male

value: DMV

value: FB


title: Tumor patient 16 (DDLPS_DD), RNAseq

tag: age at_diagnosis

value: M

value: retroperitoneum


title: 3Pseq_bam_1_S1_R1_001


title: LOVO, B-catenin90, MEKi, 1

description:
LOVO cell line transduced with lentivrus to express B-catenin delta90 construct, and then treated with 50 nM trametinib (MEKi) after 16 hours, replicate 1
LOVO_B-catenin90_TRAM_1

value: cell line

value: LOVO

tag: condition


title: Tumor patient 15 (DDLPS_DD), RNAseq

tag: location

tag: tumour size_(mm)


title: 3Pseq_UAS-PCF11_1_S3_R1_001


title: 3Pseq-sufKD-2

data_processing:
Reads that did not contain at least 10 consecutive As were filtered out using bbduk k=10 int=f hdist=0 and then adapters were trimmed also with bbduk k=13 ktrim=r useshortkmers=t mink=5 qtrim=t trimq=10 minlength=20 int=f.
Reads were mapped to the Drosophila melanogaster genome build dm6 using bowtie. Woth options -S -e 5000
Samtools was used to create indexed bam files: samtools view -S -b ${Input}.sam > ${Input}.bam ; samtools sort ${Input}.bam > ${Input}_Sorted_By_Coord.bam ; samtools index $Input
PolyAminer was run with the command: python3 PolyA_miner/PolyA-miner.py \         -mode bam \         -c1 CTRL1, CTRL2 \         -c2 KD-1,KD-2  \         -fasta Drosophila_melanogaster.BDGP6.28.dna.toplevel.fa\         -bed genes_bed.bed\         -pa bam_vs_Spermatocytes.bed \         -o output_folder_name \         -expNovel 0\         -novel_d 500\         -md 0\         -p 40\         -ip_d 40\         -ip_u 30\         -pa_m 5
Assembly: Ensembl annotation BDGP6.28
Supplementary files format and content: PolyA miner output of KDs vs Control
Supplementary files format and content: genes_bed.bed is a list of the drosophila genes in bed format
Supplementary files format and content: bam_vs_Spermatocytes.bed list of the proximal and distal siates of the ~500 genes identified from Berry et al. (2022)


title: Tumor patient 14 (DDLPS_DD), RNAseq


title: Section_116-Sample_1

tag: strain

tag: age

value: Caudal


title: Tumor patient 13 (WDLPS), RNAseq

value: WDLPS


title: LOVO, B-catenin90, DMSO, 3

description:
LOVO cell line transduced with lentivrus to express B-catenin delta90 construct, and then treated with DMSO, replicate 3
LOVO_B-catenin90_DMSO_3

value: Colorectal cancer

value: pLV B-catenin90

value: DMSO


title: Section_115-Sample_2

value: Sprague Dawley

tag: region

tag: connectivity

value: Non-FB

value: F


title: 3Pseq-sufKD-1

value: Testes


title: LOVO, B-catenin90, DMSO, 2

description:
LOVO cell line transduced with lentivrus to express B-catenin delta90 construct, and then treated with DMSO, replicate 2
LOVO_B-catenin90_DMSO_2

tag: cell line


title: 3Pseq-PCF11KD-2


title: Tumor patient 12 (DDLPS_WD), RNAseq

tag: tumour grade


title: Section_155-Sample_3

value: 12 weeks

tag: position

value: Rostral

value: D

value: Left


title: Section_130-Sample_1

value: Male

value: FB

value: Middle

tag: cluster

value: H

value: Right


title: Section_155-Sample_2

value: DMV

tag: side


title: LOVO, EV, COMBO, 3

description:
LOVO cell line transduced with lentivrus to express empty vector construct, and then treated with lentivrus to express a combination of trametinib and tazemetostat for 16 hours, replicate 3
LOVO_EV_COMBO_3

tag: tissue

value: cell line

value: LOVO

value: Colorectal cancer

value: pLV Empty Vector

value: COMBO


title: 3Pseq-PCF11-NIGKD-2

tag: genotype


title: Tumor patient 11 (lipoma), RNAseq

value: lipoma

value: M

value: trunk


title: Tumor patient 10 (DDLPS_WD), RNAseq

value: F

value: retroperitoneum


title: Section_121-Sample_2

value: Sprague Dawley

value: 12 weeks

value: Non-FB

value: Caudal

value: D


title: Section_121-Sample_3

value: Male

value: FB

value: Right


title: LOVO, EV, COMBO, 2

description:
LOVO cell line transduced with lentivrus to express empty vector construct, and then treated with lentivrus to express a combination of trametinib and tazemetostat for 16 hours, replicate 2
LOVO_EV_COMBO_2

value: cell line

value: LOVO

tag: cell type

tag: treatment


title: 3Pseq-PCF11-NIGKD-1

value: Testes


title: Tumor patient 10 (DDLPS_DD), RNAseq

tag: age at_diagnosis

tag: Sex


title: 3Pseq-PABP2KD-2


title: LOVO, EV, COMBO, 1

description:
LOVO cell line transduced with lentivrus to express empty vector construct, and then treated with lentivrus to express a combination of trametinib and tazemetostat for 16 hours, replicate 1
LOVO_EV_COMBO_1

value: Colorectal cancer

tag: condition

value: pLV Empty Vector

value: COMBO


title: Control DMSO Proximal blastema, 14dpa rep3

first: James

middle: R

last: Monaghan

address: 360 Huntington Ave.

department: Biology

institute: Northeastern University

data_processing:
Sequence reads were trimmed using Trimmomatic v0.38 for adapter content/sequence quality (HEADCROP:0 ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:25 SLIDINGWINDOW:4:30 MINLEN:36)
Quality trimmed reads were quasi-mapped against the A. mexicanum v4.7 transcriptome using salmon v0.13.1 with flags "--validateMappings --recoverOrphans --rangeFactorizationBins 4 --seqBias"
Counts matrices were generated and summarized to gene level using Trinity v2.8.5 script "abundance_estimates_to_matrix.pl"
Assembly: Ambystoma mexicanum v6  genome (AmexG_v6.0-DD) & v4.7 transcriptome (AmexT_v47)
Supplementary files format and content: Tab-delimited text file containing transcript abundances summarized to gene level

organism: Ambystoma mexicanum

source_name: Ambystoma mexicanum (sized 5 cm head to tail, aged 3 months)

extract_protocol:
RNA extraction from flash frozen tissue was performed at Genewiz.
Library construction was performed at Genewiz following manufacturer's instruction for 150-bp reads.

treatment_protocol: Talarozole (TAL) was resuspended in dimethyl sulfoxide (DMSO) to 5 mM concentration and stored at -20C until use. Animals were placed in housing water dosed with the indicated concentration of TAL or DMSO control at 4dpa. TAL or DMSO treatment was refreshed every other day for 7 days, after which animals were removed from treatment and placed in housing water.

value: 14dpa proximal blastema

value: White (d/d)

value: DMSO

tag: time

value: 14 dpa


title: LOVO, B-catenin90, DMSO, 1

description:
LOVO cell line transduced with lentivrus to express B-catenin delta90 construct, and then treated with DMSO, replicate 1
LOVO_B-catenin90_DMSO_1

value: pLV B-catenin90


title: Tumor patient 8 (WDLPS), RNAseq

value: WDLPS

value: M

tag: location

value: limb

tag: tumour size_(mm)


title: LOVO, EV, EZH2i, 3

description:
LOVO cell line transduced with lentivrus to express empty vector construct, and then treated with lentivrus to express 5 uM tazemetostat (EZH2i), replicate 3
LOVO_EV_EPZ_3


title: 3Pseq-PABP2KD-1

description: Uploaded entire PolyA miner result folder


title: 3Pseq-PCF11KD-1


title: LOVO, EV, EZH2i, 2

description:
LOVO cell line transduced with lentivrus to express empty vector construct, and then treated with lentivrus to express 5 uM tazemetostat (EZH2i), replicate 2
LOVO_EV_EPZ_2


title: Tumor patient 7 (peritumoral_fat), RNAseq

value: F

value: retroperitoneum


title: Tumor patient 8 (peritumoral_fat), RNAseq


title: 3Pseq-CstF64KD-2


title: Control DMSO Proximal blastema, 14dpa rep1


title: 3Pseq-CstF64KD-1


title: Control DMSO Distal blastema, 14dpa rep3

value: 14dpa distal blastema


title: Tumor patient 6 (peritumoral_fat), RNAseq


title: 3Pseq-CstF50KD-2


title: Control DMSO Proximal blastema, 14dpa rep2


title: 3Pseq-CstF50KD-1


title: Tumor patient 4 (DDLPS_WD), RNAseq

value: spermatic cordon


title: LOVO, EV, MEKi, 2

description:
LOVO cell line transduced with lentivrus to express empty vector construct, and then treated with lentivrus to express 50 nM trametinib (MEKi) after 16 hours, replicate 2
LOVO_EV_TRAM_2

value: cell line

value: LOVO

value: MEKi


title: Tumor patient 5 (WDLPS), RNAseq


title: LOVO, EV, MEKi, 1

description:
LOVO cell line transduced with lentivrus to express empty vector construct, and then treated with lentivrus to express 50 nM trametinib (MEKi) after 16 hours, replicate 1
LOVO_EV_TRAM_1

value: Colorectal cancer

value: pLV Empty Vector


title: LOVO, EV, MEKi, 3

description:
LOVO cell line transduced with lentivrus to express empty vector construct, and then treated with lentivrus to express 50 nM trametinib (MEKi) after 16 hours, replicate 3
LOVO_EV_TRAM_3


title: 3Pseq-CPSF6KD-2

value: Testes


title: LOVO, EV, EZH2i, 1

description:
LOVO cell line transduced with lentivrus to express empty vector construct, and then treated with lentivrus to express 5 uM tazemetostat (EZH2i), replicate 1
LOVO_EV_EPZ_1


title: Control DMSO Distal blastema, 14dpa rep2

value: White (d/d)


title: Tumor patient 3 (WDLPS), RNAseq


title: 1uM TAL Distal blastema, 14dpa rep3

value: 1 uM TAL


title: 1uM TAL Distal blastema, 14dpa rep2

value: 14 dpa


title: 3Pseq-CPSF6KD-1


title: LOVO, EV, DMSO, 3

description:
LOVO cell line transduced with lentivrus to express empty vector construct, and then treated with lentivrus to express DMSO, replicate 3
LOVO_EV_DMSO_3

value: DMSO


title: 1uM TAL Distal blastema, 14dpa rep1


title: Tumor patient 2 (DDLPS_sWD), RNAseq


title: Tumor patient 3 (peritumoral_fat), RNAseq


title: 3Pseq-cbcKD-1

value: bamGal4>cbc-KD(BL 77426)


title: 0.1uM TAL Distal blastema, 14dpa rep3

value: 0.1 uM TAL


title: Tumor patient 2 (DDLPS_DD), RNAseq


title: MG01 Xenograft Sample 2

city: New York

first: Stefan

last: Irion

state: New York

address: 415 E 29th St

institute: BlueRock Therapeutics

data_processing:
Reads were filtered and trimmed using Cutadapt v3.4
Trimmed sequence reads were aligned with STAR v2.7.8a to hg38 and mm39.
Aligned reads were sorted and indexed using SAMtools v1.12
Aligned reads were  filtered to detect only human-specific reads using XenofilteR
Human reads aligning to expressed genes were counted using HTSeq v0.13.5
Assembly: hg38/mm39
Supplementary files format and content: tab-delimited text file

source_name: brain

extract_protocol:
RNA was isolated from micro-dissected fixed histology sections using the RNeasy FFPE kit (Qiagen Cat#73504).
cDNA libraries for sequencing were generated using the Collibri 3’ mRNA Library Prep Kit for Illumina (ThermoFisher Cat#A38110024) following manufacturer's protocol

treatment_protocol: xenograft

value: brain

value: hiPSC-derived Microglia (MG01)

value: engrafted MG01

value: xenograft into mus musculus


title: LOVO, EV, DMSO, 2

description:
LOVO cell line transduced with lentivrus to express empty vector construct, and then treated with lentivrus to express DMSO, replicate 2
LOVO_EV_DMSO_2


title: 3Pseq-BAMgal4-2


title: 0.1uM TAL Distal blastema, 14dpa rep2

value: 14dpa distal blastema


title: Tumor patient 1 (DDLPS_WD), RNAseq

value: F

value: retroperitoneum


title: 3Pseq-BAMgal4-1


title: MG01 Xenograft Sample 1


title: Control DMSO Distal blastema, 14dpa rep1


title: 0.1uM TAL Distal blastema, 14dpa rep1


title: Tumor patient 1 (DDLPS_DD), RNAseq


title: 3Pseq-cbcKD-2


title: CT26 subcutaneous tumor 2

status: Public on Jul 21 2024

first: Nicholas

last: Arpaia

address: 701 West 168th Street

department: Microbiology & Immunology

institute: Columbia University Irving Medical Center

data_processing:
Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq2.17. Sequence reads were trimmed to remove adapter sequences and nucleotides with poor quality using Trimmomatic v.0.39.
Trimmed reads were aligned to the mm10 reference using STAR aligner v.2.5.2b.
Unique gene hit counts were calculated using feature Counts from Subread Package v.1.5.2. Unique reads that fell within exon regions were counted.
The gene hit counts table was used for expression analysis using DESeq2.
Assembly: mm10
Supplementary files format and content: Comma-separated text file includes raw counts for all samples
Supplementary files format and content: Comma-separated text file includes TPM values for all samples

source_name: Tumor

growth_protocol: Cells were cultured in incubators at 37°C with atmosphere of humidified 5% CO2. B16F10 cells were grown in DMEM supplemented with 10% (vol/vol) FBS, 1x GlutaMax, 1% (vol/vol) MEM Non-essential amino acids solution (Gibco-11140050), and 100 U/ml penicillin-streptomycin. CT26 and CT26-Luc cells were grown in RPMI-1640 supplemented with 10% (vol/vol) FBS, 1x GlutaMax, 1% (vol/vol) MEM Non-essential amino acids solution, and 100 U/ml penicillin-streptomycin. . For subcutaneous tumor models: 5x10^6 CT26 cells in 100μl sterile PBS were inoculated subcutaneously on the hind-flank of BALB/c mice, or 5x10^5 B16F10 melanoma cells in 100μl sterile PBS subcutaneously on the hind flank (orthotopic) of C57BL/6 mice using a 26G-needle on a 1cc syringe.

extract_protocol:
Tumors were harvested and homogenized, RNA was extracted using the Qiagen RNeasy Minikit per manufacturer’s instructions.
RNA sequencing libraries were prepared using the NEBNext Ultra RNA library Prep Kit for Illumina per manufacturer’s instructions (New England Biolabs).

treatment_protocol: No treatment given

value: Tumor

value: colon carcinoma

value: WT


title: B16F10 subcutaneous tumor 3

value: melanoma


title: CT26 subcutaneous tumor 1


title: CT26 subcutaneous tumor 3


title: LOVO, EV, DMSO, 1

description:
LOVO cell line transduced with lentivrus to express an empty vector construct, and then treated with lentivrus to express DMSO, replicate 1
LOVO_EV_DMSO_1

value: cell line

value: LOVO

value: Colorectal cancer

value: pLV Empty Vector


title: B16F10 subcutaneous tumor 2


title: CMML_Inflammatory_Mo_scRNA-Seq

city: Hachioji

first: Yoshihiro

last: Hayashi

state: Tokyo

address: 1432-1 Horinouchi

institute: Tokyo University of Pharmacy and Life Sciences

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger pipeline
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Ly6Chigh BM monocytes

extract_protocol:
Bone marrow cells were harvested from individual mice. Ly6C+CD115+ monocytes were then FACS sorted. The total RNA was isorated using RNeasy Mini Kit (Qiagen)
The molecular-tagged RNA fragments were converted into cDNA followed by library establishment for next generation sequencing using Chromium Next GEM Single Cell 3' Reagent Kits v3.1 (10x Genomics). The resulting libraries were quantified by Qubit dsDNA Assay (Thermo Fisher Scientific) and TapeStation D1000 (Agilent). The libraries were sequenced by Illumina HiSeq platform with the following configuration: read 1: 28 bp, read 2: 91 and i7 index: 8 bp, yielding approximately 400 M paired-end reads per sample

tag: strain

value: Ly6Chigh BM monocytes


title: Normal_SCs_4+LF82_(N_SCs_4+LF82)

city: Birmingham

first: Phillip

middle: D

last: Smith

state: AL

address: 1825 University Blvd

institute: University of Alabama at Birmingham

data_processing:
Illumina bcl2fastq version 2.18.0.12 was used for basecalling
Raw FASTQ files were aligned to the genome using STAR version 2.7.5b using parameters --outReadsUnmapped FastX --outSAMtype BAM SortedByCoordinate --outSAMattributes All
Transcript abundances were calculated from the aligned BAM files using HTSeq-count version 0.12.3 using parameters -r pos -t exon -i gene_id -a 10 -s no -f bam
Transcript abundances were normalized and pairwised differential expression was calculated using DESeq2 version 1.28.1 using default parameters from their vignette
Genome_build: Gencode GRCh38 p13 Release 32
Supplementary_files_format_and_content: Raw transcript abundances for each gene in each sample

source_name: Terminal ileum

growth_protocol: DMEM plus heat-inactivated FBS and antibiotics for up to 2 weeks

extract_protocol:
Collagenae digestion followed by adherence to plastic
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: With or without LF82 E. coli as above

value: Stromal cells

tag: disease state

value: Normal

tag: stimulation

value: Stimulated with LF82 E. coli


title: B16F10 subcutaneous tumor 1

tag: cell line


title: Normal_SCs_3_ (N_SCs_3)

value: No stimulation


title: Expansion

city: Shanghai

first: Mingyu

last: Xia

state: Shanghai

address: No. 83, Fenyang Road, Xuhui District

department: ENT Institute and Otorhinolaryngology Department of the Affiliated Eye and ENT Hospital, Sta

country: China

institute: Fudan University

description: Cochlear organoid derived from cochlear progenitor cells

data_processing:
Raw 10X single-cell RNA-seq data from three time points (expansion, early differentiation, and late differentiation) were demultiplexed, aligned (GRCm38), and feature-counted by Cellranger using the default settings
Cell barcode processing, feature-barcode matrix were generated by cellranger.
Genome_build: hg38
Supplementary_files_format_and_content: csv files (barcodes.csv.gz, features.tsv.gz.gz) and mtx.gz files (matrix.mtx.gz.gz)

source_name: cochlear progenitor cells

growth_protocol: Lgr5+ progenitor cells were initially expanded in 3D culture system in expansion medium based on DMEM/F-12, GlutaMAX culture medium, supplemented with penicillin/streptomycin, N2, B27, EGF , bFGF , and IGF, CHIR99021, Y-27632 and LPA and then shifted to differentiation medium composed of bFGF, BDNF, Shh, A83-01, RA, and LY4115775 during the initial 5 days, and removed LY4115775 afterward.

extract_protocol:
Organoids from passage 2 (day 8) in expansion medium, from differentiated day 5, and from differentiated day 25 were collected and incubating with 0.125% trypsin for 25 min and dissociated into single cells by mechanical pipetting. Nuclei were stained with DAPI (Sigma) on ice for 10 minutes, then cells were sorted using a MoFlo® SX FACS cytometer (Beckman Coulter). Sorted single, living cells were resuspended in 40 mL of fresh cell media.
Single-cell transcriptomic profiling was performed using the Single Cell 3’ Reagent v3 kits according to the manufacturer’s recommendations (10X Genomics

value: Organoids derived from cochlear progenitor cells

tag: culture medium

value: Lgr5+ progenitor cells were initially expanded in 3D culture system in expansion medium based on DMEM/F-12, GlutaMAX culture medium, supplemented with penicillin/streptomycin, N2, B27, EGF (20 ng/mL), bFGF (10 ng/mL), and IGF (50 ng/mL), CHIR99021 (3um), Y27-632  (10um) and LPA (2.5um)


title: Crohn's_SCs_5+LF82_(C_SCs_5+LF82)

value: Crohn's disease


title: Crohn's_SCs_5_(C_SCs_5)


title: Differentiation day 5

value: Lgr5+ progenitor cells were initially expanded in 3D culture system in expansion medium based on DMEM/F-12, GlutaMAX culture medium, supplemented with penicillin/streptomycin, N2, B27, EGF (20 ng/mL), bFGF (10 ng/mL), and IGF (50 ng/mL), CHIR99021 (3um), Y27-632  (10um) and LPA (2.5um) and then shifted to differentiation medium composed of bFGF, BDNF, Shh, A83-01, RA, and LY4115775


title: Normal_SCs_3+LF82_(N_SCs_3+LF82)


title: Crohn's_SCs_4_(C_SCs_4)


title: Crohn's_SCs_4+LF82_(C_SCs_4+LF82)


title: hiPSC-S4

city: Syracuse

first: Yuanhui

last: Song

address: 318 Bowne Hall

institute: Syracuse University

data_processing:
The unaligned reads were trimmed for bases to obtain a Phred quality score > 20, and then aligned using the Spliced Transcripts Alignment to a Reference (STAR) to the human genome (hg38).
Assembly: hg38
Supplementary files format and content: tab delimited text files include raw counts for each sample

source_name: SKIN

extract_protocol:
mRNA was extracted using Trizo, Chloroform, and isopropanol.
RNA library was finished by Azenta USA Inc.

value: SKIN

value: Drived cells

value: human induced pluripotent stem cell

value: NO


title: Neural Crest-S6

value: stem cells

value: WT

value: Neural Crest differentiation


title: Cytotrophoblast-S3

value: Cytotrophoblast differentiation


title: Ctrl_Inflammatory_Mo_scRNA-Seq

value: Ly6Chigh BM monocytes


title: Crohn's_SCs_3+LF82_(C_SCs_3+LF82)

value: Stromal cells


title: Neural Crest-S11


title: Old11D

city: Akita

first: Takako

last: Ohnuma

state: Akita

department: ARGG

institute: Akita University

hyb_protocol: After complementary RNA had been fragmented to sizes ranging from 35 to 200 bases by heating(35 min at 95℃), 10μg of RNA fragments were hybridized (16h at 45℃) to the Affimetrix Mouse Clariom S Array which interrogates over 20800 well annotated genes.

scan_protocol: The gene chips were automatically washed and stained with streptavidin-phycoerythrin bythe GeneCip Fluidis Statio 450.The chips were scannedusing the GeneChip Scanner 300 7G.

data_processing: Primary data analysis was performed with the Affymetrix Transcriptome Analysis Console(TAC) software and normalized and following the TAC user guide.

label: biotin

source_name: tissue

label_protocol: Doublw stranded cDNA synthesis and biotin-labeled cRNA was performed with GeneChip WT Plus Kit.

extract_protocol: Mouse hippocampus tissues were used as samples. Total RNA was isolated with QIAGEN Rnesy Lipid Tissue Mini kit.

value: hippocampus


title: Old18


title: Old3


title: Cytotrophoblast-S1


title: Old2D


title: Young20


title: Young7


title: Young19


title: Old8


title: Normal_SCs_4_(N_SCs_4)

source_name: terminal ileum

value: Normal


title: Crohn's_SCs_3_(C_SCs_3)

value: No stimulation


title: UC-MSC-P3-S


title: UC-MSC-1


title: Normal_SCs_1_(N_SCs_1)


title: Normal_SCs_2_(N_SCs_2)

source_name: Jejunum


title: Crohn's_SCs_2_(C_SCs_2)


title: NC-iMSC-7

value: MSC differentiation


title: hiPSC-S3


title: Crohn's_SCs_1_(C_SCs_1)


title: CT-iMSC-7


title: ClpP siRNA treated cells

city: Busan

first: Jong-Ho

last: Lee

address: 37 Nakdong-daero 550 Beon-gil

country: South Korea

institute: Dong-A University

data_processing:
FastQC v0.10.0 for quality check
Trimmomatic 0.32 for trimming
TopHat version 2.0.13 and bowtie2 2.2.3 for read mapping
Cufflinks version 2.2.1 for sequence assembly
deFuse 0.6.2 for paired end alignments clustering
Genome_build: STAR 2.4.0f1 for genomic DNA reference mapping
Supplementary_files_format_and_content: expression

source_name: in vitro cultured cells

extract_protocol:
The TruSeq RNA Sample Preparation Kit v2 (Illumina, #RS-122-2001) was used to convert poly-A containing mRNAs in total RNA to a cDNA library using poly-T oligos linked to magnetic beads.
Following mRNA purification, the RNA was physically fragmented at an elevated temperature prior to reverse transcription and cDNA generation. The fragmentation step resulted in the production of an RNA-Seq library containing inserts ranging in size from approximately 100-400 base pairs (bp).
The cDNA fragments were then subjected to an end-repair process, during which a single ‘A’ base was added to the 3’ ends and then adaptors were ligated. Finally, the products were purified and enriched by PCR to generate the final double-stranded cDNA library. The libraries were quantified using KAPA Library Quantification Kits for Illumina Sequencing platforms according to the qPCR Quantification Protocol Guide (KAPA Biosystems, KK4855) and qualified using the TapeStation D1000 ScreenTape device (Agilent Technologies, 5067-5582).

value: primary hepatocytes

value: ClpP siRNA

value: liver


title: CT-iMSC-6

value: SKIN


title: DP-MSC-1

source_name: dental pulp

value: dental pulp

value: Primary cells


title: Control siRNA (GFP) treated cells

value: GFP siRNA


title: Baf3,TPR-FGFR1-2

city: Nanjing

first: Mengyao

last: Lv

address: 305 East Zhongshan Road, Nanjing

institute: Department of Hematology, Jinling Clinical Medical College, Nanjing University of Chinese Medicine

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp with default parameters.
Clean reads were separately aligned to reference genome with orientation mode using HISAT2 software.
The mapped reads of each sample were assembled by StringTie in a reference-based approach.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Original B cells

extract_protocol:
The RNA-seq transcriptome librariy was prepared following Illumina® Stranded mRNA Prep, Ligation (San Diego, CA) using 1μg of total RNA.
After quantified by Qubit 4.0,the sequencing library was performed on NovaSeq X Plus platform(PE150) using NovaSeq Reagent Kit.

value: Original B cells

value: b lymphocyte

value: TPR-FGFR1 Overexpression


title: Baf3,TPR-FGFR1-1


title: Baf3,empty vector-3

value: WT


title: CP-MSC-P2

source_name: Chorionic Plate

value: Chorionic Plate

value: stem cells

value: NO


title: NE4

first: LIANG

last: SHENG

data_processing:
raw data processing and quality control
mapping to genome
modification site identification
differential site identification
functional enrichment analysis
Assembly: Eukaryotic Non-Strand-Specific Transcriptome Library
Supplementary files format and content: the table includes information on RNA modification sites identified in each sample

source_name: mammary cancer tissue

extract_protocol:
Trizol
preprocessing

value: mammary cancer tissue

value: without intervention


title: Baf3,empty vector-2


title: NE5


title: Cochlear organoid passage 4  2

data_processing:
fastq.gz files of paired-end read files were generated using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing on an Illumina HiSeq2500 150-bp Paired-End Platform
Kallisto and DEseq2 were used to analyze the RNA-seq data
Genome_build: mm9
Supplementary_files_format_and_content: csv files (Gene expression of each sample)

source_name: Cochlear organoid

growth_protocol: Sample:EFI, EFIC, EFICL, Cochlear organoid passage P 0 and Cochlear organoid passage P 4 all have three replicates. Lgr5+ progenitor cells were cultured in 3D expansion system with 5% matrigel.Basic expansion medium was based on DMEM/F-12, GlutaMAX culture medium, supplemented with penicillin/streptomycin, N2, B27, EGF , bFGF , and IGF ,CHIR99021, LPA and Y-27632. EFI: EGF , bFGF ,IGF and Y-27632; EFIC: EGF , bFGF, IGF, Y-27632 and CHIR99021; EFICL, Cochlear organoid: EGF , bFGF , IGF,Y-27632, CHIR99021 and LPA.

extract_protocol:
Organoids were washed by PBS for three times and harvested by centrifugation. Total RNA was extracted by trizol and flash frozen in liquid nitrogen.
The RNA-sequencing libraries were generated by the Illumina mRNA-Seq Sample Prep Kit. fastq.gz files of paired-end read files were generated using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing on an Illumina HiSeq2500 150-bp Paired-End Platform.

value: Cultured organoids from Lgr5+ cochlear progenitor cells

value: DMEM/F12 Glumax, N2, B27, PS,EGF, bFGF, IGF, CHIR99021, LPA, Y-27632


title: CV-MSC-1

source_name: chorionic villi

value: chorionic villi


title: Baf3,empty vector-1


title: NE2


title: BM-MSC

source_name: Bone marrow

value: Bone marrow


title: BM-MSC-P4


title: E5

value: voluntary exercise condition


title: Cochlear organoid passage 4  1

treatment_protocol: EFI: EGF , bFGF ,IGF and Y-27632; EFIC: EGF , bFGF, IGF, Y-27632 and CHIR99021; EFICL, Cochlear organoid: EGF , bFGF , IGF,Y-27632, CHIR99021 and LPA.


title: Baf3,TPR-FGFR1-3


title: NE1


title: E4


title: AD-MSC-P4-2

source_name: Adipose

value: Adipose


title: E3


title: Lgr5+ cochlear progenitor cells 2

value: Sorted Lgr5+ cochlear progenitor cells


title: Lgr5+ cochlear progenitor cells 1


title: E2


title: Cochlear organoid passage 4  3


title: E1


title: WT U2OS cells exposed to irofulven (HMAF), biological replicate R3

city: Zurich

first: Shana

last: Sturla

address: Schmelzbergstrasse 9

department: Department of Health Sciences and Technology

country: Switzerland

institute: ETH Zurich

data_processing:
After demultiplexing of sequencing data, each sample was represented by a fastq.gz file containing 101-nucleotide-long genomic reads. The quality of the raw sequencing data was checked via FastQC version 0.11.9. Low-quality reads and adapter-containing reads were removed via trimmomatic version 0.38 with the following parameters: SE ILLUMINACLIP:Trimmomatic-0.39/adapters/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:101. We retained only those reads that contained a validation code (TCAACAA for MoDIS_2; T(10xN)CAACAA for MoDIS_1; Supplementary Table 1). The first 17 nucleotides corresponding to the validation code and randomized index code (10xN) were clipped from the read sequences and appended to the read names via the tool extract of umi_tools/1.1.2 toolkit. The reads were mapped to human reference genome GRCh38 via bowtie2 version 2.3.5.1, using pre-built bowtie2 index from https://genome-idx.s3.amazonaws.com/bt/GRCh38_noalt_as.zip, and applying otherwise standard settings. Read duplicates were removed by the tool dedup of umi_tools version 1.1.2 toolkit, grouping reads with the same code sequence stored in the read name (method=unique). Samtools version 1.12 were employed to sort, index and generate statistics of bam files. bedtools2 version 2.29.2 were used to retrieve the coordinates of mapped and deduplicated reads and extract the sequence context of the damaged nucleotides from the reference genome. Each read represented one unit of DNA-modification signal, which we positioned at the nucleotide of the 5’ end of the read. Since a read was the reverse complement of the DNA fragment captured in the method employing MoDIS, the strand of the nucleotide bearing the signal was changed to the opposite. We implemented the described DNA-modification-signal positioning via custom scripts in Python version 3.7.4 with the modules numpy version 1.21.5, pandas version 0.25.1 and biopython version 1.79.
Assembly: GRCh38
Supplementary files format and content: In the provided sample-specific tsv-files, each line reflects one DNA modification revealed by one mapped read. The tsv-files contain the following columns: 1) the chromosome, 2) the 0-based coordinate, 3) the strand, 4) the nucleotide bearing the signal, 5) MAPQ score of the read.

growth_protocol: HAP1 cells (RRID:CVCL_Y019, Horizon Discovery) were cultivated in Iscove's Modified Dulbecco's Medium supplemented with 10% fetal bovine serum (Gibco) and 1% penicillin-streptomycin (Gibco) at 37°C, 5% CO2, 3% O2. U2OS cells (RRID:CVCL_0042) were cultivated in McCoy‘s general cell culture medium, modified with high glucose, L-glutamate, bacto-peptone and phenol red, and lacking sodium pyruvate and HEPES (4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid) (McCoy‘s 5A, Gibco 16600082), supplemented with 10% fetal bovine serum (Gibco) and 1% penicillin-streptomycin (Gibco) at 37 °C, 5% CO2.

extract_protocol:
Cells were harvested by removing the medium, washing once with 10 mL DPBS followed by addition of 1 mL 0.25% Trypsin EDTA solution (Gibco). After an incubation of 5 min at 37°C, 9 mL medium was added, cells resuspended and transferred to a Falcon centrifugal tube. Cells were centrifuged (4°C, 0.3 rcf, 5 min) and the supernatant removed. gDNA was extracted from  cell pellets using the Monarch Genomic DNA Extraction Kit following the manufacturer’s instructions. In case oxidative-modification mapping (HAP1 cells), in order to avoid artefactual oxidation, DPBS used in the cell pellet resuspension  was supplemented with 1 mM deferoxamine and 50 µM n-tert-butyl-α-phenylnitrone.
To minimize artefactual damage, samples were inverted or flicked, instead of pipette mixing, until the copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC) step. In case of endogenous-DNA-oxidation mapping, gDNA was eluted in H2O supplemented with 500 µM 8-hydroxyquinoline (HQ; Sigma) after extraction and purification. Undesired background modifications were blocked by adding 1 µL ENDOIV (NEB, 10 U/µL) and 500 µM 8-HQ to 5 µg gDNA, freshly extracted from HAP1 pellets, in 1x ThermoPol Buffer (NEB) in a final volume of 20 µL, and incubating the mixture for 20 min at 37°C. 2.5 µL ddNTP mix (Jena Biosciences, 2.5 mM), 0.5 µL 10x ThermoPol Buffer, 1.8 µL of 8-HQ (500 µM) and 0.2 µL Therminator IX (NEB, 10 U/µL) were added, followed by a 10 min incubation at 60°C. 25 µL 8-HQ (500 µM) and 80 µL Pronex beads were added for purification with an elution volume of 25 µL. To label oxidative modifications, 1 µL FPG (NEB, 8 U/µL), 1 µL ENDOIV (NEB, 10 U/µL) and 3 µL 10x NEBuffer 2 (NEB) were added for a final volume of 30 µL; the reaction mixture was incubated for 1 h at 37°C, immediately followed by adding 3.5 µL prop-dGTP (Jena Biosciences, 2.5 mM), 0.5 µL 10x NEBuffer 2 (NEB), 0.8 µL 8-HQ (500 µM) and 0.2 µL Therminator IX (NEB 10 U/µL) for 10-min incubation at 60°C. In case of mapping AP sites, 5 µg of freshly extracted U2OS gDNA was diluted with water to a final volume of 20 µL and incubated at 37°C for 18 h; then, to dephosphorylate background strand breaks, 1 µL T4 polynucleotide kinase (T4 PNK) (10 U/µL, NEB) was added to the gDNA in 1x NEBuffer 2 (NEB) in a final volume of 25 µL and incubated for 30 min at  37°C. 3 µL ddNTP mix (Jena Biosciences, 2.5 mM), 0.5 µL 10x NEBuffer 2 (NEB), 1.3 µL water and 0.2 µL Therminator IX (NEB, 10 U/µL) were added, followed by a 10 min incubation at 60°C. 20 µL water and 80 µL Pronex® beads were added for purification with an elution volume of 25 µL. To label AP sites, 1 µL Endonuclease IV (ENDOIV) (10 U/µL, NEB) and 3 µL 10x ThermoPol buffer (NEB) were added for final volume of 30 µL; the reaction mixture was incubated for 30 min at 37°C, immediately followed by adding 4 µL prop-dGTP (2.5 mM in H2O, Jena Biosciences), 5 µL prop-dATP (2 mM in H2O, Jena Biosciences), 1 µL 10x ThermoPol buffer (NEB), 0.8 µL H2O and 0.2 µL Therminator IX (10 U/µL, NEB) for 10-min incubation at 60°C. Steps for mapping either AP sites or oxidative modifications are identical from this point onwards. gDNA was purified using Pronex Magnetic Beads (Promega) with a sample:bead ratio of 50:80 and using an elution volume of 50 µL with Buffer EB. Sonication of gDNA was performed using a Q800R2 sonicator (QSonica) with the following settings: 4°C, 20% amplitude, pulse 15 s on, 5 s off, total 5 min. The resulting DNA fragments were analyzed on a Tapestation 2200 using a High Sensitivity D100 ScreenTape (Agilent Technologies). DNA was purified using Pronex beads with a sample:beads ratio of 1:2 and 50 µL elution volume. Samples were quantified using a Quantus Fluorometer. For adapter ligation, NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) was utilized using 1 µg gDNA and the pre-annealed NEB adapter (NEB_P7, NEB_P5, 15 µM; Supplementary Table 1). The manufacturer’s instruction was followed without performing the USER enzyme step. The sample was purified using Pronex beads in sample:beads ratio 1:2 and elution in 50 µL Buffer EB. Successful adapter ligation was checked on an Agilent TapeStation with a High Sensitivity D100 ScreenTape. The sample volume was then condensed to 6 µL using a vacuum concentrator. To denature gDNA, the sample was heated to 95°C for 2 min and rapidly cooled on ice. CuAAC reaction was performed using 2 µL MoDIS (100 µM equimolar mixture of MoDIS_1 and MoDIS_2; Supplementary Table 1), 4 µL DMSO, 2 µL premixed CuSO4:THPTA (THPTA from Lumiprobe; 20 mM Cu2+ and 200 mM THPTA) and 2 µL sodium phosphate buffer (1 M, pH 7.0). The reaction was started by adding 2 µL sodium ascorbate (400 mM in H2O, freshly prepared) and incubated for 60 min at 37°C. Purification was done using Pronex beads in a sample:beads ratio 1:2 and 30 µL elution volume. Biotin enrichment of sample DNA was performed using Dynabeads MyOne Streptavidin C1 (ThermoFisher). First, B&W buffer was prepared according to the manufacturer’s protocol including 0.05 % Tween 20. Then, 15 µL Dynabeads were transferred to a fresh tube, washed three times with 200 µL 1x B&W buffer and resuspended in 30 µL 2x B&W buffer. The DNA sample was denatured by heating to 95°C for 2 min and rapid cooling on ice. Then, 30 µL sample was mixed with 30 µL of the prepared Dynabeads and rotated for 15 min at RT. Afterwards, the Dynabeads were washed 3x with 1x B&W buffer by resuspending the beads, 3 min rotation and 1 min pelleting on a magnetic rack. A final wash was performed with Buffer EB and Dynabeads were resuspended in 20 µL Buffer EB. To amplify the biotin-enriched material, a PCR was performed by adding 5 µL 10x ThermoPol buffer, 5 µL dNTP mix (NEB, 2 mM), 1 µL MgSO4 (100 mM), 1 µL ex_UMI (10 µM; Supplementary Table 1), 1 µL Pr_P7 (10 µM; Supplementary Table 1) and 0.5 µL Vent (exo-) DNA Polymerase (NEB 2 U/µL). The PCR program comprised an initial denaturation step (95°C, 120 s), followed by 5 cycles of denaturation (95°C, 20 s), annealing (59°C, 20 s) and elongation (72°C, 60 s) and a final elongation step (72°C, 300 s). The sample was purified with Pronex beads in a sample:beads ratio 1:2 and an elution volume of 30 µL. Final library amplification and indexing was performed by adding 25 µL NEBNext Ultra II Q5® Master Mix (NEB), 2.5 µL i5_Index (10 µM; Supplementary Table 1) and 2.5 µL i7_Index (10 µM; Supplementary Table 1) to 20 µL sample. The PCR program comprised an initial denaturation step (98°C, 30 s), 10 cycles of denaturation (98°C, 10 s), annealing (68°C, 30 s) and elongation (72°C, 20 s), and a final elongation step (72°C, 120 s). The PCR sample was purified with the Pronex beads dual size selection protocol using an initial sample:beads ratio of 1:1, followed by a sample:beads ratio of 0.5:1 to exclude fragments longer than 1000 bp and shorter than 250 bp. The final sample concentration was adjusted to a concentration of 4 ng/µL and sequenced on an Illumina NovaSeq 6000.
OTHER: click-code-seq

treatment_protocol: For irofulven (HMAF) treatment, medium was prepared by adding HMAF (50 mM stock, dissolved in DMSO) to 10 mL medium to a final concentration of 15 μM. A control medium was prepared by adding DMSO in the same volume as the treatment to 10 mL medium. The treatment and control media were filtered with a sterile syringe filter (0.22 μm), added to the cells for further incubation for 4 h at 37°C.

value: wild type

value: irofulven


title: NE3


title: WT U2OS cells exposed to irofulven (HMAF), biological replicate R2


title: 10mgKg_10

first: Yingjia

last: Chen

address: 75 Franis St

description: Treatment 5

data_processing:
The Zymo Research RNA-Seq pipeline was originally adapted from nf-core/rnaseq pipeline v1.4.2 (https://github.com/nf-core/rnaseq). The pipelines was built using Nextflow (https://www.nextflow.io/). Differential gene expression analysis was completed using DESeq2 v1.28.0 (https://bioconductor.org/packages/DESeq2/). Functional enrichment analysis was achieved using g:Profiler python API v1.0.0 (https://biit.cs.ut.ee/gprofiler/gost). Quality control and analysis results plots were visualized using MultiQC v1.9 (https://github.com/ewels/MultiQC).
Assembly: GRCm39
Supplementary files format and content: excel file include normalized counts for each sample
Supplementary files format and content: excel file include differential gene expression analysis results between Treatment and Control groups

source_name: distal ileum

extract_protocol:
Distal ileum tissues (~20 mg) were kept on dry ice and overnight shipped to Zymo Research (Irvine, CA) for total RNA exraction.
Libraries were prepared using the Zymo-Seq RiboFree Total RNA Library Prep Kit (Cat # R3000) according to the manufacturer’s instruction manual v1.3.0.

treatment_protocol: 10 week-old male DIO mice were orally gavaged with TDCA solution (10 mg/Kg body weight) or water at an equivalent volume. After 4 weeks of treatment, mice were sacrificed. Distal ilea were harvested, snap frozen and stored at -80 C until further analysis.

value: distal ileum

value: DIO C57BL/6J

value: male

value: oral gavage with TDCA solution (10 mg/Kg body weight) for 4 weeks


title: Cdh1+ epithelium 3

source_name: cochlear sensory epithelium cells

value: Sorted Cdh1+ cochlear sensory epithelium cells


title: WT U2OS cells exposed to irofulven (HMAF), biological replicate R1


title: 10mgKg_7

description: Treatment 4

value: WT


title: Healthy donor_6

city: NY

first: Christopher

middle: Y.

last: Park

address: 550 First Avenue

institute: NYU Grossman School of Medicine

data_processing:
Following demultiplexing, data quality control, alignment, and generation of a read count matrix, DESeq2 was used for differential gene expression analysis.
Assembly: hg38
Supplementary files format and content: tab limited text file contains raw count for each sample

extract_protocol:
Bone marrow mononuclear cells (BMMCs) were isolated from BM samples using Ficoll-Paque Plus (GE Healthcare, Massachusetts, US) density gradients per manufacturer’s instructions. CD34+ cells were isolated by immunomagnetic separation using an autoMACs Pro Separator (Miltenyi Biotec GmbH, Bergisch Gladbach, Germany) following the manufacturer´s instructions. Sorted cells were snap-frozen and stored at -80ºC. Total RNA was extracted using the RNeasy Micro Kit (Qiagen, Valencia, CA, USA) following the manufacturer’s protocol. RNA integrity was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 Nano Assay kit. RNA quantities were assessed by qubit 2.0 (ThermoFisher Scientific, Massachusetts, U.S.A.) using an RNA kit (high/broad sensitivity).
Libraries were prepared using the SMART-Seq v4 Ultra Low Input RNA kit (Clontech, California, U.S.), and sequenced on a HiSeq400 sequencer (Illumina) according to manufacturer´s protocol with a read length of 2 × 150 nucleotides.

value: Bone marrow mononuclear cells (BMMCs)

value: CD34+ HSPC

value: no treatment


title: Healthy donor_5


title: Cdh1+ epithelium 2


title: Old6D

value: hippocampus


title: Healthy donor_4


title: WT U2OS cells exposed to DMSO (vehicle control), biological replicate R2

value: DMSO


title: Lgr5+ cochlear progenitor cells 3


title: Healthy donor_3

value: Bone marrow


title: 10mgKg_6

institute: Brigham and Women's Hospital

description: Treatment 3


title: WT U2OS cells exposed to DMSO (vehicle control), biological replicate R1


title: Cdh1+ epithelium 1


title: 10mgKg_4

description: Treatment 2


title: WT HAP1 cells (no exposure), biological replicate R3

value: No exposure/treatment


title: EFICL _Organoid P0_3

value: Cultured organoids from Lgr5+ cochlear progenitor cells

value: DMEM/F12 Glumax, N2, B27, PS,EGF, bFGF, IGF, CHIR99021, LPA, Y-27632


title: Healthy donor_2


title: EFICL _Organoid P0_2


title: AD-MSC-P4-1

value: Adipose

value: Primary cells

value: stem cells

value: NO


title: 10mgKg_3

description: Treatment 1

value: distal ileum

value: DIO C57BL/6J

value: male


title: Healthy donor_1


title: WT HAP1 cells (no exposure), biological replicate R2

value: wild type


title: 0mgKg_12

description: Control 5

value: WT

value: oral gavage with water for 4 weeks


title: EFICL _Organoid P0_ 1


title: Patient_14 post-AZA

value: Bone marrow mononuclear cells (BMMCs)

value: CD34+ HSPC

value: AZA treatment


title: WT HAP1 cells (no exposure), biological replicate R1


title: EFIC 3

value: DMEM/F12 Glumax, N2, B27, PS,EGF, bFGF, IGF, CHIR99021, Y-27632


title: 0mgKg_11

description: Control 4


title: Patient_14 pre-AZA

value: Bone marrow

value: no treatment


title: 0mgKg_7

description: Control 3


title: Patient_13 post-AZA


title: EFIC 2

value: Cultured organoids from Lgr5+ cochlear progenitor cells


title: 0mgKg_4

description: Control 2


title: SH2

city: shanghai

first: JL

last: CAI

address: shanghai

institute: fudan university

data_processing:
Raw RNA-seq data were subjected to quality control using FastQC (v0.11.9) and trimmed using Trim_galore (0.6.5-1).
Assembly: GRCh38
Supplementary files format and content: tab-delimmited text file includes FPKM values for each Sample

source_name: Huh7 cells

extract_protocol:
Total RNA was extracted using TRIzol Reagent (Life Technologies, CA, USA) according to the manufacturer's protocol, and RNA integrity was assessed using an Agilent Bioanalyzer 2100 (Agilent Technologies, CA, USA) to obtain RIN values. RNA with RIN values > 7 was purified using an RNAClean XP Kit (Beckman Coulter, Inc. CA, USA) and RNase-Free DNase Set (QIAGEN, GmBH, Germany).
RNA libraries were prepared for sequencing using a VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (Vazyme, Nanjing, China), and sequencing was performed on an Illumina NovaSeq 6000 system.

value: Huh7 cells

value: SRSF10 knockdown


title: SH3


title: Patient_13 pre-AZA


title: SH1


title: 0mgKg_3

description: Control 1


title: NC2


title: EFI 3

source_name: cochlear progenitor cells

value: DMEM/F12 Glumax, N2, B27, PS,EGF, bFGF, IGF, Y-27632


title: EFI 2


title: Gene expression KO1

city: Guangzhou

first: Kai

last: Yan

state: Guangdong

address: No. 106, Zhongshan 2nd Road, Guangzhou

institute: Guangdong Provincial People's Hospital

data_processing:
Clean sequencing data were compared with STAR (Version 2.10.a)
Clean sequencing data obtained through the RPKM matching method and collated as Log2 values in R (Version 4.0.5)
Heat-map, gene-set enrichment analysis was followed-up analyzed based on the expression of target genes with Pheatmap (Version 1.0.12).
Assembly: mm10
Supplementary files format and content: Matrix table with raw clonotype counts, types and other details for samples

source_name: Liver tumor

extract_protocol:
Fresh liver tissues were dissected from HCC mice or control mice, minced and dispersed with scissors in 5 mL tubes, and then digested with 1mg/mL Collagenase IV at 37℃, 120rpm for 45 mins. The cell suspension was screened with 200 mesh filter, centrifuged at 450g, 5 mins, and aspirated supernatant from cell pellet. Further, the tumor-infiltrating leukocytes were purified by 40% percoll gradient centrifugation at room temperature for 20 mins with the acceleration and brake set to medium settings. For flow sorting of macrophages, cell suspension was stained with appreciated antibodies and resuspended at a concentration of 1×107 cells/mL in 1× PBS (pH 7.4) containing 0.5 mM EDTA and 2% FBS, and analyzed with BD Aria II (18 color sorter, USA).
Cells were lysed with Trizol reagent (Invitrogen, USA) and used for microarray analysis with the 4 × 44 K Agilent Whole Mouse Genome Oligo Microarray (Novogene, China) or real-time quantitative PCR. RNA was isolated according to the standard protocol.

value: Liver tumor

value: Tumor associated macrophages

tag: age

value: 6-8 weeks

value: i.pv. Hepa 1-6


title: Gene expression KO2

value: male


title: Patient_12 pre-AZA


title: Patient_12 post-AZA


title: Patient_11 post-AZA


title: Patient_11 pre-AZA


title: LATS1/2 KO indisulam 3

city: Hiroshima

first: Toshinori

last: Ando

address: 1-2-3 Kasumi, Minami-ku

institute: Hiroshima University Hospital

data_processing:
For each sample, paired-end sequencing reads were mapped using HISAT2 version 2.1.0 to the hg38 reference human genome downloaded from Ensembl
To compute transcript abundance, uniquely mapped reads were quantified using featureCounts version 1.6.3.
Assembly: hg38 reference human genome
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

extract_protocol:
RNA was harvested by using Rneasy mini kit (Qiagen). One μg of total RNA was used for the construction of the sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® Poly(A) mRNA Magnetic Isolation Module and NEBNext® UltraTMII Directional RNA Library Prep Kit following manufacture's protocol.

value: head and neck squamous cell carcinoma

value: LATS1/2 KO

value: indisulam


title: NC1

value: WT


title: EFI 1


title: Gene expression WT1

value: Control


title: Gene expression WT2


title: VIC oxLDL rep2

city: Seoul

first: Jae-Hoon

last: Choi

address: 222 Wangsimniro, Seongdong Gu

department: Department of Life Science

institute: Hanyang University

data_processing:
The RNA reads were then aligned to the reference sequences (build mm10) using the 2-pass mode of STAR_ 2.5.0a (default parameters), and relative gene expression was quantified as transcript per million using the RSEM software v1.3.1 (default parameters).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file include TPM values

source_name: Aortic valve and mitral valve

growth_protocol: Isolated VICs were cultured in 10% FBS containing Dulbecco's modified Eagle's medium (DMEM) supplemented with 5 μg/mL insulin, 2 ng/mL EGF and 0.5 ng/mL basic FGF.

extract_protocol:
After trypsinization, RNA was extracted using an RNeasy micro kit following the manufacturer's recommended procedure. A total of 50 ng of total RNA from VICs was used to construct cDNA libraries.
Sequencing libraries were constructed using amplified cDNA with the TruSeq RNA Sample Preparation kit v2 (Cat No. RS-122-2001 & RS-122-2002, Illumina Technologies., USA) for the HiSeq2500 system (Illumina) and sequenced using the 100-bp paired-end mode of the HiSeq Rapid SBS Kit v2 (200 Cycle, Cat No. FC-402-4021) and the HiSeq® Rapid PE Cluster Kit v2 (Cat No. PE-402-4002) with an Illumina HiSeq 2500 system (Illumina Technologies, USA).

treatment_protocol: Cultured VICs were treated with 50 μg/mL of oxLDL, LDL, or an equal amount of buffer for 24 hours at 37 °C and 5% CO2.

value: valvular interstitial cells

value: Aortic valve and mitral valve

value: oxLDL


title: Patient_10 post-AZA

value: Bone marrow

value: Bone marrow mononuclear cells (BMMCs)

value: CD34+ HSPC

value: AZA treatment


title: VIC oxLDL rep3


title: LATS1/2 KO indisulam 2


title: Patient_10 pre-AZA

value: no treatment


title: SCRP_3

city: Toyama

first: Jun-Dal

last: Kim

state: Toyama

address: 2630 Sugitani

department: Department of Complex Biosystem Research (CBR), Institute of National Medicine (INM)

institute: University of Toyama

data_processing:
Reads were mapped on GRCm38/mm10 mouse reference genome and quantified using CLC Genomics Workbench version 12.0 (Qiagen).
Read counts were normalized by calculating number of reads per kilobase per million (RPKM) for each transcript in individual samples using the CLC Genomic Workbench software version 12.0 (Qiagen).
Filtering characteristics of fold-change and false discovery rate (FDR) were used to identify the DEGs.
Assembly: GRCm38/mm10
Supplementary files format and content: Excel file includes raw read counts and RPKM normalized values for all genes from each sample.

source_name: Bone marrow monocytes

extract_protocol:
Rank_cre mice, previously described (Maeda K, et al., Nature Medicine 18, 405-412, 2012), were generously provided by Prof. Kobayashi (Matsumoto Dental University). Sik3_flox mice, also previously described (Yahara Y, et al., Nature Communications 7, 10959, 2016), were provided by Prof. Tsumaki (Osaka University). Bone marrow monocytes from C57BL/6J, Rank_Cre/+, and Rank_Cre/+; Sik3_flox/flox mice were seeded at a density of 2x10⁵ cells/well in 6-well plates and cultured in α-MEM with 50 ng/ml M-CSF for two days. After the initial incubation, the cells were further cultured for two days with 50 ng/ml M-CSF and RANKL.    C57BL/6J mice were obtained from Japan SLC Inc. Bone marrow cells were isolated from mice and seeded in 10 cm dishes. One day after seeding, non-adherent bone marrow cells were re-seeded at a density of 20,000 cells per well in a 48-well plate. The cells were cultured in α-MEM with 10% FBS containing 50 ng/ml M-CSF (Peprotech) for two days to differentiate into bone marrow monocytes. Subsequently, the cells were cultured in the presence of 50 ng/ml RANKL and 50 ng/ml M-CSF for three days to induce osteoclast differentiation. Pterosin B was synthesized by i-Chemical Lab Corporation, Japan, as previously described (Yahara Y, et al., Nature Communications 7, 10959, 2016). Bone marrow monocytes were differentiated into mature osteoclasts with or without pterosin B at final concentrations of 300 μM.    Total RNA was extracted using ISOGEN II reagent (Nippon Gene). 500 ng of total RNA were ribosomal RNA-depleted using NEBNext rRNA Depletion Kit (New England Biolabs), and then converted to Illumina sequencing library using NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs).
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: agent

value: bone marrow monocytes treated with RANKL and pterosin B


title: EFIC 1

value: Cultured organoids from Lgr5+ cochlear progenitor cells

value: DMEM/F12 Glumax, N2, B27, PS,EGF, bFGF, IGF, CHIR99021, Y-27632


title: VIC oxLDL rep1

tag: tissue


title: NC3

value: Huh7 cells

tag: genotype


title: Patient_9 post-AZA

tag: cell type


title: VIC LDL rep3

tag: treatment

value: LDL


title: LATS1/2 KO DMSO 3

value: head and neck squamous cell carcinoma

value: DMSO


title: Patient_9 pre-AZA


title: VIC LDL rep2


title: SCRP_2


title: LATS1/2 KO DMSO 1

value: WT


title: SCRP_1


title: Patient_8 post-AZA


title: LATS1/2 KO DMSO 2


title: VIC Control rep3

value: untreated


title: SCR_3

value: bone marrow monocytes treated with RANKL


title: VIC LDL rep1

value: valvular interstitial cells

value: Aortic valve and mitral valve


title: Patient_8 pre-AZA

value: Bone marrow


title: SCR_2


title: VIC Control rep2


title: WT indisulam 3

value: LATS1/2 KO

value: indisulam


title: LATS1/2 KO indisulam 1


title: WT indisulam 2


title: SCR_1


title: Patient_7 post-AZA

value: Bone marrow mononuclear cells (BMMCs)

value: CD34+ HSPC

value: AZA treatment


title: Patient_6 post-AZA


title: VIC Control rep1


title: SC_2

value: vehicle


title: Patient_7 pre-AZA

value: no treatment


title: SC_3


title: SC_1


title: Patient_6 pre-AZA


title: THP-1 cells, si-CLEC5A, CSE for 48h_3

first: Erkang

last: Yi

address: 195 Dongfeng Xi Road

department: State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease

institute: The First Affiliated Hospital of Guangzhou Medical University

data_processing:
Sequencing fragments are randomly broken from mRNA. To determine which regions on the genome these fragments correspond to, we used HISAT2 software to align the quality controlled clean data reads to the reference genome (parameter: -- dta (preparation for downstream assembly), generating. sam or. bam files that contain alignment records between clean data reads and the genome. We then used the Qualimap RNA seq software process to evaluate the comparison situation (parameter: -- paid)
Calculate the gene count (gene_count. xls) using the featureCounts software in the subRead package, with the key calculation parameters being - p - t exon - g gene_id. The count here refers to the fragment count, which means that a pair of reads are counted as a whole (fragment).
Using gene_count.xls as input, genes with a detection rate (proportion of count not 0) less than 0.25 were screened out. The corrected expression levels of gene_deseq2.xls and geneuedger-TMM.xls were calculated using R language DESeq2 package and edgeR package [, respectively; These two expression tables can be used to compare the expression differences between samples or groups, but cannot be used to compare the expression differences between genes. Please note that these two files cannot be used as direct input files for DESeq2 and edger, nor can they be used to calculate FoldChange for DESeq2 and edger. DESeq2 and edger can only use gene_count.xls as input files, as they have already encoded the calibration process into the model. Please refer to the formula in the literature for the calculation of TPM
Assembly: hg38

source_name: Thp-1 cells

growth_protocol: THP-1 cells, sourced from Procell (Wuhan, China), were cultured in RPMI-1640 medium enriched with 0.05 mM β-mercaptoethanol, 10% fetal bovine serum (FBS, Gibco, USA), and 1% penicillin/streptomycin (P/S, Invitrogen, USA).

extract_protocol:
Total RNA was isolated from lung tissues and cells using the SteadyPure RNA kit (AG21022, AG, China) following an established protocol
After the construction of the library is completed, initial quantification is performed using Qubit2.0 Fluorometer to dilute the library to 1.5ng/ul. Then, Agilent 2100 bioanalyzer is used to detect the insert size of the library. Once the insert size meets expectations, qRT PCR accurately quantifies the effective concentration of the library (the effective concentration of the library is higher than 2nM) to ensure the quality of the library.

treatment_protocol: Differentiation into M0 macrophages was induced with 100 ng/ml phorbol 12-myristate 13-acetate (PMA), following established protocols.

value: Thp-1 cells

value: mononuclear macrophage

value: CLEC7A knockdown

value: PMA and CSE stimulated


title: WT DMSO 2

value: head and neck squamous cell carcinoma

value: WT

value: DMSO


title: THP-1 cells, si-NC, CSE for 48h_3


title: KO_3

value: osteoclast-specific Sik3 conditional knockout


title: THP-1 cells, si-CLEC5A, CSE for 48h_2

value: CLEC6A knockdown


title: P_421_4

city: tartu

first: Maire

last: Peters

department: Dept. of Obstetrics and gynecology

country: Estonia

institute: University of Tartu

data_processing:
barcode processing, sequence alignment, gene counting and aggregation was done using Cellranger software v7.0.0
Seurat R package was used to preprocessing, quality control/checks, sample integration, clustering analysis.
Assembly: refdata-gex-GRCh38-2020-A
Supplementary files format and content: tsv, mtx and rds files

source_name: Ectopic endometrium

extract_protocol:
Cryopreserved samples of EuE and EcE were enzymatically dissociated to obtain single-cell suspensions with viability >90%.
ScRNA libraries were constructed using 10X chromium Next GEM Single cell 3′ reagent v3.1 kit.

value: Ectopic endometrium

value: peritoneal lesions from ectopic endometrium


title: WT DMSO 3


title: THP-1 cells, si-CLEC5A, CSE for 48h_1

value: CLEC5A knockdown


title: THP-1 cells, si-NC, CSE for 48h_1


title: KO_2

value: Bone marrow