title: delta32het_pre-cDC1-3

data_processing:
ATAC-seq samples were trimmed using fastp, mapped to the mm10 genome using hisat2, and deduplicated using Picard.
Peaks were called individually for each sample using MACS2 and then peaks were iteratively merged in R to create a disjoint union peak set encompassing all samples. Genome coverage tracks were normalized based on reads in transcription start sites (TSS) and normalized bigwig files were exported using "rtracklayer::export" in R.
Assembly: mm10
Supplementary files format and content: bigWig, bedGraph

growth_protocol: BM cells were isolated from Irf8 +32+/- and +32/+41 compound heterozygous mice and CD3-, CD19-, B220-, CD105-, TER-119-, Ly-6G- and CD11b-expressing lineage-committed cells were depleted. Pre-cDC1 progenitors were sort purified.

extract_protocol:
5.0 × 104 cells were lysed in ice-cold ATAC-Resuspension Buffer (RSB) containing 0.1% NP40, 0.1% Tween-20 and 0.01% digitonin at 4 °C for 3 min, then washed with ATAC-RSB containing only 0.1% Tween-20. Nuclei were spun down by centrifugation and incubated in 50 mL of transposition buffer (25 mL 2×TD buffer, 16.5 mL PBS, 0.5 mL 1% digitonin, 0.5 mL 10% Tween-20, 5 mL H2O, 2.5 mL TDE1 Tagment DNA Enzyme (Illumina Tagment DNA TDE1 Enzyme and Buffer Kit, Illumina)) at 37 °C for 30 min in a thermomixer with 1000 rpm mixing. Transposed DNA was purified with a DNA Clean & Concentrator Kit (Zymo Research).
Libraries were prepared with a Nextera DNA Library Prep Kit.

treatment_protocol: Irf8 +32+/- and +32/+41 compound heterozygous mice were injected once daily, intraperitoneally, with 15 mg recombinant Flt-3L-Ig (BE0098; Bio X Cell) for eight consecutive days to expand pre-cDC1 progenitor cell numbers.


title: Bulge WT P56 A4

status: Public on Mar 14 2023

type: SRA

city: Irvine

first: Maksim

middle: V

last: Plikus

state: California

address: 845 Health Sciences Road

department: Developmental and Cell Biology

country: USA

institute: University of California, Irvine

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56A4

library_source: transcriptomic

data_processing:
Pair-end RNA-seq reads were aligned using STAR_2.4.2 with parameters ‘–outFilterMismatchNmax10–outFilterMismatchNoverReadLmax 0.1–outFilter-MultimapNmax 10’ to the reference genome GRCm38/mm10. We used STAR to then convert to transcriptome-based mapping with gene annotation Gencode v.M8. Gene expression was measured using RESM/1.2.25 with expression values normalized into TPM.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include TPM values for each sample

molecule: total RNA

organism: Mus musculus

source_name: Bulge WT P56

extract_protocol:
RNA libraries were prepared for sequencing using standard Illumina protocols
Smart-seq2

tag: cell type

value: Bulge stem cells

tag: genotype

value: WT

tag: tissue

value: Dorsal skin

tag: age

value: Postnatal day 56


title: WT_028

city: Baltimore

first: Jin-Young

last: Koh

state: Maryland

address: 670 W Baltimore St

department: Otorhinolaryngology-Head & Neck Surgery

institute: University of Maryland, Baltimore

library_source: transcriptomic single cell

data_processing:
The sequencing reads from fastq files were aligned to the mm10 transcriptome (GRCm38) with an index built and quantified using Kallisto pseudo-aligner. Normalized estimated counts and transcripts per kilobase million (TPM) were quantified for each cell’s transcript.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Cochlear stria vascularis

extract_protocol:
After euthanasia by CO2, the temporal bones were removed and placed into DPBS. The temporal bone was removed and opened under a dissecting microscope to access the cochlear membranous labyrinth. Once the cochlea was accessible, the stria vascularis tissue was extracted from the temporal bone and incubated for 5min at 37°C with collagenase from clostridium histolyticum solution at a working concentration of 0.3mg/500µl. The cell dissociation was completed by gently pipetting up and down. The disrupted stria vascularis tissues were placed under an inverted microscope equipped with 20x and 40x objectives and two 3D micromanipulators, each driving a pulled-glass micropipette attached to a nitrogen gas-powered Pico-Injector to control aspiration pressure. The dissociated cells were examined under the inverted microscope and were aspirated into the first pulled-glass micropipette in a slow and controlled manner then washed in fresh DPBS to remove residual collagenase solution and debris.
Nextera XT DNA sample preparation kits, including Tn5 enzymes for tagmentation, were used together with Nextera XT index kits for multiplexing. Tagmentation and amplification of adaptor-ligated fragments were carried out using half-volume reactions. For tagmentation, the input DNA was 0.125 ng. The number of amplification cycles for adaptor-ligated fragments was increased to 14. After the adaptor-ligated single-cell cDNA libraries were purified, single-cell cDNA libraries were run on the Agilent 2100 Bioanalyzer high-sensitivity DNA chips and combined in equimolar concentrations based on index balance. The concentration of pools was measured with Qubit dsDNA HS Assay Kit and Qubit 2.0 Fluorometer.

value: Stria vascularis  cells

value: Cochlear stria vascularis

tag: strain


title: Bulge WT P56 A3

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56A3


title: Bulge WT P56 A1

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56A1


title: WT_027


title: WT_039


title: delta32het_pre-cDC1-2

city: Saint Louis

first: Tiantian

last: Liu

state: MO

address: 660 S. Euclid Ave.

department: Pathology and Immunology

institute: Washington University in St. Louis

library_source: genomic

molecule: genomic DNA

source_name: bone marrow progenitor cells

value: pre-cDC1 progenitor


title: delta32het_pre-cDC1-1


title: WT_026


title: F1_pre-cDC1-3

value: +32/+41 compound heterozygous


title: F1_pre-cDC1-2


title: Immune Mut P56 Rep2

data_processing:
Pair-end RNA-seq reads were aligned using STAR_2.4.2 with parameters ‘–outFilterMismatchNmax10–outFilterMismatchNoverReadLmax 0.1–outFilter-MultimapNmax 10’ to the reference genome GRCm38/mm10. We used STAR to then convert to transcriptome-based mapping with gene annotation Gencode v.M8. Gene expression was measured using RESM/1.2.25 with expression values normalized into FPKM.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample

source_name: CD45+ cells

extract_protocol:
QIAGEN RNA Sample Prep Kit was used to isolate 10 ng of total RNA per sample. RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: CD45+ cells

tag: genotype/variation

value: mutant


title: WT_025


title: Immune WT P56 Rep2

value: wild type


title: HPSI0114ikolf2-clone1, WT, BRM014 [BRM014_PM21132_R3]

city: London

first: Cristina

last: Dias

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

description:
consensus_peaks.mLb.clN.bed.gz
consensus_peaks.mLb.clN.featureCounts.txt.gz

data_processing:
Illumina Casava software used for basecalling.
The nf-core/atacseq pipeline (version 1.1.0) was run with the parameter --min-reps_consensus 2.
For data upload reads mapping to the Y chromosome were removed as required by the MTA associated with the cell line using BBMap's filterbyname.sh function.
Assembly: hg19
Supplementary files format and content: bed file with peak regions
Supplementary files format and content: txt files with counts for each sample and each peak region

organism: Homo sapiens

growth_protocol: Dual SMAD inhibition: day 0 - day 12. Notch inhibition: 24 hrs on day 24.

extract_protocol: NEBNext HiFi 2X PCR Master Mix (New England BioLabs, M0541S)

tag: cell line

value: human induced pluripotent cells

tag: treatment

tag: treatment length

tag: time

value: day 24

tag: differentiation stage

value: Day 24 neuronal cultures


title: Immune WT P56 Rep1


title: WT_023


title: Immune WT P30 Rep2

value: Postnatal day 30


title: F1_pre-cDC1-1


title: Bevacizumab treated Acute EAE (16 dpi) BEVAC003

city: New York

first: Vilas

last: Menon

state: NY

department: Neurology

institute: Columbia University Medical Center

description:
Bevacizumab treated Acute EAE (16 dpi)
single cell RNA seq

data_processing: none provided by the submitter

source_name: Spinal cord

extract_protocol: The neural dissociation kit (P) was used to dissociate the spinal cords into a single cell suspension. Following myelin removal using Miltenyi Biotec Myelin Removal Beads II, the samples were stained with CD31-APC and PI, and live endothelial cells were FACS sorted for single cell RNA sequencing

value: Spinal cord

value: Endothelial cell

value: Complete Freund's adjuvant + Pertussis Toxin + 5 mg/kg Bevacizumab


title: Bevacizumab treated Acute EAE (16 dpi) BEVAC002


title: Bevacizumab treated Acute EAE (16 dpi) BEVAC001


title: WT_021


title: Immune WT P30 Rep1


title: WT_029


title: Myeloid Mut P56 Rep2

source_name: Myeloid cells

value: Myeloid cells


title: Myeloid Mut P56 Rep1

value: Dorsal skin


title: WT_019


title: CFA control DS014

description:
CFA control
single cell RNA seq

value: Complete Freund's adjuvant + Pertussis Toxin


title: Healthy DS013

description:
Healthy
single cell RNA seq


title: WT_018

value: Stria vascularis  cells


title: WT_020

value: Cochlear stria vascularis


title: Acute EAE (16 dpi) DS012

description:
Acute EAE (16 dpi)
single cell RNA seq

value: MOG35-55 + Complete Freund's adjuvant + Pertussis Toxin


title: Myeloid WT P56 Rep2

value: Postnatal day 56


title: WT_022


title: Myeloid WT P56 Rep1


title: Acute EAE (16 dpi) DS011

description:
Acute EAE (16 dpi)
single cell RNA seq


title: WT_024


title: Myeloid WT P30 Rep2


title: WT_017


title: Chronic EAE (28 dpi) DS009

description:
Chronic EAE (28 dpi)
single cell RNA seq


title: WT_016


title: Chronic EAE (28 dpi) DS010


title: Melanocyte Mut P56 Rep2

source_name: Melanocytes

value: Melanocytes


title: WT_015


title: WT_014


title: Healthy DS007

description:
Healthy
single cell RNA seq


title: Melanocyte Mut P56 Rep1

value: mutant


title: Melanocyte WT P56 Rep2

value: wild type


title: Chronic EAE (28 dpi) DS006


title: WT_013


title: WT_012


title: Acute EAE (16 dpi) DS005

description:
Acute EAE (16 dpi)
single cell RNA seq


title: Melanocyte WT P56 Rep1


title: WT_011


title: CFA control DS004

description:
CFA control
single cell RNA seq


title: WT_010


title: Melanocyte WT P30 Rep2


title: Chronic EAE (28 dpi) DS003


title: Melanocyte WT P30 Rep1


title: Acute EAE (16 dpi) DS002

description:
Acute EAE (16 dpi)
single cell RNA seq


title: WT_008


title: WT_009


title: Immune Mut P56 Rep1

value: CD45+ cells


title: Myeloid WT P30 Rep1


title: WT_007


title: MD1145

city: New Delhi

first: Sunil

middle: Kumar

last: Saini

state: Delhi

address: Ansari Marg

department: Department of Biophysics

country: India

institute: AIIMS, New Delhi

data_processing:
All samples were processed using an mRNA-seq pipeline implemented by Novogene Co., Ltd.
Original image data file from high- throughput sequencing Illumina platform was transformed to sequenced reads (called raw reads) by CASAVA base recognition (base calling).
Raw reads were trimmed to remove reads with adaptor contamination, remove reads when uncertain nucleotides constitute more than 10 percent of either read (N > 10%) and remove reads when low quality nucleotides (base quality less than 5) constitute more than 50 percent of the read.
Quality control of reads demonstrated a Q20(%) score of > 97.5 and an error rate < 0.03% for all the samples. The trimmed reads were mapped to human genome.
STAR software was used to accomplish the mapping. Abundance of transcripts were determined as Fragments Per Kilobase of transcript sequence per Millions base pairs (FPKM)
Genome_build: Homo Sapiens(GRCh38/hg38)
Supplementary_files_format_and_content: raw counts

source_name: Gastrocnemius muscle

extract_protocol:
Muscle tissue was collected, snap-frozen in liquid nitrogen and stored at −80°C until analysis. Total RNA from calf muscle tissues was isolated using Tri Reagent (Sigma #93289)
RNA-Seq analysis was performed using Novogene in-house protocol on the Illumina NovaSeq platform (HWI-ST1276) with paired-end 150bp sequencing strategy
RNA library is formed by polyA capture and reverse transcription of cDNA.

value: calf skeletal muscle

tag: disease state

value: Non-PAD individual

tag: progression status

value: Non-PAD

tag: Sex

value: Male

tag: race

value: White


title: CFA control DS001

description:
CFA control
single cell RNA seq

value: Spinal cord

value: Endothelial cell


title: WT_006


title: Hair germ WT P56 Rep1

source_name: Hair germ cells

value: Hair germ cells

value: Dorsal skin


title: shRen KPC1 PDAC tumors treated with Vehicle 5

city: Worcester

first: Marcus

last: Ruscetti

state: MA

address: 364 Plantation Street, LRB-613, LRB-613

department: MCCB

institute: Umass Chan Medical School

data_processing:
150-bp Paired-end reads were aligned to the mouse reference genome GRCm38.p6 (Ensembl, version 101) using STAR (version2.5.3a) (Dobin et al., 2013) with the following option setting: --outFilterMultimapNmax --outFilterScoreMinOverLread  0.15 --outFilterMatchNminOverLread  0.15  --alignSJoverhangMin 8  --twopassMode Basic  --alignSJDBoverhangMin 1  --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.1  --seedSearchStartLmax 50 --seedSearchStartLmaxOverLread 0.15 --alignIntronMin 20  --alignIntronMax 1000000  --alignMatesGapMax 1000000  --outFilterType BySJout --limitSjdbInsertNsj  2000000. A gene-by-sample count matrix was generated using featureCounts (subread version 1.6.2) (Liao et al., 2014) with the following option settings: -p  -d 25 -D 1000 -s 0  -F GTF -g gene_id -t exon. All downstream statistical analyses were done using the R (version 4.1.0) programming language (Ihaka and Gentleman, 1996). Briefly, entries of genes with extremely low expression were first removed from the gene-by-sample count matrix. Differential gene analysis was performed using DESeq2 (version 1.32.0) (Love et al., 2014) in consideration of surrogate variables for hidden variations, which were identified using svaseq  (sva version3.40.0)(Leek, 2014). Genes with absolute values of log2 (fold change) greater than one and p-values less than 0.05, which were corrected for multiple testing using the Benjamini-Hochberg procedure (Benjamini and Hochberg, 1995), were considered as significantly differentially expressed genes (DEGs).
Assembly: GRCm38.p6
Supplementary files format and content: A .txt file containing a gene-by-sample raw count matrix with Ensembl gene ID as row and sample name as column.

source_name: Pancreas

growth_protocol: To generate PDAC tumors, 5x104 KrasG12D/+;Trp53R172H/wt (KPCmut) PDAC cells expressing luciferase and GFP (LUC-GFP) were transplanted into the pancreas of 8-10 week old C57BL/6 female mice. Mice were monitored for tumor development by ultrasound on a VEVO3100 system before being randomized into various study cohorts.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen)
RNA library is formed by polyA capture, RNA fragmentation by hydrolysis,  reverse transcription, end-repair, adapter ligation, amplification and size-selectioni by following the instructions of TruSeq RNA Library Prep Kit v2 low sample protocol

treatment_protocol: Tumor-bearing mice were treated with vehicle or combined trametinib (1 mg/kg body weight), and palbociclib (100 mg/kg body weight) per os for 4 consecutive days followed by 3 days off treatment for 2 weeks before sacrafice.

value: Pancreas

value: PDAC

value: KRASG12D;P53 R172H

value: Vehicle


title: Hair germ WT P56 Rep2

value: Postnatal day 56


title: shRen KPC1 PDAC tumors treated with Vehicle 4


title: Healthy DS008

description:
Healthy
single cell RNA seq


title: shRen KPC1 PDAC tumors treated with Vehicle 3


title: Hair germ Mut P56 Rep2

value: mutant


title: Dermal papilla Mut P56 Rep1

source_name: Dermal papilla cells

value: Dermal papilla cells


title: Hair germ Mut P56 Rep1


title: WT_003

value: Stria vascularis  cells

value: Cochlear stria vascularis


title: shRen KPC1 PDAC tumors treated with Vehicle 2


title: shRen KPC1 PDAC tumors treated with Vehicle 1


title: WT_002


title: Dermal papilla WT P56 Rep2

value: wild type


title: TMD8_xeno_Tirabrutinib_10mg_12

type: RNA

city: Shimamoto-cho, Mishima-gun

first: Jun

last: Murai

state: Osaka

address: 3-1-1 Sakurai

department: Drug Discovery Technology

country: Japan

institute: Ono Pharmaceutical Co., Ltd.

description: Tumor from TMD8 xenograft model treated with 10 mg/kg of Tirabrutinib b.i.d.

hyb_protocol: 600 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to microarray for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed following the manufacturer's instructions.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028004_D_F_20120411) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: TMD8 tumor, xenografted, tirabrutinib administered, 10 mg/kg, b.i.d.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using the Low-Input QuickAmp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with a spectrophotometer.

growth_protocol: To establish the TMD8 xenograft model, TMD8 cell suspension (0.1 mL, 100 million cells/mL) was subcutaneously injected into the right flank of female C.B-17/Icr-scid/scidJcl mice.

extract_protocol: RNA was prepared using the miRNeasy kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: When the mean tumor volume in the mouse TMD8 xenograft model had reached about 150 mm3, tirabrutinib was administered to each mouse twice daily. After 21 days of drug administration and 24 h after the final dose, tumors were collected and quickly frozen with liquid nitrogen.

tag: administration

value: Tirabrutinib, 10 mg/kg, b.i.d.

tag: xenograft host

value: C.B-17/Icr-scid/scidJcl mouse

tag: tumor weight


title: Dermal papilla WT P56 Rep1


title: Dermal papilla Mut P30 Rep2

value: Postnatal day 30


title: WT_005

tag: cell type


title: Dermal papilla Mut P30 Rep1

tag: tissue


title: shRen KPC1 PDAC tumors treated with T/P 4

tag: genotype

value: T/P


title: shRen KPC1 PDAC tumors treated with T/P 3


title: Dermal papilla Mut P56 Rep2

tag: age


title: WT_004

tag: strain


title: sucra_24h_1

first: Fabio

last: Zani

address: 1 Midland Rd,

data_processing:
Raw reads were quality and adapter trimmed using cutadapt (version 2.10) before alignment
Reads were mapped and subsequent gene-level counted using RSEM 1.3.1 and STAR 2.7.6 against the mouse genome GRCm38 using annotation release 95, both from Ensembl
Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package (version 1.30.1) within the R programming environment (version 4.0.3)
Assembly: GRCm38 release 95
Supplementary files format and content: rlog log2 normalised expression values. Rows = genes; Columns = samples.

source_name: Primary murine T cells

growth_protocol: primary cd4 T cells have been growth in IMDM with Beta-mercaptoethanol in presence of activating antibodies against CD3 and CD28

extract_protocol:
TriPureTM Isolation Reagent according to manufacturer instruction
mRNA capture and library preparation were performed using the KAPA mRNA HyperPrep Kit according to the manufacter's instructions

treatment_protocol: cd4 T cells have been treated with 0.5mM Sucralose or sodium saccharine for the indicated time point. T cell in IMDM with no sweeteners served as control

tag: time point

value: Primary murine T cells

value: Sucralose


title: NAS_24h_4

tag: treatment

value: NAS


title: TMD8_xeno_Tirabrutinib_10mg_80


title: Dermal papilla WT P30 Rep2

tag: genotype/variation

value: Dorsal skin


title: TMD8_xeno_Tirabrutinib_10mg_144


title: TMD8_xeno_Tirabrutinib_10mg_16


title: shRen KPC1 PDAC tumors treated with T/P 2

value: Pancreas

tag: cell line

value: PDAC


title: TMD8_xeno_Tirabrutinib_10mg_49


title: TMD8_xeno_Tirabrutinib_10mg_38


title: NAS_24h_3


title: shRen KPC1 PDAC tumors treated with T/P 1

value: KRASG12D;P53 R172H


title: shRen KPC1 PDAC tumors treated with T/P 5


title: WT_001


title: shEzh2 KPC1 PDAC tumors treated with Vehicle 5

value: Vehicle


title: NAS_24h_2


title: Bulge Mut P56 Rep2

source_name: Bulge stem cells

value: Bulge stem cells

value: mutant

value: Postnatal day 56


title: Bulge Mut P56 Rep1


title: TMD8_xeno_Tirabrutinib_10mg_31


title: shEzh2 KPC1 PDAC tumors treated with Vehicle 4


title: TCM_24h_4

value: TCM


title: shEzh2 KPC1 PDAC tumors treated with Vehicle 3


title: TMD8_xeno_Tirabrutinib_10mg_48


title: Dermal papilla WT P30 Rep1

value: Dermal papilla cells

value: wild type


title: Bulge WT P56 Rep1


title: NAS_24h_1


title: sucra_48h_4


title: Bulge Mut P30 Rep2


title: shEzh2 KPC1 PDAC tumors treated with Vehicle 2


title: TMD8_xeno_Tirabrutinib_03mg_24

description: Tumor from TMD8 xenograft model treated with 3 mg/kg of Tirabrutinib b.i.d.

source_name: TMD8 tumor, xenografted, tirabrutinib administered, 3 mg/kg, b.i.d.

value: Tirabrutinib, 3 mg/kg, b.i.d.

value: C.B-17/Icr-scid/scidJcl mouse


title: shEzh2 KPC1 PDAC tumors treated with (T/P) 6

value: T/P


title: shEzh2 KPC1 PDAC tumors treated with Vehicle 1


title: sucra_48h_3

value: Primary murine T cells


title: Bulge Mut P30 Rep1

value: Postnatal day 30


title: TMD8_xeno_Tirabrutinib_03mg_32


title: sucra_48h_2

value: Sucralose


title: TMD8_xeno_Tirabrutinib_03mg_20


title: Bulge WT P30 Rep2

value: Dorsal skin


title: shEzh2 KPC1 PDAC tumors treated with (T/P) 5

value: Pancreas


title: sucra_48h_1


title: TMD8_xeno_Tirabrutinib_03mg_57


title: Bulge WT P56 Rep2


title: TMD8_xeno_Tirabrutinib_10mg_92

value: Tirabrutinib, 10 mg/kg, b.i.d.


title: Bulge WT P30 Rep1


title: NAS_48h_4

value: NAS


title: shEzh2 KPC1 PDAC tumors treated with (T/P) 4

value: PDAC

value: KRASG12D;P53 R172H


title: CrT-KO (Replicate 2)

city: San Juan de Alicante

first: Ángel

last: Márquez Galera

address: Av. Santiago Ramón y Cajal, s/n

country: Spain

institute: Instituto de Neurociencias

data_processing:
snRNA-seq initial analysis Quality control of sequenced reads was performed using FastQC (Babraham Institute). Sequenced samples were processed using the Cell Ranger (v.3.1.0) pipeline (10x Genomics) and aligned to a custom "pre-mRNA" GRCm38 (mm10) mouse reference genome (Ensembl annotation v99). The custom reference was built for genes with biotype as protein_coding, lincRNA or antisense, and defined the entire gene body to be an exon. Barcodes with total unique molecular identifier (UMI) count >10% of the 99th percentile of the expected recovered cells were selected for further analysis. After this filtering step, we retained a total of 35694 cells (WT_1:8282 cells; WT_2:9295 cells; KO_1:9270 cells; KO_2:8847 cells) for subsequent analyses. In all four libraries, mean read pairs per cell was above 23000 (WT_1:29018; WT_2:25703; KO_1:32417; KO_2:23627). Confident mapping to exonic regions was higher than 81% for each library; median unique counts per cell were as follows: WT_1:5925; WT_2:6006; KO_1:6700; KO_2:5548; and median detected genes per cell: WT_1:2191; WT_2:2169; KO_1:2312; KO_2:2037.
Cell quality control, filtering, and integration process Downstream analyses, such as quality control, integration, normalization, shared nearest neighbor graph-based clustering, differential expression analysis and visualization were performed using the R package Seurat (version 3.1.4) within R Statistical Computing Platform (version 3.6.3). UMI count data from each sample was normalized following a regularized negative binomial regression with Seurat function SCTransform with default parameters. To integrate the four libraries, the top 3000 gene features were selected for anchors identification based on their redundant detection across samples (SelectIntegrationFeatures). PrepSCTIntegration was run to ensure that all necessary Pearson residuals had been calculated. Next, we identified integration anchors by performing Canonical Correlation Analysis with FindIntegrationAnchors (default parameters and "SCT" as normalization method) and datasets were integrated using the pre-computed anchorset using IntegrateData function.
Dimensionality reduction and cluster detection Principal Component Analysis (PCA) dimensionality reduction was performed using the Seurat function RunPCA with default parameters. A Shared Nearest Neighbor (SNN) Graph for the integrated dataset was built using FindNeighbors over top 30 Principal Components (PCs), and cell clusters were identified by a shared nearest neighbor (SNN) modularity optimization-based clustering algorithm with FindClusters function. To explore the heterogeneity of the cortex, a first cell clustering was performed at a very low resolution (0.03), leading to the identification of 8 clusters. After further exploration of cortex cell heterogeneity by a second cell clustering at the default resolution (0.8) of the SCTransform integration workflow, the data were manually curated into 7 major cell populations (Excit: Excitatory cells, ODC: Oligodendrocytes, Inhib: Inhibitory cells, Micro: Microglia, OPC: Oligodendrocyte precursor cells, Astro: Astrocytes, Endo/Peri: Endotelial cells and/or pericytes). Uniform manifold approximation and projection (UMAP) (Becht et al., 2018) dimensional reduction technique was performed over top 30 PCs using the RunUMAP function.
Normalization and differential expression gene testing For expression plots and differentially expressed gene testing, cell expression was Log-Normalized using NormalizeData function with default parameters. Differential expression analysis was performed using logistic regression gene testing with samples as latent variables (variables to test) with FindAllMarkers function with default parameter settings. Genes differentially expressed between Slc6a8-KO (CrT-/y) and WT (CrT+/y) populations were identified using the Wilcoxon Rank Sum test with the FindMarkers function with the argument logfc.threshold = 0 and default values on the other parameters. P-value adjustment was performed using Bonferroni correction based on the total number of detected genes in the dataset.
Major populations markers heatmap We took the logistic regression gene testing with samples as latent variables without thresholds in average log fold-change over Log-Normalized expression for the 7 major populations. A total of 4866 enriched and statistically significant genes (positive log fold-change and adj p-value < 0.1) were sorted by descending average log fold-change. A proportional downsampling up to 2000 cells per population and top 10 genes from previous lists were used to plot the heatmap, showing scaled Log-Normalized expression. To generate the dot plot of gene expression and detection for the 7 major populations, 3 genes were selected for each population from the top 10 marker genes, showing scaled Log-Normalized expression.
Functional analysis GO functional enrichment analysis for each differentially expressed gene list was performed as described above.
Assembly: GRCm38 (mm10)
Supplementary files format and content: mtx

source_name: Brain

extract_protocol:
Nuclei were acutely purified from brain cortex as described previously with minor modifications (Cid et al., 2021). Brains were immediately removed into ice cold HBBS 1x. A total of four libraries were generated; two libraries per condition (CrT+/y and CrT-/y) were prepared, corresponding to independent biological replicates. For each library, the cerebral cortex of the right hemisphere was manually dissected and transferred into 1 mL of ice-cold MACS buffer (0,5% BSA, 2 mM EDTA, PBS 1x). Each cortex was then homogeneized 12-15 times with the pestle of a dounce homogeneizer (20404, Lab Unlimited, Dublin, Ireland). Cell suspensions were passed through a 40 m cell strainer, collected in a 2 mL tube and centrifuged for 15 min (500G, 4ºC). The resulting cell pellets were resuspended in 1 mL of lysis buffer (10 mM Tris-HCL, 10 mM NaCl, 3 mM MgCl2, 0,1% IGEPAL) and transferred into a 15 mL falcon tube containing 9 mL of cell lysis buffer. The cell suspension was kept 5 min on ice, inverting the tube to mix the suspension every 1 minute. Samples were then spun down at 500G for 30 min in a pre-chilled centrifuge. The nuclei pellet was resuspended in PBS 1x 1% BSA, RNase inhibitor 0,2 U/L (3335399001, Merck, Darmstadt, Germany) and 15000 nuclei were purified by flow cytometry in a BD FACS Aria III (BD Biosciences, Madrid, Spain). The whole process was carried out at 4ºC.
Purified intact nuclei were processed through all steps to generate stable cDNA libraries. For every sample, 15000 nuclei were loaded into a Chromium Single Cell A Chip (10x Genomics, Pleasanton, USA) and processed following the manufacturer’s instructions. Single-nuclei RNA-seq libraries were prepared using the Chromium Single Cell 3’ Library & Gel Bead kit v2 and i7 Multiplex kit (10x Genomics). Pooled libraries were then loaded on a HiSeq2500 instrument (Illumina) and sequenced to obtain 75 bp paired-end reads following manufacturer instructions. Libraries were sequenced to obtain more than 900 million reads in total (WT_1:>240M; WT_2:>238M; KO_1:>300M; KO_2:>209M).
snRNA-seq

value: Brain

value: Cortex cells

value: CrT-/y

value: No treatment


title: shEzh2 KPC1 PDAC tumors treated with (T/P) 3


title: TCM_24h_2

value: TCM


title: CrT-KO (Replicate 1)


title: TMD8_xeno_Tirabrutinib_03mg_70

value: Tirabrutinib, 3 mg/kg, b.i.d.


title: TMD8_xeno_Tirabrutinib_03mg_17

value: C.B-17/Icr-scid/scidJcl mouse


title: TMD8_xeno_Tirabrutinib_03mg_83


title: NAS_48h_3


title: Control (Replicate 2)

value: Control


title: shEzh2 KPC1 PDAC tumors treated with (T/P) 1

value: T/P


title: shRen KPC1 PDAC cells treated with vehicle- H3K27me3 2

description:
RV-me3
RV-H3K27me3.blacklist.rmved.size.gt.1000.q0.05.Genrich.narrowPeak
00.Cut_tag.H3K27me3.peak.count.table.txt

data_processing:
Paired-end reads were aligned to the mouse reference genome GRCm38 (Ensembl, version 101) using bwa mem (version 0.7.17) (Li and Durbin, 2009) after quality assurance with FastQC (version 0.11.5) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Alignment files in the SAM format were first sorted by coordinates and converted into the BAM format using SAMtools (version 1.9) (Li et al., 2009). Subsequently, PCR duplicates were removed from the BAM files using MarkDuplicates command of the Picard tools (version 2.9.0) (https://broadinstitute.github.io/picard/). The resulting BAM files were name sorted using SAMtools again. Peaks per condition were called using Genrich (version 0.6) (https://github.com/jsh58/Genrich) with name-sorted, de-duplicated BAM files of all biological replicates for a given condition as input and a q-value cutoff of 0.05. Given that H3K27me3 modification are widespread across inactive gene regions, peaks with sizes less than 1 kb were filtered out. Consensus peaks-by-sample count matrix were determined using DiffBind (version 3.6.1) (Ross-Innes et al., 2012). Differential peak analysis was conducted using DEseq2 (version 1.32.0) (Love et al., 2014) with hidden variations adjusted for using svaseq sva version3.40.0) (Leek, 2014). Peaks with absolute values of log2 (shrunken fold change) greater than one and p-values less than 0.05, which were corrected for multiple testing using the Benjamini-Hochberg procedure (Benjamini and Hochberg, 1995), were considered as significantly differential peaks.
Assembly: GRCm38.p6
Supplementary files format and content: .bigwig files containing the genome-wide read coverage per sample
Supplementary files format and content: .narrowPeak files containing peaks of size greater than 1 kb called by Genrich with a q-value cutoff of 0.05
Supplementary files format and content: .txt file containing a consensus peak-by-sample count matrix, with peak ID (chromosome:peakStart:peakEnd) as rownames and sample names as column names.
Library strategy: CUT&Tag

source_name: pancreas

extract_protocol:
CUT&Tag was performed largely as described in Kaya-Okur et.al. (Nature Protocols, 2020).Trypsinized cells were counted and 100,000 cells were washed and resuspended in wash buffer (20 mM HEPES pH 7.5; 150 mM NaCl; 0.5 mM Spermidine; 1× Protease inhibitor cocktail) and used for CUT&Tag. 10 µL of activated Concanavalin A coated magnetic beads (Polysciences) were added per sample and incubated at room temperature for 15 min. Bead-bound cells were resuspended in 100 µL Dig-wash Buffer (20 mM HEPES pH 7.5; 150 mM NaCl; 0.5 mM Spermidine; 0.05% Digitonin; 1× Protease inhibitor cocktail) containing 2 mM EDTA and 1ul of H3K27me3 antibody (ThermoFisher, MA5-11198). The mixture was incubated overnight at 4 °C for antibodies to bind. After pulling beads to the side of the tube using a magnetic rack and removal of unbound primary antibody, beads were resuspended in 100ul Dig-wash Buffer containing 1ul of Guinea Pig anti-Rabbit antibody (Antibodies-Online ABIN101961) and incubated for 30 mins at RT. Cells were washed 3 times with Dig-wash and then incubated with a 1:50 dilution of pA-Tn5 adapter complex in Dig-med (0.05% Digitonin, 20 mM HEPES, pH 7.5, 300 mM NaCl, 0.5 mM Spermidine, 1X Protease inhibitor cocktail) at RT for 1 hr. Cells were washed thrice in Dig-med Buffer and then resuspended in 300 µL Dig-med Buffer containing 10 mM MgCl2 and incubated at 37 °C for 1 h to activate tagmentation. To stop tagmentation, 10 µL of 0.5 M EDTA, 3 µL of 10% SDS and 1 µL of 20 mg/mL Proteinase K was added to each tube, which were incubated at 55 °C for 1 hour. DNA was extracted by performing one phenol:chloroform extraction followed by ethanol precipitation. The DNA pellet was resuspended in 22 µL of 10 mM Tris pH 8.
CUT&Tag libraries were amplified by mixing 21 µL of tagmented DNA with 2µL each of (10 µM) barcoded i5 and i7 primers, using a different combination for each sample. 25 µL NEBNext HiFi 2× PCR Master mix (NEB) was added, and PCR was performed using the following cycling conditions: 72 °C for 5 min (gap filling); 98 °C for 30 s; 17 cycles of 98 °C for 10 s and 63 °C for 30 s; final extension at 72 °C for 1 min and holding at 4 °C. 1.1× volumes of Ampure XP beads (Beckman Coulter) were incubated with libraries for 10 min room temperature to clean up the PCR reaction. Bead bound DNA was purified by washing twice with 80% ethanol and eluting in 20 µL 10 mM Tris pH 8.0.

value: pancreas

value: Vehicle

tag: antibody


title: NAS_48h_2

value: Primary murine T cells


title: Control (Replicate 1)


title: shRen KPC1 PDAC cells treated with vehicle- H3K27me3 1

description:
RV-me1
RV-H3K27me3.blacklist.rmved.size.gt.1000.q0.05.Genrich.narrowPeak
00.Cut_tag.H3K27me3.peak.count.table.txt


title: TMD8_xeno_Veh_102

description: Tumor from TMD8 xenograft model treated with vehicle

source_name: TMD8 tumor, xenografted, vehicle administered


title: Ldlr-/-Diaph1-/- mice on Western diet sample 4

first: Richard

middle: A

last: Friedman

address: 1130 St. Nicholas Av

department: Medicine

institute: Columbia University Irving  Medical Center

data_processing:
Bases were called with RTA (Illumina).
Adaptors were trimmed and reads were converted from BCL to Fastq format with bcl2fastq version 2.20 (Illumina).
Fastq files were trimmed of low quality bases and adapters with Trimmomatic.
Reads were mapped to the genome with Rsubread
Reads in each gene were counted with featureCounts
Genome_build: mm10
Supplementary_files_format_and_content: xlsx ffile with raw counts for each gene

molecule: polyA RNA

source_name: Liver cells from Diaph1-/- Ldlr-/- mice on Western diet

extract_protocol:
Liver (left lobe) was placed into RLT buffer for RNA extraction with RNeasy® Plus Mini Kit (Qiagen, #74136),
The quality of purified RNA samples was determined using a Bioanalyzer 2100 (Agilent) with an RNA Eukaryote Total RNA Nano chip
Samples have a minimum RIN of 9.0 and an average RIN of 9.53.
Samples were prepared for sequencing using the NuGEN Ovation RNA-Seq system v2 reagents for
cDNA preparation and the Ovation Ultralow DR Multiplex system for the adapter ligation step.
Libraries were amplified by 9 cycles, according to the manufacturer’s instructions.

treatment_protocol:
Mice were placed on western diet for 16 weeks at age 6 weeks. Western diet = Low Fat Clinton-Cybulsky Rodent Diet With 0.15% Cholesterol, Formulated with Standard Casein (Research Diets, D01061401C).
Mice were sacrificed at 22 weeks of age for analysis

value: liver

tag: background strain

value: male

tag: diet

value: Western diet

value: 22 weeks


title: shEzh2 KPC1 PDAC tumors treated with (T/P) 2

value: Pancreas

value: PDAC

value: KRASG12D;P53 R172H


title: TMD8_xeno_Tirabrutinib_03mg_45


title: Ldlr-/-Diaph1-/- mice on Western diet sample 3

tag: Sex


title: TCM_48h_4


title: shRen KPC1 PDAC cells treated with T/P- H3K27me3 4

description:
RTP-me4
RTP-H3K27me3.blacklist.rmved.size.gt.1000.q0.05.Genrich.narrowPeak
00.Cut_tag.H3K27me3.peak.count.table.txt


title: TCM_48h_3


title: Ldlr-/-Diaph1-/- mice on Western diet sample 2


title: TMD8_xeno_Veh_118


title: TMD8_xeno_Veh_42


title: WT_030

source_name: Cochlear stria vascularis

value: Stria vascularis  cells

value: Cochlear stria vascularis


title: TMD8_xeno_Veh_86


title: TCM_48h_2

value: TCM


title: shRen KPC1 PDAC cells treated with T/P- H3K27me3 3

description:
RTP-me3
RTP-H3K27me3.blacklist.rmved.size.gt.1000.q0.05.Genrich.narrowPeak
00.Cut_tag.H3K27me3.peak.count.table.txt


title: TMD8_xeno_Veh_111


title: NAS_48h_1

value: NAS


title: TCM_48h_1


title: Ldlr-/-Diaph1-/-  mice on Western diet sample 1


title: shRen KPC1 PDAC cells treated with T/P- H3K27me3 2

description:
RTP-me2
RTP-H3K27me3.blacklist.rmved.size.gt.1000.q0.05.Genrich.narrowPeak
00.Cut_tag.H3K27me3.peak.count.table.txt


title: sucra_24h_4

value: Sucralose


title: Ldlr-/- mice on Western diet sample 3

source_name: Liver cells from Ldlr-/- mice on Western diet

value: Ldlr-/-


title: shRen KPC1 PDAC cells treated with T/P- H3K27me3 1

description:
RTP-me1
RTP-H3K27me3.blacklist.rmved.size.gt.1000.q0.05.Genrich.narrowPeak
00.Cut_tag.H3K27me3.peak.count.table.txt

value: T/P


title: Ldlr-/- mice on Western diet sample 4


title: shEzh2 KPC1 PDAC cells treated with vehicle- H3K27me3 2

description:
EV-me3
EV-H3K27me3.blacklist.rmved.size.gt.1000.q0.05.Genrich.narrowPeak
00.Cut_tag.H3K27me3.peak.count.table.txt

value: pancreas


title: sucra_24h_3


title: shEzh2 KPC1 PDAC cells treated with vehicle- H3K27me3 3

description:
EV-me4
EV-H3K27me3.blacklist.rmved.size.gt.1000.q0.05.Genrich.narrowPeak
00.Cut_tag.H3K27me3.peak.count.table.txt

value: Vehicle


title: sucra_24h_2

value: Primary murine T cells


title: TMD8_xeno_Veh_131

value: C.B-17/Icr-scid/scidJcl mouse


title: Ldlr-/- mice on Western diet sample 1

value: liver

value: male


title: WT mice on chow  sample 4

source_name: Liver cells from WT  mice on chow

value: WT

value: chow

value: 22 weeks


title: TCM_24HR_1


title: S38W

city: Oklahoma City

first: Jonathan

middle: Daniel

last: Wren

state: OK

address: 825 NE 13th St

department: GHD

institute: OMRF

data_processing:
Raw sequencing reads (in a FASTQ format) were trimmed of residual adaptor sequences using Scythe software. Low quality bases at the beginning or the end of sequencing reads were removed using sickle then the quality of remaining reads was confirmed with FastQC.
Reads were aligned to the Olive baboon (Papio anubis) genome Panu_3.0 (Ensembl release 104) using STAR and per transcript reads were counted with  featureCounts/Subread v2.0.4.
Differentiall expression analyses was performed using edgeR package in the context of limma/voom workflow
Assembly: Panu_3.0
Supplementary files format and content: tab-delimited text file includes ENSEMBL id and raw read counts for each transcript, in each sample

organism: Papio anubis

growth_protocol: Primary fetal baboon tracheal epithelial cells (FBTECs) were cultured on air-liquid interface (ALI) to generate a pseudostratified mucociliary epithelium . Briefly, 1 x 105 cells in 100 µl of BronchiaLifeTM epithelial airway medium (BLEAM) (Cat# LL-0023, Lifeline® Cell Technology, Oceanside, CA, USA) were seeded in the apical chamber of a 0.4 µm pore-sized Transwell® insert (Cat# 3470, Corning®, Corning, NY, USA) pre-coated with human type IV collagen (Cat# C7521, Sigma Aldrich, St. Louis, MO, USA) with 1 ml of BLEAM in the basolateral chamber (ALI day -2). The following day, fresh BLEAM media was replaced in the apical and basolateral chambers (100 µl and 1 ml, respectively). Following two days of submerged culture, media from the apical chamber was removed to expose the cells to air (ALI day 0), and 1 ml of HBTEC ALI differentiation medium (Cat# LM-0050, Lifeline® Cell Technology) supplemented with Penicillin (100 I.U./ml) - Streptomycin (100 µg/ml) was added to the basolateral chamber. The media was replaced every other day and the cells allowed to differentiate for up to 28 days.

extract_protocol:
Total RNA was extracted via direct lysis of cells in the ALI well using the PureLinkTM RNA mini kit (Cat# 12183018A, Thermo Scientific, Waltham, MA, USA) and included DNase treatment (Cat# 12185-010, Thermo Scientific) on the column to remove contaminating genomic DNA. RNA concentrations were measured with a NanoPhotometer® N60 (Implen, Westlake Village, CA, USA)
RNA-sequencing was performed on a NextSeq 2000 P2 Flowcell, (Illumina, San Diego, CA, USA) following library preparation using the QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen, Vienna, Austria). The library preparation and sequencing were performed by the Genomics Core at the University of Oklahoma Health Sciences Center (OUHSC)

treatment_protocol: No treatments to report. The cells were harvested at ALI day 28.

tag: cell tyep

value: tracheal epithelial cells


title: S37W


title: S40W


title: TMD8_xeno_Veh_101

tag: administration


title: SW620-sen2

city: Suwon

first: Soon Sang

last: Park

address: Worldcup-Ro 206

country: South Korea

institute: Ajou University School of Medicine

data_processing:
Potentially existing sequencing adapters and raw quality bases in the raw reads were trimmed by Skewer ver 0.2.2.
The cleaned high quality reads after trimming the low quality bases and sequencing adapters were mapped to the reference genome by STAR ver 2.5 software.
Since the sequencing libraries were prepared strand-specifically by using Illumina’s strand-specific library preparation kit, the strand-specific library option, --library-type=fr-firststrand was applied in the mapping process.
To quantify the mapped reads on the reference genome in to the gene expression values, Cuffquant in Cufflinks ver 2.2.1[4] with
the strand-specific library option, --library-type=fr-firststrand and other default options was used. The gene annotation of the
reference genome hg38 from UCSC genome (https://genome.ucsc.edu) in GTF format was used as gene models and the expression
Assembly: values were calculated in Fragments Per Kilobase of transcript per Million fragments mapped (FPKM) unit.
Supplementary files format and content: xlsx file
Supplementary files format and content: Excel files include FPKM values for each Sample

source_name: colorectal cancer

extract_protocol:
RNA was harvested using NucleoSpin RNA, Mini kit (MN). 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using MGIEasy RNA Directional Library Prep Kit following manufacturer's protocols.

value: colorectal cancer

value: cancer cells

value: 150 uM H2O2 treated for 2 days


title: S39W


title: shEzh2 KPC1 PDAC cells treated with vehicle- H3K27me3 1

description:
EV-me1
EV-H3K27me3.blacklist.rmved.size.gt.1000.q0.05.Genrich.narrowPeak
00.Cut_tag.H3K27me3.peak.count.table.txt

value: PDAC

value: KRASG12D;P53 R172H


title: WT mice on chow  sample 3


title: SW620-sen1


title: shEzh2 KPC1 PDAC cells treated with T/P- H3K27me3 4

description:
ETP-me4
ETP-H3K27me3.blacklist.rmved.size.gt.1000.q0.05.Genrich.narrowPeak
00.Cut_tag.H3K27me3.peak.count.table.txt


title: WT mice on chow  sample 2


title: S35C


title: shEzh2 KPC1 PDAC cells treated with T/P- H3K27me3 3

description:
ETP-me3
ETP-H3K27me3.blacklist.rmved.size.gt.1000.q0.05.Genrich.narrowPeak
00.Cut_tag.H3K27me3.peak.count.table.txt


title: SW620-con2

value: control SW620


title: Ldlr-/- mice on Western diet sample 2

value: Ldlr-/-

value: Western diet


title: WT mice on chow  sample 1


title: S34C


title: TMD8_xeno_Veh_21

value: Vehicle

tag: xenograft host


title: SW620-con1


title: S33C


title: no-primary-antibody CUT&Tag WT

status: Public on Mar 13 2023

city: Seattle

first: Sonali

last: Arora

state: WA

address: 1100 Fairview Ave N,

institute: FHCRC

description: CUT&Tag for IgG control; antibody: Antibodies Online ABIN101961

data_processing:
Paired-end Mus musculus reads were mapped to UCSC mm10 using Bowtie2 version 2.2.2 (Langmead and Salzberg, 2012) with parameters --end-to-end --very-sensitive --no-mixed --no-discordant -q --phred33 -I 10 -X 700.
Continuous-valued data tracks (bedGraph and bigWig) were generated using genomecov in bedtools v2.30.0 (-bg option) and normalized as fraction of total counts.
Assembly: mm10
Supplementary files format and content: bigWig, spike-in calibration, or, read-depth normalization
Library strategy: CUT&Tag

source_name: Organoid culture of bladder urothelium

extract_protocol:
Beads (with bound nuclei) were magnetized, supernatants were removed, beads were washed once with 400 ìl antibody buffer (Wash buffer supplemented with 2 mM EDTA and 0.05% Digitonin), and resuspended in 200 ìl antibody buffer containing the primary antibody in 1:100 v/v dilution (H3K27me3 - rabbit monoclonal, Cell Signaling Technology, cat. no. 9733). Primary antibody incubations were performed on a rotating platform overnight at 4oC. Beads were magnetized, supernatant removed, washed once with 400 ìl Dig-Wash (Wash buffer supplemented with 0.05% Digitonin), resuspended in 200 ìl Dig-Wash containing guinea pig á-rabbit IgG secondary antibody (Antibodies online cat. no. ABIN101961) at 1:00 dilution. Secondary antibody incubations were performed on a rotating platform for 30 min to 1 hr at room temperature. Beads were magnetized, supernatant removed, washed twice with 400 ìl Dig-Wash to remove unbound antibodies, and resuspended in 200 ìl Dig-Med buffer (Dig-Wash buffer, except contai  ning 300 mM NaCl) with 1:200 dilution (~0.04 ìM) of pA-Tn5 pre-loaded with double-stranded adapters with 19mer mosaic ends (Kaya-Okur et al., 2019). pA-Tn5 incubations were performed on a rotating platform for 1 hr at room temperature. Beads were magnetized, supernatant removed, washed three times with 400 ìl Dig-Med to remove unbound pA-Tn5, and resuspended in 300 ìl Tagmentation buffer (Dig-Med supplemented with 10 mM MgCl2). Tagmentation reactions were performed by incubating samples at 37oC on a rotating platform for 1 hr.
Tagmentation reactions were stopped by sequentially adding 10 μl of 0.5 mM EDTA, 3.1 μl of 10% SDS (1% final), and 2 uL of 20 mg/mL Proteinase K, mixed well, and incubated in 50oC water bath for 1 hr. DNA was extracted using phenolchloroform-isoamyl alcohol (25:24:1), re-extracted with one volume CHCl3, aqueous phase (~300 μl) was transferred to fresh tube, and DNA was precipitated by adding 900 μl ethanol overnight at -20°C followed by centrifugation for 45 min at 13,000 rpm and 4°C. Pellets were rinsed with 100% ice-cold ethanol, air-dried, dissolved in 30 μL 0.1 x TE (1 mM Tris pH 8, 0.1 mM EDTA) supplemented with RNase A, and incubated in 37°C water bath for 15 min. To amplify libraries, 21 μL DNA was mixed with 2 μL each of a universal i5 primer and a uniquely barcoded i7 primer, using a different barcode for each sample, and 25 μL of NEBNext HiFi 2x PCR Master mix. Samples were placed in a thermocycler with heated lid using the following cycling conditions: 72°C for 5 min (gap filling); 98°C for 30 sec (denaturation); 13 cycles of 98°C for 10 sec and 63°C for 10 sec (combined annealing and extension); final extension at 72°C for 1 min, and held at 8oC. Post-PCR clean-up was performed using a double-sided clean-up method. 25 μL (0.5 X) of Ampure XP beads (Beckman Counter) was mixed with the libraries and incubated for 10 min at room temperature to remove large DNA fragments (>1300 bp). Beads were magnetized, supernatants were removed to fresh tubes and mixed with 45 μL (1.4 X - 0.5 X = 0.9 X) of Ampure XP beads and incubated for 10 min at room temperature. Beads were magnetized and the supernatants containing unused PCR primers were discarded. Beads were washed three times with 80% ethanol and eluted in 30 μL 10 mM Tris pH 8.0. Libraries were sequenced for 25 cycles in 25bp paired-end mode on the Illumina HiSeq 2500 platform at the Fred Hutchinson Cancer Research Center Genomics Shared Resource. The detailed, step-by-step original protocol can be found at https://www.protocols.io/view/bench-top-cut-amp-tag-kqdg34qdpl25/v3
PCR amplification using indexed primers PMID: 26083756

value: ARID1A WT


title: H3K27ac CUT&Tag KO with GSK126 treatment rep 2

description: CUT&Tag for H3K27ac; antibody: Millipore-Sigma MABE647

value: ARID1A KO


title: ARID1A CUT&Tag WT rep 2

description: CUT&Tag for ARID1A; antibody: CST 12354S


title: ARID1A CUT&Tag WT rep 1


title: H3K27ac CUT&Tag KO with GSK126 treatment rep 1


title: H3K27me3 CUT&Tag KO with GSK126 treatment rep 2

description: CUT&Tag for H3K27me3; antibody: CST 9733


title: H3K27ac CUT&Tag KO rep 2


title: H3K27me3 CUT&Tag KO with GSK126 treatment rep 1


title: H3K27me3 CUT&Tag WT DMSO


title: H3K27me3 CUT&Tag KO with ARID1A re-expression rep 1

value: ARID1A re-expression


title: H3K27me3 CUT&Tag KO with ARID1A re-expression rep 2


title: RPE-1 p53KO LMB2OE Reversine H3K27ac biol rep 2

first: Albert

middle: S

last: Agustinus

state: New York

address: 408 East 69th Street, Room 419-G

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Alignment performed using Bowtie2 v. 2.2.5 Blacklist regions from Encode. Cite: Amemiya, H.M., Kundaje, A. & Boyle, A.P. The ENCODE Blacklist: Identification of Problematic Regions of the Genome.  Sci Rep 9, 9354 (2019). https://doi.org/10.1038/s41598-019-45839-z
Bigwigs generated using Deeptools v. 3.5.1
Peak calling performed with MACS2 v. 2.2.7.1
Peaks annotated with HOMER
Assembly: hg38
Supplementary files format and content: bigwig
Library strategy: CUT&RUN

source_name: Retina (female)

growth_protocol: RPE-1 cells were grown in DMEM supplemented with 10% FBS and 1X Pen-Strep in 100 mm dish (Corning   Corning™ 100 mm TC-Treated Culture Dishes)

extract_protocol:
CUTANA CUT&RUN, Illumina sequencing, and data analysis. CUTANA(R) CUT&RUN was performed on an automated protocol (autoCUT&RUN) derived from those previously described [1-3]. In brief, for each CUT&RUN reaction 500K cells [5 million cells/mL prepared in 20 mM HEPES, pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 1 mM Trichostatin A, 1X EDTA/EGTA-free Complete Protease Inhibitor] were dispensed to individual wells of a 96-well plate, immobilized onto Concanavalin-A beads (Con-A; EpiCypher #21-1401), and incubated overnight (4°C) with 0.5 µg of antibody (IgG, H3K4me3, H3K27me3, H3K27ac) (all antibodies validated to histone post-translation modification (PTM)-defined SNAP-ChIP nucleosome standards as previously [4]). pAG-MNase (EpiCypher #15-1016) was added / activated (2 hours @ 4°C) and CUT&RUN enriched DNA purified using Serapure beads after mixing at 2:1 (Bead:DNA) ratio. Recovered DNA was quantified using PicoGreen and reactions were normalized to 5ng DNA (or entirety of the reaction if <5ng DNA was recovered) before preparing sequencing libraries (CUTANA CUT&RUN Library Prep kit;EpiCypher #14-1001). All autoCUT&RUN steps were optimized / performed on Tecan Freedom EVO robotics platforms with gentle rocking for incubation steps and magnetic capture for media exchange / washing steps.  •        [1] Marunde et al (2022) bioRxiv [doi.org/10.1101/2022.02.21.481373]  •        [2] Yusufova et al (2021) Nature 589:299 [PMID: 33299181]   •        [3] Skene et al (2018) Nat Protoc 13:1006  •        [4] Shah et al (2018) Molecular Cell 72:172 [PMID: 30244833]
Library was prepared according to Epicypher CUT&RUN Kit library prep manual https://www.epicypher.com/content/documents/manuals/14-1001-2-cut-and-run-library-prep-kit-manual.pdf

treatment_protocol: RPE-1 cells were treated with either 1:1000 DMSO (vehicle control) or 0.5 µM reversine for 48 hours, before passaging. This treatment was done long-term until passage #8)

value: Retina (female)

value: hTERT-immortalized retinal pigment epithelial cell line

tag: cut&run antibody

value: H3K27ac - EpiCypher (13-0045)

value: p53KO LMB2OE

value: Reversine 0.5 uM 48 hours before splitting, long-term


title: shEzh2 KPC1 PDAC cells treated with T/P- H3K27me3 2

description:
ETP-me2
ETP-H3K27me3.blacklist.rmved.size.gt.1000.q0.05.Genrich.narrowPeak
00.Cut_tag.H3K27me3.peak.count.table.txt

value: pancreas

tag: cell type

value: T/P


title: RPE-1 p53KO LMB2OE Reversine H3K27ac biol rep 1

tag: tissue


title: RPE-1 p53KO LMB2OE DMSO H3K27ac biol rep 1

tag: genotype

value: DMSO 10 uL 48 hours before splitting, long-term


title: RPE-1 p53KO Reversine H3K27ac biol rep 2


title: shEzh2 KPC1 PDAC cells treated with T/P- H3K27me3 1

description:
ETP-me1
ETP-H3K27me3.blacklist.rmved.size.gt.1000.q0.05.Genrich.narrowPeak
00.Cut_tag.H3K27me3.peak.count.table.txt

value: PDAC


title: RPE-1 p53KO DMSO H3K27ac biol rep 2


title: RPE-1 p53KO DMSO H3K27ac biol rep 1


title: RPE-1 p53KO Reversine H3K27ac biol rep 1


title: RPE-1 p53KO LMB2OE DMSO H3K27ac biol rep 2


title: RPE-1 p53KO LMB2OE DMSO H3K27me3 biol rep 2

value: H3K27me3 - ThermoFisher (MA5-11198)


title: RPE-1 p53KO LMB2OE Reversine H3K27me3 biol rep 2


title: NextSeq2000_A1-2

city: Tomsk

first: Irina

last: Larionova

state: Tomsk oblast

address: Lenin Ave, 36, Tomsk, Tomsk Oblast, Russia

country: Russia

institute: Tomsk State University

description:
Whole transcriptome probes
Instrument model used to produce the reads: Illumina NextSeq 2000
NextSeq2000_A1-2

data_processing:
Raw sequencing reads were primary processed in the Space Ranger v.1.3 using the count command with default parameters. Raw reads were additionally assessed with FastQC quality control algorithm, and results were visualized with MultiQC tool.
After read mapping and counting, resulted feature-barcode matrix was uploaded into R environment and processed via the Seurat R package.
Normalization of the raw read counts in feature-barcode matrix was performed with the SCTransform function in the Seurat package.
Following dimension reduction and clusterization steps, the SCT normalized counts were used in Wilcoxon rank sum test to find differentially expressed genes.
Assembly: hg38
Supplementary files format and content: .h5 Filtered HDF5 Feature-Barcode Matrix
Supplementary files format and content: .json Scale factors for slide images
Supplementary files format and content: .png High resolution slide images
Supplementary files format and content: .png Low resolution slide images
Supplementary files format and content: .csv Tissue spot positions
Library strategy: Spatial Transcriptomics

source_name: Ovarian cancer

extract_protocol:
Three tumor FFPE samples obtained from patients with high-grade serous ovarian cancer were analyzed. Patients were treated in the Department of Gynecological Oncology, Cancer Research Institute of Tomsk National Research Medical Center (Tomsk, Russia). The study was carried out according to Declaration of Helsinki (from 1964, revised in 1975 and 1983) and was approved by the local committee of Medical Ethics of Tomsk Cancer Research Institute; all patients signed informed consent for the study. Shortly, FFPE tissue sections were placed on the Capture Areas of 10x Genomics Visium slides, deparaffinized, and stained by hematoxylin and eosin. Tumor tissue slides were scanned using the Leica Aperio AT2 station (Leica, Germany) and images were processed with Aperio ScanScope.
Libraries were prepared using standard protocol provided by 10x Genomics (User Guide | CG000407). The obtained cDNA libraries were analyzed following 10x Genomics sequencing recommendation for FFPE Visium libraries. Sequencing cycles comprised 28 bp (Read 1), 10 bp (Index 1 and 2) and 50 bp (Read 2). Illumina NextSeq 2000 sequencing was performed using NextSeq 1000/2000 P2 reagents (100 cycles), whereas GeneMind Genolab M used FCM reagents (150 cycles).

value: Ovarian cancer

tag: disease state

tag: patient

tag: slide

tag: area


title: NextSeq2000_B1-2

description:
Whole transcriptome probes
Instrument model used to produce the reads: Illumina NextSeq 2000
NextSeq2000_B1-2


title: RPE-1 p53KO LMB2OE DMSO H3K27me3 biol rep 1

tag: treatment


title: RPE-1 p53KO LMB2OE Reversine H3K27me3 biol rep 1

tag: cell line


title: RPE-1 p53KO Reversine H3K27me3 biol rep 1


title: NextSeq2000_A1-1

description:
Whole transcriptome probes
Instrument model used to produce the reads: Illumina NextSeq 2000
NextSeq2000_A1-1


title: RPE-1 p53KO Reversine H3K27me3 biol rep 2


title: RPE-1 p53KO DMSO H3K27me3 biol rep 2


title: RPE-1 p53KO Reversine H3K4me3 biol rep 2

value: H3K4me3 - EpiCypher (13-0041)


title: RPE-1 p53KO LMB2OE DMSO H3K4me3 biol rep 2


title: RPE-1 p53KO DMSO H3K27me3 biol rep 1


title: RPE-1 p53KO LMB2OE DMSO H3K4me3 biol rep 1


title: RPE-1 p53KO LMB2OE Reversine H3K4me3 biol rep 2


title: RPE-1 p53KO Reversine H3K4me3 biol rep 1


title: RPE-1 p53KO LMB2OE Reversine H3K4me3 biol rep 1


title: DLD-1 cln36 H3K27ac biol rep 2

source_name: DLD-1 Cells

growth_protocol: DLD-1 cells were grown in RPMI supplemented with 10% FBS and 1X Pen-Strep in 100 mm dish (Corning   Corning™ 100 mm TC-Treated Culture Dishes)

treatment_protocol: n/a (clones and parental cells were obtained from the authors of Ly et al., Nat. Genet. 2019)

value: DLD-1 Cells


title: RPE-1 p53KO DMSO H3K4me3 biol rep 1


title: DLD-1 cln36 H3K27me3 biol rep 1


title: DLD-1 cln36 H3K27me3 biol rep 2


title: DLD-1 cln32 H3K27ac biol rep 2


title: DLD-1 cln36 H3K27ac biol rep 1


title: DLD-1 cln36 H3K4me3 biol rep 1


title: DLD-1 cln32 H3K27me3 biol rep 2


title: DLD-1 cln32 H3K27ac biol rep 1


title: DLD-1 cln36 H3K4me3 biol rep 2


title: DLD-1 cln32 H3K4me3 biol rep 2


title: DLD-1 cln32 H3K27me3 biol rep 1


title: DLD-1 cln32 H3K4me3 biol rep 1


title: DLD-1 cln26 H3K27ac biol rep 1


title: TCM_24h_3

tag: time point

value: Primary murine T cells

value: TCM


title: DLD-1 cln26 H3K27me3 biol rep 2


title: DLD-1 cln26 H3K27me3 biol rep 1


title: RPE-1 p53KO DMSO H3K4me3 biol rep 2


title: DLD-1 cln26 H3K4me3 biol rep 2


title: DLD-1 cln22 H3K27ac biol rep 2


title: DLD-1 cln22 H3K27me3 biol rep 1


title: DLD-1 cln22 H3K27ac biol rep 1


title: DLD-1 cln22 H3K4me3 biol rep 2


title: DLD-1 cln22 H3K4me3 biol rep 1


title: DLD-1 cln19 H3K27me3 biol rep 2


title: DLD-1 cln19 H3K27ac biol rep 1


title: DLD-1 cln19 H3K27me3 biol rep 1


title: DLD-1 cln19 H3K4me3 biol rep 1


title: DLD-1 cln19 H3K4me3 biol rep 2


title: DLD-1 cln26 H3K27ac biol rep 2


title: DLD-1 cln18 H3K27me3 biol rep 2


title: DLD-1 cln18 H3K27ac biol rep 1


title: DLD-1 cln18 H3K27me3 biol rep 1


title: DLD-1 cln18 H3K4me3 biol rep 2


title: DLD-1 cln17 H3K27ac biol rep 1


title: DLD-1 cln17 H3K27me3 biol rep 1


title: DLD-1 cln18 H3K4me3 biol rep 1


title: DLD-1 cln26 H3K4me3 biol rep 1


title: DLD-1 cln16 H3K27ac biol rep 2


title: DLD-1 cln16 H3K27ac biol rep 1


title: DLD-1 cln19 H3K27ac biol rep 2


title: DLD-1 cln22 H3K27me3 biol rep 2


title: DLD-1 cln17 H3K4me3 biol rep 1


title: DLD-1 cln16 H3K27me3 biol rep 2


title: S36C

value: tracheal epithelial cells


title: DLD-1 cln16 H3K27me3 biol rep 1


title: DLD-1 cln16 H3K4me3 biol rep 1


title: DLD-1 cln17 H3K4me3 biol rep 2


title: DLD-1 cln18 H3K27ac biol rep 2


title: DLD-1 cln15 H3K27me3 biol rep 1


title: DLD-1 cln15 H3K27ac biol rep 1


title: DLD-1 cln15 H3K27me3 biol rep 2


title: DLD-1 cln15 H3K27ac biol rep 2


title: DLD-1 cln13 H3K27ac biol rep 2


title: DLD-1 cln13 H3K27me3 biol rep 1


title: DLD-1 cln15 H3K4me3 biol rep 2


title: DLD-1 cln13 H3K27me3 biol rep 2


title: DLD-1 cln15 H3K4me3 biol rep 1


title: DLD-1 cln17 H3K27me3 biol rep 2


title: DLD-1 cln13 H3K4me3 biol rep 2


title: DLD-1 cln12 H3K27ac biol rep 2


title: DLD-1 cln13 H3K4me3 biol rep 1


title: DLD-1 cln17 H3K27ac biol rep 2


title: DLD-1 cln13 H3K27ac biol rep 1


title: DLD-1 cln12 H3K27me3 biol rep 1


title: DLD-1 cln12 H3K27me3 biol rep 2


title: DLD-1 cln12 H3K27ac biol rep 1


title: DLD-1 cln16 H3K4me3 biol rep 2


title: DLD-1 cln12 H3K4me3 biol rep 1


title: DLD-1 cln12 H3K4me3 biol rep 2


title: DLD-1 cln9 H3K27me3 biol rep 1


title: DLD-1 cln9 H3K4me3 biol rep 1


title: DLD-1 cln8 H3K27ac biol rep 2


title: DLD-1 cln9 H3K27ac biol rep 1


title: DLD-1 cln9 H3K27ac biol rep 2


title: DLD-1 parental H3K27ac biol rep 2


title: DLD-1 parental H3K27me3 biol rep 1


title: DLD-1 parental H3K27me3 biol rep 2


title: DLD-1 cln6 H3K27me3 biol rep 1


title: DLD-1 cln8 H3K27me3 biol rep 2


title: DLD-1 cln9 H3K27me3 biol rep 2


title: R92

type: genomic

city: Utrecht

first: Judith

middle: M.

last: Boer

address: Heidelberglaan 25

country: Netherlands

institute: Prinses Maxima Centrum

hyb_protocol: Agilent Oligo aCGH Hybridization Kit was used according to manufacturer's protocol.

scan_protocol: The Agilent G4449A arrays were scanned using an Agilent scanner. Agilent feature extraction software (version 10.5.1.1) was used to extract the data.

data_processing:
Data was processed using R-version 2.14.1. Limma version 3.10.2 (Bioconductor) was used to generate a logRatio matrix for unique probes. CGHcall version 2.14.0 (Bioconductor) was used to normalize the data, NoWave (from: van de Wiel et al., 2009, Bioinformatics) was used to dewave the data, CGHnormaliter version 1.9.1 (Bioconductor) was used to centralize the data (see Ratios.txt file). CGHcall was further used to segment the data (see Segmented.txt file).
Normalized signal intensity, log2 scale

source_name: leukemic blast, blast percentage >90%

label_protocol: 1 ug of DNA was labelled using the Agilent Genomic DNA ULS Labeling kit 5190-0420, according to manufacturer's protocol.

growth_protocol: Primary human leukemic cells were isolated at initial diagnosis (blast percentage >90%).

extract_protocol: Trizol extraction of gDNA was performed according to the manufacturer's instructions.

tag: diagnosis

value: pediatric acute lymphoblastic leukemia

tag: all subtype

value: primary leukemic cells

source_name: reference genomic DNA male pool

tag: sample type

value: reference

value: male


title: DLD-1 cln9 H3K4me3 biol rep 2


title: R100

tag: Sex


title: DLD-1 cln8 H3K4me3 biol rep 2


title: DLD-1 cln8 H3K27me3 biol rep 1


title: DLD-1 cln6 H3K27ac biol rep 2

value: H3K27ac - EpiCypher (13-0045)


title: DLD-1 parental H3K27ac biol rep 1


title: DLD-1 cln6 H3K4me3 biol rep 1


title: DLD-1 cln8 H3K27ac biol rep 1


title: DLD-1 parental H3K4me3 biol rep 2


title: DLD-1 cln6 H3K27ac biol rep 1


title: DLD-1 cln6 H3K4me3 biol rep 2


title: DLD-1 parental H3K4me3 biol rep 1


title: DLD-1 cln6 H3K27me3 biol rep 2


title: R90


title: R86


title: R83

value: B-other


title: R82


title: R79


title: R69


title: R74


title: R72


title: R60


title: R91


title: DLD-1 cln8 H3K4me3 biol rep 1


title: R51


title: R55


title: R48


title: R46


title: R37


title: R59


title: R35


title: R43


title: R29


title: R30


title: R23


title: R18


title: R32


title: R16


title: R26


title: R14


title: R11

value: high hyperdiploid


title: R9


title: R10


title: R58


title: R5


title: R2


title: A551


title: R44


title: A540


title: A549


title: A538


title: A547


title: A548


title: A545


title: A550


title: A534


title: A527


title: A543


title: A526


title: A521


title: A520


title: A519


title: A515


title: A516


title: A552


title: A512


title: A513


title: A507


title: A506

value: near tetraploidy (>65)


title: A536


title: A535


title: A501


title: A504


title: A529


title: A491


title: A541


title: A486


title: A498


title: A476


title: A484


title: A485


title: A494


title: A537


title: A497


title: A472


title: A471


title: A524


title: A483


title: A469


title: A505


title: A470


title: AsPC1, M

city: Shenzhen

first: Huang

last: Hsien-Da

address: 2001 Longxiang Boulevard, Longgang District

country: China

institute: CUHKSZ

data_processing:
nf-core/rnaseq pipeline (v3.0)
mRNA-seq raw data were processed by nf-core/rnaseq pipeline (v3.0) with the parameter of “--genome hg38 –gencode” to obtain the read count matrix for all samples.
We trimmed low-quality and adaptor sequences in raw reads using Trim Galore!.
After removing ribosomal RNA by SortMeRNA, we aligned and compared processed reads to the reference genome (hg38, UCSC) using STAR.
Supplementary files format and content: CR_10celllines_rawreads.xlsx

source_name: Pancreas

growth_protocol: Ten human cancer cell lines, including A549, HeLa, Hep G2, SKOV3, SKBR3, HCT116, MCF7, RBE, Hep 3B, and AsPC1 were  incubated at 37°C and 5% CO2 in an incubator

extract_protocol:
Total RNA was isolated with TRIzol (Invitrogen cat: 15596026) and assessed for integrity using 2100 Agilent Bioanalyzer (Agilent, USA) before library preparation.
The library preparation started with 1 μg of total RNA for each sample. For mRNA sequencing library construction, we first purified mRNA with poly-T oligo-attached magnetic beads and synthesized first-strand and second-strand cDNA. Rolling circle amplification (RCA) was performed to generate DNA nanoballs (DNBs).

treatment_protocol: Cells were treated with a series of concentrations (L,M and H) of CR for 24 h.

value: Pancreas

value: epithelial cell

value: WT


title: Hep 3B, H

source_name: Liver

value: Liver

value: Hep 3B


title: AsPC1, CTRL

value: CTRL


title: AsPC1, L


title: A463


title: AsPC1, H


title: A458


title: A453


title: A481


title: A448


title: Hep 3B, CTRL


title: RBE, H

source_name: Bile duct

value: Bile duct

value: RBE


title: RBE, L


title: Hep 3B, L


title: RBE, CTRL


title: A444


title: A452


title: MCF7, M

source_name: Breast; Mammary gland

value: Breast; Mammary gland


title: RBE, M


title: A440

value: pediatric acute lymphoblastic leukemia


title: A435

value: primary leukemic cells


title: Hep 3B, M


title: MCF7, L


title: MCF7, H


title: A430

value: reference


title: A425

value: male


title: A426


title: A428


title: A432


title: MCF7, CTRL


title: HCT116, M

source_name: Large intestine; Colon

value: Large intestine; Colon


title: HCT116, L


title: HCT116, CTRL


title: HCT116, H


title: A424

value: B-other


title: A445


title: SKBR3, M


title: SKBR3, L


title: A423


title: SKBR3, CTRL


title: SKBR3, H


title: SKOV3, H

source_name: Ovary; Ascites

value: Ovary; Ascites


title: A422


title: A419


title: A420


title: A417


title: SKOV3, L


title: A459


title: A409


title: SKOV3, CTRL


title: Hep G2, H

value: Hep G2


title: A421


title: A411


title: A407


title: Hep G2, M


title: SKOV3, M


title: A403


title: Hep G2, L


title: Hep G2, CTRL


title: A395


title: HeLa, H

source_name: Uterus; Cervix

value: Uterus; Cervix

value: HeLa


title: A393


title: A397


title: HeLa, M

value: epithelial cell

value: WT


title: HeLa, L


title: A386


title: A380


title: A381


title: A549, H

source_name: Lung

value: Lung


title: HeLa, CTRL

value: CTRL


title: A549, M


title: A379


title: A376


title: A375

value: high hyperdiploid


title: A372


title: A367


title: A549, CTRL


title: 36506_BMDM [ATAC-seq]

city: Oklahoma city

first: Philip

last: ONeill

address: 945 9th st

institute: OUHSC

data_processing:
Quality trim to a minimum of Q15
Map using GSNAP version 2012-07-20 using the commandline: gsnap -d mmul10_104 -v mmul10_104.snp138 --use-splicing=mmul10_104.splicesites --max-mismatches=0.06 -i2 -n2 -Q --gunzip --force-xs-dir --nofails -B5 -t${num_processors} --read-group-id=$j --read-group-name=$j --read-group-library=$j --read-group-platform=illumina -A sam $outfile_R1 $outfile_R2 | samtools view -bS -@ ${num_processors} - | samtools sort -@ ${num_processors} -o ./Illumina_data/${j}.sorted.bam -; samtools index ./Illumina_data/${j}.sorted.bam
sort and index using SAMTOOLS
call FPKM using CUFFLINKS
pepatac.py --output-parent $results --cores 24 --mem 16000 --sample-name $sample --input $sample.R1.fastq.gz --input2 $sample.R2.fastq.gz --single-or-paired paired --genome mmul10  --trimmer skwer --aligner bowtie2 --deduplicator samblaster --peak-caller macs2 --peak-type fixed --extend 250 --genome-size 2.7e9 --frip-ref-peaks None
Assembly: mmul10_104
Supplementary files format and content: Excel file containing FPKM values
Supplementary files format and content: Excel file containing peak counts

organism: Macaca mulatta

source_name: Bone marrow

extract_protocol:
RNA was extracted with Zymo Quick-DNA/RNA microprep kit and DNA was extracted with Active Motif ATAC-seq kit
Swift directional mRNA prep
NovaSeq 6000 using 2x150bp format

value: Bone marrow

value: BMDM

value: Control diet


title: 36637_BMDM [ATAC-seq]

value: Western diet


title: A365

value: pediatric acute lymphoblastic leukemia

value: primary leukemic cells

value: reference


title: 36452_BMDM [ATAC-seq]


title: 35715_BMDM [ATAC-seq]


title: A360

value: male


title: A354


title: A349


title: 34871_BMDM [ATAC-seq]


title: A359

value: B-other


title: 34850_BMDM [ATAC-seq]


title: A347


title: A348


title: 34816_BMDM [ATAC-seq]


title: A346


title: 34551_BMDM [ATAC-seq]


title: A549, L


title: A345


title: A343


title: 36452_CD34+ [ATAC-seq]


title: A327


title: 35540_CD34+ [ATAC-seq]


title: 35715_CD34+ [ATAC-seq]


title: A324


title: 35314_CD34+ [ATAC-seq]


title: A318


title: 35314_BMDM [ATAC-seq]


title: 34931_CD34+ [ATAC-seq]


title: 34931_BMDM [ATAC-seq]


title: A317


title: A316


title: A311


title: 34816_CD34+ [ATAC-seq]


title: 34871_CD34+ [ATAC-seq]


title: A302


title: 34850_CD34+ [ATAC-seq]


title: WC_35411 [RNA-seq]


title: 34886_CD34+ [ATAC-seq]


title: WC_34551 [RNA-seq]


title: 36506_CD34+ [ATAC-seq]


title: A314


title: WC_34931 [RNA-seq]


title: WC_34886 [RNA-seq]


title: A299


title: A287


title: A282


title: WC_35540 [RNA-seq]


title: CC_36506 [RNA-seq]


title: A295


title: A280


title: A277


title: CC_35194 [RNA-seq]


title: A337


title: CC_36452 [RNA-seq]


title: A278


title: A275


title: CC_34816 [RNA-seq]


title: A274


title: CC_36727 [RNA-seq]


title: WC_34850 [RNA-seq]


title: A272


title: A271


title: CC_30598 [RNA-seq]


title: A268


title: WC_30511 [RNA-seq]


title: WC_30508 [RNA-seq]


title: A264

value: T-ALL


title: A267


title: A260


title: A279


title: CC_30374 [RNA-seq]


title: WC_30243 [RNA-seq]


title: A256


title: A258


title: A254


title: WC_30237 [RNA-seq]


title: A253


title: CC_29906 [RNA-seq]


title: A250

value: low hypodiploid (<39)


title: A251


title: SubAa272_rep3

city: Boston

first: jinzhi

last: duan

state: Massachusetts

address: 6th Floor, Room 641, NRB, 77 Louis Pasteur Avenue

institute: Brigham and Women' hospital

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using STAR 2.7.3a  in partek software.
The reads were quantified with Quantify to annotation model (Partek E/M) with default setting.
Genome_build: mm10
Supplementary_files_format_and_content: MODE-K text files include gene account values for each Sample.

source_name: small intestine epithelia cell

growth_protocol: MODE-K cells grow in RPMI 1640 with FCS 10%,Non essential aa 1% , Hepes 10mM, anti/anti 1%.

extract_protocol:
1x10^6  MODE-K SubAa272 and Control stable cells were harvasted and extracted by RNeasy Plus Mini Kit(Qiagen,74134).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: express SubAa274

value: stable cell line


title: SubAa272_rep2

value: express SubAa273


title: SubAa272_rep1

value: express SubAa272


title: WC_29387 [RNA-seq]


title: CC_30707 [RNA-seq]


title: A249


title: A247


title: A248


title: CC_30466 [RNA-seq]


title: ctr_rep3

value: express control cassette


title: ctr_rep2


title: A246


title: ctr_rep1


title: A240


title: A241


title: A243


title: A244


title: A238

value: high hyperdiploid


title: A232


title: N_GC_94

city: Shanghai

first: Ying

last: Xie

state: Shanghai

address: 725 South Wanping Road, Shanghai

department: School of public Health

institute: Shanghai University of Traditional Chinese Medicine

description: WT

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp software
Trimmed sequence reads were mapped to GRCm39 mouse genome
Read count extraction and normalization were performed using RSEM software
Assembly: GRCm39
Supplementary files format and content: tab-delimited xls files include TPM values for each Sample

source_name: spleen

extract_protocol:
RNA was harvested using Rneasy mini plus kit (VZ6). 1.5 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: spleen

value: TNBC tumor-bearing mice

value: WT


title: N_GC_36

description: WT


title: N_GC_11

description: WT


title: A228


title: N_P_38

description: WT


title: N_P_29

description: WT


title: A226


title: A224


title: A236


title: N_I_92

description: WT


title: A222


title: A223


title: N_I_18

description: WT


title: A221


title: A235


title: A234


title: A231


title: A230


title: T_GC_37

description: Anti-PD-9 treatment in TNBC tumor-bearing mice

value: Anti-PD-1 treatment


title: T_GC_21

description: Anti-PD-8 treatment in TNBC tumor-bearing mice


title: N_I_96

description: WT


title: A220

value: pediatric acute lymphoblastic leukemia


title: SMG_m-2

city: Beijing

first: Jinghua

last: Yang

address: 32 North Third Ring Road West, Haidian District, Beijing

institute: Beijing Zhiyun data technology co. LTD

hyb_protocol: mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

scan_protocol: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 5 out of 10 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis.

data_processing: Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering. Pathway analysis and GO analysis were applied to determine the roles of these differentially expressed mRNAs played in these biological pathways or GO terms. Hierarchical Clustering and combined analysis were performed using in-house scripts.

source_name: submandibular gland, m

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications.

growth_protocol: The submandibular glands of mice are preserved at -80 degrees Celsius.

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen Life Technologies, Carlsbad, CA, USA) according to the manufacturer’s instructions.

value: submandibular gland

tag: gender

value: db/m

tag: age

value: 8 week


title: N_P_17

description: WT

tag: cell type


title: SMG_db-5

source_name: submandibular gland, db

tag: tissue

value: male

value: db/db


title: SMG_db-4

tag: genotype


title: SMG_db-3


title: SMG_db-1


title: SMG_m-4


title: A219

value: primary leukemic cells

value: reference


title: A225

value: B-other


title: SMG_m-3


title: SMG_m-1


title: T_GC_10

description: Anti-PD-7 treatment in TNBC tumor-bearing mice


title: T_P_39

description: Anti-PD-5 treatment in TNBC tumor-bearing mice


title: A216


title: T_P_43

description: Anti-PD-6 treatment in TNBC tumor-bearing mice


title: A218


title: T_I_12

description: Anti-PD-2 treatment in TNBC tumor-bearing mice


title: T_P_26

description: Anti-PD-4 treatment in TNBC tumor-bearing mice


title: A214


title: T_I_27

description: Anti-PD-3 treatment in TNBC tumor-bearing mice


title: A209


title: T_I_8

description: Anti-PD-1 treatment in TNBC tumor-bearing mice


title: A207


title: A212


title: A208


title: A205


title: A206


title: A202


title: A204


title: A213


title: A200


title: non-tumor control, replicate 1, scRNAseq

city: Little Rock

first: Fumou

last: Sun

state: Arkansas

address: 4301 W. Markham, Slot 508

department: Internal Medicine

institute: University of Arkansas for Medical Sciences

description: 10x Genomics

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

source_name: Bone marrow cells

extract_protocol:
Twenty-one days after the 5TGM1 injections, bone marrow cells were harvested. BM microenvironmental cells were sorted out with fluorescence-activated cell sorting by depleting 5TGM1-GFP+ MM cells and human CD34+ CAR-T cells. Sorted cells with a purity greater than 98% were used for scRNA-seq. Approximately 10,000 cells were targeted, and single-cell emulsions were generated with the Chromium Controller (10x Genomics, Pleasanton, CA, USA) using the Chromium Next GEM Chip G (Part Number 1000120, 10x Genomics) with the Chromium NextGEM Single Cell 3’ v3.1 kit (Part Number 1000121, 10x Genomics) following the standard protocol.
Libraries were assessed for mass concentration using the Qubit 1X dsDNA HS Assay Kit (catalog # Q33231; Invitrogen, Waltham MA, USA) and the Qubit 4 fluorometer (catalog # Q33238; Invitrogen, Waltham MA, USA). Library fragment size was assessed with the High Sensitivity NGS Fragment Analysis Kit (catalog # DNF-474-0500; Agilent, Santa Clara CA, USA) on the Fragment Analyzer System (catalog # M5310AA; Agilent, Santa Clara CA, USA). Libraries were functionally validated with the KAPA Universal Library Quantification Kit (catalog # 07960140001; Roche, Basel CH).

treatment_protocol: Eight-week-old female C57BL/KaLwRij mice were injected intravenously via the tail vein with either 100 μL PBS or 1×106 5TGM1-GFP cells stained with DiD dye and randomized into 3 groups (n = 3/group). Seven days after the 5TGM1 injections, mice were injected intravenously via the tail vein with either PBS (PBS group), 1×106 MOCK CAR-T cells (MOCK-CAR T group), or CD24-CAR-T cells (CD24-CAR T group).

value: Bone marrow cells

tag: tumor cell_injection

value: PBS


title: 5TGM1, non-treatment control, replicate 3, scRNAseq

description: 10x Genomics


title: 5TGM1, MOCK CAR-T, replicate 3, scRNAseq

description: 10x Genomics

value: MOCK CAR-T cells


title: 5TGM1, non-treatment control, replicate 1, scRNAseq

description: 10x Genomics


title: 5TGM1, non-treatment control, replicate 2, scRNAseq

description: 10x Genomics


title: 5TGM1, MOCK CAR-T, replicate 2, scRNAseq

description: 10x Genomics


title: 5TGM1, MOCK CAR-T, replicate 1, scRNAseq

description: 10x Genomics


title: A197


title: non-tumor control, replicate 2, scRNAseq

description: 10x Genomics


title: 5TGM1, CD24 CAR-T, replicate 3, scRNAseq

description: 10x Genomics

value: CD24 CAR-T cells


title: 5TGM1, CD24 CAR-T, replicate 2, scRNAseq

description: 10x Genomics


title: non-tumor control, replicate 3, scRNAseq

description: 10x Genomics


title: A196


title: A194


title: 5TGM1, CD24 CAR-T, replicate 1, scRNAseq

description: 10x Genomics


title: A191

value: near tetraploidy (>65)


title: PGCLCs, THC 100nM, biol rep 3

city: Los Angeles

first: Roxane

last: Verdikt

state: CA

address: Life Science Building 3360  621 Charles E. Young Drive S.

department: Institute for Society & Genetics

institute: UCLA

description:
PGCLC_DEGs.xlsx
PGCLC_adjusted_counts_combatseq.csv

data_processing:
Data quality check was performed using Illumina Sequencing Analysis Viewer (SAV) software.
Demultiplexing was performed with Illumina Bcl2fastq2 program (version 2.19.1.403; Illumina Inc.).
The quality of the reads was verified using FastQC (Andrews, 2010)
Reads were aligned to the mm10 reference genome (GRCm39) using STAR (Dobin et al., 2013) with the following arguments: --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts --outFilterMismatchNmax 5 --outFilterMultimapNmax 1.
The quality of the resulting alignments was assessed using QualiMap (García-Alcalde et al., 2012).
The Python package HTseq was used for gene counts (Anders et al., 2015) using the following arguments: --stranded=no --idattr=gene_id --type=exon --mode=union -r pos --format=bam.
Output files were filtered to remove genes with low count (≤10) then were used for differential gene expression analysis using DESeq2 (Love et al., 2014).
The negative binomial regression model of ComBat-seq was used to correct unwanted batch effects (Zhang et al., 2020).
Assembly: mm10
Supplementary files format and content: Excel files contain lo2FoldChange, stat, p-value and adjusted p-value for DEGs as determined by DESeq2
Supplementary files format and content: csv files contain adjusted_counts_combatseq

source_name: primordial germ cells-like cells, double-positive

extract_protocol:
Total RNA was extracted from ESCs and EpiLCs pellets using the AllPrep DNA/RNA Micro Kit (Qiagen), according to the manufacturer’s protocol. For PGCLCs, d5 embryonic bodies were harvested and cells were dissociated using TrypLE™ Select followed by resuspension in fluorescence-activated cell sorting (FACS) buffer (1×Dulbecco’s phosphate buffered saline [DPBS], 1% BSA, 1 mM EDTA, 25 mM HEPES) and cell suspension were passed through a cell strainer (70μm). Cells were sorted on a BD Biosciences FACSAria III (UCLA BSCRC Flow Cytometry Core). Practically, cell populations of interest, being double-positive (Blimp1::mVenus+ and Stella::ECFP+) were sorted and collected in microtubes containing GK15 medium. Total RNA was extracted from double-positive PGCLCs using the AllPrep DNA/RNA Micro Kit (Qiagen).
Libraries were prepared with the KAPA mRNA HyperPrep Kit (BioMek) or with the RNA library prep kit (ABClonal) following the manufacturers’ protocols. Briefly, poly(A) RNA were selected, fragmented and double-stranded cDNA synthesized using a mixture of random and oligo(dT) priming, followed by end repair to generate blunt ends, adaptor ligation, strand selection, and polymerase chain reaction (PCR) amplification to produce the final library.

value: PGCLCs

value: 100nM THC-treated


title: PGCLCs, THC 100nM, biol rep 1

value: primordial germ cells-like cells, double-positive


title: PGCLCs, THC 100nM, biol rep 2


title: A190

source_name: leukemic blast, blast percentage >90%

value: pediatric acute lymphoblastic leukemia


title: A193

source_name: reference genomic DNA male pool


title: A198


title: A188


title: PGCLCs, vehicle, biol rep 3

value: Mock-treated


title: PGCLCs, vehicle, biol rep 1


title: A199


title: A195

value: high hyperdiploid


title: EpiLCs, THC 100nM, biol rep 3

description:
EpiLC_DEGs.xlsx
epiLC_adjusted_counts_combatseq.csv

source_name: epiblast-like cells

value: epiblast-like cells

value: EpiLCs


title: A187

value: male


title: A185

value: primary leukemic cells


title: A184

value: reference


title: EpiLCs, THC 100nM, biol rep 1


title: EpiLCs, vehicle, biol rep 2


title: ESCs, THC 100nM, biol rep 3

description:
ESC_DEGs.xlsx
ESC_adjusted_counts_combatseq.csv

source_name: embryonic stem cells

value: embryonic stem cells

value: ESCs


title: EpiLCs, THC 100nM, biol rep 2


title: A178

value: B-other


title: A179


title: A180


title: A182


title: EpiLCs, vehicle, biol rep 1


title: EpiLCs, vehicle, biol rep 3


title: ESCs, THC 100nM, biol rep 2


title: ESCs, vehicle, biol rep 3


title: A173


title: A177


title: ESCs, THC 100nM, biol rep 1


title: ESCs, vehicle, biol rep 2


title: A189


title: PGCLCs, vehicle, biol rep 2


title: A172


title: ESCs, vehicle, biol rep 1


title: A171


title: A169


title: A170


title: A168


title: A167


title: A166


title: A165


title: A174


title: A176


title: LPS GMP-MoP, bio rep 3

city: Hachioji

first: Kenichi

last: Asano

state: Tokyo

address: 1432-1 Horinouchi

department: Life Sciences

institute: Tokyo University of Pharmacy and Life Sciences

data_processing:
Adaptor sequences were removed from raw data using Trimmomatic (Galaxy Version 0.38.0).
Sequencing reads after trimming were aligned to a mouse reference genome sequence (GRCm38/mm10) in the RNA STAR (Galaxy Version 2.7.8).
Read counts per gene were calculated using featureCounts (Galaxy Version 2.0.1) based on GENCODE gene annotation version M25.
The fragments per kilobase of exon per million (FPKM) normalization was done account for gene length and read counts.
Assembly: GRCm38/mm10
Supplementary files format and content: EXCEL file includes FPKM values for all samples.

source_name: BM progenitor cells

extract_protocol:
Total RNA from sorted cells was extracted with an RNeasy Micro Kit (QIAGEN).
RNA-seq libraries were prepared using the NEBNext UltraII Directional RNA Library Prep Kit (NEW ENGLAND BioLabs).

value: BM progenitor cells

tag: sample group

value: LPS GMP-MoP

value: WT

value: LPS

tag: time

value: 2 days


title: LPS proNeu2, bio rep 3

value: LPS proNeu2


title: LPS GMP, bio rep 3

value: LPS GMP


title: LPS proNeu2, bio rep 2


title: LPS proNeu1, bio rep 1

value: LPS proNeu1


title: LPS proNeu1, bio rep 3


title: LPS GMP-MoP, bio rep 1


title: A159

value: pediatric acute lymphoblastic leukemia

value: high hyperdiploid


title: LPS GMP-MoP, bio rep 2


title: LPS proNeu2, bio rep 1


title: A161


title: A160


title: LPS GMP, bio rep 2


title: LPS proNeu1, bio rep 2


title: BM progenitor cells, mRNA-derived cDNA [AsanoWTA1]

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
polyA RNA
cell names in processed files are as follows: [HTO ID]_[DataID]_[Cell barcode number]

data_processing:
Each A961 and A963 or A964 and A965 datasets were integrated with merge functions of Seurat (version 4.2.0 in R version 4.2.1.).
Cells that contained a percentage of mitochondrial transcripts > 25% were filtered out.
PCA analysis was performed against 4777 of highly-variable genes identified by FindVariableFeatures (selection.method = mvp, mean.cutoff = c(0.1, Inf), dispersion.cutoff = c(0.5, Inf)) function in Seurat.
Naïve (A963) and LPS (A965) datasets were integrated with a combination of Find Integration Anchors and Integrate Data functions using rpca reduction.
1:52 PCs were selected by Jackstraw analysis and used for clustering analysis.
UMAP was performed on significant PCs for visualization in two dimensions.
Assembly: GRCm38 release 101
Supplementary files format and content: gene-expression matrix (.txt.gz)

source_name: bone marrow

extract_protocol:
BM cells from one naïve mouse and one LPS-injected mouse were sorted by FACSAriaIII and stained with different DNA barcode-conjugated PE-streptavidins (BioLegend Totalseq PE-streptavidin (A961, A962, A963, A964, and A965)) to identify each sample origin.
Sorted cells were pooled and subject to scRNA-seq using BD RhapsodyTM Single-Cell Analysis System (BD  Biosciences), and resulted cDNA was amplified by TAS-Seq protocol. 100 cells /A961 ; 100 cells /A962 ; 15,000 cells /A963 ; 100 cells /A964 ; 15,000 cells /A965 were loaded onto BD RhapsodyTM Single-Cell Analysis System.
cDNA library was processed to sequencing library by using NEBNext UltraII FS library prep kit for Illumina (New England Biolabs).
Sequencing adapters were added to associated Totalseq PE-streptavidin libraries by PCR.
Pooled library concentration was adjusted to 2.0 nM and 12% PhiX control library v3 (Illumina) was spiked into the library.

value: cKit+Lin- progenitor cells

value: bone marrow

tag: library type

value: mRNA

tag: antibodies/tags


title: BM progenitor cells, HTO-derived cDNA [AsanoTag1]

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Hashtag-derived oligonucleotide (HTO)

library_source: other

molecule: protein

value: HTO

value: Naïve cMoP/TotalSeq-A961 ; Naïve GMP-MoP/TotalSeq-A962 ; Naïve cKit+Lin(CD90.2, CD19, NK1.1, SiglecF, Ly6G)- /TotalSeq-A963 ; LPS GMP-MoP/TotalSeq-A964 ; LPS  cKit+Lin(CD90.2, CD19, NK1.1, SiglecF, Ly6G)-/TotalSeq-A965


title: A156

value: primary leukemic cells

value: reference

value: male


title: A158


title: LPS GMP, bio rep 1

value: BM progenitor cells

tag: treatment


title: Naïve GMP-MoP, bio rep 3

value: Naïve GMP-MoP

value: WT


title: A155


title: A154

value: B-other


title: Naïve GMP-MoP, bio rep 2


title: A163


title: A164


title: A162


title: A153


title: Naïve GMP-MoP, bio rep 1


title: Naïve proNeu2, bio rep 3

value: Naïve proNeu2


title: A152


title: Naïve proNeu2, bio rep 2


title: A151


title: Naïve proNeu1, bio rep 3

value: Naïve proNeu1


title: Naïve proNeu1, bio rep 1


title: Naïve GMP, bio rep 3

value: Naïve GMP


title: Naïve GMP, bio rep 1


title: A146

value: pediatric acute lymphoblastic leukemia


title: A148


title: A143

value: high hyperdiploid


title: Naïve proNeu2, bio rep 1


title: A144


title: A147


title: Naïve cMoP, bio rep 3

value: Naïve cMoP


title: Naïve GMP, bio rep 2


title: A142


title: Naïve MDP, bio rep 3

value: Naïve MDP


title: A140


title: Naïve cMoP, bio rep 1


title: A141


title: A138

value: T-ALL


title: Naïve MDP, bio rep 2


title: A136


title: Naïve MDP, bio rep 1


title: A137


title: Mouse Tibia P56, 8

city: Pok Fu Lam

first: Peikai

last: Chen

address: Sassoon Road 5

department: Faculty of Medicine

country: Hong Kong

institute: The University of Hong Kong

description:
10X single-cell
mm10_barcodes.tsv.gz
mm10_features.tsv.gz
mm10_matrix.mtx.gz
exogenous_barcodes.tsv.gz
exogenous_features.tsv.gz
exogenous_matrix.mtx.gz

data_processing:
Data was aligned to mouse genome mm10 (reference v3.0.0 provided by 10X Genomics) by CellRanger (version 3.1.0)
Data was also aligned to a reference file of exogenous sequences, including tdTomato (1431bp), by CellRanger (version 3.1.0)
The resulting matrix files were integrated and further processed on Seurat (version 3).
Dimension reduction including CCA, PCA, tSNE and UMAP were performed
Clustering were performed, and differentially expressed genes between one cluster and another (or all remaining clusters) were performed. A further filtering of abs(log2(fold-change)) > 1/2 and FDR <0.05 was applied to ensure higher specificity and correct for multiple testing.
Assembly: mm10
Supplementary files format and content: gzip text file of gene expression file

source_name: tibia

growth_protocol: The mice grow under normal condition.

extract_protocol:
RNA extraction from disassociated cells was done according to standard 10X Genomics Protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: No special treatment was applied.

value: tibia

value: 8 weeks (P56)

value: chondro-osteogenic

value: MMP14 F/+; COL10A1cre; R26-tdT; Col1a1-2.3-GFP


title: A149

value: primary leukemic cells

value: reference

value: male


title: A135


title: Mouse Tibia P56, 7


title: A150


title: A134


title: Naïve proNeu1, bio rep 2

value: BM progenitor cells

value: WT


title: A133


title: Mouse Tibia P56, 6


title: Mouse Tibia P56, 5


title: Mouse Tibia P56, 4


title: A131


title: A130


title: A128


title: Mouse Tibia P56, 3


title: Naïve cMoP, bio rep 2


title: aPD1_aCTLA4 [S4971Nr9]

city: Amsterdam

first: PETROS

last: DIMITRIADIS

email: p.dimitriadis@nki.nl, d.rao@nki.nl

state: Noord-Holland

address: Plesmanlaan 121

institute: NETHERLANDS CANCER INSTITUTE - NKI

description: tumor grown in immune competent C57BL/6 mouse

data_processing:
The samples were mapped with STAR (v2.7.3a) to mouse reference genome  Mus_musculus.GRCm39.105 using default settings.
 The read counts were computed with HTseq-count (v0.12.4) and were analyzed with DESeq2 (v1.30.1)
Supplementary files format and content: HTseqCount

source_name: tumor, sub cutaneous

growth_protocol: MeVa2.1.dOVA tumor cell line, used for s.c injection, was cultured in Advanced DMEM media containing 10% heat inactivated fetal bovine serum, 1% penicillin-streptomycin and L-Glutamine

extract_protocol:
RNA was isolated from samples using RNeasy Mini kit (QIAGEN)
Strand-specific libraries were generated using the TruSeq Stranded mRNA sample preparation kit (Illumina Inc.,)

treatment_protocol: Mice were treated with Domatinostat (20 mg/kg, administered twice daily via oral gavage) ± Anti-PD1 (100 ug per mouse) and anti-CTLA4 (50 ug per mouse) (antibodies were administered two times per week intraperitoneal). Treatment duration was 13 days

value: tumor, sub cutaneous

tag: cell line

value: mouse tumor_MeVa2.1.dOVA

value: BrafV600E; Pten-/-; CDKN2A-/- (tumor cell line)


title: Mouse Tibia P56, 1


title: Mouse Tibia P56, 2


title: A124

tag: diagnosis

value: pediatric acute lymphoblastic leukemia

value: B-other


title: A126

tag: all subtype


title: A123

tag: sample type


title: A125

value: high hyperdiploid

tag: Sex


title: Domatinostat [S4971Nr8]

value: Domatinostat


title: A127


title: Domatinostat [S4971Nr7]


title: Domatinostat [S4971Nr6]


title: A122


title: Domatinostat [S4971Nr5]


title: vehicle_control [S4971Nr3]


title: A121


title: A120


title: vehicle_control [S4971Nr2]


title: A116


title: vehicle_control [S4971Nr1]


title: aPD1_aCTLA4_Domatinostat [S4971Nr16]


title: A114


title: A113


title: aPD1_aCTLA4_Domatinostat [S4971Nr15]


title: A111


title: aPD1_aCTLA4_Domatinostat [S4971Nr13]


title: aPD1_aCTLA4 [S4971Nr12]


title: aPD1_aCTLA4_Domatinostat [S4971Nr14]


title: aPD1_aCTLA4 [S4971Nr11]


title: A110


title: A109


title: aPD1_aCTLA4 [S4971Nr10]


title: 4T1 KIF2C ATAC biol rep 2

city: New York

data_processing:
Reads were mapped to mm10 using bowtie2 with the following parameters: -t -X2000 --no-mixed --no-discordant. Reads were filtered based on -F 1804 -q 30 using samtools and the MarkDuplicates function in Picard tools was used to remove PCR duplicates. Peak calling was done using macs2  callpeak function with the following parameters: -f BAM -g hs --nomodel --shift 37 --extsize 73 --keep-dup all -B --SPMR --call-summits -q 1e-2. Summit of peaks were extended by 250bp and merged across samples. IGVtools count function was used to generate TDF files for visualization.
Assembly: mm10
Supplementary files format and content: bed, tdf, bigwig

growth_protocol: 4T1 cells were grown in RPMI media supplemented with 10% FBS and 1X Pen-Strep in 245x245 mm dish (Corning   Corning™ TC-Treated Culture Dishes)

extract_protocol:
Extraction was performed according to Buenrostro et. al. 2015
Library prepared according to Buenrostro et. al. 2015

tag: strain

value: BALB/c

value: 4T1 TNBC Breast Cancer Cells

tag: overexpression


title: A104


title: A106


title: A108


title: A101


title: 4T1 KIF2C ATAC biol rep 3


title: vehicle_control [S4971Nr4]


title: 4T1 KIF2C ATAC biol rep 1


title: A102


title: A117


title: A99


title: 4T1 dnMCAK ATAC biol rep 3

value: dnMCAK


title: 4T1 dnMCAK ATAC biol rep 2


title: A100


title: A98


title: 4T1 dnMCAK ATAC biol rep 1