city: Durham

first: Trudy

last: Oliver

email: tgo@duke.edu, trudy.oliver@duke.edu

state: NC

address: Duke University, Box 3813, LSRC Room C138B, 308 Research Drive

department: Pharmacology & Cancer Biology

institute: Duke University

description:
Library name: RPM_Basal_Allograft_CellTagged_PreCre_rep1_GEX
10X Genomic 3' GEX

data_processing:
Demulitplexed with 10x cellranger mkfastq to create fastq files with sample index (I1, I2) and read files (R1, R2).
Reads were aligned to the custom mouse genome (mm10) plus Venus and firefly Luciferase (fLuc) sequences to aid in detecting recombination, and GFP.CDS and CellTag.UTR sequences (as described in Kong et al., Nature Protocols, 2020) for CellTagged samples using cellranger mkref. For primary tumors, reads were aligned to a distinct custom genome (mm10) plus EGFP, Cas9, Venus, and firefly Luciferase (fLuc) sequences  to aid in detecting recombination for various mouse models using cellranger mkref. Custom sequences includes as supplementary fasta files.
Count barcodes and UMIs were then generated using cellranger count or cellranger multi for CellPlexed/multiplexed samples.
For CellTag analysis, filtered bam files were generated according to the CellTagR workflow (https://github.com/morris-lab/CellTagR).
Downstream visualization and further analysis of scRNA seq data was performed in R with Seurat and/or Python with Scanpy.
Assembly: Custom mm10-2020-A plus EGFP, Cas9, Venus, fLuc sequences (for primary tumors) and Venus, fLuc, GFP.CDS, and CellTag.UTR sequences (for CellTagged organoids and allografts).
Supplementary files format and content: Filtered feature-barcode matrices from cellranger count or cellranger multi.

source_name: Basal-organoid-derived allograft tumor

extract_protocol:
Organoids were subject to dissociation by TrypLE for 30 minutes into a single cell suspension. Allograft and primary tumors were subject to enzymatic/mechanical digestion into a single cell suspension. Select samples were multiplexed with 10x Genomics CellPlex technology. 10x Genomics gel beads and reverse transcription reagents were added to cell suspensions and loaded to a chromium single cell controller to form gel-bead-in emulsions (GEMs). From GEMs, cDNA was generated from barcoded mRNA and subsequent A tailing, end repair, adaptor ligation, and sample indexing was performed according to manufacturer. Libraries were assessed on Agilent D5000 ScreenTape on an Agilent Tech 2200 tapestation system and quantified by Kapa Biosystems Library Quantification Kit for Illumina Platforms. Libraries were sequenced on the Novaseq 6000, Novaseq X Plus, or NextSeq 1000 with paired end seq targeting > ~30k reads/cell for gene expression (GEX) libraries or ~5k reads/cell for CellPlexing/Cell multiplexing oligo (CMO) libraries.
10X Genomics Single-Cell 3' RNA Dual Index v3 and 10X Genomics 3’ Feature Barcode Kit for CellPlexed samples

value: Basal-organoid-derived allograft tumor

tag: cellplex oligo

tag: celltag experiment

value: Experiment_A (RPM CellTag pre-Cre)

value: tumor

value: Rb1 fl/fl; Trp53 fl/fl;H11b-LSL-MycT58A-Ires-Luc (RPM)

value: CellTag pre-CMV-Cre


title: ChIPseq_L36plClone2_dTAG_1h_H3K4me3_Rep2

status: Public on Jul 01 2025

type: SRA

city: Stuttgart

first: Steven

middle: A

last: Johnsen

address: Auerbachstrasse 112

country: Germany

institute: Robert Bosch Center for Tumor Diseases

description: Library name: Sample039

library_source: genomic

data_processing:
Paired or end sequencing reads were mapped to the reference genome assembly hg38 using bowtie2. PCR duplicates were removed with samtools markdup and replicates were merged using samtools merge. Bigwig files were generated removing blacklist regions using reads per genomic content (RPGC) normalization with bamCoverage . MACS3 callpeak was used to call the significant peaks with non-broad cutoff of 0.05 for while using input files from respective conditions as background.
Assembly: hg38
Supplementary files format and content: Normalized bigwig for each condition
Supplementary files format and content: peaks.narrowPeak file for each condition

molecule: genomic DNA

organism: Homo sapiens

source_name: cell line

growth_protocol: AsPC1 and BxPC3 (RPMI, 10% FBS, 1% Pen-Strep), HPAFII and L36pl (phenol red free MEM, 10% FBS, 1% Pen-Strep) were maintained in humidified 5% CO2 incubator at 37C.

extract_protocol:
Chromatin immunoprecipitation was performed by crosslinking cells with 1% formaldehyde for 20 min and quenched by 1.25 M glycine for 5 min. Cells were lysed with lysis buffer (150 mM NaCl, 20 mM EDTA, 50 mM Tris-HCl, 0.5% v/v NP-40, 1% v/v Triton X-100, 10 mM NaF). Nuclear pellets were resuspended and sonicated in sonication buffer (150 mM NaCl, 20 mM EDTA, 50 mM Tris-HCl, 1% v/v NP-40, 0.5% v/v sodium deoxycholate, 10 mM NaF, 0.1% SDS) using a Bioruptor Pico (Diagenode) and a cycle setting of 30 sec on/off until fragment sizes around 200-500 bp was reached. Protease and phosphatase inhibitors were added to both lysis and sonication buffers. Samples were precleared by 50% slurry of sepharose resuspended in sonication buffer. Antibodies were added and incubated rotating overnight. Sepharose beads coupled with Protein A (rabbit antibodies) or Protein G (mouse or goat antibodies) were added to samples and incubated for 2 hr, washed, de-crosslinked, RNAse A and proteinase K treated, and DNA was extracted.
ChIP DNA was quantified with Qubit using the Qubit 1X dsDNA High Sensitivity Kit and libraries were prepped per supplier’s protocol using the MicroPlex Library Preparatioin Kit v3 (Diagenode, C05010001). The library fragment size was determined by TapeStation using the High Sensitivity D1000 Sample Buffer and High Sensitivity D1000 ScreenTape.

tag: tissue

value: cell line

tag: cell line

tag: cell type

value: Pancreatic ductal adenocarcinoma

tag: sample group


title: ChIPseq_L36plClone2_dTAG_1h_H3K4me3_Rep1

description: Library name: Sample038


title: tumor-like cells

city: Darmstadt

first: Tamara

last: Bender

address: Planckstraße 1

institute: GSI Helmholtzzentrum für Schwerionenforschun

description: Library name: TB-A29-P2

library_source: transcriptomic

data_processing:
Raw reads were preprocessed using FastP preprocessor (https://github.com/OpenGene/fastp) for trimming adapters, polyG or polyX, and aligned to the human genome (hg38) using the STAR Aligner (http://code.google.com/p/rna-star/). Data analysis of the filtered feature counts was performed using the R software (https://www.r-project.org/) with Bioconductor (https://www.bioconductor.org/).
Assembly: Human (hg38)
Supplementary files format and content: csv file with filtered feature counts for all samples

molecule: total RNA

source_name: tumor-like cells

extract_protocol:
Organoid slices (n = 3), organoids (n = 3), assembloids (n = 3), tumor spheres (n = 6), each pooled from the same biological replicate in one tube, and tumor-like cells (n = 1), were washed in cold PBS at 300xg, 5 min. RNA was isolated as described in a section “Real time RT-PCR analysis” and stored at -80 °C. Preparation of samples for sequencing including the isolation of the nuclei, and initial quality control were performed as a service by GENEWIZ/AZENTA (USA). Library preparation, sequencing and initial data processing were performed as a service by GENEWIZ/AZENTA (USA). The standard RNA-seq bundle with polyA selection with 2x150 bp was performed on the Illumina series. The estimated sequencing output was ~50 million paired-end reads per sample.
Library preparation, sequencing and initial data processing were performed as a service by GENEWIZ/AZENTA (USA). The RNA-seq library was prepared using 10X Genomics Chromium® 3` expression, and the 10X library sequencing was performed on the Illumina series. The target number of cells per sample was 6000, and number of reads per cell 50000.

value: tumor-like cells

tag: genotype

value: c-MYChigh

tag: treatment

value: control


title: organoid slice

description: Library name: TB-A27-C

source_name: organoid slice

value: organoid slice

value: neural and glia cells

value: WT


title: DSP-1001660016239-C-A12

city: Ann Arbor

first: Mohamed

last: Noureldein

address: 109 Zina Pitcher Place

department: Neurology

country: USA

institute: University of Michigan

data_processing:
Fastq files were converted to DCC files using the GeoMx NGS Pipeline software and the mm10 reference genome.
Digital Count Conversion files, containing expression count data and sequencing quality metadata, and Probe Kit Configuration files, containing probe assay and sample metadata, were imported into R. Gene expression counts with a value of 0 were shifted to 1 to facilitate downstream transformations. ROI segments were filtered and removed if they met the criteria: “<1000 raw reads”, “below 80% Aligned or 80% Trimmed”, “80% Stitched”, and “below 50% sequencing saturation”. Genes were filtered and removed if they were not detected in at least 10% of segments. Next, counts were normalized using quartile 3 normalization and visualized by uniform manifold approximation and projection, a non-linear dimensionality reduction visualization tool. Gene expression in both datasets was relatively well separated according to ROI brain region.
Assembly: mm10
Supplementary files format and content: Late_stage_count_table.csv. A count table containing normalized counts for probes and segments that passed the quality control steps mentioned in the data processing step.
Library strategy: Spatial Transcriptomics

organism: Mus musculus

source_name: Brain

growth_protocol: Two slides were for late-stage analysis and were duplicates of 4 brain sections (n=2 5XFAD 30 wk, n=2 controls 30 wk)

extract_protocol:
One brain hemisphere was fixed in 4% paraformaldehyde (PFA) for 24 h, cryoprotected in escalating sucrose gradients, embedded, and cryosectioned in coronal plane sections onto histologic slides [10 μm thickness for spatial transcriptomics sections, 14 μm thickness for subsequent fluorescent in situ hybridization (FISH)] and stored at –80 °C.
Spatial transcriptomics was performed by GeoMx DSP (NanoString, Seattle, WA), a platform for spatially analyzing gene expression in tissue in a highly multiplexed manner
Other: Spatial transcriptomics-Nanostring GeoMx DSP

value: Brain


description:
Library name: RPM_RPMA_RPR2_Basal_Organoids_CMV_CellTagged_PreCre_CMO
10X Genomic 3' CellPlex (CMO)

source_name: Tracheal-basal organoid

value: Tracheal-basal organoid

value: RPM (CMO305), RPMA (CMO307), RPR2 (CMO306)

value: Experiment_A (RPM CellTag pre-Cre); Experiment_C (RPMA CellTag pre-Cre)

value: organoid

value: Rb1 fl/fl; Trp53 fl/fl;H11b-LSL-MycT58A-Ires-Luc (RPM) and Rb1 fl/fl; Trp53 fl/fl;H11b-LSL-MycT58A-Ires-Luc; Ascl1 fl/fl (RPMA) and  Rb1 fl/fl; Trp53 fl/fl; Rbl1/p130 fl/fl (RPR2)


title: ChIPseq_L36plClone2_dTAG_1h_H3K27ac_Rep3

description: Library name: Sample037


title: tumor sphere

description: Library name: ES-M27-TS

source_name: tumor sphere

value: tumor sphere


title: organoid

description: Library name: ES-M27-O

source_name: cerebral organoid

value: cerebral organoid


title: ChIPseq_L36plClone2_dTAG_1h_H3K27ac_Rep2

description: Library name: Sample036


title: Wildtype_Basal_Organoids_GEX

description:
Library name: Wildtype_Basal_Organoids_GEX
10X Genomic 3' GEX

library_source: transcriptomic single cell

value: Wildtype (WT)


title: DSP-1001660016239-C-A11


title: DSP-1001660016239-C-A10


title: assembloid

description: Library name: ES-M27-A

source_name: cerebral organoid and tumor sphere

value: cerebral organoid and tumor sphere

value: neural, glia cells, and tumor-like cells

value: WT + c-MYChigh


title: ChIPseq_L36plClone2_dTAG_1h_H3K27ac_Rep1

description: Library name: Sample035

value: cell line

value: Pancreatic ductal adenocarcinoma


title: DSP-1001660016239-C-A09


title: cortex, E15_Emx1_Cre_Map2k1/2_dcko, experiment

city: Shanghai

first: TongYe

last: Fu

address: 138 Yi Xue Yuan Road

country: China

institute: Fudan University

description:
Library name: sample11
10x Genomics

data_processing:
High quality sequences (clean reads) were obtained by removing low quality sequences and joints. The clean reads were then processed with Cell Ranger software to obtain quantitative information on gene expression.
Assembly: mm10
Supplementary files format and content: Tab-separated value files and matrix files

source_name: cortex

extract_protocol:
Briefly, mouse embryos were dissected out and immediately submerged in fresh ice-cold Hanks balanced salt solution (Gibco 12175-095). The cortex was then cut into pieces and dissociated into a single-cell suspension using a Papain Cell Dissociation Kit (Miltenyi Biotec, catalog no. 130-092-628) according to the manufacturer’s instructions.
The Chromium dropletbased sequencing platform (10X Genomics) was used to generate scRNA-Seq libraries, following the manufacturer’s instructions (manual document part number: CG00052 Rev C). The cDNA libraries were purified, quantified using an Agilent 2100 Bioanalyzer, and sequenced on an Illumina NovaSeq 6000.

value: cortex

value: Mapk-dcko


title: cortex, E15_Map2k1/2, control

description:
Library name: sample10
10x Genomics

value: WT


title: ChIPseq_L36plClone2_dTAG_0h_KLF5_Rep2

description: Library name: Sample034


title: HEK293, Library_MI, 24h, rep2

city: Amsterdam

first: Noud

last: Klaassen

address: Plesmanlaan 121

department: Gene Regulation

country: Netherlands

institute: Netherlands Cancer Insitute

description: Library name: Motif_Insertion_Library_HEK293_Replicate2

data_processing:
See methods
Assembly: hg19
Supplementary files format and content: count tables and normalized (log2RPM) data

growth_protocol: cells were cultured according to manufacters protocol

extract_protocol:
Standard RNA extraction protocols see methods paper
Various different protocols

treatment_protocol: cells were transfected by either nucleofection or lipofection

value: Embryonic kidney


title: HEK293, Library_MI, 24h, rep1

description: Library name: Motif_Insertion_Library_HEK293_Replicate1


title: cortex, P2_hGFAP_Cre_SmoF/F, experiment

description:
Library name: sample9
10x Genomics


title: ChIPseq_L36plClone2_dTAG_0h_KLF5_Rep1

description: Library name: Sample033


description:
Library name: RPM_RPMA_RPR2_Basal_Organoids_CMV_CellTagged_PreCre_GEX
10X Genomic 3' GEX

value: Tracheal-basal organoid

value: CellTag pre-CMV-Cre


title: DSP-1001660016239-C-A08

value: Brain


title: ChIPseq_L36plClone2_dTAG_0h_H3K4me3_Rep3

description: Library name: Sample032


title: U2OS, Library_MI, 24h, rep2

description: Library name: Motif_Insertion_Library_U2OS_Replicate2

value: Osteosarcoma


title: DSP-1001660016239-C-A06


title: cortex, E18_hGFAP_Cre_SmoF/F_dnPKA, experiment

description:
Library name: sample7
10x Genomics

value: dnPKA


title: DSP-1001660016239-C-A07


title: DSP-1001660016239-C-A04


title: U2OS, Library_MI, 24h, rep1

description: Library name: Motif_Insertion_Library_U2OS_Replicate1


title: cortex, E16_5_Emx1_Cre_Super, experiment

description:
Library name: sample6
10x Genomics


title: cortex, E16_5_SuperHippo(without_Cre), control

description:
Library name: sample5
10x Genomics


title: ChIPseq_L36plClone2_dTAG_0h_H3K27ac_Rep1

description: Library name: Sample027


title: ChIPseq_L36plClone2_dTAG_0h_H3K27ac_Rep3

description: Library name: Sample029


title: ChIPseq_L36plClone2_dTAG_0h_H3K4me3_Rep1

description: Library name: Sample030


title: DSP-1001660016239-C-A01

value: No template control


title: cortex, E16_5_Wild_type_littermate, control

description:
Library name: sample3
10x Genomics


title: ChIPseq_L36plClone2_dTAG_0h_H3K27ac_Rep2

description: Library name: Sample028


title: DSP-1001660016239-C-A02


title: cortex, E16_5_hGFAP_Cre_Super, experiment

description:
Library name: sample4
10x Genomics


title: DSP-1001660016239-C-A03


title: DSP-1001660016238-F-G08


title: cortex, P2_Super_without_Cre, control

description:
Library name: sample1
10x Genomics


title: cortex, P2_hGFAP_Cre_Super, experiment

description:
Library name: sample2
10x Genomics


title: ChIPseq_L36plClone2_dTAG_0h_H3K4me3_Rep2

description: Library name: Sample031


title: cortex, P2_SmoF/F, control

description:
Library name: sample8
10x Genomics


title: ChIPseq_L36pl_KLF5_Rep1

description: Library name: Sample025


title: ChIPseq_L36pl_CTCF_Rep3

description: Library name: Sample024


title: Foxk2_KO_GM_2

first: Wu

last: Peixuan

address: Dongan road

institute: Fudan university

description:
Library name: Sample 15
gene_count_matrix.txt

data_processing:
Illumina Casava1.7 software used for basecalling.
For ChIP-seq, ChIP products were end repaired, dA-tailing and linker ligation were performed, and barcoding and Illumina adapter addition were performed by PCR amplification. Libraries were purified using QiaQuick PCR purification reagents (Qiagen, Hilden, Germany) and size selected by 0.7×and 0.2×Ampure XP beads (Beckman, California, USA).
For ATAC-seq, to profile open chromatin regions, a totol of 50,000 control and FOXK2 knockout C2C12 cells were washed once with cold PBS. Cells were lysed on ice for 3 minutes in 50 μL of ice-cold lysis buffer containing 10 mM Tris (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, 0.1% Tween 20, and 0.01% Digitonin in diethylpyrocarbonate (DEPC)-treated water. Following lysis, cells were resuspended in ice-cold RBS-Wash buffer (10 mM Tris, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween 20) and pelleted at 4 °C at 500 × g for 10 minutes. Tagmentation was performed in 1× Tagmentation buffer composed of 10 mM Tris (pH 7.4), 5 mM MgCl2, 10% DMF, 33% PBS, 0.1% Tween 20, and 0.01% Digitonin, using 100 nM Tn5 Transposase for 15 minutes at 37 °C. An equal volume of 2x Tn5 Digestion Mix (TransNGS) was added, and the tagmentated samples were purified using the QIAquick PCR Purification Kit (Qiagen). Libraries were then amplified with Illumina primers, purified again, and size-selected using 0.7× and 0.2× DNA clear beads (TransNGS). Finally, the assay of transposase accessible chromatin sequencing (ATAC-seq) libraries were sequenced on a NovaSeq platform (Anoroad) using paired-end reads of 150 bp.
For RNA-seq of C2C12 cells was carried on by the LC-Bio Technology, Hangzhou, China. The detailed operations were as follows: total RNA was extracted from cells using TRIzol reagent (Invitrogen), and the RNA quantity and purity were assessed using the Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent). Only samples with an RNA integrity number (RIN) > 7.0 were selected for subsequent library construction. Paired- end (PE) RNA sequencing was performed on the Illumina NovaseqTM 6000 platform (Illumina). The PE reads were filtered using Cutadapt (v.1.9) and then quality-checked with FastQC (v.0.11.9). Mapped reads of each sample were assembled using StringTie (v.2.1.6) with default parameters, and transcriptomes were merged using gffcompare (v.0.9.8). Transcript abundance was estimated using Ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) and StringTie, calculating fragment per kilobase of transcript per million mapped reads (FPKM). Differential gene expression analysis was performed with DESeq2 (v.1.30.0) using  default settings.
bedGraph files were generated using Bedtools (v2.29.2) with normalized values for each sample. we used the custom script to get bedpe files for interaction loops identified by using raw contact frequencies.  The custom utility was used to convert the raw contact frequencies into sparse .matrix format, and  these interaction counts were normalized for a total of 1,000,000 interactions at the same resolutions.
Assembly: mm10
Supplementary files format and content: gene_count_matrix.txt, bw

source_name: Muscle

growth_protocol: All mouse procedures were approved and monitored by the Research Ethics Committee of the School of Basic Medical Sciences, Fudan University, China. Mice were on a C57Bl/6 genetic background . Animals were housed and bred in a specific pathogen-free animal facility.

extract_protocol:
For ChIP-seq, C2C12 cells (5-10.0×106) were crosslinked  with 1% formaldehyde and then quenched in a final solution at a final concentration of 0.125 M. The chromatin was extracted and digested with micrococcal nuclease to primarily generate mononucleosomes, with a minor fraction of dinucleosomes. Digestion reaction was halted by adding 8μL of a solution containing 0.2 M EDTA and 0.2 M EGTA. The chromatin was then incubated overnight at 4°C with either 2 μL of rabbit anti-FOXK2 antibody or 2 μL control rabbit IgG antibody. Protein A/G magnetic beads (Thermo Fisher) were added for an additional 4 hour incubation. The resulting immunoprecipitates were washed thoroughly to remove unbound materials, and DNA was purified according to the manufacturer’s instructions using the SimpleChIP® Plus Enzymatic Chromatin IP Kit (CST). For RNA-seq, Total RNA was extracted from cells using TRIzol reagent (Invitrogen), and the RNA quantity and purity were assessed using the Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent). Only samples with an RNA integrity number (RIN) > 7.0 were selected for subsequent library construction. Paired- end (PE) RNA sequencing was performed on the Illumina NovaseqTM 6000 platform (Illumina). For ATAC-seq,   To profile open chromatin regions, a totol of 50,000 control and FOXK2 knockout C2C12 cells were washed once with cold PBS. Cells were lysed on ice for 3 minutes in 50 μL of ice-cold lysis buffer containing 10 mM Tris (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, 0.1% Tween 20, and 0.01% Digitonin in diethylpyrocarbonate (DEPC)-treated water. Following lysis, cells were resuspended in ice-cold RBS-Wash buffer (10 mM Tris, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween 20) and pelleted at 4 °C at 500 × g for 10 minutes. Tagmentation was performed in 1× Tagmentation buffer composed of 10 mM Tris (pH 7.4), 5 mM MgCl2, 10% DMF, 33% PBS, 0.1% Tween 20, and 0.01% Digitonin, using 100 nM Tn5 Transposase for 15 minutes at 37 °C. An equal volume of 2x Tn5 Digestion Mix (TransNGS) was added, and the tagmentated samples were purified using the QIAquick PCR Purification Kit (Qiagen). Libraries were then amplified with Illumina primers, purified again, and size-selected using 0.7× and 0.2× DNA clear beads (TransNGS).
ChIP-seq, ATAC-seq,RNA-seq

value: Muscle

value: Myoblast cell


title: Foxk2_KO_GM_3

description:
Library name: Sample 16
gene_count_matrix.txt


title: DSP-1001660016238-F-G05


title: DSP-1001660016238-F-G06


title: Foxk2_KO_GM_1

description:
Library name: Sample 14
gene_count_matrix.txt


title: ChIPseq_L36pl_CTCF_Rep1

description: Library name: Sample022


title: DSP-1001660016238-F-G04


title: Control_GM_3

description:
Library name: Sample 13
gene_count_matrix.txt


title: ChIPseq_HPAFII_KLF5_Rep2

description: Library name: Sample021

value: HPAFII


title: DSP-1001660016238-F-G02


title: Control_GM_2

description:
Library name: Sample 12
gene_count_matrix.txt


title: ChIPseq_L36pl_KLF5_Rep2

description: Library name: Sample026


title: DSP-1001660016238-F-G03


title: ChIPseq_HPAFII_KLF5_Rep1

description: Library name: Sample020


title: ChIPseq_BxPC3_KLF5_Rep2

description: Library name: Sample019


title: ChIPseq_BxPC3_KLF5_Rep1

description: Library name: Sample018


title: DSP-1001660016238-F-F12


title: ChIPseq_AsPC1_KLF5_Rep2

description: Library name: Sample017


title: Control_GM_1

description:
Library name: Sample 11
gene_count_matrix.txt


title: Foxk2-NC2-ATAC-lib

description: Library name: Sample 9


title: ChIPseq_AsPC1_KLF5_Rep1

description: Library name: Sample016


title: Foxk2-NC3-ATAC-lib

description: Library name: Sample 10


title: Foxk2-KD3-ATAC-lib

description: Library name: Sample 7


title: DSP-1001660016238-F-F11


title: ChIPseq_AsPC1_CTCF_Rep3

description: Library name: Sample015


title: ChIPseq_L36pl_CTCF_Rep2

description: Library name: Sample023


title: DSP-1001660016238-F-F09


title: Foxk2-NC1-ATAC-lib

description: Library name: Sample 8


title: ChIPseq_AsPC1_CTCF_Rep2

description: Library name: Sample014


title: DSP-1001660016238-F-F08


title: ChIPseq_AsPC1_CTCF_Rep1

description: Library name: Sample013


title: Foxk2-KD2-ATAC-lib

description: Library name: Sample 6


title: Foxk2-KD1-ATAC-lib

description: Library name: Sample 5


title: DSP-1001660016238-F-F07


title: C2C12-WT-IgG-N-cuttag-lib

description: Library name: Sample 4


title: RNAseq_L36plClone2_dTAG_4h_Rep2

description: Library name: Sample105

data_processing:
Paired end sequencing reads were mapped to the reference genome assembly hg38 using STAR). Reverse (sense strand) reads were quantified using htseq-count.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

molecule: polyA RNA

extract_protocol:
Cells were washed twice with PBS after removing cell culture medium and total RNA was extracted from cells by adding 700 µL of QIAzol, incubated for 5 min on rocker, scraped and transferred to a new tube. 140 µL chloroform was added to the samples, vortexed for 15 sec, incubated for 3 min at room temperature, and centrifuged. Aqueous phase was transferred to a new tube and mixed with an equal volume of isopropanol. Samples were incubated at -80°C 1 hour and centrifuged. RNA pellet was washed twice with 70% ethanol and the pellet was air-dried at room temperature for 5-10 min. 50 µL of RNAse-free water was used to resuspend the pellet.
Before RNA-sequencing, RNA integrity was validated by gel electrophoresis and libraries were prepped using 500 ng following supplier’s protocol - Illumina Stranded mRNA Prep, Ligation (Illumina, 20040534). The library fragment size was determined by TapeStation.


title: DSP-1001660016238-F-F06


title: DSP-1001660016238-F-G01


title: C2C12-WT-Foxk2-cuttag-lib

description: Library name: Sample 1


title: C2C12-WT-Foxk2-cuttag-rep3

description: Library name: Sample 3


title: DSP-1001660016238-F-F03


title: DSP-1001660016238-F-F10


title: DSP-1001660016238-F-F04


title: RNAseq_L36plClone2_dTAG_4h_Rep1

description: Library name: Sample104


title: C10_6

city: Jinan

first: Zhaochao

last: Liu

address: Wenhua West Road

institute: Shandong University

description: Library name: C10-6

data_processing:
The droplet-based sequencing data were subjected to alignment and quantification through the utilization of CellRanger software (version 7.2.0, designed for 3’ chemistry), employing the mm10 mouse reference genome. The Python package Scanpy (version 1.8.2)65 was employed to load the matrix containing cell-gene counts and to execute quality control procedures for both the newly generated dataset and the acquired datasets.
Assembly: mm10
Supplementary files format and content: matrix.tar

source_name: nasal mucosa

extract_protocol:
Chronic rhinosinusitis (CRS) mice model To establish CRS mice model, mice in CRS group were treated intranasally with 20μg Papain (Sigma-Aldrich, P5306-25MG, USA) which was dissolved in 20μL phosphate buffer saline (PBS) on days 0-2 and 7-11. Drug treatment The treatment dosage of C10 (MCE, HY-19357, CHN) drug solution for intranasal administration in CRS mice were 10 mg/mL, with bilateral administration (10 μl/side, bilateral intranasal instillation). Starting from the initial administration of papain, treatment was continued for 10 consecutive days, with once-daily application. The concentration 10 ng/mL of IL-13 (MCE, HY-P72795, CHN) was used to stimulate Beas-2b and HNECs for 48 hours.
We used the following quality control procedure: genes expressed in fewer than three cells were filtered out, and cells were kept for further analysis when (1) more than 200 genes were detected and (2) mitochondrial genes were expressed at a proportion < 10%.

value: nasal mucosa


title: C10_8

description: Library name: C10-8


title: RNAseq_L36plClone2_dTAG_24h_Rep3

description: Library name: Sample100


title: C10_3

description: Library name: C10-3


title: DSP-1001660016238-F-E12


title: RNAseq_L36plClone2_dTAG_48h_Rep2

description: Library name: Sample102


title: CRS_9

description: Library name: CRS9


title: RNAseq_L36plClone2_dTAG_24h_Rep2

description: Library name: Sample099


title: DSP-1001660016238-F-E11


title: DSP-1001660016238-F-F01


title: CRS_7

description: Library name: CRS7


title: RNAseq_L36plClone2_dTAG_4h_Rep3

description: Library name: Sample106


title: DSP-1001660016238-F-E10


title: RNAseq_L36plClone2_dTAG_48h_Rep3

description: Library name: Sample103


title: C2C12-WT-Foxk2-cuttag-rep2

description: Library name: Sample 2


title: DSP-1001660016238-F-F05


title: RNAseq_L36plClone2_dTAG_24h_Rep1

description: Library name: Sample098


title: CRS_2

description: Library name: CRS2


title: RNAseq_L36plClone2_dTAG_0h_Rep3

description: Library name: Sample097


title: DSP-1001660016238-F-E09


title: DSP-1001660016238-F-E07


title: CON_6

description: Library name: C6


title: DSP-1001660016238-F-E08


title: RNAseq_L36plClone2_dTAG_0h_Rep2

description: Library name: Sample096


title: DSP-1001660016238-F-F02


title: CON_7

description: Library name: C7


title: RNAseq_L36plClone2_dTAG_48h_Rep1

description: Library name: Sample101


title: RNAseq_L36pl_siNT5_Rep3

description: Library name: Sample094


title: CON_2

description: Library name: C2


title: DSP-1001660016238-F-E06


title: 065.secondary infection, 2dpi, IgG-control

city: New York

first: Donna

last: Farber

state: NY

address: 701 W168th street

department: Immunology

institute: Columbia University

description:
Library name: DA065
DA065
rnaseq_aIL10R.csv

data_processing:
RTA (Illumina) was used for bsae calling
bcl2fastq2 was used for converting BCL to fastq, coupled with adaptor trimming
pseudoallignment was performed using kallisto, aligned to GRCm39
Assembly: GRCm39
Supplementary files format and content: csv (comma-seperated table) of DESeq2 normalized counts of RNAseq data (for both tables)

source_name: lung

growth_protocol: C57BL6/J WT mice were housed in an BSL2+ SPF facility

extract_protocol:
whole lungs were homogenized using the Tissuelyser II (Qiagen) and total RNA was extracted with the Qiasymphony SP (Qiagen) according to manufacturer protocol. RNA quality was assessed by either Bioanalyzer (Agilent) or Tapestation 4200 (Agilent). Only RNA with RIN ≥ was used for these experiments.
RNAseq libraries were prepared using Illumina Truseq chemistry.

treatment_protocol: mice undergoing primary infection are naïve at the time of infection. mice undergoing primary infection were previously infected with a different strain of IAV, and after recovery, were infected again at the beginning of the experiment.

value: lung

value: whole lung homogenate

value: WT (C57BL6/J)

value: memory +IgG

tag: batch


title: DSP-1001660016238-F-E05


title: RNAseq_L36pl_siNT5_Rep2

description: Library name: Sample093

value: Pancreatic ductal adenocarcinoma


title: RNAseq_L36pl_siNT5_Rep1

description: Library name: Sample092


title: 064.secondary infection, 2dpi, IgG-control

description:
Library name: DA064
DA064
rnaseq_aIL10R.csv


title: DSP-1001660016238-F-E03

value: WT


title: RNAseq_L36pl_siKLF5_Rep3

description: Library name: Sample091


title: 063.secondary infection, 2dpi, IgG-control

description:
Library name: DA063
DA063
rnaseq_aIL10R.csv


title: DSP-1001660016238-F-E02


title: 062.secondary infection, 2dpi, IgG-control

description:
Library name: DA062
DA062
rnaseq_aIL10R.csv


title: RNAseq_L36pl_siKLF5_Rep1

description: Library name: Sample089


title: RNAseq_L36pl_siKLF5_Rep2

description: Library name: Sample090


title: 061.secondary infection, 2dpi, aIL10R-treated

description:
Library name: DA061
DA061
rnaseq_aIL10R.csv

value: memory +aIL10R


title: RNAseq_HPAFII_siNT5_Rep3

description: Library name: Sample088

source_name: HPAFII


title: RNAseq_L36plClone2_dTAG_0h_Rep1

description: Library name: Sample095


title: DSP-1001660016238-F-E01


title: DSP-1001660016238-F-D12


title: 059.secondary infection, 2dpi, aIL10R-treated

description:
Library name: DA059
DA059
rnaseq_aIL10R.csv


title: DSP-1001660016238-F-D11


title: 058.secondary infection, 3dpi

description:
Library name: DA058
DA058
rnaseq_kx.csv

value: memory (previous infection)


title: RNAseq_HPAFII_siNT5_Rep2

description: Library name: Sample087


title: RNAseq_HPAFII_siNT5_Rep1

description: Library name: Sample086


title: DSP-1001660016238-F-G07


title: DSP-1001660016238-F-E04


title: DSP-1001660016238-F-D10


title: 056.secondary infeciton, 3dpi

description:
Library name: DA056
DA056
rnaseq_kx.csv


title: 057.secondary infection, 3dpi

description:
Library name: DA057
DA057
rnaseq_kx.csv


title: DSP-1001660016238-F-D09


title: 054.secondary infection, 3dpi

description:
Library name: DA054
DA054
rnaseq_kx.csv


title: RNAseq_HPAFII_siKLF5_Rep3

description: Library name: Sample085


title: DSP-1001660016238-F-D08


title: RNAseq_HPAFII_siKLF5_Rep2

description: Library name: Sample084


title: 053.secondary infection, 2dpi

description:
Library name: DA053
DA053
rnaseq_kx.csv


title: DSP-1001660016238-F-D07


title: 060.secondary infection, 2dpi, aIL10R-treated

description:
Library name: DA060
DA060
rnaseq_aIL10R.csv


title: RNAseq_BxPC3_siNT5_Rep3

description: Library name: Sample082


title: RNAseq_BxPC3_siNT5_Rep2

description: Library name: Sample081


title: DSP-1001660016238-F-D05


title: 051.secondary infection, 2dpi

description:
Library name: DA051
DA051
rnaseq_kx.csv


title: DSP-1001660016238-F-D06


title: 050.secondary infection, 2dpi

description:
Library name: DA050
DA050
rnaseq_kx.csv


title: RNAseq_BxPC3_siNT5_Rep1

description: Library name: Sample080


title: 049.secondary infection, 1dpi

description:
Library name: DA049
DA049
rnaseq_kx.csv


title: RNAseq_BxPC3_siKLF5_Rep3

description: Library name: Sample079


title: DSP-1001660016238-F-D03


title: DSP-1001660016238-F-D04


title: DSP-1001660016238-F-D02


title: 047.secondary infection, 1dpi

description:
Library name: DA047
DA047
rnaseq_kx.csv


title: RNAseq_AsPC1_siNT5_Rep3

description: Library name: Sample076


title: 048.secondary infection, 1dpi

description:
Library name: DA048
DA048
rnaseq_kx.csv


title: RNAseq_BxPC3_siKLF5_Rep2

description: Library name: Sample078


title: RNAseq_HPAFII_siKLF5_Rep1

description: Library name: Sample083


title: 046.secondary infection, 1dpi

description:
Library name: DA046
DA046
rnaseq_kx.csv


title: RNAseq_AsPC1_siNT5_Rep2

description: Library name: Sample075


title: DSP-1001660016238-F-C11


title: DSP-1001660016238-F-D01


title: RNAseq_BxPC3_siKLF5_Rep1

description: Library name: Sample077


title: RNAseq_AsPC1_siNT5_Rep1

description: Library name: Sample074


title: DSP-1001660016238-F-C12


title: DSP-1001660016238-F-C10


title: 045.secondary infection, 0dpi

description:
Library name: DA045
DA045
rnaseq_kx.csv


title: 052.secondary infection, 2dpi

description:
Library name: DA052
DA052
rnaseq_kx.csv


title: DSP-1001660016238-F-C09


title: RNAseq_AsPC1_siKLF5_Rep2

description: Library name: Sample072


title: RNAseq_AsPC1_siKLF5_Rep3

description: Library name: Sample073


title: 044.secondary infection, 0dpi

description:
Library name: DA044
DA044
rnaseq_kx.csv


title: DSP-1001660016238-F-C08


title: 041.primary infection, 3dpi

description:
Library name: DA041
DA041
rnaseq_kx.csv

value: naïve


title: 039.primary infection, 3dpi

description:
Library name: DA039
DA039
rnaseq_kx.csv


title: DSP-1001660016238-F-C07

value: Brain


title: RNAseq_AsPC1_siKLF5_Rep1

description: Library name: Sample071


title: DSP-1001660016238-F-C06


title: ATACseq_L36plClone2_dTAG_4h_Rep3

description: Library name: Sample012

data_processing:
Paired end sequencing reads were filtered for adapter contamination with Trim Galore and mapped to the reference genome assembly hg38 using bowtie2 with --dovetail. BamTools Filter was used for removing low quality (mapQ >= 30) and mitochondrial reads. Resulting bam file was converted to a bed file with bedtools bamtobed. Peak calling and bedgraph generation was performed using macs3 callpeak using shift and extend method to center peaks at 5’ cut site (shift -100 extension size 200). The data was visualized by using bedGraphToBigWig.
Assembly: hg38
Supplementary files format and content: Normalized bigwigs and bed file for each condition

growth_protocol: L36pl cells were maintained in phenol free MEM with 10% FBS and 1% Pen-Strep in a humidified 5% CO2 incubator at 37C.

extract_protocol:
For ATAC-Seq library preparation, cells were harvested and libraries were produced using ATAC-Seq kit (Active Motif, 53150) following manufacturer’s instructions. Library concentration was determined via Qubit and fragment size was quantified with TapeStation.
For ATAC-Seq library preparation, cells were harvested and libraries were produced using ATAC-Seq kit (Active Motif, 53150) following manufacturer’s instructions. Library concentration was determined via Qubit and fragment size was quantified with TapeStation.

value: cell line


title: 038.primary infection, 3dpi

description:
Library name: DA038
DA038
rnaseq_kx.csv


title: ATACseq_L36plClone2_dTAG_4h_Rep1

description: Library name: Sample010


title: 037.primary infection, 2dpi

description:
Library name: DA037
DA037
rnaseq_kx.csv


title: DSP-1001660016238-F-C05


title: DSP-1001660016238-F-C03


title: 036.primary infection, 2dpi

description:
Library name: DA036
DA036
rnaseq_kx.csv


title: ATACseq_L36plClone2_dTAG_24h_Rep1

description: Library name: Sample007


title: 042.primary infection, 3dpi

description:
Library name: DA042
DA042
rnaseq_kx.csv


title: ATACseq_L36plClone2_dTAG_24h_Rep3

description: Library name: Sample009


title: DSP-1001660016238-F-C02


title: ATACseq_L36plClone2_dTAG_1h_Rep3

description: Library name: Sample006


title: ATACseq_L36plClone2_dTAG_24h_Rep2

description: Library name: Sample008


title: 033.primary infection, 2dpi

description:
Library name: DA033
DA033
rnaseq_kx.csv


title: ATACseq_L36plClone2_dTAG_1h_Rep2

description: Library name: Sample005


title: 032.primary infection, 1dpi

description:
Library name: DA032
DA032
rnaseq_kx.csv


title: DSP-1001660016238-F-B12


title: 031.primary infection, 1dpi

description:
Library name: DA031
DA031
rnaseq_kx.csv


title: ATACseq_L36plClone2_dTAG_4h_Rep2

description: Library name: Sample011


title: DSP-1001660016238-F-B11


title: ATACseq_L36plClone2_dTAG_1h_Rep1

description: Library name: Sample004


title: 030.primary infection, 1dpi

description:
Library name: DA030
DA030
rnaseq_kx.csv


title: ATACseq_L36plClone2_dTAG_0h_Rep3

description: Library name: Sample003


title: 029.primary infection, 1dpi

description:
Library name: DA029
DA029
rnaseq_kx.csv


title: ATACseq_L36plClone2_dTAG_0h_Rep2

description: Library name: Sample002


title: DSP-1001660016238-F-B10


title: 034.primary infection, 2dpi

description:
Library name: DA034
DA034
rnaseq_kx.csv


title: 035.primary infection, 2dpi

description:
Library name: DA035
DA035
rnaseq_kx.csv


title: DSP-1001660016238-F-C04


title: DSP-1001660016238-F-B09


title: DSP-1001660016238-F-C01


title: 027.primary infection, 0dpi

description:
Library name: DA027
DA027
rnaseq_kx.csv


title: DSP-1001660016238-F-B07


title: DSP-1001660016238-F-B08


title: ATACseq_L36plClone2_dTAG_0h_Rep1

description: Library name: Sample001


title: DSP-1001660016238-F-B06


title: SG05, MULTI-seq, LMO capture 2

city: Melbourne

first: Mark

last: Dawson

address: 305 Grattan Street

department: Cancer Research

country: Australia

institute: Peter MacCallum Cancer Centre

description: Library name: SG05-scRNA-02-MultiSeq

data_processing:
Fastq files from SG05-scRNA-01-GEX and SG05-scRNA-02-GEX were processed using Cell Ranger v.7.1.0 against the Cell Ranger mm10/GRCm38 v3.0.0 genome. Following quality control was performed using Seurat v5.1.0 filtering out cells with fewer than 200 genes or 4,000 unique molecular identifiers (UMIs). Cells with greater than 20% mitochondrial RNA were also removed.
MULTI-Seq LMOs files were processed using CITE-seq-count v1.4.5 using default settings. Seurat HTODemux methods were used to demultiplex LMO information.
Fastq files were processed using BARtab v1.4 using the single-cell workflow on non-empty droplets identified by Cell Ranger as input. The resulting data frame containing cell ID and SPLINTR barcode ID is generated. SPLINTR barcode data was added to the scRNA-seq data using AddMetaData from Seurat.
To detect SPLINTR barcodes from the scRNA-seq library, unmapped reads were extracted from BAM alignment files for each library using SAMtools v1.9. BAMs containing SPLINTR barcode reads were identified using BARtab v1.4.
Assembly: scRNA GEX: mm10/GRCm38 v3.0.0, SPLINTR amplicon and scBARtab extraction: SPLINTR GFP barcode reference library, LMO MULTI-seq: List of LMO sequences used in experiment
Supplementary files format and content: gz, tsv, mtx, BAM

growth_protocol: 1 million SPLINTR barcoded Molm-13 cells were injected into mice treated with Vehicle or Combined 5 mg/kg PF-9363 and 10mg/kg SNDX-5613 treatment. Upon disease endpoint mice were humanely euthanized before extracting cells from the bone marrow and spleen. Cells were cryogenically preserved.

extract_protocol:
Cells previously isolated from bone marrow and spleen of mice treated transplanted with SPLINTR barcoded Molm-13 cells and treated with either Vehicle or Combination and T0 (pre-transplantation population) were thawed at 37 C in a water bath before being resuspended in FACs buffer (0.5% FBS in PBS). Viable, SPLINTR barcoded cells were sorted using propidium iodide and GFP. Samples were hashtagged with MULTI-seq lipid-modified oligos (LMOs) following manufacturers instructions. LMO-tagged cells were pooled before measuring viability using trypan blue. Following this, cells were captured using 10X Genomics 3' GEX workflow following manufacturers instructions.
10X Genomics 3' GEX and MULTI-seq LMO libraries were contstructed following their respective manufacturer's instructions. For the SPLINTR library, full length cDNA from the 10X GEX library was used as input. Barcode sequences were amplified using primers which bind to the P5 adaptor and TruSeq sequences read 1 (forward primer) and constant region of barcode, i7 index, TruSeq read 2 and P7 adapter. Libraries were cleaned using 0.7X SPRI beads before runing on an agarose gel to ensure amplicon size ~450bp and quantifiying via Quibit DNA Broad Range and Agilent Tapestation DNA High Sensitivity. The 10X 3' GEX library sequencing was performed on the Illumina NovaSeq6000 with 100bp paired-end chemistry targeting 70 million reads per cell. The MULTI-seq library sequencing was performed on the Illumina NextSeq6000 with 100bp single-end chemistry targeting 70 million reads per sample. The SPLINTR barcode library sequencing was performed on the Illumina NextSeq2000 with 100bp paired-end chemistry targeting 5 million reads per cluster.


title: SG05, MULTI-seq, LMO capture 1

description: Library name: SG05-scRNA-01-MultiSeq


title: DSP-1001660016238-F-B05


title: 026.primary infection, 0dpi

description:
Library name: DA026
DA026
rnaseq_kx.csv


title: NPHP1_rep2_ALP

city: Newcastle Upon Tyne

first: Juliana

middle: Estefania

last: Arcila-Galvis

state: Selecciona un estado

address: 258A  BAxterwood Court, Newcastle Upon Tyne, Tyne and Wear, NE4 5HW

department: Biosciences Institute

country: United Kingdom

institute: Newcastle University

description:
Library name: NPHP1_rep2_ALP
column name in raw_gene_counts: NPHP1_rep2_ALP

data_processing:
Raw sequencing reads were processed by Novogene with trimming, adapter removal, and alignment to the GRCh38 genome using HISAT2, quality-checked with FastQC, and paired-end BAM reads were counted over hg38 gene exons using the summarizeOverlaps function from the Bioconductor GenomicAlignments package to produce a gene-level count matrix.
Assembly: hg38
Supplementary files format and content: raw_gene_counts.txt

source_name: primary cells

extract_protocol:
TRIzol or column/magnetic kit
mRNA library preparation (poly A enrichment)

value: primary cells

value: urine-derived renal epithelial cells (hURECs)

value: Alprostadil


title: SG05, capture 2 SPLINTR bc amplicon rep 2

description: Library name: SG05-Capture-2-Rep2


title: NPHP1_rep1_ALP

description:
Library name: NPHP1_rep1_ALP
column name in raw_gene_counts: NPHP1_rep1_ALP


title: DSP-1001660016238-F-B04


title: 014.secondary infection, 0dpi

description:
Library name: DA014
DA014
rnaseq_kx.csv


title: SG05 capture 2, SPLINTR bc amplicon rep 1

description: Library name: SG05-Capture-2-Rep1


title: NPHP1_rep2_AG556

description:
Library name: NPHP1_rep2_AG556
column name in raw_gene_counts: NPHP1_rep2_AG556


title: DSP-1001660016238-F-B03


title: 028.primary infection, 1dpi

description:
Library name: DA028
DA028
rnaseq_kx.csv


title: DSP-1001660016238-F-B02


title: 003.primary infection, 0dpi

description:
Library name: DA003
DA003
rnaseq_kx.csv


title: 002.primary infection, 0dpi

description:
Library name: DA002
DA002
rnaseq_kx.csv


title: DSP-1001660016238-F-B01


title: NPHP1_rep2_DMSO

description:
Library name: NPHP1_rep2_DMSO
column name in raw_gene_counts: NPHP1_rep2_DMSO

value: DMSO


title: SG05 capture 1, SPLINTR bc amplicon rep 1

description: Library name: SG05-Capture-1-Rep1


title: 001.primary infection, 0dpi

description:
Library name: DA001
DA001
rnaseq_kx.csv


title: 015.secondary infection, 0dpi

description:
Library name: DA015
DA015
rnaseq_kx.csv


title: SLPI overexpression vector, T0, pcr2

description: Library name: SLPI-OE-T0-PCR2

data_processing:
Fastq files were processed using the BARtab v1.4 pipeline (https://github.com/DaneVass/BARtab) for bulk population analysis. The bartools v1.0 R package (https://github.com/DaneVass/bartools) was used for further downstream quality control using default settings before analysis and visualisation.
Assembly: SPLINTR GFP barcode reference library
Supplementary files format and content: text

growth_protocol: SPLINTR barcoded Molm-13 cells were cultured at 37 C and 5% CO2 in RPMI-1640, 10% heat inactivated fetal bovine serum (FBS), 2 mM L-Glutamine, 100 IU/ml Penicillin and 100 g/ml Streptomycin. Cells were transduced with a lentiviral vector containing a SLPI overexpression vector (Ubc-SLPI-Flag-miRFP680) or empty vector (Ubc-MCS-miRFP680) and sorted 72 hours after transduction. Cells were expanded for 2 weeks before injecting 2 hundred thousand cells into each mouse via tail vein.

extract_protocol:
5E5 cells from bone marrow and spleen were lysed using Viagen DNA lysis buffer following manufacturers instructions.
DNA Barcode-sequencing libraries were constructed using an amplicon approach. Briefly, viagen lysed samples were split in half to generate PCR replicates. Barcode sequences were amplified using primers flanking the constant region of the barcode before adding i5 and i7 indexes compatible with NGS sequencing. Samples were sequenced on an Illumina NextSeq2000 using 100-bp single end chemistry targeting 2 million reads per sample.

treatment_protocol: Mice were randomised into treatment groups (Vehicle or Combination (5 mg/kg PF-9363 and 10 mg/kg SNDX-5613) n=5 per group) based on leukemia burden detected by flow cytometry before beginning treatment 4 days post tumor transplantation. Groups: Vehicle + SLPI overexpression, Combination + SLPI overexpression, Vehicle + Empty vector, Combination + Empty vector. Mice were dosed twice daily via oral gavage. At disease endpoint, mice were humanely euthanised and spleen and bone marrow were collected.


title: SLPI overexpression vector, T0, pcr1

description: Library name: SLPI-OE-T0-PCR1


title: NPHP1_rep1_DMSO

description:
Library name: NPHP1_rep1_DMSO
column name in raw_gene_counts: NPHP1_rep1_DMSO


title: Naive HSPC (+LPS) BioRep4 TechRep2 RNASeq

city: Philadelphia

first: Eric

last: Wafula

state: PA

address: 2714-2720 South Street

department: DBHi

institute: Children's Hospital of Philadelphia

data_processing:
RNA-Seq read quality was assessed using FASTQ v0.11.9 and adaptors/low-quality bases were trimmed using Trim Galore v0.6.7). The resulting high-quality read fragments were mapped onto the GRCm38 mouse reference genome using the STAR aligner v2.7.10a Then, gene-level abundance from Ensembl comprehensive annotation was estimated using RSEM v1.3.1.
Assembly: GRCm38
Supplementary files format and content: Tab-separated filtered files for RSEM gene expression matrices

source_name: Bone marrow

extract_protocol:
At sacrifice, hind legs were dissected and bone marrow (BM) cells were harvested by flushing both femur and tibia. Whole BM cells were subjected to RBC lysis and were lineage-depleted using a magnetic-activated cell sorting (MACS)-based method with EasySep Mouse Hematopoietic Progenitor Cell Isolation Kit (StemCell Technologies). Lineage-depleted BM cells were stained and HSPCs were fluorescence-activated cell sorting (FACS)-sorted using the FACSAria Fusion sorter (BD). RNA were extracted from HSPCs using RNeasy Micro Plus Kit (Qiagen) and subjected to RNA-Seq
Library were constructed using Chromium GEM V3 chemistry (10X Genomics) according to manufacturer's protocol

value: Bone marrow

value: N/A - in vivo

value: HSPC (Lin- cKit+ Sca1+)

value: LPS


title: DSP-1001660016238-F-A11


title: Pre-transduction T0, pcr2

description: Library name: Pre-EV-T0-PCR2

value: SPLINTR-GFP-Barcode


title: NPHP1_rep1

description:
Library name: NPHP1_rep1
column name in raw_gene_counts: NPHP1_rep1

value: untreated


title: NPHP1_rep2

description:
Library name: NPHP1_rep2
column name in raw_gene_counts: NPHP1_rep2


title: Naive HSPC (+LPS) BioRep4 TechRep1 RNASeq


title: Pre-transduction T0, pcr1

description: Library name: Pre-EV-T0-PCR1


title: DSP-1001660016238-F-A10


title: DSP-1001660016238-F-A09


title: 013.secondary infection, 0dpi

description:
Library name: DA013
DA013
rnaseq_kx.csv

value: lung

value: whole lung homogenate

value: WT (C57BL6/J)


title: control_rep2

description:
Library name: control_rep2
column name in raw_gene_counts: control_rep2


title: NPHP1_rep1_AG556

description:
Library name: NPHP1_rep1_AG556
column name in raw_gene_counts: NPHP1_rep1_AG556


title: Naive HSPC (+LPS) BioRep3 TechRep2 RNASeq


title: Empty Vector, T0, pcr2

description: Library name: EV-T0-PCR2

value: Ubc-MCS-miRFP680, SPLINTR-GFP-Barcode


title: SG05, capture 1 SPLINTR bc amplicon rep 2

description: Library name: SG05-Capture-1-Rep2


title: control_rep1

description:
Library name: control_rep1
column name in raw_gene_counts: control_rep1


title: DSP-1001660016238-F-A08

value: WT


title: DSP-1001660016238-F-A12

value: Brain


title: Naive HSPC (+LPS) BioRep3 TechRep1 RNASeq


title: Empty Vector, T0, pcr1

description: Library name: EV-T0-PCR1


title: SG05, 3' scRNA-seq capture 2

description: Library name: SG05-scRNA-02-GEX


title: Naive HSPC (+LPS) BioRep2 TechRep2 RNASeq


title: DSP-1001660016238-F-A07


title: M9, SPL, SLPI OE, Combination, rep 2

description: Library name: Mouse-9-SPL-PCR2

value: Combination (5 mg/kg PF-9363 and 10 mg/kg SNDX-5613)


title: DSP-1001660016238-F-A06


title: Naive HSPC (+LPS) BioRep2 TechRep1 RNASeq


title: M9, SPL, SLPI OE, Combination, rep 1

description: Library name: Mouse-9-SPL-PCR1


title: DSP-1001660016238-F-A05


title: 2317TGP-NEG, Standard Serum #2

city: Paris

first: Elodie

last: Girard

address: 11-13 rue Pierre et Marie Curie

country: France

institute: Institut Curie

description: Library name: D260T08

data_processing:
Raw counts were generated using Star (v2.6.1a) gene quantification mode (--quantMode GeneCounts) on the Gencode v19 gene database.
Raw counts were normalized using  the TMM method using EdgeR (v3.22.5) and Limma's voom function (v3.36.5).
Assembly: hg19
Supplementary files format and content: Tab-delimited text file containing raw counts for each sample
Supplementary files format and content: Tab-delimited text file containing TPM for each sample

growth_protocol: MDA-MB-2317TGP-POS and MDA-MB-2317TGP-NEG cells were propagated in DMEM supplemented with 10% FBS under standard cell culture conditions, maintained at 37.5°C in a humidified atmosphere containing 5% CO2. MDA-MB-4367TGP-POS and MDA-MB-4367TGP-NEG cells were propagated in DMEM supplemented with 10% FBS under standard cell culture conditions, maintained at 37.5°C in a humidified atmosphere containing 5% CO2.

extract_protocol:
Extraction was performed using the RNAeasy Mini Kit (Qiagen, Courtaboeuf, France), according to the manufacturer’s instructions
TruSeq Stranded mRNA

treatment_protocol: WNT activity reporter cell lines were generated by liposome-mediated transfection of the 7TGP plasmid, followed by stable selection with puromycin (3 μg/mL) for a minimum of five passages. The 7TGP reporter vector contains seven copies of TCF-binding sites upstream of a minimal promoter that drives eGFP expression in response to WNT pathway activation. Upon nuclear translocation of β-catenin and subsequent binding to TCF/LEF1 transcription factors, eGFP is expressed. Reporter activity (7TGP/eGFP status) was assessed by flow cytometry and fluorescence microscopy under optimal growth conditions. Sequential FACS sorting was performed on the stably transfected lines to enrich for either 7TGP-positive or 7TGP-negative subpopulations.

value: Mesenchymal Cell line

value: Wnt-negative cell line

value: 7TGP vector transfected MDA-MB-2317TGP-NEG


title: DSP-1001660016238-F-A04


title: Naive HSPC (+LPS) BioRep1 TechRep2 RNASeq


title: M9, BM, SLPI OE, Combination,  rep 2

description: Library name: Mouse-9-BM-PCR2


title: Naive HSPC (+LPS) BioRep1 TechRep1 RNASeq


title: 2317TGP-NEG, Standard Serum #1

description: Library name: D260T07


title: M9, BM, SLPI OE, Combination, rep 1

description: Library name: Mouse-9-BM-PCR1


title: DSP-1001660016238-F-A03


title: 2317TGP-POS, Standard Serum #2

description: Library name: D260T06

value: Wnt-positive cell Line

value: 7TGP vector transfected MDA-MB-2317TGP-POS


title: AF9_Experienced HSPC (+LPS) BioRep4 TechRep2 RNASeq

value: Bone marrow

value: N/A - in vivo


title: AF9_Experienced HSPC (+LPS) BioRep4 TechRep1 RNASeq

value: HSPC (Lin- cKit+ Sca1+)

value: LPS


title: 4367TGP-NEG, Standard Serum #2

description: Library name: D260T04

value: 7TGP vector transfected MDA-MB-4367TGP-NEG


title: M8, BM, SLPI OE, Combination,  rep 2

description: Library name: Mouse-8-BM-PCR2


title: AF9_Experienced HSPC (+LPS) BioRep3 TechRep2 RNASeq


title: DSP-1001660016238-F-A01

value: No template control


title: 2317TGP-POS, Standard Serum #1

description: Library name: D260T05


title: M8, BM, SLPI OE, Combination, rep 1

description: Library name: Mouse-8-BM-PCR1


title: DSP-1001660016238-F-A02


title: M7, SPL, SLPI OE, Vehicle, rep 2

description: Library name: Mouse-7-SPL-PCR2

value: Vehicle


title: SG05, 3' scRNA-seq capture 1

description: Library name: SG05-scRNA-01-GEX


title: DSP-1001660016237-E-H12


title: 4367TGP-POS, Standard Serum #2

description: Library name: D260T02

value: 7TGP vector transfected MDA-MB-4367TGP-POS


title: 4367TGP-NEG, Standard Serum #1

description: Library name: D260T03


title: DSP-1001660016237-E-H11


title: AF9_Experienced HSPC (+LPS) BioRep3 TechRep1 RNASeq


title: AF9_Experienced HSPC (+LPS) BioRep2 TechRep2 RNASeq


title: M7, SPL, SLPI OE, Vehicle, rep 1

description: Library name: Mouse-7-SPL-PCR1


title: M7, BM, SLPI OE, Vehicle,  rep 2

description: Library name: Mouse-7-BM-PCR2


title: AF9_Experienced HSPC (+LPS) BioRep2 TechRep1 RNASeq


title: M7, BM, SLPI OE, Vehicle, rep 1

description: Library name: Mouse-7-BM-PCR1


title: DSP-1001660016237-E-H10


title: AF9_Experienced HSPC (+LPS) BioRep1 TechRep2 RNASeq


title: 4367TGP-POS, Standard Serum #1

description: Library name: D260T01


title: DSP-1001660016237-E-H08


title: MTA1_3

city: Hefei

first: Lei

last: Chen

address: No. 678, Furong Road, Shushan District

institute: The Second Affiliated Hospital of Anhui Medical University

description: Library name: Sample6

data_processing:
Base calling, instruments and procedures (sequencing)
Data quality control
Mapping data to the reference genome
Files used for expression levels and gene counts
Genome assembly
Assembly: DESeq2.Genome
Supplementary files format and content: tab-delimited text files include reads counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: PC-3 cells

growth_protocol: The PC-3 cell line, purchased from Procell Life Science & Technology Co., Ltd. (China), was cultured at 37℃ with 5% CO₂ in DMEM/F12 medium supplemented with 10% fetal bovine serum, 100µg/mL streptomycin and 100 U/mL penicillin.

extract_protocol:
The total RNA was extracted from PC-3 cells using TRIzol Reagent (Invitrogen, cat. NO 15596026) following the methods by Chomczynski. DNA digestion was carried out after RNA extraction by DNase I. RNA quality was determined by examining A260/A280 with NanodropTM OneCspectrophotometer (Thermo Fisher Scientific Inc). RNA Integrity was confirmed by 1.5% agarose gel electrophoresis. Qualified RNAs were finally quantified by Qubit3.0 with QubitTM RNA Broad Range Assay kit (Life Technologies, Q10210).
The cDNA library was prepared according to the manufacturer's protocol, using the SMARTer Stranded Total RNA-Seq Kit version 2 (634413; Takara/Clontech). Sequencing was performed on the Illumina NovaSeq system with 150 nt paired - end reads.

treatment_protocol: Plasmid construction and lentivirus preparation, cell transfection and stable clone screening, gene expression detection, protein extraction and Western Blot analysis, RNA extraction and sequencing.

value: PC-3 cells


title: MTA1_2

description: Library name: Sample5


title: DSP-1001660016237-E-H09

value: WT


title: M5, SPL, SLPI OE, Vehicle, rep 2

description: Library name: Mouse-5-SPL-PCR2


title: AF9_Experienced HSPC (+LPS) BioRep1 TechRep1 RNASeq


title: M5, SPL, SLPI OE, Vehicle, rep 1

description: Library name: Mouse-5-SPL-PCR1


title: MTA1_1

description: Library name: Sample4


title: DSP-1001660016237-E-H07

value: Brain


title: Naive HSPC (+PBS) BioRep4 TechRep2 RNASeq

value: PBS


title: M5, BM, SLPI OE, Vehicle,  rep 2

description: Library name: Mouse-5-BM-PCR2


title: Ctrl_3

description: Library name: Sample3


title: Naive HSPC (+PBS) BioRep4 TechRep1 RNASeq


title: DSP-1001660016237-E-H06


title: M5, BM, SLPI OE, Vehicle, rep 1

description: Library name: Mouse-5-BM-PCR1


title: Ctrl_2

description: Library name: Sample2


title: Ctrl_1

description: Library name: Sample1


title: M4, SPL, SLPI OE, Vehicle, rep 2

description: Library name: Mouse-4-SPL-PCR2


title: DSP-1001660016237-E-H05


title: Naive HSPC (+PBS) BioRep3 TechRep2 RNASeq


title: DSP-1001660016237-E-H04


title: Naive HSPC (+PBS) BioRep3 TechRep1 RNASeq


title: M4, SPL, SLPI OE, Vehicle, rep 1

description: Library name: Mouse-4-SPL-PCR1


title: DSP-1001660016237-E-H03


title: MTA1-INPUT2

description: Library name: Sample4

data_processing:
Base calling, instruments and procedures (sequencing)
Data quality control
Mapping data to the reference genome
Files used for expression levels and gene counts
Genome assembly
Assembly: DESeq2.Genome
Supplementary files format and content: tab-delimited text files include peak information for each group.

extract_protocol:
UV Crosslinking (254 nm) to covalently link RNA-binding proteins (RBPs) to RNA. Cell Lysis using NP-40/Triton-based buffer with protease/RNase inhibitors. RNA Fragmentation (optional, using RNase I) to generate ~50–100 nt RNA fragments. Immunoprecipitation (IP) with target-specific antibodies and Protein A/G beads. RNA Purification via protease digestion and phenol-chloroform extraction.
RNA End Repair、Reverse Transcription (RT)、cDNA Purification & Amplification、Sequencing


title: M4, BM, SLPI OE, Vehicle, rep 2

description: Library name: Mouse-4-BM-PCR2


title: DSP-1001660016237-E-H02


title: Naive HSPC (+PBS) BioRep2 TechRep1 RNASeq


title: M4, BM, SLPI OE, Vehicle, rep 1

description: Library name: Mouse-4-BM-PCR1


title: MTA1-IP2

description: Library name: Sample2


title: DSP-1001660016237-E-H01


title: Naive HSPC (+PBS) BioRep1 TechRep2 RNASeq


title: DSP-1001660016237-E-G12


title: MTA1-IP1

description: Library name: Sample1


title: M3, SPL, SLPI OE, Combination, rep 2

description: Library name: Mouse-3-SPL-PCR2

value: Combination (5 mg/kg PF-9363 and 10 mg/kg SNDX-5613)


title: Naive HSPC (+PBS) BioRep1 TechRep1 RNASeq


title: M3, SPL, SLPI OE, Combination, rep 1

description: Library name: Mouse-3-SPL-PCR1


title: HUVEC-1, HUVEC-2, HUVEC-3

city: Kyoto

first: Koki

last: Yoshimoto

state: Kyoto

department: iCeMS

country: Japan

institute: Kyoto university

description: Library name: N164-mix-01

data_processing:
Read1(10bp of UMI + 9bp of barcode) was assigned to Read2(insert read) by following command "umi_tools extract -I read1.fastq --read2-in=read2.fastq --bc-pattern=NNNNNNNNNNCCCCCCCCC".
Adaptor sequence and low quality sequence were removed and read length below 20bp were discarded by using Trim Galore (ver.0.6.7).
Reads were mapped to the GRCh38 reference using HISAT2 (ver.2.2.1).
Gene count was obtaind by featureCounts(ver.2.0.1) and UMI duplication was ramoved by using UMI tools (ver.1.1.1).
Assembly: GRCh38
Supplementary files format and content: compressed tab separated files(.tsv.gz, .txt.gz)

source_name: blood vessel

extract_protocol:
30um of tissue sections were lysed in TRIzol reagent (Thermo Fisher Science) and extract RNA by using Direct-zol Kit (Zymo Research).
Libraries were prepared by BRB-Seq(Alpern D, et al.) method. Individual samples were reverse transcribed using dT primer with unique cell barcodes. Then replicate were mixed and amplified by PCR. 10nt of UMI followedby 9nt of cell barcode are in read1 and 81nt of RNA insert reads are in read2.

value: blood vessel

value: HUVECs

value: Endothelial cells

value: total RNA


title: M3, BM, SLPI OE, Combination,  rep 2

description: Library name: Mouse-3-BM-PCR2


title: DSP-1001660016237-E-G11


title: DSP-1001660016237-E-G10


title: AF9_Experienced HSPC (+PBS) BioRep4 TechRep2 RNASeq

value: Bone marrow


title: ES-1, ES-2, ES-3

description: Library name: N150-mix-01

value: Human ES cells


title: DSP-1001660016237-E-G09


title: Naive HSPC (+PBS) BioRep2 TechRep2 RNASeq

value: N/A - in vivo

value: HSPC (Lin- cKit+ Sca1+)


title: EC-1, EC-2, EC-3

description: Library name: N150-mix-03


title: MTA1-INPUT1

description: Library name: Sample3


title: AF9_Experienced HSPC (+PBS) BioRep3 TechRep2 RNASeq


title: AF9_Experienced HSPC (+PBS) BioRep4 TechRep1 RNASeq


title: SMARCA3 KO Input

first: Yael

last: David

department: Chemical Biology

institute: Memorial Sloan Kettering Cancer Center

description: Library name: SMARCA3 KO Input

data_processing:
ChIP sequencing reads were trimmed and filtered for quality and adapter content using version 0.4.5 of TrimGalore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore), with a quality setting of 15, and running version 1.15 of cutadapt and version 0.11.5 of FastQC. Reads were aligned to human assembly hg38 with version 2.3.4.1 of bowtie2 (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml) and were deduplicated using MarkDuplicates in version 2.16.0 of Picard Tools. To ascertain regions of chromatin accessibility, MACS2 (https://github.com/taoliu/MACS) was used with a p-value setting of 0.001. ChIP target enrichment also used MACS2 with the same parameters and scored against matched input as the control. The BEDTools suite (http://bedtools.readthedocs.io) was used to create normalized read density profiles. A global peak atlas was created by first removing blacklisted regions then merging all peaks within 500 bp for ChIP-seq or taking 500 bp windows around peak summits for ATAC and counting reads with version 1.6.1 of featureCounts (http://subread.sourceforge.net). DESeq2 was used to normalize read density (median ratio method) and to calculate differential enrichment for all pairwise contrasts. Peak-gene associations were created by assigning all intragenic peaks to that gene, and otherwise using linear genomic distance to transcription start site. Peak intersections were calculated using bedtools v2.29.1 and intersectBed with 1 bp overlap. Gene set enrichment analysis (GSEA, http://software.broadinstitute.org/gsea) was performed with the pre-ranked option and default parameters, where each gene was assigned the single peak with the largest (in magnitude) log2 fold change associated with it. Motif signatures were obtained using Homer v4.5 (http://homer.ucsd.edu). Composite and tornado plots were created using deepTools v3.3.0 by running computeMatrix and plotHeatmap on normalized bigwigs with average signal sampled in 25 bp windows and flanking region defined by the surrounding 3 kb.
Assembly: hg38
Supplementary files format and content: Bigwig files

source_name: epithelial-like

growth_protocol: HEK293T were cultured in DMEM with 10% fetal bovine serum and 1% penicillin-streptomycin at 37 °C in a humidified incubator with 5% CO2.

extract_protocol:
Freshly harvested cells were cross-linked with 1% formaldehyde (ThermoFisher Scientific #28906) for 10 min at room temperature, after which the reactions were quenched for 5 min by the addition of glycine to the final concentration of 0.125 M. Fixed cells were washed twice with PBS, snap frozen and store at -80°C. Frozen cell pellets were sent to MSKCC Epigenetics Research Innovation Lab for processing. Cells were resuspended in SDS buffer (100 mM NaCl, 50 mM Tris-HCl pH 8.0, 5 mM EDTA, 0.5% SDS, 1x protease inhibitor cocktail from Roche). The resulting nuclei were spun down, resuspended in the immunoprecipitation buffer at 1 mL per 0.5 million cells (SDS buffer and Triton Dilution buffer (100 mM NaCl, 100 mM TrisHCl pH 8.0, 5 mM EDTA, 5% Triton X-100) mixed in 2:1 ratio with the addition of 1x protease inhibitor cocktail (Millipore Sigma, #11836170001) and processed on a Covaris E220 Focused-ultrasonicator to achieve an average fragment length of 200-300 bps with the following parameters: PIP=140, Duty Factor=5, CBP/Burst per sec=200, Time = 20 min. Chromatin concentrations were estimated using the Pierce™ BCA Protein Assay Kit (ThermoFisher Scientific #23227) according to the manufacturer’s instructions. The immunoprecipitation reactions were set up in 500uL of the immunoprecipitation buffer in Protein LoBind tubes (Eppendorf, #22431081) and pre-cleared with 50uL of Protein G Dynabeads (ThermoFisher Scientific #10004D) for two hours at 4°C. After pre-clearing, the samples were transferred into new Protein LoBind tubes and incubated overnight at 4°C with 10uL of the H3K27ac antibody (CST, 8173. The next day, 50uL of BSA-blocked Protein G Dynabeads were added to the reactions and incubated for 2 hours at 4°C. The beads were then washed two times with low-salt washing buffer (150mM NaCl, 1% Triton X-100, 0.1% SDS, 2mM EDTA, 20mM TrisHCl pH8.0), two times with high-salt washing buffer (500mM NaCl, 1% Triton X-100, 0.1% SDS, 2mM EDTA, 20mM TrisHCl pH8.0), two times with LiCL wash buffer (250mM LiCl, 10mM TrisHCl pH8.0, 1mM EDTA, 1% Na-Deoxycholate, 1% IGEPAL CA-630) and one time with TE buffer (10mM TrisHCl pH8.0, 1mM EDTA). The samples were then reverse-crosslinked overnight in the elution buffer (1% SDS, 0.1 M NaHCO3) and purified using the ChIP DNA Clean & Concentrator kit (Zymo Research, #D5205) following the manufacturer’s instructions.
After quantification of the recovered DNA fragments, libraries were prepared using the ThruPLEX®DNA-Seq kit (R400676, Takara) following the manufacturer’s instructions, purified with SPRIselect magnetic beads (B23318, Beckman Coulter), and quantified using a Qubit Flex fluorometer (ThermoFisher Scientific) and profiled with a TapeStation (Agilent). The libraries were sent to MSKCC Integrated Genomics Operation core facility for sequencing on an Illumina NovaSeq 6000 (aiming for 30-40 million 100bp paired-end reads per library).

value: epithelial-like

value: human embryonic kidney


title: M20, SPL, EV, Vehicle, rep 2

description: Library name: Mouse-20-SPL-PCR2

value: Ubc-MCS-miRFP680, SPLINTR-GFP-Barcode

value: Vehicle


title: AF9_Experienced HSPC (+PBS) BioRep3 TechRep1 RNASeq


title: SMARCA3 KO 293T rep3

description: Library name: Sample 6 SMARCA3 KO 293T


title: DSP-1001660016237-E-G07

data_processing:
Fastq files were converted to DCC files using the GeoMx NGS Pipeline software and the mm10 reference genome.
Digital Count Conversion files, containing expression count data and sequencing quality metadata, and Probe Kit Configuration files, containing probe assay and sample metadata, were imported into R. Gene expression counts with a value of 0 were shifted to 1 to facilitate downstream transformations. ROI segments were filtered and removed if they met the criteria: “<1000 raw reads”, “below 80% Aligned or 80% Trimmed”, “80% Stitched”, and “below 50% sequencing saturation”. Genes were filtered and removed if they were not detected in at least 10% of segments. Next, counts were normalized using quartile 3 normalization and visualized by uniform manifold approximation and projection, a non-linear dimensionality reduction visualization tool. Gene expression in both datasets was relatively well separated according to ROI brain region.
Assembly: mm10
Supplementary files format and content: Late_stage_count_table.csv. A count table containing normalized counts for probes and segments that passed the quality control steps mentioned in the data processing step.
Library strategy: Spatial Transcriptomics

extract_protocol:
One brain hemisphere was fixed in 4% paraformaldehyde (PFA) for 24 h, cryoprotected in escalating sucrose gradients, embedded, and cryosectioned in coronal plane sections onto histologic slides [10 μm thickness for spatial transcriptomics sections, 14 μm thickness for subsequent fluorescent in situ hybridization (FISH)] and stored at –80 °C.
Spatial transcriptomics was performed by GeoMx DSP (NanoString, Seattle, WA), a platform for spatially analyzing gene expression in tissue in a highly multiplexed manner
Other: Spatial transcriptomics-Nanostring GeoMx DSP


title: DSP-1001660016237-E-G08


title: M20, SPL, EV, Vehicle, rep 1

description: Library name: Mouse-20-SPL-PCR1


title: M20, BM, EV, Vehicle,  rep 2

description: Library name: Mouse-20-BM-PCR2


title: M20, BM, EV, Vehicle, rep 1

description: Library name: Mouse-20-BM-PCR1


title: DSP-1001660016237-E-G06


title: AF9_Experienced HSPC (+PBS) BioRep2 TechRep2 RNASeq


title: SMARCA3 KO 293T rep2

description: Library name: Sample 5 SMARCA3 KO 293T


title: SMARCA3 KO 293T rep1

description: Library name: Sample 4 SMARCA3 KO 293T


title: AF9_Experienced HSPC (+PBS) BioRep2 TechRep1 RNASeq


title: AF9_Experienced HSPC (+PBS) BioRep1 TechRep2 RNASeq


title: DSP-1001660016237-E-G04


title: M2, SPL, SLPI OE, Vehicle, rep 2

description: Library name: Mouse-2-SPL-PCR2


title: M3, BM, SLPI OE, Combination, rep 1

description: Library name: Mouse-3-BM-PCR1


title: AF9_Experienced HSPC (+PBS) BioRep1 TechRep1 RNASeq


title: M2, SPL, SLPI OE, Vehicle, rep 1

description: Library name: Mouse-2-SPL-PCR1


title: WT Input

description: Library name: WT Input


title: Naive HSPC (+LPS) BioRep3 TechRep2 ATACSeq

data_processing:
ATAC-Seq quality checks were performed on raw sequence data using FASTQC, and adaptors and low-quality bases were removed using Trim Galore. Trimmed reads were then aligned to the mouse reference genome (GRCm38) using BWA (Li & Durbin, 2009) and filtered to remove PCR duplicate reads using Picard MarkDuplicates (v2.27.4) and mitochondrial DNA. Peaks were called using MACS3 (Zhang et al., 2008).
Assembly: GRCm38
Supplementary files format and content: Tab-separated files for MACS3 ATAC-Seq peaks
Supplementary files format and content: Sample Alignment bigwig files

extract_protocol:
At sacrifice, hind legs were dissected and bone marrow (BM) cells were harvested by flushing both femur and tibia. Whole BM cells were subjected to RBC lysis and were lineage-depleted using a magnetic-activated cell sorting (MACS)-based method with EasySep Mouse Hematopoietic Progenitor Cell Isolation Kit (StemCell Technologies). Lineage-depleted BM cells were stained and HSPCs were fluorescence-activated cell sorting (FACS)-sorted using the FACSAria Fusion sorter (BD). DNA extraction and ATAC-Seq preparation were performed according to the OMNI-ATAC protocol (Corces MR et al., 2017).
Library were constructed using Chromium GEM V3 chemistry (10X Genomics) according to manufacturer's protocol

value: LPS


title: WT 293T rep2

description: Library name: Sample 2 WT 293T


title: WT 293T rep1

description: Library name: Sample 1 WT 293T


title: Naive HSPC (+LPS) BioRep3 TechRep1 ATACSeq


title: DSP-1001660016237-E-G03


title: M2, BM, SLPI OE, Vehicle,  rep 2

description: Library name: Mouse-2-BM-PCR2


title: M2, BM, SLPI OE, Vehicle, rep 1

description: Library name: Mouse-2-BM-PCR1


title: Naive HSPC (+LPS) BioRep2 TechRep2 ATACSeq


title: DSP-1001660016237-E-G02


title: DSP-1001660016237-E-G01


title: SMARCA3 KO 293T 3

description:
Library name: Sample 6 SMARCA3 KO 293T
Column name in raw counts: HLTFKORNA3

data_processing:
ATAC sequencing reads were 3’ trimmed and filtered for quality and adapter content using TrimGalore (v0.5.0) and quality was assessed by FastQC (v0.11.8). Reads were aligned to human assembly hg38 with bowtie2 (v2.3.5) and were deduplicated using MarkDuplicates in Picard Tools (v2.19.0). To determine regions of altered accessibility, we followed the pipeline described by Reske et. al. Briefly, sample alignments were queried for library complexity with the Bioconductor package “ATACseqQC” (v1.16.0) and subsampled to equivalent aligned paired reads among all libraries using SAMTOOLs (v1.9). Bigwig files of the subsampled normalized reads for each sample were generated with deeptools15 (v3.2.0) for visualization in browser shots and heatmaps. Accessible regions for each sample were called using the Bioconductor package “csaw” (v1.24.3) with local enrichment of TMM normalized binned counts (method V from PMID: 32321567). Differentially accessible regions between SMARCA3 KO 293T cells and WT 293T cells were called using the Bioconductor package “edgeR” (v3.32.1) where regions with an FDR threshold <= 0.05 are considered significant. Accessible regions were annotated throughout the genome using the Bioconductor package “ChIPseeker” (PMID: 25765347) (v1.30.3).
Assembly: hg38
Supplementary files format and content: Bigwig files

extract_protocol:
The ATAC-seq. samples were generated using WT or SMARCA3 KO 293T cells. Approximately 70,000 cells of each sample were harvested and processed following the previously published protocol by the Integrated Genomics Operation of Memorial Sloan Kettering Cancer Center.
Profiling of chromatin was performed by ATAC-Seq as described by Buenrostro, et al. (2013). Briefly, 50,000 viably frozen HEK293T cells were thawed, washed in cold PBS, and lysed. The transposition reaction containing TDE1 Tagment DNA Enzyme (Illumina catalog # 20034198) was incubated at 37°C for 30 minutes. The DNA was cleaned with the MinElute PCR Purification Kit (QIAGEN catalog # 28004) and material was amplified for 5 cycles using NEBNext High-Fidelity 2X PCR Master Mix (New England Biolabs catalog # M0541L). After evaluation by real-time PCR, 8-9 additional PCR cycles were done. The final product was cleaned by aMPure XP beads (Beckman Coulter catalog # A63882) at a 1X ratio, and size selection was performed at a 0.5X ratio. Libraries were sequenced on a HiSeq 4000 in a PE100/100 run, using the HiSeq 3000/4000 SBS Kit (Illumina).  An average of 42 million paired reads were generated per sample.


title: DSP-1001660016237-E-F12


title: M18, SPL, EV, Vehicle, rep 2

description: Library name: Mouse-18-SPL-PCR2


title: DSP-1001660016237-E-G05


title: Naive HSPC (+LPS) BioRep1 TechRep2 ATACSeq


title: DSP-1001660016237-E-F11


title: M17, SPL, EV, Combination, rep 2

description: Library name: Mouse-17-SPL-PCR2


title: DSP-1001660016237-E-F10


title: WT 293T rep3

description: Library name: Sample 3 WT 293T


title: M17, SPL, EV, Combination, rep 1

description: Library name: Mouse-17-SPL-PCR1


title: Naive HSPC (+LPS) BioRep1 TechRep1 ATACSeq


title: WT 293T 3

description:
Library name: Sample 3 WT 293T
Column name in raw counts: WT293RNA3


title: DSP-1001660016237-E-F09


title: AF9_Experienced HSPC (+LPS) BioRep5 TechRep2 ATACSeq


title: WT 293T 1

description:
Library name: Sample 1 WT 293T
Column name in raw counts: WT293RNA1


title: Naive HSPC (+LPS) BioRep2 TechRep1 ATACSeq


title: WT 293T 2

description:
Library name: Sample 2 WT 293T
Column name in raw counts: WT293RNA2


title: M17, BM, EV, Combination,  rep 2

description: Library name: Mouse-17-BM-PCR2


title: AF9_Experienced HSPC (+LPS) BioRep5 TechRep1 ATACSeq


title: AF9_Experienced HSPC (+LPS) BioRep4 TechRep2 ATACSeq


title: M15, SPL, EV, Vehicle, rep 2

description: Library name: Mouse-15-SPL-PCR2


title: Information of vdj from MG08

city: Chiba

first: Hiroyuki

last: Akamine

address: chuoku inohana 1-8-1

institute: Chiba university

description:
Library name: vdj_MG08
Rhapsody

library_source: other

data_processing:
The BCL file after sequencing was converted to a FASTQ file using bcl2fastq. The multiplex FASTQ was output as adata using sample tags and index information in sevenbridges. Subsequently, to facilitate analysis, files were created that were completely divided by sample as adata.The RNA expression matrix was analyzed with scanpy (v1.9.8).
Assembly: GRCh38
Supplementary files format and content: adata file of RNA and Abseq for each sample, vdj data as xlsx

molecule: other

source_name: PBMC

extract_protocol:
Peripheral blood was collected from all participants, and SepMate (STEMCELL Technologies, ST-8645, Vancouver, Canada) was used for PBMC isolation.
T and B cells were sorted from PBMC using a BD Melody cytometer. After 30-min incubation at 4 °C with sample tags and Abseq antibodies, the cells were washed and enumerated using a hemocytometer with Trypan blue. Cell viability was assessed, and the total cell number was quantified using a BD Rhapsody Scanner. A total of 20,000 cells were targeted and loaded onto BD Rhapsody cartridges, allowing single cells to remain stationary. If sample tags were used for pooled cells from two samples, we adjusted the target cell number accordingly. The libraries were prepared according to the BD Rhapsody protocol using the WTA amplification kit. They were then quantified and quality-assessed on an Agilent TapeStation.

value: PBMC


title: DSP-1001660016237-E-F08

value: Brain


title: M18, SPL, EV, Vehicle, rep 1

description: Library name: Mouse-18-SPL-PCR1


title: SMARCA3 KO 293T 2

description:
Library name: Sample 5 SMARCA3 KO 293T
Column name in raw counts: HLTFKORNA2


title: M17, BM, EV, Combination, rep 1

description: Library name: Mouse-17-BM-PCR1


title: AF9_Experienced HSPC (+LPS) BioRep4 TechRep1 ATACSeq


title: DSP-1001660016237-E-F07


title: Information of vdj from MG07

description:
Library name: vdj_MG07
Rhapsody


title: M15, SPL, EV, Vehicle, rep 1

description: Library name: Mouse-15-SPL-PCR1


title: M15, BM, EV, Vehicle,  rep 2

description: Library name: Mouse-15-BM-PCR2


title: AF9_Experienced HSPC (+LPS) BioRep3 TechRep2 ATACSeq


title: SMARCA3 KO 293T 1

description:
Library name: Sample 4 SMARCA3 KO 293T
Column name in raw counts: HLTFKORNA1


title: DSP-1001660016237-E-F04


title: DSP-1001660016237-E-F05


title: Information of vdj from C08

description:
Library name: vdj_C08
Rhapsody


title: DSP-1001660016237-E-F03


title: M15, BM, EV, Vehicle, rep 1

description: Library name: Mouse-15-BM-PCR1


title: Information of vdj from MG06

description:
Library name: vdj_MG06
Rhapsody


title: AF9_Experienced HSPC (+LPS) BioRep2 TechRep2 ATACSeq


title: AF9_Experienced HSPC (+LPS) BioRep3 TechRep1 ATACSeq


title: DSP-1001660016237-E-F06


title: M14, SPL, EV, Combination, rep 2

description: Library name: Mouse-14-SPL-PCR2


title: M14, SPL, EV, Combination, rep 1

description: Library name: Mouse-14-SPL-PCR1


title: AF9_Experienced HSPC (+LPS) BioRep2 TechRep1 ATACSeq


title: PBMC from MG09 control

description:
Library name: MG09
Rhapsody

tag: age

tag: Sex

value: male


title: PBMC from MG08 control

description:
Library name: MG08
Rhapsody


title: DSP-1001660016237-E-F02


title: M14, BM, EV, Combination, rep 2

description: Library name: Mouse-14-BM-PCR2

value: Combination (5 mg/kg PF-9363 and 10 mg/kg SNDX-5613)


title: AF9_Experienced HSPC (+LPS) BioRep1 TechRep1 ATACSeq


title: Naive HSPC (+PBS) BioRep4 TechRep2 ATACSeq

value: PBS


title: DSP-1001660016237-E-E12


title: PBMC from MG07 control

description:
Library name: MG07
Rhapsody


title: M14, BM, EV, Combination, rep 1

description: Library name: Mouse-14-BM-PCR1


title: M13, SPL, EV, Vehicle, rep 2

description: Library name: Mouse-13-SPL-PCR2


title: PBMC from MG06 control

description:
Library name: MG06
Rhapsody


title: Naive HSPC (+PBS) BioRep4 TechRep1 ATACSeq


title: M13, SPL, EV, Vehicle, rep 1

description: Library name: Mouse-13-SPL-PCR1


title: PBMC from MG04 control

description:
Library name: MG04
Rhapsody


title: Naive HSPC (+PBS) BioRep3 TechRep2 ATACSeq


title: M13, BM, EV, Vehicle, rep 2

description: Library name: Mouse-13-BM-PCR2


title: DSP-1001660016237-E-E09


title: PBMC from MG03 control

description:
Library name: MG03
Rhapsody

value: female


title: DSP-1001660016237-E-F01


title: AF9_Experienced HSPC (+LPS) BioRep1 TechRep2 ATACSeq


title: DSP-1001660016237-E-E08


title: Naive HSPC (+PBS) BioRep3 TechRep1 ATACSeq


title: M13, BM, EV, Vehicle, rep 1

description: Library name: Mouse-13-BM-PCR1


title: PBMC from MG02 control

description:
Library name: MG02
Rhapsody


title: DSP-1001660016237-E-E07


title: Naive HSPC (+PBS) BioRep2 TechRep2 ATACSeq


title: DSP-1001660016237-E-E10


title: PBMC from MG05 control

description:
Library name: MG05
Rhapsody


title: DSP-1001660016237-E-E06


title: M11, SPL, EV, Vehicle, rep 2

description: Library name: Mouse-11-SPL-PCR2


title: DSP-1001660016237-E-E11


title: PBMC from MG01 control

description:
Library name: MG01
Rhapsody


title: Naive HSPC (+PBS) BioRep2 TechRep1 ATACSeq


title: M11, SPL, EV, Vehicle, rep 1

description: Library name: Mouse-11-SPL-PCR1


title: DSP-1001660016237-E-E05


title: Naive HSPC (+PBS) BioRep1 TechRep2 ATACSeq


title: M11, BM, EV, Vehicle,  rep 2

description: Library name: Mouse-11-BM-PCR2


title: DSP-1001660016237-E-E04


title: Naive HSPC (+PBS) BioRep1 TechRep1 ATACSeq


title: AF9_Experienced HSPC (+PBS) BioRep4 TechRep2 ATACSeq


title: M11, BM, EV, Vehicle , rep 1

description: Library name: Mouse-11-BM-PCR1


title: DSP-1001660016237-E-E03


title: M10, SPL, SLPI OE, Vehicle, rep 2

description: Library name: Mouse-10-SPL-PCR2


title: PBMC from C07 sample

description:
Library name: C07
Rhapsody


title: AF9_Experienced HSPC (+PBS) BioRep4 TechRep1 ATACSeq


title: DSP-1001660016237-E-E01


title: PBMC from C06 sample

description:
Library name: C06
Rhapsody


title: M10, SPL, SLPI OE, Vehicle, rep 1

description: Library name: Mouse-10-SPL-PCR1


title: DSP-1001660016237-E-E02


title: PBMC from C05 sample

description:
Library name: C05
Rhapsody


title: PBMC from C10 sample

description:
Library name: C10
Rhapsody


title: M10, BM, SLPI OE, Vehicle,  rep 2

description: Library name: Mouse-10-BM-PCR2


title: PBMC from C09 sample

description:
Library name: C09
Rhapsody


title: AF9_Experienced HSPC (+PBS) BioRep3 TechRep2 ATACSeq


title: M10, BM, SLPI OE, Vehicle, rep 1

description: Library name: Mouse-10-BM-PCR1


title: AF9_Experienced HSPC (+PBS) BioRep3 TechRep1 ATACSeq


title: PBMC from C04 sample

description:
Library name: C04
Rhapsody


title: DSP-1001660016237-E-D12


title: DSP-1001660016237-E-D11


title: AF9_Experienced HSPC (+PBS) BioRep2 TechRep2 ATACSeq


title: DSP-1001660016237-E-D10


title: PBMC from C08 sample

description:
Library name: C08
Rhapsody


title: M1, SPL, SLPI OE, Combination, rep 2

description: Library name: Mouse-1-SPL-PCR2


title: PBMC from C03 sample

description:
Library name: C03
Rhapsody


title: M1, SPL, SLPI OE, Combination, rep 1

description: Library name: Mouse-1-SPL-PCR1


title: AF9_Experienced HSPC (+PBS) BioRep2 TechRep1 ATACSeq


title: DSP-1001660016237-E-D09


title: AF9_Experienced HSPC (+PBS) BioRep1 TechRep2 ATACSeq


title: PBMC from C01 sample

description:
Library name: C01
Rhapsody


title: M1, BM, SLPI OE, Combination, rep 2

description: Library name: Mouse-1-BM-PCR2


title: DSP-1001660016237-E-D08


title: AF9_Experienced HSPC (+PBS) BioRep1 TechRep1 ATACSeq


title: T0, rep2, pcr2

description: Library name: T0-R2-PCR2

growth_protocol: Molm-13 cells were cultured at 37 C and 5% CO2 in RPMI-1640, 10% heat inactivated fetal bovine serum (FBS), 2 mM L-Glutamine, 100 IU/ml Penicillin and 100 g/ml Streptomycin. Cells were transduced with a lentiviral vector containing a SPLINTR barcode sequence and sorted 72 hours after transduction. Cells were expanded for 2 weeks before injecting 1 million cells into each mouse via tail vein.

treatment_protocol: Mice were randomised into treatment groups (Vehicle, 5mg/kg PF-9363, 10 mg/kg SNDX-5613 and Combination (5 mg/kg PF-9363 and 10 mg/kg SNDX-5613) n=5 per group) based on leukemia burden detected by flow cytometry before beginning treatment 7 days post tumor transplantation. Mice were dosed twice daily via oral gavage. At disease endpoint, mice were humanely euthanised and spleen and bone marrow were collected.

value: SPLINTR-GFP-Barcode


title: DSP-1001660016237-E-D07


title: M1, BM, SLPI OE, Combination, rep 1

description: Library name: Mouse-1-BM-PCR1


title: DSP-1001660016237-E-D06


title: mouse hippocampus,shHepaCAM3

first: Ziyu

last: Qiu

address: Huangshan Road

institute: USTC

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing sequencing adapter sequences and  low-quality sequences.
Index of the reference genome was built using Bowtie v2.0.6 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12.
RPKM of each gene was calculated based on the length of the gene and reads count mapped to the gene
Assembly: mm39
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: hippocampus

growth_protocol: C57BL/6 J mice were provided with adequate food and water, and housed under suitable temperature and a 12:12 h light-dark cycle.

extract_protocol:
Total RNA was extracted from brain tissues in TRIzol (Invitrogen). 2 μg of total RNA was used for construction of sequencing libraries
RNA libraries  were prepared for sequencing using standard illumina protocols.

treatment_protocol: AAV was injected into CA1 region of bilateral hippocampus to knock down hepaCAM.

value: hippocampus

value: HepaCAM knockdown


title: T0, rep2, pcr1

description: Library name: T0-R2-PCR1


title: Erythroid cells, GSK-J4  treated 2, Day7

city: zhengzhou

first: Hengchao

last: Zhang

state: Henan

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

institute: zzu

description: Library name: RNAseq_GSKJ4_2

data_processing:
The original data were filtered and compared with the reference genome, which can be downloaded from the Ensemble database (http://www.ensembl.org/index.html,human genome build GRCh38.87). Using HISAT2 version 2.2.1 (http://daehwankimlab.github.io/hisat2/) to read the counts for each gene in each sample and gene expression was assessed by StringTie (https://ccb.jhu.edu/software/stringtie/). TPM (Transcripts Per Kilobase of exon model per Million mapped reads) was calculated to evaluate the expression level. Differentially expressed genes (DEGs) were defined by p.adjust < 0.05 and fold change >1.2 using the DESeq2 version 1.38.3 (https://bioconductor.org/packages/release/bioc/html/DESeq2.html). Gene ontology (GO) enrichment analysis and visualization of DEGs was performed using the Metascape (www.metascape.org/) online tool with q < 0.05.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: Tab-delimited text file includes TPM values for each Sample

source_name: Cord blood

growth_protocol: CD34+ cells were puriﬁed from cord blood by positive selection using the magnetic-activated cell sorting magnetic beads system, according to the manufacturer’sinstructions. The purity of isolated CD34+ cells was 95% to 98%. The day of CD34+ cell harvest was recorded as day 0. The cell culture procedure consisted of 3 phases. The basic culture medium consisted of Iscove's Modified Dulbecco's Medium (IMDM), 2% human peripheral blood plasma, 3% human AB serum, 200 mg/mL human holo-transferrin, 3 IU/mL heparin and 10 μg/mL insulin. From day 0 to day 7, CD34+ cells were cultured at a concentration of 105/mL in the presence of 10 ng/mL stem cell factor (SCF), 1 ng/mL interleukin-3 (IL-3) and 3 IU/mL erythropoietin (EPO).  The cells were cultured at 37°C in the presence of 5% CO2.

extract_protocol:
Experiment procedure before sequencing: 2 million cells were collected and washed twice with PBS. RNA was extracted from cell culture using RNA extract kits (74104, Qiagen) according to the manufacturer’s instruction.
RNA was extracted and used as cDNA input, cDNA library was prepared by VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina ® (NR604-01,  Vazyme, China), and sequenced on Illumina NovaSeq 6000.

treatment_protocol: The JMJD3/UTX inhibitor GSK-J4 (Catalog #HY-5648B; MedChemExpress) was dissolved in DMSO and administered to cell cultures at a final concentration of 1 and 1.5 μM. After treated with1μM GSK-J4 for 5 days, we performed a RNA-seq of DMSO and GSK-J4 treated cells.

value: Cord blood

value: Erythroid cells

value: GSK-J4 1μM


title: DSP-1001660016237-E-D05

source_name: Brain


title: mouse hippocampus,shHepaCAM1


title: mouse hippocampus,shHepaCAM2


title: Erythroid cells, GSK-J4  treated 3, Day7

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description: Library name: RNAseq_GSKJ4_3


title: Erythroid cells, Control 3, Day7

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description: Library name: RNAseq_Control_3

value: DMSO


title: Erythroid cells, Control 2, Day7

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description: Library name: RNAseq_Control_2


title: T0, rep1, pcr1

description: Library name: T0-R1-PCR1


title: DSP-1001660016237-E-D04


title: PBMC from C02 sample

description:
Library name: C02
Rhapsody


title: mouse hippocampus,shControl2

value: WT


title: M9, SPL, SNDX-5613, rep 2

description: Library name: Mouse-9-SPL-PCR2

value: 10 mg/kg SNDX-5613


title: Erythroid cells, Control 1, Day7

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description: Library name: RNAseq_Control_1


title: DSP-1001660016237-E-D02


title: DSP-1001660016237-E-D01


title: M9, SPL, SNDX-5613, rep 1

description: Library name: Mouse-9-SPL-PCR1


title: Erythroid cells, GSK-J4  treated 1, Day7

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description: Library name: RNAseq_GSKJ4_1


title: Erythroid cells, Control, Day7

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description: Library name: CUT_Tag_IgG

data_processing:
Trim Galore version 0.6.6 was used to remove adapter and low-quality reads. Align paired-end reads using Bowtie2 version 2.5.1 with options: “--end-to-end --very-sensitive”. Peak calling uses MACS2 version 2.1.1 with threshold: q<0.01, and the differential binding sites of H3K14la were calculated using the DiffBind version 3.8.4 with the parameter log2foldchange >=1 and FDR <0.05 (https://www.cruk.cam.ac.uk/core-facilities/bioinformatics-core/software/diffbind.html). Scatterplots, correlation plots, and heatmaps are displayed using deepTools version 2.5.7. Annotation of peaks is performed using an R package ChIPseeker version 1.34.1(https://www.cruk.cam.ac.uk/core-facilities/bioinformatics-core/software/ ChIPseeker.html). The CUT&Tag peak/region <1000bp from the nearest transcriptional start site (TSS) was defined as the promoter. Hypergeometric Optimization of Motif Enrichment (HOMER) version 4.11 (http://homer.ucsd.edu/homer/) was used to search for the binding motif.
Assembly: GRCh38
Supplementary files format and content: bigWig,narrowPeak
Library strategy: CUT&Tag

extract_protocol:
Cells were harvested, counted and centrifuged for 3 min at 600×g at room temperature. 1×105 cells were washed twice in 500μL wash buffer by gentle pipetting. Concanavalin A coated magnetic beads were prepared as the kit manual described, 10 µL of activated beads were added per sample and incubated at RT for 10 min. According to the kit instructions, cells were sequentially incubated with ConA Beads, primary antibody (anti-H3K27me3 antibody, secondary antibody (Goat anti-Rabbit IgG) and Hyperactive PG-TN5/PA-TN5 Transposon and then fragmented. The fragmented DNA was extracted from the samples and amplified by PCR.
CUT&Tag libraries were constructed using Hyperactive Universal CUT&Tag Assay Kit for Illumina (TD901, Vazyme, China) and sequenced on an Illumina NovaSeq platform, and 150-bp paired-end reads were generated.

treatment_protocol: The JMJD3/UTX inhibitor GSK-J4 (Catalog #HY-5648B; MedChemExpress) was dissolved in DMSO and administered to cell cultures at a final concentration of 1 and 1.5 μM. After treated with 1μM GSK-J4 for 5 days, we performed a CUT&Tag of DMSO and GSK-J4 treated cells.


title: KO_DMSO

city: Guangzhou

first: Ding

address: Zhong Shan Er Lu, Guangzhou, Guangdong Province, China

institute: Sun yet san university

description: 10× Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: CD11b+ or CD11c+ of bronchoalveolar lavage cells

growth_protocol: The mice were maintained in a specific pathogen-free environment with a sterilized normal diet, acidified tap water (pH 2.5) using 0.002 N HCl, and autoclaved corn cob bedding.

extract_protocol:
Bronchoalveolar lavage fluid was collected from mice using HBSS, and CD11b+ or CD11c+ cells were sorted by flow cytometry. The sorted cells were then used for library preparation for single-cell transcriptome sequencing.
Appropriate number of FACS sorted CD11b+ or CD11c+ cells from BALF of mice were mixed with reverse transcription reagent and then added to the sample well in SeekOne® chip. Next, cDNA was purified from broken droplet and amplified in PCR reaction. The amplified cDNA product was then cleaned, fragmented, end repaired, A-tailed and ligated to sequencing adaptor. Finally, the indexed PCR were performed to amplified the DNA representing 3’ polyA part of expressing genes which also contained Cell Barcode and Unique Molecular Index. The indexed sequencing libraries were cleanup with SPRI beads, analyzed by Qubit (Thermo Fisher Q33226) and Agilent 4200 TapeStation (Agilent G2991BA). The libraries were then sequenced on illumina NovaSeq 6000 with PE150 read length.


title: M9, BM, SNDX-5613,  rep 2

description: Library name: Mouse-9-BM-PCR2


title: DSP-1001660016237-E-C12

first: Mohamed

institute: University of Michigan


title: M9, BM, SNDX-5613, rep 1

description: Library name: Mouse-9-BM-PCR1


title: DSP-1001660016237-E-C11


title: Erythroid cells, GSK-J4  treated rep3, Day11

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description: Library name: CUT_Tag_H3K27me3_GSKJ4_rep3


title: mouse hippocampus,shControl3


title: WT_DMSO

description: 10× Genomics

value: CD11b+ or CD11c+ of bronchoalveolar lavage cells


title: T0, rep1, pcr2

description: Library name: T0-R1-PCR2


title: WT_GW5074

description: 10× Genomics


title: M8, SPL, Combination, rep 2

description: Library name: Mouse-8-SPL-PCR2


title: Erythroid cells, GSK-J4  treated rep2, Day11

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description: Library name: CUT_Tag_H3K27me3_GSKJ4_rep2


title: Erythroid cells, GSK-J4  treated rep1, Day7

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description: Library name: CUT_Tag_H3K27me3_GSKJ4_rep1


title: DSP-1001660016237-E-C10