title: SW620, Input

data_processing:
Sample preparation and RNA library construction
Quality control and mapping
Transcript-level quantification, analysis of differentially expressed transcript (DEGs), cluster analysis, GO and KEGG enrichment of mRNA, LncRNA, circRNA.(P value < 0.05 and foldChange >2 or foldChange < 0.5 was set as the threshold for significantly differential expression.)
Assembly: human genome (GRCh38)
Supplementary files format and content: Excel files include -10*log10(pvalue) and fold enrichment for each Sample

extract_protocol:
Total RNA was isolated using the TRIZOL reagent and subjected to multiple purification steps to obtain an RNA solution of suitable concentration and purity.
RNA libraries for RIP-seq were prepared using GenSeq® Low Input RNA Library Prep Kit (GenSeq, Inc.) following manufacturer's protocols.


title: CLL196

status: Public on Feb 12 2025

type: SRA

city: Rochester

first: Jessica

last: Hohenstein

state: MN

address: 200 1st St SW

country: USA

institute: Mayo Clinic

library_source: transcriptomic

data_processing:
mRNA sequencing was generated using a HiSeq 4000 sequencer for 58 AA CLL and 292 EA CLL.  The raw RNA sequencing paired-end reads were processed through the Mayo RNA-Seq bioinformatics pipeline, MAP-RSeq version 3.1.4. Batch correction for all RNA samples was performed by removing protein coding genes with low counts, for each batch individually, resulting in 9,934 protein coding genes.  In addition, CombatSeq was run using the annotated reported race as a covariate, with CombatSeq corrected count values used for all downstream analyses.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes batch corrected gene counts each gene per sample

molecule: total RNA

organism: Homo sapiens

source_name: Peripheral blood mononuclear cells

extract_protocol:
RNA was extracted using the Quagen miRNeasy Mini Kit
Illumina TruSeq Stranded mRNA library prep protocol

tag: ancestry

value: European Ancestry (EA)

tag: tissue

value: Peripheral blood mononuclear cells

tag: disease state

value: Chronic Lymphocytic Leukemia (CLL)

tag: genotype

value: IGHV Unmutated


title: CLL195


title: CLL194


title: ctrl3_NAWM1

city: Münster

first: Carolin

last: Walter

address: Domagkstraße 9

department: Medical Faculty of the WWU Münster

country: Germany

data_processing:
All raw fastq files were processed with the Nanostring GeoMxNGSPipeline v2.3.3.10, and counts per gene were exported as Nanostring DCC files per sample.
Assembly: hg38
Supplementary files format and content: Nanostring GeoMx DCC files with read counts per gene
Library strategy: Spatial Transcriptomics

source_name: Brain, MS Autopsie

extract_protocol:
5µm thick sections were cut under RNase free codtions and processed according to the GeoMx RNA FFPE workflow (MAN-10150-02) with 10min antigen retrival at 100°C and 15min Proteinase K (0.1µg/ml in PBS) at 37°C for RNA Target exposure.
Spatial Transcriptomics libararys were prepared according to GeoMx DSP workflow (MAN-10153-02)

value: Brain, MS Autopsie

tag: cell type

value: CD68 positive

tag: location

value: NAWM


title: shNAT10 3

city: Wu Han

first: Gongcai

last: Tao

state: Hu Bei Province

address: No. 9, Zhangzhidong Road, Wuchang District

department: Department of Gastrointestinal Surgery

country: China

institute: Renmin Hospital of Wuhan University

data_processing:
Sample preparation and RNA library construction
Quality control and mapping
Gene-level quantification, analysis of differentially expressed genes (DEGs), cluster analysis, GGene-level quantification, analysis of differentially expressed genes (DEGs), cluster analysis, GO and KEGG enrichment (parameter- Quality limit: 0.05)
Transcript-level quantification, analysis of differentially expressed transcript (DEGs), cluster analysis, GO and KEGG enrichment.(P value < 0.05 and foldChange >2 or foldChange < 0.5 was set as the threshold for significantly differential expression.)
Assembly: human genome (GRCh38)
Supplementary files format and content: tab-delimited EXCEL files include RPKM values for each Sample
Supplementary files format and content: tab-delimited EXCEL files include cmprehensive information for all Samples

source_name: colorectal cancer

growth_protocol: SW620 cells were maintained in L15 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
Total RNA was isolated using the TRIZOL reagent and subjected to multiple purification steps to obtain an RNA solution of suitable concentration and purity.
RNA libraries for RNA-seq were prepared using GenSeq® Low Input RNA Library Prep Kit (GenSeq, Inc.) following manufacturer's protocols.

value: colorectal cancer

tag: cell line

value: colorectal cancer cells

value: NAT10 knockdown

tag: treatment


title: CLL193


title: ctrl2_NAWM8


title: METTL7A overexpression, trophectoderm, rep3

city: Gainesville

first: Zongliang

last: Jiang

state: FL

address: 2033 Mowry Rd

department: Animal Sciences

institute: University of Florida

data_processing:
Low-quality read and adaptors were trimmed with TrimGalore-0.6.10 (parameters: -q 20 --phred33 --fastqc --length 20 --stringency 1)
Clean reads were mapped to bovine genome bt9 (NCBI ARS-UCD 2.0) using STAR-2.7.11b (parameters: --sjdbOverhang 150 --alignIntronMax 1000000)
Raw counts were retrieved from bam files with Subread-2.0.6 (parameters: -p -M)
Raw un-normalized counts were used for differetial gene expression analysis with DEseq2-1.44.0
Gene enrichment was done with clusterprofiler-4.10.1
Assembly: NCBI ARS-UCD 2.0
Supplementary files format and content: excel files include raw counts for each sample

molecule: polyA RNA

organism: Bos indicus x Bos taurus

source_name: pre-implantation embryos

extract_protocol:
Embryos and cells were used directly for library preparation without RNA extraction.
SMART-Seq v4 Ultra Low Input RNA kit (Takara, Mountain View, CA) was used for cDNA synthesis and amplification, followed by Tn5 tagmentation and library preparation with Nextera XT DNA Library Prep Kit (Illumina, San Diego, CA). The final libraries were subject to size selection with 0.6x AMPure XP bead wash (Beckman Coulter, Indianapolis, IN).

value: pre-implantation embryos

value: WT

value: zygotic injection of in vitro transcribed METTL7A mRNA


title: METTL7A overexpression, trophectoderm, rep2


title: shNAT10 2


title: SW620, IP


title: shControl, IP, RIP 1

data_processing:
Sample preparation and RNA library construction
Quality control and mapping
Transcript-level quantification, analysis of differential acetylation, cluster analysis, GO and KEGG enrichment of differential acetylation.(P value < 0.05 and foldChange >2 or foldChange < 0.5 was set as the threshold for significantly differential expression.)
Assembly: human genome (GRCh38)
Supplementary files format and content: Exctab-delimited bed files include MACS_peak for each Sample
Supplementary files format and content: Excel files include comprehensive information for all Samples
Library strategy: ac4CRIP-Seq

extract_protocol:
Total RNA was isolated using the TRIZOL reagent and subjected to multiple purification steps to obtain an RNA solution of suitable concentration and purity.
RNA libraries for ac4CRIP-seq were prepared using GenSeq® Low Input RNA Library Prep Kit (GenSeq, Inc.) GenSeq® Low Input Whole RNA Library Prep Kit (GenSeq, Inc.) following manufacturer's protocols.


title: shNAT10 1


title: CLL192

value: IGHV Mutated


title: ctrl2_NAWM6


title: ctrl2_NAWM7


title: CLL190


title: shControl 3


title: METTL7A overexpression, Inner cell mass, rep2


title: shControl, Input, RIP 3


title: ctrl2_NAWM5


title: ctrl2_NAWM4


title: shControl 2


title: ctrl3_NAWM2


title: MS2_NAWM_rep4

data_processing:
*library strategy: Spatial Transcriptomics
All raw fastq files were processed with the Nanostring GeoMxNGSPipeline v2.3.3.10, and counts per gene were exported as Nanostring DCC files per sample.
Assembly: hg38
Supplementary files format and content: Nanostring GeoMx DCC files with read counts per gene

value: NAWM/PPWM


title: ctrl2_NAWM3


title: shControl 1


title: MS2_NAWM_rep3


title: CLL188


title: CLL186


title: CLL191


title: METTL7A overexpression, 8-cell embryo, rep2


title: METTL7A overexpression, Inner cell mass, rep3


title: ctrl2_NAWM2


title: CLL185


title: METTL7A overexpression, 2-cell embryo, rep1


title: METTL7A overexpression, Inner cell mass, rep1


title: METTL7A overexpression, trophectoderm, rep1


title: MS3b_NAWM_rep4


title: METTL7A overexpression, 8-cell embryo, rep1


title: ctrl2_NAWM1


title: METTL7A overexpression, 2-cell embryo, rep2


title: ctrl1_NAWM4


title: ctrl1_NAWM2


title: MS3b_RIM_rep4

value: lesion rim


title: Control, 8-cell embryo, rep1

value: zygotic injection of vehicle


title: Control, 8-cell embryo, rep2


title: MS3b_NAWM_rep3


title: CLL184

value: European Ancestry (EA)


title: ctrl1_NAWM1


title: ctrl1_NAWM3


title: MS3b_RIM_rep3


title: CLL182

value: Peripheral blood mononuclear cells


title: CLL181

value: African Ancestry (AA)

value: Chronic Lymphocytic Leukemia (CLL)


title: Control, 2-cell embryo, rep2


title: CLL189


title: MS24_mixed7

value: Brain, MS Autopsie

value: mixed rim


title: MS24_mixed8

value: CD68 positive


title: MS17_NAWM_rep4


title: Control, 2-cell embryo, rep1


title: CLL187


title: Control, trophectoderm, rep3


title: MS17_RIM_rep4


title: CLL183


title: MS24_mixed5


title: CLL179

value: IGHV Unmutated


title: MS24_NAWM4

value: NAWM


title: Control, trophectoderm, rep1


title: CLL180


title: MS17_NAWM_rep3


title: MS24_mixed6


title: Control, trophectoderm, rep2


title: Control, Inner cell mass, rep2


title: MS24_NAWM3


title: Control, Inner cell mass, rep3


title: CLL178


title: MS24_NAWM1


title: MS17_RIM_rep3


title: Control, Inner cell mass, rep1


title: MS24_mixed4


title: CLL177


title: CLL176


title: CLL175


title: MS24_mixed3


title: CLL173


title: MS24_NAWM2


title: Nb-W45-OE3 (biol rep 3)

city: Mérida

first: Sergio

last: García

state: Yucatán

department: Biotechnology

country: Mexico

institute: Centro de Investigación Científica de Yucatán A. C.

description: Library name: Nb-W45-OE3

data_processing:
CLC genomics workbench v. 11.0.1
Trimmomatic program was used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 were trimmed. Afterwards, reads with length shorter than 36 bp were dropped to produce trimmed data.
de novo transcriptome assembly was performed in order to reconstruct the transcript sequences without reference genome sequence.
Read count extraction and normalization were performed.
Assembly: de novo transcriptome assembly
Supplementary files format and content: raw counts, FPKM, TPM for each sample

organism: Nicotiana benthamiana

source_name: Leaves

growth_protocol: N. benthamiana plants were grown under a 12-hour light/12-hour dark cycle, with a light intensity of 100 μmol m⁻² s⁻¹, a temperature of 25 ± 1°C, and a relative humidity of approximately 70%.

extract_protocol:
Total RNA was harvested using the RNeasy Plant Minikit kit. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNAseq were prepared using TruSeq stranded mRNA library kit following the manufacturer´s protocols.

treatment_protocol: Leaves of N. benthamiana plants were infiltrated with Agrobacterium tumefaciens LBA4404 harboring either the pCAMBIA2200::MaWRKY45 construct  (overexpressing samples) or the empty vector pCAMBIA2200 (mock samples).

value: Leaves

value: MaWRKY45 CDS overexpression


title: CLL174


title: CLL172


title: Nb-W45-OE2 (biol rep 2)

description: Library name: Nb-W45-OE2

value: WT


title: OTE, air, 24 hr, batch 1, rep 6

city: Winston-Salem

first: Jeannie

last: Chan

state: NC

address: Medical Center Boulevard

department: Internal Medicine

institute: Wake Forest School of Medicine

description:
Batch1_46samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_18C_S33

data_processing:
Raw sequence reads were imported into Partek® Flow® software (Partek®) for analysis.
Cutadapt was used to trim the random barcode (4 bases) from the 5’ end and adapter (AAAAAAAAAA) from the 3’ end of the reads. Bases with a Phred quality score <20 were trimmed, and reads <15 bases in length were discarded.
High-quality reads were then aligned and quantified to the hg38 GENCODE reference database using STAR and an expectation/maximization (E/M) algorithm, respectively.
Transcript-level counts were summed to gene level, normalized with the median-of-ratios method used in DESeq2, and log2-transformed.
Assembly: hg38
Supplementary files format and content: Text file includes raw counts for 46 samples in batch 1.
Supplementary files format and content: Text file includes raw counts for 90 samples in batches 2 and 3.
Supplementary files format and content: Text file includes normalized and log2-transformed gene counts for 136 samples.

source_name: Airway organ tissue equivalent

extract_protocol:
Each frozen OTE was briefly incubated in QIAzol Lysis Reagent (QIAGEN, Inc.), and a pipette was used to remove and discard the membrane.
OTEs were then homogenized 2 x 30 seconds at 2,200 rpm using a Precellys® 2ml Tissue Homogenizing Mixed Beads Kit (Cayman Chemical) and Mini-BeadBeater-96 Cell Disruptor (BioSpec Products).
Homogenized samples were centrifuged 1 minute at 2,000 x g to remove particulate debris, and RNA was purified from lysed cells using QIAGEN’s miRNeasy Micro Kit with the optional DNase I treatment.
Quantity of RNA extracts was determined using the DeNovix RNA Assay Kit and DS-11 FX+ Spectrophotometer/Fluorometer (DeNovix®).
RNA integrity was determined using an Agilent 4200 TapeStation System (Agilent).
cDNA libraries were prepared from 50 ng of each RNA extract using a NEXTFLEX® Combo-Seq™ mRNA/miRNA Kit (PerkinElmer®) and Sciclone® G3 NGSx Workstation (PerkinElmer®).
Libraries were quantified using a KAPA Library Quantification Kit (Roche Sequencing and Life Science), with average fragment length determined by a 4200 TapeStation System (Agilent).
Libraries were normalized prior to pooling, and the pooled libraries were sequenced using an Illumina® NovaSeq 6000 System (Illumina®, Inc.), generating 76-bp single-end reads.

treatment_protocol:
OTEs were exposed to medical air (MA) or 20 ppm chlorine gas (Cl2) for 30 min. At 0, 6, 12 or 24 hours post-exposure, OTEs were collected and snap-frozen in liquid nitrogen for gene expression studies.
The experiment was repeated three times and three batches of OTEs exposed to MA or CE were collected. The experimental design included replicates of OTEs  (n = 5 or 6) exposed to MA or CE at each time point.

value: Airway organ tissue equivalent

tag: ote batch

tag: exposure

value: medical air

tag: time point

value: 24 hr


title: OTE, air, 6 hr, batch 1, rep 5

description:
Batch1_46samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_20B_S45

value: 6 hr


title: OTE, air, 12 hr, batch 1, rep 5

description:
Batch1_46samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_19C_S47

value: 12 hr


title: OTE, air, 12 hr, batch 1, rep 4

description:
Batch1_46samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_19A_S34


title: OTE, air, 6 hr, batch 1, rep 4

description:
Batch1_46samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_20A_S20


title: OTE, air, 6 hr, batch 1, rep 6

description:
Batch1_46samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_20C_S38


title: CLL170


title: MS24_mixed2


title: OTE, air, 24 hr, batch 1, rep 5

description:
Batch1_46samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_18B_S39


title: Nb-W45-OE1 (biol rep 1)

description: Library name: Nb-W45-OE1


title: CLL171


title: CLL169


title: Nb-EV3 (biol rep 3)

description: Library name: Nb-EV3

value: Mock control


title: MS28b_NAWM7


title: Nb-EV2 (biol rep 2)

description: Library name: Nb-EV2


title: OTE, air, 24 hr, batch 1, rep 4

description:
Batch1_46samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_18A_S28


title: Nb-EV1 (biol rep 1)

description: Library name: Nb-EV1


title: MS28b_NAWM8


title: OTE, chlorine, 0 hr, batch 1, rep 5

description:
Batch1_46samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_17C_S21

value: 20 ppm chlorine

value: 0 hr


title: CLL168

value: European Ancestry (EA)

value: Peripheral blood mononuclear cells

value: Chronic Lymphocytic Leukemia (CLL)

value: IGHV Mutated


title: OTE, chlorine, 0 hr, batch 1, rep 4

description:
Batch1_46samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_17A_S2


title: MS28b_NAWM6

value: Brain, MS Autopsie

value: CD68 positive


title: MS24_mixed1

value: mixed rim


title: CLL167

value: African Ancestry (AA)

value: IGHV Unmutated


title: OTE, chlorine, 6 hr, batch 1, rep 4

description:
Batch1_46samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_16A_S18

value: Airway organ tissue equivalent


title: OTE, chlorine, 6 hr, batch 1, rep 6

description:
Batch1_46samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_16C_S29


title: MS28b_mixed3


title: MS28b_mixed4


title: OTE, chlorine, 6 hr, batch 1, rep 5

description:
Batch1_46samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_16B_S41


title: MS28b_NAWM5

value: NAWM


title: bXEN_RNA_A

description: Library name: Sample 3

data_processing:
For RNAseq, multiplexed sequencing reads that passed filters were trimmed to remove low-quality reads and adaptors by Trim Galore (version 0.6.7) (-q 25 –length 20 –max_n 3 –stringency 3). The quality of reads after filtering was assessed by FastQC, followed by alignment to the bovine genome (ARS-UCD1.3) by HISAT2 (version 2.2.1) with default parameters. The output SAM files were converted to BAM files and sorted using SAMtools6 (version 1.14). Read counts of all samples were quantified using featureCounts (version 2.0.1) with the bovine genome as a reference and were adjusted to provide counts per million (CPM) mapped reads. Principal component analysis and cluster analysis were performed with R (a free software environment for statistical computing and graphics). Differentially expressed genes (DEGs) were identified using edgeR in R. Genes were considered differentially expressed when they provided a false discovery rate of <0.05 and fold change >2. ClusterProfiler was used to reveal the Gene Ontology and KEGG pathways in R. For ATACseq, all quality assessed ATAC-seq reads were aligned to the bovine reference genome using Bowtie 2.3 with following options: –very-sensitive -X 2000 –no-mixed –no-discordant. Alignments resulted from PCR duplicates or locations in mitochondria were excluded. Only unique alignments within each sample were retained for subsequent analysis. ATAC-seq peaks were called separately for each sample by MACS2 with following options: –keep-dup all –nolambda –nomodel. The ATAC-seq bigwig files were generated using bamcoverage from deeptools. The ATAC-seq signals were normalized in the Integrative Genome Viewer genome browser. The enrichment of transcriptional factor motifs in peaks was evaluated using HOMER (http://homer.ucsd.edu/homer/motif/).
Assembly: ARS-UCD1.3
Supplementary files format and content: csv, normalized read counts
Supplementary files format and content: bw, genome data that will be displayed in the Genome Browser

organism: Bos taurus

source_name: cell line

growth_protocol: To derive bXEN, the embryos were cultured in bXENM containing DMEM: F12 (Gibco) and Neurobasal medium (Gibco) (1:1), 1x N2-supplement (Gibco), 1x B27-supplement (Gibco), 1x NEAA (Gibco), 1x GlutaMAX (Gibco), 0.1 mM 2-mercaptoethanol (Gibco), 25 ng/mL FGF4 (sigma, F8424), 10 ng/mL BMP4 (R&D SYSTEMS, 314-BP-050/CF), 1uM XAV939 (sigma, X3004-5MG), 3uM A83-01 (sigma SML0788-25MG), 10ng/mL IL-6 (sigma, SRP3096). To promote the proliferation of hypoblast, 0.1% KSR, 0.1% BSA (MP biomedicals), 20ng/mL ActivinA, and PDGF (10 ng/mL, R&D SYSTEMS, BT220-010/CF) were also added during the derivation of bXEN and were optional for bXEN maintenance. All the cells were cultured at 38.5°C and 5% CO2. The culture medium was changed every other day. On day 7 or 8, outgrowths were dissociated by TrypLE (Gibco, 12605-010) for 5-7 mins at 38.5 °C and passaged. For optimal survival rate, 10 mM Rho-associated protein kinase (ROCK) inhibitor Y-27632 (Tocris,1254) was added to the culture medium for first 24 hours. Once established, both bXEN were passaged every 3-5 days at a 1:5 split ratio using TrypLE. Each well of cells was dissociated by 0.5mL TrypLE for 5 mins at 38.5°C, the same volume of DMEM/F12 with 1% BSA was used to neutralize TrypLE.

extract_protocol:
Total RNA of bXEN was extracted using RNeasy Micro Kit (Qiagen).
The RNA-seq libraries were generated using the Smart-seq2 v4 kit with minor modifications from the manufacturer’s instructions. Briefly, individual cells were lysed, and mRNA was captured and amplified with the Smart-seq2 v4 kit (Clontech). After AMPure XP beads purification, the high-quality amplified RNAs were subject to library preparation using Nextera XT DNA Library Preparation Kit (Illumina) and multiplexed by Nextera XT Indexes (Illumina). The concentration of sequencing libraries was determined using Qubit dsDNA HS Assay Kit (Life Technologies) and KAPA Library Quantification Kits (KAPA Biosystems). The size of sequencing libraries was determined using the Agilent D5000 ScreenTape with Tapestation 4200 system (Agilent). Pooled indexed libraries were then sequenced on the Illumina HiSeq X platform with 150-bp pair-end reads. For ATAC-seq, fresh cells were lysed on ice, then incubated with the Tn5 transposase (TDE1, Illumina) and tagmentation buffer. Tagmentated DNA was purified using MinElute Reaction Cleanup Kit (Qiagen). The ATAC-seq libraries were amplified by Illumina TrueSeq primers and multiplexed by index primers. Finally, high quality indexed libraries were then pooled together and sequenced on Illumina NovaSeq platform with 150-bp paired-end reads.

value: cell line

value: WT


title: MS28b_mixed2


title: OTE, air, 0 hr, batch 1, rep 5

description:
Batch1_46samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_15A_S37

value: medical air


title: CLL165


title: CLL166


title: CLL164


title: bXEN_ATAC_B

description: Library name: Sample 2

library_source: genomic

molecule: genomic DNA


title: bXEN_RNA_C

description: Library name: Sample 5


title: bXEN_RNA_B

description: Library name: Sample 4


title: OTE, air, 0 hr, batch 1, rep 6

description:
Batch1_46samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_15C_S40


title: CLL163


title: OTE, air, 6 hr, batch 1, rep 3

description:
Batch1_46samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_14C_S19

value: 6 hr


title: bXEN_ATAC_A

description: Library name: Sample 1


title: bXEN_RNA_D

description: Library name: Sample 6


title: Lung_aKO_w10

city: Los Angeles

first: Xiuju

last: Wu

state: CA

address: 650 Charles Young Dr East, CHS A2-237

institute: University of California, Los Angeles

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting were performed using Cell Ranger software v7.2.0.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

organism: Mus musculus

source_name: Lung

extract_protocol:
Freshly harvested lungs from C57BL/6J mice were enzymatically dissociated with 5mg/ml Dispase in PBS/2%FBS in room temperature for 1 hour, tissues were minced, then were incubated on the shaker (100rpm) with 50 µg/ml DNase I for 30 min. Cell suspension was washed and filtered with 70and 40 µm strainers. Tomato positive cells were sorted by fluorescence-activated cell sorting (FACS) for scRNA-seq analysis.
scRNA libraries were constructed according to the manufacturer's instructions (single cell 3' v3 protocol, 10x Genomics).

value: Lung Ve-cadherin cre tdTomato+ cells

value: Lung

tag: strain

tag: age

value: 10-12 weeks old


title: OTE, air, 6 hr, batch 1, rep 2

description:
Batch1_46samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_14B_S8


title: CLL161

value: Peripheral blood mononuclear cells


title: MS28b_mixed1


title: MS4_NAWM4


title: MS4_NAWM3


title: OTE, air, 6 hr, batch 1, rep 1

description:
Batch1_46samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_14A_S7


title: CLL160

value: Chronic Lymphocytic Leukemia (CLL)


title: K27ac_2

city: Zurich

first: shafeeq

middle: Ahmed

last: Mohammed

state: Zurich

address: wagistrasse 12

department: Centre for Translational and Experimental Cardiology

country: Switzerland

institute: University of Zurich

description: Library name: ND_H3K27ac

data_processing:
SNPsplit was then used to tag the SNPs for S129/SvJae and CAST alleles in the bam file and sort the haplotype-specific bam files for both the alleles. Bigwig files were created from the bam files using bamCoverage from deeptools (Ramirez et al., 2014) using default parameters.
Integrative Genome Viewer (IGV, version 2.15.4) (Robinson et al., 2011) was used to visualize and extract representative ChIPseq tracks. “computeMatrix” from deepTools was used to generate all heat maps and plot profiles.
Assembly: ChIPseq reads were aligned to the mm10 reference genome with Bowtie2 (version 2.5.0; (version 2.5.0; (Langmead & Salzberg, 2012)) using default parameters
Supplementary files format and content: Bigwig files were created from the bam files using bamCoverage from deeptools (Ramirez et al., 2014) using default parameters. Integrative Genome Viewer (IGV, version 2.15.4) (Robinson et al., 2011) was used to visualize and extract representative ChIPseq tracks. “computeMatrix” from deepTools was used to generate all heat maps and plot profiles.

source_name: Heart

growth_protocol: Frozen heart tissues of mouse fed with high-fat diet (HFD) and normal diet (ND) were used. About 50mg of tissue was chopped into 1-3 mm3 pieces using a scalpel blade. The tissue was disintegrated using a dounce homogenizer (pestle A) in ice-cold PBS with 1X protease inhibitor complete EDTA-free cocktail, (Roche) to get a homogenous suspension. The tissue suspension was centrifuged, and the supernatant was discarded. The pellet was resuspended in 1% formaldehyde to cross-link proteins to DNA and the reaction was stopped with glycine. The pellet was washed with ice-cold PBS with protease inhibitor. Isolated nuclei were lysed with lysis buffer (50 mM Tris-HCl, pH 8.1, 10 mM EDTA, pH 8, 1% SDS, 1X protease inhibitor). Nuclei were sonicated using a Bioruptor ultrasonic cell disruptor (Diagenode) to shear genomic DNA to an average fragment size of 200 bp. 20 μg of chromatin was diluted to a total volume of 500 μl with ChIP buffer (16.7 mM Tris-HCl, pH 8.1, 167 mM NaCl, 1.2 mM EDTA, 0.01% SDS, 1.1% Triton X-100) and incubated overnight with the ChIP-grade antibodies against H3K36me3 (D5A7, Cell Signalling Technology), H3K4me1 (ab8895, abcam), H3K4me3 (07-473, Sigma-Aldrich) and H3K27ac (ab4729, abcam).  After washing, bound chromatin was eluted with the elution buffer (1% SDS, 100 mM NaHCO3). Upon proteinase K digestion (50 °C for 3 h) and reversion of cross- linking (65 °C, overnight), DNA was purified with phenol/chloroform, and ethanol precipitated.

extract_protocol:
For ChIPseq normalization with D. melanogaster spike-in chromatin, the samples were prepared and processed as above but with the addition of 200 ng of D. melanogaster S2 chromatin.
ChIPseq reads were aligned to the mm10 reference genome with Bowtie2 (version 2.5.0; (version 2.5.0; (Langmead & Salzberg, 2012)) using default parameters. PCR duplicates were removed using samtools (Danecek et al., 2021).

treatment_protocol: The quality and quantity of the isolated DNA were determined with a Qubit® 4 Fluorometer (Life Technologies, California, USA) and the 4200 TapeStation system. Briefly, ChIP samples (1 ng) were end-repaired and polyadenylated before the ligation of Illumina compatible adapters. The adapters contain the index for multiplexing. The quality and quantity of the enriched libraries were validated using Qubit® 4 Fluorometer and the 4200 TapeStation system. The libraries were pooled to 10 nM in Tris-HCl 10 mM, pH 8.5 with 0.1% Tween 20. Sequencing was performed on the NovaSeq 6000 for 100bp single end reads (Illumina, Inc, California, USA).

value: Heart

value: Cardiomyocytes

value: ND


title: MS4_NAWM2

value: Brain, MS Autopsie

value: CD68 positive


title: MS4_NAWM1


title: OTE, chlorine, 24 hr, batch 1, rep 6

description:
Batch1_46samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_13C_S44

value: 20 ppm chlorine

value: 24 hr


title: CLL158

value: African Ancestry (AA)

value: IGHV Unmutated


title: K27ac_1

description: Library name: HFD_H3K27ac

value: HFD


title: OTE, chlorine, 24 hr, batch 1, rep 5

description:
Batch1_46samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_13B_S35

value: Airway organ tissue equivalent


title: MS28b_active4

value: active center


title: K4me1_1

description: Library name: HFD_H3K4me1


title: MS28b_active3


title: CLL156


title: CLL162


title: OTE, air, 0 hr, batch 1, rep 4

description:
Batch1_46samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_12B_S24

value: medical air

value: 0 hr


title: K4me3_2

description: Library name: ND_H3K4me3


title: K4ME1_2

description: Library name: ND_H3K4me1


title: CLL157


title: OTE, chlorine, 24 hr, batch 1, rep 4

description:
Batch1_46samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_13A_S26


title: MS28b_active2


title: OTE, air, 24 hr, batch 1, rep 3

description:
Batch1_46samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_11C_S27


title: CLL155


title: K4me3_1

description: Library name: HFD_H3K4me3


title: OTE, air, 24 hr, batch 1, rep 2

description:
Batch1_46samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_11B_S16


title: MS28b_active1


title: K36ME3_2

description: Library name: ND_K36me3


title: Lung_aWT_w10

description: 10x Genomics

value: Lung Ve-cadherin cre tdTomato+ cells

value: Lung

value: 10-12 weeks old


title: CLL154

value: Peripheral blood mononuclear cells

value: Chronic Lymphocytic Leukemia (CLL)


title: MS4_brl4

value: BRL rim


title: OTE, air, 24 hr, batch 1, rep 1

description:
Batch1_46samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_11A_S15


title: CLL153


title: CLL159


title: CLL152


title: MS4_brl2

value: Brain, MS Autopsie


title: WT, replicate 2(ChIP)

city: Zhengzhou

first: Peng

last: Wang

address: Science Avenue

institute: Zhengzhou University

description: Library name: Sample 4

data_processing:
Two biological replicates were performed in ChIP-seq analysis. Trimmomatic (version 0.36) was used to filter out low-quality reads. Clean reads were mapped to the GRCm39 genome by Bwa (version 0.7.15). Samtools (version 1.3.1) was used to remove potential PCR duplicates
Assembly: GRCm38
Supplementary files format and content: BED

source_name: Colon

extract_protocol:
Tissue was washed in cold PBS and cross-linked with 1% formaldehyde for 10 minutes and then quenched by addition of glycine. Afterwards, samples were lysed and chromatins were obtained on ice. Chromatins were sonicated to get soluble sheared chromatin (average DNA length of 200-500 bp).
Immunoprecipitated DNA was used to construct sequencing libraries following the protocol provided by the I NEXTFLEX ChIP-seq Library Prep Kit for Illumina Sequencing（NOVA-5143-02，Bio Scientific）and sequenced on Illumina Novaseq 6000 with PE 150 method

value: Colon

value: DSS


title: OTE, air, 12 hr, batch 1, rep 3

description:
Batch1_46samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_10C_S46

value: 12 hr


title: MS4_brl3

value: CD68 positive


title: WT, replicate 2(input)

description: Library name: Sample 3


title: MS4_brl1


title: CLL149

value: African Ancestry (AA)


title: WT, replicate 1(input)

description: Library name: Sample 1


title: MS27d _NAWM3

value: NAWM


title: OTE, chlorine, 6 hr, batch 1, rep 2

description:
Batch1_46samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_9B_S6

value: Airway organ tissue equivalent

value: 20 ppm chlorine

value: 6 hr


title: OTE, chlorine, 6 hr, batch 1, rep 3

description:
Batch1_46samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_9C_S17


title: MS27d _NAWM2


title: CLL150


title: OTE, chlorine, 6 hr, batch 1, rep 1

description:
Batch1_46samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_9A_S5


title: MS27d _NAWM1


title: CLL148


title: CLL147

value: IGHV Mutated


title: OTE, air, 0 hr, batch 1, rep 3

description:
Batch1_46samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_8C_S23

value: medical air

value: 0 hr


title: BM Eosinophil_SA7

city: Salzburg

first: Natalia

middle: Rodrigues Nunes

last: da Silva

address: Steingasse 11,

country: Austria

institute: Paris Lodron Universität Salzburg

description: Library name: MR71_ATAC7

data_processing:
(1) Sample quality was verified using FastQC to ensure read quality and the absence of sequencing artifacts. (2) Adapter sequences were removed, and low-quality reads were trimmed using Trimmomatic. (3) Reads were aligned to the mouse reference genome (mm10) using Bowtie2 with default parameters optimized for ATAC-seq data. (4) Duplicates were removed using Picard tools to avoid biases in peak calling. (5) Peak calling was performed using MACS2 to identify regions of open chromatin, using default narrowPeak parameters. (6) Peaks were annotated using HOMER, and differential accessibility analysis was conducted using DESeq2. (7) Quality metrics such as TSS enrichment and fragment length distribution were calculated to validate library preparation and data processing steps.
Supplementary files format and content: The processed data files are in the BED-like narrowPeak format. These files contain peak regions identified from ATAC-seq data analysis, including genomic coordinates, peak scores, signal values, and significance values (p-values and q-values). The narrowPeak files provide high-resolution information about accessible chromatin regions and transcription factor binding sites.

source_name: Bone marrow

extract_protocol:
Nuclei were isolated from a total of 80 000 viable bone marrow derived eosinophils through lysis. Briefly, cells were pelleted at 500 g for 5 minutes at 4°C prior to gentle, but thorough resuspension in 50 µl ATAC-seq resuspension buffer (10 mM Tris-HCL, 10 mM NaCl and 3 mM MgCl2 in molecular biology grade H2O) supplemented with 0.1% NP-40 (Sigma #I8896), 0.1% Tween 20  (Sigma #9005-64-5) and 0.01% digitonin (Sigma #D141). Cells were then incubated at 4°C for 3 minutes, followed by addition of 1 ml cold ATAC-seq resuspension buffer with only 0.1% Tween 20. Nuclei were then pelleted by centrifugation for 10 minutes at 500 g and 4°C. The pellet was resuspended with 50 µl of tagmentation mixture containing 25 µl of 2X tagmentation buffer (Diagenode #C01019043), 2 µl of tagmentase (Diagenode #C0170012), 1 µl of 50x EDTA-free protease inhibitor (Roche/Sigma, #11836170001), 0.5 µl of 1% digitonin, 2.5 µl 1% NP-40 and 19 µl H2O and incubated at 37°C for 30 minutes. After tagmentation, DNA was purified using the MiniElute PCR purification Kit (Qiagen). The protocol was adapted from a previously published protocol (J. M. Felton et al., Epigenetic Analysis of the Chromatin Landscape Identifies a Repertoire of Murine Eosinophil-Specific PU.1-Bound Enhancers. The Journal of Immunology 207, 1044–1054 (2021),  DOI: 10.4049/jimmunol.2000207).
Libraries were constructed according to the OMNI-ATAC protocol (Felton et al., 2021, DOI: 10.4049/jimmunol.2000207 and Corces et al, 2017, DOI: 10.1038/nmeth.4396 ). Quality was assessed with an Agilent Bioanalyzer and libraries were sequenced on the Illumina Novaseq 6000, paired-end, 150 bases each end.

value: Bone marrow

value: bone marrow derived eosinophils

value: S.aureus skin infection


title: BM Eosinophil_SA8

description: Library name: MR71_ATAC8


title: BM Eosinophil_SA6

description: Library name: MR71_ATAC6


title: CLL146

value: Peripheral blood mononuclear cells

value: Chronic Lymphocytic Leukemia (CLL)

value: IGHV Unmutated


title: OTE, air, 12 hr, batch 1, rep 2

description:
Batch1_46samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_10B_S12


title: K36ME3_1

description: Library name: HFD_K36me3

value: Heart

value: Cardiomyocytes

value: HFD


title: CLL151

value: African Ancestry (AA)


title: MS27d _mixed4

value: Brain, MS Autopsie

value: CD68 positive

value: mixed rim


title: BM Eosinophil_SA5

description: Library name: MR71_ATAC5


title: OTE, air, 12 hr, batch 1, rep 1

description:
Batch1_46samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_10A_S11

value: Airway organ tissue equivalent

value: 12 hr


title: MS27d _mixed3


title: WT, replicate 1(ChIP)

description: Library name: Sample 2

value: Colon

value: DSS


title: CLL145


title: OTE, air, 0 hr, batch 1, rep 1

description:
Batch1_46samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_7B_S3

value: medical air

value: 0 hr


title: MS27d _NAWM4

value: NAWM


title: BM Eosinophil_PBS4

description: Library name: MR71_ATAC4

value: Bone marrow

value: bone marrow derived eosinophils

value: PBS Control


title: MS27d _mixed2


title: OTE, air, 0 hr, batch 1, rep 2

description:
Batch1_46samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_8B_S4


title: BM Eosinophil_PBS3

description: Library name: MR71_ATAC3


title: OTE, chlorine, 0 hr, batch 1, rep 2

description:
Batch1_46samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_5B_S22

value: 20 ppm chlorine


title: OTE, chlorine, 0 hr, batch 1, rep 3

description:
Batch1_46samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_6B_S48


title: CLL142

value: Peripheral blood mononuclear cells

value: Chronic Lymphocytic Leukemia (CLL)


title: OTE, chlorine, 12 hr, batch 1, rep 6

description:
Batch1_46samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_4C_S43


title: BM Eosinophil_PBS2

description: Library name: MR71_ATAC2


title: MS26_NAWM4


title: CLL141

value: African Ancestry (AA)

value: IGHV Unmutated


title: BM Eosinophil_PBS1

description: Library name: MR71_ATAC1


title: MS26_NAWM3

value: Brain, MS Autopsie

value: CD68 positive


title: MS26_NAWM2


title: OTE, chlorine, 12 hr, batch 1, rep 4

description:
Batch1_46samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_4A_S36

value: Airway organ tissue equivalent


title: CLL139


title: macrophages L+S_3

city: Hangzhou

first: Yunkun

last: Lu

state: Zhejiang

address: 3 Qingchun East Rd.

department: Sir Run-Run Shaw Hospital

institute: Zhejiang University

description: Library name: Sample 10

data_processing:
Illumina Casava1.8 software was used for basecalling.
The raw data were trimmed by fastp (v0.20.1) to remove adapter sequence and reads with low sequencing quality.
Clean reads were aligned to the mouse genome (mm10) using HISAT2 (v2.1.0) with the default parameter settings.
Transcript assembly was performed by stringtie (v2.0) and expression of transcripts sharing each Ensembl_id was quantified as Fragments Per Kilobase Million (FPKM).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
Library strategy: CUT&Tag

source_name: Male Abelson murine leukemia virus-induced tumors

growth_protocol: 6×10^5 RAW264.7 cells were seeded onto one plate and cultured in DMEM with 10% FBS and 1% P/S.

extract_protocol:
2×10^5 cells per sample were used for CUT&Tag experiment
DNA was amplified with N5 and N7 primers and purified with NovoNGS DNA Clean Beads (NovoNGS® CUT&Tag® 4.0 High-Sensitivity Kit, Novoprotein, China) following manufacturer’s recommendations.

treatment_protocol: 24 h later, cells were divided into three groups and treated with: DMSO, DMSO+LPS, and LPS+Skatole respectively for 12 h.

value: macrophages

value: WT

value: p65 antibody


title: CLL144


title: macrophages L+S_2

description: Library name: Sample 9

value: Male Abelson murine leukemia virus-induced tumors


title: OTE, chlorine, 24 hr, batch 1, rep 3

description:
Batch1_46samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_3C_S25

value: 24 hr


title: CLL143


title: MS26_NAWM1

value: NAWM


title: CLL137


title: MS26_mixed4

value: mixed rim


title: OTE, chlorine, 24 hr, batch 1, rep 2

description:
Batch1_46samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_3B_S14


title: MS27d _mixed1


title: macrophages L+S_1

description: Library name: Sample 8


title: OTE, chlorine, 24 hr, batch 1, rep 1

description:
Batch1_46samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_3A_S13


title: macrophages D+L_3

description: Library name: Sample 7


title: CLL136


title: MS26_mixed3


title: macrophages D+L_2

description: Library name: Sample 6


title: MS26_mixed2


title: OTE, chlorine, 0 hr, batch 1, rep 1

description:
Batch1_46samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_2A_S1

value: 0 hr


title: OTE, chlorine, 12 hr, batch 1, rep 5

description:
Batch1_46samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_4B_S42

value: 12 hr


title: macrophages D+L_1

description: Library name: Sample 5


title: CLL135

value: European Ancestry (EA)


title: MS26_mixed1


title: CLL140

value: Peripheral blood mononuclear cells


title: CLL134

value: Chronic Lymphocytic Leukemia (CLL)

value: IGHV Mutated


title: macrophages D_3

description: Library name: Sample 4


title: MS2d_NAWM4


title: CLL138

value: African Ancestry (AA)

value: IGHV Unmutated


title: MS2d_NAWM3

value: Brain, MS Autopsie

value: CD68 positive


title: CLL133


title: macrophages D_2

description: Library name: Sample 3

value: macrophages


title: OTE, chlorine, 12 hr, batch 1, rep 1

description:
Batch1_46samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_1A_S9

value: Airway organ tissue equivalent

value: 20 ppm chlorine


title: MS2d_NAWM2


title: CLL132


title: CLL131


title: MS2d_NAWM1


title: OTE, air, 0 hr, batch 3, rep 6

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_96_S96

value: medical air


title: CLL130


title: OTE, air, 0 hr, batch 3, rep 5

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_95_S95


title: Mouse forebrain, Curio Seeker, P22

city: Toronto

first: Scott

last: Yuzwa

state: Ontario

address: 1 King's College Circle, Medical Sciences Building, Rm 6316

department: Laboratory Medicine and Pathobiology

country: Canada

institute: University of Toronto

description:
Library name: P22_Curio_Seeker
Curio Seeker

data_processing:
scRNA-seq data were processed using the BD WTA pipeline version 1 implemented in SevenBridges and Curio Seeker was processed using DNAnexus pipleline version 1.
Assembly: For scRNA-seq, GenecodevM19-2018-12-06, For Curio Seeker GRCm38
Supplementary files format and content: For scRNA-seq, comma-separated values files of count data. For Curio Seeker, Rdata (.RDS) files that contain all count and bead location data.
Library strategy: Spatial Transcriptomics

source_name: forebrain

extract_protocol:
We conducted single cell RNA sequencing (scRNAseq) on P4 pbacBarcode mice that were embryonically labelled at E14.5 via electroporation. Brains were identified as containing GFP+ cells by visual inspection under a NIGHTSEA Xite Fluorescence Flashlight System and the ventricles and cortex from the GFP containing hemisphere were isolated under a dissection microscope. Cells were reduced to single cell suspension from brain tissue via the use of Neuron Isolation Enzyme (with Papain, Thermo Fisher, Cat # 88285) containing 0.1mg/ml DNAse I (Sigma-Aldrich) in HBSS for 30 min at 37 ̊C and mechanical dissociation. GFP+/DRAQ7- cells were then isolated by fluorescence activated cell sorting (FACS), loaded into the BD Rhapsody cartridge (BD Biosciences) and were processed via the Rhapsody platform as per manufacturer’s instructions.  In addition, we performed spatial transcriptomics using the Curio Seeker platform at two ages, P4 and P22. One brain of each age was collected in the same manner by snap-freezing freshly dissected tissue in liquid nitrogen before storing at -80˚C to prevent RNA degradation. Brains were sectioned via cryostat along the rostral-caudal axis until a region approximately equivalent to 1 mm bregma in the adult brain. This region included the lateral ventricles with visible corpus callosum. At this level a 10 µm section was taken and positioned over the Curio Seeker tile with the aid of a paintbrush to place the dorsal regions of the lateral ventricles and the cortex between the edges of the tile. Sections were then mounted on the tile by gently melting the section with heat from a finger. Tiles were then processed as described in the Curio Seeker protocol .
scRNA-seq and Curio Seeker libraries were prepared according to the BD mRNA WTA Library Preparation Protocol and the Curio Seeker Spatial Mapping Kit, respectively.

value: forebrain

value: brain cells

value: wild-type


title: MS2d_brl3

value: BRL rim


title: CLL129


title: OTE, chlorine, 12 hr, batch 1, rep 3

description:
Batch1_46samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_1C_S30

value: 12 hr


title: MS2d_brl4


title: OTE, air, 24 hr, batch 3, rep 5

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_92_S92

value: 24 hr


title: Mouse forebrain, Curio Seeker, P4

description:
Library name: P4_Curio_Seeker
Curio Seeker


title: CLL128

value: European Ancestry (EA)

value: Peripheral blood mononuclear cells


title: MS2d_brl2


title: OTE, chlorine, 12 hr, batch 1, rep 2

description:
Batch1_46samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_1B_S10


title: OTE, chlorine, 0 hr, batch 3, rep 5

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_93_S93

value: 0 hr


title: OTE, air, 24 hr, batch 3, rep 4

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_91_S91


title: CLL127

value: Chronic Lymphocytic Leukemia (CLL)

value: IGHV Mutated


title: Mouse neocortex electroporated with pbBarcode at E14 and collected at P4, Replicate 2

description:
Library name: P4_IUE_Replicate2
BD Rhapsody WTA

data_processing:
scRNA-seq data were processed using the BD WTA pipeline version 1 implemented in SevenBridges and Curio Seeker was processed using DNAnexus pipleline version 1.
Assembly: For scRNA-seq, GenecodevM19-2018-12-06, For Curio Seeker GRCm38
Supplementary files format and content: For scRNA-seq, comma-separated values files of count data. For Curio Seeker, Rdata (.RDS) files that contain all count and bead location data.

source_name: whole neocortex

value: whole neocortex


title: Mouse neocortex electroporated with pbBarcode at E14 and collected at P4, Replicate Mixed

description:
Library name: P4_IUE_Replicate_Mixed
BD Rhapsody WTA


title: macrophages D_1

description: Library name: Sample 2

value: Male Abelson murine leukemia virus-induced tumors

value: WT

value: p65 antibody


title: OTE, chlorine, 24 hr, batch 3, rep 6

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_90_S90

value: Airway organ tissue equivalent

value: 20 ppm chlorine


title: MS13_active4

value: Brain, MS Autopsie

value: CD68 positive

value: active center


title: CLL126

value: IGHV Unmutated


title: Mouse neocortex electroporated with pbBarcode at E14 and collected at P4, Replicate 1

description:
Library name: P4_IUE_Replicate1
BD Rhapsody WTA

value: brain cells

value: wild-type


title: OTE, chlorine, 24 hr, batch 3, rep 5

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_89_S89

value: 24 hr


title: MS2d_brl1

value: BRL rim


title: CLL125

value: European Ancestry (EA)

value: Peripheral blood mononuclear cells


title: macrophages Blank

description: Library name: Sample 1

value: macrophages


title: MS13_active3


title: C48/80 + Anti-PD-L1, Replicate6, RNA-seq

city: Beijing

first: Yuanyuan

last: Zhang

state: Beijing

address: Panjiayuan nanli #17, Chaoyang District

department: National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital

institute: Chinese Academy of Medical Sciences and Peking Union Medical College

description:
C48/80 + Anti-PD-L1_Rep6
Mm_bulk.counts.xls

data_processing:
Demultiplexing, barcode processing, alignment, gene counting, and the generation of raw count matrix were performed by the Cell Ranger toolkit (version 3.1.0)
Assembly: GRCh38, mm10
Supplementary files format and content: Tab-separated files (TSV) and matrix files enclosed in RDS

source_name: Breast

extract_protocol:
Tumor biopsy samples were first stored in RNAlater RNA stabilization reagent (QIAGEN) after collection and kept on ice to avoid RNA degradation. Samples were then collected in the RPMI-1640 medium (Gibco), and enzymatically digested with gentle MACS Tumor Dissociation Kit (Miltenyi Biotec) for 60 min on a rotor at 37 °C according to the manufacturer’s protocol. The dissociated cells were next passed through a 40-μm cell-strainer (BD) in the RPMI-1640 medium (Invitrogen) with 10% FBS until uniform cell suspensions were obtained. Subsequently, the suspended cells were passed through cell strainers and centrifuged at 400 g for 10 min. Red blood cells were removed via the same procedure described above. After washing twice with 1x PBS (Invitrogen), the cell pellets were re-suspended in sorting buffer (PBS supplemented with 1% FBS).
Single-cell RNA-seq libraries were prepared using the Chromium Next GEM Single Cell 5’ Kit from 10x Genomics, following the manufacturer’s instructions; Bulk RNA-seq libraries were constructed in Sequanta Technologies Co., Ltd at Shanghai.

tag: patient

value: Breast

value: Total cells

tag: group

value: Post-treatment

value: Compound 48/80 plus Anti-PD-L1 antibody


title: CLL124

data_processing:
mRNA sequencing was generated using a HiSeq 4000 sequencer for 58 AA CLL and 292 EA CLL.  The raw RNA sequencing paired-end reads were processed through the Mayo RNA-Seq bioinformatics pipeline, MAP-RSeq version 3.1.4. Batch correction for all RNA samples was performed by removing protein coding genes with low counts, for each batch individually, resulting in 9,934 protein coding genes.  In addition, CombatSeq was run using the annotated reported race as a covariate, with CombatSeq corrected count values used for all downstream analyses.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes batch corrected gene counts each gene per sample

value: Chronic Lymphocytic Leukemia (CLL)

value: IGHV Mutated


title: OTE, air, 12 hr, batch 3, rep6

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_88_S88

value: Airway organ tissue equivalent

value: medical air

value: 12 hr


title: MS13_active2

data_processing:
All raw fastq files were processed with the Nanostring GeoMxNGSPipeline v2.3.3.10, and counts per gene were exported as Nanostring DCC files per sample.
Assembly: hg38
Supplementary files format and content: Nanostring GeoMx DCC files with read counts per gene
Library strategy: Spatial Transcriptomics

value: Brain, MS Autopsie

value: CD68 positive

value: active center


title: MS13_active1


title: C48/80 + Anti-PD-L1, Replicate5, RNA-seq

description:
C48/80 + Anti-PD-L1_Rep5
Mm_bulk.counts.xls


title: CLL122


title: 2-Nab-PTX+Anti-PD-L1, Replicate6, RNA-seq

description:
2-Nab-PTX+Anti-PD-L1_Rep6
Mm_bulk.counts.xls

value: Nab-paclitaxel plus Anti-PD-L1 antibody


title: OTE, air, 6 hr, batch 3, rep 6

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_84_S84

value: 6 hr


title: 8241-AC

city: Ann Arbor

first: Ashley

last: Calder

state: Michigan

address: 109 Zina Pitcher Place

institute: University of Michigan

description: Contains samples AC-1 through AC-4

data_processing:
Outputs were input into CellRanger (v7.1.0) to perform alignment, filtering, barcode counting, UMI counting, and construct feature-barcode matrices.
Assembly: mm10
Supplementary files format and content: TSV file of filtered barcode and feature files.
Supplementary files format and content: text-separated values and matrix files.

source_name: Extrahepatic bile duct

extract_protocol:
Extrahepatic bile ducts were isolated from sham/BDL mice 24 hours post-surgery. Cells were fixed and dissociated using the 10x Genomics Next GEM Single Cell Fixed RNA Sample Preparation Kit. Cells were pooled from 5-6 mice per each group.
Library preparation was performed according to 10x Genomics protocol using the Chromium Mouse Transcriptome Probe Set v1.0.1 which is derived from the mm10-2020-A transcriptome.

value: Extrahepatic bile duct

value: Whole tissue

value: sham and bile duct ligated mice 24-hours post-surgery


title: MS13_NAWM3

value: NAWM


title: MS13_NAWM4


title: OTE, air, 6 hr, batch 3, rep 5

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_83_S83


title: 2-Nab-PTX+Anti-PD-L1, Replicate5, RNA-seq

description:
2-Nab-PTX+Anti-PD-L1_Rep5
Mm_bulk.counts.xls

value: Breast

value: Total cells


title: CLL123

value: European Ancestry (EA)

value: Peripheral blood mononuclear cells

value: IGHV Unmutated


title: C48/80 + Anti-PD-L1, Replicate4, RNA-seq

description:
C48/80 + Anti-PD-L1_Rep4
Mm_bulk.counts.xls

value: Post-treatment

value: Compound 48/80 plus Anti-PD-L1 antibody


title: CLL120

value: Chronic Lymphocytic Leukemia (CLL)

value: IGHV Mutated


title: 2-Nab-PTX+Anti-PD-L1, Replicate4, RNA-seq

description:
2-Nab-PTX+Anti-PD-L1_Rep4
Mm_bulk.counts.xls


title: CLL121


title: MS13_NAWM2

value: Brain, MS Autopsie

value: CD68 positive


title: CLL119


title: CLL118


title: MS13_NAWM1


title: MS27c_NAWM8


title: OTE, chlorine, 6 hr, batch 3, rep 4

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_81_S81

value: Airway organ tissue equivalent

value: 20 ppm chlorine


title: OTE, air, 12 hr, batch 3, rep 5

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_87_S87

value: medical air

value: 12 hr


title: OTE, chlorine, 6 hr, batch 3, rep 5

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_82_S82

value: 6 hr


title: CLL117


title: OTE, chlorine, 0 hr, batch 3, rep 4

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_80_S80

value: 0 hr


title: Nab-PTX+Anti-PD-L1+DSCG, Replicate5, RNA-seq

description:
Nab-PTX+Anti-PD-L1+DSCG_Rep5
Mm_bulk.counts.xls

value: Breast

value: Nab-paclitaxel plus Anti-PD-L1 antibody plus DSCG


title: OTE, chlorine, 12 hr, batch 3, rep 5

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_85_S85


title: MS27c_NAWM7

value: NAWM


title: CLL116

value: European Ancestry (EA)

value: Peripheral blood mononuclear cells


title: OTE, chlorine, 0 hr, batch 3, rep 3

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_79_S79


title: MS27c_NAWM6


title: Nab-PTX+Anti-PD-L1, Replicate6, RNA-seq

description:
Nab-PTX+Anti-PD-L1_Rep6
Mm_bulk.counts.xls

value: Total cells

value: Post-treatment

value: Nab-paclitaxel plus Anti-PD-L1 antibody


title: Nab-PTX+Anti-PD-L1, Replicate5, RNA-seq

description:
Nab-PTX+Anti-PD-L1_Rep5
Mm_bulk.counts.xls


title: Nab-PTX+Anti-PD-L1+DSCG, Replicate6, RNA-seq

description:
Nab-PTX+Anti-PD-L1+DSCG_Rep6
Mm_bulk.counts.xls


title: CLL114

value: Chronic Lymphocytic Leukemia (CLL)

value: IGHV Unmutated


title: OTE, air, 24 hr, batch 3, rep 2

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_77_S77

value: 24 hr


title: MS27c_NAWM5

value: Brain, MS Autopsie

value: CD68 positive


title: MS27c_active8

value: active center


title: OTE, chlorine, 24 hr, batch 3, rep 4

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_76_S76

value: Airway organ tissue equivalent

value: 20 ppm chlorine


title: CLL113

value: IGHV Mutated


title: MS27c_active7


title: Nab-PTX+Anti-PD-L1, Replicate4, RNA-seq

description:
Nab-PTX+Anti-PD-L1_Rep4
Mm_bulk.counts.xls

value: Breast


title: DSCG, Replicate6, RNA-seq

description:
DSCG_Rep6
Mm_bulk.counts.xls

value: DSCG


title: OTE, air, 12 hr, batch 3, rep 4

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_74_S74

value: medical air

value: 12 hr


title: DSCG, Replicate5, RNA-seq

description:
DSCG_Rep5
Mm_bulk.counts.xls


title: Nab-PTX+Anti-PD-L1+DSCG, Replicate4, RNA-seq

description:
Nab-PTX+Anti-PD-L1+DSCG_Rep4
Mm_bulk.counts.xls

value: Nab-paclitaxel plus Anti-PD-L1 antibody plus DSCG


title: OTE, air, 12 hr, batch 3, rep 3

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_73_S73


title: MS27c_active5


title: OTE, chlorine, 24 hr, batch 3, rep 3

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_75_S75


title: CLL112

value: European Ancestry (EA)

value: Peripheral blood mononuclear cells


title: MS27c_active6


title: MS8_active4


title: Control-3, Replicate6, RNA-seq

description:
Control-3_Rep6
Mm_bulk.counts.xls

value: Total cells

value: Post-treatment

value: Control


title: DSCG, Replicate4, RNA-seq

description:
DSCG_Rep4
Mm_bulk.counts.xls


title: MS8_active3


title: OTE, chlorine, 12 hr, batch 3, rep 4

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_72_S72


title: OTE, air, 24 hr, batch 3, rep 3

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_78_S78

value: 24 hr


title: CLL115

value: Chronic Lymphocytic Leukemia (CLL)


title: CLL111


title: OTE, chlorine, 12 hr, batch 3, rep 3

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_71_S71


title: CLL108

value: IGHV Unmutated


title: Control-3, Replicate5, RNA-seq

description:
Control-3_Rep5
Mm_bulk.counts.xls


title: CLL107

value: African Ancestry (AA)


title: Control-3, Replicate4, RNA-seq

description:
Control-3_Rep4
Mm_bulk.counts.xls


title: OTE, air, 6 hr, batch 3, rep 3

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_69_S69

value: Airway organ tissue equivalent

value: 6 hr


title: C48/80, Replicate6, RNA-seq

description:
C48/80_Rep6
Mm_bulk.counts.xls

value: Compound 48/80


title: MS8_NAWM4

value: Brain, MS Autopsie

value: CD68 positive

value: NAWM


title: CLL106


title: OTE, chlorine, 6 hr, batch 3, rep 3

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_68_S68

value: 20 ppm chlorine


title: Control-2, Replicate6, RNA-seq

description:
Control-2_Rep6
Mm_bulk.counts.xls

value: Breast


title: OTE, chlorine, 6 hr, batch 3, rep 2

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_67_S67


title: CLL105

value: European Ancestry (EA)

value: IGHV Mutated


title: CLL110

value: Peripheral blood mononuclear cells


title: MS8_NAWM3


title: Anti-PD-L1, Replicate6, RNA-seq

description:
Anti-PD-L1_Rep6
Mm_bulk.counts.xls

value: Total cells

value: Post-treatment

value: Anti-PD-L1 antibody


title: CLL104

value: Chronic Lymphocytic Leukemia (CLL)


title: CLL109


title: MS8_NAWM2


title: Anti-PD-L1, Replicate4, RNA-seq

description:
Anti-PD-L1_Rep4
Mm_bulk.counts.xls


title: CLL102


title: OTE, air, 0 hr, batch 3, rep 4

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_66_S66

value: medical air

value: 0 hr


title: MS8_NAWM1


title: CLL103


title: OTE, air, 0 hr, batch 3, rep 3

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_65_S65

value: Airway organ tissue equivalent


title: OTE, air, 24 hr, batch 3, rep 1

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_64_S64

value: 24 hr


title: OTE, air, 6 hr, batch 3, rep 4

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_70_S70

value: 6 hr


title: MS27b_active6

value: Brain, MS Autopsie

value: active center


title: Anti-PD-L1, Replicate5, RNA-seq

description:
Anti-PD-L1_Rep5
Mm_bulk.counts.xls


title: MS8_active1

value: CD68 positive


title: Nab-PTX, Replicate6, RNA-seq

description:
Nab-PTX_Rep6
Mm_bulk.counts.xls

value: Nab-paclitaxel


title: MS8_active2


title: CLL101

value: IGHV Unmutated


title: MS27b_active5


title: OTE, chlorine, 24 hr, batch 3, rep 2

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_62_S62

value: 20 ppm chlorine


title: Nab-PTX, Replicate5, RNA-seq

description:
Nab-PTX_Rep5
Mm_bulk.counts.xls

value: Breast


title: CLL100

value: European Ancestry (EA)

value: Peripheral blood mononuclear cells

value: IGHV Mutated


title: MS27b_active4


title: CLL099


title: Nab-PTX, Replicate4, RNA-seq

description:
Nab-PTX_Rep4
Mm_bulk.counts.xls

value: Total cells

value: Post-treatment


title: MS27b_active3


title: OTE, chlorine, 24 hr, batch 3, rep 1

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_61_S61


title: OTE, air, 12 hr, batch 3, rep 2

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_60_S60

value: medical air

value: 12 hr


title: CLL098

value: Chronic Lymphocytic Leukemia (CLL)


title: Control-1, Replicate5, RNA-seq

description:
Control-1_Rep5
Mm_bulk.counts.xls

value: Control


title: CLL097


title: MS27b_active2


title: OTE, air, 12 hr, batch 3, rep 1

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_59_S59

value: Airway organ tissue equivalent


title: CLL096


title: Control-1, Replicate4, RNA-seq

description:
Control-1_Rep4
Mm_bulk.counts.xls


title: MS27b_active1

value: Brain, MS Autopsie


title: OTE, chlorine, 12 hr, batch 3, rep 2

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_58_S58


title: CLL095


title: MS27b_NAWM4

value: NAWM


title: MS27b_NAWM3

value: CD68 positive


title: OTE, chlorine, 12 hr, batch 3, rep 1

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_57_S57


title: OTE, air, 6 hr, batch 3, rep 2

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_56_S56

value: 6 hr


title: CLL094


title: MS27b_NAWM2


title: 7416-AC-10-BDL

data_processing:
Salmon was used to count the trimmed data against the transcriptome defined in Gencode vM33.
Assembly: GRCm39
Supplementary files format and content: Excel file of raw counts data.

extract_protocol:
RNA was harvested from the extrahepatic bile duct using a Qiagen Rneasy Micro Kit with a Dnase treatment.
Libraries were prepped using the SMART-Seq mRNA kit according to the manufacturer's protocol

value: Extrahepatic bile duct

value: Whole tissue

value: Bile duct ligated (BDL)


title: 7416-AC-8-BDL


title: OTE, air, 6 hr, batch 3, rep 1

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_55_S55


title: 7416-AC-6-BDL


title: CLL093

extract_protocol:
RNA was extracted using the Quagen miRNeasy Mini Kit
Illumina TruSeq Stranded mRNA library prep protocol

value: European Ancestry (EA)

value: IGHV Unmutated


title: OTE, chlorine, 6 hr, batch 3, rep 1

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_53_S53

value: 20 ppm chlorine


title: MS27b_NAWM1

extract_protocol:
5µm thick sections were cut under RNase free codtions and processed according to the GeoMx RNA FFPE workflow (MAN-10150-02) with 10min antigen retrival at 100°C and 15min Proteinase K (0.1µg/ml in PBS) at 37°C for RNA Target exposure.
Spatial Transcriptomics libararys were prepared according to GeoMx DSP workflow (MAN-10153-02)


title: CLL092

value: Peripheral blood mononuclear cells


title: Control-1, Replicate6, RNA-seq

description:
Control-1_Rep6
Mm_bulk.counts.xls

value: Breast

value: Total cells

value: Post-treatment


title: 7416-AC-4-BDL


title: OTE, air, 0 hr, batch 3, rep 2

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_52_S52

value: medical air

value: 0 hr


title: CLL091

value: Chronic Lymphocytic Leukemia (CLL)


title: 7416-AC-3-BDL


title: MS27b_mixed3

value: Brain, MS Autopsie

value: mixed rim


title: MS27b_mixed4

value: CD68 positive


title: CLL090

value: IGHV Mutated


title: OTE, chlorine, 0 hr, batch 3, rep 2

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_50_S50

value: Airway organ tissue equivalent


title: 7416-AC-5-Sham

value: Extrahepatic bile duct

value: Whole tissue

value: Sham


title: CLL089

value: European Ancestry (EA)


title: OTE, air, 0 hr, batch 3, rep 1

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_51_S51


title: OTE, chlorine, 0 hr, batch 3, rep 1

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_49_S49

value: 20 ppm chlorine


title: MS27b_mixed2


title: MS27b_mixed1


title: CLL088

value: Peripheral blood mononuclear cells

value: IGHV Unmutated


title: MS25b_NAWM4

value: NAWM


title: OTE, air, 0 hr, batch 2, rep 6

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_48_S48


title: 7416-AC-2-Sham


title: CLL087


title: OTE, air, 0 hr, batch 2, rep 5

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_47_S47


title: MS25b_NAWM3


title: OTE, chlorine, 0 hr, batch 2, rep 6

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_46_S46


title: Circumvallate Papillae, 1, scRNAseq

first: Wenlei

last: Ye

address: HNB 301, 3641 Watt Way

institute: University of Southern California

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were made using cell ranger 3.0.1
The filtered file (filtered_feature_bc_matrix.h5) were generated by removing cells (according to barcodes) with UMI (unique molecule identifier) number <500, yielding 3169 cells
Then, the data were processed using Scanpy v1.8.1. The final file (annotated_taste_cell_transcriptome.h5ad) were generated after clustering and annotation.
Assembly: mm10-PLUS
Supplementary files format and content: filtered_feature_bc_matrix.h5
Supplementary files format and content: annotated_taste_cell_transcriptome.h5ad

source_name: Circumvallate Papillae and surounding epithelial cells

extract_protocol:
Taste cells were isolated from 5~10 adult mice (10-week old) with mixed genders. In brief, Tyrode’s solution containing 1 mg/mL elastase (Worthington), 2.5 mg/mL dispase II (Roche), and 1 mg/mL trypsin inhibitor (Sigma-Aldrich) was injected between the epithelium and the muscle of the isolated tongue beneath the CV, which was then incubated for 20 min in Tyrode's solution bubbled with 95% O2/5% CO2. The epithelium was peeled off from the tongue. The small piece of epithelium containing the circumvallate papillae was further trimmed and incubated in about 200 uL Tyrode's solution containing 1 mg/mL elastase (Worthington), 2 mg/mL papain (Worthington) for 20 min at room temperature. Single cells were isolated by trituration in Tyrode’s solution with a fire-polished Pasteur pipette, followed by filtering using a 10 um cell strainer (PluriSelect).
Libarary was performed according to the manufacter's instructions (single cell 3' v3.1, 10x Genomics).

value: Taste receptor cells and epithelial cells

value: Lgr5-EGFP-IRES-creERT2 (JAX:008875) and Ai14 progeny (Jax:007914)

value: 10 weeks

tag: Sex

value: Mixed


title: 7416-AC-1-Sham


title: CLL085

source_name: Peripheral blood mononuclear cells

value: Chronic Lymphocytic Leukemia (CLL)


title: Olfactory bulb from normal fat diet-fed mouse 3

city: Hwasun, Jeollanam-do

first: Young-Kook

last: Kim

address: 264, Seoyang-ro

department: Department of Biochemistry

country: South Korea

institute: Chonnam National University Medical School

data_processing:
Following sequencing, the reads with low quality were removed or trimmed using Trimmomatic (Bolger et al., 2014).
The remaining sequences were aligned to the mouse genome (mm10) using the spliced transcripts alignment to a reference (STAR) (Dobin et al., 2013).
The normalized values of the fragments per kilobase of transcript per million mapped reads (FPKM) were calculated using Cuffnorm based on the GENCODE annotation (Release M23, GRCm38.p6) (Trapnell et al., 2012).
Assembly: Release M23, GRCm38.p6
Supplementary files format and content: Tab-delimited normalized values of the fragments per kilobase of transcript per million mapped reads (FPKM) in each sample

source_name: Olfactory bulb

extract_protocol:
RNA samples from the olfactory tissues of each mouse fed either  NFD or HFD were prepared for RNA sequencing (RNA-seq) analysis. Total RNA was extracted using an RNAiso Plus (Takara), and the integrity was identified with a 2100 bioanalyzer system (Agilent).
The RNA-seq libraries were prepared using the TruSeq Stranded Total RNA kit (Illumina) and the NovaSeq 6000 system (Illumina).

treatment_protocol: The normal fat diet (NFD: 3.5% fat, 8% carbohydrate, and 20% protein, purchased from DBL, RodFeed) and high fat diet (HFD: 45% fat, 35% carbohydrate, and 20% protein, purchased from Research Diets, D12451) mice were given ad libitum access to food and water during the experimental procedures. Two-month-old mice were fed a diet for four months, and three mice per group were used in the experiment.

value: Olfactory bulb

value: normal fat diet


title: MS25b_NAWM2

source_name: Brain, MS Autopsie

value: Brain, MS Autopsie

value: CD68 positive


title: MS25b_NAWM1


title: OTE, chlorine, 0 hr, batch 2, rep 5

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_45_S45

value: Airway organ tissue equivalent

value: 0 hr


title: Olfactory bulb from normal fat diet-fed mouse 2


title: CLL084


title: OTE, air, 24 hr, batch 2, rep 5

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_44_S44

value: medical air

value: 24 hr


title: MS25b_mixed4

value: mixed rim


title: 7416-AC-7-Sham

value: Extrahepatic bile duct

value: Whole tissue

value: Sham


title: CLL083

value: European Ancestry (EA)

value: Peripheral blood mononuclear cells

value: IGHV Unmutated


title: CLL082


title: OTE, air, 24 hr, batch 2, rep 4

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_43_S43


title: Olfactory bulb from high fat diet-fed mouse 3

value: high fat diet


title: OTE, chlorine, 24 hr, batch 2, rep 5

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_42_S42

value: 20 ppm chlorine


title: MS25b_mixed3


title: CLL081

value: Chronic Lymphocytic Leukemia (CLL)


title: MS25b_mixed2


title: Olfactory bulb from high fat diet-fed mouse 2

value: Olfactory bulb


title: CLL086


title: Olfactory bulb from normal fat diet-fed mouse 1

value: normal fat diet


title: MS2c _NAWM4

value: Brain, MS Autopsie

value: CD68 positive

value: NAWM


title: OTE, chlorine, 24 hr, batch 2, rep 4

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_41_S41

value: Airway organ tissue equivalent


title: CLL080

value: IGHV Mutated


title: OTE, air, 12 hr, batch 2, rep 6

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_40_S40

value: medical air

value: 12 hr


title: MS25b_mixed1

value: mixed rim


title: Olfactory bulb from high fat diet-fed mouse 1


title: OTE, air, 12 hr, batch 2, rep 5

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_39_S39


title: CLL078


title: control, replicate1, scRNAseq

city: Chengdu

first: chen

last: li

address: Renmin South Road

institute: Sichuan Univercity

description: BMKMANU DG1000

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the cellranger software v5.0.0 (https://www.10xgenomics.com/support/software/cell-ranger/latest)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: bone marrow

extract_protocol:
Freshly harvested whole bone marrow (BM) cells from Map4k4-cKO or control mice were isolated using ice-cold Hank's Balanced Salt Solution without Mg2+/Ca2+ (HBSSwo), supplemented with 10 mM HEPES at pH 7.2. Subsequently, the whole BM cells from control or Map4k4-cKO mice were respectively divided into two aliquots. One aliquot underwent treatment with red blood cell lysis buffer to remove erythrocytes, while the other was subjected to enrichment for c-Kit+ BM hematopoietic stem and progenitor cells (HSPCs) using magnetic bead separation. The isolated c-Kit+ BM HSPCs were then artificially mixed with the corresponding BM cells at a ratio of 2:3 to establish a combined c-Kit/BM cell population.
Library was performed according to the manufacter’s instructions (single cell 3’ protocol, BMKMANU DG1000). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the DG1000 Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added

value: bone marrow

value: bone marrow cells and ckit+ cells

value: control

value: 13-14 weeks old


title: MS2c _NAWM3


title: MS2c _NAWM2


title: OTE, chlorine, 12 hr, batch 2, rep 6

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_38_S38

data_processing:
Raw sequence reads were imported into Partek® Flow® software (Partek®) for analysis.
Cutadapt was used to trim the random barcode (4 bases) from the 5’ end and adapter (AAAAAAAAAA) from the 3’ end of the reads. Bases with a Phred quality score <20 were trimmed, and reads <15 bases in length were discarded.
High-quality reads were then aligned and quantified to the hg38 GENCODE reference database using STAR and an expectation/maximization (E/M) algorithm, respectively.
Transcript-level counts were summed to gene level, normalized with the median-of-ratios method used in DESeq2, and log2-transformed.
Assembly: hg38
Supplementary files format and content: Text file includes raw counts for 46 samples in batch 1.
Supplementary files format and content: Text file includes raw counts for 90 samples in batches 2 and 3.
Supplementary files format and content: Text file includes normalized and log2-transformed gene counts for 136 samples.


title: MS2c _NAWM1


title: CLL077

first: Jessica

last: Hohenstein

value: European Ancestry (EA)

value: Peripheral blood mononuclear cells

value: IGHV Unmutated


title: GEX_Y665F_BM-rep1

city: Bethesda

first: Hye Kyung

last: Lee

state: MD

address: 8 CENTER DR RM 107

department: National Institute of Diabetes and Digestive and Kidney (NIDDK)

institute: National Institutes of Health (NIH)

description: transcriptomic single cell

data_processing:
Raw sequencing data was aligned using Cellranger (version 5.0). The quality control, normalization, dimension reduction, cell clusters, UMAP projection, and cell type annotation were performed using Seurat (version 4.0). Assembly: mm10
Assembly: mm10
Supplementary files format and content: barcodes, features, matrix

growth_protocol: Single-cell suspensions were then immediately loaded on the 10X Genomics Chromium Controller with a loading target of 10,000 cells.

extract_protocol:
The downstream library constructions were performed using the Chromium Next GEM Single Cell 3′ Kit v3.1 (Dual Index) according to the manufacturer’s instructions (10x Genomics).
Libraries for sequencing were prepared using standard 10x genomics protocols.

value: Bone marrow

tag: Stage

value: 2-month-old age


title: OTE, chlorine, 12 hr, batch 2, rep 5

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_37_S37

extract_protocol:
Each frozen OTE was briefly incubated in QIAzol Lysis Reagent (QIAGEN, Inc.), and a pipette was used to remove and discard the membrane.
OTEs were then homogenized 2 x 30 seconds at 2,200 rpm using a Precellys® 2ml Tissue Homogenizing Mixed Beads Kit (Cayman Chemical) and Mini-BeadBeater-96 Cell Disruptor (BioSpec Products).
Homogenized samples were centrifuged 1 minute at 2,000 x g to remove particulate debris, and RNA was purified from lysed cells using QIAGEN’s miRNeasy Micro Kit with the optional DNase I treatment.
Quantity of RNA extracts was determined using the DeNovix RNA Assay Kit and DS-11 FX+ Spectrophotometer/Fluorometer (DeNovix®).
RNA integrity was determined using an Agilent 4200 TapeStation System (Agilent).
cDNA libraries were prepared from 50 ng of each RNA extract using a NEXTFLEX® Combo-Seq™ mRNA/miRNA Kit (PerkinElmer®) and Sciclone® G3 NGSx Workstation (PerkinElmer®).
Libraries were quantified using a KAPA Library Quantification Kit (Roche Sequencing and Life Science), with average fragment length determined by a 4200 TapeStation System (Agilent).
Libraries were normalized prior to pooling, and the pooled libraries were sequenced using an Illumina® NovaSeq 6000 System (Illumina®, Inc.), generating 76-bp single-end reads.

value: 20 ppm chlorine


title: GEX_Y665F_BM-rep2

description: transcriptomic single cell


title: CLL076

city: Rochester

address: 200 1st St SW

institute: Mayo Clinic

tag: ancestry

value: Chronic Lymphocytic Leukemia (CLL)


title: MS2c _active2

city: Münster

first: Carolin

last: Walter

address: Domagkstraße 9

tag: tissue

value: Brain, MS Autopsie

value: CD68 positive

value: active center


title: CLL074

tag: disease state


title: CLL075

tag: genotype

value: IGHV Mutated


title: MS2c _active4

tag: cell type


title: GEX_Y665H_BM-rep1

description: transcriptomic single cell


title: CLL079


title: MS2c _active3

tag: location


title: OTE, chlorine, 6 hr, batch 2, rep 6

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_34_S34

value: Airway organ tissue equivalent

value: 6 hr


title: Map4k4-cko, replicate1, scRNAseq

description: BMKMANU DG1000

value: bone marrow


title: GEX_WT_BM-rep2

description: transcriptomic single cell

value: WT


title: OTE, air, 6 hr, batch 2, rep 6

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_36_S36

value: medical air


title: CLL072


title: GEX_Y665H_BM-rep2

description: transcriptomic single cell


title: OTE, air, 6 hr, batch 2, rep 5

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_35_S35


title: OTE, chlorine, 6 hr, batch 2, rep 5

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_33_S33


title: MS21_NAWM4

value: NAWM


title: CLL073

value: European Ancestry (EA)


title: MS21_NAWM3


title: CLL071

value: Peripheral blood mononuclear cells


title: GEX_Y665F_Spleen-rep1

description: transcriptomic single cell

source_name: Spleen

value: Spleen


title: CLL070


title: GEX_WT_BM-rep1

description: transcriptomic single cell

value: Bone marrow


title: OTE, chlorine, 0 hr, batch 2, rep 3

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_31_S31

source_name: Airway organ tissue equivalent

value: 0 hr


title: GEX_Y665H_Spleen-rep1

description: transcriptomic single cell

value: 2-month-old age


title: MS21_NAWM2


title: OTE, air, 24 hr, batch 2, rep 3

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_30_S30

value: 24 hr


title: CLL069

value: Chronic Lymphocytic Leukemia (CLL)


title: GEX_WT_Spleen-rep1

description: transcriptomic single cell


title: MS21_NAWM1

value: Brain, MS Autopsie

value: CD68 positive


title: OTE, chlorine, 24 hr, batch 2, rep 3

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_28_S28

value: 20 ppm chlorine


title: MS2c _active1

value: active center


title: CLL067

value: IGHV Mutated


title: MS21_brl3

value: BRL rim


title: Skin_biopsy_Control/Pyoderma_case1

type: RNA

city: North Grafton

first: Jillian

middle: M

last: Richmond

state: Massachusetts

address: 200 Westboro Road

department: Comparative Pathobiology

institute: Tufts Cummings School of Veterinary Medicine

description: 7yo_neuteredMale_Golden Retriever

hyb_protocol: Hybridizations were performed per Nanostring manufacturer's protocol overnight for 18h in a BioRad C1000 touch thermocycler

scan_protocol: Cartridges were run on a Nanostring Sprint machine

data_processing: Data were analyzed with nSolver software version 4.0

label: fluorescent probe

organism: Canis lupus familiaris

source_name: archival skin biopsy

label_protocol: Probe labeling was performed per Nanostring manufacturer's protocol

extract_protocol: RNA was isolated from 30 micron curls from archival skin biopsies using Qiagen FFPE RNEasy kit with Deparaffinization solution per the manufacturer's instructions.

tag: disease status

value: Control/Pyoderma

value: neuteredMale

tag: breed

value: Golden Retriever


title: CLL065

value: European Ancestry (EA)


title: OTE, chlorine, 0 hr, batch 2, rep 4

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_32_S32

value: Airway organ tissue equivalent

tag: ote batch


title: MS21_brl2


title: CLL066

value: Peripheral blood mononuclear cells

value: IGHV Unmutated


title: OTE, air, 12 hr, batch 2, rep 4

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_26_S26

tag: exposure

value: medical air

value: 12 hr


title: MS21_brl1


title: CLL064


title: Skin_biopsy_Control/Pyoderma_case2

description: 9yo_neuteredMale_German Shepherd

value: German Shepherd


title: Skin_biopsy_Control/CPV_case1

value: Control/CPV

value: spayedFemale

value: Pomeranian


title: CLL063

value: Chronic Lymphocytic Leukemia (CLL)


title: OTE, air, 12 hr, batch 2, rep 3

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_25_S25

tag: time point


title: MS25a_mixed4

value: Brain, MS Autopsie

value: CD68 positive

value: mixed rim


title: OTE, chlorine, 12 hr, batch 2, rep 4

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_24_S24

value: 20 ppm chlorine


title: MS25a_mixed3


title: OTE, chlorine, 12 hr, batch 2, rep 3

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_23_S23


title: CLL068

value: IGHV Mutated


title: CLL062


title: OTE, air, 24 hr, batch 2, rep 2

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_29_S29

value: 24 hr


title: MS21_brl4

value: BRL rim


title: Skin_biopsy_EM_case3

value: EM


title: Skin_biopsy_EM_case1


title: OTE, chlorine, 24 hr, batch 2, rep 2

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_27_S27

value: Airway organ tissue equivalent


title: OTE, air, 6 hr, batch 2, rep 4

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_22_S22

value: 6 hr


title: TCR_Y665F_homo_LN-rep2

description: transcriptomic single cell

source_name: Lymph node

value: Lymph node

tag: strain

value: 2-month-old age


title: CLL061

value: European Ancestry (EA)

value: Peripheral blood mononuclear cells


title: MS25a_mixed1


title: MS25a_mixed2


title: CLL060

value: IGHV Unmutated


title: MS25a_NAWM4

value: NAWM


title: Skin_biopsy_EM_case4

tag: age

value: spayedFemale

value: Boxer


title: OTE, chlorine, 6 hr, batch 2, rep 4

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_20_S20


title: TCR_Y665F_homo_LN-rep1

description: transcriptomic single cell


title: TCR_Y665F_het_LN-rep3

description: transcriptomic single cell


title: CLL059

value: Chronic Lymphocytic Leukemia (CLL)


title: OTE, chlorine, 6 hr, batch 2, rep 3

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_19_S19


title: TCR_Y665F_het_LN-rep2

description: transcriptomic single cell


title: OTE, air, 0 hr, batch 2, rep 4

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_18_S18

value: medical air

value: 0 hr


title: MS25a_NAWM2

value: Brain, MS Autopsie

value: CD68 positive


title: Skin_biopsy_EM_case2


title: CLL057

value: IGHV Mutated


title: TCR_Y665F_het_LN-rep1

description: transcriptomic single cell


title: OTE, air, 0 hr, batch 2, rep 3

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_17_S17


title: MS25a_NAWM1


title: MS1b_mixed4

value: mixed rim


title: TCR_WT_LN-rep1

description: transcriptomic single cell

value: WT


title: CLL055


title: TCR_WT_LN-rep2

description: transcriptomic single cell


title: OTE, air, 24 hr, batch 2, rep 1

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_16_S16

value: Airway organ tissue equivalent

value: 24 hr


title: OTE, air, 6 hr, batch 2, rep 3

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_21_S21

value: 6 hr


title: OTE, chlorine, 24 hr, batch 2, rep 1

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_13_S13

value: 20 ppm chlorine


title: MS1b_mixed3


title: OTE, air, 12 hr, batch 2, rep 2

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_12_S12

value: 12 hr


title: CLL054

value: European Ancestry (EA)

value: Peripheral blood mononuclear cells

value: IGHV Unmutated


title: CLL053


title: GEX_Y665F_homo_LN-rep2

description: transcriptomic single cell

value: Lymph node

value: 2-month-old age


title: MS1b_mixed2


title: CLL058

value: Chronic Lymphocytic Leukemia (CLL)


title: OTE, air, 12 hr, batch 2, rep 1

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_11_S11

value: medical air


title: GEX_Y665F_homo_LN-rep1

description: transcriptomic single cell


title: MS25a_NAWM3

value: Brain, MS Autopsie

value: NAWM


title: CLL052

value: IGHV Mutated


title: GEX_Y665F_het_LN-rep3

description: transcriptomic single cell


title: MS1b_NAWM8

value: CD68 positive


title: CLL051


title: MS1b_NAWM7


title: MS1b_mixed1

value: mixed rim


title: CLL056


title: OTE, chlorine, 12 hr, batch 2, rep 1

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_09_S9

value: Airway organ tissue equivalent


title: CLL050


title: MS1b_NAWM6


title: GEX_Y665F_het_LN-rep1

description: transcriptomic single cell


title: OTE, air, 6 hr, batch 2, rep 2

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_08_S8


title: GEX_Y665F_het_LN-rep2

description: transcriptomic single cell


title: CLL049


title: MS1b_NAWM5


title: CLL048


title: OTE, air, 6 hr, batch 2, rep 1

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_07_S7


title: MS1b_active4

value: active center


title: OTE, chlorine, 6 hr, batch 2, rep 2

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_06_S6

value: 6 hr


title: GEX_WT_LN-rep1

description: transcriptomic single cell

value: WT


title: GEX_WT_LN-rep2

description: transcriptomic single cell


title: OTE, chlorine, 6 hr, batch 2, rep 1

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_05_S5

value: 20 ppm chlorine


title: MS1b_active3


title: CLL046

value: European Ancestry (EA)


title: OTE, chlorine, 12 hr, batch 2, rep 2

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_10_S10

value: 12 hr


title: MS1b_active2


title: CLL047

value: Peripheral blood mononuclear cells


title: Y665F_Splenocyte-rep6

data_processing:
The fastq files were subjected to QC analyses using the FastQC tool (version 0.11.9). Quality filtering and alignment of the raw reads was done using Trimmomatic (version 0.36) and subsequently aligned to the reference genome mm10 applying STAR RNA-seq aligner (version 2.7.11b), Samtools (version 1.9) and Picard (version 2.9.2). Htseq (version 0.9.1) was applied to calculate raw read counts.
Assembly: mm10
Supplementary files format and content: raw read counts from RNA-seq samples

growth_protocol: Total RNA-seq was done for the splenocyte and cytokine-stimulated T cells of wild-type and mutant mice carrying a point mutation in Stat5b-Y665.

extract_protocol:
Total RNA was extracted from frozen mammary tissue from mice and purified with RNeasy Plus Mini Kit (Invitrogen, 12183018A). Ribosomal RNA was removed from 1ug of total RNAs and cDNA was synthesized using SuperScript III (Invitrogen). Libraries for sequencing were prepared according to the manufacturer’s instructions with TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold (Illumina, RS-122-2301) and paired-end sequencing was done with a HiSeq 3000 or Novaseq 6000 instrument (Illumina).
Libraries for sequencing were prepared using standard Illumina protocols.

value: Spleen


title: CLL045

value: IGHV Unmutated


title: OTE, air, 0 hr, batch 2, rep 1

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_03_S3

value: 0 hr


title: OTE, air, 0 hr, batch 2, rep 2

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_04_S4

value: medical air


title: Y665F_Splenocyte-rep5

value: 2-month-old age


title: OTE, chlorine, 0 hr, batch 2, rep 2

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_02_S2


title: CLL043

value: Chronic Lymphocytic Leukemia (CLL)


title: CLL042


title: MS28_NAWM3

value: Brain, MS Autopsie

value: NAWM


title: OTE, chlorine, 0 hr, batch 2, rep 1

description:
Batches2and3_90samples_rawcounts.txt
Normalized Count Data_136samples.txt
OTE_01_S1


title: MS28_NAWM4

value: CD68 positive


title: CLL041

value: IGHV Mutated


title: Y665F_Splenocyte-rep4


title: Y665F_Splenocyte-rep7


title: CLL044


title: CLL040


title: MS28_NAWM1


title: SUM159 cell SMARCA4 shRNA knockdown with rescue vector control spheroids

city: Plainsboro

first: Yong

last: Wei

state: NJ

address: LTL227 Wathington Road

department: Molecular Biology

institute: Princeton University

data_processing:
Raw reads were aligned to human genome hg38 with Bowtie 2 (Langmead and Salzberg 2012) with -X 2000 and other parameters set as default, and duplicate reads were filtered. Reads from the non-targeting group (NTC) and the rescue group (KD2 + SMARCA4 OE) were merged. Peak calling was performed using the merged files with MACS 3.0 (Zhang et al. 2008) with default settings. Bam files were converted to bedgraphs and normalized to CPM using bedtools. Bedgraphs were converted to tdf files and visualized with IGV (Robinson et al. 2011). Bam files were converted to bigwig files and normalized to RPKM with Deeptools (Ramírez et al. 2016). TSS plots were generated using Deeptools function plotHeatmap.
Assembly: hg38
Supplementary files format and content: Reads from the non-targeting group (NTC) and the rescue group (KD2 + SMARCA4 OE) were merged. Peak calling was performed using the merged files with MACS 3.0 (Zhang et al. 2008) with default settings.

growth_protocol: SUM159 was cultured with Ham’s F12 (Corning) , supplemented with 10% heat-inactivated fetal bovine serum (FBS, Gemini), hydrocortisone (500 ng/ml, Sigma), insulin (10 µg/ml, Novoprotein), 3D spheroid samples were used for ATAC-seq. 120K cells were seeded with a density of 12K/ml cells to 10 cm ultra-low attachment plates and cultured in spheroid media for 9 days.

extract_protocol:
Spheroids were dissociated with Accumax (Sigma) to generate single cell suspension. Dead cells were removed with the dead cell removal kit (Miltenyi, 130-090-101) to achieve at least 85% of live cells assessed by flow cytometry.
ATAC-seq library was prepared with Nextera DNA library preparation kit (Illumina)

tag: cell line

value: Breast cancer

tag: culture system

value: 3D spheroid


title: MS28_NAWM2


title: MS1b_active1

value: active center


title: CLL039


title: SUM159 cell SMARCA4 shRNA knockdown spheroids


title: Y665H_Splenocyte-rep5


title: MS28_mixed4

value: mixed rim


title: Y665F_Splenocyte-rep1


title: Y665H_Splenocyte-rep4


title: Y665H_Splenocyte-rep3


title: SUM159 cell non-targeting shRNA control spheroids

value: NTC


title: CLL037

value: European Ancestry (EA)


title: MS28_mixed2


title: MS28_mixed3


title: SUM159 cell SMARCA4 KD1 2D culture

data_processing:
The library pools were denatured and sequenced on Illumina NovaSeq 6000 using the S Prime flowcells as pair-end 65 nt reads according to the manufacturer’s protocol.  Raw sequencing reads were filtered by Illumina NovaSeq Control Software, only the Pass-Filter (PF) reads were de-multiplexed allowing 1 mismatch and used for further analysis.
Demultiplexed raw sequence file (FASTQ) were analyzed using Partek® Flow® software package. Raw reads were aligned using STAR 2.7.8a, followed by quantification to annotation model hg38 – Ensembl Transcripts release 110. After noise filtering, counts were normalized as CPM+1
Assembly: hg38 – Ensembl Transcripts release 110.
Supplementary files format and content: Tab-Delimited text file with CPM+1 value for each sample

growth_protocol: SUM159 was cultured with Ham’s F12 (Corning) , supplemented with 10% heat-inactivated fetal bovine serum (FBS, Gemini), hydrocortisone (500 ng/ml, Sigma), insulin (10 µg/ml, Novoprotein), For 3D spheroid samples, 100K cells were seeded with a density of 10K/ml cells to 10 cm ultra-low attachment plates and cultured in spheroid media for 8-10 days before harvesting.  For 2D samples, 150K cells were seeded to 6 cm regular culture plates and cultured for 2 days before harvesting.

extract_protocol:
Total RNA were extracted using Qiagen RNAeasy kit.
The integrity of total RNA samples were assessed on Bioanalyzer 2100 using RNA 6000 Pico chip (Agilent Technologies, CA).  Messenger RNA was enriched from these samples using QIAseq FastSelect - rRNA HMR Kit (Qiagen, CA), fragmented and converted to cDNA and Illumina sequencing library using the PrepX RNA-seq library preparation protocol on the Apollo 324TM NGS Library Prep System (Takara Bio, CA).

value: 2D monolayer


title: Y665F_Splenocyte-rep3

value: Spleen


title: SUM159 cell non-targeting shRNA control 2D culture


title: Y665H_Splenocyte-rep1


title: SUM159 cell SMARCA4 shRNA knockdown with SMARCA4 expression rescue spheroids


title: MS28_mixed1


title: CLL035

value: Peripheral blood mononuclear cells

value: IGHV Unmutated


title: CLL036


title: WT_Splenocyte-rep4

value: WT


title: SUM159 cell SMARCA4 KD2 spheroids, repeat 3


title: SUM159 cell SMARCA4 KD2 spheroids, repeat 2


title: MS5c _NAWM4


title: CLL034


title: WT_Splenocyte-rep3

value: 2-month-old age


title: CLL038

value: Chronic Lymphocytic Leukemia (CLL)


title: CLL033


title: SUM159 cell SMARCA4 KD2 spheroids, repeat 1


title: MS5c _NAWM2

value: Brain, MS Autopsie


title: MS5c _NAWM3

value: NAWM


title: WT_Splenocyte-rep2


title: CLL032


title: SUM159 cell SMARCA4 KD1 spheroids, repeat 3


title: MS5c _NAWM1

value: CD68 positive


title: Y665H_Splenocyte-rep2


title: MS5c _brl4

value: BRL rim


title: CLL031


title: SUM159 cell SMARCA4 KD1 spheroids, repeat 2

value: Breast cancer


title: Y665F_T-rep3

source_name: T cells from spleen

value: T cells from spleen


title: SUM159 cell SMARCA4 KD1 spheroids, repeat 1

value: 3D spheroid


title: CLL030


title: SUM159 cell non-targeting shRNA control spheroids, repeat 3


title: CLL029


title: Y665F_T-rep1


title: MS5c _brl1


title: Y665F_T_IL-rep4


title: MS27a_active8

value: active center


title: SUM159 cell non-targeting shRNA control spheroids, repeat 1

value: NTC


title: Y665F_Splenocyte-rep2


title: Y665F_T_IL-rep3


title: Y665F_T_IL-rep2


title: MS27a_active6


title: MS27a_active7


title: CLL026

value: European Ancestry (EA)

value: IGHV Mutated


title: CLL027


title: MS5c _brl2


title: Y665F_T-rep2


title: WT_Splenocyte-rep1

value: Spleen


title: Y665F_T_IL-rep1


title: Y665H_T_IL-rep4


title: MS5c _brl3


title: CLL025

value: Peripheral blood mononuclear cells


title: MS27a_active5


title: CLL024

value: IGHV Unmutated


title: MS27a_NAWM8


title: Y665H_T_IL-rep3


title: MS27a_NAWM7


title: CLL022


title: SUM159 cell non-targeting shRNA control spheroids, repeat 2


title: CLL028


title: Y665H_T_IL-rep2


title: MS27a_NAWM6


title: CLL021


title: Y665H_T_IL-rep1


title: CLL020