title: CD8_RIP

city: Houston

first: Jia

last: Li

address: 2121 W HOLCOMBE BLVD

department: CEDP

institute: Guangzhou Medical University

description: Library name: CD8_RIP

data_processing:
For ATAC-seq:Bowtie2 with ‘-very-sensitive’ option was used to map the high-quality reads to mm10 version of mice genome. The uniquely properly paired mapped reads were extracted for downstream analysis. MACS2 with the ‘-nomodel’ and ‘-extsize 147′ was used to call ATAC peaks. DESeq2 was used to identify significantly differential (FDR <=0.05) ATAC peaks between different conditions.
For cuttag:Cutadapt was used to remove low quality bases and adaptors. Clean reads were mapped to mm10 genome by using bowtie2. MACS2 was used to call cut&tag peaks with default settings. Bam2wig.py script was used to generate bigwig tracks for visualization in IGV5.
For HiC: HiC-Pro was used to perform reads alignment, quality control, and pairing reads. The h5 file was generated by using HiC-Pro. DeepLoops was applied to predict loops.
For RNA-seq: Uniquely mapped reads were retained for gene-level quantification using the htseq-count function from the HTSeq package.
For m3C-seq, raw sequencing reads were first subjected to quality control using FastQC, and adapter trimming was performed with cutadapt (v1.9.1). High-quality reads were then aligned to the mouse reference genome (mm10) using bowtie2 with default parameters. Raw counts and coverage counts were calculated by bedtools (v2.24) software and in-house scripts, then ratio (define as: count/coverage) and fc (defined as: treat-methyl-ratio/Input-methyl-ratio)(Schwartz et al., 2014) were also calculated.
For RIP-seq, after 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3), the high quality reads were aligned to the reference genome with hisat2 software (v2.0.4). Binding sites on RNAs (peaks) were identified by MACS2 software. Then, HTSeq software (v0.9.1) was used to get the gene level raw count as the expression profiling
Assembly: mm10
Supplementary files format and content: bigwig and normalized coverage signal
Supplementary files format and content: h5 format contain hic information
Supplementary files format and content: txt and counts

source_name: Tumor

extract_protocol:
For ATAC-seq, the extracted nuclei were re-suspended fragmented buffer including 1.5 μL transposome (novoprotein N248), and incubated at 37 oC for 30 min. For CUT&Tag, cells were sorted enriched by ConA-magnetic beads, and then incubated overnight with antibody. The next day, beads were washed and incubated with anti-rabbit secondary antibody. Then the beads were washed and incubated with proteinA/G-Tnp transposome in Chitag. Next, cells were resuspended in 100 μL Tagmentation buffer (10 mM MgCl in Chitag Buffer) and incubated at 37 °C for 1 hr. The tagmentation was terminated by adding 1 μL of 10% SDS at 55 °C for 10 min. For HiC, the sorted cells were crosslinked with 1% formaldehyde and lysed in 1 ml lysis buffer. The resulting chromatin was then digested with NUB I (NEB) restriction enzymes at at 37 °C overnight. The DNA ends were blunted and labelled with biotin by Klenow DNA polymerase, followed by ligation using T4 DNA ligase (NEB). After reverse crosslinking, DNA was fragmented by sonication. For RNA-seq, RNA was extracted using the Direct-zol RNA MiniPrep kit (Zymo Research). A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations.For m3C-seq, RNA samples were subjected to alkaline hydrolysis for fragmentation. RNA fragments were dephosphorylated with antarctic phosphatase (NEB, USA) and then incubated in 1M aniline for cleavage. For RIP-seq, the RNA immunoprecipitation assay was carried out with GenSeq RIP kit (GenSeq Inc.) according to the manufacturer’s instructions. rRNAs were removed by using GenSeq rRNA Removal Kit (GenSeq, Inc.).
For ATAC-seq, the products were purified with tagment DNA extract beads (novoprotein N245), and then amplified by PCR for 14 cycles with NovoNGS index kit for illumine (N239). For CUT&Tag, the DNA fragments added 1 μL spike in (Vazyme) and were extracted by DNA extract beads, then amplified by PCR for 12 cycles with TruePrep index kit for illumine. For HiC, the DNA fragments were then end-repaired and the biotinylated DNA fragments were captured using Dynabeads MyOne Streptavidin C1 beads (Invitrogen, Termo Fisher Scientifc). The DNA on beads was ligated to the Truseq adaptors and amplifed with PCR for library construction. For RNA-seq, Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB) following manufacturer’s recommendations.For m3C-seq, RNA libraries were constructed with GenSeq® Small RNA Library Prep Kit (GenSeq Inc.) by following the manufacturer’s instructions.For,RIP-seq, RNA libraries were constructed by using rRNA-depleted RNAs with GenSeq Low Input RNA Library Prep Kit (GenSeq, Inc.) according to the manufacturer’s instructions.

value: Tumor


title: Whole blood, healthy control 8

status: Public on Mar 18 2026

type: SRA

city: Westmead

first: Nader

last: Aryamanesh

state: NSW

address: 214 Hawkesbury Rd

department: Bioinformatics

country: Australia

institute: CMRI

description: Library name: Control_8

library_source: transcriptomic

data_processing:
RNA-Seq raw fastq files were quality checked by FastQC (version 0.11.9), and trimming of adapters and quality filtering were then performed by AdapterRemoval (version 2.3.2). Trimmed and quality filtered paired-end reads were aligned to the human GRCh38 reference genome by using STAR (version 2.7.9a) with default parameters. Gene expression was quantified by counting the number of reads aligned to each Ensembl gene model using featureCounts (version 2.0.1).
Assembly: Human hg38
Supplementary files format and content: tsv file for read count matrix from the same samples.

molecule: total RNA

organism: Homo sapiens

source_name: Whole blood

growth_protocol: Stored at -80 degrees.

extract_protocol:
This workflow includes RNA extraction from PAXgene™ blood RNA tubes, depletion of ribosomal RNA via hybrid capture (Illumina Ribo-Zero), and Illumina TruSeq Stranded Total RNA Library Preparation (input 200-1000 ng of Total RNA). The stranded RNA samples are sequenced on the Illumina NovaSeq 6000 next generation sequencing platform (2 x 150 base pair) for a depth of 50 million paired end reads. The cleaned sequence reads were aligned against the Homo sapiens genome (Build version hg38), and the STAR aligner (v2.5.3a) was used to map unique reads to the genomic sequences14.
FASTQ files were processed into gene and transcript counts

treatment_protocol: Whole blood stored at -80 degrees within 1 hour of collection.

tag: tissue

value: Whole blood

tag: age

tag: treatment

value: Control

tag: Sex

value: F


title: Patient GHD28-Visit-2 [EB_28_V2B]

city: Chicago

first: Ajay

last: Rana

state: IL

address: 840 S. Wood Street

department: Surgery

country: USA

institute: University of Illinois at Chicago

description:
Library name: EB_28_V2B
Patient GHD28-Visit-2

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Assembly: GRCh38,hg38
Supplementary files format and content: analysis results; AR_FPKM.xls.txt

source_name: skeletal muscle

extract_protocol:
RNA was isolated using RNAeasy mini kit (Qiagen)
The library was checked with Qubit and real-time PCR for quantification and a bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

value: skeletal muscle

tag: treatment/time point

value: after 12 months of supervised, resistance-based muscle therapy


title: CD8-m3C_KO-2

state: Texas

description: Library name: CD8-m3C_KO-2

library_source: other

molecule: other

organism: Mus musculus


title: sperm, control lineage, male, f0 generation, biol rep2

city: Columbia

first: Ramji

last: Bhandari

state: MO

address: 1200 University Ave

department: Division of Biological Sciences

institute: University of Missouri

description: Library name: Control lineage, f0 generation, sperm 2

library_source: genomic

data_processing:
The “nf-core/methylseq” (v1.6.1) automated bioinformatic pipeline for Methylation (Bisulfite) sequencing data was used to analyze all the samples. In particular, the “nf-core/methylseq” pipeline's "Bismark workflow" was used to align the reads on the medaka genome (assembly ASM223467v1).
The Bismark coverage files of each individual sample, which describe the methylation percentages and overall coverages of methylated and unmethylated cytosines at each CpG location, were collected for further downstream analyses using methylKit R package. The samples of all the generations (f0, f1 and f2) were processed in the same way.
Assembly: ASM223467v1
Supplementary files format and content: Bismark Coverage file (*.bismark.cov.gz) for each sample

molecule: genomic DNA

organism: Oryzias latipes

source_name: sperm

extract_protocol:
DNA was extracted by using Quick-DNA Microprep Kit following manufacturer's protocol
DNA library was prepared by using NEBNext® Ultra™ II FS DNA Library Prep Kit for Illumina following manufacturer's protocol

value: sperm

tag: generation

value: male

value: control


title: Whole blood, healthy control 1

description: Library name: Control_1

value: M


title: Before pulldown_Rep 2

city: Nijmegen

first: Daphne

middle: Ai Lin

last: van den Homberg

address: Heyendaalseweg

department: Physical Organic Chemistry

country: Netherlands

institute: Radboud University

description:
Library name: DvH_14
BP2

data_processing:
RNAFramework
Sequences were trimmed and mapped to ASM584v2_genomic.gff using RNAFrameworks rf-map using the default parameters
Read count was performed using featureCounts
Assembly: NC_000913.2
Supplementary files format and content: CSV file includes raw counts for each sample

organism: Escherichia coli

growth_protocol: Bacteria were cultured at 37 °C in liquid Luria Broth (LB) medium until OD600=0.8. RNA was extracted afterwards using the Zymo Quick RNA miniprep kit. RNA was incubated with the respective probes for photoaffinity labeling and downstream analysis

extract_protocol:
RNA was isolated after desthiobiotin-streptavidin bead pulldown using (95% formamide/H2O, 10 mM EDTA) elution buffer . Eluted RNA samples were cleaned up using RNA Clean and Concentrator-5 (Zymo) and dissolved in nuclease-free water. >25 ng of RNA was used per sample for construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using the KAPA RNA Evoprep kit following manufacturer's protocols

treatment_protocol: RNA was isolated from the bacteria. Isolated RNA was used to incubate Ribocil or control photoaffinity probes in folding buffer at 37 oC for 30 min and irradiated with 365 nm light. RNA was isolated and a desthiobiotin handle was ligated to the probe 1 and 3 RNA complexes. Desthiobiotin-Streptavidin bead enrichments were performed on purified RNA and next-generation RNA library preparation and sequencing were performed.

tag: cell type

value: RNA before Streptavidin-pulldown


title: brincidofovir treated, replicate 5

type: RNA

city: Singapore

first: Jason

middle: Yongsheng

last: Chan

address: 30 Hospital Blvd

country: Singapore

institute: National Cancer Centre Singapore

description: NanoString Mouse Immunology Panel

hyb_protocol: Hybridation was performed as per manufacturer's protocol

scan_protocol: Analysed in the nCounter Digital Analyser using default protocol

data_processing: Normalization was performed using the nSolver 4.0 Advanced Analysis software using default parameters

label: not provided

source_name: EL4-C57BL6N syngeneic mouse tumor model

label_protocol: 100 ng total RNA was used as input into the hybridisation step and carried out according to the manufacturer's protocol

extract_protocol: Total RNA was extracted using RNeasy Mini Kit (Qiagen) from snap frozen EL4 cell-line derived tumors engrafted on C57BL6N mice and analyzed using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA).

value: brincidofovir treated


title: sperm, control lineage, male, f0 generation, biol rep1

description: Library name: Control lineage, f0 generation, sperm 1


title: CD8-m3C_KO-1

description: Library name: CD8-m3C_KO-1


title: MDA-MB-231, Entinostat-treatment, 24h, biol rep 2, H2A.Zac, ChIP

city: St. Louis

first: Rashmi

last: Karki

address: 660 S. Euclid Ave

institute: Washington University in St. Louis

description: Library name: Sample 11

data_processing:
ChIP-Seq datasets for histone H2A.Z ac were processed using ENCODE Uniform Processing Pipeline (v2.2.0). Raw sequencing reads (FASTQ) from replicates and their input controls were aligned to the human reference genome hg38 using Bowtie2. Low-quality reads, duplicates and non-uniquely mapped reads were removed using SAMtools. BAM files are used to create bigwig signal tracks using deepTools and were normalized as counts per million. Peak calling was performed using MACS 2.1.0.
Assembly: hg38
Supplementary files format and content: bigwig (except for input)

growth_protocol: The HeLa cell and MDA-MB-231 cells were cultured in Dulbecco’s modified Eagle’s medium  supplemented with 10% fetal bovine serum, penicillin (100 U/mL), streptomycin (100 mg/mL), and 2 mM GlutaMAX Supplement.

extract_protocol:
Chromatin was crosslinked by adding formaldehyde to the medium to a final concentration of 1% for 10 minutes at room temperature and sonicated using E220 focused-ultrasonicator (Covaris).
Fragments were sequenced on an Illumina NovaSeq X plus (300 cycles).

treatment_protocol: The cells were treated with 1µM of Entinostat for 24h. Cells were incubated at 37 °C with 5% CO2 before harvesting.

tag: cell line

value: Entinostat

tag: time


title: CD8-m3C_WT-1

description: Library name: CD8-m3C_WT-1


title: Whole blood, healthy control 2

description: Library name: Control_2


title: Control probe 4_pulldown_Rep 3

description:
Library name: DvH_12
CD3

value: RNA treated with photoaffinity Control probe 4, followed by Streptavidin-pulldown


title: MDA-MB-231, Entinostat-treatment, 24h, Input

description: Library name: Sample 12


title: Patient GHD28-Visit-1 [EB_28_V1C]

description:
Library name: EB_28_V1C
Patient GHD28-Visit-1

value: before 12 months of supervised, resistance-based muscle therapy


title: Tex_RNA_KO_2

description: Library name: Tex_KO_2


title: Patient GHD28-Visit-1 [EB_28_V1B]

description:
Library name: EB_28_V1B
Patient GHD28-Visit-1


title: Whole blood, PANS7, Week 12

description: Library name: PANS-post_7


title: Before pulldown_Rep 1

description:
Library name: DvH_13
BP1


title: MDA-MB-231, Entinostat-treatment, 24h, biol rep 1, H2A.Zac, ChIP

description: Library name: Sample 10


title: Control probe 4_pulldown_Rep 2

description:
Library name: DvH_11
CD2


title: Whole blood, PANS8, Week 12

description: Library name: PANS-post_8


title: CD8-m3C_WT-2

description: Library name: CD8-m3C_WT-2


title: Tex_RNA_KO_3

description: Library name: Tex_KO_3


title: Control probe 4_pulldown_Rep 1

description:
Library name: DvH_10
CD1


title: Whole blood, healthy control 4

description: Library name: Control_4


title: Whole blood, PANS8, baseline

description: Library name: PANS-pre_8


title: Tex_RNA_WT_3

description: Library name: Tex_WT_3


title: Control probe 3_pulldown_Rep 3

description:
Library name: DvH_9
CA3

value: RNA treated with photoaffinity Control probe 3, followed by Streptavidin-pulldown


title: MDA-MB-231, DMSO-control, 24h, biol rep 1, H2A.Zac, ChIP

description: Library name: Sample 7

value: DMSO


title: Whole blood, PANS6, Week 12

description: Library name: PANS-post_6


title: Tex_RNA_WT_1

description: Library name: Tex_WT_1

value: Tumor


title: MDA-MB-231, DMSO-control, 24h, Input

description: Library name: Sample 9


title: Whole blood, PANS7, baseline

description: Library name: PANS-pre_7

value: Whole blood


title: HeLa cells, Entinostat-treatment, 24h, Input

description: Library name: Sample 6

source_name: HeLa

value: HeLa


title: intTex_RNA_KO_3

description: Library name: intTex_KO_3


title: Tex_RNA_KO_1

description: Library name: Tex_KO_1


title: Before pulldown_Rep 3

description:
Library name: DvH_15
BP3


title: HeLa cells, Entinostat-treatment, 24h, biol rep 1, H2A.Zac, ChIP

description: Library name: Sample 4


title: intTex_RNA_KO_2

description: Library name: intTex_KO_2


title: Ribocil probe 2_pulldown_Rep 3

description:
Library name: DvH_6
RD3

value: RNA treated with photoaffinity Ribocil probe 2, followed by Streptavidin-pulldown


title: Tex_RNA_WT_2

description: Library name: Tex_WT_2


title: MDA-MB-231, DMSO-control, 24h, biol rep 2, H2A.Zac, ChIP

description: Library name: Sample 8


title: Whole blood, PANS4, baseline

description: Library name: PANS-pre_4


title: intTex_RNA_KO_1

description: Library name: intTex_KO_1


title: Whole blood, PANS3, Week 12

description: Library name: PANS-post_3


title: HeLa cells, DMSO-control, 24h, biol rep 2, H2A.Zac, ChIP

description: Library name: Sample 2


title: HeLa cells, Entinostat-treatment, 24h, biol rep 2, H2A.Zac, ChIP

description: Library name: Sample 5


title: Whole blood, PANS5, Week 12

description: Library name: PANS-post_5

value: F


title: Ribocil probe 2_pulldown_Rep 2

description:
Library name: DvH_5
RD2


title: Whole blood, PANS5, baseline

description: Library name: PANS-pre_5


title: intTex_RNA_WT_3

description: Library name: intTex_WT_3


title: Control probe 3_pulldown_Rep 2

description:
Library name: DvH_8
CA2


title: Whole blood, PANS6, baseline

description: Library name: PANS-pre_6


title: Whole blood, PANS4, Week 12

description: Library name: PANS-post_4


title: Control probe 3_pulldown_Rep 1

description:
Library name: DvH_7
CA1


title: HeLa cells, DMSO-control, 24h, biol rep 1, H2A.Zac, ChIP

description: Library name: Sample 1


title: Ribocil probe 1_pulldown_Rep 3

description:
Library name: DvH_3
RA3

value: RNA treated with photoaffinity Ribocil probe 1, followed by Streptavidin-pulldown


title: Ribocil probe 2_pulldown_Rep 1

description:
Library name: DvH_4
RD1


title: intTex_RNA_WT_2

description: Library name: intTex_WT_2


title: HeLa cells, DMSO-control, 24h, Input

description: Library name: Sample 3


title: Whole blood, PANS2, Week 12

description: Library name: PANS-post_2


title: Ribocil probe 1_pulldown_Rep 2

description:
Library name: DvH_2
RA2


title: MDA-MB-231 cells, Entinostat-treatment, 24h, bio rep 2

description: Library name: Sample 11

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software with a maximum of one mismatch in the indexing read.  RNA-seq reads were then aligned to the Ensembl GRCh38.113 primary assembly with STAR version 2.7.11b.  Gene counts were derived from the number of uniquely aligned unambiguous fragments by Subread:featureCount version 2.0.8. Isoform expression of known Ensembl transcripts were quantified with Salmon version 1.10.0.  Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected.  The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 5.04.
Assembly: hg38
Supplementary files format and content: gene_counts.txt contains all counts, CPM, FPKM, TPM

extract_protocol:
RNA was extracted from the cell by using RNeasy® Mini kit (catalog No.: 74104). Samples were eluted in nuclease free water and processed for further library preparation and sequencing.
Total RNA integrity was determined using Agilent Bioanalyzer or 4200 Tapestation.  Library preparation was performed with 5 to 10ug of total RNA with a Bioanalyzer RIN score greater than 8.0. Ribosomal RNA was removed by poly-A selection using Oligo-dT beads (mRNA Direct kit, Life Technologies). mRNA was then fragmented in reverse transcriptase buffer and heating to 94 degrees for 8 minutes. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer's instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq X Plus using paired end reads extending 150 bases.

treatment_protocol: The cells were treated with 1µM of Entinostat for 24h. Cells were incubated at 37 C with 5% CO2 before harvesting.


title: intTex_RNA_WT_1

description: Library name: intTex_WT_1


title: Tpex_RNA_KO_3

description: Library name: Tpex_KO_3


title: Whole blood, PANS2, baseline

description: Library name: PANS-pre_2


title: Whole blood, PANS1, baseline

description: Library name: PANS-pre_1


title: MDA-MB-231 cells, DMSO-control, 24h, bio rep 3

description: Library name: Sample 9


title: Ribocil probe 1_pulldown_Rep 1

description:
Library name: DvH_1
RA1


title: Tpex_RNA_WT_2

description: Library name: Tpex_WT_2


title: IgG2_Donor 8

city: Amsterdam

first: Arie Johan

last: Hoogendijk

address: Plesmanlaan 125

institute: Sanquin Research

description: Library name: JK-T97

data_processing:
Sequence quality was confirmed using FastQC (Babraham Bioinformatics).
Reads were aligned to GRCh38.104 using STAR.
A count matrix was generated FeatureCounts (using -p -g gene_id -t exon flags).
Further normalization and differential expression analysis were performed using DESeq2.
Assembly: ChGR38.v104
Supplementary files format and content: tab-delimited text file include count values for all samples

source_name: Blood

extract_protocol:
FACS-separated B cell subsets from 8 donors were sorted into DNA LoBind tubes (Eppendorf) and washed with PBS. Total RNA was isolated from B cell sorted subsets using Qiagen RNeasy Plus Universal mini kit according to the manufacturer’s instructions (Qiagen, Hilden, Germany). RNA samples were quantified using Qubit 4.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked with RNA Kit on Agilent 5300 Fragment Analyzer (Agilent Technologies, Palo Alto, CA, USA). Total RNA samples that had inadequate quantity or an RNA Integrity Number (RIN) < 8 were excluded from the library preparation.
RNA sequencing library preparation was prepared using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were first enriched with Oligo(dT) beads. Enriched mRNAs were fragmented. First strand and second strand cDNA were subsequently synthesized. The second strand of cDNA was marked by incorporating dUTP during the synthesis. cDNA fragments were adenylated at 3’ends, and indexed adapter was ligated to cDNA fragments. Limited cycle PCR was used for library amplification. The dUTP incorporated into the cDNA of the second strand enabled its specific degradation to maintain strand specificity. Sequencing libraries were validated using NGS Kit on the Agilent 5300 Fragment Analyzer (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 4.0 Fluorometer (Invitrogen, Carlsbad, CA). The sequencing libraries were multiplexed and loaded on the flowcell on the Illumina NovaSeq 6000 instrument according to the manufacturer’s instructions. The samples were sequenced using a 2x150 Pair-End (PE) configuration v1.5.

treatment_protocol: Healthy adult human peripheral blood was obtained with written informed consent in accordance to the guidelines established by the Sanquin Medical Ethical Committee and in line with the Declaration of Helsinki. Donor information is summarized in Table I. Blood samples were drawn outside of the seasonal allergy season. Peripheral blood mononucleated cells (PBMCs) were isolated from fresh buffy coats using Ficoll gradient centrifugation (lymphoprep; Axis-Shield PoC AS). PBMC fractions were screened for adequate yet normal IgG4+ MBC frequencies (0.2-1% of total CD19+). Total B cells were isolated by untouched magnetic bead separation (Pan B cell isolation kit human; Miltenyi Biotec) and studied subsets were separated using flow cytometric cell-sorting based on expression of CD19, CD27, CD38 and BCR isotype (FACS Aria III and FACS Aria IIIu, BD Biosciences). During sorting cells that expressed multiple BCRs isotypes, due to promiscuous antibody staining or recent class switch events were excluded. The following antibodies were included: anti-CD19 (clone SJ25C1, 563325), anti-IgD (clone IA6-2, 561315), and anti-IgM (clone G20-127, 562618) from BD Biosciences. Anti-IgA1 (clone B3506B4, 9130-30), anti-IgA2 (clone A9604D2, 9140-31), and anti-IgG2 (clone HP6002, 9070-02) from SouthernBiotech. Anti-IgG1 (clone HP6188, M1325), Anti-IgG3 (clone HP6095, M1270), and anti-IgG4 (clone HP6098, M1271) from Sanquin Reagents. Anti-CD27 (clone O323, 63-0279-42), anti-CD38 (clone HB7, 25-0388-42), and Live/Dead Fixable Near-IR Dead cell stain (L10119) from ThermoFisher scientific. Each antibody was titrated to optimal staining concentration using PBMCs.

value: Blood

value: B cell

tag: genotype

value: WT


title: HeLa cells, Entinostat-treatment, 24h, biol rep 3

description: Library name: Sample 6


title: Whole blood, PANS1, Week 12

description: Library name: PANS-post_1

value: M


title: MDA-MB-231 cells, DMSO-control, 24h, bio rep 1

description: Library name: Sample 7


title: Tpex_RNA_WT_1

description: Library name: Tpex_WT_1


title: IgG1_Donor 8

description: Library name: JK-T96


title: IgG3_Donor 8

description: Library name: JK-T98


title: IgA2_Donor 8

description: Library name: JK-T95


title: 10I3-PoN-H

city: Muenster

first: Marcos

middle: J

last: Araúzo-Bravo

address: Rontgenstr. 20

department: Cell and Developmental Biology

country: Germany

institute: Max Planck Institute for Molecular Biomedicine

hyb_protocol: Samples were hybridized to AffymetrixClariom D Human r1-na36-hg38, following the manufacturer’s instructions

scan_protocol: Data generation was controlled by the Affymetrix GeneChip Command Console AGCC Version 2.0.0.1029 software of AGCC Portal and the Expression Console Version 1.1 was used for data quality control and analysis application (Affymetrix).

data_processing:
Normalyzation was perform using the Affymetrix Robust Multi-array Analysis (RMA) background correction model,
Data post-processing and graphics were performed with in-house developed functions in MATLAB.
Hierarchical clusters of genes and samples were performed with the one minus the sample correlation metric and the
Unweighted Pair-Group Method using Average (UPGMA) linkage method

label: biotin

source_name: Groin

label_protocol: Biotinylated cRNA were prepared for Affymetrix arrays following the manufacturer's instructions.

extract_protocol:
After obtaining biopsies from all patients, those intended for gene expression change studies were selected, and RNA was extracted.
The change in gene expression between different biopsies from the same patient was analyzed.
Genes that varied their expression when comparing Biopsy 0 (unaffected skin, before treatment) and Biopsy 3 (unaffected skin, 6 months after treatment) were excluded from the study,
as no laser was applied to the unaffected skin, and thus no gene expression changes were expected.
Gene expression changes between Biopsies 1 and 2 (affected area before treatment and affected area after treatment) were interpreted as treatment-induced modifications.
These changes were subsequently validated by quantitative polymerase chain reaction (qPCR).
Total RNA was isolated using RNeasy mini kit (Qiagen) following the manufacturer's instructions.

treatment_protocol:
The treatment was performed under anesthetic sedation, and in some cases where contraindications existed or at the patient's request,
tumescent local anesthesia with mepivacaine and 0.9% saline solution was administered. We used the Lumenis AcuPulse CO2 ablative laser at 10,600 nm with the following parameters:
F200 scanner, 8 mm spot size, 4 mm depth, 0.50-second duration, 24 watts power.
Three passes were administered in each area until slight bleeding was achieved, indicating that the papillary dermis had been reached. Between each laser pass,
the resulting scab from the epidermal ablation was removed with a saline-soaked gauze.
Immediately afterward, medium potency topical corticosteroids (betamethasone) and a vaseline gauze were applied to the treated area.
After 48 hours, the dressing was removed, and patients were instructed to perform daily washes with water and antiseptic soap and apply an alginate dressing until complete epithelialization,
which occurred between 4 and 6 weeks. All patients were discharged with oral analgesics, and antibiotics were not prescribed unless an infection occurred during follow-up.

value: Groin

tag: moment

value: Post-Treatment

value: Not-Treated

tag: skin

value: Healthy

tag: replicate

value: replicate 1


title: HeLa cells, Entinostat-treatment, 24h, biol rep 2

description: Library name: Sample 5

value: Entinostat


title: CD8_RNA_KO_3

description: Library name: CD8_KO_3


title: HeLa cells, Entinostat-treatment, 24h, biol rep 1

description: Library name: Sample 4


title: IgA1_Donor 8

description: Library name: JK-T94


title: 9I3-PoN-H


title: IgM_Donor 8

description: Library name: JK-T93


title: CD8_RNA_KO_2

description: Library name: CD8_KO_2


title: HeLa cells, DMSO-control, 24h, biol rep 3

description: Library name: Sample 3

value: DMSO


title: IgMD_Donor 8

description: Library name: JK-T92


title: Naive_Donor 8

description: Library name: JK-T91


title: HeLa cells, DMSO-control, 24h, biol rep 2

description: Library name: Sample 2


title: 10I2-PoY-A

value: Treated

value: Affected


title: CD8_RNA_KO_1

description: Library name: CD8_KO_1

value: Tumor


title: 9I2-PoY-A


title: 9I0-PrN-H

value: Pre-Treatment


title: CD8_RNA_WT_4

description: Library name: CD8_WT_4


title: 9I1-PrN-A


title: HeLa cells, DMSO-control, 24h, biol rep 1

description: Library name: Sample 1

value: HeLa


title: 8I3-PoN-H


title: IgG4_Donor 7

description: Library name: JK-T90


title: MDA-MB-231 cells, DMSO-control, 24h, bio rep 2

description: Library name: Sample 8


title: BMMCs from MM patient 3, high-dose melphalan following auto-HSCT, TCR, rep3

city: Tianjin

first: Lina

last: Zhao

address: Huan-Hu-Xi Road

country: China

institute: Tianjin Medical University

description: Library name: Sample 9

library_source: transcriptomic single cell

data_processing:
Raw data were processed using Cell Ranger v7.2.0 with alignment to the GRCh38 reference genome, and the downstream analyses were conducted according to the guideline. Quality control criteria included removal of cells with >10% mitochondrial content, >5% hemoglobin transcripts, <200 detected genes, or >30,000 genes. DoubletFinder was applied for further doublet exclusion[1]. To integrate datasets across different cohorts and eliminate batch effects, we used Harmony for unsupervised correction while preserving biological heterogeneity. Normalized expression matrices were used for downstream analyses.
Assembly: GRCh38 reference genome
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: contig_annotations.csv

molecule: polyA RNA

source_name: BM

extract_protocol:
Standard density gradient centrifugation was used to isolate Bone Marrow Mononuclear Cells (BMMCs) from fresh blood samples, followed by washing and red blood cell lysis. Cell viability and quality control were assessed using acridine orange/propidium iodide (AO/PI) dual fluorescent staining on the LUNA instrument. The quality control criteria were as follows: cell concentration of 1000–1500 cells/μL, cell viability >90%, aggregation rate <5%, and cell diameter <30 μm. After confirming that the cell concentration and viability met the required standards, the cell suspension was placed on ice and processed for the 10× Genomics single-cell transcriptomics workflow within 30 min.
Using single cell 5 ′ Library and Gel Bead Kit V2 (10x Genomics, PN-1000263) and Chromium Single Cell K Chip Kit (10x Genomics, PN-2000182), the cell suspension was loaded onto the Chromium single cell controller (10x Genomics) to generate single-cell gel beads in the emulsion according to the manufacturer’s protocol. Captured cells were lysed and the released RNA was barcoded through reverse transcription in individual gel bead-in-emulsions (GEMs). The next steps were carried out according to the manufacturer’s user guide (Chromium Single Cell V(D)J Reagent Kits User Guide, including GEM-RT incubation, post GEM-RT Dynabead cleanup, and cDNA amplification. 5’ cDNA libraries were then sequenced on an Illumina NovaseqX sequencer.

value: BM

value: BMMCs

value: mononuclear cells


title: IgG3_Donor 7

description: Library name: JK-T89

value: Blood

value: B cell

value: WT


title: CD8_RNA_WT_3

description: Library name: CD8_WT_3


title: CD8_RNA_WT_2

description: Library name: CD8_WT_2


title: IgG2_Donor 7

description: Library name: JK-T88


title: BMMCs from MM patient 2, high-dose melphalan following auto-HSCT, TCR, rep2

description: Library name: Sample 8


title: IgG1_Donor 7

description: Library name: JK-T87


title: CD8_mettl8KO_hic

description: Library name: CD8_mettl8KO_hic

source_name: tumor

value: tumor


title: MDA-MB-231 cells, Entinostat-treatment, 24h, bio rep 3

description: Library name: Sample 12


title: MDA-MB-231 cells, Entinostat-treatment, 24h, bio rep 1

description: Library name: Sample 10


title: IgA2_Donor 7

description: Library name: JK-T86


title: BMMCs from MM patient 3, high-dose melphalan following auto-HSCT, BCR, rep3

description: Library name: Sample 6


title: BMMCs from MM patient 1, high-dose melphalan following auto-HSCT, TCR, rep1

description: Library name: Sample 7


title: BMMCs from MM patient 2, high-dose melphalan following auto-HSCT, BCR, rep2

description: Library name: Sample 5


title: IgA1_Donor 7

description: Library name: JK-T85


title: 8I0-PrN-H

value: Groin

value: Not-Treated


title: CD8_RNA_WT_1

description: Library name: CD8_WT_1


title: 8I2-PoY-A

value: Post-Treatment

value: replicate 1


title: CD8-mettl8_2

description: Library name: CD8-mettl8_2

data_processing:
For ATAC-seq:Bowtie2 with ‘-very-sensitive’ option was used to map the high-quality reads to mm10 version of mice genome. The uniquely properly paired mapped reads were extracted for downstream analysis. MACS2 with the ‘-nomodel’ and ‘-extsize 147′ was used to call ATAC peaks. DESeq2 was used to identify significantly differential (FDR <=0.05) ATAC peaks between different conditions.
For cuttag:Cutadapt was used to remove low quality bases and adaptors. Clean reads were mapped to mm10 genome by using bowtie2. MACS2 was used to call cut&tag peaks with default settings. Bam2wig.py script was used to generate bigwig tracks for visualization in IGV5.
For HiC: HiC-Pro was used to perform reads alignment, quality control, and pairing reads. The h5 file was generated by using HiC-Pro. DeepLoops was applied to predict loops.
For RNA-seq: Uniquely mapped reads were retained for gene-level quantification using the htseq-count function from the HTSeq package.
For m3C-seq, raw sequencing reads were first subjected to quality control using FastQC, and adapter trimming was performed with cutadapt (v1.9.1). High-quality reads were then aligned to the mouse reference genome (mm10) using bowtie2 with default parameters. Raw counts and coverage counts were calculated by bedtools (v2.24) software and in-house scripts, then ratio (define as: count/coverage) and fc (defined as: treat-methyl-ratio/Input-methyl-ratio)(Schwartz et al., 2014) were also calculated.
For RIP-seq, after 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3), the high quality reads were aligned to the reference genome with hisat2 software (v2.0.4). Binding sites on RNAs (peaks) were identified by MACS2 software. Then, HTSeq software (v0.9.1) was used to get the gene level raw count as the expression profiling
Assembly: mm10
Supplementary files format and content: bigwig and normalized coverage signal
Supplementary files format and content: h5 format contain hic information
Supplementary files format and content: txt and counts
Library strategy: CUT&Tag


title: 10I0-PrN-H

value: Healthy


title: 8I1-PrN-A


title: IgG4_Donor 6

description: Library name: JK-T81


title: 7C3-PoN-H

source_name: Neck

value: Neck


title: 10I1-PrN-A

value: Affected


title: IgG2_Donor 6

description: Library name: JK-T79


title: CD8_mettl8KO_2_Tcf1

description: Library name: CD8_mettl8KO_2_Tcf1


title: BMMCs from MM patient 1, high-dose melphalan following auto-HSCT, RNA, rep1

description: Library name: Sample 1


title: Tpex_RNA_KO_2

description: Library name: Tpex_KO_2

value: Tumor


title: Tpex_RNA_KO_1

description: Library name: Tpex_KO_1


title: 6I0-PrN-H

value: Pre-Treatment


title: CD8_Ctrl_hic

description: Library name: CD8_Ctrl_hic


title: Tpex_RNA_WT_3

description: Library name: Tpex_WT_3


title: CD8_mettl8KO_1_Tcf1

description: Library name: CD8_mettl8KO_1_Tcf1


title: BMMCs from MM patient 3, high-dose melphalan following auto-HSCT, RNA, rep3

description: Library name: Sample 3


title: 7C0-PrN-H


title: 6I1-PrN-A


title: CLEAR5_D27_PBMC,Protein

city: New York

first: Xiaoli

last: Mi

state: NY

address: 408 East 69th Street, 408-18

institute: Memorial Sloan Kettering Cancer Center

description: Library name: AML_3287_CLEAR5_D27_PBMC_Protein

data_processing:
FASTQ sequencing reads were processed using the Cell Ranger pipeline, which extracts cell barcodes, unique molecular identifiers (UMIs), and cDNA or antibody barcodes. It aligns cDNA reads to the human GRCh38 reference genome and generates gene and antibody UMI count matrices.
Assembly: Human reference, GRCh38 (GENCODE v32/Ensembl 98)
Supplementary files format and content: Raw count matrices:  RNA_counts.csv.gz,ADT_counts.csv.gz
Supplementary files format and content: Demultiplexing tables: cell_sample_assign.csv.gz
Supplementary files format and content: ADT and HTO feature information: CLEAR_AML_feature_README.txt
Library strategy: CITE-seq

molecule: protein

source_name: Peripheral blood mononuclear cells

extract_protocol:
Previously isolated and viably frozen peripheral blood mononuclear cells (PBMCs) from patient samples were thawed and introduced to prewarmed and filtered 1640 RPMI (Gibco, catalog #11875093) with 10% FBS. Cells were suspended in Human FcR Blocking Reagent (Miltenyi Biotec, catalog #130-059-901) diluted in Filtered DPBS (Corning, catalog #21-031-CM) + 0.5% BSA (Fisher, catalog #F2442-500ML) and incubated for 10 minutes at 4ºC.  Brilliant Staining Buffer (BD), TotalSeqTM Oligonucleotide anti-Human Hashtag antibodies (Biolegend; C0251 catalog # 394661, C0252 catalog # 394663, C0253 catalog # 394665, C0254 catalog # 394667, or C0258 catalog # 394675), surface antibody mix (CD3 PE-Cy7, Invitrogen; CD45 BV510, Biolegend) and the CAR detection antibody (G4S Linker, Cell Signaling Technologies) were added to the FcR Blocking solution and incubated at RT for 30 minutes in the dark. Cells were washed with filtered DPBS + 0.5% BSA, filtered using 30 µm filters (Sysmex), and resuspended in filtered DPBS + 2% BSA + DAPI. Cell populations were purified using Fluorescent Activated Cell Sorting (FACS), using the Aria3 Instrument (BD Biosciences). Upon purification and collection of cell populations in Protein Lo-Bind Eppendorf Tubes, samples were pooled together based off cell number (with a goal of 50-100k cells per sample) and washed with filtered Cell Staining Buffer (Biolegend, catalog # 420201). Cells were Fc Blocked using TruStain FcX (Biolegend) at 4ºC for 10 minutes and then stained with TotalseqTM Universal Cocktail (Biolegned, catalog #399905) for 30 minutes at 4ºC. The cells were washed once with Cell Staining Buffer and twice with DPBS + 0.04% BSA and then submitted to the MSKCC Integrative Genomics Core for sequencing.
Approximately 10,000 cells were targeted for each sample (or as many as were available), and several samples were multiplexed together on one lane of 10X Chromium to reach 30,000 cells targeted (when 3 samples were pooled together), following cell hashing protocol. The libraries were prepared using the 10X Single Cell Immune Profiling Solution Kit, according to the manufacturer’s instructions. Final libraries were sequenced on Illumina NovaSeq S4 platform (R1 – 26 cycles, i7 – 10 cycles, i5 – 10 cycles, R2 – 90 cycles)

value: Peripheral blood mononuclear cells

value: paired-end

tag: batch

value: Illumina NovaSeq S4


title: CD8-mettl8_1

description: Library name: CD8-mettl8_1


title: CLEAR5_D27_PBMC,RNA

description: Library name: AML_3287_CLEAR5_D27_PBMC_RNA


title: CLEAR4_CLEAR5_EOP,Protein

description: Library name: AML_3287_CLEAR4_CLEAR5_EOP_Protein

source_name: T cells

value: T cells


title: BMMCs from MM patient 1, high-dose melphalan following auto-HSCT, BCR, rep1

description: Library name: Sample 4

value: BM

value: BMMCs

value: mononuclear cells


title: CD8_Ctrl_H3K27ac

description: Library name: CD8_Ctrl_H3K27ac

value: tumor


title: IgA2_Donor 6

description: Library name: JK-T77

value: Blood

value: B cell

value: WT


title: BMMCs from MM patient 2, high-dose melphalan following auto-HSCT, RNA, rep2

description: Library name: Sample 2


title: IgA1_Donor 6

description: Library name: JK-T76


title: IgMD_Donor 6

description: Library name: JK-T74


title: 7C2-PoY-A

value: Post-Treatment

value: Treated

value: replicate 1


title: 7C1-PrN-A

value: Neck

value: Not-Treated

value: Affected


title: 5G5M-PoN-H

source_name: Gluteo

value: Gluteo

value: Healthy


title: CLEAR4_CLEAR5_EOP,RNA

description: Library name: AML_3287_CLEAR4_CLEAR5_EOP_RNA

value: paired-end

value: Illumina NovaSeq S4


title: IgG1_Donor 6

description: Library name: JK-T78


title: CD8_Ctrl1_Tcf1

description: Library name: CD8_Ctrl1_Tcf1


title: CD8_RNA_KO_4

description: Library name: CD8_KO_4

value: Tumor


title: CD8_Ctrl2_Tcf1

description: Library name: CD8_Ctrl2_Tcf1


title: IgM_Donor 6

description: Library name: JK-T75


title: Naive_Donor 6

description: Library name: JK-T73


title: CLEAR2_CLEAR3_EOP,RNA

description: Library name: AML_3287_CLEAR2_CLEAR3_EOP_RNA

value: T cells


title: IgG4_Donor 5

description: Library name: JK-T72


title: 5I0-PrN-H

value: Groin

value: Pre-Treatment


title: 5G5-PoN-H


title: 6I2-PoY-A


title: IgG3_Donor 5

description: Library name: JK-T71

value: Blood


title: Tumor-pos

city: Boston

first: Chong

last: Zuo

address: 450 Brookline Ave

institute: Dana Farber Cancer Institute

description:
Library name: Tumor-pos
10X Genomics

data_processing:
Sample data was analyzed in R with Seurat 95. The 10x Cellranger pipeline (v7.0.0) was used to align reads to the Mm10 Mus musculus genome (from 10x Genomics). CITE-seq-Count was used to count hashtag reads. Hashtag reads were used to demultiplex samples with the Seurat ‘HTODemux’ function using the default settings. Only cells classified as a “singlet”, but not as a “doublet” or “negative” by hashtag demultiplexing were kept. Following hash demultiplexing, cells were further filtered out if they contained more than 20% mitochondrial (mt-) reads. ZsGreen- and ZsGreen+ tumor-draining lymph node samples were integrated together and clusters identified in a similar manner as human samples (see below). Three clusters of lower quality cells or doublets were removed after cluster identification. Genes from the Molecular Signatures Database (MSigDB) “Hallmark Interferon Gamma Response” and “Hallmark Interferon Alpha Response” (v7.2) were z-scaled and summed to visualize an IFN score.
The three CD4 T cell clusters from the main tumor-draining lymph node dataset were subset, and new variable features were discovered. The dataset was scaled, and top 15 PCs used for UMAP embedding and clusters identified. Following cluster identification, two clusters consisting of dendritic cells and B cells were removed, and the process of generating the UMAP and clustering was repeated. The “DCs” cluster from the main tdLN dataset were subset, new variable features identified, a new UMAP generated from the top 15 PCs, and clusters identified as above. This new sub-clustered object had 2 clusters comprised of either T cells or B cells; these clusters were subsequently removed as well as any cell with Cd79b expression. This filtered, subclustered dataset was reprocessed with the above steps. Differentially expressed genes between treatment groups were identified with the ‘FindMarkers’ function.
Assembly: mm10
Supplementary files format and content: matrix files

source_name: PDAC tumor

extract_protocol:
Mice bearing ZsGreen-expressing 6694c2 tumors were treated as described above. 48 hours after treatment, tumors, spleens, and tumor-draining lymph nodes were harvested from mice. Spleens and lymph nodes were macerated. Tumors were macerated and digested in collagenase IV (Sigma #C5138) and soybean trypsin inhibitor (Life Technologies #17075029). Tumor chunks were removed via filtration with a 40 μM filter, and the resulting single cell suspension was washed with PBS. Part of the tumor, lymph node, and spleen sample was taken for flow cytometry analysis. The rest of the samples were hashed, sorted based on ZsGreen expression on a BD FACS Aria, and analyzed via single-cell sequencing analysis. 6694c2 and B16F10 tumor cells were treated with IFNγ (100 ng/mL) (Peprotech #315-05), IFNβ (1000 U/mL) (BioLegend #581302), and STING agonist (225 ug/mL) in culture for 24 hrs. Cells were harvested and RNA isolated with a QIAGEN RNAeasy Plus Mini Kit (#74134). RNA was sent to Genewiz for paired-end RNA sequencing.
Cells were then loaded onto a Chromium X with the Single Cell K Chip (PN-2000182), the Chromium Next GEM Single Cell 5ʹ GEM Kit v2 reagents, and beads (PN-1000244). Library preparation was performed with the Library Construction Kit (PN-1000190). Libraries were pooled and sequenced on an Illumina NovaSeq 6000 instrument with 2x150bp sequencing (Azenta Life Sciences).

value: PDAC tumor

value: STING agonist


title: 6I3-PoN-H

value: Post-Treatment


title: mettl8KO_hic_2

description: Library name: mettl8KO_hic

source_name: spleen

value: spleen


title: 5G4-PoN-H

value: replicate 1


title: 5I2-PoY-A

value: Treated


title: CLEAR5_screen_CLEAR4_D10_D12_PBMC_lymphs,Protein

description: Library name: AML_3245_CLEAR5_screen_CLEAR4_D10_D12_PBMC_lymphs_Protein

source_name: Peripheral blood lymphocytes

value: Peripheral blood lymphocytes


title: Whole blood, PANS3, baseline

description: Library name: PANS-pre_3

value: Whole blood

value: M


title: IgG2_Donor 5

description: Library name: JK-T70

value: B cell

value: WT


title: CD8_Ctrl_ATAC

description: Library name: CD8_Ctrl_ATAC

value: tumor


title: IgG1_Donor 5

description: Library name: JK-T69


title: SP-pos

description:
Library name: SP-pos
10X Genomics

source_name: Spleen

value: Spleen

value: single cell suspension


title: Tumor-neg

description:
Library name: Tumor-neg
10X Genomics


title: CLEAR2_CLEAR3_EOP,Protein

description: Library name: AML_3287_CLEAR2_CLEAR3_EOP_Protein

value: T cells

value: paired-end

value: Illumina NovaSeq S4


title: LN-pos

description:
Library name: LN-pos
10X Genomics

source_name: Tumor-draining lymph nodes

value: Tumor-draining lymph nodes


title: LN-neg

description:
Library name: LN-neg
10X Genomics


title: SP-neg

description:
Library name: SP-neg
10X Genomics


title: IgA1_Donor 5

description: Library name: JK-T67

value: Blood


title: IgA2_Donor 5

description: Library name: JK-T68


title: 4A5-PoN-H

source_name: Armpit

value: Armpit

value: Post-Treatment

value: Not-Treated

value: Healthy


title: CLEAR5_D9_PBMC_biolrep1,Protein

description: Library name: AML_3245_CLEAR5_D9_PBMC_biolrep1_Protein

value: Peripheral blood mononuclear cells


title: CLEAR5_screen_CLEAR4_D10_D12_PBMC_blasts,Protein

description: Library name: AML_3245_CLEAR5_screen_CLEAR4_D10_D12_PBMC_blasts_Protein

source_name: Peripheral blood AML blasts

value: Peripheral blood AML blasts


title: 5I1-PrN-A

value: Groin

value: Pre-Treatment

value: Affected

value: replicate 1


title: CLEAR5_D9_PBMC_biolrep2,RNA

description: Library name: AML_3245_CLEAR5_D9_PBMC_biolrep2_RNA


title: IgG2_Donor 4

description: Library name: JK-T61

value: B cell

value: WT


title: CLEAR5_screen_CLEAR4_D10_D12_PBMC_lymphs,RNA

description: Library name: AML_3245_CLEAR5_screen_CLEAR4_D10_D12_PBMC_lymphs_RNA

value: Peripheral blood lymphocytes


title: CLEAR5_D9_PBMC_biolrep2,Protein

description: Library name: AML_3245_CLEAR5_D9_PBMC_biolrep2_Protein

value: paired-end


title: CKO_2

city: Chengdu

first: Quan

last: Yuan

address: No.14, 3Rd Section of Ren Min Nan Road, Sichuan

institute: West China Hospital of Stomatology, Sichuan University

description: Library name: Sample 5

data_processing:
Raw RNA-seq reads were first assessed for quality using FastQC and processed with the FASTX-Toolkit. The cleaned reads were then aligned to the Mus musculus reference genome (mm10) using HISAT2. Differentially expressed genes were identified using the DESeq2 R package with thresholds of |fold change| ≥ 2 and adjusted p-value ≤ 0.05. Gene Ontology and KEGG pathway enrichment analyses were subsequently performed using the clusterProfiler R package.
Assembly: mm10
Supplementary files format and content: a csv file includes raw counts for each sample

source_name: Bone marrow

extract_protocol:
Total RNA was extracted using Trizol reagent and purified with poly-T oligo-attached magnetic beads.
Sequencing libraries were generated using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (New England Biolabs, USA) according to the manufacturer’s instructions.

treatment_protocol: Mesenchymal stem cells (MSCs) were induced toward osteogenic differentiation by culturing in osteogenic medium containing 50 μg/mL ascorbic acid, 5 mM β-glycerophosphate, and 100 nM dexamethasone.

value: Bone marrow

value: Mesenchymal stem cells

value: Pcif1 CKO

value: osteogenic differentiation


title: IgG3_Donor 4

description: Library name: JK-T62

value: Blood


title: IgG4_Donor 4

description: Library name: JK-T63


title: 4A4-PoN-H

value: Armpit

value: Post-Treatment

value: Not-Treated


title: CKO_3

description: Library name: Sample 6


title: CLEAR5_screen_CLEAR4_D10_D12_PBMC_blasts,RNA

description: Library name: AML_3245_CLEAR5_screen_CLEAR4_D10_D12_PBMC_blasts_RNA

value: Peripheral blood AML blasts

value: Illumina NovaSeq S4


title: 3I4-PoN-H

value: Groin

value: Healthy


title: 4A1-PrN-A

value: Pre-Treatment

value: Affected

value: replicate 1


title: CKO_1

description: Library name: Sample 4


title: CLEAR5_D9_PBMC_biolrep1,RNA

description: Library name: AML_3245_CLEAR5_D9_PBMC_biolrep1_RNA

value: Peripheral blood mononuclear cells


title: 3I5-PoN-H


title: WT_3

description: Library name: Sample 3

value: WT


title: 3I1-PrN-A


title: IgG1_Donor 4

description: Library name: JK-T60

value: B cell


title: CLEAR5_D14_PBMC,Protein

description: Library name: AML_3245_CLEAR5_D14_PBMC_Protein

value: paired-end


title: CLEAR5_D14_PBMC,RNA

description: Library name: AML_3245_CLEAR5_D14_PBMC_RNA


title: 4A2-PoY-A

value: Treated


title: CLEAR4_screen_D7_D14_D38_PBMC_blasts,Protein

description: Library name: AML_3236_CLEAR4_screen_D7_D14_D38_PBMC_blasts_Protein


title: IgA2_Donor 4

description: Library name: JK-T59


title: Naive_Donor 4

description: Library name: JK-T55


title: IgA1_Donor 4

description: Library name: JK-T58


title: 3I2-PoY-A


title: IgMD_Donor 4

description: Library name: JK-T56


title: IgG3_Donor 3

description: Library name: JK-T53


title: E15+24h mouse cortex, Control, CUT&Tag, H3K27ac

city: Geneva

first: Awais

last: Javed

address: Chemin des mines, 9

department: Fundamental Neurosciences

country: Switzerland

institute: University of Geneva

description:
Library name: Control_H3K27ac_CT
CUT&Tag

data_processing:
Data preprocessing and quality controls. Fastq files were mapped on the standard 10X mouse reference genome GRCm38 using cellranger (v7.2.0) for the E16 collected snRNA-seq dataset. For the E16 collected scRNA-seq, fastq files were mapped with the mouse reference genome including hEGR1 and hIRF1 sequences. For the P0 collected scRNA-seq, fastq files were mapped with the mouse reference genome including PBase, TurboRFP-NLS and JUNB sequences for quality control purposes. Counts due to ambient RNA and random barcode swapping were removed from the raw matrix using remove-background function of cellbender (v0.3.0) with epochs = 150, expected-cells=2000 for the E16 snRNA-seq dataset and epochs = 50, expected-cells=6000 for the E16 collected scRNA-seq. The newly generated sn/scRNA-seq cellbender count matrix was used for subsequent analysis. Single-cell RNA-seq P0 collected dataset was not processed through cellbender. Briefly, for the JUNB overexpression E16 collected dataset, cells with nCount_RNA < 25’000, nFeature_RNA > 1’500 and percent.mt < 0.25 were included. For the IRF1/EGR1 overexpression E16 collected dataset, cells with nCount_RNA > 500, nCount_RNA < 20’000, nFeature_RNA > 1’000 and percent.mt < 5 were included. For the P0 collected dataset, nCount_RNA < 30’000, nFeature_RNA > 1’000 and percent.mt < 10 were included. scDblFinder package (v1.16.0) was used to remove doublets by simulating ncol(sce)/1000*0.008 doublet ratio. A small number of microglia and vasculature cells were removed from the analysis.
CUT&RUN. Fastqs files were processed as outlined by 4DN CUT&RUN processing pipeline. Briefly, Fastqs files were trimmed using trimmomatic (v0.39) (ILLUMINACLIP:2:30:10; LEADING:3; TRAILING:3; SLIDINGWINDOW:4:15; MINLEN:25). Trimmed reads were then aligned with human (GRCh38-noalt) and yeast (R64-1-1) spike-in reference genomes using bowtie2 (v2.5.4) using the –dovetail option. Sambamba (v1.0.1) was used to generate indices, SAM to BAM conversion and sorting. CUT&Tag. Fastqs files were aligned with either human (GRCh38-noalt), mouse (mm10) or E.coli genome using bowtie2 (v2.5.4). Spike-in depth was quantified to normalize in later steps. Duplicates were removed using Picard (v3.4.0). Reads mapped to ENCODE blacklist regions were excluded using bedtools (v2.31.1). Samtools (v1.22.1) was used to generate indices, SAM to BAM conversion and sorting. Once the CUT&RUN/CUT&Tag bam files were preprocessed, Deeptools (v3.5.6) bamCoverage function was used to generate spike-in normalized bigwig files for visualization. SEACR (v1.3) was used to call peaks with 0.01 threshold of pvalue. The .bed peaks were then uploaded to GREAT to generate peak to gene associations. IGV genome browser (v2.18.2) was used to visualize bigwig and generate coverage plots.
Assembly: refdata-gex-mm10-2020-A (cellranger reference); refdata-gex-mm10-2020-A with RFP-NLS reporter and hJUNB (custom reference); refdata-gex-mm10-2020-A with hIRF1 and hEGR1 (custom reference) used for cellranger (sn/scRNA-seq analysis) human (GRCh38-noalt), yeast (R64-1-1), mouse (mm10) or E.coli genome used for bowtie2 (CUT&Tag/RUN analysis)
Supplementary files format and content: .h5 raw matrix files for the sn/scRNAseq, processed .rds for TrackerSeq datasets, .bed SEACR and .bigwig files for the CUT&Tag/RUN datasets
Library strategy: CUT&Tag

source_name: E16 cortex

growth_protocol: Cerebral organoids were generated from induced pluripotent stem cells (iPSCs) PC1505 line at ~80% confluency according to STEMdiff Cerebral organoid kit from STEMCELL Technologies (a standardized implementation of unguided cerebral organoid differentiation). Cells were dissociated with Accutase and resuspended in Organoid formation medium with 50 μM ROCK inhibitor. Live cells (5,000 per well) were seeded into low-attachment 96-well plates, forming embryoid bodies (EBs) after 24 hours. EBs were cultured for 5 days and subsequently transferred to Neural Induction Medium and cultured for 2 days. Neuroepithelial tissues formed, showing radially organized pseudo-stratified epithelium. On day 7, aggregates were embedded in Matrigel in Expansion Medium and cultured further. By day 10, organoids were placed in Maturation Medium, with medium changes every 3-4 days, supporting cerebral tissue development.

extract_protocol:
E16.5 dataset. Twenty-four hours following electroporation, pregnant female was anaesthetized and sacrificed. Embryos from the pregnant mouse were harvested. Embryos were first separated based on electroporated plasmids, decapitated and the cortex was dissected out in 1X HBSS. JUNB: The GFP+ cortices were separated, and the electroporated region was dissected and frozen straight away in 2 ml Eppendorf tubes. Four cortices were collected per condition. On the day of the snRNA-seq, samples were first gently thawed on ice and resuspended in 100 ul of lysis buffer composed of: 10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 0.01% NP-40, 1% BSA and 1 mM DTT. After 5 minutes of lysis on ice, 1 mL of HBSS was added. The samples were then centrifuged at 500 g for 5 minutes. After removing supernatant, the pellet was resuspended in 1 mL washing buffer composed of: 10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 1% BSA, 1 mM DTT and 0.5 U/μl RNAase inhibitor. Then, using the P1000 pipette, the samples were pipetted up and down 10 times. The samples were then centrifuged again for 5 minutes at 500 g. Supernatant was removed, 1 mL of additional washing buffer was added, and the pellet was resuspended. At this point, no clumps were seen, and the samples were passed through a 30-μm filter before FANS. Hoechst was used as a positive nuclei marker and 25’000 events representing Hoechst+GFP+ nuclei were sorted directly into empty 1.5 mL Eppendorf-tubes using Beckman Coulter MoFlo Astrios. Exactly 42.8 μL of the sorted nuclei were loaded on the first step of the 10x Next GEM v3.1 reagent kit on the Chromium controller. IRF1/EGR1: The TagBFP2-NLS+ cortices were separated, and the electroporated region was dissected and processed for cell dissociation using the Miltenyi Neural dissociation kit as described previously 87. Single cell suspensions were then passed through a 70-μm filter before FACS. Only 20,000 BFP+ cells were sorted into separate tubes for either Control, IRF1, EGR1, or IRF1+EGR1. The FAC-sorted cells were centrifuged for 5 min at 300 g and all but 42.8 μL was removed from the tube before resuspending once more and loading on the Chip G for 10x capture with Next GEM v3.1 reagent kit on the 10x Chromium X controller. P0 dataset. Four days after electroporations and after birth of pups, four litter-mates per condition were sacrificed by decapitation and the cortex was dissected out of the head in cold 1x HBSS in less than 5 mins. The electroporated region was microdissected in a fresh petri dish containing 1x HBSS and transferred into an eppendorf tube. Dissociations were performed using the Neural Dissociation kit (130-092-628; Miltenyi) by treating the microdissected tissue with Enzyme mix 1 for 7mins and then Enzyme mix 2 for 3mins. Cells were washed in sorting buffer (1x PBS, 1% BSA and 0.5 U/μl SUPERase-In RNase inhibitor (AM2694; ThermoFisher Scientific)) twice at 4 C with 300 g. 16,000 for Control and 50,000 JUNB electroporated RFP+ cells were sorted into separate tubes containing sorting buffer. Sorted cell suspension was centrifuged again for 5 min at 4 C with 300 g and all but around 43.2 μL was removed. The cell suspension was resuspended gently and processed with 10X Genomics Chromium Single Cell 3’ v3 reagent kit on the Chromium X controller.
Gene expression libraries were constructed according to the manufacturer’s guidelines (10x Genomics NextGEM v3.1 reagent kit). TrackerSeq libraries were constructed as previously described (Bandler et al. 2022).

value: E16 cortex

value: Mixed cortical cell types

value: WT CD1

value: Control


title: CLEAR4_screen_D7_D14_D38_PBMC_blasts,RNA

description: Library name: AML_3236_CLEAR4_screen_D7_D14_D38_PBMC_blasts_RNA


title: WT_2

description: Library name: Sample 2

value: Bone marrow

value: Mesenchymal stem cells

value: osteogenic differentiation


title: CLEAR4_screen_D38_PBMC_lymphs,Protein

description: Library name: AML_3236_CLEAR4_screen_D38_PBMC_lymphs_Protein

value: Peripheral blood lymphocytes

value: Illumina NovaSeq S4


title: E15+24h mouse cortex, JUNB overexpression, CUT&Tag H3K27ac

description:
Library name: JUNBOE_H3K27ac_CT
CUT&Tag

value: Junb


title: WT_1

description: Library name: Sample 1


title: E15+24h mouse cortex, IRF1+EGR1 overexpression, single cell RNA-seq

description:
Library name: Irf1_Egr1_E16_sc
10x Genomics

data_processing:
Data preprocessing and quality controls. Fastq files were mapped on the standard 10X mouse reference genome GRCm38 using cellranger (v7.2.0) for the E16 collected snRNA-seq dataset. For the E16 collected scRNA-seq, fastq files were mapped with the mouse reference genome including hEGR1 and hIRF1 sequences. For the P0 collected scRNA-seq, fastq files were mapped with the mouse reference genome including PBase, TurboRFP-NLS and JUNB sequences for quality control purposes. Counts due to ambient RNA and random barcode swapping were removed from the raw matrix using remove-background function of cellbender (v0.3.0) with epochs = 150, expected-cells=2000 for the E16 snRNA-seq dataset and epochs = 50, expected-cells=6000 for the E16 collected scRNA-seq. The newly generated sn/scRNA-seq cellbender count matrix was used for subsequent analysis. Single-cell RNA-seq P0 collected dataset was not processed through cellbender. Briefly, for the JUNB overexpression E16 collected dataset, cells with nCount_RNA < 25’000, nFeature_RNA > 1’500 and percent.mt < 0.25 were included. For the IRF1/EGR1 overexpression E16 collected dataset, cells with nCount_RNA > 500, nCount_RNA < 20’000, nFeature_RNA > 1’000 and percent.mt < 5 were included. For the P0 collected dataset, nCount_RNA < 30’000, nFeature_RNA > 1’000 and percent.mt < 10 were included. scDblFinder package (v1.16.0) was used to remove doublets by simulating ncol(sce)/1000*0.008 doublet ratio. A small number of microglia and vasculature cells were removed from the analysis.
CUT&RUN. Fastqs files were processed as outlined by 4DN CUT&RUN processing pipeline. Briefly, Fastqs files were trimmed using trimmomatic (v0.39) (ILLUMINACLIP:2:30:10; LEADING:3; TRAILING:3; SLIDINGWINDOW:4:15; MINLEN:25). Trimmed reads were then aligned with human (GRCh38-noalt) and yeast (R64-1-1) spike-in reference genomes using bowtie2 (v2.5.4) using the –dovetail option. Sambamba (v1.0.1) was used to generate indices, SAM to BAM conversion and sorting. CUT&Tag. Fastqs files were aligned with either human (GRCh38-noalt), mouse (mm10) or E.coli genome using bowtie2 (v2.5.4). Spike-in depth was quantified to normalize in later steps. Duplicates were removed using Picard (v3.4.0). Reads mapped to ENCODE blacklist regions were excluded using bedtools (v2.31.1). Samtools (v1.22.1) was used to generate indices, SAM to BAM conversion and sorting. Once the CUT&RUN/CUT&Tag bam files were preprocessed, Deeptools (v3.5.6) bamCoverage function was used to generate spike-in normalized bigwig files for visualization. SEACR (v1.3) was used to call peaks with 0.01 threshold of pvalue. The .bed peaks were then uploaded to GREAT to generate peak to gene associations. IGV genome browser (v2.18.2) was used to visualize bigwig and generate coverage plots.
Assembly: refdata-gex-mm10-2020-A (cellranger reference); refdata-gex-mm10-2020-A with RFP-NLS reporter and hJUNB (custom reference); refdata-gex-mm10-2020-A with hIRF1 and hEGR1 (custom reference) used for cellranger (sn/scRNA-seq analysis) human (GRCh38-noalt), yeast (R64-1-1), mouse (mm10) or E.coli genome used for bowtie2 (CUT&Tag/RUN analysis)
Supplementary files format and content: .h5 raw matrix files for the sn/scRNAseq, processed .rds for TrackerSeq datasets, .bed SEACR and .bigwig files for the CUT&Tag/RUN datasets


title: CLEAR3_screen_D8_D15_D28_PBMC_lymphs,RNA

description: Library name: AML_3236_CLEAR3_screen_D8_D15_D28_PBMC_lymphs_RNA


title: IgG2_Donor 3

description: Library name: JK-T52

source_name: Blood

value: Blood


title: 2S1-PrN-A

source_name: Undermammary fold

value: Undermammary fold

value: Pre-Treatment

value: Not-Treated

value: Affected

value: replicate 1


title: CLEAR4_screen_D38_PBMC_lymphs,RNA

description: Library name: AML_3236_CLEAR4_screen_D38_PBMC_lymphs_RNA

value: paired-end


title: E15+24h mouse cortex, EGR1 overexpression, single cell RNA-seq

description:
Library name: Egr1_E16_sc
10x Genomics

value: E16 cortex


title: 1G5-PoN-H

value: Gluteo

value: Post-Treatment

value: Healthy


title: IgG1_Donor 3

description: Library name: JK-T51

value: B cell

value: WT


title: E15+24h mouse cortex, IRF1 overexpression, single cell RNA-seq

description:
Library name: Irf1_E16_sc
10x Genomics

value: Mixed cortical cell types

value: WT CD1


title: 2S4-PoN-H


title: CLEAR3_screen_D8_D15_D28_PBMC_lymphs,Protein

description: Library name: AML_3236_CLEAR3_screen_D8_D15_D28_PBMC_lymphs_Protein

value: Peripheral blood lymphocytes

value: Illumina NovaSeq S4


title: CLEAR3_screen_D8_D15_D28_PBMC_blasts,Protein

description: Library name: AML_3236_CLEAR3_screen_D8_D15_D28_PBMC_blasts_Protein

value: Peripheral blood AML blasts


title: CLEAR3_screen_D8_D15_D28_PBMC_blasts,RNA

description: Library name: AML_3236_CLEAR3_screen_D8_D15_D28_PBMC_blasts_RNA


title: BLEO-IPF Nintedanib Vehicle Sample 4042732101

city: Hørsholm

first: Henrik

last: Hansen

address: Hørsholm Kongevej 11

department: Histology & NGS

country: Denmark

institute: Gubra

description: Library name: 4042732101

data_processing:
All downstream analyses were performed using R version 3.6.0.
Assembly: Reads were aligned to the GRCm38 release 96 Ensembl Mus musculus genome using STAR version 2.7.0f.
Supplementary files format and content: comma-delimited text file contains raw counts for each Sample.

source_name: Lung

extract_protocol:
The inferior lobe samples were homogenised in lysis buffer, and RNA was purified using NucleoSpin® RNA binding strips (cat. no. 740698.5, Macherey-Nagel, Dueren, Germany). RNA purity and concentration were measured using a NanoDrop 2000.
cDNA libraries were prepared using NEBNext® Ultra II Directional RNA library prep Kit for Illumina® (cat. no. E7760L, New England Biolabs, Ipswich, MA). cDNA libraries were sequenced to a depth of approximately 15 million reads per sample (single-end, 75 bp reads) on a NextSeq 500 System (Illumina, San Diego, CA) using the NextSeq 500/550 High Output Kit version 2.5 (cat. no. 20024906, Illumina).

value: Lung

value: BLEO-IPF Nintedanib Vehicle


title: E15+24h mouse cortex, Control, single cell RNA-seq

description:
Library name: Control_E16_sc
10x Genomics

value: Control


title: 1G4-PoN-H

value: Not-Treated


title: E15+24h mouse cortex, JUNB overexpression, single nucleus RNA-seq

description:
Library name: Junb_E16_sn
10x Genomics

value: Junb


title: IgA1_Donor 3

description: Library name: JK-T49

value: Blood


title: IgA2_Donor 3

description: Library name: JK-T50


title: BLEO-IPF Nintedanib Sample 4042731910

description: Library name: 4042731910

value: BLEO-IPF Nintedanib


title: 2S2-PoY-A

value: Undermammary fold

value: Treated

value: Affected

value: replicate 1


title: BLEO-IPF Nintedanib Sample 4042731873

description: Library name: 4042731873


title: CLEAR2_screen_D15_D134_PBMC_lymphs_biolrep2,Protein

description: Library name: AML_3236_CLEAR2_screen_D15_D134_PBMC_lymphs_biolrep2_Protein

value: paired-end


title: E15+24h mouse cortex, Control, single nucleus RNA-seq

description:
Library name: Control_E16_sn
10x Genomics

value: E16 cortex

value: Mixed cortical cell types


title: CLEAR2_screen_D15_D134_PBMC_lymphs_biolrep2,RNA

description: Library name: AML_3236_CLEAR2_screen_D15_D134_PBMC_lymphs_biolrep2_RNA

value: Peripheral blood lymphocytes


title: IgM_Donor 3

description: Library name: JK-T48

value: B cell

value: WT


title: 1G2-PoY-A

value: Gluteo

value: Post-Treatment


title: CLEAR2_screen_D15_D134_PBMC_lymphs_biolrep1,Protein

description: Library name: AML_3236_CLEAR2_screen_D15_D134_PBMC_lymphs_biolrep1_Protein

value: Illumina NovaSeq S4


title: CTRL Vehicle Sample 4042731953

description: Library name: 4042731953

value: Lung

value: CTRL Vehicle


title: 1G1-PrN-A

value: Pre-Treatment

value: Not-Treated


title: BLEO-IPF Nintedanib Vehicle Sample 4042731431

description: Library name: 4042731431

value: BLEO-IPF Nintedanib Vehicle


title: IgMD_Donor 3

description: Library name: JK-T47

value: Blood


title: Naive_Donor 3

description: Library name: JK-T46


title: CLEAR2_screen_D15_D134_PBMC_lymphs_biolrep1,RNA

description: Library name: AML_3236_CLEAR2_screen_D15_D134_PBMC_lymphs_biolrep1_RNA


title: P0 mouse cortex, Control, Trackerseq

description:
Library name: Control_P0_sc_TS
TrackerSeq

value: WT CD1

value: Control


title: IgG3_Donor 2

description: Library name: JK-T35


title: BLEO-IPF Nintedanib Vehicle Sample 4042712499

description: Library name: 4042712499


title: P0 mouse cortex, JUNB overexpression, Trackerseq

description:
Library name: Junb_P0_sc_TS
TrackerSeq

value: Junb


title: P0 mouse cortex, JUNB overexpression, single cell RNA-seq

description:
Library name: Junb_P0_sc_RNA
10x Genomics

source_name: P0 cortex

value: P0 cortex


title: BLEO-IPF Nintedanib Vehicle Sample 4028945088

description: Library name: 4028945088


title: CLEAR2_screen_D134_PBMC_blasts,Protein

description: Library name: AML_3236_CLEAR2_screen_D134_PBMC_blasts_Protein

value: Peripheral blood AML blasts

value: paired-end


title: IgA2_Donor 2

description: Library name: JK-T32

value: B cell


title: K2_MRTX1133_cell_hash

first: Yu-Jui

last: Ho

state: New York

address: 417 E 68th St

department: Cancer Biology & Genetics Program

description:
Library name: JR-2281_Krasi_caer_epi_HTO
10x_v3

data_processing:
All scRNA-seq datasets were demultiplexed, barcode-corrected, aligned and UMI-corrected with SEQC using mouse genome mm10 and default parameters.
Assembly: mm10
Supplementary files format and content: Unfiltered count matrices resulting from alignment and demultiplexing with our custom pipeline SEQC (v0.2.8) are deposited in the Matrix Market format for sparse matrix representation. Cell barcodes in processed data files are encoded using the DNA3Bit class of the SEQC package.
Supplementary files format and content: Merged fastq files, encoding the cell and molecule barcode information in fastq record headers, were obtained using SEQC (v0.2.8). Merged fastq files were aligned to transgenes in our KPLOH model (GFP, rtTA3-IRES-mKate2, shRen) using BWA (0.7.17-r1188). Columns in _transgene_count.tsv.gz files are: (1) record_index, (2) numeric cell barcode resulting from encoding of sequence cell barcode using the DNA3Bit class of the SEQC package, (3) arbitrary gene identifier for each transgene, (4) UMI count (5) transgene_symbol.

source_name: Pancreas

growth_protocol: Mice were generated by 8-cell injection of KPLOH (Ptf1a-Cre; LSL-KrasG12D; Rosa26-CAGS-LSL-rtTA3-IRES-mKate2; p53flox/wt; TRE-GFP-shRen.713) ESCs.

extract_protocol:
Pancretata were harvested from the indicated mouse models and processed for FACS sorting using Collagenase (1 mg/mL) & Dispase (2 U/mL) mix digestion solution and Gentle-MACS dissociator (mTDK_1 protocol), followed by a 0.05% Trypsin-EDTA step. For every sample that would be subjected to cell hashing, we used DNAse-free buffers following digestion. Samples were resuspended in 1 mL ACK-lysis buffer and incubated for 5 min at room temperature to deplete red blood cells, and washed the ACK lysis buffer with 20 mL HBSS. We blocked samples with TruStain Fc block Plus (Biolegend, 156603; clone S17011E, 1:100) for 7 min at 4°C, followed by incubation with a sample-specific TotalSeq cell hashing antibody (Biolegend, 155832, 155833, 155835, 155837, 155839, 155841; clones M1/42; 30-F11). We incubated cell hashing antibodies at a 1:50 dilution for 30 min. We washed samples 3 times with DNAse-free FACS buffer + STI, followed by filtering through a 40-μm strainer and FACS-based isolation of mKate2+/GFP+ cells (KrasG12D+ pancreatic epithelial cells expressing shp53 or shCtrl). To prepare cells for scRNA-seq, we pooled samples from the same experimental conditions into the same tube, and resuspended cells at a 1000 cells μL-1.
Cells were resuspended in 1X PBS and BSA (0.04%) and checked for viability using 0.2% (w/v) Trypan Blue staining (Countess II). All sequencing experiments were performed on samples with a minimum of 80% viable cells. Single-cell encapsulation and scRNA-seq library prep of FACS-sorted cell suspensions was performed on the Chromium instrument (10x Genomics) following the user manual (Reagent Kit 3’ v3). Each sample loaded onto the cartridge contained approximately 15,000 cells at a final dilution of ~500 cells μl-1. Transcriptomes of encapsulated cells were barcoded during reverse transcription and the resulting cDNA was purified with DynaBeads, followed by amplification per the user manual. Next, the PCR-amplified product was fragmented, A-tailed, purified with 1.2X SPRI beads, ligated to sequencing adapters and indexed by PCR. Indexed DNA libraries were double-size purified (0.6–0.8X) with SPRI beads and sequenced on an Illumina sequencer (R1 – 26 cycles, i7 – 8 cycles, R2 – 70 cycles or higher) to a depth of >50 million reads per sample (>13,000 reads per cell) at MSK’s Integrated Genomics Operation Core Facility.

treatment_protocol: GFP was induced by treatment of the resulting mice with doxycycline (200 mg/kg; Envigo) in the chow starting at 4 weeks of age. At 5 weeks of age, mice were subjected to eight-hourly intraperitoneal injections of 80 μg kg-1 of caerulein (Bachem) for two consecutive days (16 injections total). In addition,  mice were treated with MRTX1133 (30mg/kg) or vehicle concurrently with caerulein treatment, euthanizing mice within 4 h of the last MRTX1133 or vehicle dose (fifth dose, 2 days after the first dose).

value: Pancreas

value: Epithelial

value: KPLOH (p53 proficient)


title: CLEAR2_screen_D134_PBMC_blasts,RNA

description: Library name: AML_3236_CLEAR2_screen_D134_PBMC_blasts_RNA

value: Illumina NovaSeq S4


title: IgG2_Donor 2

description: Library name: JK-T34

value: WT


title: IgG1_Donor 2

description: Library name: JK-T33


title: CLEAR2_D8_PBMC_biolrep2,Protein

description: Library name: AML_3236_CLEAR2_D8_PBMC_biolrep2_Protein

source_name: Peripheral blood mononuclear cells

value: Peripheral blood mononuclear cells


title: 2S5-PoN-H

value: Undermammary fold

value: Post-Treatment

value: Healthy

value: replicate 1


title: IgA1_Donor 2

description: Library name: JK-T31

value: Blood


title: BLEO-IPF Nintedanib Sample 4028944922

description: Library name: 4028944922

value: Lung

value: BLEO-IPF Nintedanib


title: K2_MRTX1133

description:
Library name: JR-2281_Krasi_caer_epi
10x_v3


title: BLEO-IPF Nintedanib Vehicle Sample 4028945057

description: Library name: 4028945057

value: BLEO-IPF Nintedanib Vehicle


title: IgMD_Donor 2

description: Library name: JK-T29


title: CLEAR2_D8_PBMC_biolrep2,RNA

description: Library name: AML_3236_CLEAR2_D8_PBMC_biolrep2_RNA


title: P0 mouse cortex, Control, single cell RNA-seq

description:
Library name: Control_P0_sc_RNA
10x Genomics

value: P0 cortex

value: Mixed cortical cell types

value: WT CD1

value: Control


title: K2_vehicle_cell_hash

description:
Library name: JR-2281_Ctrl_caer_epi_HTO
10x_v3

value: Pancreas

value: Epithelial

value: vehicle


title: BLEO-IPF Nintedanib Sample 4028944919

description: Library name: 4028944919


title: BLEO-IPF Nintedanib Vehicle Sample 4016716514

description: Library name: 4016716514


title: K2_vehicle

description:
Library name: JR-2281_Ctrl_caer_epi
10x_v3

value: KPLOH (p53 proficient)


title: CTRL Vehicle Sample 4016716901

description: Library name: 4016716901

value: CTRL Vehicle


title: IgM_Donor 2

description: Library name: JK-T30

value: B cell

value: WT


title: CLEAR2_D37_PBMC,RNA

description: Library name: AML_3236_CLEAR2_D37_PBMC_RNA

value: Peripheral blood mononuclear cells

value: paired-end

value: Illumina NovaSeq S4


title: peripheral blood Treg, HADA, rep4

city: Beijing

first: Zhijie

last: Bai

state: 北京Beijing

address: Taiping Road, Haidian District

institute: beijing institute of radiation

description: Library name: H4

data_processing:
Raw FASTQ files were first subjected to quality control using FastQC, followed by adapter trimming and low-quality read removal with Trimmomatic. High-quality reads were then aligned to the reference genome (GRCm39) using STAR aligner. Gene expression quantification was performed using featureCounts, generating a count matrix where rows represent genes and columns represent samples.
Assembly: GRCm39
Supplementary files format and content: gene_expression_matrix.txt

source_name: peripheral blood

extract_protocol:
Peripheral blood Treg cells were sorted using flow cytometry. Due to the limited number of cells, cDNA library construction was performed using the NEBNext® Single Cell/Low Input cDNA Synthesis & Amplification Module (NEB, E6421L, E7805, E6440) according to the manufacturer’s instructions.
cDNA library construction was performed using the NEBNext® Single Cell/Low Input cDNA Synthesis & Amplification Module (NEB, E6421L, E7805, E6440)

value: peripheral blood

value: Treg


title: CLEAR2_D8_PBMC_biolrep1,RNA

description: Library name: AML_3236_CLEAR2_D8_PBMC_biolrep1_RNA


title: CTRL Vehicle Sample 4016716507

description: Library name: 4016716507

value: Lung


title: CLEAR2_D8_PBMC_biolrep1,Protein

description: Library name: AML_3236_CLEAR2_D8_PBMC_biolrep1_Protein


title: Naive_Donor 2

description: Library name: JK-T28

value: Blood


title: peripheral blood Treg, HADA, rep2

description: Library name: H2


title: IgG4_Donor 1

description: Library name: JK-T27


title: CLEAR1_D8_PBMC_biolrep2,Protein

description: Library name: AML_3236_CLEAR1_D8_PBMC_biolrep2_Protein


title: CLEAR2_D37_PBMC,Protein

description: Library name: AML_3236_CLEAR2_D37_PBMC_Protein


title: peripheral blood Treg, HADA, rep3

description: Library name: H3


title: CTRL Vehicle Sample 4016716344

description: Library name: 4016716344


title: peripheral blood Treg, HADA, rep1

description: Library name: H1


title: BLEO-IPF Nintedanib Vehicle Sample 4016716208

description: Library name: 4016716208

value: BLEO-IPF Nintedanib Vehicle


title: peripheral blood Treg, control, rep4

description: Library name: C4


title: IgG2_Donor 1

description: Library name: JK-T25


title: peripheral blood Treg, control, rep3

description: Library name: C3


title: CLEAR1_screen_PBMC_lymphs,Protein

description: Library name: AML_3040_CLEAR1_screen_PBMC_lymphs_Protein

value: Peripheral blood lymphocytes


title: IgM_Donor 1

description: Library name: JK-T21


title: BLEO-IPF Nintedanib Vehicle Sample 4016716137

description: Library name: 4016716137


title: CLEAR1_D8_PBMC_biolrep1,Protein

description: Library name: AML_3236_CLEAR1_D8_PBMC_biolrep1_Protein


title: KG1A_50_R3

city: Little Rock

first: Kimberly

middle: E

last: Stephens

state: AR

address: 4301 W. Markham St Slot 510

department: Neuroscience

institute: University of Arkansas for Medical Sciences

description: Library name: Sample-6

data_processing:
Reads trimmed for adapter sequence
Reads mapped to rn6 genome using Bowtie2
Aligned reads shifted to accommodate Tn5 footprint
Peaks called by macs
Differential accessibility done in DiffBind
Assembly: GRCH38.p14 (GENCODEv47)
Supplementary files format and content: Normalized read count table generated

source_name: cell line

extract_protocol:
Trypsinize cell culture plates and aliquot 50,000 cells/reaction
ATAC-seq libraries generated from 50,000 cells/sample using OMNI-ATACseq protocol (Corces, et al, 2015). Libraries were sequenced using 50 bp paired-end reads on a NovaSeq6000 (Illumina).

value: 50 ng Nanaomycin A


title: BLEO-IPF Nintedanib Vehicle Sample 4016716106

description: Library name: 4016716106


title: CLEAR1_D8_PBMC_biolrep1,RNA

description: Library name: AML_3236_CLEAR1_D8_PBMC_biolrep1_RNA


title: IgA1_Donor 1

description: Library name: JK-T22


title: DACE657_mKate2_multiome_ATAC

description:
Library name: DACE657_mKate2_multiome_ATAC
10x_RNA_ATAC_multiome

data_processing:
All multiome datasets were processed using cellranger-arc-2.0.0 with default parameters, using the mm10 mouse annotation as reference.
Assembly: mm10
Supplementary files format and content: Unfiltered count matrices resulting from alignment and demultiplexing are deposited in the Matrix Market format for sparse matrix representation.
Supplementary files format and content: Merged fastq files, encoding the cell and molecule barcode information in fastq record headers, were obtained using SEQC (v0.2.8). Merged fastq files were aligned to transgenes in our mouse models model (GFP, rtTA3-IRES-mKate2, shRen) using BWA (0.7.17-r1188). Columns in _transgene_count.tsv.gz files are: (1) record_index, (2) numeric cell barcode resulting from encoding of sequence cell barcode using the DNA3Bit class of the SEQC package, (3) arbitrary gene identifier for each transgene, (4) UMI count (5) transgene_symbol.

growth_protocol: Mice were generated by 8-cell injection of KCshRen (Ptf1a-Cre; LSL-KrasG12D; Rosa26-CAGS-LSL-rtTA3-IRES-mKate2; TRE-GFP-shRen.713 or TRE-GFP-shp53.1224) ESCs, or through breeding KPfC (Ptf1a-Cre; LSL-KrasG12D;  Rosa26-CAGS-LSL-rtTA3-IRES-mKate2; p53flox/wt)

extract_protocol:
Pancretata were harvested from the indicated mouse models and processed for FACS sorting using Collagenase (1 mg/mL) & Dispase (2 U/mL) mix digestion solution and Gentle-MACS dissociator (mTDK_1 protocol), followed by a 0.05% Trypsin-EDTA step. For every sample that would be subjected to cell hashing, we used DNAse-free buffers following digestion. Samples were resuspended in 1 mL ACK-lysis buffer and incubated for 5 min at room temperature to deplete red blood cells, and washed the ACK lysis buffer with 20 mL HBSS. Samples  were washed 3 times with DNAse-free FACS buffer + STI, followed by filtering through a 40-μm strainer and FACS-based isolation of mKate2+/GFP+ or mKate2+ cells (KrasG12D+ pancreatic epithelial cells). Cell suspensions were incubated with Fc block and CD45-APC or CD45-APC-Cy7 antibody to mark immune cells. Live pancreatic epithelial cells (marked as mKate2-positive, CD45-negative and DAPI-negative) or immune cells (marked as mKate2-negative, CD45-positive and DAPI-negative) were sorted using Aria3 or Aria 1 sorter, and collected in 2% 1x PBS buffer containing 2% fetal bovine serum (FBS). Single-cell suspensions were spun down and resuspended in 0.05% BSA containing 1 U/µL Invitrogen Ambion RNase Inhibitor (AM2682, Thermo Fisher Scientific).
ATAC and gene expression libraries were prepared according to the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression workflow, following 10x Genomics guidelines for ATAC, gene expression, and sequencing preparation. Cells were pelleted (300 g, 5 min, 4°C), permeabilized in chilled lysis buffer, incubated on ice for 5 min, and washed in chilled buffer containing RNase inhibitor (Protector, Roche). After centrifugation (500 g, 5 min, 4°C), nuclei were resuspended in Nuclei Buffer (10x Genomics), counted, and adjusted to 3,000 nuclei/µL.  For each reaction, up to 15,400 nuclei were diluted in isotonic Tagmentation Buffer with RNase inhibitor and mixed with ATAC Buffer B and ATAC Enzyme B (10x Genomics) for transposition (37°C, 60 min). Samples were loaded onto a Chromium Next GEM Chip J with barcoding reagents, gel beads, and partitioning oil (10x Genomics) and processed on the Chromium Controller to generate GEMs. Reverse transcription and barcoding proceeded at 37°C for 45 min and 25°C for 30 min. Later, GEMs were broken, and the aqueous phase was purified using Dynabeads MyOne SILANE (10x Genomics) and SPRIselect magnetic bead cleanups (Beckman Coulter). Barcoded ATAC and cDNA fragments were pre-amplified and purified with SPRIselect.  ATAC libraries were constructed using sample indexing PCR with 10x Genomics reagents, followed by dual-sided SPRI size selection. cDNA was amplified, cleaned, fragmented, end-repaired, A-tailed, and ligated using 10x Genomics reagents, with SPRI-based purifications throughout. Final gene expression libraries were indexed using 10x Genomics dual-index reagents and purified with SPRIselect. Sequencing was performed according to 10x Genomics recommendations on an Illumina NovaSeq 6000.

treatment_protocol: GFP was induced by treatment of KCshRen mice with doxycycline (200 mg/kg; Envigo) in the chow starting at 5-6 weeks of age.

value: Pancreas

value: KPfC (p53 flox/wt)


title: CLEAR1_D8_PBMC_biolrep2,RNA

description: Library name: AML_3236_CLEAR1_D8_PBMC_biolrep2_RNA


title: CLEAR1_screen_PBMC_blasts,RNA

description: Library name: AML_3040_CLEAR1_screen_PBMC_blasts_RNA

value: Peripheral blood AML blasts


title: p489c_shRen_caer_multiome_2_ATAC

description:
Library name: JR-1497_p489c_shRen_caer_48h_multiome_2_ATAC
10x_RNA_ATAC_multiome

value: Epithelial

value: KCshRen

value: Dox


title: KG1A_50_R1

description: Library name: Sample-4


title: CLEAR1_screen_PBMC_lymphs,RNA

description: Library name: AML_3040_CLEAR1_screen_PBMC_lymphs_RNA


title: peripheral blood Treg, control, rep1

description: Library name: C1


title: p489c_shRen_caer_multiome_2

description:
Library name: JR-1497_p489c_shRen_caer_48h_multiome_2
10x_RNA_ATAC_multiome


title: IgA2_Donor 1

description: Library name: JK-T23

value: B cell

value: WT


title: KG1A_50_R2

description: Library name: Sample-5


title: KG1A_0_R3

description: Library name: Sample-3

value: 0 ng Nanaomycin A


title: BLEO-IPF Nintedanib Sample 4016714066

description: Library name: 4016714066

value: BLEO-IPF Nintedanib


title: IgG1_Donor 1

description: Library name: JK-T24


title: BLEO-IPF Nintedanib Sample 4016716110

description: Library name: 4016716110


title: DACE657_mKate2

description:
Library name: DACE657_mKate2_multiome
10x_RNA_ATAC_multiome


title: IgMD_Donor 1

description: Library name: JK-T20


title: p489c_shRen_caer_multiome_1_ATAC

description:
Library name: JR-1497_p489c_shRen_caer_48h_multiome_1_ATAC
10x_RNA_ATAC_multiome


title: BLEO-IPF Nintedanib Sample 4016714052

description: Library name: 4016714052


title: KG1A_0_R1

description: Library name: Sample-1


title: BLEO-IPF Nintedanib Sample 4016714060

description: Library name: 4016714060


title: p489c_shRen_caer_multiome_1

description:
Library name: JR-1497_p489c_shRen_caer_48h_multiome_1
10x_RNA_ATAC_multiome


title: CLEAR1_D15_PBMC_biolrep2,RNA

description: Library name: AML_3040_CLEAR1_D15_PBMC_biolrep2_RNA

value: Peripheral blood mononuclear cells

value: paired-end

value: Illumina NovaSeq S4


title: CLEAR1_D58_PBMC,Protein

description: Library name: AML_3040_CLEAR1_D58_PBMC_Protein


title: BLEO-IPF Nintedanib Sample 4016714039

description: Library name: 4016714039

value: Lung


title: CLEAR1_D15_PBMC_biolrep2,Protein

description: Library name: AML_3040_CLEAR1_D15_PBMC_biolrep2_Protein


title: peripheral blood Treg, control, rep2

description: Library name: C2

value: peripheral blood

value: Treg


title: peripheral blood, HADA, rep2

description: Library name: H3

data_processing:
For ATAC-Seq data, raw reads were similarly quality controlled with FastQC and trimmed using Trimmomatic. Cleaned reads were aligned to the reference genome using Bowtie2, with duplicate reads marked and removed using Picard Tools. Peak calling was executed with MACS2 to identify open chromatin regions, and a count matrix of peak intensities across samples was generated using tools like featureCounts or BedTools. Finally, both gene expression and chromatin accessibility matrices were normalized and prepared for downstream analyses.
Assembly: GRCm39
Supplementary files format and content: narrowPeak

extract_protocol:
Peripheral blood samples were subjected to red blood cell lysis, followed by two washes with PBS. Approximately 50,000 leukocytes were used for each ATAC-seq experiment.
Cells were lysed on ice using a lysis buffer containing 10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl₂, and 0.1% IGEPAL CA-630 to release nuclei. The nuclear pellets were resuspended in a transposition reaction mix containing Tn5 transposase and incubated at 37°C for 30 minutes. Adapter 1 and Adapter 2 were added in equimolar amounts, and the libraries were amplified by PCR using the ATAC-seq_Novogene Kit

value: white blood cell


title: BLEO-IPF Nintedanib Sample 4016716374

description: Library name: 4016716374


title: BLEO-IPF Nintedanib Sample 4016716042

description: Library name: 4016716042


title: CLEAR1_D58_PBMC,RNA

description: Library name: AML_3040_CLEAR1_D58_PBMC_RNA


title: CLEAR1_screen_PBMC_blasts,Protein

description: Library name: AML_3040_CLEAR1_screen_PBMC_blasts_Protein


title: CTRL Vehicle Sample 4016713893

description: Library name: 4016713893

value: CTRL Vehicle


title: Organoid_ccRCC_Paetient_5_IgG1

city: Fukuoka

first: Michitaka

last: Nakano

state: Fukuoka

address: 3-1-1, Maidashi, Higashi-ku

department: Department of Medicine and Biosystemic Sciences

country: Japan

institute: Kyushu University

description: Library name: ccRCC5_Control

data_processing:
The demultiplexing, barcoded processing, gene counting and aggragation were made using the Cell Ranger software v7.2.0 (https://www.10xgenomics.com/support/software/cell-ranger/latest/getting-started/cr-what-is-cell-ranger)
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: clear cell renal carcinoma

growth_protocol: ALI organoids from ccRCC or NSCLC were generated and culture for 8 days cultures.

extract_protocol:
Cell population were extracted by FACS sorting by gating CD45+ cells or CD45+ CD11b+ HLA-DR+ CD68+ cells.
Purified cells were counted and subjected to 10X Genomics Chromium single cell 5' platform following to manufacurer's protocol using the Chromium NextGEM Single Cell 5' Kit v2 (PN-1000263).

treatment_protocol: IgG1 isotype control or anti-CD47 were added to the media.

value: clear cell renal carcinoma

value: immune cells


title: peripheral blood, control, rep2

description: Library name: C6


title: CLEAR1_EOP,RNA

description: Library name: AML_2856_CLEAR1_EOP_RNA

source_name: T cells

value: T cells


title: BLEO-IPF Nintedanib Vehicle Sample 4016714086

description: Library name: 4016714086

value: BLEO-IPF Nintedanib Vehicle


title: KG1A_0_R2

description: Library name: Sample-2


title: peripheral blood, control, rep1

description: Library name: C5


title: Organoid_ccRCC_Paetient_3_CD47

description: Library name: ccRCC3_CD47


title: Organoid_ccRCC_Paetient_5_CD47

description: Library name: ccRCC5_CD47


title: peripheral blood, HADA, rep1

description: Library name: H2


title: K3_shCtrl_batch5_cellHash

description:
Library name: shRen_caer_3weeks_repeat_cellHash
10x_v3

data_processing:
All scRNA-seq datasets were demultiplexed, barcode-corrected, aligned and UMI-corrected with SEQC using mouse genome mm10 and default parameters.
Assembly: mm10
Supplementary files format and content: Unfiltered count matrices resulting from alignment and demultiplexing with our custom pipeline SEQC (v0.2.8) are deposited in the Matrix Market format for sparse matrix representation. Cell barcodes in processed data files are encoded using the DNA3Bit class of the SEQC package.
Supplementary files format and content: Merged fastq files, encoding the cell and molecule barcode information in fastq record headers, were obtained using SEQC (v0.2.8). Merged fastq files were aligned to transgenes in our mouse models (GFP, rtTA3-IRES-mKate2, shRen, shp53) using BWA (0.7.17-r1188). Columns in _transgene_count.tsv.gz files are: (1) record_index, (2) numeric cell barcode resulting from encoding of sequence cell barcode using the DNA3Bit class of the SEQC package, (3) arbitrary gene identifier for each transgene, (4) UMI count (5) transgene_symbol.

growth_protocol: Mice were generated by 8-cell injection of KCshRen or KCshp53 (Ptf1a-Cre; LSL-KrasG12D; Rosa26-CAGS-LSL-rtTA3-IRES-mKate2; TRE-GFP-shRen.713 or TRE-GFP-shp53.1224) ESCs.

treatment_protocol: GFP was induced by treatment of the resulting mice with doxycycline (200 mg/kg; Envigo) in the chow starting at 5-6 weeks of age.

value: Pancreas

value: Epithelial

value: KCshRen

value: Dox


title: Fresh_ccRCC_Paetient_4

description: Library name: ccRCC4_Fresh

value: No treatment


title: CLEAR1_D15_PBMC_biolrep1,Protein

description: Library name: AML_3040_CLEAR1_D15_PBMC_biolrep1_Protein

value: Peripheral blood mononuclear cells


title: CTRL Vehicle Sample 4016713931

description: Library name: 4016713931


title: CTRL Vehicle Sample 4016713960

description: Library name: 4016713960


title: Organoid_ccRCC_Paetient_4_CD47

description: Library name: ccRCC4_CD47


title: ALI ccRCC organoid TAM treated by IL4_2

description: Library name: IL4 TAM_2

data_processing:
Good quality of reads were generated by removing reads containing adapters, ploy-N, and low-quality reads using fastp software
Trimmed reads were mapped on human reference genome (hg) using Hisat2 v2.0.5
Read count matrices were generated using featureCounts v1.5.0-p3 and FPKM of each gene was calculated based on the length of the gene and read count
Assembly: hg38
Supplementary files format and content: csv file includes raw counts for each sample
Supplementary files format and content: csv files include FPKM values for each sample

growth_protocol: ALI organoids from ccRCC were generated and culture for 8 days.

extract_protocol:
Cell population were extracted by FACS sorting by gating CD45+ CD11b+ HLA-DR+ CD68+ cells. TAM cells were sorted into PBS+10%FBS, followed by RNA isolation using PicoPure RNA isolation kit (Applied Biosystems, KIT0204).
Isolated RNA sample quality and quantity was assessed by BioAnalyzer RNA Pico Assay. Library construction was performed following to manufaturer's protocol for SMART-seq v4 Ultra Low Input RNA kit. Llibraries were sequenced on an Illumina NovaSeq X Plus.

treatment_protocol: IFN-γ or IL-4 were added into the cultre.

value: macrophages


title: Organoid_ccRCC_Paetient_2_CD47

description: Library name: ccRCC2_CD47


title: K3_shp53_batch5_cellHash

description:
Library name: shp53_caer_3weeks_repeat_cellHash
10x_v3


title: CLEAR1_EOP,Protein

description: Library name: AML_2856_CLEAR1_EOP_Protein

value: paired-end

value: Illumina NovaSeq S4


title: Organoid_ccRCC_Paetient_2_IgG1

description: Library name: ccRCC2_Control


title: BLEO-IPF Nintedanib Sample 4016713659

description: Library name: 4016713659

value: Lung

value: BLEO-IPF Nintedanib


title: CLEAR1_D15_PBMC_biolrep1,RNA

description: Library name: AML_3040_CLEAR1_D15_PBMC_biolrep1_RNA


title: K3_shp53_batch3_cellHash

description:
Library name: p489c_shp53_caer_3weeks_cellHash
10x_v3


title: ALI ccRCC organoid TAM treated by IFN-γ_2

description: Library name: IFN TAM_2

value: IFN-γ


title: BLEO-IPF Nintedanib Vehicle Sample 4016713856

description: Library name: 4016713856


title: BLEO-IPF Nintedanib Vehicle Sample 4016713700

description: Library name: 4016713700


title: BLEO-IPF Nintedanib Vehicle Sample 4016713786

description: Library name: 4016713786


title: Organoid_ccRCC_Paetient_4_IgG1

description: Library name: ccRCC4_Control


title: BLEO-IPF Nintedanib Sample 4016713435

description: Library name: 4016713435


title: peripheral blood, control, rep3

description: Library name: C9

value: peripheral blood

value: white blood cell


title: peripheral blood, HADA, rep3

description: Library name: H10


title: BLEO-IPF Nintedanib Sample 4016713471

description: Library name: 4016713471


title: ALI ccRCC organoid TAM treated by IL4_1

description: Library name: IL4 TAM_1

value: clear cell renal carcinoma


title: BLEO-IPF Nintedanib Vehicle Sample 4016713374

description: Library name: 4016713374


title: Organoid_ccRCC_Paetient_1_CD47

description: Library name: ccRCC1_CD47

value: immune cells


title: Fresh_ccRCC_Paetient_2

description: Library name: ccRCC2_Fresh


title: K3_shCtrl_batch3_cellHash

description:
Library name: p489c_shRen_p53exp_caer_3weeks_cellHash
10x_v3


title: K3_shCtrl_batch5

description:
Library name: shRen_caer_3weeks_repeat
10x_v3


title: Organoid_ccRCC_Paetient_3_IgG1

description: Library name: ccRCC3_Control


title: CTRL Vehicle Sample 4016713358

description: Library name: 4016713358

value: CTRL Vehicle


title: K3_shCtrl_batch3

description:
Library name: p489c_shRen_p53exp_caer_3weeks
10x_v3

value: Pancreas


title: ALI ccRCC organoid TAM treated by IL4_3

description: Library name: IL4 TAM_3


title: ALI ccRCC organoid TAM treated by IFN-γ_1

description: Library name: IFN TAM_1


title: ALI ccRCC organoid TAM treated by IFN-γ_3

description: Library name: IFN TAM_3


title: BLEO-IPF Nintedanib Sample 4016713166

description: Library name: 4016713166


title: Organoid_NSCLC_Paetient_2_CD47

description: Library name: NSCLC2_CD47

source_name: non small cell lung cancer

value: non small cell lung cancer


title: CTRL Vehicle Sample 4016713070

description: Library name: 4016713070


title: ALI ccRCC organoid TAM treated by control_1

description: Library name: Control TAM_1

value: Control


title: Fresh_NSCLC_Paetient_2

description: Library name: NSCLC2_Fresh


title: BLEO-IPF Nintedanib Vehicle Sample 4016712662

description: Library name: 4016712662

value: BLEO-IPF Nintedanib Vehicle


title: Organoid_NSCLC_Paetient_2_IgG1

description: Library name: NSCLC2_Control


title: Organoid_NSCLC_Paetient_1_CD47

description: Library name: NSCLC1_CD47