title: ADSCs:T24(10:1)-1,day 14

description: Library name: D14CoC101_1


title: Stat1-ChIP, untreated WT748A, rep.2

status: Public on Jul 09 2025

type: SRA

city: Kanagawa

first: Kazuki

last: Okuyama

address: 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama

department: IMS

country: Japan

institute: RIKEN Yokohama

description: Library name: Untreated T748A, rep.2

library_source: genomic

data_processing:
Adapter sequences were trimmed from the reads by Cutadapt (v4.0)
Mapping to the mm10 genome using bowtie2 (v2.5.0)
Removing reads with low mapping quality (MAPQ<30) , mitochondrial reads, and improperly paired reads using Filter BAM (v2.5.2)
Removing PCR duplicates by MarkDuplicates (v2.18.2.3)
Peak calling using MACS2 callpeak (v2.2.7.1) with default settings
Generate BigWig files from BedGraph using Convert BedGraph to BigWig (v1.0.1)
Regions were extended 100bp for both directions from summits while keeping the most significant summit when nearby regions were overlapped and assigned as peaks
Assembly: mm10
Supplementary files format and content: BigWig files

molecule: genomic DNA

organism: Mus musculus

source_name: Colon

extract_protocol:
Cross-linking was quenched with 1.375 M glycine for 5 minutes at room temperature. Nuclei were isolated, and chromatin was enzymatically sheared using micrococcal nuclease for 17 minutes at 37 °C. Five percent of the sheared chromatin was reserved as input, and the remainder was subjected to immunoprecipitation using anti–STAT1 antibody (1:50 dilution). Immunocomplexes were reverse cross-linked overnight at 65 °C with Proteinase K, and DNA was purified using phenol/chloroform extraction.
ChIP DNA libraries were prepared using the KAPA Hyper Prep Kit (KAPA Biosystems) according to the manufacturer’s instructions. Paired-end sequencing (2 × 101 bp) was performed on an Illumina NovaSeq 6000 platform (Illumina Inc., San Diego, CA, USA). Adapter trimming was conducted with Cutadapt (v4.8), using the following adapter sequences: Read 1: 5′-AGATCGGAAGAGCACACGTCTGAACTCCAGTCA-3′; Read 2: 5′-AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT-3′. Read quality was assessed using FastQC (default settings). Trimmed reads were aligned to the mouse reference genome (mm10) using Bowtie2 (v2.5.3) with the “very sensitive end-to-end” preset. BAM files were further processed using the Galaxy platform. Low-quality reads (MAPQ < 30), improperly paired reads, mitochondrial reads, and PCR duplicates were removed using ‘Filter’ (v2.4.2) and ‘MarkDuplicates’ (v3.1.1.0). Peak calling was performed using MACS2 callpeak (v2.2.9.1).

treatment_protocol: Briefly, IECs were isolated from DSS-treated Wt and Stat1T748A littermate mice and cross-linked with 3.7% formaldehyde for 10 minutes at room temperature.

tag: tissue

value: Colon

tag: cell type

value: Intestinal epithelial cells

tag: genotype

value: Stat1 T748A/T748A

tag: treatment

value: Stat1 (D1K9Y) Rabbit mAb


title: Stat1-ChIP, untreated WT748A, rep.1

description: Library name: Untreated T748A, rep.1


title: LCLinf_EBV_WT_rep4

city: Corbeil-Essonnes

first: Hélène

last: Polvèche

address: 28, Rue Henri Desbruères

country: France

institute: I-Stem

description: Library name: LCLinf_EBV_WT_S46

library_source: transcriptomic

data_processing:
QC : FastQC ( v0.11.9 )
Filters : cutadapt ( 4.1 ), PRINSEQ-lite ( 0.20.4 )
Mapping & QC : STAR ( 2.7.6a), samtools ( 0.1.19 )
Counting : HTSeq-count ( 0.13.5)
Assembly: GRCh38.110
Supplementary files format and content: Raw counts of each sample (txt)

molecule: total RNA

organism: Homo sapiens

source_name: Human peripheral B cells (PBL) purified from blood samples using the RosetteSep human enrichment kit (Stemcell Technologies; 15064)

extract_protocol:
Total RNA was extracted using the Direct-zolTM RNA MicroPrep Kit (Zymo Research)
RNA libraries for RNAseq were prepared by Novogen: messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

value: Lymphoblastoid cell line (LCL) established from cells infected with  B95.8 EBV (2089) recombinant viruses.

tag: time

value: Three to four weeks post infection

tag: batch


title: NTM-infected mouse lung tissue – Atg7 cKO, spatial transcriptomics

city: Seoul

first: Yeonju

last: Lee

address: 500-1 Anam-dong, Seongbuk-gu

country: South Korea

institute: Sungkyunkwan University

description:
Library name: ATG7_KO_MAV-3_CR_23_15194_FP_R_SSV_1
FFPE tissue sample

data_processing:
Sequencing reads were processed using the Space Ranger software (10x Genomics) and aligned to the mouse reference genome mm10 (2020-A).
Feature-barcode matrices and spatial image files were generated as outputs from Space Ranger.
Aggregated HDF5 matrices were imported into R and split by sample.
Spots with fewer than 300 detected genes were excluded from further analysis.
Downstream analysis was performed using the Seurat package.
Assembly: mm10 (2020-A)
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz : list of gene IDs
Supplementary files format and content: matrix.mtx.gz : gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg
Supplementary files format and content: aligned_tissue_image.jpg
Supplementary files format and content: cytassist_image.tiff
Supplementary files format and content: detected_tissue_image.jpg
Supplementary files format and content: scalefactors_json.json
Supplementary files format and content: spatial_enrichment.csv
Supplementary files format and content: tissue_hires_image.png
Supplementary files format and content: tissue_lowres_image.png
Supplementary files format and content: tissue_positions.csv
Library strategy: Spatial Transcriptomics

source_name: lung

extract_protocol:
Tissue samples were processed using Visium CytAssist Spatial Gene Expression for FFPE protocol. Lung tissues from Mav-infected Atg7 cWT and Atg7 cKO mice (21 dpi) were fixed in 10% neutral buffered formalin, embedded in paraffin, and sectioned at 5 µm thickness using a microtome. Sections were placed on Visium CytAssist slides and processed following the manufacturer’s protocol (10x Genomics #CG000409). RNA was extracted using the RNeasy FFPE Kit (Qiagen #73504) after deparaffinization (Qiagen Deparaffinization Solution #19093). RNA integrity was assessed using Agilent TapeStation (High Sensitivity RNA ScreenTape #5067-5579) by measuring DV200 values.
Libraries were prepared from FFPE tissue sections using the Visium Spatial Gene Expression for FFPE Kit, Mouse Transcriptome v1 (10x Genomics #1000521) and Dual Index Kit TS Set A (10x Genomics #1000251) following the manufacturer’s instructions. H&E staining was performed prior to permeabilization using standard reagents (Xylene, Ethanol, Eosin Y, Mayer's Hematoxylin, Bluing Reagent), and imaging was conducted using Nikon Eclipse Ti2 microscope (QC at 4X, Visium at 20X).

value: lung

value: Lung Epithelial cells, Stromal cells, Immune cells

value: Atg7fl/fl LysM-Cre+/+

value: NTM infection


title: ADSCs-3,day 14

city: Haikou

first: Denggao

last: Huang

state: Hainan

address: No.43 avenue Renmin Road

country: China

institute: Haikou people hospital

description: Library name: D14hADSCs_3

data_processing:
fastp software were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality was also verified using fastp. We used HISAT2 to map reads to the reference genome of Homo sapiens GRCh38. The mapped reads of each sample were assembled using StringTie  with default parameters.
Assembly: Homo sapiens GRCh38
Supplementary files format and content: All transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare . After the final transcriptome was generated, StringTie and was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM × exon_length(kB)]). The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and with parametric F-test comparing nested linear models (p value < 0.05) by R package edgeR

source_name: cell line

extract_protocol:
Total RNA was isolated and purified via TRIzol reagent according to the manufacturer's protocol(Vazyme)
RNA libraries for RNA-seq were prepared using Illumina NovaSeq™ 6000 according to the manufacturer's recommended protocol.

value: cell line

tag: cell line

value: ADSCs

value: stromal stem cells

value: wt

value: day 14


title: LCLinf_EBV_WT_rep2

description: Library name: LCLinf_EBV_WT_S26

value: Human peripheral B cells (PBL) purified from blood samples using the RosetteSep human enrichment kit (Stemcell Technologies; 15064)


title: Stat1-ChIP, DSS-treated T748A, rep.1

description: Library name: DSS T748A, rep.1


title: Stat1-ChIP, untreated Wt, rep.2

description: Library name: Untreated WT, rep.2

value: Stat1 +/+


title: LCLinf_EBV_dEBNALP_rep2

description: Library name: LCLinf_EBV_dEBNALP_S27

value: Lymphoblastoid cell line (LCL) established from cells infected with EBNALP KO B95.8 EBV (8060) recombinant viruses.


title: LCLinf_EBV_WT_rep1

description: Library name: LCLinf_EBV_WT_S16


title: Stat1-ChIP, untreated Wt, rep.1

description: Library name: Untreated WT, rep.1

value: Colon

value: Intestinal epithelial cells


title: LCLinf_EBV_dEBNALP_rep1

description: Library name: LCLinf_EBV_dEBNALP_S17


title: Bprim_rep4

description: Library name: Bprim_S41

value: non treated

value: prior treatment or infection


title: Bprim_rep1

description: Library name: Bprim_S11


title: Cranial bone deffect, Gel100, 7 days, biol rep 5

city: Lexington

first: Ni

last: Su

state: KY

address: 760 PRESS AVE

country: USA

institute: University of Kentucky

description:
Library name: Cranial bone deffect, Gel100
10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using Cell Ranger software (10x Genomics)
Assembly: mouse mm10
Supplementary files format and content: Tab-separated value files and matrix files

source_name: Cranial bone defect

extract_protocol:
Upon harvest at week 1, cells from the five mice were pooled together for each material composition. Scaffolds from different groups were washed with DPBS and digested in an enzyme mixture containing 0.1 mg/mL Liberase TM (Sigma-Aldrich), 0.2 U/mL Chondroitinase (Sigma-Aldrich ABC C2905), and 100 U/mL Hyaluronidase (Sigma-Aldrich H3506) for 30 minutes at 37°C on a shaker. The digested scaffolds were then passed through a 70 μm cell strainer, with any remaining tissue in the strainer being minced using a syringe plunger and washed with DPBS containing 2% FBS. Red blood cells were removed with red blood cell lysis buffer (BioLegend). Cell viability was assessed via flow cytometry, and the viable cells were sorted for library preparation
Approximately 10,000 viable cells were loaded into a 10x Chromium Controller (10x Genomics) to generate single-cell gel beads-in-emulsion (GEMs). The GEMs were processed to reverse transcribe the cells' RNA, producing cDNA, which was then amplified. This amplified cDNA was used to construct the single-cell library using the Chromium Single Cell 3' Reagent Kits v3 (10x Genomics) according to the manufacturer's protocol. The libraries were quantified with a Qubit fluorometer, and their quality was assessed using an Agilent Bioanalyzer. The resulting libraries were sequenced on an Illumina NovaSeq 6000 platform to achieve the desired sequencing depth.

treatment_protocol: The periosteum was carefully removed, and a drill was used to create a circular defect with a diameter of 3.5 mm on the cranial bone. The defect was then filled with a 3.5 mm diameter acellular scaffold, and the skin incision was sutured. Two scaffold groups were included for the study, including Gel100 and Gel50_CS50, with n=5 per group.

value: Cranial bone defect

tag: strain

value: Balb/c

tag: age

value: 6 weeks

tag: Sex

value: female

value: Gel100 scaffold

value: 1 week


title: Cranial bone deffect, Gel50_CS50, 7 days, biol rep 5

description:
Library name: Cranial bone deffect, Gel50_CS50
10x Genomics

value: Gel50_CS50 scaffold


title: Bprim_rep5

description: Library name: Bprim_S51


title: Stat1-ChIP, DSS-treated Wt, rep.2

description: Library name: DSS WT, rep.2

value: Stat1 (D1K9Y) Rabbit mAb


title: Binf_EBV_WT_48h_rep5

description: Library name: Binf_EBV_WT_48h_S52

value: infection with B95.8 EBV (2089) recombinant viruses

value: 48h post infection


title: Bprim_rep2

description: Library name: Bprim_S21

value: Human peripheral B cells (PBL) purified from blood samples using the RosetteSep human enrichment kit (Stemcell Technologies; 15064)


title: Binf_EBV_WT_48h_rep4

description: Library name: Binf_EBV_WT_48h_S42


title: Binf_EBV_WT_48h_rep2

description: Library name: Binf_EBV_WT_48h_S22


title: Binf_EBV_dEBNALP_48h_rep4

description: Library name: Binf_EBV_dEBNALP_48h_S44

value: infection with EBNALP KO B95.8 EBV (8060) recombinant viruses


title: Binf_EBV_dEBNALP_48h_rep5

description: Library name: Binf_EBV_dEBNALP_48h_S54


title: Binf_EBV_dEBNALP_48h_rep2

description: Library name: Binf_EBV_dEBNALP_48h_S24


title: ADSCs:T24(10:1)-2,day 14

description: Library name: D14CoC101_2

value: cell line

value: stromal stem cells and tumor cell

value: wt

value: co-culture

value: day 14


title: Binf_EBV_WT_48h_rep1

description: Library name: Binf_EBV_WT_48h_S12


title: Binf_EBV_dEBNALP_48h_rep1

description: Library name: Binf_EBV_dEBNALP_48h_S14


title: Stat1-ChIP, untreated Wt, rep.3

description: Library name: Untreated WT, rep.3

value: Colon

value: Intestinal epithelial cells

value: Stat1 +/+


title: Binf_EBV_dEBNA2_48h_rep5

description: Library name: Binf_EBV_dEBNA2_48h_S53

value: infection with EBNA2 KO. B95.8 EBV (3057) recombinant viruses


title: Binf_EBV_dEBNA2_48h_rep4

description: Library name: Binf_EBV_dEBNA2_48h_S43


title: Binf_EBV_dEBNA2_48h_rep1

description: Library name: Binf_EBV_dEBNA2_48h_S13


title: Bact_CD40L_IL4_48h_rep4

description: Library name: Bact_CD40L_IL4_48h_S45

value: CD40 Ligand + interleukin 4


title: Bact_CD40L_IL4_48h_rep5

description: Library name: Bact_CD40L_IL4_48h_S55


title: Binf_EBV_dEBNA2_48h_rep2

description: Library name: Binf_EBV_dEBNA2_48h_S23


title: Bact_CD40L_IL4_48h_rep2

description: Library name: Bact_CD40L_IL4_48h_S25


title: Bact_CD40L_IL4_48h_rep1

description: Library name: Bact_CD40L_IL4_48h_S15


title: Hypoxia HEK MIR210-KO replicate 4

city: Bucharest

first: Mihai Bogdan

last: Preda

state: - Select -

address: BP Hasdeu, Nr. 8, Sector 5

department: Stem Cell Biology

country: Romania

institute: Institute of Cellular Biology and Pathology "Nicolae Simionescu"

description: Library name: Hypoxia sample 8

data_processing:
Alignment of the raw fastq-data with STAR v2.6.1d to reference genome.
FeatureCounts v1.5.0-p3 was used to count the read numbers mapped of each gene.
Differential Analysis was performed using DESeq2 (v1.20.0) or EdgeR (v3.24.3) to produce normalized counts and the data were log2-transformed.
Assembly: Homo sapiens, GRCh38
Supplementary files format and content: Tab-delimitated text files include raw counts for each sample in normoxia and hypoxia

source_name: Kidney; Embryo

growth_protocol: DMEM High Glucose (4.5 g/l), with L-Glutamine + 10% heat-inactivated FBS + 1x Penicillin/Streptomycin/Amphotericin.

extract_protocol:
Total RNA using TRIzol™ Reagent (ThermoFisher Scientific).
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

treatment_protocol: Normoxia (21% O₂) or hypoxia (1% O₂) for 24 hours.

value: Kidney; Embryo

value: epithelial morphology

value: Hypoxia


title: Hypoxia HEK 210HG-KO replicate 1

description: Library name: Hypoxia sample 9


title: Hypoxia HEK 210HG-KO replicate 3

description: Library name: Hypoxia sample 11


title: Hypoxia HEK MIR210-KO replicate 1

description: Library name: Hypoxia sample 5


title: Hypoxia HEK WT replicate 4

description: Library name: Hypoxia sample 4


title: Hypoxia HEK 210HG-KO replicate 2

description: Library name: Hypoxia sample 10


title: Hypoxia HEK WT replicate 2

description: Library name: Hypoxia sample 2


title: Hypoxia HEK WT replicate 1

description: Library name: Hypoxia sample 1


title: Normoxia HEK 210HG-KO replicate 4

description: Library name: Normoxia sample 12

value: Normoxia


title: Normoxia HEK 210HG-KO replicate 2

description: Library name: Normoxia sample 10


title: Normoxia HEK 210HG-KO replicate 3

description: Library name: Normoxia sample 11


title: Hypoxia HEK WT replicate 3

description: Library name: Hypoxia sample 3


title: Hypoxia HEK MIR210-KO replicate 2

description: Library name: Hypoxia sample 6


title: Normoxia HEK MIR210-KO replicate 4

description: Library name: Normoxia sample 8


title: Normoxia HEK MIR210-KO replicate 3

description: Library name: Normoxia sample 7


title: FFPE lung slides control mouse, Day21, sample 6

city: Parma

first: Erica

last: Ferrini

address: Via Largo Belloli

country: Italy

institute: Chiesi Farmaceutici

description: Library name: 2403_Ctrl_5

data_processing:
The tool cutadapt (version 4.4) was used to remove the adapter sequence (if present) and the very short reads (reads length < 30).
The sample was mapped on Mus Musculus Gencode.vM29, obtained from GenCode, using the bioinformatics tool STAR (version 2.7.10b), with the standard parameters for paired reads.
The quantification of transcripts expressed for each sequenced samples was performed using FeatureCounts (version 2.0.3).
After pre-filtering to select for genes covered by at least 10 reads, Bioconductor package DESeq2 (version 1.42.1) was used to normalize the data, using the median of ratio, to perform the differential expression analysis.
Assembly: mm39
Supplementary files format and content: tab-delimited text includes raw counts for each Sample
Supplementary files format and content: tab-delimited text includes normalized counts for each Sample after DESeq2 analysis

extract_protocol:
Total RNA was extracted from a 10 µm thick coronal slice using the RNeasy FFPE Kit (Qiagen). . Indexed libraries were prepared from 8 ng of purified total RNA.
Indexed libraries were prepared using the SMARTer Stranded Total RNA-Seq Kit v3 – Pico Input Mammalian following the manufacturer’s instructions.

value: 7-8 weeks old

value: Male

value: lung

value: Saline


title: Normoxia HEK MIR210-KO replicate 2

description: Library name: Normoxia sample 6


title: FFPE lung slides control mouse, Day21, sample 5

description: Library name: 2402_Ctrl_4


title: Normoxia HEK MIR210-KO replicate 1

description: Library name: Normoxia sample 5


title: FFPE lung slides control mouse, Day21, sample 3

description: Library name: 2400_Ctrl_2


title: FFPE lung slides control mouse, Day21, sample 4

description: Library name: 2401_Ctrl_3


title: Normoxia HEK WT replicate 4

description: Library name: Normoxia sample 4


title: Normoxia HEK WT replicate 3

description: Library name: Normoxia sample 3


title: FFPE lung slides BLM-treated mouse, Day21, sample 7

description: Library name: 2176_BLM_7

value: Bleomycin


title: FFPE lung slides control mouse, Day21, sample 2

description: Library name: 2399_Ctrl_1


title: FFPE lung slides control mouse, Day21, sample 1

description: Library name: 2185_BLM_8


title: Hypoxia HEK 210HG-KO replicate 4

description: Library name: Hypoxia sample 12


title: Hypoxia HEK MIR210-KO replicate 3

description: Library name: Hypoxia sample 7


title: Normoxia HEK WT replicate 2

description: Library name: Normoxia sample 2


title: FFPE lung slides BLM-treated mouse, Day21, sample 6

description: Library name: 2175_BLM_6


title: FFPE lung slides BLM-treated mouse, Day21, sample 5

description: Library name: 2174_BLM_5


title: Normoxia HEK WT replicate 1

description: Library name: Normoxia sample 1


title: FFPE lung slides BLM-treated mouse, Day21, sample 3

description: Library name: 2508_BLM_3


title: Normoxia HEK 210HG-KO replicate 1

description: Library name: Normoxia sample 9


title: FFPE lung slides BLM-treated mouse, Day21, sample 1

description: Library name: 2501_BLM_1


title: Pt48_T_2

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

data_processing:
Sequencing was performed on HiSeq 2500 or NovaSeq 6000 platform in a 75-base or 101-base single-end mode.
Illumina RTA v1.18.64 or RTA v3.4.4 software was used for base calling.
Generated reads were mapped to the human (hg19) reference genome using TopHat (version 2.1.1).
The fragments per kilobase of exon per million mapped fragments (FPKMs) was calculated using Cuffdiff version 2.2.1.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: colorectal cancer

extract_protocol:
Total RNA was isolated with miRNeasy Mini or Micro Kit (QIAGEN) according to the manufacturer’s instructions.
RNA libraries were prepared using SMART-Seq HT Kit (Takara Bio, Japan) and NexteraXT DNA Library Preparation Kit (Illumina); or TruSeq stranded mRNA Library Prep Kit (Illumina).

value: colorectal cancer


title: FFPE lung slides BLM-treated mouse, Day21, sample 4

description: Library name: 2509_BLM_4


title: Pt45_T_2


title: FFPE lung slides BLM-treated mouse, Day21, sample 2

description: Library name: 2502_BLM_2


title: Pt45_T_1


title: E14.5_MGE_YAP_TAZ_KO_3

city: Memphis

first: Xinwei

last: Cao

state: TN

address: 62 Danny Thomas Pl

department: Developmental Neurobiology

institute: St. Jude Children's Research Hospital

description:
Library name: Sample 23
10x Genomics

data_processing:
General quality control and filtering: Sequences from each individual Illumina sequencing dataset were demultiplexed using bcl2fastq v2.20.0.422 (Illumina). Sequencing reads were processed using 10X Genomics Cell Ranger version 7.0.0, with reads mapping to the mouse reference genome mm10 version 2020-A (10x Genomics). Quality control filtering, clustering, dimensionality reduction, visualization, and differential gene expression were performed using Seurat v4.0.4 with R v4.1.036. Each dataset was initially filtered so that genes that were expressed in at least three or more cells and cells that expressed at least 200 genes were retained when reading in the data. Then cells were excluded if they: (1) expressed greater than 10% of unique transcripts derived from mitochondrial genes, (2) unique transcripts derived from mitochondrial genes expressing more than 3 median absolute deviations (MADs) from the median number of unique transcripts derived from mitochondrial genes, (3) had fewer than 2,500 genes expressed, or (3) had UMI counts below 5,000. Afterward, cells with more than 3 MADs from the median number of genes expressed were removed.
Assembly: mm10 version 2020-A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Medial Ganglionic Eminence

extract_protocol:
MGEs were obtained by first extracting the embryonic brain and detaching the telencephalon, followed by removing the dorsal telencephalon and finally dissecting the MGE from the rest of the subpallium in cold PBS. Both MGEs from the same embryo were dissociated using either Stem-Pro Accutase (Thermo Scientific A1110501) or a papain dissociation kit (Worthington LK003150) for less than 5 min. Cells were filtered through Flowmi cell strainers (SP Bel-Art #13680040). Cell viability was analyzed with a Countess cell counter and only samples with a viability of >90% were processed for scRNAseq.
A 3’ scRNAseq kit from 10x Genomics was used according to kit instructions. Up to 10K cells were loaded per each bead mix.

value: Medial Ganglionic Eminence

value: Neural progenitors


title: Pt42_T_2


title: E14.5_MGE_YAP_TAZ_KO_2

description:
Library name: Sample 22
10x Genomics


title: E14.5_MGE_YAP_TAZ_KO_1

description:
Library name: Sample 21
10x Genomics


title: Pt42_T_1


title: E14.5_MGE_YAP_TAZ_CONTROL_3

description:
Library name: Sample 20
10x Genomics


title: Pt40_T_2


title: Pt41_T_1


title: Pt36_T_2


title: E14.5_MGE_YAP_TAZ_CONTROL_1_Ln2

description:
Library name: Sample 17
10x Genomics


title: Pt40_T_1


title: Pt28_T_2


title: Pt41_T_2


title: E14.5_MGE_YAP_TAZ_CONTROL_1_Ln1

description:
Library name: Sample 16
10x Genomics


title: Pt36_T_1


title: E14.5_MGE_TEAD_DKO_3

description:
Library name: Sample 15
10x Genomics


title: Pt28_T_1


title: Pt48_sphere_2


title: E14.5_MGE_TEAD_DKO_2

description:
Library name: Sample 14
10x Genomics


title: E14.5_MGE_TEAD_DKO_1_Ln3

description:
Library name: Sample 13
10x Genomics


title: Pt48_T_1


title: E14.5_MGE_TEAD_DKO_1_Ln2

description:
Library name: Sample 12
10x Genomics


title: Pt48_sphere_1


title: Pt45_sphere_2


title: E14.5_MGE_TEAD_DKO_1_Ln1

description:
Library name: Sample 11
10x Genomics


title: Pt42_sphere_2


title: E14.5_MGE_YAP_TAZ_CONTROL_2_Ln2

description:
Library name: Sample 19
10x Genomics


title: Pt41_sphere_1


title: Pt41_sphere_2


title: Pt40_sphere_2


title: E14.5_MGE_TEAD_CONTROL_1_Ln1

description:
Library name: Sample 6
10x Genomics


title: E14.5_MGE_TEAD_CONTROL_3

description:
Library name: Sample 10
10x Genomics


title: E14.5_MGE_TEAD_CONTROL_1_Ln3

description:
Library name: Sample 8
10x Genomics


title: Pt40_sphere_1


title: Pt45_sphere_1


title: E15.5_MGE_3

description:
Library name: Sample 5
10x Genomics

value: Wildtype


title: E14.5_MGE_YAP_TAZ_CONTROL_2_Ln1

description:
Library name: Sample 18
10x Genomics


title: E15.5_MGE_2

description:
Library name: Sample 4
10x Genomics


title: Pt36_sphere_1


title: Pt36_sphere_2


title: E12.5_MGE_2

description:
Library name: Sample 2
10x Genomics


title: E15.5_MGE_1

description:
Library name: Sample 3
10x Genomics


title: Pt30_sphere_2


title: Pt30_sphere_1


title: E12.5_MGE_1

description:
Library name: Sample 1
10x Genomics


title: Pt28_sphere_2


title: E14.5_MGE_TEAD_CONTROL_2

description:
Library name: Sample 9
10x Genomics


title: Pt42_sphere_1


title: Y428F_PTH_1

city: Boston

first: Roland

last: Baron

state: MA

address: 188 Longwood Ave

department: Division of Bone and Mineral Research Oral Medicine, Infection & Immunity

institute: Harvard University

description: Library name: Sample 10

data_processing:
Fastq files were mapped using STAR ver. 2.7.10b  on the primary assembly mouse genome GRCm39 and basic gene annotation vM31 downloaded from GENCODE . The gene expression levels were summarized in a count matrix using RSEM . Genes with ten or more counts were filtered and normalized using DESeq2 [84]. Principal component analysis was performed using prcomp in stats [85]. The distribution of log fold changes in gene expression and adjusted p-values were drawn on volcano plots, and appropriate threshold values were determined. Significantly differentially expressed genes were summarized in heatmaps referring to interesting gene ontology terms in mSigDB (m2.cp.v2023.1.Mm.symbols.gmt). The AUC scores calculated using AUCell were scaled for each term.
Assembly: mm39

growth_protocol: Experiments were performed using W-20 bone marrow stromal cell line manteined in DMEM supplemented with 10% FBS and antibiotics in humidified athmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was isolated from cells using the RNeasy Mini Kit (Qiagen Germantown, MD, USA) according to the manufacturer’s protocol. 500ng of total RNA was used for the construction of sequencing libraries
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library.

treatment_protocol: PTH treatment was performed with 50nM and the corresponding ul used for the VEH treatment for the duration of 2h.

value: cell line

value: Bone; Marrow; Stroma

value: WT

value: PTH 50nM (2h)


title: Y428F_PTH_2

description: Library name: Sample 11


title: E14.5_MGE_TEAD_CONTROL_1_Ln2

description:
Library name: Sample 7
10x Genomics


title: Y428F_PTH_3

description: Library name: Sample 12


title: Y428F_VEH_3

description: Library name: Sample 9

value: VEH (PBS)


title: Normoxia_SCC25-3

city: shanghai

first: Haoming

last: Zhao

address: zhizaoju road

department: Department of Oral and Maxillofacial-Head and Neck Oncology

institute: Ninth People’s Hospital, School of Medicine, Shanghai Jiao Tong University

data_processing:
CLC Genomocs Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork(parameter-Quality limit:0.05
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: SCC25 were maintained in DMEM/F12 supplemented with 10% fetal bovine serum(FBS) and antibiotics in humidified atmosphere

extract_protocol:
RNA was harvested using Rneasy mini plus kit(Qiagen)
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep kit following manufacturer's protocols

treatment_protocol:
Normoxic treatment of cells was performed in a humidified 5%CO2/95% air incubator at 37℃
Hypoxic treatment of cells was performed in a tri-gas incubator (ThermoFisher Scientific, USA) flushed with a gas mixture of 1% O2, 5% CO2 and balanced N2.

value: Human oral squamous cell carcinoma cell line.


title: Y428F_VEH_2

description: Library name: Sample 8


title: Normoxia_SCC25-2


title: Normoxia_SCC25-1


title: W20_PTH_3

description: Library name: Sample 6


title: Y428F_VEH_1

description: Library name: Sample 7


title: W20_PTH_1

description: Library name: Sample 4


title: Hypoxia_SCC25-3


title: Pancreatic ductal adenocarcinoma PDO, TRACER Layer 6

city: Toronto

first: Alison

middle: P

last: McGuigan

state: ON

address: 200 College St, Rm 338

country: Canada

institute: University of Toronto

data_processing:
Demultiplexing, alignment to reference genome GRCh38 and quantification were performed from FAST files using CellRanger v6.0
Assembly: GRCh38
Supplementary files format and content: Tab-separated values file and matrix files

source_name: pancreatic ductal adenocarcinoma Stage IIB, patient-derived organoid

extract_protocol:
After 24h of culture in the rolled configuration, TRACER constructs were disassembled and sectioned into individual layers. The indiviudal layers were then incubated in a solution of HBSS supplemented trypsin 0.5x for 30 mins on an orbital shaker at 900 rpm and 37C. Samples were agitated by repeated pipetting to dislodge the organoid cells and the digestion reaction was neutralized wtih Advanced DMEM/F-12 media supplemented with 10% FBS. Cells were collected by centrifugation.
The library was prepared in accordance with manufaturer's instructions (Single Cell 5' v2 Reagent Kits, 10x genomics). Briefly, cells were washed and assessed for viability, then loaded onto a 10X single cell chip K. cDNA was recovered using a 10X recovery agent and cleaned using Silane DynaBead mix as outlined in the user guide. Purified cDNA was amplified and cleaned using SPRI select beads. 5' v2 cDNA libraries were then prepared as outlined in the Single Cell 5'v2 Reagent kid user guide.


title: W20_VEH_3

description: Library name: Sample 3


title: Pancreatic ductal adenocarcinoma PDO, TRACER Layer 5

value: pancreatic ductal adenocarcinoma Stage IIB, patient-derived organoid


title: W20_VEH_2

description: Library name: Sample 2


title: Pancreatic ductal adenocarcinoma PDO, TRACER Layer 4


title: Hypoxia_SCC25-1


title: W20_VEH_1

description: Library name: Sample 1


title: Pancreatic ductal adenocarcinoma PDO, TRACER Layer 3


title: Cong_IRI_3

city: Kyoto

first: Tetsuro

last: Kusaba

state: Kyoto

address: 465 Kajii-cho, Kamigyo-ku

department: Department of Nephrology

institute: Graduate School of Medical Science, Kyoto Prefectural University of Medicine

description:
Library name: Sample6
Column name in counts_IVCC.txt: IVCC_IRI_3

data_processing:
Sequenced reads were mapped to mouse reference genome sequences (GRCm38) using STAR v 2.7.10a (https://github.com/alexdobin/STAR/) and uniquely mapped reads were counted by the featureCounts function in the Subread package (https://subread.sourceforge.net)
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes for each Sample

source_name: Kidney

extract_protocol:
Total RNA was extracted from the cortex of kidneys using NucleoSpin® RNA (Macherey-Nagel, Duren, Germany) according to the manufacturer's protocol.
The Library preparation was performed using a TruSeq stranded mRNA sample prep kit (Illumina, San Diego, CA) according to the manufacturer's instructions.

value: Kidney

value: male

value: IRI with IVCC


title: Pt28_sphere_1


title: Cong_IRI_1

description:
Library name: Sample4
Column name in counts_IVCC.txt: IVCC_IRI_1


title: Pancreatic ductal adenocarcinoma PDO, TRACER Layer 2


title: Pancreatic ductal adenocarcinoma PDO, TRACER Layer 1


title: CLK_IRI_3

description:
Library name: Sample3
Column name in counts_IVCC.txt: CLK_IRI_3

value: IRI


title: CLK_IRI_2

description:
Library name: Sample2
Column name in counts_IVCC.txt: CLK_IRI_2


title: CLK_IRI_1

description:
Library name: Sample1
Column name in counts_IVCC.txt: CLK_IRI_1


title: tumor resection tissue, patient 10

city: Phoenix

first: Eric

last: Alsop

state: AZ

address: 445 N 5th St

institute: TGen

description: 10X genomics

data_processing:
data as run through cellranger count using 10X's provided reference genome (2020A), using the 'include-introns' option
Assembly: GRCh38, as downloaded from 10X genomics (2020A)
Supplementary files format and content: cellranger counts output matrices

molecule: nuclear RNA

source_name: resected lung tumor tissue

growth_protocol: N/A, cells were obtained directly from human lung

extract_protocol:
Single nuclei were isolated from whole lung tissue; briefly, tissue was mechanically dissociated, and nuclei were retrieved, washed, DAPI stained, and sorted to remove debris. Sorted single nuclei were loaded directly into 10x Genomics 5' chip K for polyA tagging, using the manufacturer's recommendation.
10x Genomics 5' V2

treatment_protocol: N/A, tissue samples were obtained directly from human lung, and directly used for sequencing experiments, upon thawing and processing.

tag: patient diagnosis

value: NSCLC

value: resected lung tumor tissue


title: tumor resection tissue, patient 12

description: 10X genomics


title: tumor resection tissue, patient 7

description: 10X genomics


title: tumor resection tissue, patient 8

description: 10X genomics


title: W20_PTH_2

description: Library name: Sample 5


title: Hypoxia_SCC25-2


title: MEC Brain, A24

city: San Francisco

first: Jeremy

middle: Michael

last: Shea

state: CA

address: 513 Parnassus Avenue

department: Anatomy

institute: University of California, San Francisco

data_processing:
reads were mapped and aligned using kallisto
downstream differential gene expression analysis was performed using DESeq2
Assembly: mm10 with introns included
Supplementary files format and content: Giocomo_SplitMaze_Expression.csv represents FPKM values

source_name: MEC Brain

extract_protocol:
RNA was extracted using TriZol/chloroform.
RNA seq libraries were prepared using SmartSeq library manufacturer instructions.

value: MEC Brain

value: Neuronal nuclei

tag: developmental stage

value: Aged


title: MEC Brain, A19


title: tumor resection tissue, patient 4

description: 10X genomics

molecule: polyA RNA


title: MEC Brain, A18


title: MEC Brain, A15


title: PBMC, post-tumor resection, patient 14, cell surface antibody barcode library

description:
also sequenced on Illumina NovaSeq X Plus
processed data included in matrix available on related GEX sample.

library_source: other

data_processing:
fastq files from GEX, VDJ and CSP were processed together using cellranger multi. CSP was processed using uploaded feature_README.txt file for CSP barocodes. GEX and VDJ were processed using reference downloaded from 10X's website (v. 2020A)
Assembly: GRCh38, builds downloaded from 10X's website specfic to GEX and VDJ data (v. 2020A)
Supplementary files format and content: feature, barcode and counts matrices from cellranger multi, run on combined dataset from GEX, CSP and VDJ data for each sample
Library strategy: CITE-seq

molecule: protein

source_name: PBMCs

growth_protocol: N/A, cells were obtained directly from human whole blood.

extract_protocol:
PBMCs were isolated from whole blood via density gradient separation, frozen viably, and stored in liquid nitrogen. For sequencing experiments, cells were thawed, counted, stained with CITE-seq antibodies, and loaded directly into 10x Genomics 5' chip K for polyA tagging, using the manufacturer's recommendation.
10x Genomics 5' V2

treatment_protocol: N/A, cells were obtained directly from human whole blood, and directly used for scRNA and CITE-seq experiments, upon thawing.

value: PBMCs

value: circulating peripheral mononuclear immune cells

tag: library type

value: ADT

tag: adt

value: TotalSeq™-C0083 anti-human CD16, TotalSeq™-C0084 anti-human CD56,  TotalSeq™-C0090 Mouse IgG1, κ isotype


title: MEC Brain, A17


title: tumor resection tissue, patient 2

description: 10X genomics


title: MEC Brain, MA10

value: Mature


title: PBMC, post-tumor resection, patient 12, cell surface antibody barcode library


title: PBMC, pre-tumor resection, patient 12, cell surface antibody barcode library


title: PBMC, pre-tumor resection, patient 14, cell surface antibody barcode library


title: MEC Brain, MA6


title: MEC Brain, MA8


title: PBMC, pre-tumor resection, patient 10, cell surface antibody barcode library


title: Cong_IRI_2

description:
Library name: Sample5
Column name in counts_IVCC.txt: IVCC_IRI_2


title: tumor resection tissue, patient 9

description: 10X genomics


title: MEC Brain, MA5


title: PBMC, post-tumor resection, patient 9, cell surface antibody barcode library


title: PBMC, pre-tumor resection, patient 9, cell surface antibody barcode library


title: MEC Brain, A20


title: MEC Brain, Y27

value: Young


title: MEC Brain, MA1


title: MEC Brain, MA3


title: PBMC, post-tumor resection, patient 8, cell surface antibody barcode library


title: tumor resection tissue, patient 5

description: 10X genomics


title: PBMC, pre-tumor resection, patient 8, cell surface antibody barcode library


title: MEC Brain, Y25


title: PBMC, post-tumor resection, patient 7, cell surface antibody barcode library


title: PBMC, pre-tumor resection, patient 7, cell surface antibody barcode library


title: MEC Brain, Y28


title: PBMC, post-tumor resection, patient 6, cell surface antibody barcode library


title: MEC Brain, Y23


title: MEC Brain, Y22


title: PBMC, pre-tumor resection, patient 6, cell surface antibody barcode library


title: MEC Brain, Y20


title: PBMC, post-tumor resection, patient 5, cell surface antibody barcode library


title: WT_Day3_3

city: Kanazawa

first: Sotaro

last: Fujisawa

state: Ishikawa

address: 13-1 Takara-machi

institute: Kanazawa University

data_processing:
Sequence data were assessed using FastQC, and trimmed for adapter and loq-quality bases using fastp.
Reads were aligned to the GRCm38/mm10 reference genome using STAR with default settings.
Read count and TPM were calculated using featureCounts and StringTie, respectively.
Assembly: mm10
Supplementary files format and content: tab-delimited text file include raw counts

source_name: CD8+ T cells

extract_protocol:
RNA was extracted using Rneasy Mini Kit (QIAGEN).
Sequence libraries were prepared using NEBNext Ultra RNA LP Kit.

value: CD8+ T cells

value: WT

value: Day 3


title: PBMC, pre-tumor resection, patient 5, cell surface antibody barcode library


title: PBMC, post-tumor resection, patient 4, cell surface antibody barcode library


title: PBMC, pre-tumor resection, patient 4, cell surface antibody barcode library


title: WT_Day3_1


title: WT_Day3_2


title: BatfKO_Day3_2

value: BatfKO


title: PBMC, pre-tumor resection, patient 2, cell surface antibody barcode library


title: BatfKO_Day3_3


title: BatfKO_Day3_1


title: PBMC, post-tumor resection, patient 2, cell surface antibody barcode library


title: WT_Day0_2

value: Day 0


title: BatfKO_Day0_2


title: PBMC, post-tumor resection, patient 14, VDJ recombination library

description: also sequenced on Illumina NovaSeq X Plus

data_processing:
fastq files from GEX, VDJ and CSP were processed together using cellranger multi. CSP was processed using uploaded feature_README.txt file for CSP barocodes. GEX and VDJ were processed using reference downloaded from 10X's website (v. 2020A)
Assembly: GRCh38, builds downloaded from 10X's website specfic to GEX and VDJ data (v. 2020A)
Supplementary files format and content: feature, barcode and counts matrices from cellranger multi, run on combined dataset from GEX, CSP and VDJ data for each sample
Library strategy: scVDJ-seq

value: mRNA


title: PBMC, pre-tumor resection, patient 10, VDJ recombination library


title: BatfKO_Day0_1


title: PBMC, post-tumor resection, patient 9, VDJ recombination library


title: H55Q_IRF4_2

data_processing:
Sequence data were assessed using FastQC, and trimmed for adapter and loq-quality bases using fastp.
Reads were aligned to the GRCm38/mm10 reference genome using Bowtie v2.3.5.
Unmapped, unpaired, low-quality reads, and mitochondrial reads were removed using samtools.
ENCODE blacklist regions were removed, and PCR duplicates were removed using Picard.
BED file was created using bamtobed function of BedTools.
Data were normalized by mapping the reads to E. coli DNA, the carry-over from purification of pAG-MNase (Meers et al., 2019) and normalized bigwig files were created using deepTools bamCoverage
Assembly: mm10
Supplementary files format and content: bigwig
Library strategy: CUT&RUN

extract_protocol:
DNA fragment of TF-bound regions were extracted using pAG-MNase.
Sequence libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina

value: Batf H55Q RV

tag: antibody

value: IRF4 (SantaCruz, E-7)


title: WT_Day0_1


title: H55Q_IRF4_1


title: IRF4OE_IRF4_2

value: Batf RV


title: PBMC, post-tumor resection, patient 12, VDJ recombination library


title: PBMC, pre-tumor resection, patient 14, VDJ recombination library


title: PBMC, pre-tumor resection, patient 9, VDJ recombination library


title: PBMC, post-tumor resection, patient 8, VDJ recombination library


title: IRF4OE_IRF4_1


title: PBMC, pre-tumor resection, patient 8, VDJ recombination library


title: PBMC, post-tumor resection, patient 7, VDJ recombination library


title: Empty_IRF4_2

value: Empty RV


title: Empty_IRF4_1


title: PBMC, pre-tumor resection, patient 7, VDJ recombination library


title: S43D_BATF_2

value: Batf S43D RV

value: BATF (Brookwood Biomedical, PAB4003)


title: PBMC, post-tumor resection, patient 6, VDJ recombination library

value: PBMCs

value: circulating peripheral mononuclear immune cells


title: S43D_BATF_1


title: S43A_BATF_2

value: Batf S43A RV


title: PBMC, pre-tumor resection, patient 6, VDJ recombination library


title: PBMC, post-tumor resection, patient 5, VDJ recombination library


title: PBMC, pre-tumor resection, patient 12, VDJ recombination library


title: PBMC, pre-tumor resection, patient 5, VDJ recombination library


title: H55Q_BATF_2


title: PBMC, post-tumor resection, patient 4, VDJ recombination library


title: H55Q_BATF_1


title: PBMC, pre-tumor resection, patient 4, VDJ recombination library


title: PBMC, post-tumor resection, patient 2, VDJ recombination library


title: BATFOE_BATF_1


title: PBMC, pre-tumor resection, patient 2, VDJ recombination library


title: PBMC, post-tumor resection, patient 14, gene expression library

description:
also sequenced on Illumina NovaSeq X Plus
processed data matrix also includes data for ADT

data_processing:
fastq files from GEX, VDJ and CSP were processed together using cellranger multi. CSP was processed using uploaded feature_README.txt file for CSP barocodes. GEX and VDJ were processed using reference downloaded from 10X's website (v. 2020A)
Assembly: GRCh38, builds downloaded from 10X's website specfic to GEX and VDJ data (v. 2020A)
Supplementary files format and content: feature, barcode and counts matrices from cellranger multi, run on combined dataset from GEX, CSP and VDJ data for each sample


title: PBMC, pre-tumor resection, patient 14, gene expression library


title: BATFOE_BATF_2


title: Empty_BATF_1


title: CD4cre_nIgG

value: Rabbit IgG (Invitrogen, 02-6102)


title: IRF4cKO_BATF_2


title: PBMC, post-tumor resection, patient 12, gene expression library


title: PBMC, pre-tumor resection, patient 12, gene expression library


title: PBMC, post-tumor resection, patient 9, gene expression library


title: IRF4cKO_BATF_1


title: CD4cre_BATF_2


title: PBMC, pre-tumor resection, patient 10, gene expression library


title: CD4cre_BATF_1


title: PBMC, pre-tumor resection, patient 9, gene expression library


title: H55Q_2

data_processing:
Sequence data were assessed using FastQC, and trimmed for adapter and loq-quality bases using fastp.
Reads were aligned to the GRCm38/mm10 reference genome using Bowtie v2.3.5.
Unmapped, unpaired, low-quality reads, and mitochondrial reads were removed using samtools.
ENCODE blacklist regions were removed, and PCR duplicates were removed using Picard.
BED file was created using bamtobed function of BedTools and ATAC shift was corrected as described (https://github.com/wherrylab/jogiles_ATAC).
Peak calling was performed using MACS v2 using the narrowPeak setting with q value cut-off of 0.01, -f BEDPE.
Peaks from all samples in each experiment were combined and merged using BedTools merge, and the numbers of reads in each peak was quantified using BedTools coverage
Assembly: mm10
Supplementary files format and content: bigwig

extract_protocol:
DNA fragment of open chromatin regions were extracted using Tn5 transposase (Illumina)
Sequence libraries were prepared using NEBNext High Fidelity 2x PCR Master Mix

value: Day 4


title: S43A_BATF_1

value: CD8+ T cells


title: PBMC, post-tumor resection, patient 8, gene expression library


title: H55Q_1


title: PBMC, pre-tumor resection, patient 8, gene expression library


title: BATF_2


title: PBMC, pre-tumor resection, patient 7, gene expression library


title: PBMC, post-tumor resection, patient 7, gene expression library


title: Empty_2


title: Empty_BATF_2


title: PBMC, post-tumor resection, patient 6, gene expression library


title: Empty_1


title: CD4cre_Day3_2

value: WT


title: PBMC, pre-tumor resection, patient 6, gene expression library


title: PBMC, post-tumor resection, patient 5, gene expression library


title: PBMC, pre-tumor resection, patient 5, gene expression library


title: CD4cre_Day3_1

value: Day 3


title: IRF4cKO_Day3_1


title: PBMC, post-tumor resection, patient 4, gene expression library


title: PBMC, pre-tumor resection, patient 4, gene expression library


title: WT_Day3_2


title: BatfKO_Day3_2

value: BatfKO


title: extracellular vesicle RNA, NK cell derived, pool of donors without any diagnosed cancer at the time of collection

data_processing:
fastq files  were aligned to the human genome using STAR with a custom transcriptome that includes additional lncRNAs from lncpedia
count tables were generated from the STAR alignments using featureCounts
counts from featureCounts were collapsed into a single raw counts table
Assembly: GRCh38
Supplementary files format and content: Raw counts table with sample IDs as columns and ENSEMBL IDs as rows

growth_protocol: After thawing and isolation, NK cells were maintained in growth medium (X-Vivo, Lonza, 5% human AB serum, heat inactivated, Il-2, Il-15) for 12 days, with occasional counting and medium addition; at day 12, cells were retrieved, centrifuged to remove the medium, and resuspended in EV medium (X-Vivo, Lonza, 5% human AB serum EV depleted, heat inactivated, Il-2, Il-15, Il-21) and medium was retrieved every 2 days, and frozen. Medium was then thawed, and size exclusion chromatography was used to isolate the extracellular vesicles (EVs).

extract_protocol:
The isolated Evs were treated for total RNA extraction using a commercial kit, according to the manufacturer's instructions. Plasma/serum circulating and exosomal RNA purification mini kit (Norgen Biotek) was used, followed by DNA digestion with TURBO DNA-free (ThermoFisher) and treatment with RNeasy MinElute Cleanup (Qiagen). RNA was quantified with Ribogreen Quant-iT (ThermoFisher) before library preparation.
Libraries were constructed using a workflow optimized for low input, low quality RNA sources, as is appropriate for Evs. Using the Smart-er Stranded Total RNAseq kit v3 for pico inputs (Takara Bio), RNA was converted into cDNA, PCR-amplified with unique barcodes, and treated with ribosomal RNA probes for ribosomal RNA depletion. The libraries were size selected via magnetic bead separation, PCR amplified again, size-selected again, and eluted in water. The resulting libraries were stranded, with unique molecular indices.

treatment_protocol: N/A, Evs were retrieved and used for RNAseq experiments after thawing without additional treatment.

value: extracellular vesicled derived from cultured NK cells

value: extracellular vesicled derived from cultured human primary NK cells

value: cells were kept in extracellular vesicle free medium prior to retrieval of extracellular vesicles


title: PBMC, post-tumor resection, patient 2, gene expression library

value: mRNA


title: PBMC, pre-tumor resection, patient 2, gene expression library


title: extracellular vesicle RNA, NK cell derived, patient 14, pre tumor resection sample

value: NSCLC


title: WT_Day0_2

value: Day 0


title: extracellular vesicle RNA, NK cell derived, patient 14, post tumor resection sample


title: BATF_1

value: Batf RV


title: WT_Day0_1


title: extracellular vesicle RNA, NK cell derived, patient 12, pre tumor resection sample


title: BatfKO_Day0_2


title: extracellular vesicle RNA, NK cell derived, patient 12, post tumor resection sample


title: BatfKO_Day0_1


title: extracellular vesicle RNA, NK cell derived, patient 10, pre tumor resection sample


title: extracellular vesicle RNA, NK cell derived, patient 10, post tumor resection sample


title: CD45+ Batf3 KO ADT

city: Research Triangle Park

first: Donald

middle: Nelson

last: Cook

state: NC

address: 111 T.W. Alexander Drive

department: IIDL

institute: NIEHS

description: 10x Genomics Antibody Derived Tags

data_processing:
Cell Ranger v7.0.0 "count" function to map reads and assign cell barcodes
Assembly: refdata-gex-mm10-2020-A
Supplementary files format and content: Cell Ranger Output files: barcodes.tsv.gz, features.tsv.gz, matrix.tsv.gz, filtered_feature_bc_matrix.h5
Library strategy: CITE-seq

source_name: Lung

extract_protocol:
Lungs were homogenized to a single cell suspension, FACS sorted to extract lymphocytes, then sorted again to extract lung resident CD4+ T-cells
10x Genomics 3' v3 GEM Kit with TotalseqA Antibody Derived Tags

treatment_protocol: Allergic sensitization on day 0 and 7 using lyophilized House Dust Mites, followed by HDM challenge 5 weeks post day 7

value: Lung

value: CD4+ T Lymphocytes

value: ADT

value: TotalSeq-A0987 anti-Allophycocyanin (APC), TotalSeq-A0911 anti-phycoerythrin (PE), TotalSeq-A0201 anti-mouse CD103, TotalSeq-A0197 anti-mouse CD69, TotalSeq-A0112 anti-mouse CD62L, TotalSeq-A0073 anti-mouse/human CD44


title: CD45- Batf3 KO ADT

description: 10x Genomics Antibody Derived Tags


title: extracellular vesicle RNA, NK cell derived, patient 9, pre tumor resection sample


title: IRF4cKO_Day3_2


title: CD45+ WT ADT

description: 10x Genomics Antibody Derived Tags


title: extracellular vesicle RNA, NK cell derived, patient 9, post tumor resection sample


title: CD45- WT ADT

description: 10x Genomics Antibody Derived Tags


title: CD45+ Batf3 KO GEX

description: 10x Genomics 3' GEX poly A mRNA


title: extracellular vesicle RNA, NK cell derived, patient 8, post tumor resection sample


title: WT_Day3_1


title: extracellular vesicle RNA, NK cell derived, patient 7, pre tumor resection sample


title: BatfKO_Day3_1


title: CD45+ WT GEX

description: 10x Genomics 3' GEX poly A mRNA


title: extracellular vesicle RNA, NK cell derived, patient 6, pre tumor resection sample


title: WT4-14922

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

data_processing:
Sequence images were transformed with Illumina software BaseCaller to BCL files, which was demultiplexed to fastq files with bcl2fastq v2.20
STAR version 2.7.8a was used to align the reads to the rn6 genome using 2 mismatches within 50 bases
featureCounts version 1.6.3-p1 was used to quantify reads for genes in GRCm39 version 107
Assembly: GRCm39 version 107
Supplementary files format and content: Tab-delimited gene counts

source_name: cortex

extract_protocol:
Total RNA isolation using the NucleoSpin RNA kit (Macheray-Nagel)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: cortex


title: extracellular vesicle RNA, NK cell derived, patient 5, pre tumor resection sample


title: WT6-31022


title: CD45- WT GEX

description: 10x Genomics 3' GEX poly A mRNA


title: WT1-8-241022


title: WT6-14922


title: extracellular vesicle RNA, NK cell derived, patient 5, post tumor resection sample


title: WT1-2-241022


title: E2KO7-14922

value: Emx2 KO


title: extracellular vesicle RNA, NK cell derived, patient 4, post tumor resection sample


title: extracellular vesicle RNA, NK cell derived, patient 2, pre tumor resection sample


title: extracellular vesicle RNA, NK cell derived, patient 2, post tumor resection sample


title: E2KO3-31022


title: extracellular vesicle RNA, NK cell derived, patient 8, pre tumor resection sample


title: E2KO1-7-241022


title: TALL1D ISRIB EVE 12h

city: Padova

first: Loredana

last: Urso

address: Via Gattamelata

department: IDMO

institute: Istituto Oncologico Veneto

data_processing:
The raw reads were mapped to the HG38 human reference using Dragen (version 3.9.5). Transcript quantification was performed using Dragen (version 3.9.5) and the Gencode human release v42 basic annotation.
Assembly: The raw reads were mapped to the HG38 human reference using Dragen (version 3.9.5).
Supplementary files format and content: Processed data file contain the row data count in tsv format

source_name: Blood

growth_protocol: TALL-1 cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS), 2 mM L-glutamine, 100 units/mL penicillin, and 20 units/mL streptomycin.

extract_protocol:
Total RNAs were extracted using RNeasy Plus Mini Kit (Qiagen).
The RNA-seq libraries were produced using the NEBNext rRNA Depletion Kit (NEB). All samples were sequenced in 150PE with an Illumina Platform.

treatment_protocol: TALL-1 cells were pretreated with Vehicle (DMSO) or ISRIB 25nM for two hours and then treated with with vehicle (ET-OH) or 10µM Everolimus for the indicated time point.

value: Blood

value: T-cell acute lymphoblastic leukemia

value: Isrib + everolimus


title: CD45- Batf3 KO GEX

description: 10x Genomics 3' GEX poly A mRNA


title: E2KO1-3-241022


title: TALL-1D ISRIB 12h

value: Isrib + ethanol


title: TALL-1D EVE 12h

value: Everolimus


title: Liver, Tshrf/f,Lyz2-Cre, fed High fat diet for 9 wks,insulin admin (1.5 U/kg) for 5 min in vivo after 8-hr fasting,rep3

city: Xi 'an

first: Zhang

last: Haihong

state: Shaanxi Province

address: Xiaozhai West Road

institute: Xi'an Jiaotong university

data_processing:
The raw data was handled by Skewer and data quality was checked by FastQC v0.11.2(http:// www.bioinformatics.babraham.ac.uk/projects/fastqc/ ).
Clean reads were aligned to the mm10 using STAR. StringTie.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample.

source_name: Liver

growth_protocol: 1.Primary mouse bone marrow derived macrophages(BMDMs) were isolated from TshrMKO mice and age-matched Tshrf/f littermates(male, 6 weeks old), cultured and differentiated for 7 days in DMEM containing 10% FBS and 1% penicillin/streptomycin supplemented with murine recombinant M-CSF (10ng/mL) at 37 °C with 5% CO2. 2.TshrMKO mice and age-matched Tshrf/f littermates (male, 6 weeks old) were fed a HFD for 9 weeks.

extract_protocol:
Total RNA was isolated from each thymic sample using the RNAmini kit ( Qiagen,Germany). 2ug of total RNA was used for the construction of sequencing libraries.
Strand-specific libraries were constructed using the TruSeq RNA sample preparation kit (Illumina, San Diego, CA, USA)
Sequencing was carried out using the Illumina Novaseq 6000 instrument by the commercial service of Genergy Biotechnology Co. Ltd. (Shanghai, China).

treatment_protocol: 1.Primary mouse bone marrow derived macrophages(BMDMs) were stimulated by 1ng/mL Tsh for 24 hours,24 hours.  2.Mice were sacrificed after insulin administration (1.5 U/kg) for 5 minutes in vivo after 8-hour fasting, whose liver were used to perform RNAseq.

value: Liver

value: fed a High fat diet for 9 weeks,insulin administration (1.5 U/kg) for 5 minutes in vivo after 8-hour fasting


title: TALL-1D CNTR 12h

value: Ethanol


title: extracellular vesicle RNA, NK cell derived, patient 6, post tumor resection sample

value: NSCLC

value: extracellular vesicled derived from cultured NK cells

value: extracellular vesicled derived from cultured human primary NK cells

value: cells were kept in extracellular vesicle free medium prior to retrieval of extracellular vesicles


title: Liver, Tshrf/f, fed High fat diet for 9 wks,insulin admin (1.5 U/kg) for 5 min in vivo after 8-hr fasting,rep3

value: Tshrf/f


title: TALL1D ISRIB EVE 4h


title: extracellular vesicle RNA, NK cell derived, patient 4, pre tumor resection sample


title: Liver, Tshrf/f, fed High fat diet for 9 wks,insulin admin (1.5 U/kg) for 5 min in vivo after 8-hr fasting,rep1


title: Liver, Tshrf/f, fed High fat diet for 9 wks,insulin admin (1.5 U/kg) for 5 min in vivo after 8-hr fasting,rep2


title: extracellular vesicle RNA, NK cell derived, patient 7, post tumor resection sample


title: TALL-1D EVE 4h


title: TALL-1D CNTR 4h


title: Liver, Tshrf/f,Lyz2-Cre, fed High fat diet for 9 wks,insulin admin (1.5 U/kg) for 5 min in vivo after 8-hr fasting,rep1


title: Bone marrow derived macrophages(BMDMs), Tshrf/f,Lyz2-Cre, TSH,1ng/mL,24 hours,rep2

source_name: Bone marrow

value: Bone marrow

value: Bone marrow derived macrophages

value: 1ng/mL Tsh for 24 hours


title: E2KO3-14922

value: cortex

value: Emx2 KO


title: Bone marrow derived macrophages(BMDMs), Tshrf/f,Lyz2-Cre, TSH,1ng/mL,24 hours,rep3


title: TALL1C ISRIB EVE 12h

value: Blood

value: T-cell acute lymphoblastic leukemia


title: Bone marrow derived macrophages(BMDMs),Tshrf/f, TSH,1ng/mL,24 hours,rep3


title: TALL-1C CNTR 12h


title: TALL-1C ISRIB 12h

value: Isrib + ethanol


title: TALL1C ISRIB EVE 4h

value: Isrib + everolimus


title: TALL-1C EVE 12h

value: Everolimus


title: Bone marrow derived macrophages(BMDMs), Tshrf/f,Lyz2-Cre, TSH,1ng/mL,24 hours,rep1


title: Liver, Tshrf/f,Lyz2-Cre, fed High fat diet for 9 wks,insulin admin (1.5 U/kg) for 5 min in vivo after 8-hr fasting,rep2

value: Liver

value: fed a High fat diet for 9 weeks,insulin administration (1.5 U/kg) for 5 minutes in vivo after 8-hour fasting


title: TALL-1C ISRIB 4h


title: periosteum, high fat diet, rep4

city: Baltimore

first: Aaron

middle: W

last: James

state: MD

address: 720 Rutland Ave

department: School of Medecine. Surgical Pathology

institute: Johns Hopkins University

description: 10x Genomics

data_processing:
CellRanger 6.0.1 was used to perform sample de-multiplexing, barcode processing, and single-cell gene counting (Alignment, Barcoding, and UMI Count) at the JHMI Transcriptomics and Deep Sequencing Core.
Assembly: mm10-2020-A
Supplementary files format and content: mm10
Supplementary files format and content: matrix files

source_name: periosteum

extract_protocol:
Four left femurs and tibias were dissected from ND and HFD groups at the experimental endpoint for scRNA-Seq. The bones were digested in a pre-warmed dissociation solution (3 mg ml−1 collagenase I (Worthington) and 4 mg ml−1 dispase II (Roche) in PBS) for 1.5 h min at 180 r.p.m. at 37 °C, run through a 40 μm filter (VWR) and rinsed with 3 ml medium (αMEM (Gibco) with 20% FBS, 1% penicillin/streptomycin). Periosteal cells were centrifuged at 300g for 30 min at 4 °C. The cell pellet was washed twice with PBS and spun for 10 min at 300g at 4 °C. Periosteal cells were then resuspended in HBSS at a concentration of ~1,000 cells/μl. Cell viability was assessed with Trypan blue exclusion on a Countess II (ThermoFisher Scientific) automated counter and showed >85% viability. Cells were sent to the JHMI Transcriptomics and Deep Sequencing Core.
The library was generated using the 10X Genomics Chromium controller following the manufacturer’s protocol

value: periosteum

value: C57BL/6J male

value: 16 weeks old

value: High fat diet chow


title: Bone marrow derived macrophages(BMDMs),Tshrf/f, TSH,1ng/mL,24 hours,rep1

value: Tshrf/f


title: TALL-1C CNTR 4h

value: Ethanol


title: TALL-1C EVE 4h


title: Bone marrow derived macrophages(BMDMs),Tshrf/f, TSH,1ng/mL,24 hours,rep2

value: Bone marrow

value: Bone marrow derived macrophages


title: TALL-1D ISRIB 4h


title: periosteum, high fat diet, rep3

description: 10x Genomics


title: TALL1B ISRIB EVE 12h


title: periosteum, high fat diet, rep2

description: 10x Genomics


title: TALL-1B EVE 12h


title: TALL-1B ISRIB 12h


title: periosteum, normal diet, rep4

description: 10x Genomics

value: Normal diet chow


title: periosteum, high fat diet, rep1

description: 10x Genomics


title: TALL1B ISRIB EVE 4h


title: periosteum, normal diet, rep2

description: 10x Genomics


title: periosteum, normal diet, rep3

description: 10x Genomics


title: TALL-1B EVE 4h


title: periosteum, normal diet, rep1

description: 10x Genomics


title: TALL-1B ISRIB 4h


title: TALL-1B CNTR 4h


title: WT_pIC_5

city: Paris

first: Isadora

last: Lenoel

address: 47 Boulevard de l'hopital

institute: Paris Brain Institute

data_processing:
Quality of raw data has been evaluated with FastQC
Poor quality sequences has been trimmed or removed with Trimmomatic software to retain only good quality paired reads
Illumina DRAGEN bio-IT Plateform (v3.8.4) was used for mapping on mm10 reference genome and quantification with gencode v25 annotation gtf file.
Library orientation, library composition and coverage along transcripts were checked with Picard tools.
Assembly: mm10
Supplementary files format and content: tab-delimited text files including expecting cd raw counts and TPM

source_name: Microglial cells

growth_protocol: Primary microglial cells were cultured in DMEM, 10% FCS, 50μM ß-mercaptoethanol for 16h after purification, before stimulation

extract_protocol:
After 24h of stimulation, medium was removed, and cells were lysed in lysis buffer RLT from  Rneasy mico kit (Qiagen) and preserved at -80°C until further use. RNA was then extracted using the Rneasy micro kit (qiagen) with final RNA elution in 14µL.
After 24h of stimulation, medium was removed, and cells were lysed in lysis buffer RLT from Rneasy mico kit (Qiagen) and preserved at -80°C until further use. RNA was then extracted using the Rneasy micro kit (qiagen) with final RNA elution in 14µL.
RNA concentration was determined using a nanodrop, and 300ng were used to prepare RNA-seq libraries, using the Kapa mRNA Hyperprep kit (Roche).

treatment_protocol: Culture medium of primary microglial cells was replaced 16h after plating with fresh medium (untreated, UT), or medium plus stimuli: Lipopolysaccharide (LPS, 100ng/mL), or Interleukin-4 (IL-4, 20ng/mL), or polyI:C (pIC) ; and incubated for 24h (37°C, 5%CO2)

value: Microglial cells

value: WT

value: pIC


title: HET_pIC_5

value: HET


title: KO_pIC_4

value: KO


title: NC1235,ChIRP

city: Shanghai

first: Zhibo

last: Shao

institute: Fudan University Shanghai Cancer Center

data_processing:
The ChiLin pipeline 2.0.052 was used for quality control and pre-processing of the data. We used Bowtie2 (v2.2.9)  as a read mapping tool to align to hg38, and Model-based Analysis of ChIP-Seq (MACS2)(v2.1.0.20140616) as a peak caller using the command line parameters “-SPMR -B -q 0.01 –keep-dup 1 –nomodel -hs ”. The counts of these peaks were obtained using HTseq-count (v2.0.3). The differential analyses were performed using peak counts for ChIP-seq following the DEseq2 (v1.22.2) pipeline with a False Discovery Rate threshold of 0.05 and |log2FC| > 1.
Assembly: hg38
Supplementary files format and content: bigWig

source_name: Breast

extract_protocol:
HCC1954 cells were transfected with ASOs as indicated. After 72h, cells were treated with 1% formaldehyde for 10 min at RT prior to the addition of glycine at the final concentration of 0.125 M for 5 min. Cells were washed twice with PBS and treated with Buffer A (10 mM Tris-HCl 7.5, 10 mM NaCl, 0.5% NP-40) with 1X Protease Inhibitor Cocktail (PIC) for 10 min on ice. Washed once with Buffer A+PIC, Cells were resuspended in nuclei lysis buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA pH 8.0, 1% SDS). The nuclei were sonicated for several rounds until the de-crosslinked DNA fragment was about 200-500 bp with Bioruptor Pico (5 cycles in our case). Centrifuge 12000 g at 10°C for 15min. For 100 μl cleared sonicated chromatin, add 900 μl ChIP dilution buffer (0.01% SDS, 1% Triton-X100, 1 mM EDTA pH 8.0, 16.7mM Tris-HCl pH 8.0, 167 mM NaCl) with PIC. Then, 30 μg sonicated chromatin was incubated 7.5 μl of H3K27ac (Cell Signaling, 8173), H3K9ac (Cell Signaling, 9649), H3K36me3 (Cell Signaling, 9733) antibody or 5 μg H2A.Z (Abcam, ab4174) antibody with rotation at 4°C overnight. For each reaction, mix 25 μl Protein A and 25 μl Protein G dynabeads at 1:1 ratio and blocked with 1% BSA in ChIP dilution buffer overnight. Beads were washed 3 times with ChIP dilution buffer before added into the lysates. Incubated at 4°C for 4h with rotation. The beads were washed twice with RIPA-150 (50 mM Tris-HCl, pH 8.0, 157 150 mM NaCl, 1 mM EDTA, pH 8.0, 0.1% SDS, 1% Triton X-100, 0.1% sodium deoxycholate), then twice with RIPA-500 (50 mM Tris-HCl, pH 8.0, 500 mM NaCl, 1 mM EDTA, pH 8.0, 0.1% SDS, 1% Triton X-100, 0.1% sodium deoxycholate). The beads were further washed twice with RIPA LiCl (50 mM Tris-HCl, pH 8.0, 1 mM EDTA, pH 8.0, 1% NP-40, 0.7% sodium deoxycholate, 500 mM LiCl). The beads were washed twice with TE and resuspended with 150 μl freshly made elution buffer (0.1M NaHCO3, 1% SDS) with 5 μl Proteinase K and 2 μl RNase A (Thermo, R1253). Incubated at 56 °C overnight with shaking 900 rpm.
The DNA library was prepared using a Next Ultra DNA Library Prep Kit (NEB, E7645) according to the manufacturer’s instructions. The libraries were purified with AMPure XP beads (Beckman, A63881) according to the manufacturer ’s instructions, and sequenced using Illumina platforms.

value: Breast

value: Her2-positive breast cancer cells

value: ChIRP


title: Si1235,input,ChIP

value: Control

value: input


title: HET_pIC_4


title: WT_pIC_4


title: KO_pIC_3


title: Si1235,H3K9ac,ChIP


title: NC1235,input,ChIP


title: HET_pIC_3


title: Si1235,H3K36me3,ChIP,rep2


title: NC1235,H3K9ac,ChIP


title: NC1235,H3K36me3,ChIP,rep2


title: HET_pIC_2


title: KO_pIC_2


title: NC1235,H3K36me3,ChIP,rep1


title: TALL-1B CNTR 12h

value: Blood

value: T-cell acute lymphoblastic leukemia


title: Si1235,H3K36me3,ChIP,rep1


title: KO_pIC_5


title: KO_pIC_1


title: WT_pIC_3


title: Si1235,H3K27ac,ChIP,rep1


title: Si1235,H3K27ac,ChIP,rep2


title: HET_pIC_1


title: TS, scRNA-seq

city: Beijing

first: Shufan

last: Fan

address: A3 Datun Road

institute: Institute of Zoology

description: 10x Genomics

data_processing:
The barcodes processing and gene counting were made using Cell Ranger softwere (v3.1, 10 × Genomics) with default parameters.
Gene expression data were processed using the R package Seurat (v5.1.0).
Potential doublets in individual samples were identified using the R package DoubletFinder (v2.0.3)
Assembly: hg38
Supplementary files format and content: Tab-separated values files, matrix files and reference data set files

source_name: Placenta

extract_protocol:
The day 6 ppTOs were removed from Matrigel using Cell Recovery Solution at 4°C for 30 min. Then, the ppTOs were further digested into single cells using TrypLE Express Enzyme. The enzymatic treatment was performed on a shaker at 37°C for 20 min, and pipetted every 5 min. The cells were collected by centrifugation and filtered through a 40 μm Cell Strainer. The cell viability was detected using trypan blue staining.
The construction of transcriptome libraries was performed following the standard protocol of 10X Genomics (v3). Briefly, the cDNA was purified after GEM generation, barcode addition, GEM-RT reaction and bead cleanup. The GEX libraries were generated following the protocol of 10x Genomics Chromium Single Cell 3’ Reagent Kits (v3). The concentration of each library was accurately detected for 10x Genomics sequencing.

value: Placenta

value: stem cell


title: WT_pIC_2


title: WT_pIC_1


title: BMDMs, Infected+V46, rep1

city: Daejeon

first: Taylor

last: Roh

address: 266, Munhwa-ro

department: Microbiology

institute: Chungnam National University

data_processing:
Paired-end sequencing reads were generated on the Illumina sequencing NovaSeq platform. Before starting analysis, Trimmomatic v0.38 was used to remove adapter sequences and trim bases with poor base quality. The cleaned reads were aligned to the Mus musculus (mm10) using HISAT v2.1.0 (KIM et al, 2015), based on the HISAT and Bowtie2 implementations. The reference genome sequence and gene annotation data were downloaded from NCBI Genome assembly and NCBI RefSeq database respectively. Aligned data (SAM file format) were sorted and indexed using SAMtools v 1.9. After alignment, the transcripts were assembled and quantified using StringTie v2.1.3b (Pertea, Mihaela, et al., 2015, 2016). Gene-level and Transcript-level quantification were calculated as raw read count, FPKM (Fragments Per Kilobase of transcript per Million mapped reads) and TPM (Transcripts Per Million).
Assembly: genome used for mapping: mm10
Supplementary files format and content: Normalized_data.csv

source_name: BMDMs

extract_protocol:
Total RNA concentration was calculated by Quant-IT RiboGreen (Invitrogen). To determine the DV200 (% of RNA fragments >200 bp) value, samples are run on the TapeStation RNA screentape (Agilent).
A total of 100 ng of total RNA was subjected to a sequencing library construction using the Agilent SureSelect RNA Direct kit according to the manufacturer's protocol.

value: BMDMs

value: Macrophages


title: BMDMs, Infected, rep2

value: Infected


title: NC1235,H3K27ac,ChIP,rep1


title: NC1235,H3K27ac,ChIP,rep2


title: BMDMs, Infected+V46, rep2


title: Si1235,H2AZ,ChIP,rep2


title: Si1235,H2AZ,ChIP,rep1


title: BMDMs, Infected, rep1


title: NC1235,H2AZ,ChIP,rep2


title: NC1235,RNAseq

data_processing:
RNA-seq reads were mapped by STAR (v2.7.11a)[13] to hg38, and gene counts were generated through featureCounts (v2.0.6) with parameters "-t exon  -p  --countReadPairs"
For GSEA, the ranked gene list was analysed with the GSEA Preranked v4.3.2 tool using MSigDB Hallmarks v2023.2, C2 v2023.2, C3 gene set collections
Assembly: hg38
Supplementary files format and content: txt

extract_protocol:
.The total RNA samples were treated with VAHTS mRNA Capture Beads (Vazyme) to enrich polyA+ RNA before constructing the RNA-seq libraries.
RNA-seq libraries were prepared using VAHTS mRNA-seq v2 Library Prep Kit for Illumina (Vazyme) following the manufacturer’s instructions. Briefly, polyA+ RNA samples were fragmented and then used for first- and second-strand cDNA synthesis with random hexamer primers. The cDNA fragments were treated with DNA End Repair Kit to repair the ends, then modified with Klenow to add an A at the 3’ end of the DNA fragments, and finally ligated to adapters. Purified dsDNA was subjected to 12 cycles of PCR amplification.

value: ASO-NC


title: BMDMs, Uninfected, rep1

value: WT

value: Uninfected


title: PDGFRα positive cells of WT mice cerebral cortex

city: Toyama

first: Noriko

last: Okuno

state: Toyama

institute: University of Toyama

description: CellBarcode-Rhapsody.xlsx

data_processing:
Seven Brides - BD RhapsodyTM WTA Analysis Pipeline
Assembly: GRCm38-mm10
Supplementary files format and content: RSEC_MolsPerCell.csv

source_name: Cerebral cortex

extract_protocol:
Single-cell capture, cell lysis and cDNA synthesis were performed with the BD Rhapsody cDNA kit and BD Rhapsody Single-Cell Analysis system following manufacturer's protocols.
scRNA-seq libraries  were prepared using BD RhapsodyTM WTA Reagent Kit following manufacturer's protocols.

treatment_protocol: The cerebral cortex with the meninges were dissociated, and magnetic cell sorting was performed using the CD140a antibody.

value: Cerebral cortex

value: C57BL/6J (WT)


title: BMDMs, Uninfected, rep2


title: Si1235,RNAseq

value: Breast


title: Si1235,ATACseq

data_processing:
Sequenced reads were trimmed for adaptor sequence, and then mapped to hg38 whole genome using Bowtie2 (v2.2.9) using the default parameters.MACS2 was used for peak calling.
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
For ATAC-seq, 1×105 HCC1954 cells treated with indicated ASOs were harvested and counted. Washed twice with PBS, cells are lysed in Lysis buffer (10 mM Tris-HCl pH 7.5, 10mM NaCl, 3 mM MgCl2, 0.1% NP-40, 0,1% Tween-20, 0.01% Digitonin) on ice for 5 min then centrifuge for 10min at 500 g. Pellets were resuspended in 50 μl 1X TD Buffer (Illumina, 15027865) with 7.5 μl Tn5 Transposase (Illumina, 15027865), 0.01% Digitonin, 0.1% Tween and incubated at 37°C for 30 min. DNA were purified by Monarch PCR & DNA Cleanup Kit (NEB, T1030). Eluted DNA were amplified with NEBNext High-Fidelity 2X PCR Master Mix (NEB, M0541L) and TruePrep Index Kit V2 for Illumina (Vazyme, TD202) for 10 cycles and purified by AMPure XP beads (0.5x-0.7x).
The DNA library was prepared using a Next Ultra DNA Library Prep Kit (NEB, E7645) according to the manufacturer’s instructions. The libraries were purified with AMPure XP beads (Beckman, A63881) according to the manufacturer ’s instructions, and sequenced using Illumina platforms.

value: Her2-positive breast cancer cells


title: iPSCs

city: Madison

first: Rupa

last: Sridharan

state: WI

address: 330 N. Orchard Street

department: Wisconsin Institute for Discovery

institute: University of Wisconsin

library_source: genomic single cell

data_processing:
The returned sequencing data for each sample was aligned and processed using the cellranger-atac count pipeline openly available from 10X Genomics’ website.
Assembly: mm10
Supplementary files format and content: processd data from cellranger-atac pipeline in fragments.tsv.gz format. Contains scATAC data which was used as input into ArchR

source_name: mouse induced pluripotent stem cells

growth_protocol: All cells were grown and maintained in ESC media containing Knockout DMEM, 15% FBS, L-glutamine, Pen/Strep, NEAA, 2-mercaptoethanol, and LIF with or without any combination of the A2S chemicals. Media changed during reprogramming on even numbered days.

extract_protocol:
Cells were harvested as a single-cell suspension. Nuclei were isolated from the single-cell suspension and lysed in accordance with the recommended protocol from 10X Genomics (all spin steps were carried out at 300g for 3min at RT) to obtain genomic DNA. We aimed for a targeted nuclei recovery of 4,000 and targeted read depth of 25k reads per nucleus.
Nuclei concentration was determined using the Countess II prior to transposition and library preparation using the 10X Chromium platform.

treatment_protocol: Reprogramming was induced on Day 0 with the addition of doxycycline (2 mg/ml) and a feeder layer of irradiated human neonatal foreskin fibroblasts (ATCC HFF-1 SCRC-1041). Ascorbic acid (50 mg/ml, Sigma A8960) and SGC0946 (5 mM, ApexBio A4167) are also added at this time to A2S and dual combination reprogramming samples

value: mouse induced pluripotent stem cells


title: NC1235,ATACseq


title: ESCs

source_name: mouse embryonic stem cells

value: mouse embryonic stem cells


title: MGG4-shKPNA2-003

city: Orsay

first: Giorgio

last: Seano

address: Bâtiment 110, Rue Henri Becquerel

department: INSERM U1021 - CNRS UMR3347

institute: Institut Curie

description:
D1707T66
MGG4_selinexor_sh_tpm.csv

data_processing:
The reads obtained were processed using the Curie Institute Nextflow RNA-seq analysis pipeline
reads quality was assessed using FastQC and mapped to the reference genome (hg38) using STAR software
raw reads count tables were generated using STAR
Software versions and full pipelines are available at https://github.com/bioinfo-pf-curie/RNA-seq/
Assembly: hg38
Supplementary files format and content: Matrix table with TPM gene counts for every gene and every sample (.csv)

source_name: brain

growth_protocol: cells were maintained in neurospheres using NeuroCult basal medium with NeuroCult proliferation supplement (STEMCELL technologies, #05751), 20ng/ml EGF, 20ng/ml bFGF, 5ug/ml heparin (STEMCELL Technologies, #07980) and gentamycin (Sigma) (NC complete media) in low attachment flasks (Corning, #3814)

extract_protocol:
Total RNA was extracted using RNeasy Mini kit (Qiagen)
RNA-seq libraries were constructed using 100ng to 1ug of RNA using Illumina library structure (Stranded mRNA Library preparation, Illumina), according to the manufacturer’s instructions. Samples were sequenced as 100bp paired-end runs on the Novaseq 6000 (Illumina).

treatment_protocol: In-vitro cells were treated with 5Gy of irradiation using a gamma ray irradiator 5 days before RNA extraction. For population-based RNA sequencing of MGG4 and MGG8, cells were sorted based on fluorescent intensity of reporters.

value: brain

value: patient-derived glioblastoma cell line

value: short-hairpin KPNA2


title: PDGFRα positive cells of N-PRα-KO mice cerebral cortex

description: CellBarcode-Rhapsody.xlsx

value: Nestin-Cre;Pdgfraflox/flox


title: MGG4-shCTL-003

description:
D1707T65
MGG4_selinexor_sh_tpm.csv

value: short-hairpin control


title: MGG4-shCTL-002

description:
D1707T61
MGG4_selinexor_sh_tpm.csv


title: MEF FBS Day 12

source_name: mouse embryonic fibroblasts

value: mouse embryonic fibroblasts


title: MEF FBS Day 9


title: MGG4-shKPNA2-001

description:
D1707T58
MGG4_selinexor_sh_tpm.csv


title: MGG4-shKPNA2-002

description:
D1707T62
MGG4_selinexor_sh_tpm.csv


title: MEF FBS Day 6


title: MGG4-shCTL-001

description:
D1707T57
MGG4_selinexor_sh_tpm.csv


title: NC1235,H2AZ,ChIP,rep1


title: MGG4-selinexor-004

description:
D1707T55
MGG4_selinexor_sh_tpm.csv

value: selinexor


title: MGG4-drug-CTL-004

description:
D1707T54
MGG4_selinexor_sh_tpm.csv


title: MEF S2 Day 4


title: MGG4-drug-CTL-003

description:
D1707T48
MGG4_selinexor_sh_tpm.csv


title: MEF S2 Day 6


title: MEF S2 Day 6+2


title: MEF AS Day 6+2


title: MEF AS Day 6


title: MGG4-selinexor-002

description:
D1707T43
MGG4_selinexor_sh_tpm.csv


title: MGG4-drug-CTL-002

description:
D1707T42
MGG4_selinexor_sh_tpm.csv


title: MGG4-selinexor-001

description:
D1707T37
MGG4_selinexor_sh_tpm.csv


title: MEF AS Day 4


title: MEF A2 Day 6+2


title: MEFs


title: MEF A2 Day 4


title: HUVEC,MeAIB4,rep4,12h

city: Dalian

first: Chunxiu

last: Du

address: Lushunkou District

institute: Dalian medical university

data_processing:
The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp（0.12.2）
Trimmed sequence reads were mapped to GrCM38/mm10 using hisat2（2.0.5）
Read count extraction and normalization were performed using featureCounts（1.5.0-p3）
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0)
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: HUVEC

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) according to the manufacturer’s instructions.Total amounts and integrity of RNA were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: HUVEC

value: Human umbilical vein endothelial cells

value: treated with MeAIB for 12h


title: MGG4-drug-CTL-001

description:
D1707T36
MGG4_selinexor_sh_tpm.csv


title: MEF A2 Day 6


title: HUVEC,MeAIB2,rep2,12h

value: WT


title: MEF A2S Day 6


title: MEF A2S Day 4


title: HUVEC,control4,rep4,12h

value: control


title: HUVEC,MeAIB1,rep1,12h


title: MEF FBS Day 3


title: MGG4-selinexor-003

description:
D1707T49
MGG4_selinexor_sh_tpm.csv


title: MEF A2S Day 6+2


title: MEF A2S Day 2


title: M2_WT mouse6

city: Martinsried

first: Tobias

last: Straub

address: Großhadener Str. 9

department: Biomedical Center, Bioinformatics

institute: LMU Munich

data_processing:
Expression quantification was performed using kallisto (version 0.48) with Ensembl release version 106 for M. musculus.
Assembly: Ensembl release version 106 for M. musculus
Supplementary files format and content: Kallisto output files with pseudocounts and TPM values

source_name: thymus

growth_protocol: Mice were maintained under SPF conditions in individually ventilated cages.

extract_protocol:
CD69-MHCI+ (M2) CD4SP thymocytes were FACS-sorted, pelleted and resuspended in RNA protect (Qiagen). The treated samples were stimulated for 4h first and then resuspended in RNA protect. All samples were stored at -80°C until RNA extraction. RNA isolation was performed by Eurofins Genomics, according to the INVIEW transcriptome discovery package
Eurofins INVIEW transcriptome discovery

treatment_protocol: Where indicated, the sorted thymocytes were stimulated for 4h in the presence of soluble anti-CD28 (250ng/ml) and plate-bound LLO:Iab monomer (1μg/ml). Stimulation was performed with 1.5 × 10^5 cells/well in 96-well-plates with U-bottom and HL-1™ serum-free medium (Lonza).

value: thymus

value: CD4SP M2 thymocytes

value: Lm54 Rag1-/- Ctsl fl/fl (WT)

value: 4h anti-CD28 (250ng/ml) +LLO:Iab monomer (1μg/ml)


title: HUVEC,control1,rep1,12h


title: M2_WT mouse5


title: HUVEC,control2,rep2,12h


title: M2_CtslΔTEC mouse7

value: Lm54 Rag1-/- CtsldeltaTEC


title: Unedited T cells,CD8 subset, cultured with No target cells, experiment 2, replicate 2

first: Brian

last: Mog

address: 1650 Orleans street, CRB1 room 520

institute: Ludwig Center at Johns Hopkins

description:
Mock_T_Only_CD8_2_S6_R1_001_bio_2
Library #107

data_processing:
FASTQ files were demultiplexed and only reads containing the 5’ unique molecular identifiers (UMIs: ATTGCGCAATGNNNNNNNNGGGGG) were retained after trimming adapters and extracting the UMI. Reads were aligned to hg38 with RNA STAR using gencode release 44 comprehensive gene annotation followed by UMI deduplication using UMI-tools. Gene-counts of unique reads were generated with HTseq. Differentially expressed genes were identified with DEseq2 and defined as genes with adjusted p-value less than 0.05, base-mean expression greater than 4, and absolute value of fold change greater than 1.2. Heatmaps were Z-score scaled by row on variance stabilizing transformations of the normalized count matrix produced by DEseq2. Pathway analysis was performed using the STRING tool on differentially expressed genes and Reactome gene sets were reported. The strength of enrichment was calculated with the following expression: log10(observed number of genes/expected number of genes).
Assembly: hg38
Supplementary files format and content: Individual tabular processed data files are the count outputs from the program htseq-count on samples after UMI de-deuplication. These files were the input into the DEseq2 differential expression analysis.
Supplementary files format and content: The file "DEseq2_Normalized_Counts_Unedited_STAR-3_Co-STAR-1_Co-Cultures.tabular" contains the normalized counts for each sample after DEseq2 analysis.

source_name: T cell

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated by Ficoll-Paque PLUS (Cytiva, 17144002) gradient centrifugation from healthy donor leukopaks (StemCell and Charles River). CD3+ T cells were isolated by negative selection (StemCell Technologies, 17951) and activated with Dynabeads Human T-Activator CD3/CD28 (Thermo Fisher Scientific, 11132D) at a 1:1 bead-to-cell ratio in T cell media, which consisted of RPMI-1640 (ATCC, 30-2001) supplemented with 10% FBS (Cytiva, SH30070.03), 1% penicillin-streptomycin (Thermo Fisher Scientific, 15140163), 100 IU/mL recombinant human IL-2 (Proleukin, Prometheus Laboratories), and 5 ng/mL recombinant human IL-7 (BioLegend, 581908). After 48-56 hours of activation, T cells were separated from CD3/CD28 beads by two passes over a magnet and allowed to rest while CRISPR reagents were prepared. For each electroporation condition of simultaneous TRAC knock-in and TRBC knock-out, 50 pmols of each crRNA were independently mixed with 25 pmols of Alt-R A.s. Cas12a (Cpf1) Ultra (IDT, 10001273) and 37.5 pmols of Alt-R Cpf1 Electroporation Enhancer (IDT, 1076301) in a total volume of 1.27 µl of Nuclease Free Duplex Buffer (IDT, 11-01-03-01) for at least 15 minutes before combining the two RNPs at a 1:1 volume ratio. The TRAC and TRBC RNPs were then mixed with 0.5 µg HDRT diluted in 2.4 uL OptiMEM for a final volume of 5 µL per electroporation condition. Immediately prior to electroporation, T cells were centrifuged at 90g for 10 minutes, then resuspended at 0.75-1.25 x 106 T cells in 20 µl P3 buffer (Lonza, V4XP-3032) and combined with the 5uL Cpf1 RNP and HDRT mixture. Cells were nucleofected in 16-well cuvettes (Lonza, V4XP-3032) with a 4D Nucleofector X-Unit (Lonza, AAF-1003X) using pulse code EH115. After nucleofection, 80 µl pre-warmed cytokine free T cell media was added to cells and the cuvette strip was placed in a 37 °C incubator for 20 min. The cells were then diluted in 1 mL of T cell media and transferred to a 24-well plate. T cell media was changed every 3 days until functional assays on days 11 or greater after initial activation. STAR-3 and Co-STAR-1 T cells were generated using CRISPR-HDR as described above. On days 8-9 after activation, knock-in+ T cells were isolated using the EasySep™ Release Human PSC-Derived Neural Crest Cell Positive Selection Kit (StemCell, 100-0047).

extract_protocol:
Total RNA was isolated with the RNeasy Mini Kit (Qiagen, 74104) according to the manufacturer’s instructions and quantified by RNA ScreenTape (Agilent, 5067-5576).
The SMART-Seq mRNA LP (with UMIs) kit (Takara, 634765) and the Unique Dual Index Kit (1–96) (Takara, 634752) were used to generate cDNA and prepare sequencing libraries from two independent batches of T cells, with 3 independent cDNA libraries per condition. Libraries were sequenced on a NovaSeq 6000 (Illumina) using the 100 cycle single-end configuration at approximately 25 million reads per technical replicate.

treatment_protocol: On days 13-14 after activation, unedited, STAR-3, or Co-STAR-1 T cells were cocultured with KMS26-MUT, KMS26-NULL, or no target cells at an E:T ratio of 1:5 for 18 hours followed by flow sorting of CD4+ and CD8+ T cells into RNAprotect Tissue Reagent (Qiagen, 76104).

value: T cell

tag: susbet

tag: receptor

value: Unedited

tag: co-culture condition

value: No target cells

tag: biological replicate

tag: technical replicate


title: Unedited T cells,CD8 subset, cultured with No target cells, experiment 2, replicate 3

description:
Mock_T_Only_CD8_3_S14_R1_001_bio_2
Library #108

tag: cell type


title: M2_CtslΔTEC mouse6

tag: tissue

tag: genotype

tag: treatment


title: Unedited T cells,CD8 subset, cultured with No target cells, experiment 2, replicate 1

description:
Mock_T_Only_CD8_1_S52_R1_001_bio_2
Library #106


title: HUVEC,MeAIB3,rep3,12h

tag: cell line


title: Unedited T cells,CD4 subset, cultured with No target cells, experiment 2, replicate 3

description:
Mock_T_Only_CD4_3_S13_R1_001_bio_2
Library #105


title: M2_WT mouse1


title: Unedited T cells,CD4 subset, cultured with No target cells, experiment 2, replicate 1

description:
Mock_T_Only_CD4_1_S51_R1_001_bio_2
Library #103


title: M2_CtslΔTEC mouse2


title: Unedited T cells,CD4 subset, cultured with No target cells, experiment 2, replicate 2

description:
Mock_T_Only_CD4_2_S5_R1_001_bio_2
Library #104


title: M2_CtslΔTEC mouse4


title: M2_CtslΔTEC mouse5


title: Unedited T cells,CD8 subset, cultured with KMS26-MUT, experiment 2, replicate 2

description:
Mock_Parental_CD8_2_S2_R1_001_bio_2
Library #101


title: M2_WT mouse4


title: Unedited T cells,CD8 subset, cultured with KMS26-MUT, experiment 2, replicate 1

description:
Mock_Parental_CD8_1_S48_R1_001_bio_2
Library #100


title: HUVEC,control3,rep3,12h


title: Unedited T cells,CD4 subset, cultured with KMS26-MUT, experiment 2, replicate 3

description:
Mock_Parental_CD4_3_S9_R1_001_bio_2
Library #99


title: M2_CtslΔTEC mouse1


title: M2_CtslΔTEC mouse3


title: H3K4me3, SP, HFD, Mat2ai, rep4

city: Chicago

first: Yalu

last: Zhou

state: IL

address: 303 E Superior St

department: Department of Medicine

institute: Northwestern University

data_processing:
none provided
Assembly: mm10

source_name: kidney

extract_protocol: none provided

treatment_protocol: SGTL2 MT mice were fed with HFD for 8 weeks. Then, MAT2Ai (10 mg/kg BW) was injected into intraperitoneal cavity for eight weeks.

value: kidney

tag: chip antibody

value: Sglt2 mutant

value: high-fat diet, Mat2a inhibitor


title: Unedited T cells,CD4 subset, cultured with KMS26-MUT, experiment 2, replicate 2

description:
Mock_Parental_CD4_2_S1_R1_001_bio_2
Library #98


title: M2_WT mouse3


title: H3K4me3, SP, HFD, Mat2ai, rep3


title: H3K4me3, SP, HFD, Mat2ai, rep2


title: Unedited T cells,CD8 subset, cultured with KMS26-NULL, experiment 2, replicate 1

description:
Mock_KO_CD8_1_S50_R1_001_bio_2
Library #94


title: Unedited T cells,CD8 subset, cultured with KMS26-NULL, experiment 2, replicate 2

description:
Mock_KO_CD8_2_S4_R1_001_bio_2
Library #95


title: M2_WT mouse2


title: Unedited T cells,CD4 subset, cultured with KMS26-MUT, experiment 2, replicate 1

description:
Mock_Parental_CD4_1_S47_R1_001_bio_2
Library #97


title: Unedited T cells,CD8 subset, cultured with KMS26-NULL, experiment 2, replicate 3

description:
Mock_KO_CD8_3_S12_R1_001_bio_2
Library #96


title: Unedited T cells,CD4 subset, cultured with KMS26-NULL, experiment 2, replicate 3

description:
Mock_KO_CD4_3_S11_R1_001_bio_2
Library #93


title: Unedited T cells,CD8 subset, cultured with KMS26-MUT, experiment 2, replicate 3

description:
Mock_Parental_CD8_3_S10_R1_001_bio_2
Library #102


title: Unedited T cells,CD4 subset, cultured with KMS26-NULL, experiment 2, replicate 2

description:
Mock_KO_CD4_2_S3_R1_001_bio_2
Library #92


title: H3K4me3, SP, HFD, Placebo, rep4

value: high-fat diet, Placebo


title: Co-STAR-1 T cells,CD8 subset, cultured with No target cells, experiment 2, replicate 2

description:
566_T_Only_CD8_2_S28_R1_001_bio_2
Library #89


title: H3K4me3, SP, HFD, Placebo, rep3


title: Co-STAR-1 T cells,CD8 subset, cultured with No target cells, experiment 2, replicate 3

description:
566_T_Only_CD8_3_S30_R1_001_bio_2
Library #90


title: H3K4me3, SP, HFD, Placebo, rep2


title: Unedited T cells,CD4 subset, cultured with KMS26-NULL, experiment 2, replicate 1

description:
Mock_KO_CD4_1_S49_R1_001_bio_2
Library #91


title: H3K4me3, WT, HFD, Mat2ai, rep3


title: H3K4me3, SP, HFD, Placebo, rep1


title: H3K4me3, WT, HFD, Mat2ai, rep4


title: H3K4me3, WT, HFD, Mat2ai, rep2


title: H3K4me3, WT, HFD, Mat2ai, rep1


title: Co-STAR-1 T cells,CD8 subset, cultured with KMS26-MUT, experiment 2, replicate 3

description:
566_Parental_CD8_3_S22_R1_001_bio_2
Library #84


title: Co-STAR-1 T cells,CD8 subset, cultured with No target cells, experiment 2, replicate 1

description:
566_T_Only_CD8_1_S26_R1_001_bio_2
Library #88


title: Co-STAR-1 T cells,CD4 subset, cultured with No target cells, experiment 2, replicate 2

description:
566_T_Only_CD4_2_S27_R1_001_bio_2
Library #86


title: H3K4me3, SP, HFD, Placebo, rep5


title: H3K4me3, WT, HFD, Placebo, rep4


title: H3K4me3, WT, HFD, Placebo, rep3


title: Co-STAR-1 T cells,CD4 subset, cultured with No target cells, experiment 2, replicate 3

description:
566_T_Only_CD4_3_S29_R1_001_bio_2
Library #87


title: H3K27me3, SP, HFD, Mat2ai, rep5


title: H3K4me3, WT, HFD, Placebo, rep1


title: Co-STAR-1 T cells,CD4 subset, cultured with KMS26-MUT, experiment 2, replicate 3

description:
566_Parental_CD4_3_S21_R1_001_bio_2
Library #81


title: Co-STAR-1 T cells,CD8 subset, cultured with KMS26-MUT, experiment 2, replicate 1

description:
566_Parental_CD8_1_S36_R1_001_bio_2
Library #82


title: Co-STAR-1 T cells,CD8 subset, cultured with KMS26-MUT, experiment 2, replicate 2

description:
566_Parental_CD8_2_S44_R1_001_bio_2
Library #83


title: H3K4me3, WT, HFD, Placebo, rep2


title: Co-STAR-1 T cells,CD4 subset, cultured with KMS26-MUT, experiment 2, replicate 1

description:
566_Parental_CD4_1_S35_R1_001_bio_2
Library #79


title: Co-STAR-1 T cells,CD8 subset, cultured with KMS26-NULL, experiment 2, replicate 3

description:
566_KO_CD8_3_S24_R1_001_bio_2
Library #78


title: H3K27me3, SP, HFD, Mat2ai, rep4


title: H3K27me3, SP, HFD, Mat2ai, rep2


title: H3K4me3, SP, HFD, Mat2ai, rep1


title: Co-STAR-1 T cells,CD8 subset, cultured with KMS26-NULL, experiment 2, replicate 2

description:
566_KO_CD8_2_S46_R1_001_bio_2
Library #77


title: H3K27me3, SP, HFD, Mat2ai, rep1


title: H3K27me3, SP, HFD, Placebo, rep5


title: H3K27me3, SP, HFD, Mat2ai, rep3


title: Co-STAR-1 T cells,CD4 subset, cultured with No target cells, experiment 2, replicate 1

description:
566_T_Only_CD4_1_S25_R1_001_bio_2
Library #85


title: Co-STAR-1 T cells,CD4 subset, cultured with KMS26-NULL, experiment 2, replicate 3

description:
566_KO_CD4_3_S23_R1_001_bio_2
Library #75


title: H3K27me3, SP, HFD, Placebo, rep4


title: Co-STAR-1 T cells,CD8 subset, cultured with KMS26-NULL, experiment 2, replicate 1

description:
566_KO_CD8_1_S38_R1_001_bio_2
Library #76


title: Co-STAR-1 T cells,CD4 subset, cultured with KMS26-NULL, experiment 2, replicate 2

description:
566_KO_CD4_2_S45_R1_001_bio_2
Library #74


title: Co-STAR-1 T cells,CD4 subset, cultured with KMS26-MUT, experiment 2, replicate 2

description:
566_Parental_CD4_2_S43_R1_001_bio_2
Library #80


title: Co-STAR-1 T cells,CD4 subset, cultured with KMS26-NULL, experiment 2, replicate 1

description:
566_KO_CD4_1_S37_R1_001_bio_2
Library #73


title: STAR-3 T cells,CD8 subset, cultured with No target cells, experiment 2, replicate 3

description:
417_T_Only_CD8_3_S20_R1_001_bio_2
Library #72


title: H3K27me3, SP, HFD, Placebo, rep1


title: STAR-3 T cells,CD8 subset, cultured with No target cells, experiment 2, replicate 2

description:
417_T_Only_CD8_2_S42_R1_001_bio_2
Library #71


title: STAR-3 T cells,CD8 subset, cultured with No target cells, experiment 2, replicate 1

description:
417_T_Only_CD8_1_S34_R1_001_bio_2
Library #70


title: H3K27me3, SP, HFD, Placebo, rep3


title: H3K27me3, WT, HFD, Mat2ai, rep4


title: H3K27me3, SP, HFD, Placebo, rep2


title: H3K27me3, WT, HFD, Mat2ai, rep3


title: STAR-3 T cells,CD4 subset, cultured with No target cells, experiment 2, replicate 3

description:
417_T_Only_CD4_3_S19_R1_001_bio_2
Library #69


title: H3K27me3, WT, HFD, Mat2ai, rep2


title: STAR-3 T cells,CD4 subset, cultured with No target cells, experiment 2, replicate 2

description:
417_T_Only_CD4_2_S41_R1_001_bio_2
Library #68


title: STAR-3 T cells,CD4 subset, cultured with No target cells, experiment 2, replicate 1

description:
417_T_Only_CD4_1_S33_R1_001_bio_2
Library #67


title: H3K27me3, WT, HFD, Mat2ai, rep1


title: STAR-3 T cells,CD8 subset, cultured with KMS26-MUT, experiment 2, replicate 3

description:
417_Parental_CD8_3_S16_R1_001_bio_2
Library #66


title: STAR-3 T cells,CD8 subset, cultured with KMS26-MUT, experiment 2, replicate 2

description:
417_Parental_CD8_2_S8_R1_001_bio_2
Library #65


title: H3K27me3, WT, HFD, Placebo, rep4


title: H3K27me3, WT, HFD, Placebo, rep3


title: STAR-3 T cells,CD8 subset, cultured with KMS26-MUT, experiment 2, replicate 1

description:
417_Parental_CD8_1_S54_R1_001_bio_2
Library #64


title: STAR-3 T cells,CD4 subset, cultured with KMS26-MUT, experiment 2, replicate 3

description:
417_Parental_CD4_3_S15_R1_001_bio_2
Library #63


title: IgG, WT, ND

treatment_protocol: SGTL2 WT and MT mice were fed with HFD for 18 weeks. Single nuclei was isolated from renal cortex.

value: normal diet


title: STAR-3 T cells,CD4 subset, cultured with KMS26-MUT, experiment 2, replicate 2

description:
417_Parental_CD4_2_S7_R1_001_bio_2
Library #62


title: STAR-3 T cells,CD4 subset, cultured with KMS26-MUT, experiment 2, replicate 1

description:
417_Parental_CD4_1_S53_R1_001_bio_2
Library #61


title: H3K27me3, WT, HFD, Placebo, rep1


title: H3K4me3, SP, HFD, rep2

value: high-fat diet


title: H3K27me3, WT, HFD, Placebo, rep2


title: STAR-3 T cells,CD8 subset, cultured with KMS26-NULL, experiment 2, replicate 2

description:
417_KO_CD8_2_S40_R1_001_bio_2
Library #59


title: H3K4me3, SP, HFD, rep1


title: STAR-3 T cells,CD8 subset, cultured with KMS26-NULL, experiment 2, replicate 3

description:
417_KO_CD8_3_S18_R1_001_bio_2
Library #60


title: H3K4me3, SP, HFD, rep3


title: H3K4me3, SP, ND, rep1


title: H3K4me3, WT, HFD, rep3


title: STAR-3 T cells,CD4 subset, cultured with KMS26-NULL, experiment 2, replicate 3

description:
417_KO_CD4_3_S17_R1_001_bio_2
Library #57