title: Day30,GD32 cell, replicate 1

description:
Library name: Sample63
Day30_GD32_rep1

data_processing:
mice: Raw RNA-seq reads were trimmed, filtered and assessed using Trim Galore (version: 0.6.10). High-quality reads were then mapped to the mouse genome (GRCm38/mm10) using Hisat2 (version: 2.2.1). Read counts were calculated by HTSeq (version: 0.11.3). DESeq2 package was used to perform the different expression analyses for different sample groups. Gene Set Enrichment Analysis (GSEA) was performed using the GSEA software (version:4.3.3) available at http://software.broadinstitute.org/gsea/downloads.jsp with the option pre-ranked and default parameters. Gene Ontology (GO) analysis was performed on the online platform DAVID 23 and visualized by Prism GraphPad. cell line : The raw sequencing data were processed using Trimmomatic (RRID:SCR_011848) to remove low-quality reads and adapters . The cleaned reads were then aligned to the human reference genome (hg38) and annotated using GENCODE version M20 for Homo sapiens, employing the STAR aligner (version 2.7.7a) with default parameters 30. Gene expression quantification and differential expression analysis were conducted using Cufflinks (version 2.2.1) .
Flag CUT&RUN-seq data analysis: yeast chromatin was employed as a spike-in control for normalization. FASTQ files were preprocessed using Trimmomatic (v0.39)  to remove adapter sequences and low-quality reads. Sequencing reads were aligned to a composite reference genome, integrating the human genome (hg38) and the yeast genome (Sac3). A custom Bowtie2 library was constructed using Bowtie2-build (v2.4.2) , and reads were mapped to the reference using default parameters. After alignment, paired-end reads were segregated by species. Spike-in-derived reads were used to compute a normalization factor to account for technical variability. Peak calling was performed using MACS2 (v2.2.5) with a significance threshold of p<0.001 . Normalized read counts within peaks were quantified using BEDTools .
CRISPR screen data analysis was performed using the MAGeCK algorithm(doi.org/10.1186/s13059-014-0554-4).All the candidates with Log2FC<0 (indicating a decrease in gDNA abundance over time) were used to calculate Log2FC difference (Log2FC_diff) between GD32 and WT7: Log2FC_diff =Log2FC(GD32)- log2FC(WT7). Candidates with Log2FC_diff>-0.5 are shown in the heatmap.
Assembly: mice: GRCm38/mm10 cell line: hg38
Supplementary files format and content: mice RNA seq excel file include read counts value for each sample knock-in cell  RNAseq: excel file include FPKM value for each sample CUT&RUN: bw file showing the CUT&RUN peaks CRISPR Screen: excel include the raw counts from each sample
Library strategy: CRISPR Screen

value: cell line

value: PDAC cell line

value: H2BG53D-FLAG knock-in cell


title: N. punctiforme cells, MidLight2, bio rep 2

status: Public on Oct 26 2025

type: SRA

city: Woods Hole

first: Blair

last: Paul

state: MA

address: 7 MBL St

country: USA

institute: Marine Biological Laboratory

library_source: transcriptomic

data_processing:
Alignment, normalization, and transcript abundance was performed using the Rockhopper software package with default settings.
Assembly: GCA_000020025.1
Supplementary files format and content: comma-separated text file includes each replicate's upper quartile normalized gene counts and the time point's smoothed local regression estimate of gene expression

molecule: total RNA

organism: Nostoc punctiforme PCC 73102

growth_protocol: All replicate cultures contained an initial biomass equivalent to ~47 μg chlorophyll ɑ in 25 mL of Allan and Arnon standard growth media, diluted fourfold (AA/4). Cultures were grown at 28℃ under constant shaking (130 rpm) for 12 hours of light (40 - 50 μmol photons m-2s-1), followed by 12 hours of darkness. Following 192 hours of diurnal growth, cultures were subjected to 24 hours of light (Light24), wherein Dark24 cultures were wrapped in tin foil to occlude light.

extract_protocol:
Flash-frozen sample pellets were subjected to mechanical lysis, lithium chloride precipitation, and RNeasy Plus Mini Kit and on-column DNase treatment (QIAGEN).
Bacterial mRNA enrichment was performed with NEBNext rRNA Depletion Kit (Bacteria) and RNA Sample Purification Beads. Non-directional cDNA libraries were synthesized using Invitrogen SuperScript IV First-Strand Synthesis System before library preparation with the Tecan Life Sciences Ovation Ultralow V2 DNA-Seq Library Preparation Kit. Samples were ran with the Illumina NextSeq 500/550 High Output Kit v2.5 (150 cycles).

tag: cell line

tag: Stage

value: Mid-Light

tag: light state

value: Light

tag: time

value: 186 hours


title: HCA1_STING_N, rep 3

city: Boston

first: Dan

last: Duda

address: 55 Fruit St

department: Radiation Oncology

institute: Massachusetts General Hospital

description: Library name: Sample 12

data_processing:
The quality control of RNA-seq raw data was performed by FastQC.
After quality control, the low-quality bases and adaptors contamination was removed by Cutadapt.
Next, the clean data were aligned to mouse reference genome mm39 by STAR under two-pass mode.
After data mapping, samtools and featureCounts were used to count the number of reads aligned to the gene features.
Assembly: mm39
Supplementary files format and content: R data serialization file includes count values for each sample

organism: Mus musculus

source_name: liver

extract_protocol:
Total RNA was extracted from the tumor/liver tissues or cultured cells using Qiagen kits.
RNA libraries for RNA-seq were prepared using Qiagen Stranded RNA Library Kits following manufacturer's protocols.

tag: tissue

value: liver


title: N. punctiforme cells, MidLight2, bio rep 1


title: HCA1_STING_N, rep 2

description: Library name: Sample 11


title: Adipoctye,Rosiglitazone,24hr,Replicate,24hr,4

city: Missoula

first: Travis

last: Hughes

state: MT

address: 32 Campus Drive, Skaggs BLDG RM 472

institute: University of Montana

description:
Novogene contract only says NovaSeq
gene_count_matrix_24hr.csv

data_processing:
Align to GRCh38  with HISAT2 v. 2.2.0
Convert from sam to bam files with SAMtools v. 1.15.1
Assemble with StringTie v. 2.2.1.Linux_x86_64 with GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.gtf as the reference annotation.  Only mRNA annotations were included
convert to a count table with prepDE.py from http://ccb.jhu.edu/software/stringtie/index.shtml?t=manual
Genes with less than 10 reads in each replicate for at least one condtion were removed
Run DESeq2 v. 1.32.0  in R
Assembly: GRCh38
Supplementary files format and content: comma seperated value files for differential expression analyses
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Homo sapiens

source_name: Adult Stem Cells - Zenbio

growth_protocol: Cells were grown and differentiated IAW ZenBio protocols.  They were thawed and passaged in Preadipocyte medium (PM-1) until differentiation.  They were differentiated in Differentiation Medium lacking PPARγ agonist (DM-2-PPG) supplemented with 3 μM pioglitazone.  After differentiation for 7 days, they were transferred to Adipocyte Medium (AM-1) for maintenance.

extract_protocol:
Cells were lysed with Trizol and RNA was purified using the Invitrogen RNA was isolated using the TRIzol™Plus RNA Purification Kit (Invitrogen #12183555) treated with the on-column Purelink® DNase Treatment (Invitrogen)
Total RNA was sent to Novogene

treatment_protocol: Cells were treated with PPARγ ligands or controls for 3 hours with or without a 3 hour T0070907 pretreatment or for 24 hours

value: Adult Stem Cells - Zenbio

tag: cell type

value: Adipoctye

tag: genotype

value: WT

tag: treatment

value: Rosiglitazone 24 hr


title: Day30, WT7 cell, replicate 1

city: Hong Kong

first: Tiantian

last: QIN

address: Tat Chee Avenue, Kowloon

country: China

institute: City University of Hong Kong

description:
Library name: Sample61
Day30_WT7_rep1

library_source: genomic

molecule: genomic DNA

source_name: cell line

growth_protocol: mouse RNA-seq: All mice were raised in the laboratory animal research unit (LARU) at the City University of Hong Kong with enough food and water. KI cell lines" All cells were cultured in 37 °C incubator with 5% CO2.Cells cultured in DMEM (Gibco, 12100061) with 10% fetal bovine serum (Biosera, FB-1001).

extract_protocol:
RNA was extracted from primary tumor and liver metastasis tissue by RNA Extraction Kit (Takara, 9597) following manufacturer’s instructions. KI cell line CUT&RUN seq: CUT&RUN experiment was conducted following Skene et al’s protocol (doi.org/10.17504/protocols.io.zcpf2vn) KI cell line CUT&RUN seq: Genomic DNA was extracted using the Blood & Cell Culture DNA Midi Kit (Qiagen, 13343). KI cell line CRISPR screen: CRISPR screen was conducted following zhang feng's protocal(doi: 10.1126/science.1247005). genomic DNA was extracted using the Blood & Cell Culture DNA Midi Kit (Qiagen, 13343).
RNA-seq: 1 μg total RNA was used for following library preparation by VAHTS® Universal V8 RNA-seq Library Prep Kit for Illumina (NR605). The libraries were sequenced on a NovaSeq 6000 System using 2x150 bp paired-end configuration. KI cell line CUT&RUN seq: Libraries were prepared using the Ovation Ultralow System V2 (Invitrogen, Q32854) KI cell line CRISPR screen: The sgRNA regions within the genomic DNA were amplified with Next® Ultra™ II Q5® Master Mix (NEB, M0544X) and sequenced  on the Illumina platform

treatment_protocol: mice: no treatment KI cell line RNA-seq and CUT&RUN seq : H2B-WT-FLAG and H2BG53D-FLAG knockin cells were infected with either shNT or shSPT16 lentivirus. The infected cells were selected with 3 µg/mL puromycin for 48 hours. KI cell line CRISPR screen: no treat

value: H2B_WT-FLAG knock-in cell


title: Adipoctye,MRL24,24hr,Replicate,24hr,4

value: MRL24 24 hr


title: N. punctiforme cells, Dawn2, bio rep 3

value: Pre-Dawn

value: Dark

value: 180 hours


title: HCA1_STING_N, rep 1

description: Library name: Sample 10


title: Day30, WT7 cell, replicate 2

description:
Library name: Sample62
Day30_WT7_rep2


title: HCA1_Control_N, rep 2

description: Library name: Sample 8


title: N. punctiforme cells, Dawn2, bio rep 2


title: Day0,GD32 cell, replicate 2

description:
Library name: Sample60
Day0_GD32_rep2


title: Day0,GD32 cell, replicate 1

description:
Library name: Sample59
Day0_GD32_rep1


title: Adipoctye,DMSO,24hr,Replicate,24hr,3

value: DMSO 24 hr


title: Adipoctye,Rosiglitazone,24hr,Replicate,24hr,3


title: Day30,GD32 cell, replicate 2

description:
Library name: Sample64
Day30_GD32_rep2

value: cell line


title: Day0, WT7 cell, replicate 2

description:
Library name: Sample58
Day0_WT7_rep2

value: PDAC cell line


title: HCA1_STING_T, rep 3

description: Library name: Sample 6

source_name: tumor

value: tumor


title: HCA1_Control_N, rep 1

description: Library name: Sample 7


title: HCA1_Control_N, rep 3

description: Library name: Sample 9


title: Adipoctye,MRL24,24hr,Replicate,24hr,3


title: Day0, WT7 cell, replicate 1

description:
Library name: Sample57
Day0_WT7_rep1


title: Adipoctye,GW1929,24hr,Replicate,24hr,3


title: N. punctiforme cells, MidDark2, bio rep 3

value: Mid-Dark

value: 174 hours


title: Adipoctye,GW1929,24hr,Replicate,24hr,4


title: Adipoctye,DMSO,24hr,Replicate,24hr,2


title: N. punctiforme cells, MidDark2, bio rep 1


title: N. punctiforme cells, MidDark2, bio rep 2


title: P4-H2A-GD3-KD

description: Library name: Sample55

data_processing:
mice: Raw RNA-seq reads were trimmed, filtered and assessed using Trim Galore (version: 0.6.10). High-quality reads were then mapped to the mouse genome (GRCm38/mm10) using Hisat2 (version: 2.2.1). Read counts were calculated by HTSeq (version: 0.11.3). DESeq2 package was used to perform the different expression analyses for different sample groups. Gene Set Enrichment Analysis (GSEA) was performed using the GSEA software (version:4.3.3) available at http://software.broadinstitute.org/gsea/downloads.jsp with the option pre-ranked and default parameters. Gene Ontology (GO) analysis was performed on the online platform DAVID 23 and visualized by Prism GraphPad. cell line : The raw sequencing data were processed using Trimmomatic (RRID:SCR_011848) to remove low-quality reads and adapters . The cleaned reads were then aligned to the human reference genome (hg38) and annotated using GENCODE version M20 for Homo sapiens, employing the STAR aligner (version 2.7.7a) with default parameters 30. Gene expression quantification and differential expression analysis were conducted using Cufflinks (version 2.2.1) .
Flag CUT&RUN-seq data analysis: yeast chromatin was employed as a spike-in control for normalization. FASTQ files were preprocessed using Trimmomatic (v0.39)  to remove adapter sequences and low-quality reads. Sequencing reads were aligned to a composite reference genome, integrating the human genome (hg38) and the yeast genome (Sac3). A custom Bowtie2 library was constructed using Bowtie2-build (v2.4.2) , and reads were mapped to the reference using default parameters. After alignment, paired-end reads were segregated by species. Spike-in-derived reads were used to compute a normalization factor to account for technical variability. Peak calling was performed using MACS2 (v2.2.5) with a significance threshold of p<0.001 . Normalized read counts within peaks were quantified using BEDTools .
CRISPR screen data analysis was performed using the MAGeCK algorithm(doi.org/10.1186/s13059-014-0554-4).All the candidates with Log2FC<0 (indicating a decrease in gDNA abundance over time) were used to calculate Log2FC difference (Log2FC_diff) between GD32 and WT7: Log2FC_diff =Log2FC(GD32)- log2FC(WT7). Candidates with Log2FC_diff>-0.5 are shown in the heatmap.
Assembly: mice: GRCm38/mm10 cell line: hg38
Supplementary files format and content: mice RNA seq excel file include read counts value for each sample knock-in cell  RNAseq: excel file include FPKM value for each sample CUT&RUN: bw file showing the CUT&RUN peaks CRISPR Screen: excel include the raw counts from each sample
Library strategy: CUT&Run

value: PDAC cancer cell line

value: H2BG53D-FLAG knock-in cell

value: SPT16 knockdown sh49, H2A


title: P4-H2A-GD32-KD

description: Library name: Sample56


title: HCA1_STING_T, rep 2

description: Library name: Sample 5


title: Adipoctye,Rosiglitazone,24hr,Replicate,24hr,2

value: Adult Stem Cells - Zenbio

value: Adipoctye


title: P4-H2A-WT16-KD

description: Library name: Sample54


title: HCA1_Control_T, rep 2

description: Library name: Sample 2


title: Adipoctye,MRL24,24hr,Replicate,24hr,2

value: WT


title: N. punctiforme cells, Dusk1, bio rep 3

value: Pre-Dusk

value: Light

value: 96 hours


title: N. punctiforme cells, Dawn2, bio rep 1

value: Pre-Dawn

value: Dark


title: HCA1_Control_T, rep 1

description: Library name: Sample 1


title: HCA1_Control_T, rep 3

description: Library name: Sample 3


title: P4-H2A-WT7-KD

description: Library name: Sample53

value: H2B_WT-FLAG knock-in cell


title: Adipoctye,GW1929,24hr,Replicate,24hr,2


title: P4-H2A-GD32-NT

description: Library name: Sample52

value: cell line

value: non-targeting control, H2A


title: Adipoctye,DMSO,24hr,Replicate,24hr,1

value: DMSO 24 hr


title: N. punctiforme cells, Dusk1, bio rep 2


title: G53D-KPC mice 3, metastastic tumor

description:
Library name: Sample14
Sample14

data_processing:
mice: Raw RNA-seq reads were trimmed, filtered and assessed using Trim Galore (version: 0.6.10). High-quality reads were then mapped to the mouse genome (GRCm38/mm10) using Hisat2 (version: 2.2.1). Read counts were calculated by HTSeq (version: 0.11.3). DESeq2 package was used to perform the different expression analyses for different sample groups. Gene Set Enrichment Analysis (GSEA) was performed using the GSEA software (version:4.3.3) available at http://software.broadinstitute.org/gsea/downloads.jsp with the option pre-ranked and default parameters. Gene Ontology (GO) analysis was performed on the online platform DAVID 23 and visualized by Prism GraphPad. cell line : The raw sequencing data were processed using Trimmomatic (RRID:SCR_011848) to remove low-quality reads and adapters . The cleaned reads were then aligned to the human reference genome (hg38) and annotated using GENCODE version M20 for Homo sapiens, employing the STAR aligner (version 2.7.7a) with default parameters 30. Gene expression quantification and differential expression analysis were conducted using Cufflinks (version 2.2.1) .
Flag CUT&RUN-seq data analysis: yeast chromatin was employed as a spike-in control for normalization. FASTQ files were preprocessed using Trimmomatic (v0.39)  to remove adapter sequences and low-quality reads. Sequencing reads were aligned to a composite reference genome, integrating the human genome (hg38) and the yeast genome (Sac3). A custom Bowtie2 library was constructed using Bowtie2-build (v2.4.2) , and reads were mapped to the reference using default parameters. After alignment, paired-end reads were segregated by species. Spike-in-derived reads were used to compute a normalization factor to account for technical variability. Peak calling was performed using MACS2 (v2.2.5) with a significance threshold of p<0.001 . Normalized read counts within peaks were quantified using BEDTools .
CRISPR screen data analysis was performed using the MAGeCK algorithm(doi.org/10.1186/s13059-014-0554-4).All the candidates with Log2FC<0 (indicating a decrease in gDNA abundance over time) were used to calculate Log2FC difference (Log2FC_diff) between GD32 and WT7: Log2FC_diff =Log2FC(GD32)- log2FC(WT7). Candidates with Log2FC_diff>-0.5 are shown in the heatmap.
Assembly: mice: GRCm38/mm10 cell line: hg38
Supplementary files format and content: mice RNA seq excel file include read counts value for each sample knock-in cell  RNAseq: excel file include FPKM value for each sample CUT&RUN: bw file showing the CUT&RUN peaks CRISPR Screen: excel include the raw counts from each sample

source_name: metastatic tumor

value: metastatic tumor


title: N. punctiforme cells, MidLight1, bio rep 2

value: Mid-Light

value: 90 hours


title: N. punctiforme cells, MidLight1, bio rep 3


title: G53D-KPC mice 2, metastastic tumor

description:
Library name: Sample13
Sample13


title: Adipoctye,Rosiglitazone,24hr,Replicate,24hr,1

value: Rosiglitazone 24 hr


title: P4-H2A-WT16-NT

description: Library name: Sample50

value: PDAC cancer cell line


title: P4-H2A-GD3-NT

description: Library name: Sample51

value: H2BG53D-FLAG knock-in cell


title: HCA1_STING_T, rep 1

description: Library name: Sample 4

value: tumor


title: G53D-KPC mice 1, metastastic tumor

description:
Library name: Sample12
Sample12


title: N. punctiforme cells, MidLight1, bio rep 1


title: KPC mice 3, metastastic tumor

description:
Library name: Sample11
Sample11

value: KPC


title: P4-H2A-Par-NT

description: Library name: Sample48

value: parental cell line


title: Adipoctye,GW1929,24hr,Replicate,24hr,1

value: Adult Stem Cells - Zenbio

value: Adipoctye

value: WT


title: P4-H2A-WT7-NT

description: Library name: Sample49


title: KPC mice 2, metastastic tumor

description:
Library name: Sample10
Sample10


title: HCHN_2

city: Xiamen

first: Jichen

last: Chen

state: None Selected

address: Fujian province xiamen city

institute: Xiamen University

data_processing:
illuma casava 1.7 software  used for basecalling
Sequence reads were trimmed for adaptor sequence, and masked for low complexity or low-quality sequence then mapped to mm10 whole genome using bowtie V0.12.2 with parameters
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read per kilobase of exon per magabase of library size (TPM) were caculated using a protocol
Assembly: no
Supplementary files format and content: mm10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

organism: Gracilariopsis lemaneiformis

source_name: fresh sample

growth_protocol: optional

extract_protocol:
12h light, 12h dark
RNA was harvested using Trizol reagent illumina truseq RNA sample kit (Cat#FC-122-1001) was used with 1ug of total RNA for construction
RNA libraries for RNA-seq were prepared using standard illumia protocols

treatment_protocol: optional

value: fresh sample

value: Wild type

value: CO2 concentration


title: N. punctiforme cells, Dawn1, bio rep 3

value: Pre-Dawn

value: Dark

value: 84 hours


title: N. punctiforme cells, Dawn1, bio rep 1


title: P4-Flag-GD32-KD

description: Library name: Sample47

value: cell line

value: SPT16 knockdown sh49, FLAG


title: HCHN_3


title: N. punctiforme cells, MidDark1, bio rep 3

value: Mid-Dark

value: 78 hours


title: HCLN_3


title: KPC mice 1, metastastic tumor

description:
Library name: Sample9
Sample9

value: metastatic tumor


title: N. punctiforme cells, Dawn1, bio rep 2


title: Adipoctye,MRL24,24hr,Replicate,24hr,1

value: MRL24 24 hr


title: HCHN_1


title: G53D-KPC mice 4, primary PDAC tumor

description:
Library name: Sample8
Sample8

source_name: primary tumor

value: primary tumor


title: G53D-KPC mice 3, primary PDAC tumor

description:
Library name: Sample7
Sample7


title: P4-Flag-WT16-KD

description: Library name: Sample45

value: PDAC cancer cell line

value: H2B_WT-FLAG knock-in cell


title: N. punctiforme cells, MidDark1, bio rep 1


title: HCLN_2


title: HCLN_1


title: P4-Flag-GD32-NT

description: Library name: Sample43

value: H2BG53D-FLAG knock-in cell

value: non-targeting control, FLAG


title: G53D-KPC mice 2, primary PDAC tumor

description:
Library name: Sample6
Sample6


title: G53D-KPC mice 1, primary PDAC tumor

description:
Library name: Sample5
Sample5


title: N. punctiforme cells, Dusk0, bio rep 3

value: Pre-Dusk

value: Light

value: 48 hours


title: LCHN_3

value: fresh sample

value: Wild type

value: CO2 concentration


title: N. punctiforme cells, Dusk1, bio rep 1

value: 96 hours


title: P4-Flag-GD3-NT

description: Library name: Sample42

value: cell line


title: N. punctiforme cells, Dusk0, bio rep 2


title: KPC mice 3, primary PDAC tumor

description:
Library name: Sample3
Sample3

value: KPC


title: KPC mice 4, primary PDAC tumor

description:
Library name: Sample4
Sample4


title: P4-Flag-GD3-KD

description: Library name: Sample46

value: SPT16 knockdown sh49, FLAG


title: LCHN_2


title: N. punctiforme cells, Dusk0, bio rep 1


title: N. punctiforme cells, Dawn0, bio rep 2

value: Pre-Dawn

value: Dark

value: 36 hours


title: N. punctiforme cells, Dawn0, bio rep 3


title: P4-Flag-WT7-KD

description: Library name: Sample44

value: PDAC cancer cell line


title: LCLN_2


title: P4-Flag-WT7-NT

description: Library name: Sample40

value: H2B_WT-FLAG knock-in cell


title: P4-Flag-Par-NT

description: Library name: Sample39

value: parental cell line


title: KPC mice 2, primary PDAC tumor

description:
Library name: Sample2
Sample2

value: primary tumor


title: LCHN_1


title: KPC mice 1, primary PDAC tumor

description:
Library name: Sample1
Sample1


title: LCLN_3


title: N. punctiforme cells, MidDark1, bio rep 2

value: Mid-Dark

value: 78 hours


title: N. punctiforme cells, Dawn0, bio rep 1


title: LCLN_1


title: P4-Flag-WT16-NT

description: Library name: Sample41

value: non-targeting control, FLAG


title: Min6_sgNT_2

status: Public on Oct 25 2025

city: Minato-Ku

first: Satoshi

last: Hashimoto

address: 4-6-1 shirokanedai

country: Japan

institute: The University of Tokyo

description: Library name: 10

library_source: other

data_processing:
Sequence data were trimmed and quality-checked with fastp (0.23.4)using the following options: -a TGATCGGAAGAGCACACGTCTGAA -f 2 -w 4 -q 20 -n 10 -l 20. Reads were demultiplexed by barcode sequences using a modified version of auto_barcode-master barcode_split_trim.pl (v2.1.2).
Unique molecular identifiers (UMIs) were extracted with UMI-tools (1.1.2) extract using the following options: --extract-method=string --3prime --bc-pattern=NNNNN. rRNA reads were removed using Bowtie2 (2.5.4) with the --very-sensitive option; rRNA reference sequences were obtained from Ensembl BioMart. The remaining reads were mapped to the mouse genome using STAR (2.7.11a)with default settings and indexed with samtools (1.9) index. PCR duplicates were removed using UMI-tools dedup. Ribosome density per transcript was quantified using featureCounts (2.12.3) with gencode.vM35.basic.annotation.gtf as reference. Fold changes were calculated with DESeq2 (1.38.3).
Assembly: GRCm39
Supplementary files format and content: csv file, raw conuts for each samples
Library strategy: Ribo-Seq

molecule: other

extract_protocol:
80% confluent cells were washed twice with PBS and lysed in Ribo-seq lysis buffer. 40 µg of RNA was mixed with RNase I at 25 °C for 45 min. Ribosome fraction was purified by sucrose cushion with ultracentrifuge at 542,715 × g for 1 h at 4 °C in a TLA-110 rotor. The ribosomal pellet was resuspended in 120 µL splitting buffer to dissociate ribosomes from mRNA fragments, then passed through a 100 kDa MWCO Amicon Ultra-0.5 filter. Approximately 100 µL of the non-ribosomal flow-through was mixed with 300 µL TRIzol, and RNA fragments were purified.
A linker was ligated to the 3′ end of the RNA fragments, followed by reverse transcription and circularization. The resulting cDNA was then PCR-amplified to generate the sequencing library.

value: mouse pancreatic cell lines

value: sgNT

tag: batch


title: Min6_sgL_2

description: Library name: 13


title: Min6_sgL_1

description: Library name: 12


title: Min6_sgNT_3

description: Library name: 11


title: Mouse HSPC_CCL2_treated

city: Minato-ku

first: Takaharu

last: Kimura

state: Tokyo

address: 4-6-1 Shirokanedai

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Sequence reads were processed using Cell Ranger (version 7.0.0) to align and generate feature-barcode matrices.
Assembly: mm10 (Mouse) / GRCh38 (Human)
Supplementary files format and content: Cell Ranger output files (barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz)

source_name: Bone marrow

extract_protocol:
From cultured mouse and human HSPCs, propidium iodide-negative fraction was sorted using MoFlo (Beckman Coulter), and loaded into Chromium Next GEM Chip G (10× Genomics). Gel beads-in-emulsions were generated using the Chromium Controller (10× Genomics).
Libraries were constructed using the Single Cell 3' Reagent Kit version 3.1 (10× Genomics) according to the manufacturer’s protocol. Reverse transcription and library preparation were performed on VeritiPro Thermal cycler (Thermo Fisher Scientific). Amplified cDNA and constructed libraries were evaluated on Agilent TapeStation (Agilent Technologies). The libraries were sequenced on Illumina Hiseq X (Macrogen Japan).

treatment_protocol: Mouse HSPCs and human CB CD34+ cells were cultured at 37°C under 5% CO2 with CCL2 (Pepro tech) for 10 days.

value: Bone marrow

value: HSPCs

value: Wild type


title: Min6_sgL_3

description: Library name: 14


title: Day 25 bovine embryo, replicate 2, scRNA seq

city: Storrs

first: Yue

last: Su

address: 1390 Storrs Road

institute: University of Connecticut

data_processing:
The raw data was aligned with the bovine reference genome and analyzed with the cell ranger pipeline (10x Genomics) to map gene expression results to each individual cell with the help of barcodes from the gel beads. We used R software v4.1.2 (https://www.r-project.org/) and Seurat v4.3.0 package (15) to read gene expression matrix from the .h5 file and performed further analysis. To ensure the accuracy and robustness of our results, we used DoubletFinder (16) to integrate multiple copies and remove potential doublets. Cells with less than 200 genes or more than 4,000 genes, and more than 5% mitochondrial gene expressed, as well as all genes not expressed in at least five cells, were filtered out.
Assembly: bosTau9
Supplementary files format and content: RDS file includes normalized GFP-selected counts

organism: Bos taurus

source_name: Day 25 bovine embryo

extract_protocol:
Day 25 flushed bovine chimeric embryos were cut into small pieces and treated with 2 mg/ml papain (Worthington Biochemical, LS003119), 1 mg/ml DNase I (Roche, 10104159001) and 0.5x Glutamax in 2 ml Hibernate A without calcium (BrainBits, HACA500) at 37°C for 40 min. After digestion, 2 ml DPBS with 2% FBS was added to neutralize the enzyme. The embryos were singularized by pipetting 15 to 20 times. The dissociated cell suspension was passed through a 70 μm strainer and centrifuged at 300g for 5 min at 4°C. The cell pellet was resuspended in 1 ml cold RPMI medium with 2% FBS and subjected to cell sorting. After sorting, the cell pellet was resuspended in DPBS with 2% FBS at 800 cells/μL. The concentrated cells were then loaded for 10x single cell RNA sequencing.
Prepared cells were processed for single cell transcriptome analysis using the Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1 (10x Genomics, Pleasanton, CA, USA).  Cells were diluted to the appropriate concentration per manufacturer recommendations prior to ensure proper loading.  GEM reverse transcription, cDNA amplification and library generation followed manufacturer’s protocol (10x Genomics, Pleasanton, CA, USA).

value: Day 25 bovine embryo


title: JY-bESC-9

data_processing:
The RNA-seq reads were mapped to the bovine genome (ARS-UCD1.2) using RNA STAR.
The alignment data were then annotated using featureCounts.
The raw counts were used as input for the differential expression analysis by DESeq2
Assembly: bosTau9
Supplementary files format and content: Excel file includes the normalized row counts

source_name: JY-bESC

extract_protocol:
Total RNA was isolated using miRNeasy Mini kit (Qiagen, 217004).
Total RNA samples were prepared for mRNA-Sequencing using the Illumina Stranded mRNA Ligation Sample Preparation kit following the manufacturer’s protocol.

value: JY-bESC

value: bovine embryonic stem cell


title: Day 25 bovine embryo, replicate 1, scRNA seq


title: JY-bESC-8


title: JY-bESC-6


title: Human HSPC_CCL2_treated

description: 10x Genomics

source_name: Umbilical cord

value: Umbilical cord

value: Normal


title: JY-bESC-3


title: JY-bESC-1


title: JY-bESC-4


title: 1175, Frontal cortex, mutant

first: Kellen

last: Winden

address: 300 Longwood Ave

department: Neurology

institute: Boston Children's Hospital

description: Library name: 1175KCP

data_processing:
Sequencing was performed on a NextSeq 500 (Illumina). Reads were mapped and quantified as previously published using the inDrops pipeline using the GRCm38 genome.
Assembly: GRCm38
Supplementary files format and content: Tab-separated value files and matrix files

molecule: nuclear RNA

source_name: frontal cortex

extract_protocol:
At P30, littermate Tsc2del/fl SynCre+ and Tsc2fl/fl SynCre- animals were euthanized with carbon dioxide. A piece of left frontal cortex was dissected and transferred to a dounce homogenizer with 1ml of homogenization buffer (HB) (250mM Sucrose (IBI Scientific IB37160), 25mM KCl (Sigma P9541-500G), 5mM MgCl2 (Sigma 63068-250G), 20mM Tricine-KOH (Tricine T0377-100G), spermine 150uM (Abcam ab146523), spermidine 500uM (Sigma S2501-1G), DTT 1mM (Sigma D0632-1G), pH 7.8), followed by 10 strokes of a “tight” pestle. Then 320ul of 5% IGEPAL in HB was added to the homogenate, followed by 5 more strokes with the pestle. The resulting homogenate was filtered through a 40um cell strainer and then washed with 4ml of buffer HB. This was mixed with 5ml of working solution (50% optiprep, 25mM KCl, 5mM MgCl2, 20mM Tricine-KOH, pH 7.8) to generate a nuclei suspension in 25% optiprep. A gradient was formed with (bottom to top) 1ml 40% optiprep (2ml working solution + 0.5ml HB + 4ul RNAsin (N2511; Promega)), 1ml 30% optiprep (1.5ml working solution + 1ml HB + 4ul RNAsin), and then 10ml of 25% optiprep with homogenate in ultracentrifuge tubes (16mm x 76mm UltraClear; Beckman Coulter). Gradients were centrifuged at 10,000g for 20 minutes. Nuclei were collected from the interface between the 30% and 40% optiprep layers. Nuclei suspension was washed once with PBS (Invitrogen 14190-250) + 1% (BSA EMD-Millipore 2930-100GM) + 5mM MgCl2 (Sigma 63068-250G).
Single cell RNA-Seq was provided by the Single Cell Core at Harvard Medical School, Boston, MA. Library size was quantified on a Bioanalyzer (Agilent) and concentration was quantified by qPCR (Kapa Library Quantification – Complete kit ROX low; Roche Sequencing 07960336001).

value: frontal cortex

value: mixed

value: Tsc2del/fl SynCre+


title: 1167, Frontal cortex, mutant

description: Library name: 1167KCP


title: 1159, Frontal cortex, control

description: Library name: 1159CCM

value: Tsc2fl/fl SynCre-


title: CCR7- memory CD8+ T cells, IL-15 + anti-CD3, 48hours, rep10

city: Daejeon

first: So-Young

last: Kim

state: Daejeon

address: GSMSE, 291, Daehak-ro, Yuseong-gu, Daejeon, Rep, E18-1

country: South Korea

institute: KAIST

description:
Library name: ALL_H10_48h
ALL_H10

data_processing:
Alignment of the QuantSeq 3’ mRNA-Seq reads based on a human reference sequence (hg19) was performed using Bowtie2.
Assembly: hg19
Supplementary files format and content: Raw count matrix

source_name: Peripheral blood

growth_protocol: Sorted CCR7- memory CD8+ T cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin in humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
Total RNA was extracted using TRIZOL reagent.
An RNA library was prepared using a QuantSeq 3’ mRNA-seq Library Prep Kit (Lexogen). An individual set of 500 ng total RNA was prepared, an oligo-dT primer containing an Illumina-compatible sequence at its 5’ end was hybridized to the RNA, and reverse transcription was performed. After degradation of the RNA template, second strand synthesis was processed using a random primer with an Illumina-compatible linker sequence at its 5’ end. Magnetic beads were used to purify the double-stranded library, and to eliminate reactive components. The library was amplified for the addition of complete adapter sequences needed for cluster generation and, finally, the amplified library was purified from PCR components.

treatment_protocol: Sorted CCR7- memory CD8+ T cells from healthy donors (n = 10) were stimulated for 48 hours with IL-15 (10 ng/ml), anti-CD3 (coated, 1 µg/ml), or the combination of both

value: Peripheral blood

value: Primary cell

value: CCR7- memory CD8+ T cells

value: IL-15 (10 ng/ml) + anti-CD3 (coated, 1 µg/ml)


title: CCR7- memory CD8+ T cells, IL-15 + anti-CD3, 48hours, rep9

description:
Library name: ALL_H9_48h
ALL_H9


title: CCR7- memory CD8+ T cells, IL-15 + anti-CD3, 48hours, rep8

description:
Library name: ALL_H8_48h
ALL_H8


title: 1173, Frontal cortex, control

description: Library name: 1173CCM


title: 1171, Frontal cortex, control

description: Library name: 1171CCM


title: 1084_1085, Frontal cortex

description: Library name: 1084CCM_1085KCP


title: 1160, Frontal cortex, mutant

description: Library name: 1160KCP


title: CCR7- memory CD8+ T cells, IL-15 + anti-CD3, 48hours, rep6

description:
Library name: ALL_H6_48h
ALL_H6


title: 1083_1086, Frontal cortex

description: Library name: 1083CCM_1086KCP


title: Min6_sgNT_1

description: Library name: 9

value: mouse pancreatic cell lines

value: sgNT


title: CCR7- memory CD8+ T cells, IL-15 + anti-CD3, 48hours, rep5

description:
Library name: ALL_H5_48h
ALL_H5


title: CCR7- memory CD8+ T cells, IL-15 + anti-CD3, 48hours, rep4

description:
Library name: ALL_H4_48h
ALL_H4


title: CCR7- memory CD8+ T cells, IL-15 + anti-CD3, 48hours, rep2

description:
Library name: ALL_H2_48h
ALL_H2


title: CCR7- memory CD8+ T cells, anti-CD3, 48hours, rep8

description:
Library name: CD3_H8_48h
CD3_H8

value: anti-CD3 (coated, 1 µg/ml)


title: CCR7- memory CD8+ T cells, anti-CD3, 48hours, rep7

description:
Library name: CD3_H7_48h
CD3_H7


title: CCR7- memory CD8+ T cells, anti-CD3, 48hours, rep6

description:
Library name: CD3_H6_48h
CD3_H6


title: CCR7- memory CD8+ T cells, IL-15 + anti-CD3, 48hours, rep3

description:
Library name: ALL_H3_48h
ALL_H3


title: CCR7- memory CD8+ T cells, anti-CD3, 48hours, rep5

description:
Library name: CD3_H5_48h
CD3_H5


title: CCR7- memory CD8+ T cells, anti-CD3, 48hours, rep4

description:
Library name: CD3_H4_48h
CD3_H4


title: CCR7- memory CD8+ T cells, IL-15 + anti-CD3, 48hours, rep1

description:
Library name: ALL_H1_48h
ALL_H1


title: CCR7- memory CD8+ T cells, anti-CD3, 48hours, rep2

description:
Library name: CD3_H2_48h
CD3_H2


title: CCR7- memory CD8+ T cells, anti-CD3, 48hours, rep1

description:
Library name: CD3_H1_48h
CD3_H1


title: CCR7- memory CD8+ T cells, anti-CD3, 48hours, rep9

description:
Library name: CD3_H9_48h
CD3_H9


title: CCR7- memory CD8+ T cells, IL-15, 48hours, rep9

description:
Library name: IL15_H9_48h
IL15_H9


title: CCR7- memory CD8+ T cells, anti-CD3, 48hours, rep10

description:
Library name: CD3_H10_48h
CD3_H10


title: CCR7- memory CD8+ T cells, IL-15, 48hours, rep5

description:
Library name: IL15_H5_48h
IL15_H5


title: CCR7- memory CD8+ T cells, IL-15, 48hours, rep1

description:
Library name: IL15_H1_48h
IL15_H1


title: CCR7- memory CD8+ T cells, IL-15, 48hours, rep10

description:
Library name: IL15_H10_48h
IL15_H10


title: CCR7- memory CD8+ T cells, No treatment, 48hours, rep10

description:
Library name: NOTX_H10_48h
NOTX_H10

value: No treatment


title: CCR7- memory CD8+ T cells, IL-15, 48hours, rep4

description:
Library name: IL15_H4_48h
IL15_H4


title: CCR7- memory CD8+ T cells, IL-15, 48hours, rep7

description:
Library name: IL15_H7_48h
IL15_H7


title: CCR7- memory CD8+ T cells, IL-15, 48hours, rep8

description:
Library name: IL15_H8_48h
IL15_H8


title: CCR7- memory CD8+ T cells, No treatment, 48hours, rep7

description:
Library name: NOTX_H7_48h
NOTX_H7


title: CCR7- memory CD8+ T cells, anti-CD3, 48hours, rep3

description:
Library name: CD3_H3_48h
CD3_H3


title: CCR7- memory CD8+ T cells, No treatment, 48hours, rep5

description:
Library name: NOTX_H5_48h
NOTX_H5


title: CCR7- memory CD8+ T cells, No treatment, 48hours, rep2

description:
Library name: NOTX_H2_48h
NOTX_H2


title: CCR7- memory CD8+ T cells, IL-15, 48hours, rep6

description:
Library name: IL15_H6_48h
IL15_H6


title: CCR7- memory CD8+ T cells, IL-15 + anti-CD3, 48hours, rep7

description:
Library name: ALL_H7_48h
ALL_H7


title: CCR7- memory CD8+ T cells, IL-15, 48hours, rep3

description:
Library name: IL15_H3_48h
IL15_H3


title: CCR7- memory CD8+ T cells, IL-15, 48hours, rep2

description:
Library name: IL15_H2_48h
IL15_H2


title: CCR7- memory CD8+ T cells, No treatment, 48hours, rep9

description:
Library name: NOTX_H9_48h
NOTX_H9


title: CCR7- memory CD8+ T cells, No treatment, 48hours, rep8

description:
Library name: NOTX_H8_48h
NOTX_H8


title: CCR7- memory CD8+ T cells, IL-15 + Ionomycin, 12hours, rep5

description:
Library name: ALL_H5_12h
ALL_H5

treatment_protocol: Sorted CCR7- memory CD8+ T cells from healthy donors (n = 10) were stimulated for 12 hours with IL-15 (10 ng/ml), ionomycin (500 ng/ml), or the combination of both.

value: IL-15 (10 ng/ml) + Ionomycin (500ng/ml)


title: CCR7- memory CD8+ T cells, IL-15 + Ionomycin, 12hours, rep6

description:
Library name: ALL_H6_12h
ALL_H6


title: CCR7- memory CD8+ T cells, IL-15 + Ionomycin, 12hours, rep4

description:
Library name: ALL_H4_12h
ALL_H4


title: CCR7- memory CD8+ T cells, IL-15 + Ionomycin, 12hours, rep2

description:
Library name: ALL_H2_12h
ALL_H2


title: CCR7- memory CD8+ T cells, Ionomycin, 12hours, rep10

description:
Library name: IONO_H10_12h
IONO_H10

value: Ionomycin (500ng/ml)


title: CCR7- memory CD8+ T cells, Ionomycin, 12hours, rep8

description:
Library name: IONO_H8_12h
IONO_H8


title: CCR7- memory CD8+ T cells, No treatment, 48hours, rep6

description:
Library name: NOTX_H6_48h
NOTX_H6


title: CCR7- memory CD8+ T cells, No treatment, 48hours, rep4

description:
Library name: NOTX_H4_48h
NOTX_H4


title: CCR7- memory CD8+ T cells, No treatment, 48hours, rep3

description:
Library name: NOTX_H3_48h
NOTX_H3


title: CCR7- memory CD8+ T cells, Ionomycin, 12hours, rep6

description:
Library name: IONO_H6_12h
IONO_H6


title: CCR7- memory CD8+ T cells, Ionomycin, 12hours, rep7

description:
Library name: IONO_H7_12h
IONO_H7


title: CCR7- memory CD8+ T cells, Ionomycin, 12hours, rep5

description:
Library name: IONO_H5_12h
IONO_H5


title: NSC-EV_Hip2

city: shanghai

first: negri

last: li

address: zhennan road 500

institute: tongji university

description: Library name: Sample17

data_processing:
The libraries were sequenced on a llumina Novaseq 6000 platform and 150 bp paired-end reads were generated. Raw reads for each sample were generated. Raw reads of fastq format were firstly processed using fastp1 and the low quality reads were removed to obtain the clean reads. Then clean reads for each sample were retained for subsequent analysis. The clean reads were mapped to the reference genome using HISAT22. FPKM3 of each gene was calculated and the read counts of each gene were obtained by HTSeq-count4. PCA analysis were performed using R (v 3.2.0) to evaluate the biological duplication of samples. Differential expression analysis was performed using the DESeq25. Q value < 0.05 and foldchange > 2 was set as the threshold for significantly differential expression genes (DEGs). Hierarchical cluster analysis of DEGs was performed using R (v 3.2.0) to demonstrate the expression pattern of genes in different groups and samples. The radar map of top 30 genes was drawn to show the expression of up-regulated or down-regulated DEGs using R packet g gradar. Based on the hypergeometric distribution, GO, kyoto encyclopedia of genes and genomes (KEGG) pathway, Reactome and WikiPathways enrichment analysis of DEGs were performed to screen the significant enriched term using R (v 3.2.0), respectively. R (v 3.2.0) was used to draw the column diagram, the chord diagram and bubble diagram of the significant enrichment term.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

molecule: polyA RNA

source_name: one sample from hippocampus

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Then the libraries were constructed using VAHTS Universal V10 RNA-seq Library Prep Kit (Premixed Version) according to the manufacturer’s instructions. The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China).
RNA libraries were prepared with Chromium Singlecell 3’ Reagent v3 Kits according to the manufacturer's protocol.

value: Hippocampus

value: CRS mice

value: NSC-EVs


title: CCR7- memory CD8+ T cells, IL-15, 12hours, rep8

description:
Library name: IL15_H8_12h
IL15_H8


title: NSC-EV_Hip1

description: Library name: Sample16


title: CCR7- memory CD8+ T cells, IL-15, 12hours, rep9

description:
Library name: IL15_H9_12h
IL15_H9


title: CCR7- memory CD8+ T cells, IL-15 + Ionomycin, 12hours, rep10

description:
Library name: ALL_H10_12h
ALL_H10


title: CRS_Hip3

description: Library name: Sample15

value: PBS


title: CCR7- memory CD8+ T cells, IL-15, 12hours, rep7

description:
Library name: IL15_H7_12h
IL15_H7


title: CCR7- memory CD8+ T cells, No treatment, 48hours, rep1

description:
Library name: NOTX_H1_48h
NOTX_H1


title: CRS_Hip2

description: Library name: Sample14


title: CCR7- memory CD8+ T cells, IL-15 + Ionomycin, 12hours, rep9

description:
Library name: ALL_H9_12h
ALL_H9


title: Control_Hip3

description: Library name: Sample12

value: WT mice


title: CCR7- memory CD8+ T cells, Ionomycin, 12hours, rep2

description:
Library name: IONO_H2_12h
IONO_H2


title: CCR7- memory CD8+ T cells, IL-15, 12hours, rep6

description:
Library name: IL15_H6_12h
IL15_H6


title: CCR7- memory CD8+ T cells, IL-15 + Ionomycin, 12hours, rep8

description:
Library name: ALL_H8_12h
ALL_H8


title: CCR7- memory CD8+ T cells, IL-15, 12hours, rep4

description:
Library name: IL15_H4_12h
IL15_H4


title: Control_Hip1

description: Library name: Sample10


title: CCR7- memory CD8+ T cells, IL-15 + Ionomycin, 12hours, rep7

description:
Library name: ALL_H7_12h
ALL_H7


title: CCR7- memory CD8+ T cells, IL-15, 12hours, rep2

description:
Library name: IL15_H2_12h
IL15_H2


title: CCR7- memory CD8+ T cells, IL-15 + Ionomycin, 12hours, rep3

description:
Library name: ALL_H3_12h
ALL_H3


title: CCR7- memory CD8+ T cells, IL-15 + Ionomycin, 12hours, rep1

description:
Library name: ALL_H1_12h
ALL_H1


title: CCR7- memory CD8+ T cells, IL-15, 12hours, rep1

description:
Library name: IL15_H1_12h
IL15_H1


title: CCR7- memory CD8+ T cells, No treatment, 12hours, rep10

description:
Library name: NOTX_H10_12h
NOTX_H10


title: CCR7- memory CD8+ T cells, No treatment, 12hours, rep8

description:
Library name: NOTX_H8_12h
NOTX_H8


title: CCR7- memory CD8+ T cells, Ionomycin, 12hours, rep9

description:
Library name: IONO_H9_12h
IONO_H9


title: CCR7- memory CD8+ T cells, No treatment, 12hours, rep7

description:
Library name: NOTX_H7_12h
NOTX_H7


title: CCR7- memory CD8+ T cells, No treatment, 12hours, rep6

description:
Library name: NOTX_H6_12h
NOTX_H6


title: CCR7- memory CD8+ T cells, Ionomycin, 12hours, rep4

description:
Library name: IONO_H4_12h
IONO_H4


title: CCR7- memory CD8+ T cells, Ionomycin, 12hours, rep3

description:
Library name: IONO_H3_12h
IONO_H3


title: Control_mPFC2

description: Library name: Sample2

source_name: one sample from medial prefrontal cortex

value: medial prefrontal cortex


title: NSC-EV_Hip3

description: Library name: Sample18


title: CCR7- memory CD8+ T cells, Ionomycin, 12hours, rep1

description:
Library name: IONO_H1_12h
IONO_H1


title: CD8+ T cells ADT, healthy steady state ex vivo, rep3

description:
Library name: HD_3_ADT
Contains Cell Ranger output folders for ADT for every GEM (matrix.mtx.gz, barcodes.tsv.gz, features.tsv.gz).

data_processing:
Fastq files were generated by demultiplexing the sequenced data using the mkfastq function (Cell Ranger, 10X Genomics, v3.1.0). The demultiplexed fastq files for the expressions of each gene and ADT were aligned to the reference human genome (GRCH38; 10X Cell Ranger reference GRCh38 v3.0.0). The barcode sequencing of each ADT and dCODE dextramer, filtering, barcode counting, and UMI counting were performed to generate feature-barcode matrices using the count function (Cell Ranger, v3.1.0).
Assembly: hg38
Supplementary files format and content: Cellranger_GEX.tar.gz
Supplementary files format and content: Cellranger_ADT.tar.gz
Library strategy: CITE-seq

extract_protocol:
Total CD8+ T cells were isolated from patients at acute and convalescent stages of HAV infection (n = 5) and healthy donors (n = 3) by magnetic separation, and stained with DNA barcode-labeled MHC class I dextramers conjugated with PE (dCODE dextramers). dCODE dextramer-positive and -negative CD8+ T cells were flow-sorted, and then re-mixed at a 1:9 ratio and further stained with ADTs.
Cell suspensions were pelleted, and scRNA-seq libraries were prepared using the Chromium Single Cell 5’ Library & Gel Bead Kit (PN-10000006) and 5’ Feature Barcode Library Kit (PN-1000020) (10X Genomics), following the manufacturer’s instructions.

value: CD8+ T cells

value: ex vivo


title: Control_mPFC1

description: Library name: Sample1


title: CRS_mPFC1

description: Library name: Sample4


title: CCR7- memory CD8+ T cells, IL-15, 12hours, rep10

description:
Library name: IL15_H10_12h
IL15_H10

value: Peripheral blood

value: Primary cell


title: CCR7- memory CD8+ T cells, No treatment, 12hours, rep1

description:
Library name: NOTX_H1_12h
NOTX_H1

value: CCR7- memory CD8+ T cells


title: CRS_Hip1

description: Library name: Sample13


title: CCR7- memory CD8+ T cells, IL-15, 12hours, rep5

description:
Library name: IL15_H5_12h
IL15_H5


title: Control_Hip2

description: Library name: Sample11


title: Ctl lung, HDM/OVA

first: Myoung Seung

last: Kwon

state: Yuseong-gu

address: 291, Daehak-ro, Yuseong-gu, Biomedical research center (E7)

description: 10X Genomics

data_processing:
Cell ranger 7.2.0 was used for Chromium scRNA-seq output to align reads, generate feature-barcode matrices and perform clustering and gene expression analysis.
Assembly: mm10
Supplementary files format and content: Ctl.tar contains bacodes.tsv.gz, genes.tsv.gz and matrix.mtx.gz
Supplementary files format and content: MIA.tar contains bacodes.tsv.gz, genes.tsv.gz and matrix.mtx.gz

source_name: Lung

extract_protocol:
On embryonic day 14, either PBS or LPS was administered to the pregnant mice. When the offspring reached postnatal day 10, they were sensitized and challenged intranasally with HDM and OVA. Lungs were harvested, and the tissue was digested with collagenase IV and DNase I, followed by filtration through a 70 μm strainer to obtain a single-cell suspension. From the lung cells, 5,000 CD4- and 5,000 CD4+ cells were isolated using FACS from the CD45+ cells.
Library was contracted with 10x genomics Chromium Next GEM single cell 5` V2 kit accorting to the manufacterer`s recommendations.

value: Lung

value: WT

tag: maternal treatment

tag: offspring treatment

value: HDM/OVA


title: HAV or EBV or CMV or IAV specific CD8+ T cells GEX, healthy steady state ex vivo, rep1

description:
Library name: HD_1_GEX
Contains Cell Ranger output folders for GEX for every GEM (matrix.mtx.gz, barcodes.tsv.gz, features.tsv.gz).

data_processing:
Fastq files were generated by demultiplexing the sequenced data using the mkfastq function (Cell Ranger, 10X Genomics, v3.1.0). The demultiplexed fastq files for the expressions of each gene and ADT were aligned to the reference human genome (GRCH38; 10X Cell Ranger reference GRCh38 v3.0.0). The barcode sequencing of each ADT and dCODE dextramer, filtering, barcode counting, and UMI counting were performed to generate feature-barcode matrices using the count function (Cell Ranger, v3.1.0).
Assembly: hg38
Supplementary files format and content: Cellranger_GEX.tar.gz
Supplementary files format and content: Cellranger_ADT.tar.gz


title: iPSC Neurons, WT, D30 DMSO, R8

description:
Library name: 82_NC231017_WT_Acute_VC
H10

data_processing:
Sequencing was performed on a NextSeq 500 (Illumina). Reads were mapped and quantified using STAR using the GRCh38 genome build.
Assembly: GRCh38
Supplementary files format and content: Comma separated count file

source_name: hiPSC-derived neurons

extract_protocol:
At day 40 of differentiation, cells were lysed and mRNA was extracted using the Monarch Total RNA miniprep kit (New England Biolabs). Total RNA was quantified using the Qubit.
Library construction was perfomed at the Broad Institute following the smart-seq2 protocol.

value: hiPSC-derived neurons

value: neurons

value: D30 DMSO


title: CCR7- memory CD8+ T cells, IL-15, 12hours, rep3

description:
Library name: IL15_H3_12h
IL15_H3


title: NSC-EV_mPFC3

description: Library name: Sample9


title: iPSC Neurons, NULL, D30 Rapamycin 20nM, R7

description:
Library name: 73_NC231024_NULL_Acute_RAPA
H9

value: D30 Rapamycin 20nM


title: MIA_3

data_processing:
The data were trimmed for quality control using Fastp (Chen et al., 2018), and the trimmed reads were mapped to the reference sequence of Mus musculus  using HISAT2. After mapping, StringTie was used to assemble and merge transcripts, allowing their abundance to be estimated
Assembly: GRCm38
Supplementary files format and content: tab-delimited txt file raw counts for each sample

source_name: Placenta

extract_protocol:
Timed pregnant dams at embryonic day 14 were injected with PBS or LPS (50 ug/kg). Four hours after injection, placentas were harvested, and total RNA was extracted using an RNeasy Mini Kit (Qiagen, Hilden, Germany)
RNA was processed using a TruSeq Stranded Total RNA LT Sample Prep Kit (Illumina, San Diego, CA, USA) and sequenced on an Illumina HiSeq 4000 platform (Illumina).

value: Placenta

value: LPS (50ug/kg)


title: NSC-EV_mPFC2

description: Library name: Sample8

value: CRS mice

value: NSC-EVs


title: iPSC Neurons, WT, D30 DMSO, R7

description:
Library name: 64_NC231024_WT_Acute_VC
H8


title: CRS_mPFC3

description: Library name: Sample6

value: medial prefrontal cortex

value: PBS


title: HAV or EBV or CMV or IAV specific CD8+ T cells ADT, healthy steady state ex vivo, rep1

description:
Library name: HD_1_ADT
Contains Cell Ranger output folders for ADT for every GEM (matrix.mtx.gz, barcodes.tsv.gz, features.tsv.gz).

value: CD8+ T cells

value: ex vivo


title: NSC-EV_mPFC1

description: Library name: Sample7


title: iPSC Neurons, HET, D30 DMSO, R6

description:
Library name: 56_NC231017_HET_Acute_VC
H7


title: CCR7- memory CD8+ T cells, No treatment, 12hours, rep9

description:
Library name: NOTX_H9_12h
NOTX_H9

value: Peripheral blood

value: Primary cell

value: No treatment


title: CD8+ T cells GEX, convalescent stage ex vivo, rep5

description:
Library name: HAV_5_ConV_GEX
Contains Cell Ranger output folders for GEX for every GEM (matrix.mtx.gz, barcodes.tsv.gz, features.tsv.gz).


title: CRS_mPFC2

description: Library name: Sample5


title: iPSC Neurons, WT, D10 Rapamycin 20nM, R7

description:
Library name: 40_NC230117_WT_Chronic_RAPA
H5

value: D10 Rapamycin 20nM


title: CD8+ T cells GEX, healthy steady state ex vivo, rep3

description:
Library name: HD_3_GEX
Contains Cell Ranger output folders for GEX for every GEM (matrix.mtx.gz, barcodes.tsv.gz, features.tsv.gz).


title: Control_mPFC3

description: Library name: Sample3

value: WT mice


title: MIA_1

value: WT


title: iPSC Neurons, NULL, D30 Rapamycin 20nM, R6

description:
Library name: 24_NC230801_NULL_Acute_RAPA
H3

value: hiPSC-derived neurons

value: neurons


title: Ctl_3


title: CCR7- memory CD8+ T cells, No treatment, 12hours, rep5

description:
Library name: NOTX_H5_12h
NOTX_H5

value: CCR7- memory CD8+ T cells


title: iPSC Neurons, HET, D10 Rapamycin 20nM, R4

description:
Library name: 16_NC230801_HET_Chronic_RAPA
H2


title: CCR7- memory CD8+ T cells, No treatment, 12hours, rep4

description:
Library name: NOTX_H4_12h
NOTX_H4


title: CCR7- memory CD8+ T cells, No treatment, 12hours, rep3

description:
Library name: NOTX_H3_12h
NOTX_H3


title: iPSC Neurons, WT, D10 Rapamycin 20nM, R6

description:
Library name: 8_NC231024_WT_Chronic_RAPA
H1


title: CD8+ T cells GEX, healthy steady state ex vivo, rep2

description:
Library name: HD_2_GEX
Contains Cell Ranger output folders for GEX for every GEM (matrix.mtx.gz, barcodes.tsv.gz, features.tsv.gz).


title: iPSC Neurons, WT, D10 Rapamycin 20nM, R8

description:
Library name: 48_NC231024_WT_Chronic_RAPA
H6


title: CCR7- memory CD8+ T cells, No treatment, 12hours, rep2

description:
Library name: NOTX_H2_12h
NOTX_H2


title: MIA lung, HDM/OVA

description: 10X Genomics

value: Lung

value: LPS

value: HDM/OVA


title: CD8+ T cells ADT, acute stage ex vivo, rep5

description:
Library name: HAV_5_Acute_ADT
Contains Cell Ranger output folders for ADT for every GEM (matrix.mtx.gz, barcodes.tsv.gz, features.tsv.gz).


title: iPSC Neurons, NULL, D10 DMSO, R12

description:
Library name: 104_NC230829_NULL_Chronic_VC
H12

value: D10 DMSO


title: iPSC Neurons, NULL, D30 Rapamycin 20nM, R8

description:
Library name: 92_NC231017_NULL_Acute_RAPA
H11

value: D30 Rapamycin 20nM


title: CD8+ T cells ADT, healthy steady state ex vivo, rep2

description:
Library name: HD_2_ADT
Contains Cell Ranger output folders for ADT for every GEM (matrix.mtx.gz, barcodes.tsv.gz, features.tsv.gz).


title: Ctl_2

value: Placenta

value: PBS


title: CD8+ T cells GEX, acute stage ex vivo, rep5

description:
Library name: HAV_5_Acute_GEX
Contains Cell Ranger output folders for GEX for every GEM (matrix.mtx.gz, barcodes.tsv.gz, features.tsv.gz).

value: CD8+ T cells

value: ex vivo


title: MIA_2

value: LPS (50ug/kg)


title: iPSC Neurons, NULL, D10 DMSO, R11

description:
Library name: 103_NC230829_NULL_Chronic_VC
G12


title: iPSC Neurons, WT, D30 DMSO, R6

description:
Library name: 81_NC231017_WT_Acute_VC
G10

value: D30 DMSO


title: Ctl_1


title: CD8+ T cells GEX, convalescent stage ex vivo, rep4

description:
Library name: HAV_4_ConV_GEX
Contains Cell Ranger output folders for GEX for every GEM (matrix.mtx.gz, barcodes.tsv.gz, features.tsv.gz).

value: Peripheral blood

value: Primary cell


title: iPSC Neurons, HET, D10 Rapamycin 20nM, R5

description:
Library name: 32_NC230117_HET_Chronic_RAPA
H4

value: D10 Rapamycin 20nM


title: TriAdj, replicate 1

city: Vancouver

first: Robert

middle: E. W.

last: Hancock

state: British Columbia

address: 2259 - Lower Mall Research Station

department: Department of Microbiology & Immunology

country: Canada

institute: University of British Columbia

data_processing:
Sequence reads were aligned to GRCm39/mm39 using STAR aligner version 2.7.10b.
HTseq-count version 0.11.3 was used to compile gene-level summary counts using default parameters except “-s reverse -r pos -t gene”.
Analysis using R version 3.6.3.
Low count genes (with less than 10 counts across a minimum of 3 replicates) were removed.
Raw counts were extracted using DESeq2 version 1.26.0.
Assembly: Mus musculus GRCm39 (mm39)
Supplementary files format and content: Comma separated file of summarized raw read counts (genes in rows, samples in columns)

source_name: RAW 264.7 macrophages

growth_protocol: RAW 264.7 macrophage cells were seeded in 6-well tissue culture plates at a density of 600,000 cells per well. The cells were then cultured for 24 hours in DMEM high glucose supplemented with 10% FBS and 1% penicillin, maintaining a temperature of 37°C and 5% CO2.

extract_protocol:
RNA was isolated using RNeasy Mini Kit (Qiagen)
Strand-specific cDNA libraries were prepared by selecting for poly-adenylated RNA using the KAPA RNA HyperPrep Kit (Roche).

treatment_protocol: Culture media was replaced with treatment or control solutions. After 12 hours of stimulation, RNAProtect cell was added to preserve RNA integrity.

value: RAW 264.7 macrophages

value: TriAdj


title: CD8+ T cells ADT, convalescent stage ex vivo, rep5

description:
Library name: HAV_5_ConV_ADT
Contains Cell Ranger output folders for ADT for every GEM (matrix.mtx.gz, barcodes.tsv.gz, features.tsv.gz).


title: CD8+ T cells ADT, convalescent stage ex vivo, rep4

description:
Library name: HAV_4_ConV_ADT
Contains Cell Ranger output folders for ADT for every GEM (matrix.mtx.gz, barcodes.tsv.gz, features.tsv.gz).


title: iPSC Neurons, HET, D30 DMSO, R5

description:
Library name: 55_NC231017_HET_Acute_VC
G7

value: hiPSC-derived neurons

value: neurons


title: iPSC Neurons, WT, D10 Rapamycin 20nM, R5

description:
Library name: 39_NC230117_WT_Chronic_RAPA
G5


title: iPSC Neurons, NULL, D30 DMSO, R10

description:
Library name: 72_NC231024_NULL_Acute_VC
G9


title: iPSC Neurons, HET, D10 Rapamycin 20nM, R2

description:
Library name: 31_NC230117_HET_Chronic_RAPA
G4


title: iPSC Neurons, NULL, D30 Rapamycin 20nM, R5

description:
Library name: 91_NC231017_NULL_Acute_RAPA
G11


title: CD8+ T cells GEX, acute stage ex vivo, rep4

description:
Library name: HAV_4_Acute_GEX
Contains Cell Ranger output folders for GEX for every GEM (matrix.mtx.gz, barcodes.tsv.gz, features.tsv.gz).


title: iPSC Neurons, NULL, D30 DMSO, R9

description:
Library name: 23_NC230801_NULL_Acute_VC
G3


title: iPSC Neurons, NULL, no treatment, R2

description:
Library name: 102_NC230829_NULL_NT
F12

value: D10 No treatment


title: iPSC Neurons, WT, D10 DMSO, R7

description:
Library name: 7_NC231024_WT_Chronic_VC
G1


title: TriAdj, replicate 2


title: CD8+ T cells ADT, convalescent stage ex vivo, rep3

description:
Library name: HAV_3_ConV_ADT
Contains Cell Ranger output folders for ADT for every GEM (matrix.mtx.gz, barcodes.tsv.gz, features.tsv.gz).


title: DDAB/DOPE/DSPC/CHOL (40:30:20:10) + TriAdj (2:1) + PRRSV, replicate 3


title: iPSC Neurons, WT, D30 DMSO, R5

description:
Library name: 63_NC231024_WT_Acute_VC
G8


title: iPSC Neurons, HET, D10 DMSO, R7

description:
Library name: 15_NC230801_HET_Chronic_VC
G2


title: TriAdj, replicate 3


title: CD8+ T cells GEX, convalescent stage ex vivo, rep3

description:
Library name: HAV_3_ConV_GEX
Contains Cell Ranger output folders for GEX for every GEM (matrix.mtx.gz, barcodes.tsv.gz, features.tsv.gz).


title: iPSC Neurons, NULL, D30 DMSO, R7

description:
Library name: 71_NC231024_NULL_Acute_VC
F9


title: iPSC Neurons, NULL, D30 Rapamycin 20nM, R3

description:
Library name: 62_NC231017_NULL_Acute_RAPA
F8


title: DDAB/DOPE/DSPC/CHOL (40:30:20:10) + TriAdj (3:2), replicate 2


title: iPSC Neurons, NULL, D10 Rapamycin 20nM, R8

description:
Library name: 46_NC230117_NULL_Chronic_RAPA
F6


title: iPSC Neurons, NULL, D30 DMSO, R8

description:
Library name: 90_NC231017_NULL_Acute_VC
F11


title: DDAB/DOPE/DSPC/CHOL (40:30:20:10) + TriAdj (2:1) + PRRSV, replicate 1


title: iPSC Neurons, WT, D10 DMSO, R8

description:
Library name: 47_NC231024_WT_Chronic_VC
G6


title: CD8+ T cells ADT, acute stage ex vivo, rep4

description:
Library name: HAV_4_Acute_ADT
Contains Cell Ranger output folders for ADT for every GEM (matrix.mtx.gz, barcodes.tsv.gz, features.tsv.gz).


title: DDAB/DOPE/DSPC/CHOL (40:30:20:10) + TriAdj (3:2), replicate 3


title: iPSC Neurons, WT, D30 Rapamycin 20nM, R8

description:
Library name: 54_NC231017_WT_Acute_RAPA
F7


title: CD8+ T cells ADT, acute stage ex vivo, rep3

description:
Library name: HAV_3_Acute_ADT
Contains Cell Ranger output folders for ADT for every GEM (matrix.mtx.gz, barcodes.tsv.gz, features.tsv.gz).


title: iPSC Neurons, NULL, D30 Rapamycin 20nM, R4

description:
Library name: 80_NC231024_NULL_Acute_RAPA
F10


title: CD8+ T cells GEX, acute stage ex vivo, rep3

description:
Library name: HAV_3_Acute_GEX
Contains Cell Ranger output folders for GEX for every GEM (matrix.mtx.gz, barcodes.tsv.gz, features.tsv.gz).


title: HAV or EBV or CMV or IAV specific CD8+ T cells GEX, convalescent stage ex vivo, rep2

description:
Library name: HAV_2_ConV_GEX
Contains Cell Ranger output folders for GEX for every GEM (matrix.mtx.gz, barcodes.tsv.gz, features.tsv.gz).


title: iPSC Neurons, WT, D10 DMSO, R6

description:
Library name: 38_NC230117_WT_Chronic_VC
F5


title: DDAB/DOPE/DSPC/CHOL (40:30:20:10) + TriAdj (3:2), replicate 1


title: DDAB/DOPE/DSPC/CHOL (40:30:20:10) + TriAdj (2:1), replicate 3


title: DDAB/DOPE/DSPC/CHOL (40:30:20:10) + TriAdj (2:1) + PRRSV, replicate 2


title: HAV or EBV or CMV or IAV specific CD8+ T cells ADT, convalescent stage ex vivo, rep2

description:
Library name: HAV_2_ConV_ADT
Contains Cell Ranger output folders for ADT for every GEM (matrix.mtx.gz, barcodes.tsv.gz, features.tsv.gz).


title: iPSC Neurons, HET, D30 Rapamycin 20nM, R7

description:
Library name: 22_NC230801_HET_Acute_RAPA
F3


title: HAV or EBV or CMV or IAV specific CD8+ T cells ADT, acute stage ex vivo, rep2

description:
Library name: HAV_2_Acute_ADT
Contains Cell Ranger output folders for ADT for every GEM (matrix.mtx.gz, barcodes.tsv.gz, features.tsv.gz).


title: DDAB/DOPE/DSPC/CHOL (40:30:20:10) + TriAdj (2:1), replicate 1


title: iPSC Neurons, WT, D10 Rapamycin 20nM, R4

description:
Library name: 14_NC230801_WT_Chronic_RAPA
F2


title: iPSC Neurons, NULL, D10 Rapamycin 20nM, R7

description:
Library name: 6_NC231024_NULL_Chronic_RAPA
F1


title: HAV or EBV or CMV or IAV specific CD8+ T cells GEX, acute stage ex vivo, rep2

description:
Library name: HAV_2_Acute_GEX
Contains Cell Ranger output folders for GEX for every GEM (matrix.mtx.gz, barcodes.tsv.gz, features.tsv.gz).


title: iPSC Neurons, NULL, No treatment, R1

description:
Library name: 101_NC230829_NULL_NT
E12

value: D10 None


title: iPSC Neurons, HET, D30 Rapamycin 20nM, R6

description:
Library name: 70_NC231024_HET_Acute_RAPA
E9


title: DDAB/DOPE/DSPC/CHOL (40:30:20:10) + PRRSV, replicate 3


title: iPSC Neurons, NULL, D30 Rapamycin 20nM, R2

description:
Library name: 61_NC231017_NULL_Acute_RAPA
E8


title: DDAB/DOPE/DSPC/CHOL (40:30:20:10) + PRRSV, replicate 2


title: iPSC Neurons, WT, D30 Rapamycin 20nM, R7

description:
Library name: 53_NC231017_WT_Acute_RAPA
E7


title: HAV or EBV or CMV or IAV specific CD8+ T cells GEX, acute stage ex vivo, rep1

description:
Library name: HAV_1_Acute_GEX
Contains Cell Ranger output folders for GEX for every GEM (matrix.mtx.gz, barcodes.tsv.gz, features.tsv.gz).


title: iPSC Neurons, WT, D10 DMSO, R4

description:
Library name: 37_NC230117_WT_Chronic_VC
E5

value: D10 DMSO


title: iPSC Neurons, NULL, D10 Rapamycin 20nM, R6

description:
Library name: 45_NC230117_NULL_Chronic_RAPA
E6


title: DDAB/DOPE/DSPC/CHOL (40:30:20:10) + PRRSV, replicate 1


title: iPSC Neurons, HET, D10 DMSO, R6

description:
Library name: 30_NC230117_HET_Chronic_VC
F4


title: HAV or EBV or CMV or IAV specific CD8+ T cells ADT, convalescent stage ex vivo, rep1

description:
Library name: HAV_1_ConV_ADT
Contains Cell Ranger output folders for ADT for every GEM (matrix.mtx.gz, barcodes.tsv.gz, features.tsv.gz).


title: iPSC Neurons, HET, D30 DMSO, R4

description:
Library name: 21_NC230801_HET_Acute_VC
E3


title: iPSC Neurons, HET, D10 DMSO, R5

description:
Library name: 29_NC230117_HET_Chronic_VC
E4


title: DDAB/DOPE/DSPC/CHOL (40:30:20:10) + TriAdj (2:1), replicate 2


title: iPSC Neurons, WT, D10 DMSO, R5

description:
Library name: 13_NC230801_WT_Chronic_VC
E2


title: iPSC Neurons, NULL, D10 DMSO, R10

description:
Library name: 5_NC231024_NULL_Chronic_VC
E1


title: DDAB/DOPE/DSPC/CHOL (40:30:20:10), replicate 3

value: DDAB/DOPE/DSPC/CHOL (40:30:20:10)


title: iPSC Neurons, NULL, D30 DMSO, R6

description:
Library name: 89_NC231017_NULL_Acute_VC
E11


title: scRNA-seq of hnbMOs from DS patients: 63 days in vitro

city: Nanjing

first: Yan

last: Liu

state: Jiangsu

address: 101Longmian Avenue, Jiangning District

department: School of Pharmacy

institute: Nanjing Medical University

description: Library name: 210503A_2DS3_D63_S

data_processing:
For the scRNA-seq, raw sequencing data was processed with Cell Ranger software version 3.1 (10X Genomics) for FASTQ generation and GRCh38 human reference genome was used for alignments. For filtering and unsupervised clustering, the gene expression matrixs from Cell Ranger results were used for downstream analysis, using R 4.1.1.
Assembly: hg38
Supplementary files format and content: outputs of cellranger software with h5 format, which include barcodes, gene features and expression matrix for each sample

source_name: brain organoids

extract_protocol:
For the scRNA-seq, brain organoids were dissociated by 1 ml of trypLE (Life Technology Inc) for 30 min in the condition of 37°C and 5% CO2 into single cell when differentiated in vitro for 35 days. The cell debris and other aggregates were removed by additional low-speed centrifugation. Droplet-based single-cell RNA sequencing was performed using the 10X Genomics Chromium Single Cell platform, version 3. Approximately 5,000 cells were captured for each sample onto a Chromium Single Cell 3’ Chip (10X Genomics, PN-120236), and the released RNA in each cell was barcoded through reverse transcription in individual gel beads in emulsions (GEMs).
For scRNA-seq, the quality of cDNA was accessed on Agilent 4200 (Agilent Technologies). Libraries of scRNA-seq were established by the Chromium Single Cell 3’ Library & Gel Bead Kit V3 (10X Genomics, 1000075) and then sequenced on an Illumina NovaSeq6000 with a sequencing depth of at least 750000 reads per cell.

value: brain organoids

value: neural cells


title: scRNA-seq of hnbMOs from healthy people: 63 days in vitro, IMR

description: Library name: BFCO_IMR_D63


title: DDAB/DOPE/DSPC/CHOL (40:30:20:10), replicate 2


title: HAV or EBV or CMV or IAV specific CD8+ T cells GEX, convalescent stage ex vivo, rep1

description:
Library name: HAV_1_ConV_GEX
Contains Cell Ranger output folders for GEX for every GEM (matrix.mtx.gz, barcodes.tsv.gz, features.tsv.gz).

value: CD8+ T cells


title: iPSC Neurons, HET, D30 Rapamycin 20nM, R5

description:
Library name: 87_NC231017_HET_Acute_RAPA
D11

value: D30 Rapamycin 20nM


title: iPSC Neurons, NULL, D30 DMSO, R5

description:
Library name: 79_NC231024_NULL_Acute_VC
E10


title: DDAB/DOPE/DSPC/CHOL (40:30:20:10), replicate 1


title: iPSC Neurons, NULL, D30 DMSO, R4

description:
Library name: 98_NC230614_NULL_Acute_VC
D12


title: iPSC Neurons, HET, D30 DMSO, R3

description:
Library name: 77_NC231024_HET_Acute_VC
D10


title: iPSC Neurons, HET, D30 Rapamycin 20nM, R4

description:
Library name: 69_NC231024_HET_Acute_RAPA
D9


title: scRNA-seq of hnbMOs from healthy people: 63 days in vitro, H9

description: Library name: 191641O_H9_D63


title: DDAB/DOPE (55:45) + TriAdj (2:1) + PRRSV, replicate 3


title: iPSC Neurons, NULL, D30 DMSO, R3

description:
Library name: 60_NC231017_NULL_Acute_VC
D8


title: scRNA-seq of hnbMOs from healthy people: 36 days in vitro

description: Library name: 191641L_H9_750_D36


title: HAV or EBV or CMV or IAV specific CD8+ T cells ADT, acute stage ex vivo, rep1

description:
Library name: HAV_1_Acute_ADT
Contains Cell Ranger output folders for ADT for every GEM (matrix.mtx.gz, barcodes.tsv.gz, features.tsv.gz).

value: ex vivo


title: iPSC Neurons, WT, D30 DMSO, R4

description:
Library name: 52_NC231017_WT_Acute_VC
D7

value: D30 DMSO


title: DDAB/DOPE (55:45) + TriAdj (2:1) + PRRSV, replicate 2


title: iPSC Neurons, NULL, D10 DMSO, R9

description:
Library name: 44_NC230117_NULL_Chronic_VC
D6


title: DDAB/DOPE (55:45) + TriAdj (2:1) + PRRSV, replicate 1


title: iPSC Neurons, NULL, D10 Rapamycin 20nM, R5

description:
Library name: 36_NC230117_NULL_Chronic_RAPA
D5


title: iPSC Neurons, WT, D10 Rapamycin 20nM, R3

description:
Library name: 28_NC230117_WT_Chronic_RAPA
D4


title: DDAB/DOPE (55:45) + TriAdj (3:2), replicate 3

value: DDAB/DOPE (55:45) + TriAdj (3:2)


title: iPSC Neurons, WT, D30 Rapamycin 20nM, R6

description:
Library name: 20_NC230801_WT_Acute_RAPA
D3


title: iPSC Neurons, NULL, D10 Rapamycin 20nM, R4

description:
Library name: 12_NC231024_NULL_Chronic_RAPA
D2


title: DDAB/DOPE (55:45) + TriAdj (3:2), replicate 2


title: iPSC Neurons, HET, D30 Rapamycin 20nM, R3

description:
Library name: 4_NC231024_HET_RAPA
D1


title: iPSC Neurons, NULL, D30 DMSO, R2

description:
Library name: 97_NC230614_NULL_Acute_VC
C12


title: iPSC Neurons, WT, D30 Rapamycin 20nM, R5

description:
Library name: 76_NC231024_WT_Acute_RAPA
C10


title: iPSC Neurons, HET, D30 DMSO, R2

description:
Library name: 85_NC231017_HET_Acute_VC
C11


title: Female hPXR EtOH-fed 4

type: RNA

city: Seattle

first: Julia

middle: Yue

last: Cui

state: WA

address: 4225 Roosevelt Way NE Suite #100

department: Occupational and Health Sciences

institute: University of Washington

hyb_protocol: not provided

scan_protocol: GeneChip Scanner 3000 7G Pluse with autoloader

data_processing: R using oligo package. Probes IDs annotated using the clariomsmousehttranscriptcluster.db package. The mean probe intensities higher than log2(100) in at least one group were selected for further analysis. Differential analysis between control and EtOH-exposed groups of the same genotype and sex was determined using the Linear Models for Micoarray Data (limma) package.

label: Label sense-strand cDNA

source_name: hPXREtOH, female

label_protocol: Sense-strand cDNA

extract_protocol: Affymetrix GeneChip array was used after the total RNA extraction from liver tissues.

tag: strain

value: hPXR B6NTac

value: Liver

tag: Sex

value: female


title: DDAB/DOPE (55:45) + TriAdj (3:2), replicate 1

value: RAW 264.7 macrophages


title: iPSC Neurons, HET, D30 DMSO, R1

description:
Library name: 68_NC231024_HET_Acute_VC
C9

value: hiPSC-derived neurons


title: DDAB/DOPE (55:45) + TriAdj (2:1), replicate 2

value: DDAB/DOPE (55:45) + TriAdj (2:1)


title: DDAB/DOPE (55:45) + TriAdj (2:1), replicate 3


title: Female hPXR EtOH-fed 1


title: iPSC Neurons, WT, D30 DMSO, R3

description:
Library name: 51_NC231017_WT_Acute_VC
C7

value: neurons


title: Female hPXR EtOH-fed 2


title: iPSC Neurons, NULL, D30 DMSO, R1

description:
Library name: 59_NC231017_NULL_Acute_VC
C8


title: iPSC Neurons, NULL, D10 DMSO, R8

description:
Library name: 43_NC230117_NULL_Chronic_VC
C6


title: iPSC Neurons, NULL, D10 Rapamycin 20nM, R3

description:
Library name: 35_NC230117_NULL_Chronic_RAPA
C5

value: D10 Rapamycin 20nM


title: DDAB/DOPE (55:45) + TriAdj (2:1), replicate 1


title: iPSC Neurons, WT, D10 Rapamycin 20nM, R2

description:
Library name: 27_NC230117_WT_Chronic_RAPA
C4


title: Female hPXR control-fed 3

source_name: hPXRCT, female


title: iPSC Neurons, WT, D30 DMSO, R2

description:
Library name: 19_NC230801_WT_Acute_VC
C3


title: Female hPXR control-fed 4


title: DDAB/DOPE (55:45) + PRRSV, replicate 3

value: DDAB/DOPE (55:45) + PRRSV


title: iPSC Neurons, NULL, D10 DMSO, R7

description:
Library name: 11_NC231024_NULL_Chronic_VC
C2

value: D10 DMSO


title: Female hPXR control-fed 2


title: iPSC Neurons, HET, D10 DMSO, R4

description:
Library name: 3_NC231024_HET_VC
C1


title: iPSC Neurons, NULL, D10 DMSO, R6

description:
Library name: 94_NC230614_NULL_Chronic_VC
B12


title: Female hPXR EtOH-fed 3


title: DDAB/DOPE (55:45) + PRRSV, replicate 2


title: iPSC Neurons, WT, D30 Rapamycin 20nM, R4

description:
Library name: 84_NC231017_WT_Acute_RAPA
B11


title: DDAB/DOPE (55:45) + PRRSV, replicate 1


title: Female hPXR control-fed 1


title: Male hPXR EtOH-fed 4

source_name: hPXREtOH, male

value: male


title: DDAB/DOPE (55:45), replicate 3

value: DDAB/DOPE (55:45)


title: iPSC Neurons, WT, D30 Rapamycin 20nM, R3

description:
Library name: 66_NC231024_WT_Acute_RAPA
B9


title: Male hPXR EtOH-fed 2


title: iPSC Neurons, NULL, D10 Rapamycin 20nM, R2

description:
Library name: 50_NC231024_NULL_Chronic_RAPA
B7


title: DDAB/DOPE (55:45), replicate 1


title: iPSC Neurons, HET, D30 Rapamycin 20nM, R2

description:
Library name: 58_NC231017_HET_Acute_RAPA
B8


title: iPSC Neurons, HET, D10 Rapamycin 20nM, R3

description:
Library name: 42_NC230117_HET_Chronic_RAPA
B6


title: Control, replicate 3

value: Control


title: Control, replicate 1


title: iPSC Neurons, WT, D10 DMSO, R3

description:
Library name: 26_NC230117_WT_Chronic_VC
B4


title: Control, replicate 2


title: iPSC Neurons, NULL, D10 DMSO, R5

description:
Library name: 34_NC230117_NULL_Chronic_VC
B5


title: iPSC Neurons, WT, D30 DMSO, R1

description:
Library name: 75_NC231024_WT_Acute_VC
B10


title: ITF 2357 3

city: Indianapolis

first: Xiongbin

last: Lu

state: Indiana

address: 980 W. Walnut Street, R3-C218D	MMGE

institute: Indiana University School of Medicine

description:
KPC cells, ITF2357 1uM, 48h
I3_S44

data_processing:
Base calling and quality scoreing were performed by Real-Time Analysis (RTA) v2 in Illumina NovaSeq 6000
The bcl2fastq2 Conversion software were used to convert base call (bcl) files to FASTQ files, and trim adapter sequence at the same time.
The reads were mapped to the mouse genome using STAR (v2.7.2a) RNA-seq aligner with the following parameter: “--outSAMmapqUnique 60”.
Uniquely mapped sequencing reads were assigned to GENCODE M22 genes using featureCounts (from subread v2.0.1) with the following parameters: “-s2 –p –Q 10”.
The data was filtered using read count per million (CPM) > 0.5 in more than 3 of the samples, normalized using TMM (trimmed mean of M values) method and subjected to differential expression analysis using likelihood ratio test method in edgeR (v3.38.4).
Assembly: mm10
Supplementary files format and content: differential analysis and raw counts

source_name: Pancreatic cancer

growth_protocol: KPC cells were cultured in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin.

extract_protocol:
Total RNA was extracted from KPC cells using TRIzol (Ambion) and the miRNeasy Mini kit (Qiagen).
The cDNA library was constructed using the KAPA RNA Hyper Prep Kit (Roche Corporate) and the quality was accessed by the Qubit and Agilent Bioanalyzer. The library pool was sequenced in 100b paired-end read format on NovaSeq 6000 (Illumina)

treatment_protocol: KPC cells treated with control,  ITF2357, JQ1 or I-BET151 (1uM) for 48 h .

value: Pancreatic cancer

value: KPC

value: Eukaryotic cells

value: ITF2357 treated


title: Male hPXR EtOH-fed 1

value: hPXR B6NTac


title: Male hPXR control-fed 4

source_name: hPXRCT, male

value: Liver


title: DDAB/DOPE (55:45), replicate 2


title: Male hPXR control-fed 1


title: Female WT EtOH-fed 4

source_name: WTEtOH, female

value: WT C57BL/6NTAC

value: female


title: iPSC Neurons, NULL, D10 Rapamycin 20nM, R1

description:
Library name: 18_NC230801_NULL_Chronic_RAPA
B3

value: hiPSC-derived neurons


title: Male hPXR EtOH-fed 3


title: ITF 2357 2

description:
KPC cells, ITF2357 1uM, 48h
I2_S43


title: ITF 2357 1

description:
KPC cells, ITF2357 1uM, 48h
I1_S42


title: Male hPXR control-fed 2


title: hMADS - White_D14_siGFP - Rep1

city: Toulouse Cedex 4

first: Dominique

last: Langin

address: 1 avenue du Professeur Jean Poulhès

country: France

institute: INSERM

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 10x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturer's instructions (Agilent Technologies, Santa Clara, CA). On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE v3 microarray (8X60K, Design 072363 enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min) and Wash buffer 2 (Agilent Technologies, 37°C, 1 min).

scan_protocol: Slides were scanned immediately after washing on a Agilent G2505C Microarray Scanner with Agilent Scan Control A.8.5.1 software

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent Technologies, Santa Clara, CA) using default parameters (protocol GE1_1010_Sep10 and Grid: 072363_D_F_20150612). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} We selected the spots with a minimal weight of 1 for 20 out of 24 microarrays or with a minimal weight of 3 per group from at least one experimental group. At this step, 43258 spots out of 62976 were selected. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore R library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 40115 rows each corresponding to a unique ProbeName (provided as data Matrix).

source_name: hMADS cells

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng of total RNA using the One-Color Quick Amp Labeling kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer's instructions, followed by Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, Massachusetts) purification. Dye incorporation and cRNA yield were checked using Dropsense™ 96 UV/VIS droplet reader (Trinean, Belgium).

growth_protocol: hMADS adipocytes were transfected at day 7 of differentiation with HSL-targetting (siHSL) of control (siGFP) siRNA.

extract_protocol: Total RNA from cells was extracted using RNeasy kit (Qiagen 75162).

treatment_protocol: At day 14 of differenciation, hMADS white adipocytes were subjected to low glucose/no insulin followed by high glucose/insulin to induce de novo lipogenesis (W14). hMADS adipocyte were treated with PPARγ agonist rosiglitazone between day 14 and 18 to obtain beige adipocyte (B18), or untreated to obtain control white adipocytes (W18)

tag: type

value: White

tag: knockdown

value: siGFP


title: Male hPXR control-fed 3


title: Female WT EtOH-fed 3


title: hMADS - Brite_D18_siGFP - Rep3

value: Brite


title: hMADS - Brite_D18_siHSL - Rep2

value: siHSL


title: hMADS - White_D14_siGFP - Rep3


title: hMADS - Brite_D18_siGFP - Rep1


title: iPSC Neurons, WT, D10 Rapamycin 20nM, R1

description:
Library name: 2_NC231024_WT_Chronic_RAPA
B1

value: neurons

value: D10 Rapamycin 20nM


title: hMADS - Brite_D18_siHSL - Rep1


title: I-BET151 3

description:
KPC cells, I-BET151 1uM, 48h
B3_S41

value: I-BET151 treated


title: hMADS - White_D18_siHSL - Rep1


title: hMADS - White_D14_siGFP - Rep4


title: I-BET151 2

description:
KPC cells, I-BET151 1uM, 48h
B2_S40


title: Female WT EtOH-fed 1


title: iPSC Neurons, WT, D30 Rapamycin 20nM, R2

description:
Library name: 83_NC231017_WT_Acute_RAPA
A11

value: D30 Rapamycin 20nM


title: hMADS - White_D14_siHSL - Rep4


title: I-BET151 1

description:
KPC cells, I-BET151 1uM, 48h
B1_S39

value: Pancreatic cancer


title: iPSC Neurons, HET, D10 Rapamycin 20nM, R1

description:
Library name: 10_NC231024_HET_Chronic_RAPA
B2


title: hMADS - White_D18_siHSL - Rep3


title: iPSC Neurons, NULL, D30 Rapamycin 20nM, R1

description:
Library name: 74_NC231024_NULL_Acute_RAPA
A10


title: JQ1 3

description:
KPC cells, JQ1 1uM, 48h
J3_S38

value: KPC

value: JQ1 treated


title: iPSC Neurons, WT, D30 Rapamycin 20nM, R1

description:
Library name: 65_NC231024_WT_Acute_RAPA
A9


title: Female WT control-fed 4

source_name: WTCT, female


title: JQ1 2

description:
KPC cells, JQ1 1uM, 48h
J2_S37

value: Eukaryotic cells


title: iPSC Neurons, NULL, D10 DMSO, R4

description:
Library name: 93_NC230614_NULL_Chronic_VC
A12

value: D10 DMSO


title: iPSC Neurons, HET, D30 Rapamycin 20nM, R1

description:
Library name: 57_NC231017_HET_Acute_RAPA
A8


title: JQ1 1

description:
KPC cells, JQ1 1uM, 48h
J1_S36


title: Female WT EtOH-fed 2

value: Liver


title: iPSC Neurons, NULL, D10 DMSO, R3

description:
Library name: 49_NC231024_NULL_Chronic_VC
A7


title: Female WT control-fed 1

value: WT C57BL/6NTAC


title: Ctrl 3

description:
KPC cells, Isotype control(PBS) 1uM, 48h
V3_S35

value: untreated


title: Female WT control-fed 2

value: female


title: Female WT control-fed 3


title: Ctrl 2

description:
KPC cells, Isotype control(PBS) 1uM, 48h
V2_S34


title: hMADS - Brite_D18_siGFP - Rep4


title: hMADS - White_D14_siHSL - Rep1

value: White


title: iPSC Neurons, HET, D10 DMSO, R2

description:
Library name: 41_NC230117_HET_Chronic_VC
A6

value: hiPSC-derived neurons


title: Male WT EtOH-fed 4

source_name: WTEtOH, male

value: male


title: hMADS - White_D18_siGFP - Rep2

value: siGFP


title: hMADS - White_D18_siGFP - Rep1


title: hMADS - Brite_D18_siHSL - Rep4

value: Brite

value: siHSL


title: iPSC Neurons, NULL, D10 DMSO, R2

description:
Library name: 33_NC230117_NULL_Chronic_VC
A5

value: neurons


title: Ctrl 1

description:
KPC cells, Isotype control(PBS) 1uM, 48h
V1_S33


title: Male WT EtOH-fed 2


title: Male WT EtOH-fed 1


title: iPSC Neurons, WT, D10 DMSO, R2

description:
Library name: 25_NC230117_WT_Chronic_VC
A4


title: S3_11.5d_1_zhengpei

first: Taifeng

last: Zhou

state: Massachusetts

address: 188 Longwood Avenue, REB514B

department: Developmental biology

institute: Harvard University

data_processing:
The Space Ranger software pipeline provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus spots
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every spot

source_name: Bone

extract_protocol:
The tissues were cut into 4-5 mm pieces and treated with cleanroom wipers. After removing blood stains on the tissue surface, fresh tissue was embedded with OCT then snap frozen. Cryosections were cut at 10-um thickness, mounted onto the ST arrays.Next, the tissue was dehydrated with isopropanol for 1 min followed by staining with HE. Brightfield images were taken on a Leica SCN400 F whole-slide scanner at 40x resolution.
Library preparation slides used were purchased from the Spatial Transcriptomics team. Each of the spots printed onto the array is 55um in diameter and 100um from center to center, covering an area of 6.5x6.5 mm2. Each slide includes 4 Capture Areas, each with ~5,000 unique gene expression spots.

value: Bone

tag: developmental stage

value: embryonic mouse axial skeleton


title: hMADS - Brite_D18_siGFP - Rep2


title: hMADS - Brite_D18_siHSL - Rep3


title: iPSC Neurons, NULL, D10 DMSO, R1

description:
Library name: 17_NC230801_NULL_Chronic_VC
A3


title: S13.5d_2


title: Male WT control-fed 4

source_name: WTCT, male


title: Male WT EtOH-fed 3


title: iPSC Neurons, HET, D10 DMSO, R1

description:
Library name: 9_NC231024_HET_Chronic_VC
A2


title: hMADS - White_D18_siHSL - Rep2


title: iPSC Neurons, WT, D10 DMSO, R1

description:
Library name: 1_NC231024_WT_Chronic_VC
A1


title: hMADS - White_D14_siHSL - Rep2


title: S12.5d_8


title: EAE, Vehicle, female, rep 1

status: Public on Oct 24 2025

city: Baltimore

first: Matthew

middle: D

last: Smith

state: MD

address: 600 N Wolfe Street

institute: Johns Hopkins University

description: Library name: EAE_Vehicle_I5

data_processing:
Raw sequencing data was processed with Cellranger Multi (v9.0.1, 10X Genomics) using the GRCm39-2024-A reference transcriptome, Chromium Mouse Transcriptome Probe Set v1.1.1, and 8000 nuclei per sample was specified as the expected cell count. This generated both raw and filtered feature count matrices per sample as well as a BAM file for each sample based on probe barcode. Reads not assigned to a sample were stored in unassigned_alignments.bam. The BAM files were then converted back to demultiplexed fastq files with the program bamtofastq (v1.4.1, 10X Genomics) using default options except for maximum reads per file set to 2e9 for submission to GEO.
Assembly: GRCm39-2024-A
Supplementary files format and content: Feature barcode matrices provided in HDF5 format (.H5) as generated by cellranger. Both raw and filtered matrices (filtered on nuclei as called by cellranger) are provided.

source_name: Lumbar Spine

growth_protocol: Mice were purchased from Jackson Laboratories then housed in Johns Hopkins University vivarium . Animals were housed in temperature and humidity-controlled rooms and maintained on fixed light/dark cycle.

extract_protocol:
16 days after immunization, mice were euthanized via isoflurane inhalation in bell jar followed by cardiac perfusion with chilled phosphate buffered saline. Lumbar spinal cords were manually dissected out and flash frozen immediately in liquid nitrogen then stored in liquid nitrogen. Lumbar tissue was later removed from liquid nitrogen and lysed in Nuclei Extraction Buffer (Miltenyi Biotec) with RNAse inhibitor (40U/mL RNasin Plus) in a gentleMACS tissue dissociator (Miltenyi) using octo coolers to keep nuclei chilled during digestion. Nuclei then were filtered over 100μM SmartStrainer into pre-chilled 5mL conical tube, centrifuged, then passed over a 30μM SmartStrainer. Nuclei were then incubated with magnetic anti-nucleus microbeads (Miltenyi 130-132-997) for 15 minutes at 4c then were washed and passed onto LS magnetic column in cold room. Column was washed twice then nuclei were eluted and counted. RNase inhibitor was maintained in all buffers until nuclei were fixed. Nuclei were pelleted and resuspended in Fix/Perm Buffer (4% formaldehyde, 10X Genomics PN-2000517) and incubated overnight at 4c. The following morning fixation was quenched and then underwent 10X Genomics Flex (Fixed RNA Profiling) protocol according to manufacturer recommendations including probe hybridization, pooling, washing, and then loaded onto a single lane of a Chip Q (10X Genomics PN-2000518) targeting 8000 nuclei per sample. Nuclei were partitioned into Gel Bead in Emulsion (GEMs) using a Chromium iX device (10X genomics).
Libraries were prepared according to manufacturer's recommendation (10X Genomics "Chromium Fixed RNA Profiling Reagent Kits User Guide CG000527 Rev F") in which GEMs are incubated to allow for probe ligation and GEM barcoding, then libraries were amplified in bulk followed by size selection, sample index addition (using 9 amplification cycles), followed by a final size selection step. 1 NGS library was sequenced on 1 lane of a NovaSeq X Plus 10B flow cell in 28x10x18x90 configuration in isolation (no other libraries on lane) with 10% PhiX spike-in at the Johns Hopkins Genetic Resources Core Facility. Raw fastq (not demultiplexed) were used as input into cellranger to avoid losing data due to demultiplexing errors which are more frequent on NovaSeq X when using only a single index.

treatment_protocol: Starting 2 days prior to immunization, mice were gavaged daily with either PAANIB1 (10mg/kg in 1% Tween 80, 10% polyethylene glycol, 1% hydroxy propyl methyl cellulose) or vehicle. 2 days layer mice were then immunized with 150μl of complete freund's adjuvant (8mg/mL Mtb) emulsified 1:1 with either 2mg/ml MOG35-55 (to induce EAE) or PBS (to serve as CFA only controls) for a final amount of 150μg MOG35-55 and 600μg Mtb. On the same day of immunization, and again 2 days later, mice were also injected with 500ng of pertussis toxin IP. Mice were monitored for 16 days as paralysis developed and were then euthanized at day 16 (~ peak of disease).

value: Lumbar Spine

value: Female

tag: barcode

tag: group

value: EAE

value: Vehicle

tag: disease onset

tag: disease score


title: EAE, Vehicle, female, rep 2

description: Library name: EAE_Vehicle_J1


title: EAE, Vehicle, female, rep 3

description: Library name: EAE_Vehicle_H2


title: Male WT control-fed 3

value: Liver


title: Male WT control-fed 1

value: WT C57BL/6NTAC


title: EAE, Vehicle, male, rep 3

description: Library name: EAE_Vehicle_G5

value: Male


title: EAE, Vehicle, male, rep 2

description: Library name: EAE_Vehicle_G2


title: EAE, Vehicle, male, rep 1

description: Library name: EAE_Vehicle_G1


title: hMADS - White_D14_siHSL - Rep3

tag: time


title: EAE, PAANIB1, female, rep 2

description: Library name: EAE_C831_E2

tag: tissue


title: hMADS - White_D18_siGFP - Rep3


title: Male WT control-fed 2


title: EAE, PAANIB1, male, rep 3

description: Library name: EAE_C831_B2


title: EAE, PAANIB1, male, rep 2

description: Library name: EAE_C831_B1


title: CFA, Vehicle, female, rep 2

description: Library name: CFA_Vehicle_CFA4

value: CFA


title: EAE, PAANIB1, female, rep 3

description: Library name: EAE_C831_C4


title: EAE, PAANIB1, male, rep 1

description: Library name: EAE_C831_A5


title: EAE, PAANIB1, female, rep 1

description: Library name: EAE_C831_C1


title: CFA, Vehicle, female, rep 1

description: Library name: CFA_Vehicle_CFA2


title: CFA, PAANIB1, female, rep 2

description: Library name: CFA_C831_CFA3


title: hMADS - White_D14_siGFP - Rep2

value: White


title: Unassigned Reads, rep 1

description: Library name: Unassigned_Reads

value: not determined

value: Unassigned


title: Morphine+probiotics4

city: MIAMI

first: JUNYI

last: TAO

address: 501 NW 10th Ave

institute: University of Miami

description:
Library name: Pro4
count matrix produced by cellranger

data_processing:
cellranger multi pipeline
Assembly: GRCm39
Supplementary files format and content: hdf5

source_name: midbrain

extract_protocol:
The suspensions were prepped following the Chromium Fixed RNA Profiling Reagent Kits for Multiplexed Samples User Guide.
10X FLEX pipline

value: midbrain

value: morphine+probiotics


title: Morphine-5

description:
Library name: Mor5
count matrix produced by cellranger

value: morphine


title: Morphine+probiotics1

description:
Library name: Pro1
count matrix produced by cellranger


title: CFA, PAANIB1, female, rep 1

description: Library name: CFA_C831_CFA1


title: Morphine+probiotics2

description:
Library name: Pro2
count matrix produced by cellranger


title: Morphine-3

description:
Library name: Mor3
count matrix produced by cellranger


title: Morphine-2

description:
Library name: Mor2
count matrix produced by cellranger


title: Morphine+probiotics3

description:
Library name: Pro3
count matrix produced by cellranger


title: Morphine-1

description:
Library name: Mor1
count matrix produced by cellranger


title: Control4

description:
Library name: Con4
count matrix produced by cellranger

value: saline


title: Morphine-4

description:
Library name: Mor4
count matrix produced by cellranger


title: Control3

description:
Library name: Con3
count matrix produced by cellranger


title: Control2

description:
Library name: Con2
count matrix produced by cellranger


title: Control1

description:
Library name: Con1
count matrix produced by cellranger


title: Celecoxib_rep3

first: Su-Jin

last: Baek

address: 1672, Yuseong-daero

institute: KOREA INSTITUTE of ORIENTAL MEDICINE

description:
Library name: T_10-3-2
Celecoxib_rep3

data_processing:
Read count and transcripts per million (TPM) were calculated as gene expression abundance using the RSEM software (v1.3.3) and gene annotation mm10 Gene Transfer Format (GTF) file from UCSC browser
Assembly: mm10
Supplementary files format and content: tab-delimited text files include count values for each Sample

source_name: Muscle

growth_protocol: C2C12 murine myoblasts (ATCC CRL-1772) were purchased from the ATCC (Manassas, VA, USA). Myoblasts were maintained in Dulbecco’s modified Eagle’s medium (DMEM) (Invitrogen, CARLSBAD, CA, USA) containing 10% fetal bovine serum (FBS; Gibco Grand Island, NY, USA) and 1% penicillin/streptomycin (Invitrogen) at 37°C in an atmosphere of 5% CO2. For differentiation to C2C12 myotubes, myoblasts were cultured in DMEM containing 2% horse serum (HS; Gibco) for 5 days. We used differentiated C2C12 myotubes.

extract_protocol:
One mg of total RNA was processed for preparing mRNA sequencing library using MGIEasy RNA Directional Library Prep Kit (MGI Tech, China) according to manufacturer’s instruction.
Library was quantified by QauntiFluor ssDNA System (Promega, WI, USA).

value: Muscle

tag: cell line

tag: cell type

value: Myotube

value: D


title: Resveratrol_rep3

description:
Library name: T_10-3-3
Resveratrol_rep3

tag: treatment


title: Palmitric acid_rep3

description:
Library name: T_10-3-6
Palmitric acid_rep3

value: Palmitric acid_rep3

tag: batch


title: Arachidonic acid_rep3

description:
Library name: T_10-3-4
Arachidonic acid_rep3

value: Arachidonic acid_rep3


title: Dexa_rep3

description:
Library name: T_10-3-1
Dexa_rep3


title: Calcitriol_rep3

description:
Library name: T_10-3-5
Calcitriol_rep3


title: Calcitriol_rep2

description:
Library name: T_10-2-5
Calcitriol_rep2


title: Palmitric acid_rep2

description:
Library name: T_10-2-6
Palmitric acid_rep2

value: Palmitric acid_rep2


title: Arachidonic acid_rep2

description:
Library name: T_10-2-4
Arachidonic acid_rep2

value: Arachidonic acid_rep2


title: Palmitric acid_rep1

description:
Library name: T_10-1-6
Palmitric acid_rep1

value: Palmitric acid_rep1


title: Celecoxib_rep2

description:
Library name: T_10-2-2
Celecoxib_rep2


title: Resveratrol_rep2

description:
Library name: T_10-2-3
Resveratrol_rep2


title: Arachidonic acid_rep1

description:
Library name: T_10-1-4
Arachidonic acid_rep1

value: Arachidonic acid_rep1


title: Resveratrol_rep1

description:
Library name: T_10-1-3
Resveratrol_rep1


title: Dexa_rep1

description:
Library name: T_10-1-1
Dexa_rep1


title: Celecoxib_rep1

description:
Library name: T_10-1-2
Celecoxib_rep1


title: BatchD, Vehicle_rep1

description:
Library name: D1-1-4
Batch D; 0.02% DMSO, 24 h

value: Batch D; 0.02% DMSO, 24 h


title: BatchD, Vehicle_rep3

description:
Library name: D1-1-6
Batch D; 0.02% DMSO, 24 h


title: BatchD, Vehicle_rep2

description:
Library name: D1-1-5
Batch D; 0.02% DMSO, 24 h


title: BatchD, non-treat_rep2

description:
Library name: D1-1-2
Batch D; non-treat

value: Batch D; non-treat


title: BatchD, non-treat_rep3

description:
Library name: D1-1-3
Batch D; non-treat


title: BatchC, non-treat_rep1

description:
Library name: C1-1-1
Batch C; non-treat

value: Batch C; non-treat

value: C


title: BatchD, non-treat_rep1

description:
Library name: D1-1-1
Batch D; non-treat


title: BatchC, non-treat_rep2

description:
Library name: C1-1-2
Batch C; non-treat


title: BatchB, Vehicle_rep3

description:
Library name: B1-1-6
Batch B; 0.02% DMSO, 24 h

value: Batch B; 0.02% DMSO, 24 h

value: B


title: BatchB, Vehicle_rep1

description:
Library name: B1-1-4
Batch B; 0.02% DMSO, 24 h


title: BatchB, non-treat_rep3

description:
Library name: B1-1-3
Batch B; non-treat

value: Batch B; non-treat


title: BatchC, non-treat_rep3

description:
Library name: C1-1-3
Batch C; non-treat


title: BatchB, non-treat_rep1

description:
Library name: B1-1-1
Batch B; non-treat


title: BatchB, non-treat_rep2

description:
Library name: B1-1-2
Batch B; non-treat


title: BatchA, Vehicle_rep3

description:
Library name: A1-1-6
Batch A; 0.02% DMSO, 24 h

value: Batch A; 0.02% DMSO, 24 h

value: A


title: Dexa_rep2

description:
Library name: T_10-2-1
Dexa_rep2

value: Muscle

value: Myotube


title: BatchA, Vehicle_rep1

description:
Library name: A1-1-4
Batch A; 0.02% DMSO, 24 h


title: Calcitriol_rep1

description:
Library name: T_10-1-5
Calcitriol_rep1

value: D


title: BatchB, Vehicle_rep2

description:
Library name: B1-1-5
Batch B; 0.02% DMSO, 24 h


title: BatchA, Vehicle_rep2

description:
Library name: A1-1-5
Batch A; 0.02% DMSO, 24 h


title: BatchA, non-treat_rep2

description:
Library name: A1-1-2
Batch A; non-treat

value: Batch A; non-treat


title: BatchA, non-treat_rep3

description:
Library name: A1-1-3
Batch A; non-treat


title: BatchA, non-treat_rep1

description:
Library name: A1-1-1
Batch A; non-treat


title: JGE08 (20 ug/mL dose)_rep3

description:
Library name: T_9-3-6
Rep3_Ethanol extracts (20ug/mL dose); combination ratios of two herbs into 1:2

value: extraction -> mix of Ethanol extracts of JGT (JGW08;20 ug/mL dose)_rep3