title: ND Male

description: Library name: NDWTM

value: normal diet


title: 13-NRR-032-Adult GBM

status: Public on Mar 19 2025

type: SRA

city: New York

first: Varshini

last: Vasudevaraja

state: New York

address: 240 East 38th street

country: USA

institute: NYU Langone Health

description: Library name: 13-NRR-032

library_source: transcriptomic

data_processing:
FASTQ files were aligned to the human reference genome (hg19) using the STAR aligner
Sample quality was assessed for contamination using Fastq Screen, and alignment metrics were generated with Picard RNASeqMetrics
Gene expression levels were quantified using featureCounts.
Assembly: hg19
Supplementary files format and content: csv file includes raw counts for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: Glioblastoma CNS WHO 4

extract_protocol:
Approximately 10 mg of tumor tissue was allocated for transcriptomic analysis. RNA extraction was performed using the Qiagen RNeasy Lipid Tissue Mini Kit (Catalog #74804). RNA extractions were quantified using RNA Nano Chips (Cat. #5067-1511) on an Agilent 2100 BioAnalyzer.
RNA-Seq library preps were constructed using the Illumina TruSeq Stranded mRNA Library Prep kit (Cat #20020595) according to the manufacturers recommendations.  Input was 500ng of total RNA with 10 cycles of PCR amplification.  Final libraries were visualized using High Sensitivity DNA ScreenTape (Agilent, Cat. #5067-5584) on the Agilent TapeStation 2200 instrument.  Quant-It (Invitrogen, Cat. P11495) was used for final concentration determination and libraries were pooled equimolar.  The pool was sequenced single-end on an Illumina HiSeq4000 100 Cycle flowcell with 2% PhiX spike-in.

tag: tissue

value: Glioblastoma CNS WHO 4

tag: cell type

value: bulk tumor

tag: developmental stage

value: Adult

tag: subgroup


title: control_SG - biol rep 4

city: Siegen

first: Florian

last: Centler

state: NRW

address: Am Eichenhang 50

department: School of Life Sciences

country: Germany

institute: University of Siegen

data_processing:
Trimmomatic & cutadapt was used for adapter trimming and quality filtering, monitored by FastQC
Salmon was used for mapping and quantifying transcripts
R package tximport was used for collapsing results on the gene level
Assembly: GRCh38.p14
Supplementary files format and content: tsv, salmon pseudocounts (TPM)

extract_protocol:
For the isolation of totalRNAfromexosomes and cytoplasmic RNA granule cores, mirVana™ miRNA227Isolation Kit (Invitrogen) was used according to the manufacturers protocol.
Illumina stranded total RNA, NovaSeq S1 2x100 bp

tag: cell line

value: RNA granule

tag: treatment

value: control


title: 13-NRR-028-Adult GBM

description: Library name: 13-NRR-028


title: HD_exosome - biol rep 1

value: exosome

value: HD-induced


title: mouse corneal epithelium, 3 hours after injury, scATAC-seq, rep3

city: Guangzhou

first: Yingfeng

last: Zheng

state: - Select State/Region -

address: No.7 Jinsui Road, Tianhe District

country: China

institute: Zhongshan Ophthalmic Center, Sun Yat-sen University

description:
Library name: WO-scATAC-3
10× Genomics

library_source: genomic single cell

data_processing:
Quality control parameters for scRNA-seq were used to filter cells with fewer than 1000 or more than 4200 genes, or a mitochondrial gene ratio greater than 5%. The batch effect across different samples was removed using the Harmony package. Quality control parameters for scATAC-seq were used to filter cells with less than 3200 unique fragments and enriched at TSSs below 5. Additionally, cells that mapped to blacklist regions based on the ENCODE project reference were removed.
Assembly: GRCm38.p3
Supplementary files format and content: Seurat's processed output file: scRNA_seq.rds; Integrated scRNA and scATAC.rds
Supplementary files format and content: ArchR's processed output file:scATAC_data.rar

molecule: genomic DNA

organism: Mus musculus

source_name: cornea

extract_protocol:
The dissected cornea tissues were pooled and incubated with 0.25% trypsin for 30 to 50 minutes at 37℃. The loose central corneal epithelial sheets were peeled and digested with fresh trypsin. Then cells were collected into RPMI medium containing 10% fetal bovine serum to deactivate and remove trypsin. Cell suspension was centrifuged, resuspended,and filtered using a cell strainer to ensure single-cell suspension.
scRNA-seq library generation followed 10 ×Genomics instructions. Cells were captured in droplets. Then, reverse transcription, demulsification, Dynabeads barcode cDNA purification and PCR ampification were performed successively. The amplified cDNA was used to construct the gene expression library. scATAC-seq library generation followed 10 ×Genomics instructions. The nuclei were isolated and washed according to the manufacturer's protocal. Then resuspend the nucleus by chilled Diluted Nuclei Buffer. Nuclei were then immediately used to generate 10×single cell ATAC libraries.

treatment_protocol: corneal epithelium wound

value: cornea

tag: genotype

value: wildtype

value: corneal epithelium wound


title: mouse corneal epithelium, 3 hours after injury, scATAC-seq, rep2

description:
Library name: WO-scATAC-2
10× Genomics


title: 13-NRR-010-Adult GBM

description: Library name: 13-NRR-010


title: mouse corneal epithelium, 3 hours after injury, scATAC-seq, rep1

description:
Library name: WO-scATAC-1
10× Genomics


title: Lac_Input

city: 广州

first: li

last: xiaobai

address: 381 Wushan Road, Tianhe District, Guangzhou

institute: south china university of technology

description: Library name: Lac_Input_1

library_source: genomic

data_processing:
For a specific ChIP-seq binding site, individual reads mapping to the plus or minus strand and present significant enrich. For single-end sequencing, the fragment size was estimated with MACS2 (Zhang et al., 2008) predicted method with default parameters. MACS2 scan all the genome with a specific window size and calculate the reads enrichment level. A particular number of windows were used as samples to build enrichment model and to predict fragment size. The following peak calling analysis was based on this predicted fragment size.After mapping reads to the reference genome, we used the MACS2 (version 2.1.0) peak calling software to identify regions of IP enrichment over background. A q-value threshold of 0.05 was used for all data sets. After peak calling, the distribution of chromosome distribution, peak width, fold enrichment, significant level and peak summit number per peak were all displayed.
Assembly: ensembl_homo_sapiens_grch38_106
Supplementary files format and content: The peak detection results for each sample.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit.

value: Human pancreatic cancer cells

value: l-lactate


title: 12-TABS-556-Adult GBM

description: Library name: 12-TABS-556


title: NC_Input

description: Library name: NC_Input_1


title: NC_IP

description:
Library name: NC_IP_1
NC_IP.count

tag: antibody

value: anti- H3K18la antibody


title: Lac_IP

description:
Library name: Lac_IP_1
Lac_IP.count


title: mouse corneal epithelium, 3 hours after injury, scRNA-seq, rep3

description:
Library name: WO-scRNA-3
10× Genomics

library_source: transcriptomic single cell


title: control_SG - biol rep 3


title: Normal 2

city: Chengdu

first: Li

last: Chen

state: Sichuann

address: No.17, South Renmin Road

institute: Sichuan University West China Hospital

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the CellRanger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: TS_3.0 genome annotation（http://www.treeshrewdb.org/download.html）
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

organism: Tupaia belangeri

source_name: hippocampus

extract_protocol:
100-200mg samples were flash frozen immediately after collection for downstream processing. Nucleus isolation was done as previously described(https://pubmed.ncbi.nlm.nih.gov/32587393/).  Briefly, tissue samples were cut into pieces <0.5 cm and homogenized using a glass Dounce tissue grinder (Sigma, cat.  no.  D8938).  The tissue was homogenized 25 times with pestle A and 25 times with pestle B in 2 ml of ice-cold nuclei EZ lysis buffer.  The sample was then incubated on ice for 5 min, with an additional 3 ml of cold EZ lysis buffer.  Nuclei were centrifuged at 500g for 5 min at 4 °C, washed with 5 ml ice-cold EZ lysis buffer and incubated on ice for 5 min. After centrifugation, the nucleus pellet was washed with 5 ml nuclei suspension buffer (NSB;  consisting of 1× PBS, 0.01% BSA and 0.1% RNase inhibitor (Clontech, cat.  no.  2313A)).  Isolated nuclei were resuspended in 2 ml NSB, filtered through a 35 μm cell strainer (Corning-Falcon, cat.  no.  352235) and counted.  A final concentration of 1,000 nuclei per μl was used for loading on a 10x channel.
We prepared single-nucleus RNA-seq libraries with Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 on the Chromium Controller(10× Genomics).  The nuclei suspension was loaded onto the Chromium Next GEM Chip G and ran the Chromium Controller to generate single-cell gel beads in the emulsion(GEMs) according to the manufacturer’s recommendation.   Captured nuclei were lysed and the released RNA was barcoded through reverse transcription in individual GEMs.   Barcoded, full-length cDNA was generated and libraries were constructed according to the performer’s protocol .The quality of libraries was assessed by Qubit 4.0 and the Agilent 2100.   Sequencing was performed on the Illumina NovaSeq 6000 with a sequencing depth of at least 50,000 reads per nucleus and 150 bp (PE150) paired-end reads (performed by Biomarker Technologies Corporation, Beijing, China).

value: hippocampus


title: HD_SG - biol rep 5


title: 12-TABS-546-Adult GBM

description: Library name: 12-TABS-546


title: mouse corneal epithelium, 3 hours after injury, scRNA-seq, rep2

description:
Library name: WO-scRNA-2
10× Genomics


title: control_SG - biol rep 2


title: Splenocyte, replicate 1, scRNAseq

city: Raleigh

first: Xinxia

last: Peng

address: 1060 William Moore Drive

institute: North Carolina State University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0.0
Assembly: ASM1176430v1.1
Supplementary files format and content: Tab-separated values files and matrix files

organism: Mustela putorius furo

source_name: unsorted cells Splenocyte

extract_protocol:
Cryopreserved PBMC and one splenocyte sample were used for single-cell analysis. Cells were washed in resuspension buffer (RPMI, 10% FBS), depleted of dead cells using a removal kit (Miltenyi Biotec), collected by centrifugation at 700xg, and resuspended at an appropriate concentration, between 700 and 1200 cells/ul. All cells were counted by hemocytometer and assayed for viability using a Countess II automated cell counter (Thermo Fisher Scientific, Waltham, MA). From each sample a maximum volume containing 17,000 cells, having approximately >80% viable cells, were loaded onto the 10x Chromium (10x Genomics, Pleasanton, CA) controller for a targeted cell recovery of 10,000 cells (10x Genomics, Pleasanton, CA, Chromium Next GEM Single Cell 5’ v2 UserGuide RevD). cDNA amplification was carried out at 20 cycles of amplification for all samples and assayed for quality and concentration using a Bioanalyzer 2100 and High Sensitivity DNA Kit.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, PBMCs and Splenocyte cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: unsorted cells Splenocyte


title: mouse corneal epithelium, 3 hours after injury, scRNA-seq, rep1

description:
Library name: WO-scRNA-1
10× Genomics


title: PMBC, replicate 1, scRNAseq

description: 10x Genomics

source_name: unsorted cells PBMC

value: unsorted cells PBMC


title: 12-TABS-528-Adult GBM

description: Library name: 12-TABS-528


title: Normal 1

description: 10x Genomics


title: control_exosome - biol rep 4


title: 12-TABS-523-Adult GBM

description: Library name: 12-TABS-523


title: HD_SG - biol rep 4


title: control_exosome - biol rep 5


title: KrTB-95

city: New York City

first: Jorge

last: Baquero

state: NY

address: 1300 York Avenue

department: Pharmacology

institute: Weill Cornell Medical College

description: Library name: Sample 16

data_processing:
Illumina bcl2fastq2 v2.20 was employed for basecalling.
The sequenced reads underwent trimming to eliminate low-quality bases and adapter sequences using cutadapt. Subsequently, these reads were mapped to the mouse GRCm38 reference genome using STAR v2.5.2b.
The extraction of raw read counts was accomplished through HTSeq-count v0.11.2.
Differential expression analysis was conducted using the DESeq2 v1.6.3 package.
We employed the limma package v3.22.7 to remove batch effects from processing samples from different batches.
Assembly: Mouse GRCm38
Supplementary files format and content: Excel file including gene name and log2fold changes (KrTB-D vs. KrTB and KrTB-DN vs. KrTB-N) for each gene

source_name: Tongue epithelia tissue

extract_protocol:
Qiagen's RNEasy Micro kit (Cat # 74004)
The preparation of RNA libraries utilized the TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA), following the protocols provided by the manufacturer. The libraries were sequenced with pair-end 51bp reads on the NovaSeq6000 sequencer.

treatment_protocol: Water, water+doxycycline (2 mg/ml), water+4NQO (50 μg/ml), and water+doxycycline+4NQO (2 mg/ml and 50 μg/ml)

value: Tongue epithelia tissue

tag: strain

value: KrTB-DN


title: MSC, Ground control, P1

city: Rochester

first: Alexandra

last: Krivonos

state: MN

address: 200 1st St SW

department: Quantitative Health Sciences

institute: Mayo Clinic

data_processing:
FASTQ files were processed using MAP-RSeq v3.0.2.
Splice-aware alignment against the human reference genome hg38 was performed using STAR v2.5.2b.
Expression quantification was performed using Subread v1.5.1.
Quality control was performed using RSeQC v2.6.4.
Assembly: hg38
Supplementary files format and content: TSV file containing raw gene expression values.

growth_protocol: BMSC07 mesenchymal stem cells were maintained in alpha-MEM supplemented with 16.5% fetal bovine serum (FBS) and GlutaMAX™-I Supplement in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
MSCs were trypsinized and subsequently preserved in RNAprotect solution followed by isolation utilizing the miRNeasy Mini kit.
cDNA libraries were prepared using up to 200 ng of total RNA according to the manufacturer’s instructions for the TruSeq RNA Library Prep Kit v2 (Illumina, San Diego, CA).
Libraries were sequenced at an average of 35M read pairs per sample with Illumina’s standard protocol for the Illumina cBot and HiSeq 3000/4000 PE Cluster Kit. The flow cell was sequenced as 100 X 2 paired end reads on an Illumina HiSeq 4000 using the HiSeq 3000/4000 sequencing kit and HD 3.3.52 collection software. Base-calling was performed using Illumina’s RTA version 2.7.3.

treatment_protocol: Samples in ISS group were exposed to microgravity for one week or two weeks. Paired samples in control group were kept in the lab on the groud.

value: mesenchymal stem cells

value: WT

value: normal gravity

tag: time

value: two week


title: control_SG - biol rep 1

value: RNA granule

value: control


title: KrTB-93

description: Library name: Sample 14


title: sgVdac2_4

type: RNA

city: Memphis

first: Hongbo

last: Chi

state: TN

address: 262 Danny Thomas Place

department: Immunology

institute: St Jude Children's Research Hospital

hyb_protocol: Labeled cDNA was included in a hybridization mix that was incubated on the Clariom S mouse array for 16 hours at 45◦c while rotating at 60 rpm.

scan_protocol: GeneChips were scanned using the AffymetrixGeneChip Scanner 3000 7G.

data_processing: Probe signals were quantile normalized and summarized by the RMA algorithm using the Affymetrix Expression Console software v1.1

label: biotin

source_name: B16-OVA-Cas9-sgVdac2 with no treatment

label_protocol: High-quality RNA was processed using Thermo Fisher (Affymetrix) Whole Transcript (WT) Plus assay kit

growth_protocol: B16-OVA-Cas9-sgNTC/sgVdac2 tumor cells were cultured according to ATCC guideline.

extract_protocol: Total RNA samples were prepared according to the prototol of Rneasy Micro kit from Qiagen,

treatment_protocol: B16-OVA-Cas9-sgNTC/sgVdac2 tumor cells were co-cultured with  OT-I CD8+ T cells at E:T ratio of 0.5:1 for 24h, survived tumor cells were sorted after co-culture for RNA extraction.

value: B16-OVA-Cas9-sgVdac2 with no treatment


title: MSC, ISS microgravity, O2

value: microgravity


title: HD_SG - biol rep 3

value: HD-induced


title: KrTB-4

description: Library name: Sample 13


title: control_exosome - biol rep 3

value: exosome


title: MSC, Ground control, O1


title: MSC, ISS microgravity, N2


title: sgVdac2_3


title: MSC, Ground control, N1


title: MSC, ISS microgravity, P2


title: KrTB-94

description: Library name: Sample 15


title: MSC, Ground control, J1

value: one week


title: control_exosome - biol rep 2


title: HD_exosome - biol rep 4


title: HD_exosome - biol rep 5


title: HD_SG - biol rep 2


title: sgVdac2_2


title: KrTB-47

description: Library name: Sample 8

value: KrTB-D


title: MSC, ISS microgravity, I2


title: MSC, ISS microgravity, J2


title: control_exosome - biol rep 1


title: sgNTC_4

source_name: B16-OVA-Cas9-sgNTC with no treatment

value: B16-OVA-Cas9-sgNTC with no treatment


title: KrTB-46

description: Library name: Sample 7


title: sgVdac2_1


title: MSC, Ground control, I1


title: KrTB-44

description: Library name: Sample 6


title: sgNTC_2


title: HealthyHSPC06

city: Suzhou

first: Fang

last: Fang

state: Jiangsu

address: 92 Zhongnan street

institute: Children’s Hospital of Soochow University

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: HSPC

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: HSPC


title: HealthyHSPC05


title: sgNTC_3


title: KrTB-34

description: Library name: Sample 5


title: Vdac2BimBidKO_IFNg3

source_name: Vdac2, Bim and Bid TKO B16-OVA tumor cells with IFNg treatment

growth_protocol: Cells were cultured with RPMI-1640 medium ( 10% FBS).

extract_protocol: Total RNA samples were prepared according to the prototol of Rneasy Micro kit from Qiagen

treatment_protocol: WT, Vdac2 KO, Bim/Bid dKO and Vdac2/Bim/Bid TKO B16-OVA tumor cells were treated with IFNg treatment (10ng/ml) for 24 hours.

value: B16-OVA tumor cells


title: Vdac2BimBidKO_IFNg2


title: MSC, Ground control, H1


title: sgNTC_1


title: HealthyHSPC04


title: KrTB-32

description: Library name: Sample 4

value: Tongue epithelia tissue

value: KrTB


title: KrTB-31

description: Library name: Sample 3


title: HealthyHSPC02


title: KrTB-28

description: Library name: Sample 2


title: BimBidKO_IFNg3

source_name: Bim and Bid dKO B16-OVA tumor cells with IFNg treatment


title: HealthyHSPC01


title: BimBidKO_IFNg2


title: MSC, ISS microgravity, H2

value: mesenchymal stem cells


title: KrTB-26

description: Library name: Sample 1


title: e17: week 17 organoid SFPQ-TFE3 gene fusion sample

city: UTRECHT

first: PHILIP

last: LIJNZAAD

state: Utrecht

address: HEIDELBERGLAAN 25

department: Single Cell Facility

country: Netherlands

institute: Princess Maxima Center for Pediatric Oncology

data_processing:
data were processed using the10x Genomics cellranger 7.1 suite of programs
Assembly: 10x genome 'refdata-gex-GRCh38-2020-A' (GRCh38-p13, gencode v32 July 7, 2020), extended with sequence of luciferase construct
Supplementary files format and content: gzipped TAR file of Sparse Matrix in MTX format; tab-delimited file of sample identifiers for the lx221 library

molecule: polyA RNA

source_name: fetal kidney

growth_protocol: Collected fetal kidneys were minced and digested in AdvDF+++ (Advanced DMEM/F12 containing 1× Glutamax, 10 mM HEPES and antibiotics) containing 1 mg/ml collagenase (Sigma, C9407) and 10 µM Y-27632 on an orbital shaker for 30 - 45 min at 37 °C. The suspension was subsequently washed with AdvDF+++ followed by centrifugation at 250×g. The cell pellets were seeded in growth factor-reduced BME (Trevigen, 3533-010-02) and cultured in kidney organoid medium (AdvDF+++ supplemented with 1.5% B27 supplement (Gibco), 10% R-spondin-conditioned medium, EGF (50 ng/ ml, Peprotech), FGF-10 (100 ng/ml, Peprotech), N-acetylcysteine (1.25 mM, Sigma-Aldrich), Rho-kinase inhibitor Y-27632 (10 µM, Abmole), A83-01 (5 µM, Tocris Bioscience) and Next Generation Surrogate (NGS) Wnt (0.5 nM, ImmunoPrecise Antibodies NASDAQ),

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen) or using the Macherey-Nagel RNA isolation kit according to manufacturer’s instructions. Extracted total RNA was used to produce cDNA using the GoScript reverse transcriptase system (Promega) and qRT-PCR was subsequently performed using IQ SYBR green mix (Bio-Rad) according to the manufacturer’s instructions.
The barcoding of individual transcripts from single cells, followed by cDNA amplification and library construction, were performed using 10X Genomics reagents and 10X Chromium Controller, according to the manufacturer’s user guide nr. CG000315 (“Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (Dual Index), RevC”).

value: fetal kidney

value: unknown patient material transduced with gene fusion contruct


title: e17: week 17 organoid control sample

value: unknown patient material transduced with luciferase contruct


title: macro-metastatic niche,replicate 1,scRNAseq

first: Yue

last: Jiang

state: Guangdong

address: No. 26, Erheng Road, Yuancun

institute: The Sixth Affiliated Hospital of Sun Yat-sen University

description:
Library name: MMN1
BD Rhapsody system

data_processing:
Basecalls performed using CASAVA version 1.8, Umi-tools was utilized to calculate the raw counts and cell whitelist by default parameter
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: liver

extract_protocol:
Liver single cell suspension preparation was performed by the laboratory staff of NovelBio Biopharmaceutical Technologies Ltd. Liver lysis was performed as described previously, whole mouse livers were removed, cut into small pieces on ice, and then enzymatically lysed with 1 mg/mL Collagenase II (Worthington) for 30 min on a shaker at 37°C. 70-micron cell filters were sieved and then erythrocytes were lysed in erythrocyte lysis buffer (Miltenyi Biotec), rinsed twice with PBS, and then the MACS Dead Cell Removal Kit (Miltenyi Biotec) was used to further enrich the single cell suspension.
Single cell capture was realized using the BD Rhapsody system. Whole transcriptome libraries were prepared according to the BD Rhapsody Single Cell Whole Transcriptome Amplification Workflow and 150 bp paired-end sequencing was performed using the Illumina (Illumina, San Diego, California, USA).

value: liver

value: immune cells and non-immune cell

value: Orthotopic mouse models of colorectal cancer


title: e16: fetal week 16 organoid, both control and fusion (see supplemental)

description: this library was multiplexed, see lx221-samples.txt for the identies

value: unknown patient material transduced with luciferase and SFPQ-TFE3 gene fusion contructs


title: HealthyHSPC03

value: WT


title: macro-metastatic niche,replicate 2,scRNAseq

description:
Library name: MMN2
BD Rhapsody system


title: N_48_h

city: seoul

first: Jueng Soo

last: You

address: 120 Neungdong-ro

country: South Korea

institute: Konkuk University

description: Replicate 7

hyb_protocol: Following fragmentation, 1.65 ug of cRNA were hybridized to the Agilent expression microarray according to the protocols provided by the manufacturer

scan_protocol: Arrays were scanned using the Agilent Technologies G4900DA SG12494263

data_processing: Array data export processing and analysis was performed using Agilent Feature Extraction v11.0.1.1

label: Cy3 (or Cy5)

source_name: liver cancer cell line

label_protocol: labeled cRNA were prepared from 1~5 ug total RNA using the Agilent’s Quick Amp Labeling Kit

growth_protocol: All cells were cultured at 37°C in a humidified incubator with 5% CO2.

extract_protocol: Total RNA was extracted using TRIzol reagent, digested with DNase I and reverse transcribed using a High Capacity cDNA Reverse Transcription Kit

treatment_protocol: Dimethyl α-Ketoglutarate was added to the culture media at different time points

tag: tag

value: liver cancer cell line


title: 17-03-DG, Ts65Dn, ChP

city: Orangeburg

first: Stephen

middle: D.

last: Ginsberg

address: 140 Old Orangeburg Rd

department: Center for Dementia Research

institute: Research Foundation for Mental Hygiene

description: Library name: 17-03-DG

data_processing:
FastQ files were utilized for both conditions (2N and Ts) in all three cell types (CA1 PNs, CA3 PNs, DG GCs) to analyze data in parallel. FastQ files were generated and QC of the raw reads was performed by FastQC v0.11.9. The reads with adapter contamination/ low quality were trimmed using Trimmomatic 0.39.
Trimmed sequence reads were aligned to the reference  genome (GRCm39-mm10) using STAR Aligner. Quantification was performed on alignments using Picard (2.26.2) (2019) for different measures. Gene counts were extracted using RSEM. QC was performed on alignments using RSeQC (v5.0.2).
Downstream Analysis was performed using R with the gene counts obtained from the RSEM. Genes with over 0.1 counts per million were retained followed by TMM normalization.
Assembly: mm10
Supplementary files format and content: tab delimited text files with gene counts of all samples in a region per one file
Supplementary files format and content: tab delimited text files with gene counts of one sample per one file

source_name: Ts65Dn Hippocampus

growth_protocol: Breeder pairs (female Ts65Dn and male C57Bl/6J Eicher × C3H/HeSnJ F1 mice) were purchased from Jackson Laboratories (Bar Harbor, ME, USA) and mated at the Nathan Kline Institute.

extract_protocol:
Brain tissues were immediately flash frozen and 20 μm-thick tissue sections were cryostat cut (−25°C) in the coronal plane and mounted on polyethylene naphthalate (PEN) membrane slides. Sections were stained with rapid Nissl staining protocol. CA1 and CA3 PNs along with DG GCs were identified visually in the same section and isolated by laser capture microdissection (LCM). Approximately 6 rostral hippocampi sections were dissected by LCM (approximately -1.58 to -2.54 Bregma), with mean collections of ~950 CA1, ~750 CA3 and ~1175 DG neurons collected per brain before proceeding to RNA isolation and RNA-seq library preparation. RNA from each sample was purified using miRNeasy Micro kit (Qiagen) following the manufacturer's specifications, with a the optional DNase digestion step done twice sequentially.
The SMARTer Stranded Total RNA-Seq kit-Pico input Mammalian v3  was employed with unique indexes for each sample. To normalize input, CA1, CA3 and DG RNA concentrations were used to determine sample input, with average of ~3-3.75 ng RNA input utilized per sample. Samples were fragmented for 3.75 min, with 5 cycles for PCR1 and 14 cycles for PCR2. Samples were quantified using Tapestation D1000 DNA assay.  Samples were pooled in equimolar concentrations and assayed on an Illumina NovaSeq 6000 using a S1 100cycle flow cell (v1.5) by the NYUGSOM Genome Technology Center.

treatment_protocol: Breeder pairs were assigned to receive one of two choline-controlled experimental diets: (i) control rodent diet containing 1.1 g/kg choline chloride or (ii) choline-supplemented diest containing 5.0g/kg choline chloride. Pups received choline normal or choline supplemented diet as per their respective dam's diet from E0-P21 and starting at weaning all offspring had ad libitum access to water and the control diet

value: Ts65Dn Hippocampus

value: DG granule cells

value: ChP


title: Vdac2KO_IFNg3

source_name: Vdac2 KO B16-OVA tumor cells with IFNg treatment


title: N_9_h

description: Replicate 4


title: N_24_h

description: Replicate 6


title: hCO_shNGB35D

city: Nankang

first: Yuan-Hsuan

last: Liu

state: Taipei

address: 128, Section 2, Academia Road

department: Research Center for Applied Sciences

country: Taiwan

institute: Academia Sinica

description: 10x Genomics

data_processing:
The raw sequencing data were aligned to the GRCh38 human reference genome by the Cell Ranger pipeline v.6.1.2 (10x Genomics) with default parameters to generate the cell-by-gene count matrix.
Assembly: GRCh38
Supplementary files format and content: Matrix files (h5).

source_name: cerebral organoid derived from human induced pluripotent stem cells (hiPSCs)

extract_protocol:
Cerebral organoids were washed with calcium and magnesium-free DPBS and incubated with Corning Cell Recovery Solution to dissociate the polymerized Matrigel. The collected hCOs were cut into 2 to 4 small pieces using a scalpel and washed with the DPBS several times to remove the potential debris. The pieces of the hCOs were disassociated into single-cell suspension through the Neural Tissue Dissociation Kit (Miltenyi Biotec, Bergisch Gladbach, German).
Following the manufacturer’s instruction, the single-cell RNA sequencing (scRNA-seq) libraries were prepared with the Chromium Single Cell 3’ Library & Gel Bead Kit v.3.1 (10x Genomics). The constructed libraries were sequenced following the specific procedures (R1:28 cycles, R2: 91 cycles, and i7 index: 8 cycles) by a sequencing system (NovaSeq 6000, Illumina, San Diego CA).

tag: shRNA

value: shNGB

tag: time point

value: day 35


title: 16-272-DG, Ts65Dn, ChP

description: Library name: 16-272-DG


title: N_12_h

description: Replicate 5


title: Vdac2BimBidKO_IFNg1

value: B16-OVA tumor cells


title: Vdac2KO_IFNg2


title: hCO_control35D

description: 10x Genomics

value: cerebral organoid derived from human induced pluripotent stem cells (hiPSCs)

value: control


title: nucleus pulposus cells treated with Erastin and miR_Exo_3

city: Chongqing

first: Wenkai

last: Wang

state: Chongqing

address: Gaotanyan main street

institute: Army Medical University

description:
Library name: Sample 12
Model+miR_Exo_3

data_processing:
The mapped reads of each sample were assembled using StringTie with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software. After the final transcriptome was generated, StringTie and ballgown were used to estimate the expression levels of all transcripts and perform expression level for mRNAs by calculating FPKM.
Assembly: mRatBN7.2
Supplementary files format and content: txt files include FPKM values for each sample

organism: Rattus norvegicus

source_name: intervertebral disc

growth_protocol: Nucleus pulposus cells (NPCs) were cultured in DMEM/F12 medium, supplemented with 10% FBS and 1% penicillin-streptomycin, and incubated in a humidified atmosphere of 5% CO2 at 37°C.

extract_protocol:
Total RNA from NPCs was isolated using a TRIzol reagent (Invitrogen, U.S.A.).
The cleaved RNA fragments were reversetranscribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a Tbase overhang for ligating the adapter to the A-tailed fragmented DNA. Singleor dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads.

treatment_protocol: To induce ferroptosis, NPCs were incubated with Erastin at 0.1-5 μM for 48 h. for exosomes administration, NPPC-Exo were added into cell mediums at a concentration of 50 μg/mL.

value: intervertebral disc

value: nucleus pulposus cells


title: N_6_h

description: Replicate 3


title: Vdac2KO_IFNg1


title: N_0_h_1

description: Replicate 1


title: N_0_h_2

description: Replicate 1


title: BimBidKO_IFNg1


title: N_3_h

description: Replicate 2


title: WT_IFNg1

source_name: WT B16-OVA tumor cells with IFNg treatment


title: WT_IFNg2


title: hCO_control24D

description: 10x Genomics

value: day 24


title: nucleus pulposus cells treated with Erastin and miR_Exo_1

description:
Library name: Sample 10
Model+miR_Exo_1


title: 15-245-DG, Ts65Dn, ChP

description: Library name: 15-245-DG


title: hCO_shNGB24D

description: 10x Genomics


title: 16-206-DG, Ts65Dn, ChP

description: Library name: 16-206-DG


title: GRH1 pbmc，at End CPB,in red blood transfusion group

first: Ping

last: Yang

state: 中国 +86

address: 37 Guo Xue Alley, Wuhou District

institute: West China Hospital

description: 10x Genomics

data_processing:
CellRanger software (version 7.0.0, 10X Genomics) was used to analyze the sequencing data, and gene expression information for each cell was obtained.
Assembly: Ensembol V105
Supplementary files format and content: Tab-separated values and Matrix files

source_name: pbmc

extract_protocol:
Peripheral blood mononuclear cells were isolated by density gradient centrifugation using Ficoll Hypaque density solution. Cells were used only if >80% were viable based on trypan blue staining, in which case they were subjected to single-cell RNA sequencing.
An appropriate volume of peripheral blood mononuclear cells was loaded onto a 10X Genomics Chromium instrument to capture 8000 single cells according to the manufacturer’s instructions for the 10X Genomics Chromium Single-Cell 5’ kit (version 2). Subsequent cDNA amplification and library construction were performed according to the standard protocol. Libraries were sequenced on an Illumina NovaSeq 6000 sequencing system (paired-end multiplexing run, 150 bp) at LC-Bio Technology (Hangzhou, China) at a minimum depth of 20,000 reads per cell.

value: pbmc

tag: age

value: 57 years old

value: red blood cell transfusion


title: WT_IFNg3


title: nucleus pulposus cells treated with Erastin and NPPC_Exo_3

description:
Library name: Sample 9
Model+NPPC_Exo_3


title: 15-199-DG, Ts65Dn, ChP

description: Library name: 15-199-DG


title: 15-198-DG, Ts65Dn, ChP

description: Library name: 15-198-DG


title: GRH1 pbmc，at Pre-grugery,in red blood transfusion group

description: 10x Genomics


title: nucleus pulposus cells treated with Erastin and NPPC_Exo_2

description:
Library name: Sample 8
Model+NPPC_Exo_2


title: 15-140-DG, Ts65Dn, ChP

description: Library name: 15-140-DG


title: Vdac2-Apaf1-dKO-24h 3

source_name: B16-OVA-Cas9-sgVdac2 + Apaf1

growth_protocol: B16-OVA-Cas9-sgNTC/Vdac2 tumor cells were cultured according to ATCC guideline.

treatment_protocol: Tumor cells were treated with mouse IFNg at 10ng/ml

value: treatment for 24h


title: 15-36-DG, Ts65Dn, ChP

description: Library name: 15-36-DG


title: nucleus pulposus cells treated with Erastin and NPPC_Exo_1

description:
Library name: Sample 7
Model+NPPC_Exo_1


title: WXY1 pbmc，at Pre-grugery,in red blood transfusion group

description: 10x Genomics

value: 63 years old


title: nucleus pulposus cells treated with miR_Exo_3

description:
Library name: Sample 6
miR_Exo_3


title: 14-90-DG, Ts65Dn, ChP

description: Library name: 14-90-DG


title: GTL1 pbmc，at End CPBin no transfusion group

description: 10x Genomics

value: 66 years old

value: No transfusion


title: nucleus pulposus cells treated with Erastin and miR_Exo_2

description:
Library name: Sample 11
Model+miR_Exo_2


title: 16-90-DG, 2N, ChP

description: Library name: 16-90-DG

source_name: Disomic Hippocampus

value: Disomic Hippocampus

value: DG granule cells


title: GTL1 pbmc，at Pre-grugery,in no transfusion group

description: 10x Genomics


title: 16-273-DG, 2N, ChP

description: Library name: 16-273-DG

value: ChP


title: nucleus pulposus cells treated with miR_Exo_1

description:
Library name: Sample 4
miR_Exo_1


title: ASJ1 pbmc，at End CPBin no transfusion group

description: 10x Genomics

value: 61 years old


title: 15-336-DG, 2N, ChP

description: Library name: 15-336-DG


title: WXY1 pbmc，at End CPB,in red blood transfusion group

description: 10x Genomics


title: nucleus pulposus cells treated with NPPC_Exo_3

description:
Library name: Sample 3
NPPC_Exo_3


title: ASJ1 pbmc，at Pre-grugery,in no transfusion group

description: 10x Genomics


title: nucleus pulposus cells treated with NPPC_Exo_2

description:
Library name: Sample 2
NPPC_Exo_2


title: 15-334-DG, 2N, ChP

description: Library name: 15-334-DG


title: LC_1 pbmc，at End CPBin no transfusion group

description: 10x Genomics

value: 51 years old


title: nucleus pulposus cells treated with NPPC_Exo_1

description:
Library name: Sample 1
NPPC_Exo_1


title: nucleus pulposus cells treated with miR_Exo_2

description:
Library name: Sample 5
miR_Exo_2


title: 15-296-DG, 2N, ChP

description: Library name: 15-296-DG


title: LC_1 pbmc，at Pre-grugery,in no transfusion group

description: 10x Genomics


title: Vdac2-Bak1-dKO-24h 3

source_name: B16-OVA-Cas9-sgVdac2 + Bak1


title: 15-269-DG, 2N, ChP

description: Library name: 15-269-DG


title: km, cmyb_pu.1, replicate 1

first: Wei

state: Guangdong Province

address: 382 Waihuan E Rd, Panyu District

department: School of Medicine

institute: South China University of Technology

description: 10x Genomics

data_processing:
10X Genomics Cell Ranger software (version 3.1.0) was used to convert raw BCL files to FASTQ files, alignment and counts quantification.
Doublet GEMs was achieved by using the tool DoubletFinder (v2.0.3) by the generation of artificial doublets, using the PC distance to find each cell’s proportion of artificial k nearest neighbors (pANN) and ranking them according to the expected number of doublets
The cell by gene matrices for each sample were individually imported to Seurat  version 3.1.1 for downstream analysis. Cells with unusually high number of UMIs (≥40000) or mitochondrial gene percent (≥15%) were filtered out. We also excluded cells with less than 200 or more than 3500 genes detected.
After removing unwanted cells from the dataset, we employed a global-scaling normalization method “LogNormalize” that normalizes the gene expression measurements for each cell by the total expression, multiplies this by a scale factor (10,000 by default), and log-transforms the results.
Seurat embed cells in a shared-nearest neighbor (SNN) graph, with edges drawn between cells via similar gene expression patterns. To partition this graph into highly interconnected quasi-cliques or communities, we first constructed the SNN graph based on the euclidean distance in PCA space and refined the edge weights between any two cells based on the shared overlap in their local neighborhoods (Jaccard distance). We then cluster cells using the Louvain[6] method to maximize modularity. For visualization of clusters, t-distributed Stochastic Neighbor Embedding (t-SNE) were generated using the same PCs.
Assembly: GRCz11 Ensembl release 100
Supplementary files format and content: tab-separated values files, matrix files

organism: Danio rerio

source_name: kidney marrow

extract_protocol:
Kidney marrow were isolated from 1-year-old fish, placed in PBS with 5% fetal bovine serum, triturated by pipet, and filtered through a 40-μm cell strainer. The cells were counted and the proportion of living cells was calculated. After ensuring that the proportion of living cells was ≥90%, the cell concentration was adjusted to 1 000 cells/μL.
Libraries were generated and sequenced from the cDNAs with Chromium Next GEM Single Cell 3’ Reagent Kits v3.1. Briefly, blood cell suspensions were loaded on a 10X Genomics GemCode Single-cell instrument to generates single-cell Gel Bead-In-EMlusion (GEMs). Upon dissolution of the Gel Bead in a GEM, primers containing an Illumina® R1 sequence, a 16 nt 10x Barcode, a 10 nt Unique Molecular Identifier (UMI), and a poly-dT primer sequence were released and mixed with cell lysate and Master Mix. Barcoded, full-length cDNAs were then reverse-transcribed from poly-adenylated mRNA. The pooled barcoded cDNA was then cleaned up with silane magnetic beads, amplified by PCR to generate sufficient mass for library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

tag: development stage

value: kidney marrow

value: blood cells


title: ADSC_sphere

city: Tainan City

first: Yi-Kai

last: Hong

state: Please select an option below

address: No.1, Daxue Rd., East Dist.

institute: National Cheng Kung University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Whole cells

extract_protocol:
ASCs and spheroids were digested with 0.05 % trypsin (Invitrogen) for 1 and 10 min, respectively. Subsequently, cells were centrifuged at 800 rpm for 5 min, and the pellets were resuspended in growth medium with 10% FBS. The cell concentration was determined by Countstar (Aber Instruments Ltd, Aberystwyth, UK). The target cell concentration of 1 × 106 cells per milliliter was achieved by adding appropriate volumes of growth medium with 10% FBS.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Whole cells


title: Vdac2-Apaf1-dKO-24h 1


title: km, pu.1, replicate 1

description: 10x Genomics


title: ADSC

description: 10x Genomics


title: Vdac2-Apaf1-dKO-24h 2


title: km, cmyb, replicate 1

description: 10x Genomics

value: cmybhyper


title: Cal-62 cells, NSUN2 knockout 50, replication 2

city: Tianjin

first: Xiukun

last: Hou

address: Huanhu Road

institute: Tianjin Cancer Institute and Hospital

data_processing:
Illumina RTA software used for image identification and basecalling.
Adaptor sequence and low-quality sequence were trimmed by Trim Galore, then sequence reads were mapped to mm10 genome using Hisat2 with default parameters.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: hg38
Supplementary files format and content: tab-delimited text file include Normalized count values for each Sample.

source_name: Cal-62 cells

extract_protocol:
Total RNA was extracted with Trizon Reagen (CWBIO) and was subjected to DNase Ｉ(Thermo Scientific) for 30min
Next generation sequencing library preparations were constructed according to the manufacturer’s protocol (VAHTS mRNA-seq V2 Library Prep Kit for Illumina). The mRNA fragmentation and priming was performed using VAHTSFirst Strand Synthesis Reaction Buffer and VAHTS Random Primers. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second-strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The purified double-stranded cDNA（byAxyPrep Mag PCR Clean-up (Axygen)was then treated with End Prep Enzyme Mix to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using AxyPrep Mag PCR Clean-up (Axygen), and fragments of ~360 bp (with the approximate insert size of 300 bp) were recovered. Each sample was then amplified by PCR for 11 cycles using P5 and P7 primers, with both primers carrying sequences which can anneal with flow cell to perform bridge PCR and P7 primer carrying a six-base index allowing for multiplexing. The PCR products were cleaned up using AxyPrep Mag PCR Clean-up (Axygen), validated using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), and quantified by Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA, USA).

tag: disease

value: Thyroid cancer

value: Cal-62 cells


title: 14-125-DG, 2N, ChP

description: Library name: 14-125-DG


title: 16-206-CA3, Ts65Dn, ChP

description: Library name: 16-206-CA3

value: Ts65Dn Hippocampus

value: CA3 pyramidal Neurons


title: 17-03-CA3, Ts65Dn, ChP

description: Library name: 17-03-CA3


title: 15-36-CA3, Ts65Dn, ChP

description: Library name: 15-36-CA3


title: km, wildtype, replicate 1

description: 10x Genomics

value: wt


title: V2-KO-24h 3

value: treatment for 24h


title: Vdac2-Bak1-dKO-24h 1


title: Day0_Gata2 rep3

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

institute: University clinics Freiburg

description: Library name: S26

data_processing:
Low-quality reads and adapter sequences were trimmed with Trimmomatic  (v0.38), employing the following parameters: HEADCROP:3 TRAILING:10 MINLEN:25
Alignment and quantification was done using STAR  (v2.5.2b)
Assembly: mm10
Supplementary files format and content: tab-delimited text file including raw read count per gene for each sample

source_name: Bone marrow

extract_protocol:
RNA was extracted from BM-derived lineage marker negative cells with the RNeasy Micro kit (Qiagen).
Sequencing libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina) or SMARTer Ultra Low RNA kit (Clontech) for illumina sequencing

value: Bone marrow

value: LSK cells


title: Cal-62 cells, NSUN2 knockout 49, replication 2


title: Vdac2-Bak1-dKO-24h 2


title: Cal-62 cells, NSUN2 knockout 49, replication 1


title: Day0_Gata2 rep2

description: Library name: S25


title: V2-KO-24h 1


title: 15-245-CA3, Ts65Dn, ChP

description: Library name: 15-245-CA3


title: Apaf1-KO-24h 2

value: IFNg treatment for 24h


title: Apaf1-KO-24h 1


title: Apaf1-KO-24h 3


title: V2-KO-24h 2


title: Day0_Gata2 rep1

description: Library name: S24


title: Cal-62 cells, NSUN2 knockout 50, replication 1


title: Cal-62 cells, NSUN2 knockout control, replication 4


title: Day0_WT rep2

description: Library name: S23


title: Bak1-KO-24h 3


title: 15-140-CA3, Ts65Dn, ChP

description: Library name: 15-140-CA3


title: Bak1-KO-24h 1


title: 16-90-CA3, 2N, ChP

description: Library name: 16-90-CA3

value: Disomic Hippocampus


title: 15-199-CA3, Ts65Dn, ChP

description: Library name: 15-199-CA3

value: ChP


title: Cal-62 cells, NSUN2 knockout control, replication 1


title: Day2_WT rep3

description: Library name: S5


title: 16-273-CA3, 2N, ChP

description: Library name: 16-273-CA3


title: Cal-62 cells, NSUN2 knockout control, replication 3


title: Bak1-KO-24h 2


title: 14-90-CA3, Ts65Dn, ChP

description: Library name: 14-90-CA3


title: Vdac2-Apaf1-dKO-0h 3

value: no treatment


title: WT-24h 2


title: Day0_WT rep1

description: Library name: S22


title: WT-24h 3


title: Cal-62 cells, NSUN2 knockout control, replication 2


title: MCF7 ETOH FOXA1 CUT&RUN

city: Aurora

first: Kiran

last: Vinod Paul

institute: University of Colorado-Anschutz medical campus

description: triplicates

data_processing:
Library strategy: CUT&RUN
Adaptrer trimming was done for raw fastq files cutadapt
Alignment to the reference genome was done using Bowtie2
The aligned bam files were indexed and sorted using samtools
The wig files with the peak tags were generated from the sorted bam files
Genome_build: GRCh38
Supplementary_files_format_and_content: wig

source_name: Breast cancer cell line

growth_protocol: Cells were estrogen withdrawn for 72 hours in MEM phenol-free media supplemented with 10% DCC FBS and 2mM glutagro

extract_protocol:
CUT&RUN was performed according to the protocol as described (Skene and Henikoff, 2017).
CUT&RUN libraries were prepared for sequencing using standard Illumina protocols at the University of Colorado Denver Genomics and Microarray Core facility.

treatment_protocol: Cells were treated with either ETOH (vehicle control) or 10^-10M E2 (estradiol) for one hour. Each sample was ran in triplicates.

value: ETOH (vehicle control)

value: Breast cancer cell line


title: Day2_WT rep2

description: Library name: S4


title: MCF7 E2 FOXA1 CUT&RUN

description: triplicates

value: E2 (10^-10M estradiol)


title: Day2_Gata2 rep2

description: Library name: S3


title: 15-336-CA3, 2N, ChP

description: Library name: 15-336-CA3


title: Day2_Gata2 rep1

description: Library name: S2


title: 15-334-CA3, 2N, ChP

description: Library name: 15-334-CA3


title: MCF7 E2 ERα CUT&RUN

description: triplicates


title: 15-296-CA3, 2N, ChP

description: Library name: 15-296-CA3


title: MCF7 ETOH ERα CUT&RUN

description: triplicates


title: 15-269-CA3, 2N, ChP

description: Library name: 15-269-CA3


title: Vdac2-Apaf1-dKO-0h 2


title: OCI-AML3 FLT3-ITD 100 nM FHD-286 2

city: Houston

first: Xiaoping

last: Su

state: Texas

address: 7300 Brompton St, Apt 5633

institute: MD Anderson Cancer Center

description: Library name: KBr_OCIFLT3_ITD_100FHD_2

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw data FASTQ files were generated by standard illumina base calling pipeline. Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, Reads were aligned to hg38 reference genome using STAR with default parameters
STAR was used to generate the "raw count" from an aligned bam againt transcript file
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each annotated gene for each sample

growth_protocol: AML OCI-AML3 and OCI-AML3-FLT3-ITD cells were cultured in 20% FBS containing RPMI media.

extract_protocol:
Total RNA was isolated with a kit from Ambion, Inc. The RNA was DNAse I treated to eliminate genomic DNA, then the purified RNA was utilized to make libraries for next generation sequencing.
Bulk RNA Libraries were constructed following standard Illumina protocols for RNA sequencing in a sequencing and microarray core facility. Indexed cDNA libraries were minimally PCR amplified, pooled and sequenced.

treatment_protocol: AML cells were treated with FHD-286 (100 nM) for 16 hours at 37°C and harvested into RNA lysis buffer. Lysed cells were frozen at -80°C until they were processed for total RNA.

value: cell line


title: PD1neg CD8+ T cells from Vdac2 KO B16OVA tumor3

data_processing:
Adapter sequences were removed using cutadapt v.1.9
and aligned them to the mouse genome mm10 (GRCm38_68 from Sanger; ftp://ftp-mouse.sanger.ac.uk/ref/GRCm38_68.fa) using the Burrows–Wheeler algorithm32 (version 0.5.9-r26-dev, default parameter)
duplicated reads were then marked with Picard (version 1.65 (1160)) and only non-duplicated reads were kept, using samtools (parameter ‘-q 1 -F 1024’ version 0.1.18 (r982:295))
After adjustment using the Tn5 shift (by which reads were offset by +4 bp for the sense strand and −5 bp for the antisense strand), we separated reads into nucleosome-free, mononucleosome, dinucleosome and trinucleosome by fragment size
performed peak-calling for nucleosome-free reads using MACS2 (version 2.1.0.20150603, default parameters with ‘–extsize 200 –nomodel’, merged by bedtools if within 100 bp) for individual samples
Assembly: mm10
Supplementary files format and content: Consensus peaks and fragment counts for all samples

source_name: tumor

growth_protocol: Cells were expanded by culture with RPMI-1640 medium ( 10% FBS), then inject into C57BL/6 mice through subcutaneously injection (1 million cells per mouse).

extract_protocol:
Cells were lysed in 50 μl ATAC-seq lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630 detergent) on ice for 10 min. Resulting nuclei were pelleted at 500g for 10 min at 4 °C. Supernatant was carefully removed with a pipette and discarded. The pellet was resuspended in 50 μl transposase reaction mix (25 μl 2 × TD buffer, 22.5 μl nuclease-free water, 2.5 μl transposase) and incubated for 30 min at 37 °C. After the reaction, the DNA was cleaned up using the Qiagen MinElute kit
The barcoding reaction was run using the NEBNext HiFi kit on the basis of the manufacturer’s instructions and amplified for five cycles

treatment_protocol: Mice were sac'd at day 14 after tumor injection. CD8+ T cells were harvested from tumor tissues using a cell sorter.

value: tumor

value: Primary CD8+ T cells

value: Wild-type

value: PD1– CD8+ T cells sort-purified


title: 14-125-CA3, 2N, ChP

description: Library name: 14-125-CA3

value: CA3 pyramidal Neurons


title: WT-24h 1

extract_protocol: Total RNA samples were prepared according to the prototol of Rneasy Micro kit from Qiagen,


title: OCI-AML3 FLT3-ITD 100 nM FHD-286 1

description: Library name: KBr_OCIFLT3_ITD_100FHD_1


title: 17-03-CA1, TS, ChP

description: Library name: 17-03-CA1

value: Ts65Dn Hippocampus

value: CA1 pyramidal Neurons


title: PD1neg CD8+ T cells from Vdac2 KO B16OVA tumor2


title: OCI-AML3-FLT3-ITD Control 3

description: Library name: KBr_OCIFLT3_ITD_0_3

value: Control


title: 16-272-CA1, TS, ChP

description: Library name: 16-272-CA1


title: PD1neg CD8+ T cells from Vdac2 KO B16OVA tumor1


title: OCI-AML3-FLT3-ITD Control 2

description: Library name: KBr_OCIFLT3_ITD_0_2


title: 16-206-CA1, TS, ChP

description: Library name: 16-206-CA1


title: Day2_WT rep1

description: Library name: S1

value: Bone marrow

value: LSK cells


title: PD1neg CD8+ T cells from WT B16OVA tumor4


title: PD1neg CD8+ T cells from Vdac2 KO B16OVA tumor4


title: V2-KO-0h 3


title: Vdac2-Bak1-dKO-0h 1


title: OCI-AML3-FLT3-ITD Control 1

description: Library name: KBr_OCIFLT3_ITD_0_1


title: Vdac2-Bak1-dKO-0h 2


title: Apaf1-KO-0h 2


title: 15-36-CA1, TS, ChP

description: Library name: 15-36-CA1


title: PD1neg CD8+ T cells from WT B16OVA tumor3


title: V2-KO-0h 2


title: Apaf1-KO-0h 1


title: Bak1-KO-0h 3


title: Vdac2-Apaf1-dKO-0h 1


title: Apaf1-KO-0h 3


title: V2-KO-0h 1


title: OCI-AML3 100 nM FHD-286 2

description: Library name: KBr_OCIAML3_100FHD_2


title: OCI-AML3 100 nM FHD-286 3

description: Library name: KBr_OCIAML3_100FHD_3


title: 15-199-CA1, TS, ChP

description: Library name: 15-199-CA1


title: OCI-AML3 100 nM FHD-286 1

description: Library name: KBr_OCIAML3_100FHD_1


title: PD1neg CD8+ T cells from WT B16OVA tumor1


title: Vdac2-Bak1-dKO-0h 3


title: OCI-AML3 Control 3

description: Library name: KBr_OCIAML3_0_3


title: Bak1-KO-0h 2


title: PD1pos CD8+ T cells from Vdac2 KO B16OVA tumor4

value: PD1+ CD8+ T cells sort-purified


title: PD1neg CD8+ T cells from WT B16OVA tumor2


title: WT-0h 3


title: Bak1-KO-0h 1


title: PD1pos CD8+ T cells from Vdac2 KO B16OVA tumor3


title: 15-245-CA1, TS, ChP

description: Library name: 15-245-CA1

value: ChP


title: OCI-AML3 Control 2

description: Library name: KBr_OCIAML3_0_2


title: 15-140-CA1, TS, ChP

description: Library name: 15-140-CA1


title: OCI-AML3 Control 1

description: Library name: KBr_OCIAML3_0_1


title: 16-90-CA1, 2N, ChP

description: Library name: 16-90-CA1

value: Disomic Hippocampus


title: PD1pos CD8+ T cells from Vdac2 KO B16OVA tumor2


title: Rag2KO-hCSF1KI-AppSAA 7

city: Rotselaar

first: Daan

last: Moechars

address: Catharinalaan 43

country: Belgium

institute: KULeuven

description: Library name: SAA_7

data_processing:
Reads were aligned against a combined mus musculus (mm10) and homo sapiens (GRCh38) database using STAR (v.2.7.11a), quality checked using FASTQC (v.0.11.9) and counted using featureCounts (v.2.0.1). Messenger RNAs with fewer than 10 counts in at least 5 samples were discarded.
Assembly: combined database with mm10 and GRCh38
Supplementary files format and content: count matrix in csv format

source_name: stem cell derived microglia

growth_protocol: H9 embryonic stem cell derived microglia were differentiated following the MIGRATE protocol (Fattorelli et al. 2021 Nature Protocols) and xenotransplanted into the brains of AppSAA or AppHu mice at postnatal day 4.

extract_protocol:
At 6 months of age the human microglia were extracted from the mouse brain using the Neural Dissociation Kit (P; Miltenyi, 130-092-628) following manufacturer's instructions. After myelin removal using 30% Percoll, the cell pellets were washed (DPBS with 2% FBS & 2mM EDTA) and blocked with FcR blocking solution (1/10; Milteny, 130-092-575) and subsequently stained with the viability dye eFluor780 (1/1000; Thermo Fisher 65-0865-14) and the antibodies anti-CD11b (1/50; Miltenyi 130-113-806), anti-human CD45 (1/50; BD Bioscience 555485) and anti-mouse CD45 (1/200; BD Bioscience 563890). Human microglia (defined as CD11b positive and human CD45 positive)  were sorted using the Miltenyi MACS Quant Tyto cell sorter, pelleted and stored at -80C until further processing. RNA extraction was performed using the Qiagen RNeasy Mini kit (Qiagen 74104) according to the manufacturer's protocol. Extracted RNA was eluted in 45ul of RNAse-free water and stored at -80C.
RNA concentration, purity and integrity were determined using the Nanodrop ND-8000 and Bioanalyzer 2100 and full length cDNA was created using 1ng of total RNA as input for the SMART-Seq HT PLUS protocol tusing a 1-step RT-PCR (Takara Bio; version 011921). Next, 4ng of purified double-stranded cDNA was enzymatically fragmented and stem-loop adapters were ligated. Next, libraries were amplified and indexed, generating Illumina-compatible libraries with unique dual identifiers (UDIs) following manufacturer's protocol. Each sample sequence library was pooled equimolar and sequenced on the AVITI 2x75 Cloudbreak High, single read (101-8-8-0).

value: stem cell derived microglia

value: microglia


title: PD1pos CD8+ T cells from WT B16OVA tumor4


title: PD1pos CD8+ T cells from Vdac2 KO B16OVA tumor1


title: PD1pos CD8+ T cells from WT B16OVA tumor3


title: 15-336-CA1, 2N, ChP

description: Library name: 15-336-CA1


title: 16-273-CA1, 2N, ChP

description: Library name: 16-273-CA1


title: Rag2KO-hCSF1KI-AppSAA 8

description: Library name: SAA_8


title: 15-334-CA1, 2N, ChP

description: Library name: 15-334-CA1


title: WT-0h 2

data_processing: Probe signals were quantile normalized and summarized by the RMA algorithm using the Affymetrix Expression Console software v1.1

value: no treatment


title: sgVdac2 + sgSting1-24h 3

source_name: B16-OVA-Cas9-sgVdac2 + Sting1

value: B16-OVA-Cas9-sgVdac2 + Sting1

value: IFNg treatment for 24h


title: sgNTC + sgSting1-24h 3

source_name: B16-OVA-Cas9-sgNTC + Sting1

value: B16-OVA-Cas9-sgNTC + Sting1


title: 14-90-CA1, TS, ChP

description: Library name: 14-90-CA1

source_name: Ts65Dn Hippocampus


title: sgVdac2 + sgSting1-24h 2


title: 15-296-CA1, 2N, ChP

description: Library name: 15-296-CA1


title: PD1pos CD8+ T cells from WT B16OVA tumor1

value: tumor

value: Primary CD8+ T cells

value: Wild-type


title: B16OVAVdac2KO4

growth_protocol: Cells were expanded by culture with RPMI-1640 medium (10% FBS), then inject into C57BL/6 mice through subcutaneously injection (1 million cells per mouse).

treatment_protocol: Mice were sac'd at day 15 after tumor injection. Ametrine+ tumor cells were harvested from tumor tissues using a cell sorter.

value: B16OVA tumor

value: tumor cell

value: VDAC2 KO

value: no chronic IFNg stimulation


title: WT-0h 1


title: Rag2KO-hCSF1KI-AppKI 8

description: Library name: KI_8


title: 14-125-CA1, 2N, ChP

description: Library name: 14-125-CA1

value: CA1 pyramidal Neurons


title: 15-269-CA1, 2N, ChP

description: Library name: 15-269-CA1


title: Rag2KO-hCSF1KI-AppSAA 6

description: Library name: SAA_6


title: 15-198-CA1, TS, ChP

description: Library name: 15-198-CA1

value: Ts65Dn Hippocampus


title: Rag2KO-hCSF1KI-AppKI 7

description: Library name: KI_7


title: B16OVAVdac2KO2


title: Rag2KO-hCSF1KI-AppSAA 4

description: Library name: SAA_4


title: 17-21-DG, 2N, ChN

description: Library name: 17-21-DG

value: DG granule cells

value: ChN


title: B16OVAVdac2KO1


title: Rag2KO-hCSF1KI-AppKI 6

description: Library name: KI_6

value: stem cell derived microglia


title: 17-56-DG, 2N, ChN

description: Library name: 17-56-DG

value: Disomic Hippocampus


title: B16OVAVdac2KO3


title: Rag2KO-hCSF1KI-AppSAA 5

description: Library name: SAA_5

value: microglia


title: Rag2KO-hCSF1KI-AppKI 4

description: Library name: KI_4


title: Rag2KO-hCSF1KI-AppKI 3

description: Library name: KI_3


title: 17-172-DG, 2N, ChN

description: Library name: 17-172-DG


title: B16OVANTC4

value: WT


title: 17-154-DG, 2N, ChN

description: Library name: 17-154-DG


title: sgNTC + sgSting1-24h 2

value: IFNg treatment for 24h


title: sgNTC + sgSting1-24h 1

value: B16-OVA-Cas9-sgNTC + Sting1


title: B16OVANTC3

value: tumor


title: N9

type: genomic

city: Palo Alto

first: Takaya

last: Ishii

state: California

address: 3165 PORTER DRIVE

institute: Stanford University

hyb_protocol: Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: The arrays were scanned with the Illumina iScan platform.

data_processing: RnBeads Package in R environment (v4.3.1)

label: Cy5 and Cy3

source_name: brain

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from brain tissue using the MasterPure DNA extraction kit (MCD85201, Epicentre, Madison, WI, USA). DNA quality was assessed using NanoDrop spectrometry (Q32850, ThermoFisher Scientific, Waltham, MA, USA) and quantification was completed using the Qubit dsDNA Broad Range Assay Kit.

value: brain

tag: disease state

value: non-POD

tag: Sex

value: Male


title: sgVdac2 + sgSting1-24h 1

first: Hongbo

institute: St Jude Children's Research Hospital

tag: cell type

value: B16-OVA-Cas9-sgVdac2 + Sting1


title: sgVdac2-24h 3


title: N8

tag: tissue

value: Female


title: 15-147-DG, 2N, ChN

state: New York

description: Library name: 15-147-DG


title: sgVdac2-24h 2


title: B16OVANTC2

value: B16OVA tumor

value: tumor cell

value: no chronic IFNg stimulation


title: sgNTC-24h 2


title: sgVdac2-24h 1


title: sgNTC-24h 1


title: B16OVANTC1


title: 15-145-DG, 2N, ChN

description: Library name: 15-145-DG

value: DG granule cells


title: N7


title: 17-192-DG, TS, ChN

description: Library name: 17-192-DG

value: Ts65Dn Hippocampus

value: ChN


title: N6


title: B16OVAIFNgVdac2KO4

value: VDAC2 KO

value: with chronic IFNg stimulation


title: B16OVAIFNgVdac2KO3


title: B16OVAIFNgVdac2KO2


title: 17-157-DG, TS, ChN

description: Library name: 17-157-DG


title: sgVdac2 + sgSting1-0h 2

value: no treatment


title: sgVdac2 + sgSting1-0h 3


title: N4


title: 17-153-DG, TS, ChN

description: Library name: 17-153-DG


title: N2


title: B16OVAIFNgVdac2KO1


title: N3


title: B16OVAIFNgNTC4

value: WT


title: 16-490-DG, TS, ChN

description: Library name: 16-490-DG


title: sgVdac2 + sgSting1-0h 1


title: sgNTC + sgSting1-0h 3

value: B16-OVA-Cas9-sgNTC + Sting1


title: N1


title: B16OVAIFNgNTC3

value: tumor


title: N5

value: brain


title: 17-173-DG, TS, ChN

description: Library name: 17-173-DG


title: B16OVAIFNgNTC2


title: sgNTC + sgSting1-0h 1


title: D9

value: POD


title: 17-56-CA3, 2N, ChN

description: Library name: 17-56-CA3

value: Disomic Hippocampus

value: CA3 pyramidal Neurons


title: B16OVAIFNgNTC1


title: 17-21-CA3, 2N, ChN

description: Library name: 17-21-CA3


title: 17-172-CA3, 2N, ChN

description: Library name: 17-172-CA3


title: D8

value: Female


title: sgNTC + sgSting1-0h 2


title: sgVdac2-0h 1


title: Vdac2KO-2-VDJ

description: CD45+ immune cells and tumor cells from B16-OVA-Cas9-sgVdac2 tumors (TCR)

data_processing:
The Cell Ranger 6.0 Single-Cell Software Suite (10x Genomics) was implemented to process the raw sequencing data from the Illumina HiSeq run.
Assembly: mm10
Supplementary files format and content: cell ranger count matrix for single cells in each sample for scRNAseq and filtered contig annotations for scTCR-seq

source_name: Tumor

growth_protocol: B16-OVA-Cas9-sgNTC/Vdac2 tumor cells were injected subcutaneously in C57BL/6 mice, mice were sacrificed at day 14, and then tumors were isolated

extract_protocol:
CD45+ immune cells and tumor cells were  loaded onto  the Chromium Controller according to their respective cell counts to target 9000 single cell GEMs (gel beads in emulsion) per sample.
Libraries were prepared using the Chromium Single Cell 5’ v2 Library and Gel Bead Kit (10x Genomics)

treatment_protocol: CD45+ immune cells and tumor cells from B16-OVA-Cas9-sgNTC/Vdac2 tumors at day 14 after tumor inoculation in C57BL/6 mice

value: Tumor

value: B16-OVA-Cas9 melanoma

value: CD45+ immune cells and B16-OVA cells


title: D7


title: 16-357-DG, TS, ChN

description: Library name: 16-357-DG

value: DG granule cells


title: sgVdac2-0h 3


title: sgVdac2-0h 2


title: D6

value: Male


title: Vdac2KO-1-VDJ

value: CD45+ immune cells and tumor cells from B16-OVA-Cas9-sgVdac2 tumors (TCR)


title: 17-154-CA3, 2N, ChN

description: Library name: 17-154-CA3

value: ChN


title: sgNTC-0h 2


title: 15-147-CA3, 2N, ChN

description: Library name: 15-147-CA3


title: NTC-2-VDJ

description: CD45+ immune cells and tumor cells from B16-OVA-Cas9-sgNTC tumors (TCR)

value: NTC


title: D5


title: 15-145-CA3, TS, ChN

description: Library name: 15-145-CA3

value: Ts65Dn Hippocampus


title: NTC-1-VDJ

value: CD45+ immune cells and tumor cells from B16-OVA-Cas9-sgNTC tumors (TCR)


title: Vdac2KO-2-GEX

description: CD45+ immune cells and tumor cells from B16-OVA-Cas9-sgVdac2 tumors (gene expression)


title: sgNTC-0h 1

value: no treatment


title: 17-192-CA3, TS, ChN

description: Library name: 17-192-CA3


title: sgNTC-0h 3


title: sgNTC-24h 3

value: IFNg treatment for 24h


title: KO_16h 4

value: IFNg treatment for 16h


title: D3

value: brain

value: POD


title: Vdac2KO-1-GEX

value: CD45+ immune cells and tumor cells from B16-OVA-Cas9-sgVdac2 tumors (gene expression)


title: D2


title: 17-157-CA3, TS, ChN

description: Library name: 17-157-CA3

value: CA3 pyramidal Neurons


title: KO_16h 2


title: D1

value: Female


title: NTC-2-GEX

description: CD45+ immune cells and tumor cells from B16-OVA-Cas9-sgNTC tumors (gene expression)

value: Tumor

value: B16-OVA-Cas9 melanoma


title: 17-153-CA3, TS, ChN

description: Library name: 17-153-CA3


title: NTC-1-GEX

value: CD45+ immune cells and B16-OVA cells

value: CD45+ immune cells and tumor cells from B16-OVA-Cas9-sgNTC tumors (gene expression)


title: 16-490-CA3, TS, ChN

description: Library name: 16-490-CA3


title: D4

value: Male


title: CAGE_set1∆set2∆_Replicate_2

city: Bethesda

first: Poonam

last: Poonia

state: MD

address: 6 Center Drive, Bldg 6, Room 240

department: NICHD

institute: NIH

data_processing:
For ribo-seq/RNA-Seq samples, Fastq records are trimmed with fastxtoolkit (version 0.0.14) to remove adapters sequences. rRNA sequence was removed with Bowtie2 (version 2-2.3.5.1) then mapped to yeast genome (sacCer3) with HISAT2 (version 2.1.1). Perfect reads were extracted with samtools (version 1.9) for downstream analysis. Normalized wiggle files and reads counts are generated with RiboSeq tools (https://github.com/hzhanghenry/RiboProR). For RNA-seq, the same protocol mentioned above for ribo-seq analysis was followed.
The sequenced CAGE reads of each sample were aligned to the reference genome of S. cerevisiae S288c (Assembly version: sacCer3) using HISAT2. CAGE reads mapped to rRNA genes were identified using rRNAdust (http://fantom.gsc.riken.jp/5/sstar/Protocols:rRNAdust), and were excluded from subsequent TSS analyses. CAGE reads with a mapping quality score (MAPQ) > 20 were considered uniquely mapped reads and were used for subsequent analyses. CAGE signals of biological replicates were then merged as a single sample. The transcription abundance of each TSS was quantified as the numbers of CAGE tags/reads supporting the TSS per million mapped reads (TPM). For RNA-Seq samples in parallel with CAGE-Seq, Fastq files after passing the QC and the adapter content check they were mapped to yeast genome (sacCer3) with STAR aligner, then PCR duplicates were removed by samtools.
For SMPAT-Seq: Sequencing reads from the Sequel instrument come in the form of continuous reads around a “rolling circle.” The insert is read over multiple passes in each direction. These insert passes are referred to as subreads. Multiple passes gives circular consensus sequences (CCS; also referred to as HiFi). CCS reads were demultiplexed to individual samples using the program “lima” (v2.6 or above) using the appropriate sample barcodes utilized during library construction. Samtools was used to convert demultiplexed sample CCS reads to fastq format for further processing and alignment. CCS read IDs are assigned to transcripts through the use of PacBio minimap2 to align reads to Ensembl Saccharomyces cerevisiae.R64-1-1 release 109. To determine and assign a poly(A) tail length to a CCS ID, reads are evaluated in either direction for a poly(A) stretch abutting the adapter utilized in library construction. A one base mismatch is tolerated for the adapter sequence pattern matching.
Assembly: sacCer3 and Saccharomyces cerevisiae.R64-1-1 release 109
Supplementary files format and content: Processed data (.txt) files contain raw reads for each file. For Ribo and parallel RNA-Sequencing, each file contains five columns providing: systemmatic gene name (Gene_ID), total reads (trx), reads in CDS, reads in 5' UTR and reads in 3' UTR. For RNA-sequencing, with spike-in normalization, processed file is a matrix with 6 columns providing: systemmatic gene name (Gene_ID), chromosome (Chr), start and end coordinates of genes (Start and End), strand information (Strand), length of the gene in basepairs (length) and multiple columns with read counts for different samples. For CAGE-sequencing the file contains three columns providing: Chromosome (Chr), Position of detected TSS (pos), strand information (strand) and 14 columns with read counts for different samples. For SMPAT-Seq, report.txt file contains multiple columns providing: Gene name (#Gene), Counts for each gene (Counts), mean poly(A) tail lengths (MeanPolyA), Standard error (STDERR), Minimum poly(A) tail length (Min), Quartile1 (Q1), median poly(A) tail lengths (Median), Quartile 3rd (Q3), Maximun poly(A) tail lengths (Max) and ListOfValues.

organism: Saccharomyces cerevisiae

source_name: BY4741 DG184 (MATa his3-∆1 leu2-∆0 ura3-∆0 met15-∆0 set2∆::KanMX4 set1∆::hphMX4)

growth_protocol: Yeast cells cells were cultured in SC medium at 30°C till OD600 ~0.6-0.8.

extract_protocol: CAGE libraries were constructed from 5µg of total RNA of each strain using the nAnT-iCAGE protocol (Murata et al. 2014) by K.K. DNAFORM of Japan. Briefly, first strand cDNAs were transcribed to the 5’ end of capped RNAs and attached to CAGE “barcode” tags. Each nAnT-iCAGE library used linkers with specific barcodes and was sequenced using Illumina NextSeq500 (single-end, 75-bp reads).

value: Yeast whole cells

value: No additional treatment


title: WT_16h 4

last: Chi

address: 262 Danny Thomas Place


title: H37Rv_Untreated@0+16h_b15_2

city: Seattle

first: Ethan

last: Bustad

state: WA

address: 1900 Ninth Ave.

department: CGIDR

institute: Seattle Children's Research Institute

description: Library name: Rv_T16_Set_B_1_R2_S48

data_processing:
Libraries were sequenced at the University of Washington Northwest Genomics Center with the Illumina NextSeq 500 High Output v2 kit (Illumina Inc., San Diego, CA). The sequencing run generated an average of 75 million base-pair paired-end raw read counts per library.
Read alignment and gene expression estimation was carried out using a custom processing pipeline in R that harnesses the Bowtie 2 utilities, which is publicly accessible at https://github.com/robertdouglasmorrison/DuffyTools, and https://github.com/robertdouglasmorrison/DuffyNGS.
TPM (transcripts per million) reads were calculated and used as the expression value reported in the second processed data file.
Assembly: Accession # AL123456.3 | Mycobacterium tuberculosis H37Rv complete genome
Supplementary files format and content: FrontiersInTb_INDIGO1Sherman_GEO_processed_reads.txt is a matrix of aligned read values representing the expression levels of each gene for each sample. Each row represents a different sample, and each column represents the expression of each gene. The first 6 columns give the metadata information associated with each sample.
Supplementary files format and content: FrontiersInTb_INDIGO1Sherman_GEO_processed_tpm.txt is a matrix of TPM values representing the expression levels of each gene for each sample. Each row represents a different sample, and each column represents the expression of each gene. The first 6 columns give the metadata information associated with each sample.

organism: Mycobacterium tuberculosis H37Rv

source_name: Bacteria

growth_protocol: Mycobacterium tuberculosis was routinely grown in Middlebrook 7H9 broth supplemented with 10% OADC and 0.05% Tyloxapol or 0.025% Tween80 (v/v) at 37°C on a rotary shaker.

extract_protocol:
Bacterial pellets suspended in TRIzol were transferred to a tube containing Lysing Matrix B (QBiogene) and vigorously shaken in a homogenizer. The mixture was centrifuged, and RNA was extracted from the supernatant with chloroform, followed by RNA precipitation by isopropanol and high-salt solution (0.8 M Na citrate, 1.2 M NaCl). Total RNA was purified using a RNeasy kit following the manufacturer’s recommendations (Qiagen). rRNA was depleted from samples using a custom-designed set of biotinylated oligonucleotides based on the method described in PMID: 32317317.
Illumina sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep kit for Illumina (New England Biolabs, Ipswich, MA) according to the manufacturer’s instructions, and using the AMPure XP reagent (Agencourt Bioscience Corporation, Beverly, MA) for size selection and cleanup of adaptor-ligated DNA. We used the NEBNext Multiplex Oligos for Illumina (Dual Index Primers Set 1) to barcode the libraries to enable sample multiplexing per sequencing run. The prepared libraries were quantified using the Kapa quantitative PCR (qPCR) quantification kit.

value: Bacteria

value: Wildtype

value: Untreated

tag: batch

value: 16 hours


title: CAGE_set1∆set2∆_Replicate_1


title: H37Rv_Untreated@0+16h_b15_1

description: Library name: Rv_T16_Set_B_1_R1__S47


title: 16-357-CA3, TS, ChN

description: Library name: 16-357-CA3

data_processing:
FastQ files were utilized for both conditions (2N and Ts) in all three cell types (CA1 PNs, CA3 PNs, DG GCs) to analyze data in parallel. FastQ files were generated and QC of the raw reads was performed by FastQC v0.11.9. The reads with adapter contamination/ low quality were trimmed using Trimmomatic 0.39.
Trimmed sequence reads were aligned to the reference  genome (GRCm39-mm10) using STAR Aligner. Quantification was performed on alignments using Picard (2.26.2) (2019) for different measures. Gene counts were extracted using RSEM. QC was performed on alignments using RSeQC (v5.0.2).
Downstream Analysis was performed using R with the gene counts obtained from the RSEM. Genes with over 0.1 counts per million were retained followed by TMM normalization.
Assembly: mm10
Supplementary files format and content: tab delimited text files with gene counts of all samples in a region per one file
Supplementary files format and content: tab delimited text files with gene counts of one sample per one file

extract_protocol:
Brain tissues were immediately flash frozen and 20 μm-thick tissue sections were cryostat cut (−25°C) in the coronal plane and mounted on polyethylene naphthalate (PEN) membrane slides. Sections were stained with rapid Nissl staining protocol. CA1 and CA3 PNs along with DG GCs were identified visually in the same section and isolated by laser capture microdissection (LCM). Approximately 6 rostral hippocampi sections were dissected by LCM (approximately -1.58 to -2.54 Bregma), with mean collections of ~950 CA1, ~750 CA3 and ~1175 DG neurons collected per brain before proceeding to RNA isolation and RNA-seq library preparation. RNA from each sample was purified using miRNeasy Micro kit (Qiagen) following the manufacturer's specifications, with a the optional DNase digestion step done twice sequentially.
The SMARTer Stranded Total RNA-Seq kit-Pico input Mammalian v3  was employed with unique indexes for each sample. To normalize input, CA1, CA3 and DG RNA concentrations were used to determine sample input, with average of ~3-3.75 ng RNA input utilized per sample. Samples were fragmented for 3.75 min, with 5 cycles for PCR1 and 14 cycles for PCR2. Samples were quantified using Tapestation D1000 DNA assay.  Samples were pooled in equimolar concentrations and assayed on an Illumina NovaSeq 6000 using a S1 100cycle flow cell (v1.5) by the NYUGSOM Genome Technology Center.

value: Ts65Dn Hippocampus

value: ChN


title: H37Rv_Untreated@0+16h_b14_5

description: Library name: Rv_T16_Set_A_2__R2_S34


title: H37Rv_Untreated@0+16h_b14_4

description: Library name: Rv_T16_Set_A_2__R1__S33


title: 17-56-CA1, 2N, ChN

description: Library name: 17-56-CA1

value: Disomic Hippocampus

value: CA1 pyramidal Neurons


title: CAGE_WT_SET1SET2_Replicate_2

source_name: BY4741 (MATa his3-∆1 leu2-∆0 ura3-∆0 met15-∆0)


title: 17-21-CA1, 2N, ChN

description: Library name: 17-21-CA1

source_name: Disomic Hippocampus


title: CAGE_WT_SET1SET2_Replicate_1


title: WT_16h 2

value: IFNg treatment for 16h


title: WT_16h 3


title: KO_16h 3


title: H37Rv_Untreated@0+16h_b14_3

description: Library name: Rv_T16_Set_A_1__R3_S27


title: CAGE_spt6-1004_Replicate_2

growth_protocol: Yeast cells cultured in SC medium at 30°C and shifted to 39°C for 90 min before harvesting.

value: 39°C for 90 min


title: KO_16h 1


title: 17-172-CA1, 2N, ChN

description: Library name: 17-172-CA1


title: WT_16h 1


title: KO_12h 4

value: IFNg treatment for 12h


title: H37Rv_Untreated@0+16h_b14_2

description: Library name: Rv_T16_Set_A_1__R2_S26


title: 17-154-CA1, 2N, ChN

description: Library name: 17-154-CA1


title: KO_12h 3


title: CAGE_spt6-1004_Replicate_1


title: H37Rv_Untreated@0+16h_b14_1

description: Library name: Rv_T16_Set_A_1__R1__S25


title: 15-147-CA1, 2N, ChN

description: Library name: 15-147-CA1


title: CAGE_WT_SPT6_Replicate_2


title: 17-173-CA3, TS, ChN

description: Library name: 17-173-CA3

value: CA3 pyramidal Neurons


title: H37Rv_Untreated@0+0h_b15_2

description: Library name: Rv_T0_Set_B_1_R2_S46

value: 0 hours


title: KO_12h 2


title: 15-145-CA1, 2N, ChN

description: Library name: 15-145-CA1


title: CAGE_WT_SPT6_Replicate_1


title: PD1pos CD8+ T cells from WT B16OVA tumor2

value: tumor

value: Primary CD8+ T cells

value: Wild-type

value: PD1+ CD8+ T cells sort-purified


title: H37Rv_Untreated@0+0h_b15_1

description: Library name: Rv_T0_Set_B_1_R1__S45

value: Bacteria


title: KO_12h 1


title: WT_12h 4


title: 17-173-CA1, TS, ChN

description: Library name: 17-173-CA1


title: H37Rv_Untreated@0+0h_b14_5

description: Library name: Rv_T0_Set_A_2__R2_S32

value: Wildtype


title: 17-157-CA1, TS, ChN

description: Library name: 17-157-CA1


title: CAGE_pab1-AID+NAA_Replicate_3

source_name: W303 PMY2 (MATa ade2-1 ura3-1 his3-11,15 trp1-1 leu2-3,112 can1-100 lys2::PADH1-OsTIR1-7myc-TADH1 pab1-AID (71-114)-9myc::hphNT1)

growth_protocol: Yeast cells were cultured in YPD at 30°C for one division and thereafter NAA was added to a final concentration of 1mM and growth was continued for 6h.

value: Yeast whole cells

value: 1mM 1-Napthaleneacetic acid (NAA)


title: CAGE_pab1-AID+NAA_Replicate_2


title: CAGE_pab1-AID+NAA_Replicate_1


title: H37Rv_Untreated@0+0h_b14_4

description: Library name: Rv_T0_Set_A_2__R1__S31

value: Untreated


title: WT_12h 3


title: H37Rv_Untreated@0+0h_b14_3

description: Library name: Rv_T0_Set_A_1__R3_S24


title: H37Rv_Untreated@0+0h_b14_2

description: Library name: Rv_T0_Set_A_1__R2_S23


title: 17-153-CA1, TS, ChN

description: Library name: 17-153-CA1

value: Ts65Dn Hippocampus

value: ChN


title: WT_12h 2


title: CAGE_WT+NAA_Replicate_2

source_name: W303 PMY1 (MATa ade2-1 ura3-1 his3-11,15 trp1-1 leu2-3,112 can1-100 lys2::PADH1-OsTIR1-7myc-TADH1)

growth_protocol: Yeast cells pre-cultured in liquid YPD medium at 30°C for 3h and thereafter NAA was added to a final concentration of 1mM and growth was continued for 6h.


title: H37Rv_Untreated@0+0h_b14_1

description: Library name: Rv_T0_Set_A_1__R1__S22


title: 16-357-CA1, TS, ChN

description: Library name: 16-357-CA1

value: CA1 pyramidal Neurons


title: WT_12h 1


title: CAGE_WT+NAA_Replicate_1


title: KPR172HC_Npy1r_KO_10

city: Darlinghurst

first: Leonard

last: Goldstein

address: 384 Victoria St

country: Australia

institute: Garvan Institute of Medical Research

description: Library name: FS42259888

data_processing:
RNA-seq data were processed using Nextflow pipeline nf-core/rnaseq (3.16.0). Briefly sequence reads were aligned to mouse reference genome assembly GRCm39 using STAR (2.7.10a) and expression counts estimated for Gencode basic gene annotation M35 using RSEM (1.3.1).
Assembly: Mus musculus (GRCm39)
Supplementary files format and content: Expression count matrix

source_name: pancreatic tumor tissue

growth_protocol: KPR172HC mice (Pdx1-Cre, LSL-KrasG12D/+, LSL-Trp53R172H/+; Hingorani et al. Cancer Cell 2005; Morton et al. PNAS 2009) were crossed with Npy1r-/- mice (Zhang et al. International Journal of Obesity 2010; Yan et al. Nature Communications 2021) to generate Pdx1-Cre, LSL-KrasG12D/+, LSL-Trp53R172H/+, Npy1r wildtype mice and Pdx1-Cre, LSL-KrasG12D/+, LSL-Trp53R172H/+, Npy1r-/- mice. All mice were bred at Australian BioResources (ABR), and genotyping was performed at Garvan Molecular Genetics (GMG) facility. Mice were kept in ventilated cages on a 12-hour light/dark cycle with 24-hour access to food and water. Mice with the appropriate genotypes were enrolled into the study at ~6 weeks of age and euthanized upon reaching study endpoint, which included development of signs of ascites, overnight weight loss of ≥ 10% or weight loss of ≥ 20% compared to the maximum body weight, hunching posture and signs of pain. Animal experiments were conducted in compliance with the Australian code of practice for the care and use of animals for scientific purposes and the Garvan/St. Vincent’s Animal Ethics committee (guidelines 19/06, 19/10, 19/13, 22/08, 22/09, 22/10).

extract_protocol:
RNA was extracted using the QIAGEN RNeasy Mini Kit (#74104) according to the manufacturer’s instructions.
Libraries were generated using the Illumina® Stranded mRNA Library Preparation Kit according to the manufacturer’s protocol

value: pancreatic tumor tissue

value: Pdx1-Cre; LSL-KrasG12D/+; LSL-Trp53R172H/+; Npy1r-/-


title: KO_8h 4

city: Memphis

value: IFNg treatment for 8h


title: H37Rv_Untreated@0+16h_b8_3

description: Library name: H37Rv_ND_RPE_T16_R3_S18

value: 16 hours


title: KO_8h 3


title: H37Rv_Untreated@0+16h_b8_2

description: Library name: H37Rv_ND_RPE_T16_R2_S17


title: KPR172HC_Npy1r_KO_9

description: Library name: FS42259887


title: CC39034059

city: Birmingham

first: Kaleen

middle: M

last: Lavin

state: Alabama

address: 908 20th Street South, Room 201-C

department: Medicine

institute: University of Alabama at Birmingham

data_processing:
FASTQs from different flow cells were combined for a given sample using NGmerge
alignment via TopHat
Assembly: ensembl Hg19
Supplementary files format and content: processed data are RPKM normalized read counts

source_name: skeletal muscle

extract_protocol:
TRIzol method. Homogenized samples were thawed on ice followed by the addition of 200µL of chloroform and thorough mixing, then a  5 min incubation at room temperature, followed by centrifugation for 15 min at 40ºC at 12000g.  The clear, aqueous top layer was collected and total RNA was precipitated by adding 100% cold ethanol to the extracted portion until a final concentration of 35% ethanol was achieved. Samples were then incubated for 30 minutes at 200C and centrifuged for 15 minutes at 40C at 16000g.  75% ethanol was used to wash the RNA pellet twice, and the RNA pellet was left to air-dry after which it was resuspended in 20µL of nuclease-free, ultra-pure diethlpyrocarbonate-treated water.
Libraries were created using a non-strand specific library of polyA RNA (Illumina TruSeq RNA Sample Prep Kit v2, Illumina, San Diego, CA)

value: skeletal muscle

tag: participant id

tag: diet

value: HiCarb

tag: timepoint

value: IP


title: KO_8h 1

tag: treatment


title: KPR172HC_Npy1r_KO_8

description: Library name: FS42259886

tag: genotype


title: WT_8h 4

tag: strain


title: KPR172HC_Npy1r_KO_7

description: Library name: FS42259885


title: H37Rv_Untreated@0+16h_b8_1

description: Library name: H37Rv_ND_RPE_T16_R1_S16

tag: time


title: CAGE_WT+NAA_Replicate_3


title: 16-490-CA1, TS, ChN

first: Stephen

institute: Research Foundation for Mental Hygiene

description: Library name: 16-490-CA1


title: CC39034058

value: Base


title: H37Rv_Untreated@0+0h_b8_3

description: Library name: H37Rv_ND_RPE_T0_R3_S15

value: 0 hours


title: WT_8h 3


title: CC39034057


title: H37Rv_Untreated@0+0h_b8_2

description: Library name: H37Rv_ND_RPE_T0_R2_S14

value: Bacteria


title: KPR172HC_Npy1r_KO_6

description: Library name: FS42259884


title: CC39034060


title: CC39034056


title: KPR172HC_Npy1r_KO_4

description: Library name: FS42259882


title: H37Rv_Untreated@0+0h_b8_1

description: Library name: H37Rv_ND_RPE_T0_R1_S13

value: Wildtype


title: CC39034055


title: KO_8h 2


title: WT_8h 1


title: H37Rv_Untreated@0+16h_b9_3

description: Library name: H37Rv_ND_PZA_T16_R3_S6


title: H37Rv_Untreated@0+16h_b9_2

description: Library name: H37Rv_ND_PZA_T16_R2_S5


title: KO_4h 3

value: IFNg treatment for 4h


title: KPR172HC_Npy1r_KO_2

description: Library name: FS42259880


title: CC39034053


title: H37Rv_Untreated@0+16h_b9_1

description: Library name: H37Rv_ND_PZA_T16_R1_S4


title: KO_4h 2


title: WT_8h 2


title: KPR172HC_Npy1r_KO_1

description: Library name: FS42259879


title: CC39034052


title: H37Rv_Untreated@0+0h_b9_3

description: Library name: H37Rv_ND_PZA_T0_R3_S3


title: KPR172HC_Npy1r_WT_10

description: Library name: FS42259868

value: Pdx1-Cre; LSL-KrasG12D/+; LSL-Trp53R172H/+; Npy1r WT


title: KPR172HC_Npy1r_KO_5

description: Library name: FS42259883


title: KO_4h 1


title: CC39034051


title: WT_4h 4


title: KPR172HC_Npy1r_WT_9

description: Library name: FS42259867


title: KPR172HC_Npy1r_KO_3

description: Library name: FS42259881


title: CC39034050


title: WT_4h 3


title: H37Rv_Untreated@0+0h_b9_1

description: Library name: H37Rv_ND_PZA_T0_R1_S1

value: Untreated


title: CC39034054


title: WT_4h 2


title: H37Rv_PZA@5mg/mL+16h_b9_3

description: Library name: H37Rv_5mg_ml_PZA_T16_R3_S9

value: PZA, 5mg/mL


title: KPR172HC_Npy1r_WT_8

description: Library name: FS42259866


title: KO_4h 4


title: KPR172HC_Npy1r_WT_7

description: Library name: FS42259865


title: CC39034048

value: LowCarb


title: H37Rv_PZA@5mg/mL+16h_b9_2

description: Library name: H37Rv_5mg_ml_PZA_T16_R2_S8


title: KPR172HC_Npy1r_WT_6

description: Library name: FS42259864


title: H37Rv_PZA@5mg/mL+16h_b9_1

description: Library name: H37Rv_5mg_ml_PZA_T16_R1_S7


title: CC39034046


title: H37Rv_PZA@2mg/mL+16h_b9_3

description: Library name: H37Rv_2mg_ml_PZA_T16_R3_S12

value: PZA, 2mg/mL


title: KPR172HC_Npy1r_WT_4

description: Library name: FS42259862

value: pancreatic tumor tissue


title: KO_0h 3

value: no treatment


title: WT_4h 1


title: H37Rv_PZA@2mg/mL+16h_b9_1

description: Library name: H37Rv_2mg_ml_PZA_T16_R1_S10


title: KO_0h 2


title: CC39034044


title: KPR172HC_Npy1r_WT_2

description: Library name: FS42259860


title: WT_0h 4


title: KPR172HC_Npy1r_WT_1

description: Library name: FS42259859


title: H37Rv_RPE@0.025ug/mL+16h_b8_2

description: Library name: H37Rv_0_025ug_ml_RPE_T16_R3_S21

value: RPE, 0.025ug/mL


title: CC39034043


title: H37Rv_RPE@0.025ug/mL+16h_b8_1

description: Library name: H37Rv_0_025ug_ml_RPE_T16_R1_S19

value: 16 hours


title: CC39034042

value: skeletal muscle


title: CC39034047


title: KO_0h 1


title: KPR172HC_Npy1r_WT_5

description: Library name: FS42259863


title: CC39034041

value: HiCarb


title: WT_0h 3


title: H37Rv_Untreated@0+16h_b7_3

description: Library name: H37RvNDT16R3_S6_R1


title: Whole lung, LNP injected, rep2

city: Shanghai

first: Jing

last: Yan

address: 800, Dongchuan road

institute: Shanghai Jiaotong University

description:
Library name: BLM+LNP2
10x Genomics

data_processing:
The Cell Ranger pipeline was used for processing all samples after sequencing (10× Genomics, V3.1.0). Raw sequencing data were demultiplexed and fastq files were generated using Illumina bcl2fastq software V 2.20. The scRNA-seq data were aligned to the mouse reference genome mm10 and row count matrices were imported to the R package Seurat V3.1.1. Cells were excluded due to the gene number (<500), UMI counts (<8000) and mitochondrial gene percentage (<25%). We used DoubleFinder package for individual samples to remove doublets and 47,129 cells were obtained after filtering. Clustering was then run using the functions FindVariableFeatures, FindNeighbors and Findclusters with resolution = 0.8 and dims = 1:20. The output UMAP graph were generated by DimPlot. Marker genes were identified using FindAllMarkers R package focusing on genes expressed by more than 10% of cells within a cluster and with a log fold change greater than 0.26. GO analysis was performed using the function FindMerkers. Merge function was used to create one merged Seurat object of BLM and CD5/βLNP treatment groups. This merged object was processed with differential gene expression and GO term analysis per cluster. Cells were manual annotated as a specific subset for a marker after qualitative evaluation of feature plot and violin plots. Clusters of macrophage, T cell, alveolar cell and fibroblast were re-clustered with the same strategy. We performed pseudotime analysis on the UMAP embeddings using Monocle 3. Slingshot analysis were using the function Slingshot R package, specifying starting cluster as “AT2” or “Tn cells”. We used the Nichenetr default pipeline to predict enriched ligand-receptor pairs signaling to macrophages. The regulatory potential of top 20 ligand-receptor pairs (showed top 13) was represented in a dot plot.
Assembly: Ensembl_v105_mus_musculus
Supplementary files format and content: Tab-separated valued files and matrix files

source_name: lung

extract_protocol:
The rinsed tissue was added to the dissociation solvent (0.35% collagenase IV5,2 mg/ml papain,In 120 Units/ml DNase I) and incubated at 37℃ in a water bath shaker (100rpm) for 20min.After centrifugation, cell precipitates were collected and the cells were suspended with 100ul 1×PBS(0.04% BSA) solution.Red blood cells and dead cells are then removed.
For scRNA-seq library preparation, cells were loaded onto the 10× Genomics Chromium instrument and 10× Genomics Chromium Single-Cell 3’kit V3 reagents were used according to the manufacturer’s protocols. The samples were pooled into libraries and sequenced on the Illumina NovaSeq 6000 at a minimum depth of 20,000 reads per cell.

value: lung

value: pulmonary cell

value: LNP


title: Whole lung, LNP injected, rep1

description:
Library name: BLM+LNP1
10x Genomics


title: CC39034045


title: H37Rv_PZA@2mg/mL+16h_b9_2

description: Library name: H37Rv_2mg_ml_PZA_T16_R2_S11

value: Bacteria


title: KPR172HC_Npy1r_WT_3

description: Library name: FS42259861


title: CC39034040

value: Base


title: sgVdac2OTI_4

source_name: B16-OVA-Cas9-sgVdac2 with OT-I CD8+ T cells treatment

growth_protocol: B16-OVA-Cas9-sgNTC/sgVdac2 tumor cells were cultured according to ATCC guideline.

value: B16-OVA-Cas9-sgVdac2 with OT-I CD8+T cell treatment


title: CC39034039


title: WT_0h 2


title: H37Rv_Untreated@0+16h_b7_1

description: Library name: H37RvNDT16R1_S4_R1

value: Wildtype


title: Whole lung, Saline injected, rep2

description:
Library name: BLM+Saline2
10x Genomics

value: Saline


title: CC39034038

value: IP


title: Whole lung, Saline injected, rep1

description:
Library name: BLM+Saline1
10x Genomics


title: H37Rv_Untreated@0+16h_b7_2

description: Library name: H37RvNDT16R2_S5_R1

value: Untreated


title: CC39034037

value: LowCarb


title: H37Rv_Untreated@0+0h_b7_3

description: Library name: H37RvNDT0R3_S3_R1

value: 0 hours


title: H37Rv_Untreated@0+0h_b7_2

description: Library name: H37RvNDT0R2_S2_R1


title: Eye, T cells, recipient mice 4, scRNAseq

first: Vijay

last: Nagarajan

state: Maryland

address: 10 Center Drive, 10/10N248

department: National Eye Institute

institute: National Institutes Of Health

description: 10x Genomics

data_processing:
Sequencing reads were demultiplexed and aligned using CellRanger (7.1.0) with the default parameters. The output matrix files were converted into a Seurat object for quality control and clustering. Standard scRNA-seq analysis (quality control, clustering, and marker gene detection) was performed using Seurat (v4.3.0)
Assembly: mm10
Supplementary files format and content: Filtered feature barcode matrix files in H5 format

source_name: Eye

growth_protocol: All animals were maintained under specific-pathogen-free conditions at NIH animal facility on standard chow and water ad libitum. Treatment and use of animals followed institutionally approved animal study protocol (ASP# NEI-688) and Animal Research Advisory Committee (ARAC) guidelines.

extract_protocol:
Fresh naive T cells sorted from donor mice and CD90.2 donor cells retrieved from the recipients’ eyes one week after intravitreal injection were collected for scRNA-seq. Donor T cells in the eyes retrieved from each of the four recipient mice were individually labeled with Anti-mouse TotalSeqB hashtags.
Strictly following the manufacturer’s protocols, we incubated individual samples with unique hashtags and sorting antibodies before FACS sorting. Viability of sorted cells were greater than 90%. The concentration of sorted single-cell suspensions was adjusted to 700–1200 cells/μl before loading the 10X chromium chip. Samples were processed with the Chromium Next GEM Single Cell 3’ reagent kit in the Chromium X platform following the standard protocol for 3’ Gene Expression assay (10X genomics). The gene expression and cell surface libraries were sequenced on Illumina NovaSeq 6000 platform.

value: Eye

value: 6-10 weeks old

value: T cells

value: CD90.1 congenic wildtype (WT) B10.RIII


title: CC39034036

value: skeletal muscle


title: Eye, Naïve T cells, donor mice

description: 10x Genomics

value: Tcra-/- R161H Foxp3GFP reporter mice


title: CC39034049

value: HiCarb


title: sgVdac2OTI_2


title: sgVdac2OTI_3


title: CC39034035


title: H37Rv_Untreated@0+0h_b7_1

description: Library name: H37RvNDT0R1_S1_R1


title: Eye, T cells, recipient mice 3, scRNAseq

description: 10x Genomics


title: H37Rv_PA824@3.2uM+16h_b7_3

description: Library name: H37Rv_3_2uM_PA824_T16_R3_S33_R1

value: 16 hours


title: H37Rv_Untreated@0+0h_b9_2

description: Library name: H37Rv_ND_PZA_T0_R2_S2

value: Bacteria


title: sgVdac2OTI_1


title: CC39034034

value: Base


title: sgNTC_OTI_4

source_name: B16-OVA-Cas9-sgNTC with OT-I CD8+ T cells treatment

value: B16-OVA-Cas9-sgNTC with OT-I CD8+T cell treatment


title: Eye, T cells, recipient mice 2, scRNAseq

description: 10x Genomics


title: KO_0h 4

value: no treatment


title: sgNTC_OTI_3


title: H37Rv_PA824@3.2uM+16h_b7_2

description: Library name: H37Rv_3_2uM_PA824_T16_R2_S32_R1

value: Wildtype


title: Eye, T cells, recipient mice 1, scRNAseq

description: 10x Genomics


title: CC39034033


title: H37Rv_PA824@3.2uM+16h_b7_1

description: Library name: H37Rv_3_2uM_PA824_T16_R1_S31_R1