title: Liver_ABT-263_11

city: Los Angeles

first: Ivan

middle: Alexander

last: Salladay-Perez

address: 615 Charles E Young Dr S

department: Department of Microbiology Immunology and Molecular Genetics

institute: University of California, Los Angeles

description:
Library name: sample11
11_Liver_ABT_S11_L008

data_processing:
Roughly 100 M high quality reads were sequenced per sample using a Novaseq x Plus (Illumina). Raw data in FASTAq format was filtered for adapter sequences or low-quality sequences using SOAPnuke. Reads were aligned to the mm10 reference genome using STAR.
Assembly: Aligned reads were processed using TopHat and a counts matrix was generated using FeatureCounts.
Supplementary files format and content: Raw reads were processed using the latest version of base R commands as of May 2025 (4.5.0)

growth_protocol: BMDMs used in experiments were derived from bone marrow extracted from the femurs of euthanized mice (6-12 weeks old male C57BL/6J) by mortar and pestle. Femurs were placed in the mortar and were washed with 70% ethanol to sterilize followed by two washes with complete RPMI (cRPMI; standard RPMI (Corning) supplemented with 10% fetal calf serum, penicillin-streptomycin solution (Corning), 1mM sodium pyruvate solution (Corning), 2 mM L-Glutamine solution (Corning), 10nM HEPES buffer (Corning), and 50μM 2-mercaptoethanol). After washing, 10 ml of cRPMI was added to the mortar and the femur bones were gently crushed. The resulting media was collected and filtered through a 70μm filter and placed in a conical tube. The filtered supernatant was centrifuged at 100 g (150 RCF) for 5 minutes. Cells were resuspended, counted and plated at a density of 3E6 cells/10 cm dish in 10 ml of macrophage growth media (cRPMI containing 25% M-CSF containing L929 conditioned media (made in house)). Cells were left to grow for 7 days to differentiate and were supplemented with 5 ml of macrophage growth media on day 5. On day 7, BMDMs (yielding 10-12x106 cells/10cm dish) were lifted off the plate using cold PBS containing 5mM EDTA. BMDMs were counted and replated in macrophage growth media overnight prior to experiments

extract_protocol:
Mouse BMDM cell-culture experiments, RNA was isolated using RNA STAT 60 (Amsbio) as per the manufacturer’s protocol. ~ 2000 ng of RNA was converted to complementary DNA using a High Capacity cDNA Reverse Transcription Kit (Applied Biosystems).
Mouse BMDM were lysed with RNA STAT 60 (Amsbio) and ~50 ng per uL of RNA was submitted to the UCLA’s Technology Center for Genomics & Bioinformatics (TCGB) core for library preparation and 2x100 paired-end sequencing.

treatment_protocol: On the day of experiments, macrophage growth media was replaced with cRPMI 6 hours prior to stimulation to remove M-CSF. M2 polarization was performed by stimulating macrophages with 10 ng/ml recombinant mouse IL-4 (Peprotech). For M1 polarization macrophages were stimulated with 100 ng/ml LPS (LPS EK-Ultrapure, Invivogen). To induce senescence, day 7 BMDMs were either irradiated (10 Gy) or treated with doxorubicin (Fisher) for 24 hours at 250 nM in 60% cRPMI: 40 MGM. DNA damaged cells were left in culture for 10 days and media components were replaced every 2-3 days. As a negative control, a mock irradiated or drug treated condition was cultured in parallel and required passing every 2-3 days. All senescent macrophage experiments were performed 10-13 days post DNA damage.

value: Liver

value: APOE*Leiden-CETP

tag: batch


title: OCSCC34, Post, CD3, TCR

status: Public on Feb 10 2026

type: SRA

city: Saint Louis

first: Sidharth

last: Puram

address: 660 Euclid Ave

country: USA

institute: Washington University in St Louis

description: Library name: OCSCC34_Post_CD3_TCR

library_source: transcriptomic single cell

data_processing:
FASTQ files were aligned to a pre-built human reference genome hg19 (10X Genomics, July 24, 2019) using CellRanger v3.1.0 (10X Genomics) 'count' command with default options.
VDJ librarires (prepared from the 5' Single Cell Librarires) were aligned to a pre-built human reference genome hg19 (10X Genomics, July 24, 2019) using CellRanger v3.1.0 (10X Genomics) 'vdj' command with default options.
Assembly: hg19
Supplementary files format and content: filtered_feature_bc_matrix.h5 files include raw cell x count matrix CellRanger ouptut for each Sample
Supplementary files format and content: all_contig_annotations.csv files include TCR clonotype information cell for each Sample
Supplementary_files_format_and_content: GSE301741_Seurat_Object_QCpass_137020cells_withMetaData.rds is a matrix and metadata object of all post-filtered high quality (QC passing) cells, created using Seurat (v5), with cell typing, TCR assignment, and subtypes as described in the accompanying citation.

molecule: polyA RNA

organism: Homo sapiens

source_name: Oral Cavity

extract_protocol:
Fresh biopsies  from primary tumor sites  were dissociated using a Human Tumor Dissociation Kit (Miltenyi Biotec #130-095-929) followed by ACK red blood cell lysis. The single-cell suspension was sorted via magnetic column using either human CD45 magnetic MicroBeads (Miltenyi) or human CD3 magnetic MicroBeads (Miltenyi).  The positive and negative cell fractions were then mixed in a 1:2 ratio of positive:negative fractions to enrich for malignant/stromal cells.
Samples were processed using either the Chromium Single Cell 3’ (V2 Chemistry) or 5' (V2) platform with a target of ∼10,000 cells (10x Genomics) following the manufacturer’s instructions. T-cell receptor VDJ l and were sequenced on Illumina NovaSeq machines with a target minimum read count of 0.5 billion per sample

treatment_protocol: Clinical trial protocol under which patients is published and available at Pubmed ID: 37683037

tag: tissue

value: Oral Cavity

tag: timepoint

value: Post

tag: library type

value: TCR

tag: cell type

tag: disease

value: HNSCC


title: Control_St_T1_A

city: Seattle

first: David

last: Wiener

state: Washington

department: School of Oceanography

institute: University of Washington

description:
Library name: Control_St_T1_A
Column name in AMsummary & TPsummary.csv:  Control_St_T1_A

library_source: transcriptomic

data_processing:
Sequence reads were trimmed using Trimmomatic 0.39, run in paired-end mode with the adaptor and other Illumina-specific sequences (ILLUMINACLIP) set to TruSeq3-PE.fa:2:30:10:1, leading and trailing quality thresholds of 25, a sliding window trimming approach (SLIDINGWINDOW) of 4:15, an average quality level (AVGQUAL) of 20, and a minimum length (MINLEN) of 60.
Paired-end reads were aligned with STAR v2.7.10b to the T. pseudonana genome (Thaps3, FilteredModels2) plus an additional “chromosome” containing an updated version of the ribosomal sequences or to a combined T. pseudonana -A. macleodii Te101.  Default parameters were used, with the maximum intron length limited to 500 nucleotides (‘–alignIntronMax 500’).
Reads per chromosome were calculated using the samtools idxstats command
Assigned to gene models using featureCounts
Assembly: T. pseudonana genome (Thaps3, FilteredModels2) & A. macleodii Te101 genome
Supplementary files format and content: AMsummary.csv and TPsummary.csv contain gene counts per gene model for each organism (A. macleodii and T. pseudonana).
Supplementary files format and content: ReadsPerChr.csv contains the number of reads aligned per chromosome for each treatment (Total RNA, PolyA selection, and Ribodepletion).

organism: Thalassiosira pseudonana

growth_protocol: T. pseudonana CCMP 1335 strain was maintained as a semicontinuous batch culture in 30ml L1+Si medium (NCMA) at 20°C with a 16:8h light cycle, under ~160µmol photons m−2 s−1. Before the experiments, diatom cells were acclimated to exponential growth after a minimum of three 1:10 dilutions and diluted in L1+Si medium to reach the designated growth phases before coculture. Growth was monitored by relative fluorescence units (RFU) using a fluorometer. In the exponential phase, cultures doubled in cell number approximately over 24 Hrs. Stationary phase cultures were defined as those sampled 7 days after the last doubling event when the culture reached ~800,000 cells/ml. Mid-exponential/Exponential cultures were defined as having undergone two doubling events before reaching stationary (~200,000 cells/ml). Early exponential phase cultures were defined as five doubling events before reaching stationary (~25,000 cells/ml).

extract_protocol:
Total RNA was extracted from 0.2 µm polycarbonate membrane filters using the Zymo Direct-zol RNA MiniPrep Plus kit for all samples.
For T. pseudonana transcriptome ribodepletion calibration, three samples obtained from exponentially growing cells were prepared: Total RNA, poly(A) selected with oligo dT-beads (Dynabeads mRNA DIRECT Kit, Life Technologies), and ribodepleted using a tailored Thalassiosira pseudonana riboPOOL following the manufacturer’s instructions. For Duo-RNA-seq, samples were prepared in triplicate for each time point and ribodepleted using the T.pseudonana riboPOOL combined with the Pan-Bacteria riboPOOL, with beads mixed in a 1:1 ratio. At this point, libraries were submitted for preparation, and sequencing to the Northwest Genomics Center (University of Washington) using a NextSeq (Illumina) platform.

treatment_protocol: For the coculture experiments, glycerol stocks of A. macleodii EP were streaked on marine agar plates (marine broth (MB) with 1.5% w/v agar) and grown at 25°C for 48 hours. Single colonies were grown overnight in Marine Broth with shaking at 25°C until an OD600 of ~0.5 was reached, measured using a NanoDrop One Microvolume UV-Vis Spectrophotometer. Cultures were then diluted 1:10 and allowed to double twice (~3:30 hours) before removing the media and washing twice with L1+Si. Finally, A. macleodii cells were added to the diatom culture to a ~40000 cells/ml concentration. All experiments were performed in L1+Si medium.

tag: cell line

tag: time

tag: treatment

value: Control


title: Control_Exp_T3_C

description:
Library name: Control_Exp_T3_C
Column name in AMsummary & TPsummary.csv:  Control_Exp_T3_C


title: Liver_ABT-263_9

state: CA

description:
Library name: sample9
9_Liver_ABT_S9_L008

organism: Mus musculus

source_name: Liver

tag: genotype


title: Liver_Veh_4

description:
Library name: sample4
4_Liver_Veh_S4_L008

value: HFHCD+Veh


title: LSCC20, Post, CD3, TCR

description: Library name: LSCC20_Post_CD3_TCR

source_name: Larynx

value: Larynx


title: LSCC20, Post, CD3, 5prime

description: Library name: LSCC20_Post_CD3_5prime


title: Control_Exp_T2_B

description:
Library name: Control_Exp_T2_B
Column name in AMsummary & TPsummary.csv:  Control_Exp_T2_B


title: LSCC20, Post, CD3, 3prime

description: Library name: LSCC20_Post_CD3_3prime


title: Control_Exp_T2_A

description:
Library name: Control_Exp_T2_A
Column name in AMsummary & TPsummary.csv:  Control_Exp_T2_A


title: Control_Exp_T1_C

description:
Library name: Control_Exp_T1_C
Column name in AMsummary & TPsummary.csv:  Control_Exp_T1_C


title: Control_Exp_T1_B

description:
Library name: Control_Exp_T1_B
Column name in AMsummary & TPsummary.csv:  Control_Exp_T1_B


title: OCSCC35, Post, CD3, TCR

description: Library name: OCSCC35_Post_CD3_TCR


title: OCSCC35, Pre, CD3, 5prime

description: Library name: OCSCC35_Pre_CD3_5prime

value: Pre


title: Sen_sg_Rosa26_12

description:
Library name: sample12
S-25-0849-12_S137_L006

data_processing:
Roughly 100 M high quality reads were sequenced per sample using a Novaseq x Plus (Illumina). Raw data in FASTAq format was filtered for adapter sequences or low-quality sequences using SOAPnuke. Reads were aligned to the mm10 reference genome using STAR.
Aligned reads were processed using TopHat and a counts matrix was generated using FeatureCounts.
Assembly: not provided
Supplementary files format and content: Raw reads were processed using the latest version of base R commands as of May 2025 (4.5.0)

source_name: Bone-marrow derived

value: Bone-marrow derived

value: Primary

value: Macrophage

value: senescent


title: OCSCC35, Post, CD3, 5prime

description: Library name: OCSCC35_Post_CD3_5prime


title: Liver_ABT-263_10

description:
Library name: sample10
10_Liver_ABT_S10_L008


title: OCSCC34, Pre, CD3, TCR

description: Library name: OCSCC34_Pre_CD3_TCR


title: Control_St_T2_C

description:
Library name: Control_St_T2_C
Column name in AMsummary & TPsummary.csv:  Control_St_T2_C


title: Sen_sg_Rosa26_11

description:
Library name: sample11
S-25-0849-11_S136_L006


title: Sen_sg_Rosa26_10

description:
Library name: sample10
S-25-0849-10_S135_L006


title: OPSCC41, Post, CD3, TCR

description: Library name: OPSCC41_Post_CD3_TCR

source_name: Oropharynx

value: Oropharynx


title: Liver_ABT-263_8

description:
Library name: sample8
8_Liver_ABT_S8_L008


title: Liver_ABT-263_7

description:
Library name: sample7
7_Liver_ABT_S7_L008


title: OPSCC41, Post, CD3, 5prime

description: Library name: OPSCC41_Post_CD3_5prime


title: OCSCC31, Pre, CD3, TCR

description: Library name: OCSCC31_Pre_CD3_TCR


title: OCSCC31, Pre, CD3, 5prime

description: Library name: OCSCC31_Pre_CD3_5prime


title: OCSCC34, Post, CD3, 5prime

description: Library name: OCSCC34_Post_CD3_5prime


title: Sen_sg_Cmpk2_7

description:
Library name: sample7
S-25-0849-07_S132_L006


title: OCSCC19, Post, CD3, 5prime

description: Library name: OCSCC19_Post_CD3_5prime


title: Liver_Veh_6

description:
Library name: sample6
6_Liver_Veh_S6_L008


title: Control_sg_Rosa26_6

description:
Library name: sample6
S-25-0849-06_S131_L006


title: OCSCC34, Pre, CD3, 5prime

description: Library name: OCSCC34_Pre_CD3_5prime


title: OCSCC13, Pre, CD45pos, 5prime

description: Library name: OCSCC13_Pre_CD45pos_5prime


title: Control_sg_Rosa26_5

description:
Library name: sample5
S-25-0849-05_S130_L006


title: OCSCC19, Post, CD3, TCR

description: Library name: OCSCC19_Post_CD3_TCR


title: Liver_Veh_5

description:
Library name: sample5
5_Liver_Veh_S5_L008


title: OCSCC13, Post, CD45pos, 5prime

description: Library name: OCSCC13_Post_CD45pos_5prime


title: OCSCC31, Post, CD3, TCR

description: Library name: OCSCC31_Post_CD3_TCR


title: Liver_Veh_3

description:
Library name: sample3
3_Liver_Veh_S3_L008


title: genomic_DNAmethylation_207179240127_R03C01

type: genomic

city: Vancouver

first: Wendy

last: Robinson

state: BC

address: 950 W 28th Ave

department: Medical Genetics

country: Canada

institute: University of British Columbia

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to beadchips (Infinium MethylationEPIC v1.0) using standard Illumina protocol.

scan_protocol: Arrays were imaged using a iSCAN using standard Illumina settings.

data_processing: Raw .idat files were read into R (v4.3.1). minfi preprocessNoob() and wateRmelon dasen() normalization.

label: Cy3 and Cy5

molecule: genomic DNA

source_name: placental chorionic villi

label_protocol: Standard Illumina protocol.

extract_protocol: Three ~0.4 cm3 samples of chorionic villi were taken from three distinct cotyledons (sites) from below the surface of the fetal-facing side of the placenta. Genomic DNA was extracted with the PerkinElmer Chemagic 360 System (PerkinElmer, USA) using a process based on the PerkinElmer chemagen M-PVA Magnetic Bead technology. Purified DNA from the three cotyledons was pooled in equal amounts then 500ng was bisulfite converted using the standard Illumina Protocol.

value: placental chorionic villi

tag: resourcescomposite

tag: socialpositioncomposite

tag: disadvantagecomposite

tag: Sex

value: XY

tag: ga

tag: syncytiotrophoblast

tag: cytotrophoblast

tag: stromal

tag: endothelial

tag: hofbauer

tag: nrbc

value: Plate 4


title: OCSCC31, Post, CD3, 5prime

description: Library name: OCSCC31_Post_CD3_5prime

tag: tissue

tag: timepoint

tag: library type

tag: cell type


title: OCSCC33, Post, CD3, TCR

description: Library name: OCSCC33_Post_CD3_TCR

tag: disease


title: OCSCC13, Post, CD45neg, 3prime

description: Library name: OCSCC13_Post_CD45neg_3prime


title: Liver_Veh_2

description:
Library name: sample2
2_Liver_Veh_S2_L008

value: Liver

tag: genotype

value: APOE*Leiden-CETP

tag: treatment

tag: batch


title: OCSCC33, Post, CD3, 5prime

description: Library name: OCSCC33_Post_CD3_5prime

value: Oral Cavity

value: Post


title: Liver_Veh_1

description:
Library name: sample1
1_Liver_Veh_S1_L008


title: aCD27, bio rep 3, GEX

city: Durham

last: Severson

state: North Carolina

address: 2301 Erwin Road

department: Department of Surgery

institute: Duke University Health System

description:
Library name: aCD27_3_GEX
GEX (5' library): read 1 contains 16 bp cell barcode and 10 bp UMI; read 2 contains cDNA transcripts

data_processing:
Using the CellRanger multi pipeline, raw reads were mapped to a custom reference constructed by supplementing the standard mouse reference genome (mm39) fasta and gtf files with human HER2 and CD27 genes. The resulting CellRanger outputs were concatenated into a single Seurat object in R v4.4.0 using Seurat v5.3.0.
Cells were filtered by UMIs detected (500 ≤ UMI ≤ 1500), genes expressed (200 ≤ Features ≤ 5000), and mitochondrial reads (mitochondrial cDNA ≤ 10%). This resulted in a single-cell expression matrix containing 77,135 cells. Cells were also initially filtered for doublets using scDblFinder v1.18.0.
Data were normalized using scTransform and integrated using RPCA integration to mitigate batch effects with Seurat. Normalized, filtered, and integrated single-cell transcriptomes were typed using Seurat-generated cluster marker genes (Wilcoxon test) and known immunologic markers.
To further mitigate doublet cells’ impact on downstream analysis, cells were filtered based on canonical immune type marker gene expression to exclude out-group markers. Specifically, macrophages and dendritic cells were filtered to remove any cells expressing B cell, T cell, or innate lymphoid markers. Similarly, T cells and innate lymphoid cells were filtered for unexpected marker expression. Mitotic cells were classified based on macrophage/dendritic or T cell markers; cells lacking either marker were designated mitotic, while cells expressing both markers were removed as presumed doublets. This filtering resulted in a robust dataset of 58,171 cells by 50,172 genes.
Assembly: mm39 supplemented with human CD27 and HER2 genes
Supplementary files format and content: counts.txt is the raw counts for final set of typed cells.
Supplementary files format and content: cell_assignment.txt is the annotated cells including type assignments, sample origin,  and experimental arm
Supplementary files format and content: mm39_supplemented_reference_seq.gtf contains the annotation utilized for building a CellRanger reference containing mm39 standard reference supplemented with CD27 and HER2 genes

molecule: total RNA

source_name: implanted tumor

growth_protocol: The MM3MG-HER2del16 cells were orthotopically implanted into the mammary fat pad of female 8-12 weeks old F1 offspring mice, by crossing between HuCD27-Tg with regular Balb/Cor Jh-Balb/C (1x106 cells/animal).

extract_protocol:
Tumors were minced with razor blade and then digested with dissociation media (RPMI media supplemented with collagenase, dispase II, DNase and Calcium chloride (5mM))for 30 minutes in 37oC using a rotating platform. Digested tumor cells were filtered with 40μm filter and counted using Countess 3 (Invitrogen). Resuspend the cells pass through filter to 10x106 cells/ml in 1% BSA/PBS; followed by staining with Live/Dead Far-Red (ThermoFisher) and FITC conjugated anti-mouse CD45 antibody (Biolegend) on ice for 20 minutes. CD45 positive live cells were sorted with Sony MA900 multiapplication cell sorter at the Duke Cancer Institute Flow Cytometry core. The sorted cells were resuspended in 45ul of 0.04% BSA/PBS, stained with trypan blue and counted with hemocytometer.
Cells (10,000) were used for GEM generation and barcoding, followed by the construction of V(D)J library and 5’ gene expression (GEX) libraries using the Chromium Next GEM single cells 5’ V2 (Dual Index; 10X Genomics) according to manufacturer’s protocol.

treatment_protocol: Vaccination was given by footpad injection of 20ul of AdHER2 (2x1011 vp/ml) into both footpad of mice, alongside with 10ug of anti-human CD27 antibody varlilumab. Alternatively, either 20ul of AdHER2 (2x1011 vp/ml)  or 10ug of anti-human CD27 antibody varlilumab alone was injected. Alternatively, isotype control IgG was injected.

value: implanted tumor

tag: cell line

value: breast cancer

value: CD27 agonism alone


title: OCSCC30, Post, CD3, TCR

description: Library name: OCSCC30_Post_CD3_TCR

value: TCR

value: HNSCC


title: Sen_sg_Cmpk2_9

description:
Library name: sample9
S-25-0849-09_S134_L006

value: Bone-marrow derived


title: Sen_sg_Cmpk2_8

description:
Library name: sample8
S-25-0849-08_S133_L006

value: Primary


title: OCSCC13, Pre, CD45pos, TCR

description: Library name: OCSCC13_Pre_CD45pos_TCR

value: Pre


title: OCSCC30, Post, CD3, 5prime

description: Library name: OCSCC30_Post_CD3_5prime


title: OCSCC13, Post, CD45pos, TCR

description: Library name: OCSCC13_Post_CD45pos_TCR


title: Control_sg_Cmpk2_3

description:
Library name: sample3
S-25-0849-03_S128_L006

value: Macrophage

value: Control


title: OCSCC3, Post, CD45neg, 3prime

description: Library name: OCSCC3_Post_CD45neg_3prime


title: Control_sg_Cmpk2_2

description:
Library name: sample2
S-25-0849-02_S127_L006


title: OCSCC1, Pre, CD45pos, 5prime

description: Library name: OCSCC1_Pre_CD45pos_5prime


title: OCSCC1, Pre, CD45neg, 3prime

description: Library name: OCSCC1_Pre_CD45neg_3prime


title: OCSCC12, Post, CD3, TCR

description: Library name: OCSCC12_Post_CD3_TCR


title: Control_sg_Rosa26_4

description:
Library name: sample4
S-25-0849-04_S129_L006


title: Control_sg_Cmpk2_1

description:
Library name: sample1
S-25-0849-01_S126_L006


title: OCSCC3, Pre, Unsorted, 5prime

description: Library name: OCSCC3_Pre_Unsorted_5prime

value: Unsorted


title: OCSCC3, Pre, Unsorted, TCR

description: Library name: OCSCC3_Pre_Unsorted_TCR


title: OCSCC3, Post, CD45ratio, TCR

description: Library name: OCSCC3_Post_CD45ratio_TCR


title: aCD27, bio rep 2, GEX

description:
Library name: aCD27_2_GEX
GEX (5' library): read 1 contains 16 bp cell barcode and 10 bp UMI; read 2 contains cDNA transcripts


title: aCD27PosAdHER2, bio rep 3, GEX

description:
Library name: aCD27PosAdHER2_3_GEX
GEX (5' library): read 1 contains 16 bp cell barcode and 10 bp UMI; read 2 contains cDNA transcripts

value: Combined CD27 agonism and AdHER2 vaccination


title: aCD27, bio rep 3, TCR

description:
Library name: aCD27_3_TCR
TCR (5’ T-cell receptor library):  read 1 contains 16 bp cell barcode and 10 bp UMI; read 2 contains rearranged TCR cDNA sequences

library_source: other

data_processing:
Using the CellRanger multi pipeline, raw reads were mapped to a custom reference constructed by supplementing the standard mouse reference genome (mm39) fasta and gtf files with human HER2 and CD27 genes. The resulting CellRanger outputs were concatenated into a single Seurat object in R v4.4.0 using Seurat v5.3.0.
Cells were filtered by UMIs detected (500 ≤ UMI ≤ 1500), genes expressed (200 ≤ Features ≤ 5000), and mitochondrial reads (mitochondrial cDNA ≤ 10%). This resulted in a single-cell expression matrix containing 77,135 cells. Cells were also initially filtered for doublets using scDblFinder v1.18.0.
Data were normalized using scTransform and integrated using RPCA integration to mitigate batch effects with Seurat. Normalized, filtered, and integrated single-cell transcriptomes were typed using Seurat-generated cluster marker genes (Wilcoxon test) and known immunologic markers.
To further mitigate doublet cells’ impact on downstream analysis, cells were filtered based on canonical immune type marker gene expression to exclude out-group markers. Specifically, macrophages and dendritic cells were filtered to remove any cells expressing B cell, T cell, or innate lymphoid markers. Similarly, T cells and innate lymphoid cells were filtered for unexpected marker expression. Mitotic cells were classified based on macrophage/dendritic or T cell markers; cells lacking either marker were designated mitotic, while cells expressing both markers were removed as presumed doublets. This filtering resulted in a robust dataset of 58,171 cells by 50,172 genes.
Assembly: mm39 supplemented with human CD27 and HER2 genes
Supplementary files format and content: counts.txt is the raw counts for final set of typed cells.
Supplementary files format and content: cell_assignment.txt is the annotated cells including type assignments, sample origin,  and experimental arm
Supplementary files format and content: mm39_supplemented_reference_seq.gtf contains the annotation utilized for building a CellRanger reference containing mm39 standard reference supplemented with CD27 and HER2 genes
Library strategy: TCR-Seq

molecule: other


title: aCD27, bio rep 2, TCR

description:
Library name: aCD27_2_TCR
TCR (5’ T-cell receptor library):  read 1 contains 16 bp cell barcode and 10 bp UMI; read 2 contains rearranged TCR cDNA sequences


title: aCD27PosAdHER2, bio rep 2, TCR

description:
Library name: aCD27PosAdHER2_2_TCR
TCR (5’ T-cell receptor library):  read 1 contains 16 bp cell barcode and 10 bp UMI; read 2 contains rearranged TCR cDNA sequences


title: OCSCC12, Post, CD3, 5prime

description: Library name: OCSCC12_Post_CD3_5prime


title: WF,bladder cancer patient

city: Chongqing

first: Li

middle: qiu

last: Liu

address: No. 10, Changjiang Road, Daping, Yuzhong District, Chongqing

country: China

institute: Chongqing Daping Hospital

description:
Library name: Sample5
single cell RNA-Seq

data_processing:
Basecalls performed using CASAVA version 1.8
Cellranger was utilized to calculate the raw counts and cell whitelist by default parameter
We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:  MT% < 40%;  Cell Gene Number < 10000;  Cell Gene Number > 200. PCA and tSNE analysis was used for the single cell to cell relation description. The fastMNN function  (k = 5, d = 50, approximate = TRUE, auto.order = TRUE) from R package scran (v1.10.2) was used to apply mutual nearest neighbor method to correct for batch effect among samples.  Graphcluster was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Assembly: GRCh38
Supplementary files format and content: MTX file and TSV file contain counts for each barcodes and genes

source_name: bladder cancer

extract_protocol:
Single-cell RNA-seq experiment was performed by experimental personnel in the laboratory of NovelBio Co.,Ltd. The tissues were surgically removed and kept in MACS Tissue Storage Solution (Miltenyi Biotec) until processing. The tissue samples were processed as described below. Briefly, samples were first washed with phosphate-buffered saline (PBS), minced into small pieces (approximately 1mm3) on ice and enzymatically digested with collagenase I (Worthington) and DNase I (Worthington) for 45 min at 37°C, with agitation . After digestion, samples were sieved through a 70µm cell strainer, and centrifuged at 300g for 5 min. After the supernatant was removed, the pelleted cells were suspended in red blood cell lysis buffer (Miltenyi Biotec) to lyse red blood cells.  After washing with PBS containing 0.04% BSA, the cell pellets were re-suspended in PBS containing 0.04% BSA and re-filtered through a 35μm cell strainer. Dissociated single cells were then stained with AO/PI for viability assessment using Countstar Fluorescence Cell Analyzer. The single-cell suspension was further enriched with a MACS dead cell removal kit (Miltenyi Biotec).
Single-cell RNA sequencing (scRNA-seq) was performed using 10X Genomics Chromium platform. Related operations including Generation of gel beads in emulsion (GEMs), barcoding, GEM-RT cleanup, complementary DNA amplification and library construction were all carried out following the manufacturer’s protocol.

value: bladder cancer


title: LJX,bladder cancer patient

description:
Library name: Sample4
single cell RNA-Seq


title: OCSCC3, Post, CD45ratio, 5prime

description: Library name: OCSCC3_Post_CD45ratio_5prime


title: aCD27PosAdHER2, bio rep 1, GEX

description:
Library name: aCD27PosAdHER2_1_GEX
GEX (5' library): read 1 contains 16 bp cell barcode and 10 bp UMI; read 2 contains cDNA transcripts


title: aCD27, bio rep 1, TCR

description:
Library name: aCD27_1_TCR
TCR (5’ T-cell receptor library):  read 1 contains 16 bp cell barcode and 10 bp UMI; read 2 contains rearranged TCR cDNA sequences


title: aCD27, bio rep 1, GEX

description:
Library name: aCD27_1_GEX
GEX (5' library): read 1 contains 16 bp cell barcode and 10 bp UMI; read 2 contains cDNA transcripts


title: aCD27PosAdHER2, bio rep 4, GEX

description:
Library name: aCD27PosAdHER2_4_GEX
GEX (5' library): read 1 contains 16 bp cell barcode and 10 bp UMI; read 2 contains cDNA transcripts


title: aCD27PosAdHER2, bio rep 4, TCR

description:
Library name: aCD27PosAdHER2_4_TCR
TCR (5’ T-cell receptor library):  read 1 contains 16 bp cell barcode and 10 bp UMI; read 2 contains rearranged TCR cDNA sequences


title: OCSCC1, Pre, CD45pos, TCR

description: Library name: OCSCC1_Pre_CD45pos_TCR


title: Human FLI1CUT&Tag FLI1, Rep3

first: Jeong Hyun

last: Ji

address: 615 Charles E Young Dr S, Rm 247

description: Library name: Human_FLI1CUT_Tag_FLI1_Rep3

library_source: genomic

data_processing:
FastQC (v0.12.0), Trimmomatic (v0.39), and Bowtie2 (v2.5.4)
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

source_name: NK cells

extract_protocol:
Nuclei were harvested using nuclear extraction buffer (20mM HEPES, 10mMKCl, 0.1% Triton X-100, 20% glycerol, protease inhibitor [Sigma 11836170001], 0.5mM spermidine)
CUT&Tag libraries were constructed as previously described in Cheng et al., 2023.

value: NK cells


title: AdHER2, bio rep 3, TCR

description:
Library name: AdHER2_3_TCR
TCR (5’ T-cell receptor library):  read 1 contains 16 bp cell barcode and 10 bp UMI; read 2 contains rearranged TCR cDNA sequences

value: AdHER2 vaccination


title: AdHER2, bio rep 3, GEX

description:
Library name: AdHER2_3_GEX
GEX (5' library): read 1 contains 16 bp cell barcode and 10 bp UMI; read 2 contains cDNA transcripts


title: aCD27PosAdHER2, bio rep 3, TCR

description:
Library name: aCD27PosAdHER2_3_TCR
TCR (5’ T-cell receptor library):  read 1 contains 16 bp cell barcode and 10 bp UMI; read 2 contains rearranged TCR cDNA sequences


title: OCSCC1, Post, CD45pos, TCR

description: Library name: OCSCC1_Post_CD45pos_TCR

value: Oral Cavity


title: AdHER2, bio rep 2, GEX

description:
Library name: AdHER2_2_GEX
GEX (5' library): read 1 contains 16 bp cell barcode and 10 bp UMI; read 2 contains cDNA transcripts


title: Human ATACseq NTC, Rep2

description: Library name: Human_ATACseq_NTC_Rep2

data_processing:
FastQC (v0.12.0), Trimmomatic (v0.39), and Bowtie2 (v2.5.4)
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
Nuclei were harvested using ATAC Lysis Buffer (Zymo).
ATAC libraries were constructed using the Zymo-Seq ATAC Library kit following manufacturer's instructions.

value: NTC


title: Human ATACseq NTC, Rep1

description: Library name: Human_ATACseq_NTC_Rep1


title: AdHER2, bio rep 2, TCR

description:
Library name: AdHER2_2_TCR
TCR (5’ T-cell receptor library):  read 1 contains 16 bp cell barcode and 10 bp UMI; read 2 contains rearranged TCR cDNA sequences

value: implanted tumor


title: Human ATACseq FLI1 KO, Rep3

description: Library name: Human_ATACseq_FLI1KO_Rep3

value: FLI1 KO


title: AdHER2, bio rep 1, GEX

description:
Library name: AdHER2_1_GEX
GEX (5' library): read 1 contains 16 bp cell barcode and 10 bp UMI; read 2 contains cDNA transcripts

value: breast cancer


title: aCD27PosAdHER2, bio rep 2, GEX

description:
Library name: aCD27PosAdHER2_2_GEX
GEX (5' library): read 1 contains 16 bp cell barcode and 10 bp UMI; read 2 contains cDNA transcripts


title: OCSCC1, Post, CD45neg, 3prime

description: Library name: OCSCC1_Post_CD45neg_3prime

value: Post


title: OCSCC1, Post, CD45pos, 5prime

description: Library name: OCSCC1_Post_CD45pos_5prime

value: HNSCC


title: E0771_FePD1_TIL

city: Indianapolis

first: Qingfei

last: Wang

state: IN

address: Walther Hall-R3 C243

department: Division of Hematology/Oncology, Department of Medicine

institute: Indiana University School of Medicine

description:
Library name: Sample 4
PIP-seq

data_processing:
The sequencing data were aligned using PIPseeker v3 according to the user’s guide (Doc ID:FB 0002787, Fluent BioSciences).
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: mammary tumor

extract_protocol:
Single-cell suspensions from E0771 tumors with indicated treatment were prepared by using mouse tumor dissociation kit (Cat#130-096-730, Miltenyi Biotec) in combination with the gentleMACS Octo Dissociator. In brief, fresh E0771 tumors were resected and minced with sterile scissors into approximately 1- to 2- mm3 pieces, then transferred into gentleMACS C Tube with 5 mL enzyme mix prepared as recommended in the protocol (5 mL enzyme mix for maximal 1g tumor tissue). Program ‘37C_m_TDK_2’ was used with the heating function. After termination of the program, samples were resuspended after adding 10 mL of DMEM/F12 medium supplemented with 2% FBS and passed through a 40 mm cell strainer (BD Biosciences). Cell suspension was centrifuged at 350g for 5 minutes and resuspended in PBS. Cells were then stained with zombie violet fixable viability dye (Cat#423114, BioLegend) on ice for 15 minutes followed by a 20-minute incubation with TruStain FcX. Subsequently, cells were incubated with APC anti-mouse CD45 antibody (Cat#103112, BioLegend)on ice for 30 minutes. After washing wash twice with cell staining buffer (Cat# 420201, BioLegend), FACS was conducted on BD FACSAria Fusion Cell Sorter (BD Biosciences) to isolate live CD45+ cells.
Sorted CD45+ cells were suspended at a concentration of 5,000 live cells/L with cell suspension buffer provided in the PIPseq T20 3ʹ Single Cell RNA Kit V4. A total of 40,000 cells puls 40 units of RNase inhibitor were added into pre-templated instant partitions (PIPs). Samples were processed following the workflow of capture and lysis, mRNA isolation, complementary DNA (cDNA) synthesis, cDNA amplification, library preparation, library pooling, and sequencing according to the user’s guide (Doc ID:FB0002130, Fluent BioSciences).

value: mammary tumor

value: CD45+ cells

value: wild type

value: PD-1 + Iron


title: E0771_PD1_TIL

description:
Library name: Sample 3
PIP-seq

value: PD-1 antibody


title: Human FLI1CUT&Tag IgG, Rep1

description: Library name: Human_FLI1CUT_Tag_IgG_Rep1

value: IgG


title: E0771_Ctrl_TIL

description:
Library name: Sample 1
PIP-seq

value: Control


title: E0771_Fe_TIL

description:
Library name: Sample 2
PIP-seq

value: Iron


title: aCD27PosAdHER2, bio rep 1, TCR

description:
Library name: aCD27PosAdHER2_1_TCR
TCR (5’ T-cell receptor library):  read 1 contains 16 bp cell barcode and 10 bp UMI; read 2 contains rearranged TCR cDNA sequences

value: Combined CD27 agonism and AdHER2 vaccination


title: Ctrl, bio rep 3, GEX

description:
Library name: Ctrl_3_GEX
GEX (5' library): read 1 contains 16 bp cell barcode and 10 bp UMI; read 2 contains cDNA transcripts

value: isotype control IgG


title: ZKY,bladder cancer patient

description:
Library name: Sample3
single cell RNA-Seq

value: bladder cancer


title: A. baumannii 17978WT, stationary, rep 2

city: Austin

first: Mady

last: Telford

state: TX

address: 2506 Speedway

department: Molecular Biosciences

institute: The University of Texas at Austin

description: Library name: 17978WT_B

data_processing:
CLC Genomics Workbench 24.0.1
Assembly: ATCC 17978 (NCBI:txid400667)
Supplementary files format and content: gene expression comparison output from CLC comparing RNA expression of WT to ΔMccAB1

organism: Acinetobacter baumannii

source_name: gram-negative bacteria

growth_protocol: Strains were grown in Mueller-Hinton broth static at 30C for 24 hours.

extract_protocol:
Total RNA was extracted using the Direct-zol RNA Miniprep Kit (Zymo). RNA was depleted of DNA (Turbo DNAse - Thermo) and ribosomes (QiaSeq Fast Select - Qiagen). 2.7 ug total RNA was used for library construction.
RNA libraries for RNA-seq were constructed using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina sequencing according to manuafacturer's protocols.

treatment_protocol: Genetic deletion was performed sing recombineering

tag: strain

value: gram-negative bacteria

value: wildtype

value: stationary phase


title: Ctrl, bio rep 3, TCR

description:
Library name: Ctrl_3_TCR
TCR (5’ T-cell receptor library):  read 1 contains 16 bp cell barcode and 10 bp UMI; read 2 contains rearranged TCR cDNA sequences

value: implanted tumor

value: breast cancer


title: ZRJ,bladder cancer patient

description:
Library name: Sample2
single cell RNA-Seq


title: DMSO, scATAC-seq

city: Shanghai

first: Xiangyi

last: Chen

address: No. 1239, Siping Road, Shanghai, China

institute: Weida Li

description:
Library name: DMSO, scATAC-seq
10x Genomics

library_source: genomic single cell

data_processing:
scRNA-seq：The demultiplexing, barcoded processing, gene counting and aggregation were made using the DNBelab_C4_scRNA_v2.3. scATAC-seq：data processed data was generated using cellranger ATAC v1.1.0 software.
Assembly: scRNA-seq:GRCH38;scATAC-seq:GRCH38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: pancreas

extract_protocol:
scRNA-seq：SC-islets were dissociated into single cells with TrypLE and resuspended with DPBS with 0.5% fat-acid -free BSA. Added DNase I to eliminate the DNA released form the dead cells to prevent cell caking and placed the tubes containing cells on ice for preservation. scATAC-seq: Cells were isolated per 10x Genomics manufacture instructions. Nuclei isolation was performed according to the protocol of 10× Genomics.
scRNA-seq：DNBelab C Series High-throughput Single-Cell RNA Library (MGI, #940-000047-00) was utilized for scRNA-seq library preparation. In brief, the single-cell suspensions were converted to barcoded scRNA-seq libraries through steps including droplet encapsulation, emulsion breakage, mRNA captured beads collection, reverse transcription, cDNA amplification and purification. cDNA production was sheared to short fragments with 250-400 bp, and indexed sequencing libraries were constructed according to the manufacturer’s protocol. Qualification was performed using Qubit ssDNA Assay Kit (Thermo Fisher Scientific) and Agilent Bioanalyzer 2100. All libraries were further sequenced by the MGISEQ-2000RS with pair-end sequencing. The sequencing reads contained 30-bp read 1 (including the 10-bp cell barcode 1, 10-bp cell barcode 2 and 10-bp unique molecular identifiers (UMI)), 100-bp read 2 for gene sequences and 10-bp barcodes read for sample index.scATAC-seq: The library was constructed according to the Chromiun signal Cell ATAC Reagent Kits protocol (10× Genomics).

value: pancreas

value: hES-derived islet organoid

value: dmso


title: Subject 9, Pre-vaccination tumor, biol rep 2

city: Columbus

first: Katherine

middle: E

last: Miller

state: OH

address: 700 Children's Dr.

department: Institute for Genomic Medicine

institute: Nationwide Children's Hospital

description:
Library name: SC130_GBM132_pre_GEX
10X 5' snRNAseq

data_processing:
BCL files were converted to FASTQ files using Cell Ranger v7.1.0 mkfastq pipeline. Cell Ranger v7.1.0 multi was used to perform alignment to the human genome reference GRCh38, filtering, barcode counting, and UMI counting (default settings). Gene expression libraries were sequenced on the NovaSeq6000 with a run recipe of 26x10x10x90 targeting 500 million reads per sample (50,000 reads/cell; estimated 10,000 cells/sample).
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: glioblastoma tumor

extract_protocol:
Nuclei were isolated from frozen tumor sections following the 10X Chromium Nuclei Isolation Kit Sample Prep User Guide (CG000505 Rev A). To enrich for T cells, nuclei were stained with 5 ul of Alexa Fluor® 488 anti-NFATc1 antibody (Biolegend 649604) per 1 ml of Wash and Resuspension Buffer for 30 min in the dark at 4 degrees Celsius. To minimize sample loss, we did not perform a wash after the incubation. 10 ul of 7-AAD (ThermoFisher Scientific A1310), a nucleic acid dye that intercalates into double-stranded DNA, was added to the sample prior to loading onto the BigFoot cell sorter running Sasquatch 1.19.13 software (ThermoFisher Scientific). Nuclei were gated on single cells, then 7-AAD positive, and then a liberal Alexa Fluor® 488 gate (102) was set to initially sort about 14,000 nuclei. This initial liberal gate was done to ensure we capture T cells but also other immunocytes, microenvironment, and tumor cells. We then moved the Alexa Fluor® 488 gate to 103 to enrich for the T cells and sorted up to 2,000 additional nuclei with this stringent gate. A maximum total of 16,000 sorted nuclei were sorted directly into 10X Genomics Master Mix and loaded onto a Next GEM Chip K.
The Chromium Next GEM Single Cell 5’ v2 (Dual Index) User Guide (Rev E) was then followed according to the manufacturer’s recommendations for library preparation.

value: glioblastoma tumor

tag: Sex

value: Male


title: YCK,bladder cancer patient

description:
Library name: Sample1
single cell RNA-Seq


title: A. baumannii 17978WT, stationary, rep 3

description: Library name: 17978WT_C


title: Human FLI1CUT&Tag IgG, Rep3

description: Library name: Human_FLI1CUT_Tag_IgG_Rep3

value: NK cells


title: Ctrl, bio rep 2, TCR

description:
Library name: Ctrl_2_TCR
TCR (5’ T-cell receptor library):  read 1 contains 16 bp cell barcode and 10 bp UMI; read 2 contains rearranged TCR cDNA sequences


title: Ctrl, bio rep 2, GEX

description:
Library name: Ctrl_2_GEX
GEX (5' library): read 1 contains 16 bp cell barcode and 10 bp UMI; read 2 contains cDNA transcripts


title: Human FLI1CUT&Tag IgG, Rep2

description: Library name: Human_FLI1CUT_Tag_IgG_Rep2

value: IgG


title: Ctrl, bio rep 1, TCR

description:
Library name: Ctrl_1_TCR
TCR (5’ T-cell receptor library):  read 1 contains 16 bp cell barcode and 10 bp UMI; read 2 contains rearranged TCR cDNA sequences


title: A. baumannii 17978ΔMccAB1, stationary, rep 1

description: Library name: 17978ΔMccAB1_A


title: Subject 2, Post-vaccination tumor, biol rep 2

description:
Library name: SC104_GBM123_post_GEX
10X 5' snRNAseq

value: Female


title: Subject 2, Post-vaccination tumor, biol rep 1

description:
Library name: SC099_GBM_Post_GEX
10X 5' snRNAseq


title: Ctrl, bio rep 1, GEX

description:
Library name: Ctrl_1_GEX
GEX (5' library): read 1 contains 16 bp cell barcode and 10 bp UMI; read 2 contains cDNA transcripts


title: Human FLI1CUT&Tag FLI1, Rep1

description: Library name: Human_FLI1CUT_Tag_FLI1_Rep1


title: Subject 2, Pre-vaccination tumor, biol rep 1

description:
Library name: SC098_GBM_Pre_GEX
10X 5' snRNAseq


title: SU6656, scRNA-seq (oligo)

description:
Library name: SU6656, scRNA-seq (oligo)
DNBelab C


title: Human ATACseq NTC, Rep3

description: Library name: Human_ATACseq_NTC_Rep3

value: NTC


title: Subject 9, Post-vaccination Tumor Resection

description:
Library name: GNOS-PV01-132_S-2022-034405-R
Bulk RNAseq

data_processing:
Reads were aligned to the human reference genome build GRCh38 using a custom in-house pipeline and the splice-aware aligner STAR (RRID-:SCR_004463).
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Tumor RNA was DNase treated and ribodepleted.
Library construction was performed using using NEBNext Ultra II Directional RNA library kit for Illumina (New England BioLabs). Paired end 151 bp reads were sequenced on the NovaSeq6000 at a minimum of 80 million reads per sample.


title: Human FLI1CUT&Tag FLI1, Rep2

description: Library name: Human_FLI1CUT_Tag_FLI1_Rep2


title: SU6656, scRNA-seq (cDNA)

description:
Library name: SU6656, scRNA-seq (cDNA)
DNBelab C


title: Subject 9, Pre-vaccination Tumor Region 2

description:
Library name: 21-2835_GNOS-PVO1-132_R2_S-2021-041197-R
Bulk RNAseq


title: genomic_DNAmethylation_207179240129_R04C01

value: placental chorionic villi

tag: resourcescomposite

tag: socialpositioncomposite

tag: disadvantagecomposite

value: XX

tag: ga

tag: syncytiotrophoblast

value: Plate 4


title: DMSO, scRNA-seq (oligo)

description:
Library name: DMSO, scRNA-seq (oligo)
DNBelab C


title: AdHER2, bio rep 1, TCR

description:
Library name: AdHER2_1_TCR
TCR (5’ T-cell receptor library):  read 1 contains 16 bp cell barcode and 10 bp UMI; read 2 contains rearranged TCR cDNA sequences

value: AdHER2 vaccination


title: DMSO, scRNA-seq (cDNA)

description:
Library name: DMSO, scRNA-seq (cDNA)
DNBelab C


title: Subject 8, Post-vaccination Tumor Resection Middle Lesion

description:
Library name: GT-20-124_1865566
Bulk RNAseq


title: Subject 8, Post-vaccination Tumor Resection Deep Lesion

description:
Library name: GT-20-124_1865564
Bulk RNAseq


title: Human ATACseq FLI1 KO, Rep2

description: Library name: Human_ATACseq_FLI1KO_Rep2

value: FLI1 KO


title: SU6656, scATAC-seq

description:
Library name: SU6656, scATAC-seq
10x Genomics


title: Subject 8, Pre-vaccination Tumor Region 3

description:
Library name: GBM145_GNOS-PV01_124_TISSUE_C
Bulk RNAseq


title: GFPscreen_GFP+tronslons_replicate1

first: Vighnesh

last: Ghatpande

state: Texas

address: 2500 Speedway

institute: University of Texas at Austin

description: Library name: Twist_rep1_GFP

data_processing:
NGS reads were trimmed to remove vector-specific PCR handles using Cutadapt104 v1.18 with the following parameters: “-g ^CGTGAGGATCTATTTCCGGTGAATTC -G ^GGTGAACAGCTCCTCGCCCTTGCTGGATCC”. Trimmed reads were aligned to the APPRIS release M25 (GRCm38.p6) transcriptome using bowtie2105 v2.3.4.3. The resulting sorted indexed bam files were used to generate a count table using a custom script.
Assembly: APPRIS release M25 (GRCm38.p6) transcriptome
Supplementary files format and content: bam

extract_protocol:
Following recovery cells were trypsinized and resuspended in 1mL PBS+ 1% FBS to reduce clumping. 100µL of the cells were stored as input and remaining 900µL cells were passed through a cell strainer to achieve single cell suspension and immediately sorted using a Sony MA900 FACS machine using the maximum purity settings. Singlets were gated using a SSC-H vs SSC-W plot followed by sequential gating using a FSC-A vs FSC-H plot. Singlet cells showing a 10 fold increase in GFP were considered GFP positive and sorted in PBS+ 5% BSA to increase centrifugation efficiency. Sorted cells were centrifuged and the pellets were used for genomic DNA isolation using Zymo mini DNA isolation kit.
The 5′UTR sequences upstream of the nostartGFP were amplified from 2 µg gDNA in a 100µL PCR reaction divided into four 25 µL reactions for 22 cycles using custom made Illumina indexing primers to generate amplicon libraries (Supplemental table S8). PCR products were cleaned with AmpureXP beads and quantified on a bioanalyzer. Guide amplicon libraries were sequenced using NovaSeq 6000 (Illumina) with a PE150 chemistry.

treatment_protocol: 2.5 x 106 mESCs were infected with the lentiviral library at an MOI of 0.3 and a library representation of 500X in T75 flask overnight. Next day, the media was replaced with 2i ES growth media, and cells were allowed to grow for 24 hours. Infected cells were selected using 2i ES growth media + 0.3µg/mL puromycin for the next 48 hours. The surviving cells were recovered in 2i ES growth media for next 48 hours.

value: Embryonic stem cells


title: Subject 9, Post-vaccination tumor, biol rep 2

description:
Library name: SC131_GBM132_post_GEX
10X 5' snRNAseq


title: GFPscreen_Input_tronslons_replicate2

description: Library name: Twist_rep2_Input


title: GFPscreen_GFP+tronslons_replicate2

description: Library name: Twist_rep2_GFP


title: Subject 9, Pre-vaccination Tumor Region 1

description:
Library name: 21-2834_GNOS-PVO1-132_R1_S-2021-041195-R
Bulk RNAseq


title: Human ATACseq FLI1 KO, Rep1

description: Library name: Human_ATACseq_FLI1KO_Rep1


title: A. baumannii 17978ΔMccAB1, stationary, rep 3

description: Library name: 17978ΔMccAB1_C

value: gram-negative bacteria

value: stationary phase


title: A. baumannii 17978WT, stationary, rep 1

description: Library name: 17978WT_A

value: wildtype


title: Subject 8, Post-vaccination Tumor Resection Superficial Lesion

description:
Library name: GT-20-124_1865565
Bulk RNAseq


title: Subject 9, Post-vaccination tumor, biol rep 1

description:
Library name: SC106_GBM132_post_GEX
10X 5' snRNAseq


title: Subject 8, Pre-vaccination Tumor Region 1

description:
Library name: GBM145_GNOS-PV01_124_TISSUE_A
Bulk RNAseq


title: Subject 9, Pre-vaccination tumor, biol rep 1

description:
Library name: SC105_GBM132_pre_GEX
10X 5' snRNAseq


title: A. baumannii 17978ΔMccAB1, stationary, rep 2

description: Library name: 17978ΔMccAB1_B


title: Subject 7, Pre-vaccination Tumor Region 3

description:
Library name: 21-1041-1_GBM143_GNOS-PV01-122C_RNA
Bulk RNAseq


title: Subject 7, Pre-vaccination Tumor Region 2

description:
Library name: 21-1040-1_GBM143_GNOS-PV01-122B_RNA
Bulk RNAseq


title: Heart CD45+ leukocytes, MI and NK depletion, ADT

city: Würzburg

first: Alexander

middle: M.

last: Leipold

address: Josef-Schneider-Str. 2

country: Germany

institute: Helmholtz Institute for RNA-based Infection Research

description: Library name: B10_2_ADT

data_processing:
Pre-processing of sequencing results to generate count matrices (gene expression, ADT and HTO barcode counts) was performed using the 10x genomics Cell Ranger pipeline where ADT and HTO sequences were concatenated and treated as Custom library with default settings and aligning to the mm10 genome build and Ensembl annotations.
Further processing was done with Seurat (cell and gene filtering, hashtag identification, clustering, differential gene expression analysis).
Assembly: mm10
Supplementary files format and content: CellRanger output: molecule_info.h5; filtered_feature_bc_matrix.tar.gz containing Cellranger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Library strategy: CITE-seq

molecule: protein

source_name: heart

extract_protocol:
5 minutes before being euthanasia, the mice were injected i.v. with 2.5µg anti-CD45.2 APC (clone 104, Biolegend, cat. #109814) under isoflurane anesthesia to label circulating immune cells. The heart was perfused with PBS, excised, and the infarct, peri-infarct area, and adjacent viable myocardium collected, weighed and digested for 1 hour at 37°C under agitation in RPMI containing 450U/ml collagenase I (Sigma-Aldrich, #C0130), 125U/ml Collagenase XI (Sigma-Aldrich, C7657), 60U/ml Hyaluronidase (Sigma-Aldrich, H3506), 60U/ml DNAse (Roche #11284932001). After digestion, the cell suspensions were passed through a 70µm cell strainer and washed twice in MACS buffer (PBS+0.5% BSA+2mM EDTA) and incubated for 5 minutes on ice with TruStain FcX™ (anti-mouse CD16/32, Biolegend #101320, 10µg/ml). Afterwards, cells were incubated with mouse CD45 microbeads (Miltenyi, 130-052-301, 1:10 final concentration), and anti-mouse CD45.2-AlexaFluor488. After 10 minutes incubation at 4°C, TotalSeq-A hashtag antibodies (Biolegend) were added as follows: hashtag 1 to 5 controls; hashtags 6 to 10: NK-depleted. Cells were incubated for an additional 15 minutes at 4°C, washed twice in MACS buffer, pooled, and magnetic selection was performed using LS Columns (Miltenyi (# 130-042-401) and MidiMACS separators (Miltenyi # 130-042-302). Sorted CD45+ cells were washed twice with PBS containing 0.04% BSA (Sigma-Aldrich A1595) and incubated for 25 minutes at 4°C in PBS/0.04% FCS containing Fixable Viability Dye eFluor™ 780 (ThermoFisher #65-0865-14, 1:1000) and anti-mouse TotalSeqA-Antibodies (ADT panel). Cells were washed with PBS/0.04% FCS, resuspended and viable CD45.2-AlexaFluor488+ CD45.2-APC- cells sorted using a BD FACS Aria III with a 100µm nozzle. Cells were resuspended, counted (final concentration 1,650 cells/µl).
Genomics Chromium using Chromium Next GEM Single Cell 3' High Throughput (HT) Reagent Kits v3.1 were used for library construction with the aim to recover 40,000 cells.

treatment_protocol: 8-12 week old male C57BL6J mice underwent permanent coronary ligation to induce myocardial infarction and were injected i.p. with a depleting mouse anti-mouse NK1.1 monoclonal antibody (200µg/mouse, BioxCell BE0036 clone PK136) or with isotype 1 hour after coronary artery ligation. Five days after myocardial infarction, cells were extracted from the infarcted heart as described in "extract protocol”

value: heart

value: male

value: CD45+ leukocytes

value: MI/MI+NK cell depletion

value: Library 1

value: ADT

tag: hto/adt


title: PB-TWM,bladder cancer patient

description:
Library name: Sample8
BD Rhapsody

data_processing:
Basecalls performed using CASAVA version 1.8
10X Genomics: Cellranger was utilized to calculate the raw counts and cell whitelist by default parameter. BD Rhapsody:The feature-barcode matrices were obtained by aligning reads to the human genome (GRCh38) using STARsolo with default parameter.
Assembly: GRCh38
Supplementary files format and content: MTX file and TSV file contain counts for each barcodes and genes

source_name: PBMC

extract_protocol:
Single-cell RNA-seq experiment was performed by experimental personnel in the laboratory of NovelBio Co.,Ltd. The tissues were surgically removed and kept in MACS Tissue Storage Solution (Miltenyi Biotec) until processing. The tissue samples were processed as described below. Briefly, samples were first washed with phosphate-buffered saline (PBS), minced into small pieces (approximately 1mm3) on ice and enzymatically digested with collagenase I (Worthington) and DNase I (Worthington) for 45 min at 37°C, with agitation . After digestion, samples were sieved through a 70µm cell strainer, and centrifuged at 300g for 5 min. After the supernatant was removed, the pelleted cells were suspended in red blood cell lysis buffer (Miltenyi Biotec) to lyse red blood cells. After washing with PBS containing 0.04% BSA, the cell pellets were re-suspended in PBS containing 0.04% BSA and re-filtered through a 35μm cell strainer. Dissociated single cells were then stained with AO/PI for viability assessment using Countstar Fluorescence Cell Analyzer. The single-cell suspension was further enriched with a MACS dead cell removal kit (Miltenyi Biotec).
10X Genomics: Single-cell RNA sequencing (scRNA-seq) was performed using 10X Genomics Chromium platform. Related operations including Generation of gel beads in emulsion (GEMs), barcoding, GEM-RT cleanup, complementary DNA amplification and library construction were all carried out following the manufacturer’s protocol. BD Rhapsody:BD Rhapsody system  were used to capture the single cells and construct the scRNA-Seq libraries.

tag: tissue

value: PBMC


title: BC-LNM-TWM,bladder cancer patient

description:
Library name: Sample7
BD Rhapsody

source_name: lymph node

value: lymph node


title: Subject 7, Pre-vaccination Tumor Region 1

description:
Library name: 21-1039-1_GBM143_GNOS-PV01-122A_RNA
Bulk RNAseq

value: glioblastoma tumor

value: Male


title: Subject 2, Pre-vaccination tumor, biol rep 2

description:
Library name: SC103_GBM123_pre_GEX
10X 5' snRNAseq

value: Female


title: BC-TWM,bladder cancer patient

description:
Library name: Sample6
BD Rhapsody

value: bladder cancer


title: Subject 9, Pre-vaccination Tumor Region 3

description:
Library name: 21-2836_GNOS-PVO1-132_R3_S-2021-041199-R
Bulk RNAseq


title: Subject 6, Pre-vaccination Tumor Region 2

description:
Library name: GNOS-PV01-113_B_RNA
Bulk RNAseq


title: 22Rv1_BL01D1_R03

city: shanghai

first: Yao

last: Zhu

state: shanghai

address: dongan road 270

department: urology

institute: Fudan University

description: Library name: Sample 6

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools. featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

extract_protocol:
Total RNA from each sample was extracted using  TRIzol Reagent (Invitrogen).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

value: Prostate cancer


title: Subject 5, Pre-vaccination Tumor Region 2

description:
Library name: 21-0495_GBM130_GNOS-PV01-110B_RNA
Bulk RNAseq


title: Subject 5, Pre-vaccination Tumor Region 1

description:
Library name: 21-0494_GBM130_GNOS-PV01-110A_RNA
Bulk RNAseq


title: 22Rv1_Control03

description: Library name: Sample 3

value: vehicle


title: Subject 8, Pre-vaccination Tumor Region 2

description:
Library name: GBM145_GNOS-PV01_124_TISSUE_B
Bulk RNAseq


title: GFPscreen_Input_tronslons_replicate1

description: Library name: Twist_rep1_Input

value: Embryonic stem cells


title: 22Rv1_Control02

description: Library name: Sample 2


title: Subject 4, Pre-vaccination Tumor Region 2

description:
Library name: 21-0217_GBM129B_GNOS-PV01-109_R
Bulk RNAseq


title: Heart CD45+ leukocytes, MI and NK depletion, HTO

description: Library name: B10_2_HTO

value: HTO


title: CESC 7

first: Chuntao

last: Tao

state: State...

address: China

institute: Chongqing Medical University

description: Library name: Sample 14

data_processing:
After transfecting SiHa cells with the siRNAs, total cellular RNA was extracted using RNA TRIzol Reagent (Invitrogen, USA) and stored at -80°C. The RNA quality met the control standards. RNA sequencing analysis was performed by Knorigene Technologies (Chongqing, China) and the data was analyzed with bioinformatics technology.
Assembly: hg38
Supplementary files format and content: xlsx

source_name: CESC tissue

extract_protocol:
RNA was isolated using TRIZOL reagent (Invitrogen, MA, USA) Poly-A pull-down was used to enrich for mRNAs, and libraries were prepared using the Illumina TruSeq RNA kit. Libraries were pooled and sequenced on an Illumina HiSeq2000 machine with 150 bp paired-end reads.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: CESC tissue


title: Heart CD45+ leukocytes, MI and NK depletion, GEX

description: Library name: B10_2

value: heart

value: mRNA


title: Lung_metastasis_1

city: London

first: Mariia

last: Yuneva

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

description: Library name: PAN5774A4

data_processing:
Fastq files were quantified using SpaceRanger (version 1.3.1) from 10x Genomics. The Visium samples were loaded into R as SpatialExperiment objects. Raw counts in the Visium data were log1p normalized using PhiSpace R package via PhiSpace::logTransf. Cell type deconvolution was performed using the partial least squares regression model PhiSpace::PhiSpaceR_1ref(phenotypes = “CellType”, PhiSpaceAssay = “log1p”, regMethod = “PLS”), using a scRNA-seq dataset as reference.
Assembly: MM10 reference provided by 10XGenomics (refdata-gex-mm10-2020-A)
Supplementary files format and content: *.jpg files. Visium images of tissue.
Supplementary files format and content: tab separated files containing barcodes, features and count matrix. One per sample.
Library strategy: Spatial Transcriptomics

source_name: lung

extract_protocol:
Tissue sections were mounted on a Visium Spatial Gene Expression Slide with four capture areas, each containing ~5,000 spatially barcoded spots. Following fixation and hematoxylin and eosin (H&E) staining, tissue permeabilization was performed for 18 minutes—a duration determined through prior tissue optimization using the 10x Genomics Tissue Optimization protocol (CG000238).mRNA released from permeabilized tissue was hybridized to oligonucleotides on the slide, and reverse transcription was carried out in situ to generate spatially barcoded cDNA.
library preparation followed the manufacturer's protocol (Visium Spatial Gene Expression Reagent Kits User Guide, CG000239 Rev F), including second-strand synthesis, cDNA amplification, enzymatic fragmentation, end repair, adaptor ligation, and sample index PCR. Libraries were sequenced on an Illumina platform (NovaSeq 6000) using paired-end sequencing (Read 1: 28 bp, Read 2: 90 bp) at a target depth of (50k reads per cell/spot).

value: lung

value: mammary gland tumour

value: orthotopic injection of 4T1 cells into the mammary fat pad, lung metastasis


title: Lung_normal_1

description: Library name: PAN5774A3

value: control (no treatment)


title: Subject 6, Pre-vaccination Tumor Region 3

description:
Library name: GNOS-PV01-113_C_RNA
Bulk RNAseq


title: TCD-BM (BC002), cGVDH sample 1 (BC003), BETi (BC004) Flex multiplex

description:
Library name: GSL_MK_4004_Mouse_Flex
10X Single Cell Fixed RNA Profling

data_processing:
BCL files were converted to FASTQ files using Cell Ranger v8.0.0 mkfastq pipeline. Cell Ranger v8.0.0 multi was used to perform alignment to themouse reference genome (mm10 2020), filtering, barcode counting, and UMI counting (default settings). Gene expression libraries were sequenced on the NovaSeq6000 with a run recipe of 28x10x10x90 targeting 250 million reads per sample (25,000 reads/cell; estimated 10,000 cells/sample). Flex multiplex sample was demultiplexed using the following sample:barcode assignments: TCD-BM (BC002), cGVDH sample 1 (BC003), BETi (BC004)
Assembly: mm10
Supplementary files format and content: matrix.h5

source_name: Lung

extract_protocol:
Whole lungs were placed in dissociation media (Blank DMEM supplemented with 10mg/mL DNASE and 1.5mg/mL Collagenase IV) and dissociated via m_Lung_02 program of octoMACS dissociator, followed by an incubation at 370C/30min and a repeated dissociation. Solution was then filtered through a 100mM filter into a single cell suspension.
Single cell suspensions were fixed and processed using the 10X Genomics NextGem Fixed RNA Profiling kit according to the manufacturer recommendations. We targeted 10,000 single cells per sample and multiplexed four samples together.

value: Lung


title: Subject 6, Pre-vaccination Tumor Region 1

description:
Library name: GNOS-PV01-113_A_RNA
Bulk RNAseq


title: Subject 5, Pre-vaccination Tumor Region 3

description:
Library name: 21-0496_GBM130_GNOS-PV01-110C_RNA
Bulk RNAseq


title: 22Rv1_BL01D1_R02

description: Library name: Sample 5


title: Normal 7

description: Library name: Sample 7

source_name: normal cervical tissue

value: normal cervical tissue


title: SiHa_siDLEU2

description: Library name: Sample 16

source_name: SiHa cell line

value: SiHa cell line


title: Subject 4, Pre-vaccination Tumor Region 3

description:
Library name: 21-0218_GBM129C_GNOS-PV01-109_R
Bulk RNAseq

value: glioblastoma tumor


title: SiHa_siNC

description: Library name: Sample 15


title: CESC 5

description: Library name: Sample 12


title: 22Rv1_BL01D1_R01

description: Library name: Sample 4


title: Normal 5

description: Library name: Sample 5


title: CESC 4

description: Library name: Sample 11


title: CESC 6

description: Library name: Sample 13


title: 22Rv1_Control01

description: Library name: Sample 1


title: Subject 4, Pre-vaccination Tumor Region 1

description:
Library name: 21-0216_GBM129A_GNOS-PV01-109_R
Bulk RNAseq

value: Female


title: Normal 3

description: Library name: Sample 3


title: CESC 3

description: Library name: Sample 10


title: Subject 3, Pre-vaccination Tumor Region 3

description:
Library name: GNOS-PV01-106C-DUNN-R
Bulk RNAseq

value: Male


title: Chow1

city: Ann Arbor

first: You

last: Lu

state: MI

address: 210 Washtenaw Avenue

department: Life Sciences Institute

institute: University of Michigan

description: Library name: sample1

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were performed using the 10x Genomics Cell Ranger software v8.0.1 with 'include-introns' set to false.
Assembly: GRCm38
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

source_name: liver

growth_protocol: Mice were housed in specific pathogen-free facilities under 12-h light-dark cycles with free access to food and water.

extract_protocol:
Liver tissue was snap-frozen in liquid nitrogen and homogenized in lysis buffer supplemented with RNase inhibitorusing a glass dounce homogenizer. The nuclei suspension was filtered through a 70-mm cell strainer, briefly centrifuged, washed and strained again through a 40-mm cell strainer. The nuclei suspension was then FACS sorted on a BD FACS Discover S8 Cell Sorter.
Sequencing libraries were prepared using the 10x Genomics Chromium Next GEM Single Cell 3’ RNA Library & Gel Bead Kit (v3) using the 10x Genomics Chromium X instrument  according to the manufacturer’s protocol.

treatment_protocol: Male mice were fed either on regular chow or with a MASH diet containing 40 kcal% fat, 20 kcal % fructose, and 2% cholesterol (D09100310, Research Diets) starting at the age of 10-12 weeks for five months.

value: liver

value: wild-type

value: regular chow diet


title: cGVHD sample 2 Flex singleplex

description:
Library name: cGVHD_2
10X Single Cell Fixed RNA Profling


title: Normal 2

description: Library name: Sample 2


title: MASH2

description: Library name: sample5

value: AMYLIN liver NASH diet


title: Subject 2, Pre-vaccination Tumor Region 4

description:
Library name: GBM123_Region-4-R
Bulk RNAseq


title: CESC 2

description: Library name: Sample 9

value: CESC tissue


title: Normal 4

description: Library name: Sample 4


title: MASH1

description: Library name: sample4


title: CESC 1

description: Library name: Sample 8


title: Subject 3, Pre-vaccination Tumor Region 2

description:
Library name: GNOS-PV01-106B-DUNN-R
Bulk RNAseq


title: e13.5c13

city: New York

first: Weijia

last: Zhang

state: NY

address: 1 Gustave L. Levy Pl

department: Renal

institute: Icahn School of Medicine at Mount Sinai

description:
Library name: PL8
Group6

data_processing:
The sequences were aligned to the genome with popular STAR aligner and the read count for each transcript was extracted from the alignment with htseq program. Transcript with reads <100 across all samples were filtered out. The read counts were normalized to the same total read counts level at sample level, log2 transformed, and then quantile normalized.
Assembly: mm10
Supplementary files format and content: raw_counts.txt

source_name: placenta

extract_protocol:
Mice with timed pregnancies were perfused with 60cc sterile PBS and RNA from whole fetal-placental units (E8.5-9.5) or whole placentas (E12.5-13.5) was isolated using Qiagen kits.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

value: placenta

tag: gestational age

tag: disease state

value: Control


title: mES cells, Trf2f/f,Upf1HM, rep3

city: Bethesda

first: J. Robert

last: Hogg

state: MD

address: 50 South Drive, Room 2341

department: Biochemistry and Biophysics Center

institute: National Heart, Lung, and Blood Institute

description: Library name: Upf1_3

data_processing:
Reads were trimmed to remove adapters and low-quality bases using Cutadapt before alignment with the reference genome (mm39) and the annotated transcripts using STAR (v2.7.6a).
The long-read transcript annotation for mouse embryonic stem cells (ES_consolidated.bed) from Pardo-Palacios et al. was obtained and converted to GTF format using UCSC Genome Browser utilities (bedToGenePred). The resulting GTF file was then filtered to retain only full splice match (FSM) isoforms using a custom R script.
Transcriptomes were assembled from individual mouse ESCs RNA-seq samples using StringTie (v2.1.4).
For each sample, alignment files in BAM format were processed using StringTie with a minimum isoform fraction threshold of 0.05 (-f 0.05) and guided by the previously filtered GTF annotation reference (-G ES_consolidated.gtf). Trimming was disabled (-t) to preserve full-length transcript structures. Assembled transcriptomes were filtered to retain only isoforms with an expression level greater than 1 TPM using a custom R script (StringTie_filter_gtf.R). Filtered sample-level annotations were merged in two stages using StringTie’s --merge function: first, within each experimental condition (Smg5-/-, Smg6-/-, Upf1HM, Ctrl), and then across all conditions to generate a unified annotation. The merged GTF file was sorted and indexed using IGVTools
To refine transcript models and remove likely spurious or low-abundance isoforms, we applied the AnnotationCleaner pipeline (https://github.com/isaacvock/AnnotationCleaner)
A STAR index was generated from the cleaned annotation, and raw FASTQ files were aligned to the custom transcriptome using STAR (v2.7.6a). Count matrices were generated using RSEM (v1.3.3) with corresponding custom indices.
Assembly: mm39
Supplementary files format and content: gtf file contains custom transcriptome annotations
Supplementary files format and content: CSV file contains raw counts from RSEM

source_name: mESC

growth_protocol: Cells were  grown on 0.1% gelatin at 37 °C and 5% CO2 in ES medium (DMEM (Gibco) supplemented with 15% FBS (Omega Scientific), 1,000 U/ml LIF (Millipore Sigma), 2i (1 μM PD03259010, 3 μM CHIR99021, Sigma Aldrich), 0.1 mM non-essential amino acids (Gibco), 1 mM sodium pyruvate (Gibco), 0.143 mM 2-β-mercaptoethanol (Millipore Sigma) and 0.5 mg/ml penicillin, streptomycin and l-glutamine (Gibco))

extract_protocol:
Total RNA was isolated using the RNeasy Plus Mini Kit (Qiagen).
Ribosomal RNA was depleted from total RNA using the Illumina® Ribo-Zero Plus, and libraries were prepared using the Illumina® Stranded Total RNA Prep, Ligation kit.

value: mESC

value: Trf2f/f, Upf1HM


title: Normal 6

description: Library name: Sample 6


title: Subject 2, Post-vaccination Tumor Resection

description:
Library name: GT-20-102_RNA
Bulk RNAseq


title: Subject 2, Pre-vaccination Tumor Region 3

description:
Library name: GBM123_Region-3-R
Bulk RNAseq


title: Subject 3, Pre-vaccination Tumor Region 1

description:
Library name: GNOS-PV01-106A-DUNN-R
Bulk RNAseq


title: Subject 2, Pre-vaccination Tumor Region 2

description:
Library name: GBM123_Region-2-R
Bulk RNAseq


title: e13.5c11

description:
Library name: PL69
Group6


title: e13.5c9

description:
Library name: PL19
Group6


title: e13.5c7

description:
Library name: PL63
Group6


title: Subject 1, Pre-vaccination Tumor Region 3

description:
Library name: 20-1320_GNOS-PV-010_REGION3_RNA
Bulk RNAseq


title: mES cells, Trf2f/f, Smg6-/-, rep2

description: Library name: Smg6_2

value: Trf2f/f, Smg6-/-


title: Normal 1

description: Library name: Sample 1


title: e13.5c12

description:
Library name: PL70
Group6


title: Subject 2, Pre-vaccination Tumor Region 1

description:
Library name: GBM123_Region-1-R
Bulk RNAseq


title: e13.5c10

description:
Library name: PL20
Group6


title: e13.5c6

description:
Library name: PL62
Group6


title: Chow3

description: Library name: sample3


title: mES cells, Trf2f/f, Smg6-/-, rep3

description: Library name: Smg6_3


title: Subject 1, Pre-vaccination Tumor Region 2

description:
Library name: 20-1319_GNOS-PV-010_REGION2_RNA
Bulk RNAseq


title: mES cells, Trf2f/f,Upf1HM, rep2

description: Library name: Upf1_2


title: mES cells, Trf2f/f,Upf1HM, rep1

description: Library name: Upf1_1


title: e13.5c4

description:
Library name: PL4
Group6


title: e13.5c5

description:
Library name: PL5
Group6


title: e13.5c8

description:
Library name: PL9
Group6


title: Chow2

description: Library name: sample2


title: mES cells, Trf2f/f, Smg6-/-, rep1

description: Library name: Smg6_1


title: e13.5c3

description:
Library name: PL2
Group6


title: e13.5c2

description:
Library name: PL1
Group6


title: e13.5c1

description:
Library name: PL10
Group6


title: Subject 1, Pre-vaccination Tumor Region 1

description:
Library name: 20-1318_GNOS-PV-010_REGION1_RNA
Bulk RNAseq


title: mES cells, Trf2f/f, Smg5-/-, rep3

description: Library name: Smg5_3

value: Trf2f/f, Smg5-/-


title: e13.5nr11

description:
Library name: PL71
Group5

value: Non-resorbed

value: huTLR8 transgenic


title: A13Lg shKLF5-5 ATAC biol rep2

city: Baltimore

first: Weiqiang

last: Zhou

address: 615 N. Wolfe Street

department: Department of Biostatistics

institute: Johns Hopkins University Bloomberg School of Public Health

description: Library name: A13D_shRNA_4_ATAC

data_processing:
The single-cell multiomics data was aligned to the human reference genome hg38 using Cell Ranger ARC.
Assembly: hg38
Supplementary files format and content: Cell Ranger ARC output files: filtered_feature_bc_matrix.h5

extract_protocol:
“Nuclei Isolation for Single Cell Multiome ATAC + Gene Expression Sequencing” (Demonstrated protocol CG000365, Rev D; 10x Genomics)
10X Chromium

tag: cell type

value: Lung Metastasis


title: e13.5nr9

description:
Library name: PL51
Group5


title: A13Lg shKLF5-5 GEX biol rep2

description: Library name: A13D_shRNA_4_RNA


title: mES cells, Trf2f/f, Smg5-/-, rep2

description: Library name: Smg5_2


title: mES cells, Trf2f/f, Smg5-/-, rep1

description: Library name: Smg5_1


title: e13.5nr8

description:
Library name: PL23
Group5


title: e13.5nr10

description:
Library name: PL57
Group5


title: A13Lg shKLF5-5 GEX biol rep1

description: Library name: A13D_shRNA_3_RNA


title: e13.5nr7

description:
Library name: PL7
Group5


title: mES cells, Trf2f/f, rep3

description: Library name: WT_3


title: e13.5nr5

description:
Library name: PL55
Group5


title: mES cells, Trf2f/f, rep2

description: Library name: WT_2


title: e13.5nr4

description:
Library name: PL53
Group5


title: mES cells, Trf2f/f, rep1

description: Library name: WT_1


title: e13.5nr2

description:
Library name: PL22
Group5


title: A13Lg shCtrl-5 ATAC biol rep2

description: Library name: A13D_scrambled5_4_ATAC


title: e13.5nr6

description:
Library name: PL58
Group5


title: e13.5nr3

description:
Library name: PL49
Group5


title: e13.5nr1

description:
Library name: PL21
Group5


title: A13Lg shKLF5-5 ATAC biol rep1

description: Library name: A13D_shRNA_3_ATAC


title: e13.5r7

description:
Library name: PL52
Group4

value: Resorbed


title: A13Lg shCtrl-5 GEX biol rep2

description: Library name: A13D_scrambled5_4_RNA


title: e13.5r6

description:
Library name: PL38
Group4


title: e13.5r5

description:
Library name: PL68
Group4


title: HKO_MASH

description: Library name: sample2

treatment_protocol: Male mice were fed with a MASH diet containing 40 kcal% fat, 20 kcal % fructose, and 2% cholesterol (D09100310, Research Diets) starting at the age of 10-12 weeks for five months.

value: Themis Alb-Cre


title: A13Lg Parental ATAC

description: Library name: A13D_ATAC


title: e13.5r4

description:
Library name: PL56
Group4


title: A13Lg Parental GEX

description: Library name: A13D_RNA


title: KO_MASH diet_liver 3

description: Library name: sample6

data_processing:
The reads were trimmed using Cutadapt v2.3
Reads were mapped to the reference genome GRCm38 (ENSEMBL 102), using STAR v2.7.8a
Count estimates to genes were calculated with RSEM v1.3.3
Assembly: GRCm38
Supplementary files format and content: tab-delimited file containing gene ID and annotation, with count estimates for each gene each library

extract_protocol:
Total RNA was extracted from frozen liver samples with Trazol reagent (Alkali Scientific) following manufacturer's guideline.
Sequencing libraries were generated with NEBNext UltraExpress RNA Library Prep Kit  (NEB) following manufacturer's guideline.

treatment_protocol: Mice were fed a MASH diet containing 40 kcal% fat, 20 kcal % fructose, and 2% cholesterol (D09100310, Research Diets) starting at the age of 10-12 weeks for three months.

value: Themis KO


title: WT_MASH

description: Library name: sample1

value: liver

value: Themis flox/flox


title: e13.5r1

description:
Library name: PL36
Group4


title: A13Lg shCtrl-5 GEX biol rep1

description: Library name: A13D_scrambled5_3_RNA


title: KO_MASH diet_liver 2

description: Library name: sample5


title: A13Lg shCtrl-5 ATAC biol rep1

description: Library name: A13D_scrambled5_3_ATAC


title: e8.5c11

description:
Library name: PL66
Group3


title: KO_MASH diet_liver 1

description: Library name: sample4


title: e8.5c10

description:
Library name: PL65
Group3


title: A13Pr2 Parental ATAC

description: Library name: A13B_ATAC

value: Primary PDAC tumor


title: e13.5r2

description:
Library name: PL37
Group4


title: e8.5c8

description:
Library name: PL61
Group3


title: e13.5r3

description:
Library name: PL50
Group4


title: e8.5c9

description:
Library name: PL13
Group3


title: WT_MASH diet_liver 2

description: Library name: sample2

value: wild-type C57BL6/J

value: AMYLIN liver NASH diet


title: A13Pr2 Parental GEX

description: Library name: A13B_RNA


title: A13Pr2 shCtrl ATAC

description: Library name: A13B_scrambled5_ATAC


title: e8.5c7

description:
Library name: PL60
Group3

value: placenta


title: e8.5c5

description:
Library name: PL26
Group3

value: Control


title: WT_MASH diet_liver 3

description: Library name: sample3


title: A13Pr2 shCtrl GEX

description: Library name: A13B_scrambled5_RNA


title: e8.5c3

description:
Library name: PL24
Group3


title: e8.5c2

description:
Library name: PL12
Group3


title: e8.5c4

description:
Library name: PL25
Group3


title: A13Pr2 shKLF5-5 ATAC

description: Library name: A13B_shRNA5_ATAC


title: KO2

description: Library name: sample4

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were performed using the 10x Genomics Cell Ranger software v6.1.0
Assembly: GRCm38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: cortex and hippocampus

extract_protocol:
Cortex and hippocampus were dissected and homogenized in Lysis Buffer (EZ Prep Nuclei Kit, Sigma-Aldrich) with RNAase Inhibitor and filtered through a 30 mm MACS strainer. The samples were briefly centrifuged, washed and strained again before resuspended in washing buffer (10 mM Tris buffer pH 8.0, 5 mM KCl, 12.5 mM MgCl2, 1% BSA with RNAse inhibitor). The nuclei were then FACS sorted on a MoFlo Astrios Cell Sorter. The final nuclei suspension was adjusted to 750–1200 nuclei/μL.
Sequencing libraries were prepared using the 10x Genomics Chromium Next GEM Single Cell 3’ RNA Library & Gel Bead Kit (v3) using the 10x Genomics Chromium X instrument  according to the manufacturer’s protocol.

value: cortex and hippocampus

value: Sel1L Syn-Cre


title: e8.5nr11

description:
Library name: PL44
Group2


title: WT_MASH diet_liver 1

description: Library name: sample1


title: KO1

description: Library name: sample3


title: A13Pr2 shKLF5-5 GEX

description: Library name: A13B_shRNA5_RNA


title: e8.5c6

description:
Library name: PL59
Group3


title: e8.5nr7

description:
Library name: PL46
Group2


title: A13Lg shKLF5-5 biol rep 2

description: Library name: A13DKLF5sh52

data_processing:
Alignment with Salmon. Differential gene expression analysis with DEseq2
Assembly: hg38
Supplementary files format and content: .sf files are quantification matrices with counts (TPM) per transcripts

extract_protocol:
RNeasy Mini kit (Qiagen)
Strand-specific mRNA libraries were generated using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England BioLabs #E7760). mRNA was isolated using the Poly(A) mRNA Magnetic Isolation Module (New England BioLabs #E7490)

value: Lung PDAC Metastasis


title: WT1

description: Library name: sample1

value: Sel1L flox/flox


title: e8.5nr6

description:
Library name: PL45
Group2

value: Non-resorbed


title: e8.5c1

description:
Library name: PL11
Group3


title: A13Lg shKLF5-5 biol rep 1

description: Library name: A13DKLF5sh51


title: e8.5nr9

description:
Library name: PL17
Group2

value: huTLR8 transgenic


title: e8.5nr3

description:
Library name: PL32
Group2


title: e8.5nr4

description:
Library name: PL33
Group2


title: e8.5nr10

description:
Library name: PL34
Group2


title: e8.5nr2

description:
Library name: PL16
Group2


title: WT2

description: Library name: sample2


title: e8.5nr5

description:
Library name: PL42
Group2


title: A13Lg shCtrl-5 biol rep 1

description: Library name: A13DKLF5sc51


title: A13Lg shCtrl-5 biol rep 2

description: Library name: A13DKLF5sc52


title: PB@PM 5

first: ling

middle: ling

last: xu

address: tianlin street

institute: shanghai jiaotong university

description: Library name: Sample 15

data_processing:
Data quality control Use fastp v 0.19.3 to filter the original data, mainly to remove reads with adapters; when the N content in any sequencing reads exceeds 10% of the base number of the reads, remove the paired reads; when any sequencing reads When the number of low quality (Q<=20) bases contained in reads exceeds 50% of the bases of the reads, this paired reads will be removed. All subsequent analyses are based on clean reads.
Reads mapping to the reference genome Download the reference genome and its annotation files from the designated website, use HISAT v2.1.0 to construct the index, and compare clean reads to the reference genome.New transcript prediction Use StringTie v1.3.4d for new gene prediction. StringTie applies network streaming algorithms and optional de novo to splice transcripts. Compared with Cufflinks and other software, StringTie can splice a more complete and accurate transcript, and the splicing speed is faster.
Quantification of gene expression levels Use featureCounts v1.6.2 to calculate the gene alignment, and then calculate the FPKM of each gene based on the gene length. FPKM is currently the most commonly used method to estimate gene expression levels.
Difference analysis DESeq2 v1.22.1 was used to analyze the differential expression between the two groups, and the P value was corrected using the Benjamini & Hochberg method. The corrected P value and |log2foldchange| are used as the threshold for significant difference expression.
Differential gene enrichment analysis The enrichment analysis is performed based on the hypergeometric test. For KEGG, the hypergeometric distribution test is performed with the unit of pathway; for GO, it is performed based on the GO term.GSEA Use gsea--3.0.jar for gene set enrichment analysis.
Assembly: mm10
Supplementary files format and content: gene fpkm files

growth_protocol: The mouse MIRI model was established as previously reported45. Briefly, after mice were anesthetized by inhalation using 3% isoflurane (1 L/min), an incision (≈2 cm) was made with sterile scissors at the thoracic location of the mice where the heartbeat was most intense. A 4-0 purse-string suture was created, and the thorax above the heart was bluntly dissected through the fourth intercostal space using curved forceps. The chest was lightly pressed to squeeze out the heart from the chest cavity and position the heart in the sutured opening. At this time, it was ensured that there was as little air in the chest cavity as possible. A 6-0 surgical suture was used to tie a surgical slipknot on the left anterior descending coronary artery, with one end of the suture being exposed outside the chest. The heart was immediately placed back into the chest cavity, with the excess air expelled, and the epidermis was sutured closed. After 45 minutes, the slipknot for cardiac reperfusion was opened. Surgical wounds were sutured using sterile 5-0 sutures, and the mice were returned to the rearing cage for continued feeding.

extract_protocol:
Total RNA was extracted using the TRIzol reagent according to the manufacturer's protocol. 1 ug of total RNA was used for the construction of sequencing libraries.
Then the libraries were constructed using TruSeq Stranded mRNALTSample Prep Kit(Ilumina,San Diego, CA, USA) .RNA degradation and contamination was monitored on 1% agarose gels. RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA) . RNA concentration was measured using Qubit® RNA Assay Kit in Qubit®2.0 Flurometer (Life Technologies, CA, USA). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations.  Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.  In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq6000 platform and 150 bp paired-end reads were generated.

treatment_protocol: Mice were divided into four groups: Sham group, MIRI group, MIRI+PB group, and MIRI+PB@PM group. Next, 0.5mg/kg PB or PB@PM (containing 0.5mg/kg PB) was administrated via the tail vein to the corresponding group at 1 hour and 24 hours after reperfusion, and the equal amount of 0.9% saline was applied to the Sham and MIRI groups.

value: heart

value: cardiomyocyte

value: total RNA


title: e8.5nr8

description:
Library name: PL47
Group2


title: PB@PM 3

description: Library name: Sample 13


title: PB@PM 2

description: Library name: Sample 12


title: e8.5nr1

description:
Library name: PL15
Group2


title: e8.5r2

description:
Library name: PL31
Group1

value: Resorbed


title: e8.5r3

description:
Library name: PL41
Group1


title: PB@PM 4

description: Library name: Sample 14


title: A13Lg shKLF5-7 biol rep 1

description: Library name: A13D_sh7_1


title: A13Lg shKLF5-7 biol rep 2

description: Library name: A13D_sh7_2


title: e8.5r4

description:
Library name: PL43
Group1


title: MIRI 5

description: Library name: Sample 10


title: A13Lg shCtrl-7 biol rep 2

description: Library name: A13D_sc7_2


title: MIRI 4

description: Library name: Sample 9


title: Culture mature days  (Lane 1-4)

city: Thuwal

first: Xabier

last: Martinez de Morentin

address: Kaust

country: Saudi Arabia

institute: KAUST

description: Library name: atac_fastq_control_mature_days

data_processing:
Demultiplexing, barcode processing, and UMI counting performed with 10x Genomics Cell Ranger 3.0.1 (scRNA-seq). Reads aligned to GRCh38 using STAR. Quality filtering: cells with <3,250 counts or <1,500 features removed; genes expressed in <3 cells removed; mitochondrial reads ≥10% removed. Doublets removed using DoubletFinder (7.5% estimated rate).
Assembly: Human genome reference GRCh38 (Ensembl).
Supplementary files format and content: scRNA-seq: counts matrices (.mtx), barcodes (.csv), gene/features (.csv). scATAC-seq: cistopic_obj (.pkl)

source_name: Brain

growth_protocol: NPCs derived from XCL1 DCXpGFP were cultured on CellMatrix Basement Membrane Gel coated plates in NPC expansion medium (DMEM/F-12 supplemented with Growth Kit for Neural Progenitor Cell Expansion). Cells were incubated at 37°C with 5% CO₂, seeded at 0.30 ×10⁶ per well for expansion, and 8×10⁴ cells/cm² for differentiation.

extract_protocol:
Cells were harvested by Accutase detachment, washed with DPBS, and centrifuged at 13,000 rpm. Cell pellets were resuspended in 0.05% BSA in PBS. Dead cells were stained with TO-PRO-3 and viable cells were sorted using MoFlo Astrios EQs based on negative TOPRO-3 signal.
scRNA-seq: 10x Genomics NEXTGEM Single Cell 3’ v3.1 Kit; cells loaded at 500–1,000 cells/µL on Chromium Controller to generate GEMs. cDNA synthesized, PCR-amplified, fragmented, end-repaired, A-tailed, and ligated to Illumina adapters. Libraries indexed and quality-controlled with Qubit and TapeStation. Sequencing on NextSeq500 (Read1:28 cycles, Read2:55 cycles, i7 index: 8 cycles). scATAC-seq: Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit, following 10x Genomics protocol.

treatment_protocol: For control, differentiation medium was added from Day 1 to Day 20. For disease condition, Aβ 1-42 peptide (50 nM) was added concurrently with differentiation medium from Day 1, with medium changes every 2–3 days. Cells were harvested at Days 0, 7, 13, and 20.

value: Brain

value: XCL1 DCXpGFP


title: PB@PM 1

description: Library name: Sample 11


title: Culture mature days with ba condition added  (Lane 1-4)

description: Library name: atac_fastq_ba_mature_days


title: Culture intermediate days  (Lane 1-4)

description: Library name: atac_fastq_control_intermediate_days


title: A13Lg shCtrl-7 biol rep 1

description: Library name: A13D_sc7_1


title: MIRI 3

description: Library name: Sample 8


title: e8.5r1

description:
Library name: PL14
Group1


title: MIRI 2

description: Library name: Sample 7


title: Basal culture scATAC  (Lane 1-4)

description: Library name: atac_fastq_basal


title: Culture early days with ba condition added  (Lane 1-4)

description: Library name: atac_fastq_ba_early_days


title: Culture intermediate days with ba condition added  (Lane 1-4)

description: Library name: atac_fastq_ba_intermediate_days


title: Blood, AD, RJJ

city: Guangzhou

first: xie

last: xinyang

address: 58 Zhongshan Second Road, Yuexiu District, Guangzhou City, Guangdong Province

institute: The First Affiliated Hospital, Sun Yat-sen University

description:
Library name: sample6
10x Genomics

data_processing:
Sequencing data were demultiplexed and converted to FASTQ format using Illumina bcl2fastq software (v2.20). The FASTQ files were processed using the Cell Ranger pipeline (v6.1.1) for sample demultiplexing, barcode assignment, and single-cell 3′ gene counting. Data were aligned to the Ensembl GRCh38 reference genome. The output from Cell Ranger was imported into Seurat (v3.1.1) for dimensionality reduction, clustering, and transcriptomic analysis.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Peripheral blood

extract_protocol:
Human basophils from patients with atopic dermatitis and healthy controls were isolated from 10 mL of peripheral blood using the EasySep™ Direct Human Basophil Isolation Kit for downstream scRNA-seq.
A single-cell 3′ library was constructed using the 10x Genomics Chromium Single-Cell 3′ kit (v3). R1 (read 1 primer sequence) are added to the molecules during GEM incubation. P5, P7, a sample index, and R2 (read 2 primer sequence) are added during library construction via End Repair, A- tailing, Adaptor Ligation, and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification.

treatment_protocol: All samples were collected from 10mL peripheral blood of patients with atopic dermatitis and healthy controls

value: Peripheral blood


title: Culture after 13 days rep 1  (Lane 1-4)

description: Library name: rna_fastq_control_13_days_re


title: Culture early days  (Lane 1-4)

description: Library name: atac_fastq_control_early_days


title: MIRI 1

description: Library name: Sample 6


title: Blood, AD, ZWQ

description:
Library name: sample7
10x Genomics


title: Culture after 20 days  (Lane 1-4)

description: Library name: rna_fastq_control_20_days


title: Culture after 13 days  (Lane 1-4)

description: Library name: rna_fastq_control_13_days


title: Blood, AD, DZ

description:
Library name: sample4
10x Genomics


title: Culture after 20 days rep 1  (Lane 1-4)

description: Library name: rna_fastq_control_20_days_re


title: control 5

description: Library name: Sample 5


title: Blood, HC, YHK

description:
Library name: sample3
10x Genomics


title: Culture after 7 days  (Lane 1-4)

description: Library name: rna_fastq_control_7_days


title: Culture after 20 days with ba condition added rep 1  (Lane 1-4)

description: Library name: rna_fastq_ba_20_days_re


title: Culture after 20 days with ba condition added  (Lane 1-4)

description: Library name: rna_fastq_ba_20_days


title: Blood, AD, FZX

description:
Library name: sample5
10x Genomics


title: control 4

description: Library name: Sample 4


title: Blood, HC, LWH

description:
Library name: sample2
10x Genomics


title: Culture after 13 days with ba condition added  (Lane 1-4)

description: Library name: rna_fastq_ba_13_days


title: Culture after 13 days with ba condition added rep 1  (Lane 1-4)

description: Library name: rna_fastq_ba_13_days_re


title: Blood, HC, CYZ

description:
Library name: sample1
10x Genomics


title: Culture after 7 days with ba condition added  (Lane 1-4)

description: Library name: rna_fastq_ba_7_days


title: control 2

description: Library name: Sample 2


title: Aged Mlkl-/- HSC, ATAC-seq, rep3

city: Memphis

first: Masayuki

last: Yamashita

state: TN

address: 262 Danny Thomas Place

department: Division of Experimental Hematology, Department of Hematology

institute: St. Jude Children's Research Hospital

description: Library name: Aged_Mlkl-/-_Rep3

data_processing:
Sequencing reads were mapped to the mouse reference genome (mm10) with Bowtie2 (v2.5.3).
Peaks were called with MACS2 (v2.2.7.1) using the nomodel function and a q-value cutoff of 0.001.
All called peaks overlapping by at least one base pair were merged using bedtools (v2.31.0) merge to generate a comprehensive peak catalog.
Reads at each peak in the catalog were quantified with the bedtools map function.
Differentially accessible regions were detected using edgeR (v3.30.3).
Assembly: mm10
Supplementary files format and content: BED file containing peak summits for each sample.
Supplementary files format and content: BigWig file providing signal tracks for visualization across the genome.

source_name: bone marrow

extract_protocol:
Cells were lysed in cold lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, and 0.1% IGEPAL CA-630). Nuclei were spun down and immediately subjected to the transposase reaction.
Nuclei were incubated in transposase reaction mix consisting of Tagment DNA buffer (Illumina) and Tagment DNA enzyme (Illumina). Transposed fragments were purified with MinElute PCR Purification Kit (QIAGEN). Libraries were amplified using NEBNext High Fidelity 2×PCR Master Mix (New England Biolabs) with index primers, size-selected between 240 and 360 base pairs by using BluePippin (Sage Science), and sequenced on a NextSeq500 (Illumina) with 70 bp single-read length.

value: bone marrow

value: hematopoietic stem cell

value: Mlkl-/-

tag: age

value: 18 months old


title: control 1

description: Library name: Sample 1