title: hnscc_30.ROI_011.Stroma.buds

description:
Library name: DSP-1001660021755-B-C12
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling

value: Head and neck squamous cell carcinoma


title: RNA-seq of Mus musculus: FL_C_IgG1_GC_DZ

status: Public on Apr 17 2026

type: SRA

city: St. Louis

first: Julian

last: Zhou

state: MO

address: 425 S. Euclid Ave.

department: Pathology & Immunology

country: USA

institute: Washington University in St. Louis

description: Library name: FL_C_IgG1_GC_DZ

library_source: transcriptomic

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software with a maximum of one mismatch in the indexing read.
RNA-seq reads were then aligned to the Ensembl GRCm39.113 primary assembly with STAR version 2.7.11b.
Gene counts were derived from the number of uniquely aligned unambiguous fragments by Subread:featureCount version 2.0.8.
Assembly: GRCm39
Supplementary files format and content: Excel spreadsheet file includes raw counts for each Sample

molecule: polyA RNA

organism: Mus musculus

source_name: spleen and draining lymph node

extract_protocol:
RNA and DNA were isolated with the AllPrep DNA/RNA kit (Qiagen Cat#80204) according to manufacturer instructions and stored at -80°C.
Library preparation was performed with 3-10ng of total RNA with a Bioanalyzer RIN score greater than 8.0. ds-cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per manufacturer's protocol. cDNA was fragmented using a Covaris E220 sonicator using peak incident power 18, duty factor 20%, cycles per burst 50 for 120 seconds. cDNA was blunt-ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq X Plus using paired-end reads extending 150 bases.

tag: tissue

value: spleen and draining lymph node

tag: cell type

value: GC B cells


title: hnscc_27.ROI_001.Stroma.non_budding

city: Heidelberg

first: Jan

last: Budczies

address: Im Neuenheimer Feld 224

department: Institute of Pathology

country: Germany

institute: University Hospital Heidelberg

description:
Library name: DSP-1001660021755-B-D02
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling

data_processing:
BCL to FASTQ conversion was performed using DRAGEN and the following command line options: dragen --bcl-conversion-only true --bcl-input-directory /path/to/BCL/directory --output-directory /path/to/FASTQ --sample-sheet /path/to/SeqCodeIndices/SeqCodeIndices.csv FASTQ files were processed using the NanoString GeoMx NGS Pipeline v2.3.3.10 and the following command line options: geomxngspipeline --in=/path/to/FASTQ --out=/path/to/DCC --ini=/path/to/GNP_config.ini The following default options were used: --quality-trim-score=20 (score used for quality trimming), --trim-adapter=true (enable/disable adapter trimming), --adapter-trim-match-length=10 --adapter-trim-max-mismatch=3 , --stitching-max-mismatch=2, --stitch-shift=true, --barcode-max-mismatch=1, --dedup-hd=1. For all downstream analysis, the deduplicated read counts were used. For each segment, additional quality control thresholds were applied. The minimum number of reads per segment was set at 40,000, the minimum number of successfully stitched reads at 80%, and the minimum number of aligned reads at 70%. Additionally, sequencing saturation was required to be at least 50%, while non-template control (NTC) wells were limited to a maximum of 1,000 counts. Each segment (that is a specific ROI-AOI combination) contained a set of negative probes; the geometric mean of the counts of the negative probes was calculated per segment and used to define the limit of quantification (LOQ), according to the formula LOQ = max (2, NegGeoMean × NegGeoSD2), where NegGeoMean is the geometric mean of the counts of the negative probes and NegGeoSD is the geometric standard deviation of the counts of the negative probes for a given segment. Essentially, the LOQ is defined as 2 standard deviations above the negative control mean and at minimum as at least 2 counts. Using the segment-specific LOQ thresholds, segments with exceptionally low signal (fewer than 5% of the genes detected above LOQ) and genes with low detection rates (fewer than 10% of the segments having detected a given gene above LOQ) were filtered out. The final post-QC dataset consisted of 239 segments and 7,795 genes. The raw counts were normalized to upper quartile (UQ or Q3) normalized counts and, for each case, the mean of the normalized counts for each gene was calculated for segments belonging to the same segment type.
Assembly: hg38
Supplementary files format and content: DCC files containing the raw counts for each probe.
Library strategy: Spatial Transcriptomics

molecule: total RNA

organism: Homo sapiens

source_name: Head and neck squamous cell carcinoma

growth_protocol: FFPE blocks

extract_protocol:
Slides were imaged in three fluorescence channels (FITC/525 nm, Cy3/568 nm, and Texas Red/615 nm) to visualize morphology markers, and regions of interest were segmented based on the expression of the morphology markers. For each tumor, two regions of interest (ROIs) were sampled from the bulk of the tumor and the surrounding stromal tissue. In budding cases, an additional two to three ROIs were sampled, focusing specifically on tumor bud cells and the adjacent stroma. Each ROI is then divided in distinct areas of illumination (AOIs) based on the morphology markers PanCK and CD45. PanCK-negative/CD45-positive cells were assigned the “immune” AOI,  PanCK-negative/CD45-negative cells were assigned the “stroma” AOI, and PanCK-positive/CD45-negative cells were assigned the “tumor” AOI. Each AOI was sequentially illuminated with UV and the UV-cleavable released tags were collected into 96-well plates.
The library preparation was performed according to the GeoMx DSP NGS Readout User Manual. In short, the 96-well plate was dried by being left on the bench top overnight covered by a permeable membrane which was subsequently replaced by another permeable membrane and the plate was then spinned down. The samples were then rehydrated with ten µL nuclease-free water and the plate was pulse-centrifuged to 1000 x g. GeoMx Seq Code primers were used to amplify the WTA tags and add Illumina adaptor sequences and sample demultiplexing barcodes. The GeoMx Seq Code primer plate was thawed and the GeoMx Seq Code primer plate and the GeoMx NGS Master Mix were pulse-centrifuged to 1000 x g. The subsequent PCR reaction was set up on a PCR plate with two μL of GeoMx NGS Master Mix, four μL of GeoMx Seq Code primer mix (added to the corresponding PCR plate well), and four μL of DSP aspirate (added to the corresponding PCR plate well) used per well. The PCR plate was sealed with a PCR plate sticker, pulse centrifuged to 1000 x g, and incubated in the thermocycler with a 100°C heated lid. The cycling conditions were as follows: UDG treatment at 37°C for 30 min, followed by UDG deactivation at 50°C for ten min. Initial denaturation was performed at 95°C for three minutes. Amplification consisted of 18 cycles of denaturation at 95°C for 15 sec, annealing at 65°C for 60 sec, and extension at 68°C for 30 sec. A final extension was carried out at 68°C for five minutes, followed by an indefinite hold at 4°C. The PCR products were pooled using four μL of each PCR product (including the NTC) and the remainder of the NTC PCR product was placed into a separate tube. The tubes with the sample pool and the NTC went through the same AMPure cleanup protocol using the 1.2-fold volume AMPure XP beads and the libraries were sequenced on an Illumina NextSeq 550 with 27x27 paired end reads.

treatment_protocol: Tumor sections from formalin-fixed, paraffin-embedded (FFPE) tissue of primary tumors of immunohistochemically p16-negative HNSCC patients were mounted on 24 slides. Tissue microarrays (TMAs) were constructed, incorporating selected tumor regions from two to three representative cases per array. The selected areas measured approximately 25-50 mm². Each slide included a tumor section from a budding case, and on 19 of the 24 slides, an additional section from a non-budding case was also included. Sample preparation was performed as described in the GeoMx DSP Manual Slide Prep User Manual (following the RNA FFPE instructions). In short, five μm thick FFPE tissue sections were mounted on BOND Plus slides. The slides were baked in a 60°C drying oven for 75 minutes and were deparaffinized and rehydrated with three five-minute washes in CitriSolv, two five-minute washes in 100% EtOH, one five-minute wash in 95% EtOH, and one one-minute wash in 1x PBS. The slides were then dipped into DEPC-treated water (at ~99°C) for ten seconds and immediately transferred to a ~99°C 1X Tris-EDTA jar and incubated for 15 minutes for target retrieval. After incubation, the slides were moved to room temperature 1x PBS and were washed for five minutes. The samples were then digested with one µg/mL Proteinase K for 15 minutes at 37°C and washed with 1x PBS for five minutes. The slides were then washed in 10% NBF for five minutes, two times in NBF Stop Buffer for five minutes each time, and one time in 1x PBS for five minutes. The samples were then incubated overnight (16 hours) at 37°C with Buffer R and the Human Whole Transcriptome Atlas (WTA) RNA detection probes in a light-non-permeable humid chamber, ensuring humid conditions by arranging DEPC-treated water-soaked Kimwipes on the bottom of the chamber . The reagent concentrations were adjusted for each run, where 200 μL x n Buffer R, 25 μL x n WTA Probe Mix, and 25 μL x n DEPC-treated water were used for the final solution, with n referring to the number of slides analyzed per run. 200 μL of the final solution was applied on each slide and HybriSlip Hybridization Covers (Grace BioLabs) covered the tissue during incubation. To remove off-target probes, two 25-minute stringent washes were performed in 50% formamide in 2x SSC at 37°C. The slides were then washed twice with 2x SCC for two minutes each time. For the morphology marker staining, the slides were placed in the light-non-permeable humidity chamber, covered with 200 μL Buffer W each at room temperature for 30 minutes. Then the Buffer W was removed and up to 200 μL of morphology marker solution (22 μL x n Syto 13, 5.5 μL x n PanCK, 5.5 μL x n CD45, filling in with Buffer W to reach 220 μL x n final volume, where n is the number of slides per run) was applied on each slide in the humidity chamber. The slides were stained for one hour in the humidity chamber at room temperature. After staining, the solution was removed and the slides were washed in 2x SCC two times for five minutes each time and loaded on the GeoMx DSP instrument.


title: RNA-seq of Mus musculus: FL_C_IgG1_GC_LZ

description: Library name: FL_C_IgG1_GC_LZ


title: Tet2fl/fl CD45+ TILs, 5' GEX, biol rep 2

city: Tsukuba

first: AI NHAN THI

last: LE

state: Ibaraki Prefecture

address: 2-1-1 Amakubo, University of Tsukuba Global Village, 305-8575

department: Department of Hematology

country: Japan

institute: Graduate School of Comprehensive Human Sciences, University of Tsukuba

description:
Library name: GEX_WT_89
10x Genomics 5' GEX library

library_source: transcriptomic single cell

data_processing:
Raw sequencing data were demultiplexed and mapped to the mouse reference genome (GRCm39) using Cell Ranger v8.0.1 (10x Genomics, RRID: SCR_017344) with default parameters.
For GEX libraries, gene expression count matrices were generated using the Cell Ranger count pipeline.
For TCR libraries, V(D)J contig annotations were generated using the Cell Ranger vdj pipeline. Filtered contig annotations were used for downstream TCR repertoire analysis.
Downstream analysis including quality control, clustering, dimensionality reduction, differential gene expression, trajectory inference, and TCR repertoire analysis was performed using Seurat (v5.0.1), Monocle3 (v1.3.7), AUCell (v1.26.0), and scRepertoire (v2.3.0) in R (v4.4.1).
Assembly: GRCm39
Supplementary files format and content: Per-sample Cell Ranger output: barcodes.tsv.gz (cell barcodes), features.tsv.gz (gene IDs and names), matrix.mtx.gz (UMI count matrix in Matrix Market Exchange Format).
Supplementary files format and content: Per-sample filtered_contig_annotations.csv: Cell Ranger V(D)J output containing TCR contig annotations, V(D)J gene assignments, CDR3 sequences, and clonotype information for each cell barcode.

source_name: liver metastatic tumor

extract_protocol:
Tumor-infiltrating leukocytes were isolated from liver metastatic tumors by enzymatic digestion with collagenase A (0.75 mg/ml) and DNase I (50 µg/ml) followed by density gradient centrifugation using Histopaque-1083. Cells were washed and resuspended in PBS supplemented with 1% BSA, stained with BV421 anti-mouse CD45.2 antibody (clone 104, BioLegend, Cat#109832) and 7-AAD viability solution (ThermoFisher Scientific, Cat#00-6993-50), and CD45+ live cells were sorted using BD FACSAria III (BD Biosciences, RRID: SCR_016695).
Sorted CD45+ live cells were processed to generate barcoded 5' gene expression (GEX) libraries and TCR V(D)J-enriched libraries using the Chromium Next GEM Single Cell 5' Kit v1.1 (10x Genomics, Cat#1000165) and GEM Single Cell V(D)J Reagent Kits v1.1 (10x Genomics, Cat#1000181), targeting 10,000 cells per library, following the manufacturer's instructions (CG000208 Rev G). Library quality and concentration were assessed using the Bioanalyzer High Sensitivity DNA Kit (Agilent Technologies, Cat#5067-4626) and KAPA Library Quantification Kit (Kapa Biosystems, Cat#KK4873).

value: liver metastatic tumor

value: CD45+ tumor-infiltrating leukocytes

tag: genotype


title: 20251218_WT

city: Oklahoma

first: Christopher

middle: Lee

last: Sansam

state: OK

address: 825 NE 13th Street

department: Cell Cycle and Cancer Biology Program

institute: Oklahoma Medical Research Foundation

description:
Library name: 20251218_WT
Vehicle control; Sequential EdU (50 µM, 10 min) → BrdU (50 µM, 10 min) pulse labeling followed by thymidine chase (250 µM, 40 min); HMW genomic DNA extracted and sequenced by Oxford Nanopore WGS.

library_source: genomic

data_processing:
Basecalling and alignment: Dorado v0.8.1 high-accuracy mode; alignments to hg38/GRCh38.
Replication tract detection and fork calling: DNAscent v4.0.3 (forkSense), minimum read length 20 kb.
Pipeline: ReplisomeTracer v1.0.2 used to orchestrate basecalling/alignment, DNAscent analyses, and output formatting.
Assembly: hg38 / GRCh38
Supplementary files format and content: Processed data include DNAscent detect BAM files and forkSense output archives. forkSense archives contain BED/TSV-style segmentations of EdU- and BrdU-labeled tracts and calls for leftward/rightward forks, initiation (origin) sites, and termination sites, along with per-read tract length summaries.

molecule: genomic DNA

growth_protocol: HCT116 TICRR gene-trap (mClover) cell lines were maintained under standard mammalian cell culture conditions and plated in 6‑cm dishes for labeling experiments.

extract_protocol:
High–molecular weight genomic DNA was extracted from 1×10^6 cells per sample using the Monarch HMW DNA Extraction Kit for Cells and Blood (NEB #T3050S).
Sequencing libraries were prepared from 400 ng HMW genomic DNA using the Oxford Nanopore Rapid Barcoding Kit 96 V14 (SQK‑RBK114.96) per manufacturer instructions and sequenced on a PromethION flow cell (FLO‑PRO114M) using a PromethION 2 Solo device.

treatment_protocol: Where indicated, cells were treated with the WEE1 inhibitor MK‑1775 (1 µM) for 40 min prior to labeling and maintained in MK‑1775 during EdU and BrdU labeling (total MK‑1775 exposure 1 h). Cells were sequentially pulse-labeled with EdU (50 µM, 10 min) followed by BrdU (50 µM, 10 min), then chased with thymidine (250 µM, 40 min). Vehicle controls were processed identically without MK‑1775.

tag: cell line

value: TICRR-GT[SA-mClover- ex20-22(WT)]

tag: treatment

value: vehicle

tag: batch


title: Vav1CreTet2KO CD45+ TILs, TCR, biol rep 2

description:
Library name: TCR_KO_05
10x Genomics TCR V(D)J enriched library


title: Tet2fl/fl CD45+ TILs, 5' GEX, biol rep 1

description:
Library name: GEX_WT_75
10x Genomics 5' GEX library


title: Vav1CreTet2KO CD45+ TILs, 5' GEX, biol rep 2

description:
Library name: GEX_KO_05
10x Genomics 5' GEX library


title: hnscc_30.ROI_009.Stroma.buds

description:
Library name: DSP-1001660021755-B-C10
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: 20251122_SBI_MK

description:
Library name: 20251122_SBI_MK
MK‑1775 (1 µM) for 40 min prior to labeling and during EdU/BrdU pulses; Sequential EdU (50 µM, 10 min) → BrdU (50 µM, 10 min) pulse labeling followed by thymidine chase (250 µM, 40 min); HMW genomic DNA extracted and sequenced by Oxford Nanopore WGS.

value: TICRR-GT[SA-mClover- ex20-22(DeltaSBI)]


title: Vav1CreTet2KO CD45+ TILs, TCR, biol rep 1

description:
Library name: TCR_KO_04
10x Genomics TCR V(D)J enriched library


title: hnscc_30.ROI_008.Tumor.non_budding

description:
Library name: DSP-1001660021755-B-C09
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: Vav1CreTet2KO CD45+ TILs, 5' GEX, biol rep 1

description:
Library name: GEX_KO_04
10x Genomics 5' GEX library


title: C3H10T1/2 DNMT3A/B-double knockout (DKO) cells clone 5

city: Montréal

first: Jacek

last: Majewski

state: QC

address: 740 Av. du Docteur-Penfield

department: Human Genetics

country: Canada

institute: McGill University

description: Library name: DNMT3AB_KO_c5

data_processing:
Reads were aligned using the STAR aligner (v2.6.1d)
Aligning parameters: --outFilterMultimapNmax 10 --outSAMmapqUnique 60 --outSAMunmapped Within
Assembly: mm10
Supplementary files format and content: gene raw counts

growth_protocol: C3H10T1/2 mouse mesenchymal stem cells (ATCC) were cultured in DMEM supplemented with 10% fetal bovine serum (FBS), 1% GlutaMax, and 1% penicillin–streptomycin at 37 °C in a humidified incubator with 5% CO₂.

extract_protocol:
Total RNA was extracted from approximately 1 million cells using AllPrep DNA/RNA/miRNA Universal Kit (QIAGEN) according to the manufacturer’s instructions, including on-column DNase I treatment. RNA quality was assessed using an Agilent 2100 Bioanalyzer prior to library preparation.
RNA libraries for RNA-seq were generated using the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Human/Mouse/Rat (Illumina) according to the manufacturer’s instructions.

value: Mesenchymal stem cells


title: hnscc_30.ROI_008.Stroma.non_budding

description:
Library name: DSP-1001660021755-B-C08
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: C3H10T1/2 DNMT3A/B-double knockout (DKO) cells clone 1

description: Library name: DNMT3AB_KO_c1


title: hnscc_30.ROI_009.Tumor.buds

description:
Library name: DSP-1001660021755-B-C11
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: 20251122_SBI

description:
Library name: 20251122_SBI
Vehicle control; Sequential EdU (50 µM, 10 min) → BrdU (50 µM, 10 min) pulse labeling followed by thymidine chase (250 µM, 40 min); HMW genomic DNA extracted and sequenced by Oxford Nanopore WGS.


title: C3H10T1/2 PRDX1MT cells (CRISPR edit at Prdx1 intron 5 splice acceptor site)

description: Library name: PRDX1_KO_c10


title: hnscc_30.ROI_004.Tumor.non_budding

description:
Library name: DSP-1001660021755-B-C07
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: C3H10T1/2 wiltype (WT) cells (unedited)

description: Library name: parental_1

value: WT


title: 20251104_SBI_MK

description:
Library name: 20251104_SBI_MK
MK‑1775 (1 µM) for 40 min prior to labeling and during EdU/BrdU pulses; Sequential EdU (50 µM, 10 min) → BrdU (50 µM, 10 min) pulse labeling followed by thymidine chase (250 µM, 40 min); HMW genomic DNA extracted and sequenced by Oxford Nanopore WGS.


title: 20251122_WT

description:
Library name: 20251122_WT
Vehicle control; Sequential EdU (50 µM, 10 min) → BrdU (50 µM, 10 min) pulse labeling followed by thymidine chase (250 µM, 40 min); HMW genomic DNA extracted and sequenced by Oxford Nanopore WGS.


title: hnscc_30.ROI_002.Tumor.budding

description:
Library name: DSP-1001660021755-B-C05
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: Denerv_951

city: Jerusalem

first: Hodaya

last: Polonsky

address: Givat Ram

department: Edmond & Lily Safra Center for Brain Sciences

country: Israel

institute: The Hebrew University of Jerusalem

description:
Library name: Mouse_Sample_3
For the proccesed obj_classified.rds file the orig.ident column for each sample correspond to the title column.

data_processing:
Batch A and B: Demultiplexing, cell calling and gene counting were done using the Cell Ranger software v 9.0.0.
Batch C:  Demultiplexing, cell calling and gene counting were done using the Cell Ranger software v 7.0.0.
Assembly: Mouse mm10
Supplementary files format and content: Second tab- seperated values files and matrix files

source_name: brain

extract_protocol:
Brains were excised excluding the medulla, without dissecting meninges and choroid plexus, and manually chopped (0.5–1.0 mm2 in size), before enzymatic dissociation using 0.4mg/ml Collagenase D, 2mM HEPES (BI Industries), 10μg/ml DNase (Sigma), and 2% FCS for 20 min at 37°C. For density gradient separation, the pellet was resuspended with 37% Percoll in PBS and centrifuged at 800g for 20 min at 4°C with no brake; the supernatant was then discarded. Cells were suspended in ice-cold sorting buffer (PBS supplemented with 2  mM  EDTA and 2% FCS) supplemented with anti-mouse CD16/32 (1:100, no. 101302,  BioLegend) to block Fc receptors before labeling with fluorescent antibodies against cell-surface epitopes (Supplementary Table 1). For scRNA sequencing, samples were gated for CD45+ CD11b+ after exclusion of debris and doublets, and sorted using an ARIA-III instrument (BD  Biosciences), and analyzed with BD FACSDiva (BD Biosciences) software. Isolated single cells were sorted into 1.5ml Eppendorf tubes containing PBS enriched with 10% ultra-pure BSA and then immediately subjected to library preparation for scRNA sequencing.
n single-cell RNA libraries were prepared using 10x Chromium Next Gem Single cell 3' reagent kit (version 3.1) according to the manufacturer's instructions

treatment_protocol: Splenic denervation was performed following the protocol of Zhang with minor adjustments (Zhang X, Lei B, Yuan Y, Zhang L, Hu L, Jin S, Kang B, Liao X, Sun W, Xu F, Zhong Y, Hu J, Qi H. 2020. Brain control of humoral immune responses amenable to behavioural modulation. Nature 581: 204-8)

value: brain

value: myeloid cells

tag: age

value: 5 mo

tag: Sex

value: Male

value: splenic-denervation

value: C


title: Sham_949

description:
Library name: Mouse_Sample_2
For the proccesed obj_classified.rds file the orig.ident column for each sample correspond to the title column.

value: Female

value: control


title: Denerv_956

description:
Library name: Mouse_Sample_4
For the proccesed obj_classified.rds file the orig.ident column for each sample correspond to the title column.


title: 20251104_SBI

description:
Library name: 20251104_SBI
Vehicle control; Sequential EdU (50 µM, 10 min) → BrdU (50 µM, 10 min) pulse labeling followed by thymidine chase (250 µM, 40 min); HMW genomic DNA extracted and sequenced by Oxford Nanopore WGS.


title: 20251104_WT_MK

description:
Library name: 20251104_WT_MK
MK‑1775 (1 µM) for 40 min prior to labeling and during EdU/BrdU pulses; Sequential EdU (50 µM, 10 min) → BrdU (50 µM, 10 min) pulse labeling followed by thymidine chase (250 µM, 40 min); HMW genomic DNA extracted and sequenced by Oxford Nanopore WGS.


title: Sham_948

description:
Library name: Mouse_Sample_1
For the proccesed obj_classified.rds file the orig.ident column for each sample correspond to the title column.


title: hnscc_30.ROI_002.Stroma.budding

description:
Library name: DSP-1001660021755-B-C04
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling

value: Head and neck squamous cell carcinoma


title: scRNA-seq of denervated and sham myeloid cells (Multiplexed Pool)- Sham_627, Denerv_628, Denerv_636, Sham_646

description:
Library name: denerv_B
This sample represents a multiplexed pool of 4 biological samples. Individual processed data files for each condition (Sample Sham_627, Denerv_628, Denerv_636, Sham_646) are provided as separate files. For the proccesed obj_classified.rds file the orig.ident column for each sample correspond to the title column.
Male; Male; Male; Female

value: pooled male and female

value: control; splenic-denervation; splenic-denervation; control

value: B


title: scRNA-seq of denervated and sham myeloid cells (Multiplexed Pool)- Denerv_581, Sham_586, Denerv_591, Sham_645

description:
Library name: denerv_A
This sample represents a multiplexed pool of 4 biological samples. Individual processed data files for each condition (Sample Denerv_581, Sham_586, Denerv_591, Sham_645) are provided as separate files. For the proccesed obj_classified.rds file the orig.ident column for each sample correspond to the title column.

value: splenic-denervation; control; splenic-denervation; control

value: A


title: 20251122_WT_MK

description:
Library name: 20251122_WT_MK
MK‑1775 (1 µM) for 40 min prior to labeling and during EdU/BrdU pulses; Sequential EdU (50 µM, 10 min) → BrdU (50 µM, 10 min) pulse labeling followed by thymidine chase (250 µM, 40 min); HMW genomic DNA extracted and sequenced by Oxford Nanopore WGS.

value: TICRR-GT[SA-mClover- ex20-22(WT)]


title: KO_3

city: Wenzhou

first: Xinyu

last: Yang

state: Not applicable

address: Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, 325035, China.

department: School of Pharmaceutical Sciences

country: China

institute: Wenzhou Medical University

description:
Library name: sample3
FPKM.KO_3

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: LUNG

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

value: LUNG

value: alveolar epithelial Type II

value: KIAA1199 knockout


title: hnscc_25.ROI_006.Tumor.buds

description:
Library name: DSP-1001660021755-B-C01
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: KO_1

description:
Library name: sample1
FPKM.KO_1


title: hnscc_30.ROI_001.Stroma.budding

description:
Library name: DSP-1001660021755-B-C02
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_30.ROI_004.Stroma.non_budding

description:
Library name: DSP-1001660021755-B-C06
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_30.ROI_001.Tumor.budding

description:
Library name: DSP-1001660021755-B-C03
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: over_En1-IgG

city: shenyang

first: Wei

last: Wang

address: No. 155 Nanjing North Street

institute: China Medical University Affiliated First Hospital

description:
Library name: sample 2
over_En1-IgG

data_processing:
Raw reads in fastq format were processed to remove contaminating adapter sequences using Trimmomatics
Quality distribution plot and base content distribution were generated by FASTQC
CUT&Tag reads were aligned to the hg38 genome using BWA（0.7.13-r1126） . Only uniquely mapping reads with at most two mismatches were retained.
Peaks were called uing MACS v2.1.2 with the significance cut-off q-value <=0.05
bigWig files were generated using the deeptools. Peak files were generated using MACS v2 with default settings.
Assembly: En1
Supplementary files format and content: bigWig

organism: Rattus norvegicus

extract_protocol:
CUT&Tag assay was performed as described previously with modifications(Hatice et al., 2019 ). Briefly，100000 cells were washed twice gently with wash buffer (20 mM HEPES pH 7.5; 150 mM NaCl; 0.5 mM Spermidine; 1× Protease inhibitor cocktail).
To amplify libraries, 21μL DNA was mixed with 2μL of a universal i5 and auniquely barcoded i7 primer. A volume of 25 μL NEBNext HiFi 2× PCR Master mix was added and mixed. The sample was placed in a Thermocycler with a heated lid using the following cycling conditions: 72 °C for 5 min (gap filling); 98 °C for 30 s; 14 cycles of 98 °C for 10 s and 63 °C for 30 s; final extension at 72 °C for 1 min and hold at 8 °C. libraried clean-up was performed XP beads (Beckman Counter).

value: Pheochromocytoma cells

value: WT

value: Highglucose DMEM (Hyclone) + 10% FBS (FB1058, Biosera) + 1% penicillinstreptomycin (ST488S)  24 h


title: FL_3

description:
Library name: sample6
FPKM.FL_3

value: KIAA1199 wildtype


title: FL_2

description:
Library name: sample5
FPKM.FL_2


title: KO_2

description:
Library name: sample2
FPKM.KO_2


title: 20251104_WT

description:
Library name: 20251104_WT
Vehicle control; Sequential EdU (50 µM, 10 min) → BrdU (50 µM, 10 min) pulse labeling followed by thymidine chase (250 µM, 40 min); HMW genomic DNA extracted and sequenced by Oxford Nanopore WGS.

value: vehicle


title: FL_1

description:
Library name: sample4
FPKM.FL_1


title: over_En1

description:
Library name: sample 1
over_En1

value: over En1


title: HLI-4

first: Zhaohang

last: Wu

address: Chashan

description: Library name: HLI-4

data_processing:
Illumina novaseq 6000 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
Assembly: Beta_vulgaris.GCF_000511025.2_RefBeet-1.2.2
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: gastrocnemius muscle

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: gastrocnemius muscle

value: HLI


title: testis_WT_4

city: Padova

first: Marco

last: Sandri

state: Padova

address: Via Orus 2

department: Biomedical Sciences

country: Italy

institute: University of Padova

description: Library name: Mytho_WT_4

data_processing:
Reads were aligned using STAR v2.7.1a on  Ensembl GRCz11,  release 107
FeatureCounts v 1.5.1 was used to quantify gene expression as raw fragment counts
Assembly: Ensembl GRCz11, release 107
Supplementary files format and content: tab delimited txt file reporting raw counts at the gene level, one single file include counts of all samples

organism: Danio rerio

source_name: testes

extract_protocol:
TRIzol (ThermoFisher Scientific)
Total RNA samples (1 µg) were used for library preparation (Illumina’s TruSeq Stranded mRNA LT Sample Prep Kit with poly A selection)

value: testes

tag: tumor


title: HLI-3

description: Library name: HLI-3


title: hnscc_25.ROI_006.Stroma.buds

description:
Library name: DSP-1001660021755-B-B12
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling

value: Head and neck squamous cell carcinoma


title: HLI-2

description: Library name: HLI-2


title: HLI-1

description: Library name: HLI-1


title: HLI-5

description: Library name: HLI-5


title: hnscc_25.ROI_005.Tumor.buds

description:
Library name: DSP-1001660021755-B-B11
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: Sham-5

description: Library name: Sham-5

value: Sham


title: Sham-3

description: Library name: Sham-3


title: Sham-4

description: Library name: Sham-4


title: testis_WT_2

description: Library name: Mytho_WT_2


title: hnscc_25.ROI_004.Tumor.non_budding

description:
Library name: DSP-1001660021755-B-B09
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_25.ROI_005.Stroma.buds

description:
Library name: DSP-1001660021755-B-B10
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: P16 testis, Hsf5 knockdown, biol rep1

city: Wuhan

first: shen

last: jin

state: Hubei

address: No. 299, Bayi Road, Wuchang District, Wuhan City

institute: Wuhan university

description: Library name: SAMPLES3

data_processing:
Adaptor sequences were removed from 3′ end of the raw fastq file using cutadapt with parameters(-m 16 --trimmed-only). Then these reads were aligned to non-coding RNAs, piRNA clusters,  genomic transposable element sequences retrieved from RepeatMasker and  mouse genome(UCSC mm39)
Assembly: UCSC mm39
Supplementary files format and content: tab-delimited txt file includes raw counts for each Sample

source_name: testis

extract_protocol:
Total RNA was used as input material for the RNA sample preparations. Briefly, 3’ and 5’ adaptors were ligated to 3’ and 5’ end of small RNA, respectively.
Then the first strand cDNA was synthesized after hybridization with reverse transcription primer. The double-stranded cDNA library was generated through PCR enrichment. After purification and size selection, libraries with insertions between18~40 bp were ready for sequencing.

value: testis

value: Hsf5 knockdown


title: hnscc_25.ROI_004.Stroma.non_budding

description:
Library name: DSP-1001660021755-B-B08
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: testis_WT_1

description: Library name: Mytho_WT_1


title: P16 testis, Wild type, biol rep1

description: Library name: SAMPLES1


title: testis_mythoKO_1

description: Library name: Mytho_KO_1


title: testis_mythoKO_2

description: Library name: Mytho_KO_2


title: Sham-1

description: Library name: Sham-1


title: P16 testis, Hsf5 knockdown, biol rep2

description: Library name: SAMPLES4


title: Surface_Protein_Tumor

city: Münster

first: Carlos

last: Silvestre Roig

address: Von Esmarch Str. 56

institute: University of Münster

description:
Library name: SURF_B4-AK36792-AK36793_HNW33DSX5_S18_L003
Contains HTO and ADT

library_source: other

data_processing:
Demultiplexing, barcode processing, gene counting and aggregation were made using Cellranger V7.0.1
Assembly: mm10
Supplementary files format and content: CellRanger output files filtered_feature_bc_matrix representing raw counts, barcodes and gene information.
Library strategy: CITE-seq

molecule: protein

source_name: Tumor

extract_protocol:
Mice were euthanized by ketamine/xylazine overdose, the blood was collected by heart puncture after which the mice were flushed with 10 ml of ice-cold PBS. Subsequently, organs were harvested and directly processed for functional assays or flow cytometry analysis. Blood was collected in a tube containing EDTA and incubated with erythrocyte lysis buffer (Biolegend) for 6 minutes on ice for erythrocyte lysis. After washing, cells were centrifugated and resuspended in HANKs buffer (HBSS w/o Mg and Ca + 0.06% BSA + 0.3mM EDTA). For isolation of bone marrow cells, the femur was harvested and flushed using 5 mL of HANKs buffer using a syringe with a 21G needle. Splenic cells were obtained by the mince and smashing of the spleen over a 70um filter. Fresh tumor samples were digested in an enzyme mixture (DMEMc (Dulbecco´s modified Eagle´s medium (Thermo Fisher Scientific, Massachusetts, USA) supplemented with 10% fetal bovine serum (PAN-Biotech, Aidenbach, Germany) and 100 U/mL penicillin‒streptomycin (Thermo Fisher Scientific)) supplemented with 0.2 μg/mL dispase, 0.2 μg/mL collagenase A, and 100 μg/mL DNase I (Merck, Darmstadt, Germany)), with 1 mL per sample for 45 min at 500 rpm and 37 °C. The cells were passed through 100 μm sterile strainers (Cell Trics, Partec, Sysmex Europe GmbH, Goerlitz, Germany) and centrifuged at 300 × g and 4 °C for 5 min, after which the supernatant was discarded. Bone marrow, splenic or tumor cells were subjected to erythrocyte lysis in 1mL of erythrocyte lysis buffer (Biolegend) for 1 minute on ice. After washing, cells were centrifugated and resuspended in HANKs buffer. Samples were then normalized across conditions to obtain similar number of target cells (myeloid cell populations and progenitors). Normalized samples were then incubated with hashtag antibodies  specific for each organ, mouse and condition. After extensive washing, cells were FACS-sorted.
Sorted cells were then loaded into the 10x Genomic platform and processed with 10X Chromium Next GEM Single-Cell 3′ Reagent Kit with Feature Barcoding technology following manufacturer’s instructions. he HTO counts are appended to the end matrix.mtx.gz files, with identifiers in the features file starting with "HTO...".

value: Tumor

value: WT, Genotype_02 (gene knockout mouse model)

value: MPOC tumor

tag: library type

value: HTO and ADT


title: P16 testis, Wild type, biol rep2

description: Library name: SAMPLES2


title: testis_WT_3

description: Library name: Mytho_WT_3


title: hnscc_25.ROI_003.Stroma.non_budding

description:
Library name: DSP-1001660021755-B-B06
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_25.ROI_003.Tumor.non_budding

description:
Library name: DSP-1001660021755-B-B07
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: testis_mythoKO_seminoma_2

description: Library name: KO_seminoma_3

value: seminoma


title: hnscc_25.ROI_002.Tumor.budding

description:
Library name: DSP-1001660021755-B-B05
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: Surface_Protein_Bone_Marrow

description:
Library name: SURF_B2-AK36049-AK43596_HNW33DSX5_S16_L003
Contains HTO and ADT

source_name: Bone marrow

value: Bone marrow


title: Surface_Protein_Blood

description:
Library name: SURF_B1-AK36043-AK43597_HNW33DSX5_S15_L003
Contains HTO and ADT

source_name: Blood

value: Blood


title: hnscc_25.ROI_002.Stroma.budding

description:
Library name: DSP-1001660021755-B-B04
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: Sham-2

description: Library name: Sham-2

value: WT


title: Surface_Protein_Spleen

description:
Library name: SURF_B3-AK36778-AK36779_HNW33DSX5_S17_L003
Contains HTO and ADT

source_name: Spleen

value: Spleen


title: testis_mythoKO_seminoma_1

description: Library name: KO_seminoma_1


title: scRNA_Spleen

description: Library name: RNA_B3_S10_L004

value: mRNA


title: scRNA_Tumor

description: Library name: RNA_B4_S11_L004


title: scRNA_Blood

description: Library name: RNA_B1_S8_L004


title: THR278

city: New York City

first: Matthew

last: Muller

state: NY

address: 550 First Avenue

department: Department of Medicine

institute: New York University

description: Library name: Sample 71

data_processing:
Data processing and quality control were performed using the SeqNSlide Pipeline
Quality control of sequencing reads was assessed using FastQC (v.0.11.9) and MultiQC (v.1.10.1)
Reads were trimmed using fastqc (v.0.20.1) and trimmomatic, and mapped to human reference genome hg38 using STAR (v.2.7.7a).
Genomic features were then assigned using Subread featureCounts (v.1.6.3)
Assembly: hg38
Supplementary files format and content: space-delimited text file includes raw counts per sample per gene

source_name: whole blood

extract_protocol:
Peripheral whole blood RNA was collected into PAXgene Blood RNA tubes (Becton Dickinson and Company, Franklin Lakes, New Jersey) and stored at −80 C. Automated RNA extraction was performed using the QIAsymphony PAXgene Blood RNA Kit (PreAnalytiX, Qiagen/BD). RNA yield and integrity were evaluated prior to sequencing.
Library preparation was performed with the Illumina TruSeq kit (Illumina, San Diego, CA) using 200 ng of total RNA per sample as input. Libraries were amplified for 12 PCR cycles, then quantified, normalized, and pooled for sequencing. Sequencing was carried out on an Illumina HiSeq 4000 platform (v4 chemistry, single-read configuration).

value: whole blood

tag: phenotype

value: CAD

value: Female

tag: race

value: Other

tag: ethnicity

value: Hispanic/Latino


title: scRNA_Bone_Marrow

description: Library name: RNA_B2_S9_L004


title: hnscc_25.ROI_001.Tumor.budding

description:
Library name: DSP-1001660021755-B-B03
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling

value: Head and neck squamous cell carcinoma


title: THR270

description: Library name: Sample 70

value: Male

value: White

value: Non-Hispanic


title: hnscc_32.ROI_006.Tumor.non_budding

description:
Library name: DSP-1001660021755-B-B01
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_25.ROI_001.Stroma.budding

description:
Library name: DSP-1001660021755-B-B02
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: Neutro,SP,rep3

description: Library name: Neutro_SP_rep3

data_processing:
Fastq files were trimmed from Nextera adapters using fastp (0.23.2)
Trimmed fastq files were aligned to GRCm38 (GENCODE vM25) with bowtie2 (2.5.0) with options "-X 2000 --very-sensitive" and duplicates were marked with samblaster (0.1.26)
Alignments were filtered for mappings to chr1-19, chrX/Y and further filtered with samtools with options "-q20 -F3332" to retain alignments with mapping quality above 20, removing unmapped reads, non-primary and supplementary alignments and marked duplicated.
For peak calling, we first extracted transposase insertion sites from the filtered BAM files using bedtools (v2.30.0) and awk using the command "bedtools bamtobed -i filtered.bam | mawk 'OFS=      {if ($6 == +) print $1, $2+4, $2+5, ., ., $6} {if ($6 == -) print $1, $3-5, $3-4, ., ., $6}'". Then we called peaks with macs2 (2.2.7.1) on each of the resulting BED files using the callpeak command with options "--keep-dup=all --nomodel --extsize 100 --shift -50 --min-length 250 -g mm -f BED". Peaks were filtered against overlap with the merge of the ENCODE mm10 blacklist and a blacklist for homologs of the mitochondrial genome in the nuclear genome, available at https://github.com/Boyle-Lab/Blacklist/tree/master/lists and https://github.com/buenrostrolab/mitoblacklist/tree/master/fasta .
NarrowPeak files from biological replicates (that is celltype_organ) were grouped and those peaks were retained that showed a reciprocal overlap of at least 50% in at least two replicates of the group. That resulted in one set of peaks per group which were subsequently merged using bedtools merge to create the template "regulome".
The matrix of raw counts based on the regulome BED file was then created with featureCounts from subread (2.0.1) using the options "--read2pos 5 --readExtension3 4" using the per-sample filtered bam files as input.
For subsequent downstream analysis please refer to the code documentation in our paper.
Assembly: GRCm38.p6 (GENCODE vM25)
Supplementary files format and content: Matrix of raw counts for both the entire (unfiltered) regulome. Matrices (filtered for sufficient counts using edgeR filterByExpr with min.count=100) containing raw counts, cpm, logcpm, and normalization offsets (the latter produced with csaw function normOffsets). Metadata file with per-sample annotations. The metadata contains a column with a size factor that was used to normalize the genome browser tracks (bedGraph/bigwig files) shown in the paper. To use it, divide the 4th column of a bedGraph/bigwig file by this per-sample size factor.

source_name: SP

extract_protocol:
Mice were euthanized by ketamine/xylazine overdose, the blood was collected by heart puncture after which the mice were flushed with 10 ml of ice-cold PBS. Subsequently, organs were harvested and directly processed for functional assays or flow cytometry analysis. Blood was collected in a tube containing EDTA and incubated with erythrocyte lysis buffer (Biolegend) for 6 minutes on ice for erythrocyte lysis. After washing, cells were centrifugated and resuspended in HANKs buffer (HBSS w/o Mg and Ca + 0.06% BSA + 0.3mM EDTA). For isolation of bone marrow cells, the femur was harvested and flushed using 5 mL of HANKs buffer using a syringe with a 21G needle. Splenic cells were obtained by the mince and smashing of the spleen over a 70um filter. Bone marrow, and splenic cells were subjected to erythrocyte lysis in 1mL of erythrocyte lysis buffer (Biolegend) for 1 minute on ice. After washing, cells were centrifugated and resuspended in HANKs buffer. Samples were then normalized across conditions to obtain similar number of target cells (myeloid cell populations and progenitors). Normalized samples were then incubated with hashtag antibodies  specific for each organ, mouse and condition. After extensive washing, cells were FACS-sorted.
Sorted cells were immediately subjected to library preparation using the OmniATAC protocol, PCR-amplified and sequenced on Novaseq-6000.

treatment_protocol: C57BL6/J female mice were administered with cyclophosphamide (CPM), followed by daily administration of 5 mg/kg of AMD3100 (AMD).

value: SP

value: Neutro

value: WT BL6

value: AMD


title: Neutro,Bld,rep3

description: Library name: Neutro_Bld_rep3

source_name: Bld

value: Bld


title: THR266

description: Library name: Sample 68


title: Neutro,SP,rep4

description: Library name: Neutro_SP_rep4


title: THR264

description: Library name: Sample 67


title: THR268

description: Library name: Sample 69


title: hnscc_32.ROI_005.Tumor.buds

description:
Library name: DSP-1001660021755-B-A11
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: Neutro,Bld,rep2

description: Library name: Neutro_Bld_rep2


title: Neutro,SP,rep1

description: Library name: Neutro_SP_rep1


title: hnscc_32.ROI_006.Stroma.non_budding

description:
Library name: DSP-1001660021755-B-A12
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: Neutro,SP,rep2

description: Library name: Neutro_SP_rep2


title: Neutro,BM,rep4

description: Library name: Neutro_BM_rep4

source_name: BM

value: BM


title: hnscc_32.ROI_005.Stroma.buds

description:
Library name: DSP-1001660021755-B-A10
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: Neutro,Bld,rep1

description: Library name: Neutro_Bld_rep1


title: Neutro,BM,rep2

description: Library name: Neutro_BM_rep2


title: THR254

description: Library name: Sample 65


title: Neutro,BM,rep1

description: Library name: Neutro_BM_rep1


title: hnscc_32.ROI_004.Tumor.buds

description:
Library name: DSP-1001660021755-B-A09
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: Neutro,BM,rep3

description: Library name: Neutro_BM_rep3


title: THR262

description: Library name: Sample 66

value: Black


title: THR253

description: Library name: Sample 64


title: imNeu,Bld,rep3

description: Library name: imNeu_Bld_rep3

value: imNeu


title: hnscc_32.ROI_004.Stroma.buds

description:
Library name: DSP-1001660021755-B-A08
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: THR244

description: Library name: Sample 63

value: whole blood


title: imNeu,Bld,rep1

description: Library name: imNeu_Bld_rep1


title: imNeu,Bld,rep2

description: Library name: imNeu_Bld_rep2


title: imNeu,SP,rep1

description: Library name: imNeu_SP_rep1


title: imNeu,SP,rep4

description: Library name: imNeu_SP_rep4


title: hnscc_32.ROI_003.Tumor.non_budding

description:
Library name: DSP-1001660021755-B-A07
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: imNeu,BM,rep3

description: Library name: imNeu_BM_rep3


title: imNeu,SP,rep2

description: Library name: imNeu_SP_rep2


title: imNeu,BM,rep4

description: Library name: imNeu_BM_rep4


title: THR216

description: Library name: Sample 59

value: CAD

value: Asian


title: hnscc_32.ROI_003.Stroma.non_budding

description:
Library name: DSP-1001660021755-B-A06
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_32.ROI_002.Stroma.budding

description:
Library name: DSP-1001660021755-B-A04
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: imNeu,BM,rep1

description: Library name: imNeu_BM_rep1


title: THR217

description: Library name: Sample 60


title: THR236

description: Library name: Sample 62


title: PreN,SP,rep4

description: Library name: PreN_SP_rep4

value: PreN


title: THR232

description: Library name: Sample 61


title: imNeu,SP,rep3

description: Library name: imNeu_SP_rep3


title: PreN,SP,rep3

description: Library name: PreN_SP_rep3


title: imNeu,BM,rep2

description: Library name: imNeu_BM_rep2


title: hnscc_32.ROI_002.Tumor.budding

description:
Library name: DSP-1001660021755-B-A05
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: PreN,SP,rep2

description: Library name: PreN_SP_rep2


title: hnscc_32.ROI_001.Tumor.budding

description:
Library name: DSP-1001660021755-B-A03
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: PreN,SP,rep1

description: Library name: PreN_SP_rep1


title: THR213

description: Library name: Sample 57

value: Female

value: Hispanic/Latino


title: THR215

description: Library name: Sample 58

value: Male


title: hnscc_32.ROI_001.Stroma.budding

description:
Library name: DSP-1001660021755-B-A02
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling

value: Head and neck squamous cell carcinoma


title: THR211

description: Library name: Sample 56

value: Other


title: PreN,BM,rep4

description: Library name: PreN_BM_rep4


title: PreN,BM,rep3

description: Library name: PreN_BM_rep3


title: PreN,BM,rep2

description: Library name: PreN_BM_rep2


title: EDL933 25 micromolar norepinephrine, biological replicate 3

city: Cambridge

first: Abigail

last: McShane

state: MA

address: 77 Massachusetts Ave

department: Biological Engineering

institute: Massachusetts Institute of Technology

description: Library name: D24-6676

data_processing:
Raw sequencing reads were processed to obtain the raw abundance matrix of tRNAs using an optimized version of the custom data analytical pipeline designed for AQRNA-seq.
Assembly: Sequence reads were mapped to an custom E. coli O157:H7 EDL933 tRNA reference sequence library.
Supplementary files format and content: A tab-delimited text file containing raw abundance (i.e., read counts) across different tRNA isoacceptors.

molecule: other

organism: Escherichia coli

source_name: Escherichia coli O157:H7 EDL933

growth_protocol: An overnight culture of EHEC O157:H7 strain EDL933 was diluted 1:100 in 3mL DMEM low glucose (supplemented with HEPES and pyruvate, no serum) with 0, 25, and 50 micromolar norepinephrine, at 37C, 180rpm. Cells were grown for 5hrs (to early stationary phase).

extract_protocol:
The isolation of small RNAs from bacterial cells was performed using the PureLink miRNA Isolation Kit with slight modifications. Cells were lysed using TRIzol (Sigma-Aldrich), followed by chloroform treatment and centrifugation to separate the RNA-containing aqueous phase. Total RNAs were passed through Spin Cartridges with different ethanol concentrations to selectively bind and separate large and small RNAs. Finally, the small RNAs were eluted in RNase-free water after washing and a final centrifugation step.
cDNA libraries were prepared using 75 ng of small RNAs as the input, following a variation of the AQRNA-seq library constuction protocol (PMCID: PMC8355021, PMID: 38372376) with two modifications. First, the use of a high-processivity reverse transcriptase replaced the need for AlkB demethylation. Second, an ExoI digestion was included immediately after the reverse transcription step to mitigate primer-dimer formation and eliminate the need for gel purification. Constructed libraries were subjected to quality assessment using Fragment Analyzer and qPCR.

treatment_protocol: Norepinephrine bitartrate salt was eluted in water to a stock concentration of 50mM and filter sterilized. This was diluted into growth media to give final media concentrations of 25 and 50 micromolar, respectively.

value: Escherichia coli O157:H7 EDL933

value: 25 micromolar norepinephrine


title: PreN,BM,rep1

description: Library name: PreN_BM_rep1

value: WT BL6


title: GMP,SP,rep4

description: Library name: GMP_SP_rep4

value: SP

value: GMP

value: AMD


title: THR180

description: Library name: Sample 55

value: White

value: Non-Hispanic


title: GMP,SP,rep3

description: Library name: GMP_SP_rep3


title: EDL933 50 micromolar norepinephrine, biological replicate 3

description: Library name: D24-6677

value: 50 micromolar norepinephrine


title: EDL933 50 micromolar norepinephrine, biological replicate 2

description: Library name: D24-6674


title: EDL933 25 micromolar norepinephrine, biological replicate 2

description: Library name: D24-6673


title: EDL933 0 micromolar norepinephrine, biological replicate 3

description: Library name: D24-6675

value: 0 micromolar norepinephrine


title: EDL933 0 micromolar norepinephrine, biological replicate 2

description: Library name: D24-6672


title: RNA_01_Blood, Sham, IgG, Splenectomy, Partial_irradiation_anti-CXCR2

description:
Library name: E1
E1_E2_matrix_raw.mtx.gz
E1_E2_matrix_filtered.mtx.gz
E1_E2_barcodes_raw.tsv.gz
E1_E2_barcodes_filtered.tsv.gz
E1_E2_features_raw.tsv.gz
E1_E2_features_filtered.tsv.gz
E1_E2_metadata.xlsx
feature_reference.xlsx

data_processing:
Demultiplexing, barcode processing, gene counting and aggregation were made using Cellranger V3.1 and V6.02
Assembly: mm10
Supplementary files format and content: CellRanger output files from the two folders raw_feature_bc_matrix and filtered_feature_bc_matrix representing raw counts, barcodes and gene information.

extract_protocol:
Mice were euthanized by ketamine/xylazine overdose, the blood was collected by heart puncture after which the mice were flushed with 10 ml of ice-cold PBS. Subsequently, organs were harvested and directly processed for functional assays or flow cytometry analysis. Blood was collected in a tube containing EDTA and incubated with erythrocyte lysis buffer (Biolegend) for 6 minutes on ice for erythrocyte lysis. After washing, cells were centrifugated and resuspended in HANKs buffer (HBSS w/o Mg and Ca + 0.06% BSA + 0.3mM EDTA). For isolation of bone marrow cells, the femur was harvested and flushed using 5 mL of HANKs buffer using a syringe with a 21G needle. Splenic cells were obtained by the mince and smashing of the spleen over a 70um filter. Bone marrow or splenic cells were subjected to erythrocyte lysis in 1mL of erythrocyte lysis buffer (Biolegend) for 1 minute on ice. After washing, cells were centrifugated and resuspended in HANKs buffer. Samples were then normalized across conditions to obtain similar number of target cells (myeloid cell populations and progenitors). Normalized samples were then incubated with hashtag antibodies  specific for each organ, mouse and condition. After extensive washing, were FACS-sorted.
Sorted cells were then loaded into the 10x Genomic platform and processed with 10X Chromium Next GEM Single-Cell 3′ Reagent Kit with Feature Barcoding technology following manufacturer’s instructions. he HTO counts are appended to the end matrix.mtx.gz files, with identifiers in the features file starting with "HTO...".

value: Blood

value: WT

value: saline or CPM/AMD


title: GMP,BM,rep3

description: Library name: GMP_BM_rep3

value: BM


title: RNA_02_Blood, Sham, IgG, Splenectomy, Partial_irradiation_anti-CXCR2

description:
Library name: E2
E1_E2_matrix_raw.mtx.gz
E1_E2_matrix_filtered.mtx.gz
E1_E2_barcodes_raw.tsv.gz
E1_E2_barcodes_filtered.tsv.gz
E1_E2_features_raw.tsv.gz
E1_E2_features_filtered.tsv.gz
E1_E2_metadata.xlsx
feature_reference.xlsx


title: Surface_02_Blood, Sham, IgG, Splenectomy, Partial_irradiation_anti-CXCR2

description:
Library name: A2
E1_E2_matrix_raw.mtx.gz
E1_E2_matrix_filtered.mtx.gz
E1_E2_barcodes_raw.tsv.gz
E1_E2_barcodes_filtered.tsv.gz
E1_E2_features_raw.tsv.gz
E1_E2_features_filtered.tsv.gz
E1_E2_metadata.xlsx
feature_reference.xlsx

data_processing:
Demultiplexing, barcode processing, gene counting and aggregation were made using Cellranger V3.1 and V6.02
Assembly: mm10
Supplementary files format and content: CellRanger output files from the two folders raw_feature_bc_matrix and filtered_feature_bc_matrix representing raw counts, barcodes and gene information.
Library strategy: CITE-seq


title: THR177

description: Library name: Sample 53

value: whole blood

value: CAD

value: Male


title: THR170

description: Library name: Sample 51

value: Female


title: Surface_01_Blood, Sham, IgG, Splenectomy, Partial_irradiation_anti-CXCR2

description:
Library name: A1
E1_E2_matrix_raw.mtx.gz
E1_E2_matrix_filtered.mtx.gz
E1_E2_barcodes_raw.tsv.gz
E1_E2_barcodes_filtered.tsv.gz
E1_E2_features_raw.tsv.gz
E1_E2_features_filtered.tsv.gz
E1_E2_metadata.xlsx
feature_reference.xlsx


title: RNA_Bone Marrow and Spleen, CPM/AMD treatment and Treatment 1, Day 2

description:
Library name: 20034-0018
20034_matrix_raw.mtx.gz
20034_matrix_filtered.mtx.gz
20034_barcodes_raw.tsv.gz
20034_barcodes_filtered.tsv.gz
20034_features_raw.tsv.gz
20034_features_filtered.tsv.gz
metadata.xlsx
feature_reference.xlsx

source_name: Bone marrow, Spleen

value: Bone marrow, Spleen

value: CPM/AMD


title: THR166

description: Library name: Sample 50

value: Asian


title: EDL933 50 micromolar norepinephrine, biological replicate 1

description: Library name: D24-6671

value: Escherichia coli O157:H7 EDL933


title: RNA_Blood and Organ 1, CPM/AMD treatment and Treatment 1, Day 2

description:
Library name: 20034-0017
20034_matrix_raw.mtx.gz
20034_matrix_filtered.mtx.gz
20034_barcodes_raw.tsv.gz
20034_barcodes_filtered.tsv.gz
20034_features_raw.tsv.gz
20034_features_filtered.tsv.gz
metadata.xlsx
feature_reference.xlsx

source_name: Blood, Organ 1

value: Blood, Organ 1


title: RNA_Bone Marrow and Spleen, CPM/AMD treatment and Treatment 1, Day 1

description:
Library name: 20034-0016
20034_matrix_raw.mtx.gz
20034_matrix_filtered.mtx.gz
20034_barcodes_raw.tsv.gz
20034_barcodes_filtered.tsv.gz
20034_features_raw.tsv.gz
20034_features_filtered.tsv.gz
metadata.xlsx
feature_reference.xlsx


title: GMP,BM,rep1

description: Library name: GMP_BM_rep1

value: GMP

value: WT BL6

value: AMD


title: THR176

description: Library name: Sample 52

value: Other

value: Non-Hispanic


title: EDL933 25 micromolar norepinephrine, biological replicate 1

description: Library name: D24-6670

value: 25 micromolar norepinephrine


title: THR157

description: Library name: Sample 49

value: White


title: RNA_Blood and Organ 1, CPM/AMD treatment and Treatment 1, Day 1

description:
Library name: 20034-0015
20034_matrix_raw.mtx.gz
20034_matrix_filtered.mtx.gz
20034_barcodes_raw.tsv.gz
20034_barcodes_filtered.tsv.gz
20034_features_raw.tsv.gz
20034_features_filtered.tsv.gz
metadata.xlsx
feature_reference.xlsx

value: WT


title: EDL933 0 micromolar norepinephrine, biological replicate 1

description: Library name: D24-6669

value: 0 micromolar norepinephrine


title: RNA_Bone Marrow and Spleen, Saline treatment and Treatment 1, Day 2

description:
Library name: 20034-0014
20034_matrix_raw.mtx.gz
20034_matrix_filtered.mtx.gz
20034_barcodes_raw.tsv.gz
20034_barcodes_filtered.tsv.gz
20034_features_raw.tsv.gz
20034_features_filtered.tsv.gz
metadata.xlsx
feature_reference.xlsx

value: Saline


title: THR152

description: Library name: Sample 47

value: whole blood

value: CAD

value: Male

value: Hispanic/Latino


title: THR153

description: Library name: Sample 48

value: Female


title: RNA_Blood and Organ 1, Saline treatment and Treatment 1, Day 1

description:
Library name: 20034-0011
20034_matrix_raw.mtx.gz
20034_matrix_filtered.mtx.gz
20034_barcodes_raw.tsv.gz
20034_barcodes_filtered.tsv.gz
20034_features_raw.tsv.gz
20034_features_filtered.tsv.gz
metadata.xlsx
feature_reference.xlsx


title: Surface_Protein_Bone Marrow and Spleen, CPM/AMD treatment and Treatment 1, Day 2

description:
Library name: 20034-0008
20034_matrix_raw.mtx.gz
20034_matrix_filtered.mtx.gz
20034_barcodes_raw.tsv.gz
20034_barcodes_filtered.tsv.gz
20034_features_raw.tsv.gz
20034_features_filtered.tsv.gz
metadata.xlsx
feature_reference.xlsx

value: Bone marrow, Spleen

value: CPM/AMD


title: SP_MEP_rep2

description: Library name: lane3_TCCTGA

data_processing:
STAR alignment, Gene quantification using Salmon, differential expression was made using Deseq2
Assembly: mm10
Supplementary files format and content: csv file with FPKM values for each sample

extract_protocol:
TotalRNA was isolated using PicoPure Kit (Thermofisher) following manufacturer's protocol.
SMARTer smRNA-Seq Kit was used to generate Illumina libraries.

value: Spleen

value: MEP


title: SP_MEP_rep3

description: Library name: lane4_CGAGGC


title: Surface_Protein_Blood and Organ 1, CPM/AMD treatment and Treatment 1, Day 2

description:
Library name: 20034-0007
20034_matrix_raw.mtx.gz
20034_matrix_filtered.mtx.gz
20034_barcodes_raw.tsv.gz
20034_barcodes_filtered.tsv.gz
20034_features_raw.tsv.gz
20034_features_filtered.tsv.gz
metadata.xlsx
feature_reference.xlsx

value: Blood, Organ 1


title: SP_MEP_rep4

description: Library name: lane4_TCCTGA


title: Surface_Protein_Bone Marrow and Spleen, CPM/AMD treatment and Treatment 1, Day 1

description:
Library name: 20034-0006
20034_matrix_raw.mtx.gz
20034_matrix_filtered.mtx.gz
20034_barcodes_raw.tsv.gz
20034_barcodes_filtered.tsv.gz
20034_features_raw.tsv.gz
20034_features_filtered.tsv.gz
metadata.xlsx
feature_reference.xlsx


title: SP_MEP_rep1

description: Library name: lane3_CGAGGC


title: THR150

description: Library name: Sample 46


title: THR149

description: Library name: Sample 45


title: Surface_Protein_Blood and Organ 1, Saline treatment and Treatment 1, Day 2

description:
Library name: 20034-0003
20034_matrix_raw.mtx.gz
20034_matrix_filtered.mtx.gz
20034_barcodes_raw.tsv.gz
20034_barcodes_filtered.tsv.gz
20034_features_raw.tsv.gz
20034_features_filtered.tsv.gz
metadata.xlsx
feature_reference.xlsx


title: SP_LSK_rep3

description: Library name: lane4_GGACTC

value: LSK


title: RNA_Blood and Organ 1, Saline treatment and Treatment 1, Day 2

description:
Library name: 20034-0013
20034_matrix_raw.mtx.gz
20034_matrix_filtered.mtx.gz
20034_barcodes_raw.tsv.gz
20034_barcodes_filtered.tsv.gz
20034_features_raw.tsv.gz
20034_features_filtered.tsv.gz
metadata.xlsx
feature_reference.xlsx


title: Surface_Protein_Bone Marrow and Spleen, Saline treatment and Treatment 1, Day 1

description:
Library name: 20034-0002
20034_matrix_raw.mtx.gz
20034_matrix_filtered.mtx.gz
20034_barcodes_raw.tsv.gz
20034_barcodes_filtered.tsv.gz
20034_features_raw.tsv.gz
20034_features_filtered.tsv.gz
metadata.xlsx
feature_reference.xlsx


title: Surface_Protein_Blood and Organ 1, Saline treatment and Treatment 1, Day 1

description:
Library name: 20034-0001
20034_matrix_raw.mtx.gz
20034_matrix_filtered.mtx.gz
20034_barcodes_raw.tsv.gz
20034_barcodes_filtered.tsv.gz
20034_features_raw.tsv.gz
20034_features_filtered.tsv.gz
metadata.xlsx
feature_reference.xlsx


title: THR147

description: Library name: Sample 44

value: Asian

value: Non-Hispanic


title: THR143

description: Library name: Sample 43

value: White


title: RNA_Bone Marrow and Spleen, Saline treatment and Treatment 1, Day 1

description:
Library name: 20034-0012
20034_matrix_raw.mtx.gz
20034_matrix_filtered.mtx.gz
20034_barcodes_raw.tsv.gz
20034_barcodes_filtered.tsv.gz
20034_features_raw.tsv.gz
20034_features_filtered.tsv.gz
metadata.xlsx
feature_reference.xlsx

value: WT


title: Surface_Protein_Bone Marrow and Spleen, Saline treatment and Treatment 1, Day 2

description:
Library name: 20034-0004
20034_matrix_raw.mtx.gz
20034_matrix_filtered.mtx.gz
20034_barcodes_raw.tsv.gz
20034_barcodes_filtered.tsv.gz
20034_features_raw.tsv.gz
20034_features_filtered.tsv.gz
metadata.xlsx
feature_reference.xlsx


title: SP_LSK_rep4

description: Library name: lane4_TAAGGC


title: THR141

description: Library name: Sample 42


title: BCA and Blood, ZT13, 5 mice, HTO

first: Oliver

last: Soehnlein

address: Von-Esmarch-Str. 56

department: Institute of Experimental Pathology

institute: University Hospital Münster

description:
Library name: X5_HTO
hashtag-derived oligonucleotide (HTO)
X5_matrix_raw.mtx.gz
X5_matrix_filtered.mtx.gz
X5_barcodes_raw.tsv.gz
X5_barcodes_filtered.tsv.gz
X5_features_raw.tsv.gz
X5_features_filtered.tsv.gz

data_processing:
Fastq files for both gene expression and hashtag oligos were preprocessed with default CellRanger 9.0.0 using the mm10 reference from 10X. The HTO counts are appended to the end matrix.mtx.gz files, with identifiers in the features file starting with "HTO...".
Hashtag oligo counts were demultiplexed using the Bioconductor package DropletUtils.
Assembly: mm10
Supplementary files format and content: CellRanger output files from the two folders raw_feature_bc_matrix and filtered_feature_bc_matrix representing raw counts, barcodes and gene information.
Library strategy: CITE-seq

source_name: BCA, Blood

extract_protocol:
Mice were euthanized by ketamine/xylazine overdose, the blood was collected by heart puncture after which the mice were flushed with 10 ml of ice-cold PBS. Subsequently, organs were harvested and directly processed for functional assays or flow cytometry analysis. Blood was collected in a tube containing EDTA and incubated with erythrocyte lysis buffer (Biolegend) for 6 minutes on ice for erythrocyte lysis. After washing, cells were centrifugated and resuspended in HANKs buffer (HBSS w/o Mg and Ca + 0.06% BSA + 0.3mM EDTA). For isolation of bone marrow cells, the femur was harvested and flushed using 5 mL of HANKs buffer using a syringe with a 21G needle. Splenic cells were obtained by the mince and smashing of the spleen over a 70um filter.  For lung perfusion, heart and lungs from PBS-perfused mouse were gently harvested and placed on ice in a Petri dish. A needle was inserted into the right ventricle, at the level of the pulmonary artery, and lungs was slowly perfused with 20 ml of ice-cold PBS + 5 mM EDTA to detach adherent cells. For liver perfusion, PBS-perfused mice were placed on a cooling pad, the portal vein was canulated using a catheter and fixed in place with tissue adhesive (Surgibond). Once the catheter was fixed in place, the liver was gently harvested and placed on ice in a Petri dish. Liver was then slowly perfused with 20 ml of ice-cold PBS + 5 mM EDTA using a perfusion pump (2ml/min) to detach adherent cells. For isolating aortic cells, the brachiocephalic artery was isoalted, cleaned from surrounding fat and digested in 1 ml RPMI with 10% FCS and 1.25 mg/ml Liberase at 37 °C for 1 hour. Brachiocephalic artery (BCA), bone marrow, splenic cells as well as lung and liver perfusates were subjected to erythrocyte lysis in 1mL of erythrocyte lysis buffer (Biolegend) for 1 minute on ice. After washing, cells were centrifugated and resuspended in HANKs buffer. Samples were then normalized across conditions to obtain similar number of target cells (myeloid cell populations and progenitors). Normalized samples were then incubated with hashtag antibodies specific for each organ, mouse and condition (samples X1, X2, X4, X5) or only organ (samples X3, X6). After extensive washing, cells were pooled FACS-sorted.
Sorted cells were then loaded into the 10x Genomic platform and processed with 10X Chromium Next GEM Single-Cell 3′ Reagent Kit with Feature Barcoding technology following manufacturer’s instructions.

value: BCA, Blood

value: ApoE-/-

value: 16w HFD


title: Surface_Protein_Blood and Organ 1, CPM/AMD treatment and Treatment 1, Day 1

description:
Library name: 20034-0005
20034_matrix_raw.mtx.gz
20034_matrix_filtered.mtx.gz
20034_barcodes_raw.tsv.gz
20034_barcodes_filtered.tsv.gz
20034_features_raw.tsv.gz
20034_features_filtered.tsv.gz
metadata.xlsx
feature_reference.xlsx


title: SP_LSK_rep2

description: Library name: lane3_TAAGGC


title: THR140

description: Library name: Sample 41

value: whole blood

value: CAD


title: Enriched BCA, ZT13, 5 mice, HTO

description:
Library name: X4_HTO
hashtag-derived oligonucleotide (HTO)
X4_matrix_raw.mtx.gz
X4_matrix_filtered.mtx.gz
X4_barcodes_raw.tsv.gz
X4_barcodes_filtered.tsv.gz
X4_features_raw.tsv.gz
X4_features_filtered.tsv.gz

source_name: BCA

value: BCA


title: Blood, BM, Spleen, Liver, Lung, ZT13, pooled mice, HTO

description:
Library name: X6_HTO
hashtag-derived oligonucleotide (HTO)
X6_matrix_raw.mtx.gz
X6_matrix_filtered.mtx.gz
X6_barcodes_raw.tsv.gz
X6_barcodes_filtered.tsv.gz
X6_features_raw.tsv.gz
X6_features_filtered.tsv.gz

source_name: Blood, BM, Spleen, Liver, Lung

value: Blood, BM, Spleen, Liver, Lung


title: SP_LSK_rep1

description: Library name: lane3_GGACTC


title: control_2

description:
Library name: DSP-1001660021806-C-A01
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling

data_processing:
BCL to FASTQ conversion was performed using DRAGEN and the following command line options: dragen --bcl-conversion-only true --bcl-input-directory /path/to/BCL/directory --output-directory /path/to/FASTQ --sample-sheet /path/to/SeqCodeIndices/SeqCodeIndices.csv FASTQ files were processed using the NanoString GeoMx NGS Pipeline v2.3.3.10 and the following command line options: geomxngspipeline --in=/path/to/FASTQ --out=/path/to/DCC --ini=/path/to/GNP_config.ini The following default options were used: --quality-trim-score=20 (score used for quality trimming), --trim-adapter=true (enable/disable adapter trimming), --adapter-trim-match-length=10 --adapter-trim-max-mismatch=3 , --stitching-max-mismatch=2, --stitch-shift=true, --barcode-max-mismatch=1, --dedup-hd=1. For all downstream analysis, the deduplicated read counts were used. For each segment, additional quality control thresholds were applied. The minimum number of reads per segment was set at 40,000, the minimum number of successfully stitched reads at 80%, and the minimum number of aligned reads at 70%. Additionally, sequencing saturation was required to be at least 50%, while non-template control (NTC) wells were limited to a maximum of 1,000 counts. Each segment (that is a specific ROI-AOI combination) contained a set of negative probes; the geometric mean of the counts of the negative probes was calculated per segment and used to define the limit of quantification (LOQ), according to the formula LOQ = max (2, NegGeoMean × NegGeoSD2), where NegGeoMean is the geometric mean of the counts of the negative probes and NegGeoSD is the geometric standard deviation of the counts of the negative probes for a given segment. Essentially, the LOQ is defined as 2 standard deviations above the negative control mean and at minimum as at least 2 counts. Using the segment-specific LOQ thresholds, segments with exceptionally low signal (fewer than 5% of the genes detected above LOQ) and genes with low detection rates (fewer than 10% of the segments having detected a given gene above LOQ) were filtered out. The final post-QC dataset consisted of 239 segments and 7,795 genes. The raw counts were normalized to upper quartile (UQ or Q3) normalized counts and, for each case, the mean of the normalized counts for each gene was calculated for segments belonging to the same segment type.
Assembly: hg38
Supplementary files format and content: DCC files containing the raw counts for each probe.
Library strategy: Spatial Transcriptomics

organism: synthetic construct

source_name: No tissue (negative control)

extract_protocol:
Slides were imaged in three fluorescence channels (FITC/525 nm, Cy3/568 nm, and Texas Red/615 nm) to visualize morphology markers, and regions of interest were segmented based on the expression of the morphology markers. For each tumor, two regions of interest (ROIs) were sampled from the bulk of the tumor and the surrounding stromal tissue. In budding cases, an additional two to three ROIs were sampled, focusing specifically on tumor bud cells and the adjacent stroma. Each ROI is then divided in distinct areas of illumination (AOIs) based on the morphology markers PanCK and CD45. PanCK-negative/CD45-positive cells were assigned the “immune” AOI,  PanCK-negative/CD45-negative cells were assigned the “stroma” AOI, and PanCK-positive/CD45-negative cells were assigned the “tumor” AOI. Each AOI was sequentially illuminated with UV and the UV-cleavable released tags were collected into 96-well plates.
The library preparation was performed according to the GeoMx DSP NGS Readout User Manual. In short, the 96-well plate was dried by being left on the bench top overnight covered by a permeable membrane which was subsequently replaced by another permeable membrane and the plate was then spinned down. The samples were then rehydrated with ten µL nuclease-free water and the plate was pulse-centrifuged to 1000 x g. GeoMx Seq Code primers were used to amplify the WTA tags and add Illumina adaptor sequences and sample demultiplexing barcodes. The GeoMx Seq Code primer plate was thawed and the GeoMx Seq Code primer plate and the GeoMx NGS Master Mix were pulse-centrifuged to 1000 x g. The subsequent PCR reaction was set up on a PCR plate with two μL of GeoMx NGS Master Mix, four μL of GeoMx Seq Code primer mix (added to the corresponding PCR plate well), and four μL of DSP aspirate (added to the corresponding PCR plate well) used per well. The PCR plate was sealed with a PCR plate sticker, pulse centrifuged to 1000 x g, and incubated in the thermocycler with a 100°C heated lid. The cycling conditions were as follows: UDG treatment at 37°C for 30 min, followed by UDG deactivation at 50°C for ten min. Initial denaturation was performed at 95°C for three minutes. Amplification consisted of 18 cycles of denaturation at 95°C for 15 sec, annealing at 65°C for 60 sec, and extension at 68°C for 30 sec. A final extension was carried out at 68°C for five minutes, followed by an indefinite hold at 4°C. The PCR products were pooled using four μL of each PCR product (including the NTC) and the remainder of the NTC PCR product was placed into a separate tube. The tubes with the sample pool and the NTC went through the same AMPure cleanup protocol using the 1.2-fold volume AMPure XP beads and the libraries were sequenced on an Illumina NextSeq 550 with 27x27 paired end reads.

value: No tissue (negative control)


title: SP_GMP_rep4

description: Library name: lane4_TAGGCA

value: GMP


title: BCA and Blood, ZT1, 5 mice, HTO

description:
Library name: X2_HTO
hashtag-derived oligonucleotide (HTO)
X2_matrix_raw.mtx.gz
X2_matrix_filtered.mtx.gz
X2_barcodes_raw.tsv.gz
X2_barcodes_filtered.tsv.gz
X2_features_raw.tsv.gz
X2_features_filtered.tsv.gz


title: Blood, BM, Spleen, Liver, Lung, ZT1, pooled mice, HTO

description:
Library name: X3_HTO
hashtag-derived oligonucleotide (HTO)
X3_matrix_raw.mtx.gz
X3_matrix_filtered.mtx.gz
X3_barcodes_raw.tsv.gz
X3_barcodes_filtered.tsv.gz
X3_features_raw.tsv.gz
X3_features_filtered.tsv.gz


title: THR136

description: Library name: Sample 40

value: Male


title: control_1

description:
Library name: DSP-1001660021758-A-A01
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: control_3

description:
Library name: DSP-1001660021757-D-A01
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: THR103

description: Library name: Sample 37

value: Hispanic/Latino


title: SP_GMP_rep2

description: Library name: lane3_TAGGCA

value: Spleen


title: control_4

description:
Library name: DSP-1001660021755-B-A01
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: Blood, BM, Spleen, Liver, Lung, ZT13, pooled, GEX mice

description:
Library name: X6_mRNA
polyA RNA

data_processing:
Fastq files for both gene expression and hashtag oligos were preprocessed with default CellRanger 9.0.0 using the mm10 reference from 10X. The HTO counts are appended to the end matrix.mtx.gz files, with identifiers in the features file starting with "HTO...".
Hashtag oligo counts were demultiplexed using the Bioconductor package DropletUtils.
Assembly: mm10
Supplementary files format and content: CellRanger output files from the two folders raw_feature_bc_matrix and filtered_feature_bc_matrix representing raw counts, barcodes and gene information.


title: THR129

description: Library name: Sample 38


title: THR135

description: Library name: Sample 39


title: THR179

description: Library name: Sample 54


title: Enriched BCA, ZT1, 5 mice, HTO

description:
Library name: X1_HTO
hashtag-derived oligonucleotide (HTO)
X1_matrix_raw.mtx.gz
X1_matrix_filtered.mtx.gz
X1_barcodes_raw.tsv.gz
X1_barcodes_filtered.tsv.gz
X1_features_raw.tsv.gz
X1_features_filtered.tsv.gz


title: SP_GMP_rep1

description: Library name: lane3_CGTACT


title: SP_GMP_rep3

description: Library name: lane4_CGTACT


title: Enriched BCA, ZT13, 5 mice, GEX

description:
Library name: X4_mRNA
polyA RNA


title: SP_CMP_rep3

description: Library name: lane4_AGGCAG

value: CMP


title: THR102

description: Library name: Sample 36


title: BCA and Blood, ZT13, 5 mice, GEX

description:
Library name: X5_mRNA
polyA RNA


title: THR090

description: Library name: Sample 34

value: Asian


title: C95

city: Toronto

first: Rachel

middle: D

last: Edgar

state: ON

address: 101 College Street

department: Ajmera Transplant Centre

institute: University Health Network

description:
Library name: C95-3_A1
Stored 2 years, 1 year room temperature 1 year 4°C

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files
Sequences were aligned to human genome GRCh38 using Space Ranger’s default settings
Gene expression levels were quantified using Space Ranger’s default settings
Assembly: GRCh38-2020-A (10x reference package)
Supplementary files format and content: binned_outputs_square_002um_filtered_feature_bc_matrix_barcodes.tsv.gz: list of spatial barcodes for 2um bins
Supplementary files format and content: binned_outputs_square_002um_filtered_feature_bc_matrix_features.tsv.gz: list gene IDs for 2um bins
Supplementary files format and content: binned_outputs_square_002um_filtered_feature_bc_matrix_matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format for 2um bins
Supplementary files format and content: binned_outputs_square_002um_spatial_scalefactors_json.json: scale factors in json format for 2um bins
Supplementary files format and content: binned_outputs_square_002um_spatial_tissue_positions.parquet: spatial coordinates for 2um bins
Supplementary files format and content: binned_outputs_square_008um_filtered_feature_bc_matrix_barcodes.tsv.gz: list of spatial barcodes for 8um bins
Supplementary files format and content: binned_outputs_square_008um_filtered_feature_bc_matrix_features.tsv.gz: list gene IDs for 8um bins
Supplementary files format and content: binned_outputs_square_008um_filtered_feature_bc_matrix_matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format for 8um bins
Supplementary files format and content: binned_outputs_square_008um_spatial_scalefactors_json.json: scale factors in json format for 8um bins
Supplementary files format and content: binned_outputs_square_008um_spatial_tissue_positions.parquet: spatial coordinates for 8um bins
Supplementary files format and content: binned_outputs_square_016um_filtered_feature_bc_matrix_barcodes.tsv.gz: list of spatial barcodes for 16um bins
Supplementary files format and content: binned_outputs_square_016um_filtered_feature_bc_matrix_features.tsv.gz: list gene IDs for 16um bins
Supplementary files format and content: binned_outputs_square_016um_filtered_feature_bc_matrix_matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format for 16um bins
Supplementary files format and content: binned_outputs_square_016um_spatial_scalefactors_json.json: scale factors in json format for 16um bins
Supplementary files format and content: binned_outputs_square_016um_spatial_tissue_positions.parquet: spatial coordinates for 16um bins
Supplementary files format and content: cloupe_008um.cloupe: Loupe Browser visualization file
Supplementary files format and content: feature_slice.h5: feature count matrix
Supplementary files format and content: metrics_summary.csv: sample quality metrics
Supplementary files format and content: molecule_info.h5: per-molecule barcode and UMI information
Supplementary files format and content: probe_set.csv: probe design and annotation table
Supplementary files format and content: spatial_aligned_fiducials.jpg: fiducial markers aligned to slide
Supplementary files format and content: spatial_cytassist_image.tiff: cytAssist-captured tissue image
Supplementary files format and content: spatial_detected_tissue_image.jpg: tissue segmentation mask
Supplementary files format and content: spatial_tissue_hires_image.png: high resolution tissue image
Supplementary files format and content: spatial_tissue_lowres_image.png: low resolution tissue image
Supplementary files format and content: web_summary.html: summary of some data metrics
Library strategy: Spatial Transcriptomics

source_name: Liver Caudate

extract_protocol:
Formalin-fixed paraffin-embedded liver tissue was cut into 5-µm sections.
Spatial transcriptome sequencing libraries were prepared following the Visium HD Gene Expression User Guide

value: Liver Caudate

value: Female


title: Blood, BM, Spleen, Liver, Lung, ZT1, pooled mice, GEX

description:
Library name: X3_mRNA
polyA RNA


title: ATP2B1 scRNAseq

first: Angelica

last: Varesi

institute: University of Toronto

description:
Library name: ATP2B1_scRNAseq
Single Cell Multiome ATAC + Gene Expression v1

data_processing:
scMultiome data generated in this study were aligned to GRCh38 using CellRanger-ARC (v2.0.2), which was subsequently used to aggregate samples and normalize read counts to a uniform median depth.
Assembly: hg38
Supplementary files format and content: CellRanger output files: atac_fragments.tsv.gz, filtered_feature_bc_matrix.tar.gz and raw_feature_bc_matrix.tar.gz

source_name: Cord Blood

extract_protocol:
Cord Blood CD34+ enrichment (Miltenyi Biotec)
CD49f+ATP2B1+, CD49f+ATP2B1- and CD49f-ATP2B1- samples were processed for library preparation as described in (Zeng and Nagree et al., Biorxiv 2023), link (https://www.biorxiv.org/content/10.1101/2023.09.11.557271v2)

value: Cord Blood

value: Hematopoietic Stem Cells


title: SP_CMP_rep2

description: Library name: lane3_CTCTCT

value: WT


title: C113

description:
Library name: C113_only
Stored for 2 years at 4°C

source_name: Liver Right Lobe

value: Liver Right Lobe


title: SP_CMP_rep1

description: Library name: lane3_AGGCAG


title: THR095

description: Library name: Sample 35

value: whole blood

value: Non-Hispanic


title: SP_CMP_rep4

description: Library name: lane4_CTCTCT


title: BCA and Blood, ZT1, 5 mice, GEX

description:
Library name: X2_mRNA
polyA RNA

value: BCA, Blood

value: ApoE-/-

value: 16w HFD


title: THR058

description: Library name: Sample 33

value: CAD

value: White


title: Enriched BCA, ZT1, 5 mice, GEX

description:
Library name: X1_mRNA
polyA RNA

value: BCA


title: Sample32 Preterm GFP (-) non NPCs At PC20.5

city: Melbourne

first: Mehran

last: Piran

state: VIC

address: 19 Innovation Walk

department: Anatomy and Developmental Biology

country: Australia

institute: Monash University

description: Library name: S32_preterm20

data_processing:
FASTQ files were first assessed for quality using base-level metrics including per-base sequence content, GC content, adaptor contamination, and sequence duplication levels. Overrepresented sequences and adaptor content were flagged and used to guide preprocessing decisions. Trimming of nucleotides at both the 3′ and 5′ ends, as well as removal of overrepresented sequences using TrimGlore and BBDuK, was carried out using a combination of trimming strategies and overrepresented sequence removal. Pre-processed reads were aligned to the mouse reference genome, GRCm39, using STAR. Read count quantification was implemented using featureCounts tool. MultiQC was used to summarise alignment metrics across samples.
Assembly: GRCm39
Supplementary files format and content: Each file is a gene-level annotation and quantification table, in tab-delimited text format, where each row represents an Ensembl gene ID, with accompanying genomic and expression information. The "Chr", "Start", and "End" columns list the chromosome and genomic coordinates, sometimes with multiple semicolon-separated entries reflecting exons or transcript variants, while the **Strand** column indicates the DNA strand orientation (`+` or `-`, or multiple values if features span both). The "Length" column gives the size of the annotated region in base pairs, and the "Counts"  column reports the number of sequencing reads mapped to each gene, serving as a measure of expression.

source_name: kidney

growth_protocol: All animal experiments were approved by the Institutional Animal Care and Use Committee of the Hadassah Hebrew University. All mice were housed in the Hebrew University Specific Pathogen–Free Animal Facility Unit. The study utilized CD1 outbred mice, including transgenic mice. Specifically, we used the transgenic mice line Tg(Six2-EGFP/cre) Amc (herein Six2 Cre+/tg). Heterozygous Six2 Cre+/tg embryos were generated by mating male Six2 Cre+/tg  mice (8 to 10 weeks old) with wild-type (WT) CD1 females (8 to 10 weeks old). The day of vaginal plug detection was considered embryonic day 0.5 of pregnancy. Pregnant females were randomly assigned to the different experimental groups. At PC19.5 and PC 20.5, kidneys from each letter and each group were dissected from all pups, and no gender-specific analysis was performed.

extract_protocol:
The pups kidney were carefully dissected and excised in ice-cold HBSS buffer. Using a surgical scalpel, the kidneys were sliced and chopped into approximately 0.5- to 1-mm pieces on ice. The chopped kidney fragments were then transferred into an HBSS solution supplemented with 1 mg/ml collagenase (11213865001; Sigma-Aldrich) and dispase (D4693-1G; Sigma-Aldrich) and incubated at 37°C for 30 minutes. The cell suspension was filtered through a 40-mm nylon cell strainer (Corning) and washed twice with cold HBSS. Six2 Cre+/tg GFP(+) and GFP(-) NPCs were isolated by cell flow cytometry-based cell sorting at the Hebrew University Faculty of Medicine Core Facility. For RNA extraction, 50,000-100,000 cells were washed in cold HBSS, and total RNA was extracted using the Qiagen RNeasy Micro Kit (74004; Qiagen).
Libraries were prepared from RNA samples using a SMARTer® Stranded Total RNA-Seq Kit v4 (Takara Bio). The libraries were barcoded and pooled for multiplex sequencing. The pooled DNA library was loaded on a NovaSeq 6000 SP Reagent Kit v1.5 (100 cycles) cartridge (Illumina) and sequenced on an Illumina Novaseq 6000 System using a single-read sequencing condition of 100 cycles.

treatment_protocol: The pregnant mice were randomly assigned to one of two groups : Preterm group,pregnant females were injected with a single subcatanouse dose of mifepristone at the post conception (PC) day 17.5 leading to delivery at PC18.5 and Term group. pregnant mice were injected with the same dose at PC18.5 to deliver at PC19.5. On PC19.5 and PC20.5, the pups were dissected, kidneys were extracted and the nephron progenitor cells and non nephron progenitor cells were sorted.

value: kidney

value: non NPC

value: Heterozygous CD-1 WT/ Six2 Cre+/tg embryos

value: Mifepristone at PC17.5


title: BM_MEP_rep4

description: Library name: lane2_TCCTGA

source_name: Bone marrow

value: Bone marrow

value: MEP


title: THR049

description: Library name: Sample 31

value: Male

value: Hispanic/Latino


title: C107

description:
Library name: C107_D1
Stored for 1 year at 4°C

value: Liver Caudate


title: Sample30 Preterm GFP (-) non NPCs At PC20.5

description: Library name: S30_preterm20


title: THR047

description: Library name: Sample 30

value: whole blood


title: BM_MEP_rep3

description: Library name: lane2_CGAGGC

value: WT


title: ATP2B1 scATACseq

description:
Library name: ATP2B1_scATAC
Single Cell Multiome ATAC + Gene Expression v1

library_source: genomic single cell

value: Cord Blood

value: Hematopoietic Stem Cells


title: HEK293T, 10X-Cys, biol rep 3

city: Martinsried

first: Assa

last: Yeroslaviz

state: Bavaria

address: Am Klopferspitz 18

department: computational Biology

institute: Max-Planck-Institute for biochemistry

description: Library name: 10x_Cys_9

data_processing:
Reads were mapped to the human genome GRCh38 using STAR version 2.7.10b
reads were quantified using HTseq tool69 in Python
sample normalization and differential expression analysis was done using DESeq2 package70 (R 4.3.3, DESeq version 1.42.0)
Assembly: GRCh38
Supplementary files format and content: tab-delimited file containing DESeq2-normalized counts for each sample per column

source_name: cultured cells

extract_protocol:
Cells were lysed using 1 mL of TRIzol™ (Thermo Fisher Scientific) and the samples were stored at -80 °C overnight. Subsequently, 200 μL of chloroform was added and the RNA phase was collected following centrifugation for 10 minutes at 4°C at 12700 rpm. The RNA fraction was precipitated with 500 μL of 2-propanol and washed with 1 ml of EtOH 70%. Finally, the pellet was left to dry and resuspend in 25 μL of RNAse-free water.
Bulk mRNA sequencing libraries were prepared with 1ug of total RNA of each sample using the NEBNext Ultra™ II Directional RNA Library Prep Kit for Illumina® (E7760, NEB) with NEBNext® Poly(A) mRNA Magnetic Isolation Module (E7490, NEB), according to standard manufacturer’s protocol. Total RNA and the final library quality controls were performed using Qubit™ Flex Fluorometer (Q33327, Thermo Fisher Scientific) and 4200 TapeStation System (G2991BA, Agilent) before and after library preparation. The libraries were sequenced on Element AVITI (2 x 75 bp, on average 20M reads per sample) and demultiplexed by bases2fastq software (Element).

value: cultured cells

value: embryonal kidney


title: BM_MEP_rep2

description: Library name: lane1_TCCTGA


title: Sample28 Preterm GFP (-) non NPCs At PC20.5

description: Library name: S28_preterm20


title: HEK293T, 10X-Cys, biol rep 4

description: Library name: 10x_Cys_10


title: HEK293T, 10X-Cys, biol rep 2

description: Library name: 10x_Cys_8


title: THR044

description: Library name: Sample 29

source_name: whole blood

value: CAD

value: Black

value: Non-Hispanic


title: THR056

description: Library name: Sample 32

value: Female

value: White


title: Sample26 Preterm GFP (-) non NPCs At PC20.5

description: Library name: S26_preterm20

value: kidney

value: non NPC

value: Heterozygous CD-1 WT/ Six2 Cre+/tg embryos

value: Mifepristone at PC17.5


title: THR040

description: Library name: Sample 28

value: Male


title: BM_LSK_rep4

description: Library name: lane2_TAAGGC

value: Bone marrow

value: LSK


title: HEK293T, 10X-Cys, biol rep 1

description: Library name: 10x_Cys_7


title: BM_LSK_rep3

description: Library name: lane2_GGACTC

value: WT


title: Sample22 Term GFP (-) non NPCs At PC20.5

description: Library name: S22_term20

value: Mifepristone at PC18.5


title: Sample24 Term GFP (-) non NPCs At PC20.5

description: Library name: S24_term20


title: HEK293T, 1X-Cys, biol rep 3

description: Library name: 1X_Cys_5


title: THR039

description: Library name: Sample 27

value: whole blood


title: THR033

description: Library name: Sample 26


title: HEK293T, 1X-Cys, biol rep 4

description: Library name: 1X_Cys_6

value: cultured cells


title: BM_MEP_rep1

description: Library name: lane1_CGAGGC

value: MEP


title: Sample20 Term GFP (-) non NPCs At PC20.5

description: Library name: S20_term20


title: HEK293T, 1X-Cys, biol rep 2

description: Library name: 1X_Cys_4

value: embryonal kidney


title: Sample16 Preterm GFP (-) non NPCs At PC19.5

description: Library name: S16_preterm19


title: BM_LSK_rep2

description: Library name: lane1_TAAGGC


title: BM_LSK_rep1

description: Library name: lane1_GGACTC


title: BM_GMP_rep4

description: Library name: lane2_TAGGCA

value: GMP


title: THR025

description: Library name: Sample 23

value: CAD

value: Hispanic/Latino


title: THR027

description: Library name: Sample 24

value: White

value: Non-Hispanic


title: Sample18 Term GFP (-) non NPCs At PC20.5

description: Library name: S18_term20

value: kidney

value: non NPC


title: Sample14 Preterm GFP (-) non NPCs At PC19.5

description: Library name: S14_preterm19

value: Heterozygous CD-1 WT/ Six2 Cre+/tg embryos

value: Mifepristone at PC17.5


title: THR028

description: Library name: Sample 25

value: Male


title: BM_GMP_rep3

description: Library name: lane2_CGTACT

value: Bone marrow


title: THR022

description: Library name: Sample 22

value: Female


title: Sample12 Preterm GFP (-) non NPCs At PC19.5

description: Library name: S12_preterm19


title: HEK293T, 1X-Cys, biol rep 1

description: Library name: 1X_Cys_3


title: HEK293T, 0X-Cys, biol rep 1

description: Library name: 0X_Cys_1


title: HEK293T, 0X-Cys, biol rep 2

description: Library name: 0X_Cys_2


title: BM_GMP_rep2

description: Library name: lane1_TAGGCA

value: WT


title: BM_GMP_rep1

description: Library name: lane1_CGTACT


title: Healthy Control 2, Fluorophore positive, Tetramer positive, IGK/L targeted

city: Chapel Hill

first: Office of Genomics Research

last: UNC Lineberger Comprehensive Cancer Center

state: NC

address: 125 Mason Farm Road, CB #7599 5105-5106 Marsico Hall

institute: University of North Carolina at Chapel Hill

description: Library name: HC2 TPOS IGKL

data_processing:
Airrflow NF-core pipeline v4.1.1
Assembly: Hg38
Supplementary files format and content: IgH/K/L consensus clonotypes, TSV format
Library strategy: BCR-Seq

source_name: Peripheral blood mononuclear cells

growth_protocol: Cells were cultured inImmunoCult Human B cell expansion kit media (StemCell Catalog #100-0645) media containing CD40L (Bio-Techne, 6245-CL, 0.5 μg/mL), CpG oligodeoxynucleotide (InvivoGen, tlrl-2006, 1 μg/mL) in humidified conditions with 5% CO2 at 37degrees

extract_protocol:
RNeasy Plus Micro Kit
Takara SMARTer Human BCR IgG IgM H/K/L Profiling Kit

treatment_protocol: MPO antigen (Elastin, No. MY862, 1 ng/mL) was added to all cells

value: Peripheral blood mononuclear cells

value: B cells


title: THR021

description: Library name: Sample 21

value: whole blood


title: PACE236

description: Library name: Sample 20

value: PAD


title: BM_CMP_rep4

description: Library name: lane2_CTCTCT

value: CMP


title: Sample10 Preterm GFP (-) non NPCs At PC19.5

description: Library name: S10_preterm19


title: PACE235

description: Library name: Sample 19


title: Healthy Control 2, Fluorophore negative, IGK/L targeted

description: Library name: HC2 ANEG IGKL


title: Sample8 Term GFP (-) non NPCs At PC19.5

description: Library name: S8_term19

value: Mifepristone at PC18.5