title: exs10KOS0 population-Rep1

description:
S0 population replication 1
FACs experiments with surface marker CD71/Ter119 divided the fetal liver cells into S0-S5 population from immature to mature erythroid cells.


title: Placenta, RNA Control4 Rep1

status: Public on Jul 01 2026

type: SRA

city: London

first: Pradeepa

middle: M

last: Madapura

state: UK

address: 4 Newark Street, Whitechapel

country: United Kingdom

institute: Queen Mary University of London

library_source: transcriptomic

data_processing:
The reads were processed and mapped using STAR aligner. The mapped data obtained as bam files were further used for merging, sorting and indexing. The sorted bam files were converted to bigwigs via deepTools (version 3.5.1) bamCoverage tool with --skipNAs  –normalizeUsing  RPKM --smoothLength 60  --centerReads options.
PolyA RNA-seq
Assembly: GRCh38/hg38
Supplementary files format and content: bigwig containing signal for RNAseq

molecule: total RNA

organism: Homo sapiens

source_name: Placenta tissue

growth_protocol: Healthy control and preeclampsia placenta biopsies were used for performing CUT&Tag and RNA sequencing

extract_protocol:
RNA was isolated from placental biopsies using TRI reagent solution (ThermoFisher Scientific, AM9738), and genomic DNA was eliminated by treating RNA samples with Turbo RNAse free DNAse1 (ThermoFisher Scientific AM1907).
RNA sequencing library preparation using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (NEB #E7765), followed by libraries, were sequenced as 150 bp paired-end reads using Novaseq 6000.
PolyA RNA-seq

tag: tissue

value: Placenta tissue

tag: group

value: Control


title: Control_Ax_2_input

first: Braulio

last: Martinez De La Cruz

address: Gower Street

department: LMCB

institute: UCL

description:
Library name: S22
Column name in processed data file matches "title" in this file

data_processing:
Sequencing data was processed using nf-core/rnaseq (https://zenodo.org/records/7998767) of the nf-core collection of workflows. Reads were pre-processed including quality filtered and trimmed before being mapped to GRCm38, using a combination of fastqc, samtools, star, salmon, trimgalore (full list of software and processes in table S3) set with default parameters. Mapped reads were deduplicated and quantified to produce gene counts which were used as input for differential gene expression. Differential gene expression was performed with the SARTools pipeline using DESeq2. Differential gene expression analysis was performed using edgeR using TMM normalization. Only genes with more than 15 total counts with at least 10 counts in one of the samples were considered for further processing. Surrogate Variable Analysis was used to remove batch effects. Linear models were fitted through all eight conditions (~ SV1 + SV2 + compartment * seqmethod * treatment). Gene Ontology analysis was performed using Metascape and plots were created with ggplot2 (Wickham, 2009) on R (R Core Team, 2014).
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files with raw and size normalised counts per gene for each sample

organism: Mus musculus

source_name: Nervous

growth_protocol: Primary sympathetic neurons from p0-p2 mice were seeded on the top compartment of trans-well membranes and cultured in "NGF medium" composed of DMEM + 10% FBS + 1% Pen/Strep + 2 mM L-Glutamine supplemented with 100 ug/ml NGF and 10 uM Ara-C for at least 14 days before treatment

extract_protocol:
Cells were washed 3x in 1x PBS, and the top and bottom of a trans-well membrane was scraped for Cell Bodies/Axonal fractions, respectively. The fractions were collected, pelleted, and PBS was replaced with cell lysis buffer from PureLink RNA Micro Kit
After saving 10% RNA for inputs, RNA was sheared into ~200 bp fragments using the NEBNext® Magnesium RNA Fragmentation Module (New England Biolabs, Cat. E6150S). After purification with AMPure XP beads (Beckman Coulter, Cat. A63880), meRIP was performed as described above. RNA size, quality, and concentration were verified via TapeStation High Sensitivity RNA ScreenTape Analysis. Using the Watchmaker RNA Library Prep Kit with Polaris available under aCC-BY-NC-ND 4.0 International license. (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made bioRxiv preprint doi: https://doi.org/10.1101/2025.09.01.671701; this version posted September 3, 2025. The copyright holder for this preprint 17 Depletion (Watchmaker Genomics, Cat. 7BK0002-024), rRNA and Goblin RNA depletion, first and second strand cDNA synthesis, sequencing library prep and amplification were performed in one continuous workflow.

treatment_protocol: Medium was removed, cells were washed 3x with 1xPBS, and medium without NGF was added for 18 hours. Cells were then restimulated by replacing medium with NGF medium for 1 hour.

value: Nervous

tag: cell type

value: Sympathetic neurons

tag: cell subset

value: Ax

tag: genotype

value: Wildtype

tag: treatment

value: Growth under NGF


title: Restim_Ax_1

description:
Library name: S13
Column name in processed data file matches "title" in this file

data_processing:
Sequencing data was processed using nf-core/rnaseq (https://zenodo.org/records/7998767) of the nf-core collection of workflows. Reads were pre-processed including quality filtered and trimmed before being mapped to GRCm38, using a combination of fastqc, samtools, star, salmon, trimgalore (full list of software and processes in table S3) set with default parameters. Mapped reads were deduplicated and quantified to produce gene counts which were used as input for differential gene expression. Differential gene expression was performed with the SARTools pipeline using DESeq2. Differential gene expression analysis was performed using edgeR using TMM normalization. Only genes with more than 15 total counts with at least 10 counts in one of the samples were considered for further processing. Surrogate Variable Analysis was used to remove batch effects. Linear models were fitted through all eight conditions (~ SV1 + SV2 + compartment * seqmethod * treatment). Gene Ontology analysis was performed using Metascape and plots were created with ggplot2 (Wickham, 2009) on R (R Core Team, 2014).
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files with raw and size normalised counts per gene for each sample
Library strategy: MeRIP-Seq

value: Restimulation with NGF after 18 hours of starvation


title: T26_0056

type: genomic

city: Tübingen

first: Daniel

middle: J.

last: Merk

address: Otfried-Müller-Str. 27

country: Germany

institute: Hertie-Institute for Clinical Brain Research

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hypridized to human Infinium MethylationEPIC version 2 array using standard Illumina protocols

scan_protocol: Arrays were imaged using BeadArray Reader and standard recommended Illumina scanner protocols

data_processing:
SeSAMe pipline (v1.24.0)
Average Beta values

label: Cy3 and Cy5

molecule: genomic DNA

source_name: meningioma

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA from human meningiomas was extracted using QIAamp DNA Blood Mini Kit

value: meningioma


title: exs10WTS45 population-Rep3

city: bethesda

first: Xiang

last: Guo

state: MD

address: 50 south drive, blg50

department: NIDDK

country: USA

institute: NIH

description:
S4 and S5 population replication 3
FACs experiments with surface marker CD71/Ter119 divided the fetal liver cells into S0-S5 population from immature to mature erythroid cells.

data_processing:
Sequenced reads were trimmed for adaptor sequence,  then mapped to mouse Gencode m12  whole genome using hisat2 v2.1.0 with default parameters respectively. Multimappnig reads were filtered using samtoools 1.9, uniquely aligned reads were then mapped to gene features using Subread featureCounts v1.6.4
Differential expression between groups of samples was tested using R version 3.5.1 with DESeq2 1.20.0
Assembly: mouse GRCm38
Supplementary files format and content: tab-delimited text files include gene count values for each Sample ...

source_name: fetal livers

growth_protocol: DIS3 and EXOSC10 WT and KO mice were housed in NIDDK mouse core facility, in accordance with guidelines of the Animal Care and Use Committee of the National Institutes of Health under a Division of Intramural Research, NIDDK approved animal study protocols. Fetal livers isolated from E14.5 control and knockout mice.

extract_protocol:
Total RNA was isolated using RNeasy Plus Micro Kit and Arcturus PicoPure RNA Isolation Kit
RNA sequencing libraries were generating from 100ng-1 ug of RNA using Illumina Stranded Total RNA Rrep Ligation with Ribo-Zero Plus following manufacturer’s protocol.

value: fetal livers

tag: strain

value: WT

tag: age

value: Embryonic day 14.5


title: Placenta, RNA PE+IUGR3 Rep2

value: PE+IUGR


title: Restim_CB_4

description:
Library name: S12
Column name in processed data file matches "title" in this file

value: CB


title: T26_0131


title: T26_0068


title: Placenta, RNA PE+IUGR3 Rep1


title: exs10WTS45 population-Rep2

description:
S4 and S5 population replication 2
FACs experiments with surface marker CD71/Ter119 divided the fetal liver cells into S0-S5 population from immature to mature erythroid cells.


title: Restim_CB_3

description:
Library name: S11
Column name in processed data file matches "title" in this file


title: exs10WTS45 population-Rep1

description:
S4 and S5 population replication 1
FACs experiments with surface marker CD71/Ter119 divided the fetal liver cells into S0-S5 population from immature to mature erythroid cells.


title: Placenta, RNA PE5 Rep2

value: PE


title: T26_0278


title: Restim_CB_2

description:
Library name: S10
Column name in processed data file matches "title" in this file


title: exs10WTS3 population-Rep3

description:
S3 population replication 3
FACs experiments with surface marker CD71/Ter119 divided the fetal liver cells into S0-S5 population from immature to mature erythroid cells.


title: Placenta, RNA PE5 Rep1


title: Subject 127, EuE, ALDH-High

city: Houston

first: Peixin

last: Jiang

state: TX

address: 1515 Holcombe Blvd

institute: UT MD Anderson Cancer Center

description:
Library name: Sample 3
EH2

data_processing:
Raw sequencing reads were preprocessed using fastp for low-quality reads filtering and adapter-trimming.
Reads were aligned to reference genome using STAR Aligner.
The gene count table was generated using featureCounts.
The raw counts were filtered, normalized, and analyzed using DESeq2.
Assembly: GRCh38
Supplementary files format and content: Tab-sperated value files.

source_name: Endometriosis lesion

extract_protocol:
We used Direct-zol RNA Miniprep Kit (Zymo Research) to extract RNA.
Library was prepared using Illumina TruSeq RNA Library Prep Kit and sequenced with Illumina Novaseq.

value: Endometriosis lesion

value: Epithelium


title: Restim_CB_1

description:
Library name: S9
Column name in processed data file matches "title" in this file


title: HSF, ctrl-1

city: Shanghai

first: Xin

last: Huang

state: China

address: zhizaoju Road 639

country: China

institute: Ninth People's Hospital affiliated to Shanghai Jiao Tong University School of Medicine

data_processing:
Quality control: the image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition. Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads mapping to the reference genome: Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5). We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Quantification of gene expression level: featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis: (For DESeq2 with biological replicates) Differential expression analysis of three conditions/groups (three biological replicates per condition) was performed using the DESeq2 R package (1.20.0). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . padj<0.05 and |log2(foldchange)| > 1 were set as the threshold for significantly differential expression.
Assembly: hg38
Supplementary files format and content: BAM

source_name: not applicable

growth_protocol: HSF cells were maintained in DMEM (Gibco) supplemented with 10% fetal bovine serum (Gibco) and 1% P/S (Gibco) in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
Total RNA was extracted from cultured HSF using TRIzol reagent (Invitrogen, Carlsbad, CA, USA)
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained.

treatment_protocol: HSF cells were treated with human recombinant SPP1 (MedChemExpress, HY-P70499) with concenration of 10nM for 24h. Control group of cells were treated with solvent control for 24h. Three independent experimental replicates were performed and planed for RNA-sequencing.

value: not applicable

tag: cell line

value: HSF

value: Human skin fibroblast cell line

value: solvent control


title: exs10WTS3 population-Rep2

description:
S3 population replication 2
FACs experiments with surface marker CD71/Ter119 divided the fetal liver cells into S0-S5 population from immature to mature erythroid cells.


title: Placenta, RNA PE4 Rep2

value: Placenta tissue


title: T26_0138


title: Sample 43-I; Control_Male

city: New York

first: Molly

middle: S

last: Estill

state: NY

address: 1 Gustave L. Levy Place

department: Neuroscience

institute: Mount Sinai School of Medicine

description: Library name: 43-I

library_source: genomic

data_processing:
FASTQ files were processed with the NGS-Data-Charmer pipeline (https://github.com/shenlab-sinai/NGS-Data-Charmer). In brief, adapter trimming was performed, followed by alignment to the mm10 genome build using HISAT2, and duplicate alignments were removed using the Picard ‘MarkDuplicates’ module. Peaks were called with MACS2 (v2.2.6;-f BAMPE -q 0.01 --keep-dup) using IgG as background, and annotated withChIPseeker (v1.22.1).
Assembly: mm10
Supplementary files format and content: Narrowpeak files were annotated with ChIPSeekeR. Each annotated file contains peak locations and the associated genomic annotations of the peaks.
Library strategy: CUT&Run

source_name: Dorsal Hippocampus

extract_protocol:
The dorsal two-thirds of the right hippocampus was sub-dissected to use for CUT&RUN analysis. CUT&RUN was performed using a primary anti-ΔFOSB antibody.
Libraries were generated using the NEB Next® Ultra™ II DNA Library Prep Kit (New England BioLabs) and sequenced on an Illumina HiSeq 4000 with a 2 × 150 bp paired-end configuration at a minimum depth of 30 million reads per sample.

treatment_protocol: 2–3-month-old Alzheimer's model mice expressing human Amyloid Precursor Protein (APP) were injected with YL0441 in the right dorsal hippocampus. YL0441 or vehicle was infused for three days into the hippocampus. Mice were then anesthetized with commercial euthanasia solution, transcardially perfused with ice-cold 0.9% saline solution, and the brains collected and hemisected.

value: Dorsal Hippocampus

tag: Sex

value: Male

value: Control

value: APP

value: IgG

tag: batch


title: T26_0108

value: meningioma


title: Control_Ax_4

description:
Library name: S8
Column name in processed data file matches "title" in this file

value: Nervous

value: Sympathetic neurons

value: Ax

value: Wildtype

value: Growth under NGF


title: exs10WTS3 population-Rep1

description:
S3 population replication 1
FACs experiments with surface marker CD71/Ter119 divided the fetal liver cells into S0-S5 population from immature to mature erythroid cells.

value: fetal livers

value: WT

value: Embryonic day 14.5


title: Placenta, RNA PE4 Rep1

value: PE


title: Control_Ax_3

description:
Library name: S7
Column name in processed data file matches "title" in this file


title: exs10WTS2 population-Rep3

description:
S2 population replication 3
FACs experiments with surface marker CD71/Ter119 divided the fetal liver cells into S0-S5 population from immature to mature erythroid cells.


title: T26_0207


title: Placenta, RNA PE+IUGR2 Rep2

value: PE+IUGR


title: T26_0007


title: Control_Ax_2

description:
Library name: S6
Column name in processed data file matches "title" in this file


title: Placenta, RNA PE+IUGR2 Rep1

value: Placenta tissue


title: T26_0254


title: MN8_ADT

city: Bethesda

first: Laura

last: Dillon

state: Maryland

address: Room 10CRC 6-5142, 10 Center Drive

department: Hematology Branch

institute: National Heart Lung and Blood Institute, NIH

description: Patient 8 single-cell Protein

library_source: other

data_processing:
Patient samples were analyzed using Cell Ranger version 3.1.0 (10x Genomics) to obtain the UMI counts for GEX. The number of barcode mismatches was set to be 0 to minimize the demultiplexing error. The ADT libraries were quantified by CITE-seq-Count (https://github.com/Hoohm/CITE-seq-Count) with 15000 expected cells, and cells with overlapping cell barcodes (CB) in GEX results were included in the multimodal analysis.
Assembly: Single-cell cellranger used the pre-built GRCh38 in the pipeline.
Supplementary files format and content: Single-cell processed data contain the gene and protein expression matrices with cell barcodes.

molecule: protein

source_name: Bone marrow

growth_protocol: Bone marrow (BM) aspirate was collected from 12 AML patients with known abnormalities on chr7 according to cytogenetics studies

extract_protocol:
Bone marrow mononuclear cells (BMMCs) were purified from BM aspirate using density centrifugation, cryopreserved, and stored in liquid nitrogen.
The 10x Genomics 3’v2 Single Cell Profiling platform was used for scRNAseq. After staining and cell concentration adjustment, cells were loaded onto a Chromium Chip A with master mix, gel beads, and partitioning oil according to manufacturer’s instructions. Desired number of captured cells was 3000-4000. Reverse transcription (RT) of mRNA into barcoded first strand cDNA was performed on the emulsion by incubating at 53°C for 45 min in an Eppendorf Mastercycler X50a. After RT, emulsions were broken and cDNA purified using Dynabeads MyOne SILANE. At this stage, cDNA was amplified by PCR (98°C for 45 seconds; 13 cycles of 98°C for 20 sec, 67°C for 30 sec, 72°C for 1 min; 72°C for 1 min). Additional primers were added to ensure adequate amplification of oligo tags to later generate antibody-derived tag (ADT) sequencing libraries. Amplified cDNA was mixed with 0.6X SPRIselect magnetic beads (Beckman Coulter); after magnetic separation, supernatant was transferred for ADT library generation, and the remaining pellet was used for constructing the gene expression (GEX) library. Concentration of amplified cDNA was measured at a 1:10 dilution with a High Sensitivity (HS)-D5000 chip on an Agilent Tapestation.  For the GEX library, 50ng of amplified cDNA was carried forward for library construction. Fragmentation, end-repair, and A-tailing was performed (32°C for 5 min; 65°C for 30 min), followed by double-sided size selection using SPRIselect beads. Adaptor ligation (20°C for 15 min), cleanup with SPRIselect beads, and PCR amplification with sample indexing primers (98C for 45 seconds, 14 cycles of 90C for 20 sec, 54C for 30 sec, 72°C for 20 sec; 72°C for 1 min) were performed in that order. A final double size-selection was again done using SPRIselect beads. To make ADT libraries, sample index PCR using unique indices was performed with the transferred supernatant taken immediately after initial cDNA amplification (98°C for 45 seconds; 9 cycles of 98°C for 20 sec, 54°C for 30 sec, 72°C for 20 sec; 72°C for 1 min) using Kapa HiFi Hotstart Readymix (Kapa), followed by a single sided size selection cleanup with SPRIselect beads.

treatment_protocol: No treatment

value: Bone marrow

tag: disease

value: Acute Myeloid Leukemia (AML) with Abnormalities on Chromosome 7

tag: library type

value: ADT


title: Control_Ax_1

description:
Library name: S5
Column name in processed data file matches "title" in this file


title: exs10WTS2 population-Rep1

description:
S2 population replication 1
FACs experiments with surface marker CD71/Ter119 divided the fetal liver cells into S0-S5 population from immature to mature erythroid cells.


title: exs10WTS2 population-Rep2

description:
S2 population replication 2
FACs experiments with surface marker CD71/Ter119 divided the fetal liver cells into S0-S5 population from immature to mature erythroid cells.


title: Placenta, RNA PE3 Rep2


title: Control_CB_4

description:
Library name: S4
Column name in processed data file matches "title" in this file

value: CB


title: Neonatal rat cardiomyocyte, GFP, rabbit YAP antibody

city: CINCINNATI

first: Shijie

last: Zhang

state: OH

address: 3333 Burnet Ave, T4.325

department: Heart institute

institute: Cincinnati Children's hospital medical center

description: Library name: NRCMs_GFP_rabbit_YAP_Ab

data_processing:
For RNA seq, raw sequencing data (FASTQ files) were processed using fastp for quality control. Reads containing adapters, poly-N regions, or low-quality bases were removed. Clean reads were evaluated for quality using Q20, Q30, and GC content metrics. All downstream analyses were based on high-quality clean reads. Clean reads were aligned to the rat reference genome (rn7, Ensembl release 106) using HISAT2 (v2.2.1) with default parameters. Mapped reads were quantified at the gene level with StringTie (v2.2.1), and transcript abundances were reported as raw counts and TPM values. Raw count matrices were imported into R (v4.3.1) and processed with DESeq2 (v1.38.3). CUT&RUN libraries were sequenced and processed by trimming adapters and aligning reads to the rat reference genome (rn7) using Bowtie2. Duplicate and low-quality reads (MAPQ < 30) were removed with SAMtools. Peaks were identified using MACS v2.1.0 with a significance threshold of q-value ≤ 0.01. For quantification, consensus peak regions across replicates were generated with BEDTools. Peak scores (−log10 adjusted p-values from MACS2) were assigned to genomic intervals and summed within each gene body ±2 kb flanking regions, yielding a total peak score per gene. Mapped reads were extended to 150 bp, normalized to reads per million (RPM), and converted to bigWig format for visualization.
Assembly: rn7
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample and bigWig
Library strategy: CUT&Run

organism: Rattus norvegicus

source_name: Heart

growth_protocol: M199 supplemented with 10% fetal bovine serum, 2 mM glutamine, and 1× penicillin/streptomycin. Cells were cultured at 37°C with 5% CO₂.

extract_protocol:
RNA was harvested using RNeasy Mini Plus Kit (Qiagen). 1.3 μg of total RNA was used for the construction of sequencing libraries. For CUT&RUN, DNA was released by incubation with 1/100 volume of 10% SDS and 1/80 volume of 2.5 mg/mL Proteinase K (Thermo Fisher) for at least 1 hour at 55 °C. DNA was then purified by phenol/chloroform/isoamyl alcohol extraction, followed by ethanol precipitation with glycogen, and resuspended in nuclease-free water.
For RNA seq, messenger RNA (mRNA) was purified from total RNA using poly-T oligo-attached magnetic beads. Following fragmentation, first-strand cDNA was synthesized using random hexamer primers, and second-strand cDNA synthesis was performed using dUTP instead of dTTP to maintain strand specificity. Directional libraries were prepared through a series of steps, including end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification. Library quality was assessed using Qubit fluorometry, real-time PCR, and fragment size distribution by Bioanalyzer. Libraries were pooled based on effective concentration and desired sequencing depth, then subjected to Illumina sequencing.  For CUT&RUN, DNA was released by incubation with 1/100 volume of 10% SDS and 1/80 volume of 2.5 mg/mL Proteinase K (Thermo Fisher) for at least 1 hour at 55 °C. DNA was then purified by phenol/chloroform/isoamyl alcohol extraction, followed by ethanol precipitation with glycogen, and resuspended in nuclease-free water. For CUT&RUN, Sequencing libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs) with minor modifications. End repair was carried out for 30 minutes at 20 °C, followed by A-tailing at 65 °C for 30 minutes. After adapter ligation (30 minutes at 20 °C), DNA fragments were purified using 1.8× SPRIselect beads (Beckman Coulter), then amplified via PCR for 17 cycles using NEBNext Ultra II Q5 Master Mix (New England Biolabs). Final libraries were purified with 0.9× SPRIselect beads and quantified with the Qubit dsDNA HS Assay Kit (Agilent Technologies).

value: Heart

value: Cardiomyocyte

value: wild type

value: Ad-GFP


title: T26_0063

value: meningioma


title: exs10WTS1 population-Rep3

description:
S1 population replication 3
FACs experiments with surface marker CD71/Ter119 divided the fetal liver cells into S0-S5 population from immature to mature erythroid cells.


title: Placenta, RNA PE3 Rep1


title: Control_CB_3

description:
Library name: S3
Column name in processed data file matches "title" in this file

value: Nervous

value: Sympathetic neurons

value: Wildtype


title: exs10WTS1 population-Rep2

description:
S1 population replication 2
FACs experiments with surface marker CD71/Ter119 divided the fetal liver cells into S0-S5 population from immature to mature erythroid cells.

value: fetal livers

value: WT


title: Placenta, RNA Control3 Rep2

value: Control


title: T26_0074


title: T26_0268


title: T26_0198


title: Placenta, RNA Control3 Rep1


title: exs10WTS1 population-Rep1

description:
S1 population replication 1
FACs experiments with surface marker CD71/Ter119 divided the fetal liver cells into S0-S5 population from immature to mature erythroid cells.

value: Embryonic day 14.5


title: Control_CB_1

description:
Library name: S1
Column name in processed data file matches "title" in this file

value: Growth under NGF


title: exs10WTS0 population-Rep3

description:
S0 population replication 3
FACs experiments with surface marker CD71/Ter119 divided the fetal liver cells into S0-S5 population from immature to mature erythroid cells.


title: Placenta, RNA PE1 Rep2

value: Placenta tissue

value: PE


title: T26_0103


title: Control_CB_2

description:
Library name: S2
Column name in processed data file matches "title" in this file


title: Placenta, RNA PE1 Rep1


title: exs10WTS0 population-Rep2

description:
S0 population replication 2
FACs experiments with surface marker CD71/Ter119 divided the fetal liver cells into S0-S5 population from immature to mature erythroid cells.


title: CBRestimTRAP4

description:
Library name: CB-Restim-TRAP-4_S40_R1_001.fastq.gz
Column name in processed data file matches "title" in this file

molecule: polyA RNA

extract_protocol:
Cells were washed 3x in 1x PBS, and the top and bottom of a trans-well membrane was scraped for Cell Bodies/Axonal fractions, respectively. Axon-TRAP was performed as described in Shigeoka et al., (2018; doi:10.1007/978-1-4939-7213-5_5) on each cell body/axon fraction, then RNA was purified with a PureLink RNA Micro kit according to manufacturer's protocols.
After saving 10% RNA for inputs, Using the NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina® (New England Biolabs, Cat. E6420S), first and second strand cDNA synthesis, sequencing library prep and amplification were all performed in one continuous workflow. Libraries were QC’d and then sequenced according to the manufacturer’s instructions using Illumina NextSeq 2000 platform (100 cycles) to generate ~30 million 101 bp single-end reads.

treatment_protocol: Medium was removed, cells were washed 3x with 1xPBS, and medium without NGF was added for 18 hours. Cells were then restimulated by replacing medium with NGF medium for 1 hour. Simultaneously, cells were treated with puromycin for 15 mins.

tag: assay

value: RiboTag

value: Restimulation with NGF after 18 hours of starvation


title: CBRestimTRAP1

description:
Library name: CBRestimTRAP1_S13_R1_001.fastq.gz
Column name in processed data file matches "title" in this file

value: CB


title: T26_0128


title: exs10WTS0 population-Rep1

description:
S0 population replication 1
FACs experiments with surface marker CD71/Ter119 divided the fetal liver cells into S0-S5 population from immature to mature erythroid cells.


title: T26_0029


title: Placenta, RNA Control2 Rep1


title: CBRestimInput4

description:
Library name: CB-Restim-Input-4_S7_R1_001.fastq.gz
Column name in processed data file matches "title" in this file


title: Placenta, RNA Control2 Rep2


title: exs10KOtotal -Rep4

description: total fetal livers

value: exs10 KO


title: CBRestimInput1

description:
Library name: CBRestimInput1_S31_R1_001.fastq.gz
Column name in processed data file matches "title" in this file


title: exs10KOtotal -Rep3

description: total fetal livers


title: Placenta, RNA PE+IUGR1 Rep2

value: PE+IUGR


title: T26_0130


title: exs10KOtotal -Rep2

description: total fetal livers


title: CBplusNGFTRAP3

description:
Library name: CBplusNGFTRAP3_S3_R1_001.fastq.gz
Column name in processed data file matches "title" in this file


title: exs10KOtotal -Rep1

description: total fetal livers


title: CBplusNGFTRAP1

description:
Library name: CBplusNGFTRAP1_S1_R1_001.fastq.gz
Column name in processed data file matches "title" in this file


title: T26_0171


title: T26_0126


title: Placenta, RNA PE2 Rep2


title: Placenta, RNA PE2 Rep1


title: exs10WTtotal -Rep4

description: total fetal livers


title: T26_0046


title: exs10WTtotal -Rep3

description: total fetal livers


title: Placenta, RNA Control1 Rep2


title: T26_0006


title: CBplusNGFInput3

description:
Library name: CBplusNGFInput3_S21_R1_001.fastq.gz
Column name in processed data file matches "title" in this file


title: T26_0091


title: Placenta, RNA Control1 Rep1


title: exs10WTtotal -Rep1

description: total fetal livers


title: exs10WTtotal -Rep2

description: total fetal livers


title: CBplusNGFInput1

description:
Library name: CBplusNGFInput1_S19_R1_001.fastq.gz
Column name in processed data file matches "title" in this file


title: T26_0042


title: dis3KOS45 population-Rep3

description:
S4 and S5 population replication 3
FACs experiments with surface marker CD71/Ter119 divided the fetal liver cells into S0-S5 population from immature to mature erythroid cells.

value: dis3 KO


title: HT1080 wild-type TMP195-2

city: New Orleans

first: Terry

middle: J

last: Watt

state: LA

address: 1 Drexel Dr.

department: Chemistry

institute: Xavier University of Louisiana

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trimmomatic v0.39 with default settings
Trimmed sequence reads were mapped to GrCh38.83 using bowtie2 v2.4.5 as implemented by RSEM v1.3.3, with default settings
Mapped sequences were annotated and counted using RSEM v1.3.3 with default settings
Read count extraction was performed using tximport v1.26.1
Read count statistical analysis was performed using DESeq2 v1.38.2
Assembly: Human NCBI genome build GrCH38 build 83
Supplementary files format and content: Expected counts from RSEM output for all conditions and ENSEMBL entries, cross-referenced to gene names and UNIPROT entries

source_name: Connective tissue

growth_protocol: HT1080 cells were maintained in MEM supplemented with 10% fetal bovine serum (FBS) and penicillin/streptomycin in humidified atmosphere with 5% CO2 at 37 °C

extract_protocol:
3x10^6 cells were pelleted, resuspended in MEM with 5% glycerol, and frozen at -80 °C. Cells were shipped on dry ice, and total RNA extracted by Creative Genomics using a commercially available kit. Quality of RNA was verified using RNA Screen Tape (Agilent). RNA was rRNA-depleted using the Ribo-Zero plus kit (Illumina).
Libraries were prepared using the PE150 platform (Illumina) following the manufacturer's instructions.

value: Connective tissue

value: fibrosarcoma

value: 1 µM TMP195, 2 days


title: T26_0044

value: meningioma


title: AxRestimTRAP3

description:
Library name: AxRestimTRAP3_S18_R1_001.fastq.gz
Column name in processed data file matches "title" in this file

value: Nervous

value: Sympathetic neurons

value: Ax


title: HT1080 wild-type TMP195-1

value: WT


title: T26_0018


title: dis3KOS45 population-Rep2

description:
S4 and S5 population replication 2
FACs experiments with surface marker CD71/Ter119 divided the fetal liver cells into S0-S5 population from immature to mature erythroid cells.

value: fetal livers

value: Embryonic day 14.5


title: AxRestimTRAP2

description:
Library name: AxRestimTRAP2_S17_R1_001.fastq.gz
Column name in processed data file matches "title" in this file


title: HT1080 KDAC7H709A 4


title: T26_0135


title: AxRestimInput3

description:
Library name: AxRestimInput3_S36_R1_001.fastq.gz
Column name in processed data file matches "title" in this file


title: T26_0261


title: dis3KOS3 population-Rep2

description:
S3 population replication 2
FACs experiments with surface marker CD71/Ter119 divided the fetal liver cells into S0-S5 population from immature to mature erythroid cells.


title: HT1080 KDAC7H709A 2


title: AxRestimInput2

description:
Library name: AxRestimInput2_S35_R1_001.fastq.gz
Column name in processed data file matches "title" in this file


title: T26_0014


title: HT1080 KDAC7H709A 1


title: T26_0226


title: AxplusNGFTRAP4

description:
Library name: Ax-Plus-NGF-TRAP-4_S2_R1_001.fastq.gz
Column name in processed data file matches "title" in this file

value: Growth under NGF


title: dis3KOS3 population-Rep1

description:
S3 population replication 1
FACs experiments with surface marker CD71/Ter119 divided the fetal liver cells into S0-S5 population from immature to mature erythroid cells.


title: dis3KOS2 population-Rep3

description:
S2 population replication 3
FACs experiments with surface marker CD71/Ter119 divided the fetal liver cells into S0-S5 population from immature to mature erythroid cells.


title: HT1080 KDAC4H976Y 4


title: T26_0008


title: AxplusNGFTRAP2

description:
Library name: AxplusNGFTRAP2_S5_R1_001.fastq.gz
Column name in processed data file matches "title" in this file

value: RiboTag


title: T26_0256


title: HT1080 KDAC4H976Y 3


title: dis3KOS2 population-Rep1

description:
S2 population replication 1
FACs experiments with surface marker CD71/Ter119 divided the fetal liver cells into S0-S5 population from immature to mature erythroid cells.


title: HT1080 KDAC4H976Y 2


title: T26_0194


title: Subject 129, EuE, ALDH-High

description:
Library name: Sample 4
EH4

value: Endometriosis lesion

value: Epithelium


title: dis3KOS1 population-Rep3

description:
S1 population replication 3
FACs experiments with surface marker CD71/Ter119 divided the fetal liver cells into S0-S5 population from immature to mature erythroid cells.


title: HT1080 KDAC4H976Y 1


title: AxplusNGFInput3

description:
Library name: AxplusNGFInput3_S24_R1_001.fastq.gz
Column name in processed data file matches "title" in this file


title: T26_0180


title: dis3KOS1 population-Rep2

description:
S1 population replication 2
FACs experiments with surface marker CD71/Ter119 divided the fetal liver cells into S0-S5 population from immature to mature erythroid cells.


title: HT1080 KDAC4H803A 4


title: AxplusNGFInput2

description:
Library name: AxplusNGFInput2_S23_R1_001.fastq.gz
Column name in processed data file matches "title" in this file


title: T26_0012


title: dis3KOS1 population-Rep1

description:
S1 population replication 1
FACs experiments with surface marker CD71/Ter119 divided the fetal liver cells into S0-S5 population from immature to mature erythroid cells.


title: HT1080 KDAC4H803A 3


title: HSF, ctrl-2

value: not applicable

value: HSF

value: Human skin fibroblast cell line

value: solvent control


title: EpH4_2D_PM_treatment_2

city: Linz

first: Tamara

last: Lang

address: Krankenhausstraße 5

department: Pathophysiology

country: Austria

institute: Johannes Kepler Universität

description:
Library name: MM-PM_4
Column name in "Counts_all.csv": MM-PM_4

data_processing:
CLC Genomics Workbench v 24.0.2
Reads were trimmed for quality (Phred < 13), adapter sequences, polyG tails and reads with > 2 ambiguous bases using CLC Genomics Workbench.
Trimmed reads were mapped to GRCm39 using CLC Genomics Workbench. (Parameters: Mismatch Cost: 2; Insertion Cost: 3; Deletion Cost: 3; Length Fraction: 0.8; Similaryity Fraction: 0.8; Maximum number of hits for a read: 10; Auto-detect paired distances)
Read count extraction and (RPKM) normalization were performed using CLC Genomics Workbench.
Assembly: GRCm39
Supplementary files format and content: Comma-Separated-Values-File. Includes gene names and properties. Describes the expression in each sample as raw total counts and RPKM-normalized values.
Supplementary files format and content: Comma-Separated-Values-File. Includes gene names and identifiers. Describes the raw count and (RPKM-) normalized expression of all genes in the sample.

source_name: epithelial

extract_protocol:
Total RNA was extracted using the ReliaPrep RNA Miniprep System according to the manufacturer's protocol. 750 ng of total RNA was used for the construction of sequencing libraries
RNA libraries for RNA-Seq were prepared using the Illumina Stranded mRNA Prep, Ligation Kit following the manufacturer's protocol.

value: epithelial

value: Epithelial cell of the mammary gland


title: T26_0274

value: meningioma


title: dis3KOS0 population-Rep3

description:
S0 population replication 3
FACs experiments with surface marker CD71/Ter119 divided the fetal liver cells into S0-S5 population from immature to mature erythroid cells.

value: dis3 KO


title: AxplusNGFTRAP3

description:
Library name: AxplusNGFTRAP3_S6_R1_001.fastq.gz
Column name in processed data file matches "title" in this file

value: Nervous

value: Sympathetic neurons


title: dis3KOS2 population-Rep2

description:
S2 population replication 2
FACs experiments with surface marker CD71/Ter119 divided the fetal liver cells into S0-S5 population from immature to mature erythroid cells.


title: HT1080 KDAC4H803A 2

value: Connective tissue

value: fibrosarcoma


title: EpH4_2D_PM_treatment_1

description:
Library name: MM-PM_3
Column name in "Counts_all.csv": MM-PM_3

value: WT


title: T26_0275


title: dis3KOS0 population-Rep2

description:
S0 population replication 2
FACs experiments with surface marker CD71/Ter119 divided the fetal liver cells into S0-S5 population from immature to mature erythroid cells.

value: fetal livers

value: Embryonic day 14.5


title: T26_0009


title: HT1080 KDAC4H803A 1


title: EpH4_2D_Control_2

description:
Library name: MM-WT_2
Column name in "Counts_all.csv": MM-WT_2

value: Control


title: dis3KOS0 population-Rep1

description:
S0 population replication 1
FACs experiments with surface marker CD71/Ter119 divided the fetal liver cells into S0-S5 population from immature to mature erythroid cells.


title: AxplusNGFInput4

description:
Library name: Ax-Plus-NGF-Input-4_S37_R1_001.fastq.gz
Column name in processed data file matches "title" in this file

value: Ax

value: RiboTag

value: Growth under NGF


title: Hela, SH, FOSL2, rep5

city: Milan

first: Jose

middle: Manuel

last: Garcia-Manteiga

address: Via Olgettina 58

department: Center for Translational Genomics and Bioinformatics

country: Italy

institute: OSR - San Raffaele Scientific Institute

data_processing:
Basecalls were performed using bcl2fastq v2.20 for Novaseq output.
Cut&Tag-seq reads were trimmed with Cutadapt v3.4 to remove adapters
Cut&Tag reads were aligned to the UCSC T2Tv2.0 genome using Bowtie 2 version 2.4.3. -k 100 parameter was used to allow multiple alignments. --very-sensitive --no-mixed -no-discordant -I 10 -X 700
Duplicate alignments were marked with SAMBLASTER and filtered using SAMTOOLS v1.9 to include only primary alignments (-F 2308)
To create Cut&Tag-seq coverage plots, the locations of the mapped Cut&Tag-seq reads were centered, renormalized (to bins per million, bpm), duplicates ignored and reformatted in the bigWig file format using bamCoverage from Deeptools v3.5.1. A smooth widow of 500bp on 10bp bin size was applied
Peaks (narrow) were called uing MACS v2.2.7.1 with the significance cut-off q-value <=0.05
Assembly: T2Tv2.0
Supplementary files format and content: bw: bigWig
Supplementary files format and content: narrowPeak: narrowPeaks called with MACS
Library strategy: Cut&Tag

source_name: HeLa

growth_protocol: HeLa cells were grown in DMEM complete medium

extract_protocol:
Nuclei from HeLa cells were extracted with NE1 buffer (Hepes-KOH 1M, pH7.9; KCl 1M; Spermidine 2M; Triton X-100 10%; glycerol; protease inhibitors; H2O) and cryopreserved in 10% DMSO and wash buffer (Hepes 1M, pH 7.5; NaCl 5M; Spermidine 2M; protease inhibitors; H2O). 8 x 10e4 nuclei were lightly cross-linked (0,1% formaldehyde) for 2 minutes and blocked by addition of 1.25 M glycine.
Cut&Tag libraries were prepared with dual index oligos as described by Buenrostro et al. 2015. Amplification was performed with NEBNext 2X PCR Master mix (New England BioLabs, ME541L). Library purification was performed using HighPrep PCR Cleanup (Magbio Genomics, AC-60500) and paired-end sequenced through NovaSeq 6000 SP

treatment_protocol: HeLa cells were lentiviral transduced with a specific short hairpin RNA for NSD3 long isoform (sh_NSD3L) or a non-targeting (sh_ctrl)

value: HeLa

value: Human Cervical Cancer

tag: cut&tag antibody

value: 19967S (CellSignal)


title: T26_0243


title: EpH4_2D_Control_1

description:
Library name: MM-WT_1
Column name in "Counts_all.csv": MM-WT_1

value: epithelial

value: Epithelial cell of the mammary gland


title: dis3WTS45 population-Rep3

description:
S4 and S5 population replication 3
FACs experiments with surface marker CD71/Ter119 divided the fetal liver cells into S0-S5 population from immature to mature erythroid cells.


title: Heart, QD, Sample 3

city: San Diego

first: Pura

last: Muñoz-Cánoves

state: CA

address: 5510 Morehouse Dr

institute: Altos Labs

description:
Library name: QD_Heart_Sample3
Column name in Calls_Cobos_bulkRNA-TPM.csv: QD_Heart_Sample3

data_processing:
Sequencing data was processed using the Nextflow nf-core pipeline. Raw reads were trimmed using Trimgalore (v.0.6.10) and quantified using Salmon (v.1.10.3) and the reference genome GRCm39. Counts were summarized using tximport (v1.30.0).
Assembly: GRCm39
Supplementary files format and content: Calls_Cobos_bulkRNA-TPM.csv: comma separated text file with TPM counts

extract_protocol:
Total RNA was isolated from snap-frozen TA muscles and hearts using miRNeasy Mini Kit (Qiagen, #1038703).
Libraries were prepared using the Watchmaker mRNA Library Prep Kit v1.1.0823.

value: Heart

value: Male

value: dasatinib and quercetin

tag: treatement duration

value: 4 months

tag: treatment fequency

value: Twice per week

tag: starting age

value: 12 months

tag: collection age

value: 16 months


title: Hela, SH, FOSL2, rep4

tag: cell type


title: T26_0011

tag: tissue

value: meningioma


title: Hela, SH, FOSL2, rep3


title: dis3WTS45 population-Rep2

description:
S4 and S5 population replication 2
FACs experiments with surface marker CD71/Ter119 divided the fetal liver cells into S0-S5 population from immature to mature erythroid cells.

value: fetal livers

tag: genotype

value: WT

value: Embryonic day 14.5


title: Heart, QD, Sample 2

description:
Library name: QD_Heart_Sample2
Column name in Calls_Cobos_bulkRNA-TPM.csv: QD_Heart_Sample2

value: Female

tag: treatment


title: T26_0262


title: Hela, SH, FOSL2, rep2

value: HeLa


title: Heart, QD, Sample 1

description:
Library name: QD_Heart_Sample1
Column name in Calls_Cobos_bulkRNA-TPM.csv: QD_Heart_Sample1


title: T26_0148


title: dis3WTS45 population-Rep1

description:
S4 and S5 population replication 1
FACs experiments with surface marker CD71/Ter119 divided the fetal liver cells into S0-S5 population from immature to mature erythroid cells.

tag: strain


title: dis3WTS3 population-Rep3

description:
S3 population replication 3
FACs experiments with surface marker CD71/Ter119 divided the fetal liver cells into S0-S5 population from immature to mature erythroid cells.

tag: age


title: Hela, SH, FOSL2, rep1

tag: cell line

value: Human Cervical Cancer


title: T26_0001


title: Heart, Vehicle, Sample 4

description:
Library name: Veh_Heart_Sample4
Column name in Calls_Cobos_bulkRNA-TPM.csv: Veh_Heart_Sample4

tag: Sex

value: vehicle


title: T26_0097


title: Placenta, RNA PE+IUGR1 Rep1

value: Placenta tissue

tag: group

value: PE+IUGR


title: CBplusNGFTRAP4

description:
Library name: CB-Plus-NGF-TRAP-4_S39_R1_001.fastq.gz
Column name in processed data file matches "title" in this file

value: Nervous

value: Sympathetic neurons

tag: cell subset

value: CB

value: RiboTag

value: Growth under NGF


title: Heart, Vehicle, Sample 3

description:
Library name: Veh_Heart_Sample3
Column name in Calls_Cobos_bulkRNA-TPM.csv: Veh_Heart_Sample3

value: Heart

value: 4 months

value: Twice per week

value: 12 months


title: Hela, SCR, FOSL2, rep2

value: 19967S (CellSignal)

value: shCTRL


title: T26_0027

value: meningioma


title: dis3WTS3 population-Rep2

description:
S3 population replication 2
FACs experiments with surface marker CD71/Ter119 divided the fetal liver cells into S0-S5 population from immature to mature erythroid cells.

value: fetal livers

value: WT

value: Embryonic day 14.5


title: CBplusNGFInput4

description:
Library name: CB-Plus-NGF-Input-4_S38_R1_001.fastq.gz
Column name in processed data file matches "title" in this file


title: dis3WTS3 population-Rep1

description:
S3 population replication 1
FACs experiments with surface marker CD71/Ter119 divided the fetal liver cells into S0-S5 population from immature to mature erythroid cells.


title: Heart, Vehicle, Sample 2

description:
Library name: Veh_Heart_Sample2
Column name in Calls_Cobos_bulkRNA-TPM.csv: Veh_Heart_Sample2

value: Female

value: vehicle

value: 16 months


title: Hela, SCR, FOSL2, rep1

value: HeLa

value: Human Cervical Cancer


title: T26_0125


title: dis3WTS2 population-Rep3

description:
S2 population replication 3
FACs experiments with surface marker CD71/Ter119 divided the fetal liver cells into S0-S5 population from immature to mature erythroid cells.


title: Heart, Vehicle, Sample 1

description:
Library name: Veh_Heart_Sample1
Column name in Calls_Cobos_bulkRNA-TPM.csv: Veh_Heart_Sample1

value: Male


title: CAR_T8_mobilized

city: Atlanta

first: Krishnendu

last: Roy

state: Georgia

address: 345 ferst drive NW, marcus nanotechnology building, room no 3102B, 3rd floor

department: IBB

institute: Georgia tech

description:
10x Genomics Chromium
scRNA libraries

library_source: transcriptomic single cell

data_processing: The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)

source_name: Blood

extract_protocol:
Cryopreserved CAR-T cells were thawed at 37C for 2 minutes and was processed according to 10x Genomics gene expression protocol.
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Blood

value: Tcells

value: CART expansion

value: mobilized


title: T26_0266


title: dis3WTS2 population-Rep2

description:
S2 population replication 2
FACs experiments with surface marker CD71/Ter119 divided the fetal liver cells into S0-S5 population from immature to mature erythroid cells.


title: CAR_T7_steadystate

description:
10x Genomics Chromium
scRNA libraries

value: steadystate


title: dis3WTS2 population-Rep1

description:
S2 population replication 1
FACs experiments with surface marker CD71/Ter119 divided the fetal liver cells into S0-S5 population from immature to mature erythroid cells.


title: CAR_T6_mobilized

description:
10x Genomics Chromium
scRNA libraries


title: Tibialis anterior, Vehicle, Sample 4

description:
Library name: Veh_TA_Sample4
Column name in Calls_Cobos_bulkRNA-TPM.csv: Veh_TA_Sample4

source_name: Tibialis anterior

value: Tibialis anterior

value: 2 months

value: Twice per week

value: 3 months

value: 5 months


title: Tibialis anterior, Vehicle, Sample 3

description:
Library name: Veh_TA_Sample3
Column name in Calls_Cobos_bulkRNA-TPM.csv: Veh_TA_Sample3


title: T26_0061

value: meningioma


title: T26_0270


title: HT1080 wild-type TMP195-3

value: Connective tissue

value: fibrosarcoma

value: WT

value: 1 µM TMP195, 2 days


title: AxRestimTRAP4

description:
Library name: Ax-Restim-TRAP4_S4_R1_001.fastq.gz
Column name in processed data file matches "title" in this file

value: Nervous

value: Sympathetic neurons

value: Ax

value: RiboTag

value: Restimulation with NGF after 18 hours of starvation


title: Tibialis anterior, Vehicle, Sample 2

description:
Library name: Veh_TA_Sample2
Column name in Calls_Cobos_bulkRNA-TPM.csv: Veh_TA_Sample2

value: Female

value: vehicle


title: CAR_T5_steadystate

description:
10x Genomics Chromium
scRNA libraries

value: Blood

value: Tcells

value: CART expansion

value: steadystate


title: dis3WTS1 population-Rep3

description:
S1 population replication 3
FACs experiments with surface marker CD71/Ter119 divided the fetal liver cells into S0-S5 population from immature to mature erythroid cells.

value: fetal livers

value: Embryonic day 14.5


title: T26_0112

value: meningioma


title: dis3WTS1 population-Rep2

description:
S1 population replication 2
FACs experiments with surface marker CD71/Ter119 divided the fetal liver cells into S0-S5 population from immature to mature erythroid cells.


title: CAR_T4_mobilized

description:
10x Genomics Chromium
scRNA libraries

value: mobilized


title: T26_0041


title: Tibialis anterior, Vehicle, Sample 1

description:
Library name: Veh_TA_Sample1
Column name in Calls_Cobos_bulkRNA-TPM.csv: Veh_TA_Sample1

value: Tibialis anterior

value: Male

value: 2 months

value: Twice per week

value: 3 months

value: 5 months


title: dis3WTS1 population-Rep1

description:
S1 population replication 1
FACs experiments with surface marker CD71/Ter119 divided the fetal liver cells into S0-S5 population from immature to mature erythroid cells.

value: WT


title: Tibialis anterior, QD, Sample 4

description:
Library name: QD_TA_Sample4
Column name in Calls_Cobos_bulkRNA-TPM.csv: QD_TA_Sample4

value: dasatinib and quercetin


title: CAR_T3_steadystate

description:
10x Genomics Chromium
scRNA libraries


title: dis3WTS0 population-Rep3

description:
S0 population replication 3
FACs experiments with surface marker CD71/Ter119 divided the fetal liver cells into S0-S5 population from immature to mature erythroid cells.


title: T26_0092


title: dis3KOS45 population-Rep1

description:
S4 and S5 population replication 1
FACs experiments with surface marker CD71/Ter119 divided the fetal liver cells into S0-S5 population from immature to mature erythroid cells.

value: dis3 KO


title: CAR_T2_mobilized

description:
10x Genomics Chromium
scRNA libraries

value: Blood


title: T26_0083


title: Tibialis anterior, QD, Sample 3

description:
Library name: QD_TA_Sample3
Column name in Calls_Cobos_bulkRNA-TPM.csv: QD_TA_Sample3


title: AxRestimInput4

description:
Library name: Ax-Restim-Input-4_S8_R1_001.fastq.gz
Column name in processed data file matches "title" in this file

value: Nervous

value: Sympathetic neurons

value: Ax

value: RiboTag

value: Restimulation with NGF after 18 hours of starvation


title: dis3WTS0 population-Rep2

description:
S0 population replication 2
FACs experiments with surface marker CD71/Ter119 divided the fetal liver cells into S0-S5 population from immature to mature erythroid cells.

value: fetal livers

value: Embryonic day 14.5


title: Tibialis anterior, QD, Sample 2

description:
Library name: QD_TA_Sample2
Column name in Calls_Cobos_bulkRNA-TPM.csv: QD_TA_Sample2

value: Tibialis anterior


title: dis3KOS3 population-Rep3

description:
S3 population replication 3
FACs experiments with surface marker CD71/Ter119 divided the fetal liver cells into S0-S5 population from immature to mature erythroid cells.


title: T26_0107

value: meningioma


title: HT1080 KDAC7H709A 3

value: Connective tissue

value: fibrosarcoma


title: CAR_T1_steadystate

description:
10x Genomics Chromium
scRNA libraries

value: Tcells

value: CART expansion

value: steadystate


title: dis3WTS0 population-Rep1

description:
S0 population replication 1
FACs experiments with surface marker CD71/Ter119 divided the fetal liver cells into S0-S5 population from immature to mature erythroid cells.

value: WT


title: Hela, SH, UBF, rep4

data_processing:
library strategy: Cut&Tag
Basecalls were performed using bcl2fastq v2.20 for Novaseq output.
Cut&Tag-seq reads were trimmed with Cutadapt v3.4 to remove adapters
Cut&Tag reads were aligned to the UCSC T2Tv2.0 genome using Bowtie 2 version 2.4.3. -k 100 parameter was used to allow multiple alignments. --very-sensitive --no-mixed -no-discordant -I 10 -X 700
Duplicate alignments were marked with SAMBLASTER and filtered using SAMTOOLS v1.9 to include only primary alignments (-F 2308)
To create Cut&Tag-seq coverage plots, the locations of the mapped Cut&Tag-seq reads were centered, renormalized (to bins per million, bpm), duplicates ignored and reformatted in the bigWig file format using bamCoverage from Deeptools v3.5.1. A smooth widow of 500bp on 10bp bin size was applied
Peaks (narrow) were called uing MACS v2.2.7.1 with the significance cut-off q-value <=0.05
Assembly: T2Tv2.0
Supplementary files format and content: bw: bigWig
Supplementary files format and content: narrowPeak: narrowPeaks called with MACS only for NSD3 Cut&Tag

value: HeLa

value: Human Cervical Cancer

value: sc-13125 (SantaCruzBiotecnology)


title: Tibialis anterior, QD, Sample 1

description:
Library name: QD_TA_Sample1
Column name in Calls_Cobos_bulkRNA-TPM.csv:  QD_TA_Sample1

value: Male

value: dasatinib and quercetin

value: 2 months

value: Twice per week

value: 3 months

value: 5 months


title: T26_0059


title: T26_0111


title: S560s28_KO_laser_no

city: Hamburg

first: Andreas

last: Neueder

address: Falkenried 94

department: Center for Molecular Neurobiology (ZMNH)

institute: University Medical Center Hamburg-Eppendorf

description: Library name: S560s28

data_processing:
FastQ files were quality checked with FastQC v0.11.5. All files passed QC. The reads were pseudo aligned against Ensembl mus musculus GRCm39 release vM35 and quantified using salmon v1.10.3. Counts were imported using tximport v1.32.0 into DESeq2 v1.44.0 and a intercept matrix was used to generate the normalised counts expression matrix (S560_normalized_counts.tsv)
Assembly: Ensembl mus musculus GRCm39 release vM35
Supplementary files format and content: S560_normalized_counts.tsv This file contains the normalised count matrix.

source_name: choroidia

extract_protocol:
Total RNA was extracted from mouse choroid tissue stabilized in RNAlater buffer according to the “Purification of total RNA from animal and human tissue” protocol of the RNeasy Micro Kit (QIAGEN, Hilden, Germany). In brief, the tissue sample was stored in RNAlater and shipped at 2-8 °C. After centrifuging for 5 minutes at 5,000 x g, the RNAlater was removed and the sample was disrupted and homogenized in 350 µl RLT buffer containing 1% beta-mercaptoethanol with Precellys CK14 ceramic beads (1 cycle of 15 seconds at 5500 rpm) using a Precellys 24 Homogenisator (Bertin Corp., Rockville, MD, USA). Next the sample was centrifuged for 2 min at full speed and 350 µl of the cleared supernatant was transferred to a new tube. One volume of 70 % ethanol was added and the sample was applied to a RNeasy MinElute spin column followed by an on-column DNase digestion and several wash steps. Finally total RNA was eluted in 14 μl of nuclease free water. Purity and integrity of the RNA was assessed on the Agilent 2100 Bioanalyzer with the RNA 6000 Nano LabChip reagent set (Agilent, Palo Alto, CA, USA).
Library preparation and RNAseq were carried out as described in the SMART-Seq mRNA LP User Manual (Takara Bio, Inc., CA, USA), the Illumina NextSeq 2000 Sequencing System Guide (Illumina, Inc., San Diego, CA, USA), and the KAPA Library Quantification Kit - Illumina/ABI Prism Protocol (Roche Sequencing Solutions, Inc., Pleasanton, CA, USA). In brief, approximately 10 ng of total-RNA was used to generate first strand cDNA. Double stranded cDNA was amplified by LD-PCR (8 cycles) and purified via magnetic bead clean-up. After validating the quality and quantity, approximately 500 pg of cDNA was enzymatically fragmented and stem-loop adapters were ligated. Then libraries were PCR amplified (14 cycles) and indexed, generating Illumina-compatible libraries with unique dual indexes (UDIs). After a magnetic bead purification, the libraries were quantified using the KAPA Library Quantification Kit. Equimolar amounts of each library were sequenced on an Illumina NextSeq 2000 instrument controlled by the NextSeq 2000 Control Software (NCS) v1. 5.0.42699, using one 100 cycles P3 Flow Cell with the dual index, paired-end (PE) run parameters. Image analysis and base calling were done by the Real Time Analysis Software (RTA) v3.10.30. The resulting .cbcl files were converted into .fastq files with the bcl2fastq v2.20 software.

treatment_protocol: To induce choroidal neovascularization, mice were anaesthetized by intraperitoneal administration of ketamine hydrochloride  and xylazine. Pupillary dilatation was achieved by applying  tropicamide and phenylephrine hydrochloride. Six laser spots (150 mW, 200 μm and 100 ms) were applied to each eye using a frequency-doubled Nd:YAG-Laser.

value: choroidia

value: KO


title: Hela, SH, UBF, rep2


title: dis3KOtotal -Rep4

description: total fetal livers

value: fetal livers

value: dis3 KO

value: Embryonic day 14.5


title: Hela, SH, UBF, rep3


title: T26_0026

value: meningioma


title: dis3KOtotal -Rep2

description: total fetal livers


title: Hela, SH, UBF, rep1


title: S560s26_WT_laser_no

description: Library name: S560s26


title: Hela, SH, PolI, rep5

value: sc-293272 (SantaCruzBiotecnology)


title: T26_0048


title: dis3WTtotal -Rep4

description: total fetal livers

value: WT


title: dis3KOtotal -Rep1

description: total fetal livers


title: S560s25_KO_laser_no

description: Library name: S560s25


title: Hela, SH, PolI, rep4

value: HeLa


title: S560s24_KO_laser_no

description: Library name: S560s24


title: T26_0142


title: dis3WTtotal -Rep3

description: total fetal livers


title: Hela, SH, PolI, rep3

value: Human Cervical Cancer


title: S560s23_KO_laser_no

description: Library name: S560s23


title: Hela, SH, PolI, rep2


title: S560s22_WT_laser_no

description: Library name: S560s22


title: S560s21_WT_laser_no

description: Library name: S560s21


title: dis3WTtotal -Rep1

description: total fetal livers


title: Hela, SH, PolI, rep1


title: T26_0284


title: S560s19_WT_laser_yes

description: Library name: S560s19


title: Hela, SH, NSD3, rep4

value: 11345-AP (ProteinTect)


title: T26_0283


title: Cis7d_2: Cis7d Group rep2 bulkRNA-seq

city: Nanjing

first: Bingquan

last: Deng

state: Jiangsu

address: Nanjing Medical University, No.109 Longmian Avenue, Jiangning District

institute: Nanjing Medical University

data_processing:
Using the Illumina paired-end RNA-seq approach
Paired-end clean reads were mapped to the mouse reference genome GRCm38 using Hisat (vision 2.0)
StringTie and Ballgown was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM
FastQC (Version 0.10.1) was used for evaluating the quality of sequenced data
The mRNAs at a cut-off of 10 reads were compared and considered as differentially expressed if the fold change >2 and P value <0.05
Genome_build: GRCm38
Supplementary_files_format_and_content: text files included FPKM values for each Sample

source_name: Kidney

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) from kidney samples of the 3 groups (Sham, Cis3d, Cis7d, n=3) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Agilent 2100 with RIN number >7.0.
A total amount of 2 μg RNA per sample was used as input material for the RNA sample preparations. cDNA libraries were generated using NEB Next Ultra Directional RNA Library Prep Kit (NEB) following the manufacturer’s instructions, and then sequenced using the Illumina sequencing technology on an Illumina Hiseq4000 at LC Bio (Hangzhou, China) according to the recommended protocols

treatment_protocol: 3/7 days after intraperitoneal injection of 20mg/kg (body weight) cisplatin, Sham group injected with the same volume of normal saline

value: kidney

value: 7 days after intraperitoneal injection of cisplatin


title: Hela, SH, NSD3, rep3


title: S560s18_KO_laser_yes

description: Library name: S560s18


title: T26_0136


title: Cis7d_1: Cis7d Group rep1 bulkRNA-seq


title: Hela, SH, NSD3, rep2


title: S560s17_WT_laser_yes

description: Library name: S560s17


title: T26_0079


title: Cis3d_3: Cis3d Group rep3 bulkRNA-seq

value: 3 days after intraperitoneal injection of cisplatin


title: S560s16_WT_laser_yes

description: Library name: S560s16


title: T26_0036


title: S560s15_KO_laser_yes

description: Library name: S560s15


title: Hela, SCR, UBF, rep4

value: shCTRL

value: sc-13125 (SantaCruzBiotecnology)


title: Cis3d_1: Cis3d Group rep1 bulkRNA-seq


title: Hela, SCR, UBF, rep3


title: T26_0117


title: S560s14_KO_laser_yes

description: Library name: S560s14


title: NS_3: Sham Group rep3 bulkRNA-seq

value: Intraperitoneal injection of saline


title: Hela, SCR, UBF, rep2


title: S560s13_WT_laser_yes

description: Library name: S560s13

value: choroidia


title: T26_0024


title: NS_2: Sham Group rep2 bulkRNA-seq


title: Hela, SCR, UBF, rep1


title: S560s27_WT_laser_no

description: Library name: S560s27


title: S560s12_WT_laser_yes

description: Library name: S560s12


title: T26_0187


title: NS_1: Sham Group rep1 bulkRNA-seq


title: Hela, SCR, PolI, rep4


title: S560s11_WT_laser_yes

description: Library name: S560s11


title: T26_0240


title: Hela, SCR, PolI, rep3


title: T26_0170


title: S560s07_KO_laser_yes

description: Library name: S560s07

value: KO


title: Hela, SCR, PolI, rep2


title: T26_0124


title: Hela, SCR, PolI, rep1


title: T26_0005


title: Hela, SCR, NSD3, rep4


title: hMSC_donor2_ctrl_24h_exp1_rep1

type: RNA

city: Warsaw

first: Alicja

last: Trebinska-Stryjewska

address: gen. S. Kaliskiego 2

department: Institute of Optoelectronics

country: Poland

institute: Military University of Technology

description:
257236328904_1_3
hMCS donor2, control, 24h, experiment 1, replicate 1

hyb_protocol: 600 ng of Cy3-labeled cRNA was fragmented following the manufacturer's protocol at 60°C for 30 min; fragmentation reaction was stopped by adding 2 × Hi-RPM Hybridization buffer. Fragmented Cy3-labeled cRNA was hybridized to Agilent-072363 SurePrint G3 Human Gene Expression v3 8x60K microarrays for 17 h at 65°C in a rotating hybridization oven. After hybridization, microarrays were washed following manufacturer's instructions with GE Wash Buffer 1 and 2 (Agilent).

scan_protocol: Microarray slides were scanned immediately after washing with the SureScan Microarray Scanner (Agilent) using the Agilent Microarray Scan Control program version 9.1 with the following settings: resolution of 3 µm; dye channel green; green PMT sensitivity of 100%.

data_processing: Data from scanned images were extracted with the Feature Extraction Software 12.0 using default parameters (protocol: GE1_1200_Jun14, grid: 072363_D_F_20190214) to obtain the background-subtracted and detrended processed signal intensities. Obtained results were further processed with GeneSpring version 14.9, and log2-transformed normalized signal intensities were obtained after normalization by a percentile shift (75th percentile). The baseline was set to the median of all samples.

source_name: hMCS donor2, control, 24h

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng of Total RNA using the Low Input Quick Amp Labeling Kit, One Color (Agilent) according to manufacturer's instructions, followed by RNAeasy column purification (Qiagen). Addition of RNA Spike-In, One color (Agilent) served as an internal control. Cy3-labeled cRNA quality and quantity were assessed using 2100 Agilent Bioanalyzer (Agilent) and Agilent RNA 6000 Nano Reagent (Agilent).

growth_protocol: Poietics Normal Human Bone Marrow Derived Mesenchymal Stem Cells (hMSC) (Lonza) from two different donors were propagated in MSCGM Mesenchymal Stem Cell Growth Medium BulletKit (Lonza), and antibiotic/antimycotic in 5% carbon dioxide at 37ºC until semi-confluent.

extract_protocol: Immediately, 4 h or 24 h after treatment, cells were trypsinized, harvested, washed twice in ice-cold PBS and centrifuged at 150xg (hMSC donor 1) or 300xg (hMSC donor 2) for 5 min at 4ºC; cell pellets were frozen at -80ºC. Total RNA was isolated from the frozen pellets using the RNeasy Mini Kit (QIAGEN) according to manufacturer's instructions (including on-column DNaseI treatment). RNA was quantified using the QuantiFluor RNA System and Quantus Fluorometer (Promega). RNA quality was assessed with 2100 Agilent Bioanalyzer and Agilent RNA 6000 Nano Reagent. RIN ranged from 9.2 to 10.0.

treatment_protocol: Human MSC were used for experiments at the fourth or fifth passage, at 80% confluence. Before the exposure, standard hMSC medium in 175 cm2 cell culture flask was replaced with 10 ml of new, warm medium. Cells were exposed to a single high-peak power electromagnetic pulse (peak field: 1 Mv/m, rise time: 3 ns, pulse width: 30 ns, center frequency: 50 MHz). Cells were either harvested immediately after treatment or cultured for another 4 h or 24 h after adding 40 ml of standard hMSC medium. Sham-treated cells were prepared as above, except during exposure they were placed in a Faraday cage (80 dB attenuation for frequencies ranging from 100 kHz to 1 GHz). Control cells were kept in an incubator in standard cell culture conditions before harvesting.

tag: age of the donor

value: 24 years

tag: sex of the donor

value: Female

tag: race/ethnicity of the donor

value: Black

value: Control

tag: time


title: S560s04_KO_laser_yes

description: Library name: S560s04


title: T26_0151

value: meningioma


title: Hela, SCR, NSD3, rep3

tag: cut&tag antibody


title: S560s03_WT_laser_yes

description: Library name: S560s03

value: WT


title: hMSC_donor1_ctrl_24h_exp2_rep1

description:
257236328903_2_3
hMSC donor1, control, 24h, experiment 2, replicate 1

source_name: hMSC donor1, control, 24h

value: Normal Human Bone Marrow Derived Mesenchymal Stem Cells (hMSC)

value: 22 years

value: Male

value: Hispanic/Latino


title: S560s02_WT_laser_yes

description: Library name: S560s02


title: T26_0077


title: hMSC_donor1_ctrl_24h_exp2_rep2

description:
257236328903_2_4
hMSC donor1, control, 24h, experiment 2, replicate 2


title: dis3KOtotal -Rep3

description: total fetal livers

value: fetal livers

value: dis3 KO

value: Embryonic day 14.5


title: Hela, SCR, NSD3, rep2

value: HeLa

value: Human Cervical Cancer

value: shCTRL

value: 11345-AP (ProteinTect)


title: T26_0265


title: Hela, SCR, NSD3, rep1


title: S560s01_WT_laser_yes

description: Library name: S560s01

value: choroidia


title: T26_0094


title: T26_0276


title: dis3WTtotal -Rep2

description: total fetal livers


title: hMSC_donor1_ctrl_24h_exp1_rep2

description:
257236328903_1_4
hMSC donor1, control, 24h, experiment 1, replicate 2


title: T26_0106


title: LUAD_SMI

city: Singapore

first: Damien

last: Chua

address: 11 Mandalay Road

department: Lee Kong Chian School of Medicine

country: Singapore

institute: Nanyang Technological University, Singapore

description: Nanostring CosMx SMI Raw output file

source_name: LUAD tissue biopsy

label_protocol: Library was prepared with CosMx slides and reagent kits according to manufacturer's workflow and sequenced using the CosMx Spatial Molecular Imager (NanoString Technologies, Inc., USA).

extract_protocol: formalin-fixed paraffin-embedded (FFPE) tissue blocks were sectioned at 5 μm thickness

value: LUAD


title: Cis7d_3: Cis7d Group rep3 bulkRNA-seq

value: kidney

value: 7 days after intraperitoneal injection of cisplatin


title: Group4_5DPI_125, HTO

first: Chrysothemis

last: Brown

state: New York

department: Immuno-Oncology Program

institute: Memorial Sloan Kettering Cancer Center

description:
Library name: Group4_5DPI_125_HTO
HTO library from lung and medLN of neonatal mice

data_processing:
Single-cell RNA-seq FASTQ files were aligned to mm10 (Cell Ranger mouse reference genome mm10-2020-A) and counted by Cell Ranger v8.0.1 with default parameters. HTO sequencing data were aligned to the HTO barcodes, and UMIs were counted for each cell using CITE-seq-Count. Samples were then demultiplexed using the SHARP v0.1.3 pipeline. The singlet barcodes were further filtered based on the number of RNA-seq transcripts (>400 and <22,000), the number of detected genes (>400 and <8,000), and the fraction of mitochondrial transcripts (<8%). Following quality control filtering, raw counts were library-size normalized and log-transformed (‘log-normalized’ expression values) using Scanpy v1.10.3. A nearest-neighbor graph was constructed using the top 50 principal components (PCs) with 30 nearest neighbors. Clustering was performed using PhenoGraph (k = 30, clustering_algo = ‘louvain’). Cell clustering was visualized using UMAP, computed from the nearest neighbor graph built by PhenoGraph.
Assembly: mm10-2020-A
Supplementary files format and content: CellRanger processed output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: Output files for hashtag: Group1_124_PND10_HTO_barcodes.tsv.gz, Group1_124_PND10_HTO_features.tsv.gz, Group1_124_PND10_HTO_matrix.mtx.gz Group2_124_PND10_HTO_barcodes.tsv.gz, Group2_124_PND10_HTO_features.tsv.gz, Group2_124_PND10_HTO_matrix.mtx.gz Group3_124_PND10_HTO_barcodes.tsv.gz, Group3_124_PND10_HTO_features.tsv.gz, Group3_124_PND10_HTO_matrix.mtx.gz Group4_124_PND10_HTO_barcodes.tsv.gz, Group4_124_PND10_HTO_features.tsv.gz, Group4_124_PND10_HTO_matrix.mtx.gz Group1_125_PND10_HTO_barcodes.tsv.gz, Group1_125_PND10_HTO_features.tsv.gz, Group1_125_PND10_HTO_matrix.mtx.gz Group2_125_PND10_HTO_barcodes.tsv.gz, Group2_125_PND10_HTO_features.tsv.gz, Group2_125_PND10_HTO_matrix.mtx.gz Group3_125_PND10_HTO_barcodes.tsv.gz, Group3_125_PND10_HTO_features.tsv.gz, Group3_125_PND10_HTO_matrix.mtx.gz Group4_125_PND10_HTO_barcodes.tsv.gz, Group4_125_PND10_HTO_features.tsv.gz, Group4_125_PND10_HTO_matrix.mtx.gz, Group1_124_5DPI_HTO_barcodes.tsv.gz, Group1_124_5DPI_HTO_features.tsv.gz, Group1_124_5DPI_HTO_matrix.mtx.gz Group2_124_5DPI_HTO_barcodes.tsv.gz, Group2_124_5DPI_HTO_features.tsv.gz, Group2_124_5DPI_HTO_matrix.mtx.gz Group3_124_5DPI_HTO_barcodes.tsv.gz, Group3_124_5DPI_HTO_features.tsv.gz, Group3_124_5DPI_HTO_matrix.mtx.gz Group4_124_5DPI_HTO_barcodes.tsv.gz, Group4_124_5DPI_HTO_features.tsv.gz, Group4_124_5DPI_HTO_matrix.mtx.gz Group1_125_5DPI_HTO_barcodes.tsv.gz, Group1_125_5DPI_HTO_features.tsv.gz, Group1_125_5DPI_HTO_matrix.mtx.gz Group2_125_5DPI_HTO_barcodes.tsv.gz, Group2_125_5DPI_HTO_features.tsv.gz, Group2_125_5DPI_HTO_matrix.mtx.gz Group3_125_5DPI_HTO_barcodes.tsv.gz, Group3_125_5DPI_HTO_features.tsv.gz, Group3_125_5DPI_HTO_matrix.mtx.gz Group4_125_5DPI_HTO_barcodes.tsv.gz, Group4_125_5DPI_HTO_features.tsv.gz, Group4_125_5DPI_HTO_matrix.mtx.gz
Supplementary files format and content: Analysis results from Scanpy including pheno louvain clusters, celltype annotations, treatment groups and UMAP
Library strategy: CITE-seq

source_name: Lung and medLN

extract_protocol:
For single cell RNA seq of stem-like progenitors, pre-DCs and differentiated-DCs, lung and mediastinal lymph nodes from OPN+/+ or OPN-/- reared neonates treated with D-PLA were pooled from six biological replicates. Cells were incubated with 𝛼-CD16/32-BV605 in PBS-2% FBS for 20 min at 4°C to block binding to Fc receptors. Cell surface antigens were then stained for 30 mins at 4°C in PBS-2% FBS. Cells from distinct tissues were ‘stained’ with BioLegend TotalSeq B oligo-conjugated antibodies consisting of a pool of antibodies directed against CD45 (BioLegend; Clone 30-F11) and H2 MHC Class I alloantigens (BioLegend; clone M1/42). Immediately prior to fluorescent-assisted cell sorting (FACS), cells were resuspended in sorting buffer with SYTOX blue (Invitrogen; Cat# S34857) for dead cell exclusion. Live, lineage (CD3, CD19, NK1.1, Siglec-F, TCRβ, TCR𝛾𝛿)- singlets were then sort purified into six distinct populations: cDCs (CD11chi MHCII+ B220-), pDCs (CD11clo/int B220+ SiglecH+), pre-cDCs (CD11chi MHCII- CD135+ CD172a-), MDP/CDPs (CD11c- MHCII- cKIT+ SCA1- CD135+), LMPP/CMPs (CD34+ cKIT+ CD127- SCA1+/- CD16/32-) and CLPs (CD34- cKIT+ CD127+ Flt3+). Cells were sorted into cRPMI (Gibco; Cat# 11875093), each of the sort populations were counted and then pooled together to a final concentration of ~1600 cells per µL according to 10X Genomics guidelines for optimal cell recovery.
Single Cell Gene Expression was performed on a Chromium X (10X Genomics) following the user guide manual for Chromium GEM-X Single Cell 3’ Reagent Kit V4 (CG000732; Rev B). Briefly, cell viability was confirmed >90% with 0.5% (v/v) Trypan Blue (Sigma-Aldrich; Cat# T8154) staining and hemocytometer quantification. Cells were then captured in gel bead emulsions (GEMs). Following reverse transcription and cell barcoding, the GEMs were broken and cDNA purified using Dynabeads MyOne SILANE (Invitrogen; Cat# 37002D) followed by PCR amplifications as instructed by the manual. ~240,000 cells were targeted in total. Cells from different tissues and replicates were multiplexed together on one lane of 10X Chromium X using Hash Tag Oligonucleotides - HTO following a previously described protocol (Stoeckius et al., 2018). The final 3’ Gene Expression and cell surface protein libraries were loaded in a ratio of 9:1 and sequenced on an Illumina NextSeq 2000 (2 x P3 Flow Cell 1200mil reads) platform (Read 1 – 28 cycles, i7 index – 10 cycles, i5 index – 10 cycles, Read 2 – 90 cycles).

value: Lung and medLN

value: Lymphocytes

value: post-natal day 15

tag: host strain

tag: foster mother_strain

value: Osteopontin-/-

value: PLA

tag: infection

tag: library type

value: HTO


title: T26_0043

first: Daniel

last: Merk

institute: Hertie-Institute for Clinical Brain Research

data_processing:
SeSAMe pipline (v1.24.0)
Average Beta values

source_name: meningioma

extract_protocol: Genomic DNA from human meningiomas was extracted using QIAamp DNA Blood Mini Kit

tag: tissue

value: meningioma


title: DF1_3D_L3

first: meng

middle: yu

address: Xiaoling Wei street

institute: Nanjing Agricultural University (Weigang Campus)

data_processing:
For data processing, the clean reads were mapped to the Gallus_gallus reference genome, which was performed using HISAT2 v2.0.5.
Reads were assigned and counted to genes using the FPKM. The resulting matrix of read counts was then loaded into RStudio (R version 3.4.2), and DESeq2 were used to identify differentially expressed genes.
Functional enrichment (GO annotation, KEGG) of gene sets with different expression patterns was performed using clusterProfiler.
The heat maps were drawn by the function 'pheatmap' of R packages 'pheatmap' and correlation coefficients were calculation by the function 'cor' in R. Scatter plots were generated using the 'ggplot2' package to graphically reveal genes that differ significantly between two samples.
Assembly: GCF_000002315.6_GRCg6a
Supplementary files format and content: tab-delimited FPKM file includes FPKM values for each Sample

organism: Gallus gallus

extract_protocol:
Total RNA was extracted using the trizol method ,according to the manufacturer's instructions.
The poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads. Then the selected RNA was fragmented and copied into first strand cDNA, which was followed by second strand cDNA synthesis. These cDNA fragments then had the addition of a single 'A' base and subsequent ligation of the adapter. The products were then purified and enriched with PCR amplification. PCR yield was quantified and samples were pooled together to make a single strand DNA circle (ssDNA circle), which gave the final library.

tag: cell type

value: Fibroblasts

tag: genotype

value: WT


title: Group3_5DPI_125, HTO

description:
Library name: Group3_5DPI_125_HTO
HTO library from lung and medLN of neonatal mice

tag: age

tag: treatment

value: OPN


title: T26_0228

address: Otfried-Müller-Str. 27


title: hMSC_donor1_ctrl_24h_exp1_rep1

description:
257236328903_1_3
hMSC donor1, control, 24h, experiment 1, replicate 1

tag: cell line

value: Normal Human Bone Marrow Derived Mesenchymal Stem Cells (hMSC)

value: 22 years

value: Male

value: Hispanic/Latino

value: Control


title: hMSC_donor2_ctrl_4h_exp2_rep2

description:
257236328904_2_2
hMCS donor2, control, 4h, experiment 2, replicate 2

source_name: hMCS donor2, control, 4h

value: 24 years

value: Female

value: Black

value: 4 h


title: T26_0255


title: DF1_3D_L2

tag: group


title: T26_0037


title: Group2_5DPI_125, HTO

description:
Library name: Group2_5DPI_125_HTO
HTO library from lung and medLN of neonatal mice

value: Lung and medLN

value: Lymphocytes

value: post-natal day 15

value: PBS


title: Hela, SH, NSD3, rep1

value: HeLa

value: Human Cervical Cancer

value: 11345-AP (ProteinTect)


title: Cis3d_2: Cis3d Group rep2 bulkRNA-seq

tag: strain

value: kidney

value: 3 days after intraperitoneal injection of cisplatin


title: DF1_3D_L1

value: Fibroblasts

value: WT


title: Group1_5DPI_125, HTO

description:
Library name: Group1_5DPI_125_HTO
HTO library from lung and medLN of neonatal mice

value: HTO


title: T26_0269

value: meningioma


title: DF1_3D_E3


title: T26_0004


title: hMSC_donor2_ctrl_0h_exp1_rep2

description:
257236328904_1_2
hMCS donor2, control, 0h, experiment 1, replicate 2

source_name: hMCS donor2, control, 0h

value: Normal Human Bone Marrow Derived Mesenchymal Stem Cells (hMSC)

tag: age of the donor

value: 24 years

value: Control

value: 0 h


title: Group4_5DPI_124, HTO

description:
Library name: Group4_5DPI_124_HTO
HTO library from lung and medLN of neonatal mice

value: Lung and medLN

value: Osteopontin-/-

value: PLA


title: hMSC_donor2_ctrl_0h_exp1_rep1

description:
257236328904_1_1
hMCS donor2, control, 0h, experiment 1, replicate 1

tag: sex of the donor

value: Female

value: Black


title: T26_0288


title: T26_0271


title: DF1_3D_E1


title: DF1_3D_E2


title: Group3_5DPI_124, HTO

description:
Library name: Group3_5DPI_124_HTO
HTO library from lung and medLN of neonatal mice

value: Lymphocytes

value: post-natal day 15

value: OPN


title: DF1_2D_3


title: T26_0250


title: T26_0086


title: hMSC_donor1_ctrl_0h_exp2_rep2

description:
257236328903_2_2
hMSC donor1, control, 0h, experiment 2, replicate 2

source_name: hMSC donor1, control, 0h

value: 22 years

value: Male

tag: race/ethnicity of the donor

value: Hispanic/Latino


title: Group2_5DPI_124, HTO

description:
Library name: Group2_5DPI_124_HTO
HTO library from lung and medLN of neonatal mice

value: PBS

value: HTO


title: hMSC_donor1_ctrl_0h_exp2_rep1

description:
257236328903_2_1
hMSC donor1, control, 0h, experiment 2, replicate 1

value: Normal Human Bone Marrow Derived Mesenchymal Stem Cells (hMSC)

tag: time


title: Group1_5DPI_124, HTO

description:
Library name: Group1_5DPI_124_HTO
HTO library from lung and medLN of neonatal mice


title: hMSC_donor1_ctrl_0h_exp1_rep2

description:
257236328903_1_2
hMSC donor1, control, 0h, experiment 1, replicate 2


title: DF1_2D_2

value: Fibroblasts

value: WT


title: Group4_5DPI_125, GEX

description:
Library name: Group4_5DPI_125_mRNA
GEX (3' mRNA) library from lung and medLN of neonatal mice

value: mRNA


title: T26_0045

value: meningioma


title: hMSC_donor1_ctrl_0h_exp1_rep1

description:
257236328903_1_1
hMSC donor1, control, 0h, experiment 1, replicate 1

value: Control

value: 0 h


title: DF1_2D_1


title: T26_0033


title: Group3_5DPI_125, GEX

description:
Library name: Group3_5DPI_125_mRNA
GEX (3' mRNA) library from lung and medLN of neonatal mice

value: Lung and medLN

value: Osteopontin-/-


title: P. berghei ANKA trophozoite stage cells, CAP knockout, replicate 5

city: Chengdu

first: chen

last: li

address: Renmin South Road

institute: Sichuan Univercity

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic (v0.32) (default parameters)
Trimmed sequence reads were mapped to P. berghei genome (PlasmoDBv56) using STAR (v2.7.1a) with default parameters
Read count extraction were performed using GenomicAlignments (v1.24.0)
Read count extraction were normalization using DESeq2 (v1.24.0)
Assembly: P. berghei genome (PlasmoDBv56)
Supplementary files format and content: Tab-delimited txt files includes raw counts for each Sample
Supplementary files format and content: Tab-delimited txt files include RPKM values for each Sample

organism: Plasmodium berghei

source_name: Trophozoites

growth_protocol: Red blood cells infected by P. berghei ANKA parasites were injected into mice by intraperitoneal (i.p) injection. Trophozoite parasites were acquired by collecting blood at a parasitemia stage of 1-3%, followed by filtration, lysis with Red Blood Cell Lysis Buffer, and washing with PBS to isolate the parasites.

extract_protocol:
Total RNA was extracted and purified by RiboPureTM kit, and ribosomal RNA was removed using Illumina Ribo-Zero Plus rRNA Depletion Kit, and the rRNA-free residue was precipitated by ethanol
Sequencing libraries were generated using the rRNA-depleted RNA by NEB Next Ultra Directional RNA Library Prep Kit for Illumina (NEB, USA) following the manufacturer’s recommendations

treatment_protocol: The CAP knockout mutants were generated in PbA-NIH and PbA-SZ by transfecting a linearized DNA construct generated based on plasmid pL0034 (MRA-849, www.mr4.org) under the positive selection with pyrimethamine.

value: Trophozoites

value: CAP knockout


title: Group2_5DPI_125, GEX

description:
Library name: Group2_5DPI_125_mRNA
GEX (3' mRNA) library from lung and medLN of neonatal mice

value: Lymphocytes

value: post-natal day 15


title: S560s06_KO_laser_yes

description: Library name: S560s06

value: choroidia

value: KO


title: T26_0248

city: Tübingen


title: hMSC_donor2_ctrl_24h_exp2_rep2

description:
257236328904_2_4
hMCS donor2, control, 24h, experiment 2, replicate 2

value: 24 years

value: Female

value: Black


title: hMSC_donor2_HPEM_24h_exp2_rep3

description:
257236328909_2_4
hMCS donor2, HPEM, 24h, experiment 2, replicate 3

source_name: hMCS donor2, HPEM, 24h

value: Normal Human Bone Marrow Derived Mesenchymal Stem Cells (hMSC)

value: Exposed to a high power electromagnetic pulse (HPEM), 1 MV/m


title: hMSC_donor2_ctrl_24h_exp2_rep1

description:
257236328904_2_3
hMCS donor2, control, 24h, experiment 2, replicate 1


title: hMSC_donor2_HPEM_24h_exp2_rep2

description:
257236328898_2_4
hMCS donor2, HPEM, 24h, experiment 2, replicate 2


title: CFF-16HBEge cells mock-transduced, 48h

city: Cork

first: Lucia

last: Nicosia

state: Co. Cork

address: College Road

country: Ireland

institute: University College Cork

description: Library name: NC2

data_processing:
The samples were sequenced using a 2x150 Pair-End (PE) configuration v1.5. Image analysis and base calling were conducted by the NovaSeq Control Software v1.7 on the NovaSeq instrument. Raw sequence data (.bcl files) generated from Illumina NovaSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq program version 2.20. One mismatch was allowed for index sequence identification.
After investigating the quality of the raw data, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Homo sapiens reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step. Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
Assembly: Trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL.
Supplementary files format and content: Excel spreadsheet (.xlsx) with raw read counts, with genes as rows and samples as columns. The first column contains Ensembl gene identifiers, columns 2-10 contain integer count values for biological triplicates of each condition (eVLP, NC, PLAS), and the final column contains gene symbols.
Supplementary files format and content: Excel spreadsheets with Differential Gene Expression and Gene Ontology analysis results.

extract_protocol:
Total RNA from each condition was extracted ~48 hours post-treatment using the Monarch® Total RNA Miniprep Kit (NEB, T2010S) according to manufacturer’s protocols.
RNA sequencing library preparation was performed using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina by following the manufacturer’s recommendations (NEB, Ipswich, MA, USA). Briefly, mRNAs were first enriched with Oligo(dT) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. The second strand of cDNA was marked by incorporating dUTP during the synthesis. cDNA fragments were end repaired and adenylated at 3’ ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by limited-cycle PCR. The incorporated dUTP in second strand cDNA quenched the amplification of second strand, which helped to preserve the strand specificity. Sequencing libraries were validated using NGS Kit on the Agilent 5300 Fragment Analyzer (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 4.0 Fluorometer (Invitrogen, Carlsbad, CA).

value: gene edited human bronchial epithelial cells

value: CFTR G542X/G542X

value: mock-transduction

tag: batch

value: 48 hours post treatment


title: Group1_5DPI_125, GEX

description:
Library name: Group1_5DPI_125_mRNA
GEX (3' mRNA) library from lung and medLN of neonatal mice

value: Lung and medLN

tag: host strain

value: PBS

value: mRNA


title: P. berghei ANKA trophozoite stage cells, CAP knockout, replicate 4

value: Trophozoites

value: CAP knockout


title: Group4_5DPI_124, GEX

description:
Library name: Group4_5DPI_124_mRNA
GEX (3' mRNA) library from lung and medLN of neonatal mice

value: Lymphocytes

value: post-natal day 15

tag: foster mother_strain

value: Osteopontin-/-

value: PLA


title: T26_0247

value: meningioma


title: P. berghei ANKA trophozoite stage cells, CAP knockout, replicate 3


title: hMSC_donor2_ctrl_24h_exp1_rep2

description:
257236328904_1_4
hMCS donor2, control, 24h, experiment 1, replicate 2

value: 24 years

value: Female

value: Black

value: Control


title: T26_0141


title: hMSC_donor2_HPEM_24h_exp2_rep1

description:
257236328897_2_4
hMCS donor2, HPEM, 24h, experiment 2, replicate 1

value: Normal Human Bone Marrow Derived Mesenchymal Stem Cells (hMSC)

value: Exposed to a high power electromagnetic pulse (HPEM), 1 MV/m


title: P. berghei ANKA trophozoite stage cells, CAP knockout, replicate 2


title: S560s05_KO_laser_yes

description: Library name: S560s05

value: choroidia

value: KO


title: Group3_5DPI_124, GEX

description:
Library name: Group3_5DPI_124_mRNA
GEX (3' mRNA) library from lung and medLN of neonatal mice

value: Lung and medLN

value: OPN

tag: infection


title: hMSC_donor2_HPEM_24h_exp1_rep2

description:
257236328898_1_4
hMCS donor2, HPEM, 24h, experiment 1, replicate 2


title: T26_0099


title: P. berghei ANKA trophozoite stage cells, CAP knockout, replicate 1

value: Trophozoites


title: T26_0098


title: Group2_5DPI_124, GEX

description:
Library name: Group2_5DPI_124_mRNA
GEX (3' mRNA) library from lung and medLN of neonatal mice

value: PBS

tag: library type

value: mRNA


title: P. berghei ANKA trophozoite stage cells, wild type, replicate 5

value: Wild type


title: hMSC_donor2_HPEM_24h_exp1_rep3

description:
257236328909_1_4
hMCS donor2, HPEM, 24h, experiment 1, replicate 3


title: P. berghei ANKA trophozoite stage cells, wild type, replicate 4


title: Group1_5DPI_124, GEX

description:
Library name: Group1_5DPI_124_mRNA
GEX (3' mRNA) library from lung and medLN of neonatal mice

tag: tissue

value: Lymphocytes

value: post-natal day 15


title: T26_0253

value: meningioma


title: Group4_PND10_125, HTO

description:
Library name: Group4_PND10_125_HTO
HTO library from lung and medLN of neonatal mice

tag: cell type

value: post-natal day 10

value: Osteopontin-/-

value: PLA

value: uninfected

value: HTO


title: hMSC_donor1_HPEM_24h_exp2_rep3

description:
257236328902_2_4
hMSC donor1, HPEM, 24h, experiment 2, replicate 3

source_name: hMSC donor1, HPEM, 24h

value: Normal Human Bone Marrow Derived Mesenchymal Stem Cells (hMSC)

value: 22 years

value: Male

value: Hispanic/Latino

value: Exposed to a high power electromagnetic pulse (HPEM), 1 MV/m


title: P. berghei ANKA trophozoite stage cells, wild type, replicate 3

value: Trophozoites

tag: genotype


title: hMSC_donor1_HPEM_24h_exp2_rep2

description:
257236328901_2_4
hMSC donor1, HPEM, 24h, experiment 2, replicate 2


title: Group3_PND10_125, HTO

description:
Library name: Group3_PND10_125_HTO
HTO library from lung and medLN of neonatal mice

value: Lung and medLN

tag: age

value: OPN


title: T26_0249


title: T26_0252


title: hMSC_donor1_HPEM_24h_exp2_rep1

description:
257236328900_2_4
hMSC donor1, HPEM, 24h, experiment 2, replicate 1

tag: treatment


title: hMSC_donor2_HPEM_24h_exp1_rep1

description:
257236328897_1_4
hMCS donor2, HPEM, 24h, experiment 1, replicate 1

tag: cell line

value: 24 years

value: Female

value: Black


title: P. berghei ANKA trophozoite stage cells, wild type, replicate 2

value: Wild type


title: T26_0246

value: meningioma


title: Group2_PND10_125, HTO

description:
Library name: Group2_PND10_125_HTO
HTO library from lung and medLN of neonatal mice

value: Lymphocytes

value: post-natal day 10

value: Osteopontin-/-

value: PBS


title: T26_0244


title: Group1_PND10_125, HTO

description:
Library name: Group1_PND10_125_HTO
HTO library from lung and medLN of neonatal mice

value: uninfected

value: HTO


title: Control parent 305

city: Istanbul

first: Elif

last: ÖNEL

address: Buyukdere Street

country: Turkey

institute: Istanbul Technicial University

description: DNA is isolated from peripheral blood samples via salting-out procedure is genotyped using HumanOmniExpress-24-v1-0-B.

hyb_protocol: Allele-specific staining was performed for chips.

scan_protocol: BeadArray Reader (Illumina) is used after bead chips are stained.

data_processing:
GenomeStudio v2.0 is used for deriving genotypes.
value definition: Genotype:  AA,AB,BB,or 00 (no call)

label: biotin

label_protocol: DNA fragmentation is applied.

extract_protocol: DNA is isolated from peripheral blood samples via salting-out procedure.

value: Blood

tag: Sex


title: P. berghei ANKA trophozoite stage cells, wild type, replicate 1


title: T26_0025


title: T26_0114


title: hMSC_donor1_HPEM_24h_exp1_rep2

description:
257236328901_1_4
hMSC donor1, HPEM, 24h, experiment 1, replicate 2

value: Normal Human Bone Marrow Derived Mesenchymal Stem Cells (hMSC)

value: 22 years

value: Male

value: Hispanic/Latino


title: Patient 405


title: Group4_PND10_124, HTO

description:
Library name: Group4_PND10_124_HTO
HTO library from lung and medLN of neonatal mice

value: Lung and medLN

value: PLA


title: T26_0150


title: Group3_PND10_124, HTO

description:
Library name: Group3_PND10_124_HTO
HTO library from lung and medLN of neonatal mice

value: OPN


title: hMSC_donor1_HPEM_24h_exp1_rep1

description:
257236328900_1_4
hMSC donor1, HPEM, 24h, experiment 1, replicate 1

value: Exposed to a high power electromagnetic pulse (HPEM), 1 MV/m


title: Group2_PND10_124, HTO

description:
Library name: Group2_PND10_124_HTO
HTO library from lung and medLN of neonatal mice


title: hMSC_donor2_sham_24h_exp2_rep3

description:
257236328909_2_3
hMCS donor2, sham, 24h, experiment 2, replicate 3

source_name: hMCS donor2, sham, 24h

value: 24 years

value: Female

value: Black

value: Sham-exposed


title: T26_0169

value: meningioma


title: Group1_PND10_124, HTO

description:
Library name: Group1_PND10_124_HTO
HTO library from lung and medLN of neonatal mice

value: Lymphocytes

value: post-natal day 10

value: PBS


title: T26_0211


title: Group4_PND10_125, GEX

description:
Library name: Group4_PND10_125_mRNA
GEX (3' mRNA) library from lung and medLN of neonatal mice

value: Osteopontin-/-

value: uninfected

value: mRNA


title: T26_0161


title: Patient 401

value: Blood