title: NU-DHL1 IgG1 WT replicate 2

description: Library name: NUDHL1_IgG1_WT_2


title: 251_TNY9NWK

status: Public on Dec 17 2025

type: SRA

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

country: USA

institute: Benaroya Research Institute

description: Library name: lib33108

library_source: transcriptomic

data_processing:
Base calls were processed to FASTQs on BaseSpace (Illumina), and a base call quality-trimming step was applied to remove low-confidence base calls from the ends of reads.
Reads were processed using workflows managed on the Galaxy platform; reads were trimmed by 1 base at the 3’ end, and then trimmed from both ends until base calls had a minimum quality score of at least 30 (Galaxy FASTQ Trimmer tool v1.0.0)
FastqMcf (v1.1.2, https://benthamopen.com/ ABSTRACT/TOBIOIJ-7-1) was used to remove any remaining adapter sequence.
Reads were aligned by STAR1 2.4.2a to GRCh38
Gene counts were generated using HTSeq-count (v0.4.1). Quality metrics were compiled from PICARD (v1.134, http://broadinstitute.github.io/picard/), FASTQC (v0.11.3, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), Samtools (v1.2)30, and HTSeq-count (v0.4.1).
Assembly: GRCh38
Supplementary files format and content: Raw counts are provided in .csv format. Each row is a gene, each column is a sample.

molecule: total RNA

organism: Homo sapiens

source_name: whole blood

extract_protocol:
Whole blood was collected in Tempus Blood RNA Tubes (Thermo Fisher Scientific), RNA was extracted using MagMax for Stabilized Blood Tubes RNA Isolation Kit (Thermo Fisher Scientific), followed by globin reduction using GlobinClear Human (Thermo Fisher Scientific).
To generate sequencing libraries, total RNA (0.5 ng) was added to reaction buffer from the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara), and reverse transcription was performed followed by PCR amplification to generate full-length amplified cDNA. Sequencing libraries were constructed using the NexteraXT DNA sample preparation kit (Illumina) to generate Illumina-compatible barcoded libraries. Libraries were pooled and quantified using a Qubit Fluorometer (Life Technologies). Dual-index, single-read sequencing of pooled libraries was carried out on a HiSeq 2500 sequencer (Illumina) with 58-base reads, using HiSeq v4 Cluster and SBS kits (Illumina) with a target depth of 5 million reads per sample.

tag: tissue

value: whole blood

tag: donor id

tag: age

tag: gender

value: male

tag: visit

tag: group

value: Placebo


title: NU-DHL1 IgG1 WT replicate 1

city: London

first: Pavel

last: Tolar

address: Institute of Immunity and Transplantation, Rowland Hill St

country: United Kingdom

institute: University College London

description: Library name: NUDHL1_IgG1_WT_1

data_processing:
Data were processed by Novogene Novomagic. Raw reads were filtered to remove reads containing adapters or reads of low quality (containing undetermined nucleotides or Qphred <= 5 bases accounting for more than 50% of the entire read length). Reads were mapped to the reference genome using the HISAT2. Gene counts were extracted and gene expression levels were estimated by calculating the number of fragments per kilobase of transcript sequence per millions base pairs sequenced (FPKM).
Assembly: GRCh38
Supplementary files format and content: Excel spreadsheet containing raw read counts and FPKM values of the individual samples

molecule: polyA RNA

source_name: B Lymphoma

growth_protocol: Cells were cultured in RPMI (Gibco) supplemented with 10% heat-inactivated fetal bovine serum (FBS), 1X MEM non-essential amino acids (Gibco), 1X GlutaMAX (Gibco), 50µM 2-mercaptoethanol (Sigma Aldrich), 100U/ml penicillin and 100µg/ml streptomycin and maintained at 37°C in humidified incubators with 5% CO2. The cell lines were authenticated by STR and tested mycoplasma-free.

extract_protocol:
RNA was isolated from 5x106 cells by Novogene using QIAGEN Rneasy
Library was constructed by Novogene using mRNA library preparation (poly A enrichment)

treatment_protocol: Stable WSU-FSCCL cells expressing Cas9 were established. The WSU-FSCCL Cas9 cells were lentivirally transduced with a dual-targeting sgRNA lentiGuide-mCherry construct  targeting IgM and IgG1 switch regions. mCherry+ IgM+ or mCherry+ IgG+ cells were sorted by flow cytometry. IGHG1 mutation W375* was introduced into IgG1+ cells by prime editing and cells were cultured for 15 weeks during which W375* cells overgrew WT cells (>77%). NU-DHL1 cells were nucleofected with Cas9/sgRNA complexes targeting the IgM and IgG1 switch regions. IgM+ or  IgG+ cells were sorted by flow cytometry. IGHG1 mutation W375* was introduced into IgG1+ cells by prime editing and cells were cultured for 15 weeks during which W375* cells overgrew WT cells (>95%).

value: B Lymphoma

tag: cell line

tag: treatment

value: Class-switching induced by CRISPR/Cas9 targeting of IgM and IgG1 immunoglobulin switch regions

value: Flow sorting for cells expressing surface IgG1


title: AMB_201117_9mo_5E_6E_4_P1-3-B21-I5

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Library strategy: snmC-seq3
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

molecule: genomic DNA

organism: Mus musculus

extract_protocol:
Regions of mouse brain were dissected.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: strain

value: 9 months

tag: brain region

value: CP

value: M


title: AMB_201117_9mo_5E_6E_4_P1-3-B21-L5


title: NU-DHL1 IgM replicate 2

description: Library name: NUDHL1_IgM_2

value: Flow sorting for cells expressing surface IgM


title: AMB_201117_9mo_5E_6E_4_P1-3-B21-K18


title: NU-DHL1 IgM replicate 3

description: Library name: NUDHL1_IgM_3


title: AMB_201117_9mo_5E_6E_4_P1-3-B21-I18


title: AMB_201117_9mo_5E_6E_4_P1-3-B21-H18


title: 249_TNY93CX

description: Library name: lib33106

value: ATG


title: AMB_201117_9mo_5E_6E_4_P1-3-B21-I17


title: 250_TNY7WAG

description: Library name: lib33107

value: female


title: AMB_201117_9mo_5E_6E_4_P1-3-B21-H5


title: NU-DHL1 IgM replicate 1

description: Library name: NUDHL1_IgM_1


title: AMB_201117_9mo_5E_6E_4_P1-3-B21-H17


title: AMB_201117_9mo_5E_6E_4_P1-3-B21-H6


title: 252_TNY9NX3

description: Library name: lib33109


title: 247_TNY8752

description: Library name: lib33104


title: 248_TNY953X

description: Library name: lib33105

value: ATG-GCSF


title: AMB_201117_9mo_5E_6E_4_P1-3-B21-G5


title: AMB_201117_9mo_5E_6E_4_P1-3-B21-G6


title: AMB_201117_9mo_5E_6E_4_P1-3-B21-J17


title: AMB_201117_9mo_5E_6E_4_P1-3-B21-G17


title: 246_TNY8MUL

description: Library name: lib33103


title: PTSD2

city: Charleston

first: Liu

last: Liu

state: South Carolina

address: 173 Ashley Ave. CRI 610

institute: Medical University of South Carolina

description:
Library name: SAMPLE5
10x Genomics

library_source: transcriptomic single cell

data_processing:
Raw sequencing reads were processed by Novogene, including alignment to the GRCh38 human reference genome using Cell Ranger (10x Genomics), UMI collapsing, and barcode filtering to generate gene expression matrices. Downstream analysis was performed in R using Seurat, including quality control, normalization, clustering, and cell type annotation. The final processed data are provided as a Seurat RDS object containing all six samples.
Assembly: GRCh38
Supplementary files format and content: Processed data are provided as a Seurat RDS object containing gene expression matrices and cell-level annotations for all six samples.

source_name: hippocampus

extract_protocol:
RNA extraction and library preparation were performed by Novogene (San Jose, CA) following standard 10x Genomics Chromium Single Cell 3′ v3.1 protocols.
Single-nucleus 3′ RNA libraries were prepared by Novogene (San Jose, CA) using the 10x Genomics Chromium Single Cell 3′ v3.1 platform following the manufacturer’s instructions. Library construction included barcoding of individual nuclei, cDNA synthesis, amplification, and preparation for Illumina sequencing.

value: hippocampus

tag: Sex

value: Female


title: PTSD3

description:
Library name: SAMPLE6
10x Genomics


title: PTSD1

description:
Library name: SAMPLE4
10x Genomics
Fastq files for lane L003 of sample PTSD1 were corrupted during download and therefore not included in this submission. Processed RDS files still contain all data including reads from L003.


title: AMB_201117_9mo_5E_6E_4_P1-3-B21-F5


title: AMB_201117_9mo_5E_6E_4_P1-3-B21-F18


title: AMB_201117_9mo_5E_6E_4_P1-3-B21-F6


title: 244_TNY667W

description: Library name: lib33101


title: AMB_201117_9mo_5E_6E_4_P1-3-B21-F17


title: 243_TNY4HV1

description: Library name: lib33100


title: Con2

description:
Library name: SAMPLE2
10x Genomics


title: Con1

description:
Library name: SAMPLE1
10x Genomics


title: AMB_201117_9mo_5E_6E_4_P1-3-B21-E17


title: AMB_201117_9mo_5E_6E_4_P1-3-B21-D6


title: CVG-1-mock, biol rep2

city: Pittsburgh

first: Hyun Jung

last: Park

state: PA

address: 1013 River Oaks Dr.

institute: University of Pittsburgh-Pittsburgh Campus

description: Library name: Sample 6

data_processing:
Reads from six libraries, representing duplicates for each condition (mock, A-485-treated, dCBP-1-treated), were trimmed by Trimmomatic v.0.38 with default setting for paired-end reads, followed by alignment with STAR v.2.7.10b using human genome reference GRCh38.p14. The aligned reads were quantified by featureCounts from SubRead v.1.5.1.
The quantified expression was analyzed in R statistical environment v.4.3.1. Differential gene expression analysis was performed using DESeq2 1.40.2, differentially expressed genes were defined by having Benjamini and Hochberg-adjusted p value < 0.05 and |log2 fold change|
Gene set enrichment analysis between conditions was performed by fgsea v.1.26.0 on hallmark gene signature obtained from Molecular Signature Database and tumor transcriptional metaprograms from Gavish et al. (2023)(58). Per-sample gene set enrichment was calculated by gene set variation analysis (GSVA) v.1.48.3. Gene ontology over-representation analysis was performed on the concordantly up-/downregulated genes between CBP/p300 inhibitor treatments and pan T antigen knockdown in CVG-1 cells using clusterProfiler v.4.14.6, overrepresented terms were visualized in descending order of gene ratio, i.e. number of genes in the query gene set found in a particular GO biological process term divided by the total number of genes in the query gene set.
Assembly: hg19
Supplementary files format and content: tab-delimeted text file includes raw counts for each gene

growth_protocol: MKL-1, MKL-2, MS-1, CVG-1, BroLi, WaGa, UISO, NCI- H146, and NCI-H69 cell lines were maintained in RPMI medium (Corning) supplemented with 10% fetal bovine serum (VWR) and non-essential amino acids (Corning). BJ fibroblasts (ATCC, CRL-2522), U87, U251, U2OS, 293, and 293FT cells (Invitrogen) were cultured in Dulbecco’s modified Eagle’s Medium (Corning) with 10% fetal bovine serum (VWR) and non-essential amino acids (Corning). Cells were kept at 37°C and 5% CO2. CBP/p300 inhibitors A-485 (Selleckchem) and dCBP-1 (MedChemExpress) were prepared as 10 mM and 100 μM stocks in DMSO, respectively; mock treatments contained 0.1 % DMSO. All cell lines were screened for mycoplasma every two months.

extract_protocol:
Total RNA was extracted with Trizol (Invitrogen) and quantified using Qubit 3.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked using Agilent TapeStation 4200 (Agilent Technologies, Palo Alto, CA, USA).   ERCC RNA Spike-In Mix (Cat: #4456740) from ThermoFisher Scientific, was added to normalized total RNA prior to library preparation following manufacturer’s protocol.
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were initially enriched with Oligod(T) beads.  Enriched mRNAs were fragmented for 15 minutes at 94 °C. Converted the RNA molecules into complementary DNA (cDNA) and incorporated UMIs during reverse transcription. 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 PCR with limited cycles. The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 3.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA). The sequencing libraries were clustered on a flowcell. After clustering, the flowcell was loaded on the Illumina NovaSeq instrument according to manufacturer’s instructions.  The samples were sequenced using a 2x150bp Paired End (PE) configuration. Image analysis and base calling were conducted by the Control software. Raw sequence data (.bcl files) generated by the sequencer were converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.

treatment_protocol: MCV-positive MCC cell lines (3x104 of MKL-1, MKL-2, MS-1, CVG-1, and WaGa), MCV-negative UISO cell line (1x104), small cell neuroendocrine carcinoma cell lines (8x103 of NCI-H146 and NCI-H69), glioblastoma cell lines (4x103 of U87 and U251), osteosarcoma U2OS cell line (4x103), adenovirus E1A-immortalized embryonic kidney 293 cell lines (3x103) and foreskin BJ cell line (6x103) were seeded in a 96 well plate with triplicates for each measurement time in 200 µL of medium containing mock, 5 µM A-485, or 100 nM dCBP-1. On days 1, 3, 5, 7, and 9, 95 µL of media was removed and 8 µL of Resazurin (Cell Signaling) was added. Measurements took place 4 hours after addition. Minimum of 2 repeats were performed.

tag: cell type

value: Merkel cell carcinoma


title: AMB_201117_9mo_5E_6E_4_P1-3-B21-E6


title: 242_TNY667N

description: Library name: lib33099


title: 241_TNY8GH4

description: Library name: lib33098


title: AMB_201117_9mo_5E_6E_4_P1-3-B21-G18


title: AMB_201117_9mo_5E_6E_4_P1-3-B21-D18


title: AMB_201117_9mo_5E_6E_4_P1-3-B21-D17


title: AMB_201117_9mo_5E_6E_4_P1-3-B21-C6


title: 240_TNY041L

description: Library name: lib33097


title: AMB_201117_9mo_5E_6E_4_P1-3-B21-C5


title: 245_TNY5XXT

description: Library name: lib33102


title: 239_TNY84WX

description: Library name: lib33096


title: CVG-1-d-CBP1, biol rep2

description: Library name: Sample 4

value: 100 nM dCBP-1


title: Con3

description:
Library name: SAMPLE3
10x Genomics


title: CVG-1-d-CBP1, biol  rep1

description: Library name: Sample 3


title: AMB_201117_9mo_5E_6E_4_P1-3-B21-C17


title: 238_TNY11HL

description: Library name: lib33095

value: whole blood


title: AMB_201117_9mo_5E_6E_4_P1-3-B21-E5


title: AMB_201117_9mo_5E_6E_4_P1-3-B21-E18


title: AMB_201117_9mo_5E_6E_4_P1-3-B21-B6


title: CVG-1-A-485, biol rep2

description: Library name: Sample 2


title: AMB_201117_9mo_5E_6E_4_P1-3-B21-D5


title: AMB_201117_9mo_5E_6E_4_P1-3-B21-B18


title: AMB_201117_9mo_5E_6E_4_P1-3-B21-B5


title: 236_TNY7UJ7

description: Library name: lib33093

value: male


title: 237_TNY3JKA

description: Library name: lib33094


title: AMB_201117_9mo_5E_6E_4_P1-3-B21-B17


title: CVG-1-A-485, biol rep1

description: Library name: Sample 1


title: AMB_201117_9mo_5E_6E_4_P1-3-B21-A6


title: CVG-1-mock, biol rep1

description: Library name: Sample 5


title: AMB_201117_9mo_5E_6E_4_P1-3-B21-A18


title: 234_TNY5UGM

description: Library name: lib33091


title: AMB_201117_9mo_5E_6E_4_P1-3-B21-A17


title: 235_TNY3JNA

description: Library name: lib33092


title: tHER2CAR_OR7A10Stop_24hr_Rep3

city: West Haven

first: Sidi

last: Chen

state: CT

address: 850 West Campus Drive

institute: Yale University

description: Library name: 90b-24_Rep3

data_processing:
Raw FASTQ files were first assessed for quality using FastQC (v0.12.1). Reads were then aligned to the GRCh38 reference genome using the STAR aligner, and gene-level quantification was performed using Gencode annotations (GRCh38_v45). Gene count tables were merged using a custom R script, and genes with fewer than 20 total counts across all samples and conditions were considered universally not expressed and subsequently filtered out. The resulting raw count matrix was normalized and subjected to differential expression analysis using DESeq2 (v1.42.1). DESeq2 fit a complete generalized linear model (GLM) based on negative binomial distribution. The design matrix of the complete model (design = ~ OE*CAR) for stimulated population includes main effect of OR7A10 overexpression, main effect from CAR construct, and the interaction terms between the two variable.
Assembly: GRCh38_v45
Supplementary files format and content: Tab-delimited txt file that contains the raw count matrix

source_name: NK Cells

extract_protocol:
Total mRNA were  extracted using Qiagen RNeasy Plus Kits
The mRNA library preparations were performed using a NEBNext® Ultra™ RNA Library Prep Kit, and samples were multiplexed using barcoded primers provided by NEBNext® Multiplex Oligos for Illumina® (Index Primers Set 2). Libraries were sequenced using a NovaSeq X plus (Illumina) platform.

treatment_protocol: Human primary NK cells were infected with OR7A10(STOP), OR7A10, truncated-CAR;OR7A10(STOP), truncated-CAR;OR7A10, CAR;OR7A10(STOP), or CAR;OR7A10 lentiviral constructs and stimulated with HT29 cancer cells at a 1 : 1  E : T  ratio for 0 or 24 hours. CAR-NK cells were stained with APC-CD56 antibody and isolated with anti-APC magnetic beads.

value: NK Cells


title: AMB_201117_9mo_5E_6E_4_P1-3-B21-C18


title: tHER2CAR_OR7A10Stop_24hr_Rep1

description: Library name: 90b-24_Rep1


title: AMB_201117_9mo_5E_6E_4_P1-2-B6-P3


title: tHER2CAR_OR7A10Stop_0hr_Rep3

description: Library name: 90b_Rep3


title: 232_TNY5CAG

description: Library name: lib33089


title: tHER2CAR_OR7A10Stop_0hr_Rep2

description: Library name: 90b_Rep2


title: AMB_201117_9mo_5E_6E_4_P1-2-B6-P16


title: AMB_201117_9mo_5E_6E_4_P1-2-B6-O4


title: tHER2CAR_OR7A10Stop_24hr_Rep2

description: Library name: 90b-24_Rep2


title: 231_TNY5TL0

description: Library name: lib33088


title: AMB_201117_9mo_5E_6E_4_P1-2-B6-O3


title: 233_TNY7L77

description: Library name: lib33090


title: AMB_201117_9mo_5E_6E_4_P1-2-B6-O16


title: 230_TNY6JYW

description: Library name: lib33087


title: AMB_201117_9mo_5E_6E_4_P1-3-B21-A5


title: tHER2CAR_OR7A10Stop_0hr_Rep1

description: Library name: 90b_Rep1


title: 229_TNY776W

description: Library name: lib33086


title: AMB_201117_9mo_5E_6E_4_P1-2-B6-N3


title: AMB_201117_9mo_5E_6E_4_P1-2-B6-N4


title: AMB_201117_9mo_5E_6E_4_P1-2-B6-O15


title: AMB_201117_9mo_5E_6E_4_P1-2-B6-N15


title: tHER2CAR_OR7A10_24hr_Rep2

description: Library name: 90-24_Rep2


title: AMB_201117_9mo_5E_6E_4_P1-2-B6-P4


title: 228_TNY38T5

description: Library name: lib33085


title: AMB_201117_9mo_5E_6E_4_P1-2-B6-M4


title: tHER2CAR_OR7A10_24hr_Rep1

description: Library name: 90-24_Rep1


title: AMB_201117_9mo_5E_6E_4_P1-2-B6-M3


title: 227_TNY65WJ

description: Library name: lib33084


title: AMB_201117_9mo_5E_6E_4_P1-2-B6-M16


title: tHER2CAR_OR7A10_0hr_Rep3

description: Library name: 90_Rep3


title: AMB_201117_9mo_5E_6E_4_P1-2-B6-P15


title: 226_TNY65YY

description: Library name: lib33083


title: AMB_201117_9mo_5E_6E_4_P1-2-B6-M15


title: AMB_201117_9mo_5E_6E_4_P1-2-B6-L4


title: tHER2CAR_OR7A10_0hr_Rep2

description: Library name: 90_Rep2


title: AMB_201117_9mo_5E_6E_4_P1-2-B6-L3


title: 225_TNY664U

description: Library name: lib33082


title: AMB_201117_9mo_5E_6E_4_P1-2-B6-L16


title: tHER2CAR_OR7A10_0hr_Rep1

description: Library name: 90_Rep1


title: AMB_201117_9mo_5E_6E_4_P1-2-B6-L15


title: 224_TNY660M

description: Library name: lib33081


title: AMB_201117_9mo_5E_6E_4_P1-2-B6-K4


title: tHER2CAR_OR7A10_24hr_Rep3

description: Library name: 90-24_Rep3


title: AMB_201117_9mo_5E_6E_4_P1-2-B6-N16


title: AMB_201117_9mo_5E_6E_4_P1-2-B6-K3


title: OR7A10Stop_24hr_Rep3

description: Library name: 79b-24_Rep3


title: 222_TNY7JJ6

description: Library name: lib33079


title: OR7A10Stop_24hr_Rep2

description: Library name: 79b-24_Rep2


title: OR7A10Stop_24hr_Rep1

description: Library name: 79b-24_Rep1


title: 221_TNY605H

description: Library name: lib33078


title: AMB_201117_9mo_5E_6E_4_P1-2-B6-J3


title: AMB_201117_9mo_5E_6E_4_P1-2-B6-J4


title: AMB_201117_9mo_5E_6E_4_P1-2-B6-K15


title: OR7A10Stop_0hr_Rep3

description: Library name: 79b_Rep3


title: AMB_201117_9mo_5E_6E_4_P1-2-B6-J16


title: 220_TNYHH0T

description: Library name: lib33077

value: Placebo


title: AMB_201117_9mo_5E_6E_4_P1-2-B6-I4


title: OR7A10Stop_0hr_Rep2

description: Library name: 79b_Rep2


title: AMB_201117_9mo_5E_6E_4_P1-2-B6-J15


title: AMB_201117_9mo_5E_6E_4_P1-2-B6-I3


title: 219_TNYGKMR

description: Library name: lib33076


title: OR7A10Stop_0hr_Rep1

description: Library name: 79b_Rep1


title: AMB_201117_9mo_5E_6E_4_P1-2-B6-I16


title: AMB_201117_9mo_5E_6E_4_P1-2-B6-I15


title: OR7A10_24hr_Rep3

description: Library name: 79-24_Rep3


title: 218_TNYHUMA

description: Library name: lib33075


title: AMB_201117_9mo_5E_6E_4_P1-2-B6-H4


title: AMB_201117_9mo_5E_6E_4_P1-2-B6-H3


title: 223_TNY6050

description: Library name: lib33080


title: AMB_201117_9mo_5E_6E_4_P1-2-B6-K16


title: AMB_201117_9mo_5E_6E_4_P1-2-B6-H16


title: AMB_201117_9mo_5E_6E_4_P1-2-B6-H15


title: OR7A10_24hr_Rep2

description: Library name: 79-24_Rep2


title: 216_TNYCC37

description: Library name: lib33073


title: AMB_201117_9mo_5E_6E_4_P1-2-B6-G4


title: OR7A10_24hr_Rep1

description: Library name: 79-24_Rep1


title: AMB_201117_9mo_5E_6E_4_P1-2-B6-G3


title: 214_TNYARJP

description: Library name: lib33071


title: 215_TNYA3YG

description: Library name: lib33072


title: AMB_201117_9mo_5E_6E_4_P1-2-B6-G16


title: AMB_201117_9mo_5E_6E_4_P1-2-B6-G15


title: OR7A10_0hr_Rep3

description: Library name: 79_Rep3


title: OR7A10_0hr_Rep2

description: Library name: 79_Rep2


title: AMB_201117_9mo_5E_6E_4_P1-2-B6-F3


title: 213_TNYA41T

description: Library name: lib33070


title: AMB_201117_9mo_5E_6E_4_P1-2-B6-F16


title: AMB_201117_9mo_5E_6E_4_P1-2-B6-F15


title: 212_TNY9HTR

description: Library name: lib33069


title: AMB_201117_9mo_5E_6E_4_P1-2-B6-F4


title: HER2CAR_OR7A10Stop_24hr_Rep3

description: Library name: 77b-24_Rep3


title: OR7A10_0hr_Rep1

description: Library name: 79_Rep1


title: 217_TNYCUA6

description: Library name: lib33074


title: 211_TNYCAMP

description: Library name: lib33068


title: AMB_201117_9mo_5E_6E_4_P1-2-B6-E4


title: AMB_201117_9mo_5E_6E_4_P1-2-B6-E15


title: AMB_201117_9mo_5E_6E_4_P1-2-B6-E3


title: 210_TNY9TJG

description: Library name: lib33067


title: HER2CAR_OR7A10Stop_24hr_Rep2

description: Library name: 77b-24_Rep2


title: HER2CAR_OR7A10Stop_24hr_Rep1

description: Library name: 77b-24_Rep1


title: AMB_201117_9mo_5E_6E_4_P1-2-B6-D4


title: 209_TNY7M21

description: Library name: lib33066


title: AMB_201117_9mo_5E_6E_4_P1-2-B6-D3


title: 208_TNY6RTH

description: Library name: lib33065


title: AMB_201117_9mo_5E_6E_4_P1-2-B6-D16


title: AMB_201117_9mo_5E_6E_4_P1-2-B6-D15


title: HER2CAR_OR7A10Stop_0hr_Rep3

description: Library name: 77b_Rep3


title: AMB_201117_9mo_5E_6E_4_P1-2-B6-C3


title: AMB_201117_9mo_5E_6E_4_P1-2-B6-C4


title: AMB_201117_9mo_5E_6E_4_P1-2-B6-C16


title: 207_TNY6U58

description: Library name: lib33064


title: HER2CAR_OR7A10Stop_0hr_Rep2

description: Library name: 77b_Rep2


title: AMB_201117_9mo_5E_6E_4_P1-2-B6-C15


title: HER2CAR_OR7A10_24hr_Rep3

description: Library name: 77-24_Rep3


title: 206_TNY6U41

description: Library name: lib33063


title: HER2CAR_OR7A10Stop_0hr_Rep1

description: Library name: 77b_Rep1


title: AMB_201117_9mo_5E_6E_4_P1-2-B6-E16


title: AMB_201117_9mo_5E_6E_4_P1-2-B6-B3


title: AMB_201117_9mo_5E_6E_4_P1-2-B6-B16


title: AMB_201117_9mo_5E_6E_4_P1-2-B6-B15


title: HER2CAR_OR7A10_24hr_Rep2

description: Library name: 77-24_Rep2


title: AMB_201117_9mo_5E_6E_4_P1-2-B6-B4


title: AMB_201117_9mo_5E_6E_4_P1-2-B6-A3


title: 204_TNYAHNY

description: Library name: lib33061


title: HER2CAR_OR7A10_0hr_Rep3

description: Library name: 77_Rep3


title: 205_TNYAKNT

description: Library name: lib33062


title: AMB_201117_9mo_5E_6E_4_P1-2-B6-A4


title: AMB_201117_9mo_5E_6E_4_P1-2-B6-A15


title: 203_TNY941A

description: Library name: lib33060


title: 202_TNY99HY

description: Library name: lib33059


title: AMB_201117_9mo_5E_6E_4_P1-2-B6-A16


title: AMB_201117_9mo_5E_6E_4_P1-1-I24-P2


title: AMB_201117_9mo_5E_6E_4_P1-1-I24-P14


title: HER2CAR_OR7A10_0hr_Rep2

description: Library name: 77_Rep2


title: 201_TNY7PN5

description: Library name: lib33058


title: HER2CAR_OR7A10_0hr_Rep1

description: Library name: 77_Rep1


title: AMB_201117_9mo_5E_6E_4_P1-1-I24-P13


title: 200_TNY7PPH

description: Library name: lib33057


title: AMB_201117_9mo_5E_6E_4_P1-1-I24-P1


title: AMB_201117_9mo_5E_6E_4_P1-1-I24-O2


title: OR7A10_stop

description: Library name: OR7A10_stop

data_processing:
Single-cell transcriptomics datasets for OR7A10-OE and OR7A10-(stop) samples were preprocessed and aligned to the human transcriptome reference (GRCh38 Gencode V37) using CellRanger v4.3.0 (default settings) (10X Genomics).
Assembly: GRCh38 Gencode V37
Supplementary files format and content: Standard CellRanger output files

source_name: Tumor infiltrating CAR-NK

extract_protocol:
CAR-NK Tumors were harvested, digested with Collagenase IV. Cells were then stained with APC-CD56 antibody and isolated with anti-APC magnetic beads.
Chromium Next GEM Sign Cell 5’ Regent kits V2 (10X Genomics) were used to prepare the library, according to manufacturer’s instructions. The scRNA-seq libraries were sequenced on the NovaSeq X system (Illumina) using a paired-end 150 bp read length.

value: Tumor infiltrating CAR-NK

value: Primary CAR-PBNK-hIL-15

tag: genotype


title: HER2CAR_OR7A10_24hr_Rep1

description: Library name: 77-24_Rep1


title: OR7A10

description: Library name: OR7A10


title: AMB_201117_9mo_5E_6E_4_P1-1-I24-O1

value: 9 months


title: 198_TNY9AWT

description: Library name: lib33055


title: AMB_201117_9mo_5E_6E_4_P1-1-I24-O13

value: CP


title: SF5

city: Zurich

first: Genome

last: Informatics

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich (FGCZ)

country: Switzerland

institute: ETH ZURICH / University of Zurich

description: Library name: SF5

data_processing:
RNA-seq reads were pseudoaligned with Kallisto using the genome build GENCODE Homo sapiens GRCh38 Release 42
Assembly: Grch38
Supplementary files format and content: Kallisto transcript text files

source_name: Superficial endometriosis

extract_protocol:
RNA isolation with RNAesy mini kit (Qiagen) according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Superficial endometriosis

value: Endometrial stromal cell


title: SF4

description: Library name: SF4


title: AMB_201117_9mo_5E_6E_4_P1-1-I24-N1

value: M


title: 196_TNY9924

description: Library name: lib33053

value: female


title: SF3

description: Library name: SF3


title: AMB_201117_9mo_5E_6E_4_P1-1-I24-M2


title: AMB_201117_9mo_5E_6E_4_P1-1-I24-N2


title: 195_TNY47AY

description: Library name: lib33052

value: ATG


title: AMB_201117_9mo_5E_6E_4_P1-1-I24-M14


title: AMB_201117_9mo_5E_6E_4_P1-1-I24-N14


title: 197_TNY8H60

description: Library name: lib33054


title: 194_TNY47C3

description: Library name: lib33051


title: AMB_201117_9mo_5E_6E_4_P1-1-I24-L2


title: AMB_201117_9mo_5E_6E_4_P1-1-I24-M1


title: SF2

description: Library name: SF2


title: 193_TNY900U

description: Library name: lib33050


title: AMB_201117_9mo_5E_6E_4_P1-1-I24-O14


title: AMB_201117_9mo_5E_6E_4_P1-1-I24-L14


title: 199_TNY9R73

description: Library name: lib33056


title: AMB_201117_9mo_5E_6E_4_P1-1-I24-L1


title: OMA5

description: Library name: OMA5

source_name: Endometrioma

value: Endometrioma


title: AMB_201117_9mo_5E_6E_4_P1-1-I24-L13


title: 192_TNY6M4N

description: Library name: lib33049


title: AMB_201117_9mo_5E_6E_4_P1-1-I24-K2


title: OMA4

description: Library name: OMA4


title: 191_TNY6666

description: Library name: lib33048

value: ATG-GCSF


title: AMB_201117_9mo_5E_6E_4_P1-1-I24-K14


title: AMB_201117_9mo_5E_6E_4_P1-1-I24-N13


title: AMB_201117_9mo_5E_6E_4_P1-1-I24-K13


title: OMA3

description: Library name: OMA3


title: AMB_201117_9mo_5E_6E_4_P1-1-I24-M13


title: 190_TNY5XH5

description: Library name: lib33047


title: AMB_201117_9mo_5E_6E_4_P1-1-I24-J14


title: AMB_201117_9mo_5E_6E_4_P1-1-I24-J2


title: 189_TNY69C0

description: Library name: lib33046


title: AMB_201117_9mo_5E_6E_4_P1-1-I24-K1


title: AMB_201117_9mo_5E_6E_4_P1-1-I24-J13


title: OMA1

description: Library name: OMA1


title: SF1

description: Library name: SF1


title: AMB_201117_9mo_5E_6E_4_P1-1-I24-J1


title: AMB_201117_9mo_5E_6E_4_P1-1-I24-I13


title: AMB_201117_9mo_5E_6E_4_P1-1-I24-I2


title: DE4

description: Library name: DE4

source_name: Deep endometriosis lesion

value: Deep endometriosis lesion


title: DE5

description: Library name: DE5


title: 186_TNY8JGA

description: Library name: lib33043


title: AMB_201117_9mo_5E_6E_4_P1-1-I24-I14


title: AMB_201117_9mo_5E_6E_4_P1-1-I24-H14


title: AMB_201117_9mo_5E_6E_4_P1-1-I24-I1


title: AMB_201117_9mo_5E_6E_4_P1-1-I24-H13


title: 184_TNY56GK

description: Library name: lib33041


title: AMB_201117_9mo_5E_6E_4_P1-1-I24-H2


title: 187_TNXUWA

description: Library name: lib33044


title: AMB_201117_9mo_5E_6E_4_P1-1-I24-H1


title: AMB_201117_9mo_5E_6E_4_P1-1-I24-G2


title: OMA2

description: Library name: OMA2


title: AMB_201117_9mo_5E_6E_4_P1-1-I24-G14


title: DE1

description: Library name: DE1


title: 183_TNY5WVY

description: Library name: lib33040


title: AMB_201117_9mo_5E_6E_4_P1-1-I24-G13


title: C5

description: Library name: C5

source_name: Eutopic endometrium

value: Eutopic endometrium


title: 182_TNY666Y

description: Library name: lib33039

value: whole blood


title: 188_TNY697V

description: Library name: lib33045

value: male


title: AMB_201117_9mo_5E_6E_4_P1-1-I24-F2


title: C4

description: Library name: C4


title: DE3

description: Library name: DE3


title: C3

description: Library name: C3


title: AMB_201117_9mo_5E_6E_4_P1-1-I24-F14


title: AMB_201117_9mo_5E_6E_4_P1-1-I24-F13


title: 181_TNY080W

description: Library name: lib33038


title: AMB_201117_9mo_5E_6E_4_P1-1-I24-F1


title: AMB_201117_9mo_5E_6E_4_P1-1-I24-G1


title: 185_TNY797T

description: Library name: lib33042


title: DE2

description: Library name: DE2


title: 180_TNY6778

description: Library name: lib33037


title: AMB_201117_9mo_5E_6E_4_P1-1-I24-E14


title: AMB_201117_9mo_5E_6E_4_P1-1-I24-E2


title: AMB_201117_9mo_5E_6E_4_P1-1-I24-E13


title: AMB_201117_9mo_5E_6E_4_P1-1-I24-E1


title: C1

description: Library name: C1


title: AMB_201117_9mo_5E_6E_4_P1-1-I24-D2


title: C2

description: Library name: C2


title: 178_TNY44VW

description: Library name: lib33035


title: AMB_201117_9mo_5E_6E_4_P1-1-I24-D13


title: 177_TNY65YG

description: Library name: lib33034


title: 179_TNY676Y

description: Library name: lib33036


title: PC-3 cells, treated, 48 hours, rep3

city: Stony Brook

first: Agnieszka

middle: B.

last: Bialkowska

state: New York

address: HSC-T17 Room 090

department: Dept. of Medicine

institute: Stony Brook University

description: Library name: SBFI-1143_48_3

data_processing:
RNA-seq
Data was analyzed using usegalaxy platform and R
Sample quality was checked using FASTQC and Trimmomatic
The paired-ended sequences were aligned to hg38 using HISAT2
To quantify the number of reads per gene, featureCounts was used
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: prostate cancer cell line

growth_protocol: Human PC-3 cells were maintained in RPMI640 medium supplemented with 10% fetal bovine serum (FBS) and 1% Pencillin/Streptomycin in a humidified atmosphere at 37°C and 5% CO2.

extract_protocol:
RNA was isolated using Qiagen Rneasy Mini Kit
RNA library and sequencing was performed by Novogene. mRNA library preparation (poly A enrichment) and sequencing was performed using NovaSeq X Plus (PE150).

treatment_protocol: PC-3  cells were trypsinized, counted, and seeded (6x105 cells/well) in a 100mm plate format in RPMI640 medium supplemented with 2% fetal bovine serum (FBS) and 1% Pencillin/Streptomycin in a humidified atmosphere at 37°C and 5% CO2. After 24 hours of incubation, media was aspirated and replaced with treatment-supplemented media (0.2% DMSO or 15uM SBFI-1143). Cells were then treated for 24 and 48 hours total, followed by total RNA extraction and quantification

value: prostate cancer cell line

tag: batch


title: AMB_201117_9mo_5E_6E_4_P1-1-I24-D1


title: AMB_201117_9mo_5E_6E_4_P1-1-I24-D14


title: 176_TNY7J8N

description: Library name: lib33033

value: Placebo


title: PC-3 cells, treated, 48 hours, rep2

description: Library name: SBFI-1143_48_2


title: PC-3 cells, treated, 48 hours, rep1

description: Library name: SBFI-1143_48_1


title: AMB_201117_9mo_5E_6E_4_P1-1-I24-C14


title: 175_TNY6M28

description: Library name: lib33032


title: 174b_TNYHH4N

description: Library name: lib33031


title: AMB_201117_9mo_5E_6E_4_P1-1-I24-B2


title: AMB_201117_9mo_5E_6E_4_P1-1-I24-C13


title: PC-3 cells, control,48 hours, rep3

description: Library name: DMSO_48_3

value: DMSO, 48h


title: PC-3 cells, control,48 hours, rep2

description: Library name: DMSO_48_2


title: AMB_201117_9mo_5E_6E_4_P1-1-I24-C1


title: AMB_201117_9mo_5E_6E_4_P1-1-I24-B14


title: PC-3 cells, control, 48 hours, rep1

description: Library name: DMSO_48_1


title: AMB_201117_9mo_5E_6E_4_P1-1-I24-B13


title: 174_TNYG36N

description: Library name: lib33030


title: 173_TNYGCNP

description: Library name: lib33029


title: AMB_201117_9mo_5E_6E_4_P1-1-I24-B1


title: AMB_201117_9mo_5E_6E_4_P1-1-I24-A2


title: AMB_201117_9mo_5E_6E_4_P1-1-I24-A13


title: AMB_201117_9mo_5E_6E_4_P1-1-I24-A14


title: 171_TNYHPNL

description: Library name: lib33027


title: AMB_201117_9mo_5E_6E_4_P1-1-I24-A1


title: 172_TNYHPM7

description: Library name: lib33028


title: PC-3 cells, treated, 24 hours, rep1

description: Library name: SBFI-1143_24_1


title: PC-3 cells, treated, 24 hours, rep3

description: Library name: SBFI-1143_24_3


title: AGY2256_T30NaCl_R6

city: Madison

first: Audrey

last: Gasch

state: WI

address: 425G Henry mall

department: Genetics

institute: University of Wisconsin

description:
Library name: Gasch-A12-072025
Gasch-A12-072025

data_processing:
Trimmed reads with Trimmomatic 0.39
Reading mapping to S288c genome using Bowtie 2 version 2.4.4
Read counts calculated with HTSeq-count version 0.6.0
Assembly: default yeast reference, SGD R64-1-1 equivalent to UCSC sacCer3
Supplementary files format and content: raw HTSeq counts

organism: Saccharomyces cerevisiae BY4741

growth_protocol: Cells were grown in low fluorescence media in shake flasks to mid log phase in batch cultures in shaker flasks at 30C. TET-Dot6 (and the wild-type samples paired with them) were also grown in 50 µg/mL Doxycycline.

extract_protocol:
Total RNA was extracted using hot phenol lysis and purified using the RNeasy MinElute Cleanup Kit (QIAGEN, Hilden, Germany) and DNase digestion.
RNA-seq libraries were prepared using a TruSeq Stranded Total RNA kit (Illumina), and PCR purified using AMPure XP beads (Beckman Coulter, Indianapolis, IN).

treatment_protocol: Cells were harvested at time 0 before Sodium chloride was added. NaCl was added to 0.7M final concentration and cells were collected at 10, 20, 30, 40, 50, 60, and 90 min after treatment (some samples were only collected at 20 and 30 minutes).

tag: media

value: low fluorescence media

tag: stress

value: 30 minutes post NaCl stress


title: AGY2256_T0NaCl_R6

description:
Library name: Gasch-A8-072025
Gasch-A8-072025

value: unstressed


title: AGY2256_T20NaCl_R6

description:
Library name: Gasch-A10-072025
Gasch-A10-072025

value: 20 minutes post NaCl stress


title: AMB_201117_9mo_5E_6E_4_P1-1-I24-C2

value: 9 months

value: CP


title: AGY4_T30NaCl_R6

description:
Library name: Gasch-A11-072025
Gasch-A11-072025

value: wild-type


title: 169_TNYAP77

description: Library name: lib33025

value: female


title: AGY4_T20NaCl_R6

description:
Library name: Gasch-A9-072025
Gasch-A9-072025


title: AGY4_T0NaCl_R6

description:
Library name: Gasch-A7-072025
Gasch-A7-072025


title: 170_TNYG745

description: Library name: lib33026


title: AGY2256_T20NaCl_R5

description:
Library name: Gasch-A4-072025
Gasch-A4-072025


title: PC-3 cells, treated, 24 hrs, rep4

description: Library name: PC-3_SBFI-103_24h_4

treatment_protocol: PC-3  cells were trypsinized, counted, and seeded (6x105 cells/well) in a 100mm plate format in RPMI640 medium supplemented with 2% fetal bovine serum (FBS) and 1% Pencillin/Streptomycin in a humidified atmosphere at 37°C and 5% CO2. After 24 hours of incubation, media was aspirated and replaced with treatment-supplemented media (0.2% DMSO or 15uM SBFI-103). Cells were then treated for 24 hours total, followed by total RNA extraction and quantification


title: 168_TNYAP84

description: Library name: lib33024


title: PC-3 cells, control, 24 hours, rep1

description: Library name: DMSO_24_1

value: DMSO, 24h


title: 167_TNYCU89

description: Library name: lib33023

value: ATG


title: AGY4_T30NaCl_R5

description:
Library name: Gasch-A5-072025
Gasch-A5-072025


title: AGY2256_T0NaCl_R5

description:
Library name: Gasch-A2-072025
Gasch-A2-072025


title: PC-3 cells, treated, 24 hrs, rep3

description: Library name: PC-3_SBFI-103_24h_3


title: 166_TNY7NWU

description: Library name: lib33022

value: ATG-GCSF


title: AGY4_T20NaCl_R5

description:
Library name: Gasch-A3-072025
Gasch-A3-072025


title: PC-3 cells, treated, 24 hours, rep2

description: Library name: SBFI-1143_24_2


title: PC-3 cells, treated, 24 hrs, rep2

description: Library name: PC-3_SBFI-103_24h_2


title: 165_TNY9HY7

description: Library name: lib33021


title: AGY4_T0NaCl_R5

description:
Library name: Gasch-A1-072025
Gasch-A1-072025


title: AGY594_T30NaCl_R4

description:
Library name: Gasch-B12-062025
Gasch-B12-062025

value: dot6 tod6 deletion


title: PC-3 cells, control, 24 hours, rep3

description: Library name: DMSO_24_2


title: 164_TNYAKJM

description: Library name: lib33020

value: whole blood


title: AGY594_T0NaCl_R4

description:
Library name: Gasch-B4-062025
Gasch-B4-062025


title: PC-3 cells, control, 24 hrs, rep4

description: Library name: PC-3_DMSO_4


title: PC-3 cells, control, 24 hrs, rep3

description: Library name: PC-3_DMSO_3


title: AGY524_T20NaCl_R4

description:
Library name: Gasch-B7-062025
Gasch-B7-062025

value: tod6 deletion


title: AGY524_T30NaCl_R4

description:
Library name: Gasch-B11-062025
Gasch-B11-062025


title: AGY2256_T30NaCl_R5

description:
Library name: Gasch-A6-072025
Gasch-A6-072025


title: AGY524_T0NaCl_R4

description:
Library name: Gasch-B3-062025
Gasch-B3-062025


title: AGY523_T30NaCl_R4

description:
Library name: Gasch-B10-062025
Gasch-B10-062025

value: dot6 deletion


title: 162_TNYAM63

description: Library name: lib33018


title: 161_TNY9TG3

description: Library name: lib33017

value: male


title: AGY523_T20NaCl_R4

description:
Library name: Gasch-B6-062025
Gasch-B6-062025


title: AGY523_T0NaCl_R4

description:
Library name: Gasch-B2-062025
Gasch-B2-062025


title: PC-3 cells, control, 24 hrs, rep2

description: Library name: PC-3_DMSO_2

value: prostate cancer cell line


title: PC-3 cells, control, 24 hrs, rep1

description: Library name: PC-3_DMSO_1


title: AGY4_T30NaCl_R4

description:
Library name: Gasch-B9-062025
Gasch-B9-062025

value: low fluorescence media


title: 160_TNYA79M

description: Library name: lib33016


title: Hela S3 clone2 Metaphase biol rep2

city: Evanston

first: Xiaozhong

last: Wang

state: IL

address: 2200 Campus Dr

department: Molecular Biosciences

institute: Northwestern University

description: Library name: Metaphase Hela clone2 Chemical map biol rep2

data_processing:
For chemical mapping, we sequenced two biological replicates twice for each state: interphase and metaphase. The resulting reads were mapped to Ensembl Genome assembly GRCh38.p13 (GCA_000001405.28, Release 108) using STAR software tool, and the only reads mapped to unique sites were used to calculate the chemical cleavage.
The second set of the technical replicate for each chemical map was performed in the sequencing facility using a dark cycle protcol which resulted in the first bp being ignored, we corrected for this by shifting the identified 5 prime cleavage sites for each read by 1 bp upstream. For chemical maps, the resulting cleavage frequencies from the two technical replicates of each condition were merged for downstream analysis. And biological replicates are merged in later analysis as described in the manuscript.
We  identified the cleavage pattern around the dyad, and the R package NuCMap that implements the deconvolution algorithm was used to compute the nucleosome center positioning (NCP) score at every genomic location (https://github.com/jipingw/NuCMap). We defined the unique nucleosome map based on the magnitude of NCP scores using a greedy algorithm, by requiring two neighboring dyad positions to be spaced >= 120 bp
Based on all defined nucleosomes, we selected the top 90% as our unique nucleosome set/map that represents the most prominent dyad positions.
Assembly: GCA_000001405.28, Release 108
Supplementary files format and content: bigwig tracks displaying corrected NCP score for each genomic position
Supplementary files format and content: bigwig track displaying unique nucleosome set position and associated score

source_name: Hela S3

growth_protocol: HeLa S3 derived cell lines were cultured in high glucose Dulbecco’s modified Eagle’s (DMEM) (Corning) medium supplemented with 10% fetal bovine serum (FBS), 1% (v/v) Penicillin/Streptomycin, 1% (v/v) Glutamine, and 1 mM sodium pyruvate.

extract_protocol:
Cleaved genomic DNA was extracted from the rinsed cell pellets using proteinase K digestion followed by phenol/chloroform extraction, ethanol precipitation. The purified DNA was resolved on a 1.8% NuSieve 3:1 (Lonza) agarose gel. DNA fragments (~100 to 300 bp) were gel-purified and prepared for paired-end sequencing
NEBNext Ultra II DNA Lib prep

treatment_protocol: For synchronization of HeLa S3 cells to prometaphase, 2 x10 6 cells per 10cm cell culture plate seeded on the previous day were synchronized to early S phase by double thymidine (2 mM) treatment over the course of two days. This was followed by a 5-hour release in fresh media and an 8-hour nocodazole arrest at a final concentration of 100 ng/ml. Mitotic cells were then collected by shaking off and centrifugation.

value: Hela S3

value: double thymidine + nocodazole


title: 159_TNY9AWA

description: Library name: lib33015

value: Placebo


title: AGY524_T30NaCl_R3

description:
Library name: Gasch-A11-062025
Gasch-A11-062025

value: 30 minutes post NaCl stress


title: AGY4_T0NaCl_R4

description:
Library name: Gasch-B1-062025
Gasch-B1-062025

value: unstressed


title: AGY594_T20NaCl_R4

description:
Library name: Gasch-B8-062025
Gasch-B8-062025

value: 20 minutes post NaCl stress


title: Hela S3 clone2 Metaphase biol rep1

description: Library name: Metaphase Hela clone2 Chemical map biol rep1


title: PC-3 cells, treated, 24 hrs, rep1

description: Library name: PC-3_SBFI-103_24h_1


title: AGY524_T20NaCl_R3

description:
Library name: Gasch-A8-062025
Gasch-A8-062025


title: 158_TNY7PMP

description: Library name: lib33014


title: AGY524_T0NaCl_R3

description:
Library name: Gasch-A2-062025
Gasch-A2-062025


title: 163_TNY8M8H

description: Library name: lib33019

value: female


title: AGY523_T30NaCl_R3

description:
Library name: Gasch-A10-062025
Gasch-A10-062025


title: Hela S3 clone2 Interphase biol rep2

description: Library name: Interphase Hela clone2 Chemical map biol rep2


title: AGY523_T20NaCl_R3

description:
Library name: Gasch-A6-062025
Gasch-A6-062025


title: AGY523_T0NaCl_R3

description:
Library name: Gasch-A3-062025
Gasch-A3-062025


title: AGY4_T30NaCl_R3

description:
Library name: Gasch-A9-062025
Gasch-A9-062025

value: wild-type


title: Hela S3 clone2 Interphase biol rep1

description: Library name: Interphase Hela clone2 Chemical map biol rep1


title: 156_TNY9V2W

description: Library name: lib33012


title: AGY4_T20NaCl_R3

description:
Library name: Gasch-A5-062025
Gasch-A5-062025


title: Hela S3 clone2 Interphase

description: Library name: Interphase Hela clone2 Mnase-Seq

data_processing:
The resulting reads were mapped to Ensembl Genome assembly GRCh38.p13 (GCA_000001405.28, Release 108) using STAR software tool, uniquely mapped reads were used.
Nucleosome occupancy is a center weighted occupancy calculated as described in methods using the NuCMap R package (https://github.com/jipingw/numap)
Assembly: GCA_000001405.28, Release 108
Supplementary files format and content: bigwig tracks displaying center weighted nucleosome occupancy score
Supplementary files format and content: bigwig tracks displaying unique nucleosome set and associated center nucleosome occupancy score

extract_protocol:
The digested genomic DNA was purified followed by an overnight proteinase K digestion. Mononucleosomal DNA fragments were resolved on a 1.5% agarose gel and gel-purified for sequencing
NEBNext Ultra II DNA Lib prep


title: AGY4_T20NaCl_R4

description:
Library name: Gasch-B5-062025
Gasch-B5-062025


title: pRS315-FUS(1-163)12E, 1h Rapamycin

city: Garching

first: Frauke

last: Huth

address: James-Franck Str. 1

department: Department of Biosciences

country: Germany

institute: Technical University Munich

description:
Library name: sample_14
Rapamycin induced Abf1 Anchor-Away pRS315-FUS(1-163)12E, 1h Rapamycin, total RNA

data_processing:
The S.cerevisiae reference genome SacCer3 build R64-1-1 was used for alignment with STAR. Expression was quantified using rsem-calculate-expression.
Assembly: SacCer3 R64-1-1
Supplementary files format and content: Each file is a tab separated values file and contains the gene name (gene_id), transcripts per million (tpms) as well as absolute counts (counts).

organism: Saccharomyces cerevisiae

growth_protocol: The Abf1 anchor away strain ABF1-aa-V5 clone A9 was obtained from Wim de Jonge and Frank Holstege (de Jonge et al., Mol Syst Biol. 2020). The strain was transformed with pRS315-based plasmids encoding wildtype Abf1, select Abf1 constructs, or the empty pRS315 plasmid as a control. At least three independent clones were isolated and stored as glycerol cultures after transformation and used for biologically independent replicate experiments. Anchor away strains were grown to log phase, ca. OD600 of 0.4, in YNB –leucine media.

extract_protocol:
Total RNA was prepared with the RNeasy kit (Qiagen). 4 OD600 units of cells were washed with PBS (50 mM phosphate buffer pH 7, 150 mM NaCl) and flash frozen in liquid nitrogen. The cell wall was broken up by incubation with beta-mercaptoethanol and Zirconia bead-beating (6x 3 min 30 Hz with 3 min breaks). The cell lysate was cleared by centrifugation, mixed with ethanol, and bound to a column provided in the kit. The optional DNaseI digestion on the column was carried out. RNA was washed on the resin, eluted, and digested using DNase I in solution.
After ethanol precipitation, the total RNA preparation was converted into sequencing libraries with the NEBNext Ultra II directional RNA library prep kit for Illumina.

treatment_protocol: The strains were incubated for the indicated amount of time with 8 µg/mL rapamycin.

value: ABF1-aa-V5 clone A9

value: RNeasy kit (Qiagen) with DNaseI digestion; NEBNext Ultra II directional RNA library prep kit for Illumina.


title: 154_TNY8HX6

description: Library name: lib33010

value: ATG


title: pRS315-FUS(1-163)12E YM, 1h Rapamycin

description:
Library name: sample_12
Rapamycin induced Abf1 Anchor-Away pRS315-FUS(1-163)12E YM, 1h Rapamycin, total RNA


title: HelaS3 clone 2 Metaphase

description: Library name: Metaphase Hela clone 2 RNA-Seq

data_processing:
reads were aligned to Ensembl Genome assembly GRCh38.p13 (GCA_000001405.28, Release 108) using STAR software tool to generate reads per gene count output
Assembly: GCA_000001405.28, Release 108
Supplementary files format and content: tab delimited format files containing raw counts per gene

extract_protocol:
Total RNA was extracted from cultured HeLa cells using TRIzol Reagent (Life Technologies) following the manufacturer’s protocol.
NEBNext Ultra II DNA Lib prep


title: Hela S3 clone2 Metaphase

description: Library name: Metaphase Hela clone2 Mnase-Seq


title: pRS315-WT Abf1, 1h Rapamycin

description:
Library name: sample_10
Rapamycin induced Abf1 Anchor-Away pRS315-WT Abf1, 1h Rapamycin, total RNA


title: HelaS3 clone 2 Interphase

description: Library name: Interphase Hela clone 2 RNA-Seq


title: HelaS3 clone 1-2 Metaphase

description: Library name: Metaphase Hela clone 1-2 RNA-Seq


title: 152_TNY9WLL

description: Library name: lib33008

value: whole blood

value: ATG-GCSF


title: SGD chromatin with drosophila histones, Abf1 DBD only, 10 nM INO80, replicate 2

description:
Library name: scino80_kpni_abf1dbd_dm_sc_r2
MNase treated SGD chromatin (plasmid library with pGP546 backbone) with drosophila histones, Abf1 DBD only, 10 nM INO80, replicate 2

data_processing:
bam files were converted to bed files using bamToBed and subsequently converted into bigWig files while trimming the ranges to the center 50 bp of the MNase fragments.
Assembly: SacCer3 R64-1-1
Supplementary files format and content: Each file is a bigWig file containing the coverage derived from 50 bp windows centered on the dyad determined from the MNase-Seq fragments.

extract_protocol:
The Remodelling assay was conducted according to Chacin (Nature, 2023) and Oberbeckmann. (Nat. Commun., 2021), however without ammonium sulfate in the reaction buffer.
Similarly, preparation for Illumina sequencing followed Chacin (Nature, 2023) and Oberbeckmann, but was conducted in paired-end mode.

value: plasmid library with pGP546 backbone

value: 20 mM HEPES pH 7.5, 55 mM NaCl, 3 mM MgCl2, 2.5 mM DTT, 2.5 mM ATP, 0.5 mM EGTA, 12% glycerol


title: SGD chromatin with drosophila histones, FUS(1-163)12E, 10 nM INO80, replicate 2

description:
Library name: scino80_kpni_abf1fus12e_dm_sc_r2
MNase treated SGD chromatin (plasmid library with pGP546 backbone) with drosophila histones, FUS(1-163)12E, 10 nM INO80, replicate 2


title: pRS315-IDR2, 1h Rapamycin

description:
Library name: sample_11
Rapamycin induced Abf1 Anchor-Away pRS315-IDR2, 1h Rapamycin, total RNA


title: HelaS3 clone 1-2 Interphase

description: Library name: Interphase Hela clone 1-2 RNA-Seq


title: SGD chromatin with drosophila histones, WT Abf1

description:
Library name: mock_abf1wt_kpni
MNase treated SGD chromatin (plasmid library with pGP546 backbone) with drosophila histones, WT Abf1


title: 150_TNY93AR

description: Library name: lib33006

value: male


title: SGD chromatin with drosophila histones, WT Abf1, 20 nM INO80

description:
Library name: 20nmscino80_abf1wtkpni_dm_sc_mhigh_15m
MNase treated SGD chromatin (plasmid library with pGP546 backbone) with drosophila histones, WT Abf1, 20 nM INO80

value: 26.6 mM Na·HEPES pH 7.5, 1 mM Tris·HCl pH 7.6, 85.5 mM NaCl, 8 mM KCl, 10 mM creatine phosphate, 3 mM MgCl2, 2.5 mM ATP, 0.1 mM EDTA, 0.6 mM EGTA, 1 mM DTT, 14% glycerol, 20 ng/µl creatine kinase


title: 153_TNY99YH

description: Library name: lib33009


title: SGD chromatin with drosophila histones, Abf1 DBD only, 20 nM INO80

description:
Library name: 20nmscino80_abf1dbdkpni_dm_sc_mhigh_15m
MNase treated SGD chromatin (plasmid library with pGP546 backbone) with drosophila histones, Abf1 DBD only, 20 nM INO80


title: AGY4_T0NaCl_R3

description:
Library name: Gasch-A1-062025
Gasch-A1-062025

value: low fluorescence media


title: 149_TNY6XMH

description: Library name: lib33005


title: 157_TNY9CC9

description: Library name: lib33013


title: 155_TNY7TG1

description: Library name: lib33011


title: 151_TNY8H3R

description: Library name: lib33007


title: SGD chromatin with drosophila histones, Abf1 DBD only, 6.7 nM INO80

description:
Library name: 7nmscino80_abf1dbdkpni_dm_sc_mhigh_15m
MNase treated SGD chromatin (plasmid library with pGP546 backbone) with drosophila histones, Abf1 DBD only, 6.7 nM INO80


title: SGD chromatin with drosophila histones, replicate 2

description:
Library name: sgd_dm_sc_r2
MNase treated SGD chromatin (plasmid library with pGP546 backbone) with drosophila histones, replicate 2


title: SGD chromatin with drosophila histones, WT Abf1, 6.7 nM INO80

description:
Library name: 7nmscino80_abf1wtkpni_dm_sc_mhigh_15m
MNase treated SGD chromatin (plasmid library with pGP546 backbone) with drosophila histones, WT Abf1, 6.7 nM INO80


title: 148_TNY7TA3

description: Library name: lib33004


title: SGD chromatin with drosophila histones, WT Abf1, 10 nM INO80, replicate 2

description:
Library name: scino80_kpni_abf1wt_dm_sc_r2
MNase treated SGD chromatin (plasmid library with pGP546 backbone) with drosophila histones, WT Abf1, 10 nM INO80, replicate 2


title: KYSE150, GFP-TFAP2β-ΔIDR3, replicate 3

city: Chengdu

first: Lu

last: Pu

state: Sichuan

address: #37 Guoxue Alley, Wuhou District

country: China

institute: west china hospital

description:
Library name: Sample12
Column name in All_gene_counts.txt: T433-3

data_processing:
The RNA libraries were sequenced on the Illumina NovaSeq X Plus platform.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trim-galore
Trimmed sequence reads were mapped to Homo_sapiens.GRCh38 using HISAT2
StringTie was applied to assemble the mapped reads.
FPKM(Fragments Per Kilobase of transcript per Million fragments mapped) was applied to measure the expression level of a gene or transcript by StringTie using maximum flow algorithm.
Assembly: hg38
Supplementary files format and content: xls file includes raw counts for each Sample

growth_protocol: RMPI 1640, 10% fetal bovine serum, 1×penicillin-streptomycin. Cells were cultured at 37 ℃ at 5% CO2

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was usedfor the construction of sequencing libraries.
RNA libraries for RNA-seg were prepared using SMARTER mRNA-Seg Library Prep Kitfollowing manufacturer's protocols.

value: esophageal squamous cell carcinoma cell

tag: sample group


title: KYSE150, GFP-TFAP2β-ΔIDR3, replicate 1

description:
Library name: Sample10
Column name in All_gene_counts.txt: T433-1


title: SGD chromatin with drosophila histones, Abf1 DBD only, 2 nM INO80

description:
Library name: 2nmscino80_abf1dbdkpni_dm_sc_mhigh_15m
MNase treated SGD chromatin (plasmid library with pGP546 backbone) with drosophila histones, Abf1 DBD only, 2 nM INO80


title: SGD chromatin with drosophila histones, WT Abf1, 0.7 nM INO80

description:
Library name: 1nmscino80_abf1wtkpni_dm_sc_mhigh_15m
MNase treated SGD chromatin (plasmid library with pGP546 backbone) with drosophila histones, WT Abf1, 0.7 nM INO80


title: SGD chromatin with drosophila histones, WT Abf1, 2 nM INO80

description:
Library name: 2nmscino80_abf1wtkpni_dm_sc_mhigh_15m
MNase treated SGD chromatin (plasmid library with pGP546 backbone) with drosophila histones, WT Abf1, 2 nM INO80


title: KYSE150, GFP-TFAP2β-Mut_IDR3, replicate 3

description:
Library name: Sample9
Column name in All_gene_counts.txt: M433-3


title: 146_TNY95Y1

description: Library name: lib33002

tag: tissue


title: SGD chromatin with drosophila histones, Abf1 DBD only, 0.7 nM INO80

description:
Library name: 1nmscino80_abf1dbdkpni_dm_sc_mhigh_15m
MNase treated SGD chromatin (plasmid library with pGP546 backbone) with drosophila histones, Abf1 DBD only, 0.7 nM INO80


title: SGD chromatin with drosophila histones, 10 nM INO80, replicate 2

description:
Library name: scino80ml_dm_sc_med-low_2h_1to5_5m
MNase treated SGD chromatin (plasmid library with pGP546 backbone) with drosophila histones, 10 nM INO80, replicate 2


title: 145_TNY76WA

description: Library name: lib33001

tag: donor id


title: KYSE150, GFP-TFAP2β-Mut_IDR3, replicate 2

description:
Library name: Sample8
Column name in All_gene_counts.txt: M433-2


title: SGD chromatin with drosophila histones, 10 nM INO80, replicate 1

description:
Library name: scino80f_dm_sc_med-low_2h_1to5_5m
MNase treated SGD chromatin (plasmid library with pGP546 backbone) with drosophila histones, 10 nM INO80, replicate 1


title: SGD chromatin with drosophila histones

description:
Library name: sgd_dm_sc_med-low_2h_1to5_5m
MNase treated SGD chromatin (plasmid library with pGP546 backbone) with drosophila histones


title: KYSE150, GFP-TFAP2β-ΔIDR3, replicate 2

description:
Library name: Sample11
Column name in All_gene_counts.txt: T433-2


title: SGD chromatin with human histones, WT Abf1, 10 nM INO80

description:
Library name: scino80_hs_sc_h_kpniabf1-WT
MNase treated SGD chromatin (plasmid library with pGP546 backbone) with human histones, WT Abf1, 10 nM INO80


title: 144_TNY8NVU

description: Library name: lib33000

tag: age


title: SGD chromatin with human histones, FUS(1-163)12E, 10 nM INO80

description:
Library name: scino80_hs_sc_h_kpniabf1-FUS12E
MNase treated SGD chromatin (plasmid library with pGP546 backbone) with human histones, FUS(1-163)12E, 10 nM INO80


title: SGD chromatin with human histones, WT Abf1

description:
Library name: hs_sc_h_kpniabf1-WT
MNase treated SGD chromatin (plasmid library with pGP546 backbone) with human histones, WT Abf1


title: KYSE150, GFP-TFAP2β-Mut_IDR3, replicate 1

description:
Library name: Sample7
Column name in All_gene_counts.txt: M433-1


title: SGD chromatin with human histones, Abf1 DBD only, 10 nM INO80

description:
Library name: scino80_hs_sc_h_kpniabf1-DBD
MNase treated SGD chromatin (plasmid library with pGP546 backbone) with human histones, Abf1 DBD only, 10 nM INO80


title: KYSE150, GFP-TFAP2β, replicate 3

description:
Library name: Sample6
Column name in All_gene_counts.txt: AP2-3


title: Mycelium grown for 7 days in low phosphate medium + one day in high phosphate, sample number 2

city: Lausanne

first: Giovanna

last: Ambrosini

address: Station 19

institute: EPFL

description: Library name: LPspike2

data_processing:
For RNA quantification, Kallisto (v0.48.0) was used, a k-mer counting software that uses pseudoalignments to reduce quantification error and improve speed. An average pseudoalignment rate of 90% was achieved.
Differential transcript expression analysis was performed with Sleuth (0.30.0).
In order to examine the sense/antisense read coverage for two transcripts of interest, namely Kcs1 and Ddp1, under different phosphate conditions, reads were realigned using STAR (v2.7.11a).
Assembly: Lacbi2
Supplementary files format and content: HDF5-formatted binary files including run info, abundance esimates, bootstrap estimates, and transcript length information. This file can be read in by Sleuth.

organism: Laccaria bicolor

source_name: free-living mycelium

growth_protocol: Dikaryotic strain L. bicolor S238N was grown in liquid P5 medium with 7 mM inorganic phosphate (HP samples) or without phosphate (LP samples) for 7days. One set of cultures grown without phosphate for 7 day was spiked with 7 mM phosphate and grown for one additional day (LPspike sample). Cultures were maintained at 23 °C in dark chamber with 100 rpm shaking.

extract_protocol:
Total cellular RNA was extracted from all the samples using Qiagen RNA extraction kit.
RNA-seq libraries were prepared from 1 ug of total RNA with the Illumina TruSeq Stranded mRNA reagents (Illumina) using a unique dual indexing strategy, and following the official protocol automated on a Sciclone liquid handling robot (PerkinElmer). Libraries were quantified by a fluorometric method (QubIT, Life Technologies) and their quality assessed on a Fragment Analyzer (Agilent Technologies). Sequencing was performed on an Illumina NovaSeq 6000 for 300 cycles (paired end 150 nt reads) and an average of 40 million reads was obtained per sample.

value: free-living mycelium

value: mycelium

value: strain S238N

value: low phosphate + high phosphate spike


title: 143_TNY69CR

description: Library name: lib32999

data_processing:
Base calls were processed to FASTQs on BaseSpace (Illumina), and a base call quality-trimming step was applied to remove low-confidence base calls from the ends of reads.
Reads were processed using workflows managed on the Galaxy platform; reads were trimmed by 1 base at the 3’ end, and then trimmed from both ends until base calls had a minimum quality score of at least 30 (Galaxy FASTQ Trimmer tool v1.0.0)
FastqMcf (v1.1.2, https://benthamopen.com/ ABSTRACT/TOBIOIJ-7-1) was used to remove any remaining adapter sequence.
Reads were aligned by STAR1 2.4.2a to GRCh38
Gene counts were generated using HTSeq-count (v0.4.1). Quality metrics were compiled from PICARD (v1.134, http://broadinstitute.github.io/picard/), FASTQC (v0.11.3, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), Samtools (v1.2)30, and HTSeq-count (v0.4.1).
Assembly: GRCh38
Supplementary files format and content: Raw counts are provided in .csv format. Each row is a gene, each column is a sample.

extract_protocol:
Whole blood was collected in Tempus Blood RNA Tubes (Thermo Fisher Scientific), RNA was extracted using MagMax for Stabilized Blood Tubes RNA Isolation Kit (Thermo Fisher Scientific), followed by globin reduction using GlobinClear Human (Thermo Fisher Scientific).
To generate sequencing libraries, total RNA (0.5 ng) was added to reaction buffer from the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara), and reverse transcription was performed followed by PCR amplification to generate full-length amplified cDNA. Sequencing libraries were constructed using the NexteraXT DNA sample preparation kit (Illumina) to generate Illumina-compatible barcoded libraries. Libraries were pooled and quantified using a Qubit Fluorometer (Life Technologies). Dual-index, single-read sequencing of pooled libraries was carried out on a HiSeq 2500 sequencer (Illumina) with 58-base reads, using HiSeq v4 Cluster and SBS kits (Illumina) with a target depth of 5 million reads per sample.

tag: gender

value: Placebo


title: KYSE150, GFP-TFAP2β, replicate 2

description:
Library name: Sample5
Column name in All_gene_counts.txt: AP2-2


title: 141_TNY75HG

description: Library name: lib32997

value: female

tag: visit


title: KYSE150, GFP, replicate 3

description:
Library name: Sample3
Column name in All_gene_counts.txt: NC-3

value: GFP


title: 147_TNY89T6

description: Library name: lib33003

tag: group


title: Mycelium grown for 7 days in low phosphate medium + one day in high phosphate, sample number 1

description: Library name: LPspike1


title: Mycelium grown for 7 days in high phosphate medium, sample number 3

description: Library name: HP3

value: high phophate


title: Mycelium grown for 7 days in high phosphate medium, sample number 4

description: Library name: HP4


title: 140_TNY60TC

description: Library name: lib32996


title: Mycelium grown for 7 days in high phosphate medium, sample number 2

description: Library name: HP2


title: KYSE150, GFP, replicate 2

description:
Library name: Sample2
Column name in All_gene_counts.txt: NC-2

tag: cell line


title: KYSE150, GFP, replicate 1

description:
Library name: Sample1
Column name in All_gene_counts.txt: NC-1


title: Mycelium grown for 7 days in low phosphate medium, sample number 3

description: Library name: LP3

tag: treatment

value: low phosphate


title: 139_TNY60YX

description: Library name: lib32995

value: whole blood


title: Mycelium grown for 7 days in low phosphate medium, sample number 1

description: Library name: LP1


title: 138_TNY7WKK

description: Library name: lib32994

value: ATG


title: Mycelium grown for 7 days in low phosphate medium, sample number 2

description: Library name: LP2


title: 142_TNY8H7A

description: Library name: lib32998


title: Mycelium grown for 7 days in low phosphate medium + one day in high phosphate, sample number 3

description: Library name: LPspike3


title: 19N_0.Ile

first: Cara

middle: L

last: Green

address: 2500 Overlook Terrace

institute: University of Wisconsin-Madison

description: Library name: 19N

data_processing:
Analysis of significantly differentially expressed genes (DEGs) was completed in R version 4.3.0. using edgeR and limma. Gene names were converted to gene symbol and Entrez ID formats using the mygene package. Genes with too many missing values were removed, if genes were present in less than one diet/age group they were removed. To reduce the impact of external factors not of biological interest that may affect expression, data was normalized to ensure the expression distributions of each sample are within a similar range. We normalized using the trimmed mean of M-values (TMM), which scales to library size. Heteroscedasticity was accounted for using the voom function, DEGs were identified using an empirical Bayes moderated linear model, and log coefficients and Benjamini-Hochberg (BH) adjusted p-values were generated for each comparison of interest.
Assembly: Reads were aligned to the mouse (Mus musculus) with genome-build GRCm38.p5 of accession NCBI:GCA_000001635.7[DL9]  and expected counts were generated with ensembl gene IDs.
Supplementary files format and content: Processed data file containing log2 fold-changes, gene IDs and unadjusted and Benjamini-Hochberg adjusted p-values. Haws2025_JBC_TableS2_Liver_RNAseqSummary.xlsx

source_name: Liver

extract_protocol:
RNA was extracted from liver with TRI Reagent (Thermo Fisher, AM9738), then treated with DNase (Invitrogen, 12185010) and purified with RNA purification kit (Ambion, 12183025). The concentration and purity of RNA was determined using a NanoDrop 2000c spectrophotometer (Thermo Fisher Scientific, Waltham, MA) and RNA was diluted to 100-400 ng/µl for sequencing. The RNA was then submitted to the University of Wisconsin-Madison Biotechnology Center Gene Expression Center & DNA Sequencing Facility, and RNA quality was assayed using an Agilent RNA NanoChip.
RNA libraries were prepared using the TruSeq Stranded Total RNA Sample Preparation protocol (Illumina, San Diego, CA) with 250ng of mRNA, and cleanup was done using RNA Clean beads (lot #17225200).

value: Liver


title: KYSE150, GFP-TFAP2β, replicate 1

description:
Library name: Sample4
Column name in All_gene_counts.txt: AP2-1


title: 19L_0.Ile

description: Library name: 19L


title: Blood GF 3

city: New York

first: Julia

last: Brown

address: 413 E 69th Street, 1252A

institute: Weill Cornell Medicine

description: Library name: Blood GF 3

data_processing:
Filtered barcode matrices generated by CellRanger v3.1.0 for each sample were first merged using Seurat merge function and then assessed for nFeature_RNA, nCount_RNA, and percentage of mitochondrial gene expression (%mito). To remove low-quality/dying cells from the data, only cells with 500 < nFeaure RNA < 4000, and %mito > 7.8 (90% quantile of %mito in all cells) were retained. Scrublet v0.2.2 was used to systematically remove doublets/multiplets in the data with a Scrublet score > 0.2. Additionally, we also removed cells with Ppbp expression that may be derived from platelet cells or platelet-related doublets that weren’t detected by Scrublet. Finally, 44,754 singlets were used for downstream analysis.
We followed the Seurat guided clustering tutorial (https://satijalab.org/seurat/articles/pbmc3k_tutorial.html) for single cell data analysis with a few key modifications. Briefly, quality-filtered cells were first normalized and scaled (regress out nCount-RNA) followed by principal component analysis (PCA) on highly variable features. To account for sample-sample variation and improve cell cluster identification, single-cell batch integration that simultaneously integrated across samples (q=1) and tissues (q=0.5) was performed using Harmony v1.0. Top 20 harmony embeddings were used to run UMAP and to perform clustering analysis (resolution = 0.3). Clusters with low CD45 (Ptprc) expression or with less than 100 cells were excluded from downstream analysis. Fourteen final clusters from 43,682 cells were defined and annotated. The FindAllMarkers function with Wilcox method was used to identify cell-type-specific markers comparing every cluster against the rest of the clusters. Similar analysis was also performed to identify differentially expressed genes between SPF and GF mice for clusters of interest. Markers that likely originated from ambient RNAs (e.g., Igkc in Tregs) were manually removed from the top differentially expressed gene list.
Assembly: GRCm38.p6
Supplementary files format and content: CellRanger filtered feature-barcode matrix files

source_name: Blood

extract_protocol:
Single cell suspensions were generated from blood, uterine horns and placenta tissues from GF or SPF E16.5 pregnant mice. Five placentas were pooled from each dam, and two dams were used per group. Blood, placenta, and uterine single-cell suspensions were stained with anti-CD45 APC antibody (clone 30-F11, BioLegend 103112) diluted 1:200 in FACS buffer (PBS + 1% bovine serum albumin; Sigma A2153) and enriched via MACS sorting using Miltenyi Biotec anti-APC beads (Miltenyi Biotec 130-090-855) diluted 1:10 in FACS buffer following the manufacturer’s instructions. The purified cells were resuspended at 750 cells/µL and viability was verified using an Invitrogen Countess automated cell counter. >10,000 live CD45+ cells from each tissue (blood, uterine horns or placenta) from each mouse, 3 mice per group, were FACS sorted and subjected to the 10X genomics pipeline.
Library preparation and sequencing was performed by the Weill Cornell Genomics Core, using the 10X Genomics Universal 3' Gene Expression v3.1 pipeline.

value: Blood

tag: condition

value: GF


title: 137_TNXV6T

description: Library name: lib32993

value: male


title: Blood GF 1

description: Library name: Blood GF 1


title: 136_TN5PGY

description: Library name: lib32992

value: ATG-GCSF


title: 09N_0.Ile

description: Library name: 09N


title: Blood SPF 2

description: Library name: Blood SPF 2

value: SPF


title: 135_TNY705W

description: Library name: lib32991


title: 134_TNY4XGR

description: Library name: lib32990


title: Blood SPF 1

description: Library name: Blood SPF 1


title: 09R_0.Ile

description: Library name: 09R


title: 09L_0.Ile

description: Library name: 09L


title: Uterus GF 3

description: Library name: Uterus GF 3

source_name: Uterus

value: Uterus


title: Control group sample Ctrl-3

city: Hangzhou

first: Da

last: Qian

state: Zhejiang

address: No. 158 Shangtang Road

department: Breast Surgery

institute: Zhejiang Provincial People's Hospital

description: Library name: Ctrl-3

data_processing:
Data filtering The sequencing data was filtered with SOAPnuke  by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).
RNA identification Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Gene Quantification Differential Expression Analysis Expression level of gene was calculated by RSEM (v1.3.1) . The heatmap was drawn by pheatmap (v1.0.8)  according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5)  (or DEGseq or PoissonDis)with Q value ≤ 0.05 (or FDR ≤ 0.001).
Gene Annotation To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05) .
Assembly: GRCr8
Supplementary files format and content: tab-delimited text files include fpkm values for each Sample

organism: Rattus norvegicus

source_name: rat microvascular tissue

extract_protocol:
1. Experimental Procedures 1.1 Sample Lysis 1.1.1 Transfer appropriate tissue sample into corresponding tissue grinding tube (tissue≤30 mg, cell≤1×107). 1.1.2 Add 600 μL Buffer RLT Plus. Homogenize the lysate for using a rotor–stator homogenizer, stay at room temperature for 5 min. 1.1.3 Centrifuge at 12,000×g for 3 min in room temperature, transfer the supernatant to AllPrep DNA spin column. 1.1.4 Centrifuge 12,000×g for 30 s in room temperature, transfer the solution from the collection tube for the RNA purification. 1.1.5 Transfer the DNA spin column to the new collection tube for DNA purification. 1.2 DNA Purification 1.2.1 Add 500μL Buffer AW1 to AllPrep DNA spin column, centrifuge at 10,000×g for 30 s and discard the filtrate. 1.2.2 Add 500μL Buffer AW2 to AllPrep DNA spin column, centrifuge at 10,000×g for 30 s and discard the filtrate. 1.2.3 Centrifuge at 16,000×g for 2 min, transfer the AllPrep DNA spin column to 1.5mL centrifuge tube. 1.2.4 Add 50μL Buffer EB to AllPrep DNA spin column, stay at room temperature for 1 min. 1.2.5 Centrifuge at 16,000×g for 2 min and collect the DNA. 1.3 RNA Purification 1.3.1 Add the equal volume of 70% ethanol to the collection tube, mix by pipetting. 1.3.2 Transfer 700 μL mixed solution, to a RNeasy spin column placed in a 2 mL collection tube. 2.3.3 Centrifuge at 10,000×g for 30 s and allow it to empty by gravity flow. 1.3.4 Add 700 μL Buffer RW1 to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate. 1.3.5 Add 500 μL Buffer RPE to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate. 1.3.6 Add 500 μL Buffer RPE to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate. 1.3.7 Centrifuge at 16,000×g for 2 min and transfer the RNeasy spin column to the 1.5 mL centrifuge tube. 1.3.8 Add 35 μL RNase-free water to RNeasy spin column. Stay at room temperature for 1min. 1.3.9 Centrifuge at 16,000×g for 2 min at room temperature to collect RNA.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase, which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP Solution. An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: rat microvascular tissue

value: primary rat microvascular vascular smooth muscle cells

value: Control


title: Treated group sample LCARIIN-1

description: Library name: LCARIIN-1

value: treated with Icariin


title: 133_TNY9GLH

description: Library name: lib32989


title: Treated group sample LCARIIN-3

description: Library name: LCARIIN-3


title: Treated group sample LCARIIN-2

description: Library name: LCARIIN-2


title: Control group sample Ctrl-2

description: Library name: Ctrl-2


title: 132_TNYGKCJ

description: Library name: lib32988


title: 05N_0.Ile

description: Library name: 05N


title: Uterus GF 1

description: Library name: Uterus GF 1


title: Control group sample Ctrl-1

description: Library name: Ctrl-1


title: 05L_0.Ile

description: Library name: 05L


title: 131_TNYCU5J

description: Library name: lib32987

value: Placebo


title: CTR_4

city: Jingzhou

first: Tinghua

last: Huang

address: Jingmi Road #266

institute: Yangtze University

description: Library name: Sample16

data_processing:
Data filtering was conducted to obtain clean reads and to remove low quality reads present in the raw reads as recommended by the manufacturer. Hisat2 was used to map clean reads to the reference genome (GRCg7b), which was extracted from the NCBI genome database. The calculated reads count per gene were estimated by Htseq-count and used for comparing the difference in gene expression among samples.
Assembly: GRCg7b
Supplementary files format and content: Reads count

organism: Gallus gallus

growth_protocol: HD11 cells were cultured in RPMI 1640 complete medium (Containing 8% of FBS, 3% of CS and 1% of penicillin-streptomycin), kept at 41°C in 5% CO2, and were passaged every three days at a ratio of 1:3.

extract_protocol:
RNA was prepared using RNAeasy mini kit (Qiagen). 2ug of total RNA was used for the construstion of the sequencing labraries
Sequencing libraries were prepared using the Illumina Truseq RNA sample preparation kit according to the manufacturer’s protocol (Illumina Inc., USA).

treatment_protocol: Approximately 12 hours before challenging, HD11 cells were seeded into 6-well cell plates at a concentration of 2×106 cells per well in RPMI 1640 containing 100 μM SeMC, the concentration of Procyanidin B1 has been verified to be fit for cell viability. Cells were stimulated with 100 ng/ mL lipopolysaccharide for 6h, washed and further lysed with 1mL Trizol regent.

value: Macrophage-like

value: CTR


title: 19R_0.Ile

description: Library name: 19R


title: Uterus SPF 1

description: Library name: Uterus SPF 1


title: 05R_0.Ile

description: Library name: 05R


title: 130_TNYG1NY

first: Stephanie

last: Osmond

address: 1201 9th Ave

institute: Benaroya Research Institute

description: Library name: lib32986

value: female


title: Placenta GF 3

description: Library name: Placenta GF 3

source_name: Placenta

value: Placenta


title: CTR_3

description: Library name: Sample15


title: 03N_0.Ile

description: Library name: 03N


title: CTR_2

description: Library name: Sample14


title: 129_TNY44TG

description: Library name: lib32985

source_name: whole blood

value: whole blood


title: Placenta GF 1

description: Library name: Placenta GF 1


title: 03L_0.Ile

description: Library name: 03L

value: Liver


title: 128_TNY9T3U

description: Library name: lib32984

value: ATG


title: CTR_1

description: Library name: Sample13


title: 127_TNY9GHK

description: Library name: lib32983


title: 03R_0.Ile

description: Library name: 03R


title: Placenta SPF 2

description: Library name: Placenta SPF 2


title: PB1_4

description: Library name: Sample12


title: Placenta SPF 1

description: Library name: Placenta SPF 1


title: 17N_0.Leu

description: Library name: 17N


title: PB1_3

description: Library name: Sample11


title: 126_TNY93JG

description: Library name: lib32982


title: Uterus SPF 2

description: Library name: Uterus SPF 2


title: 125_TNY70PX

description: Library name: lib32981


title: 17L_0.Leu

description: Library name: 17L


title: 17R_0.Leu

description: Library name: 17R


title: PB1_2

description: Library name: Sample10


title: 124_TNY88W7

description: Library name: lib32980


title: PB1_1

description: Library name: Sample9


title: 14N_0.Leu

description: Library name: 14N


title: 123_TNYA3W2

description: Library name: lib32979


title: LPS_PB1_4

description: Library name: Sample8


title: heart, infarctzone_8

city: Freiburg

first: Diana

last: Lindner

address: Hugstetter Straße 55

department: University Heart Center Freiburg-Bad Krozingen

institute: University Hospital Freiburg

description: Library name: sample16_heart

data_processing:
Illumina bcl2fastq software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and bad quality as well as MACE specific polyA stretches; PCR artifacts were deduplicated based on Unique Molecular Identifier sequences
Cleaned reads were mapped onto mm10 genome using bowtie2 and raw counts were obtained using HTSeq
Differential gene expression was calculated using DESeq2.
Assembly: mm10
Supplementary files format and content: rawcounts

source_name: heart - infarctzone

extract_protocol:
Total RNA Isolation was performed using the miRNeasy mini kit (Qiagen, Germany). As suggested, DNase I (Qiagen, Germany) was applied to the column to avoid genomic DNA contamination.
Three prime End sequencing using GenXPro-MACE-Seq kit (GenXPro GmbH, Frankfurt Germany) including UMIs for PCR-dupliacate removal. Massive Analysis of cDNA ends (MACE-Seq)

value: heart - infarctzone

value: wildtype

value: MI


title: heart, infarctzone_6

description: Library name: sample14_heart


title: heart, infarctzone_7

description: Library name: sample15_heart


title: 14L_0.Leu

description: Library name: 14L


title: 122_TNYA3H3

city: Seattle,

description: Library name: lib32978

value: male


title: LPS_PB1_3

description: Library name: Sample7


title: heart, infarctzone_5

description: Library name: sample13_heart


title: 14R_0.Leu

description: Library name: 14R


title: 121_TNY9U68

description: Library name: lib32977

value: ATG-GCSF


title: LPS_PB1_2

description: Library name: Sample6


title: 13N_0.Leu

description: Library name: 13N


title: heart, infarctzone_9

description: Library name: sample17_heart


title: LPS_PB1_1

description: Library name: Sample5


title: 119_TNY8ML1

description: Library name: lib32975


title: 13R_0.Leu

description: Library name: 13R


title: 13L_0.Leu

description: Library name: 13L


title: LPS_4

description: Library name: Sample4

value: LPS


title: heart, infarctzone_4

description: Library name: sample12_heart


title: heart, infarctzone_2

description: Library name: sample10_heart


title: LPS_3

description: Library name: Sample3


title: 08N_0.Leu

description: Library name: 08N


title: heart, infarctzone_1

description: Library name: sample9_heart


title: 117_TNY93C9

description: Library name: lib32973


title: 118_TNY954G

description: Library name: lib32974


title: 08L_0.Leu

description: Library name: 08L


title: LPS_2

description: Library name: Sample2


title: heart, sh_8

description: Library name: sample8_heart

source_name: heart

value: heart

value: sham


title: 115_TNY8P0Y

description: Library name: lib32971


title: Healthy control 4

type: genomic

city: Ningbo

first: Qingxiao

last: Hong

state: Zhejiang province

address: No.1 Zhuangyu South Road

department: Department of psychiatry

institute: Afffliated Kangning Hospital of Ningbo University

description: Healthy participants that were recruited as the healthy controls, these people had no other major illnesses and no substance addictions

hyb_protocol: Bisulphite converted DNA was amplifed, fragmented and hybridized to human infnium MethylationEpIc Beadchip (lumina) using standard llumina protocolArrays were imaged using BeadArray Reader (HiScan) and standard recommended llumina scanner settingRnBeads package in R environment (v4.1.1)

scan_protocol: Arrays were imaged using BeadArray Reader(HiScan) and standard recommended Illumina scanner setting

data_processing:
RnBeads package in R environment
processed data values: Average Beta

label: biotin

source_name: Peripheral blood

label_protocol: Standard lllumina Protocol

extract_protocol: DNA extraction was performed using the DNeasy Blood & Tissue Kit (QIAGEN) following the manufacturer's instructions.

value: Peripheral blood

value: Male

value: leukocyte

value: Not available

value: Nothing


title: 120_TNY7PM5

description: Library name: lib32976

value: Placebo


title: 116_TNY82X9

description: Library name: lib32972

value: whole blood


title: 20N_0.Met

description: Library name: 20N

value: Liver


title: 08R_0.Leu

description: Library name: 08R


title: heart, sh_6

description: Library name: sample6_heart


title: Healthy control 3


title: heart, sh_5

description: Library name: sample5_heart


title: heart, infarctzone_3

description: Library name: sample11_heart


title: 113_TNY5XTG

description: Library name: lib32969

value: female

value: ATG


title: 20L_0.Met

description: Library name: 20L


title: heart, sh_4

description: Library name: sample4_heart

value: wildtype


title: 20R_0.Met

description: Library name: 20R


title: 112_TNY3X7J

description: Library name: lib32968


title: Healthy control 1


title: heart, sh_3

description: Library name: sample3_heart


title: 16N_0.Met

description: Library name: 16N


title: 111_TNY3THJ

description: Library name: lib32967


title: Methamphetamine-dependent individual 4

description: Men that met the Diagnostic and Statistical Manual of Mental Disorders (Fifth Edition) criteria for methamphetamine dependence

value: Methamphetamine


title: LPS_1

description: Library name: Sample1

value: Macrophage-like


title: heart, sh_7

description: Library name: sample7_heart


title: 16L_0.Met

description: Library name: 16L


title: heart, sh_2

description: Library name: sample2_heart


title: 110_TNYPR4

description: Library name: lib32966

value: ATG-GCSF


title: Methamphetamine-dependent individual 3


title: heart, sh_1

description: Library name: sample1_heart


title: Methamphetamine-dependent individual 2


title: 16R_0.Met

description: Library name: 16R


title: 114_TNY5XUA

description: Library name: lib32970


title: MI_28d_7

description: Library name: sample24_kidney

data_processing:
Unprocessed sequencing reads were adapter-trimmed and quality-trimmed using Cutadapt
Deduplication based on UMIs (Unique Molecular Identifier) was performed using in-house tools. FastQC was used to assess the quality of sequencing reads.
Processed sequencing reads were mapped with a reference genome using Bowtie2 or nvBowtie from nvbio
Quantification of mapped reads to each gene was performed using HTSeq
Raw counts were geometric-mean-normalized using DESeq2 and TPM-normalized by dividing each count with the sum of all counts for each sample multiplied by one million.
Assembly: mm39
Supplementary files format and content: raw count and tpm count

source_name: kidney

value: kidney

value: MI

tag: time


title: 10N_0.Met

description: Library name: 10N


title: 109_TNY694C

description: Library name: lib32965


title: Healthy control 2

tag: Sex


title: 108_TNY8CP6

description: Library name: lib32964

value: male


title: 10L_0.Met

description: Library name: 10L


title: Methamphetamine-dependent individual 1

value: Peripheral blood

tag: cell type


title: 107_TNY8CLR

description: Library name: lib32963


title: SScF_P02_Eso100uM

city: San Antonio

first: Shaheer

last: Koniyan

state: TX

address: 4939 Charles Katz Dr

department: Radiation Oncology

institute: UT San Antonio

description: Library name: SScF_P02_Eso100uM

data_processing:
Reads aligned to hg38 using STAR Aligner
Reads were counted using StringTie
Assembly: UCSC/GRChg38
Supplementary files format and content: Raw counts as a TSV file

source_name: Primary Fibroblasts

growth_protocol: The cells were cultured in Dulbecco’s Modified Eagle medium (DMEM; Gibco, cat # 11995) supplemented with 10% fetal bovine serum (FBS; Gibco, cat # A5256801) and 1% penicillin-streptomycin (Gibco, cat # 15140122), and maintained at 37°C in 5% CO2

extract_protocol:
Total RNA was extracted from cell lysates using Zymo’s Direct-zol RNA MiniPrep Kit (Zymo Research, cat # R2052), which included an on-column DNase digestion step to eliminate genomic DNA contamination. RNA concentration and purity were analyzed using a NanoDrop spectrophotometer
Stranded mRNA-seq library preparation kit

treatment_protocol: Esomeprazole sodium (Tecoland, batch # 20240126) was used at final concentrations ranging from 10 to 100 uM for 24 hours.

tag: tissue source

value: Skin

value: Male

value: Primary Fibroblasts

tag: disease type

value: SSc Limited


title: MI_28d_5

description: Library name: sample22_kidney

tag: genotype


title: 10R_0.Met

description: Library name: 10R


title: MI_28d_4

description: Library name: sample21_kidney


title: 04N_0.Met

description: Library name: 04N


title: SScF_P02_Eso50uM

description: Library name: SScF_P02_Eso50uM


title: MI_28d_3

description: Library name: sample20_kidney


title: SScF_P02_Eso20uM

description: Library name: SScF_P02_Eso20uM


title: 104_TNY0Y3N

description: Library name: lib32960


title: MI_28d_2

description: Library name: sample19_kidney


title: 04R_0.Met

description: Library name: 04R


title: SScF_P02_Eso10uM

description: Library name: SScF_P02_Eso10uM


title: 103_TNY7WRV

description: Library name: lib32959


title: SScF_P02_Eso0uM

description: Library name: SScF_P02_Eso0uM


title: 15N_Rapa

description: Library name: 15N


title: MI_28d_1

description: Library name: sample18_kidney


title: MI_5d_9

description: Library name: sample17_kidney


title: MI_28d_6

description: Library name: sample23_kidney


title: 101_TNY6K5C

description: Library name: lib32957

value: Placebo


title: 15L_Rapa

description: Library name: 15L


title: SScF_P01_Eso100uM

description: Library name: SScF_P01_Eso100uM


title: 102_TNY0KAT

description: Library name: lib32958

value: whole blood


title: MI_5d_8

description: Library name: sample16_kidney


title: 106_TNY8MMY

description: Library name: lib32962


title: SScF_P01_Eso50uM

description: Library name: SScF_P01_Eso50uM


title: 15R_Rapa

description: Library name: 15R

value: Liver


title: MI_5d_7

description: Library name: sample15_kidney


title: 100_TNY7HX8

description: Library name: lib32956

value: female


title: 105_TNY87AU

description: Library name: lib32961

value: ATG


title: SScF_P01_Eso20uM

description: Library name: SScF_P01_Eso20uM


title: SScF_P01_Eso10uM

description: Library name: SScF_P01_Eso10uM


title: 12N_Rapa

description: Library name: 12N


title: MI_5d_6

description: Library name: sample14_kidney

value: wildtype


title: 99_TNY5WX3

description: Library name: lib32955


title: 04L_0.Met

description: Library name: 04L


title: 12L_Rapa

description: Library name: 12L


title: 98_TNY797M

description: Library name: lib32954


title: MI_5d_5

description: Library name: sample13_kidney


title: 12R_Rapa

description: Library name: 12R


title: 97_TNY6G5G

description: Library name: lib32953


title: MI_5d_4

description: Library name: sample12_kidney


title: 06N_Rapa

description: Library name: 06N


title: 96_TNY03LV

description: Library name: lib32952


title: MI_5d_3

description: Library name: sample11_kidney


title: 06L_Rapa

description: Library name: 06L


title: R2_D3_CpG-A+230V5

city: Shanghai

first: Haomin

address: 399 Libing Road

institute: 3SBio Inc.

description:
Library name: r2_Donor3_sam12
MobiNova-100

data_processing:
Mobivision-v3.2 software was used to map reads to a reference genome and quantify gene expression levels.  Data analysis and clustering were performed using the “seurat” R package of R software (version 4.3.3).
Assembly: GRCh38
Supplementary files format and content: filtered_matrix

source_name: PBMC

growth_protocol: PBMCs were cultured in RPMI 1640 medium supplemented with 10% FBS

extract_protocol:
Cells were loaded onto a Chip A Single-Cell Kit v2.1 (MobiDrop (Zhejiang) Co., Ltd., Cat. No. S050100301, Zhejiang, China) to generate droplets with MobiNova-100 (MobiDrop (Zhejiang) Co., Ltd., Cat. No. A1A40001). Each cell was prepared in a droplet that contained a gel bead linked with up to millions of oligos (cell unique barcodes). After encapsulation, the droplets are cut by light with a MobiNovaSP-100 (MobiDrop (Zhejiang) Co., Ltd., Cat. No. A2A40001), while the oligos diffused into the reaction mixture. The mRNAs were captured by cell barcodes with cDNA amplification in droplets. Following reverse transcription, cDNAs with barcodes were amplified, and a library was constructed using the High Throughput Single-Cell 3' Transcriptome Kit v2.1 (MobiDrop (Zhejiang) Co., Ltd., Cat. No. S050200301) and the 3' Dual Index Kit (MobiDrop (Zhejiang) Co., Ltd., Cat. No. S050300301). The resulting libraries were subsequently sequenced on an Illumina NovaSeq Xplus System.
Generating the “water in oil” droplets based on the microflu-idics technology, by identifying the fluorescence signal in the droplets, and deflecting droplets to different channels using dielectrophoresis, thereby fulfilling highly efficient cell sorting.MobiNova-100 Single Cell System utilizes patented barcoding and microfluidic technologies to achieve reliable single cell partitioning and effective cell capture in minutes.

treatment_protocol: Aliquots of 5×10⁶ cells were transferred to 96-well culture plates, after which 50 μL of 230 variants that were diluted in culture medium to achieve a final concentration of 4 nM were added to each well, and the cells were preincubated at 37 °C with 5% CO₂ for 1 hour. Afterward, 50 μL of CpG2216 was added to each well to achieve a final concentration of 2 μg/mL. The cultures were maintained at 37 °C with 5% CO₂ for 18 hours prior to harvesting the cells by centrifugation. The pellets were subsequently washed twice with PBS and processed for the sequencing analysis

value: PBMC

tag: batch


title: R2_D3_CpG-A+230V3

description:
Library name: r2_Donor3_sam11
MobiNova-100


title: 95_TN88C1

description: Library name: lib32951


title: 06R_Rapa

description: Library name: 06R


title: R2_D3_CpG-A

description:
Library name: r2_Donor3_sam10
MobiNova-100


title: MI_5d_2

description: Library name: sample10_kindey


title: R2_D3_Ctrl

description:
Library name: r2_Donor3_sam9
MobiNova-100

value: Ctrl


title: MI_5d_1

description: Library name: sample9_kindey


title: 93_TNY5UTK

description: Library name: lib32949


title: R2_D2_CpG-A+230V5

description:
Library name: r2_Donor2_sam8
MobiNova-100


title: 94_TNY7J7L

description: Library name: lib32950


title: sh_8

description: Library name: sample8_kidney

value: sham


title: SScF_P01_Eso0uM

description: Library name: SScF_P01_Eso0uM


title: 02N_Rapa

description: Library name: 02N


title: 92_TNYJ528

description: Library name: lib32948


title: sh_7

description: Library name: sample7_kidney

value: kidney


title: 18N_Ctl

description: Library name: 18N


title: 02L_Rapa

description: Library name: 02L


title: 91_TNYH9W8

description: Library name: lib32947


title: R2_D2_CpG-A+230V3

description:
Library name: r2_Donor2_sam7
MobiNova-100


title: 90_TNYG1M6

description: Library name: lib32946

value: ATG-GCSF


title: R2_D2_Ctrl

description:
Library name: r2_Donor2_sam5
MobiNova-100


title: sh_5

description: Library name: sample5_kidney


title: R2_D2_CpG-A

description:
Library name: r2_Donor2_sam6
MobiNova-100


title: 89_TNYCC30

description: Library name: lib32945

value: male


title: sh_4

description: Library name: sample4_kidney


title: R2_D1_CpG-A+230V5

description:
Library name: r2_Donor1_sam4
MobiNova-100


title: 18R_Ctl

description: Library name: 18R


title: sh_3

description: Library name: sample3_kidney


title: 18L_Ctl

description: Library name: 18L


title: 88_TNYA3XC

description: Library name: lib32944


title: R2_D1_CpG-A+230V3

description:
Library name: r2_Donor1_sam3
MobiNova-100


title: 87_TNY9T38

description: Library name: lib32943


title: sh_2

description: Library name: sample2_kidney


title: R2_D1_CpG-A

description:
Library name: r2_Donor1_sam2
MobiNova-100


title: 86_TNY7NUM

description: Library name: lib32942


title: 02R_Rapa

description: Library name: 02R


title: 11L_Ctl

description: Library name: 11L


title: R2_D1_Ctrl

description:
Library name: r2_Donor1_sam1
MobiNova-100


title: 11R_Ctl

description: Library name: 11R


title: R1_CpG-A+230V5

description:
Library name: r1_sam4
MobiNova-100


title: sh_1

description: Library name: sample1_kidney


title: sh_6

description: Library name: sample6_kindey


title: 07N_Ctl

description: Library name: 07N


title: 84_TNY87RC

description: Library name: lib32940


title: 85_TNY79CW

description: Library name: lib32941