title: ROI.052.Stroma

description:
Library name: DSP-1001660011191-D-D10
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 052 | Stroma


title: ROI.050.Stroma

status: Public on May 09 2025

type: SRA

city: Chicago

first: CRI

last: Bioinformatics

state: IL

address: 5801 S. Ellis Ave.

country: USA

institute: University of Chicago

description:
Library name: DSP-1001660011191-D-D08
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 050 | Stroma

library_source: transcriptomic

data_processing:
Raw count data were processed and normalized using the R package GeoMxTools (GeoMx_NGS_Pipeline_2.3.3.10). Details on thresholds, settings, and normalization are provided in Supplementary Table 11 of the original article.
Assembly: GRCh38.p13
Supplementary files format and content: Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: normalized gene counts
Library strategy: Spatial Transcriptomics

molecule: total RNA

organism: Homo sapiens

source_name: HGSOC, FFPE

growth_protocol: A tissue microarray (TMA) comprising 55 cores (2 mm diameter each) from non-tumorous adjacent stroma (n = 10), ovarian cancer (n = 29), and omental metastases (n = 16) was constructed using samples from 30 patients with high-grade serous ovarian cancer (HGSOC).

extract_protocol:
mRNA expression in FFPE tissues was measured using the GeoMx Human Whole Transcriptome Atlas (NanoString, GMX-RNA-NGS HuWTA-4), which targets 18,000 protein-coding genes via UV-cleavable oligonucleotide barcodes. Probe hybridization and immunofluorescent staining were performed according to the GeoMx FFPE slide preparation protocol. Briefly, the slide was baked overnight at 37°C, followed by deparaffinization, rehydration, target retrieval, and proteinase K (0.1 μg/mL) treatment. After post-fixation, in situ probe hybridization was performed overnight. Morphology markers used for immunofluorescent staining included: pan-cytokeratin (pan-CK; Novus Biologicals, NBP2-33200AF532, AF532, 1:40), CD45 (NBP2-34528AF594, AF594, 1:20), CD163 (Abcam, ab218294, AF647, 1:100), and SYTO 13 nuclear stain (NanoString, 121300303, FITC, 1:10). Slides were scanned at 20x magnification using the GeoMx Digital Spatial Profiler. Regions of interest (ROIs) were selected by a pathologist based on morphology marker staining, guided by H&E staining to exclude necrotic areas and big vessels. ROIs were subdivided into areas of interest (AOIs), and only those containing ≥50 cells based on manual counting were included. Four AOI types were collected: (1) panCK+ cancer epithelium, (2) CD163+ monocytes/macrophages, (3) CD45+ CD163- immune cells, and (4) stroma (panCK- CD163- CD45-). Oligonucleotide barcodes from AOIs were collected into 96-well plates via UV ablation.
Subsequent PCR amplification, pooling, quality control, and sequencing were conducted following the GeoMx DSP-NGS protocol. Libraries were purified using two rounds of Ampure XP magnetic beads (1.2:1 bead-to-library ratio) with the HighPrep PCR Clean-up System (MAGBIO, AC-60500), then sequenced on an Illumina NovaSeq PE50 flow cell at a depth of 100x/μm².

treatment_protocol: All included patients were treatment naiive.

tag: tissue

value: HGSOC, FFPE

tag: cell type

value: Stroma

tag: treatment

value: chemotherapy-naïve

tag: roi

tag: nanostring id

tag: sample location

value: ovary


title: p1107-plusN-02_0130

city: New York

first: Ji

last: Huang

state: NY

address: 12 Waverly Place

department: Center for Genomics & Systems Biology

institute: New York University

data_processing:
All RNA-seq raw reads for maize TARGET experiments were first processed to remove optical duplicates (Clumpify) and adapters (BBDuk). The trimmed reads were aligned to the maize version 4 genome using BBMap. The mapped reads were assigned to gene loci using featureCounts with the latest annotation AGPv4.32. Genes passing the expression threshold (>1 CPM per sample) were normalized using upper-quantile normalization (EDASeq 2.18.0) and replicate samples (RUVSeq 1.18.0). Differential gene expression analysis was conducted using edgeR to identify target genes for each TF, comparing empty vector- and TF-transfected samples with and without N treatment in parallel. The union of DEGs (FDR<0.05) from minus- and plus-N conditions was considered the target genes for a given TF.
Assembly: maize genome version 4
Supplementary files format and content: tsv file includes the 23 TF-to-gene edges

molecule: polyA RNA

organism: Zea mays

source_name: leaf protoplast

growth_protocol: All maize TARGET experiments were performed using the p1107 plasmid as described previously (Shanks et al. 2022). The maize transfection protocol was adapted from our Arabidopsis TARGET protocol (Bargmann et al. 2013; Brooks et al. 2019) and Dr. Jen Sheen’s protocol (https://molbio.mgh.harvard.edu/sheenweb/protocols.html) with some modifications. The maize seeds were soaked overnight and planted in pots filled with Turface MVP. The pots were placed at the growth chamber, under 16 h light/8 h dark diurnal cycle, at temperatures 27 and 24°C respectively and 70% humidity for three days. After seeds were germinated and about 5cm above ground, the pots were moved to the dark room at temperature 27°C and 70% humidity for etiolation for seven days.

extract_protocol:
TF vector and control empty vector transfected protoplasts were FACS sorted for RFP signals into 150 µL TRI regent for RNA extraction (Zymo, R2061). The RNA quality was checked on the Agilent TapeStation (5067-5576).
We used Lexogen QuantSeq 3' mRNA-Seq Library Prep Kit (Lexogen, 015.2x96) for RNASeq library preparation.

treatment_protocol: On the day of the TARGET experiment, etiolated middle section (~4cm) of the second leaves were cut into 1 mm pieces and soaked in the cell-wall digestion solution (1.5% cellulase RS, 0.3% macerozyme R10 (Yakult Honsha), 0.6M mannitol, 10 mM MES (pH 5.7), 1 mM CaCl2, 5 mM b-mercaptoethanol, and 0.1% BSA) in a petri dish. The petri dish was vacuum infiltrated for 30 minutes and shaken for 95min at 50 rpm in the dark, followed by 10 min at 70 rpm to fully release cells. Maize protoplast cells were filtered through a 40 µm cell strainer (BD Falcon, USA) and spun down for 2 min at 280g. The cells were washed with 10mL Buffer (10mM MES, pH 5.7, 0.6M mannitol, 10 mM KCl) three times. After the final wash, cells were resuspended in the Buffer to 1.0x106 cells/mL and were ready for transfection.

value: leaf protoplast

tag: batch

tag: plasmid

value: EV

tag: genotype

value: plusN


title: p1107-plusN-03_0130


title: p1107-minusN-02_0130

value: minusN


title: p1107-plusN-01_0130


title: ROI.050.CD45

description:
Library name: DSP-1001660011191-D-D07
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 050 | CD45


title: p1107-minusN-03_0130


title: ROI.051.Cancer Cells

description:
Library name: DSP-1001660011191-D-D09
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 051 | Cancer Cells

value: Cancer Cells


title: p1107-minusN-01_0130


title: p1107-plusN-02_0116


title: ROI.050.CD163

description:
Library name: DSP-1001660011191-D-D06
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 050 | CD163


title: ROI.049.Stroma

description:
Library name: DSP-1001660011191-D-D05
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 049 | Stroma

value: omentum


title: p1107-plusN-03_0116


title: ROI.049.Cancer Cells

description:
Library name: DSP-1001660011191-D-D04
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 049 | Cancer Cells


title: notrap_30m_rep2

city: Nankang, Taipei

first: Hung-Che

last: Lin

address: 128 Academia Road, Section 2

country: Taiwan

institute: Academia sinica

description: Library name: Sample2

data_processing:
we conducted quality control using FastQC
The STAR was employed for alignment of sequencing reads to the reference genome, C. elegans (PRJNA13758) from WormBase WS273, and subsequent mapping
RSEM facilitated accurate quantification of gene and isoform abundances.
For normalization of gene counts, we employed edgeR (3), implementing a sophisticated procedure involving DGEList object creation, stringent filtering based on count and repeat thresholds, and subsequent normalization.
Assembly: PRJNA13758
Supplementary files format and content: tsv files with all the counts for all samples

organism: Caenorhabditis elegans

source_name: whole organism

growth_protocol: C. elegans (wild-type N2 and nhr-66 STOP-IN mutants) were cultured to the late L4 stage under standard conditions with OP50 E. coli as the food source. Arthrobotrys oligospora was grown on 9-cm agar plates for 5 days to establish non-trapping cultures.

extract_protocol:
Total RNA was extracted from lyophilized samples via a Trizol-chloroform based protocol
Library preparation for total RNA samples (Genomic Core Facility, Institute of Molecular Biology, Academia Sinica) were carried out using the Illumina TruSeq stranded mRNA library preparation kit.

treatment_protocol: Late L4 nematodes were transferred to A. oligospora plates and exposed for 30 minutes under non-trapping conditions. After exposure, nematodes were washed twice in M9 buffer to remove residual fungi and bacteria.

value: whole organism

tag: strain

value: Bristol


title: ROI.049.CD45

description:
Library name: DSP-1001660011191-D-D03
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 049 | CD45


title: p1107-minusN-03_0116


title: p1107-minusN-02_0116


title: ROI.049.CD163

description:
Library name: DSP-1001660011191-D-D02
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 049 | CD163


title: ROI.047.CD163

description:
Library name: DSP-1001660011191-D-C10
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 047 | CD163


title: p1107-plusN-02_20190625


title: ROI.048.Cancer Cells

description:
Library name: DSP-1001660011191-D-D01
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 048 | Cancer Cells


title: p1107-minusN-01_0116


title: ROI.047.Stroma

description:
Library name: DSP-1001660011191-D-C12
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 047 | Stroma


title: p1107-plusN-04_20190625


title: ROI.046.CD45

description:
Library name: DSP-1001660011191-D-C07
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 046 | CD45


title: ROI.044.Stroma

description:
Library name: DSP-1001660011191-D-C04
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 044 | Stroma


title: p1107-minusN-02_20190625


title: p1107-plusN-01_20190625


title: p1107-plusN-03_20190625


title: ROI.046.Stroma

description:
Library name: DSP-1001660011191-D-C09
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 046 | Stroma


title: p1107-plusN-01_0116


title: ROI.047.CD45

description:
Library name: DSP-1001660011191-D-C11
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 047 | CD45


title: p1107-plusN-04_0619


title: p1107-plusN-02_0619


title: p1107-minusN-03_20190625


title: p1107-minusN-04_20190625


title: ROI.046.CD163

description:
Library name: DSP-1001660011191-D-C06
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 046 | CD163


title: ROI.045.Cancer Cells

description:
Library name: DSP-1001660011191-D-C05
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 045 | Cancer Cells


title: p1107-minusN-01_20190625


title: p1107-plusN-03_0619


title: ROI.044.CD163

description:
Library name: DSP-1001660011191-D-C02
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 044 | CD163


title: ROI.046.Cancer Cells

description:
Library name: DSP-1001660011191-D-C08
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 046 | Cancer Cells


title: ROI.044.CD45

description:
Library name: DSP-1001660011191-D-C03
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 044 | CD45


title: p1107-minusN-01_0619


title: ROI.043.Cancer Cells

description:
Library name: DSP-1001660011191-D-B12
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 043 | Cancer Cells


title: p1107NLSmyc-plusN-04_20210524


title: ROI.042.Stroma

description:
Library name: DSP-1001660011191-D-B09
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 042 | Stroma


title: p1107-minusN-04_0619


title: ROI.043.Stroma

description:
Library name: DSP-1001660011191-D-C01
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 043 | Stroma


title: ROI.042.CD163

description:
Library name: DSP-1001660011191-D-B06
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 042 | CD163


title: p1107-minusN-03_0619


title: p1107NLSmyc-plusN-01_20210524


title: ROI.042.CD45

description:
Library name: DSP-1001660011191-D-B07
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 042 | CD45


title: ROI.040.Stroma

description:
Library name: DSP-1001660011191-D-B04
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 040 | Stroma


title: p1107-minusN-02_0619


title: ROI.041.Stroma

description:
Library name: DSP-1001660011191-D-B05
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 041 | Stroma


title: ROI.043.CD163

description:
Library name: DSP-1001660011191-D-B10
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 043 | CD163


title: p1107-plusN-01_0619


title: ROI.039.Stroma

description:
Library name: DSP-1001660011191-D-B03
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 039 | Stroma


title: p1107NLSmyc-minusN-04_20210524


title: ROI.039.Cancer Cells

description:
Library name: DSP-1001660011191-D-B02
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 039 | Cancer Cells


title: p1107NLSmyc-plusN-02_20210524


title: p1107NLSmyc-minusN-03_20210524


title: p1107NLSmyc-plusN-03_20210524


title: ROI.043.CD45

description:
Library name: DSP-1001660011191-D-B11
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 043 | CD45


title: p1107NLSmyc-minusN-02_20210524


title: p1107NLSmyc-minusN-01_20210524


title: ROI.039.CD163

description:
Library name: DSP-1001660011191-D-B01
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 039 | CD163


title: ROI.042.Cancer Cells

description:
Library name: DSP-1001660011191-D-B08
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 042 | Cancer Cells


title: ROI.038.Stroma

description:
Library name: DSP-1001660011191-D-A12
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 038 | Stroma


title: G2plantp1107NLSmyc-plusN-02_20210523


title: ROI.036.Stroma

description:
Library name: DSP-1001660011191-D-A10
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 036 | Stroma


title: ROI.036.CD45

description:
Library name: DSP-1001660011191-D-A09
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 036 | CD45


title: G2plantp1107NLSmyc-plusN-04_20210523


title: ROI.036.CD163

description:
Library name: DSP-1001660011191-D-A08
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 036 | CD163


title: G2plantp1107NLSmyc-minusN-02_20210523


title: G2plantp1107NLSmyc-plusN-03_20210523


title: ROI.037.Cancer Cells

description:
Library name: DSP-1001660011191-D-A11
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 037 | Cancer Cells


title: p1107NLSmyc-plusN-03_20210517


title: ROI.034.CD45

description:
Library name: DSP-1001660011191-D-A04
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 034 | CD45


title: G2plantp1107NLSmyc-plusN-01_20210523


title: G2plantp1107NLSmyc-minusN-04_20210523


title: p1107NLSmyc-minusN-04_20210517


title: G2plantp1107NLSmyc-minusN-03_20210523


title: p1107NLSmyc-minusN-02_20210517


title: ROI.034.Stroma

description:
Library name: DSP-1001660011191-D-A06
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 034 | Stroma


title: G2plantp1107NLSmyc-minusN-01_20210523


title: ROI.034.Cancer Cells

description:
Library name: DSP-1001660011191-D-A05
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 034 | Cancer Cells


title: p1107NLSmyc-plusN-04_20210517


title: ROI.034.CD163

description:
Library name: DSP-1001660011191-D-A03
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 034 | CD163


title: ROI.032.CD45

description:
Library name: DSP-1001660009163-C-H07
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 032 | CD45


title: ROI.033.Stroma

description:
Library name: DSP-1001660011191-D-A02
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 033 | Stroma


title: p1107NLSmyc-plusN-02_20210517


title: No Template Control 2

description:
Library name: DSP-1001660011191-D-A01
Not shown on Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx

source_name: No Template Control

value: No Template Control


title: ROI.033.CD45

description:
Library name: DSP-1001660009163-C-H11
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 033 | CD45


title: ROI.031.Stroma

description:
Library name: DSP-1001660009163-C-H05
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 031 | Stroma


title: p1107NLSmyc-minusN-03_20210517


title: p1107NLSmyc-minusN-02_20210510


title: ROI.031.CD45

description:
Library name: DSP-1001660009163-C-H03
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 031 | CD45


title: ROI.032.Stroma

description:
Library name: DSP-1001660009163-C-H09
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 032 | Stroma


title: ROI.033.CD163

description:
Library name: DSP-1001660009163-C-H10
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 033 | CD163


title: p1107NLSmyc-minusN-01_20210517


title: ROI.032.Cancer Cells

description:
Library name: DSP-1001660009163-C-H08
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 032 | Cancer Cells


title: ROI.035.Cancer Cells

description:
Library name: DSP-1001660011191-D-A07
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 035 | Cancer Cells


title: p1107NLSmyc-plusN-02_20210510


title: ROI.033.Cancer Cells

description:
Library name: DSP-1001660009163-C-H12
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 033 | Cancer Cells


title: ROI.032.CD163

description:
Library name: DSP-1001660009163-C-H06
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 032 | CD163


title: p1107NLSmyc-minusN-01_20210510


title: p1107NLSmyc-plusN-01_20210517


title: ROI.031.Cancer Cells

description:
Library name: DSP-1001660009163-C-H04
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 031 | Cancer Cells


title: p1107NLSmyc-plusN-01_20210510


title: ROI.030.CD45

description:
Library name: DSP-1001660009163-C-G11
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 030 | CD45


title: p1107NLSmyc-plusN-03_20210510


title: p1107NLSmyc-plusN-04_20210503


title: p1107NLSmyc-plusN-03_20210503


title: ROI.030.Stroma

description:
Library name: DSP-1001660009163-C-H01
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 030 | Stroma


title: p1107NLSmyc-minusN-04_20210503


title: ROI.030.Cancer Cells

description:
Library name: DSP-1001660009163-C-G12
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 030 | Cancer Cells


title: ROI.030.CD163

description:
Library name: DSP-1001660009163-C-G10
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 030 | CD163


title: ROI.029.Stroma

description:
Library name: DSP-1001660009163-C-G09
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 029 | Stroma


title: p1107NLSmyc-plusN-02_20210503


title: ROI.029.Cancer Cells

description:
Library name: DSP-1001660009163-C-G08
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 029 | Cancer Cells


title: p1107NLSmyc-minusN-03_20210503


title: p1107NLSmyc-minusN-03_20210510


title: p1107NLSmyc-plusN-01_20210503


title: ROI.031.CD163

description:
Library name: DSP-1001660009163-C-H02
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 031 | CD163


title: ROI.029.CD45

description:
Library name: DSP-1001660009163-C-G07
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 029 | CD45


title: p1107NLSmyc-minusN-01_20210503


title: NAC109_01d042609-plusN-03


title: ROI.028.Stroma

description:
Library name: DSP-1001660009163-C-G05
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 028 | Stroma


title: ROI.029.CD163

description:
Library name: DSP-1001660009163-C-G06
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 029 | CD163


title: NAC109_01d042609-plusN-02


title: NAC109_01d042609-plusN-01


title: ROI.028.Cancer Cells

description:
Library name: DSP-1001660009163-C-G04
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 028 | Cancer Cells


title: ROI.028.CD45

description:
Library name: DSP-1001660009163-C-G03
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 028 | CD45


title: NAC109_01d042609-minusN-03


title: ROI.028.CD163

description:
Library name: DSP-1001660009163-C-G02
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 028 | CD163


title: NAC109_01d042609-minusN-02


title: NAC109_01d042609-minusN-01


title: ROI.026.Cancer Cells

description:
Library name: DSP-1001660009163-C-F12
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 026 | Cancer Cells


title: ROI.025.Stroma

description:
Library name: DSP-1001660009163-C-F11
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 025 | Stroma


title: MYBR3_01d038270-plusN-03


title: ROI.025.CD163

description:
Library name: DSP-1001660009163-C-F10
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 025 | CD163


title: MYBR3_01d038270-plusN-01


title: MYBR3_01d038270-plusN-02


title: p1107NLSmyc-minusN-02_20210503


title: ROI.023.Stroma

description:
Library name: DSP-1001660009163-C-F08
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 023 | Stroma


title: ROI.023.Cancer Cells

description:
Library name: DSP-1001660009163-C-F07
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 023 | Cancer Cells


title: MYBR3_01d038270-minusN-01


title: MYBR3_01d038270-minusN-02


title: ROI.023.CD45

description:
Library name: DSP-1001660009163-C-F06
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 023 | CD45


title: ROI.024.Stroma

description:
Library name: DSP-1001660009163-C-F09
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 024 | Stroma


title: MYB34_01d042830-plusN-03


title: ROI.023.CD163

description:
Library name: DSP-1001660009163-C-F05
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 023 | CD163


title: ROI.022.Cancer Cells

description:
Library name: DSP-1001660009163-C-F03
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 022 | Cancer Cells


title: MYB34_01d042830-plusN-01


title: ROI.022.Stroma

description:
Library name: DSP-1001660009163-C-F04
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 022 | Stroma


title: MYB34_01d042830-plusN-02


title: ROI.022.CD163

description:
Library name: DSP-1001660009163-C-F02
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 022 | CD163


title: MYB34_01d042830-minusN-01


title: HB6_01d005951-plusN-03


title: ROI.020.CD45

description:
Library name: DSP-1001660009163-C-E11
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 020 | CD45


title: ROI.020.Stroma

description:
Library name: DSP-1001660009163-C-E12
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 020 | Stroma


title: ROI.027.Stroma

description:
Library name: DSP-1001660009163-C-G01
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 027 | Stroma


title: ROI.020.CD163

description:
Library name: DSP-1001660009163-C-E10
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 020 | CD163


title: ROI.021.Cancer Cells

description:
Library name: DSP-1001660009163-C-F01
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 021 | Cancer Cells


title: HB6_01d005951-plusN-01


title: MYBR3_01d038270-minusN-03


title: ROI.019.Stroma

description:
Library name: DSP-1001660009163-C-E09
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 019 | Stroma


title: HB6_01d005951-minusN-03


title: HB6_01d005951-plusN-02


title: ROI.019.Cancer Cells

description:
Library name: DSP-1001660009163-C-E08
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 019 | Cancer Cells


title: ROI.019.CD45

description:
Library name: DSP-1001660009163-C-E07
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 019 | CD45


title: ROI.019.CD163

description:
Library name: DSP-1001660009163-C-E06
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 019 | CD163


title: bZIP9_01d046937-plusN-03


title: ROI.018.Stroma

description:
Library name: DSP-1001660009163-C-E05
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 018 | Stroma


title: bZIP9_01d046937-plusN-02


title: bZIP9_01d046937-plusN-01


title: MYB34_01d042830-minusN-03


title: ROI.018.CD45

description:
Library name: DSP-1001660009163-C-E03
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 018 | CD45


title: bZIP9_01d046937-minusN-02


title: MYB34_01d042830-minusN-02


title: ROI.018.CD163

description:
Library name: DSP-1001660009163-C-E02
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 018 | CD163


title: bZIP9_01d046937-minusN-01


title: ROI.017.Stroma

description:
Library name: DSP-1001660009163-C-E01
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 017 | Stroma


title: NAC66_01d040318-plusN-03


title: ROI.017.Cancer Cells

description:
Library name: DSP-1001660009163-C-D12
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 017 | Cancer Cells


title: ROI.017.CD45

description:
Library name: DSP-1001660009163-C-D11
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 017 | CD45


title: NAC66_01d040318-plusN-02


title: HB6_01d005951-minusN-02


title: NAC66_01d040318-minusN-03


title: ROI.017.CD163

description:
Library name: DSP-1001660009163-C-D10
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 017 | CD163


title: NAC66_01d040318-plusN-01


title: ROI.016.Cancer Cells

description:
Library name: DSP-1001660009163-C-D08
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 016 | Cancer Cells


title: ROI.016.Stroma

description:
Library name: DSP-1001660009163-C-D09
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 016 | Stroma


title: NAC66_01d040318-minusN-01


title: ROI.015.Stroma

description:
Library name: DSP-1001660009163-C-D06
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 015 | Stroma


title: HB6_01d005951-minusN-01


title: ROI.018.Cancer Cells

description:
Library name: DSP-1001660009163-C-E04
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 018 | Cancer Cells


title: ROI.015.Cancer Cells

description:
Library name: DSP-1001660009163-C-D05
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 015 | Cancer Cells


title: NAC66_01d040318-minusN-02


title: ROI.016.CD163

description:
Library name: DSP-1001660009163-C-D07
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 016 | CD163


title: MYB56_01d030678-plusN-03


title: bZIP9_01d046937-minusN-03


title: ROI.014.Stroma

description:
Library name: DSP-1001660009163-C-D03
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 014 | Stroma


title: MYB56_01d030678-minusN-03


title: MYB56_01d030678-plusN-01


title: MYB56_01d030678-minusN-02


title: ROI.013.Stroma

description:
Library name: DSP-1001660009163-C-D02
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 013 | Stroma


title: MYB56_01d030678-minusN-01


title: ROI.012.Cancer Cells

description:
Library name: DSP-1001660009163-C-C12
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 012 | Cancer Cells


title: ROI.012.Stroma

description:
Library name: DSP-1001660009163-C-D01
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 012 | Stroma


title: 5699-plusN-03


title: ROI.011.Stroma

description:
Library name: DSP-1001660009163-C-C11
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 011 | Stroma


title: 5699-plusN-02


title: 5699-plusN-01


title: ROI.011.Cancer Cells

description:
Library name: DSP-1001660009163-C-C10
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 011 | Cancer Cells


title: ROI.011.CD163

description:
Library name: DSP-1001660009163-C-C08
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 011 | CD163


title: 5699-minusN-03


title: 5699-minusN-02


title: ROI.011.CD45

description:
Library name: DSP-1001660009163-C-C09
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 011 | CD45


title: MYB56_01d030678-plusN-02


title: 5699-minusN-01


title: ROI.010.Cancer Cells

description:
Library name: DSP-1001660009163-C-C07
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 010 | Cancer Cells


title: ROI.009.CD163

description:
Library name: DSP-1001660009163-C-C03
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 009 | CD163


title: Orphan42_01d028752-plusN-01


title: ROI.009.Stroma

description:
Library name: DSP-1001660009163-C-C05
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 009 | Stroma


title: ROI.015.CD163

description:
Library name: DSP-1001660009163-C-D04
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 015 | CD163


title: Orphan42_01d028752-plusN-02


title: ROI.008.Stroma

description:
Library name: DSP-1001660009163-C-C02
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 008 | Stroma


title: ROI.009.CD45

description:
Library name: DSP-1001660009163-C-C04
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 009 | CD45


title: Orphan42_01d028752-minusN-03


title: Orphan42_01d028752-minusN-01


title: Orphan42_01d028752-minusN-02


title: G2_01d039260-plusN-03


title: ROI.008.CD45

description:
Library name: DSP-1001660009163-C-B12
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 008 | CD45


title: ROI.008.CD163

description:
Library name: DSP-1001660009163-C-B11
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 008 | CD163


title: G2_01d039260-plusN-02


title: ROI.007.Stroma

description:
Library name: DSP-1001660009163-C-B10
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 007 | Stroma


title: ROI.008.Cancer Cells

description:
Library name: DSP-1001660009163-C-C01
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 008 | Cancer Cells


title: ROI.007.Cancer Cells

description:
Library name: DSP-1001660009163-C-B09
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 007 | Cancer Cells


title: ROI.007.CD45

description:
Library name: DSP-1001660009163-C-B08
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 007 | CD45


title: ROI.010.CD163

description:
Library name: DSP-1001660009163-C-C06
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 010 | CD163


title: G2_01d039260-minusN-02


title: ROI.007.CD163

description:
Library name: DSP-1001660009163-C-B07
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 007 | CD163


title: EREB115_01d021208-plusN-03


title: ROI.006.Stroma

description:
Library name: DSP-1001660009163-C-B06
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 006 | Stroma


title: G2_01d039260-minusN-01


title: G2_01d039260-minusN-03


title: ROI.006.CD163

description:
Library name: DSP-1001660009163-C-B04
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 006 | CD163


title: Orphan42_01d028752-plusN-03


title: EREB115_01d021208-minusN-03


title: EREB115_01d021208-plusN-02


title: ROI.005.Cancer Cells

description:
Library name: DSP-1001660009163-C-B02
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 005 | Cancer Cells


title: ROI.005.Stroma

description:
Library name: DSP-1001660009163-C-B03
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 005 | Stroma


title: EREB115_01d021208-plusN-01


title: ROI.005.CD45

description:
Library name: DSP-1001660009163-C-B01
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 005 | CD45


title: ROI.006.Cancer Cells

description:
Library name: DSP-1001660009163-C-B05
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 006 | Cancer Cells


title: EREB115_01d021208-minusN-01


title: ROI.005.CD163

description:
Library name: DSP-1001660009163-C-A12
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 005 | CD163


title: G2_01d039260-plusN-01


title: G2plantG2_01d039260-plusN-04


title: G2plantG2_01d039260-plusN-03


title: EREB115_01d021208-minusN-02


title: ROI.003.Stroma

description:
Library name: DSP-1001660009163-C-A10
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 003 | Stroma


title: G2plantG2_01d039260-plusN-02


title: G2plantG2_01d039260-plusN-01


title: ROI.003.CD45

description:
Library name: DSP-1001660009163-C-A08
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 003 | CD45


title: G2plantG2_01d039260-minusN-04


title: ROI.002.Stroma

description:
Library name: DSP-1001660009163-C-A06
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 002 | Stroma


title: ROI.001.Stroma

description:
Library name: DSP-1001660009163-C-A05
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 001 | Stroma


title: G2plantG2_01d039260-minusN-03


title: G2plantG2_01d039260-minusN-01


title: ROI.001.Cancer Cells

description:
Library name: DSP-1001660009163-C-A04
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 001 | Cancer Cells


title: WRKY107_01d033965-plusN-03


title: G2plantG2_01d039260-minusN-02


title: ROI.001.CD45

description:
Library name: DSP-1001660009163-C-A03
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 001 | CD45


title: WRKY107_01d033965-plusN-01


title: ROI.001.CD163

description:
Library name: DSP-1001660009163-C-A02
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 001 | CD163


title: No Template Control 1

description:
Library name: DSP-1001660009163-C-A01
Not shown on Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx


title: ROI.004.Stroma

description:
Library name: DSP-1001660009163-C-A11
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 004 | Stroma


title: WRKY107_01d033965-minusN-03


title: WRKY107_01d033965-minusN-01


title: WRKY107_01d033965-minusN-02


title: ROI.003.Cancer Cells

description:
Library name: DSP-1001660009163-C-A09
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 003 | Cancer Cells


title: CN7

description: Library name: CN7

library_source: transcriptomic single cell

data_processing:
Cell Ranger v7.1.0 was used for gene counting.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: omental metastases

extract_protocol:
Buffer preparation: ST buffer was prepared as a 2x stock solution containing 292 mM NaCl, 20 mM Tris-HCL (pH 7.5), 2 mM CaCl2, and 42 mM MgCl2 in nuclease-free water. This served as a base for preparing ST wash buffer and TST lysis buffer. Lysis buffer (TST) was prepared by diluting the 2x ST buffer stock solution with nuclease-free water and adding the following reagents: Tween-20 (0.03% final), BSA (0.01% final) and recombinant RNAse inhibitor (final concentration: 0.25 U/µL). Nuclei isolation: Omental metastases samples were collected from seven HGSOC patients, snap frozen, and stored at -80°C. 60 to 100 mg of frozen tissue was used for each dissociation. Tissue samples were chopped in cold TST buffer using a razor blade until a homogenous pulp was obtained, followed by filtration through a 40 µm filter. The filtered nuclei solution was centrifuged at 500 g for 5 min at 4°C. The pellet was resuspended in cold ST buffer and filtered through a 20 µm sieve placed on a DNA low-bind microcentrifuge tube to remove smaller debris. The filter was rinsed with PBS-0.04% BSA and centrifuged. The nuclei were then resuspended in PBS-0.04% BSA and counted. Nuclei concentration was adjusted to 1,000 nuclei/µL by diluting with PBS-0.04% BSA. If the sample was clumpy, it was again strained through a 20 µm filter.
The isolated nuclei were loaded onto a Chromium Next GEM Chip (10X Genomics) following the manufacturer's protocol at a concentration of 10,000 cells/nuclei per well. We used the Chromium Next GEM Single Cell 5' Reagent Kits, including Single Cell V(D)J Reagent Kits v1.1 with Chip G.

value: omental metastases

value: HGSOC


title: NAC61_01d024543-plusN-03


title: WRKY107_01d033965-plusN-02


title: CN4

description: Library name: CN4


title: CN2

description: Library name: CN2


title: CN6

description: Library name: CN6


title: NAC61_01d024543-minusN-03


title: CN3

description: Library name: CN3


title: CN5

description: Library name: CN5


title: NAC61_01d024543-plusN-01


title: ROI.003.CD163

description:
Library name: DSP-1001660009163-C-A07
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 003 | CD163


title: NAC61_01d024543-plusN-02


title: NAC61_01d024543-minusN-02


title: CN1

description: Library name: CN1


title: NAC61_01d024543-minusN-01


title: Pt 45 W12 L Roflumilast

city: Aarhus

first: Hakim

last: Ben Abdallah

state: Denmark

address: Palle Juul-Jensens Boulevard 45

department: Dermatology and Venerology

country: Denmark

institute: Aarhus University Hospital

description:
Library name: 96
2x150 Sequence mode to obtain at approx. 20 million read pairs

data_processing:
R package Subread (version 2.10.3)
Raw reads were aligned to the human reference genome (GRCh38.p14 primary assembly)
Gene counts were obtained by uniquely aligned unambiguous reads
Assembly: GRCh38.14 primary assembly
Supplementary files format and content: xlsx

source_name: Skin

extract_protocol:
Total RNA was isolated using the SV 96 Total RNA Isolation System (Promega) according to the manufacturer’s instructions
RNA sequencing library was prepared with 100 ng of total RNA using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina

value: Skin


title: Pt 45 W4 L Roflumilast

description:
Library name: 95
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: Pt 45 W0 L Roflumilast

description:
Library name: 94
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: NAC5_01d005208-plusN-02


title: Pt 45 W0 NL Roflumilast

description:
Library name: 93
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: NAC5_01d005208-plusN-01


title: NAC5_01d005208-minusN-02


title: Pt 44 W12 L Placebo

description:
Library name: 92
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: Pt 44 W0 L Placebo

description:
Library name: 90
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: Pt 44 W4 L Placebo

description:
Library name: 91
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: NAC5_01d005208-minusN-01


title: NAC5_01d005208-minusN-03


title: bHLH92_01d011187-plusN-03


title: Pt 43 W4 L Roflumilast

description:
Library name: 87
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: Pt 43 W12 L Roflumilast

description:
Library name: 88
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: Pt 43 W0 NL Roflumilast

description:
Library name: 85
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: bHLH92_01d011187-minusN-03


title: bHLH92_01d011187-plusN-01


title: bHLH92_01d011187-minusN-02


title: bHLH92_01d011187-plusN-02


title: Pt 43 W0 L Roflumilast

description:
Library name: 86
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: Pt 41 W12 L Roflumilast

description:
Library name: 80
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: Pt 42 W4 L Placebo

description:
Library name: 83
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: Pt 42 W12 L Placebo

description:
Library name: 84
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: Pt 41 W0 L Roflumilast

description:
Library name: 78
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: NAC5_01d005208-plusN-03


title: WRKY36_01d049173-plusN-03


title: Pt 30 W12 L Placebo

description:
Library name: 76
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: Pt 30 W4 L Placebo

description:
Library name: 75
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: WRKY36_01d049173-plusN-02


title: WRKY36_01d049173-plusN-01


title: Pt 30 W0 L Placebo

description:
Library name: 74
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: WRKY36_01d049173-minusN-02


title: WRKY36_01d049173-minusN-03


title: Pt 27 W12 L Placebo

description:
Library name: 72
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: MYB81_01d039893-plusN-03


title: WRKY36_01d049173-minusN-01


title: Pt 27 W4 L Placebo

description:
Library name: 71
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: Pt 27 W0 L Placebo

description:
Library name: 70
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: MYB81_01d039893-plusN-01


title: Pt 27 W0 NL Placebo

description:
Library name: 69
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: MYB81_01d039893-minusN-03


title: Pt 20 W4 L Placebo

description:
Library name: 67
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: bHLH92_01d011187-minusN-01


title: MYB81_01d039893-minusN-02


title: MYB81_01d039893-minusN-01


title: Pt 20 W0 L Placebo

description:
Library name: 66
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: Pt 19 W12 L Roflumilast

description:
Library name: 64
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: MYB121_01d032694-plusN-03


title: Pt 19 W0 L Roflumilast

description:
Library name: 62
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: Pt 19 W4 L Roflumilast

description:
Library name: 63
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: Pt 19 W0 NL Roflumilast

description:
Library name: 61
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: MYB121_01d032694-plusN-02


title: Pt 13 W12 L Roflumilast

description:
Library name: 60
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: MYB121_01d032694-minusN-01


title: Pt 13 W4 L Roflumilast

description:
Library name: 59
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: bHLH47_01d029339-plusN-03


title: Pt 13 W0 L Roflumilast

description:
Library name: 58
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: MYB121_01d032694-minusN-03


title: MYB81_01d039893-plusN-02


title: bHLH47_01d029339-plusN-02


title: MYB121_01d032694-minusN-02


title: Pt 20 W12 L Placebo

description:
Library name: 68
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: bHLH47_01d029339-plusN-01


title: Pt 12 W4 L Placebo

description:
Library name: 55
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: bHLH47_01d029339-minusN-03


title: Pt 12 W12 L Placebo

description:
Library name: 56
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: Pt 12 W0 L Placebo

description:
Library name: 54
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: bHLH47_01d029339-minusN-01


title: Pt 03 W4 L Roflumilast

description:
Library name: 51
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: bHLH47_01d029339-minusN-02


title: MYB21_01d035605-plusN-03


title: Pt 12 W0 NL Placebo

description:
Library name: 53
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: Pt 03 W0 L Roflumilast

description:
Library name: 50
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: MYB21_01d035605-plusN-02


title: MYB121_01d032694-plusN-01


title: MYB21_01d035605-plusN-01


title: Pt 10 W12 L Roflumilast

description:
Library name: 48
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: Pt 10 W4 L Roflumilast

description:
Library name: 47
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: MYB21_01d035605-minusN-03


title: Pt 13 W0 NL Roflumilast

description:
Library name: 57
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: Pt 10 W0 L Roflumilast

description:
Library name: 46
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: Pt 08 W12 L Roflumilast

description:
Library name: 44
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: KN1-plusN-03


title: MYB21_01d035605-minusN-01


title: Pt 08 W0 L Roflumilast

description:
Library name: 42
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: KN1-plusN-02


title: Pt 08 W4 L Roflumilast

description:
Library name: 43
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: Pt 46 W12 L Placebo

description:
Library name: 40
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: KN1-minusN-02


title: MYB21_01d035605-minusN-02


title: Pt 46 W4 L Placebo

description:
Library name: 39
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: KN1-minusN-01


title: Pt 10 W0 NL Roflumilast

description:
Library name: 45
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: Pt 08 W0 NL Roflumilast

description:
Library name: 41
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: KN1-plusN-01


title: Pt 46 W0 L Placebo

description:
Library name: 38
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: KN1-minusN-03


title: GLK44_01d034160-plusN-02


title: Pt 46 W0 NL Placebo

description:
Library name: 37
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: Pt 40 W12 L Placebo

description:
Library name: 36
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: GLK44_01d034160-plusN-01


title: Pt 40 W4 L Placebo

description:
Library name: 35
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: GLK44_01d034160-minusN-03


title: Pt 40 W0 L Placebo

description:
Library name: 34
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: GLK44_01d034160-minusN-02


title: Pt 40 W0 NL Placebo

description:
Library name: 33
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: GLK44_01d034160-minusN-01


title: Pt 39 W4 L Roflumilast

description:
Library name: 31
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: Pt 39 W12 L Roflumilast

description:
Library name: 32
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: B4_ZmMYB38_-N_rep2


title: Pt 39 W0 L Roflumilast

description:
Library name: 30
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: B4_ZmMYB38_+N_rep3


title: Pt 39 W0 NL Roflumilast

description:
Library name: 29
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: B4_ZmMYB38_+N_rep1


title: GLK44_01d034160-plusN-03


title: Pt 38 W0 L Placebo

description:
Library name: 26
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: B4_ZmMYB38_+N_rep2


title: B4_EV_-N_rep2


title: Pt 38 W0 NL Placebo

description:
Library name: 25
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: Pt 37 W12 L Roflumilast

description:
Library name: 24
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: Pt 37 W4 L Roflumilast

description:
Library name: 23
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: B4_EV_+N_rep2


title: Pt 37 W0 L Roflumilast

description:
Library name: 22
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: Pt 37 W0 NL Roflumilast

description:
Library name: 21
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: B4_EV_-N_rep1


title: B4_EV_+N_rep3


title: B4_EV_+N_rep1


title: B2_ZmMYB38_-N_rep3


title: Pt 36 W4 L Roflumilast

description:
Library name: 19
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: Pt 36 W0 L Roflumilast

description:
Library name: 18
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: Pt 36 W0 NL Roflumilast

description:
Library name: 17
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: B2_ZmMYB38_-N_rep2


title: B2_ZmMYB38_-N_rep1


title: B2_ZmMYB38_+N_rep3


title: Pt 38 W12 L Placebo

description:
Library name: 28
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: B4_ZmMYB38_-N_rep1


title: B4_EV_-N_rep3


title: Pt 35 W12 L Roflumilast

description:
Library name: 16
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: Pt 38 W4 L Placebo

description:
Library name: 27
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: Pt 35 W0 NL Roflumilast

description:
Library name: 13
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: Pt 35 W4 L Roflumilast

description:
Library name: 15
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: Pt 35 W0 L Roflumilast

description:
Library name: 14
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: B2_EV_+N_rep3


title: B2_EV_-N_rep1


title: B2_EV_-N_rep2


title: Pt 36 W12 L Roflumilast

description:
Library name: 20
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: B2_EV_+N_rep2


title: Pt 34 W0 L Placebo

description:
Library name: 10
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: Pt 34 W4 L Placebo

description:
Library name: 11
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: Pt 34 W0 NL Placebo

description:
Library name: 9
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: MTS90mR3-noN

data_processing:
The UMI-incorporated RNA-Seq libraries were analyzed following Lexogen's guidance (https://www.lexogen.com/quantseq-3mrna-sequencing/). The reads' UMI were extracted from raw fastq ﬁles using `extract` command from UMI-tools v1.1.1. The fastq ﬁles were trimmed by fastp 0.21.0. The clean fastq ﬁles were aligned to maize genome version 4 downloaded from Ensembl Plant using STAR 2.7.6a. The identical UMI reads were deduplicated using `dedup` command from UMI-tools v1.1.1. The read counts matrix was generated by featureCounts v2.0.1 from the deduplicated bam ﬁles.
Assembly: maize genome version 4
Supplementary files format and content: tab-delimited text file includes raw count matrix for the maize root NxTime data.
Supplementary files format and content: tab-delimited text file includes quantile normalized expression matrix for the maize root NxTime data.
Supplementary files format and content: tab-delimited text file includes the output edge weight from Dynamic Factor Graph.

source_name: Ten day old seedling root

growth_protocol: On day one, seeds (B73) were soaked in sterilized water overnight. On the next day, seeds were sterilized in a glass beaker with 50% commercial bleach (CLOROX) for 20min. Then the seeds were rinsed five times with sterilized water, each time for 20mins. Six sterilized seeds were paper rolled on a double-layered, pre-rinsed 60cm x 10cm paper towel. Seeds were placed 2cm below the paper edge. The paper rolls with seeds were covered with foil paper and stored in a plastic container filled with 200ml water. Plants were checked daily. All plants were grown in the growth chamber at New York University (16h light- 8h dark, 27ºC at light-24ºC at dark cycle, 70% relative humidity). Water in each container was replaced by nitrate-free MS hydroponic medium (Caisson Labs- MSP10-50LT) on day six. On day eight, the germinated seedlings were taken out of the paper rolls and endosperms were removed with a razor blade by hand. After the removal of the endosperms, seedlings were grown in the fresh nitrate-free MS hydroponic medium. All plants were handled between 10 am and 12 pm Eastern Standard Time.

extract_protocol:
About 100 mg finely ground tissues were used for RNA extraction using the Zymo Direct-zol RNA Miniprep Kits (R2052). The RNA quality was checked on a Nanodrop and Agilent TapeStation (5067-5576).
The Lexogen QuantSeq 3' mRNA-Seq Library Prep Kit (015.2x96) with UMI (081.96) was used for the mRNA library preparation. The libraries were pooled and sequenced on the Illumina NextSeq 500 platform at NYU-CGSB Genomics Core using the HighOutput 1x75bp mode.

treatment_protocol: The seedlings were starved from nitrogen for two days. On the day of the sampling (day ten), two hours after the start of the light period (10 am), seedlings were transferred to the fresh hydroponic medium containing either the Nitrogen in MS medium (20 mM KNO3 + 20 mM NH4NO3) or 20 mM KCl and harvested at time intervals 0, 5, 10, 15, 20, 30, 45, 60, 90, and 120 minutes. Ten percent of nitrogen in the MS medium was labelled with the 15N isotope (Cambridge Isotope lab- NLM-390-1). Shoots and roots from three seedlings were combined as one biological replicate. Three biological replicates were collected per time point per treatment. They were immediately flash-frozen in liquid nitrogen and stored in an -80ºC freezer.

value: Ten day old seedling root

value: noN


title: Pt 33 W12 L Placebo

description:
Library name: 8
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: Pt 33 W4 L Placebo

description:
Library name: 7
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: MTS90mR3-N

value: N


title: MTS90mR2-N


title: MTS90mR2-noN


title: Pt 33 W0 L Placebo

description:
Library name: 6
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: Pt 34 W12 L Placebo

description:
Library name: 12
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: B2_ZmMYB38_+N_rep2


title: MTS90mR1-noN


title: B2_ZmMYB38_+N_rep1


title: Pt 32 W12 L Placebo

description:
Library name: 4
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: B2_EV_+N_rep1


title: MTS60mR3-N


title: Pt 32 W0 NL Placebo

description:
Library name: 1
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: MTS60mR2-N


title: MTS90mR1-N


title: Pt 32 W4 L Placebo

description:
Library name: 3
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: Pt 33 W0 NL Placebo

description:
Library name: 5
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: 08-175-Cetuximab-1

first: Milad

last: Ibrahim

address: 550 1st Avenue

department: Dermatology

institute: NYU Langone

data_processing:
The sequencing reads were aligned to the human genome (build hg19/GRCh37) using the splice-aware STAR aligner. PCR duplicates were removed using the Picard toolkit. The HTSeq package generated a count matrix for each annotated gene. DESeq2 was used to normalize the counts matrix and to identify differentially expressed genes using negative binomial generalized linear models.
Assembly: hg19/GRCh37
Supplementary files format and content: normalized counts

source_name: Melanoma

extract_protocol:
Total RNA was extracted and treated with DNAse using the RNeasy Plus Micro Kit (Qiagen, Cat#74034) according to the manufacturer’s instructions
Illimina TruSeq Stranded Total RNA Ribo-Zero H/M/R Gold

value: Melanoma

tag: cell line

value: patient isolated cell line xenograft

value: NF1 mutant

value: Cetuximab


title: Pt 32 W0 L Placebo

description:
Library name: 2
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: MTS60mR2-noN


title: 08-175-Cetuximab-2


title: MTS60mR1-noN


title: 08-175IgG-3

value: IgG


title: 08-175IgG-2


title: MTS60mR1-N


title: MTS5mR3-noN


title: B4_ZmMYB38_-N_rep3

value: leaf protoplast

value: minusN


title: MTS5mR3-N


title: MTS5mR2-noN


title: 08-175IgG-1


title: 07-127_shEGFR-3

value: patient isolated cell lline

value: EGFR knockdown


title: 07-127_shEGFR-2


title: MTS60mR3-noN


title: MTS5mR1-noN


title: 07-127_shEGFR-1


title: 08-175-Cetuximab-3


title: MTS45mR3-noN


title: 07-127_shScramble-2

value: Control


title: 07-127_shScramble-1


title: MTS45mR3-N


title: MTS45mR2-noN


title: 18-082

source_name: Lymph Node

value: Lymph Node

value: patient derived

value: melanoma


title: MTS45mR2-N


title: 17-073

value: NF1 wild type


title: 16-289


title: 16-304


title: MTS45mR1-N

value: Ten day old seedling root


title: 16-133

source_name: Brain

value: Brain


title: MTS45mR1-noN

value: noN


title: MTS30mR3-noN


title: MTS30mR2-noN


title: 16-036


title: 15-393

source_name: Paraspinal muscle

value: Paraspinal muscle


title: 07-127_shScramble-3

value: Melanoma


title: MTS5mR2-N

value: N


title: 14-266


title: 15-041


title: MTS30mR1-noN


title: MTS5mR1-N


title: 13-247

value: NF1 mutant


title: MTS30mR1-N


title: 13-313


title: MTS20mR3-N


title: 13-146


title: MTS20mR2-N


title: 13-045

source_name: Scalp

value: Scalp


title: 12-273BM


title: 12-273


title: MTS20mR1-noN


title: MTS20mR1-N


title: MTS30mR3-N


title: MTS15mR3-noN


title: 12-126


title: MTS30mR2-N


title: MTS15mR3-N


title: MTS15mR2-noN


title: 12-019


title: MTS20mR3-noN


title: MTS15mR2-N


title: 11-336


title: 11-001


title: MTS120mR4-noN


title: 11-211


title: 11-103


title: MTS120mR3-N


title: 11-161


title: MTS15mR1-noN


title: MTS120mR2-noN


title: MTS20mR2-noN


title: MTS15mR1-N


title: MTS120mR3-noN


title: 10-230BM


title: 10-230

source_name: Parotid Gland

value: Parotid Gland


title: MTS120mR2-N


title: 12-108


title: 09-135


title: 09-203


title: MTS120mR1-N


title: 12-215


title: MTS120mR1-noN


title: 09-085


title: MTS10mR3-N


title: MTS10mR3-noN


title: MTS10mR2-noN


title: MTS10mR2-N


title: 07-127

source_name: Subcutaneous

value: Subcutaneous


title: MTS10mR1-noN


title: Sk-Mel-28-H3K4ME3-shNF1-3

library_source: genomic

data_processing:
Sequencing results were demultiplexed and converted to FASTQ format using Illumina bcl2fastq software. Reads were aligned to the human genome (build hg19/GRCh37) with Bowtie 2  using local alignment. Only confidently mapped reads (mapping quality >20) were retained. Duplicate reads were discarded using Picard. MACS  was utilized to perform broad peak calling without modelling, a q-value cutoff of 0.05 and --shift -37 and --extsize 73
Assembly: hg19/GRCh37
Supplementary files format and content: Bigwig files
Library strategy: CUT&RUN

molecule: genomic DNA

extract_protocol:
100K cells were counted, resuspended in  wash buffer at room temperature, and added to activated ConA beads. Next, anti-H3K4Me3 (Cell Signaling Technology, 9751) antibody was added at a final 1:50 dilution. Antibodies and permeabilized cells were incubated overnight at 4°C. Next, pAG-MNase was added, and the mixture was incubated for 10 minutes at room temperature, followed by 2 hours on a nutator at 4°C. Stop master mix was added, and samples were incubated at 37 ̊C for 10 minutes before CUT&RUN-enriched DNA fragments were purified with the Qiagen MinElute PCR purification kit (28006). DNA extractions were quantified using Qubit (Invitrogen).
DNA-Seq library preps were constructed using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina kit (E7103) and amplified for 15 cycles.


title: 08-175


title: Sk-Mel-28-H3K4ME3-shNF1-2


title: MTS0mR3-noN


title: MTS0mR2-noN


title: Sk-Mel-28-H3k4ME3-shScramble-3


title: 10-040


title: Sk-Mel-28-H3K4ME3-shNF1-1


title: MTS0mR1-noN


title: 18-082-H3K4Me3


title: Sk-Mel-28-H3k4ME3-shScramble-2


title: MTS90mS3-N

data_processing:
The UMI-incorporated RNA-Seq libraries were analyzed following Lexogen's guidance (https://www.lexogen.com/quantseq-3mrna-sequencing/). The reads' UMI were extracted from raw fastq ﬁles using `extract` command from UMI-tools v1.1.1. The fastq ﬁles were trimmed by fastp 0.21.0. The clean fastq ﬁles were aligned to maize genome version 4 downloaded from Ensembl Plant using STAR 2.7.6a. The identical UMI reads were deduplicated using `dedup` command from UMI-tools v1.1.1. The read counts matrix was generated by featureCounts v2.0.1 from the deduplicated bam ﬁles.
Assembly: maize genome version 4
Supplementary files format and content: tab-delimited text file includes raw count matrix for the maize shoot NxTime data.
Supplementary files format and content: tab-delimited text file includes quantile normalized expression matrix for the maize shoot NxTime data.
Supplementary files format and content: tab-delimited text file includes the output edge weight from Dynamic Factor Graph.

source_name: Ten day old seedling shoot

value: Ten day old seedling shoot


title: MTS90mS2-noN


title: 16-304-H3K4Me3


title: MTS90mS2-N


title: 16-133-H3K4Me3


title: 16-289-H3K4Me3


title: Sk-Mel-28-H3k4ME3-shScramble-1


title: MTS60mS3-noN


title: 15-041-H3K4Me3


title: MTS90mS1-N


title: MTS10mR1-N


title: 13-247-H3K4Me3


title: MTS60mS3-N


title: 14-266-H3K4Me3


title: 16-036-H3K4Me3


title: 13-313-H3K4Me3


title: MTS60mS2-N


title: MTS90mS1-noN


title: 13-045-H3K4Me3


title: 17-073-H3K4Me3


title: MTS60mS1-N


title: MTS90mS3-noN


title: 12-215-H3K4Me3


title: 12-273BM-H3K4Me3


title: MTS5mS3-noN


title: MTS5mS3-N


title: MTS5mS2-noN


title: 12-126-H3K4Me3


title: MTS5mS2-N


title: 12-019-H3K4Me3


title: 12-108-H3K4Me3


title: 11-336-H3K4Me3


title: MTS60mS2-noN


title: MTS5mS1-noN


title: MTS5mS1-N


title: 11-161-H3K4Me3


title: MTS45mS3-noN


title: 11-211-H3K4Me3


title: 11-001-H3K4Me3


title: MTS60mS1-noN


title: MTS45mS2-noN


title: MTS45mS3-N


title: 11-103-H3K4Me3


title: 10-230BM-H3K4Me3


title: MTS45mS1-noN


title: 10-040-H3K4Me3


title: MTS45mS2-N


title: 10-230-H3K4Me3


title: MTS30mS3-noN


title: 09-203-H3K4Me3


title: MTS45mS1-N


title: 09-135-H3K4Me3


title: MTS30mS2-noN


title: MTS30mS2-N


title: MTS30mS3-N


title: 09-085-H3K4Me3


title: 08-175-H3K4Me3


title: 07-127-H3K4Me3


title: MTS30mS1-noN


title: MTS30mS1-N


title: 18-082-H3K27Ac

extract_protocol:
100K cells were counted, resuspended in  wash buffer at room temperature, and added to activated ConA beads. Next, , anti-H3K27Ac (Cell Signaling Technology, 8173)  antibody was added at a final 1:50 dilution. Antibodies and permeabilized cells were incubated overnight at 4°C. Next, pAG-MNase was added, and the mixture was incubated for 10 minutes at room temperature, followed by 2 hours on a nutator at 4°C. Stop master mix was added, and samples were incubated at 37 ̊C for 10 minutes before CUT&RUN-enriched DNA fragments were purified with the Qiagen MinElute PCR purification kit (28006). DNA extractions were quantified using Qubit (Invitrogen).
DNA-Seq library preps were constructed using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina kit (E7103) and amplified for 15 cycles.


title: MTS20mS3-noN


title: 17-073-H3K27Ac


title: MTS20mS2-N


title: MTS20mS3-N


title: 16-304-H3K27Ac


title: MTS20mS2-noN


title: MTS20mS1-N


title: MTS15mS3-noN


title: MTS20mS1-noN


title: 16-036-H3K27Ac


title: 16-133-H3K27Ac


title: 14-266-H3K27Ac


title: 13-247-H3K27Ac


title: 16-289-H3K27Ac


title: 13-045-H3K27Ac


title: 15-041-H3K27Ac


title: MTS15mS1-noN


title: MTS15mS2-N


title: MTS15mS3-N


title: 12-108-H3K27Ac


title: 12-215-H3K27Ac


title: MTS15mS1-N


title: 12-019-H3K27Ac


title: MTS120mS2-noN


title: 12-126-H3K27Ac


title: MTS120mS2-N


title: MTS120mS3-noN


title: 11-211-H3K27Ac


title: 11-336-H3K27Ac


title: MTS120mS1-noN


title: MTS10mS3-noN


title: 11-161-H3K27Ac


title: 11-103-H3K27Ac


title: MTS120mS1-N


title: 11-001-H3K27Ac


title: MTS15mS2-noN


title: 12-273BM-H3K27Ac


title: 10-230BM-H3K27Ac


title: 10-040-H3K27Ac


title: MTS10mS1-noN


title: MTS10mS2-noN


title: MTS10mS2-N


title: MTS10mS1-N


title: 09-203-H3K27Ac


title: 09-085-H3K27Ac


title: 08-175-H3K27Ac


title: MTS0mS1


title: MTS0mS2


title: MTS120mS3-N


title: 07-127-H3K27Ac


title: MTS0mS3


title: KN1 protoplast input

description: maize KN1 protoplast input sample

data_processing:
The sequenced raw fastq reads were trimmed by fastp 0.21.0. Clean reads were aligned to the maize genome version 4 downloaded from Ensembl Plant using bowtie 2.4.2 with default parameters. Aligned reads with MAPQ values smaller than 10 were discarded using samtools 1.11.
The peaks were called using macs2.2.7.1 with non-ChIP DNA as control.
Assembly: maize genome version 4
Supplementary files format and content: tab-delimited text file include KN1 binding peaks and their distance to the closest genes.

source_name: Protoplast

growth_protocol: The maize seeds were soaked overnight and planted in pots filled with Turface MVP. The pots were placed at the growth chamber, under 16 h light/8 h dark diurnal cycle, at temperatures 27 and 24°C respectively and 70% humidity for three days. After seeds were germinated and about 5cm above ground, the pots were moved to the dark room at temperature 27°C and 70% humidity for etiolation for seven days.

extract_protocol:
The isolated protoplasts were transfected by p1107-KN1 plasmid. We performed BLRP-ChIP-Seq on the cells.
DNA was purified using the ChIP DNA Clean & Concentrator™ kit (Zymo D5205). DNA concentration was measured using Qubit. The cells were incubated in dark overnight. We used NEBNext® Ultra™ II DNA Library Prep Kit (NEB E7645S) for sequencing libraries. The libraries were sequenced on the Illumina NextSeq 500 platform at NYU-CGSB Genomics Core using the HighOutput 1x75bp mode.

value: Protoplast

value: Leaf protoplast


title: KN1 protoplast ChIP

description: maize KN1 protoplast ChIP sample


title: 17-073-ATAC

data_processing:
Sequencing results were demultiplexed and converted to FASTQ format using Illumina bcl2fastq software. Reads were aligned to the human genome (build hg19/GRCh37) with Bowtie 2  using local alignment. Only confidently mapped reads (mapping quality >20) were retained. Duplicate reads were discarded using Picard. MACS  was utilized to perform broad peak calling without modelling, a q-value cutoff of 0.05 and --shift -37 and --extsize 73
Assembly: hg19/GRCh37
Supplementary files format and content: Bigwig files

extract_protocol:
200K cells were collected, washed once with cold PBS, and pelleted by centrifugation for 5min at 4°C. Cell pellets were re-suspended in 50μl of lysis buffer per 50,000 cells processed (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% Igepal CA-630), and nuclei were pelleted by centrifugation for 25min with 500 g at 4°C using a swing-out rotor with low acceleration and brake settings. Nuclei were re-suspended in 25ul of cold sterile water and added to a PCR strip tube along with 25ul of Illumina tagmentation buffer and 2.5ul of Illumina tagmentation enzyme (Illumina, cat# 20034198) per reaction. The sample was tagmented for 30 mins @ 37˚C. then cleaned using a Qiagen minelute cleanup column kit (cat # 28206)
The cleaned DNA was input into PCR using NEB High-Fidelity PCR 2X Master Mix (25ul), 2.5ul of universal primer @ 25uM concentration, and 2.5ul of a unique index primer @25uM concentration per sample. Both the universal and unique index primers (24 unique primers total) were ordered from IDT. The samples underwent 10-11 total cycles of PCR amplification then cleaned with Ampure XP beads (45ul, 0.9x ratio) to remove excess primer dimer from the final library

value: Lymph Node


title: KO ESC ATAC-seq_r2

city: Shanghai

first: Xinyu

last: Wang

address: Siping Road 1239

country: China

institute: Tongji University

description:
Library name: Sample14
KO ESC ATAC-seq replicate2

data_processing:
RNA-seq: For raw paired-end RNA-seq reads, trim_galore v0.4.5 was used to remove low-quality bases and adapter sequences. HISAT2 was used to align the clean sequence data to the mouse reference genome (mm10). StringTie was used to quantify gene expression from the aligned sequences for each gene, and htseq-count was used to count reads number for each gene. The mouse gene annotation file was obtained from the mouse GENCODE release (GRCm38.99). ULI-MNase-seq: For raw paired-end MNase-seq reads, trim_galore v0.4.5 was used to remove low-quality bases and adapter sequences. Clean MNase-seq reads were aligned to the mouse reference genome (mm10) using the bwa v0.7.12 mem command. Reads with a mapping quality (MAPQ) less than 10 was removed for downstream analysis. To create nucleosome profiles, the aligned paired-end reads was extended to 146bp length based on each read center. All the nucleosome profiles was scaled to 500 million reads in total. ATAC-seq: For raw paired-end ATAC-seq reads, trim_galore v0.4.5 was used to remove low-quality bases and adapter sequences. The clean sequence data were aligned to the mouse reference genome (mm10) using bowtie2 v2.3.5. For downstream analysis, the read counts were normalized based on the numbers of reads per kilobase of bin per million reads (RPKM).
Assembly: mm10
Supplementary files format and content: MNase signal file, gene expression quantification file and ATAC signal file

organism: Mus musculus

source_name: mouse ESC

growth_protocol: Specific pathogen-free (SPF) mice were housed in the animal facility at Tongji University,Shanghai, China, and they were fed a standard diet. The temperature and light were strictly controlled (24 °C; 12 h light and 12 h dark). Smarca4flox/flox mice are from previous study(Qi et al. 2021). All animal experiments were performed in accordance with the University of Health Guide for the Care and Use of Laboratory Animals and were approved by the Biological Research Ethics Committee of Tongji University. To get MII oocytes for ICSI, B6D2F1 or Smarca4flox/flox Gdf9 Cre C57BL/6 female mice (8–12-weeks old) were superovulated by injection with 7 IU each of pregnant mare serum gonadotropin (PMSG), followed by injection of 5 IU of human chorionic gonadotropin (hCG) (San-Sheng Pharmaceutical) 48 h later.

extract_protocol:
Brg1 knockout R1 ES cell lines are generated by CRISPR-Cas9 technology targeting the exon 4 & 5 of Smarca4. All cell lines have been regularly tested negatively for mycoplasm contamination and were cultured on mitomycin C-treated mouse embryonic fibroblasts in ES medium containing DMEM (Merck Millipore) supplemented with 15% (v/v) FBS (Hyclone), 1 mM l-glutamine (Merck Millipore), 0.1 mM mercaptoethanol (Merck Millipore), 1% non-essential amino acid stock (Merck Millipore), penicillin/streptomycin (100×, Merck Millipore), nucleosides (100×, Merck Millipore) and 1,000 U ml–1 leukaemia inhibitory factor (Merck Millipore).
For mESCs, the sequencing libraries were prepared using KAPA Stranded RNA-Seq Kit with RiboErase(Kapa Biosystems, KK8483) and KAPA HyperPrep Kit for the Illumina platform (Roche, kk8504) following manufacturer’s protocol. Paired-end sequencing with 150-bp read length was performed on the HiSeq X Ten (Illumina) platform.

value: mouse ESC

value: Smarca4 KO


title: 16-289-ATAC

value: patient derived

value: melanoma

value: NF1 wild type


title: 16-304-ATAC


title: WT ESC ATAC-seq_r2

description:
Library name: Sample12
WT ESC ATAC-seq replicate2

value: wild type


title: 16-133-ATAC

value: Brain


title: WT ESC ATAC-seq_r1

description:
Library name: Sample11
WT ESC ATAC-seq replicate1


title: KO ESC ATAC-seq_r1

description:
Library name: Sample13
KO ESC ATAC-seq replicate1


title: 10-230-H3K27Ac


title: 15-041-ATAC


title: 16-036-ATAC


title: 14-266-ATAC


title: 15-393-ATAC

value: Paraspinal muscle


title: 09-135-H3K27Ac


title: KO ESC RNA-seq_r1

description:
Library name: Sample8
KO ESC RNA-seq replicate1


title: KO ESC RNA-seq_r2

description:
Library name: Sample9
KO ESC RNA-seq replicate2


title: WT ESC RNA-seq_r1

description:
Library name: Sample5
WT ESC RNA-seq replicate1


title: WT ESC RNA-seq_r2

description:
Library name: Sample6
WT ESC RNA-seq replicate2


title: 13-247-ATAC


title: KO ESC ULI-MNase-seq_r1

description:
Library name: Sample3
KO ESC ULI-MNase-seq replicate1


title: 13-045-ATAC


title: WT ESC ULI-MNase-seq_r2

description:
Library name: Sample2
WT ESC ULI-MNase-seq replicate2


title: WT ESC ULI-MNase-seq_r1

description:
Library name: Sample1
WT ESC ULI-MNase-seq replicate1


title: 13-313-ATAC


title: 12-215-ATAC


title: 13-146-ATAC


title: KO ESC ULI-MNase-seq_r2

description:
Library name: Sample4
KO ESC ULI-MNase-seq replicate2


title: 12-273BM-ATAC


title: 12-108-ATAC


title: yYY520, DSB, biol rep1

city: Boston

first: Kaifu

last: Chen

address: 300 Longwood Ave

department: Cardiology

institute: Boston Children's Hospital

description: Library name: yYY520 biol rep 1 exp1

data_processing:
Large insertion detection: https://github.com/gucascau/iDSBins.git
Large insertion feature: https://github.com/gucascau/LargeInsertionFeature.git
Assembly: saccharomyces_cerevisiae_R64-2-1_20150113
Supplementary files format and content: BED file that contain the single donor.  Each column represents : "Donor  Chromosome",  "Donor Start","Donor End", " CaseID", "Score", "Donor Strand ", and  "Representative Read"
Supplementary files format and content: BED file for poly insertions.  Each column represents : "Donor  Chromosome",  "Donor Start","Donor End", " CaseID", "Score", "Donor Strand ", and  "Representative Read"

organism: Saccharomyces cerevisiae

source_name: mutant isogenic to JKM139

extract_protocol:
All colonies on YP-galactose plates were collected, combined, and mixed vigorously. Approximately 80 μL cells were spun down for isolating genomic DNA. Standard glass beads-phenol/chloroform/isoamyl alcohol (25:24:1) method. The DNA was dissolved in water and adjusted to a concentration of 10 ng/μL. The construction of the amplicon sequencing library was adapted from Illumina’s protocol #15044223 Rev. B. Briefly, the sequencing libraries were constructed with two rounds of PCR using KAPA HiFi HotStart ReadyMix polymerase (Roche, 7958927001). For the first round of PCR, 3.2 μL genomic DNA and 0.5 μL 10 μM primers were used for a total volume of 25 μL. The forward and reverse primers targeting the MATa locus are located 11 bp upstream or 18 bp downstream of the HO cleavage site respectively, containing Illumina adapter sequence and 3 bases unique home index as described (7). The thermocycling conditions were: 95 °C for 5 min; 22 cycles of 98 °C for 20 s, 65 °C for 30 s, 72 °C for 3 min; 72 °C for 10 min. After the first round of PCR, 18μL PCR product was purified with an equal volume of AMPure XP beads (Beckman Coulter, A63880). The DNA was eluted with 52.5 μL of 10 mM Tris (pH 8.5) and used as the templates for the second round of PCR. For the second round of PCR, 5 μl template DNA, 5 μL index primer N7xx and 5 μL index primer S5xx from Nextera XT V2 Index kit (Illumina, FC-131-2001) were used for the total volume of 50 μL. The following conditions were used for the second round of PCR: 95 °C for 5 min; 8 cycles of 95 °C for 30 s, 55 °C for 30 s, 72 °C for 3 min; 72 °C for 10 min. Then, the PCR product was purified with 1.2x volume of AMPure XP beads and eluted with 10 mM Tris pH 8.5. The average size of each sample was measured with TapeStation and the DNA concentration was measured with Qubit dsDNA BR Assay Kit (ThermoFisher, Q32850)
The DNA was diluted to a concentration of 4 nM. An equal volume of DNA from ~20 samples was pooled into the library. The 0.2 M NaOH was used to denature the pooled library and PhiX library (Illumina, FC‐110‐3001). After diluting the libraries with pre-chilled HT1 to 12 pM, pooled library and PhiX library were mixed with the ratio 9:1, further denatured by incubating at 96 °C for 2 min and immediately put in an ice-water bath for 5 min

value: mutant isogenic to JKM139


title: JL195, DSB, 0.5mMmM H2O2 4hr, rep1 exp1

description: Library name: JL195 biol rep1 exp1

value: mgm1 + H2O2

value: 0.5mM hydrogen peroxide 4hr


title: 12-273-ATAC


title: 12-126-ATAC


title: JL179, DSB, 0.5mMmM H2O2 4hr, rep1 exp2

description: Library name: JL179 biol rep1 exp2

value: grx5 + H2O2


title: 11-211-ATAC

value: NF1 mutant


title: YY532, DSB, 0.5mMmM H2O2 4hr, rep1 exp2

description: Library name: YY532 biol rep 1 exp2

value: WT (respiration deficient) + H2O2


title: JKM139, DSB, 0.5mMmM H2O2 4hr, rep1 exp13

description: Library name: JKM139 biol rep1 exp13

value: WT + H2O2


title: MTS10mS3-N

value: Ten day old seedling shoot

value: N


title: ZZ414, DSB, 0.5mM H2O2 4hr, biol rep1

description: Library name: ZZ414 biol rep1

value: mec1 tel1 sml1 + H2O2


title: YY466, DSB, 0.5mM H2O2 4hr, biol rep1

description: Library name: YY466 biol rep1

value: rad51 + H2O2


title: yYY520 biol rep1

description: Library name: yYY520 biol rep1


title: PKT182, DSB, , biol rep1

description: Library name: PKT182 biol rep1


title: 10-230BM-ATAC

value: patient derived


title: PKT180, DSB, , biol rep1

description: Library name: PKT180 biol rep1


title: 11-161-ATAC

value: melanoma


title: 10-230-ATAC

value: Parotid Gland

value: NF1 wild type


title: 11-001-ATAC

value: Brain


title: PKT179, DSB, , biol rep1

description: Library name: PKT179 biol rep1


title: 10-040-ATAC

value: Lymph Node


title: 09-203-ATAC


title: JL307, DSB, , biol rep5

description: Library name: JL307 biol rep1

value: mutant isogenic to JKM139


title: JL306, DSB, , biol rep4

description: Library name: JL306 biol rep1

value: ntg1 ntg2 mgm1


title: 09-085-ATAC


title: JL296, DSB, , biol rep2

description: Library name: JL296 biol rep1

value: apn1 mgm1


title: 12-019-ATAC


title: 09-135-ATAC


title: JL295, DSB, , biol rep1

description: Library name: JL295 biol rep1

value: apn2 mgm1


title: JL230, DSB, YPD 0.5mM auxin ON, biol rep1

description: Library name: JL230 biol rep1

value: NAR1-AID + YPD + auxin

value: Growth in YPD and 0.5mM auxin overnight


title: JL292, DSB, , biol rep1

description: Library name: JL292 biol rep1


title: JL19, DSB, 500mM CPT 6hr, biol rep1

description: Library name: JL19 biol rep1 exp15

value: mgm1 + CPT

value: 500mM CPT 6hr


title: 07-127-ATAC

value: Subcutaneous

value: NF1 mutant


title: MEF2C-/- (KO) iMGLs, treated with 5 μM BMS, in the presence  of 100 ng/mL LPS for 12 hours, rep3

city: Beijing

first: Lu

last: Shi

address: Shuangqing road

department: School of Pharmaceutical Sciences

institute: Tsinghua University

data_processing:
Illumina Casava1.7 software used for basecalling.
TrimGalore software (with Cutadapt v0.6.10) was employed to trim adaptor. The alignment to the hg38 reference genome was performed using hisat2 (v2.2.1) with default parameters. The gene expression count matrix were generated by featureCounts (v2.0.6) using hg38 RefSeq gene annotation obtained from UCSC table browser. To allow the comparison of gene expression profiles, the normalized expression values for each transcript were calculated as Fragments Per Kilobase per Million mapped reads (FPKM)
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: iMGLs

growth_protocol: iMGLs differentiation base medium was prepared using DMEM/F12 (Thermo Fisher Scientific, 11320033), supplemented with 2% ITS-G (Thermo Fisher Scientific, 41400045), 2% B27 (Thermo Fisher Scientific, 17504044), 0.5% N2 (Thermo Fisher Scientific, 17502048), 200 μM monothioglycerol, 1×Glutamax, 1×NEAA, and 5 mg/mL insulin. iMGLs were cultured in iMGLs differentiation base medium supplemented with 25 ng/mL MCSF, 100 ng/mL IL-34, 50 ng/mL TGFβ1, 100 ng/mL CD200 (R&D Systems, 2724-CD-050), and 100 ng/mL CX3CL1 (Peprotech, 300-31).

extract_protocol:
total RNAs were extracted using TRIzol reagent according to the manufacturer’s instruction.
RNA libraries were prepared for sequencing using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, E7530) according to the manufacturer’s instruction

treatment_protocol: iMGLs treated with or without 5 μM BMS, in the presence or absence of 100 ng/mL LPS for 12 hours

value: iMGLs

value: microglia

value: MEF2C knockout

value: Treated 100 ng/mL LPS and 5 μM BMS for 12 h


title: JL19, DSB, 500mM HU 6hr, biol rep1

description: Library name: JL19 biol rep1 exp16

value: mgm1 + HU

value: 500mM CPT 6 hr


title: MEF2C-/- (KO) iMGLs, treated with 5 μM BMS, in the presence  of 100 ng/mL LPS for 12 hours, rep2


title: MEF2C-/- (KO) iMGLs, treated with DMSO, in the presence  of 100 ng/mL LPS for 12 hours, rep3

value: Treated 100 ng/mL LPS for 12 h


title: JKM139, DSB, 500mM HU 6hr, biol rep1

description: Library name: JKM139 biol rep2

value: mutant isogenic to JKM139

value: WT + HU

value: 500mM HU 6hr


title: JKM139, DSB, 500mM CPT 6hr, biol rep1

description: Library name: JKM139 biol rep1

value: WT + CPT


title: MEF2C-/- (KO) iMGLs, treated with DMSO, in the presence  of 100 ng/mL LPS for 12 hours, rep1


title: yYY515, DSB, biol rep1

description: Library name: yYY515 biol rep1


title: MEF2C-/- (KO) iMGLs, treated with DMSO for 12 hours, rep2

value: Normal condition


title: yYY363, DSB, biol rep2

description: Library name: yYY363 biol rep2


title: JL298, DSB, , biol rep3

description: Library name: JL298 biol rep1

value: ntg1 ntg2


title: 08-175-ATAC

value: patient derived

value: melanoma


title: yYY363, DSB, biol rep1

description: Library name: yYY363 biol rep1


title: WT iMGLs, treated with DMSO, in the presence  of 100 ng/mL LPS for 12 hours, rep2

value: wild type


title: WT iMGLs, treated with DMSO, in the presence  of 100 ng/mL LPS for 12 hours, rep3


title: WT iMGLs, treated with DMSO for 12 hours, rep3


title: JL77, DSB, biol rep1

description: Library name: JL77 biol rep1


title: JL71, DSB, biol rep2

description: Library name: JL71B biol rep2

value: dnm1 mgm1


title: WT iMGLs, treated with DMSO, in the presence  of 100 ng/mL LPS for 12 hours, rep1

value: iMGLs


title: WT iMGLs, treated with DMSO for 12 hours, rep2

value: microglia


title: MEF2C-/- (KO) iMGLs, treated with 5 μM BMS, in the presence  of 100 ng/mL LPS for 12 hours, rep1

value: MEF2C knockout


title: JL71, DSB, biol rep1

description: Library name: JL71B biol rep1


title: JL70, DSB, biol rep2

description: Library name: JL70 biol rep2


title: JL77, DSB, biol rep2

description: Library name: JL77 biol rep2


title: S24-KinprolaPKA_low_Rep3

city: Heidelberg

first: Deen

last: Sun

address: Jahnstrasse 29

department: Chemical Biology

country: Germany

institute: Max Planck Institute for Medical Research

data_processing:
The RNA sequencing data was aligned against human genome GRCh38 by STAR (v.2.5.3a)
The reads mapped to multiple loci were filtered
The gene counts were quantified against GENCODE annotation (v.32) by the featureCounts function from Subread (v.1.5.3) with default setting
Assembly: Human genome GRCh38
Supplementary files format and content: Tab-delimited text files include log2(FPKM) values for each Sample

extract_protocol:
RNA was harvested using Arcturus PicoPure Kit (Thermo Fisher).
Takara SMARTer Ultra-low RNA HV Kit was used for RNA conversion. NEBNext® Multiplex Oligos for Illumina® and NEB Next High Fidelity Master Mix were used for RNA Library Prep following manufacturer's protocols.

value: Patient derived glioblastoma cell line

value: KinprolaPKA


title: WT iMGLs, treated with DMSO for 12 hours, rep1


title: S24-KinprolaPKA_medium_Rep3


title: JL70, DSB, biol rep1

description: Library name: JL70 biol rep1


title: NH18-1406

city: Utrecht

first: Cristian

last: Ruiz-Moreno

state: Utrecht

address: 25 Heidelberglaan

country: Netherlands

institute: Prinses Máxima Centrum

data_processing:
CellRanger v3.1.0 (10X Genomics) toolkit was used for demultiplexing BCL into FASTQ. Alignment was performed to the reference human genome GRCh38 with default parameters to obtain the filtered gene count matrix.
Quality control, data normalization, dimensional reduction, clustering, and differential gene expression analyses were performed using Seurat (v4.0) and Scanpy (v1.8.2).
Refference mapping was performed using the Azimuth algorithm part of the Seurat package.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files that contain the gene expression level (UMI) of each individual cell

extract_protocol:
Nuclei were isolated using an NP40 with salts/tris based lysis buffer. Single-nuclei partition into GEMs was performed using the Chromium Controller and 10x Genomics reagents.
Single Cell Gene Expression 3’ v3 (10X Genomics)

tag: sample preservation

value: Snap-frozen

tag: sample preparation

value: Nuclei

value: Primary tumor

tag: diagnosis

value: IDH-wildtype glioblastoma

tag: gender

value: male

tag: age


title: MEF2C-/- (KO) iMGLs, treated with DMSO, in the presence  of 100 ng/mL LPS for 12 hours, rep2

value: Treated 100 ng/mL LPS for 12 h


title: yYY515, DSB, biol rep2

description: Library name: yYY515 biol rep2

value: mutant isogenic to JKM139


title: JL19B, DSB, biol rep2

description: Library name: JL19B biol rep2


title: MEF2C-/- (KO) iMGLs, treated with DMSO for 12 hours, rep1

value: Normal condition


title: NH19-123


title: S24-KinprolaPKA_high_Rep3


title: JL179A, DSB, biol rep1

description: Library name: JL179A biol rep1


title: NH19-565

value: female


title: NH17-2069


title: JL19B, DSB, biol rep1

description: Library name: JL19B biol rep1


title: MEF2C-/- (KO) iMGLs, treated with DMSO for 12 hours, rep3


title: S24-KinprolaPKA_low_Rep2


title: NH17-1258


title: NH17-1245


title: JL169A, DSB, biol rep1

description: Library name: JL169A biol rep1


title: NH17-1953


title: 11-103-ATAC

value: Brain

value: patient derived

value: melanoma

value: NF1 mutant


title: NH17-161


title: S24-KinprolaPKA_medium_Rep2


title: NH17-442

value: missing


title: JL120, DSB, biol rep2

description: Library name: JL120 biol rep2


title: JL132A, DSB, biol rep1

description: Library name: JL132A biol rep1


title: S24-KinprolaPKA_high_Rep2


title: NH16-2366


title: CD4-TCell_LCMV_CMO

city: Chapel Hill

first: Matthew

last: Niederhuber

state: NC

address: 250 Bell Tower Dr.

institute: UNC-Chapel Hill

data_processing:
cellranger (v8.0.0) multi used to demultiplex and get per sample outputs (barcodes.tsv, features.tsv, matrix.mtx)
Assembly: mm39
Supplementary files format and content: cellranger multi per sample output: {sample}_barcodes.tsv.gz, {sample}_features.tsv.gz, {sample}_matrix.mtx.gz

source_name: Spleen

extract_protocol:
Single cell suspension of splenocytes was obtained by mechanical disruption of spleen from infected mice with a syringe plunger over a 70um filter. CD4 T-cells were enriched by negative selection using biotinylated antibodies against CD8, B220, and TER-119 and Mojosort Streptavidin Nanobeads according to the manufacturers instructions (Biolegend). CD4 enriched cells were stained for 30 minutes at 4C with fixable viability dye (Tonbo)  n dPBS, 1 hour at 37C with I-Ab GP66-77 tetramer in 10% RPMI, and 30 mins at 4C with antibodies against CD4, PD1, and TotalSeqB (Biolegend) in FACS buffer (dPBS  + 1% BSA/  + 0.12% Sodium Azide). Virus-specific CD4 T-cells were FACS sorted on a Sony SH800z by expression of CD4 and GP66 tetramer. Sorted cells from each sample were combined in roughly equal numbers
Chromium GEM-X Single Cell 3' Kit v4 according to the manufacturers instructions (10x)

value: mixed (B6.LckCre x KMT2Dfl/fl, B6.LckCre Control)

value: 10-14 weeks

value: Spleen

value: CD4+ T-cell

tag: library type

value: CMO


title: NH17-2680

value: Snap-frozen

value: Nuclei

tag: tissue

value: Primary tumor


title: JL120, DSB, biol rep1

description: Library name: JL120 biol rep1

tag: cell type


title: S24-KinprolaPKA_medium_Rep1

value: Patient derived glioblastoma cell line

value: KinprolaPKA

tag: treatment


title: S24-Kinprolaon_low_Rep3

value: Kinprolaon


title: JL119, DSB, biol rep2

description: Library name: JL119 biol rep2

value: mutant isogenic to JKM139


title: S24-Kinprolaon_medium_Rep3


title: S24-KinprolaPKA_high_Rep1


title: CD4-TCell_LCMV_GEX

value: mRNA


title: JL272, DSB, biol rep2

description: Library name: JL272 biol rep2


title: JL119, DSB, biol rep1

description: Library name: JL119 biol rep1


title: S24-Kinprolaon_high_Rep2


title: JL105, DSB, biol rep1

description: Library name: JL105 biol rep1


title: JL272Fe, DSB, 3mM Fe 6hr, biol rep1

description: Library name: JL272Fe biol rep1

value: 3mM Fe 6hr


title: JL272Fe, DSB, 3mM Fe 6hr, biol rep2

description: Library name: JL272Fe biol rep2


title: JL272, DSB, biol rep1

description: Library name: JL272 biol rep1


title: dia2, DSB, biol rep2

description: Library name: dia2 biol rep2


title: dia2, DSB, biol rep1

description: Library name: dia2 biol rep1


title: Muscle, Aged, biol rep5, ATAC

city: Shatin, NT

first: CHUHAN

last: LI

state: shatin

address: The Chinese University of Hong Kong, Central Ave

country: Hong Kong

institute: CUHK

description:
10x Genomics
Aged_5_barcodes.tsv.gz
Aged_5_features.tsv.gz
Aged_5_matrix.mtx.gz

data_processing:
Cell Ranger ARC v2.0.1 count functions to aggregate reads across sequencing lanes into a single set of barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz
Subsequently, the processed matices were read in by Seurat 5.0.1 and Signac 1.12.0 for following analysis.
Assembly: hg38
Supplementary files format and content: CellRanger ARC output files: Tab-separated values files and matrix files
Library strategy: single-cell multiome (RNA+ATAC)

source_name: hamstring muscle

extract_protocol:
Whole live muscle mononuclear cells were freshly isolated by FACs sorting
whole muscle cells were isolated with an additional step of viability validation by 7-AAD (Thermo Scientific, 00-6993-50) staining. Red blood cells were eliminated by ACK buffers (150M NH4Cl, 100mM KHCO3, 10mM EDTA-2Na) before sorting. After sorting, live cells were washed with 0.04% BSA in PBS twice and resuspended in the BSA solution. Nuclei were isolated from the suspended cells according to the manufacturer’s instruction CG000366 • Rev D. Isolated nuclei were counted under a microscope and Typan blue was used to examine the number and integrity. The isolated nuclei were then resuspended at an appropriate concentration (5000-10000 nuclei/μl). Library construction was performed following the manufacturer’s instructions for generation of Gel Bead-In Emulsions (GEMs) using the 10x Chromium system. The single-cell multiome (RNA+ATAC) library were sequenced by Illumina NovaSeq S4 instrument.

value: hamstring muscle

tag: group

value: Aged

value: muscle mononuclear cell


title: pol32, DSB, biol rep2

description: Library name: pol32 biol rep2


title: whi2, DSB, biol rep1

description: Library name: whi2 biol rep1


title: S24-Kinprolaon_high_Rep1


title: S24-Kinprolaon_high_Rep3


title: pol32, DSB, biol rep1

description: Library name: pol32 biol rep1


title: Muscle, Aged, biol rep4, ATAC

description:
10x Genomics
Aged_4_barcodes.tsv.gz
Aged_4_features.tsv.gz
Aged_4_matrix.mtx.gz


title: top1, DSB, biol rep2

description: Library name: top1 biol rep2


title: JL217A, DSB, biol rep1

description: Library name: JL217A biol rep1

value: atp1-111 mgm1


title: S24-KinprolaPKA_low_Rep1


title: top1, DSB, biol rep1

description: Library name: top1 biol rep1


title: Muscle, Aged, biol rep3, ATAC

description:
10x Genomics
Aged_3_barcodes.tsv.gz
Aged_3_features.tsv.gz
Aged_3_matrix.mtx.gz


title: Muscle, Aged, biol rep5, GEX

molecule: nuclear RNA


title: S24-Kinprolaon_low_Rep2


title: Muscle, Aged, biol rep3, GEX


title: S24-Kinprolaon_medium_Rep2


title: S24-Kinprolaon_low_Rep1


title: sir2, DSB, biol rep1

description: Library name: sir2 biol rep1


title: S24-Kinprolaon_medium_Rep1


title: rsc2, DSB, biol rep1

description: Library name: rsc2 biol rep1


title: rsc2, DSB, biol rep2

description: Library name: rsc2 biol rep2


title: Muscle, Aged, biol rep1, ATAC

description:
10x Genomics
Aged_1_barcodes.tsv.gz
Aged_1_features.tsv.gz
Aged_1_matrix.mtx.gz


title: Muscle, Aged, biol rep2, ATAC

description:
10x Genomics
Aged_2_barcodes.tsv.gz
Aged_2_features.tsv.gz
Aged_2_matrix.mtx.gz


title: rad5, DSB, biol rep1

description: Library name: rad5 biol rep1


title: Muscle, Young, biol rep5, GEX

description:
10x Genomics
Young_5_barcodes.tsv.gz
Young_5_features.tsv.gz
Young_5_matrix.mtx.gz

value: Young


title: Muscle, Aged, biol rep1, GEX


title: Muscle, Young, biol rep5, ATAC


title: rrm3, DSB, biol rep1

description: Library name: rrm3 biol rep1


title: Muscle, Young, biol rep4, ATAC

description:
10x Genomics
Young_4_barcodes.tsv.gz
Young_4_features.tsv.gz
Young_4_matrix.mtx.gz


title: Muscle, Young, biol rep3, ATAC

description:
10x Genomics
Young_3_barcodes.tsv.gz
Young_3_features.tsv.gz
Young_3_matrix.mtx.gz


title: pso2, DSB, biol rep2

description: Library name: pso2 biol rep2


title: Muscle, Young, biol rep4, GEX


title: Muscle, Aged, biol rep4, GEX


title: pso2, DSB, biol rep1

description: Library name: pso2 biol rep1


title: rev3, DSB, biol rep1

description: Library name: rev3 biol rep1


title: rev3, DSB, biol rep2

description: Library name: rev3 biol rep2


title: sir2, DSB, biol rep2

description: Library name: sir2 biol rep2


title: Muscle, Young, biol rep1, ATAC

description:
10x Genomics
Young_1_barcodes.tsv.gz
Young_1_features.tsv.gz
Young_1_matrix.mtx.gz


title: Muscle, Young, biol rep2, ATAC

description:
10x Genomics
Young_2_barcodes.tsv.gz
Young_2_features.tsv.gz
Young_2_matrix.mtx.gz


title: Muscle, Aged, biol rep2, GEX


title: csm3, DSB, biol rep1

description: Library name: csm3 biol rep1


title: rad30, DSB, biol rep2

description: Library name: rad30 biol rep2