title: RNA-Seq of Campeiostachys nutans: salt-BSMV_CnbHLH130-leaf-3

city: Yangling

first: Juanjuan

last: Fu

state: Shaanxi

address: No.22 Xinong Road

institute: Northwest A&F University

description: Library name: S_BSMV_CnbHLH130_3

data_processing:
The adapter sequences were removed, and raw reads containing ambiguous bases ‘N’ > 5 % or those what were low-quality (more than 20 % Q ≤ 10 bases) were re_x0002_moved.
The Inchworm, Chrysalis, and Butterfly modules of Trinity software (version: v2.0.6) was used for de novo assembly of the clean reads
The Inchworm pro_x0002_gram assembled the reads into the unique sequences of transcripts;
Chrysalis program clusters the Inchorm Contigs into clusters and constructs complete de Bruijn graphs for each cluster.
Butterfly program con_x0002_structed the transcripts. Then use Tgicl v2.0.6 clustered transcripts to unigenes, which involves sequence splicing and redundancy removal to acquire non-redundant uni_x0002_genes.
Assembly: The assembled genome and annotation file have been deposited in the China National GeneBank DataBase (CNGB) under accession CNP0006257. (Article source: Analysis of allohexaploid wheatgrass genome reveals its Y haplome origin in Triticeae and high-altitude adaptation.)
Supplementary files format and content: genes_fpkm_expression.txt

organism: Campeiostachys nutans

source_name: leaf

extract_protocol:
Total RNA was extracted using a Trizol reagent according to the manufacturer’s protocol (Takara Bio Inc., Otsu, Japan). The integrity and purity of the RNA was determined by using the Agilent 2100 RNA 6000 Kit and electrophoresis on 1 % agarose gel.
De novo transcriptome sequencing of the samples was performed by Illumina Novaseq™ 4000 instrument at the Lc. Biotech Co., Ltd. (Hangzhou, China, http://www.lc-bio.com/) following the manufacturer’s procedure.

value: leaf

value: CnbHLH130-silenced line

value: salt

tag: infection

value: BSMV


title: WT, Cyclin E overexpression

status: Public on Jul 20 2026

type: genomic

city: Kitakyushu

first: Masaoki

last: Kohzaki

state: Fukuoka

address: 1-1 Iseigaoka Yahatanishi-ku

department: Institute of Industrial Ecological Sciences

country: Japan

institute: University of Occupational and Environmental Health, Japan

description:
Affymetrix CytoScan HD Array
WT_CyclinE_OE_clone2_151201

hyb_protocol: Genomic DNA was processed and hybridized to the Affymetrix CytoScan HD Array according to the manufacturer's instructions.

scan_protocol: Arrays were scanned using the GeneChip Scanner according to the manufacturer's recommendations.

data_processing:
The original experiments were analyzed using an earlier version of Chromosome Analysis Suite (ChAS). For GEO submission, archived CEL files were reprocessed using ChAS version 4.5 to generate CYCHP files. Copy number analysis was performed using the hg19 (GRCh37) human reference genome.
Primary data consist of raw CEL files generated using the Affymetrix CytoScan HD Array. Processed CYCHP files were generated using Chromosome Analysis Suite (ChAS) version 4.5.

label: biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: WT U2OS cells

label_protocol: Genomic DNA labeling was performed according to the manufacturer's protocol for the Affymetrix CytoScan HD Array.

growth_protocol: U2OS cells (WT and RECQL4-deficient) were cultured in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin at 37°C in a humidified atmosphere containing 5% CO₂.

extract_protocol: Genomic DNA was extracted from cultured U2OS cells using standard procedures.

treatment_protocol: WT and RECQL4-deficient U2OS cells carrying a Tet-off Cyclin E expression construct were cultured under non-induced (NE) or Cyclin E-overexpressing (OE) conditions. Cells were exposed or not exposed to 3 Gy ionizing radiation prior to genomic DNA extraction.

tag: cell line

tag: genotype

value: WT

tag: irradiation

value: 0 Gy

tag: cyclin e induction

value: Cyclin E induction


title: lncRNAseq GFP negative_rep1

status: Public on Jul 19 2026

type: SRA

city: Guangzhou

first: Man

last: Zhang

state: Guangdong

address: No.9, XingDaoHuanBei Road, Guangzhou International Bio-island, Haizhu District

department: Department of Basic Research

country: China

institute: Guangzhou Laboratory

description: Library name: lncRNAseq_GFPneg_rep1

library_source: transcriptomic

data_processing:
The raw RNA-seq reads were processed using TrimGalore to remove adapter sequences and low-quality bases. The cleaned reads were then aligned to the mouse Gencode (vM15) transcriptome with RSEM. Gene expression values were normalized across samples using the variance modeling tool DESeq2
Assembly: mm10
Supplementary files format and content: Tab-separated values files

molecule: total RNA

organism: Mus musculus

extract_protocol:
Cellular total RNA was collected using a Trizol extraction method
RNA libraries were constrcted using the Illumina Ribo-Zero plus rRNA Depletion kit (20037135, Illumina)

tag: cell type

value: mESC


title: RNA-Seq of Campeiostachys nutans: salt-BSMV_CnbHLH130-leaf-2

description: Library name: S_BSMV_CnbHLH130_2

tag: tissue

tag: treatment


title: GFP positive H3K27ac rep2

description:
Library name: GFPpos_H3K27ac_5000_rep2
GFPpos_H3K27ac_5000_rep2

library_source: genomic

data_processing:
The raw reads were processed using TrimGalore to remove adapter sequences and low-quality bases. The cleaned reads were aligned to the mouse mm10 genome using bowtie2 To analyze repetitive sequences, the multi-mapped reads were kept but only the best alignment was reported; if more than one equivalent best alignment was found, then one random alignment was reported. ATAC-seq peaks were called by MACS3  by default settings. Alignment bam files were transformed into read coverage files (bigwig format) using deepTools with the RPKM  normalization method.
Assembly: mm10
Supplementary files format and content: bigwig

source_name: DUX-induced E14Tg2a

extract_protocol:
ChIP-seq libraries were constrcted using the published ULI-NChIP-seq protocol
ChIP-seq libraries were constrcted using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (E7645S, NEB) and the NEBNext® Multiplex Oligos for Illumina® (Index Primers Set 1) (E7335S, NEB)

value: DUX-induced E14Tg2a

value: DUX-induced 2CLCs

tag: antibody


title: RNA-Seq of Campeiostachys nutans: salt-BSMV_CnbHLH130-leaf-1

description: Library name: S_BSMV_CnbHLH130_1


title: GFP positive H3K4me3 rep2

description:
Library name: GFPpos_H3K4me3_5000_rep2
GFPpos_H3K4me3_5000_rep2


title: WT, Cyclin E not induced, 3 Gy

description:
Affymetrix CytoScan HD Array
WT_3Gy_CyclinE_NE_clone2_151201

value: 3 Gy

value: no


title: mature DCs, 48h, control, rep1

city: Wageningen

first: Benthe

last: van der Lugt

address: Akkermaalsbos 2

country: Netherlands

institute: Wageningen University & Research

description: Library name: Ctrl24_1

data_processing:
The RNAseq reads were used to quantify transcript abundances. To this end, the tool Cutadapt (version 1.16) was used to trim adapters from the reads and HISAT2 (version 2.2.1) was used to map the reads to the GRCh38.p13 (release 42) human genome assembly-based transcriptome sequences as annotated by the GENCODE consortium. HISAT2 (version 2.2.1.) output was converted and sorted by chromosomal position using Samtools (version 1.9). RSeQC (v3.0.1) and PRINSEQ (v0.20.4) were used for quality control. HTSeq (version 0.11.2) was used to count reads in transcripts using gene-level quantification. Differential gene expression was determined using the package limma (version 3.50.3) utilizing the obtained scaled gene-level counts. Briefly, before statistical analyses, non-specific filtering of the count table was performed to increase detection power, based on the requirement that a gene should have an expression level greater than around 10 counts in at least three samples. Differences in library size were adjusted by the trimmed mean of M-values normalization method, implemented in the package edgeR (version 3.36.0).
Assembly: GRCh38.p13 (release 38)
Supplementary files format and content: Text file including the normalized counts for each sample.

growth_protocol: THP-1 human monocytic cells were maintained in 100-mm tissue culture dishes in RPMI 1640 medium supplemented with 2 mM L-glutamine, 100 U/mL penicillin, 0.1 mg/mL streptomycin, 50 µM 2-mercaptoethanol, and 10% heat-inactivated fetal bovine serum (FBS), hereafter referred to as cell culture medium. Cells were cultured at 37°C in a humidified atmosphere containing 5% CO₂ and maintained according to the ATCC recommendations (TIB-202), being passaged twice weekly and reseeded at a density of 2–4×10⁵ viable cells/mL to maintain exponential growth. For differentiation, THP-1 cells were seeded at a density of 1x10^5 cells/mL in T-35 tissue culture flasks and cultured for five days in cell culture medium supplemented with rhIL-4 (1500 U/mL) and GM-CSF (1500 U/mL) to induce differentiation into immature dendritic cells (iDCs).

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions. Briefly, cells were lysed in RLT buffer supplemented with β-mercaptoethanol, and total RNA was purified using RNeasy spin columns including on-column DNase digestion. RNA was eluted in RNase-free water and stored at −80 °C until use. RNA concentration and purity were assessed by measuring absorbance at 230, 260, and 280 nm using a NanoReady F-3100 spectrophotometer (Life Real, Zhejiang, China). The A260/A280 and A260/A230 ratios were used to evaluate RNA purity.
After poly(A) selection, library preparation was performed using the NEBNext Ultra RNA Library Preparation kit.

treatment_protocol: On day five of differentiation, iDCs were seeded at a density of 1×10⁶ cells/mL in 12-well plates containing complete treatment medium and exposed for 24 h to PFOA (10 µg/mL), PFOS (10 µg/mL), or vehicle control (0.1% DMSO, v/v). Following the initial 24-h exposure, a maturation cocktail consisting of rhIL-4 (3,000 IU/mL), rhGM-CSF (1,500 IU/mL), rhTNF-α (2,000 IU/mL), and ionomycin (200 ng/mL) was added to induce maturation into mature dendritic cells (mDCs). PFAS and control compounds remained present throughout the maturation period. Cells were harvested after 24 or 72 h of maturation, corresponding to total exposure times of 48 and 96 h, respectively.

value: 0.1% DMSO


title: mature DCs, 48h, PFOA , rep2

description: Library name: PFOA24_2

value: 24.4 μM PFOA


title: GFP negative H3K27ac rep2

description:
Library name: GFPneg_H3K27ac_5000_rep2
GFPneg_H3K27ac_5000_rep2


title: RNA-Seq of Campeiostachys nutans: BSMV_CnbHLH130-leaf-2

description: Library name: BSMV_CnbHLH130_2

value: control


title: WT parental clone

description:
Affymetrix CytoScan HD Array
WT_original_clone_151117


title: RNA-Seq of Campeiostachys nutans: BSMV_CnbHLH130-leaf-3

description: Library name: BSMV_CnbHLH130_3


title: RNA-Seq of Campeiostachys nutans: BSMV_CnbHLH130-leaf-1

description: Library name: BSMV_CnbHLH130_1


title: GFP negative H3K27ac rep1

description:
Library name: GFPneg_H3K27ac_rep1
GFPneg_H3K27ac_rep1


title: GFP negative H3K4me3 rep2

description:
Library name: GFPneg_H3K4me3_rep2
GFPneg_H3K4me3_rep2


title: RNA-Seq of Campeiostachys nutans: salt-BSMV_r-leaf-3

description: Library name: S_BSMV_r_3

value: non-silenced control


title: GFP negative H3K4me3 rep1

description:
Library name: GFPneg_H3K4me3_rep1
GFPneg_H3K4me3_rep1


title: GFP positive H3K27ac rep1

description:
Library name: GFPpos_H3K27ac_rep1
GFPpos_H3K27ac_rep1


title: WT, Cyclin E not induced

description:
Affymetrix CytoScan HD Array
WT_CyclinE_NE_clone2_151201


title: RNA-Seq of Campeiostachys nutans: salt-BSMV_r-leaf-1

description: Library name: S_BSMV_r_1


title: RNA-Seq of Campeiostachys nutans: salt-BSMV_r-leaf-2

description: Library name: S_BSMV_r_2


title: GFP positive H3K4me3 rep1

description:
Library name: GFPpos_H3K4me3_rep1
GFPpos_H3K4me3_rep1


title: DUX-induced 2CLCs scRNAseq

description:
Library name: Dox-plus_scRNAseq
Dox-plus_scRNAseq

library_source: transcriptomic single cell

data_processing:
Basic quality control for raw sequencing reads were performed using FastQC(v0.11.9). Sequencing adaptors and low-quality reads/bases were further removed using TrimGalore (v0.6.5).
Clean reads were then aligned to the mouse reference genome (mm10) using STAR (v2.7.6a) and only uniquely mapped reads were retained.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

source_name: DUX-induced E14Tg3a

extract_protocol:
Cells purfied by FACS were used for scRNA-seq library construction.
scRNA-seq libraries were constructed according to the standard protocol of Chromium Next GEM Chip G Single Cell Kit (1000121, 10x Genomics) .

value: DUX-induced E14Tg3a


title: GFP positive H3K4me1 rep2

description:
Library name: GFPpos_H3K4me1_rep2
GFPpos_H3K4me1_rep2


title: RNA-Seq of Campeiostachys nutans: BSMV_r-leaf-3

description: Library name: BSMV_r_3

value: leaf


title: mESC scRNAseq

description:
Library name: Dox-minus_scRNAseq
Dox-minus_scRNAseq


title: GFP negative H3K4me1 rep2

description:
Library name: GFPneg_H3K4me1_rep2
GFPneg_H3K4me1_rep2


title: GFP positive input rep2

description:
Library name: GFPpos_input_rep2
GFPpos_input_rep2

value: input


title: NP-D@MP [N12]

first: Dongbing

last: Ding

address: 600 Tianhe Road, Tianhe District, Guangzhou City, Guangdong Province

institute: The Third Affiliated Hospital of Sun Yat-sen University

data_processing:
Illumina Casava1.7 software used for basecalling.
Suquenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al. Nucleic Acids Research, 2009. In short exons from all isoforms.
Assembly: mm8
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Colon

extract_protocol:
Retinas were removed, flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (cat#FC-122-1001) was used with 1 ug of total RNA for the construction.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Colon

value: Tumor


title: GFP positive H3K4me1 rep1

description:
Library name: GFPpos_H3K4me1_rep1
GFPpos_H3K4me1_rep1


title: Donor 6 RARAF 1 Gy

city: Kingston

first: Michael

last: Antosh

state: RI

address: 2 Lippitt Rd

country: USA

institute: University of Rhode Island

description: Library name: Sample 55

data_processing:
Alignment: HISAT2
Quality check: FastQC
Analysis: deseq2
Assembly: GRCh38 Reference Genome
Supplementary files format and content: normalized data,from deseq2 output (csv file)
Supplementary files format and content: read counts (csv file)

source_name: Whole blood

growth_protocol: Sampled from donors under IRB protocol IRB-AAAS5693 at Columbia University.

extract_protocol:
Blood samples preserved in PAXgene RNA stabilization reagent were sent to Azenta, where total RNA was extracted followed by globin reduction.
QIAGEN Fast Select rRNA HMR and Globin Kit, plus NEGNext Ultra II RNA Library preparation kit.  Note: sequencer model number listed may be incorrect.

treatment_protocol: Each sample was irradiated with 42% photons and 58% neutrons, at either the RINSC source or the RARAF source.

value: Whole blood

tag: irradiation site

value: RARAF

tag: radiation dose_(gy)

tag: age

tag: Sex

value: Female


title: Epithelial cells 3

city: East Lansing

first: Axel

middle: Dizan

last: Schmitter-Sanchez

state: MI

address: 775 Woodlot Dr

department: Medicine

institute: Michigan State University

description: Library name: KTC_3

data_processing:
Reads were aligned to the Ensembl Mouse GRCm39 genome using STAR Aligner. DESeq2 was used to normalize raw counts and determine the differential expression of chemokine receptor genes among the epithelial and Langerhans cell samples.
Assembly: Ensembl Mouse GRCm39
Supplementary files format and content: A tab-delimited text matrix containing raw read counts per gene for each sample.

source_name: Ear epidermis

extract_protocol:
Single cell suspension was collected from four huLangerin-CreER; Rosa-stop-tdTomato; Cx3cr1-GFP; K14-H2B-Cerulean mice during homeostasis. Ears were incubated epidermis side up in 2.5% Trypsin solution at 37°C for 90 min, and the epidermis was removed from the dermis. Single cell suspension was achieved by mincing, cutting, and running the sample through a 70 µm filter. LCs and epithelial cells were sorted using fluorescence-activated cell sorting (FACS) based on their red (LCs) and blue (epithelial cells) fluorescence.
Libraries were prepared using the KAPA mRNA HyperPrep Kit with dUTP-based strand specificity. Libraries were normalized to 10 nM, then loaded onto an Illumina NovaSeq flow cell. The sequencing was performed using 100 bp paired-end sequencing on an Illumina HiSeq NovaSeq.

value: Ear epidermis

value: Epithelial cells

value: 8 weeks


title: RNA-Seq of Campeiostachys nutans: BSMV_r-leaf-1

description: Library name: BSMV_r_1

value: BSMV


title: RNA-Seq of Campeiostachys nutans: BSMV_r-leaf-2

description: Library name: BSMV_r_2


title: GFP positive input rep1

description:
Library name: GFPpos_input_rep1
GFPpos_input_rep1

value: DUX-induced E14Tg2a

value: DUX-induced 2CLCs


title: GFP negative H3K4me1 rep1

description:
Library name: GFPneg_H3K4me1_rep1
GFPneg_H3K4me1_rep1

value: mESC


title: NP-D@MP [N11]


title: tcx5tcx6_Zeocin_B

city: Shanghai

first: wenjie

last: liang

address: Guoquan North Road

institute: Fudan university

description: Library name: Sample12

data_processing:
Raw fastq reads were quality-controlled with fastp. Clean reads were mapped to Arabidopsis TAIR10 reference genome using STAR with default parameters.
Assembly: Arabidopsis thaliana TAIR10 (Ensembl Plants version TAIR10.46)
Supplementary files format and content: Tab-separated plain text matrix containing raw read counts of all Arabidopsis protein-coding genes generated by featureCounts.

organism: Arabidopsis thaliana

source_name: seedling

growth_protocol: Arabidopsis thaliana seeds of all genotypes were surface-sterilized with 75% ethanol and 5% sodium hypochlorite, then stratified at 4 °C for 2 days in dark. Sterilized seeds were sown on 1/2 MS solid medium containing 1% sucrose. Seedlings were grown under long-day conditions (16 h light / 8 h dark) at 22 °C for 7 days before chemical treatment.

extract_protocol:
Total RNA was extracted from frozen Arabidopsis seedling tissue using TRIzol reagent following the manufacturer’s instructions. RNA integrity was assessed by agarose gel electrophoresis and Agilent 2100 Bioanalyzer; only RNA samples with RIN ≥ 7.0 were retained for library construction. Residual genomic DNA contamination was eliminated via DNase I digestion.
mRNA was enriched from total RNA using oligo(dT) magnetic beads. Fragmented mRNA was reverse-transcribed into first-strand cDNA, followed by second-strand cDNA synthesis. End repair, A-tailing and adapter ligation were performed, then fragments of 200–300 bp were purified for PCR amplification to construct paired-end RNA-seq libraries. All libraries were sequenced on Illumina platform with paired-end 150 bp read length.

value: seedling

value: Zeocin


title: GFP negative input rep1

description:
Library name: GFPneg_input_rep1
GFPneg_input_rep1


title: NP-D@MP [N10]


title: GFP positive ATAC rep2

description: Library name: GFPpos_ATAC_rep2

extract_protocol:
The DNA was extracted using MinElute PCR Purification Kit (28004, QIAGEN) following the manufacturer’s instructions.
The ATAC-seq libraries were generated according to a previous ATAC-seq protocol


title: NP-D@M [N9]


title: GFP positive ATAC rep1

description: Library name: GFPpos_ATAC_rep1


title: GCRC1915 | 024

city: Montreal

first: Morag

last: Park

state: Quebec

address: 1160 Ave des Pins Ouest, Room 514

department: Goodman Cancer Institute

country: Canada

institute: McGill University

description: Library name: B064_2_WTA_GS6_CD31_GLUT1 | 024

library_source: other

data_processing:
The raw data (FASTQ) was converted to DCC files for upload into Bruker Spatial's proprietary software. Data were Q3 normalized, and target mRNAs that were detected in at least 1% of the ROIs were retained in the analysis.
Assembly: Nanostring synthetic WTA barcode reference
Supplementary files format and content: DCC and pkd files. Pkc files to convert FASTQ to DCC files using Bruker Spatial's pipeline for uploads into GeoMx Analysis Software
Library strategy: Spatial Transcriptomics

molecule: other

source_name: breast cancer

extract_protocol:
PDX tissues were fixed in formalin, embedded in paraffin, and sectioned onto positively charged slides for GeoMx DSP WTA analysis. Barcodes attached to antisense probes were released by UV-illumination and collected.
Releasates from each area-of-illumination (GLUT1 or GS6) were collected into a well of a 96-well plate and dual-index Illumina sequencing adapters were added by PCR amplification. Libraries were pooled and sequenced on an Illumina NovaSeq 6000.

value: breast cancer

tag: tumor stage

value: III

tag: model

value: PDX

value: Untreated


title: tcx5tcx6_A

description: Library name: Sample11


title: sog1_Zeocin_B

description: Library name: Sample10


title: GFP negative ATAC rep2

description: Library name: GFPneg_ATAC_rep2


title: NP-D@M [N8]

value: Colon

value: Tumor


title: GCRC1915 | 023

description: Library name: B064_2_WTA_GS6_CD31_GLUT1 | 023


title: sog1_Zeocin_A

description: Library name: Sample9


title: GFP negative ATAC rep1

description: Library name: GFPneg_ATAC_rep1


title: NP-D@M [N7]


title: GCRC1915 | 022

description: Library name: B064_2_WTA_GS6_CD31_GLUT1 | 022


title: GFP negative input rep2

description:
Library name: GFPneg_input_rep2
GFPneg_input_rep2

value: input


title: sog1_B

description: Library name: Sample8


title: NP@M [N6]


title: GCRC1915 | 021

description: Library name: B064_2_WTA_GS6_CD31_GLUT1 | 021

value: Female


title: BT mutant,scRNAseq

first: Zhongle

last: Cai

address: No.573, Xujiahui Road, Huangpu District, Shanghai

institute: ruijin hospital

description: 10x Genomics

data_processing:
The Cell Ranger software pipeline provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

extract_protocol:
Single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA. Then Cells were added to each channel. After generation of GEMs, reverse transcription reactions were engaged barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific). Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed,  and index adaptor ligated and library amplification.
RNA libraries  were prepared with Chromium Single cell 3’ Reagent v3 Kits according to the manufacturer’s protocol.

value: colonized with BT mutant


title: sog1_A

description: Library name: Sample7


title: GCRC1915 | 020

description: Library name: B064_2_WTA_GS6_CD31_GLUT1 | 020


title: NP@M [N5]


title: NP@M [N4]


title: Donor 6 RINSC 0.5 Gy

description: Library name: Sample 54

value: Whole blood

value: RINSC


title: PBS,scRNAseq

description: 10x Genomics

value: PBS


title: GCRC1915 | 019

description: Library name: B064_2_WTA_GS6_CD31_GLUT1 | 019


title: OE_E2FADPA_B

description: Library name: Sample6


title: GCRC1915 | 018

description: Library name: B064_2_WTA_GS6_CD31_GLUT1 | 018


title: scRNA-Seq of mus musculus: adult mouse_Gq2_ lungs

first: Xiaoyu

last: Sun

address: 160 Pujian Road, Shanghai

institute: Renji Hospital, Shanghai Jiaotong University, School of Medicine,

description:
Library name: Mouse_Gq2_lung_BD_Rhapsody
Lung tissue from male C57BL/6J mouse, 12 weeks, 3 days post LPS and SLC activtaion for 7 times, replicate 2

data_processing:
The demultiplexing,barcoded processing,gene counting and aggregation were made using the BD Rhapsod Sequence Analysis Pipeline 2.3(https://bd-rhapsody-bioinfo-docs.genomics.bd.com/top_introduction.html）
Assembly: GRCm39 / mm39
Supplementary files format and content: Tab-separated values files and matrix files

source_name: lung

growth_protocol: Male C57BL/6J mice (12 weeks old) were housed in a specific pathogen-free (SPF) facility with free access to food and water under a 12-hour light/dark cycle.

extract_protocol:
Lung tissues were enzymatically digested and filtered to obtain single-cell suspensions. Dead cells were removed following the manufacturer's protocol.
Single-cell RNA-seq libraries were prepared using the BD Rhapsody Single-Cell Analysis System, following the manufacturer's protocol. Single cells were captured in microwell arrays and co-localized with barcode-labeled beads. Following lysis and mRNA hybridization, beads were collected for reverse transcription, ExoI digestion, and cDNA amplification according to the BD Rhapsody whole-transcriptome amplification workflow. Library quality was assessed using an Agilent Bioanalyzer and Qubit, and sequencing was performed on the DNBSEQ-T7 platform with 150 bp paired-end reads.

treatment_protocol: Mice were randomly assigned to control (PBS), LPS-treated (1 mg/kg), or SLC-Gq activation + LPS groups. Lung tissues were collected 3 days after treatment.

value: lung

value: LPS(1mg/kg)+SLC activation


title: Col_0_Zeocin_B

description: Library name: Sample4

value: WT


title: BT WT,scRNAseq

description: 10x Genomics

value: colonized with BT WT


title: CD103+ Lung DCs After 18h Cell Culture 2

city: Ann Arbor

first: Stephen

middle: J.

last: Gurczynski

address: 109 Zina Pitcher Pl, Room 4062

department: Internal Medicine

institute: University Of Michigan

description: Library name: A3

data_processing:
Differential Gene expression and data processing performed in R and Python using DESEQ2
Assembly: Mus musculus GRCm38
Supplementary files format and content: processed data is provided as a .csv file containing gene hit counts normalized via DESEQ2.

source_name: Lung

extract_protocol:
Total lung rna was extraced via qiagen RNAeasy columns following manufacturer's protocol.
Library and sequencing performed by Azenta

value: Lung

value: CD103+ DCs

value: 18h Post-Culture


title: scRNA-Seq of mus musculus: adult mouse_Gq1_lungs

description:
Library name: Mouse_Gq1_lung_BD_Rhapsody
Lung tissue from male C57BL/6J mouse, 12 weeks, 3 days post LPS and SLC activtaion for 7 times, replicate 1


title: PBS [N3]


title: PBS [N2]


title: OE_E2FADPA_A

description: Library name: Sample5

value: seedling


title: Col_0_Zeocin_A

description: Library name: Sample3

value: Zeocin


title: PBS [N1]

value: Colon


title: scRNA-Seq of mus musculus: adult mouse_LPS2_lungs

description:
Library name: Mouse_LPS2_lung_BD_Rhapsody
Lung tissue from male C57BL/6J mouse, 12 weeks, 3 days post LPS, replicate 2


title: scRNA-Seq of mus musculus: adult mouse_Ctr2_ lungs

description:
Library name: Mouse_Ctr2_lung_BD_Rhapsody
Lung tissue from male C57BL/6J mouse, 12 weeks, 3 days post PBS, replicate 2


title: scRNA-Seq of mus musculus: adult mouse_LPS1_lungs

description:
Library name: Mouse_LPS1_lung_BD_Rhapsody
Lung tissue from male C57BL/6J mouse, 12 weeks, 3 days post LPS, replicate 1


title: Col_0_B

description: Library name: Sample2


title: Col_0_A

description: Library name: Sample1


title: GCRC1915 | 017

description: Library name: B064_2_WTA_GS6_CD31_GLUT1 | 017

value: breast cancer

value: III

value: PDX

value: Untreated


title: Multiome, Hippocampus, Old CFC, ATAC

city: London

first: Paul

last: Lavender

address: Guy's Hospital, Great Maze Pond

country: United Kingdom

institute: King's College London

description:
Library name: OC_multiome_ATAC
ATAC library. Read1 contains cell barcode and umi, read2 contains atac sequence.

library_source: genomic single cell

data_processing:
Reads were demultiplexed using cellranger-arc mkfastq.
Reads were aligned to the mm10 Mus musculus genome using cellranger-arc count.
Assembly: mm10
Supplementary files format and content: Cellranger-arc output files: matrix.mtx.gz, barcodes.tsv, features.tsv.
Supplementary files format and content: atac fragments files: atac_fragments.tsv.gz.

source_name: Hippocampus

extract_protocol:
Nuclei isolated from the mouse hippocampus were profiled with the 10x Genomics Single Cell Multiome ATAC + Gene Expression kit (Cat#1000285), and captured using the 10x Genomics Chromium controller.
10x Genomics Single Cell Multiome ATAC + Gene Expression kit (Cat#1000285).

value: Hippocampus

value: Wildtype

value: Contextual Fear Conditioning

tag: batch


title: Multiome, Hippocampus, Old CFC, GEX

description:
Library name: OC_multiome_RNA
3’ mRNA library. Read1 contains cell barcode and umi, read2 contains transcript.


title: Multiome, Hippocampus, Old Naive, ATAC

description:
Library name: ON_multiome_ATAC
ATAC library. Read1 contains cell barcode and umi, read2 contains atac sequence.


title: tcx5tcx6_H3K4me3_2

description: Library name: Material11

data_processing:
Raw fq.gz reads were quality checked by fastp.Clean reads were aligned to TAIR10 Arabidopsis reference genome using Bowtie2, only uniquely mapped reads were retained.
Assembly: Arabidopsis thaliana TAIR10 (Ensembl Plants TAIR10.46)
Supplementary files format and content: Normalized bigWig (.bw) files representing genome-wide H3K4me3 read density tracks for all ChIP and Input samples.

extract_protocol:
Cross-linking of chromatin was performed with 1% formaldehyde on fresh seedling tissue, followed by quenching with glycine. Nuclei were isolated and chromatin was fragmented by sonication. Immunoprecipitation was carried out using anti-H3K4me3 antibody. Input chromatin without antibody incubation was retained as control. DNA was reverse-crosslinked, purified and recovered for library construction.
Purified ChIP and Input DNA fragments were end-repaired, A-tailed and ligated to Illumina sequencing adapters. DNA fragments in the size range of 150–300 bp were purified and amplified by PCR to construct paired-end ChIP-seq libraries. All libraries were sequenced on Illumina platform with paired-end 150 bp reads.

tag: chip antibody

value: H3K4me3 antibody


title: polycystic ovary syndrome (PCOS) pregnant group_6

city: Nanjing

first: Shimin

last: Wu

address: Nanjing

institute: Affiliated Hospital of Nanjing University of Chinese Medicine

description:
Library name: PCOS6
polycystic ovary syndrome (PCOS) pregnant group

data_processing:
Raw RNA-seq reads were trimmed to remove adapter sequences and low-quality reads using fastp. Clean reads were aligned to the human reference genome using HISAT2. Gene expression levels were quantified using featureCounts. FPKM/TPM values and raw read counts were generated for subsequent differential expression analysis and bioinformatic interpretation.
Assembly: GRCh38 (Ensembl human reference genome)
Supplementary files format and content: Excel workbook Gene_differential_expression.xlsx containing gene-level processed expression values across samples

source_name: Placenta

extract_protocol:
Total RNA was extracted from human term placental tissues using standard Trizol reagent-based extraction protocol. RNA purity and integrity were assessed by NanoDrop and agarose gel electrophoresis. Qualified total RNA was used for subsequent library construction.
mRNA was enriched from total RNA using oligo(dT) magnetic beads. After fragmentation, the first-strand and second-strand cDNA were synthesized. The purified cDNA fragments were end-repaired, A-tailed and ligated with sequencing adapters. After PCR amplification and purification, the final RNA-seq libraries were quality-checked and sequenced on an Illumina platform.

value: Placenta

value: Primary placental tissue (mixed placental cell population)

value: Wild-type, no genetic modification


title: scRNA-Seq of mus musculus: adult mouse_Ctr1_lungs

description:
Library name: Mouse_Ctr1_lung_BD_Rhapsody
Lung tissue from male C57BL/6J mouse, 12 weeks, 3 days post PBS, replicate 1

value: lung

value: PBS


title: tcx5tcx6_H3K4me3_1

description: Library name: Material10


title: polycystic ovary syndrome (PCOS) pregnant group_8

description:
Library name: PCOS8
polycystic ovary syndrome (PCOS) pregnant group


title: Multiome, Hippocampus, Old Naive, GEX

description:
Library name: ON_multiome_RNA
3’ mRNA library. Read1 contains cell barcode and umi, read2 contains transcript.


title: polycystic ovary syndrome (PCOS) pregnant group_7

description:
Library name: PCOS7
polycystic ovary syndrome (PCOS) pregnant group


title: polycystic ovary syndrome (PCOS) pregnant group_5

description:
Library name: PCOS5
polycystic ovary syndrome (PCOS) pregnant group


title: sog1_Zeocin_H3K4me3_2

description: Library name: Material9


title: sog1_Zeocin_H3K4me3_1

description: Library name: Material8


title: polycystic ovary syndrome (PCOS) pregnant group_3

description:
Library name: PCOS3
polycystic ovary syndrome (PCOS) pregnant group


title: Multiome, Hippocampus, Young CFC, ATAC

description:
Library name: YC_multiome_ATAC
ATAC library. Read1 contains cell barcode and umi, read2 contains atac sequence.


title: polycystic ovary syndrome (PCOS) pregnant group_4

description:
Library name: PCOS4
polycystic ovary syndrome (PCOS) pregnant group


title: Multiome, Hippocampus, Young CFC, GEX

description:
Library name: YC_multiome_RNA
3’ mRNA library. Read1 contains cell barcode and umi, read2 contains transcript.


title: Semaglutide8_1

city: Berkeley

first: Yufan

last: Feng

address: Morgan hall

institute: University of California, Berkeley

description: Library name: Semaglutide8_1

data_processing:
Data analysis was processed on the Galaxy public server (usegalaxy.org). In brief, after removing low-quality reads and adaptor sequences, reads were aligned to the mouse genome (mm10) using 'HISAT2' (Galaxy Version 2.2.1). Gene level raw counts were generated using 'HTSeq' (Galaxy Version 2.0.5). Differential gene expression was analyzed using 'DESeq2' (Galaxy Version 2.11.40.8).
Assembly: mm10
Supplementary files format and content: Tab-delimited text file containing gene-level raw read counts generated by HTSeq-count.

source_name: Liver

extract_protocol:
Total RNA of liver samples was extracted using the RNeasy Mini Kit (Qiagen) following the manufacturer’s instructions.
PolyA-enriched libraries were prepared by Novogene and sequenced on NovaSeq XPlus 25B

value: Liver

value: Semaglutide


title: Semaglutide9_1

description: Library name: Semaglutide9_1


title: sog1_H3K4me3_1

description: Library name: Material6

value: seedling


title: Semaglutide2_2

description: Library name: Semaglutide2_2


title: Semaglutide4_1

description: Library name: Semaglutide4_1


title: polycystic ovary syndrome (PCOS) pregnant group_1

description:
Library name: PCOS1
polycystic ovary syndrome (PCOS) pregnant group


title: Multiome, Hippocampus, Young Naive, GEX

description:
Library name: YN_multiome_RNA
3’ mRNA library. Read1 contains cell barcode and umi, read2 contains transcript.


title: normal pregnant control group_6

description:
Library name: Control6
normal pregnant control group

value: normal pregnant control group


title: normal pregnant control group_5

description:
Library name: Control5
normal pregnant control group


title: Ctrl8_7

description: Library name: Ctrl8_7

value: Ctrl


title: normal pregnant control group_4

description:
Library name: Control4
normal pregnant control group


title: Col-0_Zeocin_H3K4me3_1

description: Library name: Material3


title: Col-0_H3K4me3_2

description: Library name: Material2


title: Ctrl4_7

description: Library name: Ctrl4_7


title: Col-0_H3K4me3_1

description: Library name: Material1


title: Ctrl2_7

description: Library name: Ctrl2_7


title: DPC CH+F9 3

status: Public on Jul 18 2026

type: RNA

city: Mitaka-shi

first: Reina

last: Hayakawa

state: Tokyo

address: Shinkawa 6-20-2

department: Department of dermatology

institute: Kyorin university faculty of medicine

description: Gene expression data from dermal papilla cells 3 cultured with CHIR+F9

hyb_protocol: Following fragmentation, 2.3 ug of cRNA were hybridized for 16 hr at 45C on GeneChip dermal papilla Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the DELL GeneArray Scanner 3000 7G (Affymetrix Inc.) .

data_processing: The data were analyzed with Transcriptome Analysis Console version 4.0 (TAC 4.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Dermal papilla cells 3 cultured with CH+F9

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Dermal papilla cells and fibloblasts were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM; Sigma-Aldrich, St. Louis, MO, United States) containing 10% fetal bovine serum (FBS; Biowest, Nuaillé, France), and follicle dermal papilla cell medium (DP medium; PromoCELL, Heidelberg, Germany) at 37℃ in air containing 5% CO2. Dermal papilla cells at passage 3-8, and fibloblasts at passage 5-9 were used. Dermal papilla cells were cultured with DP medium until 70% confluency for 7 days and then the medium was changed to DMEM containing activators as described below and cultured for 7 days. In DPAC, dermal papilla cells were cultured in 10% FBS–DMEM containing BIO（1mM；Sigma, St. Louis, MO, USA）, rBMP2 （200ng/mL；R&D, Minneapolis, MN, USA）, and bFGF（20ng/mL；PEPROTECH, Rocky Hill, NJ, USA）. As a new dermal papilla cell activation medium, DMEM containing CHIR99021（CH: Cayman Chemical, MI, USA）（2µM）solved in dimethyl sulfoxide (DMSO) or FGF9（F9: R&D, Minneapolis, MN, USA）(50ng/mL) or the combination of CH and F9 were developed.

extract_protocol: Using the RNeasy Mini Kit (Qiagen, Hilden, Germany), extraction of total RNA from dermal papilla cells cultured in respective conditions was performed according to the manufacturer's instructions.

treatment_protocol: Cultured dermal papilla cells were rinsed with PBS.

value: human dermal papilla cells

value: male

value: human dermal papilla cells from 46 year old male


title: Fibro

description: Gene expression data from fibroblasts cultured with control

source_name: Fibroblasts

value: human fibroblasts

value: female

value: human fibroblasts from 20 year old female


title: DPC CH+F9 2

description: Gene expression data from dermal papilla cells 2 cultured with CHIR+F9

source_name: Dermal papilla cells 2 cultured with CH+F9

value: human dermal papilla cells from 53 year old male


title: Semaglutide5_3

description: Library name: Semaglutide5_3


title: polycystic ovary syndrome (PCOS) pregnant group_2

description:
Library name: PCOS2
polycystic ovary syndrome (PCOS) pregnant group

value: Placenta


title: sog1_H3K4me3_2

description: Library name: Material7

value: H3K4me3 antibody


title: CD103+ Lung DCs After 18h Cell Culture 3

description: Library name: A4

value: Lung

value: CD103+ DCs

value: 18h Post-Culture


title: Multiome, Hippocampus, Young Naive, ATAC

description:
Library name: YN_multiome_ATAC
ATAC library. Read1 contains cell barcode and umi, read2 contains atac sequence.

value: Hippocampus

value: Wildtype


title: Input-H3K4me3

description: Library name: Material5

value: seedling


title: Ctrl5_1

description: Library name: Ctrl5_1

value: Liver


title: HEK293T cell line, ZNF460_sh-1

city: Hangzhou

first: Ke

state: Zhejiang

address: No. 1369, West Wenyi Road

institute: Zhejiang university

description: Library name: Sample 4

data_processing:
tRNA expression matrix was generated from two-step alignment.
Assembly: artificial genome -> mature tRNA
Supplementary files format and content: spave-delimited text files includes tRNA expression for all samples

extract_protocol:
To validate the candidate regulators, we performed knockdown experiments in human HEK293T cells, which were cultured in DMEM supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin, maintained at 37 °C with 5% CO2. shRNAs targeting MEF2C and ZNF460 were cloned into the pLKO.1 vector (Sigma-Aldrich). Total RNA was extracted using TRIzol reagent and reverse-transcribed with the HiScript II 1st Strand cDNA Synthesis Kit, followed by qPCR using SYBR Green Master Mix with GAPDH as the internal control.
For smRNA sequencing, libraries were prepared using the NEB Next Small RNA Library Kit with 1 µg of total RNA per sample.


title: HEK293T cell line, ZNF460_sh-2

description: Library name: Sample 5


title: Ctrl9_7

description: Library name: Ctrl9_7

value: Ctrl


title: Col-0_Zeocin_H3K4me3_2

description: Library name: Material4


title: normal pregnant control group_2

description:
Library name: Control2
normal pregnant control group

value: Primary placental tissue (mixed placental cell population)

value: Wild-type, no genetic modification

value: normal pregnant control group


title: normal pregnant control group_3

description:
Library name: Control3
normal pregnant control group


title: HEK293T cell line, MEF2C_sh-1

description: Library name: Sample 2


title: HEK293T cell line, MEF2C_sh-2

description: Library name: Sample 3


title: rat brain tissue; boldine-treated blast-exposed; Sample_35_S6

city: Bronx

first: Alexey

last: Kozlenkov

address: 130 W Kingsbridge Road

institute: Icahn School of Medicine at Mount Sinai

description:
Library name: Sample_35_S6
column name in raw counts Blast_Boldine.counts.txt: Sample_35_S6

data_processing:
raw paired-end reads were preprocessed using HTStream (v1.3.3), which sequentially performed contaminant screening, PCR duplicate removal, adapter trimming, ambiguous base removal, and sliding-window quality trimming using default options, followed by a minimum length filter to discard reads shorter than 50 base pairs (option “-m 50”).
Reads were aligned to the rat genome (rn7, mRatBN7.2)  using STAR  [ver. 2.7.11b], with gene models provided by the corresponding NCBI RefSeq GTF annotation.
Gene-level counts were quantified from exon-mapped reads using the featureCounts command (“featureCounts -T 4 -s 2 -p -t exon -g gene_name”) from the Subread software tool (ver. 2.0.1)
Differential expression was analyzed in R using DESeq2, with low-count genes removed via DESeq2’s independent filtering
Assembly: rat genome (rn7, mRatBN7.2)
Supplementary files format and content: per-gene counts matrix, quantified from exon-mapped reads using the featureCounts command (Subread software tool)

organism: Rattus norvegicus

source_name: brain

extract_protocol:
RNA was isolated using Trizol method according to provided protocol (ThermoFisher)
RNA-seq libraries were prepared with TruSeq Total Stranded RNA kit (Illumina)

value: brain

value: WT

value: boldine-treated blast-exposed


title: DPC DPAC 1

description: Gene expression data from dermal papilla cells 1 cultured with DPAC

source_name: Dermal papilla cells 1 cultured with DPAC

value: human dermal papilla cells

value: male

value: human dermal papilla cells from 43 year old male


title: rat brain tissue; boldine-treated blast-exposed; Sample_32_S5

description:
Library name: Sample_32_S5
column name in raw counts Blast_Boldine.counts.txt: Sample_32_S5


title: HEK293T cell line, NTC

description: Library name: Sample 1


title: normal pregnant control group_1

description:
Library name: Control1
normal pregnant control group

value: Placenta


title: rat brain tissue; boldine-treated blast-exposed; Sample_20_S4

description:
Library name: Sample_20_S4
column name in raw counts Blast_Boldine.counts.txt: Sample_20_S4


title: DPC control 1

description: Gene expression data from dermal papilla cells 1 cultured with control

source_name: Dermal papilla cells 1 cultured with control


title: rat brain tissue; boldine-treated blast-exposed; Sample_19_S6

description:
Library name: Sample_19_S6
column name in raw counts Blast_Boldine.counts.txt: Sample_19_S6


title: rat brain tissue; boldine-treated blast-exposed; Sample_12_S4

description:
Library name: Sample_12_S4
column name in raw counts Blast_Boldine.counts.txt: Sample_12_S4


title: rat brain tissue; boldine-treated blast-exposed; Sample_17_S5

description:
Library name: Sample_17_S5
column name in raw counts Blast_Boldine.counts.txt: Sample_17_S5


title: rat brain tissue; untreated blast-exposed; Sample_6_S3

description:
Library name: Sample_6_S3
column name in raw counts Blast_Boldine.counts.txt: Sample_6_S3

value: untreated blast-exposed


title: rat brain tissue; untreated blast-exposed; Sample_9_S3

description:
Library name: Sample_9_S3
column name in raw counts Blast_Boldine.counts.txt: Sample_9_S3


title: rat brain tissue; untreated blast-exposed; Sample_7_S2

description:
Library name: Sample_7_S2
column name in raw counts Blast_Boldine.counts.txt: Sample_7_S2


title: rat brain tissue; untreated blast-exposed; Sample_5_S2

description:
Library name: Sample_5_S2
column name in raw counts Blast_Boldine.counts.txt: Sample_5_S2


title: rat brain tissue; untreated blast-exposed; Sample_4_S1

description:
Library name: Sample_4_S1
column name in raw counts Blast_Boldine.counts.txt: Sample_4_S1


title: DPC F9 3

description: Gene expression data from dermal papilla cells 3 cultured with F9

source_name: Dermal papilla cells 3 cultured with F9

value: human dermal papilla cells from 46 year old male


title: rat brain tissue; untreated blast-exposed; Sample_1_S1

description:
Library name: Sample_1_S1
column name in raw counts Blast_Boldine.counts.txt: Sample_1_S1


title: DPC CH 2

description: Gene expression data from dermal papilla cells 2 cultured with CHIR

source_name: Dermal papilla cells 2 cultured with CH

value: human dermal papilla cells from 53 year old male


title: DPC CH 3

description: Gene expression data from dermal papilla cells 3 cultured with CHIR

source_name: Dermal papilla cells 3 cultured with CH


title: Ler_Cvi_RIL_LOW_RIL182_G10_L1-1

city: Freising

first: Zhilin

state: Bavaria

address: Emil-Ramann-Str. 4

department: School of Life Sciences

country: Germany

institute: Technical University of Munich

description:
Library name: Sample55
Low epimutation rate RIL, G10, lineage L1-1

data_processing:
Reads trimmed with Trimmomatic (v0.38) with options "ILLUMINACLIP:TruSeq3-PE.fa:2:30:10:1:true", "LEADING:3", "TRAILING:3", "SLIDINGWINDOW:4:15", "MINLEN:36"
Reads aligned with STAR (v2.7.6a) with options "--alignIntronMin 60", "--alignIntronMax 6000"
Counts gathered for features using HTSeq-count (v0.13.5) with options "--mode=union". The strandedness parameter was set to --stranded=reverse for Ler_Cvi_RIL samples, and to --stranded=no for overexpression (OX), mutant, and control samples.
Assembly: TAIR10 genome and Araport11 annotation
Supplementary files format and content: HTSeq count files (.txt) with the following columns: <locus> <read count>

growth_protocol: Transgenic overexpression lines and mutant plants were grown under long-day conditions (16h light/8h dark) at 22C on soil. T1 plants were selected in the presence of 50 ug/ml kanamycin. RIL plants were grown on half-strength MS plates under long-day conditions (16h light/8h dark) at 25C for 7-9 days.

extract_protocol:
For VIM overexpression and mutant lines, total RNA was extracted from leaves of 4 to 12-week-old T1 plants with the Monarch Total RNA Miniprep Kit (N2010, NEB) and tested with Qubit RNA BR Assay (Q33223, Thermo Fisher). For Ler x Cvi RILs, total RNA was extracted from bulk seedlings following the TRIzol extraction method.
For VIM overexpression and mutant lines, library preparation and 150 bp paired-end sequencing were performed by Novogene on an Illumina NovaSeq X Plus platform. For Ler x Cvi RILs, libraries were constructed using the TruSeq Stranded mRNA Library Kit (No.20020594, Illumina) with a custom dual index workflow. Paired-end 150 bp sequencing was performed on an Illumina NovaSeq 6000 platform.

value: Ler x Cvi RIL RIL182


title: Ler_Cvi_RIL_LOW_RIL182_G03_L2-2

description:
Library name: Sample54
Low epimutation rate RIL, G03, lineage L2-2

value: seedling


title: Ler_Cvi_RIL_LOW_RIL182_G03_L1-2

description:
Library name: Sample52
Low epimutation rate RIL, G03, lineage L1-2


title: CD103+ Lung DCs After 18h Cell Culture 1

description: Library name: A1

value: Lung

value: CD103+ DCs

value: 18h Post-Culture


title: DPC DPAC 3

description: Gene expression data from dermal papilla cells 3 cultured with DPAC

source_name: Dermal papilla cells 3 cultured with DPAC


title: DPC control 3

description: Gene expression data from dermal papilla cells 3 cultured with control

source_name: Dermal papilla cells 3 cultured with control


title: DPC F9 2

description: Gene expression data from dermal papilla cells 2 cultured with F9

source_name: Dermal papilla cells 2 cultured with F9


title: Ler_Cvi_RIL_LOW_RIL150_G10_L2-2

description:
Library name: Sample50
Low epimutation rate RIL, G10, lineage L2-2

source_name: seedling

value: Ler x Cvi RIL RIL150


title: Ler_Cvi_RIL_LOW_RIL182_G03_L1-1

description:
Library name: Sample51
Low epimutation rate RIL, G03, lineage L1-1


title: DPC DPAC 2

description: Gene expression data from dermal papilla cells 2 cultured with DPAC

source_name: Dermal papilla cells 2 cultured with DPAC


title: Ler_Cvi_RIL_LOW_RIL150_G10_L2-1

description:
Library name: Sample49
Low epimutation rate RIL, G10, lineage L2-1


title: Ler_Cvi_RIL_LOW_RIL182_G03_L2-1

description:
Library name: Sample53
Low epimutation rate RIL, G03, lineage L2-1


title: Ler_Cvi_RIL_LOW_RIL150_G10_L1-1

description:
Library name: Sample48
Low epimutation rate RIL, G10, lineage L1-1


title: Ler_Cvi_RIL_LOW_RIL150_G03_L2-2

description:
Library name: Sample47
Low epimutation rate RIL, G03, lineage L2-2


title: Ler_Cvi_RIL_LOW_RIL149_G10_L2-1

description:
Library name: Sample46
Low epimutation rate RIL, G10, lineage L2-1

value: Ler x Cvi RIL RIL149


title: Ler_Cvi_RIL_LOW_RIL149_G10_L1-2

description:
Library name: Sample45
Low epimutation rate RIL, G10, lineage L1-2


title: Ler_Cvi_RIL_LOW_RIL149_G03_L2-1

description:
Library name: Sample44
Low epimutation rate RIL, G03, lineage L2-1


title: Ler_Cvi_RIL_LOW_RIL149_G03_L1-1

description:
Library name: Sample43
Low epimutation rate RIL, G03, lineage L1-1


title: DPC control 2

description: Gene expression data from dermal papilla cells 2 cultured with control

source_name: Dermal papilla cells 2 cultured with control


title: Ler_Cvi_RIL_HIGH_RIL155_G10_L2-1

description:
Library name: Sample42
High epimutation rate RIL, G10, lineage L2-1

value: Ler x Cvi RIL RIL155


title: Ler_Cvi_RIL_HIGH_RIL155_G10_L1-1

description:
Library name: Sample40
High epimutation rate RIL, G10, lineage L1-1


title: Ler_Cvi_RIL_HIGH_RIL155_G10_L1-2

description:
Library name: Sample41
High epimutation rate RIL, G10, lineage L1-2


title: Ler_Cvi_RIL_HIGH_RIL155_G03_L2-2

description:
Library name: Sample39
High epimutation rate RIL, G03, lineage L2-2


title: Ler_Cvi_RIL_HIGH_RIL155_G03_L1-1

description:
Library name: Sample37
High epimutation rate RIL, G03, lineage L1-1


title: Ler_Cvi_RIL_HIGH_RIL050_G10_L2-2

description:
Library name: Sample36
High epimutation rate RIL, G10, lineage L2-2

value: Ler x Cvi RIL RIL050


title: Ler_Cvi_RIL_HIGH_RIL050_G03_L2-1

description:
Library name: Sample34
High epimutation rate RIL, G03, lineage L2-1


title: DPC F9 1

description: Gene expression data from dermal papilla cells 1 cultured with F9

source_name: Dermal papilla cells 1 cultured with F9


title: Ler_Cvi_RIL_HIGH_RIL050_G10_L1-2

description:
Library name: Sample35
High epimutation rate RIL, G10, lineage L1-2


title: Ler_Cvi_RIL_HIGH_RIL015_G10_L2-2

description:
Library name: Sample31
High epimutation rate RIL, G10, lineage L2-2

value: Ler x Cvi RIL RIL015


title: Ler_Cvi_RIL_HIGH_RIL015_G03_L1-2

description:
Library name: Sample28
High epimutation rate RIL, G03, lineage L1-2


title: Ler_Cvi_RIL_HIGH_RIL015_G03_L1-1

description:
Library name: Sample27
High epimutation rate RIL, G03, lineage L1-1


title: DPC CH 1

description: Gene expression data from dermal papilla cells 1 cultured with CHIR

source_name: Dermal papilla cells 1 cultured with CH

value: human dermal papilla cells


title: Ler_Cvi_RIL_HIGH_RIL155_G03_L1-2

description:
Library name: Sample38
High epimutation rate RIL, G03, lineage L1-2


title: Ler_Cvi_RIL_HIGH_RIL015_G03_L2-2

description:
Library name: Sample30
High epimutation rate RIL, G03, lineage L2-2


title: RIL50_G010_L01_2_4 ATAC-seq

description: Library name: Sample7

data_processing:
Adapters were trimmed using Trimmomatic v0.39, and paired-end reads were aligned to the TAIR10 genome using BWA-MEM (v0.7.17).
Sorted BAM files were deduplicated using Picard MarkDuplicates (v2.23.8; REMOVE_DUPLICATES=true).
Peaks were called with MACS2 (v2.2.9.1) using BEDPE input mode and Arabidopsis genome size (1.35e8), with parameters --keep-dup all, --SPMR, and -q 0.05. All downstream analyses were restricted to chromosomes 1–5.
Assembly: A. thaliana(TAIR10)
Supplementary files format and content: MACS2-generated narrowPeak file in BED format representing ATAC-seq peaks

source_name: shoot

growth_protocol: The Arabidopsis thaliana RIL-lines were grown under long day conditions (16h light/8h dark) on ½ MS plates at 25 °C for 7-9 days.

extract_protocol:
For the nuclei extraction, approximately 200mg of shoots were collected. The samples were chopped down in 1ml pre-chilled lysis buffer (10mM MES-KOH pH5.4, 10mM NaOH, 250mM sucrose, 0.1mM spermine, 0.5mM spermidine, 1mM DTT, 1%BSA, 0.5% TritonX-100) and filtered through a 40µm and a 20µm strainer, with a centrifugation step in between (500xg, 5min). The nuclei were finally pelleted with a gradient solution (35% Percoll in lysis buffer) in a swing centrifuge at 500 xg for 10 min and resuspended in tagmentation buffer (10 mM TAPS-NaOH pH 8.0, 5 mM MgCl2). Nuclei quality and concentration were checked with DAPI staining at a cell counter.
50k-100k purified nuclei were incubated with 3µl Tn5 enzyme in 40µl tagmentation buffer (s.o.) at 37°C for 30 min. The products were purified using a PCR-extraction kit (NEB Monarch PCR & DNA Clean-up, #T1030) and then amplified for 10-12 cycles using Q5 polymerase (NEBNext HiFi 2x PCR Mastermix, #M0541). PCR conditions were followed as described previously (Buenrostro et al. 2013). Amplified libraries were purified with AMPure beads and concentrations were determined using Qubit and qPCR (Roche KAPA Library Quantification Kit) prior to sequencing. Paired-end 150 bp sequencing was performed on an Illumina NovaSeq 6000 platform.

value: shoot

value: Ler X Cvi RIL

tag: ril line

tag: generation

tag: lineage

tag: sublineage


title: RIL50_G03_L02_1_3 ATAC-seq

description: Library name: Sample6

tag: genotype


title: Ler_Cvi_RIL_HIGH_RIL050_G03_L1-2

description:
Library name: Sample33
High epimutation rate RIL, G03, lineage L1-2


title: RIL50_G010_L02_2_4 ATAC-seq

description: Library name: Sample8


title: DPC CH+F9 1

description: Gene expression data from dermal papilla cells 1 cultured with CHIR+F9

source_name: Dermal papilla cells 1 cultured with CH+F9

value: male

value: human dermal papilla cells from 43 year old male


title: RIL50_G03_L01_1_3 ATAC-seq

description: Library name: Sample5


title: Ler_Cvi_RIL_HIGH_RIL050_G03_L1-1

description:
Library name: Sample32
High epimutation rate RIL, G03, lineage L1-1


title: Ler_Cvi_RIL_HIGH_RIL015_G03_L2-1

description:
Library name: Sample29
High epimutation rate RIL, G03, lineage L2-1


title: RIL192_G09_L02_2

description: Library name: Sample371

data_processing:
Run MethylStar pipeline (Shahryary et al., 2020), using TAIR10 as a reference.
Cytosine-level methylation states were called as either methylated (“M”), unmethylated (“U”) or intermediate methylated (“I”) using a three-state Hidden Markov Model (Taudt et al. 2018).
Assembly: A. thaliana(TAIR10)
Supplementary files format and content: Tab-delimited text files for methylome generated using METHimpute (Taudt et al. 2018)

source_name: leaf tissue

growth_protocol: The MAMP was grown in climate-controlled chambers for nine selfing generations (Long day conditions, 16-h-day lengths, 18 C).

extract_protocol:
Samples were collected from young above-ground tissue. Leaf tissue was flash frozen in liquid nitrogen and DNA was extracted using a Qiagen Plant DNeasy kit (Qiagen, Valencia, CA, USA) based on the manufacturer’s instructions.
MethylC-seq libraries were prepared based on the protocol described in Urich et al., (2015). Libraries were sequenced at Genewiz on a NovaSeq 6000 platform (Illumina) in a paired-end 150bp format.

value: leaf tissue


title: RIL149_G010_L02_1_4 ATAC-seq

description: Library name: Sample4


title: RIL192_G09_L02_1

description: Library name: Sample370


title: RIL192_G09_L01_2

description: Library name: Sample369


title: RIL149_G010_L01_2_4 ATAC-seq

description: Library name: Sample3


title: RIL149_G03_L01_1_3 ATAC-seq

description: Library name: Sample1


title: RIL149_G03_L02_1_3 ATAC-seq

description: Library name: Sample2


title: RIL192_G02_L02_3

description: Library name: Sample366


title: RIL192_G09_L01_1

description: Library name: Sample368


title: RIL192_G02_L02_4

description: Library name: Sample367


title: RIL192_G02_L01_3

description: Library name: Sample364


title: RIL192_G02_L01_4

description: Library name: Sample365


title: RIL191_G02_L02_4

description: Library name: Sample361


title: RIL191_G09_L02_2

description: Library name: Sample363


title: RIL191_G09_L02_1

description: Library name: Sample362


title: RIL190_G09_L02_2

description: Library name: Sample359


title: RIL190_G09_L01_2

description: Library name: Sample358


title: RIL191_G02_L02_3

description: Library name: Sample360


title: RIL190_G02_L02_4

description: Library name: Sample356


title: RIL190_G02_L02_3

description: Library name: Sample355


title: RIL190_G09_L01_1

description: Library name: Sample357


title: RIL186_G09_L01_1

description: Library name: Sample348


title: RIL190_G02_L01_4

description: Library name: Sample354


title: RIL186_G02_L02_3

description: Library name: Sample350


title: RIL186_G09_L01_2

description: Library name: Sample349


title: RIL186_G02_L01_3

description: Library name: Sample346


title: RIL182_G02_L01_4

description: Library name: Sample341


title: RIL175_G09_L02_2

description: Library name: Sample333


title: RIL175_G09_L02_1

description: Library name: Sample334


title: RIL175_G02_L02_3

description: Library name: Sample328


title: RIL173_G09_L02_1

description: Library name: Sample326


title: RIL173_G09_L01_2

description: Library name: Sample325


title: RIL175_G09_L01_1

description: Library name: Sample332


title: RIL173_G02_L02_4

description: Library name: Sample323


title: RIL172_G02_L02_3

description: Library name: Sample317


title: RIL172_G09_L01_1

description: Library name: Sample319


title: RIL170_G09_L02_1

description: Library name: Sample315


title: RIL170_G02_L01_4

description: Library name: Sample313


title: RIL168_G09_L01_1

description: Library name: Sample309


title: RIL168_G02_L02_3

description: Library name: Sample308


title: RIL186_G02_L01_4

description: Library name: Sample347


title: RIL186_G02_L02_4

description: Library name: Sample351


title: RIL180_G02_L01_3

description: Library name: Sample335


title: RIL180_G09_L02_1

description: Library name: Sample339


title: RIL180_G02_L02_3

description: Library name: Sample336


title: RIL167_G09_L02_2

description: Library name: Sample306


title: RIL173_G09_L01_1

description: Library name: Sample324


title: RIL167_G09_L01_1

description: Library name: Sample305


title: RIL167_G02_L02_4

description: Library name: Sample304


title: RIL167_G02_L02_3

description: Library name: Sample303


title: RIL172_G02_L01_4

description: Library name: Sample320


title: RIL167_G02_L01_3

description: Library name: Sample301


title: RIL166_G09_L02_2

description: Library name: Sample300


title: RIL166_G09_L01_1

description: Library name: Sample298


title: RIL166_G02_L02_4

description: Library name: Sample297


title: RIL165_G09_L02_1

description: Library name: Sample293


title: RIL165_G09_L01_2

description: Library name: Sample292


title: RIL165_G02_L02_4

description: Library name: Sample290


title: RIL165_G02_L02_3

description: Library name: Sample289


title: RIL167_G02_L01_4

description: Library name: Sample302


title: RIL165_G02_L01_3

description: Library name: Sample288


title: RIL166_G09_L01_2

description: Library name: Sample299


title: RIL166_G02_L01_4

description: Library name: Sample296


title: RIL163_G02_L02_3

description: Library name: Sample286


title: RIL163_G09_L01_2

description: Library name: Sample287


title: RIL166_G02_L01_3

description: Library name: Sample295


title: RIL163_G02_L01_4

description: Library name: Sample285


title: RIL165_G09_L02_2

description: Library name: Sample294


title: RIL163_G02_L01_3

description: Library name: Sample284


title: RIL162_G09_L02_2

description: Library name: Sample282


title: RIL162_G02_L02_4

description: Library name: Sample280


title: RIL162_G09_L02_1

description: Library name: Sample281


title: RIL162_G02_L02_3

description: Library name: Sample279


title: RIL162_G02_L01_4

description: Library name: Sample278


title: RIL162_G02_L01_3

description: Library name: Sample277


title: RIL165_G09_L01_1

description: Library name: Sample291


title: RIL190_G02_L01_3

description: Library name: Sample353


title: RIL186_G09_L02_1

description: Library name: Sample352


title: RIL158_G09_L02_2

description: Library name: Sample276


title: RIL182_G02_L02_4

description: Library name: Sample343


title: RIL182_G09_L01_1

description: Library name: Sample344


title: RIL158_G02_L02_4

description: Library name: Sample274


title: RIL182_G02_L01_3

description: Library name: Sample345


title: RIL158_G09_L01_2

description: Library name: Sample275


title: RIL158_G02_L02_3

description: Library name: Sample273


title: RIL180_G09_L02_2

description: Library name: Sample340


title: RIL180_G09_L01_1

description: Library name: Sample338


title: RIL182_G02_L02_3

description: Library name: Sample342


title: RIL180_G02_L02_4

description: Library name: Sample337


title: RIL158_G02_L01_4

description: Library name: Sample272


title: RIL158_G02_L01_3

description: Library name: Sample271


title: RIL175_G02_L01_3

description: Library name: Sample329


title: RIL173_G09_L02_2

description: Library name: Sample327


title: RIL175_G02_L02_4

description: Library name: Sample331


title: RIL155_G09_L01_2

description: Library name: Sample269


title: RIL155_G09_L02_1

description: Library name: Sample270


title: RIL175_G02_L01_4

description: Library name: Sample330


title: RIL173_G02_L02_3

description: Library name: Sample322


title: RIL155_G09_L01_1

description: Library name: Sample268


title: RIL173_G02_L01_3

description: Library name: Sample321


title: RIL155_G02_L02_4

description: Library name: Sample267


title: RIL155_G02_L01_3

description: Library name: Sample266


title: RIL155_G02_L02_3

description: Library name: Sample265


title: RIL154_G09_L02_1

description: Library name: Sample263


title: RIL154_G09_L01_2

description: Library name: Sample264


title: RIL154_G02_L02_4

description: Library name: Sample262


title: RIL154_G02_L02_3

description: Library name: Sample261


title: RIL153_G09_L02_1

description: Library name: Sample258


title: RIL154_G02_L01_4

description: Library name: Sample260


title: RIL153_G09_L01_2

description: Library name: Sample257


title: RIL153_G09_L02_2

description: Library name: Sample259


title: RIL172_G02_L02_4

description: Library name: Sample318


title: RIL153_G09_L01_1

description: Library name: Sample256


title: RIL153_G02_L02_4

description: Library name: Sample255


title: RIL151_G09_L01_2

description: Library name: Sample252


title: RIL153_G02_L01_3

description: Library name: Sample254


title: RIL153_G02_L01_4

description: Library name: Sample253


title: RIL151_G09_L01_1

description: Library name: Sample251


title: RIL151_G02_L02_4

description: Library name: Sample250


title: RIL150_G09_L02_1

description: Library name: Sample248


title: RIL151_G02_L02_3

description: Library name: Sample249


title: RIL150_G02_L02_4

description: Library name: Sample245


title: RIL149_G09_L02_1

description: Library name: Sample244


title: RIL150_G09_L01_1

description: Library name: Sample247


title: RIL149_G02_L02_3

description: Library name: Sample242


title: RIL149_G02_L01_4

description: Library name: Sample241


title: RIL147_G02_L01_3

description: Library name: Sample240


title: RIL147_G09_L01_2

description: Library name: Sample237


title: RIL147_G09_L02_1

description: Library name: Sample238


title: RIL146_G02_L02_3

description: Library name: Sample230


title: RIL146_G09_L02_1

description: Library name: Sample233


title: RIL146_G02_L01_4

description: Library name: Sample229


title: RIL146_G02_L02_4

description: Library name: Sample231


title: RIL147_G02_L01_4

description: Library name: Sample235


title: RIL143_G02_L01_3

description: Library name: Sample227


title: RIL143_G09_L02_2

description: Library name: Sample226


title: RIL143_G02_L01_4

description: Library name: Sample224


title: RIL142_G09_L02_2

description: Library name: Sample222


title: RIL142_G09_L01_2

description: Library name: Sample221


title: RIL140_G02_L01_4

description: Library name: Sample218


title: RIL140_G02_L01_3

description: Library name: Sample217


title: RIL136_G09_L01_2

description: Library name: Sample215


title: RIL140_G02_L02_4

description: Library name: Sample216


title: RIL136_G09_L01_1

description: Library name: Sample214


title: RIL136_G02_L02_4

description: Library name: Sample213


title: RIL136_G02_L01_4

description: Library name: Sample211


title: RIL135_G09_L01_2

description: Library name: Sample210


title: RIL135_G02_L02_3

description: Library name: Sample208


title: RIL135_G02_L01_4

description: Library name: Sample207


title: RIL135_G02_L01_3

description: Library name: Sample206


title: RIL133_G09_L02_1

description: Library name: Sample204


title: RIL133_G09_L01_2

description: Library name: Sample203


title: RIL133_G02_L02_3

description: Library name: Sample201


title: RIL133_G02_L01_3

description: Library name: Sample199


title: RIL127_G09_L02_2

description: Library name: Sample195


title: RIL127_G09_L02_1

description: Library name: Sample194


title: RIL127_G02_L02_4

description: Library name: Sample191


title: RIL127_G02_L02_3

description: Library name: Sample190


title: RIL140_G09_L01_2

description: Library name: Sample219


title: RIL135_G02_L02_4

description: Library name: Sample209


title: RIL127_G02_L01_3

description: Library name: Sample189


title: RIL127_G02_L01_4

description: Library name: Sample188


title: RIL133_G09_L02_2

description: Library name: Sample205


title: RIL126_G09_L02_2

description: Library name: Sample187


title: RIL126_G02_L02_3

description: Library name: Sample186


title: RIL133_G02_L01_4

description: Library name: Sample200


title: RIL132_G09_L02_2

description: Library name: Sample198


title: RIL126_G02_L01_4

description: Library name: Sample185


title: RIL132_G02_L02_3

description: Library name: Sample197


title: RIL132_G02_L01_4

description: Library name: Sample196


title: RIL126_G02_L01_3

description: Library name: Sample184


title: RIL126_G02_L02_4

description: Library name: Sample183


title: RIL125_G09_L02_2

description: Library name: Sample181


title: RIL125_G09_L01_2

description: Library name: Sample179


title: RIL125_G02_L01_4

description: Library name: Sample178


title: RIL120_G02_L01_4

description: Library name: Sample176


title: RIL125_G02_L02_4

description: Library name: Sample177


title: RIL120_G09_L02_2

description: Library name: Sample175


title: RIL120_G09_L02_1

description: Library name: Sample174


title: RIL120_G09_L01_1

description: Library name: Sample173


title: RIL120_G02_L02_3

description: Library name: Sample172


title: RIL116_G09_L01_2

description: Library name: Sample170


title: RIL120_G02_L01_3

description: Library name: Sample171


title: RIL116_G02_L02_3

description: Library name: Sample168


title: RIL116_G02_L02_4

description: Library name: Sample169


title: RIL116_G02_L01_4

description: Library name: Sample167


title: RIL116_G02_L01_3

description: Library name: Sample166


title: RIL112_G02_L02_4

description: Library name: Sample164


title: RIL112_G09_L01_2

description: Library name: Sample165


title: RIL112_G02_L02_3

description: Library name: Sample163


title: RIL108_G09_L02_1

description: Library name: Sample162


title: RIL108_G02_L02_4

description: Library name: Sample161


title: RIL108_G02_L02_3

description: Library name: Sample160


title: RIL108_G02_L01_4

description: Library name: Sample159


title: RIL108_G02_L01_3

description: Library name: Sample158


title: RIL101_G09_L02_2

description: Library name: Sample157


title: RIL101_G09_L01_1

description: Library name: Sample156


title: RIL101_G02_L02_3

description: Library name: Sample155


title: RIL101_G02_L02_4

description: Library name: Sample154


title: RIL101_G02_L01_4

description: Library name: Sample153


title: RIL101_G02_L01_3

description: Library name: Sample152


title: RIL125_G02_L02_3

description: Library name: Sample182


title: RIL72_G02_L02_4

description: Library name: Sample151


title: RIL125_G09_L02_1

description: Library name: Sample180


title: RIL72_G09_L02_2

description: Library name: Sample150


title: RIL72_G02_L01_4

description: Library name: Sample146


title: RIL72_G09_L01_1

description: Library name: Sample148


title: RIL72_G02_L02_3

description: Library name: Sample147


title: RIL72_G09_L02_1

description: Library name: Sample149


title: RIL71_G09_L01_2

description: Library name: Sample145


title: RIL71_G09_L02_2

description: Library name: Sample144


title: RIL149_G09_L01_2

description: Library name: Sample243


title: RIL71_G09_L02_1

description: Library name: Sample143


title: RIL150_G09_L02_2

description: Library name: Sample246


title: RIL71_G02_L02_4

description: Library name: Sample142


title: RIL147_G02_L02_4

description: Library name: Sample236


title: RIL147_G09_L02_2

description: Library name: Sample239


title: RIL146_G09_L02_2

description: Library name: Sample234


title: RIL71_G02_L01_3

description: Library name: Sample140


title: RIL71_G02_L02_3

description: Library name: Sample141


title: RIL70_G09_L02_1

description: Library name: Sample139


title: RIL146_G02_L01_3

description: Library name: Sample228


title: RIL70_G02_L01_3

description: Library name: Sample137


title: RIL70_G02_L02_4

description: Library name: Sample138


title: RIL146_G09_L01_2

description: Library name: Sample232


title: RIL68_G02_L01_4

description: Library name: Sample136


title: RIL143_G02_L02_3

description: Library name: Sample223


title: RIL68_G02_L01_3

description: Library name: Sample135


title: RIL68_G09_L02_1

description: Library name: Sample133


title: RIL68_G09_L01_2

description: Library name: Sample132


title: ZNF143, biol rep1

city: Toronto

first: Luomeng

last: Tan

state: Ontario

address: 101 College St

institute: University of Toronto

description: Library name: Sample 3

data_processing:
We trimmed the adapters and filtered out low-quality reads using the default settings of fastp (version 0.19.8).
We aligned the reads to the hg38 using Bowtie2 (version 2.4.4) with options "--local -D 20 -R 6 -N 1 -L 18 -i S,1,0.25 --phred33 --no-unal --no-discordant --no-mixed -I 10 -X 700". We aligned reads to the spike-in genome sacCer3 with additional options "--no-overlap --no-dovetail".
We filtered the aligned reads to only keep reads from fragments with a length ≤ 120 bp with deepTools alignmentSieve (version 3.5.1) for both the target genome and the spike-in genome.
We called peaks with MACS2 (version 2.2.7.1) and SEACR (version 1.3). We used MACS2 subcommands including pileup, bdgopt, bdgcmp, bdgpeakcall following the tutorial from MACS2 Git repository (https://github.com/macs3-project/MACS/wiki/Advanced%3A-Call-peaks-using-MACS2-subcommands). We called SEACR peaks using the stringent mode without normalization.
Assembly: hg38
Supplementary files format and content: BED files of aligned reads
Library strategy: CUT&Run

growth_protocol: We cultured the K562 cells in RPMI-1640 (Hyclone) supplemented with 100 U/mL penicillin (Gibco), 100 μg/μL streptomycin (Gibco), 292 μg/μL L-glutamine (Gibco), and 10 % FBS (Gibco). We maintained the cells at 37 °C and 5 % CO2 with routine testing to confirm the lack of Mycoplasma infection.

extract_protocol:
We adapted the CUT&RUN protocol and all buffer recipes from Skene and colleagues (Skene et al., 2018) and performed the experiments in 0.2 mL tubes as we recently described (Ishak et al., 2025). Briefly, we washed and immobilized 200 000 K562 cells on 10 μL of activated concanavalin A–coated magnetic beads (Polysciences BioMag®Plus cat. no. 86057-3). We incubated cells in 0.2 mL antibody buffer containing 1: 100 diluted primary antibody (anti-C/EBP𝛽, Santa Cruz Biotechnology (Dallas, Texas, USA) cat. no. sc-7962, anti-ZNF143 Proteintech (Rosemont, IL, USA) cat. no. 16618-1-AP; RRID: AB_2218324, or anti-IgG , Abcam (UK) cat. no. ab37415; RRID: AB_2631996) for 2 h at 4 °C with rotation. Then, we washed the cells with 0.2 mL of digitonin wash buffer. Next, we incubated the cells in 0.2 mL of digitonin wash buffer containing recombinant pA-MNase (expressed and purified in house) diluted to a final concentration of ∼ 0.8 ng/μL for 1 h at 4 °C with rotation. We then discarded the buffer and replaced it with 150 μL of digitonin wash buffer. Using an ice-water bath, we cooled the tubes to 0 °C for 5 min and added CaCl2 to activate pA-MNase-mediated digestion for 30 min. After 30 min , we added 2x STOP buffer containing chelating agents and heterologous Saccharomyces cerevisiae spike-in DNA to stop the reaction. We incubated the cells at 37 °C for 10 min and centrifuged the cells at 16 000 × g for 5 min at 4 °C. We isolated the DNA from the supernatant containing soluble chromatin fragments via phenol chloroform extraction.
We performed library preparation of 5 ng of CUT&RUN DNA using NEBNext Ultra II DNA Library Preparation Kit for Illumina ( NEB, cat. no. E7645L) as per manufacturer’s protocol. We uniquely indexed each sample using NEBNext Multiplex Oligos for Illumina (Index Primers Set 1, cat. no. E7335L and Index Primers Set 2, cat. no. E7500L). We sequenced all libraries at Princess Margaret Genomics Centre (PMGC, Toronto, ON) on an Illumina NextSeq 500 High-Output flow cell using paired-end 2 × 150 bp read length configuration.

tag: cell line

tag: cell type

value: lymphoblast cells

value: WT

tag: cut&run antibody

value: ZNF143 (Proteintech, #16618-1-AP)


title: IgG, biol rep1

description: Library name: Sample 4

value: IgG (Abcam, #ab37415)


title: IgG, biol rep2

description: Library name: Sample 5


title: CEBPB, biol rep2

description: Library name: Sample 2

value: C/EBPB (Santa Cruz Biotechnology, #sc-7962)


title: RIL68_G02_L02_4

description: Library name: Sample130

tag: tissue


title: CEBPB, biol rep1

description: Library name: Sample 1


title: RIL68_G02_L02_3

description: Library name: Sample129


title: Barnyard_96well_rep96

city: Carlsbad

first: Tom

last: Chen

state: CA

address: 6155 Corte Del Cedro

department: R&D

institute: Universal Sequencing Technology Corp.

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep96

data_processing:
Sequencing reads were processed with AmpliDrop software v1.0. Cell calling and data processing was generated with Cell Ranger v5.1
Within AmpliDrop software analysis, after bcl files been converted to fastq files, the pipeline generated three types of fastq files: cDNA reads, been called as "R1"; sample index reads, with 8 nucleotides, been called as "I1"; and barcode reads, with 20 nucleotides, been called as "I2", in which six nucleotides at positions of 4, 5, 10, 11, 16, and 17 were used as code. The pipeline was then demultiplexing the samples based on the sample index combined with the code used. However, the sample index and code sequences were not saved after demultiplexing. To evaluate the fastq quality, the pipeline ran the fastqc tool on each set of fastq files for the demultiplexed sample. After the barcodes were error collected and the cDNA reads were trimmed with the potential adapter sequences and poly-A nucleotides, the pipeline ran a merging algorithm to merge the barcodes that were located in the same droplet. At the end of the pipeline, the fastq files were converted into 10X Genomic cellranger compatible format.
Assembly: hg38 and mm10
Supplementary files format and content: _barcodes.tsv.gz contains all cellular barcodes, tab separated text file, gzipped; _features.tsv.gz contains feature annotations, tab separated text file, gzipped, column1: feature id, column2: feature name, and column3: type of feature, i.e., "Gene Expression"; _matrix.mtx.gz contains UMI counts in each gene and in each cellular barcode, with mtx format, gzipped.

organism:
Homo sapiens
Mus musculus

source_name: embryonic kidney and fibroblast cell lines

growth_protocol: All cell lines were grown in an incubator at 37C and 5% CO2 with media conditions as suggested by ATCC (293T, NIH-3T3, MCF7, HCT-116, and Jurkat) or Sigma (A2780 and A2780cis) supplemented with pen/strep antibiotics. Cells were generally grown close to confluency at the moment of collecting the cells. The WT83 clone6 of human induced-pluripotent stem cells (hiPSCs), derived from a typically developing Caucasian male 29,72, were grown on growth factor-reduced Matrigel, coated 6-cm dishes in mTeSR Plus without antibiotics. For propagation, cells were dissociated with Versene, EDTA, or Relers. To generate forebrain organoids, we followed a semi-guided protocol with a few modifications. Human iPSCs were grown in mTeSR Plus to a confluency of approximately 70% in a 6-cm plate and dissociated with a 1:1 mix of accutase/DPBS. Approximately, three million hiPSCs with a viability >95% were transferred into ultra-low attachment 6-well plates with mTeSR plus media supplemented with the SMAD inhibitors SB-431542 and Dorsomorphin, and the Rho-associated proteinase kinase (ROCK) inhibitor (RI) Y-27632. Plates were placed on orbital shaker. Alternatively, 2 million hiPSCs were transferred to a well of AggreWell-800 plate, pre-coated with Anti-Adherent Solution in mTeSR plus supplemented with RI. The AggreWell plate was centrifugated and transferred to incubator overnight. The following day, embryoid bodies (EB) were transferred to a well of 6-well plate changing the media to fresh mTsERplus supplemented with SB and Dorsomorphin as described above. Regular media and factors changes to complete generation of forebrain organoids were performed in M2 medium composed of Neurobasal supplemented with 1% Glutamax, 1% MEM non-essential amino acids solution, NEAA, and 1x B27 performing half/medium changes every two days for the first month or twice a week after.

extract_protocol:
Peripheral venous blood was drawn from voluntary donor using EDTA-treated tubes and LymphoprepTM and stored at 4°C. Cells were resuspended in 1x phosphate-buffered saline buffer solution (1xPBS) supplemented with 2% bovine serum albumin, BSA, and layered over 1.5 mL Lymphoprep Density Gradient Medium in a 15 mL conical tube, according to the manufacturer’s protocol.  The solution was centrifuged at 800xg for 20 min at room temperature without brake.  The mononuclear cell layer at the gradient interface was collected in a new tube and washed in PBS/2% FBS (10 mL total volume) and centrifuged at 120xg for 10 min at room temperature without brake.  The wash step was repeated two more times, and the cells were resuspended in PBS for sequencing library preparation.  The cells not used immediately were cryopreserved in 90% FBS/10% DMSO.
3' scRNA-seq (AmpliDrop technology); Dissociated cells (typically, >90-95% viable) in 0.1% BSA-supplemented 1x DPBS buffer were processed with AmpliDrop 3’ scRNA-seq kits following the manufacturer’s recommendations. Briefly, more than 200,000 cells were typically fixed at room temperature for 45 minutes and permeabilized for 10 minutes. For the RT and tagmentation reactions, we used 60,000 fixed and permeabilized cells. RT was conducted at 50°C for 10 minutes, and 10 cycles at 60°C for 30 sec and 50°C for 3 min, and tagmentation was conducted at 37°C for 15 minutes. Cell encapsulation was based on the following mixing protocol: 50 mixes of 170 µL at Speed 2 followed by 10 mixes of 170 µL at Speed 3. The emulsions were then moved to a thermocycler to run the following PCR/barcoding program: 72°C for 5 min, 98°C for 1 min, 26 cycles with 98°C for 15 sec, 61°C for 40 sec, and 72°C for 30 sec, and 5 cycles with 98°C for 15 sec, 50°C for 2 min, and 72°C for 40 sec, ending with 72°C for 2 min. After PCR/barcoding, the emulsions were dissolved, and the DNA was recovered from the solution  with the same volume of SPRI beads from MagBio genomics. The libraries were cleaned up with 80% ethanol for three times and finally eluted in 38 µL of 0.1x TE buffer, and half of this volume was used for indexing using Illumina adapters. Typically, we amplified the library with 9 to 12 cycles depending on the expected number of cell output (12 cycles for 1,000-2,000 cells and 9 cycles for 7,000-10,000 cells). The PCR indexing program is the following: 98°C for 30 sec, and 9-12 cycles with 98°C for 20 sec, 61°C for 30 sec, and 72°C for 30 sec, ending with 72°C for 2 min. After PCR, the library (40 µL) was diluted to 100 µL with TE buffer and cleaned up with 90 µL of SPRI beads. After washing with 80% ethanol twice, the library was eluted in 30 µL of 0.1x TE buffer. Libraries were then subject to quality control, sizing, and quantification using Agilent 4150 TapeStation system with High Sensitivity D1000 ScreenTape and Reagents.

treatment_protocol: No treatments were performed on cell lines. For seven-month-old organoids (Exp 1), mildly-perturbed conditions refer to a regimen of pipette aspiration with a wide-origfice 1mL tip and transfer of the organoids to a metal platform to mimic a mild physical manipulation of these multicellular structures. Severely-perturbed conditions refer to smashing the organoids to generate deformative compression to mimic a highly damaging physicial manipulation. Both treatments required maintaining the organoids for approximately 90 minutes outside the incubator. In the incubator, both sets of organoids were maintained withouth motion for 3 days. Non-perturbed organoids were maintained under orbital shaking all the time. For six-month-old organoids (Exp 2), everything was as in Exp1 but the non-perturbed group of organoids was also maintained 90 minutes outside the incubator. For two-month-old organoids (Exp3), one set was grown under orbital shaking always, while the other set was kept withouth motion for three days before library preparation.

value: 293T and NIH3T3

value: Human embryonic kidney and mouse embryonic fibroblasts

tag: treatment


title: Barnyard_96well_rep95

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep95

value: embryonic kidney and fibroblast cell lines


title: Barnyard_96well_rep94

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep94


title: RIL65_G02_L02_3

last: Zhang

description: Library name: Sample126


title: Barnyard_96well_rep93

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep93


title: Barnyard_96well_rep91

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep91


title: Barnyard_96well_rep92

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep92


title: RIL65_G02_L01_3

description: Library name: Sample125


title: RIL63_G09_L01_2

description: Library name: Sample123


title: RIL63_G02_L02_4

description: Library name: Sample124


title: Barnyard_96well_rep90

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep90


title: RIL63_G02_L02_3

description: Library name: Sample122


title: Barnyard_96well_rep89

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep89


title: Barnyard_96well_rep88

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep88


title: RIL63_G02_L01_4

description: Library name: Sample121


title: RIL61_G09_L02_2

description: Library name: Sample120


title: Barnyard_96well_rep87

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep87


title: Barnyard_96well_rep86

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep86


title: RIL61_G09_L01_2

description: Library name: Sample119


title: RIL61_G02_L01_4

description: Library name: Sample117


title: RIL61_G02_L01_3

description: Library name: Sample116


title: Barnyard_96well_rep83

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep83


title: Barnyard_96well_rep82

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep82


title: RIL59_G09_L02_2

description: Library name: Sample115


title: Barnyard_96well_rep81

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep81


title: RIL59_G09_L02_1

description: Library name: Sample114


title: Barnyard_96well_rep80

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep80


title: RIL59_G09_L01_1

description: Library name: Sample113


title: Barnyard_96well_rep79

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep79


title: RIL59_G02_L02_4

description: Library name: Sample112


title: Barnyard_96well_rep78

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep78


title: RIL59_G02_L02_3

description: Library name: Sample111


title: Barnyard_96well_rep77

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep77


title: RIL168_G09_L01_2

description: Library name: Sample310


title: Barnyard_96well_rep76

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep76


title: RIL59_G02_L01_3

description: Library name: Sample109


title: RIL59_G02_L01_4

description: Library name: Sample110


title: Barnyard_96well_rep75

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep75


title: RIL58_G09_L02_2

description: Library name: Sample108


title: RIL58_G09_L01_2

description: Library name: Sample107


title: Mouse CD8+ TILs, Slc7a11 KO anti-CTLA4, TCR-seq

city: Beijing

first: Haopeng

last: Hong

address: Xicheng street

institute: Peking University First Hospital

description:
Library name: TCR_KO_CTLA4
Paired-end 150 bp TCR repertoire sequencing of mouse tumor-infiltrating CD8-positive T cells.

data_processing:
Raw FASTQ files were processed with the Cell Ranger VDJ pipeline to generate per-sample clonotype calls and filtered contig annotation tables.
Assembly: Mus musculus mm10
Supplementary files format and content: Per-sample Cell Ranger VDJ CSV files: clonotypes.csv contains TCR clonotype abundance and CDR3 sequence information; filtered_contig_annotations.csv contains filtered TCR contig annotation records.
Library strategy: TCR-Seq

source_name: tumor

extract_protocol:
Mouse tumor tissues were dissociated into single-cell suspensions, and tumor-infiltrating CD8-positive T cells were isolated for TCR repertoire sequencing.
TCR repertoire libraries were prepared from genomic DNA and sequenced as paired-end 150 bp reads on an Illumina NovaSeq 6000 instrument.

treatment_protocol: Tumor-bearing mice were assigned to IgG control or anti-CTLA4 antibody treatment groups as indicated for each sample.

value: tumor

value: tumor-infiltrating CD8-positive T cell

value: Slc7a11 knockout

value: anti-CTLA4 antibody


title: Barnyard_96well_rep73

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep73


title: RIL58_G02_L02_4

description: Library name: Sample106


title: Mouse CD8+ TILs, Slc7a11 KO IgG control, TCR-seq

description:
Library name: TCR_KO_IgG
Paired-end 150 bp TCR repertoire sequencing of mouse tumor-infiltrating CD8-positive T cells.

value: IgG control


title: Barnyard_96well_rep72

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep72


title: Mouse CD8+ TILs, WT IgG control, TCR-seq

description:
Library name: TCR_WT_IgG
Paired-end 150 bp TCR repertoire sequencing of mouse tumor-infiltrating CD8-positive T cells.

value: wild type


title: Mouse CD8+ TILs, Slc7a11 KO anti-CTLA4

description:
Library name: scRNA_KO_CTLA4
10x Genomics Chromium single-cell RNA-seq; Slc7a11 knockout anti-CTLA4 treatment; 7773 cells after QC according to vendor Cell Ranger report.

data_processing:
Raw FASTQ files were processed with Cell Ranger v7.0.0 to generate per-sample filtered feature-barcode matrices. Downstream quality control, dimensionality reduction, clustering, and differential expression analyses were performed using the filtered gene expression count matrices.
Assembly: Mouse mm10
Supplementary files format and content: Per-sample Cell Ranger filtered feature-barcode HDF5 files containing gene expression count matrices for high-quality cells.

extract_protocol:
Mouse tumor tissues were dissociated into single-cell suspensions. Tumor-infiltrating CD8-positive T cells were isolated and prepared for 10x Genomics Chromium single-cell RNA-seq library construction.
Single-cell suspensions were processed using the 10x Genomics Chromium platform. Gel beads, cells, and reagents were loaded to generate GEMs; barcoded cDNA libraries were constructed according to the 10x Genomics single-cell gene expression protocol and sequenced on an Illumina NovaSeq 6000.


title: RIL55_G09_L02_1

description: Library name: Sample104

value: Ler X Cvi RIL


title: Mouse CD8+ TILs, Slc7a11 KO IgG

description:
Library name: scRNA_KO_IgG
10x Genomics Chromium single-cell RNA-seq; Slc7a11 knockout IgG control; 9025 cells after QC according to vendor Cell Ranger report.


title: Barnyard_96well_rep70

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep70


title: Mouse CD8+ TILs, WT anti-CTLA4

description:
Library name: scRNA_WT_CTLA4
10x Genomics Chromium single-cell RNA-seq; WT anti-CTLA4 treatment; 12194 cells after QC according to vendor Cell Ranger report.


title: Mouse CD8+ TILs, WT IgG

description:
Library name: scRNA_WT_IgG
10x Genomics Chromium single-cell RNA-seq; WT IgG control; 8971 cells after QC according to vendor Cell Ranger report.


title: Barnyard_96well_rep69

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep69


title: C2C12, SRF-RELA_3

city: Brussels

first: Jean-Baptiste

last: Demoulin

address: av Hippocrate 75, B1.74.05

department: de Duve Institute

country: Belgium

institute: Université catholique de Louvain

description: Library name: SRF-RELA_3

data_processing:
Read quality control was performed using FastQC software v0.11.8 (Andrews S, Babraham Bioinformatics)
Low quality reads were trimmed and adapters were removed using Trimmomatic software v0.39
Reads were aligned using the HISAT2 software v2.12.1 [9] on GRCm38 genome
Gene counts were generated using featureCounts software from subread-2.0.0 and Ensembl  Mus_musculus.GRCm38.94.gtf annotation file
Assembly: Ensembl  Mus_musculus.GRCm38.94.gtf
Supplementary files format and content: raw counts

growth_protocol: Mouse C2C12 myoblasts were cultured in Dulbecco’s modified Eagle’s medium (DMEM) (Lonza, Basel, Switzerland) supplemented with 10% fetal bovine serum

extract_protocol:
Total RNA was extracted with TriPure Isolation Reagent (Sigma-Aldrich) and cleaned from residual genomic DNA with DNase on column (NucleoSpin RNA, Macherey-Nagel, Düren, Germany)
Libraries were prepared using the TruSeq Stranded mRNA kit and sequenced on a NovaSeq 6000 Sequencing System (Illumina, San Diego, CA, USA)

value: mouse myoblast cell line

value: SRF-RELA


title: C2C12, SRF-RELA_2

description: Library name: SRF-RELA_2


title: RIL55_G02_L02_4

description: Library name: Sample102

value: leaf tissue


title: C2C12, SRF-RELA_1

description: Library name: SRF-RELA_1


title: RIL55_G02_L02_3

description: Library name: Sample101


title: C2C12, SRF-PDGFRB_2

description: Library name: SRF-PDGFRb_2

value: SRF-PDGFRB


title: Barnyard_96well_rep67

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep67

value: WT


title: RIL55_G09_L01_2

description: Library name: Sample103


title: C2C12, SRF-PDGFRB_1

description: Library name: SRF-PDGFRb_1


title: RIL55_G02_L01_4

description: Library name: Sample100


title: C2C12, SRF-ICA1L_3

description: Library name: SRF-ICA1L_3


title: Barnyard_96well_rep68

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep68


title: Barnyard_96well_rep66

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep66


title: C2C12, SRF-ICA1L_2

description: Library name: SRF-ICA1L_2


title: C2C12, SRF-ICA1L_1

description: Library name: SRF-ICA1L_1


title: Barnyard_96well_rep65

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep65


title: C2C12, SRF-FOXO1_3

description: Library name: SRF-FOXO1_3


title: RIL54_G09_L01_2

description: Library name: Sample98


title: C2C12, SRF-FOXO1_1

description: Library name: SRF-FOXO1_1


title: Barnyard_96well_rep63

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep63


title: C2C12, SRF_2

description: Library name: SRF_2

value: SRF


title: RIL55_G02_L01_3

description: Library name: Sample99


title: RIL58_G02_L02_3

description: Library name: Sample105


title: C2C12, SRF-FOXO1_2

description: Library name: SRF-FOXO1_2


title: Barnyard_96well_rep71

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep71


title: Mouse CD8+ TILs, WT anti-CTLA4, TCR-seq

description:
Library name: TCR_WT_CTLA4
Paired-end 150 bp TCR repertoire sequencing of mouse tumor-infiltrating CD8-positive T cells.


title: C2C12, SRF_3

description: Library name: SRF_3


title: RIL54_G02_L02_4

description: Library name: Sample97


title: Barnyard_96well_rep64

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep64


title: RIL54_G02_L01_4

description: Library name: Sample96


title: C2C12, SRF_1

description: Library name: SRF_1


title: RIL68_G09_L02_2

description: Library name: Sample134


title: RIL54_G02_L01_3

description: Library name: Sample95


title: C2C12, pMSCV_2

description: Library name: pMSCV_2

value: pMSCV


title: Barnyard_96well_rep62

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep62

value: 293T and NIH3T3


title: C2C12, pMSCV_1

description: Library name: pMSCV_1


title: C2C12, pMSCV_3

description: Library name: pMSCV_3


title: RIL54_G02_L02_3

description: Library name: Sample94


title: RIL68_G09_L01_1

description: Library name: Sample131


title: Barnyard_96well_rep61

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep61

value: Human embryonic kidney and mouse embryonic fibroblasts


title: Brain_cHSPC_transplantation_rep3

city: Stanford

first: Marius

middle: Marc-Daniel

last: Mader

address: 265 Campus Drive

institute: Stanford University

data_processing:
Sequencing reads were mapped to the mouse reference transcriptome (mm39 [GRCm39], primary assembly) using STAR (version 2.7.10a; Samtools version 1.16.1) with default parameters.
Aligned reads mapping to genes were counted with the htseq-count command (intersection-strict mode, stranded=no; HTSeq package version 0.11.2).
Assembly: mm39
Supplementary files format and content: HTSeq count data (first column = gene name; second column = counts)

source_name: Brain

extract_protocol:
Brain myeloid cells were isolated via brain dissociation and fluorescence activated cell sorting directly into TRIzol LS Reagent (ThermoFisher Invitrogen), using a CD45+CD11b+GFP+ gate for graft-derived myeloid cells and a conventional CD45low/intermediate CD11b+ gate for naïve microglia. Total RNA was extracted and then purified using a Qiagen RNeasy MinElute Cleanup Kit (Qiagen, 74204) according to the manufacturer’s protocols. Quality and quantity of RNA was assessed on a Bioanalyzer (Agilent), and samples with RNA integrity number (RIN) >8 were used for subsequent library preparation.
The NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina (New England Biolabs, E6420S) was used to generate cDNA and libraries according to the manufacturer’s protocol. The libraries were indexed using the NEBNext Multiplex Oligos for Illumina (New England Biolabs, E6420S) and cleaned up using SPRI select reagent (Beckman Beckman Coulter, B23317).

value: Brain

tag: strain

value: Graft-derived brain myeloid cells

value: female

value: culturally expanded hematopoietic stem and progenitor cell transplantation and CSF1R inhibition


title: RIL65_G09_L02_2

description: Library name: Sample127


title: RIL65_G09_L01_1

description: Library name: Sample128


title: Brain_cHSPC_transplantation_rep1


title: RIL50_G09_L02_2

description: Library name: Sample93


title: Barnyard_96well_rep60

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep60

value: embryonic kidney and fibroblast cell lines


title: Brain_cHSPC_transplantation_rep2


title: Barnyard_96well_rep59

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep59


title: Barnyard_96well_rep58

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep58


title: Brain_primaryHSC_transplantation_rep1

value: primary hematopoietic stem cell transplantation and CSF1R inhibition


title: RIL50_G02_L02_3

description: Library name: Sample91


title: Brain_wholeBoneMarrow_transplantation_rep3

value: whole bone marrow transplantation and CSF1R inhibition


title: Barnyard_96well_rep57

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep57


title: Brain_primaryHSC_transplantation_rep2


title: Barnyard_96well_rep56

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep56


title: Brain_noIntervention_microglia_rep4

value: Microglia

value: no intervention


title: Brain_wholeBoneMarrow_transplantation_rep1


title: Barnyard_96well_rep85

description:
AmpliDrop
231221_293T_NIH3T3_96well_rep85


title: RIL50_G09_L01_2

description: Library name: Sample92

value: Ler X Cvi RIL


title: Brain_primaryHSC_transplantation_rep3


title: tamoxifen_rep4

source_name: hematopoietic cell (early myeloid differentiation)

extract_protocol:
Cells were dissociated with Trypsin followed by staining for magnetic-activated and fluorescence activated cell sorting. CD45+ cells were isolated directly into TRIzol LS Reagent. RNA was isolated and concentrated with the RNA Clean & Concentrator-5 kit (Zymo) according to the manufacturer’s instructions including DNase treatment.
NEBNext Ultra II RNA Library PrepKit (performed by Novogene)


title: RIL37_G02_L02_4

description: Library name: Sample87

value: leaf tissue


title: RIL50_G02_L01_3

description: Library name: Sample89