title: 8h-PD-1

description:
Library name: N6502
N6502_quant sf

value: Human coronary artery endothelial cells


title: Visium retina (Taeniopygia guttata), biological replicate 3

status: Public on Nov 11 2025

type: SRA

city: Aarhus C

first: Christian

last: Damsgaard

address: C F Møllers Alle 3

department: Department of Biology

country: Denmark

institute: Aarhus University

description:
Library name: 27
10x Genomics Visium Spatial Gene Expression v1, 55 µm resolution

library_source: transcriptomic

data_processing:
Visium: Raw BCL files were converted to FASTQ using bcl2fastq. FASTQ files were processed with SpaceRanger v3.1.1 using the count pipeline and species-specific reference genomes (AnoCar3.1, TaeGut1, Cliv_2.1, GRCg7b). The outputs include filtered_feature_bc_matrix, spatial coordinates, histology images, and QC metrics. Chromium: FASTQ files were processed with CellRanger v7.1.0 using the count pipeline and the Taeniopygia guttata (TaeGut1) reference genome. The outputs include the filtered_feature_bc_matrix. No additional filtering, ambient RNA removal (e.g., SoupX), doublet removal, or further QC was performed before deposition.
Assembly: Anolis carolinensis — AnoCar3.1 Taeniopygia guttata — TaeGut1 Columba livia — Cliv_2.1 Gallus gallus — GRCg7b
Supplementary files format and content: Each sample is provided as a single compressed tar archive (sampleID.tar.gz). For Visium: contains filtered_feature_bc_matrix/ (matrix.mtx.gz, features.tsv.gz, barcodes.tsv.gz), spatial/ (tissue_positions.csv, scalefactors_json.json), histology image (.tif), and QC metrics (metrics_summary.csv). For Chromium: contains filtered_feature_bc_matrix/ (matrix.mtx.gz, features.tsv.gz, barcodes.tsv.gz) and optional per-cell metadata (metadata.csv if available).
Library strategy: spatial transcriptomics

molecule: polyA RNA

organism: Taeniopygia guttata

source_name: Eye

extract_protocol:
Retinas were dissected from freshly euthanized adult animals. For Visium libraries, eyes were embedded in OCT, cryosectioned (10 µm), and mounted on 10x Genomics Visium slides. For Chromium single-cell libraries, retinas were enzymatically and mechanically dissociated into single cells following the 10x Genomics recommended protocol.
Spatial transcriptomics libraries were prepared using the 10x Genomics Visium Spatial Gene Expression kit v1 (poly-A capture, 55 µm spot resolution). Single-cell RNA-seq libraries were prepared using the 10x Genomics Chromium Single Cell 3′ v3 chemistry. All libraries were sequenced on an Illumina HiSeq 4000 with paired-end 2 × 150 bp reads.

tag: tissue

value: Eye


title: Single-cell RNA-seq retina (Taeniopygia guttata), biological replicate 3

description:
Library name: 37
10x Genomics Chromium Single Cell 3′ v3

library_source: transcriptomic single cell

data_processing:
Visium: Raw BCL files were converted to FASTQ using bcl2fastq. FASTQ files were processed with SpaceRanger v3.1.1 using the count pipeline and species-specific reference genomes (AnoCar3.1, TaeGut1, Cliv_2.1, GRCg7b). The outputs include filtered_feature_bc_matrix, spatial coordinates, histology images, and QC metrics. Chromium: FASTQ files were processed with CellRanger v7.1.0 using the count pipeline and the Taeniopygia guttata (TaeGut1) reference genome. The outputs include the filtered_feature_bc_matrix. No additional filtering, ambient RNA removal (e.g., SoupX), doublet removal, or further QC was performed before deposition.
Assembly: Anolis carolinensis — AnoCar3.1 Taeniopygia guttata — TaeGut1 Columba livia — Cliv_2.1 Gallus gallus — GRCg7b
Supplementary files format and content: Each sample is provided as a single compressed tar archive (sampleID.tar.gz). For Visium: contains filtered_feature_bc_matrix/ (matrix.mtx.gz, features.tsv.gz, barcodes.tsv.gz), spatial/ (tissue_positions.csv, scalefactors_json.json), histology image (.tif), and QC metrics (metrics_summary.csv). For Chromium: contains filtered_feature_bc_matrix/ (matrix.mtx.gz, features.tsv.gz, barcodes.tsv.gz) and optional per-cell metadata (metadata.csv if available).

source_name: Retina

value: Retina


title: WT rep2

city: Shanghai

first: Haibo

last: Zhou

state: Shanghai

address: Shangdong Middle street

country: China

institute: Renji Hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using HISAT2 (Kim et al., 2015;Pertea et al., 2016).
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using StringTie(Pertea et al., 2016).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include normalized counts for each Sample.

organism: Mus musculus

source_name: Bone marrow

extract_protocol:
Total RNA was extracted by Trizol reagent (Invitrogen) and determined by Bioanalyzer 2100 (Agilent, Santa Clara, CA, USA).
Next-generation libraries of mRNA-seq were prepared using VAHTS mRNA-seq v2 Library Prep Kit for Illumina® (Vazyme, Nanjing, China). The Library quality was determined by Bioanalyzer 2100 (Agilent, Santa Clara, CA, USA).

value: Bone marrow

tag: cell line

value: Primary hematopoietic stem cell

tag: cell type

value: Hematopoietic stem cell

tag: genotype


title: 8h-BRK-1

city: Hannover

first: Felix

last: Polten

address: Carl-Neuberg-Str. 1

country: Germany

institute: Hanover Medical School

description:
Library name: N6500
N6500_quant sf

data_processing:
BCL files were converted to FASTQ files using bcl2fastq Conversion Software version v2.20.0.422.
Raw data were processed and quality-controlled using the nf-core/rnaseq RNA sequencing analysis pipeline (version 3.9, SciLifeLab).
Normalization and differential expression analysis was performed on the internal Galaxy (version 20.05) instance of the RCU Genomics, Hannover Medical School, Germany with DESeq2 (Galaxy Tool Version 2.11.40.6) with default settings except for “Output normalized counts table”, which was set to “Yes” and all additional filters were disabled (“Turn off outliers replacement”, “Turn off outliers filtering”, and “Turn off independent filtering” set “Yes”).
Assembly: Genome reference and annotation data were obtained from https://www.gencodegenes.org/ (Homo sapiens, GRCh38.p14; release 46).
Supplementary files format and content: .gz are processed raw files as described above
Supplementary files format and content: .xlsx are processed pairwise comparisons as indicated

molecule: total RNA

organism: Homo sapiens

source_name: Human coronary artery endothelial cells

extract_protocol:
HCAECs were grown in 6 cm plates (Thermo Fisher Scientific , 3 × 105 cells per plate), stimulated for 8 hours, and lysed in RLT buffer (Qiagen).
The New England Biolabs NEBNext Poly(A) mRNA Magnetic Isolation Module was used for mRNA enrichment from 500 ng total RNA per sample. cDNA libraries were generated following the New England Biolabs NEB Next Ultra II workflow with 8 cycles of PCR. A DNA purification step was introduced at the end of the procedure using 1.2× Agencourt AMPure XP beads (Beckman Coulter). Fragment length distribution was monitored with the Bioanalyzer High Sensitivity DNA Analysis kit (Agilent). Libraries were quantified using the Qubit dsDNA HS Assay (Thermo Fisher Scientific). Individually barcoded libraries were pooled, denatured, diluted to 1.8 pmol l–1, and sequenced with an Illumina NextSeq 550 High Output Flowcell Kit (75 cycles) (20024906; Illumina), using the following settings: 38 bp each as sequence reads 1 and 2; 8 bp each as index reads 1 and 2. Samples obtained an average sequencing depth of 27 million reads.


title: OPC, Hippocampus, GABA, repeat2

city: SHENZHEN

first: Yixun

last: Su

state: GUANGDONG

address: 628 Zhenyuan Road

institute: The Seventh Affiliated Hospital, Sun Yat-sen University

data_processing:
Clean reads after filtering were aligned to the reference genome with HISAT.
Bowtie2 were used to align the clean reads to the reference genes.
Differential expression analysis was performed using DESeq2.
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: xlsx file includes normalized read count.

source_name: Hippocampus

growth_protocol: For Cultured OPC, OPC were isolated and cultured in OPC proliferation medium for 2 days, followed by 200 uM GABA or 200 uM Glutamate treatment for 24 h, then subjected to RNA sample collection by Trizol.

extract_protocol:
For acute-isolated OPC, Mice were anesthetized and transcardially perfused with ice-cold HBSS. The brains were isolated with the meninges removed, followed by dissection of the cortex and hippocampus, which were then minced and digested by 1% papain. OPCs were isolated from the resulting cell suspension via immunopanning and directly lysed on the panning plate by Trizol.
Poly-A selected method was used to prepare the RNA-seq library. Sequencing was performed on the DNBSEQ platform with SE50 sequencing length

value: Hippocampus

value: Cultured OPC

value: wild type

tag: treatment

value: GABA treatment


title: OPC, mPFC, GABA, repeat3

source_name: mPFC

value: mPFC


title: KO rep2


title: Visium retina (Taeniopygia guttata), biological replicate 2

description:
Library name: 26
10x Genomics Visium Spatial Gene Expression v1, 55 µm resolution


title: IgG CST CUT&Tag rep2

library_source: genomic

data_processing:
The trimmomatic software was employed to remove adapter and low quality reads. [Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30(15):2114–20.] Before read mapping, clean reads were obtained from the raw reads by removing the adaptor sequences. The clean reads were then aligned to the GRCm38/mm10 genome sequences using the bwa program. The bam files were subjected to macs2 software for peak calling with cut off q value < 0.05. Reads distributions across peaks or genes were analyzed using the deeptools. The HOMER's findMotifsGenome.pl tool was used for motif analysis and peaks were annotated by ChIPseeker.
Assembly: mm10
Supplementary files format and content: BigWig, narrowPeak
Library strategy: CUT&Tag

molecule: genomic DNA

extract_protocol:
Live cells were prepared by using Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme, China) according to the protocol.
Libraries were constructed by using TruePrep  Index  Kit  V2  for  Illumina (Vazyme, China).

value: Primary hematopoietic stem cells

value: hematopoietic stem cells


title: 8h-Kontrolle-1

description:
Library name: N6498
N6498_quant sf


title: WT rep1


title: Visium retina (Taeniopygia guttata), biological replicate 1

description:
Library name: 25
10x Genomics Visium Spatial Gene Expression v1, 55 µm resolution


title: 8h-Kontrolle-2

description:
Library name: N6499
N6499_quant sf


title: IgG CST CUT&Tag rep1


title: OPC, mPFC, repeat3


title: Kc_histoneH4_(241125_BT_Dm_3510)

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

country: USA

institute: Fred Hutchinson Cancer Research Center

description:
Library name: Kc_histoneH4
Kc cells histone H4

data_processing:
1. We used cutadapt 2.9 with parameters "-j 8 --nextseq-trim 20 -m 20 -a  AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -Z" to trim adapters from 50bp paired-end reads.
2. We used Bowtie2 2.4.4 with options "--very-sensitive-local --soft-clipped-unmapped-tlen --dovetail --no-mixed --no-discordant -q --phred33 -I 10 -X 1000" to map the paired-end 50bp reads to the dm6 Drosophia melanogaster or hg19 Homo sapiens reference sequence obtained from UCSC.
3. We used samtools 1.14 "view" to extract properly paired reads from the alignments.
4. We used bedtools 2.30.0 "genomecov" to make a normalized count track which is the fraction of counts at each base pair scaled by the size of the reference sequence so that if the counts were uniformly distributed across the reference sequence there would be one at each position (Supplementary file .bw)
Assembly: dm6 or hg19
Supplementary files format and content: bigwig
Library strategy: CUT&Tag

organism: Drosophila melanogaster

extract_protocol:
CUT&Tag chromatin profiling To perform CUT&Tag [Kaya-Okur et al 2019] with Drosophila tissue, we dissected 20 imaginal wing discs from male 3rd instar larvae in PBS buffer, and transferred them to a tube containing Accutase (Stemcell Technologies, #07920) at 25 ̊C for 30 minutes. We then added an equal volume of 30% BSA to block proteases, and ran the material through a 30 1⁄2 gauge needle once to dissociate tissue. Tissue suspensions were divided between 4-8 reaction tubes, and bound with BioMag Plus ConA (Bangs Inc., #531) magnetic beads. For CUT&Tag with Drosophila Kc167 cells and human K562 cells, 50,000 cells were bound to ConA beads for each sample, and then lightly fixed with 0.1% formaldehyde at room temperature for 1 minute. Tissue and cell culture samples were then incubated with the following CUT&Tag solutions sequentially: primary antibodies diluted in Wash+ buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 0.05% triton-X100, 2 mM EDTA, 1% BSA, with Roche cOmplete protease inhibitor) overnight at 4 ̊C, secondary antibodies (in Wash+ buffer) for 1 hour at room temperature, and then incubated with pAGTn5 (Epicypher 15-1017) in 300Wash+ buffer (20 mM HEPES pH 7.5, 300 mM NaCl, 0.5 mM spermidine, 0.05% triton-X100 with cOmplete protease inhibitor) for 1 hour. After one wash with 300Wash+ buffer, tissue samples were incubated in 300Wash+ buffer supplemented with 10 mM MgCl2 for 1 hour at 25 ̊C to tagment chromatin. Cell culture samples were incubated with CUTAC buffer (10 mM TAPS pH 8.5, 20% dimethylformamide) supplemented with 5 mM MgCl2 for 1 hour at 25˚C for tagmentation. Samples were washed with 10 mM TAPS pH 8.5 and DNA was released with 0.1% SDS, 0.012 U/μL thermolabile protease K (NEB P8111S) in 10 mM TAPS at 37 ̊C and inactivated at 55 ̊C. Libraries were enriched with 14 cycles of PCR and sequenced in dual-indexed paired-end mode (PE50) on the Illumina NextSeq 2000 platform at the Fred Hutchinson Cancer Center Genomics Shared Resource. Paired-end reads were mapped to Drosophila (dm6) or human (hg19 February 2019) assemblies using Bowtie2 using parameters, e.g.: --end-to-end --very-sensitive --no-mixed --no-discordant -q --phred33 -I 10 -X 700.
PMID 31036827

tag: antibody

value: anti-histone H4 Abcam ab31830


title: OPC, mPFC, GABA, repeat1


title: Kc_H3K27ac_(241125_BT_Dm_3505)

description:
Library name: Kc_H3K27ac
Kc cells H3K27ac

value: anti-H3K27ac Epicypher 13-0058


title: OPC, mPFC, repeat2


title: PPP2CA CST CUT&Tag rep1


title: Kc_Mxc_(240709_BT_Dm_3195)

description:
Library name: Kc_Mxc
Kc cells Mxc

value: anti-Mxc


title: Lung_normoxia_recMФs_rep2

type: RNA

city: Tianjin

first: Shumin

last: Guo

address: 22 Qixiangtai Road, Heping District

institute: Tianjin Medical University

description: Gene expression of recruited macrophages under normoxia

hyb_protocol: 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed

scan_protocol: The hybridized arrays scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing:
Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies).
After quantile normalization of the raw data, genes that at least 3 out of 12 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis.

source_name: lung recruited macrophages, normoxia,replicate 2

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology). Briefly, total RNA from each sample was linearly amplified and labeled with Cy3-UTP. The Labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60°C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA.

extract_protocol: Total RNA of sorted resident macrophages and recruited macrophages from approximately 3 mice per sample, 3 samples in each group (SuHx and normoxia). Microarray analyses were performed by aksomics (Shanghai, China). RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

value: lung

value: lung recruited macrophages

tag: condition

value: Control


title: Lung_normoxia_recMФs_rep3

source_name: lung recruited macrophages, normoxia,replicate 3


title: OPC, mPFC, repeat1

description: Cortex


title: Lung_normoxia_recMФs_rep1

source_name: lung recruited macrophages, normoxia,replicate 1


title: K562_histoneH4_R2_(241125_BT_Hs_3517)

description:
Library name: K562_histoneH4_R2
K562 cells histone H4


title: CUT&RUN_PPP2CA KO rep3

data_processing:
The trimmomatic software was employed to remove adapter and low quality reads. [Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30(15):2114–20.] Before read mapping, clean reads were obtained from the raw reads by removing the adaptor sequences. The clean reads were then aligned to the GRCm38/mm10 genome sequences using the bwa program. The bam files were subjected to macs2 software for peak calling with cut off q value < 0.05. Reads distributions across peaks or genes were analyzed using the deeptools. The HOMER's findMotifsGenome.pl tool was used for motif analysis and peaks were annotated by ChIPseeker.
Assembly: mm10
Supplementary files format and content: BigWig, narrowPeak
Library strategy: CUT&RUN

extract_protocol:
Live cells were prepared by using the Hyperactive pG-MNase CUT&RUN Assay Kit for Illumina (Vazyme, China) according to the protocol.
Libraries were constructed by using TruePrep  Index  Kit  V2  for  Illumina (Vazyme, China).


title: K562_histoneH4_R3_(241125_BT_Hs_3518)

description:
Library name: K562_histoneH4_R3
K562 cells histone H4


title: Baf155 KO OPC, Hippocampus, repeat4

value: Acute isolated OPC


title: CUT&RUN_PPP2CA KO rep2

value: Bone marrow


title: Baf155 KO OPC, Hippocampus, repeat6


title: OPC, mPFC, GABA, repeat2


title: K562_H3K27ac_R3_(241125_BT_Hs_3514)

description:
Library name: K562_H3K27ac_R3
K562 cells H3K27ac


title: Baf155 KO OPC, Hippocampus, repeat5


title: CUT&RUN_PPP2CA WT rep2


title: CUT&RUN_PPP2CA KO rep1


title: K562_histoneH4_R1_(241125_BT_Hs_3516)

description:
Library name: K562_histoneH4_R1
K562 cells histone H4


title: CUT&RUN_PPP2CA WT rep3


title: Lung_normoxia_resMФs_rep2

description: Gene expression of resident macrophages under normoxia

source_name: lung resident macrophages, normoxia,replicate 2

value: lung resident macrophages


title: Baf155 KO OPC, mPFC, repeat1


title: Hx10, scRNAseq

city: Madrid

first: Yosra

last: Berrouayel

address: Arturo Duperier, 4

country: Spain

institute: Universidad Autónoma de Madrid

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.1.0
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: embryoid bodies

extract_protocol:
Embryoid bodies cells were dissociated using Accumax and filtered using a 70 µm cell strainer. The resulting cells were washed twice using a two-step process: first with 10% FBS in DPBS (Ca2+/Mg2+ free), and then with 0.04% BSA in DPBS (Ca2+/Mg2+ free). Subsequently, an appropriate volume of 0.04% BSA in DPBS (Ca2+/Mg2+ free) was added to achieve the desired cell concentration (> 106 cells/ml).
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics). Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then purified using silane magnetic beads, amplified by PCR and the appropiate sized fragments were selected for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: embryoid bodies

value: mESC

value: 8 d in normoxia + 48 h in hypoxia


title: Kc_RNAPIIS5p_(240820_BT_Dm_3417)

description:
Library name: Kc_RNAPIIS5p
Kc cells RNAPIIS5p

value: anti-RNAPII-S5p CST D9N5I


title: PPP2CA CST CUT&Tag rep2


title: K562_H3K27ac_R2_(241125_BT_Hs_3513)

description:
Library name: K562_H3K27ac_R2
K562 cells H3K27ac


title: Baf155 KO OPC, mPFC, repeat2


title: Lung_normoxia_resMФs_rep1

source_name: lung resident macrophages, normoxia,replicate 1


title: Hela_Zfmut_Rep2

city: Changsha

first: Bi

last: Shi

address: #2 Lushan South Road

institute: Hunan University

description: RNA-seq

data_processing:
For RNA-seq, 20-30 million reads per sample were mapped to human reference genome (hg19) or mouse reference genome (mm10)using hista. Transcript assembly was performed using HTseq v0.10.0. Assembled RNA-seq count files were imported into RStudio software for analysis of differential expression with DESeq2 v3.8 package.
Assembly: hg19, mm10
Supplementary files format and content: count file for RNA-seq

source_name: Cell line

growth_protocol: Mouse bone marrow cells harvest for primary transplantation were cultured in IMDM medium (Gibco) with 20% FBS, 100ug/mL Pen/Strep, 50 ug/mL SCF, 50 ug/mL Flt3 ligand, 10 ug/mL mouse IL-6, 50 ug/mL Tpo and 50 ug/mL mouse IL-3 (PeproTech). Hela cells were cultured in DMEM (Gibco) with 10% FBS and 100 ug/mL Pen/Strep.

extract_protocol:
For RNA-seq, RNA was extracted with Qiagen miRNA-ease RNA extraction kit.
For RNA-seq , NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina was used for library prepapration.

value: Cell line

value: Hela cells

value: Hela cell with an ZF domain mutated AKAP95 overexpression


title: CUT&RUN_PPP2CA WT  rep1

value: Primary hematopoietic stem cells

value: hematopoietic stem cells


title: Lung_SuHx_recMФs_rep2

description: Gene expression of resident macrophages under SuHx

source_name: lung recruited macrophages, SuHx,replicate 2

value: Pulmonary arterial hypertension


title: K562_H3K27ac_R1_(241125_BT_Hs_3512)

description:
Library name: K562_H3K27ac_R1
K562 cells H3K27ac

value: anti-H3K27ac Epicypher 13-0058


title: Lung_SuHx_recMФs_rep3

source_name: lung recruited macrophages, SuHx,replicate 3

value: lung


title: Lung_normoxia_resMФs_rep3

source_name: lung resident macrophages, normoxia,replicate 3


title: Lung_SuHx_recMФs_rep1

source_name: lung recruited macrophages, SuHx,replicate 1

value: lung recruited macrophages


title: Hx8, scRNAseq

description: 10x Genomics

value: 7.33 d in normoxia + 16 h in hypoxia


title: CTL OPC, Hippocampus, repeat3

value: Hippocampus

value: Acute isolated OPC


title: Nx10, scRNAseq

description: 10x Genomics

value: 10 d in normoxia


title: Hela_Zfmut_Rep1

description: RNA-seq


title: Lung_SuHx_resMФs_rep2

source_name: lung resident macrophages, SuHx,replicate 2

value: lung resident macrophages


title: Baf155 KO OPC, mPFC, repeat3

value: mPFC


title: Hela_Wt_Rep1

description: RNA-seq

value: Hela cell with an empty vector overexpression


title: CTL OPC, mPFC, repeat3


title: CTL OPC, Hippocampus, repeat2


title: Hela_Wt_Rep2

description: RNA-seq


title: spleen, CuC, rep7

city: Tainan

first: Po-Min

last: Chiang

state: TAIWAN

address: No. 35, Xiaodong Road,, Rm. 7068

department: Institute of Clinical Medicine

country: Taiwan

institute: National Cheng Kung University

data_processing:
The count files in RDS format were acquired from fastq files using zUMIs.
Assembly: GRCh38 (mouse), GRCh38 (human), B73-NAM 5.0 (maize)
Supplementary files format and content: RDS for raw counts; h5ad for the filted barcodes and combined datasets.

molecule: nuclear RNA

source_name: spleen

extract_protocol:
The cells were fixed directly with 10x volumes of methanol at -20°C. The murine tissues were lyzed by pestle in a pH3 citrate buffer (pancreas, liver, and spleen) or a lysis buffer contaning a RNase inhibitor (spleen). The maize roots and shoots were dissociated with dounce homogenizer (20 strokes) in spermidine- or divalent cation-containing buffers supplemented with the RNase inhibitor. The released nuclei from these tissues were filtered through 800-mesh-size nylon membrane, purified using iodixanol density-gradient centrifugation (30%), and fixed in a organic solvent as with the cells.
The barcoded cells/nuclei containing cDNA were lyzed. The cDNA were tailed with a PCR handle using TdT. Following second-strand systhesis and preamplification with KAPA HiFi, the cDNA were purified with carboxylic paramagnetic beads in a PEG/NaCl solution. The eluted DNA were tagmenmented with Tn5 and amplified with KAPA HiFi using primers containg P5 and P7 ends and multiplex indices. The amplified products were subjected to size selection, targeting libraries with peaks in the 450bp region.

value: spleen

value: whole organ

value: mixed

value: WT

value: one-pot lysis


title: spleen, CuC, rep6


title: Nx8, scRNAseq

description: 10x Genomics

value: embryoid bodies

value: mESC

value: 8 d in normoxia


title: CTL OPC, Hippocampus, repeat1


title: maize shoot, homebrew TdT

description: spiked with human (HEK293T cells and hPSCs) and mouse (OP9DL1) nuclei as the mixed-species control

organism: Zea mays

source_name: shoot

value: shoot


title: spleen, CuC, rep5


title: CTL OPC, mPFC, repeat1


title: Lung_SuHx_resMФs_rep1

source_name: lung resident macrophages, SuHx,replicate 1

value: lung

value: Pulmonary arterial hypertension


title: Lung_SuHx_resMФs_rep3

source_name: lung resident macrophages, SuHx,replicate 3


title: CTL OPC, mPFC, repeat2

source_name: mPFC


title: maize shoot, commercial TdT


title: Hela_KD_Rep2

description: RNA-seq

value: Cell line

value: Hela cells

value: Hela cells AKAP95 knock-down


title: maize root, homebrew TdT

description: spiked with human cells (hPSCs) as the mixed-species control

source_name: root

value: root


title: Hela_PSmut_Rep1

description: RNA-seq

value: Hela cell with an IDR region mutated AKAP95 overexpression


title: maize root, commerical TdT


title: rapeseed, control, Day2, biol  rep 3

city: chongqing

first: binnian

last: tian

address: tianshenglu

institute: binniantian

data_processing:
Triticum aestivum and Brassica napus Genomics
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Triticum aestivum or Brassica napus genomic benchwork
Trimmed sequence reads were mapped to Triticum aestivum or Brassica napus genomic benchwork
Read count extraction and normalization were performed using Triticum aestivum or Brassica napus genomic benchwork
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Brassica napus

source_name: Rapeseed stem

growth_protocol: wheat and rapeseed seedlings grow on MS

extract_protocol:
RNA was harvested using TRIzol Plus RNA Purification Kit (Takara). 3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Rapeseed stem

value: QingYou 1

value: control

tag: time

value: Day 2


title: Hela_PSmut_Rep2

description: RNA-seq


title: Hela_KD_Rep3

description: RNA-seq


title: spleen, CuC, rep4

value: spleen

value: whole organ

value: mixed

value: WT


title: HEK293T and MS5, 500 cells, rep3

organism:
Homo sapiens
Mus musculus

source_name: cell line

value: cell line

value: HEK293T and MS5

value: human embryonic kidney and murine bone marrow stromal cells


title: rapeseed, control, Day2, biol  rep 1


title: Hela_Scr_Rep3

description: RNA-seq

value: Hela cells control knock-down


title: rapeseed, control, Day2, biol  rep 2


title: spleen, CuC, rep3

value: one-pot lysis


title: INJN

city: 北京市

first: 美莲

last: 蔡

state: 北京市

address: 北京市昌平区生命科学园医科路9号院3号楼西门，闹中心二期A2货架

institute: 北京脑科学与类脑研究中心

description:
Library name: sample 3
Achilles tendon from P3 mouse with tendon injury

data_processing:
Data comparison, gene quantification, and cell identification were performed using CellRanger, the official 10X Genomics software.
Assembly: GRCm39
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Achilles tendon

extract_protocol:
Freshly collected neonate and adult tendon tissue from mice were flushed with ice-cold HBSSwo(Mg2+/Ca2+ free supplemented with 10mM HEPES, pH7.2) .The tissues were re-suspended in digestion buffers (HBSS containing Mg2 +Ca2+ supplemented with 2 ml collagenase type and 40 Uml DNase) and incubated at 37 ° C for 30 min. After washing, the cells were re-suspended in HBSS-/- with 0.04% w/v BSA.
In brief, single cells are encapsulated with beads carrying cell barcode sequences in GEMs droplets. The GEMs droplets containing cells are collected, and within these droplets, the cells lyse and release mRNA. The mRNA binds to the cell barcode primers on the beads, completing the reverse transcription reaction. Subsequently, the GEMs are broken, and the cDNA is recovered and enriched through PCR amplification, followed by library construction of the cDNA.

value: Achilles tendon

value: injury


title: Hela_Scr_Rep1

description: RNA-seq

value: Cell line

value: Hela cells


title: HEK293T and MS5, 500 cells, rep2


title: liver and spleen, pH3, rep2

source_name: liver and spleen

value: liver and spleen


title: spleen, CuC, rep2


title: Hela_KD_Rep1

description: RNA-seq

value: Hela cells AKAP95 knock-down


title: INJA

address: 北京市昌平区生命科学园医科路9号院3号楼西门，闹中心二期A2货架

institute: 北京脑科学与类脑研究中心

description:
Library name: sample 4
Achilles tendon from 6-8weeks old mouse with tendon injury


title: spleen, CuC, rep1


title: Neonate

address: 北京市昌平区生命科学园医科路9号院3号楼西门，闹中心二期A2货架

institute: 北京脑科学与类脑研究中心

description:
Library name: sample 1_neonate
Achilles tendon from P3 mouse without injury

value: control


title: Hela_Scr_Rep2

description: RNA-seq


title: liver and spleen, pH3, rep1


title: maize shoot, commercial TdT, rep2

description: Library name: S13b

extract_protocol:
The cells were fixed directly with 10x volumes of methanol at -20°C. The murine tissues were lyzed by pestle in a pH3 citrate buffer or a lysis buffer contaning a RNase inhibitor. The maize roots and shoots were dissociated with dounce homogenizer (20 strokes) in spermidine- or divalent cation-containing buffers supplemented with the RNase inhibitor. The released nuclei from these tissues were filtered through 800-mesh-size nylon membrane, purified using iodixanol density-gradient centrifugation (30%), and fixed in a organic solvent as with the cells.
The barcoded cells/nuclei containing cDNA were lyzed. The cDNA were tailed with a PCR handle using TdT. Following second-strand systhesis and preamplification with KAPA HiFi, the cDNA were purified with carboxylic paramagnetic beads in a PEG/NaCl solution. The eluted DNA were tagmenmented with Tn5 and amplified with KAPA HiFi using primers containg P5 and P7 ends and multiplex indices. The amplified products were subjected to size selection, targeting libraries with peaks in the 450bp region.

value: shoot


title: AKAP_KI_CLIP

description: CLIP-seq

data_processing:
For CLIP-seq, Reads were aligned to the human reference genome hg19 (GRCh37) using bowtie2 version 2.3.2. The ChIPseq peaks from each sample were called at P <10-4 with MACS2. Bigwig files were generated with Homer softwares.
Assembly: hg19
Supplementary files format and content: bigwig

growth_protocol: Hela cells were cultured in DMEM (Gibco) with 10% FBS and 100 ug/mL Pen/Strep.

extract_protocol:
CLIP RNA was pulled down by anti-flag beads.
For CLIP-seq, NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina was used for library prepapration.

value: AKAP-Flag Konck-in Hela cells

value: RNA immunopreciptation with anti-flag antibody


title: Adult

address: 北京市昌平区生命科学园医科路9号院3号楼西门，闹中心二期A2货架

institute: 北京脑科学与类脑研究中心

description:
Library name: sample 2
Achilles tendon from 6-8weeks old mouse without injury

source_name: Tendon cell

extract_protocol:
Freshly collected neonate and adult tendon tissue from mice were flushed with ice-cold HBSSwo(Mg2+/Ca2+ free supplemented with 10mM HEPES, pH7.2) .The tissues were re-suspended in digestion buffers (HBSS containing Mg2 +Ca2+ supplemented with 2 ml collagenase type and 40 Uml DNase) and incubated at 37 ° C for 30 min. After washing, the cells were re-suspended in HBSS-/- with 0.04% w/v BSA.
In brief, single cells are encapsulated with beads carrying cell barcode sequences in GEMs droplets. The GEMs droplets containing cells are collected, and within these droplets, the cells lyse and release mRNA. The mRNA binds to the cell barcode primers on the beads, completing the reverse transcription reaction. Subsequently, the GEMs are broken, and the cDNA is recovered and enriched through PCR amplification, followed by library construction of the cDNA.
We used single cell RNA sequencing (scRNA-seg) to analyze the  diversity of tendon cells at different ages


title: wheat, control, Day2, biol  rep 3

organism: Triticum aestivum

source_name: Wheat root

value: Wheat root

value: Zheng 9023

value: Day 2


title: pancreas, pH3, rep6

source_name: pancreas

value: pancreas

value: whole organ

value: mixed

value: WT


title: AKAP_WT_CLIP

description: CLIP-seq

source_name: Cell line

value: wild-type Hela cells


title: HEK293T and MS5, 500 cells, rep1

value: cell line

value: HEK293T and MS5

value: human embryonic kidney and murine bone marrow stromal cells


title: AKAP_KI_ChIP

description: ChIP-seq

data_processing:
For ChIP-seq, Reads were aligned to the human reference genome hg19 (GRCh37) using bowtie2 version 2.3.2. The ChIPseq peaks from each sample were called at P <10-4 with MACS2. Bigwig files were generated with Homer softwares.
Assembly: hg19
Supplementary files format and content: bigwig

extract_protocol:
For Chip-seq, genomic DNA was pulled down by respective antibodies.
For ChIP-seq, library was prepared using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina.

value: Cell line

value: Hela cells

value: ChIP with anti-Flag antibody


title: wheat, control, Day2, biol  rep 1

value: control


title: AKAP_WT_ChIP

description: ChIP-seq


title: pancreas, pH3, rep5

value: one-pot lysis


title: wheat, control, Day2, biol  rep 2


title: KO_MA9_Rep2

description: RNA-seq

source_name: Bone marrow

value: Bone marrow

value: AKAP95 knockout

value: Overexpression of MLL-AF9 oncogenic fusion protein


title: pancreas, pH3, rep4


title: maize shoot, commercial TdT, rep3

description: Library name: S13c

value: shoot


title: KO_MA9_Rep1

description: RNA-seq


title: wheat, treated, Day6, biol  rep 3

value: Wheat root

value: Zheng 9023

value: Sclerotinia sclerotiorum

value: Day 6


title: pancreas, pH3, rep3

value: pancreas

value: whole organ

value: mixed

value: WT


title: Low_ActD

description: ChIP-seq

value: Cell line

value: treated with low level of Actinomycin D, ChIP with anti-flag antibody


title: WT_MA9_Rep3

description: RNA-seq

value: wild-type


title: WT_MA9_Rep2

description: RNA-seq


title: maize shoot, commercial TdT, rep1

description: Library name: S13a


title: High_ActD

description: ChIP-seq

value: Hela cells

value: treated with high level of Actinomycin D, ChIP with anti-flag antibody


title: wheat, treated, Day6, biol  rep 2


title: wheat, treated, Day6, biol  rep 1


title: KO_MA9_Rep3

description: RNA-seq

value: Bone marrow


title: pancreas, pH3, rep2

value: one-pot lysis


title: WT_MA9_Rep1

description: RNA-seq

value: Overexpression of MLL-AF9 oncogenic fusion protein


title: B78 Lu+ICI RepD  [scTCR-seq]

status: Public on Nov 10 2025

city: Madison

first: Zachary

last: Morris

address: 1111 Highland Avenue

institute: University of Wisconsin

description:
instrument model: Chromium iX
Lu177-NM600+ICI RepD  [scTCR-seq]

data_processing:
scRNA-seq data were processed by Cell Ranger (version 7.2.0) to demultiplexing, barcode processing, and gene counting. Reads were aligned to the mouse genome (version mm10).
scTCR-seq data were processd by Cell Ranger (version 7.2.0) to demultiplexing, barcode processing, VDJ contig assembly and clonotype VJ gene annotation. Reads were aligned to the mouse genome (version mm10)
Assembly: mm10
Supplementary files format and content: scRNA-seq: tab-seperated value files and matrix files
Supplementary files format and content: scTCR-seq: csv-separated values files containing summary metrics per run, list of every clonotype regardless of single cell data, and filtered and annotated clonotypes per barcode

source_name: Flank tumor

extract_protocol:
Tumors were dissected from three mice/treatment group, pooled by treatment, minced, and digested using the Miltenyi Biotech tumor dissociation kit (mouse, tough tumor dissociation protocol) for 40 min at 37 °C. Cells were then strained through a 70 µm filter and washed with RPMI-1640 (Corning), and resuspended in 6 mL of RPMI-1640. Tumor infiltrating lymphocytes were isolated by Ficoll-Paque density gradient centrifugation as previously described. Briefly, 4 mL of Ficoll-Paque (Cytiva) was added to a 15 mL tube, and the entire cell suspension was carefully layered on top. The samples were centrifuged at 600 rcf for 20 minutes with no brake or accelerator. Cells were collected from the layer interface, rinsed with RPMI-1640 at 375 rcf, strained through a 40 µm filter, and counted on a Countess 3 automated cell counter (Invitrogen). All samples had viability > 90%, and were resuspended at a concentration of 1.2 *106 cells/mL in RPMI-1640 for single-cell RNA sequencing.
Single-cell suspensions from isolated CD45+ cells were loaded on a Chromium iX single cell instrument (10x Genomics) to generate single-cell beads in emulsion and scRNA-seq libraries were prepared. For Gel bead in EMulsion (GEM) generation and library preparation, the following materials from 10x Genomics were used: Chromium Next GEM Single Cell 5′ Kit v2 (PN-1000263); VDJ Amplification, Mouse TCR Kit (PN-1000254); 5’ Feature Barcode Kit (PN-1000256); Library Construction Kit (PN-1000190); Chromium Next GEM Chip K Single Cell Kit (PN-1000286); Dual Index Kit TT Set A (PN-1000215); Dual Index Kit TN Set A (PN-1000254). The Chromium Next GEM Single Cell 5′ v2 User Guide was followed. Single-cell barcoded cDNA libraries were quantified using a Qubit Fluorometer with Qubit dsDNA HS reagent (Invitrogen) and assayed using a Tapestation D1000 screentape (Agilent).

value: Flank tumor

value: B78 melanoma

value: Immune cells

tag: strain

value: Lu+ICI


title: B78 Y+ICI RepD  [scTCR-seq]

description:
instrument model: Chromium iX
Y90-NM600+ICI RepD  [scTCR-seq]

value: Y+ICI


title: DMSO

description: ChIP-seq

value: DMSO treatment, ChIP with anti-flag antibody


title: B78 EBRT+ICI RepD  [scTCR-seq]

description:
instrument model: Chromium iX
EBRT+ICI RepD  [scTCR-seq]

value: EBRT+ICI


title: B78 Ac+ICI RepD  [scTCR-seq]

description:
instrument model: Chromium iX
Ac225-NM600+ICI RepD [scTCR-seq]

value: Ac+ICI


title: B78 ICI RepD  [scRNA-seq]

description:
instrument model: Chromium iX
ICI RepD  [scRNA-seq]

value: ICI


title: B78 Y+ICI RepD  [scRNA-seq]

description:
instrument model: Chromium iX
Y90-NM600+ICI RepD  [scRNA-seq]


title: B78 ICI RepD  [scTCR-seq]

description:
instrument model: Chromium iX
ICI RepD  [scTCR-seq]


title: pancreas, pH3, rep1

value: pancreas

value: whole organ

value: mixed

value: WT


title: B78 Lu+ICI RepD  [scRNA-seq]

description:
instrument model: Chromium iX
Lu177-NM600+ICI RepD  [scRNA-seq]


title: B78 Ac+ICI RepD [scRNA-seq]

description:
instrument model: Chromium iX
Ac225-NM600+ICI RepD  [scRNA-seq]


title: Deaf1 ChIP - C2C12 - replicate 2

city: Cardiff

first: NATHAN

last: HARMSTON

address: Museum Avenue

country: United Kingdom

institute: Cardiff University

description: Library name: IP_DEAF1_2

data_processing:
BWA
MACS2
Assembly: mm10
Supplementary files format and content: narrowPeak containing Deaf1 peaks

extract_protocol:
ChIP was performed in C2C12 myocytes using the Simple ChIP Plus Enzymatic Chromatin IP Kit. C2C12 myocytes were crosslinked with 1% Formaldehyde and quenched with glycine. DNA co-immunoprecipitations with control IgG antibody or Deaf` antibody (Bethyl Laboratories, #A303-187A)
ChIP was performed in C2C12 myocytes using the Simple ChIP Plus Enzymatic Chromatin IP Kit. C2C12 myocytes were crosslinked with 1% Formaldehyde and quenched with glycine. DNA co-immunoprecipitations with control IgG antibody or Deaf` antibody (Bethyl Laboratories, #A303-187A)

value: myocytes


title: Deaf1 ChIP - C2C12 - replicate 1

description: Library name: IP_DEAF1_1


title: WGBS_nrpe1-1

first: Li

last: He

address: No. 3888 Chenhua Road

department: Shanghai Center for Plant Stress Biology

institute: CAS Center for Excellence in Molecular Plant Science (CEMPS)

data_processing:
For data analysis, the raw paired-end reads were processed using a custom pipeline. Adapters and low-quality bases were trimmed using fastp with default parameters, and the clean reads were aligned to the TAIR10 genome using BSMAP with parameters “-v 2 -p 24 -S 1”, allowing for up to two mismatches. The methratio.py script extracted methylation ratios with parameters “-d -o -r -z -p”. The output was further processed to generate BedGraph and BigWig files for different methylation contexts (CG, CHG, CHH, and all) using awk and bedGraphToBigWig.
Assembly: TAIR10
Supplementary files format and content: bigWig, genome-wide C methylation levels
Supplementary files format and content: bigWig, genome-wide CG methylation levels
Supplementary files format and content: bigWig, genome-wide CHG methylation levels
Supplementary files format and content: bigWig, genome-wide CHH methylation levels

organism: Arabidopsis thaliana

source_name: Leaf

growth_protocol: All plants were grown under long-day conditions (16 h light/8 h dark). For seedling growth, Arabidopsis seeds were plated on 1/2 Murashige and Skoog (MS) medium with 0.6% agar and 1.5% sucrose and stratified for 7 days at 4 ℃ in darkness before being transferred to the growth chamber (16 h light/8 h dark, 22 ℃). For experiments with adult plants, seedlings were transplanted into soil in the growth chamber.

extract_protocol:
Genomic DNA was extracted from leaves using DNeasy Plant Mini Kit (Qiagen)
Libraries were then prepared using Ultra II DNA Library Prep Kit (NEB) in conjunction with EpiTect Plus Bisulfite Kit (Qiagen) following the manufacturer’s instructions.

value: Leaf


title: WGBS_WT-2


title: WGBS_nrpe1-2


title: WGBS_WT-1


title: Input ChIP - C2C12 - replicate 2

description: Library name: Input2


title: WGBS_methylation-FWA-T2-M30-line2-minus-2


title: WGBS_methylation-FWA-T2-M30-line2-minus-1


title: mESC Clone_8

city: London

first: Veronique

last: Azuara

state: London

address: Institute of Reproductive and Developmental Biology, Hammersmith Hospital Campus

department: Metabolism, Digestion and Reproduction

institute: Imperial College London

data_processing:
Image analysis and base calling was carried out in CASAVA (1.8 .2)  by Source Bioscience, UK
Quality of sequenced reads was assessed using FastQC, and reads were trimmed for adaptor sequences and low quality reads (<15) using Trimmomatic-0.33 to remove Illumina adaptors and low quality bases (< 15).
Pseudo-mapping and quantification of transcripts was carried out with Kallisto v0.43.1 using reference mouse transcriptome mm10 (GRCm38, Ensembl v94).
Assembly: mm10
Supplementary files format and content: tab-delimited text files with abundance measurements as an output from Kallisto quantification for each sample

growth_protocol: ESCs were cultured at 37°C, 5% CO2 on 0.1% gelatin-coated culture plates in GMEM-BHK12 basal medium (Gibco, 21710-025) supplemented with 10% foetal bovine serum (FBS) (Gibco, 10270-106), Leukaemia Inhibitory Factor (LIF) (made in-house), 0.1 mM b-mercaptoethanol (Gibco, 31350010), 0.25% (w/v), sodium bicarbonate (Gibco, 25080094), 1 mM sodium pyruvate (Gibco, 11360070), 0.1 mM non-essential amino acids (Gibco, 11140050), 2 mM L-glutamine (Gibco, 25030149) and 25 U/ml penicillin/streptomycin (Gibco, 11548876).

extract_protocol:
ESCs were collected using TrypLE (Gibco, 12604013) and lysed in RLT buffer from Qiagen kit (Cat# 74106). RNA was extracted according to the manufacturer's instructions.
RNA-sequencing libraries were prepared using TruSeq Stranded mRNA library prep kit (by Source Biosciences, UK).

value: Mouse embryonic stem cells


title: mESC Clone_6


title: mESC Clone_4


title: WGBS_methylation-FWA-T2-M22-line1-minus-2


title: mESC Clone_1


title: WGBS_methylation-FWA-T2-M22-line1-minus-1


title: WGBS_methylation-FWA-T2-M14-line1-plus


title: WGBS_methylation-FWA-T2-M14-line1-minus-2


title: WGBS_methylation-FWA-T2-M14-line1-minus-1


title: mESC Clone_13


title: mESC Clone_14


title: WGBS_methylation-FWA-T2-M30-line2-plus


title: mESC Clone_11


title: mESC Clone_10


title: WGBS_methylation-FWA-T2-M12-line2-plus


title: H1,ZNF263 OE,rep3

city: shanghai

first: shao

last: zhen

address: 320 Yueyang Road

institute: Shanghai Institute of Nutrition and Health

description: Library name: H1-263-3

data_processing:
RNA-seq reads were aligned to hg19 reference genome using STAR with RefSeq annotated genes.
Gene expression levels were counted using featureCounts.
Differential expression analysis comapring each sample with vehicle-treated WT hESCs was performed by DESeq2.
Assembly: hg19
Supplementary files format and content: featureCounts quantification
Supplementary files format and content: featureCounts quantification results

extract_protocol:
Total RNA was extracted with TRIzol™ (ThermoFisher), 500 ng RNA was used for sequencing library construction.
polyA RNA was enriched with NEBNext® Poly(A) mRNA Magnetic Isolation Module (New England Biolabs), then corresponding RNA libararies were prepared with NEBNext® Ultra II RNA Library Prep Kit for Illumina® (New England Biolabs).

value: Human embryonic stem cell

value: ZNF263 Overexpression


title: B78 EBRT+ICI RepD  [scRNA-seq]

description:
instrument model: Chromium iX
EBRT+ICI RepD  [scRNA-seq]

value: Flank tumor

value: B78 melanoma


title: H1,ZNF263 OE,rep2

description: Library name: H1-263-2


title: WGBS_methylation-FWA-T2-M6-line1-minus-1


title: H1,WT,rep2

description: Library name: H1-vec-2


title: WGBS_methylation-FWA-T2-M22-line1-plus


title: WGBS_methylation-FWA-T1-pR-dCas9-line2


title: WGBS_methylation-FWA-T2-M12-line2-minus-2


title: H1,ZNF263 OE,rep1

description: Library name: H1-263-1


title: H1,WT,rep3

description: Library name: H1-vec-3


title: WGBS_methylation-FWA-T2-M6-line1-plus


title: Input - C2C12 - replicate 1

description: Library name: Input1


title: WGBS_methylation-FWA-T1-pR-dCas9_without_gRNA-line2


title: mESC Clone_17


title: WGBS_methylation-FWA-T1-pR-dCas9-line1


title: WGBS_methylation-FWA-T2-M6-line1-minus-2


title: H1,ZNF263 KO,ZIC2 OE rep2

description: Library name: H1-2-10-ZIC2-2

value: ZNF263 homozygous KO & ZIC2 Overexpression


title: WGBS_methylation-FWA-T1-M40-line2


title: H1,ZNF263 KO,ZIC2 OE rep3

description: Library name: H1-2-10-ZIC2-3


title: H1,WT,rep1

description: Library name: H1-vec-1


title: WGBS_methylation-FWA-T1-M40-line1


title: WGBS_methylation-FWA-T2-M12-line2-minus-1


title: WGBS_methylation-FWA-T1-M39-line2


title: H1,ZNF263 KO,rep1

description: Library name: H1-2-10-vec-1

value: ZNF263 homozygous KO


title: WGBS_methylation-FWA-T1-pR-dCas9_without_gRNA-line1


title: WGBS_methylation-FWA-T1-M30-line1


title: H1,ZNF263 KO,ZIC2 OE rep1

description: Library name: H1-2-10-ZIC2-1


title: H1,ZNF263 KO,rep3

description: Library name: H1-2-10-vec-3


title: H1,ZNF263 KO,rep2

description: Library name: H1-2-10-vec-2


title: WGBS_methylation-FWA-T1-M30-line2


title: human CD34+-derived CD19+CD10+CD20dim B progenitors, PI3KGOF, Day 21, biol rep 1, B

city: Boston

first: Anna-Lena

last: Neehus

state: MA

address: 1 Blackfan Circle

institute: Boston Children's Hospital

description:
Library name: Sample 10
PIK3CD-B_R1_001.fastq.gz

data_processing:
RSEM (v1.3.0)
Assembly: GRCh38, Ensembl v104
Supplementary files format and content: tab-delimited txt file including tpm quantile normalized data

source_name: Blood

growth_protocol: Human CD34+ were cultered at 37°C in StemSpan Serum-Free Expansion Medium (SFEM) II supplemented with 1% L-Glutamine (200 mM), 1% Penicillin-Streptomycin (10,000 U/mL), 1× CC100 cytokine cocktail (containing FLT3L. SCF. IL-3 and IL-6) and 100 ng/mL TPO for 5 days. Cells were then co-cultured on MS5 stroma cells in IMDM supplemented with 5% FBS, 1% Penicillin-Streptomycin, 55 µM 2-mercaptoethanol and 20 ng/mL IL-7 for a total of 21 days.

extract_protocol:
RNA was extract by using Total RNA Purification Micro Kit (Norgen Biotek) with DNase I treatment.
Library construction was performed at Genewiz (from Azenta life science) using Ultra-Low-Input Option

treatment_protocol: Nucleofection was performed using the Lonza 4D-Nucleofector system with the P3 Primary Cell 4D-Nucleofector (20 µL cuvette) for CD34⁺ HSPCs on day 2 after thawing. CRISPR/Cas9 RNPs and adenine base editors are delivered to HSPC with guide RNA. Program DZ-100 was used for nucleofection.

value: Blood

value: CD34+ derived cells

value: B cell progenitor

value: PIK3CD p.C416R

value: base editing

tag: batch

value: day 21


title: human CD34+-derived CD19+CD10+CD20dim B progenitors, PI3KGOF, Day 21, biol rep 1, A

description:
Library name: Sample 9
PIK3CD-A_R1_001.fastq.gz


title: WGBS_methylation-FWA-T1-M39-line1


title: human CD34+-derived CD19+CD10+CD20dim B progenitors, CBL KO, Day 21, biol rep 2, B

description:
Library name: Sample 8
CBL-B-2_R1_001.fastq.gz

value: CBL KO

value: gene knockout


title: WGBS_methylation-FWA-T1-M22-line2


title: human CD34+-derived CD19+CD10+CD20dim B progenitors, CBL KO, Day 21, biol rep 1, B

description:
Library name: Sample 6
CBL-B


title: WGBS_methylation-FWA-T1-M16-line1


title: WGBS_methylation-FWA-T1-M14-line2


title: WGBS_methylation-FWA-T1-M14-line1


title: human CD34+-derived CD19+CD10+CD20dim B progenitors, CBL KO, Day 21, biol rep 2, A

description:
Library name: Sample 7
CBL-A-2_R1_001.fastq.gz


title: WGBS_methylation-FWA-T1-M12-line2


title: human CD34+-derived CD19+CD10+CD20dim B progenitors, AAVS1 KO, Day 21, biol rep 2, B

description:
Library name: Sample 4
AAVS1-B-2_R1_001.fastq.gz


title: human CD34+-derived CD19+CD10+CD20dim B progenitors, CBL KO, Day 21, biol rep 1, A

description:
Library name: Sample 5
CBL-A


title: WGBS_methylation-FWA-T1-M12-line1


title: WGBS_methylation-FWA-T1-M16-line2


title: PC9_persister_panobinostat

city: La Jolla

first: August

last: Williams

state: CA

address: 9500 Gilman Dr.

department: Dermatology

institute: UC San Diego

description: Library name: Sample 6

data_processing:
Reads were aligned, samples aggregated, and expression quantified using 10X pipeline cellranger-3.1.0
Assembly: GRCh38
Supplementary files format and content: Filtered feature barcode matrix (10X)

source_name: Lung cancer

growth_protocol: PC9 cells were cultured in RPMI with 5% fetal bovine serum (FBS) and 1% Antimycotic/Antibiotic (AA). Cells were split with 0.25% trypsin. Cells were maintained in 5% CO2 at 37 degrees Celcius.

extract_protocol:
Cells were washed with PBS, trypsinized, centrifuged at 400 xg, then resuspended at 1,000 cells per µL in PBS.
Single cells were processed with 10X Chromium Single Cell 3' Reagents Kit v3 with all steps performed as recommended by the manufacturer.

treatment_protocol: Persister cells were derived in 100 nM erlotinib for 10 days. 1 µM RSL3 for 24 hours, or 7.5 nM panobinostat (LBH589) for 48 hours were added to parental cells, or to 100 nM erlotinib media for persister cells.

value: Lung cancer

value: PC9 lung adenocarcinoma

value: 100 nM erlotinib for 10 days, then addition of 7.5 nM panobinostat to erlotinib media for 48 hours


title: human CD34+-derived CD19+CD10+CD20dim B progenitors, AAVS1 KO, Day 21, biol rep 1, A

description:
Library name: Sample 1
AAVS1-A


title: WGBS_methylation-FWA-T1-M6-line2

value: Leaf


title: human CD34+-derived CD19+CD10+CD20dim B progenitors, AAVS1 KO, Day 21, biol rep 2, A

description:
Library name: Sample 3
AAVS1-A-2_R1_001.fastq.gz


title: PC9_parental_panobinostat

description: Library name: Sample 5

value: 7.5 nM panobinostat for 48 hours


title: WGBS_methylation-FT-T2-M30-line2-plus


title: WGBS_methylation-FWA-T1-M6-line1


title: human CD34+-derived CD19+CD10+CD20dim B progenitors, AAVS1 KO, Day 21, biol rep 1, B

description:
Library name: Sample 2
AAVS1-B


title: WGBS_methylation-FT-T2-M30-line2-minus-2


title: PC9_parental

description: Library name: Sample 1

value: untreated


title: PC9_parental_RSL3

description: Library name: Sample 3

value: 1 uM RSL3 for 24 hours


title: H1,1-10 KO,rep2,endoderm

description: Library name: H1 1-10 rep2-EN

data_processing:
RNA-seq reads were aligned to hg19 reference genome using STAR with RefSeq annotated genes.
Gene expression levels were counted using featureCounts.
Differential expression analysis comapring each sample with vehicle-treated WT hESCs was performed by DESeq2.
Assembly: hg19
Supplementary files format and content: DESeq2 output for normalization data
Supplementary files format and content: DESeq2 output for differential analysis results

value: Human embryonic stem cell


title: PC9_persister_RSL3

description: Library name: Sample 4

value: 100 nM erlotinib for 10 days, then addition of 1 uM RSL3 to erlotinib media for 24 hours


title: PC9_persister

description: Library name: Sample 2

value: 100 nM erlotinib for 10 days


title: WGBS_methylation-FT-T2-M30-line2-minus-1


title: WGBS_methylation-FT-T2-M22-line2-plus


title: H1,1-10 KO,rep3,endoderm

description: Library name: H1 1-10 rep3-EN

value: ZNF263 homozygous KO


title: WGBS_methylation-FT-T2-M14-line1-plus


title: WGBS_methylation-FT-T2-M22-line2-minus-2


title: H1,WT,rep3,endoderm

description: Library name: H1 WT rep3-EN

value: WT


title: H1,1-10 KO,rep1,endoderm

description: Library name: H1 1-10 rep1-EN


title: WGBS_methylation-FT-T2-M22-line2-minus-1


title: WGBS_methylation-FT-T2-M14-line1-minus-2


title: WGBS_methylation-FT-T2-M14-line1-minus-1


title: 331, cervix, on-RT#2

city: St. Louis

first: Julie

middle: K.

last: Schwarz

state: MO

department: Radiation Oncology

institute: Washington University in St. Louis

description:
Library name: CE331_3
10X Genomics

data_processing:
After single-nuclei prep and sequencing, Cell Ranger (v3.1.0) from 10x Genomics (with Count functionality) was used for aligning reads to the human genome (GRCh38) with the addition of pre-mRNA references. The resulting gene-by-cell UMI count matrix was used by the R package Seurat (v.3.1.0) for all subsequent processing.
Quality filters were applied to the data to remove barcodes that fell into any of the following categories: too few genes expressed (possible debris), too many associated UMIs (possibly more than one cell), and too high mitochondrial gene expression (possible dead cell). The cut-offs for these filters were based on recommendations by Seurat package documentation.
For each sample, we obtained the unfiltered feature-barcode matrix per sample by passing the demultiplexed FASTQs to Cell Ranger v.3.1.0 ‘count’ command using default parameters and the prebuilt GRCh38 genome reference v.3.0.0 (GRCh38 and Ensembl 93) for scRNA. Seurat v.3.1.2 was used for all subsequent analyses. First, a series of quality filters was applied to the data to remove those barcodes that fell into any one of these categories recommended by Seurat: too few total transcript counts (<300); possible debris with too few genes expressed (<200) and too few unique molecular identifiers (UMIs) (<1,000); possible more than one cell with too many genes expressed (>10,000) and too many unique molecular identifiers (>10,000); possible dead cell or a sign of cellular stress and apoptosis with too high proportion of mitochondrial gene expression over the total transcript counts (>10%). We constructed a Seurat object using the unfiltered feature-barcode matrix for each sample. Each sample was scaled and normalized using Seurat’s ‘SCTransform’ function to correct for batch effects (with parameters: vars.to.regress = c(‘nCount_RNA’, ‘percent.mito’), variable.features n = 2,000). Any merged analysis or subsequent subsetting of cells/samples underwent the same scaling and normalization method. Cells were clustered using the original Louvain algorithm and top 30 PCA dimensions via ‘FindNeighbors’ and ‘FindClusters’ (with parameters: resolution = 0.5) functions. The resulting merged and normalized matrix was used for the subsequent analysis.
Assembly: GRCh38
Supplementary files format and content: RDS file with Seurat’s ‘SCTransform’ function to correct for batch effects (with parameters: vars.to.regress = c(‘nCount_RNA’, ‘percent.mito’), variable.features n = 2,000).

source_name: primary cervical cancer

extract_protocol:
Fresh tissue samples were collected and transported directly to the lab for processed. For each tumor, approximately 10-20 mg of tissue were cut into small pieces with a blade. Enzymes and reagents from the Human Tumor Dissociation Kit (Miltenyi Biotec, 130-095-929) were added to the tissue pieces and resuspended gently in DMEM. The suspension was transferred to a gentleMACS C-tube (Miltenyi Biotec, 130-093-237) for use on the gentleMACS Octo Dissociator with Heaters (Miltenyi Biotec, 130-096-427, RRID:SCR_025922) following the programmed dissociation protocol (37h_TDK_1) for 30 to 60 minutes. Post processing, samples were filtered through a 40 μm Mini-Strainer (PluriSelect no. 43-10040-60) into a tube on ice. Samples were them spun down at 400 g for 5 minutes at 4 °C and underwent ACK lysis (Thermo Fisher, A1049201) if a red pellet was observed  followed by additional clean up spins with the same parameters. Cells were then counted and resuspended in a solution of PBS with 0.5% BSA for loading onto the Chromium. A detailed version of the protocol can also be found here: https://www.protocols.io/view/wu-sc-prep-protocol-for-solid-tumors-v2-1-yxmvmkp5bg3p/v1.
Utilizing the Chromium Next GEM Single Cell 3′ GEM, Library & Gel Bead Kit v.3.1 and Chromium instrument (10X genomics, RRID:SCR_024537), approximately 17,500 to 25,000 cells were partitioned into nanoliter droplets to achieve single-cell resolution for a maximum of 10,000 to 15,000 individual cells per sample (10x Genomics, 1000269). The resulting cDNA was tagged with a common 16-nucleotide (nt) cell barcode and 10-nt Unique Molecular Identifier during the reverse transcriptase (RT) reaction. Full-length cDNA from poly-A mRNA transcripts was enzymatically fragmented and size-selected to optimize the cDNA amplicon size (approximately 400 bp) for library construction (10x Genomics). The concentration of the 10x single-cell library was accurately determined through qPCR (Kapa Biosystems) to produce cluster counts appropriate for the HiSeq 4000 (RRID:SCR_016386 or NovaSeq-6000 platform (Illumina, RRID:SCR_016387). Then, 26 × 98-bp sequence data were generated targeting 50,000 read pairs per cell, which provided digital gene expression profiles for each individual cell.

value: primary cervical cancer

tag: case id


title: WGBS_methylation-FT-T1-pR-dCas9-line1

city: Shanghai


title: WGBS_methylation-FT-T1-pR-dCas9-line2


title: H1,WT,rep2,endoderm

description: Library name: H1 WT rep2-EN


title: H1,WT,rep1,endoderm

description: Library name: H1 WT rep1-EN


title: WGBS_methylation-FWA-T1-M22-line1


title: 332, cervix, pre-RT

description:
Library name: CE332_1
10X Genomics

value: pre-RT


title: WGBS_methylation-FT-T2-M12-line1-plus


title: 331, cervix, on-RT#1

description:
Library name: CE331_2
10X Genomics


title: WGBS_methylation-FT-T1-M30-line2


title: WGBS_methylation-FT-T1-M30-line1


title: 331, cervix, pre-RT

description:
Library name: CE331_1
10X Genomics


title: 330, cervix, pre-RT

description:
Library name: CE330_1
10X Genomics


title: 327, cervix, pre-RT

description:
Library name: CE327_1
10X Genomics


title: WGBS_methylation-FT-T1-M22-line1


title: WGBS_methylation-FT-T1-M22-line2


title: 326, cervix, pre-RT

description:
Library name: CE326_1
10X Genomics


title: 326, cervix, on-RT#1

description:
Library name: CE326_2
10X Genomics


title: WGBS_methylation-FT-T1-M14-line2


title: 326, cervix, on-RT#2

description:
Library name: CE326_3
10X Genomics


title: WGBS_methylation-FT-T1-M12-line1


title: WGBS_methylation-FT-T2-M12-line1-minus


title: 325, cervix, pre-RT

description:
Library name: CE325_1
10X Genomics


title: 323, cervix, pre-RT

description:
Library name: CE323_1
10X Genomics


title: 324, cervix, pre-RT

description:
Library name: CE324_1
10X Genomics


title: WGBS_methylation-FT-T1-M6-line2


title: WGBS_methylation-FT-T1-M12-line2


title: WGBS_methylation-FT-T1-M6-line1


title: WGBS_methylation-FT-T1-M14-line1


title: 322, cervix, on-RT#2

description:
Library name: CE322_3
10X Genomics


title: WGBS_methylation-FT_demethylation-FWA-T1-pR-dCas9_without_gRNA-line2


title: WGBS_fwa-1


title: 322, cervix, on-RT#1

description:
Library name: CE322_2
10X Genomics


title: 322, cervix, pre-RT

description:
Library name: CE322_1
10X Genomics


title: WGBS_demethylation-SDC-WT_background-T2-D30-line10-plus-2


title: 321, cervix, on-RT#2

description:
Library name: CE321_3
10X Genomics


title: WGBS_demethylation-SDC-WT_background-T2-D30-line10-plus-1


title: WGBS_fwa-2


title: 700514_857890, cervix, preRT

description: Library name: 700514_857890_preRT

data_processing:
RNA quantification was done using our internal pipeline (https://github.com/ding-lab/cptac_rna_expression). Briefly, raw fastq files were aligned to the human reference genome GRCh38 using STAR (2.7.6a); raw read count was then quantified by featureCounts (1.6.4). Gencode v22 was used for gene annotation. After obtaining raw read count, Fragments Per Kilobase of transcript per Million mapped reads (FPKM) and FPKM Upper Quartile (FPKM-UQ) values were calculated by following the GDC’s formula ( https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/Expression_mRNA_Pipeline/).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file of raw gene counts for each sample

extract_protocol:
Total RNA was extracted with TRI reagent (Millipore Sigma, T9424) and treated with DNase I (Qiagen, 79254) using an RNeasy MinElute Cleanup Kit (Qiagen, 74204). Library preparation was performed with 500ng to 1μg of total RNA.
Ribosomal RNA was blocked using FastSelect reagents (Qiagen) during complementary DNA synthesis. RNA was fragmented in reverse transcriptase buffer with FastSelect reagent and heated to 94°C for 5min, 75°C for 2 min, 70°C for 2 min, 65°C for 2 min, 60°C for 2 min, 55°C for 2 min, 37 °C for 5 min and 25°C for 5 min. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer’s instructions) and random hexamers. A second strand reaction was performed to yield double-stranded cDNA (ds-cDNA). cDNA was blunt ended, had an A base added to the 3′ ends and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 S4 instrument (RRID:SCR_016387), generating approximately 30 million paired-end 2×150 reads per library.

value: preRT

value: Batch 2


title: 700514_856882, cervix, 3weeks

description: Library name: 700514_856882_3weeks


title: WGBS_demethylation-SDC-WT_background-T2-D12-line1-plus-2


title: 323, cervix, on-RT#2

description:
Library name: CE323_3
10X Genomics


title: 700514_856882, cervix, preRT

description: Library name: 700514_856882_preRT


title: WGBS_demethylation-SDC-WT_background-T2-D12-line1-plus-1


title: 700514_854828, cervix, 3weeks

description: Library name: 700514_854828_3weeks


title: 700514_856677, cervix, preRT

description: Library name: 700514_856677_preRT


title: WGBS_demethylation-SDC-WT_background-T2-D12-line1-minus-2


title: WGBS_demethylation-SDC-nrpe1_background-T2-D28-line12-minus-2


title: WGBS_demethylation-SDC-WT_background-T2-D12-line1-minus-1


title: WGBS_demethylation-SDC-nrpe1_background-T2-D30-line1-minus-1


title: 323, cervix, on-RT#1

description:
Library name: CE323_2
10X Genomics


title: WGBS_demethylation-SDC-nrpe1_background-T2-D30-line1-plus


title: 700514_854740, cervix, preRT

description: Library name: 700514_854740_preRT


title: WGBS_demethylation-SDC-nrpe1_background-T2-D30-line1-minus-2


title: WGBS_demethylation-SDC-nrpe1_background-T2-D28-line12-minus-1


title: 700514_856678, cervix, preRT

description: Library name: 700514_856678_preRT


title: 700514_854740, cervix, 3weeks

description: Library name: 700514_854740_3weeks


title: 700514_853690, cervix, 3weeks

description: Library name: 700514_853690_3weeks


title: 700514_853690, cervix, preRT

description: Library name: 700514_853690_preRT


title: WGBS_demethylation-SDC-nrpe1_background-T2-D24-line2-minus-2


title: 700514_853689, cervix, 3weeks

description: Library name: 700514_853689_3weeks


title: WGBS_demethylation-SDC-nrpe1_background-T2-D24-line2-plus


title: 700514_856678, cervix, 3weeks

description: Library name: 700514_856678_3weeks


title: WGBS_methylation-FT_demethylation-FWA-T1-pR-dCas9_without_gRNA-line1


title: 700514_856677, cervix, 3weeks

description: Library name: 700514_856677_3weeks


title: 700514_857890, cervix, 3weeks

description: Library name: 700514_857890_3weeks


title: WGBS_demethylation-SDC-WT_background-T2-D30-line10-minus


title: WGBS_demethylation-SDC-nrpe1_background-T2-D24-line2-minus-1


title: 700514_853689, cervix, preRT

description: Library name: 700514_853689_preRT


title: WGBS_demethylation-SDC-nrpe1_background-T2-D18-line1-plus


title: WGBS_demethylation-SDC-nrpe1_background-T2-D28-line12-plus-1


title: WGBS_demethylation-SDC-nrpe1_background-T2-D28-line12-plus-2


title: 700514_854828, cervix, preRT

description: Library name: 700514_854828_preRT


title: 700514_852395, cervix, 3weeks

description: Library name: 700514_852395_3weeks


title: 700514_852395, cervix, preRT

description: Library name: 700514_852395_preRT


title: WGBS_demethylation-SDC-nrpe1_background-T2-D18-line1-minus-1


title: WGBS_demethylation-SDC-nrpe1_background-T2-D12-line2-minus-2


title: WGBS_demethylation-SDC-nrpe1_background-T2-D12-line2-minus-1


title: WGBS_demethylation-SDC-nrpe1_background-T1-pR-dCas9-line2


title: WGBS_demethylation-SDC-nrpe1_background-T2-D18-line1-minus-2


title: 700514_851577, cervix, 3weeks

description: Library name: 700514_851577_3weeks


title: WGBS_demethylation-SDC-nrpe1_background-T2-D12-line2-plus


title: 700514_852129, cervix, preRT

description: Library name: 700514_852129_preRT


title: 700514_849729, cervix, preRT

description: Library name: 700514_849729_preRT

value: Batch 1


title: 700514_849729, cervix, 3weeks

description: Library name: 700514_849729_3weeks


title: 700514_853562, cervix, 3weeks

description: Library name: 700514_853562_3weeks


title: 700514_851577, cervix, preRT

description: Library name: 700514_851577_preRT


title: WGBS_demethylation-SDC-nrpe1_background-T1-pR-dCas9_without_gRNA-line1


title: 700514_848915, cervix, 3weeks

description: Library name: 700514_848915_3weeks


title: WGBS_demethylation-SDC-nrpe1_background-T1-D30-line2


title: 700514_848915, cervix, preRT

description: Library name: 700514_848915_preRT


title: WGBS_demethylation-SDC-nrpe1_background-T1-D30-line1


title: 700514_848914, cervix, 3weeks

description: Library name: 700514_848914_3weeks


title: WGBS_demethylation-SDC-nrpe1_background-T1-D24-line2


title: WGBS_demethylation-SDC-nrpe1_background-T1-D24-line1


title: 700514_848746, cervix, 3weeks

description: Library name: 700514_848746_3weeks


title: 700514_848914, cervix, preRT

description: Library name: 700514_848914_preRT


title: 700514_853562, cervix, preRT

description: Library name: 700514_853562_preRT


title: WGBS_demethylation-SDC-nrpe1_background-T1-D18-line2


title: 700514_852129, cervix, 3weeks

description: Library name: 700514_852129_3weeks


title: WGBS_demethylation-SDC-nrpe1_background-T1-D18-line1


title: 700514_848746, cervix, preRT

description: Library name: 700514_848746_preRT


title: WGBS_demethylation-SDC-nrpe1_background-T1-pR-dCas9-line1


title: WGBS_demethylation-SDC-nrpe1_background-T1-pR-dCas9_without_gRNA-line2


title: 700514_848331, cervix, 3weeks

description: Library name: 700514_848331_3weeks


title: 700514_848331, cervix, preRT

description: Library name: 700514_848331_preRT


title: PML_2

city: Montréal

first: Vincent

last: Giguère

state: QC

address: 1160 Pine Ave West, McIntyre Bldg Room 710

department: Goodman Cancer Centre

country: Canada

institute: McGill University

description: Library name: PML_2

data_processing:
Duplicate sequencing files were merged together. ChIP-seq reads were first trimmed for adapter sequences and low-quality score bases using Trimmomatic v0.36. The resulting reads were mapped to the human reference genome (hg38) using BWA-MEM v0.7.12 in paired-end mode at default parameters. Only reads that had a unique alignment (mapping quality > 20) were retained and PCR duplicates were removed using Picard tools v2.0.1.
Peaks (summit +/- 150 bp) were called using MACS2 software suite v2.1.1.20160309 at an FDR < 0.05 using sequenced libraries of respective input DNA as control. Peaks in mitochondrial chromosome and scaffold regions were removed.
Peak annotations and intersections were performed using HOMER v4.11.1.
Assembly: hg38
Supplementary files format and content: Bigwig files for ChIP and input samples as well as a ChIP peak annotated text file

growth_protocol: MDA-MB-231 cells were maintained in DMEM supplemented with 10% serum and 5% penicillin-streptomycin.

extract_protocol:
Cross-linked protein-DNA complexes were enriched with a PML-specific antibody, de-crosslinked, treated with RNase A and Proteinase K and purified using a QIAquick PCR purification kit (Qiagen, Cat#28106).
Libraries were prepared at Novogene Bioinformatics Technology Co. Ltd using the NEBNext Ultra II DNA Library Prep Kit and sequenced as paired-end 150bp reads on an Illumina NovaSeq 6000 sequencer.

value: Human triple-negative breast cancer

tag: chip antibody

value: PML (Bethyl Laboratories, A301-167A)


title: WGBS_demethylation-SDC-nrpe1_background-T1-D12-line1


title: WGBS_demethylation-FWA-T2-D30-line2-plus


title: PML_1

description: Library name: PML_1


title: WGBS_demethylation-FWA-T2-D30-line2-minus-2


title: input_2

description: Library name: input_2


title: WGBS_demethylation-FWA-T2-D24-line2-minus-1


title: shPML_3

description: Library name: shPML_3

data_processing:
Raw data (raw reads) of fastq format were processed through in-house perl scripts to remove reads containing adapter and poly-N sequences and reads with low quality.
Paired-end clean reads were aligned to the  Homo Sapiens reference genome hg19 using STAR software v2.5
HTSeq software v0.6.1 was used to count the number of reads mapped per gene. Then, FPKM (Fragments per kilobase of transcript sequence per millions base pairs sequenced) of each gene was calculated based on the length of the gene and read counts mapped to the gene.
Assembly: hg19
Supplementary files format and content: tab-delimited text file including the read count values for all 6 samples (n=3 per condition)
Supplementary files format and content: tab-delimited text file including the FPKM values for all 6 samples (n=3 per condition)

extract_protocol:
Total RNA was extracted from cells using a RNeasy Mini Kit (Qiagen, Cat#74106) with DNAse I digestion (Qiagen, Cat#79254).
Libraries were prepared at Novogene Bioinformatics Technology Co., Ltd using the NEBNext Ultra RNA Library Prep kit according to manufacturer's recommendations and sequenced as paired-end 150bp reads on an Illumina NovaSeq 6000 sequencer.

treatment_protocol: MDA-MB-231 cells with shPML-mediated knockdown or empty vector shControl (shC).

value: shPML


title: shPML_2

description: Library name: shPML_2


title: WGBS_demethylation-FWA-T2-D30-line2-minus-1

value: Leaf


title: input_1

description: Library name: input_1


title: WGBS_demethylation-FWA-T2-D18-line1-plus


title: shC_3

description: Library name: shC_3

value: shControl


title: WGBS_demethylation-FWA-T2-D18-line1-minus-1


title: shPML_1

description: Library name: shPML_1


title: shC_2

description: Library name: shC_2


title: WGBS_demethylation-FWA-T2-D12-line1-minus-2


title: WGBS_demethylation-SDC-nrpe1_background-T1-D12-line2


title: shC_1

description: Library name: shC_1


title: WGBS_demethylation-FWA-T2-D12-line1-plus


title: Plasmacytoid dendritic cells

city: Philadelphia

first: Khanh

middle: Bao

last: Trang

state: PA

address: 3615 Civic Center Blvd

department: Human Genetics

institute: Children's Hospital of Philadelphia

data_processing:
Bases were called using Illumina bcl2fastq2 conversion v2.29
Paired-end reads from two replicates were pre-processed using the HICUP pipeline v0.7.4, with bowtie as aligner and hg38 as the reference genome.
The alignment .bam file were parsed to .pairs format using pairtools v0.3.0 and pairix v0.3.7, and eventually converted to pre-binned Hi-C matrix in .cool format by cooler v0.8.10 with multiple resolutions (500bp, 1kbp, 2kbp, 2.5kbp, 4kbp, 5kbp, 10kbp, 25kbp, 40kbp, 50kbp, 100kbp, 250kbp, 500kbp, 1Mbp and 2.5Mbp) and normalized with ICE method
For each sample, eigenvectors were determined from an ICE balanced Hi-C matrix with 40kb resolution using cooltools v0.3.2 and first principal components were used to determine A/B compartments with GC% of genome region as reference track to determine the sign
For each cell type, significant intra-chromosomal interaction loops were determined under multiple resolutions (1kb, 2kb and 4kb) using the Hi-C loop caller Fit-Hi-C2 v2.0.7 (FDR<1e-6) on merged replicates matrix. The consensus chromatin loops within resolution were identified by combining all three stages. The final consensus interaction loops for visualization were collected by merging loops from all the resolutions with preference to keep the highest resolution.
Assembly: hg38
Supplementary files format and content: BEDPE with paired chromatin contact regions

source_name: PBMCs

growth_protocol: From 250 million frozen PBMCs we recovered 0.865 million pan-Dendritic Cells with Stem Cell Pan-DC pre-enrichment kit. All the subpopulations of DCs- Plasmocytoid Dendritic Cells, conventional DC CD141+ and conventional DC CD1c+ were identified after pan-DC enrichment.

extract_protocol:
Hi-C library preparation on FACS-sorted cells was performed using the Arima-HiC kit (Arima Genomics Inc), according to the manufacturer’s protocols. Briefly, cells were crosslinked using formaldehyde. Crosslinked cells were then subject to the Arima-HiC protocol, which utilizes multiple restriction enzymes to digest chromatin.
Arima-HiC sequencing libraries were prepared by first shearing purified proximally-ligated DNA and then size-selecting 200-600 bp DNA fragments using AmpureXP beads (Beckman Coulter). The size-selected fragments were then enriched using Enrichment Beads (provided in the Arima-HiC kit), and then converted into Illumina-compatible sequencing libraries with the Swift Accel-NGS 2SPlus DNA Library Kit (Swift, 21024) and Swift 2S Indexing Kit (Swift, 26148). The purified, PCR-amplified DNA underwent standard QC (qPCR, Bioanalyzer, and KAPA Library Quantification [Roche, KK4824]) and was sequenced with unique single indexes on the Illumina NovaSeq 6000 Sequencing System using 200 bp reads.

value: PBMCs

value: Plasmacytoid dendritic cells

tag: markers

tag: biomaterial provider

value: Wells Laboratory - Children’s Hospital of Philadelphia


title: Natural killer cells

value: Natural killer cells


title: CD1c+conventional dendritic cells

value: conventional dendritic cells

value: CD1c+conventional dendritic cells


title: WGBS_demethylation-FWA-T2-D12-line1-minus-1


title: WGBS_demethylation-FWA-T1-pR-dCas9-line2


title: WGBS_demethylation-FWA-T2-D24-line2-plus


title: WGBS_demethylation-FWA-T2-D10-line2-plus


title: T helper 2cells

data_processing:
Bases were called using Illumina bcl2fastq2 conversion v2.29
Paired-end reads from replicates were pre-processed using the HICUP pipeline (v0.5.9) with the default parameters. Reads were aligned to hg38 using bowtie2.
Significant interactions were called CHiCAGO (v1.1.8) with default parameters except for bin-size set to 2,500. In addition to our analysis per individual DpnII fragment (1frag), we also called interactions by binning four fragments, which improves detection of long-distance interactions. Significant promoter interactions using the read count from promoters included in our reference bait.
Significant interactions at 4-DpnII fragment resolution were also called using CHiCAGO with artificial baitmap and .rmap files where four DpnII fragments were concatenated. Interactions with a CHiCAGO score > 5 in at least one cell type in either 1-fragment or 4-fragment resolution were considered significant.
Assembly: hg38
Supplementary files format and content: BEDPE with paired chromatin contact regions
Library strategy: Promoter-Focused Capture-C

source_name: T helpercells

extract_protocol:
For each library, 10e7 fixed cells were thawed at 37ºC, followed by centrifugation at RT for 5 mins at 14,000 rpm. The cell pellet was resuspended in 1 mL of dH2O supplemented with 5 μL 200X protease inhibitor cocktail, incubated on ice for 10 mins, then centrifuged. The cell pellet was resuspended to a total volume of 650 μL in dH2O. Both samples underwent a pre-digestion incubation with the addition of 0.3% SDS, 1x NEBuffer DpnII, and dH2O for 1hr at 37ºC in a Thermomixer shaking at 1,000rpm. A 1.7% solution of Triton X-100 was added to each tube and shaking was continued for another hour. After the pre-digestion incubation, 10 μL of DpnII (was added only to each sample tube, and continued shaking until the end of the day. An additional 10 µL of DpnII was added to each digestion reaction and digestion continued overnight. The next day, another additional 10 µL of DpnII was added and the incubation continued for another 2-3 hours. 100 μL of each digestion reaction was then removed, pooled into one 1.5 mL tube. The remaining samples were heat inactivated at 65°C for 20 min at 1000 rpm in a Thermomixer, and cooled on ice for 20 additional minutes. Digested samples were ligated with 8 μL of T4 DNA ligase (HC 30U/uL) and 1X ligase buffer at 1,000 rpm overnight at 16°C in a Thermomixer. The next day, an additional 2 µL of T4 DNA ligase was spiked into each sample and incubated for another few hours. The ligated samples were then de-crosslinked overnight at 65°C with Proteinase K along with the pre-digestion and digestion controls. The following morning, both controls and ligated samples were incubated for 30 min at 37°C with RNase A, followed by phenol/chloroform/isoamyl alcohol extraction and ethanol precipitation at -20°C.
The 3C libraries were centrifuged at 3000 rpm for 45 min at 4°C 14,000 rpm, to pellet the samples. DNA pellets were resuspended in 70% ethanol and again centrifuged as described above. The 3C library pellets were resuspended in 300 μL dH2O and stored at −20°C. 10 μg of isolated DNA from 3C libraries of each library was sheared in dH2O using a QSonica Q800R to an average fragment size of 350bp. After shearing, DNA was purified using AMPure XP beads. One microgram of adaptor-ligated library was used as input for the SureSelect XT capture kit using manufacturer protocol and our custom-designed 41K promoter Capture-C probe set.

value: T helpercells

value: T helper 2cells

value: Levings Lab - BC Children's Hospital


title: Epstein-Barr Virus transformed lymphoblastoid cell line

source_name: Lymphoblastoid

value: Lymphoblastoid

value: Lymphoblastoid cells


title: Gonodal WAT macrophages, deleted sample 8, LysMCretdT-Fthfl/fl>R26CreFthfl/fl bone marrow chimera

city: Oeiras

first: Rui

last: Martins

address: Rua da Quinta Grande 6

department: Inflammation

country: Portugal

institute: Gulbenkian Institute for Molecular Medicine

description: Library name: W8M

data_processing:
Fastq reads were aligned against the mouse reference genome GRCm39 using the annotation GENCODE M27 (STAR; v.2.5.2a)
Read summarization was performed using FeatureCounts (v1.5.0-p1)m by assigning uniquely mapped reads to genomic features
Gene expression tables were imported into the R programming language and environment (v.4.1.0)
Analysis of differential gene expression was performed using the DESeq2 R package (Love et al., 2014) (v.1.31.7)
Gene expression was modeled per organ based on chimera genotype combination.
Genes not expressed or presenting an average expression inferior to 5 counts across the 18 samples were removed resulting in 22,529 (liver), 23,327 (WAT) and 29,821 (heart) genes for downstream differential gene expression analysis
Assembly: GRCm39
Supplementary files format and content: Single table containing the normalized counts per feature (geneid) and sample

source_name: Gonodal WAT macrophages, from LysMCretdT-Fthfl/fl>R26CreFthfl/fl bone marrow chimera 19 days post tamoxifen induced deletion of Fth, Sample 8

extract_protocol:
Viable, CD45+, CD11b+, dTomato+ (LysM+), Ly6G-, CD3-, CD19- cells (monocytes/macrophages) were sorted directly into QIAgen RLT+ buffer and used for SMART-seq2 cDNA library generation
Full-length cDNAs and sequencing libraries were generated following the SMART-Seq2 protocol, as previously described (Picelli et al, 2014). Quality control (Agilent Technologies) and "tagmentation" - PCR-mediated adaptor addition and amplification of the adapted libraries was performed following the Nextera library preparation protocol (llumina Tagment DNA Enzyme and Buffer, Illumina #20034211; KAPA HiFi HotStart ReadyMix, Roche #07958935001; Nextera XT Index Kit v2 Set A, Illumina #15052163; Nextera XT Index Kit v2 Set D, Illumina #15052166), essentially as previously described (Baym et al, 2015). Libraries were sequenced (NextSeq2000 sequencing; Illumina) using 100 SE P2 and sequence information was extracted in FastQ format, using Illumina DRAGEN FASTQ Generation v3.8.4, producing on average approximately 38x10^6 (liver), 32x10^6 (WAT) and 43x10^6 (heart) reads per sample.

treatment_protocol: Bone marrow chimeras (LysMCretdT>Fthfl/fl; LysMCretdT>R26CreFthfl/fl; LysMCretdT-Fthfl/fl>R26CreFthfl/fl) were given Tamoxifen (50mg/kg, in 100µl corn oil, 5% Ethanol) 3 times, every other day.

value: Tamoxifen 50mg/kg 3x, every other day


title: WGBS_demethylation-FWA-T1-D24-line2


title: WGBS_demethylation-FWA-T1-D24-line1


title: Regulatory T cells

source_name: Regulatory T cells

value: Regulatory T cells


title: WGBS_demethylation-FWA-T2-D24-line2-minus-2


title: WGBS_demethylation-FWA-T1-D30-line2


title: T regulatory type 1 cells

value: T regulatory type 1 cells


title: Gonodal WAT macrophages, deleted sample 4, LysMCretdT-Fthfl/fl>R26CreFthfl/fl bone marrow chimera

description: Library name: W4M

source_name: Gonodal WAT macrophages, from LysMCretdT-Fthfl/fl>R26CreFthfl/fl bone marrow chimera 19 days post tamoxifen induced deletion of Fth, Sample 4


title: WGBS_demethylation-FWA-T1-D18-line2


title: Gonodal WAT macrophages, rescued sample 7, LysMCretdT>R26CreFthfl/fl bone marrow chimera

description: Library name: W7M

source_name: Gonodal WAT macrophages, from LysMCretdT>R26CreFthfl/fl bone marrow chimera 19 days post tamoxifen induced deletion of Fth Sample 7


title: Gonodal WAT macrophages, rescued sample 2, LysMCretdT>R26CreFthfl/fl bone marrow chimera

description: Library name: W2M

source_name: Gonodal WAT macrophages, from LysMCretdT>R26CreFthfl/fl bone marrow chimera 19 days post tamoxifen induced deletion of Fth Sample 2


title: Regulatory T cells (Donor 3199)

data_processing:
Bases were called using Illumina bcl2fastq2 conversion v2.29
The pair-end fastq files were mapped to the genome assembly hg19 by STAR (v2.6.0c) independently for each replicate.
The GencodeV19 annotation was used for gene feature annotation and the raw read count for gene feature was calculated by htseq-count (v0.6.1) with parameter settings -f bam - r pos -s yes -t exon -m union.
The gene features localized on chrM or annotated as rRNAs, small coding RNA, or pseudo genes were removed from the final sample-by-gene read count matrix.
Assembly: hg19
Supplementary files format and content: HTSeq raw count

extract_protocol:
RNA was isolated from ∼ 1 million of each cell stage using Trizol Re-agent (Invitrogen), purified using the Directzol RNA Miniprep Kit (Zymo Research), and depleted of contaminating genomic DNA using DNAse I. Purified RNA was checked for quality on a Bioanlayzer 2100 using the Nano RNA Chip and samples with RIN>7 were used for RNA-seq library preparation. RNA samples were depleted of rRNA using QIAseq Fastselect RNA removal kit (Qiagen).
Samples were then processed for the preparation of libraries using the SMARTer Stranded Total RNA Sample Prep Kit (Takara Bio USA) according to the manufacturer’s instructions. Briefly, the purified first-strand cDNA is amplified into RNA-seq libraries using SeqAmp DNA Polymerase and the Forward and the Reverse PCR Primers from the Illumina Indexing Primer Set HT for Illumina. Quality and quantity of the libraries was assessed using the Agilent 2100 Bioanalyzer system and Qubit fluorometer (Life Technologies). Sequencing was performed on the NovaSeq 6000 platform at the CHOP Center for Spatial and Functional Genomics.


title: WGBS_demethylation-FWA-T1-D12-line2


title: T helper 1cells

value: T helper 1cells


title: WGBS_demethylation-FWA-T2-D18-line1-minus-2

value: Leaf


title: Gonodal WAT macrophages, deleted sample 3, LysMCretdT-Fthfl/fl>R26CreFthfl/fl bone marrow chimera

description: Library name: W3M

source_name: Gonodal WAT macrophages, from LysMCretdT-Fthfl/fl>R26CreFthfl/fl bone marrow chimera 19 days post tamoxifen induced deletion of Fth, Sample 3


title: T helper 17cells

value: T helper 17cells


title: WGBS_demethylation-FWA-T1-D30-line1


title: Gonodal WAT macrophages, deleted sample 9, LysMCretdT-Fthfl/fl>R26CreFthfl/fl bone marrow chimera

description: Library name: W9M

source_name: Gonodal WAT macrophages, from LysMCretdT-Fthfl/fl>R26CreFthfl/fl bone marrow chimera 19 days post tamoxifen induced deletion of Fth, Sample 9


title: WGBS_demethylation-FWA-T1-pR-dCas9-line1


title: Liver macrophages, deleted sample 9, LysMCretdT-Fthfl/fl>R26CreFthfl/fl bone marrow chimera

description: Library name: L9M

source_name: Liver macrophages, from LysMCretdT-Fthfl/fl>R26CreFthfl/fl bone marrow chimera 19 days post tamoxifen induced deletion of Fth, Sample 9


title: Liver macrophages, deleted sample 8, LysMCretdT-Fthfl/fl>R26CreFthfl/fl bone marrow chimera

description: Library name: L8M

source_name: Liver macrophages, from LysMCretdT-Fthfl/fl>R26CreFthfl/fl bone marrow chimera 19 days post tamoxifen induced deletion of Fth, Sample 8


title: Regulatory T cells (Donor 9632)


title: Liver macrophages, deleted sample 4, LysMCretdT-Fthfl/fl>R26CreFthfl/fl bone marrow chimera

description: Library name: L4M

source_name: Liver macrophages, from LysMCretdT-Fthfl/fl>R26CreFthfl/fl bone marrow chimera 19 days post tamoxifen induced deletion of Fth, Sample 4


title: Regulatory T cells - activated (Donor 3199)

value: LPS-activated


title: Liver macrophages, deleted sample 3, LysMCretdT-Fthfl/fl>R26CreFthfl/fl bone marrow chimera

description: Library name: L3M

source_name: Liver macrophages, from LysMCretdT-Fthfl/fl>R26CreFthfl/fl bone marrow chimera 19 days post tamoxifen induced deletion of Fth, Sample 3


title: WGBS_demethylation-FWA-T2-D10-line2-minus

source_name: Leaf


title: Liver macrophages, deleted sample 10, LysMCretdT-Fthfl/fl>R26CreFthfl/fl bone marrow chimera

description: Library name: L10M

source_name: Liver macrophages, from LysMCretdT-Fthfl/fl>R26CreFthfl/fl bone marrow chimera 19 days post tamoxifen induced deletion of Fth, Sample 10


title: Liver macrophages, rescued sample 7, LysMCretdT>R26CreFthfl/fl bone marrow chimera

description: Library name: L7M

source_name: Liver macrophages, from LysMCretdT>R26CreFthfl/fl bone marrow chimera 19 days post tamoxifen induced deletion of Fth Sample 7


title: Regulatory T cells - activated (Donor 2000)


title: Regulatory T cells (Donor 1064)


title: T regulatory type 1 cells (Donor 9632)


title: Liver macrophages, control sample 6, LysMCretdT>Fthfl/fl bone marrow chimera

description: Library name: L6M

source_name: Liver macrophages from LysMCretdT>Fthfl/fl bone marrow chimera 19 days post tamoxifen induced deletion of Fth - Sample 6

value: LysMCretdT>Fthfl/fl bone marrow chimera


title: Liver macrophages, rescued sample 1, LysMCretdT>R26CreFthfl/fl bone marrow chimera

description: Library name: L1M

source_name: Liver macrophages, from LysMCretdT>R26CreFthfl/fl bone marrow chimera 19 days post tamoxifen induced deletion of Fth Sample 1


title: Zone 3-Cre; Af/f; Cact (5 months)

city: Dallas

first: Hao

last: Zhu

state: TX

address: 5323 Harry Hines Blvd

institute: UTSW

description: Library name: 2_CABT_5_month

data_processing:
FASTQ files for single-cell libraries were analyzed using the Tapestri V2 pipeline as previously described. Reads were aligned against a custom mouse genome (mm10) with the floxed and recombined sequences for Arid2 and Ctnnb1 each included as additional dummy chromosomes. Nuclear genotypes were determined based on the presence of reads specific for WT, floxed, or deleted Ctnnb1 or Arid2
Bam files were manually inspected (Samtools v-1.3) to ensure fragments aligned to the flox-recombined references were appropriate in length.
Tapestri V2 h5 output files containing the read depth info for each cell were imported into R and processed
Assembly: mm10 with floxed recombined sequences for Arid2 and Ctnnb1 included as additional chromosomes
Supplementary files format and content: *.h5 : multi-omics formatted HDF5 file output from Tapestri pipeline with read counts and genotype information on a per-cell level

source_name: Liver

extract_protocol:
All steps were performed according to the Mission Bio “Tapestri® Single-Cell DNA Sequencing V2” user manual. Viable mouse hepatocytes were isolated using two-step enzyme digestion through the inferior vena cava, and nuclei were purified as previously described. Samples were then proceeded with encapsulation, lysis and digestion, barcoding, targeted PCR, emulsion breaking, and PCR product digestion and purification.
Barcoded samples were PCR-amplified using a custom amplicon panel for each relevant floxed site, designed such that recombination would lead to PCR products differing in both length and sequence. PCR products were isolated from individual droplets, purified using Ampure XP beads, and used as template for library amplification, incorporating i5/i7 Illumina indices.

value: Liver

value: C57BL/6J and Swiss Webster mix


title: Gonodal WAT macrophages, deleted sample 10, LysMCretdT-Fthfl/fl>R26CreFthfl/fl bone marrow chimera

description: Library name: W10M

source_name: Gonodal WAT macrophages, from LysMCretdT-Fthfl/fl>R26CreFthfl/fl bone marrow chimera 19 days post tamoxifen induced deletion of Fth, Sample 10


title: Zone 1-Cre; Af/f; Cact (5 months)

description: Library name: 1_GABT_5_month


title: Gonodal WAT macrophages, rescued sample 1, LysMCretdT>R26CreFthfl/fl bone marrow chimera

description: Library name: W1M

source_name: Gonodal WAT macrophages, from LysMCretdT>R26CreFthfl/fl bone marrow chimera 19 days post tamoxifen induced deletion of Fth Sample 1


title: WGBS_demethylation-FWA-T1-D18-line1


title: T regulatory type 1 cells (Donor 1064)

source_name: Regulatory T cells


title: Heart macrophages macrophages, deleted sample 9, LysMCretdT-Fthfl/fl>R26CreFthfl/fl bone marrow chimera

description: Library name: H9M

source_name: Heart macrophages, from LysMCretdT-Fthfl/fl>R26CreFthfl/fl bone marrow chimera 19 days post tamoxifen induced deletion of Fth, Sample 9


title: Regulatory T cells (Donor 2000)


title: Gonodal WAT macrophages, control sample 6, LysMCretdT>Fthfl/fl bone marrow chimera

description: Library name: W6M

source_name: Gonodal WAT macrophages from LysMCretdT>Fthfl/fl bone marrow chimera 19 days post tamoxifen induced deletion of Fth - Sample 6


title: Gonodal WAT macrophages, control sample 5, LysMCretdT>Fthfl/fl bone marrow chimera

description: Library name: W5M

source_name: Gonodal WAT macrophages from LysMCretdT>Fthfl/fl bone marrow chimera 19 days post tamoxifen induced deletion of Fth - Sample 5


title: Heart macrophages macrophages, deleted sample 3, LysMCretdT-Fthfl/fl>R26CreFthfl/fl bone marrow chimera

description: Library name: H3M

source_name: Heart macrophages, from LysMCretdT-Fthfl/fl>R26CreFthfl/fl bone marrow chimera 19 days post tamoxifen induced deletion of Fth, Sample 3


title: Heart macrophages macrophages, rescued sample 7, LysMCretdT>R26CreFthfl/fl bone marrow chimera

description: Library name: H7M

source_name: Heart macrophages, from LysMCretdT>R26CreFthfl/fl bone marrow chimera 19 days post tamoxifen induced deletion of Fth Sample 7


title: Heart macrophages macrophages, deleted sample 10, LysMCretdT-Fthfl/fl>R26CreFthfl/fl bone marrow chimera

description: Library name: H10M

source_name: Heart macrophages, from LysMCretdT-Fthfl/fl>R26CreFthfl/fl bone marrow chimera 19 days post tamoxifen induced deletion of Fth, Sample 10


title: Gonodal WAT macrophages, control sample 12, LysMCretdT>Fthfl/fl bone marrow chimera

description: Library name: W12M

source_name: Gonodal WAT macrophages from LysMCretdT>Fthfl/fl bone marrow chimera 19 days post tamoxifen induced deletion of Fth - Sample 12


title: Heart macrophages macrophages, rescued sample 2, LysMCretdT>R26CreFthfl/fl bone marrow chimera

description: Library name: H2M

source_name: Heart macrophages, from LysMCretdT>R26CreFthfl/fl bone marrow chimera 19 days post tamoxifen induced deletion of Fth Sample 2


title: Regulatory T cells - activated (Donor 9632)


title: WGBS_demethylation-FWA-T1-D12-line1

source_name: Leaf


title: WGBS_demethylation-FWA-T1-D10-line2


title: WGBS_demethylation-FWA-T1-D10-line1


title: ATACseq_WT

library_source: other

data_processing:
For data analysis, raw paired-end reads were trimmed using Trim Galore with the “--nextera” and “--paired” parameters, and quality control was conducted using FastQC. Trimmed reads were aligned to the TAIR10 reference genome using Bowtie2, and the aligned reads were converted to BAM format using Samtools. The BAM files were sorted and indexed using Samtools, and duplicates were marked and removed with Picard's “MarkDuplicates” function. Reads with a mapping quality score above 30 were filtered using Samtools, and mitochondrial and chloroplast DNA reads were removed using AWK and Samtools. The filtered BAM files were converted to BedGraph format using bedtools and subsequently to BigWig format using the bedGraphToBigWig tool for efficient visualization.
Assembly: TAIR10
Supplementary files format and content: bigWig, peaks

molecule: other

extract_protocol:
ATAC-seq was performed following a published protocol. The rosette leaves of 5-week-old WT plants were collected for nuclei extraction.
Tn5 tagmentation.

value: wild type


title: Heart macrophages macrophages, rescued sample 1, LysMCretdT>R26CreFthfl/fl bone marrow chimera

description: Library name: H1M

source_name: Heart macrophages, from LysMCretdT>R26CreFthfl/fl bone marrow chimera 19 days post tamoxifen induced deletion of Fth Sample 1


title: Liver macrophages, rescued sample 2, LysMCretdT>R26CreFthfl/fl bone marrow chimera

description: Library name: L2M

source_name: Liver macrophages, from LysMCretdT>R26CreFthfl/fl bone marrow chimera 19 days post tamoxifen induced deletion of Fth Sample 2


title: Heart macrophages macrophages, control sample 6, LysMCretdT>Fthfl/fl bone marrow chimera

description: Library name: H6M

source_name: Heart macrophages from LysMCretdT>Fthfl/fl bone marrow chimera 19 days post tamoxifen induced deletion of Fth - Sample 6