title: NP207_66h: CD8b+/CD44-/CD45.1/+CD45.2+ naive T cells bearing the NP207 TCR

city: Boston

first: Jonathan

middle: S.

last: Duke-Cohan

state: MA

address: 450 Brookline Avenue JF517

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description:
Library name: Sample cells NP207 66h
Column name in processed data files: NP207_66h

data_processing:
The paired output fasta files for each sample were checked for quality using FastQC, and adapters trimmed using FastqMcf and Cutadapt
Contaminating non-polyA-tailed RNA sequence, mitochondrial genome sequences, ribosomal RNAs and transfer RNAs were then removed using Bowtie2
The resulting filtered reads were aligned to the mouse reference genome assembly GRCm39 using STAR v2.7.3a
HTSeq-count was then used to count the reads aligned to each gene
Differential gene expression was performed using DESeq2
Assembly: GRCm39
Supplementary files format and content: "gene_readcounts_of_all_samples.csv" contains raw gene reads for all samples in CSV format
Supplementary files format and content: "gene_TPM_of_all_samples.csv" contains normalized TPM for all samples in CSV format

extract_protocol:
Total RNA from the samples was isolated using the BD Arcturus PicoPure kit with on-column DNase digestion.
Libraries were prepared using the SMART-Seq v4 Ultra Low Input kit with Tagmentation (Takara Bio USA, Inc.), Illumina adapters were added, and each sample library sequenced on the NovaSeq X Plus platform (2 x 250 bp paired end sequencing, 40 x 106 reads/sample).

treatment_protocol: Source cells are naive CD8 T cells, isolated from the lymph nodes and spleen of retrogenic mice, each bearing a unique transduced TCR specific for the NP366 peptide of influenza A virus, that were then seeded on irradiated spleen cells loaded with NP366 peptide and cultured for 66 h with sampling of cells at 0 h, 12 h, 36 h, and 66 h. Retrogenic T cells were isolated from the samples by FACS and deposited directly into lysis buffer for RNA extraction and transcriptome analysis

value: naive CD8+ T cells

value: retrogenic NP207 TCR

value: developed in vivo, cultured in vitro


title: FUCO-2_2

status: Public on Aug 05 2026

type: SRA

city: Shenzhen

first: Chen

last: Yang

address: 1068 Xueyuan Avenue, Nanshan District, Shenzhen,China

country: China

institute: Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences

description: Library name: con_14

library_source: transcriptomic

data_processing:
Raw sequencing reads (FASTQ files) were quality-checked using Fastp
The cleaned reads were aligned to the GRCh38/hg38 reference genome using STAR
Gene-level counts were generated using featureCounts
Differential expression analysis was performed using the DESeq2 R package with default parameters.
Functional enrichment analysis of KEGG pathways was performed on the DEGs using the clusterProfilerR package with the enrich KEGG function.
Assembly: GRCh38/hg38
Supplementary files format and content: FFA_gene.csv is a comma-separated values (CSV) text file containing the processed raw gene expression count matrix for all samples. The first column provides gene annotation identifiers, and each subsequent column represents the expression data for a single sample.

molecule: total RNA

organism: Homo sapiens

source_name: liver

extract_protocol:
RNA was extracted from tissues or cells using standard extraction methods, followed by stringent quality control of the RNA samples, primarily through quantification with Nanodrop and assessment of RNA integrity using the Agilent 4200 TapeStation.
A total of 1 µg total RNA per sample was used as input material for the mRNA library reparation. Most of Eukaryote 'mRNA have polyA tails, which are enriched by Oligo (dT) agnetic beads. Then, the obtained mRNA was randomly interrupted by bivalent cations, and the irst strand of cDNA was synthesized in the 1st Strand Enzymes Reverse transcriptase system sing the segmented mRNA as the template and the random oligonucleotide as the primer, and the econd strand of cDNA was synthesized using the 2nd Strand Enzymes and dNTPs. Purified ouble-stranded cDNA undergoes end repair, A-tailing, and ligation with sequencing adapters. DNA with an insert size of approximately 200-300 bp is screened. PCR amplification is erformed and the PCR product is purified again, ultimately obtaining a library.And then, library uality was assessed on the Agilent 4200 TapeStation.

tag: tissue

value: liver

tag: cell line

tag: cell type

value: liver cancer cells


title: MDA-MB-468, H3K36me1, rep1

first: Changbin

last: Sun

address: Dapeng

department: Agricultural Genomics Institute at Shenzhen

institute: Chinese Academy of Agricultural Sciences

library_source: genomic

data_processing:
Sequencing reads from mChIP-seq were demultiplexed to samples by the barcodes in the 5’ end of Read2 using fastq-multx (version 1.4.2) (https://github.com/brwnj/fastq-multx) with a mismatch setting of 0. Then, reads of each sample with adapter contamination and low quality were trimmed and filtered using fastp with parameters as -f 10 -t 5 -F 30 -T 5 --complexity_threshold=30 –n_base_limit=5  --length_required 60 (version 0.23.2) and aligned to the human reference genomes hg38, mouse reference genome mm10, or budding yeast genome sacCer3 using bowtie2 (version 2.2.5) with default parameters. Uniquely mapping reads with mapping quality more than 30 were kept using samtools (version 1.9) and duplicates were removed using picard MarkDuplicates (v2.26.10, http://broadinstitute.github.io/picard).
Assembly: BW25113 genome for E. coli, sacCer3 genome for yeast, GRCh38 genome for humans, mm10 genome for mice
Supplementary files format and content: bigWig

molecule: genomic DNA

extract_protocol:
Cells were fixed with 1% formaldehyde at room temperature for 10 min and quenched by glycine with 0.125 M final concentration. sonicated using Covaris SE220 (75 W, 20% Duty factor, 1,000 cycles per burst) for 5 min at 4°C to obtain fragments with the peak size around 200 bp.
The tailing and ssDNA ligation method used to label sample chromatin, and then multiple barcoded samples were pooled and split for immunoprecipitation with relevant antibodies as standard ChIP-seq. After immunoprecipitation, the purified ChIPed DNA was resuspended in 18 µl of water and extended in an 40 µl reaction containing 1 × KAPA HiFi HotStart ReadyMix and 0.25 µM P7TruSeqHTRev at 98 for 30 sec and 63 °C for 5 min followed by purification with 1.2 × volume of SPRIselect™ beads. Then, the purified DNA was ligated to the second adapter in a 40 µl reaction (1× T4 DNA ligase buffer, 0.5 µM P5TruSeqHT/P5SPlint mixture (1:1), and 10 Weiss units of T4 DNA ligase) at 25 °C for 30 minutes and purified with 1.0 × volume of SPRIselect™ beads. Lastly, library was amplified in 50 μl of PCR reaction Mix containing eluted DNA, 0.5 μM of P5 index primer, 0.5 μM P7 index primers, and 25 μl of KAPA HiFi HotStart ReadyMix (2 ×) (Kapa Biosystems) for 12-16 cycles (each cycle with 20 s at 98°C, 30 s at 58°C, 1 min at 68°C). DNA of 200–700 bp was isolated using a double SPRIselect bead cleanup (0.6 × and 0.85 × volume).

value: Breast adenocarcinoma

tag: chip antibody


title: NP204_66h: CD8b+/CD44-/CD45.1/+CD45.2+ naive T cells bearing the NP204 TCR

country: USA

description:
Library name: Sample cells NP204 66h
Column name in processed data files: NP204_66h

organism: Mus musculus

tag: genotype

value: retrogenic NP204 TCR

tag: treatment


title: HL-why1/3/reca1

city: Hefei

first: Wenjie

last: Wang

state: Anhui

address: No. 130, Changjiang West Road

institute: Anhui Agricultrual University

description: Library name: Sample30

data_processing:
The duplicated reads with both the same forward and reverse reads were removed according to scripts (https://github.com/PEHGP/DEtail-seq/blob/master/RemoveSamReads.py)
The rest reads were aligned to the reference genome with Bowtie2 using --local settings.
For visualization and splitting strands, the aligned reads files (BAM) including the second read in pairs were converted to the first single base bigWig file with 1bp bins using bamCoverage from deepTools with --binSize 1 --Offset 1 --samFlagInclude 128 --filterRNAstrand forward/reverse. The option --filterRNAstrand forward means Crick strand and -- filterRNAstrand reverse means Watson strand.
Normalization was performed by deepTools based on RPGC with correction by the count of reads mapped to I-CeuI sites from each sample, and the signals around I-CeuI sites (± 2 bp) were deleted in the final normalized bigWig files.
Assembly: Tair10
Supplementary files format and content: bw

organism: Arabidopsis thaliana

source_name: true leaf

extract_protocol:
The chloroplasts were embedded in 0.5% low-melting-point agarose (Promega) and lysed in 1% sarkosyl, 0.45 M EDTA (pH 8.0), 10 mM Tris-HCl (pH 8.0), and 2 mg/mL proteinase K at 48°C for 16 h with shaking. The agarose plugs were washed in TE buffer six times at 37°C, with the first two washes containing 1 mM PMSF. Cut agarose plug into 12 pieces and incubated in 1 ml TE with 10 μg/ml RNase A at 37°C overnight. The agarose pieces were washed five times with 1 ml TE buffer at 37°C for 6 min, then stored in plug storage solution (0.05 M EDTA pH 8.0, 60% glycerol) at -20°C until all samples were ready for the next step.
The DNA library was constructed with Scale ssDNA-seq Lib Prep Kit for Illumina V2 (ABclonal, RK20228). Five agarose pieces (~30 mg) were washed three times with 200 μl 1× CutSmart buffer (NEB) at 37°C for 6 min. The spike-in was performed by incubating the agarose pieces with 15 U I-CeuI (NEB) in 150 μl 1× CutSmart buffer at 37°C for 12 h. After digestion, the agarose pieces were washed three times with 500 μl TE buffer at 37°C for 6 min, followed by twice washes with 200 μl Low EDTA TE (ABclonal) at 37°C for 6 min. The agarose pieces were incubated in 80 μl T7 Tailing & Ligation buffer (ABclonal) at 37°C for 12 h. Then, heated the agarose pieces at 98°C for 2 min. The DNA in the agarose was recovered using a DNA purification kit (Magen, Catalog No D2111-02) and eluted with Low EDTA TE. The DNA was then sonicated to ~250 bp using Focused-ultrasonicator (Covaris S220). To finish the library preparation, the subsequent steps were performed according to the manufacturer's protocol exactly.

value: true leaf

value: High light


title: FUCO-2_1

description: Library name: con_13


title: HL-polIb

description: Library name: Sample29

value: polIb


title: RPMI-8226, H3K36me1, rep1

value: Multiple myeloma


title: FUCO-1_3

description: Library name: con_12


title: NP202_66h: CD8b+/CD44-/CD45.1/+CD45.2+ naive T cells bearing the NP202 TCR

description:
Library name: Sample cells NP202 66h
Column name in processed data files: NP202_66h

value: retrogenic NP202 TCR


title: SK-MEL-2, H3K36me1, rep1

value: Melanoma


title: HL-polIa

description: Library name: Sample28

value: polIa


title: NP204_36h: CD8b+/CD44-/CD45.1/+CD45.2+ naive T cells bearing the NP204 TCR

description:
Library name: Sample cells NP204 36h
Column name in processed data files: NP204_36h


title: CCRF-CEM, H3K36me1, rep1

source_name: CCRF-CEM

value: CCRF-CEM

value: Childhood T acute lymphoblastic leukemia


title: FUCO-1_1

description: Library name: con_10


title: HL-why1/3

description: Library name: Sample27


title: NP207_36h: CD8b+/CD44-/CD45.1/+CD45.2+ naive T cells bearing the NP207 TCR

description:
Library name: Sample cells NP207 36h
Column name in processed data files: NP207_36h


title: FUCO-1_2

description: Library name: con_11


title: T47D, H3K36me1, rep1

value: Invasive breast carcinoma


title: NP202_36h: CD8b+/CD44-/CD45.1/+CD45.2+ naive T cells bearing the NP202 TCR

description:
Library name: Sample cells NP202 36h
Column name in processed data files: NP202_36h

value: naive CD8+ T cells


title: HL-reca1

description: Library name: Sample26


title: PC-3, H3K36me1, rep1

value: Prostate carcinoma


title: HL-Col0

description: Library name: Sample25

tag: ecotype

value: wildtype


title: FUCO-0.5_3

description: Library name: con_9

value: liver


title: NP207_12h: CD8b+/CD44-/CD45.1/+CD45.2+ naive T cells bearing the NP207 TCR

description:
Library name: Sample cells NP207 12h
Column name in processed data files: NP207_12h

value: retrogenic NP207 TCR

value: developed in vivo, cultured in vitro


title: NP204_12h: CD8b+/CD44-/CD45.1/+CD45.2+ naive T cells bearing the NP204 TCR

description:
Library name: Sample cells NP204 12h
Column name in processed data files: NP204_12h

value: retrogenic NP204 TCR


title: RL-sigma6

description: Library name: Sample24

value: true leaf

value: Red light


title: K562, H3K36me1, rep1

value: Chronic myeloid leukemia


title: FUCO-0.5_2

description: Library name: con_8

value: liver cancer cells


title: SK-OV-3, H3K36me1, rep1

value: Ovarian serous cystadenocarcinoma


title: Model_3

description: Library name: con_6


title: RL-why1/3/polIb

description: Library name: Sample23


title: SW620, H3K36me1, rep1

value: Colon adenocarcinoma


title: NP202_12h: CD8b+/CD44-/CD45.1/+CD45.2+ naive T cells bearing the NP202 TCR

description:
Library name: Sample cells NP202 12h
Column name in processed data files: NP202_12h

value: retrogenic NP202 TCR


title: RL-why1/3/reca1

description: Library name: Sample22


title: FUCO-0.5_1

description: Library name: con_7


title: HCT116, H3K36me1, rep1

value: Colon carcinoma


title: Model_2

description: Library name: con_5


title: NP207_0h: CD8b+/CD44-/CD45.1/+CD45.2+ naive T cells bearing the NP207 TCR

description:
Library name: Sample cells NP207 0h
Column name in processed data files: NP207_0h


title: NP204_0h: CD8b+/CD44-/CD45.1/+CD45.2+ naive T cells bearing the NP204 TCR

description:
Library name: Sample cells NP204 0h
Column name in processed data files: NP204_0h


title: RL-polIb

description: Library name: Sample21

value: polIb


title: HL-60, H3K36me1, rep1

value: Adult acute myeloid leukemia


title: Model_1

description: Library name: con_4


title: RL-polIa

description: Library name: Sample20

value: polIa


title: NP202_0h: CD8b+/CD44-/CD45.1/+CD45.2+ naive T cells bearing the NP202 TCR

description:
Library name: Sample cells NP202 0h
Column name in processed data files: NP202_0h

value: naive CD8+ T cells


title: Con_3

description: Library name: con_3


title: MOLT-4, H3K36me1, rep1

value: Adult T acute lymphoblastic leukemia


title: RL-why1/3

description: Library name: Sample19


title: Sample_P39_NULL_F

city: Ann Arbor

first: Michigan

middle: CDB

last: Bioinformatics

state: MI

address: 109 Zina Pitcher Pl

department: Cell & Developmental Biology

institute: University of Michigan

description:
Library name: Sample_P39_NULL_F
Column Name in raw counts: Sample_P39_NULL_F

data_processing:
FASTQ files were mapped to the GRCm39.vm30 reference using STAR version 2.7.10a and the ENCODE standard options from the version documentation
The reference matching GTF file was used with featureCounts from the Bioconductor R package Rsubread to create the counts matrix
The edgeR Bioconductor package was used to filter low expressing genes using the “filterByExpr” function, calculate log counts per million, and normalization factors using the weighted trimmed mean of M-values (TMM) method
The Limma Biocoductor package, with the precision weights, “voom” approach was used to perform linear models
Assembly: GRCm39.vm30
Supplementary files format and content: counts_all.tsv is a tab separated matrix of raw counts from featurecounts function of RSubread

source_name: whole paws

extract_protocol:
RNA was isolated and purified from whole paws using TriZOL reagent (Fisher Scientific, #1559601) using the manufacturer’s instructions.
RNA samples were transferred to an external contractor (Novogene) for RNA quality control, RNA ribo-depletion library preparation, and next-generation sequencing

value: whole paws

tag: days postnatal

tag: litter

tag: Sex

value: F


title: NCI-H226, H3K36me1, rep1

value: Pleural epithelioid mesothelioma


title: Sample_P38_WT_F

description:
Library name: Sample_P38_WT_F
Column Name in raw counts: Sample_P38_WT_F

value: WT


title: RL-reca1

description: Library name: Sample18

value: true leaf


title: con_2

description: Library name: con_2

value: liver


title: Con_1

description: Library name: con_1


title: NCI-H522, H3K36me1, rep1

value: Lung adenocarcinoma


title: RL-Col0

description: Library name: Sample17

value: wildtype

value: Red light


title: Sample_P37_WT_F

description:
Library name: Sample_P37_WT_F
Column Name in raw counts: Sample_P37_WT_F


title: Repli-C mAID-mClover-SMC1 +HU +Aux +SMC1-4E R4

city: Madrid

first: Daniel

last: Gimenez

address: Calle de Melchor Fernández Almagro, 3

country: Spain

institute: CNIO

description: Library name: Repli-C_mAID-mClover-SMC1_+HU_+Aux_+SMC1-4E_R4

data_processing:
Repli-C data were processed using a standardized Hi-C analysis pipeline. Raw paired-end sequencing reads were quality-trimmed using Trim Galore (quality threshold = 20, minimum length = 30 bp) and aligned to the hg38 human reference genome using BWA-MEM (10) ) with Hi-C-specific parameters (-5SP -T0). Aligned reads were processed with the pairtools suite: contacts were parsed with a minimum mapping quality of 40 (--min-mapq 40), allowing walks of up to 5 unique alignments (--walks-policy 5unique) with a maximum inter-alignment gap of 30 bp. Parsed pairs were sorted, and PCR duplicates were removed while retaining duplicate marking statistics. Valid contact pairs were converted to “.hic” format using Juicer Tools (v1.22.01) and to multi-resolution cool format (.mcool) using HiCExplorer with Knight-Ruiz (KR) matrix balancing normalization. For comparative analyses between conditions, biological replicates were merged using pairtools merge, and datasets were downsampled to equalize sequencing depth across conditions using pairtools sample. Downsampling fractions were calculated to match the condition with the lowest sequencing depth, ensuring unbiased comparisons
Assembly: hg38
Supplementary files format and content: .hic
Library strategy: HiChIP

extract_protocol:
Cells were treated with 1 µg/mL dox for 48h, 2 µ M auxin for 5 h where indicated. 10 µM EdU was added for 15 min, either before collection or before washing and treating cells with 2 mM HU for 2 h. Repli-C was performed using the Dovetail® HiChIP MNase Kit with modifications. Cells were collected by trypsinization, the chromatin was fixed with DSG and formaldehyde, and permeabilized with 0.25% Triton-X in PBS. EdU was clicked to digoxigenin by incubating in click reaction (0.1 M Tris pH 8.5, 0.1 M sodium-L-ascorbate, 2 mM CuSO4 and 0.3 mM digoxigenin-azide (ATTBio)). After, cross-linked chromatin was digested in situ with MNase then extracted upon cell lysis using a combination of RIPA lysis and gentle sonication using Bioruptor Pico in RIPA buffer. The chromatin fragments were incubated with anti-digoxigenin antibody pre-coupled to A/G-coated beads, overnight rotating at 4ºC. Next, the chromatin ends were repaired and ligated to a biotinylated bridge adapter followed by proximity ligation of adapter-containing ends.
After proximity ligation, the crosslinks were reversed, the associated proteins were degraded, and the DNA was purified then converted into a sequencing library  using Illumina-compatible adaptors. Biotin-containing fragments were isolated using streptavidin beads prior to PCR amplification.

value: OsTIR (F74G)

value: HU + Auxin + SMC1-4E-3xFLAG


title: NL-sigma6

description: Library name: Sample16

value: Normal light


title: OVCAR-8, H3K36me1, rep1

value: High grade ovarian serous adenocarcinoma


title: NCI-H23, H3K36me1, rep1


title: Sample_P35_NULL_F

description:
Library name: Sample_P35_NULL_F
Column Name in raw counts: Sample_P35_NULL_F


title: CD161 positive, CD34-, CD94-negative innate lymphocyte progenitors purified from peripheral blood

city: Frederick

first: Yongmei

last: Zhao

state: MD

address: Post Office Box B

department: Advanced Biomedical Computational Science

institute: Frederick National Labroatory for Cancer Research

description: Library name: ILCP

data_processing:
Sequencing reads were processed using Biomodal duet v1.5.0 software (Biomodal) to generate aligned BAM files and genome-wide methylation profiles.
Differential methylation analysis using Modality XPLR v1.0.0 software (Biomodal) was performed across developmental stages to identify regions with changes in cytosine modification.
Assembly: hg38
Supplementary files format and content: Processed epigenetic quantification plain text reports include three quantification files per sample: one containing mC calls; one containing hmC calls; and one containing modC calls. From Biomodall evoC reports, modC calls are the union of the mC calls, the hmC calls, and any undifferentiated modC calls (where a modification was detected but it was not possible to determine whether the modification was an mC or a hmC).
Supplementary files format and content: Processed epigenetic quantification reports in BED format from BedMethyl, which include three quantification files per sample: one containing mC calls; one containing hmC calls; and one containing modC calls.

source_name: Blood

growth_protocol: Cells were obtained from healthy donor apheresis cones through negative selection of non-NK lineage markers followed by FACS sorting for cells representing the four stages of development studied

extract_protocol:
DNA was extracted using the QIAamp DNA Mini Kit Qiagen).
Genomic DNA libraries were prepared using the duet evoC assay kit (Biomodal), which enables simultaneous detection of 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC). Libraries were constructed according to the manufacturer’s protocol and subjected to whole genome sequencing.

treatment_protocol: Fresh ex vivo cells obtained by FACS sorting

value: Blood

tag: developmental stage


title: Repli-C mAID-mClover-SMC1 +HU +Aux +SMC1WT R4

description: Library name: Repli-C_mAID-mClover-SMC1_+HU_+Aux_+SMC1WT_R4

value: HU + Auxin+ SMC1WT-3xFLAG


title: NL-why1/3/polIb

description: Library name: Sample15


title: Repli-C mAID-mClover-SMC1 +HU +Aux +SMC1-4E R3

description: Library name: Repli-C_mAID-mClover-SMC1_+HU_+Aux_+SMC1-4E_R3


title: A498, H3K36me1, rep1

value: Renal cell carcinoma


title: Sample_P33_NULL_M

description:
Library name: Sample_P33_NULL_M
Column Name in raw counts: Sample_P33_NULL_M

value: M


title: Repli-C mAID-mClover-SMC1 +HU +Aux +SMC1WT R3

description: Library name: Repli-C_mAID-mClover-SMC1_+HU_+Aux_+SMC1WT_R3


title: NL-why1/3/reca1

description: Library name: Sample14


title: DU145, H3K36me1, rep1

value: Prostate carcinoma


title: NL-polIb

description: Library name: Sample13

value: polIb


title: Sample_P32_WT_M2

description:
Library name: Sample_P32_WT_M2
Column Name in raw counts: Sample_P32_WT_M2

value: whole paws


title: Sample_P32_WT_M1

description:
Library name: Sample_P32_WT_M1
Column Name in raw counts: Sample_P32_WT_M1

value: WT


title: Repli-C mAID-mClover-SMC1 +HU +Aux +SMC1-4E R2

description: Library name: Repli-C_mAID-mClover-SMC1_+HU_+Aux_+SMC1-4E_R2


title: U251, H3K36me1, rep1

value: Astrocytoma


title: Sample_P31_WT_M

description:
Library name: Sample_P31_WT_M
Column Name in raw counts: Sample_P31_WT_M


title: NL-polIa

description: Library name: Sample12

value: true leaf

value: polIa


title: Repli-C mAID-mClover-SMC1 +HU +Aux +SMC1WT R2

description: Library name: Repli-C_mAID-mClover-SMC1_+HU_+Aux_+SMC1WT_R2


title: Sample_P07_NULL_F

description:
Library name: Sample_P07_NULL_F
Column Name in raw counts: Sample_P07_NULL_F

value: F


title: NL-why1/3

description: Library name: Sample11


title: A549, H3K36me1, rep1

value: Lung adenocarcinoma


title: Repli-C mAID-mClover-SMC1 +HU +Aux +SMC1-4E R1

description: Library name: Repli-C_mAID-mClover-SMC1_+HU_+Aux_+SMC1-4E_R1

value: OsTIR (F74G)


title: 786-O, H3K36me1, rep1


title: NL-reca1

description: Library name: Sample10


title: Sample_P04_WT_F

description:
Library name: Sample_P04_WT_F
Column Name in raw counts: Sample_P04_WT_F


title: Repli-C mAID-mClover-SMC1 +HU +Aux +SMC1WT R1

description: Library name: Repli-C_mAID-mClover-SMC1_+HU_+Aux_+SMC1WT_R1


title: NCI-H460, H3K36me1, rep1

value: Lung large cell carcinoma


title: SNB19, H3K36me1, rep1


title: Repli-C mAID-mClover-SMC1 +Aux +SMC1-4E R4

description: Library name: Repli-C_mAID-mClover-SMC1_+Aux_+SMC1-4E_R4

value: Auxin + SMC1-4E-3xFLAG


title: BL-sigma6

description: Library name: Sample8

value: Blue light


title: Sample_P03_WT_M

description:
Library name: Sample_P03_WT_M
Column Name in raw counts: Sample_P03_WT_M


title: Sample_P02_WT_F

description:
Library name: Sample_P02_WT_F
Column Name in raw counts: Sample_P02_WT_F


title: SK-MEL-28, H3K27me3, rep1

value: Cutaneous melanoma


title: Sample_P01_WT_M

description:
Library name: Sample_P01_WT_M
Column Name in raw counts: Sample_P01_WT_M


title: BL-why1/3/polIb

description: Library name: Sample7


title: MDA-MB-468, H3K27me3, rep1

value: Breast adenocarcinoma


title: Repli-C mAID-mClover-SMC1 +Aux +SMC1-4E R3

description: Library name: Repli-C_mAID-mClover-SMC1_+Aux_+SMC1-4E_R3


title: Sample_P01_NULL_M

description:
Library name: Sample_P01_NULL_M
Column Name in raw counts: Sample_P01_NULL_M


title: BL-why1/3/reca1

description: Library name: Sample6


title: Repli-C mAID-mClover-SMC1 +Aux +SMC1WT R3

description: Library name: Repli-C_mAID-mClover-SMC1_+Aux_+SMC1WT_R3

value: Auxin+ SMC1WT-3xFLAG


title: A549, H3K36me2, rep2


title: RPMI-8226, H3K27me3, rep1

value: Multiple myeloma


title: SK-MEL-2, H3K27me3, rep1

value: Melanoma


title: BL-polIb

description: Library name: Sample5

value: polIb


title: BL-polIa

description: Library name: Sample4


title: TK58

first: Jason

last: Williams

address: 77 Ave Louis Pasteur, Building HIM Room 660

department: Dermatology

institute: Brigham and Women's Hospital

description:
Library name: TK58_CD8_Tumor Rejected Skin_CD103+CD69+
3 mice pooled, day 46 post TAM

data_processing:
Sequencing data was processed and analyzed using Partek software.  Alignment was performed by the STAR alignment method.  Raw read counts were processed by TMM normalization.  Differentially expressed genes were determined by normalization to spleen CD8 samples with a cutoff fold-change > 2 and adjusted p-value <0.05.
Assembly: GRCm39
Supplementary files format and content: Gene counts

source_name: Tumor Rejected Skin

extract_protocol:
Autochthonous BPO tumors were digested with collagenase IV, DNase IV, and hyaluronidase V for 30 min at 37C. Tumors were mashed through a cell strainer and Ficolled to remove dead cells. Single cell suspensions were stained with antibodies and cell sorted.
Library preparation and RNA sequencing was performed by the Dana-Farber Molecular Biology Core Facilities using Takara SmartSeq v4 reagents for low input mRNASeq. Samples with an RNA quality (RIN) score >7 were used for sequencing.  Full-length cDNA was fragmented to an average size of 200 bp, and sequencing libraries were prepared from 2 ng of sheared cDNA. Double-stranded DNA libraries were quantified by Qubit fluorometer and Agilent TapeStation 2200. Uniquely dual-indexed libraries were pooled in equimolar amounts, assessed for cluster efficiency and pool balance with shallow sequencing on an Illumina MiSeq

value: Tumor Rejected Skin

value: CD8+ T cell


title: Repli-C mAID-mClover-SMC1 +Aux +SMC1WT R2

description: Library name: Repli-C_mAID-mClover-SMC1_+Aux_+SMC1WT_R2


title: CCRF-CEM, H3K27me3, rep1

value: CCRF-CEM

value: Childhood T acute lymphoblastic leukemia


title: TK54

description:
Library name: TK54_CD8_Tumor Rejected Skin_CD103+CD69+
3 mice pooled, day 46 post TAM


title: Repli-C mAID-mClover-SMC1 +Aux +SMC1-4E R1

description: Library name: Repli-C_mAID-mClover-SMC1_+Aux_+SMC1-4E_R1


title: T47D, H3K27me3, rep1

value: Invasive breast carcinoma


title: BL-reca1

description: Library name: Sample2

value: true leaf


title: PC-3, H3K27me3, rep1

value: Prostate carcinoma


title: BL-Col0

description: Library name: Sample1

value: wildtype


title: TK42

description:
Library name: TK42_CD8_TumorAdjSkin_CD103+CD69+
3 mice pooled, day 46 post TAM

source_name: Tumor Adj Skin

value: Tumor Adj Skin


title: why1/3/polIb-NL-AsA

description: Library name: Sample9

value: Normal light and 0.5 mM ascorbic acid


title: Repli-C mAID-mClover-SMC1 +HU R2

description: Library name: Repli-C_mAID-mClover-SMC1_+HU_R2

value: OsTIR (F74G)

value: HU


title: TK36

description:
Library name: TK36_CD8_TIL_CD103+CD69-
3 mice pooled, day 46 post TAM

source_name: Tumor

value: Tumor


title: SK-OV-3, H3K27me3, rep1

value: Ovarian serous cystadenocarcinoma


title: Repli-C mAID-mClover-SMC1 +HU +Aux R2

description: Library name: Repli-C_mAID-mClover-SMC1_+HU_+Aux_R2

value: HU + Auxin


title: K562, H3K27me3, rep1

value: Chronic myeloid leukemia


title: why1/3/polIb-NL

description: Library name: Sample8

value: Normal light


title: TK35

description:
Library name: TK35_CD8_TIL_CD103-CD69-
3 mice pooled, day 46 post TAM


title: Col0-NL-H2O2

description: Library name: Sample7

value: Normal light and 2 mM H2O2


title: Repli-C mAID-mClover-SMC1 +Aux R2

description: Library name: Repli-C_mAID-mClover-SMC1_+Aux_R2

value: Auxin


title: SW620, H3K27me3, rep1

value: Colon adenocarcinoma


title: HCT116, H3K27me3, rep1

value: Colon carcinoma


title: TK33

description:
Library name: TK33_CD8_TIL_CD103-CD69+
3 mice pooled, day 46 post TAM

value: CD8+ T cell


title: Repli-C mAID-mClover-SMC1 +HU +Aux R1

description: Library name: Repli-C_mAID-mClover-SMC1_+HU_+Aux_R1


title: HL-60, H3K27me3, rep1

value: Adult acute myeloid leukemia


title: Repli-C mAID-mClover-SMC1 +HU R1

description: Library name: Repli-C_mAID-mClover-SMC1_+HU_R1


title: MOLT-4, H3K27me3, rep1

value: Adult T acute lymphoblastic leukemia


title: Col0-NL

description: Library name: Sample4

value: true leaf

value: wildtype


title: TK22

description:
Library name: TK22_CD8_TumorAdjSkin_CD103+CD69+
3 mice pooled, day 42 post TAM

value: Tumor Adj Skin


title: Repli-C mAID-mClover-SMC1 +Aux R1

description: Library name: Repli-C_mAID-mClover-SMC1_+Aux_R1

value: OsTIR (F74G)


title: NCI-H226, H3K27me3, rep1

value: Pleural epithelioid mesothelioma


title: Col0-HL

description: Library name: Sample3

value: High light


title: TK16

description:
Library name: TK16_CD8_TIL_CD103+CD69-
3 mice pooled, day 42 post TAM

value: Tumor


title: NCI-H522, H3K27me3, rep1

value: Lung adenocarcinoma


title: Repli-C mAID-mClover-SMC1 R1

description: Library name: Repli-C_mAID-mClover-SMC1_R1


title: TK15

description:
Library name: TK15_CD8_TIL_CD103-CD69-
3 mice pooled, day 42 post TAM


title: Micro-C mAID-mClover-SMC1 +Aux +SMC1-4E R2

description: Library name: Micro-C_mAID-mClover-SMC1_+Aux_+SMC1-4E_R2

data_processing:
Micro-C data were processed using a standardized Hi-C analysis pipeline. Raw paired-end sequencing reads were quality-trimmed using Trim Galore (quality threshold = 20, minimum length = 30 bp) and aligned to the hg38 human reference genome using BWA-MEM (10) ) with Hi-C-specific parameters (-5SP -T0). Aligned reads were processed with the pairtools suite: contacts were parsed with a minimum mapping quality of 40 (--min-mapq 40), allowing walks of up to 5 unique alignments (--walks-policy 5unique) with a maximum inter-alignment gap of 30 bp. Parsed pairs were sorted, and PCR duplicates were removed while retaining duplicate marking statistics. Valid contact pairs were converted to “.hic” format using Juicer Tools (v1.22.01) and to multi-resolution cool format (.mcool) using HiCExplorer with Knight-Ruiz (KR) matrix balancing normalization. For comparative analyses between conditions, biological replicates were merged using pairtools merge, and datasets were downsampled to equalize sequencing depth across conditions using pairtools sample. Downsampling fractions were calculated to match the condition with the lowest sequencing depth, ensuring unbiased comparisons
Assembly: hg38
Supplementary files format and content: .hic

extract_protocol:
The Micro-C library was prepared using the Dovetail® Micro-C Kit according to the manufacturer’s protocol. Briefly, cells were treated with 1 µg/mL dox for 48 h, 2 µM auxin for 5 h where indicated. The chromatin was fixed with disuccinimidyl glutarate (DSG) and formaldehyde in the nucleus. The cross-linked chromatin was then digested in situ with micrococcal nuclease (MNase). Following digestion, the cells were lysed with SDS to extract the chromatin fragments and the chromatin fragments were bound to Chromatin Capture Beads. Next, the chromatin ends were repaired and ligated to a biotinylated bridge adapter followed by proximity ligation of adapter-containing ends.
After proximity ligation, the crosslinks were reversed, the associated proteins were degraded, and the DNA was purified and then converted into a sequencing library using Illumina-compatible adaptors. Biotin-containing fragments were isolated using streptavidin beads prior to PCR amplification. The library was sequenced on an Illumina Novaseq X

tag: replicate

value: Auxin + SMC1-3D-3xFLAG


title: TK14

description:
Library name: TK14_CD8_TIL_CD103+CD69+
3 mice pooled, day 42 post TAM


title: Micro-C mAID-mClover-SMC1 +Aux +SMC1WT R2

description: Library name: Micro-C_mAID-mClover-SMC1_+Aux_+SMC1WT_R2

value: Auxin+ SMC1WT-3xFLAG


title: NCI-H23, H3K27me3, rep1


title: atrnh1c, 3-week-old, true leaf, 37°C, replicate2

library_source: other

data_processing:
The duplicated reads with both the same forward and reverse reads were removed according to scripts (https://github.com/PEHGP/DEtail-seq/blob/master/RemoveSamReads.py)
The rest reads were aligned to the reference genome with Bowtie2 using --local settings.
For visualization and splitting strands, the aligned reads files (BAM) including the second read in pairs were converted to the first single base bigWig file with 1bp bins using bamCoverage from deepTools with --binSize 1 --Offset 1 --samFlagInclude 128 --filterRNAstrand forward/reverse. The option --filterRNAstrand forward means Crick strand and -- filterRNAstrand reverse means Watson strand.
Normalization was performed by deepTools based on RPGC with correction by the count of reads mapped to I-CeuI sites from each sample, and the signals around I-CeuI sites (± 2 bp) were deleted in the final normalized bigWig files.
Assembly: Tair10
Supplementary files format and content: bw
Library strategy: DEtail-seq

molecule: other

treatment_protocol: For tissue at different ages, the seeds were sown at the same time, while the tissues were collected every week as indicated for chloroplast isolation. For temperature treatment, the seedlings were grown on plates for 19 days, then transferred into growth chambers and grown under different temperatures with long-day conditions as indicated for 2 days. The aerial parts were harvested for chloroplast isolation. For photoperiod treatment, the seedlings were grown on plates for 16 days, then transferred into growth chambers and grown under different photoperiods as indicated for 5 days. The aerial parts were harvested for chloroplast isolation.

value: 16 h light/8 h dark, 37°C

tag: time

value: 2 days


title: Micro-C mAID-mClover-SMC1 +Aux R2

description: Library name: Micro-C_mAID-mClover-SMC1_+Aux_R2

value: Auxin


title: TK13

description:
Library name: TK13_CD8_TIL_CD103-CD69+
3 mice pooled, day 42 post TAM


title: TK43

description:
Library name: TK43_CD8_TumorAdjSkin_CD103-CD69-
3 mice pooled, day 46 post TAM


title: A498, H3K27me3, rep1

value: Renal cell carcinoma


title: TK126

description:
Library name: TK126_CD8_SPL_CD69+
3 mice pooled, day 46 post TAM

source_name: Spleen

value: Spleen

value: CD8+ T cell


title: atrnh1c, 3-week-old, true leaf, 22°C, replicate2

value: 16 h light/8 h dark, 22°C


title: DU145, H3K27me3, rep1

value: Prostate carcinoma


title: Micro-C mAID-mClover-SMC1 R2

description: Library name: Micro-C_mAID-mClover-SMC1_R2


title: atrnh1c, 3-week-old, true leaf, 4°C, replicate2

value: true leaf

value: 16 h light/8 h dark, 4°C


title: U251, H3K27me3, rep1

value: Astrocytoma


title: TK125

description:
Library name: TK125_CD8_SPL_CD69-
3 mice pooled, day 46 post TAM


title: Micro-C mAID-mClover-NIPBL +Aux R2

description: Library name: Micro-C_mAID-mClover-NIPBL_+Aux_R2

value: OsTIR (F74G)

value: mAID-mClover-NIBPL


title: Col-0, 3-week-old, true leaf, 42°C, replicate2

value: 16 h light/8 h dark, 42°C

value: 5 hours


title: TK124

description:
Library name: TK124_CD8_SPL_CD69+
3 mice pooled, day 42 post TAM


title: Col-0, 3-week-old, true leaf, 37°C, replicate2


title: Micro-C mAID-mClover-SMC1 +Aux +SMC1-4E R1

description: Library name: Micro-C_mAID-mClover-SMC1_+Aux_+SMC1-4E_R1

value: Auxin + SMC1-3D-3xFLAG


title: TK123

description:
Library name: TK123_CD8_SPL_CD69-
3 mice pooled, day 42 post TAM


title: Col-0, 3-week-old, true leaf, 22°C, replicate2


title: EED-Mutant RPR2 tumor 1350

first: Yixiang

last: Li

address: 450 Brookline Ave

description: Library name: EED-Mutant 1350

library_source: transcriptomic single cell

data_processing:
Cell ranger version 9.0.0 pipeline (10× Genomics) was used to align sequencing data to the custom mouse reference genome and generate the gene-level counts matrix.
Assembly: Custom reference genome was established by adding EGFP and Cas9 sequence to the mouse genome (mm10-2020-A).
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Lung tumor

growth_protocol: Tumors were harvested at necropsy and were flash-frozen

extract_protocol:
The single-nuclei RNA sequencing (snRNA-seq) sample preparation from EED-Mutant RPR2 tumors were performed using Chromium Nuclei Isolation Kit with RNase Inhibitor (10x Genomics, PN-1000494) following manufacture’s instruction (10x Genomics, CG000124). Briefly, 30mg snap-frozen tumor tissue from 3 independent EED-Mutant RPR2 mice was disassociated in Lysis Buffer with pestle and centrifuged for 20s, in 16,000 rcf under 4 ºC to a column to collect lysed nuclei in the flowthrough. Debris in the flowthrough containing nuclei was removed by Debris Removal Buffer before nuclei were washed 2 times with 5min, 500 rcf, 4 ºC spin. Nuclei was then counted using ViaStain AOPI Staining Solution (Revvity, CS2-0106-5ML) on a Nexcelom Cellometer K2 Fluorescent Cell Counter (Revvity, CMT-K2-MX-150) and resuspended in 1,000 nuclei/ul DPBS with 0.04% ultra-pure Bovine Serum Albumin (Invitrogen, AM2616).
About 20,000 nuclei were loaded onto a ChromiumTM X instrument (10× Genomics) according to the manufacturer’s instructions.  The snRNAseq libraries were processed using Chromium GEM-X Single Cell 5' Kit v3 (10× Genomics). Quality controls for amplified cDNA libraries and final sequencing libraries were performed using Bioanalyzer High Sensitivity DNA Kit (Agilent). Libraries were subsequently quantified by Qubit fluorometer and Agilent TapeStation 4200. Library pooling and indexing was evaluated with shallow sequencing on an Illumina MiSeq. Subsequently, libraries were sequenced by the Molecular Biology Core Facilities at Dana-Farber Cancer Institute on an Illumina NovaSeq X Plus with the following read program: 28bp, 10bp, 10bp, 90bp.

value: Lung tumor


title: NCI-H460, H3K27me3, rep1

value: Lung large cell carcinoma


title: Micro-C mAID-mClover-NIPBL R2

description: Library name: Micro-C_mAID-mClover-NIPBL_R2


title: A549, H3K27me3, rep1

value: Lung adenocarcinoma


title: 786-O, H3K27me3, rep1


title: Micro-C mAID-mClover-SMC1 +Aux R1

description: Library name: Micro-C_mAID-mClover-SMC1_+Aux_R1

value: Auxin


title: NL-Col0

description: Library name: Sample9

value: wildtype

value: Normal light


title: SNB19, H3K27me3, rep1


title: Micro-C mAID-mClover-SMC1 +Aux +SMC1WT R1

description: Library name: Micro-C_mAID-mClover-SMC1_+Aux_+SMC1WT_R1

value: Auxin+ SMC1WT-3xFLAG


title: Repli-C mAID-mClover-SMC1 +Aux +SMC1WT R4

description: Library name: Repli-C_mAID-mClover-SMC1_+Aux_+SMC1WT_R4


title: Col-0, 3-week-old, true leaf, 12°C, replicate2

value: 16 h light/8 h dark, 12°C

value: 2 days


title: Micro-C mAID-mClover-SMC1 R1

description: Library name: Micro-C_mAID-mClover-SMC1_R1


title: EED-Mutant RPR2 tumor 1339

description: Library name: EED-Mutant 1339


title: Repli-C mAID-mClover-SMC1 +Aux +SMC1-4E R2

description: Library name: Repli-C_mAID-mClover-SMC1_+Aux_+SMC1-4E_R2

value: Auxin + SMC1-4E-3xFLAG


title: TK61

description:
Library name: TK61_CD8_SPL_CD69+
3 mice pooled

value: Spleen

value: CD8+ T cell


title: SK-MEL-28, H3K27ac

value: Cutaneous melanoma

value: H3K27ac (Abcam:#ab4729)


title: Col-0, 3-week-old, true leaf, 4°C, replicate2

value: true leaf

value: 16 h light/8 h dark, 4°C


title: PDGFNO rep3

city: yunnan

first: wang

middle: yi

last: chao

address: Jingming South Road, Chenggong District, Kunming City, Yunnan Province

institute: Kunming University of Science and Technology

description: Library name: sample6

data_processing:
Raw reads were trimmed for adapter sequences and low-quality bases using fastp(default parameters version:0.23.2).
Clean reads were aligned to the Macaca mulatta reference genome (Macaca_mulatta.Mmul_10) using HISAT2(version: 2.1.0) with default parameters.
Aligned files were converted to BAM and sorted by coordinate using samtools sort. Gene-level read counts were quantified using featureCounts (version: 2.0.1).
Assembly: Mmul_8.0.1
Supplementary files format and content: Tab-separated values files and matrix files

organism: Macaca mulatta

source_name: Testis

extract_protocol:
Tissue samples undergo dissociation and lysis  with QC validation
RNA-seq includes mRNA enrichment, fragmentation, and Illumina adapter ligation

value: Testis

tag: batch


title: Micro-C mAID-mClover-NIPBL +Aux R1

description: Library name: Micro-C_mAID-mClover-NIPBL_+Aux_R1

value: OsTIR (F74G)

value: mAID-mClover-NIBPL


title: Col-0, 3-week-old, true leaf, 17°C, replicate2

value: 16 h light/8 h dark, 17°C


title: BL-why1/3

description: Library name: Sample3

value: Blue light


title: Repli-C mAID-mClover-SMC1 +Aux +SMC1WT R1

description: Library name: Repli-C_mAID-mClover-SMC1_+Aux_+SMC1WT_R1


title: MDA-MB-468, H3K27ac

value: Breast adenocarcinoma


title: atrnh1c, 3-week-old, true leaf, CD, replicate2

value: 24 h dark, 22°C

value: 5 days


title: Micro-C mAID-mClover-NIPBL R1

description: Library name: Micro-C_mAID-mClover-NIPBL_R1


title: PDGFNO rep2

description: Library name: sample5


title: RPMI-8226, H3K27ac

value: Multiple myeloma


title: EED-Mutant RPR2 tumor 1345

description: Library name: EED-Mutant 1345

value: Lung tumor


title: atrnh1c, 3-week-old, true leaf, SD, replicate2

value: 8 h light/16 h dark, 22°C


title: RNA-seq_pt113_stroma_t2

city: Bethesda

first: Adam

middle: G.

last: Sowalsky

address: 37 Convent Drive Building 37 Room 1062B

department: Genitourinary Malignancies Branch

institute: National Cancer Institute

description:
Library name: A8-102-19
Paired-end RNA-seq for stroma sample A8-102-19 from patient 113, timepoint 2

data_processing:
Base-calling was performed with RTA RTA4
Sample demultiplexing was performed with Bcl2fastq v2.20
FASTQ files were pre-processed to remove sequencing adaptors with Trimmomatic v0.36.
Paired-end trimmed FASTQ files were aligned to hg19 using STAR.
RSEM was used to estimate read counts and TPM for each genomic feature.
Assembly: hg19
Supplementary files format and content: tab separated values, gene symbol, description, counts
Supplementary files format and content: tab separated values, gene symbol, description, transcripts-per-million (TPM)

source_name: prostate

growth_protocol: FFPE human prostate tissues were sectioned onto PEN membrane slides, and regions of interest were laser capture microdissected. Whole blood was collected into EDTA tubes.

extract_protocol:
Total RNA was extracted from microdissected tissue using the Qiagen RNeasy FFPE kit. RNA was extracted from frozen buffy coats using the Macharay-Nagel NucleoSpin RNA Blood kit
rRNA-depleted RNA was converted into cDNA and assembled into strand-specific libraries using the NEBNext Ultra II Directional RNA-Seq kit and the NEBNext Globin and rRNA depletion library construction kit.

value: prostate

tag: patient id

value: stroma

tag: behavior

value: delayed

tag: gleason score

tag: age at_time_of_sample

value: male

tag: timepoint

tag: race

value: White


title: PDGFNO rep1

description: Library name: sample4

tag: tissue


title: TK34

description:
Library name: TK34_CD8_TIL_CD103+CD69+
3 mice pooled, day 46 post TAM

value: Tumor

tag: cell line

value: CD8+ T cell

tag: cell type


title: SK-MEL-2, H3K27ac

value: Melanoma

tag: chip antibody

value: H3K27ac (Abcam:#ab4729)


title: atrnh1c, 3-week-old, true leaf, LD, replicate2

value: true leaf

tag: treatment

value: 16 h light/8 h dark, 22°C

tag: genotype


title: PDGF rep2

description: Library name: sample2

value: Testis


title: RNA-seq_pt113_benign_t2

description:
Library name: A8-102-18
Paired-end RNA-seq for benign gland sample A8-102-18 from patient 113, timepoint 2

value: benign gland

tag: Sex


title: Repli-C mAID-mClover-SMC1 R2

description: Library name: Repli-C_mAID-mClover-SMC1_R2

value: OsTIR (F74G)


title: atrnh1c, 3-week-old, true leaf, CL, replicate2

tag: developmental stage

value: 24 h light, 22°C

value: 5 days


title: CCRF-CEM, H3K27ac

value: CCRF-CEM

value: Childhood T acute lymphoblastic leukemia


title: Col0-NL-AsA

description: Library name: Sample6

tag: ecotype

value: wildtype

value: Normal light and 0.5 mM ascorbic acid


title: PDGF rep3

description: Library name: sample3


title: Col0-HL-AsA

description: Library name: Sample5

value: High light and 0.5 mM ascorbic acid


title: RNA-seq_pt113_tumor_t2

description:
Library name: A8-102-17
Paired-end RNA-seq for tumor sample A8-102-17 from patient 113, timepoint 2

value: prostate

value: tumor

value: delayed

value: male

value: White


title: RNA-seq_pt113_buffy_t2

description:
Library name: A21-E10-9
Paired-end RNA-seq for buffy sample A21-E10-9 from patient 113, timepoint 2

source_name: buffy coat

value: buffy coat

value: buffy


title: PDGF rep1

description: Library name: sample1

value: Testis


title: PC-3, H3K27ac

value: Prostate carcinoma

value: H3K27ac (Abcam:#ab4729)


title: Col-0, 3-week-old, true leaf, SD, replicate2

value: true leaf

value: 8 h light/16 h dark, 22°C

tag: time


title: aged_NB  rep7

description: Library name: sample47

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v9.0.0 (https://www.10xgenomics.com/cn/support/software/cell-ranger)
Assembly: Mmul_10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Following the 10x Genomics single-cell protocol for cell extraction
RNA libraries for RNA-seg were prepared using 10X Library Prep Kitfollowing manufacturer's protocols.


title: Col-0, 3-week-old, true leaf, LD, replicate2

value: 16 h light/8 h dark, 22°C

value: 5 days


title: RNA-seq_pt113_buffy_t1

description:
Library name: A21-E10-5
Paired-end RNA-seq for buffy sample A21-E10-5 from patient 113, timepoint 1


title: K562, H3K27ac

value: Chronic myeloid leukemia


title: SK-OV-3, H3K27ac

value: Ovarian serous cystadenocarcinoma


title: aged_NB  rep6

description: Library name: sample46


title: Col-0, 3-week-old, true leaf, CL, replicate2

value: 24 h light, 22°C


title: RNA-seq_pt79_stroma_both

description:
Library name: A8-102-9
Paired-end RNA-seq for stroma sample A8-102-9 from patient 79, timepoint both

value: prostate

value: stroma

value: both


title: SW620, H3K27ac

value: Colon adenocarcinoma


title: aged_NB  rep5

description: Library name: sample45


title: why1/3/atrnh1c, 3-week-old, true leaf, replicate2

value: 16 h light/8 h dark, 22°C/20°C


title: RNA-seq_pt79_benign_both

description:
Library name: A8-102-11
Paired-end RNA-seq for benign gland sample A8-102-11 from patient 79, timepoint both

value: benign gland

value: delayed

value: male

value: White


title: reca1/atrnh1c, 3-week-old, true leaf, replicate2


title: HCT116, H3K27ac

value: Colon carcinoma

value: H3K27ac (Abcam:#ab4729)


title: aged_B  rep8

description: Library name: sample44

value: Testis


title: HL-60, H3K27ac

value: Adult acute myeloid leukemia


title: RNA-seq_pt79_tumor_t2

description:
Library name: A8-102-10
Paired-end RNA-seq for tumor sample A8-102-10 from patient 79, timepoint 2

value: tumor


title: RNA-seq_pt79_buffy_t2

description:
Library name: A21-E10-10
Paired-end RNA-seq for buffy sample A21-E10-10 from patient 79, timepoint 2

value: buffy coat

value: buffy


title: atrnh1c, 3-week-old, true leaf, replicate2

value: true leaf


title: aged_B  rep7

description: Library name: sample43


title: MOLT-4, H3K27ac

value: Adult T acute lymphoblastic leukemia


title: Col-0, 3-week-old, true leaf, replicate2


title: aged_B  rep6

description: Library name: sample42


title: aged_B  rep5

description: Library name: sample41


title: Col-0, 1-week-old, root, replicate2

source_name: root

value: root


title: RNA-seq_pt79_buffy_t1

description:
Library name: A21-E10-2
Paired-end RNA-seq for buffy sample A21-E10-2 from patient 79, timepoint 1


title: Col-0, 5-week-old, caulin leaf, replicate2

source_name: caulin leaf

value: caulin leaf


title: aged_NB  rep3

description: Library name: sample39


title: Col-0, 5-week-old, old leaf, replicate2

source_name: old leaf

value: old leaf


title: RNA-seq_pt75_benign_t2

description:
Library name: A8-102-4
Paired-end RNA-seq for benign gland sample A8-102-4 from patient 75, timepoint 2

value: prostate

value: progressor


title: NCI-H23, H3K27ac

value: Lung adenocarcinoma


title: aged_NB  rep2

description: Library name: sample38


title: RNA-seq_pt75_tumor_t2

description:
Library name: A8-102-3
Paired-end RNA-seq for tumor sample A8-102-3 from patient 75, timepoint 2

value: male


title: A498, H3K27ac

value: Renal cell carcinoma


title: Col-0, 5-week-old, young true leaf, replicate2

source_name: young true leaf

value: young true leaf

value: 16 h light/8 h dark, 22°C/20°C


title: Sublibrary_4 from multiplexed Anableps retina samples

city: Baton Rouge

first: Patricia

last: Schneider

state: Louisiana

address: LSU 131 Life Sciences Building

department: Biological Sciences

institute: Louisiana State University

description: Library name: Aa_sub4

data_processing:
Sequence reads were mapped to Anableps anableps Genome Assembly GCA_014839685.1. SnRNA-seq FASTQ files were processed using the TrailmakerTM pipeline module (https://app.trailmaker.parsebiosciences.com/; v1.4.0, Parse Biosciences, 2024)
Assembly: GCA_014839685.1
Supplementary files format and content: Anableps_retina.rds - RDS file from Trailmaker

molecule: nuclear RNA

organism: Anableps anableps

source_name: Whole retina

extract_protocol:
Nuclei were fixed and frozen using the Evercode Nuclei Fixation Kit v3 (#NF100, #NF200) from Parse Biosciences following the manufacturer’s protocol.
snRNA-seq libraries were generated using Parse Biosciences combinatorial barcoding technology.  Fixed and frozen nuclei from each sample were processed to generate barcoded libraries aiming for 7,000 nuclei per sample using the Evercode WT v3 Kit (#WT100A-D, #WT200) as per manufacturer’s instructions. Samples were multiplexed during barcoding and sequenced as multiple technical sublibraries at the depth of 20,000 reads per nuclei in an Illumina Novaseq Xplus platform (paired-end, 150bp).

value: Whole retina

value: multiple

value: adult


title: RNA-seq_pt75_buffy_t2

description:
Library name: A21-E10-1
Paired-end RNA-seq for buffy sample A21-E10-1 from patient 75, timepoint 2

value: buffy coat

value: White


title: BAP_epidermis_rep2

type: RNA

city: Berlin

first: Heike

last: Sprenger

address: Max-Dohrn-Strasse 8-10

department: Food Safety

country: Germany

institute: German Federal Institute for Risk Assessment

hyb_protocol: GeneChip™ Hybridization, Wash, and Stain Kit Fluidics stations FS450-007

scan_protocol: GeneChip Scanner 3000 7G

data_processing: Data processing and statistical data evaluation was performed in the R environment. The raw data were normalized and summarized using the RMA (robust multi-array average) algorithm from the R package oligo version 1.68.2. The genes were associated with vendor-provided annotation information (Release 36, Thermo Fisher Scientific, https://www.thermofisher.com/order/catalog/product/sec/assets?url=TFS-Assets/LSG/Support-Files/Clariom_S_Human.r1.na36.hg38.a1.transcript.csv.zip) and control genes were removed after background correction. Furthermore, irrelevant genes with low expression were removed so that 21,194 probes corresponding to 19,304 genes remained (intensity > 4 in at least 2 samples). After applying quality metrices to normalized data, it was determined that one biological replicate from control models at timepoint 4 was an outlier. Thus, that sample was further excluded from the microarray data analysis.   Differential gene expression (DGE) analysis was performed by the R package limma version 3.60.2: linear models were fit and moderated t-statistics computed by the eBayes function. The linear models were fitted, and moderated t-statistics were computed using the eBayes function. Subsequently, the Benjamini-Hochberg correction was applied to exclude false-positive results, and the differentially expressed genes were considered significant with an adjusted p-value<0.05 and a log2FC>0.5 as well as log2FC<-0.5.

label: biotin

source_name: bacterial mixture BAP_epidermis

label_protocol: Terminal deoxynucleotidyl transferase (TdT) using the proprietary DNA Labeling Reagent that is covalently linked to biotin

growth_protocol: Tissues were cultivated at 37°C and 5% CO2 in antibiotic-free maintenance medium (EFT-400-ABF) obtained from MatTek.

extract_protocol: Total RNA of the epidermis and dermis was extracted using Trizol ® reagent (Ambion) following manufacturer´s protocol.

treatment_protocol: Tissues were inoculated with different bacterial mixtures, which were previously isolated from skin swabs. As vehicel control, PBS was used.

value: MatTek's EpiDermFT

value: human-derived epidermal keratinocytes

value: NHEK

value: bacterial inoculation, mixture BAP


title: DU145, H3K27ac

value: Prostate carcinoma

value: H3K27ac (Abcam:#ab4729)


title: RNA-seq_pt75_PIN_t1

description:
Library name: A8-102-2
Paired-end RNA-seq for PIN sample A8-102-2 from patient 75, timepoint 1

value: prostate

value: PIN

value: progressor


title: aged_B rep3

description: Library name: sample35

value: Testis


title: Col-0, 2-week-old, young true leaf, replicate2

value: young true leaf


title: RNA-seq_pt75_tumor_t1

description:
Library name: A8-102-1
Paired-end RNA-seq for tumor sample A8-102-1 from patient 75, timepoint 1

value: tumor

value: male


title: A549, H3K27ac

value: Lung adenocarcinoma


title: Col-0, 4-week-old, cotyledon, replicate2

source_name: cotyledon

value: cotyledon

value: 16 h light/8 h dark, 22°C/20°C


title: aged_B rep2

description: Library name: sample34


title: RNA-seq_pt75_buffy_t1

description:
Library name: A21-E10-7
Paired-end RNA-seq for buffy sample A21-E10-7 from patient 75, timepoint 1

value: buffy coat

value: buffy

value: White


title: 786-O, H3K27ac

value: Renal cell carcinoma


title: aged_B rep1

description: Library name: sample33


title: RNA-seq_pt66_benign_t2

description:
Library name: A8-101-23
Paired-end RNA-seq for benign gland sample A8-101-23 from patient 66, timepoint 2

value: benign gland


title: GeoMx-DSP-1001660022457-B-E11

city: Rochester

first: Alexandra

last: Krivonos

state: MN

address: 200 1st St SW

department: Quantitative Health Sciences

institute: Mayo Clinic

description: Library name: GeoMx-DSP-1001660022457-B-E11

data_processing:
The samples were sequenced on an Illumina NextSeq 2000 P3 instrument at PE50. Sequencing depth was calculated based on a total area of 9,002,857 μm2 and 900 million read pairs determined from the GeoMx GeoMx-DSP generated Lab Worksheet.
Sequencing-generated FASTQ files were processed using the NanoString GeoMx NGS pipeline to generate DCC files used in downstream data analysis.
Assembly: mm10
Supplementary files format and content: GeoMx_sample_metadata.csv includes the samples metadata
Supplementary files format and content: vwf+_VWF+_DE_analysis.xlsx Differential expression results from NanoString GeoMx WTA analysis; log₂ fold change, FDR, p-value, and mean expression values for genes in one tissue segment subset
Supplementary files format and content: cd68+_CD68+_DE_analysis.xlsx - Differential expression results from NanoString GeoMx WTA analysis; log₂ fold change, FDR, p-value, and mean expression values for genes in one tissue segment subset
Supplementary files format and content: ela2+_ELA+_DE_analysis.xlsx - Differential expression results from NanoString GeoMx WTA analysis; log₂ fold change, FDR, p-value, and mean expression values for genes in one tissue segment subset
Supplementary files format and content: else_ELSE_DE_analysis.xlsx - Differential expression results from NanoString GeoMx WTA analysis; log₂ fold change, FDR, p-value, and mean expression values for genes in one tissue segment subset
Library strategy: Spatial Transcriptomics

source_name: liver

growth_protocol: human liver FFPE

extract_protocol:
Fresh tissues from surgery were processed for FFPE embedding, 5um section were cut.
Slides were flourensently labeled with  endothelial cell marker Von Willebrand Factor (VWF), macrophage and monocyte marker CD68, and neutrophil marker Elastase (ELA2). Regions of interest (ROIs) were manually draw based on their zonal location within the liver lobule: periportal zone 1, midzonal zone 2, and pericentral zone 3. Each ROI consisted of four segments: segment 4 for VWF+ area, segment 1 for CD68+ area, segment 2 for ELA2+ area, and segment 3 was called ‘else’ to refer to non-stained areas within the ROI. Photo-cleaved oligonucleotide tags were collected from 377 AOI. PCR amplification and liabrary pprepareation were done using GeoMx Human Whole Transcriptome Atlas (WTA) accorrding to manufacture's instruction.

treatment_protocol: 3 patients with normal, 3 patients with steatosis and 4 patients with MASH

value: liver

tag: condition

tag: segment

tag: zone

tag: batch


title: NCI-H460, H3K27ac

value: Lung large cell carcinoma

value: H3K27ac (Abcam:#ab4729)


title: Col-0, 2-week-old, cotyledon, replicate2


title: prepuberty_NB rep8

description: Library name: sample32


title: RNA-seq_pt66_stroma_t2

description:
Library name: A8-101-22
Paired-end RNA-seq for stroma sample A8-101-22 from patient 66, timepoint 2

value: prostate

tag: patient id

value: stroma

tag: behavior

tag: gleason score

tag: age at_time_of_sample


title: SNB19, H3K27ac

tag: cell line

value: Astrocytoma


title: Col-0, 1-week-old, cotyledon, replicate2

tag: tissue


title: prepuberty_NB rep7

description: Library name: sample31

value: Testis


title: RNA-seq_pt66_buffy_t2

description:
Library name: A21-E10-4
Paired-end RNA-seq for buffy sample A21-E10-4 from patient 66, timepoint 2

tag: cell type

value: progressor

tag: timepoint

tag: race


title: SK-MEL-28, H3K18ac, rep1

value: Cutaneous melanoma

tag: chip antibody

value: H3K18ac (Abcam:#ab1191)


title: atrnh1c, 3-week-old, true leaf, 37°C

source_name: true leaf

value: true leaf

tag: developmental stage

tag: treatment

value: 16 h light/8 h dark, 37C

value: 2 days

tag: genotype


title: prepuberty_NB rep6

description: Library name: sample30


title: RNA-seq_pt66_PIN_t1

description:
Library name: A8-101-21
Paired-end RNA-seq for PIN sample A8-101-21 from patient 66, timepoint 1

value: PIN

tag: Sex

value: male


title: Col-0, 3-week-old, cotyledon, replicate2

value: cotyledon

value: 16 h light/8 h dark, 22°C/20°C


title: MDA-MB-468, H3K18ac, rep1

value: Breast adenocarcinoma


title: atrnh1c, 3-week-old, true leaf, 22°C

value: 16 h light/8 h dark, 22C

tag: time


title: prepuberty_NB rep5

description: Library name: sample29


title: Col-0, 3-week-old, true leaf, CD, replicate2

value: 24 h dark, 22°C

value: 5 days


title: RNA-seq_pt66_tumor_t1

description:
Library name: A8-101-20
Paired-end RNA-seq for tumor sample A8-101-20 from patient 66, timepoint 1

value: prostate

value: tumor

value: White


title: T47D, H3K27ac

value: Invasive breast carcinoma

value: H3K27ac (Abcam:#ab4729)


title: aged_NB  rep8

description: Library name: sample48

value: Testis


title: RPMI-8226, H3K18ac, rep1

value: Multiple myeloma

value: H3K18ac (Abcam:#ab1191)


title: atrnh1c, 3-week-old, true leaf, 4°C

value: true leaf

value: 16 h light/8 h dark, 4C

value: 2 days


title: RNA-seq_pt113_tumor_t1

description:
Library name: A8-102-16
Paired-end RNA-seq for tumor sample A8-102-16 from patient 113, timepoint 1

value: delayed

value: male


title: prepuberty_B rep8

description: Library name: sample28


title: Col-0, 3-week-old, true leaf, 42°C

value: 16 h light/8 h dark, 42C

value: 5 hours


title: SK-MEL-2, H3K18ac, rep1

value: Melanoma


title: RNA-seq_pt66_buffy_t1

description:
Library name: A21-E10-6
Paired-end RNA-seq for buffy sample A21-E10-6 from patient 66, timepoint 1

value: buffy coat

value: buffy

value: progressor


title: prepuberty_B rep7

description: Library name: sample27


title: RNA-seq_pt59_stroma_both

description:
Library name: A8-101-16
Paired-end RNA-seq for stroma sample A8-101-16 from patient 59, timepoint both

value: prostate

value: stroma

value: nonprogressor

value: both

value: White


title: Col-0, 3-week-old, true leaf, 37°C

value: 16 h light/8 h dark, 37C


title: prepuberty_B rep6

description: Library name: sample26

value: Testis


title: CCRF-CEM, H3K18ac, rep1

source_name: CCRF-CEM

value: CCRF-CEM

value: Childhood T acute lymphoblastic leukemia

value: H3K18ac (Abcam:#ab1191)


title: RNA-seq_pt59_PIN_t2

description:
Library name: A8-101-18
Paired-end RNA-seq for PIN sample A8-101-18 from patient 59, timepoint 2

value: PIN

value: male


title: T47D, H3K18ac, rep1

value: Invasive breast carcinoma


title: Col-0, 3-week-old, true leaf, 22°C

value: true leaf

value: 16 h light/8 h dark, 22C

value: 2 days


title: prepuberty_B rep5

description: Library name: sample25


title: RNA-seq_pt79_tumor_t1

description:
Library name: A8-102-8
Paired-end RNA-seq for tumor sample A8-102-8 from patient 79, timepoint 1

value: tumor

value: delayed


title: RNA-seq_pt59_tumor_t2

description:
Library name: A8-101-17
Paired-end RNA-seq for tumor sample A8-101-17 from patient 59, timepoint 2

value: prostate


title: PC-3, H3K18ac, rep1

value: Prostate carcinoma


title: Col-0, 3-week-old, true leaf, 17°C

value: 16 h light/8 h dark, 17C


title: NCI-H226, H3K27ac

value: Pleural epithelioid mesothelioma

value: H3K27ac (Abcam:#ab4729)


title: prepuberty_NB rep4

description: Library name: sample24

value: Testis


title: RNA-seq_pt59_buffy_t2

description:
Library name: A21-E10-11
Paired-end RNA-seq for buffy sample A21-E10-11 from patient 59, timepoint 2

value: buffy coat

value: buffy

value: nonprogressor

value: White


title: K562, H3K18ac, rep1

value: Chronic myeloid leukemia

value: H3K18ac (Abcam:#ab1191)


title: aged_NB  rep4

description: Library name: sample40


title: NCI-H522, H3K27ac

value: Lung adenocarcinoma


title: RNA-seq_pt75_stroma_t2

description:
Library name: A8-102-5
Paired-end RNA-seq for stroma sample A8-102-5 from patient 75, timepoint 2

value: stroma

value: progressor

value: male


title: Col-0, 3-week-old, true leaf, 12°C

value: true leaf

value: 16 h light/8 h dark, 12C

value: 2 days


title: prepuberty_NB rep3

description: Library name: sample23


title: RNA-seq_pt59_PIN_t1

description:
Library name: A8-101-15
Paired-end RNA-seq for PIN sample A8-101-15 from patient 59, timepoint 1

value: prostate

value: PIN


title: OVCAR-8, H3K27ac

value: High grade ovarian serous adenocarcinoma

value: H3K27ac (Abcam:#ab4729)


title: prepuberty_NB rep2

description: Library name: sample22

value: Testis


title: Col-0, 3-week-old, true leaf, 4°C

value: 16 h light/8 h dark, 4C


title: RNA-seq_pt59_tumor_t1

description:
Library name: A8-101-14
Paired-end RNA-seq for tumor sample A8-101-14 from patient 59, timepoint 1

value: tumor

value: nonprogressor


title: SK-OV-3, H3K18ac, rep1

value: Ovarian serous cystadenocarcinoma


title: SW620, H3K18ac, rep1

value: Colon adenocarcinoma

value: H3K18ac (Abcam:#ab1191)


title: prepuberty_NB rep1

description: Library name: sample21


title: RNA-seq_pt55_stroma_both

description:
Library name: A8-101-9
Paired-end RNA-seq for stroma sample A8-101-9 from patient 55, timepoint both

value: stroma

value: both

value: White


title: atrnh1c, 3-week-old, true leaf, CD

value: true leaf

value: 24 h dark, 22C

value: 5 days


title: HCT116, H3K18ac, rep1

value: Colon carcinoma


title: atrnh1c, 3-week-old, true leaf, SD

value: 8 h light/16 h dark, 22C


title: RNA-seq_pt55_benign_t2

description:
Library name: A8-101-12
Paired-end RNA-seq for benign gland sample A8-101-12 from patient 55, timepoint 2

value: prostate

value: benign gland

value: progressor

value: male


title: Col-0, 5-week-old, mature leaf, replicate2

source_name: mature leaf

value: mature leaf

value: 16 h light/8 h dark, 22°C/20°C


title: prepuberty_B rep4

description: Library name: sample20

value: Testis


title: atrnh1c, 3-week-old, true leaf, LD

value: 16 h light/8 h dark, 22C


title: HL-60, H3K18ac, rep1

value: Adult acute myeloid leukemia

value: H3K18ac (Abcam:#ab1191)


title: RNA-seq_pt55_tumor_t2

description:
Library name: A8-101-10
Paired-end RNA-seq for tumor sample A8-101-10 from patient 55, timepoint 2

value: tumor


title: prepuberty_B rep3

description: Library name: sample19


title: atrnh1c, 3-week-old, true leaf, CL

value: 24 h light, 22C


title: prepuberty_B rep2

description: Library name: sample18


title: aged_NB  rep1

description: Library name: sample37


title: RNA-seq_pt55_buffy_t2

description:
Library name: A21-E10-8
Paired-end RNA-seq for buffy sample A21-E10-8 from patient 55, timepoint 2

value: buffy coat

value: buffy

value: White


title: MOLT-4, H3K18ac, rep1

value: Adult T acute lymphoblastic leukemia


title: NCI-H226, H3K18ac, rep1

value: Pleural epithelioid mesothelioma


title: Col-0, 3-week-old, true leaf, CD

value: true leaf

value: 24 h dark, 22C

value: 5 days


title: RNA-seq_pt55_tumor_t1

description:
Library name: A8-101-8
Paired-end RNA-seq for tumor sample A8-101-8 from patient 55, timepoint 1

value: prostate

value: progressor

value: male


title: NCI-H522, H3K18ac, rep1

value: Lung adenocarcinoma


title: Col-0, 3-week-old, true leaf, SD

value: 8 h light/16 h dark, 22C


title: OVCAR-8, H3K18ac, rep1

value: High grade ovarian serous adenocarcinoma


title: Col-0, 3-week-old, true leaf, LD

value: 16 h light/8 h dark, 22C


title: RNA-seq_pt19_tumor_t2

description:
Library name: A8-101-4
Paired-end RNA-seq for tumor sample A8-101-4 from patient 19, timepoint 2

value: tumor


title: Col-0, 3-week-old, true leaf, CL

value: 24 h light, 22C


title: adult_NB rep7

description: Library name: sample15

value: Testis


title: adult_NB rep6

description: Library name: sample14


title: NCI-H23, H3K18ac, rep1

value: H3K18ac (Abcam:#ab1191)


title: RNA-seq_pt19_stroma_t1

description:
Library name: A8-101-3
Paired-end RNA-seq for stroma sample A8-101-3 from patient 19, timepoint 1

value: stroma

value: White


title: A498, H3K18ac, rep1

value: Renal cell carcinoma


title: adult_NB rep5

description: Library name: sample13


title: why1/3/atrnh1c, 3-week-old, true leaf

value: true leaf

value: 16 h light/8 h dark, 22C/20C


title: DU145, H3K18ac, rep1

value: Prostate carcinoma


title: RNA-seq_pt19_tumor_t1

description:
Library name: A8-101-1
Paired-end RNA-seq for tumor sample A8-101-1 from patient 19, timepoint 1

value: prostate


title: RNA-seq_pt19_buffy_t1

description:
Library name: A21-E10-3
Paired-end RNA-seq for buffy sample A21-E10-3 from patient 19, timepoint 1

value: buffy coat

value: buffy

value: progressor


title: atrnh1c, 3-week-old, true leaf


title: U251, H3K18ac, rep1

value: Astrocytoma


title: adult_B rep7

description: Library name: sample11


title: A549, H3K18ac, rep1

value: Lung adenocarcinoma


title: Col-0, 3-week-old, true leaf


title: adult_B rep6

description: Library name: sample10


title: 786-O, H3K18ac, rep1


title: Col-0, 1-week-old, root

value: root


title: adult_B rep5

description: Library name: sample9


title: GeoMx-DSP-1001660022456-E-G07

description: Library name: GeoMx-DSP-1001660022456-E-G07

value: liver

tag: condition

tag: segment

tag: zone


title: adult_NB rep4

description: Library name: sample8


title: Col-0, 5-week-old, seed

source_name: seed

value: seed


title: TY-DOX-DAC-2

city: Minneapolis

first: David

last: Largaespada

address: 515 Delaware St SE

department: Department of Pediatrics

institute: University of Minnesota

description: Library name: UMGC-Lar-170-TY-DOX-DAC-2

data_processing:
Data were processed using the CHURP (v. 0.2.2) pipeline
Assembly: hg38
Supplementary files format and content: text file contains raw counts for all samples

source_name: tumor

growth_protocol: Cell lines were maintained in DMEM or RPMI + 10% or 20% FBS + P/S at 37C with 5% CO2

extract_protocol:
RNA was extracted with the RNEasy mini purification kit (Qiagen) and TURBO DNase (Invitrogen) was added to remove genomic DNA contamination
Libraries were prepped using the TruSeq Stranded mRNA kit

value: tumor

value: MPNST

value: treated with DOX for 7 days; DAC for 4 days


title: SNB19, H3K18ac, rep1

value: H3K18ac (Abcam:#ab1191)


title: Col-0, 5-week-old, valve

source_name: valve

value: valve


title: TY-DOX-DAC-1

description: Library name: UMGC-Lar-170-TY-DOX-DAC-1


title: adult_NB rep3

description: Library name: sample7

source_name: Testis

value: Testis


title: Col-0, 5-week-old, caulin leaf

value: caulin leaf

value: 16 h light/8 h dark, 22C/20C


title: adult_NB rep2

description: Library name: sample6


title: TY-DOX-AZA-2

description: Library name: UMGC-Lar-170-TY-DOX-AZA-2

value: treated with DOX for 7 days; AZA for 4 days


title: Col-0, 5-week-old, old leaf

value: old leaf


title: adult_NB rep1

description: Library name: sample5


title: TY-DOX-AZA-1

description: Library name: UMGC-Lar-170-TY-DOX-AZA-1


title: RPMI-8226, H2AZ, rep1

value: Multiple myeloma

value: H2A.Z (Abcam:#ab4174)


title: Col-0, 5-week-old, mature leaf

value: mature leaf


title: adult_B rep4

description: Library name: sample4


title: TY-DMSO-DMSO-2

description: Library name: UMGC-Lar-170-TY-DMSO-DMSO-2

value: treated with DMSO for 7 days; DMSO for 4 days


title: GeoMx-DSP-1001660022456-E-F04

description: Library name: GeoMx-DSP-1001660022456-E-F04

value: Portal-Periportal

tag: batch


title: SK-MEL-2, H2AZ, rep1

value: Melanoma


title: adult_B rep3

description: Library name: sample3


title: TY-DMSO-DMSO-1

description: Library name: UMGC-Lar-170-TY-DMSO-DMSO-1


title: reca1/atrnh1c, 3-week-old, true leaf

value: true leaf


title: Col-0, 5-week-old, young true leaf

value: young true leaf


title: CCRF-CEM, H2AZ, rep1

value: CCRF-CEM

value: Childhood T acute lymphoblastic leukemia


title: adult_B rep2

description: Library name: sample2


title: TY-DMSO-DAC-2

description: Library name: UMGC-Lar-170-TY-DMSO-DAC-2

value: tumor

value: MPNST

value: treated with DMSO for 7 days; DAC for 4 days


title: GeoMx-DSP-1001660022456-E-F09

description: Library name: GeoMx-DSP-1001660022456-E-F09

value: liver


title: T47D, H2AZ, rep1

value: Invasive breast carcinoma


title: TY-DMSO-DAC-1

description: Library name: UMGC-Lar-170-TY-DMSO-DAC-1


title: PC-3, H2AZ, rep1

value: Prostate carcinoma


title: adult_B rep1

description: Library name: sample1

value: Testis


title: Col-0, 4-week-old, cotyledon

value: cotyledon

value: 16 h light/8 h dark, 22C/20C


title: RTN_7d_CO2_6

city: Wauwatosa

first: Ibrahim

last: Vazirabad

state: Wisconsin

address: 8915 W Connell Ave

department: Physiology

institute: Medical College of Wisconsin

description: Library name: R2024.925

data_processing:
Filtered reads were obtained by running fastp v0.24.0 with default parameters.
Filtered reads were aligned to the goat reference (ARS1) using STAR v2.7.10b with gene-level counts generated by FeatureCounts v2.0.6.
Differential expression analysis was performed by EdgeR v4.6
Assembly: ARS1
Supplementary files format and content: gene name, log2 fold change, log2CPM, and FDR per comparison are included for all differentially expressed genes.

organism: Capra hircus

source_name: RTN

growth_protocol: Five groups (n = 6) of adult (≥ 2 years) outbred (Alpine, Saanen, Toggenburg, etc.) female goats were assigned to the protocol.

extract_protocol:
RNA was isolated using the Qiagen RNeasy Lipid Tissue Kit per the manufacturer’s recommendations, including on-column DNase digestion
RNA-seq libraries were constructed using the SMART-SEQ v4 Ultra Low Input RNA Kit for Sequencing and the Nextera XT DNA Library Preparation Kit. Sequencing produced 100-bp paired end reads across up to two lanes.

treatment_protocol: The five groups were randomly assigned to different environmental CO2 exposures, either 24 hr of control (room air), 3 hours of 6% CO2, 24 hours of 6% CO2, 7 days of 6% CO2, or 7 days of control (room air).

value: RTN


title: HL-60, H3K27me3, rep3

data_processing:
Sequencing reads from mChIP-seq were demultiplexed to samples by the barcodes in the 5’ end of Read2 using fastq-multx (version 1.4.2) (https://github.com/brwnj/fastq-multx) with a mismatch setting of 0. Then, reads of each sample with adapter contamination and low quality were trimmed and filtered using fastp with parameters as -f 10 -t 5 -F 30 -T 5 --complexity_threshold=30 –n_base_limit=5  --length_required 60 (version 0.23.2) and aligned to the human reference genomes hg38, mouse reference genome mm10, or budding yeast genome sacCer3 using bowtie2 (version 2.2.5) with default parameters. Uniquely mapping reads with mapping quality more than 30 were kept using samtools (version 1.9) and duplicates were removed using picard MarkDuplicates (v2.26.10, http://broadinstitute.github.io/picard).
Assembly: BW25113 genome for E. coli, sacCer3 genome for yeast, GRCh38 genome for humans, mm10 genome for mice
Supplementary files format and content: bigWig

value: Adult acute myeloid leukemia


title: EMS404 cells, transfected with scrambled siRNA and treated with TGFb rep2

city: Lille

first: Lefebvre

last: Philippe

state: Nord

address: Blvd Pr. J.Leclerc

country: France

institute: Inserm

description: Library name: siNtTGF2

data_processing:
After initial QCs (OD260/280, RIN), oligo dT selection, random (N6) primed reverse transcription, end repair and adaptator ligation, cDNAs samples were paired-end sequenced (100 b) on the DNBSEQ BGI platform.
Sequence data filtering was performed using BGI SOAPnuke (v 1.5.2)(parameters: -I 15 -q 0.2 -n 0.05) and cleaned data were store as a Fastq file.  HISAT [v 2.0.4, (Kim et al, 2015)] was used to align valid reads on the mouse genome (mm10)(parameters:--sensitive –no-discordant –no mixed -I 1 -X 1000 -p8 –rnastrandness RF).  Bowtie2 [v2.2.5, (Langmead & Salzberg, 2012)](parameters: -q –phred64 –sensitive –dpad0 –gbar99999999 –mp1,1 -np 1 –score-min L,0,-0.1 -p 16 -k 200) was used to map reads of the reference transcriptome.  RSEM was used to determine gene expression levels [v1.2.8, (Li & Dewey, 2011)].  DEseq2 was used to identify differentially expressed genes [q value < 0.05, (Love et al, 2014)].
Assembly: mm10
Supplementary files format and content: Is a csv file, contains FPKM values fro each sample
Supplementary files format and content: csv

growth_protocol: Cells were transfected with indicated siRNAs and then treated 48 hours later with TGFb for an additional 24 hours period

extract_protocol:
Cellular RNAs were extracted from cells using the Macherey-Nagel™ Nucleospin™ Mini kit (#872061) or Qiagen RNeasy Micro kit (#74004), depending on sample abundance, following the manufacturers’ protocols. RNA concentration and purity were assessed with a Nanodrop One (ThermoFisher Scientific) or Qubit fluorometer and RNA HS Assay kit (#Q32852). RNA integrity was evaluated using a Bioanalyzer 2100 (Agilent). Samples with RIN <6.0 were discarded.
RNA libraries were built at BGI

value: hepatic stellate cells

tag: strain

value: Express human TLR4, SV40 immortalized


title: K562, H2AZ, rep1

extract_protocol:
Cells were fixed with 1% formaldehyde at room temperature for 10 min and quenched by glycine with 0.125 M final concentration. sonicated using Covaris SE220 (75 W, 20% Duty factor, 1,000 cycles per burst) for 5 min at 4°C to obtain fragments with the peak size around 200 bp.
The tailing and ssDNA ligation method used to label sample chromatin, and then multiple barcoded samples were pooled and split for immunoprecipitation with relevant antibodies as standard ChIP-seq. After immunoprecipitation, the purified ChIPed DNA was resuspended in 18 µl of water and extended in an 40 µl reaction containing 1 × KAPA HiFi HotStart ReadyMix and 0.25 µM P7TruSeqHTRev at 98 for 30 sec and 63 °C for 5 min followed by purification with 1.2 × volume of SPRIselect™ beads. Then, the purified DNA was ligated to the second adapter in a 40 µl reaction (1× T4 DNA ligase buffer, 0.5 µM P5TruSeqHT/P5SPlint mixture (1:1), and 10 Weiss units of T4 DNA ligase) at 25 °C for 30 minutes and purified with 1.0 × volume of SPRIselect™ beads. Lastly, library was amplified in 50 μl of PCR reaction Mix containing eluted DNA, 0.5 μM of P5 index primer, 0.5 μM P7 index primers, and 25 μl of KAPA HiFi HotStart ReadyMix (2 ×) (Kapa Biosystems) for 12-16 cycles (each cycle with 20 s at 98°C, 30 s at 58°C, 1 min at 68°C). DNA of 200–700 bp was isolated using a double SPRIselect bead cleanup (0.6 × and 0.85 × volume).

value: Chronic myeloid leukemia

value: H2A.Z (Abcam:#ab4174)


title: Col-0, 4-week-old, young true leaf

data_processing:
The duplicated reads with both the same forward and reverse reads were removed according to scripts (https://github.com/PEHGP/DEtail-seq/blob/master/RemoveSamReads.py)
The rest reads were aligned to the reference genome with Bowtie2 using --local settings.
For visualization and splitting strands, the aligned reads files (BAM) including the second read in pairs were converted to the first single base bigWig file with 1bp bins using bamCoverage from deepTools with --binSize 1 --Offset 1 --samFlagInclude 128 --filterRNAstrand forward/reverse. The option --filterRNAstrand forward means Crick strand and -- filterRNAstrand reverse means Watson strand.
Normalization was performed by deepTools based on RPGC with correction by the count of reads mapped to I-CeuI sites from each sample, and the signals around I-CeuI sites (± 2 bp) were deleted in the final normalized bigWig files.
Assembly: Tair10
Supplementary files format and content: bw

extract_protocol:
The chloroplasts were embedded in 0.5% low-melting-point agarose (Promega) and lysed in 1% sarkosyl, 0.45 M EDTA (pH 8.0), 10 mM Tris-HCl (pH 8.0), and 2 mg/mL proteinase K at 48°C for 16 h with shaking. The agarose plugs were washed in TE buffer six times at 37°C, with the first two washes containing 1 mM PMSF. Cut agarose plug into 12 pieces and incubated in 1 ml TE with 10 μg/ml RNase A at 37°C overnight. The agarose pieces were washed five times with 1 ml TE buffer at 37°C for 6 min, then stored in plug storage solution (0.05 M EDTA pH 8.0, 60% glycerol) at -20°C until all samples were ready for the next step.
The DNA library was constructed with Scale ssDNA-seq Lib Prep Kit for Illumina V2 (ABclonal, RK20228). Five agarose pieces (~30 mg) were washed three times with 200 μl 1× CutSmart buffer (NEB) at 37°C for 6 min. The spike-in was performed by incubating the agarose pieces with 15 U I-CeuI (NEB) in 150 μl 1× CutSmart buffer at 37°C for 12 h. After digestion, the agarose pieces were washed three times with 500 μl TE buffer at 37°C for 6 min, followed by twice washes with 200 μl Low EDTA TE (ABclonal) at 37°C for 6 min. The agarose pieces were incubated in 80 μl T7 Tailing & Ligation buffer (ABclonal) at 37°C for 12 h. Then, heated the agarose pieces at 98°C for 2 min. The DNA in the agarose was recovered using a DNA purification kit (Magen, Catalog No D2111-02) and eluted with Low EDTA TE. The DNA was then sonicated to ~250 bp using Focused-ultrasonicator (Covaris S220). To finish the library preparation, the subsequent steps were performed according to the manufacturer's protocol exactly.

value: young true leaf


title: RTN_7d_CO2_5

description: Library name: R2024.924


title: SK-OV-3, H2AZ, rep1

value: Ovarian serous cystadenocarcinoma


title: Col-0, 2-week-old, cotyledon


title: SW620, H2AZ, rep1

value: Colon adenocarcinoma


title: RTN_7d_CO2_3

description: Library name: R2024.922


title: TY-DMSO-1

description: Library name: UMGC-Lar-170-TY-DMSO-1

value: tumor

value: MPNST

value: treated with DMSO for 4 days


title: HCT116, H2AZ, rep1

value: Colon carcinoma


title: Col-0, 2-week-old, true leaf, rep2


title: RTN_7d_CO2_2

description: Library name: R2024.921


title: TY-DAC-2

description: Library name: UMGC-Lar-170-TY-DAC-2

value: treated with DAC for 4 days


title: HL-60, H2AZ, rep1


title: Col-0, 2-week-old, true leaf, rep1


title: RTN_7d_CO2_1

description: Library name: R2024.920


title: TY-DAC-1

description: Library name: UMGC-Lar-170-TY-DAC-1


title: MOLT-4, H2AZ, rep1

value: Adult T acute lymphoblastic leukemia


title: D. Clec7a-KO_4

city: Houston

first: haichao

last: wei

state: TX

address: 1825 Pressler St., SRB 637.C, 1825 Pressler St., SRB 637.C

institute: UTHealth

description:
Library name: Sample16
10x Genomics

data_processing:
Raw single-cell RNA sequencing reads were first processed individually for each sample using the 10x Genomics CellRanger software suited with default parameters, and aligned to the mouse reference genome (mm10). Following alignment and gene counting, data from all samples were imported into the Seurat R package for downstream analysis and subsequently merged into a single dataset. To ensure data quality, stringent filtering criteria were applied. Cells with fewer than 300 detected genes were removed to exclude low-quality or empty droplets, while cells with more than 7,000 genes were discarded to minimize the inclusion of doublets. In addition, genes expressed in fewer than three cells across the dataset were excluded. To control for artifacts associated with stressed or dying cells, we further removed cells in which mitochondrial transcripts represented more than 10% of total expression. Finally, mitochondrial genes themselves were excluded from the expression matrix to reduce confounding signals.
Normalization was performed in Seurat using default log-normalization parameters. To address batch variation across samples, we applied the FindIntegrationAnchors function followed by IntegrateData, thereby aligning datasets into a shared expression space. Dimensionality reduction was then carried out with principal component analysis (PCA), retaining the top 30 principal components for downstream clustering. Cell clustering was performed using the FindClusters function at a resolution of 0.1, and results were visualized with Uniform Manifold Approximation and Projection (UMAP). Clusters were annotated based on well-established cell-type marker genes, enabling robust identification of major cell populations. Specific cell types, including microglia, astrocyte, neuron, and endothelial cells, were further isolated using Seurat’s subset function.
For complementary pseudo bulk RNA-seq analysis, raw gene counts were extracted from the Seurat object (RNA assay) and aggregated by sample group and cell type, producing a gene-by-sample count matrix that reflects average expression across groups. The resulting matrix was processed with DESeq2, using size factor estimation and standard normalization procedures, thereby generating normalized expression profiles comparable to those obtained from conventional bulk RNA-seq. These pseudobulk values were used for downstream statistical testing and integrative comparisons.
Assembly: mm10
Supplementary files format and content: Tab-sepatated values files and matrix files

source_name: spinal cord

extract_protocol:
The whole spinal cord (SC) tissue was harvest and dissociated. After anesthesia, mice were transcardially perfused with cold PBS, SCs were extracted from the spines by flushing with PBS. SCs dissociation were performed using a Neural tissue dissociation kit (Miltenyi Biotec, #130-092-628) following the manufacturer’s instructions with some modifications 1) Add Enzyme mix 1 (100μl Enzyme P in 3800 μl Buffer X) and Enzyme mix 2 (20μl Enzyme A in 40 μl Buffer Y) to each spinal cord in order, incubate it in 37°C water bath with gently inverting every 3-5 min to resuspend settled tissues. 2) Dissociate tissue mechanically using the wide-tipped, fire-polished Pasteur pipette in decreasing diameter. 3) Filter the single-cell suspension through a 70μm cell strainer. 4) Cells were resuspended in cold PBS supplemented with 0.5% BSA containing Myelin Removal Beads II (Miltenyi Biotec, #130-096-733) to remove myelin, following the manufacturer’s protocol. After myelin removal, Cell number and viability were measured by TC20 Automated Cell Counter (Bio-Rad). The single-cell suspensions were kept on ice for no longer than 30min until further processing.
Library was prepared with the Chromium Single Cell 3’ Kit v3.1 (10x Genomics) following the manufacturer’s instructions.Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from celll lysate contained in every single GEM was retrotranscripted to cDNA, which contains an llumina R1 primer sequecne, Unique Molecular Identifier (UMI) and the 10x Barcode. The barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. Libraries were pooled based on their molar concentrations and sequenced on a NextSeq 550 instrument (Ilumina) with S2 paired end read of 100 bases reading length and 10 bases of Indexing.

value: All cell types

value: spinal cord

tag: age


title: RTN_7d_Control_6

description: Library name: R2024.919

value: RTN


title: TY-AZA-2

description: Library name: UMGC-Lar-170-TY-AZA-2

tag: cell line

value: treated with AZA for 4 days


title: TY-DMSO-AZA-2

description: Library name: UMGC-Lar-170-TY-DMSO-AZA-2

tag: tissue

value: treated with DMSO for 7 days; AZA for 4 days


title: Col-0, 3-week-old, cotyledon

value: cotyledon

value: 16 h light/8 h dark, 22C/20C


title: NCI-H226, H2AZ, rep1

tag: cell type

value: Pleural epithelioid mesothelioma

value: H2A.Z (Abcam:#ab4174)


title: TY-DMSO-AZA-1

description: Library name: UMGC-Lar-170-TY-DMSO-AZA-1


title: D. Clec7a-KO_3

description:
Library name: Sample10
10x Genomics


title: RTN_7d_Control_5

description: Library name: R2024.918


title: TY-AZA-1

description: Library name: UMGC-Lar-170-TY-AZA-1


title: TY-DMSO-2

description: Library name: UMGC-Lar-170-TY-DMSO-2


title: RTN_7d_CO2_4

description: Library name: R2024.923


title: NCI-H522, H2AZ, rep1

value: Lung adenocarcinoma


title: Col-0, 1-week-old, cotyledon


title: D. Clec7a-KO_2

description:
Library name: Sample7
10x Genomics


title: RTN_7d_Control_4

description: Library name: R2024.917


title: STS26T-DMSO-2

description: Library name: UMGC-Lar-170-STS26T-DMSO-2


title: OVCAR-8, H2AZ, rep1

value: High grade ovarian serous adenocarcinoma


title: D. Clec7a-KO_1

description:
Library name: Sample4
10x Genomics


title: adult_NB rep8

description: Library name: sample16

value: Testis


title: RTN_7d_Control_3

description: Library name: R2024.916


title: prepuberty_B rep1

description: Library name: sample17


title: STS26T-DMSO-1

description: Library name: UMGC-Lar-170-STS26T-DMSO-1

value: tumor

value: MPNST


title: NCI-H23, H2AZ, rep1


title: RNA-seq_pt19_benign_t2

description:
Library name: A8-101-5
Paired-end RNA-seq for benign gland sample A8-101-5 from patient 19, timepoint 2

source_name: prostate

value: prostate

tag: patient id

value: benign gland

tag: behavior

value: progressor

tag: gleason score

tag: age at_time_of_sample

value: male

tag: timepoint

value: White


title: C. nTg_3

description:
Library name: Sample12
10x Genomics

value: All cell types

value: spinal cord

value: nTg


title: RTN_7d_Control_2

description: Library name: R2024.915

value: RTN

tag: treatment


title: STS26T-DAC-2

description: Library name: UMGC-Lar-170-STS26T-DAC-2

value: treated with DAC for 4 days


title: A498, H2AZ, rep1

value: Renal cell carcinoma

tag: chip antibody


title: C. nTg_2

description:
Library name: Sample9
10x Genomics


title: RTN_7d_Control_1

description: Library name: R2024.914


title: DU145, H2AZ, rep1

value: Prostate carcinoma

value: H2A.Z (Abcam:#ab4174)


title: STS26T-DAC-1

description: Library name: UMGC-Lar-170-STS26T-DAC-1


title: VRC_7d_CO2_6

description: Library name: R2024.913

source_name: VRC

value: VRC


title: C. nTg_1

description:
Library name: Sample8
10x Genomics


title: STS26T-AZA-2

description: Library name: UMGC-Lar-170-STS26T-AZA-2

value: treated with AZA for 4 days


title: RNA-seq_pt19_PIN_t1

description:
Library name: A8-101-2
Paired-end RNA-seq for PIN sample A8-101-2 from patient 19, timepoint 1

value: PIN

tag: Sex

tag: race


title: U251, H2AZ, rep1

value: Astrocytoma


title: B. SOD1G93A/Clec7a-KO_4

description:
Library name: Sample15
10x Genomics

value: SOD1G93A/Clec7a KO


title: VRC_7d_CO2_5

description: Library name: R2024.912


title: STS26T-AZA-1

description: Library name: UMGC-Lar-170-STS26T-AZA-1

value: tumor

value: MPNST


title: A549, H2AZ, rep1

value: Lung adenocarcinoma


title: B. SOD1G93A/Clec7a-KO_3

description:
Library name: Sample13
10x Genomics


title: adult_B rep8

description: Library name: sample12

value: Testis


title: ST88-14-DMSO-2

description: Library name: UMGC-Lar-170-ST88-14-DMSO-2

value: treated with DMSO for 4 days


title: VRC_7d_CO2_4

description: Library name: R2024.911


title: B. SOD1G93A/Clec7a-KO_2

description:
Library name: Sample3
10x Genomics

value: All cell types

value: spinal cord


title: 786-O, H2AZ, rep1


title: ST88-14-DMSO-1

description: Library name: UMGC-Lar-170-ST88-14-DMSO-1


title: B. SOD1G93A/Clec7a-KO_1

description:
Library name: Sample2
10x Genomics


title: TY-DOX-DMSO-2

description: Library name: UMGC-Lar-170-TY-DOX-DMSO-2

value: treated with DOX for 7 days; DMSO for 4 days


title: VRC_7d_CO2_3

description: Library name: R2024.910


title: VRC_7d_CO2_2

description: Library name: R2024.909


title: NCI-H460, H2AZ, rep1

value: Lung large cell carcinoma


title: SNB19, H2AZ, rep1


title: ST88-14-DAC-2

description: Library name: UMGC-Lar-170-ST88-14-DAC-2

value: treated with DAC for 4 days


title: VRC_7d_CO2_1

description: Library name: R2024.908


title: A. SOD1G93A_3

description:
Library name: Sample6
10x Genomics


title: ST88-14-DAC-1

description: Library name: UMGC-Lar-170-ST88-14-DAC-1


title: HepG2 input replicate 3

city: Philadelphia

first: Matthew

middle: C

last: Pahl

state: PA

address: 3615 Civic Center Blvd

department: Center for Spatial and Functional Genomics

institute: Children's Hospital of Philadelphia

data_processing:
fastq files were processed using the Encode pipeline (https://www.encodeproject.org/chip-seq/histone/), with reads aligned to hg19 and peaks called with macs2
Assembly: hg19
Supplementary files format and content: narrowPeak_files

source_name: Liver

growth_protocol: HepG2 Cells ([HEPG2 (ATCC, HB8065TM)) were maintained in Eagle's Minimum Essential Medium (ATCC, 30 2003) supplemented with 10% heat inactivated fetal bovine serum (Gibco,16000044) and 1X Antibiotic-Antimycotic (Gibco, 15240096) at standard tissue culture conditions; 37C and 5% CO2.

extract_protocol:
Fixed cells were subjected to sonication following the NEXSON procedure. Briefly, nuclei were isolated by sonication using a Q Sonica Sonicator with settings of 15 seconds On, 30 seconds Off for 8 cycles at 20% power (2 minutes total sonication time).  Nuclei were centrifuged at 1250 RCF and resuspended in CHIP Buffer.  DNA was sheared using sonicator settings of 30 seconds On, 30 seconds Off at 80% power for 4 cycles of 5 minutes each (20min. total sonication time). Samples were centrifuged at 18,000 RCF and supernatant was collected and tested on an agarose gel to check for size, phenol extracted, precipitated, and resuspended.  ChIP was carried out with 300ng sheared DNA and the Chip-IT High Sensitivity Kit (Active Motif, 53040) according to kit instructions with the following antibodies from Active Motif: H3K27ac (39685), H3K4me1 (39297), H3K4me3 (61379), and anti-mouse IgG (53017).
Libraries were generated from the resulting material using the ThruPLEX Tag-seq Library Kit (Takara, 030520), PCR amplified for 10-16 cycles then purified and size selected using AMPure XP Beads.  Completed libraries were checked for quality and quantity on a BioAnalyzer 2100 and Qubit respectively.  Libraries passing QC were pooled at 1nM and sequenced on a Novaseq 6000 using an S1 flow cell (51bp paired end read length, dual indexed).

value: Liver

value: Hepatocellular carcinoma

value: anti-mouse IgG (Active Motif:53017)


title: TY-DOX-DMSO-1

description: Library name: UMGC-Lar-170-TY-DOX-DMSO-1


title: VRC_7d_Control_6

description: Library name: R2024.907

value: VRC


title: A. SOD1G93A_2

description:
Library name: Sample5
10x Genomics


title: ST88-14-AZA-2

description: Library name: UMGC-Lar-170-ST88-14-AZA-2

value: treated with AZA for 4 days


title: HepG2 input replicate 2


title: HepG2 input replicate 1


title: A. SOD1G93A_1

description:
Library name: Sample1
10x Genomics


title: ST88-14-AZA-1

description: Library name: UMGC-Lar-170-ST88-14-AZA-1


title: VRC_7d_Control_4

description: Library name: R2024.905


title: anti-CD47, 12 weeks treatment, 12 weeks high-fat diet

city: Heidelberg

first: Murat

last: Kirtay

address: Im Neuenheimer Feld 410

department: Department of Cardiology, Angiology, and Pneumology

institute: Heidelberg University Hospital

description:
Library name: anti-CD47_prevention
10x Genomics

data_processing:
Mouse single-cell RNA-sequencing data were preprocessed using 10x Cell Ranger cloud software (Cell Ranger v9.0.0), which included data demultiplexing, barcode processing, alignment, and single-cell 3′ gene counting.
Assembly: mouse mm10
Supplementary files format and content: tsv and matrix files

source_name: aorta

extract_protocol:
The isolated aortas were digested for 40 min at 37 °C in RPMI medium containing 450 U/ml Collagenase I, 125 U/ml Collagenase XI, and 60 U/ml Hyaluronidase. The digested tissue was meshed through a 70-µm cell strainer to obtain a single-cell suspension. The cells were resuspended in FACS Buffer (2 % FCS, 2 mM EDTA in PBS) and subsequently stained with SYTOX Green viability dye (L/D), TER119-BV510, and CD45-PerCP Cy5.5 for 30 min at 4 °C. Viable SYTOX Green- TER119- aortic CD45+ cells were sorted using a 100-µm nozzle by excluding CD45-BV510+ circulating leukocytes.
Samples were loaded into the 10x Chromium system to generate single-cell barcoded droplets using the Single Cell 3’ Solution v3.4 Reagent Kit (10x Genomics) following the manufacturer’s specifications. Generated libraries were sequenced using a NextSeq 2000 Sequencing System in paired-end mode to reach approximately 200,000 reads per single cell.

value: aorta

value: male

value: CD45+ leukocytes

tag: genotype

value: Ldlr-/-

value: 12 weeks anti-CD47, 12 weeks high-fat diet


title: VRC_7d_Control_5

description: Library name: R2024.906


title: HepG2 H3K4me3 replicate 3

value: H3K4me3 (Active Motif:61379)


title: JH-2-002-CL-DMSO-2

description: Library name: UMGC-Lar-170-JH-2-002-CL-DMSO-2

value: tumor

value: MPNST

value: treated with DMSO for 4 days


title: IgG, 12 weeks treatment, 12 weeks high-fat diet

description:
Library name: IgG_prevention
10x Genomics

value: 12 weeks IgG, 12 weeks high-fat diet


title: VRC_7d_Control_3

description: Library name: R2024.904


title: HepG2 H3K4me3 replicate 2


title: JH-2-002-CL-DMSO-1

description: Library name: UMGC-Lar-170-JH-2-002-CL-DMSO-1


title: SK-MEL-28, H2AZ, rep1

first: Changbin

last: Sun

address: Dapeng

institute: Chinese Academy of Agricultural Sciences

value: Cutaneous melanoma

value: H2A.Z (Abcam:#ab4174)


title: anti-CD47, 6 weeks treatment, 14 weeks high-fat diet

description:
Library name: anti-CD47_intervention
10x Genomics

value: 6 weeks anti-CD47, 14 weeks high-fat diet


title: VRC_7d_Control_2

description: Library name: R2024.903


title: JH-2-002-CL-DAC-2

description: Library name: UMGC-Lar-170-JH-2-002-CL-DAC-2

value: treated with DAC for 4 days


title: MDA-MB-468, H2AZ, rep1

value: Breast adenocarcinoma


title: HepG2 H3K4me3 replicate 1

value: Liver

value: Hepatocellular carcinoma


title: IgG, 6 weeks treatment, 14 weeks high-fat diet

description:
Library name: IgG_intervention
10x Genomics

value: aorta

value: 6 weeks IgG, 14 weeks high-fat diet


title: JH-2-002-CL-DAC-1

description: Library name: UMGC-Lar-170-JH-2-002-CL-DAC-1


title: HepG2 H3K4me1 replicate 3

value: H3K4me1 (Active Motif:39297)


title: Lung,UninvolvedIBA6

city: Mountain View

first: Lester

last: Kobzik

state: California

address: 320 Logue Avenue

institute: Cellecta, Inc

description: Library name: UninvolvedIBA6

data_processing:
To obtain raw counts, raw sequencing files were converted to .DCC files via Nanostring geomxngspipeline function. The DCC files were uploaded to the DSP instrument and automatically associated with individual scans.  Sequencing and Probe QC was performed using default parameters.
Assembly: GRCm38.p6
Supplementary files format and content: RawCountTablePaucibacillaryvsMultibacillary.txt: Count table for paucibacillary and multibacillary lesions with gene names and probe details
Library strategy: Spatial Transcriptomics

source_name: Lung

extract_protocol:
Formalin-fixed paraffin-embedded lung sections were prepared for spatial analysis.
Spatial transcriptomics libraries were prepared using samples corresponding to ROI (regions of interest) of paucibacillary and multibacillary lesions as per manufacturer’s instructions.

treatment_protocol: Mice were injected into their hocks with 10E6 M. Tb Erdman strain, followed by euthanasia 14 weeks later with harvesting and fixation of lungs.

value: Lung

value: Tuberculosis infection

tag: sample group

value: UninvolvedIBA


title: NTS_7d_CO2_6

description: Library name: R2024.901

source_name: NTS

value: NTS


title: VRC_7d_Control_1

description: Library name: R2024.902

value: VRC