title: HEK293T, non-targeting control, biol rep 3

city: Melbourne

first: Honglin

last: Chen

state: VIC

address: 305 Grattan St, North Melbourne VIC

country: Australia

institute: PeterMacCallum Cancer Centre

description:
Library name: NT3
Matrix column: NT3

data_processing:
cutadapt 4.4: paired-end reads processed with quality trimming (quality-cutoff 20) and minimum-length filtering (minimum-length 20, pair-filter any); error rate 0.1, times 1, overlap 3. No adapter sequence specified (quality and length trimming only).
STAR 2.7.4a: trimmed reads aligned to hg19 (GRCh37) with --quantMode GeneCounts, --sjdbGTFfile gencode.v19.annotation.gtf, --sjdbOverhang 36
Gene-level counts taken from STAR ReadsPerGene.out.tab, Counts_secondStrand column (reverse-stranded library)
Per-sample count columns joined on gene ID into a single matrix; STAR summary rows (N_unmapped, N_multimapping, N_noFeature, N_ambiguous) removed
Assembly: hg19 (GRCh37) + mCherry and RfxCas13d
Supplementary files format and content: Tab-delimited text (transcriptomic_count_matrix.tsv); rows = GENCODE v19 gene IDs, columns = raw read counts per sample (NT1-3, TAR1-3)

growth_protocol: 37 degree and 10% CO2 in DMEM media with 10% heat-inactivated fetal bovine serum (Thermo Fisher, 10100147), 100 mg/mL Penicillin/-Streptomycin (Thermo Fisher, 151401220), and 2 mM GlutaMAX (Thermo Fisher, A1286001).

extract_protocol:
Total RNA was isolated by standard Trizol-chloroform extraction according to manufacturer’s instruction (Thermo Fisher, 15596026), followed by DNase treatment with RQ1 RNase-Free DNase according to manufacturer’s instruction (Promega, M6101). RNA integrity was analysed by Agilent 2200 Tapestation (Agilent, G2964AA) with RNA ScreenTape (Agilent, 5067- 5576) according to the manufacturer’s instructions
Poly(A)+ mRNA was enriched from total RNA, then chemically fragmented. First-strand cDNA was synthesised by random priming, followed by second-strand synthesis incorporating dUTP for strand marking. Libraries were prepared using the Illumina Stranded mRNA Prep protocol with adapter ligation and sample indexing, then amplified by PCR with a uracil-sensitive polymerase (yielding reverse-stranded libraries). Library preparation and sequencing were performed by the Australian Genome Research Facility (AGRF), Melbourne.

treatment_protocol: RfxCas13d paired with either non-targeting crRNA (negative control) or mCherry-targeting crRNA

value: non-targeting


title: HCT116, treated with 100 nM RTX, replicate 2, long RNA

status: Public on Jul 08 2026

type: SRA

city: Budapest

first: Angela

last: Bekesi

address: Műegyetem rakpart 3.

department: Department of Applied Biotechnology and Food Science

country: Hungary

institute: Budapest University of Technology and Economics, Faculty of Chemical Technology and Biotechnology

description:
Library name: RTX_HCT116_rep2.lRNA
RTX_lRNA_2

library_source: transcriptomic

data_processing:
For lRNA-seq data, quality was checked using fastQC, residual rRNA-related reads were removed in silico, then polyG, adapter, and low-quality sequences were trimmed using the fastp tool. For sRNA-seq data, quality was checked using fastQC, and adapter and low-quality sequences were trimmed using the Trimmomatic tool.
Clean reads were aligned to the human reference genome GRCh38  using HiSAT2, or STAR aligners for lRNA and sRNA data, respectively.
Aligned data were filtered for the core chromosomes.
For lRNA-seq data, treated samples were compared to the corresponding non-treated ones using the Cufflinks package (cuffnorm and cuffdiff), and the two drug treatments were also directly compared. For sRNA-seq data, FeatureCounts was used to count reads on annotated mature miRNA genes (miRBase) as well as on sRNA, snRNA, and snoRNA genes as defined by Gencode v34, and samples were compared using the deseq2 R package.
Read coverage tracks were calculated for the forward and reverse strands, respectively, using bamCoverage of the deeptools package.
Assembly: GRCh38
Supplementary files format and content: The *forward.filtered.bw and *reverse.filtered.bw files contain the strand-selective coverage tracks in bigwig format.
Supplementary files format and content: The *cuffdiff.gene_exp.tsv files  (9) are tab-separated text files, which contain the results of differential expression analysis (cuffdiff output for lRNAs).
Supplementary files format and content: The lRNA_genes_cuffnorm.FPKM_table.annot.tsv file is a tab-separated text file, which contains all the FPKM values and the annotation details of the lRNAs, calculated using cuffnorm.
Supplementary files format and content: The ALL_sRNA_counts.tsv file is a tab-separated text file, which contains all the count values and several identifiers of the sRNAs and miRNAs. Counts were calculated with featureCounts.
Supplementary files format and content: The *deseq2.tsv files (9) are tab-separated text files, which contain the results of differential expression analysis for sRNAs and miRNAs calculated by deseq2.

molecule: total RNA

organism: Homo sapiens

growth_protocol: Cells were maintained in McCoy’s 5A medium supplemented with 10% FBS and 1% PenStrep.

extract_protocol:
Total RNA was isolated using TRIzol reagent (Invitrogen) according to the manufacturer's protocol. RNA quality was assessed by agarose gel electrophoresis, and concentration was measured using a NanoDrop 2000C UV-Vis spectrophotometer (Thermo Fisher Scientific).
Stranded RNA sequencing libraries for short RNAs (<200 nt) and long RNAs (>200 nt) were prepared separately. Library preparations, including rRNA depletion and quality control, as well as the sequencing, were performed by Novogene Co., Ltd. (China) as a whole-transcriptome sequencing service. The small RNA library was sequenced using the Illumina 50 pb single-end protocol, which yielded 20 M reads. The long RNA library was sequenced on a Novaseq 6000 platform using Illumina 150 paired-end protocol, which resulted in approximately 150 M reads for each sample.

treatment_protocol: Cells were cultured in 6-well plates, treated with 100 nM RTX or 20 µM 5FdUR for 48 hours.

tag: cell line

tag: cell type

value: colon adenocarcinoma

tag: genotype

value: MMR deficient

tag: treatment

value: 100 nM RTX


title: HCT116, treated with 100 nM RTX, replicate 1, long RNA

description:
Library name: RTX_HCT116_rep1.lRNA
RTX_lRNA_1


title: MDS388

city: Taipei

first: Yu-Hung

last: Wang

address: N0 7, Chung-Shan South Rd

country: Taiwan

institute: National Taiwan University Hospital

description: MDS

data_processing:
Reads were then aligned to the human genome (GRCh38) and gene annotated with its corresponding GTF files (GENCODE GRCh38) using STAR version 2.4.2a with the settings –outFilterMultimapNmax 20 –outFilterType BySJout –alignSJoverhangMin 8 –quantMode GeneCounts.
Assembly: GRCh38
Supplementary files format and content: Read counts in .csv format

source_name: human BM Mononuclear cells

extract_protocol:
RNA was extracted from fresh BM samples of patients and healthy donors and sent for RNA sequencing.
The purified RNA was used to prepare the sequencing library using the TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA, USA) following the manufacturer’s recommendations. Briefly, mRNA was purified from total RNA (1 μg) using oligo(dT)-coupled magnetic beads and fragmented into small pieces at elevated temperatures.
First-strand cDNA was synthesized using reverse transcriptase and random primers. After the generation of double-strand cDNA and adenylation on the 3’ ends of DNA fragments, the adaptors were ligated and purified with the AMPure XP system (Beckman Coulter, Beverly, USA). The quality of the libraries was assessed using an Agilent Bioanalyzer 2100 system and a real-time polymerase chain reaction (PCR) system. The qualified libraries were then sequenced on an Illumina NovaSeq 6000 platform with 150 bp paired-end reads generated by Genomics, BioSci & Tech Co., New Taipei City, Taiwan. The bases with low quality and sequences from adapters in the raw data were removed using Cutadapt (v 3.0).

value: human BM Mononuclear cells


title: MDS386

description: MDS


title: HCT116, non-treated, replicate 2, long RNA

description:
Library name: NT_HCT116_rep2.lRNA
NT_lRNA_2


title: MDS381

description: MDS


title: HCT116, non-treated, replicate 1, longRNA

description:
Library name: NT_HCT116_rep1.lRNA
NT_lRNA_1


title: C140_2

status: Public on Jul 09 2026

city: Nantong,Jiangsu,China

first: Xiaorong

last: Zhou

state: Jiangsu province

address: 19 Qixiu Road

country: China

institute: Nantong University

description:
Library name: Sample 11
Column name in gene_fpkm.txt: C140_2

data_processing:
Differential expression analysis was performed using the DESeq2 R package, and the genes with adjusted p values < 0.05 and log fold change (logFC) > 1 or < -1 were designated as differentially expressed genes (DEGs).
Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses of DEGs were performed using the clusterProfiler package (version 4.8.3) in R.
Enriched GO terms and KEGG pathways were filtered with adjusted P-value < 0.05 and q-value < 0.5. Gene Set Enrichment Analysis (GSEA) was performed using the clusterProfiler package
Assembly: mm10
Supplementary files format and content: csv

organism: Mus musculus

source_name: tumor

growth_protocol: All animal-related procedures were performed following the ethical guidelines of the Animal Experimentation Institution of Nantong University, and all animal experiments were approved by the Ethics Committee.

extract_protocol:
Tumors were collected three days after the third cycle of CTX treatment, washed with PBS, and submitted for RNA isolation, quality check, and subsequent RNA sequencing by the Novogene (Beijing, China) on the Illumina platform.
Tumors were collected three days after the third cycle of CTX treatment, washed with PBS, and submitted for RNA isolation, quality check, and subsequent RNA sequencing by the Novogene (Beijing, China) on the Illumina platform.

treatment_protocol: In the subcutaneous tumor formation experiment, 4T1 cells resuspended in 100 μL PBS buffer were inoculated into the subcutaneous mammary gland area of each mice (1×10⁶ cells). Nine days later, when the tumor volume reached approximately 100 mm³, the mice were randomly divided into three groups according to the experimental grouping designing. The control group was intraperitoneally injected with 100 μL PBS, and the experimental groups were intraperitoneally injected with 100 or 140 mg/kg CTX in 100 μL PBS, respectively. All groups were injected once every 6 days. On the third day after the third treatment cycle, the mice were euthanized, and the tumor tissues were harvested for bulk RNA sequencing and scRNA-seq.

tag: tissue

value: tumor

value: TNBC cell

value: 140mg/kg CTX


title: MDS380

description: MDS


title: HCT116_MMR_UGI, treated with 20 µM 5FdUR, replicate 2,short RNA

description:
Library name: 5FdUR_UGI_HCT116MMR_rep2.sRNA
FdUR_UGIMMR_sRNA_2

value: MMR restored by an additional copy of healthy chr3, UGI transgene:uracil-DNA glycosylase inhibitor

value: 20 µM 5FdUR


title: HCT116_MMR_UGI, treated with 20 µM 5FdUR, replicate 1, short RNA

description:
Library name: 5FdUR_UGI_HCT116MMR_rep1.sRNA
FdUR_UGIMMR_sRNA_1


title: MDS374

description: MDS


title: HCT116_MMR_UGI, treated with 100 nM RTX, replicate 2, short RNA

description:
Library name: RTX_UGI_HCT116MMR_rep2.sRNA
RTX_UGIMMR_sRNA_2


title: MDS376

description: MDS


title: HCT116_MMR_UGI, treated with 100 nM RTX, replicate 1, short RNA

description:
Library name: RTX_UGI_HCT116MMR_rep1.sRNA
RTX_UGIMMR_sRNA_1


title: MDS373

description: MDS


title: HCT116_MMR_UGI, non-treated, replicate 2, short RNA

description:
Library name: NT_UGI_HCT116MMR_rep2.sRNA
NT_UGIMMR_sRNA_2


title: MDS366

description: MDS


title: MDS365

description: MDS


title: HCT116_MMR_UGI, non-treated, replicate 1, short RNA

description:
Library name: NT_UGI_HCT116MMR_rep1.sRNA
NT_UGIMMR_sRNA_1


title: MDS354

description: MDS


title: HCT116_MMR_UGI, treated with 20 µM 5FdUR, replicate 1, long RNA

description:
Library name: 5FdUR_UGI_HCT116MMR_rep1.lRNA
5FdUR_UGIMMR_lRNA_1


title: HCT116_MMR_UGI, treated with 20 µM 5FdUR, replicate 2, long RNA

description:
Library name: 5FdUR_UGI_HCT116MMR_rep2.lRNA
5FdUR_UGIMMR_lRNA_2


title: MDS357

description: MDS


title: C100_4

description:
Library name: Sample 8
Column name in gene_fpkm.txt: C100_4

value: 100mg/kg CTX


title: MDS348

description: MDS


title: HCT116_MMR_UGI, treated with 100 nM RTX, replicate 2, long RNA

description:
Library name: RTX_UGI_HCT116MMR_rep2.lRNA
RTX_UGIMMR_lRNA_2


title: MDS337

description: MDS


title: HCT116_MMR_UGI, treated with 100 nM RTX, replicate 1, long RNA

description:
Library name: RTX_UGI_HCT116MMR_rep1.lRNA
RTX_UGIMMR_lRNA_1


title: MDS336

description: MDS


title: MDS327

description: MDS


title: HCT116_MMR_UGI, non-treated, replicate 2, long RNA

description:
Library name: NT_UGI_HCT116MMR_rep2.lRNA
NT_UGIMMR_lRNA_2


title: HCT116_MMR_UGI, non-treated, replicate 1, longRNA

description:
Library name: NT_UGI_HCT116MMR_rep1.lRNA
NT_UGIMMR_lRNA_1


title: MDS313

description: MDS


title: MDS3220

description: MDS


title: HCT116_UGI, treated with 20 µM 5FdUR, replicate 1, short RNA

description:
Library name: 5FdUR_UGI_HCT116_rep1.sRNA
FdUR_UGI_sRNA_1

value: MMR deficient, UGI transgene:uracil-DNA glycosylase inhibitor


title: HCT116_UGI, treated with 20 µM 5FdUR, replicate 2,short RNA

description:
Library name: 5FdUR_UGI_HCT116_rep2.sRNA
FdUR_UGI_sRNA_2


title: MDS307

description: MDS


title: MDS305

description: MDS


title: MDS303

description: MDS


title: HCT116_UGI, treated with 100 nM RTX, replicate 1, short RNA

description:
Library name: RTX_UGI_HCT116_rep1.sRNA
RTX_UGI_sRNA_1


title: HCT116_UGI, treated with 100 nM RTX, replicate 2, short RNA

description:
Library name: RTX_UGI_HCT116_rep2.sRNA
RTX_UGI_sRNA_2


title: HCT116_UGI, non-treated, replicate 2, short RNA

description:
Library name: NT_UGI_HCT116_rep2.sRNA
NT_UGI_sRNA_2


title: MDS267

description: MDS


title: MDS261

description: MDS


title: HCT116_UGI, non-treated, replicate 1, short RNA

description:
Library name: NT_UGI_HCT116_rep1.sRNA
NT_UGI_sRNA_1


title: HCT116_UGI, treated with 20 µM 5FdUR, replicate 2, long RNA

description:
Library name: 5FdUR_UGI_HCT116_rep2.lRNA
5FdUR_UGI_lRNA_2


title: HCT116_UGI, treated with 20 µM 5FdUR, replicate 1, long RNA

description:
Library name: 5FdUR_UGI_HCT116_rep1.lRNA
5FdUR_UGI_lRNA_1


title: HCT116_UGI, treated with 100 nM RTX, replicate 2, long RNA

description:
Library name: RTX_UGI_HCT116_rep2.lRNA
RTX_UGI_lRNA_2


title: MDS1912

description: MDS


title: MDS2225

description: MDS


title: HCT116_UGI, treated with 100 nM RTX, replicate 1, long RNA

description:
Library name: RTX_UGI_HCT116_rep1.lRNA
RTX_UGI_lRNA_1


title: MDS1904

description: MDS


title: HCT116_UGI, non-treated, replicate 2, long RNA

description:
Library name: NT_UGI_HCT116_rep2.lRNA
NT_UGI_lRNA_2


title: MDS255

description: MDS


title: MDS1903

description: MDS


title: HCT116_UGI, non-treated, replicate 1, longRNA

description:
Library name: NT_UGI_HCT116_rep1.lRNA
NT_UGI_lRNA_1


title: MDS1902

description: MDS


title: Co_Tp_48_14K

city: San Diego

first: Yasmin

last: Vasquez

state: CA

address: 3612 Mount Ariane Dr

country: USA

institute: Lassen Therapeutics

description: Library name: Sample 96

data_processing:
Raw image data from Illumina sequencing were converted to FASTQ format using CASAVA base calling. Low-quality reads were filtered out by removing reads containing adapter contamination, reads with >10% undetermined bases (N), and reads with >50% low-quality bases (Q < 5).
Clean reads were aligned to the Homo sapiens (hg38) reference genome using HISAT2, a graph-based alignment algorithm. Gene expression quantification was performed using FPKM (Fragments Per Kilobase of transcript per Million mapped reads).
Assembly: Homo sapiens (hg38)
Supplementary files format and content: FASTQ (.fq), Raw sequencing reads (four-line format: identifier, sequence, +, quality)
Supplementary files format and content: FPKM matrix, Normalized expression values (FPKM per gene per sample)

source_name: Orbital adipose/connective tissue

growth_protocol: Following collection, tissues were minced into 1–2 mm pieces, placed in T75 culture flasks containing 15 mL of growth media high glucose Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 20% fetal bovine serum and 1% penicillin/ streptomycin, and incubated at 37°C with 5% CO2. Culture medium was renewed every 3–4 days and tissue was maintained in culture for 2-3 weeks to allow the orbital fibroblasts to migrate out of the tissue and adhere.  Floating debris was cleared, and attached cells were expanded and used up to 6 passages.

extract_protocol:
RNA was isolated from orbital fibroblast cells using the RNeasy Plus Mini kit (Cat#74134, Qiagen) according to manufacturer instructions.
Messenger RNA (mRNA) was purified from total RNA using poly-T oligo–attached magnetic beads to isolate polyadenylated transcripts. The purified mRNA was then fragmented into short fragments, which served as templates for first-strand cDNA synthesis using random hexamer primers. The second-strand cDNA was synthesized using dTTP, generating non-directional libraries. Following cDNA synthesis, fragments were subjected to end repair, A-tailing, and adapter ligation. Ligated products were then size-selected, PCR-amplified, and purified to obtain the final sequencing libraries. Library quality and quantity were assessed using a Qubit fluorometer for concentration measurement, real-time PCR for accurate quantification, and a Bioanalyzer for insert size distribution. Final libraries were pooled according to effective concentration and sequenced on an Illumina platform to generate paired-end reads.

treatment_protocol: Orbital fibroblasts were seeded in 6-well plates at a density of 1 x 10^5 cells/well (2 mL volume) in growth media and incubated at 37°C with 5% CO2. After 24 hours media was replaced with DMEM supplemented with penicillin, streptomycin and 1% FBS for an additional 24 hours (starvation media).  Serum-starved cells were pretreated with LASN01 antibody at 1 µg/mL or 10 µg/mL Teprotumumab in starvation media for 1hr. Cells were subsequently treated with agonists IL-11 (10ng/mL), or a combination of IL-11 and IGF-1 (100ng/mL) for 6 or 48hr.

value: Orbital adipose/connective tissue

value: primary fibroblast

value: thyroid eye disease


title: MDS1901

description: MDS


title: MKs derived from UCB

city: Hangzhou

first: Yanmin

last: He

state: Zhejiang

address: 789 Jianye Road

department: Institute of Transfusion medicine

institute: Blood center of Zhejiang Province

description:
Library name: Sample 1
10×Genomics

library_source: transcriptomic single cell

data_processing:
The primary analytical pipeline for the scRNA-seq analysis followed the recommended protocols from 10× Genomics. The R package Seurat v5.0.0 was utilized for downstream analysis.
Assembly: Homo
Supplementary files format and content: The processed data files are in the RDS format, which is a standard R data file used to save R objects. This file contains a seurat object, which has been processed for single-cell RNA-seq analysis.

source_name: Megakaryocytes

extract_protocol:
The cultured cells were directly subjected to the 10×Genomics Chromium platform to produce single-cell gel beads in emulsion.
The library construction using the Chromium Single Cell 3′ Reagent Kit v3 (10×Genomics), according to the manufacturer's instructions.

value: Megakaryocytes

value: Megakaryocytes differentiation

tag: time

value: Day 14


title: Co_L1_48_14K

description: Library name: Sample 95


title: MDS1900

description: MDS


title: Co_48_14K

description: Library name: Sample 94


title: MDS1899

description: MDS


title: IL_L1_48_14K

description: Library name: Sample 93


title: MDS1898

description: MDS


title: MDS1897

description: MDS


title: IL_48_14K

description: Library name: Sample 92


title: MDS1896

description: MDS


title: MDS1895

description: MDS


title: Veh_48_14K

description: Library name: Sample 91


title: MDS1894

description: MDS


title: Co_Tp_48_12K

description: Library name: Sample 90


title: Co_L1_48_12K

description: Library name: Sample 89


title: MDS1891

description: MDS


title: MDS1893

description: MDS


title: MDS1881

description: MDS


title: IL_L1_48_12K

description: Library name: Sample 87


title: BMDMs, rIL-18_biol rep 1

city: Wuhan

first: Jin

address: 1095# Jiefang Ave.

institute: Huazhong University of Science and Technology

description: Library name: Sample 4

data_processing:
2.1 Data quality control The raw sequencing reads contain low-quality and adapter-contaminated reads. Therefore, we performed quality control using the default parameters of fastp to filter out unqualified reads. The resulting clean reads were used for further analysis. The filtering criteria for reads are as follows: (1) Trim reads containing adapter sequences. (2) If a single-end read contains more than 5 bases of "N," remove the corresponding paired-end reads. (3) If a single-end read contains more than 40% low-quality bases (Q ≤ 15), remove the corresponding paired-end reads.
2.2 Sequence alignment to the reference genome Clean Reads were quickly and accurately compared with the reference genome using HISAT2 software to obtain information on the positioning of Reads on the reference genome.
2.3 New transcript prediction Transcripts of each sample were assembled using StringTie software (http://ccb.jhu.edu/software/stringtie/index.shtml), and then the transcripts of all samples were merged into a set of transcript sets.
2.4 Gene expression level quantification Featurecounts were used to calculate the number of reads mapped to each gene. The FPKM of each gene is then calculated based on the length of the gene and the number of reads mapped to that gene is calculated.
2.5 Differential expression analysis For samples with biological replicates, differential expression analysis between the two comparative combinations was performed using DESeq2 software. The method of Benjamini and Hochberg was used to adjust the resulting P-values to control for false discovery rates. Genes found to have adjusted P-values <0.05 by DESeq2 were assigned as differentially expressed. For the absence of biological replicates using edgeR, read counts were adjusted by a scaling normalization factor through the edgeR program package for each sequencing library prior to performing differential gene expression analysis. Differential expression analysis for both conditions was performed using the edgeR package (3.22.5). P-values were adjusted using the Benjamini& Hochberg method. The corrected P values as well as |log2foldchange| were used as the threshold for significant differential expression.
Assembly: Mus musculus.GRCm39.111
Supplementary files format and content: csv file include FPKM values for each sample

source_name: Bone marrow

extract_protocol:
1.1 RNA extraction and quality inspection The total RNA from tissues or cells was extracted using the RNAprep Pure Plant Plus Kit (TIANGEN). The RNA samples then underwent stringent quality control, primarily through the Agilent 2100 Bioanalyzer, which precisely detects RNA integrity. Specific experimental steps: 1. Homogenization: Quickly grind 100 mg of plant leaves or fruit flesh into powder in liquid nitrogen. Add 500 μl of lysis buffer and vortex vigorously to mix thoroughly. 2. Centrifuge at 12,000 rpm (~13,400×g) for 2 minutes. 3. Transfer the supernatant to the CS filter column and centrifuge at 12,000 rpm for 2 minutes. Carefully transfer the supernatant from the collection tube to a new RNase-Free centrifuge tube, avoiding contact between the pipette tip and the cell debris sediment. 4. Slowly add 0.4 times the volume of the supernatant of absolute ethanol, mix well, and transfer the resulting solution along with any precipitate to the CR3 adsorption column. Centrifuge at 12,000 rpm (~13,400×g) for 15 seconds, discard the waste liquid in the collection tube, and place the CR3 adsorption column back into the collection tube. 5. Add 350 μl of protein removal solution RW1 to the CR3 adsorption column and centrifuge at 12,000 rpm for 15 seconds. Discard the waste liquid in the collection tube and place the CR3 adsorption column back into the collection tube. 6. Add 80 μl of DNase I working solution to the center of the CR3 adsorption column and incubate at room temperature for 15 minutes. 7. Add 350 μl of protein removal solution RW1 to the CR3 adsorption column and centrifuge at 12,000 rpm for 15 seconds. Discard the waste liquid and place the CR3 adsorption column back into the collection tube. 8. Add 500 μl of wash solution RW to the CR3 adsorption column and centrifuge at 12,000 rpm for 15 seconds. Discard the waste liquid and place the CR3 adsorption column back into the collection tube. 9. Repeat step 8. 10. Centrifuge at 12,000 rpm for 2 minutes. Place the CR3 adsorption column into a new RNase-Free centrifuge tube, and carefully add 50 μl of RNase-Free ddH₂O to the center of the adsorption membrane. Incubate at room temperature for 2 minutes, then centrifuge at 12,000 rpm for 1 minute to obtain the RNA solution.
1.2 Library construction After the RNA quality is confirmed, the Hieff NGS® Ultima Dual-mode RNA Library Prep Kit (Premixed version) (Yeasen) is used for transcriptome library construction, strictly following the instructions regarding recommended reagents and consumables. First, utilizing the characteristic that most eukaryotic mRNA contains a polyA tail, polyA-tailed mRNA is enriched using Oligo(dT) magnetic beads. Subsequently, the first strand of cDNA is synthesized, and immediately after the reaction, the second strand of cDNA is synthesized, followed by end repair/A-tailing. Specific MGI® adapters are ligated to the ends of the products. After adapter ligation, PCR amplification is performed to obtain the cDNA library. These steps are typical in conventional library construction. For sequencing on the DNBSEQ-T7 platform, to obtain DNA nanoballs, the double-stranded products from the cDNA library must undergo denaturation, circularization, and digestion to generate single-stranded circular cDNA, which is used to prepare DNA nanoballs.

treatment_protocol: Primary BMDMs were stimulated with rIL-18 (100 ng/mL, Sigma) for 24 h, and RNA-seq was performed on control and treated groups. Three biological replicates per group were included.

value: Bone marrow

value: Bone marrow-derived macrophages (BMDMs)

value: WT


title: MDS1879

description: MDS

value: human BM Mononuclear cells


title: MDS1878

description: MDS


title: BMDMs, Control_biol rep 3

description: Library name: Sample 3

value: PBS


title: MDS1877

description: MDS


title: MDS1868

description: MDS


title: Veh_48_12K

description: Library name: Sample 85


title: BMDMs, Control_biol rep 2

description: Library name: Sample 2


title: MDS1865

description: MDS


title: MDS1866

description: MDS


title: BMDMs, Control_biol rep 1

description: Library name: Sample 1


title: Co_L1_48_11K

description: Library name: Sample 83


title: MDS1864

description: MDS


title: MDS1861

description: MDS


title: CMR 5 Month AAV-TBG-Cre Mouse 2

city: Philadelphia

first: Abhinav

last: Illendula

address: 333 Cottman Avenue

institute: Fox Chase Cancer Center

description:
Library name: CMR_5_Month_Sample2
10X Genomics

data_processing:
Raw sequencing data files were processed using Cell Ranger v.8.0.1 from 10x Genomics, and reads were mapped to the GRCm39 reference genome modified to include the tdTomato sequence found in RtdT mice. All other parameters were kept as default. The resultant data was then processed using the Seurat 5.0.2 package in R.
Cells which did not meet QC criteria (n_feature count between 400-7000 and mitochondrial genes <20% for the normal liver samples and 950-7000, <20% for the CLD samples) were filtered out prior to downstream analysis.
Assembly: GRCm39
Supplementary files format and content: Matrix h5

source_name: Liver

extract_protocol:
The abdominal  vena cava was cannulated with the thoracic vena cava clamped. The portal vein was snipped and 20 mL HBSS -/- buffer was perfused. Then, HBSS +/+ with 4 mg/mL Liberase was perfused until the liver was digested to acheive a single-cell suspension. Cells were washed with HBSS -/- and incubated with DAPI. Cells were sorted on FACAria II into DMEM supplemented with 10% FBS.
Cell partitioning into Gel Beads-in-emulsions (GEMs) and barcoding was carried out using the Chromium Controller, following the manufacturer’s protocol. Barcoded cDNA libraries were prepared from GEMs for each mouse, and sequencing was performed on an Illumina HiSeq X platform (PE150).

treatment_protocol: AAV8-TBG-Cre tail-vein injection

value: Liver

value: AAV8:TBG>Cre 5 month


title: MDS1860

description: MDS


title: Co_48_11K

description: Library name: Sample 82


title: MDS1859

description: MDS


title: CMR 5 Month AAV-TBG-Cre Mouse 1

description:
Library name: CMR_5_Month_Sample1
10X Genomics


title: MDS1858

description: MDS


title: CMR 3 Month AAV-TBG-Cre Mouse 2

description:
Library name: CMR_3_Month_Sample2
10X Genomics

value: AAV8:TBG>Cre 3 month


title: IL_L1_48_11K

description: Library name: Sample 81


title: MDS1857

description: MDS


title: MDS1856

description: MDS


title: Veh_48_11K

description: Library name: Sample 79


title: MDS1854

description: MDS


title: MDS1853

description: MDS


title: Co_Tp_48_8K

description: Library name: Sample 78


title: MDS1851

description: MDS


title: CR 3 Month AAV-TBG-Cre Mouse 1

description:
Library name: CR_3_Month_Sample1
10X Genomics


title: MDS1849

description: MDS


title: MDS1850

description: MDS


title: CR 1 Month AAV-TBG-Cre Mouse 3

description:
Library name: CR_1_Month_Sample3
10X Genomics

value: AAV8:TBG>Cre 1 month


title: MDS1848

description: MDS


title: Co_48_8K

description: Library name: Sample 76


title: CR 1 Month AAV-TBG-Cre Mouse 2

description:
Library name: CR_1_Month_Sample2
10X Genomics


title: MDS1829

description: MDS


title: MDS1825

description: MDS


title: IL_L1_48_8K

description: Library name: Sample 75


title: CR 1 Month AAV-TBG-Cre Mouse 1

description:
Library name: CR_1_Month_Sample1
10X Genomics


title: MDS1822

description: MDS


title: IL_48_8K

description: Library name: Sample 74


title: Mouse WT DIV7 cortical neuron replicate 3

city: Ann Arbor

first: Shigeki

last: Iwase

state: MI

address: 1241 E. Catherine St., 5815 Medical Science II

department: Department of Human Genetics

institute: University of Michigan Medical School

description:
Library name: DIV7NN_WT_empty2
Wild-type mouse DIV7 cortical neuron RNA-seq used as a reference transcriptome for Figure 7A PCA analysis.

data_processing:
Raw sequencing reads were demultiplexed to generate FASTQ files.
Adapter sequences and low-quality bases were trimmed from raw reads using Cutadapt.
Trimmed reads were aligned to the mouse reference genome using STAR.
Gene-level expression estimates were generated using RSEM.
Mouse ESC and DIV7 cortical neuron expression data were integrated with published Kasper et al. mouse ESC-derived NPC/neuron RNA-seq data and analyzed by principal component analysis to evaluate developmental transcriptome progression.
Assembly: Mouse reference genome GRCm39 / mm39 with Ensembl gene annotation.
Supplementary files format and content: Gene-level count matrix in tab-delimited text format. Rows correspond to genes and columns correspond to mouse ESC and DIV7 cortical neuron RNA-seq samples.

molecule: polyA RNA

source_name: cerebral cortex

growth_protocol: Wild-type mouse embryonic stem cells were cultured under standard mouse ESC culture conditions. Wild-type primary cortical neuron cultures were prepared from embryonic day 16.5 mouse cortices and maintained in neuronal culture medium for 7 days in vitro. Mouse ESCs and DIV7 cortical neurons were used as developmental reference samples for comparison with published mouse Rai1-deficient ESC-derived neural progenitor and neuron RNA-seq datasets.

extract_protocol:
Cells were collected from mouse ESC cultures or DIV7 cortical neuron cultures. Total RNA was extracted using TRIzol reagent and purified using the RNeasy Mini Kit according to the manufacturer’s protocol.
Bulk mRNA-seq libraries were prepared from total RNA using oligo-dT priming to enrich polyadenylated RNA. Libraries were prepared for Illumina sequencing and sequenced using paired-end reads.

treatment_protocol: No perturbation treatment was applied to these samples. Mouse ESCs and DIV7 cortical neurons were collected as wild-type reference transcriptomes representing pluripotent and differentiated neuronal states, respectively. These samples were used to place published Kasper et al. Rai1-deficient mouse differentiation RNA-seq data into a PCA-defined ESC-to-neuron developmental trajectory.

value: cerebral cortex

value: primary cortical neuron

value: cortical neuron

tag: batch


title: MDS1819

description: MDS


title: MDS1817

description: MDS


title: MDS1816

description: MDS


title: Mouse WT DIV7 cortical neuron replicate 2

description:
Library name: DIV7NN_WT_empty1
Wild-type mouse DIV7 cortical neuron RNA-seq used as a reference transcriptome for Figure 7A PCA analysis.


title: Co_Tp_6_14K

description: Library name: Sample 72

value: Orbital adipose/connective tissue

value: primary fibroblast


title: MDS1815

description: MDS


title: Mouse WT DIV7 cortical neuron replicate 1

description:
Library name: DIV7NN_WT3
Wild-type mouse DIV7 cortical neuron RNA-seq used as a reference transcriptome for Figure 7A PCA analysis.


title: MDS1814

description: MDS


title: MDS1813

description: MDS


title: Co_L1_6_14K

description: Library name: Sample 71

value: thyroid eye disease


title: brain, 694_BG, basal ganglia

city: Madison

first: Hasan

last: Khatib

state: Wisconsin

address: 1675 Observatory Drive

department: Animal and Dairy Sciences

institute: University of Wisconsin Madison

description:
Library name: 694_BG
694_BG

data_processing:
Alignment (STAR)
Read counts (Rsubread)
Differential expression analysis (DEseq2 R package)
Annotation
Assembly: ARS-UI_Ramb_v3.0
Supplementary files format and content: read counts

organism: Ovis aries

source_name: Brain

extract_protocol:
RNA were extracted with either TRIzol reagent  (for sheep samples) or  Zymo Quick-RNA miniprep plus extraction kit (rat samples) followed by DNase I treatment before RNA sequencing.
RNA sequencing was performed for all samples using the NovaSeq X Plus platform with two 25B lanes, using V1.0 sequencing kits, and as 150 bp paired-end reads. Sheep RNA-Seq libraries were prepared with the Kapa Hyper Stranded mRNA library kit. Rat RNA-Seq libraries were prepared with the Watchmaker Stranded mRNA library kit. The libraries were pooled, quantified by qPCR, and sequenced on one 25B lane for 151 cycles from both ends of the fragments.

treatment_protocol: No specific treatment was applied.

value: Brain


title: MDS1812

description: MDS


title: Mouse WT ESC replicate 3

description:
Library name: B1_WT_0
Wild-type mouse embryonic stem cell RNA-seq used as a reference transcriptome for Figure 7A PCA analysis.

source_name: embryonic stem cell

value: embryonic stem cell

value: WT ESC

value: ESC


title: MDS1811

description: MDS


title: Veh_48_8K

description: Library name: Sample 73


title: Co_6_14K

description: Library name: Sample 70


title: MDS1810

description: MDS


title: Mouse WT ESC replicate 2

description:
Library name: A2_WT_0
Wild-type mouse embryonic stem cell RNA-seq used as a reference transcriptome for Figure 7A PCA analysis.

value: WT


title: BMDMs, rIL-18_biol rep 3

description: Library name: Sample 6

value: Bone marrow

value: Bone marrow-derived macrophages (BMDMs)


title: MDS1892

description: MDS

value: human BM Mononuclear cells


title: Co_48_12K

description: Library name: Sample 88


title: MDS1809

description: MDS


title: BMDMs, rIL-18_biol rep 2

description: Library name: Sample 5


title: IL_48_12K

description: Library name: Sample 86


title: IL_L1_6_14K

description: Library name: Sample 69


title: MDS1807

description: MDS


title: Mouse WT ESC replicate 1

description:
Library name: A1_WT_0
Wild-type mouse embryonic stem cell RNA-seq used as a reference transcriptome for Figure 7A PCA analysis.


title: MDS1867

description: MDS


title: IL_6_14K

description: Library name: Sample 68


title: MDS1792

description: MDS


title: NLSD7-R4

city: Abu Dhabi

first: Piergiorgio

last: Percipalle

state: abu dhabi

address: NYUAD Saadiyat Island

country: United Arab Emirates

institute: Biology

description:
Library name: SAMPLE 12
Nuclear Localization signal Day 7-R4

data_processing:
NASQAR: A web-based platform for High-throughput sequencing data analysis and visualization was used to do Differential Expression transcriptional analysis. Through NASQAR, DEseq2 was used to perform pairwise differential expression comparisons between WT and KO mESCs and generate a Volcano plot, Distance heatmap and a PCA plot. GO analysis was also done on NASQAR to generate GO plots for Cellular Components and Molecular Functions. Heatmaps were generated in R (v4.3.0) using the pheatmap package to visualize the expression patterns of selected gene sets across wild-type (WT), β-actin knockout (KO), and nuclear-localized β-actin (NLS) mESCs at Day 0. Raw gene expression matrices from bulk RNA-seq were first imported using the readr package. Gene sets related to specific biological functions (e.g., stemness, lineage commitment, extracellular matrix) were defined manually, and the corresponding expression values were extracted from the full dataset using the dplyr package. Replicates for each condition (WT_1–3, KO_1–3, NLS_1–3) were retained as individual columns or averaged using rowMeans() to create representative condition-specific profiles when required. Expression values were transformed into a numeric matrix. The matrix was then scaled row-wise (z-score) to allow for comparison of relative expression across samples. Heatmaps were plotted using pheatmap with hierarchical clustering applied to genes (rows), while preserving the experimental condition order for samples (columns). A custom diverging color palette (navy–white–firebrick3) was used to depict low to high expression.
Assembly: mouse mm10
Supplementary files format and content: raw counts
Supplementary files format and content: .txt files

source_name: Embryonic stem cells

growth_protocol: P60 culture dishes were coated with 3 mL of 0.1% gelatin solution and incubated at 37 °C for 15 min. Mouse embryonic stem cell (mESC) medium was pre-warmed to 37 °C. The gelatin solution was then replaced with 5 mL of mESC medium. A total of 5.0 × 10⁵ cells were seeded for each condition: wild type (WT), β-actin knockout (KO), and nuclear-localized β-actin (NLS). Cultures were maintained at 37 °C and 5% CO₂ for 2 days after seeding. Once cultures reached 70–90% confluency, cells were processed for RNA extraction.

extract_protocol:
RNA was extracted using RNAzol RT (Molecular Research Center, Catalog #R4533), a reagent designed for the isolation of total and small RNA from human, animal, plant, bacterial, and viral samples. Cells were washed with calcium- and magnesium-free DPBS and dissociated with TrypLE for 1 min. TrypLE was aspirated, then 1 mL of mESC medium was added, and cells were gently pipetted to detach them from the culture dish. The cell suspension was transferred to a 15-mL conical tube and pelleted by centrifugation at 500 × g for 3 min. The supernatant was removed, and 500 µL of RNAzol RT was added directly to the pellet. The pellet was fully resuspended by pipetting to ensure complete lysis and homogenization, and the lysate was transferred to a 1.5- mL microcentrifuge tube. A total of 0.2 mL of RNase-free water was added to each tube. Samples were capped, shaken vigorously for 15 s, and incubated for 15 min at room temperature. The mixture was centrifuged at 12,000 × g for 15 min at 4 °C, producing a pellet containing DNA, proteins, and polysaccharides, while RNA remained in the upper phase. The supernatant was carefully transferred to a new tube without disturbing the pellet. An equal volume of 100% isopropanol was added to the supernatant to precipitate RNA. Samples were incubated for 10 min at room temperature and then centrifuged at 12,000 × g for 10 min, forming a white RNA pellet. RNA pellets were washed twice with 75% ethanol (0.4–0.6 mL per mL of initial supernatant). Each wash was followed by centrifugation at 8,000 × g for 3 min at room temperature, after which the ethanol was removed by pipetting. The final RNA pellet was resuspended in 20 µL of RNase-free water without air-drying. Samples were vortexed at room temperature for 2 min to ensure complete solubilization.
45 NEB Ultra II RNA, PolyA selected

value: Embryonic stem cells

value: mESC

tag: sample group


title: MDS1790

description: MDS


title: MDS1793

description: MDS


title: Co_Tp_48_11K

description: Library name: Sample 84


title: Veh_6_14K

description: Library name: Sample 67


title: MDS1788

description: MDS


title: NLSD7-R3

description:
Library name: SAMPLE 11
Nuclear Localization signal Day 7-R3


title: MDS1785

description: MDS


title: Co_Tp_6_12K

description: Library name: Sample 66


title: MDS1784

description: MDS


title: MDS1781

description: MDS


title: MDS1779

description: MDS


title: Co_L_6_12K

description: Library name: Sample 65


title: NLSD7-R2

description:
Library name: SAMPLE 10
Nuclear Localization signal Day 7-R2


title: NLSD7-R1

description:
Library name: SAMPLE 9
Nuclear Localization signal Day 7-R1


title: MDS1778

description: MDS


title: Co_6_12K

description: Library name: Sample 64


title: IL_48_11K

description: Library name: Sample 80


title: MDS1775

description: MDS


title: KOD7-R4

description:
Library name: SAMPLE 8
Knock Out Day14-R4


title: MDS1855

description: MDS


title: CMR 3 Month AAV-TBG-Cre Mouse 1

description:
Library name: CMR_3_Month_Sample1
10X Genomics

value: Liver

value: AAV8:TBG>Cre 3 month


title: IL_L_6_12K

description: Library name: Sample 63


title: MDS1772

description: MDS


title: MDS1771

description: MDS


title: KOD7-R3

description:
Library name: SAMPLE 7
Knock Out Day14-R3


title: IL_6_12K

description: Library name: Sample 62


title: MDS1769

description: MDS


title: MDS1761

description: MDS


title: Veh_6_12K

description: Library name: Sample 61


title: KOD7-R1

description:
Library name: SAMPLE 5
Knock Out Day14-R1


title: MDS1759

description: MDS


title: MDS1750

description: MDS


title: Co_Tp_6_11K

description: Library name: Sample 60


title: WTD7-R4

description:
Library name: SAMPLE 4
Wild type Day-R4


title: MDS1748

description: MDS


title: Co_L1_6_11K

description: Library name: Sample 59


title: MDS1746

description: MDS


title: MDS1745

description: MDS


title: WTD7-R3

description:
Library name: SAMPLE 3
Wild type Day-R3


title: Co_6_11K

description: Library name: Sample 58


title: MDS1744

description: MDS


title: WTD7-R2

description:
Library name: SAMPLE 2
Wild type Day7-R2


title: MDS1742

description: MDS


title: IL_L1_6_11K

description: Library name: Sample 57


title: MDS1741

description: MDS


title: IL_6_11K

description: Library name: Sample 56


title: MDS1730

description: MDS


title: MDS1723

description: MDS


title: MDS1721

description: MDS


title: Veh_6_11K

description: Library name: Sample 55


title: CMRtdT 6.5 month Mouse 1173 Tumor 3

description: Library name: Mouse_2_Tumor_3

data_processing:
Raw sequencing data files were mapped to the GRCm38 reference genome using BWA. Duplicates were removed using Picard. Transcript levels were quantified by Sailfish in Transcripts per Million (TPM) and only 1:1 mouse human gene expression levels were retained.
Assembly: GRCm38

extract_protocol:
Tumors were excised from the livers. DNA and RNA were extracted and purified using the Qiagen AllPrep DNA/RNA Mini Kit according to the manufacturer's instructions.
mRNA libraries were prepared by Novogene according to the poly A enrichment protocol and sequencing was performed on an Illumina NovaSeq 6000 platform  (PE150)

value: CMRtdT

value: HFD 6.5 months


title: CMRtdT 6.5 month Mouse 1173 Tumor 2

description: Library name: Mouse_2_Tumor_2


title: MDS1717

description: MDS


title: MDS1716

description: MDS


title: Co_Tp_6_8K

description: Library name: Sample 54

value: Orbital adipose/connective tissue


title: MDS1715

description: MDS


title: CMRtdT 6.5 month Mouse 1173 Tumor 1

description: Library name: Mouse_2_Tumor_1


title: Co_L1_6_8k

description: Library name: Sample 53

value: primary fibroblast


title: MDS1705

description: MDS


title: MDS1703

description: MDS


title: CMRtdT 6.5 month Mouse 1172 Tumor 3

description: Library name: Mouse_1_Tumor_3


title: MDS1700

description: MDS


title: CMRtdT 6.5 month Mouse 1172 Tumor 2

description: Library name: Mouse_1_Tumor_2


title: Co_6_8K

description: Library name: Sample 52

value: thyroid eye disease


title: MDS1697

description: MDS


title: IL_L1_6_8K

description: Library name: Sample 51


title: MDS1695

description: MDS


title: CMRtdT 6.5 month Mouse 1172 Tumor 1

description: Library name: Mouse_1_Tumor_1


title: MDS1681

description: MDS


title: IL_6_8K

description: Library name: Sample 50


title: MDS1674

description: MDS


title: MDS1773

description: MDS


title: mGF palmitate+IL-1β 16

city: Augusta

first: Ana

middle: Carolina

last: Morandini

state: GA

address: 1120 15th Street

institute: Augusta University

description: Library name: Sample16

data_processing:
Adapter sequences and low-quality bases were removed using Trimmomatic v0.39. The resulting high-quality reads were aligned to the GENCODE Mus musculus reference genome (GRCm39 vM33) using the STAR v2.7.10a aligner. A gene-level count matrix was then generated from the aligned reads using HTSeq v2.0.9
Assembly: GRCm39 vM33
Supplementary files format and content: tab-delimited  gene count matrix for each sample

source_name: gingiva

growth_protocol: Primary murine gingival fibroblasts (mGF) were obtained from murine gingival explants from the gingiva surrounding the maxillary second molar of 3-6 month-old C57Bl6 mice. Fibroblasts were isolated and cultured in Dulbecco's Modified Eagle's Medium (DMEM) supplemented with 20% fetal bovine serum and antibiotics in a 5% CO2 incubator at 37°C and the growth media was replaced every other day.

extract_protocol:
Total RNA was extracted from mGF using Invitrogen PureLink RNA Mini Kit (ThermoFisher Scientific). 540 ng of Total RNA was used for the construction of sequencing libraries.
RNA-seq libraries were prepared using the SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian Kit (Takara Bio) following the manufacturer’s instructions.

treatment_protocol: Experiments were performed using cells between the 2nd and 8th passages. For cell treatments the following reagents were used: 200 µM BSA Control for BSA Fatty Acid Complexes (5 mM) as a vehicle, 200 µM BSA-Palmitate Saturated Fatty Acid Complex (5 mM) (Cayman); 1 ng/mL mouse recombinant Il-1β (R&D),  100μM Adenosine (MilliporeSigma) combined with 10μM EHNA (MilliporeSigma) to prevent adenosine degradation.

value: gingiva

value: mGF

value: gingival fibroblasts

value: Palmitate + IL-1β


title: MDS1666

description: MDS


title: Veh_6_8K

description: Library name: Sample 49


title: mGF palmitate+IL-1β 15

description: Library name: Sample15

value: WT


title: MDS1664

description: MDS


title: Co_Tp_48_9

description: Library name: Sample 48


title: MDS1661

description: MDS


title: mGF palmitate+IL-1β 14

description: Library name: Sample14


title: MDS1660

description: MDS


title: Co_L1_48_9

description: Library name: Sample 47


title: MDS1659

description: MDS


title: mGF palmitate+IL-1β 13

description: Library name: Sample13


title: MDS1749

description: MDS


title: MDS1657

description: MDS


title: Co_48_9

description: Library name: Sample 46


title: MDS1630

description: MDS


title: mGF palmitate 12

description: Library name: Sample12

value: Palmitate


title: MDS1626

description: MDS


title: mGF palmitate 11

description: Library name: Sample11


title: WTD7-R1

description:
Library name: SAMPLE 1
Wild type Day7-R1


title: MDS1623

description: MDS


title: IL_48_9

description: Library name: Sample 44


title: MDS1622

description: MDS


title: mGF palmitate 10

description: Library name: Sample10


title: MDS1621

description: MDS


title: Veh_48_9

description: Library name: Sample 43


title: MDS1617

description: MDS


title: MDS1615

description: MDS


title: Co_Tp_48_6K

description: Library name: Sample 42


title: MDS1613

description: MDS


title: mGF palmitate 9

description: Library name: Sample9


title: mGF IL-1β 8

description: Library name: Sample8


title: MDS1712

description: MDS


title: MDS1610

description: MDS


title: IL_L1_48_9

description: Library name: Sample 45


title: Co_L1_48_6K

description: Library name: Sample 41


title: MDS1608

description: MDS


title: MDS1605

description: MDS


title: Co_48_6K

description: Library name: Sample 40


title: MDS1604

description: MDS


title: mGF IL-1β 6

description: Library name: Sample6


title: mGF IL-1β 7

description: Library name: Sample7


title: MDS1600

description: MDS


title: IL_L1_48_6K

description: Library name: Sample 39


title: mGF IL-1β 5

description: Library name: Sample5


title: IL_48_6K

description: Library name: Sample 38


title: MDS1593

description: MDS


title: MDS1598

description: MDS


title: MDS1633

description: MDS


title: MDS1592

description: MDS


title: mGF BSA 4

description: Library name: Sample4

value: BSA


title: Veh_48_6K

description: Library name: Sample 37


title: MDS1591

description: MDS

value: human BM Mononuclear cells


title: MDS1589

description: MDS


title: MDS1588

description: MDS


title: mGF BSA 3

description: Library name: Sample3


title: Co_Tp_48_5K

description: Library name: Sample 36


title: MDS1584

description: MDS


title: mGF BSA 2

description: Library name: Sample2


title: MDS1578

description: MDS


title: Co_L1_48_5K

description: Library name: Sample 35


title: MDS1575

description: MDS


title: mGF BSA 1

description: Library name: Sample1


title: MDS1573

description: MDS


title: MDS1572

description: MDS


title: MDS1570

description: MDS


title: IL_L1_48_5K

description: Library name: Sample 33


title: MDS1558

description: MDS


title: Co_48_5K

description: Library name: Sample 34


title: MDS1557

description: MDS


title: IL_48_5K

description: Library name: Sample 32


title: MDS1556

description: MDS


title: MDS1545

description: MDS


title: MDS1540

description: MDS


title: MDS1527

description: MDS


title: Co_Tp_48_1K

description: Library name: Sample 30


title: Veh_48_5K

description: Library name: Sample 31


title: MDS1525

description: MDS


title: MDS1517

description: MDS


title: Co_L1_48_1K

description: Library name: Sample 29


title: MDS1516

description: MDS


title: MDS1513

description: MDS


title: Co_48_1K

description: Library name: Sample 28


title: MDS1512

description: MDS


title: MDS1510

description: MDS


title: IL_L1_48_1K

description: Library name: Sample 27


title: MDS1507

description: MDS


title: MDS1506

description: MDS


title: IL_48_1K

description: Library name: Sample 26


title: MDS1495

description: MDS


title: MDS1494

description: MDS


title: Mouse kidney, cKOt genotype, ZT16, (library 34)

city: Lausanne

first: Leonore

last: Wigger

address: Amphipôle Building

country: Switzerland

institute: Swiss Institute of Bioinformatics

description:
Library name: ZT16_KO4
column name in processed data file: ZT16_K4_lib34

data_processing:
Sequencing data were demultiplexed, filtered for failed reads, and written to FASTQ files using the bcl2fastq2 conversion software (version 2.20, Illumina).
Preprocessing and quality control were performed with the command-line tool fastp (v0.23.2)
Alignment to the Ensembl genome Mus_musculus.GRCm39.110 was performed with the command-line tool RSEM (v1.3.3), using the STAR method (--star).
Gene count matrices from RSEM were used for downstream analyses.
Assembly: GRCm39.110
Supplementary files format and content: Read count matrix for all annotated genes

source_name: Kidney

growth_protocol: All experiments were performed on male mice housed under 12-hours light/12-hours dark cycles with ad libitum access to drinking water and a standard laboratory chow diet (KLIBA NAFAG diet 3800). A Bmal1lox/lox/Pax8-rtTA/LC-1 Cre mouse strain was bred on the genetic background of the C57BL/6J mouse from The Jackson Laboratory. Eight weeks old Bmal1lox/lox/Pax8-rtTA/LC1 mice (referred as cKOt mice) and their Bmal1lox/lox littermates (referred as CTRL or control mice) were treated for 2 weeks with Doxycycline (DOX; 2 mg/ml in drinking water along with 20mg/ml sucrose) to induce the Cre recombinase inactivation of the Bmal1 (Arntl) gene.

extract_protocol:
RNA was directly extracted from kidney tissue (renal tubule) using RNAeasy MiniElute Spin Column (Qiagen).
RNA-seq libraries were prepared from 200 ng of total RNA with the Illumina TruSeq Stranded mRNA reagents (Illumina) using a unique dual indexing strategy.

value: Kidney

value: cKOt

tag: circadian time


title: Veh_48_1K

description: Library name: Sample 25


title: Mouse kidney, cKOt genotype, ZT16, (library 22)

description:
Library name: ZT16_KO3
column name in processed data file: ZT16_K3_lib22


title: MDS1486

description: MDS


title: MDS1484

description: MDS


title: Co_L1_6_9

description: Library name: Sample 23


title: Mouse kidney, cKOt genotype, ZT16, (library 10)

description:
Library name: ZT16_KO1
column name in processed data file: ZT16_K1_lib10


title: MDS1475

description: MDS


title: MDS1474

description: MDS


title: Mouse kidney, control genotype, ZT16, (library 65)

description:
Library name: ZT16_C6
column name in processed data file: ZT16_C6_lib65

value: Ctrl


title: MDS1473

description: MDS


title: IL_L1_6_9

description: Library name: Sample 21


title: MDS1462

description: MDS


title: Mouse kidney, control genotype, ZT16 ,(library 21)

description:
Library name: ZT16_C4
column name in processed data file: ZT16_C4_lib21


title: MDS1454

description: MDS


title: IL_6_9

description: Library name: Sample 20


title: MDS1450

description: MDS


title: Mouse kidney, control genotype, ZT16, (library 61)

description:
Library name: ZT16_C3
column name in processed data file: ZT16_C3_lib61


title: MDS1438

description: MDS


title: Veh_6_9

description: Library name: Sample 19


title: MDS1432

description: MDS


title: Mouse kidney, control genotype, ZT16, (library 09)

description:
Library name: ZT16_C1
column name in processed data file: ZT16_C1_lib09


title: MDS1430

description: MDS


title: Co_Tp_6_6K

description: Library name: Sample 18


title: Mouse kidney, cKOt genotype, ZT04, (library 52)

description:
Library name: ZT04_KO4
column name in processed data file: ZT04_K4_lib52


title: MDS1422

description: MDS


title: MDS1420

description: MDS


title: Co_6_6K

description: Library name: Sample 16


title: Co_Tp_6_9

description: Library name: Sample 24


title: MDS1665

description: MDS


title: MDS1418

description: MDS


title: Co_6_9

description: Library name: Sample 22


title: MDS1480

description: MDS


title: KOD7-R2

description:
Library name: SAMPLE 6
Knock Out Day14-R2

value: Embryonic stem cells

value: mESC


title: MDS1416

description: MDS


title: MDS1415

description: MDS


title: Mouse kidney, cKOt genotype, ZT04, (library 39)

description:
Library name: ZT04_KO1
column name in processed data file: ZT04_K1_lib39


title: MDS1414

description: MDS


title: Veh_6_6K

description: Library name: Sample 13


title: MDS1425

description: MDS


title: Co_L1_6_6K

description: Library name: Sample 17


title: MDS1421

description: MDS


title: Mouse kidney, cKOt genotype, ZT04, (library 04)

description:
Library name: ZT04_KO3
column name in processed data file: ZT04_K3_lib04


title: IL_L1_6_6K

description: Library name: Sample 15


title: Mouse kidney, cKOt genotype, ZT16, (library 42)

description:
Library name: ZT16_KO2
column name in processed data file: ZT16_K2_lib42


title: IL_6_6K

description: Library name: Sample 14


title: MDS1491

description: MDS


title: Mouse kidney, cKOt genotype, ZT04, (library 66)

description:
Library name: ZT04_KO2
column name in processed data file: ZT04_K2_lib66


title: MDS1409

description: MDS


title: MDS1476

description: MDS


title: MDS1411

description: MDS


title: Mouse kidney, control genotype, ZT04, (library 03)

description:
Library name: ZT04_C6
column name in processed data file: ZT04_C6_lib03


title: MDS1412

description: MDS


title: Mouse kidney, control genotype, ZT04, (library 62)

description:
Library name: ZT04_C5
column name in processed data file: ZT04_C5_lib62


title: Co_Tp_6_5K

description: Library name: Sample 12


title: MDS1407

description: MDS


title: Mouse kidney, control genotype, ZT04, (library 27)

description:
Library name: ZT04_C4
column name in processed data file: ZT04_C4_lib27


title: MDS1405

description: MDS


title: Co_L1_6_5K

description: Library name: Sample 11


title: MDS1404

description: MDS


title: MDS1406

description: MDS


title: Mouse kidney, control genotype, ZT04, (library 15)

description:
Library name: ZT04_C3
column name in processed data file: ZT04_C3_lib15


title: MDS1401

description: MDS


title: Co_6_5K

description: Library name: Sample 10


title: MDS1402

description: MDS


title: MDS1403

description: MDS


title: Female High Fat Diet Dioxin-Exposed Replicate 6

city: Louisville

first: Banrida

last: Wahlang

address: 505 S Hancock Street

department: Medicine

institute: University of Louisville

description:
Library name: FEH-48
Female mice fed a High Fat Diet with Dioxin Exposure serving as replicate 6

data_processing:
Raw data quality was evaluated with FastQC. Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36
The trimmed reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b
Differential gene expression analysis was conducted with the DESeq2 R package
Assembly: GRCm38
Supplementary files format and content: tab-delimited file includes normalized counts for each sample
Supplementary files format and content: Transcripts Per Million (TPM)

extract_protocol:
RNA was extracted using RNeasy plus mini kit (catalog: 74134; Qiagen)
Pre-made libraries were used (Azenta Life Sciences)

value: Liver

tag: strain

tag: Sex

value: Female

value: High Fat Diet + Dioxin Exposure


title: IL_L1_6_5K

description: Library name: Sample 9

value: Orbital adipose/connective tissue

value: primary fibroblast

value: thyroid eye disease


title: Female High Fat Diet Dioxin-Exposed Replicate 5

description:
Library name: FEH-46
Female mice fed a High Fat Diet with Dioxin Exposure serving as replicate 5


title: MDS1400

description: MDS


title: IL_6_5K

description: Library name: Sample 8


title: MDS1399

description: MDS


title: Female High Fat Diet Dioxin-Exposed Replicate 4

description:
Library name: FEH-45
Female mice fed a High Fat Diet with Dioxin Exposure serving as replicate 4


title: MDS1396

description: MDS


title: Veh_6_5K

description: Library name: Sample 7


title: MDS1392

description: MDS


title: Co_Tp_6_1K

description: Library name: Sample 6


title: MDS1394

description: MDS


title: MDS1391

description: MDS


title: MDS1390

description: MDS


title: Female High Fat Diet Dioxin-Exposed Replicate 2

description:
Library name: FEH-39
Female mice fed a High Fat Diet with Dioxin Exposure serving as replicate 2


title: Co_L1_6_1K

description: Library name: Sample 5


title: MDS1389

description: MDS


title: MDS1388

description: MDS


title: Female High Fat Diet Dioxin-Exposed Replicate 1

description:
Library name: FEH-38
Female mice fed a High Fat Diet with Dioxin Exposure serving as replicate 1


title: MDS1387

description: MDS


title: MDS1384

description: MDS


title: IL_L1_6_1K

description: Library name: Sample 3


title: Female High Fat Diet Control Replicate 6

description:
Library name: FCH-36
Female mice fed a High Fat Diet with vehicle control serving as replicate 6

value: High Fat Diet


title: Co_6_1K

description: Library name: Sample 4


title: Female High Fat Diet Control Replicate 5

description:
Library name: FCH-34
Female mice fed a High Fat Diet with vehicle control serving as replicate 5


title: MDS1385

description: MDS


title: MDS1383

description: MDS


title: MDS1382

description: MDS


title: IL_6_1K

description: Library name: Sample 2


title: Female High Fat Diet Control Replicate 4

description:
Library name: FCH-31
Female mice fed a High Fat Diet with vehicle control serving as replicate 4


title: Veh_6_1K

description: Library name: Sample 1


title: MDS1381

description: MDS


title: MDS1380

description: MDS


title: MDS1378

description: MDS


title: MDS1379

description: MDS


title: ARHGAP18KO_4

city: Buffalo

first: Jonathan

middle: E

last: Bard

state: New York

address: 701 Ellicott Street

department: Genomics and Bioinformatics Core

institute: University at Buffalo

description: Library name: ARHGAP18KO_4

data_processing:
Bcl2fastq2 Demultiplexing
NF-Core RNA-Seq  v3.18.0-gb96a753 analysis pipeline, producing salmon quantifications
Assembly: GRCh38.p14
Supplementary files format and content: tab delimited per-sample gene quantifications from salmon

growth_protocol: Jeg3 cells were purchased from ATCC.org (Cat# Htb-36) and maintained in a humidified incubator at 37°C and 5% CO2. Media for Jeg3 cells used in 1× MEM (Thermo Fisher Scientific; Cat# 10370088) with penicillin/streptomycin (Thermo Fisher Scientific; Cat# 15070063), 10% fetal bovine serum (FBS; Thermo Fisher Scientific; Cat# 26140079), and GlutaMAX (Thermo Fisher Scientific; Cat# 35050061). Corning 100 × 20 mm Petri-style TC-treated culture dishes (Cat# 430167) were used for maintaining cultures.

extract_protocol:
Qiagen Rneasy Mini plus extraction
RiboZero Total Stranded Illumina RNA Library Prep

treatment_protocol: ARHGAP18 knockout cells were created and characterized (Lombardo et al., 2024). In summary of these methods, multiple CRISPR single-guide RNAs against the sequence 5′-CAGCGGCAAGGACCAGACCG-3′ or 5′-CAGCGGCAAGGACCAGACCG-3′ were cloned into puromycin-resistant pLenti-CRISPRV2 (Addgene; Cat# 49535) which was transfected into 293TN cells with psPAX3 and pCMV-VSV-G (a gift from Jan Lammerding, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY) for 48–72 hr.  Jeg3 cells were then transduced with virus supplemented with Polybrene to 8 µg/mL twice a day for 2 days, followed by puromycin selection at 2 µg/mL. Mixed populations of selected cells were single-cell sorted and then screened by western blotting. ARHGAP18 expression vectors were created and described in (Lombardo et al., 2024).

value: Placental


title: Female High Fat Diet Control Replicate 3

description:
Library name: FCH-29
Female mice fed a High Fat Diet with vehicle control serving as replicate 3


title: Female High Fat Diet Control Replicate 2

description:
Library name: FCH-27
Female mice fed a High Fat Diet with vehicle control serving as replicate 2


title: Female High Fat Diet Dioxin-Exposed Replicate 3

description:
Library name: FEH-41
Female mice fed a High Fat Diet with Dioxin Exposure serving as replicate 3


title: MDS1376

description: MDS


title: MDS1375

description: MDS


title: ARHGAP18KO_3

description: Library name: ARHGAP18KO_3


title: Female High Fat Diet Control Replicate 1

description:
Library name: FCH-25
Female mice fed a High Fat Diet with vehicle control serving as replicate 1


title: MDS1374

description: MDS


title: ARHGAP18KO_2

description: Library name: ARHGAP18KO_2


title: MDS1372

description: MDS


title: Male High Fat Diet Dioxin-Exposed Replicate 6

description:
Library name: MEH-24
Male mice fed a High Fat Diet with Dioxin Exposure serving as replicate 6

value: male


title: MDS1371

description: MDS


title: ARHGAP18KO_1

description: Library name: ARHGAP18KO_1


title: MDS1373

description: MDS


title: Male High Fat Diet Dioxin-Exposed Replicate 5

description:
Library name: MEH-23
Male mice fed a High Fat Diet with Dioxin Exposure serving as replicate 5


title: MDS1386

description: MDS


title: WTJeg3_4

description: Library name: WTJeg3_4

value: WT


title: MDS1369

description: MDS


title: MDS1368

description: MDS


title: Male High Fat Diet Dioxin-Exposed Replicate 4

description:
Library name: MEH-20
Male mice fed a High Fat Diet with Dioxin Exposure serving as replicate 4


title: MDS1367

description: MDS


title: WTJeg3_3

description: Library name: WTJeg3_3


title: MDS1365

description: MDS


title: MDS1366

description: MDS


title: WTJeg3_2

description: Library name: WTJeg3_2


title: MDS1364

description: MDS


title: MDS1363

description: MDS


title: Male High Fat Diet Dioxin-Exposed Replicate 1

description:
Library name: MEH-14
Male mice fed a High Fat Diet with Dioxin Exposure serving as replicate 1


title: MDS1362

description: MDS


title: MDS1361

description: MDS


title: 3367696_JWH007_Group_INPUT

city: Memphis

first: Beisi

last: Xu

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hosipital

description: Library name: sample 7

library_source: genomic

data_processing:
Paired-end 50-cycle sequencing was performed on NovaSeq6000 sequencer following the manufacturer’s instructions (Illumina) Raw reads were first trimmed using TrimGalore (v0.6.3). Filtered reads are then aligned the Homo sapiens reference genome GRCh38 using BWA (0.7.17-r1188).
Duplicated reads are then marked using the “bamsormadup” function from the biobambam2 tool (v2.0.87) PCR duplicates and low mapping quality reads (MAPQ < 1) were removed using samtools (version 1.9, parameter ‘-q 1 -F 1024’).
The uniquely mapped reads were then used to estimate the average fragment length in each sample based on the cross-correlation profile calculated from SPP (v1.11) [PMID:19029915]. The smallest fragment size estimated by SPP was used to center and extend reads to generate bigwig files. The bigiwig signal in all samples is scaled to 15 million reads (ie: scaling-factor=15e6/libSize).
Assembly: hg38
Supplementary files format and content: bigwig

molecule: genomic DNA

source_name: Blood

growth_protocol: SEM cells were grown in RPMI-1640 with L-Glutamine (Cellgro) containing 10% fetal bovine serum (FBS) (Hyclone) and 1% penicillin/ streptomycin (Thermo Fisher Scientific). The cells maintained at 37 Celsius, 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 5 min with gentle rocking at room temperature, and chromatin was prepared using the Covaris TruChIP Chromatin Shearing Kit (Covaris, 520154). Chromatin was sheared by the Covaris M220 ultrasonicator (duty factor of 10, cycles/burst 200 for 10 min at set point 6°C). After clarification by centrifugation at 8,000 x g for 10 mins, the chromatin was moved to a new 1.5 mL Eppendorf tube, and the buffer was amended for immunoprecipitation (final concentration: 50 mM Tris HCL pH 7.4, 100 mM NaCl, 1 mM EDTA, 1 % SDS, 0.5 % Na Deoxycholate plus protease inhibitors). Chromatin was incubated with anti-HA magnetic beads (Pierce) at 4 °C overnight with gentle rotation. On a magnetic stand, the beads were washed twice with wash buffer 1 (50 mM Tris HCL pH 7.4, 1 M NaCl, 1 mM EDTA, 1 % NP-40, 0.1 % SDS, 0.5 % Na Deoxycholate plus protease inhibitors) and once with wash buffer 2 (20 mM Tris HCL pH 7.4, 10 mM MgCl2, 0.2 % Tween-20 plus protease inhibitors). The beads in wash buffer 2 were transferred to a new 1.5 mL Eppendorf tube and placed on a magnetic stand to remove the wash buffer. Decrosslinking was carried out in 1X TE plus 1 % SDS, proteinase K, and 400 mM NaCl at 65 °C for 4 h, followed by phenol, chloroform, and isopropyl alcohol precipitation of the DNA.
Libraries were constructed using NEBNext Ultra II NEB Library Prep Kit and NEBNext Multiplex oligos (Illumina).

treatment_protocol: Cells were treated with 1uM 5-Ph-IAA (Abcam) or DMSO for 24 hours, and doxycycline 1ug/mL for 18 hours.

value: Blood

value: SEM

value: B cell precursor leukemia

value: t(4;11) KMT2A-AFF1 (MLL-AFF1; MLL-AF4)

tag: antibody


title: MDS1358

description: MDS

value: human BM Mononuclear cells


title: Male High Fat Diet Control Replicate 6

description:
Library name: MCH-11
Male mice fed a High Fat Diet with vehicle control serving as replicate 6


title: MDS1357

description: MDS


title: 3367689_JWH006_C17.2_CTCF-Q666

description: Library name: sample 6

value: CTCF


title: MDS1356

description: MDS


title: Male High Fat Diet Control Replicate 5

description:
Library name: MCH-9
Male mice fed a High Fat Diet with vehicle control serving as replicate 5


title: MDS1355

description: MDS


title: MDS1354

description: MDS


title: Male High Fat Diet Control Replicate 4

description:
Library name: MCH-7
Male mice fed a High Fat Diet with vehicle control serving as replicate 4


title: MDS1352

description: MDS


title: 3367687_JWH004_C5_CTCF-Q666

description: Library name: sample 4


title: MDS1351

description: MDS


title: MDS1350

description: MDS


title: Male High Fat Diet Control Replicate 3

description:
Library name: MCH-6
Male mice fed a High Fat Diet with vehicle control serving as replicate 3


title: MDS1348

description: MDS


title: 3367686_JWH003_C17.2_CTCF-WT

description: Library name: sample 3


title: Male High Fat Diet Control Replicate 2

description:
Library name: MCH-3
Male mice fed a High Fat Diet with vehicle control serving as replicate 2


title: MDS1347

description: MDS


title: Male High Fat Diet Dioxin-Exposed Replicate 3

description:
Library name: MEH-17
Male mice fed a High Fat Diet with Dioxin Exposure serving as replicate 3


title: 3367685_JWH002_C3.2_CTCF-WT

description: Library name: sample 2


title: MDS1346

description: MDS


title: 3367684_JWH001_C5_CTCF-WT

description: Library name: sample 1


title: Female Low Fat Diet Dioxin-Exposed Replicate 6

description:
Library name: FEL-47
Female mice fed a Low Fat Diet with Dioxin Exposure serving as replicate 6

value: Low Fat Diet + Dioxin Exposure


title: Male High Fat Diet Control Replicate 1

description:
Library name: MCH-1
Male mice fed a High Fat Diet with vehicle control serving as replicate 1

value: Liver


title: Male High Fat Diet Dioxin-Exposed Replicate 2

description:
Library name: MEH-15
Male mice fed a High Fat Diet with Dioxin Exposure serving as replicate 2


title: MDS1344

description: MDS


title: WTJeg3_1

description: Library name: WTJeg3_1


title: MDS1343

description: MDS


title: 3367688_JWH005_C3.2_CTCF-Q666

description: Library name: sample 5


title: patient-derived organoids, sample TORG146

city: San Francisco

first: Jennifer

middle: M

last: Rosenbluth

state: California

address: 10 Koret Way

institute: University of California San Francisco

description: Library name: T146

data_processing:
Methods by Novogene: Data Quality Control. Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Methods by Novogene: Readsmapping to the reference genome. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean 1 reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Methods by Novogene: Quantification of gene expression level. Gene expression levels were quantified using RSEM, providing transcript abundance estimates for downstream analyses.
Assembly: Homo_sapiens_Ensemble_75
Supplementary files format and content: RSEM (.genes file providing transcript abundance estimates)

source_name: breast cancer

extract_protocol:
Organoids passage 4 or higher were harvested when confluent using TRIzol® reagent (ThermoFisher, Cat. No. 15596018). Cells were lysed using chloroform (SigmaAldrich, Cat. No. C2432-1L) in preparation for using the Purelink RNA Mini Kit® Protocol (ThermoFisher, cat# 12183020). Samples were eluted in 30ul RNA-Free water through two serial elutions. Samples were stored at -80°C until submission for library preparation and sequencing.
Methods by Novogene: Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

value: breast cancer

value: organoids

value: breast cancer cells


title: Female Low Fat Diet Dioxin-Exposed Replicate 5

description:
Library name: FEL-46
Female mice fed a Low Fat Diet with Dioxin Exposure serving as replicate 5

value: Female


title: MDS1341

description: MDS


title: MDS1340

description: MDS


title: Female Low Fat Diet Dioxin-Exposed Replicate 4

description:
Library name: FEL-43
Female mice fed a Low Fat Diet with Dioxin Exposure serving as replicate 4


title: MDS1333

description: MDS


title: MDS1337

description: MDS


title: Female Low Fat Diet Dioxin-Exposed Replicate 3

description:
Library name: FEL-42
Female mice fed a Low Fat Diet with Dioxin Exposure serving as replicate 3


title: patient-derived organoids, sample TORG139

description: Library name: T139


title: MDS1338

description: MDS


title: patient-derived organoids, sample TORG64

description: Library name: T64


title: patient-derived organoids, sample TORG61

description: Library name: T61


title: MDS1331

description: MDS


title: Female Low Fat Diet Dioxin-Exposed Replicate 2

description:
Library name: FEL-40
Female mice fed a Low Fat Diet with Dioxin Exposure serving as replicate 2


title: MDS1330

description: MDS


title: Female Low Fat Diet Dioxin-Exposed Replicate 1

description:
Library name: FEL-37
Female mice fed a Low Fat Diet with Dioxin Exposure serving as replicate 1


title: patient-derived organoids, sample TORG58

description: Library name: T58


title: patient-derived organoids, sample TORG56

description: Library name: T56


title: MDS1328

description: MDS


title: MDS1326

description: MDS


title: Female Low Fat Diet Control Replicate 6

description:
Library name: FCL-36
Female mice fed a Low Fat Diet with vehicle control serving as replicate 6

value: Low Fat Diet


title: MDS1327

description: MDS


title: MDS1325

description: MDS


title: patient-derived organoids, sample TORG53

description: Library name: T53


title: MDS1324

description: MDS


title: Female Low Fat Diet Control Replicate 5

description:
Library name: FCL-35
Female mice fed a Low Fat Diet with vehicle control serving as replicate 5


title: MDS1323

description: MDS


title: MDS1342

description: MDS


title: patient-derived organoids, sample TORG51

description: Library name: T51


title: Female Low Fat Diet Control Replicate 4

description:
Library name: FCL-31
Female mice fed a Low Fat Diet with vehicle control serving as replicate 4


title: MDS1320

description: MDS


title: patient-derived organoids, sample TORG45

description: Library name: T45


title: MDS1321

description: MDS


title: MDS1318

description: MDS


title: MDS1317

description: MDS


title: Female Low Fat Diet Control Replicate 3

description:
Library name: FCL-29
Female mice fed a Low Fat Diet with vehicle control serving as replicate 3


title: patient-derived organoids, sample TORG43

description: Library name: T43


title: MDS1316

description: MDS


title: Female Low Fat Diet Control Replicate 2

description:
Library name: FCL-26
Female mice fed a Low Fat Diet with vehicle control serving as replicate 2


title: MDS1314

description: MDS


title: MDS1312

description: MDS


title: patient-derived organoids, sample TORG40

description: Library name: T40


title: Female Low Fat Diet Control Replicate 1

description:
Library name: FCL-25
Female mice fed a Low Fat Diet with vehicle control serving as replicate 1


title: patient-derived organoids, sample TORG39

description: Library name: T39


title: MDS1311

description: MDS


title: MDS1308

description: MDS


title: Male Low Fat Diet Dioxin-Exposed Replicate 6

description:
Library name: MEL-24
Male mice fed a Low Fat Diet with Dioxin Exposure serving as replicate 6


title: MDS1309

description: MDS


title: WT_PTX / 13051-JM-0006

city: Nashville

first: Shristi

last: Shrestha

address: 2213 Garland Ave

institute: Vanderbilt University

description: Library name: 13051-JM-0006

data_processing:
RNA sequencing reads were adapter-trimmed and quality-filtered using Trimgalore v0.6.7 (Krueger et al., 2023).
An alignment reference was generated from the hg38 human genome and GENCODE comprehensive gene annotations (v26), to which trimmed reads were aligned and counted using Spliced Transcripts Alignment to a Reference (STAR) v2.7.9a (Dobin et al., 2013) with the –quantMode GeneCounts parameter.
About 104-136 million reads were acquired per sample. DESeq2 package v1.36.0 (Love et al. 2014) was used to perform sample-level quality control, low count filtering, normalization and downstream differential gene expression analysis.
Assembly: hg38
Supplementary files format and content: tab-delimited text file containing raw counts for each sample
Supplementary files format and content: tab-delimited text file containing normalized counts for each sample

source_name: triple-negative breast cancer cells

growth_protocol: MDA-MB-231b cells were cultured in Gibco DMEM (4.5g/L glucose) (ThermoFisher, #11995065) .

extract_protocol:
RNA was extracted using QIAzol (Qiagen, #79306), according to manufacturer's protocols.
cDNA library was constructed using qScript cDNA supermix (Quantabio, #95048), according to manufacturer's protocols.

treatment_protocol: Cells were treated for two days in complete media containing either 50nM Paclitaxel (PTX) (Sigma Aldrich, #T7191) or DMSO.

value: triple-negative breast cancer cells

value: paclitaxel (PTX)


title: MDS1307

description: MDS

data_processing:
Reads were then aligned to the human genome (GRCh38) and gene annotated with its corresponding GTF files (GENCODE GRCh38) using STAR version 2.4.2a with the settings –outFilterMultimapNmax 20 –outFilterType BySJout –alignSJoverhangMin 8 –quantMode GeneCounts.
Assembly: GRCh38
Supplementary files format and content: Read counts in .csv format

extract_protocol:
RNA was extracted from fresh BM samples of patients and healthy donors and sent for RNA sequencing.
The purified RNA was used to prepare the sequencing library using the TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA, USA) following the manufacturer’s recommendations. Briefly, mRNA was purified from total RNA (1 μg) using oligo(dT)-coupled magnetic beads and fragmented into small pieces at elevated temperatures.
First-strand cDNA was synthesized using reverse transcriptase and random primers. After the generation of double-strand cDNA and adenylation on the 3’ ends of DNA fragments, the adaptors were ligated and purified with the AMPure XP system (Beckman Coulter, Beverly, USA). The quality of the libraries was assessed using an Agilent Bioanalyzer 2100 system and a real-time polymerase chain reaction (PCR) system. The qualified libraries were then sequenced on an Illumina NovaSeq 6000 platform with 150 bp paired-end reads generated by Genomics, BioSci & Tech Co., New Taipei City, Taiwan. The bases with low quality and sequences from adapters in the raw data were removed using Cutadapt (v 3.0).


title: Male Low Fat Diet Dioxin-Exposed Replicate 5

description:
Library name: MEL-23
Male mice fed a Low Fat Diet with Dioxin Exposure serving as replicate 5

value: male


title: MDS1306

description: MDS


title: WT_PTX / 13051-JM-0002

description: Library name: 13051-JM-0002

value: WT


title: MDS1334

description: MDS


title: MDS1305

description: MDS


title: Male Low Fat Diet Dioxin-Exposed Replicate 4

description:
Library name: MEL-19
Male mice fed a Low Fat Diet with Dioxin Exposure serving as replicate 4


title: MDS1303

description: MDS


title: WT_PTX / 13051-JM-0003

description: Library name: 13051-JM-0003


title: MDS1299

description: MDS


title: MDS1302

description: MDS


title: Male Low Fat Diet Dioxin-Exposed Replicate 3

description:
Library name: MEL-18
Male mice fed a Low Fat Diet with Dioxin Exposure serving as replicate 3


title: Male Low Fat Diet Dioxin-Exposed Replicate 2

description:
Library name: MEL-16
Male mice fed a Low Fat Diet with Dioxin Exposure serving as replicate 2


title: MDS1297

description: MDS


title: MDS1294

description: MDS


title: WT_DMSO / 13051-JM-0005

description: Library name: 13051-JM-0005

value: DMSO


title: MDS1293

description: MDS


title: Male Low Fat Diet Dioxin-Exposed Replicate 1

description:
Library name: MEL-13
Male mice fed a Low Fat Diet with Dioxin Exposure serving as replicate 1


title: MDS1289

description: MDS


title: WT_DMSO / 13051-JM-0001

description: Library name: 13051-JM-0001


title: Male Low Fat Diet Control Replicate 6

description:
Library name: MCL-11
Male mice fed a Low Fat Diet with vehicle control serving as replicate 6


title: MDS1288

description: MDS


title: MDS1292

description: MDS


title: GLI2_KO_PTX / 13051-JM-0012

description: Library name: 13051-JM-0012


title: MDS1284

description: MDS


title: MDS1282

description: MDS


title: Male Low Fat Diet Control Replicate 5

description:
Library name: MCL-9
Male mice fed a Low Fat Diet with vehicle control serving as replicate 5


title: GLI2_KO_PTX / 13051-JM-0010

description: Library name: 13051-JM-0010


title: MDS1281

description: MDS


title: Male Low Fat Diet Control Replicate 4

description:
Library name: MCL-8
Male mice fed a Low Fat Diet with vehicle control serving as replicate 4


title: MDS1279

description: MDS


title: MDS1278

description: MDS


title: GLI2_KO_PTX / 13051-JM-0008

description: Library name: 13051-JM-0008


title: Male Low Fat Diet Control Replicate 3

description:
Library name: MCL-6
Male mice fed a Low Fat Diet with vehicle control serving as replicate 3


title: MDS1276

description: MDS


title: Male Low Fat Diet Control Replicate 2

description:
Library name: MCL-3
Male mice fed a Low Fat Diet with vehicle control serving as replicate 2


title: GLI2_KO_DMSO / 13051-JM-0009

description: Library name: 13051-JM-0009


title: MDS1275

description: MDS


title: MDS1274

description: MDS


title: GLI2_KO_DMSO / 13051-JM-0011

description: Library name: 13051-JM-0011


title: MDS1273

description: MDS


title: Male Low Fat Diet Control Replicate 1

description:
Library name: MCL-2
Male mice fed a Low Fat Diet with vehicle control serving as replicate 1


title: WT_DMSO / 13051-JM-0004

description: Library name: 13051-JM-0004


title: GLI2_KO_DMSO / 13051-JM-0007

description: Library name: 13051-JM-0007


title: MDS1272

description: MDS


title: MDS1271

description: MDS


title: Kidney, young

city: Greifswald

first: Yao

state: State

address: Felix-Hausdorff-Straße 3

country: Germany

institute: University Medicine Greifswald

description: Library name: Sample3

data_processing:
The FASTQ files were processed and aligned to GRCm39 mouse reference genome using MobiVision software (version 3.2 ) from 10x Genomics, with unique molecular identifier (UMI) counts summarized for each barcode.
Assembly: Mouse mm10
Supplementary files format and content: Helicobacter pylori ASM2599845v1
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Under sterile conditions, thefreshly collected kidneys  were washed twice with pre-cooled RPMI 1640 medium containing 0.04% BSA. The tissues were then mechanically dissociated into approximately 0.5 mm³ fragments using surgical scissors and transferred into freshly prepared enzymatic digestion solution. The digestion mixture contained RPMI 1640 (Conring, cat.no. 10-040-CVR), 0.04% BSA (MACS, cat.no. 1000076), and 0.2% collagenase II (Gibco, cat.no. 17101015). The samples were incubated at 37°C for 30-60 minutes with gentle inversion every 5-10 minutes.The digested cell suspension was filtered through a BD 40 μm cell strainer (Falcon, cat.no. 352340) 1-2 times. The filtrate was centrifuged at 300 × g for 5 minutes at 4°C. The cell pellet was resuspended in appropriate medium, mixed with an equal volume of red blood cell lysis buffer (Miltenyi, cat.no. 130-094-183), and incubated at 4°C for 10 minutes. After centrifugation at 300 × g for 5 minutes, the supernatant was discarded. The pellet was washed once with medium followed by another centrifugation at 300 × g for 5 minutes, and the final supernatant was removed.Finally，the cells were re-suspended with 1ml RPMI 1640 medium (Conring, cat.no.10-040-CVR) with 0.04% BSA added. Single-cell suspension concentration and cell viability were then evaluated by Luna-FL cell counter (Logos Biosystems，Korea) or Trypan Blue staining method.
The freshly prepared single-cell suspension was adjusted to a concentration of 700–1200 cells/μl. Library preparation and loading were performed following the manufacturer’s protocol for the MobiCube High-throughput Single Cell 3 ′ Transcriptome Set V2.1 (cat.no.PN-S050200301). The constructed libraries were sequenced on the Illumina Nova 6000 PE150  platform for high-throughput sequencing.

value: Kidney

tag: age

value: young

value: control


title: MDS1269

city: Taipei

first: Yu-Hung

address: N0 7, Chung-Shan South Rd

institute: National Taiwan University Hospital

description: MDS

value: human BM Mononuclear cells


title: MDS1265

description: MDS


title: OCI-AML-3 H1-3 cells, clone 2 replique 2

city: Marseille

first: Estelle

middle: Anna

last: Duprez

address: 23 bvd lei roure

department: OHIO

country: France

institute: CRCM-INSERM

description: Library name: RNAseq_OCI3_H1.3_KO2_rep2

data_processing:
paired-end reads were aligned to the human GRCh38 reference genome using Subread-align (v1.5.0) with default parameters. Gene expression quantification was performed by counting mapped tags at gene levels using featureCounts. Differentially expressed genes were identified using DESeq2 (v1.26.0)
Assembly: GRCh38 genome
Supplementary files format and content: RPKM

source_name: OCI-AML-3 H1-3KO clone 2

growth_protocol: Cells were growth in MEMα medium supplemented with 10% fetal bovine serum, 100 U/mL penicillin and 100 U/mL streptomycin under standard culture conditions (37°C, 5% CO2)

extract_protocol:
Total RNA was extracted from one the OCI-AML3 parental cell line and two KOs (KO clone #1 and KO clone #2). Each experimental condition includes three biological replicates using the RNeasy® Mini Kit (Qiagen; 74104)
Libraries were prepared with rRNA depletion with a Kapa mRNA HyperPrep kit (Roche, #KR1352-v7.21) and sequenced using the Illumina Novaseq6000 platform, 100-bp paired-end reads, at 50 million reads per sample and Nextseq500, 75-bp paired-end reads, 30 million reads per sample.

value: OCI-AML-3 H1-3KO clone 2

value: Acute myeloid leukemia

value: OCI-AML-3 H1-3 KO clone 2


title: MDS1261

description: MDS


title: Kidney, old DQ

description: Library name: Sample1

value: old

value: DQ


title: MDS1267

description: MDS


title: MDS1257

description: MDS


title: Kidney, old

description: Library name: Sample2


title: OCI-AML-3 H1-3 cells, clone 2 replique 1

description: Library name: RNAseq_OCI3_H1.3_KO2_rep1


title: MDS1256

description: MDS


title: 16793_mouse_Uninfected_Day_0

city: Aurora

first: Jo

last: Hendrix

state: CO

department: Pulmonology

institute: University of Colorado

description: Library name: mm_16793

data_processing:
After sequencing, bacterial reads were trimmed by Skewer v0.2.2 using an adapter sequence of 5’- CTGTCTCTTATACACATCT-3’, a length of 50-175 bases, and an end quality of 20. Individual reads were reunited with their mate pair using PairFQ lite v0.17.0. Paired-end reads were then aligned to the 2016 Mtb Erdman reference assembly using Bowtie2 v2.5.0 with default parameters. Mapped sequences were counted using HtSeq v1.0 with the default parameters. The SEARCH-TB panel amplifies Mtb 3,568 genes. Genes with high incidences of 0 expression values were excluded.
Sequenced mouse reads were processed using Trimmomatic v0.39 to remove TruSeq3-PE-2 adapter sequences, trim leading and trailing bases with a quality score below 3, and filter for reads longer than 36 bases after trimming. Reads were aligned to the mm39 genome assembly (GCA_000001635.9) and using Star v2.7.10b with default parameters. The genome assembly and associated annotation file were acquired from the University of California Santa Cruz Genomics Institute. Additional alignment metrics were collected using Picard v2.27.5. Genes with excessive number of zero values (>90%) or low variance across samples were removed from analysis, resulting in a final dataset of 29,579 host genes.
Assembly: 2016 Mtb Erdman reference assembly for Mtb sequencing reads. mm39 genome assembly (GCA_000001635.9) for murine sequencing reads.
Supplementary files format and content: Read counts per organism gene are provided in .txt format

source_name: Lung homogenate

growth_protocol: All animal procedures were conducted according to relevant national and international guidelines and approved by the Colorado State University Animal Care and Use Committee as described in the Supplemental Information. For the chronic infection model, 30 BALB/c female mice (7-9 weeks old) were infected with a low dose aerosol (LDA) of Mtb Erdman using the Glas-Col Inhalation Exposure System. This resulted in the deposition of 2.40 ± 0.07 (SEM) log10 CFU in lungs one day post-infection. Five mice were sacrificed on days 1, 7, 11, 19, 28, and 56 post-infection for lung specimen collection, respectively. Following sacrifice, the lungs were aseptically harvested and sectioned into the left lobe, upper right lob, and lower right robes for subsequent analysis.

extract_protocol:
Murine tissue samples were snap frozen in 7 mL Precellys tubes (Bertin) under liquid nitrogen. To each tissue sample, 1.5 mL GTC-TCEP buffer was added and samples were homogenized at 7,200 rpm for 16s using a Precellys Evolution (Bertin). Homogenates were incubated at room temperature for 5 minutes while protected from light. Unlysed mycobacterial cells were pelleted at 10,000g for 3 minutes, then resuspended in 0.8 mL RLT+ BME buffer (Qiagen, TCEP concentration 0.75 mM). Mycobacterial cells were lysed on a Precellys Evolution (Bertin) at 6,500 rpm for 30s three times, resting on ice for 5 minutes each time, and stored at -80C. After storage at -80C, murine lysates were thawed, and RNA was purified using the Maxwell simplyRNA tissue kit (murine samples) using the Maxwell RSC instrument following the manufacturer’s instructions with the following modifications. Additional kit DNase was added at twice the manufacturer’s recommended amount. Purified RNA was quantified using the Quantifluor RNA system (Promega).
Murine RNA was purified with Maxwell simplyRNA tissue kit while bacterial RNA was prepared for SEARCH-TB using Illumina’s AmpliSeq for Illumina Custom and Community RNA Panels kit.

treatment_protocol: no treatment was given.

value: Lung homogenate

value: BALB/c


title: MDS1254

last: Wang

description: MDS

source_name: human BM Mononuclear cells


title: OCI-AML-3 WT1 cells, replique 3

description: Library name: RNAseq_OCI3_WT1_rep3

source_name: OCI-AML-3 parental

value: OCI-AML-3 parental

value: OCI-AML-3 WT


title: MDS1252

description: MDS


title: 16792_mouse_Uninfected_Day_0

description: Library name: mm_16792


title: MDS1248

description: MDS


title: OCI-AML-3 WT1 cells, replique 2

description: Library name: RNAseq_OCI3_WT1_rep2


title: 16791_mouse_Uninfected_Day_0

description: Library name: mm_16791


title: MDS1244

description: MDS


title: OCI-AML-3 WT1 cells, replique 1

description: Library name: RNAseq_OCI3_WT1_rep1


title: MDS1243

description: MDS


title: 16790_mouse_Uninfected_Day_0

description: Library name: mm_16790


title: MDS1242

description: MDS


title: OCI-AML-3 H1-3 KO clone 2 cells, (Input)

description: Library name: ChIPseq_OCI3_H1.3_KO2_Input

data_processing:
Sequencing quality control was determined using the FastQC tool (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and aggregated across samples using MultiQC (v1.7)
Reads with a Phred quality score of less than 30 were filtered out and mapped to a human (Hg38) genome using using default parameters of Bowtie2 (v2.3.4.3) Only mapped reads were filtered in using samtools (v1.9). Duplicate tags were removed using Picard Tools
Peaks were called  using MACS2 callpeak (v2.1.2)  in broad mode (--broad broad-cutoff=0.05 -q 0.01 --nomodel)
bigWigs files were generated  using the deepTools suite (v3.2.1)
Assembly: GRCh38 reference genome
Supplementary files format and content: Bigwig

extract_protocol:
Cells were fix with 1% formaldehyde. Cell lysates were clarified from sonicated nuclei using a Diagenode Bioruptor, and histone-DNA complexes were isolated with antibody incubated over-night. Rabit IgG (Cell signaling; #2729S) was used as a control. Genomic DNA was purified using the i-Pure V2 kit (Diagenode)
Libraries were generated using the MicroPlex Library Preparation Kit (Diagenode) following the manufacturer's instructions and analyzed on a 2100 Bioanalyzer system (Agilent) prior sequencing

treatment_protocol: H1.3-V5 DNA was cloned into a doxycycline-inducible plasmid pLix-403 (Addgene) using the GATEWAY strategy. The plasmid (pLix403-H1.3-V5) was transfected into OCI-AML3 cells by electroporation using the Amaxa Kit V (program X-001) according to the manufacturer’s protocol. Transfected cells were selected 48 h after electroporation with puromycin 2 µg/mL, which was kept in the culture medium to maintain pressure selection. Expression of the H1.3-V5 construct was obtained with 1 µg/mL doxycycline and induction of expression was assessed by Western blot

value: CRISPR-Cas9 H1.3 KO

tag: chip antibody


title: 16789_mouse_Uninfected_Day_0

description: Library name: mm_16789


title: MDS1240

description: MDS


title: MDS1237

description: MDS


title: OCI-AML-3 H1-3 KO clone 2 cells, H1.2 antibody (ChIP)

description: Library name: ChIPseq_OCI3_H1.3_KO2_H1.2


title: MDS1236

description: MDS


title: OCI-AML-3 H1-3 cells, clone 2 replique 3

description: Library name: RNAseq_OCI3_H1.3_KO2_rep3


title: 15672_mouse_LDA_Day_56

description: Library name: mm_15672


title: OCI-AML-3 H1-3 KO clone 2 cells, H3K27me3 antibody (ChIP)

description: Library name: ChIPseq_OCI3_H1.3_KO2_H3K27me3

value: H3K27me3 (Cell Signaling; #9733S)


title: MDS1230

description: MDS


title: MDS1213

description: MDS


title: MDS1215

description: MDS


title: 15671_mouse_LDA_Day_56

description: Library name: mm_15671


title: 15670_mouse_LDA_Day_56

description: Library name: mm_15670


title: MDS1177

description: MDS


title: MDS1169

description: MDS


title: MDS1166

description: MDS


title: 15669_mouse_LDA_Day_56

description: Library name: mm_15669


title: MDS1164

description: MDS


title: MDS1163

description: MDS


title: OCI-AML-3 H1-3 KO clone 2 cells, H1 antibody (ChIP)

description: Library name: ChIPseq_OCI3_H1.3_KO2_H1

value: H1 (Active Motif; #39707)


title: OCI-AML-3 H1-3 KO clone 1 cells, (Input)

description: Library name: ChIPseq_OCI3_H1.3_KO1_Input

source_name: OCI-AML-3 H1-3KO clone 1

value: OCI-AML-3 H1-3KO clone 1


title: OCI-AML-3 H1-3 KO clone 1 cells, H1.2 antibody (ChIP)

description: Library name: ChIPseq_OCI3_H1.3_KO1_H1.2


title: MDS1161

description: MDS


title: 15667_mouse_LDA_Day_28

description: Library name: mm_15667


title: MDS1082

description: MDS


title: MDS1145

description: MDS


title: OCI-AML-3 H1-3 KO clone 1 cells, H3K27me3 antibody (ChIP)

description: Library name: ChIPseq_OCI3_H1.3_KO1_H3K27me3


title: MDS1080

description: MDS


title: 15666_mouse_LDA_Day_28

description: Library name: mm_15666


title: MDS1077

description: MDS


title: MDS1076

description: MDS


title: OCI-AML-3 H1-3 KO clone 1 cells, H3K9me3 antibody (ChIP)

description: Library name: ChIPseq_OCI3_H1.3_KO1_H3K9me3

value: H3K9me3 (Active Motif; #39161)


title: MDS1075

description: MDS


title: 15665_mouse_LDA_Day_28

description: Library name: mm_15665


title: OCI-AML-3 H1-3 KO clone 1 cells, H1 antibody (ChIP)

description: Library name: ChIPseq_OCI3_H1.3_KO1_H1


title: MDS1074

description: MDS


title: 15664_mouse_LDA_Day_28

description: Library name: mm_15664


title: MDS1073

description: MDS


title: OCI-AML-3 WT1 cells, assocated with the H1.3 ChIP (Input)

description: Library name: ChIPseq_OCI3_WT1_Input_H1.3

value: WT


title: MDS1072

description: MDS


title: OCI-AML-3 H1-3 KO clone 2 cells, H3K9me3 antibody (ChIP)

description: Library name: ChIPseq_OCI3_H1.3_KO2_H3K9me3


title: MDS1068

description: MDS


title: 15663_mouse_LDA_Day_28

description: Library name: mm_15663


title: OCI-AML-3 WT1 cells, H1.3 antibody (ChIP)

description: Library name: ChIPseq_OCI3_WT1_H1.3


title: MDS1065

description: MDS


title: 15662_mouse_LDA_Day_19

description: Library name: mm_15662


title: MDS1056

description: MDS


title: OCI-AML-3 WT1 cells, (Input)

description: Library name: ChIPseq_OCI3_WT1_Input


title: 15668_mouse_LDA_Day_56

description: Library name: mm_15668


title: MDS1052

description: MDS


title: 15661_mouse_LDA_Day_19

description: Library name: mm_15661


title: MDS1050

description: MDS


title: OCI-AML-3 WT1 cells, H1.2 antibody (ChIP)

description: Library name: ChIPseq_OCI3_WT1_H1.2


title: 15660_mouse_LDA_Day_19

description: Library name: mm_15660