title: Saline_C_3

city: New York

first: Li

last: Gan

address: 413 East 69th Street, 9th Floor BB904

institute: Weill Cornell Medicine

description:
Library name: Sample 13
mRNA expression in mouse striatum

data_processing:
Gene counts were obtained by aligning reads to the mouse genome (mm10) with Cell Ranger software (v.6.1.2) (10x Genomics).
To account for unspliced nuclear transcripts, reads mapping to pre-mRNA were counted. Cell Ranger 6.1.2 default parameters were used to call cell barcodes. Genes expressed in ≤3 cells were removed. Cells were filtered using dataset-specific thresholds for detected genes, UMI counts, and mitochondrial content: LID (nFeature_RNA 300–4,000; nCount_RNA <20,000; percent.mt <5%), LID_PLX (nFeature_RNA 300–5,000; nCount_RNA <15,000; percent.mt <1%), and LID_sTREM2 (nFeature_RNA 300–6,000; nCount_RNA <35,000; percent.mt <5%).
Potential doublet cells were predicted and removed using DoubletFinder for each sample.
SoupX was used to identify and remove ambient RNA from the dataset (Young et al., 2020)
Seurat v3.2.2 R package used for analysis
Assembly: mm10 genome
Supplementary files format and content: barcodes.tsv.gz: cellular barcodes present in datase
Supplementary files format and content: features.tsv.gz: IDs of quantified genes
Supplementary files format and content: matrix.mtx.gz: a matrix of count values, where rows are associated with the gene IDs above and columns correspond to the cellular barcodes.

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2019
Chromium Single Cell 3' Reagent Kits v3.1 (10x Genomics)

value: striatum

value: Male

value: non-lesioned saline-treated


title: 34OC

status: Public on Aug 03 2026

type: SRA

city: Pisa

first: Francesca

last: Scebba

address: Piazza martiri della libertà 33

country: Italy

institute: Scuola Superiore Sant'Anna

description: Library name: 30804-068

library_source: transcriptomic

data_processing:
Analysis was performed using CLC Genomics Server 21.0.4 with the QIAseq miRNA Quantification workflow and standard parameters. Reads were mapped to miRBase v22 after trimming of common sequences, UMIs, and adapters, followed by filtering of reads shorter than 15 nt or longer than 55 nt. Reads were then deduplicated based on their UMIs by grouping reads with the same start position, strand, and identical UMI. Singleton UMI groups were merged into non-singleton groups when their UMI differed by a single nucleotide (SNP), with assignment to the largest matching group.
All reads that don’t map to miRBase, neither with perfect matches nor as isomiRs (maximum 2 mismatches and/or alternative start/end position of 2 nt), are mapped the human genome GRCh38 with ENSEMBL GRCh38 version 97 annotation. This is carried out using the “RNA-Seq Analysis” workflow of CLC Genomics Server with standard parameters.
The ‘Empirical analysis of DGE’ algorithm of the CLC Genomics Workbench 21.0.4 was used for differential expression analysis with default settings.
Assembly: miRBase version 22
Supplementary files format and content: excel file with total miRNa count for each miRNA and each sample

molecule: total RNA

organism: Homo sapiens

source_name: saliva

extract_protocol:
RNA was isolated from 200 μl using the miRNeasy Serum/Plasma Kit (QIAGEN) according to manufacturer’s instructions
The library preparation was done using the QIAseq miRNA Library Kit (QIAGEN). A total of 5 μl total RNA was converted into miRNA NGS libraries. After adapter ligation, UMIs were introduced in the reverse transcription step. The cDNA was amplified using PCR (22 cycles) and during the PCR indices were added. After PCR the samples were purified. Library preparation was quality controlled using capillary electrophoresis (Agilent DNA 1000 Chip)

tag: tissue

value: saliva

tag: gender

value: female

tag: treatment

value: ovarian cancer


title: E42_1_ISVZ

city: Kunming

first: lei

last: shi

state: Yunnan

address: No.17 Longxin Road

country: China

institute: Kunming Institute of Zoology

description: Library name: Sample 25

data_processing:
Illumina  software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Chinese_treeshrew_genome_2.0(http://www.treeshrewdb.org/)whole genome using Hisat2
Gene expression counts per sample were calculated. First ly, align RNA seq reads to the Chinese_treeshrew_genome_2.0(http://www.treeshrewdb.org/)  by using  Hista2 to generate sam files; Then, sam files were sorted by samtools to generate sorted sam files; Finally, htseq-count program was used to quantify gene reads counts for every sample.
Assembly: Chinese_treeshrew_genome_2.0
Supplementary files format and content: Tab-delimited text files were calculated gene expression read counts  for each Sample

organism: Tupaia belangeri chinensis

source_name: Fetal cortex

extract_protocol:
The fetal tree shrew brain tissues were partitioned into several sections, after that, the specimens were embedded in OCT and then gradually frozen in an ethnol /dry ice, and stored at −80°C until processing. Frozen tissue was cryosectioned at 30μm onto polyethylene naphthalate (PEN) slides (Leica Microsystems) and place immediately into microslide box on dry ice, and stored at -80°C until use.   Taking the section slides from the -80°C freezer and put them on a blotting paper for 30s, and then transfer the slides into the 95% EtOH for 30s, 75% EtOH for 30s and 50% EtOH for 30s, place the slides on a blotting paper. Add 400ul Nissl stain solution on the slide, and incubate at room temperature for 40s. Proceed through the dehydration series (50%, 75% and 95% EtOH) till the two rounds of 100% EtOH, and leave the slides in the final xylene jar for 5 min. After air-drying in the fume hood for 5 min, proceed immediately with laser capture microdissection (LCM).   Laser microdissection was performed on a Leica LMD6000 (Leica Microsystems). Microdissected tissues including CP, OSVZ, SVZ and VZ were collected directly into QIAzol buffer from the miRNeasy Mini Kit (Qiagen) in a 0.2ml tubes, vortexed, centrifuged, and frozen at −80 °C. RNA was isolated following the manufacturer’s directions for the miRNeasy Mini Kit. RNA samples were run on the Agilent 2100 Bioanalyzer (Agilent Technologies).
RNA sequencing library construction followed VAHTs mRNA-seq V3 Library Prep Kit for Illumina (Vazyme, #NR611). The total RNA input was 0.7-1ug, mRNA (with ploy-A) binds to mRNA capture beads (with Oligo dT), mRNA is eluted from beads and then fragmented, synthesis of the 1st strand of cDNA using random primers, synthesis of the 2nd strand of cDNA after RNase H digestion. Size selection and library amplication after end repair and adapter ligation, the final RNA sequencing library length is between 320-420bp. Library quality determination analyzed by an Agilent Technologies 2100 Bioanalyzer.

value: Fetal cortex

tag: cortical layer

value: Inner sub-ventricular zone

tag: age

value: Embryonic 42 days


title: 84OC

description: Library name: 30804-067


title: E42_1_IZ

description: Library name: Sample 26

value: Intermediate zone


title: RTStop, 7-deaza-guanine, LiCl, PDS, rep1

city: Chapel Hill

first: Daniel

last: Dominguez

state: NC

address: 120 Mason Farm

department: Pharmacology

country: USA

institute: UNC Chapel Hill

description:
Library name: stG4_7dG_LiCl_PDS_Rep1
Column name in stG4_raw_counts.txt: St_7dG_LiCl_Rep1_PDS

data_processing:
Raw reads were trimmed of the universal Illumina adapter sequences using cutadapt.
Specifically:
cutadapt -j 10 -m 18 -a TGGAATTCTCGGGTGTCAAGG -g GAGTTCTACAGTCCGACGATC -o ${line}_primer_trim.fastq ${line}.fastq
Raw counts were generated by STAR mapping against (structural_pool.fasta, structural_pool.gtf). Specifically:
#### STAR index ####
STAR   --runMode genomeGenerate      --runThreadN 8   --genomeDir STAR_idx/library  --genomeFastaFiles structural_pool.fasta     --sjdbGTFfile structural_pool.gtf --genomeSAindexNbases 8
#### STAR count ####
#### notice: no mismatch
STAR --runThreadN 16 \
--genomeDir /STAR_idx/library \
--readFilesIn ./${line}_primer_trimmed.fastq \
--outFileNamePrefix STAR/${line} \
--sjdbGTFfile structural_pool.gtf \
--outFilterMultimapNmax 1 \
--outFilterMismatchNmax 0 \
--genomeLoad NoSharedMemory \
--outSAMtype BAM Unsorted \
--outReadsUnmapped Fastx \
--quantMode GeneCounts
Assembly: structural_pool.fasta, structural_pool.gtf
Supplementary files format and content: stG4_raw_counts.txt: All raw read counts for each sequence in the pool

organism: synthetic construct

source_name: RT Stop

extract_protocol:
In vitro transcribed synthetic RNA pools were made with guanine or 7dG. RT stop: RNAs were annealed in noted cations, then incubated with water or pyridostatin (where noted) for 10 minutes. RNA was reverse transcribed (RT) by SuperScript III in first strand buffer substituted with the noted cations for 40 minutes. Unless specifcially noted, RT was performed at 40ºC. After 40 minutes, samples were heated at 100ºC for 5 minutes, then proceeded to library preparation. RBNS: RNAs were annealed in KCl (or 7dG in LiCl), and allowed to incubate with noted proteins conjugated to streptavidin binding proteins. Bound RNA was eluted from streptavidin magnetic beads and concentrated by phenol-chloroform extraction. Subsequent RT was performed with SuperScript III in first strand buffer substituted with LiCl.
RT samples were PCR amplified with Phusion DNA polymerase to attach Illumina adapters and subsequently agarose gel purified. Concentrations were assessed by the Qubit dsDNA assay, and equivalent nanograms of each sample were pooled for sequencing.

value: RT Stop

tag: guanine or_7dg

tag: rt temperature

tag: cation (and/or_pds)_treatment

value: LiCl, PDS

tag: biological replicate


title: Col-0 control (bri1-1 and brl-tm), replicate 1

city: Freising

first: Brigitte

last: Poppenberger

state: Freising

address: Liesel-Beckmann-Str. 1

country: Germany

institute: Technical University of Munich

description:
Library name: FCHHL23CCX2_L2_ARArldtH005810-8_1
Wild-type Arabidopsis thaliana Col-0, replicate 1. Control for bri1-1 and brl-tM mutants.

library_source: genomic

data_processing:
Raw WGBS reads were processed using the MethylStar pipeline (v1.2.3). Reads were quality-checked with FastQC and trimmed using Trim Galore. Adapter- and quality-trimmed reads were aligned to the Arabidopsis thaliana TAIR10 reference genome using Bismark (v0.23.0) with Bowtie2. Methylation calling was performed using METHimpute (v1.18.0) to generate probabilistic estimates of cytosine methylation in CG, CHG, and CHH contexts. Strand-specific cytosine methylation profiles were converted to bigWig format using custom scripts.
DMRs were called using the jDMR-grid tool (published preliminary in Hazarika et al., 2022; available on GitHub repository: https://github.com/jlab-code/jDMRgrid/), comparing each mutant to its designated control wild-type to avoid batch effects. genome into non-sliding 100 bp regions with bins. We used all consecutive bins in the analysis. As filtering approach, we used jDMR build-in control/treatment strategy, for which both of the replicate have the same state call (replicate.consensus = 1).
Separate controls were used for the ces-D/qM and bri1-1/brl-tM mutant groups.
All coordinates are based on the TAIR10 (v57) genome build.
Assembly: TAIR10 v57
Supplementary files format and content: bigWig files: strand-specific cytosine methylation levels (CG, CHG, CHH contexts)
Supplementary files format and content: METHimpute files: CX-like reports generated from METHimpute implemented in MethylStar pipeline (CG, CHG, CHH and all contexts)

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: 21 dag soil-grown aerial tissue

growth_protocol: Seeds were germinated on ½ MS medium (Duchefa Biochemie), transferred to soil 7–8 days after germination, and grown under long-day conditions (16 h light / 8 h dark, 80 µmol m⁻² s⁻¹, 50% humidity) in a growth cabinet (Bright Boy, CLF Plant Climatics, Wertingen, Germany) at 21 ± 2 °C.

extract_protocol:
DNA was extracted from 100 mg of aerial tissue of 3-week-old plants using the DNeasy Plant Mini Kit (Qiagen, Hilden, Germany). DNA was precipitated using sodium acetate, ethanol, and glycogen, and quality-checked before submission.
DNA was bisulfite-converted and used for library preparation by BGI Genomics (Tech Solution NGS Lab, Hong Kong) using the DNBseq WGBS protocol for sequencing on the Illumina HiSeq X Ten platform.

treatment_protocol: For Hpa-infected samples, 2-week-old plants were spray-inoculated with Hyaloperonospora arabidopsidis isolate Noco2 (5 × 10⁴ conidiospores/mL). Control samples were mock-treated with water. Plants were incubated at 18 °C under high humidity (90–100%) and 16 h light / 8 h dark conditions.

value: 21 dag soil-grown aerial tissue

tag: genotype

tag: batch


title: Metrnl-null, AAV9–Metrnl, Myocardial infarction (day 4) #1

city: Barcelona

first: Ana

last: Planavila Porta

state: Catalunya

address: Avinguda Diagonal, 643

department: Bioquímica i Biomedicina Molecular

country: Spain

institute: Universitat de Barcelona

description:
Library name: KOMetInf_1
normalized_counts.csv sample column: barcode_1_5

library_source: transcriptomic single cell

data_processing:
Cell Ranger - 10x Genomics
Downstream analyses, including normalization, dimensionality reduction, clustering, and cell-type annotation, were performed using standard single-cell RNA sequencing analysis pipelines.
Assembly: GRCm39 mouse reference genome
Supplementary files format and content: normalized_counts.csv : CSV file with data of normalized counts for all samples

molecule: nuclear RNA

organism: Mus musculus

source_name: Heart

growth_protocol: Mice were housed at 22 °C under a 12-h light cycle  (lights on from 08.00 am to 08.00 pm) with 50% ±5% relative humidity with free access to water and a standard diet.

extract_protocol:
Cardiac tissue for single-nucleus RNA sequencing (snRNA-seq) was processed and performed by the Novogene platform (Sacramento, CA). Briefly, frozen samples were mechanically homogenized in nuclei isolation buffer using Dounce homogenization, followed by filtration and centrifugation to obtain a clean nuclear suspension. Nuclei were stained with DAPI and sorted by fluorescence-activated nuclei sorting (FANS) to enrich for intact singlet nuclei. Purified nuclei were processed using the 10x Genomics Chromium platform for droplet-based encapsulation, barcoding, and library preparation according to the manufacturer’s instructions, with optimization for nuclear RNA capture.
Isolated and tagged nuclear RNA reads were sequenced with NovaSeq X Plus. Shortly, reads were aligned to the reference genome with intronic regions included to account for pre-mRNA, and unique molecular identifiers (UMIs) were used for transcript quantification. Gene expression matrices were generated and subjected to quality control to exclude low-quality nuclei and potential doublets.

treatment_protocol: 7-days old wild type (Wt) or Meteorin-like null (Metrnl⁻/⁻) mice were injected intraperitoneally (i.p.) 30 microliter of purified AAV9-Null or AAV9-Metrnl (10e13 gc/mL) At 14 weeks of age. The three groups of mice (Wt AAV9-Null, Metrnl⁻/⁻ AAV9-Null and Metrnl⁻/⁻ AAV9-Metrnl) were induced a myocardial infarction (MI) by left anterior descending (LAD) coronary artery ligation. 4 days after the myocardial infarction, mice were euthanised under anesthesia using a cardioplegic solution.

value: Heart

value: Metrnl-/-

value: AAV9-Metrnl + myocardial infarction


title: E42_1_CPo

description: Library name: Sample 24

value: Outer cortical plate


title: 164HS

description: Library name: 30804-066

value: healthy


title: ces-qM, replicate 2

description:
Library name: FCH7H5GCCX2_L5_ARAqwrMAAAFAAA-29
Arabidopsis thaliana ces-qM loss-of-function mutant, replicate 2.

value: ces-qM


title: Metrnl-null, AAV9–Null, Myocardial infarction (day 4) #2

description:
Library name: KONullInf_2
normalized_counts.csv sample column: barcode_1_4

value: AAV9-Null + myocardial infarction


title: E42_1_CPi

description: Library name: Sample 23

value: Inner cortical plate


title: ces-qM, replicate 1

description:
Library name: FCH7H5GCCX2_L5_ARAqwrMAAAEAAA-28
Arabidopsis thaliana ces-qM loss-of-function mutant, replicate 1.


title: Metrnl-null, AAV9–Null, Myocardial infarction (day 4) #1

description:
Library name: KONullInf_1
normalized_counts.csv sample column: barcode_1_3


title: 136OC

description: Library name: 30804-064

value: saliva

value: female


title: Wild type, AAV9–Null, Myocardial infarction (day 4) #2

description:
Library name: WTNullInf_2
normalized_counts.csv sample column: barcode_1_2

value: Wt


title: E37_3_IZ

description: Library name: Sample 21

value: Fetal cortex

value: Embryonic 37 days


title: ces-D, replicate 2

description:
Library name: FCH7H5GCCX2_L5_ARAqwrMAAADAAA-19
Arabidopsis thaliana ces-D gain-of-function mutant, replicate 2.

value: ces-D


title: E37_3_MZ

description: Library name: Sample 22

value: Marginal zone


title: 138OC

description: Library name: 30804-062

value: ovarian cancer


title: Wild type, AAV9–Null, Myocardial infarction (day 4) #1

description:
Library name: WTNullInf_1
normalized_counts.csv sample column: barcode_1_1


title: E37_3_CPo

description: Library name: Sample 20


title: Col-0 control (ces-D and ces-qM), replicate 2

description:
Library name: FCH7H5GCCX2_L5_ARAqwrMAAABAAA-17
Wild-type Arabidopsis thaliana Col-0, replicate 2. Control for ces-D and ces-qM mutants.

value: 21 dag soil-grown aerial tissue


title: MS666

city: Baltimore

first: Myong-Hee

last: Sung

state: Maryland

address: 251 Bayview Boulevard

department: National Institute on Aging

institute: National Institutes of Health

description: Library name: Sample 60

data_processing:
Stranded 151-bp paired-end reads were aligned to the mouse reference genome (GRCm39, Genome Reference Consortium (GRC) 2020) using STAR v2.7.11b (Dobin et al., 2013). The reads were counted per gene using RSEM v1.3.3 (Li & Dewey, 2011). Downstream processing was performed in R using edgeR.
Assembly: GRCm39
Supplementary files format and content: xlsx file including FPKM for all samples

source_name: Immortalized Ear Fibroblast GR NLS-iRFP-NLS

extract_protocol:
Primary ear fibroblasts were isolated from adult DKI mice and cultured as previously described (Rahman et al., 2022). Briefly, dissected ear tissue was minced, enzymatically dissociated, and plated in standard growth medium (DMEM supplemented with 10% FBS, 1% penicillin, streptomycin, and L-glutamine). Cells were maintained in phenol-red-containing medium to facilitate pH monitoring during long-term culture. To generate stable immortalized fibroblast lines, primary cultures were expanded and routinely passaged every 72 hours for approximately 20-25 passages, at which point they exhibited hallmark features of immortalized fibroblasts, including sustained proliferation and stable expression of endogenous fluorescent RelA and c-Rel reporters.
Immortalized mouse ear fibroblasts were seeded at medium confluence in 6-cm tissue culture dishes and cultured overnight at 37 °C in humidified incubator with 5% CO2 to ensure recovery and stable basal transcriptional activity. The following day, cultures were transferred to incubators pre-equilibrated to 24 °C, 34 °C, 37 °C, or 40 °C and were allowed to adapt for 2 hours to establish temperature-specific steady states prior to stimulation. Cells were then either left untreated (0h) or stimulated with recombinant murine TNF-α (10ng/mL) or IL-1β (10ng/mL) for 1 hour or 3 hours. At each time point, cells were lysed directly on the plate using RLT buffer (Qiagen). Lysates were stored at -80°C until processing. Total RNA quantity and purity were assessed using a NanoDrop spectrophotometer (ThermoFisher). Three independent biological replicates were collected for each experimental condition. In total, 60 RNA-seq libraries were generated: 48 stimulated samples (4 temperatures x 2 cytokines x 2 time-points x 3 biological replicates) and 12 unstimulated baseline controls collected at 0h across the four temperatures (3 replicates each).

tag: cell line

tag: temperature

value: Treated 3h IL-1b

tag: replicate


title: Col-0 control (ces-D and ces-qM), replicate 1

description:
Library name: FCH7H5GCCX2_L5_ARAqwrMAAAAAAA-16
Wild-type Arabidopsis thaliana Col-0, replicate 1. Control for ces-D and ces-qM mutants.


title: E37_3_CPi

description: Library name: Sample 19


title: 141OC

description: Library name: 30804-061


title: 142OC

description: Library name: 30804-060


title: E37_2_MZ

description: Library name: Sample 18


title: MS665

description: Library name: Sample 59

value: Immortalized Ear Fibroblast GR NLS-iRFP-NLS

value: Treated 1h IL-1b


title: AdjNormal_M131N

type: RNA

city: Darlinghurst

first: Merrin Mary

last: Eapen

state: NSW

address: 384 Victoria St

country: Australia

institute: Garvan Institute of Medical Research

description: Adjacent normal liver tissue, Xenium spatial transcriptomics performed using a 462-gene panel.

hyb_protocol: Probe hybridization was carried out overnight at 50°C according to manufacturer's protocol either using a 462-gene (Tumor 1, Tumor 2, and Adjacent Normal) or a 319-gene (Tumor 3) Xenium Standalone Custom panel, followed by ligation, and rolling circle amplification. Cell segmentation staining was performed using Xenium Multi-Tissue Stain Mix, followed by autofluorescence quenching and nuclei staining.

scan_protocol: The tissue sections were imaged on 10x Genomics Xenium In Situ Analyzer.

data_processing: Raw data was processed using the Xenium Onboard Analysis software.

label: Xenium probe set

source_name: Liver

label_protocol: Xenium probe set

extract_protocol: tissue preparation protocol: The samples were sectioned at 5µm thickness and placed onto Xenium slides. This was followed by deparaffinization, rehydration, and decrosslinking of the tissue sections.

value: Liver

tag: tissue preservation method

value: FFPE

value: matched adjacent normal liver sample

tag: sample identifier


title: 144OC

description: Library name: 30804-059


title: E37_2_IZ

description: Library name: Sample 17

value: Intermediate zone


title: 146HS

description: Library name: 30804-058

value: healthy


title: E37_2_CPo

description: Library name: Sample 16

value: Outer cortical plate


title: E37_2_CPi

description: Library name: Sample 15

value: Inner cortical plate


title: 147HS

description: Library name: 30804-057

value: saliva

value: female


title: tumor2_M131T

description: CRLM tumor tissue section, Xenium spatial transcriptomics performed using a 462-gene panel.

value: CRLM tumor


title: tumor1_M242T


title: MS661

description: Library name: Sample 55


title: 163HS

description: Library name: 30804-056


title: E37_1_IZ

description: Library name: Sample 14

value: Fetal cortex

value: Embryonic 37 days


title: MS660

description: Library name: Sample 54


title: WT_cx20_5dpf_3

city: Durham

last: Levic

address: 307 Research Drive

department: Cell Biology

institute: Duke University

description: Library name: Sample 6

data_processing:
Trimmomatic(v0.38) was used to trim sequencing adapters
Reads were aligned to the zebrafish genome (GRCz11)  using STAR 2.7.11.a
Reads were counted using featureCounts in the Subread package (v1.6.3)
Assembly: GRCz11
Supplementary files format and content: tab-delimited text files includes counts for each sample

organism: Danio rerio

source_name: Whole larvae

extract_protocol:
Total RNA from n=40 larvae (3 replicates) was extracted in Trizol, treated with DNase, and then purified using RNA Clean & Concentrator-5 columns (Zymo).
RNA-sequencing libraries were made from ≥500ng of total RNA extracted from whole larvase using the Illumina Stranded mRNA prep kit.

value: Whole larvae

value: All cells

tag: cell type

value: Wildtype

value: 5 dpf


title: 152HS

description: Library name: 30804-055

tag: tissue


title: WT_cx20_5dpf_2

description: Library name: Sample 5


title: MS659

description: Library name: Sample 53

value: Immortalized Ear Fibroblast GR NLS-iRFP-NLS

value: Treated 3h TNF-a


title: 71OC

description: Library name: 30804-054

tag: gender

value: ovarian cancer


title: E28_2_VZ

description: Library name: Sample 12

value: Ventricular zone

value: Embryonic 28 days


title: MS658

description: Library name: Sample 52

tag: treatment

value: Treated 1h TNF-a


title: WT_cx20_5dpf_1

description: Library name: Sample 4


title: E28_2_OSVZ

description: Library name: Sample 11

tag: cortical layer

value: Outer sub-ventricular zone


title: SNPC4_72h_input_dataset2_replicate3

status: Public on Aug 04 2026

first: John

last: Kim

state: MD

address: 3400 Charles Street

department: Department of Biology

institute: Johns Hopkins University

description:
Library name: ChIP2021-047-SNPC4-72h-WW
snpc-4::3xflag 72h SNPC-4 ChIP-seq input dataset2 replicate3

data_processing:
Demultiplexed raw data were processed as described previously (Choi et al., 2021).
Global enrichment of SNPC-1.2 ChIP-seq signal at piRNA clusters on chromosome IV was assessed by calculating normalized read coverage across consecutive, non-overlapping 1-kb bins across the C. elegans genome.
Binding profiles and heatmaps for SNPC-1.1, SNPC-1.2, SNPC-1.3, and SNPC-4 at piRNA and snRNA loci were generated using MACS v2.1.2 (Zhang et al., 2008) and deepTools (Ramírez et al., 2016).
Fold-enrichment signal tracks were produced from read count-normalized genome-wide pileup and lambda track outputs using callpeak (bdgcmp in MACS2). Enrichment signal track regions overlapping with regions in the ENCODE ce 11 blacklist (https://github.com/Boyle-Lab/Blacklist/) were removed from further analysis.
Assembly: WBcel235
Supplementary files format and content: narrowPeak, bigWig

organism: Caenorhabditis elegans

source_name: whole worm

extract_protocol:
Liquid culture growth at 20°C was performed as described previously (Zanin et al., 2011). Approximately 2.5 million animals were grown per 2-L flask in 500 mL complete S Basal medium. For staged collections at 48 and 72 h post-L1 hatching, animals were harvested at 48 h and remaining animals were transferred to fresh complete S Basal containing HB101. For SNPC-1.2 ChIP, animals were cleaned by sucrose flotation prior to live cross-linking. Cross-linking was performed by nutating animals in 2.6% formaldehyde for 30 min at room temperature and quenched by addition of glycine (final concentration 0.125 M) for 5 min. Animals were then washed 3 times in water, flash-frozen in liquid nitrogen, and stored at -80°C until use.  ChIP was performed as described previously (Weiser et al., 2017), with the addition of proteinase K during de-crosslinking. Extracted DNA was resuspended in 18 µL 1 M Tris-EDTA pH 8 and 2 µL of 20 mg/mL RNase A (Invitrogen). SNPC-1.1 ChIP was performed using germline nuclei isolated from animals as described previously (Kirshner et al., 2025).
ChIP-seq libraries were prepared and multiplexed using the Ovation Ultralow Library Systems v2 kit (NuGEN Technologies) according to the manufacturer’s protocol. Libraries were sequenced as 50-bp paired-end reads on a NovaSeq 6000 platform (Illumina).

value: whole worm

tag: age

value: 72h gravid adult

value: input


title: MS657

description: Library name: Sample 51

value: Unstimulated


title: E28_2_MZ

description: Library name: Sample 10

value: Fetal cortex

value: Marginal zone


title: 189HS

description: Library name: 30804-052

value: saliva

value: female

value: healthy


title: Mut_cx20_5dpf_2

description: Library name: Sample 2

value: Whole larvae

value: All cells

value: pdcd7/cx20 mutant

value: 5 dpf


title: MS656

description: Library name: Sample 50

value: Immortalized Ear Fibroblast GR NLS-iRFP-NLS

value: Treated 3h IL-1b


title: 39BC

description: Library name: 30804-051

value: breast cancer


title: E28_2_IZ

description: Library name: Sample 9

value: Intermediate zone

value: Embryonic 28 days


title: Mut_cx20_5dpf_1

description: Library name: Sample 1


title: MS655

description: Library name: Sample 49

value: Treated 1h IL-1b


title: E28_2_ISVZ

description: Library name: Sample 8

value: Inner sub-ventricular zone


title: Naked mole-rat, liver, NMR32

city: London

first: Diego

last: Villar

address: 4 Newark Street, Blizard Institute

country: United Kingdom

institute: Queen Mary University of London

description: Library name: Hgla_Liver_Rep4

data_processing:
Sequencing adaptors and low-quality reads were removed using Cutadapt with the following parameters: a minimum read length of 25 bp after trimming (-m 25), a minimum sequence quality score of 30 (-q 30), and the removal of any reads containing more than one N base (--max-n 1).
Trimmed reads from each species were pseudo-aligned and quantified to their respective reference transcriptome using Salmon v.013.1, with a decoy-aware index. The pseudo-mapping process included corrections for GC content bias (--gcBias) and sequence-specific biases (--seqBias). Quantification was performed at the transcript level.
For each species, we summarised transcript-level abundance estimates generated by Salmon to the gene level using the tximport v1.24 R package, with counts corrected for effective transcript length via the lengthScaledTPM method. To enable cross-species comparisons, we retained only one-to-one orthologous genes. We then merged gene-level count matrices across species and imported them into DESeq2. We normalised the combined dataset across all samples using the median-of-ratios method implemented in DESeq2, which adjusts for library size by computing sample-specific size factors as the median of ratios of observed counts to a pseudo-reference (the geometric mean across samples for each gene). To account for technical variation introduced by different data sources, we included a batch term in the DESeq2 model (~species + data source). Finally, we applied the variance-stabilising transformation (VST) to the normalised counts, which were then used for downstream analyses.
Assembly: The reference genome and transcriptomes for naked mole-rat (HetGla1.0), Damara mole-rat (DMRv1.0), guinea pig (Cavpor3.0) and mouse (GRCm38) were downloaded from Ensembl v102
Supplementary files format and content: Vst-normalised counts across 13,929 one-to-one orthologous for each sample in the study

organism: Heterocephalus glaber

source_name: liver

extract_protocol:
Total RNA was extracted from 10-50 mg of tissue samples, previously flash-frozen in dry ice and kept at -80C. Briefly, frozen tissue samples were homogenised in lysis buffer (RNAEasy, Qiagen) using homogenisation beads (Precellys hard tissue homogenising tubes CK28) in a FastPrep-24 tissue homogeniser (MP Biosciences) with three 20 s pulses at a speed of 4.5 m/s. Homogenised tissue lysates were used directly for RNA extraction using a commercial RNA extraction kit (RNEasy, Qiagen).
500 ng of total RNA from each sample were used for preparation of total RNA-sequencing libraries with NEBNext UltraTM II RNA Library Prep Kit for Illumina (New England Biolabs). Briefly, total RNA was depleted of ribosomal RNA (rRNA) with rRNA Depletion Kit v2 (New England Biolabs) and RNA sample purification beads. rRNA-depleted RNA was used for preparation of cDNA and RNA-sequencing libraries following manufacturer specifications, with 12-15 minutes of RNA fragmentation at 94C and 10 cycles of PCR amplification. RNA-sequencing libraries were quantified by quantitative PCR with Kapa Illumina library quantification kit (Roche diagnostics) in a Roche LC480 instrument. RNA-seq libraries were then pooled in equimolar concentrations and sequenced in an Illumina NovaSeq instrument by commercial supplier Novogene UK.

value: liver

tag: Sex

value: male

tag: age (months)

tag: individual


title: MS654

description: Library name: Sample 48

value: Treated 3h TNF-a


title: PA-24h

city: Cambridge

first: Irina

last: Mohorianu

address: Puddicombe Way

department: Wellcome-MRC Cambridge Stem Cell Institute

institute: University of Cambridge

data_processing:
Quality of fastq files was assessed with FastQC v0.11.3, MultiQC v1.8.
Alignment and protein-coding gene quantification was performed using 10x cellranger v3.1.0
Normalization of expression was levels was performed with sctransform (Hafemeister and Satija, 2019)
Genome_build: GRCh38
Supplementary_files_format_and_content: csv files of raw and post-QC normalized expression levels

source_name: human induced pluripotent stem cells, primary human cholangiocytes, human immortalised stellate cells line

growth_protocol: hIPSC-derived hepatocytes, macrophages, cholangiocytes and stellate cells were seeded at physiologic ratio and grown in a collagen based 3D system for up to 1week.

extract_protocol:
The single cell solution from each sample was loaded onto the Chromium single cell controller by 10X genomics, a droplet-based single cell capture platform.
Single cells were lysed and tagged by a bead containing unique molecular identifiers (UMIs), and encapsulated in an oil droplet.; this emulsion was amplified through reverse-transcription, and subsequent library preparation was performed following the 10X Genomics manual instructions.

treatment_protocol: 3D co-cultures were treated with free fatty acids (Oleic Acid or Palmitic Acid) for 24hrs up to 1week.

value: palmitic acid 0.25uM

tag: time point

value: 24 hours

tag: disease state

value: NAFLD


title: 167HS

description: Library name: 30804-049

value: saliva

value: female

value: healthy


title: Naked mole-rat, liver, NMR30

description: Library name: Hgla_Liver_Rep3


title: MS653

description: Library name: Sample 47

value: Treated 1h TNF-a


title: 4T1 mammary carcinoma tumor, FMI.12 mtDNA mutant, mtscATAC-seq

city: Los Angeles

first: Michael

last: Teitell

state: CA

address: 675 Charles E Young Drive South

department: Pathology and Laboratory Medicine

institute: University of California Los Angeles

description:
Library name: 4T1FMI
single-cell ATAC-seq (mtscATAC-seq) with mitochondrial genotyping

data_processing:
Cell Ranger ATAC (v2.1.0) / Cell Ranger ARC (v2.0.2, multiome) were used to align reads to the mouse mm10 reference (NUMT-masked) and to call peaks, fragments, and per-cell matrices.
Mitochondrial single-cell genotyping was performed with mgatk (v0.9.0) to generate per-position, per-cell base counts (A/C/G/T), coverage, and depth tables.
Heteroplasmy and mtDNA variant statistics were computed per cell from the mgatk output.
Cell type annotation and downstream analysis were performed in R/Signac/Seurat.
Assembly: mm10 (GRCm38); chrM (16,299 bp)
Supplementary files format and content: mtscATAC-seq per sample: fragments.tsv.gz (+.tbi), filtered_peak_bc_matrix.h5, peaks.bed, singlecell.csv; mgatk: {A,C,G,T}.txt.gz and coverage.txt.gz (CSV: position,barcode,fwd,rev / position,barcode,coverage), depthTable.txt, chrM_refAllele.txt, variant_stats.tsv.gz, cell_heteroplasmic_df.tsv.gz.
Supplementary files format and content: Multiome per sample: atac_fragments.tsv.gz (+.tbi), filtered_feature_bc_matrix.h5 (Gene Expression + Peaks), per_barcode_metrics.csv; plus mgatk mtDNA files as above.

source_name: mammary carcinoma

growth_protocol: rho0 B16 melanoma and 4T1 mammary carcinoma cells were repopulated with defined homoplasmic single-nucleotide mtDNA variants by MitoPunch mitochondrial transfer to generate isogenic, mtDNA-barcoded tumor cell lines, maintained in DMEM/10% FBS at 37C, 5% CO2.

extract_protocol:
Tumors were dissociated to single-cell/nuclei suspensions; nuclei were isolated for single-cell ATAC-seq / 10x Multiome following 10x Genomics protocols.
Libraries were prepared with the 10x Genomics Chromium Single Cell ATAC kit (mtscATAC-seq samples) or the 10x Genomics Chromium Single Cell Multiome ATAC + Gene Expression kit (NOD scid samples), per manufacturer instructions.

treatment_protocol: Barcoded tumor cells were implanted into syngeneic (B16 in C57BL/6; 4T1 in BALB/c) or immunodeficient NOD scid mice and grown in vivo; tumors were harvested for single-cell profiling.

value: mammary carcinoma

value: tumor and tumor-infiltrating cells

tag: genotype

value: rho0 4T1 repopulated with homoplasmic mtDNA mutant (FMI.12)

value: tumor in BALB/c host, in vivo


title: 168HS

description: Library name: 30804-048


title: Naked mole-rat, liver, NMR31

description: Library name: Hgla_Liver_Rep2


title: MS652

description: Library name: Sample 46

tag: cell line

value: Immortalized Ear Fibroblast GR NLS-iRFP-NLS

value: Unstimulated


title: E28_1_OSVZ

description: Library name: Sample 5

value: Fetal cortex

value: Outer sub-ventricular zone

value: Embryonic 28 days


title: Naked mole-rat, liver, NMR35

description: Library name: Hgla_Liver_Rep1

value: liver

value: male


title: 169HS

description: Library name: 30804-047


title: MS651

description: Library name: Sample 45

tag: temperature

value: Treated 3h IL-1b


title: E28_1_MZ

description: Library name: Sample 4

value: Marginal zone


title: 171HS

description: Library name: 30804-046

value: saliva


title: MS650

description: Library name: Sample 44

value: Treated 1h IL-1b

tag: replicate


title: Naked mole-rat, heart, NMR34

description: Library name: Hgla_Heart_Rep3

source_name: heart

value: heart


title: 173HS

description: Library name: 30804-045

value: female

value: healthy


title: E28_1_VZ

description: Library name: Sample 6

value: Ventricular zone


title: MS649

description: Library name: Sample 43

value: Treated 3h TNF-a


title: E28_1_IZ

description: Library name: Sample 3

value: Intermediate zone


title: Naked mole-rat, heart, NMR35

description: Library name: Hgla_Heart_Rep2


title: 174HS

description: Library name: 30804-044


title: 230HS

description: Library name: 30804-050


title: HH 30 SAN Vehicle treatment pool 1

city: Chapel Hill/ 27599

last: Bressan

address: 100 Mason Farm Rd

department: Cell Biology and Physiology

institute: University of North Carolina Chapel Hill

description:
Library name: SAN_veh_1
column name in Log2_exp:SAN_veh_1

data_processing:
RNA sequencing quality assurance was run using FastQC
Index construction and read mapping were performed using Kallisto
Differntial gene analysis was preformed using edgeR and limma
Assembly: bGalGal1.mat.broiler.GRCg7b
Supplementary files format and content: cvs file including log2 counts for expressed genes

organism: Gallus gallus

source_name: HH stage 30 SAN

extract_protocol:
RNA was extracted using a standard Trizol/chloroform protocol.
Library preparation was conducted using the Illumina Stranded Total RNA-SEQ with Ribo-Zero Kit

treatment_protocol: Isolated primary tissue was cultured in DMEM/F12 with 15% FBS, 1% penicillin-streptomycin, and 1% amphotericin B with 0.25ug/ml CN03 or 1ul dH20 (vehicle)

value: HH stage 30 SAN

value: Vehicle


title: E28_1_ISVZ

description: Library name: Sample 2

value: Fetal cortex

value: Inner sub-ventricular zone


title: Naked mole-rat, heart, NMR30

description: Library name: Hgla_Heart_Rep1


title: 180HS

description: Library name: 30804-043


title: MS648

description: Library name: Sample 42

value: Immortalized Ear Fibroblast GR NLS-iRFP-NLS

value: Treated 1h TNF-a


title: E28_1_CP

description: Library name: Sample 1

value: Cortical plate

value: Embryonic 28 days


title: E28_2_CP

description: Library name: Sample 7


title: 183HS

description: Library name: 30804-042


title: MS647

description: Library name: Sample 41

value: Unstimulated


title: C4

city: palo alto

first: Joseph

last: wu

address: 265 Campus Drive

institute: Stanford university

description: Library name: C4

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trimmomatic.
Trimmed sequence reads were mapped to hg38 using STAR.
Gene- and transcript-level expression abundances were quantified using RSEM.Expression values were reported as expected counts, transcripts per million (TPM), and fragments per kilobase of transcript per million mapped reads (FPKM).
Assembly: hg38
Supplementary files format and content: *.isoforms.results.gz includes isoform-level expression results for each Sample
Supplementary files format and content: *.genes.results.gz includes Gene-level expression results for each Sample

source_name: ipsc C line

growth_protocol: COs are generated by mixing iPSC-CMs and iPSC-CFs

extract_protocol:
Qiazol for RNA extraction
Bulk RNA sequencing. The library is generated by Novogene

treatment_protocol: Drug treatment for 72 hrs

value: ipsc C line

value: iPSC-CO (CM+CF)

tag: differentiation stage

value: male

value: WT


title: R11 ctrl smoker

city: Heidelberg

first: Fabienne Dorothea

last: Lusky

address: Röntgenstr. 1

institute: Thoraxklinik at Heidelberg University Hospital

hyb_protocol: We used the excellent Expression Profiling services of the Microarray Core Facility, German Cancer Research Center (DKFZ), all information can be found on their website

data_processing: For statistical analysis we used R and the bioconductor package simpleaffy and affy, we transformed our data using RMA Algorithm

label: biotin

source_name: Whole blood

extract_protocol: We used the  PAXgene Blood RNA Kit according to the manufacturer’s instructions (PreAnalytiX, Hombrechtikon, CH)

treatment_protocol: Whole blood RNA was collected in PAXGene blood RNA tubes and incubated at room temperature for 2 hours to maximize cell lysis. Samples were stored frozen at  -80°C until processing

tag: sample type

value: control group

tag: group


title: 184HS

description: Library name: 30804-041

tag: tissue

value: saliva

value: female

value: healthy


title: C3

description: Library name: C3

tag: cell type


title: MS646

description: Library name: Sample 40

tag: treatment

value: Treated 3h IL-1b


title: R10 ctrl smoker

scan_protocol: We used the excellent Expression Profiling services of the Microarray Core Facility, German Cancer Research Center (DKFZ), all information can be found on their website


title: 214HS

description: Library name: 30804-040

tag: gender


title: MS645

description: Library name: Sample 39

value: Treated 1h IL-1b


title: C2

description: Library name: C2


title: R9 ctrl smoker

label_protocol: We used the excellent Expression Profiling services of the Microarray Core Facility, German Cancer Research Center (DKFZ), all information can be found on their website


title: Metrnl-null, AAV9–Metrnl, Myocardial infarction (day 4) #2

description:
Library name: KOMetInf_2
normalized_counts.csv sample column: barcode_1_6

value: Heart

value: Metrnl-/-

value: AAV9-Metrnl + myocardial infarction


title: R8 ctrl smoker


title: 203HS

description: Library name: 30804-038


title: MS643

description: Library name: Sample 37

value: Immortalized Ear Fibroblast GR NLS-iRFP-NLS

value: Treated 1h TNF-a


title: MS644

description: Library name: Sample 38

value: Treated 3h TNF-a


title: 215HS

description: Library name: 30804-039


title: B4

description: Library name: B4

source_name: ipsc B line

value: ipsc B line


title: C1

description: Library name: C1

value: ipsc C line

value: Veh


title: MS642

description: Library name: Sample 36

value: Unstimulated


title: 165HS

description: Library name: 30804-065

source_name: saliva


title: 137OC

description: Library name: 30804-063

value: ovarian cancer


title: ces-D, replicate 1

description:
Library name: FCH7H5GCCX2_L5_ARAqwrMAAACAAA-18
Arabidopsis thaliana ces-D gain-of-function mutant, replicate 1.

value: 21 dag soil-grown aerial tissue

value: ces-D

tag: batch


title: R6 ctrl smoker

value: control group


title: R7 ctrl smoker


title: 213HS

description: Library name: 30804-037

value: saliva

value: female

value: healthy


title: B3

description: Library name: B3

value: iPSC-CO (CM+CF)

tag: Sex

value: male

value: WT


title: MS641

description: Library name: Sample 35

value: Immortalized Ear Fibroblast GR NLS-iRFP-NLS

value: Treated 3h IL-1b


title: B2

description: Library name: B2


title: 209HS

description: Library name: 30804-036


title: 205HS

description: Library name: 30804-035


title: MS640

description: Library name: Sample 34

value: Treated 1h IL-1b


title: R5 ctrl smoker


title: MS639

description: Library name: Sample 33

value: Treated 3h TNF-a


title: B1

description: Library name: B1

value: ipsc B line


title: R4 ctrl smoker


title: 204HS

description: Library name: 30804-034


title: A4

description: Library name: A4

source_name: ipsc A line

value: ipsc A line


title: R3 ctrl smoker


title: MS664

description: Library name: Sample 58


title: tumor3_M397T

description: CRLM tumor tissue section, Xenium spatial transcriptomics performed using a 319-gene panel.

value: Liver

tag: tissue preservation method

value: FFPE

value: CRLM tumor

tag: sample identifier


title: MS662

description: Library name: Sample 56

value: Unstimulated


title: MS663

description: Library name: Sample 57

value: Treated 1h TNF-a


title: MS638

description: Library name: Sample 32


title: 199HS

description: Library name: 30804-033

value: saliva


title: A3

description: Library name: A3


title: 196HS

description: Library name: 30804-032

value: female


title: MS637

description: Library name: Sample 31


title: MS636

description: Library name: Sample 30


title: 194HS

description: Library name: 30804-031

value: healthy


title: A1

description: Library name: A1

value: iPSC-CO (CM+CF)

value: Veh


title: A2

description: Library name: A2

value: male

value: WT


title: R1 ctrl smoker

value: control group


title: MS635

description: Library name: Sample 29

value: Immortalized Ear Fibroblast GR NLS-iRFP-NLS

value: Treated 1h IL-1b


title: N10 ctrl non-smoker


title: N9 ctrl non-smoker


title: 191HS

description: Library name: 30804-030


title: MS634

description: Library name: Sample 28

value: Treated 3h TNF-a


title: Muscle, male, Nega, rep2

city: Toon

first: Hiroshi

last: Sakai

state: Ehime

address: Shitsukawa

department: Proteo-Science Center

country: Japan

institute: Ehime University

description: Library name: Human_Male_Naga_rep2

data_processing:
To align the reads, the mm10 (for mouse) or  GRCm38 (for human) reference genomes were employed, utilizing Bowtie2 with the default parameters. Removal of duplicated reads was carried out using Samtools (rmdup). Subsequent analysis focused solely on the uniquely mapped reads.
BigWig files were generated using `bamCoverage` in deepTools (version 3.4.1) with the following options: `--binSize 100 --normalizeUsing CPM`.
To identify AR peaks across samples, peak calling was performed with MACS2 on BAM files merged from biological replicates (n = 4). Peak calling for AR was performed against the corresponding control sample using MACS2 with a P-value cutoff of 0.01 and the following options: --call-summits --nomodel --nolambda.
Assembly: mm10, GRCm38
Supplementary files format and content: bigWig

source_name: semitendinosus muscle

extract_protocol:
Cryosections (10 µm thick) were individually transferred to wells of a µ-Plate 96 Well Bottom plate (Ibidi, Cat# 89626). Sections were fixed for 5 min in 4% paraformaldehyde prepared in PBS containing 0.3% Triton X-100 and subsequently washed with PBS. Nonspecific binding was blocked sequentially with 5% goat serum in PBS. The sections were incubated overnight at 4°C with the primary antibody diluted in  5% goat serum in PBS. The sections were then incubated with the ChIL probe in PBS containing M.O.M. Protein Concentrate (Vector Laboratories,Cat# BMK-2202) and NaCl at a final concentration of 0.5 M.
ChIL-seq libraries were generated using a previously described ChIL protocol (Harada et al., 2018), with several modifications. The Tn5-binding and fill-in reactions were extended to 1 and 2 hours, respectively. T7 RNA polymerase from Toyobo was used at 100 U per well, and the libraries were amplified by 15 cycles of PCR. Amplified libraries were purified using a DNA Clean & Concentrator column (Zymo Research, Cat# D4013), followed by size selection with AMPure beads (Beckman Coulter, Cat# A63880) at a bead-to-sample volume ratio of 0.5. The resulting libraries had an average fragment-size range of 200 to 500 bp.

value: semitendinosus muscle


title: 222HS

description: Library name: 30804-029


title: E37_1_CP

description: Library name: Sample 13

source_name: Fetal cortex

value: Fetal cortex

tag: cortical layer

value: Cortical plate

tag: age

value: Embryonic 37 days


title: Muscle, male, Nega, rep1

description: Library name: Human_Male_Naga_rep1


title: N8 ctrl non-smoker


title: MS633

description: Library name: Sample 27


title: Muscle, male, H3K27ac, rep2

description: Library name: Human_Male_H3K27ac_rep2

tag: chil antibody

value: H3K27ac (MAB, Cat# MABI0309)


title: N7 ctrl non-smoker


title: MS632

description: Library name: Sample 26

tag: cell line

value: Unstimulated


title: 35OC

description: Library name: 30804-027

value: saliva

value: ovarian cancer


title: Muscle, male, H3K27ac, rep1

description: Library name: Human_Male_H3K27ac_rep1


title: N6 ctrl non-smoker


title: MS631

description: Library name: Sample 25

tag: temperature

value: Treated 3h IL-1b


title: Muscle, male, AR, rep4

description: Library name: Human_Male_AR_rep4

value: AR (Abcam, Cat# ab108341)


title: 48BC

description: Library name: 30804-026

value: female

value: breast cancer


title: N5 ctrl non-smoker


title: Muscle, male, AR, rep3

description: Library name: Human_Male_AR_rep3

value: male


title: N4 ctrl non-smoker

value: control group


title: R2 ctrl smoker


title: 12BC

description: Library name: 30804-024


title: MS629

description: Library name: Sample 23

value: Immortalized Ear Fibroblast GR NLS-iRFP-NLS

tag: replicate


title: Muscle, male, AR, rep2

description: Library name: Human_Male_AR_rep2


title: N3 ctrl non-smoker


title: MS628

description: Library name: Sample 22

value: Treated 1h TNF-a


title: N2 ctrl non-smoker


title: Muscle, male, AR, rep1

description: Library name: Human_Male_AR_rep1


title: MS627

description: Library name: Sample 21


title: Muscle, female, H3K27ac, rep2

description: Library name: Human_Female_H3K27ac_rep2


title: 15BC

description: Library name: 30804-022


title: MS626

description: Library name: Sample 20


title: C400+4 follow-up

value: follow-up

value: CHTIO


title: N1 ctrl non-smoker


title: Muscle, female, H3K27ac, rep1

description: Library name: Human_Female_H3K27ac_rep1

value: semitendinosus muscle


title: 18BC

description: Library name: 30804-020


title: MS625

description: Library name: Sample 19

value: Treated 1h IL-1b


title: C331+4 follow-up


title: HepG2 RNA-2

city: Mysuru

first: Prasanna

last: Kumar S

address: Department of Biochemistry, JSS Medical College, Mysuru

country: India

institute: JSS Medical College

description:
Library name: SAM6329
Column name in RawCounts.txt : SAM6329

data_processing:
The mRNA libraries were prepared using the NEB Ultra II directional RNA-Seq Library Kit (NEB, USA).
The first-strand and second-strand cDNA synthesis were carried out using reverse transcriptase and DNA Polymerase I enzymes, respectively, followed by adapter ligation.
Prior to sequencing, the fragment sizes were analysed using HS NGS Fragment kit (1-6000bp) (Agilent, USA) on a Fragment analyser.
We performed RNA-seq on an Illumina NovaSeq V1.5 instrument according to the manufacturer’s protocol. Briefly, the ribosomal RNA depletion was carried out using Qiagen FastSelect rRNAHMR (Qiagen, Germany)
Subsequently, the mapping of the aligned paired reads was performed against the reference genome (GRCh38) using STAR (v.2.7.11b). The DETGs were identified using DESeq2. The fold change was calculated using the thresholds (−2≤log2(FC)≥+2, p≤ 0.05). FDR correction for p-value was calculated using the Benjamini-Hochberg (BH) method, where q< 0.05 was considered significant.
Assembly: GRCh38
Supplementary files format and content: tab delimited text files include raw counts of all genes for each sample

growth_protocol: We procured HCC cell lines from NCCS, Pune, India, through their standard procurement procedure (http://ncmr.nccs.res.in/home). The cell line, HepG2, was maintained in MEM with 10% fetal bovine serum supplementation. For spheroid generation, HepG2 cells were used, and the tumuroids were generated by using a modified forced suspension method as described previously. The control RNA samples were procured from TakaraBio, Japan.

extract_protocol:
Whole RNA was isolated using the standard Trizol extraction method from control and HepG2 HCC spheroids.
The mRNA libraries were prepared using the NEB Ultra II directional RNA-Seq Library Kit (NEB, USA).The ribosomal RNA depletion was carried out using Qiagen FastSelect rRNAHMR (Qiagen, Germany)

tag: genotype

value: HCC cell line

value: HepG2 spheroid RNA


title: MS624

description: Library name: Sample 18

value: Treated 3h TNF-a


title: 19BC

last: Scebba

address: Piazza martiri della libertà 33

institute: Scuola Superiore Sant'Anna

description: Library name: 30804-019

data_processing:
Analysis was performed using CLC Genomics Server 21.0.4 with the QIAseq miRNA Quantification workflow and standard parameters. Reads were mapped to miRBase v22 after trimming of common sequences, UMIs, and adapters, followed by filtering of reads shorter than 15 nt or longer than 55 nt. Reads were then deduplicated based on their UMIs by grouping reads with the same start position, strand, and identical UMI. Singleton UMI groups were merged into non-singleton groups when their UMI differed by a single nucleotide (SNP), with assignment to the largest matching group.
All reads that don’t map to miRBase, neither with perfect matches nor as isomiRs (maximum 2 mismatches and/or alternative start/end position of 2 nt), are mapped the human genome GRCh38 with ENSEMBL GRCh38 version 97 annotation. This is carried out using the “RNA-Seq Analysis” workflow of CLC Genomics Server with standard parameters.
The ‘Empirical analysis of DGE’ algorithm of the CLC Genomics Workbench 21.0.4 was used for differential expression analysis with default settings.
Assembly: miRBase version 22
Supplementary files format and content: excel file with total miRNa count for each miRNA and each sample

extract_protocol:
RNA was isolated from 200 μl using the miRNeasy Serum/Plasma Kit (QIAGEN) according to manufacturer’s instructions
The library preparation was done using the QIAseq miRNA Library Kit (QIAGEN). A total of 5 μl total RNA was converted into miRNA NGS libraries. After adapter ligation, UMIs were introduced in the reverse transcription step. The cDNA was amplified using PCR (22 cycles) and during the PCR indices were added. After PCR the samples were purified. Library preparation was quality controlled using capillary electrophoresis (Agilent DNA 1000 Chip)

value: saliva


title: HepG2 RNA-1

description:
Library name: SAM6328
Column name in RawCounts.txt : SAM6328


title: C323+4 follow-up

tag: sample type


title: MS623

description: Library name: Sample 17


title: Normal Liver RNA-2

description:
Library name: SAM6327
Column name in RawCounts.txt : SAM6327

source_name: Control normal liver RNA commercially procured from TakaraBIo, Japan Cat# #636531-Lot no.  1210374 A

value: Normal Liver RNA


title: 81OC

description: Library name: 30804-018

value: ovarian cancer


title: MS622

description: Library name: Sample 16

source_name: Immortalized Ear Fibroblast GR NLS-iRFP-NLS

value: Unstimulated


title: 113OC

description: Library name: 30804-017

value: female


title: C322+4 follow-up

tag: group


title: MS621

description: Library name: Sample 15

value: Treated 3h IL-1b


title: C312+4 follow-up


title: MS620

description: Library name: Sample 14


title: 53OC

description: Library name: 30804-015

tag: tissue


title: BJNHem20 cells, OCIAD2 OV, day 2, replicate 3

city: Bengaluru

first: Kajal

last: Kamat

state: Karnataka

address: Srirampura cross, Near Rachenahalli lake, jakkur P.O.

department: Moleculr Biology and Genetics Unit

institute: Jawaharlal Nehru Centre for Advanced Scientific Research

description:
Library name: Sample 20
OCIAD2_OV_EMP_D2_B4

data_processing:
Raw fastq files were checked for their data quality using FastQC tool, followed by adapter trimming and were finally aligned to the human reference genome (GRCh38) with HISAT2. Gene expression counts were determined by the Feature Counts program of the Subread R package, using the default parameters.
Assembly: hg38
Supplementary files format and content: excel file including raw counts for all samples
Supplementary files format and content: csv file with normalized counts

source_name: Embryonic

extract_protocol:
Total RNA was extracted using the TriZol method. mRNA enrichment was performed with NEBNext Poly(A) mRNA Magnetic Isolation Module.
cDNA library was prepared using the NEBNext® Ultra™ II Directional RNA Library Prep kit with Sample Purification Beads. The libraries were sequenced on the NovaSeq 6000 platform (Illumina) with 2×100 bp sequencing read length, generating over 100 million paired-end reads per sample.

value: Embryonic

value: BJNhem20 OCIAD2 OV

tag: cell type

value: Blastocyst derived embryonic stem cell line

value: OCIAD2 overexpression

value: mesendoderm differentiation, day 2


title: C320+4 follow-up

value: follow-up

value: CHTIO


title: BJNHem20 cells, OCIAD2 OV, day 2, replicate 4

description:
Library name: Sample 21
OCIAD2_OV_EMP_D2_B5

tag: treatment


title: C290+4 follow-up


title: MS619

description: Library name: Sample 13

value: Immortalized Ear Fibroblast GR NLS-iRFP-NLS


title: 59OC

city: Pisa

description: Library name: 30804-014

tag: gender


title: BJNHem20 cells, OCIAD2 OV, day 2, replicate 2

description:
Library name: Sample 19
OCIAD2_OV_EMP_D2_B3


title: 219HS

description: Library name: 30804-028

value: healthy


title: MS618

description: Library name: Sample 12

value: Treated 1h TNF-a


title: 41BC

description: Library name: 30804-013

value: breast cancer


title: C288+4 follow-up


title: MS617

description: Library name: Sample 11


title: 44BC

description: Library name: 30804-012

value: saliva


title: BJNHem20 cells, OCIAD2 CRISPR 33 (KO), day 2, replicate 4

description:
Library name: Sample 17
OCIAD2_CRISPR33_EMP_D2_B5

value: BJNhem20 OCIAD2 CRISPR 33

value: OCIAD2 knockout


title: C283+4 follow-up


title: 14BC

description: Library name: 30804-025


title: C280+4 follow-up


title: 43BC

description: Library name: 30804-011


title: BJNHem20 cells, OCIAD2 CRISPR 33 (KO), day 2, replicate 3

description:
Library name: Sample 16
OCIAD2_CRISPR33_EMP_D2_B4


title: MS615

description: Library name: Sample 9

value: Treated 1h IL-1b


title: 42BC

description: Library name: 30804-010

value: female


title: BJNHem20 cells, OCIAD2 CRISPR 33 (KO), day 2, replicate 2

description:
Library name: Sample 15
OCIAD2_CRISPR33_EMP_D2_B3


title: C262+4 follow-up


title: 13BC

description: Library name: 30804-023


title: C261+4 follow-up


title: MS614

description: Library name: Sample 8

value: Treated 3h TNF-a


title: BJNHem20 cells, OCIAD2 CRISPR 33 (KO), day 2, replicate 1

description:
Library name: Sample 14
OCIAD2_CRISPR33_EMP_D2_B2

value: Embryonic


title: 50OC

description: Library name: 30804-009

value: ovarian cancer


title: MS613

description: Library name: Sample 7


title: C251+4 follow-up


title: BJNHem20 cells, WT, day 2, replicate 4

description:
Library name: Sample 13
WT_EMP_D2_B5

value: Blastocyst derived embryonic stem cell line

value: wildtype


title: 16BC

description: Library name: 30804-021


title: 49OC

description: Library name: 30804-008


title: MS612

description: Library name: Sample 6

value: Unstimulated


title: BJNHem20 cells, WT, day 2, replicate 3

description:
Library name: Sample 12
WT_EMP_D2_B4

value: mesendoderm differentiation, day 2


title: C239+4 follow-up

value: follow-up

value: CHTIO


title: MS611

description: Library name: Sample 5

value: Immortalized Ear Fibroblast GR NLS-iRFP-NLS

value: Treated 3h IL-1b


title: C238+4 follow-up


title: 8BC

description: Library name: 30804-006

value: breast cancer


title: BJNHem20 cells, WT, day 2, replicate 2

description:
Library name: Sample 11
WT_EMP_D2_B3


title: MS610

description: Library name: Sample 4


title: 7OC

description: Library name: 30804-005

value: saliva


title: C235+4 follow-up


title: BJNHem20 cells, WT, day 2, replicate 1

description:
Library name: Sample 10
WT_EMP_D2_B2


title: BJNHem20 cells, OCIAD2 OV, day 0, replicate 3

description:
Library name: Sample 9
OCIAD2_OV_D0_B3

value: BJNhem20 OCIAD2 OV

value: OCIAD2 overexpression

value: day 0


title: MS609

description: Library name: Sample 3


title: MS608

description: Library name: Sample 2

value: Treated 1h TNF-a


title: 3BC

description: Library name: 30804-003

value: female


title: C221+4 follow-up


title: BJNHem20 cells, OCIAD2 OV, day 0, replicate 2

description:
Library name: Sample 8
OCIAD2_OV_D0_B2

value: Embryonic


title: BJNHem20 cells, OCIAD2 OV, day 0, replicate 1

description:
Library name: Sample 7
OCIAD2_OV_D0_B1


title: ces-D, DMSO treatment, replicate 1

description:
Library name: cesD_DMSO_1_ZKDN260001861-1A_23F5LMLT4
Arabidopsis thaliana ces-D loss-of-function mutant, replicate 1. DMSO treatment.

data_processing:
Raw WGBS reads were processed using the MethylStar pipeline (v1.2.3). Reads were quality-checked with FastQC and trimmed using Trim Galore. Adapter- and quality-trimmed reads were aligned to the Arabidopsis thaliana TAIR10 reference genome using Bismark (v0.23.0) with Bowtie2. Methylation calling was performed using METHimpute (v1.18.0) to generate probabilistic estimates of cytosine methylation in CG, CHG, and CHH contexts. Strand-specific cytosine methylation profiles were converted to bigWig format using custom scripts.
DMRs were called using the jDMR-grid tool (published preliminary in Hazarika et al., 2022; available on GitHub repository: https://github.com/jlab-code/jDMRgrid/), comparing each mutant to its designated control wild-type to avoid batch effects. genome into non-sliding 100 bp regions with bins. We used all consecutive bins in the analysis. As filtering approach, we used jDMR build-in control/treatment strategy, for which both of the replicate have the same state call (replicate.consensus = 1).
wt DMSO and wt eBL-treated controls were used for the ces-D/qM mutant eBL treatment groups.
All coordinates are based on the TAIR10 (v57) genome build.
Assembly: TAIR10 v57
Supplementary files format and content: bigWig files: strand-specific cytosine methylation levels (CG, CHG, CHH contexts)
Supplementary files format and content: METHimpute files: CX-like reports generated from METHimpute implemented in MethylStar pipeline

source_name: 21 dag 1/2MS-grown aerial tissue

growth_protocol: Seedlings were germinated and grown on ½ MS medium (Duchefa Biochemie) under long-day conditions (16 h light / 8 h dark, 80 µmol m⁻² s⁻¹, 50% humidity) for 21 d in a growth cabinet (Bright Boy, CLF Plant Climatics, Wertingen, Germany) at 21 ± 2 °C.

extract_protocol:
DNA was extracted from 100 mg of aerial tissue of 3-week-old plants using the DNeasy Plant Mini Kit (Qiagen, Hilden, Germany). DNA was precipitated using sodium acetate, ethanol, and glycogen, and quality-checked before submission, and by Novogene DNA QC workflows.
DNA was bisulfite-converted and used for methylation library preparation by Novogene (Novogene GmbH, Munich, Germany) for sequencing on the Illumina NovaSeq X Plus Series (PE150)  platform.

treatment_protocol: For eBL-treated samples, plants were spray exogenously sprayed with 10µM 2,4-Epibrassinolide and harvested material was snap-frozen in LN after 3h. Control samples were mock-treated with DMSO.

value: 21 dag 1/2MS-grown aerial tissue

value: ces-D

value: DMSO

tag: batch


title: BJNHem20 cells, OCIAD2 CRISPR 33 (KO), day 0, replicate 3

description:
Library name: Sample 6
OCIAD2_CRISPR33_D0_B3

value: BJNhem20 OCIAD2 CRISPR 33

value: Blastocyst derived embryonic stem cell line

value: OCIAD2 knockout


title: C218+4 follow-up

value: follow-up

value: CHTIO


title: C220+4 follow-up


title: ces-D, DMSO treatment, replicate 2

description:
Library name: cesD_DMSO_2_ZKDN260001862-1A_23F5LMLT4
Arabidopsis thaliana ces-D loss-of-function mutant, replicate 2. DMSO treatment.


title: HT-1080 cells w/ siHNRNPH1 replicate 3

city: Bethesda

first: Natasha

middle: J

last: Caplen

address: 37 Convent Dr, Bldg 37, Rm 6128

department: National Cancer Institute

description:
Library name: HT-1080 siHNRNPH1 Rep3
column name in HT1080.RSEM.transcript.variants.expected_count.all_samples.txt: HT1080_HNRNPH1_3

data_processing:
Short-read RNA-seq data was processed using the CCR Collaborative Bioinformatics Resource (CCBR) RNAseq pipeline, RENEE (https://ccbr.github.io/RENEE/latest/#table-of-contents).
PacBio long read RNA-seq data was processed using the official Iso-Seq software, installed as a bioconda package.
Assembly: GRCh38.p13 Release 41, Ensembl version 107
Supplementary files format and content: RSEM.transcript.variants.expected_count.all_samples.txt is a tab-delimited counts file containing transcript variant counts for each sample (short-read data)
Supplementary files format and content: gff files include full length transcript data from long-read RNA-seq. Can be viewed in IGV.

growth_protocol: HEK-293T cells were grown in DMEM and HT-1080 cells were grown in EMEM. Media was supplemented with 10% FBS and Plasmocin prophylactic at 37°C, 5% CO2.

extract_protocol:
We isolated RNA from three biological replicates 48-hours post-transfection using the Maxwell 16 LEV simplyRNA purification kit (Promega, Madison, WI).
Library preparation information for both short-read and long-read sequenicng runs can be found here: https://crtp.ccr.cancer.gov/sf/protocols-resources/

treatment_protocol: To deplete HNRNPH1, we plated 250,000 cells per well of a six-well plate and transfected cells with 20 nM siRNA complexed with 4.5 µL/well Lipofectamine RNAi-Max (Invitrogen, Thermo Fisher Scientific).


title: BJNHem20 cells, OCIAD2 CRISPR 33 (KO), day 0, replicate 2

description:
Library name: Sample 5
OCIAD2_CRISPR33_D0_B2


title: C217+4 follow-up


title: ces-D, eBL treatment, replicate 1

last: Poppenberger

address: Liesel-Beckmann-Str. 1

description:
Library name: cesD_eBL_1_ZKDN260001867-1A_23F5LMLT4
Arabidopsis thaliana ces-D loss-of-function mutant, replicate 1. eBL treatment.

value: eBL


title: HT-1080 cells w/ siHNRNPH1 replicate 2

description:
Library name: HT-1080 siHNRNPH1 Rep2
column name in HT1080.RSEM.transcript.variants.expected_count.all_samples.txt: HT1080_HNRNPH1_2


title: BJNHem20 cells, OCIAD2 CRISPR 33 (KO), day 0, replicate 1

description:
Library name: Sample 4
OCIAD2_CRISPR33_D0_B1


title: ces-D, eBL treatment, replicate 2

description:
Library name: cesD_eBL_2_ZKDN260001868-1A_23F5LMLT4
Arabidopsis thaliana ces-D loss-of-function mutant, replicate 2. eBL treatment.


title: HT-1080 cells w/ siHNRNPH1 replicate 1

description:
Library name: HT-1080 siHNRNPH1 Rep1
column name in HT1080.RSEM.transcript.variants.expected_count.all_samples.txt: HT1080_HNRNPH1_1


title: BJNHem20 cells, WT, day 0, replicate 3

description:
Library name: Sample 3
WT_D0_B3

value: wildtype


title: ces-qM, DMSO treatment, replicate 1

description:
Library name: qM_DMSO_1_ZKDN260001863-1A_23F5LMLT4
Arabidopsis thaliana ces-qM loss-of-function mutant, replicate 1. DMSO treatment.

value: ces-qM


title: HT-1080 cells w/ siNegative replicate 3

description:
Library name: HT-1080 siNegative Rep3
column name in HT1080.RSEM.transcript.variants.expected_count.all_samples.txt: HT1080_Neg_3

value: siNegative


title: 6BC

first: Francesca

description: Library name: 30804-004

value: saliva

value: breast cancer


title: BJNHem20 cells, WT, day 0, replicate 2

description:
Library name: Sample 2
WT_D0_B2

value: day 0


title: MS607

description: Library name: Sample 1

value: Immortalized Ear Fibroblast GR NLS-iRFP-NLS

value: Unstimulated


title: C206+4 follow-up


title: C202+4 follow-up


title: ces-qM, DMSO treatment, replicate 2

description:
Library name: qM_DMSO_2_ZKDN260001864-1A_23F5LMLT4
Arabidopsis thaliana ces-qM loss-of-function mutant, replicate 2. DMSO treatment.

value: 21 dag 1/2MS-grown aerial tissue


title: HT-1080 cells w/ siNegative replicate 2

description:
Library name: HT-1080 siNegative Rep2
column name in HT1080.RSEM.transcript.variants.expected_count.all_samples.txt: HT1080_Neg_2


title: 2BC

description: Library name: 30804-002

value: female


title: BJNHem20 cells, WT, day 0, replicate 1

description:
Library name: Sample 1
WT_D0_B1

value: Embryonic


title: 1BC

description: Library name: 30804-001


title: ces-qM, eBL treatment, replicate 1

description:
Library name: qM_eBL_1_ZKDN260001869-1A_232NGVLT3
Arabidopsis thaliana ces-qM loss-of-function mutant, replicate 1. eBL treatment.


title: MS630

description: Library name: Sample 24

value: Treated 1h IL-1b


title: CD4T cells, lu-3

city: Hangzhou

first: Jiajia

last: Wang

address: 866 Yuhangtang Road

institute: Zhejiang University

description:
Library name: lu-3
lu-3

data_processing:
RNA-Seq
Illumina Casava 2.19 software was used for basecalling.
Assembly: ensembl_94_homo_sapiens_grch38_primary
Supplementary files format and content: Tab-delimited text file include readcount values for each sample.

source_name: Blood

growth_protocol: CD4⁺ T cells were differentiated under Th1 conditions for 5 days

extract_protocol:
Total RNA was extracted and quality-checked before library preparation using the NEBNext® Ultra™ RNA Library Prep Kit (Novogene).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: with or without 10 µM lutein

value: Blood

value: PBMC

value: anti-CD3/28+anti-IL4+IL-12+10μM Lutein


title: HT-1080 cells w/ siNegative replicate 1

description:
Library name: HT-1080 siNegative Rep1
column name in HT1080.RSEM.transcript.variants.expected_count.all_samples.txt: HT1080_Neg_1


title: ces-qM, eBL treatment, replicate 2

city: Freising

institute: Technical University of Munich

description:
Library name: qM_eBL_2_ZKDN260001870-1A_23F5LMLT4
Arabidopsis thaliana ces-qM loss-of-function mutant, replicate 2. eBL treatment.


title: HEK-293T cells w/ siHNRNPH1 replicate 3

description:
Library name: HEK-293T siHNRNPH1 Rep3
column name in HEK293T.RSEM.transcript.variants.expected_count.all_samples.txt: HEK293T_HNRNPH1_3


title: CD4T cells, lu-2

description:
Library name: lu-2
lu-2


title: Col-0 control (ces-D and ces-qM), DMSO treatment, replicate 1

description:
Library name: WT_DMSO_1_ZKDN260001859-1A_232NGVLT3
Wild-type Arabidopsis thaliana Col-0, replicate 1. Control for DMSO treatment.

value: DMSO


title: HEK-293T cells w/ siHNRNPH1 replicate 2

description:
Library name: HEK-293T siHNRNPH1 Rep2
column name in HEK293T.RSEM.transcript.variants.expected_count.all_samples.txt: HEK293T_HNRNPH1_2


title: CD4T cells, lu-1

description:
Library name: lu-1
lu-1


title: C198+4 follow-up

value: follow-up

value: CHTIO


title: C176+4 follow-up


title: C180+4 follow-up


title: C169+4 follow-up


title: Col-0 control (ces-D and ces-qM), DMSO treatment, replicate 2

description:
Library name: WT_DMSO_2_ZKDN260001860-1A_23F5LMLT4
Wild-type Arabidopsis thaliana Col-0, replicate 2. Control for DMSO treatment.


title: HEK-293T cells w/ siHNRNPH1 replicate 1

description:
Library name: HEK-293T siHNRNPH1 Rep1
column name in HEK293T.RSEM.transcript.variants.expected_count.all_samples.txt: HEK293T_HNRNPH1_1


title: C204+4 follow-up


title: C185+4 follow-up


title: C210+4 follow-up


title: Col-0 control (ces-D and ces-qM), eBL treatment, replicate 1

description:
Library name: WT_eBL_1_ZKDN260001865-1A_23F5LMLT4
Wild-type Arabidopsis thaliana Col-0, replicate 1. Control for eBL treatment.

value: eBL


title: CD4T cells, anti-3

description:
Library name: anti-3
anti-3


title: HEK-293T cells w/ siNegative replicate 3

description:
Library name: HEK-293T siNegative Rep3
column name in HEK293T.RSEM.transcript.variants.expected_count.all_samples.txt: HEK293T_Neg_3

value: siNegative


title: C162+4 follow-up


title: CD4T cells, anti-2

description:
Library name: anti-2
anti-2


title: Col-0 control (ces-D and ces-qM), eBL treatment, replicate 2

description:
Library name: WT_eBL_2_ZKDN260001866-1A_23F5LMLT4
Wild-type Arabidopsis thaliana Col-0, replicate 2. Control for eBL treatment.


title: HEK-293T cells w/ siNegative replicate 2

description:
Library name: HEK-293T siNegative Rep2
column name in HEK293T.RSEM.transcript.variants.expected_count.all_samples.txt: HEK293T_Neg_2


title: CD4T cells, anti-1

description:
Library name: anti-1
anti-1


title: Normal Liver RNA-1

description:
Library name: SAM6326
Column name in RawCounts.txt : SAM6326

source_name: Control normal liver RNA commercially procured from TakaraBIo, Japan Cat# #636531-Lot no. 2305184

value: Normal Liver RNA


title: mESC-Gata4 (M.EcoGII-RNAPIISer2_mintbody), CUT&Tag, RNAPIISer2p, Shield, pluripotent, rep3

city: Pasadena

first: Yodai

last: Takei

state: California

address: 1200 E California Blvd

institute: California Institute of Technology

description: Library name: mESC_Gata4_clone2_1_CUTTag_Ser2p_c4_rep3

data_processing:
The demultiplexing was performed with ‘bases2fastq’ tool (Element Biosciences). For the barcoded nb-Tn5 samples, the demultiplexing of the adapter barcodes was further performed with custom bash scripts making use of basic shell commands and the ‘seqtk’ package (seqtk-v1.5 https://github.com/lh3/seqtk).
Sequencing data was processed using the cutnrun pipeline v3.2.2 from nf-core (https://nf-co.re/cutandrun/3.2.2) with Nextflow v23.10.1.
Reads were aligned to the UCSC mm10 or hg38 genome using bowtie2 v.2.4.4, keeping only reads with a minimum alignment q score of 20. For the adapter barcoded samples, 42 bp from the 5’ end were removed with parameters --clip_r1 42 --clip_r2 42.
Aligned reads were masked using the CUT&RUN suspect list regions.
Bigwigs were generated from the alignments using the bamCoverage function of deeptools v3.5.1.
Assembly: mm10 or hg38
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

growth_protocol: E14 mouse embryonic stem cells (E14Tg2a.4) were maintained on 0.1% gelatin coated plates under the serum/LIF condition in DMEM supplemented with 15% ES-grade fetal bovine serum (FBS), 1,000 units/mL leukemia inhibitory factor (LIF), 1× non-essential amino acids, 1 mM sodium pyruvate, 55 μM 2-mercaptoethanol, and 1× Penicillin-Streptomycin-Glutamine. mESC-Gata4 cells were maintained on 0.1% gelatin coated plates under the serum/LIF/2i condition by supplementing the serum/LIF medium with 1 μM PD0325901 and 3 μM CHIR99021. The human HCT116 cells (ATCC CCL‐247) were maintained in McCoy's 5A (modified) medium supplemented with 10% FBS and 1× Penicillin-Streptomycin. All cell lines were cultured at 37°C with 5% CO2.

extract_protocol:
Cells were fixed with 50 μL of 1% formaldehyde in 1× PBS at room temperature for 5 minutes on 96-well plates.
Cells were permeabilized with 0.5% Triton-X in 1× PBS. For LagTag, additional treatment with 5% RNaseA/T1 Mix as well as NaOH denaturation were performed. These treatments were omitted in CUT&Tag experiments unless noted. Samples were incubated with primary antibodies in blocking buffer (1× PBS, 1% BSA, and 0.05% Triton-X), then with nb-Tn5 transposomes (in-house) in wash 300 buffer (20 mM HEPES pH 7.4, 300 mM NaCl, and 0.05% Triton-X) supplemented with 0.1% BSA. Tagmentation was then performed in wash 300 buffer supplemented with 10 mM MgCl2 and 0.1% BSA. The DNA fragments were extracted using 20 μL SDS release buffer (10 mM TAPS buffer pH 8.5, 0.2% SDS, and 5% thermolabile proteinase K), then neutralized with 12 μL of 10% Triton-X for PCR input. Libraries were prepared by mixing 21 μL input, 2 μL each of i5 and i7 primers (10 μM stock), and 25 μL of NEBNext High-Fidelity 2X PCR Master Mix. PCR was performed as follows: 5 min at 58°C, 5 min at 72°C, and 45 sec at 98°C followed by 13-15 cycles of 15 sec at 98°C and 10 sec at 60°C, and a final extension at 72°C for 1 min. The amplified libraries were purified using 1.3× magnetic beads.

treatment_protocol: The mESC-Gata4 differentiation to endodermal cells was induced by 1 μg/mL Dox induction and LIF withdrawal for 24 hours. For LagTag, the adenine methyltransferase fusion proteins were stabilized with 1 μM Shield-1 for 16 hours in the engineered cells.

value: embryonic stem cell

value: 1 μM Shield-1 for 16 hours for endpoint recording

tag: antibody

value: RNAPIISer2p (Cell Signaling 13499S)


title: HEK-293T cells w/ siNegative replicate 1

institute: National Institutes of Health

description:
Library name: HEK-293T siNegative Rep1
column name in HEK293T.RSEM.transcript.variants.expected_count.all_samples.txt: HEK293T_Neg_1


title: M2 Macrophage, sample 4

city: Grand Forks

first: Colin

last: Combs

state: North Dakota

address: 1301 N Columbia Rd

department: Biomedical Sciences

institute: University of North Dakota

description: Library name: M2_4

data_processing:
RNA-Seq libraries were sequenced on an Illumina NovaSeq 6000, and 35 million 150 bp paired-end reads were obtained per sample. Preliminary quality control analysis of fastq files was performed with FastQC v0.11.9.
Adapters were trimmed using Trimmomatic v0.39
Reads were aligned to a human genome (hg38) with HISAT2 v2.2.1 software.
Successfully mapped clean reads were assigned to genomic features using featureCounts in Rsubread v2.18.0
Differentially expressed genes between sample groups were determined using DESeq2 v1.44.0 with a significance threshold of <0.05 Benjamini-Hochberg adjusted p-value.
Assembly: Reads were aligned to a human genome (hg38) with HISAT2 v2.2.1 software.
Supplementary files format and content: tab-delimited text files including fpkm normalized count values for each sample in the matrix.

growth_protocol: The triple negative breast cancer cell line MDA-MB-231 and human THP-1 cells were obtained from ATCC (Manassas, VA, USA). Cells were maintained in D-MEM/F-12 medium (Gibco, Life Technologies, Grand Island, NY, USA) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin (Thermo Fisher Scientific Inc., MA, USA). The cells were incubated at 37 °C in a humidified incubator with 5% CO2.

extract_protocol:
Cells were washed in PBS and lysed using RNAzol RT according to the RNAzol® RT Column Kit (Molecular Research Center, Cincinnati, OH) protocol. Briefly, the lysate was mixed with water and centrifuged at 12,000×g to remove DNA and proteins. Lysate was then diluted at a 1:1 ratio with isopropanol and added to a column before another 12,000×g centrifugation. RNA was then washed twice with 100% ethanol to remove impurities. RNA was then eluted using RNase-free deionized water and stored at -80°C. Concentrations were measured using a Qubit 4 Fluorometer, and purity was checked using a NanoDrop One spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA).
Total RNA integrity was determined using Agilent Bioanalyzer or 4200 Tapestation. Library preparation was performed with 500ng to 1ug of total RNA. Ribosomal RNA was removed by an RNase-H method using RiboErase kits (Kapa Biosystems). mRNA was then fragmented in reverse transcriptase buffer and heating to 94 degrees for 8 minutes. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer's instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags.

treatment_protocol: Macrophage Differentiation and Polarization: THP-1 cells were stimulated with 100 nM phorbol-12-myristate 13-acetate (PMA) (Sigma-Aldrich, Saint Louis, MO, USA) in D-MEM/F-12 medium for 24 hours. Afterward, cells were activated for 24 hours into M1-like macrophages by treatment with 50ng/mL IFN-γ (R&D Systems Inc., Minneapolis, MN, USA) or into M2-like macrophages by treatment with 50ng/mL IL-4 (R&D Systems Inc., Minneapolis, MN, USA).  3D Co-cultured Spheroids: 10,000 MDA-MB-231 cells were seeded into each well of a Nunclon Sphera-treated U-shaped-bottom microplate (Thermo Fisher Scientific Inc., MA, USA). After 24 h, 5,000 polarized M1-like or M2-like macrophages were seeded into each well for co-cultures. Monocultures and co-cultures were incubated for another 4 days at 37 °C in a humidified incubator with 5% CO2 before analysis or drug treatment.

value: M2-like macrophage polarized peripheral blood monocyte

value: THP-1 cells were stimulated with 100 nM phorbol-12-myristate 13-acetate (PMA) in D-MEM/F-12 medium for 24 hours. Afterward, cells were activated for 24 hours into M2-like macrophages by treatment with 50ng/mL IL-4.


title: 106OC

description: Library name: 30804-016

value: saliva

value: female

value: ovarian cancer


title: C159+4 follow-up


title: C161+4 follow-up


title: mESC-Gata4 (M.EcoGII-RNAPIISer2_mintbody), CUT&Tag, RNAPIISer2p, Shield, pluripotent, rep2

description: Library name: mESC_Gata4_clone2_1_CUTTag_Ser2p_c4_rep2


title: M2 Macrophage, sample 3

description: Library name: M2_3


title: AUa2-6_S12

city: Boston

first: Anil

last: Upreti

state: MA

address: 20 Staniford St

department: Ophthalmology, Harvard Medical School

institute: Schepens Eye Research Institute, Mass Eye and Ear

description: Library name: ARPE19 EFEMP1 R345W C

data_processing:
Raw read sequences were analyzed for quality using FastQC and MultiQC. Adapters and low-quality bases were trimmed using Cutadapt 3.4  and Trim Galore 0.6.5-1 with the parameters -q 20 --phred33 --length 20.
Human genome GRCh38 was indexed using Hisat2 (2.1.0-4), incorporating splice junctions from Gencode GTF gencode.v46.primary_assembly.annotation.gtf file. Stringtie 2.1.5  and gencode GTF annotation gencode. v46.primary_assembly.annotation.gtf was used to generate gene counts. DESeq2 1.34.0 was used to determine differential expression.
Assembly: GRCh38
Supplementary files format and content: ARPE19 normalized count matrix file from DESeq2
Supplementary files format and content: HMREC normalized count matrix file from DESeq2

source_name: ARPE19 R345W

growth_protocol: ARPE19 cells were purchased from ATCC (CRL-2302). RPE media was prepared as previously described (38). N2 Medium Supplement 1/100 (vol/vol), glutamine 1/100 (vol/vol), non-essential amino acid solution 1/100 (vol/vol), hydrocortisone (20 µg/l), taurine (250 mg/l) and triiodo-thyronin (0.013 µg/l) in alpha MEM + 5% heat inactivated FBS (Hyclone, Logan, UT, USA) or without FBS. 100µg/ml Normocin was used as an antibiotic and antifungal agent. Cells were grown on transwells and cultured for 30 days. Human retinal microvascular endothelial cells (HRMECs) purchased at P3 from Cell Systems Corporation (Kirkland, WA, USA) were incubated at 37°C with 5% CO2. HRMECs were plated at P6 using endothelial growth media (EGM‐2) (Lonza, Basel, Switzerland) supplemented with 2% FBS (Atlanta Biologicals, GA, USA), 1% penicillin/streptomycin, and 1% L‐glutamine (Lonza). Cells were treated at P7 in endothelial basal media (EBM‐2) (Lonza) supplemented with 2% FBS, 1% penicillin/streptomycin, and 1% L‐glutamine.

extract_protocol:
consisting of 100,000 cells. Total RNA was extracted from using the RNeasy Plus Mini Kit (Qiagen; 74134), following the manufacturer’s instructions. RNA quality was assessed using an Tapestation and samples with an RNA Integrity Number (RIN) >8 were used for sequencing.
Libraries were constructed by Simches Research Center, Next Generation Sequencing Core, Massachusetts General Hospital (Boston, MA, USA) using a NEBNext Ultra II Directional RNA Library Prep Kit (Ipswich, MA, USA).

treatment_protocol: Transfections were performed using 25 nM ASO mismatch control (M2) or EFEMP1 ASO diluted in optiMEM reduced serum media (ThermoFisher Scientific; 31985070). Diluted constructs were packaged using Lipofectamine RNAiMAX Transfection reagent (ThermoFisher Scientific; 13778150) in optiMEM, and administered to the explants for 48 hours before the media was exchanged with normal growth medium

value: ARPE19 R345W

value: Epithelial

value: MUT


title: mESC-Gata4 (M.EcoGII-RNAPIISer2_mintbody), CUT&Tag, RNAPIISer2p, Shield, pluripotent, rep1

description: Library name: mESC_Gata4_clone2_1_CUTTag_Ser2p_c4_rep1


title: C150+4 follow-up


title: AUa2-5_S11

description: Library name: ARPE19 EFEMP1 R345W B


title: M2 Macrophage, sample 2

description: Library name: M2_2


title: C289+4 follow-up


title: C149+4 follow-up


title: mESC-Gata4 (M.EcoGII-RNAPIISer2_mintbody), CUT&Tag, RNAPIISer2p, Shield, differentiation, rep3

description: Library name: mESC_Gata4_clone2_1_CUTTag_Ser2p_c3_rep3

value: 1 μg/mL Dox induction and LIF withdrawal for 24 hours for endodermal differentiation along with 1 μM Shield-1 for 16 hours for endpoint recording


title: AUa2-4_S10

description: Library name: ARPE19 EFEMP1 R345W A


title: M2 Macrophage, sample 1

description: Library name: M2_1


title: mESC-Gata4 (M.EcoGII-RNAPIISer2_mintbody), CUT&Tag, RNAPIISer2p, Shield, differentiation, rep2

description: Library name: mESC_Gata4_clone2_1_CUTTag_Ser2p_c3_rep2


title: C139+4 follow-up

value: follow-up


title: AUa2-3_S9

description: Library name: ARPE19 C

value: WT


title: M1 Macrophage, sample 4

description: Library name: M1_4

value: M1-like macrophage polarized peripheral blood monocyte

value: THP-1 cells were stimulated with 100 nM phorbol-12-myristate 13-acetate (PMA) in D-MEM/F-12 medium for 24 hours. Afterward, cells were activated for 24 hours into M1-like macrophages by treatment with 50ng/mL IFN-γ.


title: mESC-Gata4 (M.EcoGII-RNAPIISer2_mintbody), CUT&Tag, RNAPIISer2p, Shield, differentiation, rep1

description: Library name: mESC_Gata4_clone2_1_CUTTag_Ser2p_c3_rep1


title: C138+4 follow-up


title: BJNHem20 cells, OCIAD2 OV, day 2, replicate 1

description:
Library name: Sample 18
OCIAD2_OV_EMP_D2_B2

value: Embryonic

value: BJNhem20 OCIAD2 OV

value: Blastocyst derived embryonic stem cell line

value: OCIAD2 overexpression

value: mesendoderm differentiation, day 2


title: AUa2-2_S8

description: Library name: ARPE19 B


title: M1 Macrophage, sample 3

description: Library name: M1_3


title: TA, Control, biol rep1

description: Library name: Control rep1

data_processing:
Adaptor sequences and low-quality sequences were removed, and reads with a length below 20bp were discarded using TrimGalore (v0.6.7)
The processed reads were then mapped to the GRCm38 reference genome using HISAT2 (v2.2.1).
Read counts for each gene were obtained using featureCounts (v2.0.1).
Differentially expressed genes were identified using DESeq2 (v1.36.0) with a threshold of |log2FC| > 1 and padj < 0.1.
Assembly: GRCm38
Supplementary files format and content: Comma-separated values file includes normalized counts for each Sample

molecule: polyA RNA

source_name: TA muscles

extract_protocol:
Total RNA was isolated from tibialis anterior (TA) muscles using ISOGEN (Nippon Gene) according to the manufacturer’s instructions.
Directional RNA-seq libraries were prepared from 500 ng of RNA per sample using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina, NEBNext Poly(A) mRNA Magnetic Isolation Module, and NEBNext Multiplex Oligos for Illumina (New England Biolabs), according to the manufacturer’s instructions.

value: TA muscles

value: Control


title: mESC-Gata4 (M.EcoGII-RNAPIISer2_mintbody), CUT&Tag, RNAPIISer2p, pre-Shield, pluripotent, rep3

description: Library name: mESC_Gata4_clone2_1_CUTTag_Ser2p_c2_rep3

value: embryonic stem cell

value: 1 μM Shield-1 for 16 hours for prior recording

value: RNAPIISer2p (Cell Signaling 13499S)


title: Mut_cx20_5dpf_3

city: Durham

first: Daniel

last: Levic

address: 307 Research Drive

institute: Duke University

description: Library name: Sample 3

data_processing:
Trimmomatic(v0.38) was used to trim sequencing adapters
Reads were aligned to the zebrafish genome (GRCz11)  using STAR 2.7.11.a
Reads were counted using featureCounts in the Subread package (v1.6.3)
Assembly: GRCz11
Supplementary files format and content: tab-delimited text files includes counts for each sample

source_name: Whole larvae

extract_protocol:
Total RNA from n=40 larvae (3 replicates) was extracted in Trizol, treated with DNase, and then purified using RNA Clean & Concentrator-5 columns (Zymo).
RNA-sequencing libraries were made from ≥500ng of total RNA extracted from whole larvase using the Illumina Stranded mRNA prep kit.

value: Whole larvae

value: All cells

value: pdcd7/cx20 mutant

value: 5 dpf


title: C133+4 follow-up

value: follow-up


title: AUa2-1_S7

description: Library name: ARPE19 A

value: Epithelial

value: WT


title: M1 Macrophage, sample 2

description: Library name: M1_2

value: M1-like macrophage polarized peripheral blood monocyte

value: THP-1 cells were stimulated with 100 nM phorbol-12-myristate 13-acetate (PMA) in D-MEM/F-12 medium for 24 hours. Afterward, cells were activated for 24 hours into M1-like macrophages by treatment with 50ng/mL IFN-γ.


title: mESC-Gata4 (M.EcoGII-RNAPIISer2_mintbody), CUT&Tag, RNAPIISer2p, pre-Shield, pluripotent, rep2

description: Library name: mESC_Gata4_clone2_1_CUTTag_Ser2p_c2_rep2


title: MS616

city: Baltimore

first: Myong-Hee

last: Sung

address: 251 Bayview Boulevard

description: Library name: Sample 10

data_processing:
Stranded 151-bp paired-end reads were aligned to the mouse reference genome (GRCm39, Genome Reference Consortium (GRC) 2020) using STAR v2.7.11b (Dobin et al., 2013). The reads were counted per gene using RSEM v1.3.3 (Li & Dewey, 2011). Downstream processing was performed in R using edgeR.
Assembly: GRCm39
Supplementary files format and content: xlsx file including FPKM for all samples

extract_protocol:
Primary ear fibroblasts were isolated from adult DKI mice and cultured as previously described (Rahman et al., 2022). Briefly, dissected ear tissue was minced, enzymatically dissociated, and plated in standard growth medium (DMEM supplemented with 10% FBS, 1% penicillin, streptomycin, and L-glutamine). Cells were maintained in phenol-red-containing medium to facilitate pH monitoring during long-term culture. To generate stable immortalized fibroblast lines, primary cultures were expanded and routinely passaged every 72 hours for approximately 20-25 passages, at which point they exhibited hallmark features of immortalized fibroblasts, including sustained proliferation and stable expression of endogenous fluorescent RelA and c-Rel reporters.
Immortalized mouse ear fibroblasts were seeded at medium confluence in 6-cm tissue culture dishes and cultured overnight at 37 °C in humidified incubator with 5% CO2 to ensure recovery and stable basal transcriptional activity. The following day, cultures were transferred to incubators pre-equilibrated to 24 °C, 34 °C, 37 °C, or 40 °C and were allowed to adapt for 2 hours to establish temperature-specific steady states prior to stimulation. Cells were then either left untreated (0h) or stimulated with recombinant murine TNF-α (10ng/mL) or IL-1β (10ng/mL) for 1 hour or 3 hours. At each time point, cells were lysed directly on the plate using RLT buffer (Qiagen). Lysates were stored at -80°C until processing. Total RNA quantity and purity were assessed using a NanoDrop spectrophotometer (ThermoFisher). Three independent biological replicates were collected for each experimental condition. In total, 60 RNA-seq libraries were generated: 48 stimulated samples (4 temperatures x 2 cytokines x 2 time-points x 3 biological replicates) and 12 unstimulated baseline controls collected at 0h across the four temperatures (3 replicates each).

value: Immortalized Ear Fibroblast GR NLS-iRFP-NLS

value: Treated 3h IL-1b


title: C129+4 follow-up


title: AUa4-21_S21

description: Library name: EFEMP1 ASO C

source_name: HMREC

value: HMREC

value: Endothelial

value: ASO


title: M1 Macrophage, sample 1

description: Library name: M1_1


title: mESC-Gata4 (M.EcoGII-RNAPIISer2_mintbody), CUT&Tag, RNAPIISer2p, pre-Shield, pluripotent, rep1

description: Library name: mESC_Gata4_clone2_1_CUTTag_Ser2p_c2_rep1

value: embryonic stem cell


title: C116+4 follow-up


title: MDA-MB-231 Coculture with M2 Macrophages, sample 4

description: Library name: 231+M2_4

source_name: MDA-MB-231 and THP-1

value: MDA-MB-231 and THP-1

value: triple negative breast cancer cell line and M2-like macrophage polarized peripheral blood monocyte THP-1 cells

value: Following 24 hours of stimulation with 100 nM PMA in D-MEM/F, THP-1 cells were activated for 24 hours with 50 ng/mL IL-4 to induce an M2-macrophage state. 10,000 MDA-MB-231 cells were seeded into each well of a Nunclon Sphera-treated U-shaped-bottom microplate along with 5,000 polarized M2-like macrophages cells and co-cultured for 4 days at 37 °C in a humidified incubator with 5% CO2.


title: AUa4-20_S20

description: Library name: EFEMP1 ASO B


title: mESC-Gata4 (M.EcoGII-RNAPIISer2_mintbody), CUT&Tag, RNAPIISer2p, pre-Shield, differentiation, rep3

description: Library name: mESC_Gata4_clone2_1_CUTTag_Ser2p_c1_rep3

value: 1 μM Shield-1 for 16 hours for prior recording, followed by 1 μg/mL Dox induction and LIF withdrawal for 24 hours for endodermal differentiation

value: RNAPIISer2p (Cell Signaling 13499S)


title: C113+4 follow-up

source_name: Whole blood


title: MDA-MB-231 Coculture with M2 Macrophages, sample 3

description: Library name: 231+M2_3


title: AUa4-18_S18

description: Library name: ASO Mismatch C


title: C112+4 follow-up


title: mESC-Gata4 (M.EcoGII-RNAPIISer2_mintbody), CUT&Tag, RNAPIISer2p, pre-Shield, differentiation, rep2

description: Library name: mESC_Gata4_clone2_1_CUTTag_Ser2p_c1_rep2


title: AUa4-19_S19

description: Library name: EFEMP1 ASO A


title: MDA-MB-231 Coculture with M2 Macrophages, sample 2

description: Library name: 231+M2_2


title: AUa4-17_S17

description: Library name: ASO Mismatch B


title: mESC-Gata4 (M.EcoGII-RNAPIISer2_mintbody), CUT&Tag, RNAPIISer2p, pre-Shield, differentiation, rep1

description: Library name: mESC_Gata4_clone2_1_CUTTag_Ser2p_c1_rep1


title: C109+4 follow-up


title: C107+4 follow-up


title: AUa4-16_S16

description: Library name: ASO Mismatch A


title: C102+4 follow-up


title: mESC-Gata4, multi-LagTag, condition 6, M.EcoGII-RNAPIISer2p_mintbody m6A (rb), RNAPIISer2p (ms), rep2

description: Library name: mESC_Gata4_clone2_1_multi_LagTag_6_rb_m6A_Ser2p_ms_Ser2p_rep2

data_processing:
The demultiplexing was performed with ‘bases2fastq’ tool (Element Biosciences). For the barcoded nb-Tn5 samples, the demultiplexing of the adapter barcodes was further performed with custom bash scripts making use of basic shell commands and the ‘seqtk’ package (seqtk-v1.5 https://github.com/lh3/seqtk).
Sequencing data was processed using the cutnrun pipeline v3.2.2 from nf-core (https://nf-co.re/cutandrun/3.2.2) with Nextflow v23.10.1.
Reads were aligned to the UCSC mm10 or hg38 genome using bowtie2 v.2.4.4, keeping only reads with a minimum alignment q score of 20. For the adapter barcoded samples, 42 bp from the 5’ end were removed with parameters --clip_r1 42 --clip_r2 42.
Aligned reads were masked using the CUT&RUN suspect list regions.
Bigwigs were generated from the alignments using the bamCoverage function of deeptools v3.5.1.
Assembly: mm10 or hg38
Supplementary files format and content: bigWig

value: m6A (Invitrogen MA5-35350), RNAPIISer2p (Cosmo Bio USA MCA-MABI0602-100-EX)


title: AUa4-14_S14

description: Library name: NTC B


title: MDA-MB-231 Coculture with M1 Macrophages, sample 2

description: Library name: 231+M1_2

value: triple negative breast cancer cell line and M1-like macrophage polarized peripheral blood monocyte THP-1 cells

value: Following 24 hours of stimulation with 100 nM PMA in D-MEM/F, THP-1 cells were activated for 24 hours with 50 ng/mL ifn-γ to induce an M1-macrophage state. 10,000 MDA-MB-231 cells were seeded into each well of a Nunclon Sphera-treated U-shaped-bottom microplate along with 5,000 polarized M1-like macrophages cells and co-cultured for 4 days at 37 °C in a humidified incubator with 5% CO2.


title: AUa4-15_S15

description: Library name: NTC C

value: WT


title: mESC-Gata4, multi-LagTag, condition 5, M.EcoGII-RNAPIISer2p_mintbody m6A (rb), RNAPIISer2p (ms), rep3

description: Library name: mESC_Gata4_clone2_1_multi_LagTag_5_rb_m6A_Ser2p_ms_Ser2p_rep3

value: 1 μg/mL Dox induction and LIF withdrawal for 24 hours for endodermal differentiation


title: C89+4 follow-up

value: follow-up


title: MDA-MB-231 Coculture with M1 Macrophages, sample 1

description: Library name: 231+M1_1


title: mESC-Gata4, multi-LagTag, condition 5, M.EcoGII-RNAPIISer2p_mintbody m6A (rb), RNAPIISer2p (ms), rep2

description: Library name: mESC_Gata4_clone2_1_multi_LagTag_5_rb_m6A_Ser2p_ms_Ser2p_rep2