title: BAV_31

description: Library name: Sample 18


title: BMDM, HDL, CAC_6

status: Public on Dec 11 2025

type: SRA

city: Nashville

first: Kasey

last: Vickers

address: 2220 Pierce Ave, PRB 312

country: USA

institute: VUMC

description: Library name: CAC_6

library_source: transcriptomic

data_processing:
Reads were trimmed to remove adapter sequences using Cutadapt (v4.8)
Quality control on both raw reads and adaptor-trimmed reads was performed using FastQC (v0.12.1)(www.bioinformatics.babraham.ac.uk/projects/fastqc)
Reads were aligned to the Gencode GRCm38.p6 genome using STAR (v2.7.11a). Gencode vM25 gene annotations were provided to STAR to improve the accuracy of mapping. featureCounts (v2.0.6) was used to count the number of mapped reads to each gene.
ComplexHeatmap was used for cluster analysis and visualization. Significantly differential expressed genes with absolute fold change >= 1.5 and FDR adjusted p value <= 0.05 were detected by DESeq2 (v1.42.1)
Genome Ontology and KEGG pathway over-representation analysis was performed on differentially expressed genes using the WebGestaltR package (v1.0.0). Gene set enrichment analysis was performed using GSEA package (v4.3.2) on database (v2022.1.Hs)
Assembly: mouse GRCm38.p6
Supplementary files format and content: tsv file includes fpkm for each sample

molecule: total RNA

organism: Mus musculus

source_name: Mouse bone marrow

growth_protocol: Murine bone marrow cells were isolated from the femurs and tibiae of mice and cultured for seven days in treated cell culture plates. Cells were maintained in DMEM supplemented with 10% heat-inactivated fetal bovine serum (Thermo Fisher), 1% penicillin/streptomycin (Gibco), L-glutamine (300 mg/L, Thermo Fisher), sodium pyruvate (110 mg/L), and mGM-CSF (40 ng/ml, PeproTech) for bone marrow-derived macrophage differentiation.

extract_protocol:
Total cellular RNA was isolated using Total RNA Purification kits (Norgen)
Libraries were generated using the NEBNext Ultra II Directional RNA library prep kit for Illumina with multiplex oligos set 1 (NEB).

treatment_protocol: Cells were treated with healthy control or CAC native HDL (1mg/mL) for 6h

tag: tissue

value: Mouse bone marrow

tag: cell type

value: Bone marrow derived macrophages

tag: treatment

value: HDL, CAC>21


title: Murine CNS Treg from Naive Stage (250 cells) BioRep3

city: Munich

first: Thomas

last: Korn

email: thomas.korn@tum.de, c.sie@tum.de

address: Ismaninger Str. 22

department: Experimental Neuroimmunology

country: Germany

institute: Technical University of Munich

description: Library name: CNS_Naive_R3

data_processing:
The sequencing data were processed using the Drop-seq pipeline (PMID: 26000488) to generate UMI tables organized by sample and gene.
Assembly: The GRCm38 reference genome was aligned with transcript and gene annotations derived from ENSEMBL.
Supplementary files format and content: TXT files with gene counts (one gene per row, one sample per column)

source_name: CNS

extract_protocol:
250-2000 Treg or Tconv cells (viability > 90%) were sorted directly into TCL buffer (QIAGEN) plus 1% 2-Mercaptoethanol (Merk) and stored at -80°C until all samples were ready for RNA extraction. The RNA was extracted and purified using the RNAeasy Plus Micro Kit (QIAGEN). The RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies).
Barcode-specific cDNA was synthesized via reverse transcription with Maxima RT polymerase (Thermo Fisher), utilizing an oligo-dT primer containing barcodes, unique molecular identifiers (UMIs), and adaptor sequences. The 5′ end of the cDNA was then extended using primers complementary to the template switch oligo (TSO) site, followed by amplification of full-length cDNA. The cDNA was fragmented using the Nextera XT kit (Illumina), and the 3′-end fragments were amplified with primers incorporating Illumina P5 and P7 overhangs. The P5 and P7 sites were modified to optimize cluster recognition during sequencing, enabling sequencing of the cDNA in read1 and the barcodes/UMIs in read2.

value: CNS

tag: cell line

value: Treg

value: 250 cells

tag: genotype

value: Foxp3-GFP mice (C57BL/6)

tag: eae stage

value: Naïve

tag: batch

value: Bio rep 3


title: Ind3_VEH_0.1_24

city: Galveston

first: Michelle

middle: C.

last: Ward

address: 301 University blvd.

institute: UTMB

description: Library name: iPSC-CM_Ind3_VEH_0.1_24

data_processing:
Raw sequencing reads were assessed for quality using MultiQC (v1.26) (Ewels et al., 2016) on Linux-based systems. Reads were aligned to the human reference genome (GRCh38/hg38) using the Rsubread package (v2.16.1) (Liao et al., 2019). Gene-level quantification was performed using the featureCounts() function with the default exon-based annotations provided by Rsubread. Resulting count matrices were imported into R for downstream analysis. Expression values were transformed into log2 counts per million using the cpm() function from the edgeR package (v4.0.16) (Chen et al., 2016).
Assembly: hg38
Supplementary files format and content: Paul_CX_counts.txt

molecule: polyA RNA

organism: Homo sapiens

growth_protocol: Human iPSC-derived cardiomyocytes were cultured on Matrigel-coated plates at 37°C with 5% CO₂ under atmospheric oxygen conditions using Cardiomyocyte Maintenance Medium composed of 500 mL glucose-free DMEM (A14430-01, ThermoFisher Scientific), 50 mL fetal bovine serum (MT35015CV, Corning), 990 mg galactose (G5388, Sigma-Aldrich), 5 mL 100 mM sodium pyruvate (11360-070, ThermoFisher Scientific), 2.5 mL 1 M HEPES (H3375, Sigma-Aldrich), 5 mL 100X GlutaMAX (35050-061, ThermoFisher Scientific), and 5 mL penicillin-streptomycin.

extract_protocol:
Frozen iPSC-derived cardiomyocyte pellets were thawed on ice and lysed in Buffer RLT supplemented with 1% β-mercaptoethanol, prepared fresh under a fume hood. Lysates were homogenized using QIAshredder columns (Qiagen; 79656) and mixed with 70% ethanol prior to binding to RNeasy Mini spin columns (Qiagen; 74106). On-column DNase I digestion (Qiagen; 79256) was performed using freshly prepared DNase/RDD buffer mix and incubated for 15 minutes at room temperature. Columns were washed sequentially with RW1 and RPE buffers, and RNA was eluted in 30 µL RNase-free water. All centrifugation steps were carried out at >10,000 rpm as recommended. Eluted RNA was immediately placed on ice and stored at –80 °C. RNA integrity and concentration were assessed prior to library preparation.
Polyadenylated mRNA was isolated from 150 ng of total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (E7490L; New England Biolabs). Strand-specific RNA-seq libraries were generated using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7765S; NEB), with dual indexing performed using NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs, E6440S). Libraries were prepared in two balanced batches, each containing all treatment conditions and timepoints for three individuals (Batch 1: Individuals 1–3; Batch 2: Individuals 4–6). Final library quality and size distribution were evaluated using the Agilent 2100 Bioanalyzer prior to sequencing.

treatment_protocol: 1.5 million iPSC-derived cardiomyocytes were seeded per well in 6-well plates. On day 30 of differentiation, cells were treated with 0.1 µM or 0.5 µM CX-5461, Doxorubicin (DOX), or vehicle control in fresh cardiomyocyte maintenance media. Cells were harvested at 3 and 24 hours post-treatment. All steps were performed on ice unless otherwise specified. Culture media was aspirated, and cells were washed twice with 1 mL cold PBS. Cells were then scraped in 1 mL PBS into 1.5 mL Eppendorf tubes, followed by a second scrape using 500 µL PBS to collect any remaining cells. Cell suspensions were centrifuged at 7,000 rpm for 8 minutes at 4 °C. The supernatant was carefully removed, and the resulting cell pellets were flash-frozen in ethanol/dry ice and stored at –80 °C until RNA extraction.

tag: Sex

value: female

value: induced pluripotent stem cell-derived cardiomyocytes

tag: time


title: Veh-5 (snATAC)

city: Pittsburgh

first: Iliya

last: Lefterov

state: PA

address: 130 De Soto St

department: Environmental and Occupational Health

institute: University of Pittsburgh

description: Library name: A3000

library_source: genomic single cell

data_processing:
Cell Ranger ATAC
ArchR v1.0.1
Signac v1.14.0
Assembly: mm10
Supplementary files format and content: fragment files and single cell barcode files for each sample from 10x cell ranger atac output.

molecule: genomic DNA

source_name: brain

extract_protocol:
Mice were perfused with cold PBS, and half of each brain tissue, excluding olfactory and cerebellum, were immediately dissected and dissociated using Adult Brain Dissociation Kit (Miltenyi). Nuclei were isolated from frozen cells according to 10x demonstrated protocol (CG000169 and CG000212).
Libraries were prepared using the Chromium Next GEM Single Cell ATAC Kit v2 and Chip H Single Cell Kit (10x Genomics) according to manufacturer’s instructions.

treatment_protocol: The treatment group got 10-day oral administration of Bexarotene (100mg/kg/day), and the control group were treated with vehicle solution (corn oil with 1% DMSO).

value: brain

value: APP/PS+

value: Vehicle


title: Murine Spleen Tconv from EAE Recovery BioRep4

description: Library name: SPL_Tconv_Rec_R4

source_name: Spleen

value: Spleen

value: Tconv

value: 2000 cells

value: EAE Recovery

value: Bio rep 4


title: Murine Spleen Treg from EAE Recovery BioRep2

description: Library name: SPL_Treg_Rec_R2

value: Bio rep 2


title: Murine Spleen Treg from EAE Recovery BioRep1

description: Library name: SPL_Treg_Rec_R1

value: Bio rep 1


title: Bexa-4 (snATAC)

description: Library name: A2971

value: Bexarotene


title: BAV_35

city: nanjing

first: yuanyuan

last: wang

address: 818 Tianyuan E Rd, Nanjing, JIANGSU

country: China

institute: nanjing medical university

description: Library name: Sample 19

data_processing:
The RNA sequencing data was aligned to the reference genome (hg19) using STAR.
Assembly: hg19
Supplementary files format and content: Tab-separated values files

source_name: aortic valve leaflets

growth_protocol: collect aortic valve leaflets of the bicuspid aortic valve(BAV), tricuspid aortic valve(TAV) and control samples.

extract_protocol:
Total RNAs was extracted from aortic valve leaflets using RNAiso Plus (Takara, 9109). Magnetic beads with oligo-dT were using to isolate mRNA from total RNA.
Library was performed according to the manufacter’s instructions.

value: aortic valve leaflets

tag: group

value: BAV

value: Female

tag: age


title: mT-2

city: Chengdu

first: Weibo

last: Liang

address: Renmin South Road

institute: Sichuan University

description: Library name: Sample 2

library_source: genomic

data_processing:
The paired-end reads from ATAC-seq were processed to remove Illumina adapter sequences using the following parameters: -q 25 –phred33 –length 35 -e 0.1 –stringency 4 –paired. Subsequently, these trimmed sequences were aligned to the reference genomes using bowtie2 (version 2.3.5.1, RRID:SCR_016368), with the mm10 reference genome utilized for mouse samples and hg19 reference genome for human samples. The resulting alignments were sorted using samtools (version 1.5, RRID:SCR_002105). To eliminate duplicate reads, sambamba (version 1.0.0, RRID:SCR_024328) was employed with the markdup -r option. Mitochondrial DNA reads were filtered out using the grep -v chrM command. Bed files were generated using bedtools (version 2.31.0, RRID:SCR_006646) bamtobed command. Peak calling was performed using macs2(version 2.1.0.20150731, RRID:SCR_013291) with the callpeak command and parameters set at -g mm/hs –nomodel -shift -100 -extsize 200. For further analysis, read counts were normalized by calculating reads per kilobase of bin per million reads (RPKM) using deeptools(version 3.3.2, RRID:SCR_016366) bamCoverage with the –normalizeUsing RPKM option.
Assembly: Mouse mm10
Supplementary files format and content: bw files for each sample

source_name: Hippocampus

growth_protocol: All mice were housed in cages with ad libitum access to food and water and acclimated to standard conditions (12 h light/dark cycle, temperature: 22–25 °C, relative humidity: 40-60%) for at least one week before the experiment.

extract_protocol:
In brief, the sample was transferred from DMEM+10% FBS to a pre-chilled 2 ml Dounce (Sigma-Aldrich, USA) containing 1 ml of cold 1×homogenization buffer (HB) and thawed for 5 min. The sample was homogenized using an "A" loose pestle until resistance subsided (approximately 10 strokes), followed by further homogenization with a "B" tight pestle for an additional 20 strokes. The homogenate was filtered using a 70 µm Flowmi (Biosharp, China) strainer during transfer to a pre-chilled 2 ml LoBind tube (Eppendorf, USA). Nuclei were pelleted by centrifugation for 5 min at 4 °C and 350 RCF in a fixed-angle centrifuge (Eppendorf, USA). Aspirate the supernatant and discard until a volume of 50ul of liquid remains in the tube. The nuclei were gently resuspended in a total volume of 400 µl of 1×HB. An equal volume (400 µl) of 50% Iodixanol Solution (Sigma-Aldrich, USA) was added and thoroughly mixed by pipetting. A layer of 600 µl of 30% Iodixanol solution was carefully added underneath the 25% mixture, followed by a layer of 600 µl of 40% Iodixanol solution under the 30% mixture. The layered mixtures were then centrifuged for 20 min at 4 °C and 3,000 RCF in a pre-chilled swinging bucket centrifuge with the brake switched off. Care was taken to handle the tubes gently to avoid disturbing the gradient. The nuclei band was collected using a 200 µl volume and transferred to a fresh tube. The nuclei were then diluted by adding 500 µl of ATAC-RSB-Tween Buffer.
The nuclei were enumerated using acridine orange/propidium iodide (AO/PI) (Sigma-Aldrich, USA) staining at a 1:1 ratio of AO/PI to the sample, and an automated cell counter hemocytometer (Countstar, China). Subsequently, 50,000 nuclei were transferred into a 1.5 ml LoBind tube containing 1000 μl of ATAC-RSB-Tween Buffer. The nuclei were centrifuged for 10 min at 500 RCF at 4 °C in a fixed-angle centrifuge. After discarding the supernatant, the nuclei were resuspended in 35 μl of ddH2O and transferred into an EP tube. ATAC-seq library preparation was conducted using the TruePrep DNA Library Prep Kit V2 for Illumina TD501(Vazyme, China). A volume of 15 μl of Tn5 reaction mix (10 μl of 5×TTBL and 5 μl of TTE Mix V50) was added following the kit instructions and thoroughly mixed. The mixture was incubated at 37 °C for 30 min. The resulting product was purified using a MinElute column (MinElute PCR Purification Kit, Qiagen, Germany). The PCR reaction setup included the purified fragmented DNA (24 μl), 5×TAB (10 μl), PPM (5 μl), N5** (5 μl), N7** (5 μl), and TAE (1 μl). PCR amplification was carried out according to the recommended protocol in the manual. The number of cycles was determined based on pre-experiment qPCR, set at 12 cycles, calculated as the cycle number at which the curve reaches the plateau phase in qPCR plus 5. Subsequently, the DNA product was purified again using a MinElute column (MinElute PCR Purification Kit, Qiagen, Germany). DNA sorting was performed using VAHTS DNA Clean Beads (N411 Vazyme) according to the 0.55×/1.0×scheme. Fragmentation analysis of the DNA was conducted using a Cartridge Kit (BiOptic, Taiwan). Finally, the libraries were sequenced using Illumina NovaSeq 6000 sequencing.

treatment_protocol: Each mTBI mouse received a single mild controlled cortical impact (CCI).Sham-operated control mice underwent the same procedures except for the impact.

value: Hippocampus

value: mTBI


title: Murine Spleen Treg from EAE Peak BioRep4

description: Library name: SPL_Treg_Peak_R4

value: Treg

value: Foxp3-GFP mice (C57BL/6)

value: EAE Peak


title: Ind3_VEH_0.5_24

description: Library name: iPSC-CM_Ind3_VEH_0.5_24

value: female

value: induced pluripotent stem cell-derived cardiomyocytes


title: BMDM, HDL, Control_3

description: Library name: Control_3

value: Mouse bone marrow

value: Bone marrow derived macrophages

value: HDL, Control


title: Ind3_CX_0.5_3

description: Library name: iPSC-CM_Ind3_CX_0.5_3


title: Veh-4 (snATAC)

description: Library name: A2989

value: brain

value: APP/PS+

value: Vehicle


title: BAV_6

description: Library name: Sample 11

value: Male


title: BMDM, HDL, Control_2

description: Library name: Control_2


title: Murine Spleen Tconv from EAE Recovery BioRep1

description: Library name: SPL_Tconv_Rec_R1

value: Spleen

value: Tconv

value: 2000 cells

value: EAE Recovery

value: Bio rep 1


title: Ind3_CX_0.5_24

description: Library name: iPSC-CM_Ind3_CX_0.5_24


title: Ind3_DOX_0.5_3

description: Library name: iPSC-CM_Ind3_DOX_0.5_3


title: Murine Spleen Tconv from EAE Recovery BioRep5

description: Library name: SPL_Tconv_Rec_R5

value: Bio rep 5


title: BMDM, HDL, Control_1

description: Library name: Control_1


title: Murine Spleen Tconv from EAE Peak BioRep3

description: Library name: SPL_Tconv_Peak_R3

value: Foxp3-GFP mice (C57BL/6)

value: Bio rep 3


title: Ind3_CX_0.1_3

description: Library name: iPSC-CM_Ind3_CX_0.1_3

value: female


title: Ind3_DOX_0.1_3

description: Library name: iPSC-CM_Ind3_DOX_0.1_3

value: induced pluripotent stem cell-derived cardiomyocytes


title: Bexa-5 (snATAC)

description: Library name: A2997

value: Bexarotene


title: Murine Spleen Tconv from EAE Peak BioRep2

description: Library name: SPL_Tconv_Peak_R2

value: EAE Peak

value: Bio rep 2


title: BAV_5

description: Library name: Sample 16

value: aortic valve leaflets

value: BAV

value: Female


title: TAV_284

description: Library name: Sample 8

value: TAV


title: BAV_153

description: Library name: Sample 13


title: Ind3_DOX_0.1_48

description: Library name: iPSC-CM_Ind3_DOX_0.1_48


title: Murine Spleen Tconv from EAE Peak BioRep1

description: Library name: SPL_Tconv_Peak_R1

value: Spleen


title: Ind2_VEH_0.5_48

description: Library name: iPSC-CM_Ind2_VEH_0.5_48


title: TAV_110

description: Library name: Sample 6


title: BAV_81

description: Library name: Sample 12

value: Male


title: Bexa-2 (snATAC)

description: Library name: A2913

value: brain

value: APP/PS+


title: Ind3_DOX_0.5_24

description: Library name: iPSC-CM_Ind3_DOX_0.5_24


title: Veh-1 (snATAC)

description: Library name: A2905

value: Vehicle


title: Murine Spleen Treg from EAE Peak BioRep1

description: Library name: SPL_Treg_Peak_R1

value: Treg

value: 2000 cells

value: Bio rep 1


title: Ind3_CX_0.5_48

description: Library name: iPSC-CM_Ind3_CX_0.5_48

value: female


title: Murine Spleen Tconv from EAE Peak BioRep4

description: Library name: SPL_Tconv_Peak_R4

value: Tconv

value: Foxp3-GFP mice (C57BL/6)

value: Bio rep 4


title: Ctrl Cre left ventricle rep4

city: Heidelberg

first: Ashraf

last: Rangrez

address: Im Neuenheimer Feld 410

institute: Heidelberg University Hospital

description: Library name: Sample 8

data_processing:
RNA-seq data are aligned using Hisat2 v2.0.5. Reads are assigned to transcripts using featureCounts
Differential expression analysis of the data was performed using edgeR
Assembly: mm10
Supplementary files format and content: Microsoft Excel Worksheet containing read count and analyzed results

source_name: left ventricle

extract_protocol:
Qiagen RNeasy Universal kit for RNA extraction
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis. Libraries prepared using Novogene NGS RNA Library Prep Set (PT042) were sequenced on Illumina NovaSeq 6000 platform S4 flow cell.

treatment_protocol: Male CMI3OE and Ctrl mice were treated with Tamoxifen (30mg/kg) by gavage for 3 days. Echocardiography was performed and left ventricle was harvested for RNA-seq on day5.

value: left ventricle

value: left ventricle tissue

value: Ctrl Cre

value: Oral Tamoxifen 30mg/kg


title: Murine CNS Treg from EAE Recovery BioRep4

description: Library name: CNS_Treg_Rec_R4

value: CNS

value: EAE Recovery


title: Ind3_DOX_0.1_24

description: Library name: iPSC-CM_Ind3_DOX_0.1_24

value: induced pluripotent stem cell-derived cardiomyocytes


title: Murine CNS Treg from EAE Recovery BioRep3

description: Library name: CNS_Treg_Rec_R3

value: Bio rep 3


title: Bexa-3 (snATAC)

description: Library name: A2960

value: brain

value: APP/PS+

value: Bexarotene


title: Veh-3 (snATAC)

description: Library name: A2914

value: Vehicle


title: TAV_310

description: Library name: Sample 9

value: aortic valve leaflets

value: TAV

value: Female


title: TAV_326

description: Library name: Sample 10

value: Male


title: Ctrl Cre left ventricle rep2

description: Library name: Sample 6


title: Murine Spleen Tconv from EAE Recovery BioRep2

description: Library name: SPL_Tconv_Rec_R2

value: Spleen

value: Tconv

value: 2000 cells

value: Foxp3-GFP mice (C57BL/6)

value: Bio rep 2


title: Ind2_VEH_0.5_3

description: Library name: iPSC-CM_Ind2_VEH_0.5_3

value: female


title: Veh-2 (snATAC)

description: Library name: A2899


title: Murine Spleen Tconv from EAE Recovery BioRep3

description: Library name: SPL_Tconv_Rec_R3

value: EAE Recovery


title: Ctrl Cre left ventricle rep1

description: Library name: Sample 5

value: left ventricle

value: left ventricle tissue

value: Ctrl Cre

value: Oral Tamoxifen 30mg/kg


title: Ind2_VEH_0.1_3

description: Library name: iPSC-CM_Ind2_VEH_0.1_3

value: induced pluripotent stem cell-derived cardiomyocytes


title: Ind2_VEH_0.1_24

description: Library name: iPSC-CM_Ind2_VEH_0.1_24


title: CMI3OE left ventricle rep4

description: Library name: Sample 4


title: Ind3_CX_0.1_24

description: Library name: iPSC-CM_Ind3_CX_0.1_24


title: TAV_264

description: Library name: Sample 7


title: Bexa-1 (snATAC)

description: Library name: A2902

value: brain

value: APP/PS+

value: Bexarotene


title: Ind3_CX_0.1_48

description: Library name: iPSC-CM_Ind3_CX_0.1_48


title: CMI3OE left ventricle rep3

description: Library name: Sample 3


title: single-cell RNA seq of early weaning piglet_EWP3

city: Hangzhou

first: Wenjie

last: Tang

address: Yuhangtang Road

institute: Zhejiang university

description: one sample from early weaned piglet ileum tissue

data_processing:
Sample demultiplexing, barcode processing and unique molecular identifier (UMI) counting were processed using the Cell Ranger pipeline with default and recommended parameters (https://support.10xgenomics.com/single-cell-geneexpression/software/pipelines,version3.1.0) and scRNA-seq data were aligned to Ensembl genome sus scrofa reference genome annotations. A total of 50,025 single cells captured from NSP and EWP (n=3) were processed using 10X Genomics Chromium Single Cell 3’ Solution.
Genome_build: mm10
Supplementary_files_format_and_content: matrix table with raw gene counts for every gene and every cell

organism: Sus scrofa

source_name: Ileum tissue of early weaning piglet

extract_protocol:
The tissue was dissociated into 5 ml of digestion solution (0.35% collagenase IV5, 2 mg/ml papain, 120 unit/ml DNase I) in 37 °C water bath with shaking for 20 min at 100 rpm. Digestion was terminated with the PBS containing fetal bovine serum (FBS, 50% v/v), then pipetting 6 times with Pasteur pipette. The resulting cell suspension was filtered by passing through 70 μm stacked cell strainer and centrifuged at 300g for 5 min at 4 °C. The cell pellet was resuspended in 100ul PBS (0.04% BSA) and with 1 ml 1 × red blood cell lysis buffer (MACS, 10×) and incubated at 37 °C for 5 min to lyse remaining blood cells. And then, the suspension was resuspended in 50 μl of 1× PBS (0.04% BSA) after removing dead cells by Miltenyi® Dead Cell Removal Kit (MACS, 10× Genomics).
Single-cell suspension was loaded to 10x Chromium to capture appropriate amount of single cell according to the manufacturer instructions of 10x Genomics Chromium Single-Cell 3’ kit (V3). The following amplification of cDNA and library construction was performed per the standard manufacture’s protocol. Libraries were subjected to an Illumina NovaSeq 6000 sequencing system (paired-end multiplexing run,150 bp)

value: 26 days

value: early weaning

value: Ileum

tag: breed

value: Landrace x Yorkshire


title: Murine CNS Treg from EAE Peak BioRep3

description: Library name: CNS_Treg_Peak_R3

value: CNS

value: Treg

value: 2000 cells

value: EAE Peak

value: Bio rep 3


title: CTL_120

description: Library name: Sample 2

value: aortic valve leaflets

value: CTRL

value: Female


title: Ind2_DOX_0.5_3

description: Library name: iPSC-CM_Ind2_DOX_0.5_3

value: female


title: TAV_73

description: Library name: Sample 5

value: TAV

value: Male


title: Murine CNS Treg from EAE Recovery BioRep1

description: Library name: CNS_Treg_Rec_R1

value: Foxp3-GFP mice (C57BL/6)

value: EAE Recovery

value: Bio rep 1


title: single-cell RNA seq of early weaning piglet_EWP1

value: 26 days

value: early weaning


title: CTL_119

description: Library name: Sample 1


title: Murine CNS Treg from EAE Recovery BioRep2

description: Library name: CNS_Treg_Rec_R2

value: Bio rep 2


title: Murine CNS Treg from EAE Peak BioRep2

description: Library name: CNS_Treg_Peak_R2

value: CNS


title: single-cell RNA seq of suckling piglet_NSP3

description: one sample from suckling piglet ileum tissue

source_name: Ileum tissue of suckling piglet

value: normal breast-feeding

value: Ileum

value: Landrace x Yorkshire


title: Ind2_VEH_0.5_24

description: Library name: iPSC-CM_Ind2_VEH_0.5_24

value: induced pluripotent stem cell-derived cardiomyocytes


title: Murine CNS Treg from EAE Recovery BioRep5

description: Library name: CNS_Treg_Rec_R5

value: Treg

value: 2000 cells

value: Bio rep 5


title: CTL_200

description: Library name: Sample 3

value: aortic valve leaflets

value: CTRL

value: Female


title: Ctrl Cre left ventricle rep3

description: Library name: Sample 7

value: left ventricle

value: left ventricle tissue

value: Ctrl Cre

value: Oral Tamoxifen 30mg/kg


title: CTL_261

description: Library name: Sample 4

value: Male


title: Murine CNS Tconv from EAE Recovery BioRep4

description: Library name: CNS_Tconv_Rec_R4

value: Tconv

value: Foxp3-GFP mice (C57BL/6)

value: EAE Recovery

value: Bio rep 4


title: Ind2_DOX_0.1_24

description: Library name: iPSC-CM_Ind2_DOX_0.1_24

value: female


title: Murine CNS Treg from EAE Peak BioRep4

description: Library name: CNS_Treg_Peak_R4

value: CNS

value: EAE Peak


title: single-cell RNA seq of suckling piglet_NSP1

value: 26 days

value: normal breast-feeding

value: Ileum

value: Landrace x Yorkshire


title: AAV-EGFP-CMI3OE left ventricle rep2

description: Library name: Sample 6

data_processing:
RNA-seq data are aligned using Hisat2 v2.0.5. Reads are assigned to transcripts using featureCounts
Differential expression analysis of the data was performed using edgeR
Assembly: mm10
Supplementary files format and content: Microsoft Excel Worksheet containing analyzed read counts

treatment_protocol: Male CMI3OE mice were treated with AAV-PGC-1a  and AAV-EGFP for 3 weeks and IRF3-2D expression was induced by tamoxifen gavage (30mg/kg) for 3 days. Left ventricle was harvested on day5 for RNA-seq.


title: AAV-EGFP-CMI3OE left ventricle rep1

description: Library name: Sample 5


title: AAV-PGC-1a-CMI3OE left ventricle rep4

description: Library name: Sample 4


title: CMI3OE left ventricle rep1

description: Library name: Sample 1


title: Ind2_VEH_0.1_48

description: Library name: iPSC-CM_Ind2_VEH_0.1_48

value: induced pluripotent stem cell-derived cardiomyocytes


title: Ind2_DOX_0.1_48

description: Library name: iPSC-CM_Ind2_DOX_0.1_48


title: AAV-EGFP-CMI3OE left ventricle rep4

description: Library name: Sample 8

value: left ventricle


title: Ind2_DOX_0.5_24

description: Library name: iPSC-CM_Ind2_DOX_0.5_24


title: Murine CNS Tconv from EAE Recovery BioRep5

description: Library name: CNS_Tconv_Rec_R5

value: 2000 cells

value: Bio rep 5


title: Murine CNS Tconv from EAE Peak BioRep4

description: Library name: CNS_Tconv_Peak_R4


title: CMI3OE left ventricle rep2

description: Library name: Sample 2

value: left ventricle tissue

value: Oral Tamoxifen 30mg/kg


title: Ind2_CX_0.5_48

description: Library name: iPSC-CM_Ind2_CX_0.5_48


title: Ind2_DOX_0.1_3

description: Library name: iPSC-CM_Ind2_DOX_0.1_3


title: Ind2_CX_0.1_48

description: Library name: iPSC-CM_Ind2_CX_0.1_48


title: AAV-PGC-1a-CMI3OE left ventricle rep2

description: Library name: Sample 2


title: single-cell RNA seq of suckling piglet_NSP2


title: HG+ORG_S22

city: Badajoz

first: María

last: Gómez Álvarez

state: Badajoz

address: Parque de Cornalvo, 29

country: Spain

institute: IVI Foundation

description: Library name: Sample 22

data_processing:
The quality of raw RNA sequencing reads was assessed using FastQC (v0.11.9), and summary reports were generated with MultiQC (v1.27.1). Adapters and low-quality bases were trimmed using Trimmomatic (v0.39). Trimmed reads were aligned to the Mus musculus reference genome (GRCm39) using HISAT2 (v2.2.1) with --dta for transcriptome-aware alignment. SAM files were converted to sorted BAM format using SAMtools (v1.21) (Li et al., 2009). Gene-level counts were generated with featureCounts (v2.0.3) (Subread package) using the mouse genome annotation. Raw counts were processed in R (v4.3.1) using DESeq2 (v1.42.1) (Love et al., 2014). Low-expression genes were filtered (rowSums ≥ 10 counts in ≥ 3 samples), and data were normalized via the median-of-ratios method.  Differential expression was tested using DESeq2’s negative binomial Wald test, applying Benjamini-Hochberg (FDR) correction with a threshold of |log2FC| > 1 and adjusted p-value < 0.05. Gene Ontology (GO) and KEGG pathway analyses were performed using clusterProfiler (v4.10.1) for gene set enrichment analysis (GSEA). ENSEMBL IDs were mapped to ENTREZIDs using org.Mm.eg.db (v3.18.0). Principal component analysis (PCA) and hierarchical clustering were conducted on variance-stabilized transformed (VST) data using ggplot2 (v3.5.2) and pheatmap (v1.0.12).
Assembly: Trimmed reads were aligned to the Mus musculus reference genome (GRCm39) using HISAT2 (v2.2.1)
Supplementary files format and content: tab-delimited text file includes filtered counts for each sample
Supplementary files format and content: gene_counts.csv

source_name: endometrium

extract_protocol:
The endometrial tissue was carefully separated from the myometrium by applying gentle pressure along the uterine horns using the back of curved forceps, facilitating the expulsion of the endometrial layer. Total RNA was extracted from the isolated endometrial tissue from each horn (n = 23, 2 samples were discarded due to technical problems) using the RNAeasyVR Mini Kit (74014, Qiagen, Hilden, Germany), following the manufacturer’s protocol.
For mRNA library preparation, total RNA was processed using the Illumina Stranded mRNA Prep Kit (20020595, Illumina, San Diego, CA, USA). Initially, mRNA molecules were selectively purified using oligo-dT beads that bind to poly(A) tails. These fragments were then fragmented and hybridized with random hexamers to synthesize the first-strand of complementary DNA (cDNA). The second-strand cDNA was generated using deoxyuridine triphosphate (dUTP) to enable strand specificity. The resulting double-stranded cDNA was ligated to indexed adapters and subsequently enriched via polymerase chain reaction (PCR). The resulting cDNA libraries were quantified using fluorometry and their fragment sizes were assessed with the Agilent 2100 Bioanalyzer. An equimolar pool of all samples was prepared and sequenced on the NextSeq 550 platform (Illumina, San Diego, CA, USA) using single-end 75-cycle sequencing (1 × 75 bp) with a High Output Reagent Cartridge (400 M reads).

value: endometrium

value: tissue

value: endometrial tissue


title: Murine CNS Treg from EAE Peak BioRep1

description: Library name: CNS_Treg_Peak_R1

value: Treg

value: Foxp3-GFP mice (C57BL/6)

value: Bio rep 1


title: Ind2_CX_0.1_3

description: Library name: iPSC-CM_Ind2_CX_0.1_3

value: female


title: single-cell RNA seq of early weaning piglet_EWP2

value: 26 days

value: early weaning


title: HG+ORG_S19

description: Library name: Sample 19


title: AAV-PGC-1a-CMI3OE left ventricle rep1

description: Library name: Sample 1


title: HG+ORG_S23

description: Library name: Sample 23


title: Murine CNS Tconv from EAE Peak BioRep2

description: Library name: CNS_Tconv_Peak_R2

value: CNS

value: Tconv

value: EAE Peak

value: Bio rep 2


title: Ind2_DOX_0.5_48

description: Library name: iPSC-CM_Ind2_DOX_0.5_48

value: induced pluripotent stem cell-derived cardiomyocytes


title: HG+ORG_S21

description: Library name: Sample 21


title: Ind2_CX_0.1_24

description: Library name: iPSC-CM_Ind2_CX_0.1_24


title: Murine CNS Tconv from EAE Peak BioRep1

description: Library name: CNS_Tconv_Peak_R1

value: 2000 cells


title: AAV-EGFP-CMI3OE left ventricle rep3

description: Library name: Sample 7

value: left ventricle

value: left ventricle tissue


title: HG_S17

description: Library name: Sample 17

value: endometrium


title: Ind1_VEH_0.5_48

description: Library name: iPSC-CM_Ind1_VEH_0.5_48


title: Murine CNS Tconv from EAE Recovery BioRep2

description: Library name: CNS_Tconv_Rec_R2

value: EAE Recovery


title: RNA-seq_Tby cells, lung, cGVHD, Rep1

city: Monrovia

first: Xiwei

last: Wu

state: CA

address: 655 HUNTINGTON DR.

institute: City of Hope

data_processing:
Basecalls performed using  using RTA workflow version 1.18.64
Sequenced reads were trimmed for adaptor sequence,  low-complexity or low-quality sequence using trimmomatic v0.39 and fastp v0.20.1, then mapped to hg19 whole genome using STAR v2.7.4a with parameters --twopassMode Basic --outSAMstrandField intronMotif
Raw counts of sequencing reads for genes were perfomred using featureCounts method in Rsubread V2.01.
Read counts normalization, Reads Per Kilobase of exon per Megabase of library size (RPKM), and detection of differentailly expressed genes were processed using edgeR v3.28.1.
Assembly: mm10
Supplementary files format and content: tab-delimited text files with raw counts of sequencing reads per gene for each Sample

source_name: Lung

extract_protocol:
total RNA isolation with Trizol
KAPA mRNA HyperPrep kit was used for RNA sequencing library preparation according to kit user manual; PolyA enriched, stranded RNA sequencing library

value: Lung

value: Ly108-CD69- CD4+Tby


title: HG_S16

description: Library name: Sample 16

value: tissue

value: endometrial tissue


title: Ind2_CX_0.5_24

description: Library name: iPSC-CM_Ind2_CX_0.5_24

value: female


title: Ind1_VEH_0.5_24

description: Library name: iPSC-CM_Ind1_VEH_0.5_24


title: RNA-seq_Trm cells, lung, cGVHD, Rep3

value: Ly108-CD69+ CD4+Trm


title: Murine CNS Tconv from EAE Recovery BioRep3

description: Library name: CNS_Tconv_Rec_R3

value: Foxp3-GFP mice (C57BL/6)

value: Bio rep 3


title: HiC_ZSCAN4OECTRL

city: Paris

first: Yann

last: Loe-Mie

address: 25 rue du Dr Roux

department: Computational Biology

country: France

institute: Institut Pasteur

description: Library name: HiC_ZSCAN4OE_CTRL

data_processing:
Hi-C data was processed using the nf-core/hic
Normalization was then carried out using the ICE
Assembly: mm10
Supplementary files format and content: MCOOL multi resolution maps.

growth_protocol: Cells were maintained in Serum+Lif (S/L) medium (KnockOut DMEM supplemented with 15% ES cell qualified FBS, 1% GlutaMAX, 1% MEM non-essential amino acids, 1% penicillin-streptomycin, 0.1 mM 2-mercaptoethanol, 10 ng/mL Lif (Miltenyi Biotec, Cat #130-099-895) on gelatine-coated plates in a humidified incubator (37°C, 5% CO2). ES R1 cell line was maintained under the same conditions. To sort MERVL Tomato-positive and Tomato-negative cells, mouse ESCs were seeded in 150mm culture dishes at 5 million cells per plate. To isolate MERVL Tomato-negative ESCs overexpressing Zscan4, cells were treated with doxycycline for 48 hours and then sorted based on negative Tomato signal and positive GFP signal. In case of treatments, the compounds were supplemented in the media while seeding. After 48h (or 24h post siRNA transfection), cells were trypsinized and resuspended in PBS.  Prior to sorting using The BD FACSAria™ III Cell Sorter, cells were incubated with DRAQ7 (Invitrogen, Cat#D15106) for 10 mins in the dark at room temperature to exclude non-viable cells.

extract_protocol:
Hi-C was performed on FACS-sorted cells for all the experiments. 500,000 cells were fixed with 2% formaldehyde and frozen for at least 12 hrs at -80°C prior to Hi-C experiments. Hi-C was performed using the Arima Hi-C+ kit (Arima Genomics) according to the manufacturer's instructions. DNA was sheared using Covaris.
Sequencing libraries were prepared using the Collibri kit (Invitrogen, Cat#A38612024W). For sequencing, PE35 sequencing was carried out using NextSeq 500/550 High Output Kit v2.5 (75 Cycles) (Illumina, Cat# 20024906).

treatment_protocol: All the drug treatments were carried out for 48hrs in S/L media unless mentioned otherwise. Curaxin (CBl0137) treatment: 0.5mM; Polyamine inhibition: 0.25mM of DFMO and 15mM of AMXT-1501. PladienolideB (PlaB) treatment: 2.5nM; Doxycycline: 1000ng/ml. Mouse ESCs were plated in Serum/Lif medium in 6-well plates or in 150mm culture plates at 0.2 x 10^6 cells per well or 4 x 10^6 cells per plate. On the following day, the cells were transfected with a combination of two siRNAs against Zscan4; Ambion: Cat#4390771, ID: s233512 and Horizon discovery: J-162176-02-0050) or ON-TARGETplus Non-targeting Control siRNAs using Lipofectamine RNAiMAX at 50pM each per well for a 6-well plate and 1nM for 150mm culture plates. The transfection was repeated the following day and cells were harvested 24h post-transfection.

value: ESC (MERVL -, GFP +)

value: Mervl::dtTomato, GFP, iZscan4


title: RNA-seq_Trm cells, lung, cGVHD, Rep2


title: Ind1_VEH_0.1_48

description: Library name: iPSC-CM_Ind1_VEH_0.1_48


title: HG_S14

description: Library name: Sample 14


title: HiC_ZSCAN4OE_DOX

description: Library name: HiC_ZSCAN4OE_DOX

value: doxycycline


title: Murine CNS Tconv from EAE Recovery BioRep1

description: Library name: CNS_Tconv_Rec_R1

value: CNS

value: Tconv

value: Bio rep 1


title: AAV-PGC-1a-CMI3OE left ventricle rep3

description: Library name: Sample 3

value: left ventricle

value: left ventricle tissue

value: Oral Tamoxifen 30mg/kg


title: HiC_CTCF_CURAXIN

description: Library name: HiC_CTCF_CURAXIN

value: ESC (unsorted)

value: CTCF-AID

value: curaxin


title: Ind2_CX_0.5_3

description: Library name: iPSC-CM_Ind2_CX_0.5_3

value: induced pluripotent stem cell-derived cardiomyocytes


title: PBS_S10

description: Library name: Sample 10

value: endometrium

value: tissue

value: endometrial tissue


title: Murine CNS Tconv from EAE Peak BioRep3

description: Library name: CNS_Tconv_Peak_R3

value: 2000 cells

value: Foxp3-GFP mice (C57BL/6)

value: EAE Peak

value: Bio rep 3


title: Ind1_DOX_0.5_3

description: Library name: iPSC-CM_Ind1_DOX_0.5_3

value: female


title: PBS_S9

description: Library name: Sample 9


title: HiC_RAD21_CTRL

description: Library name: HiC_RAD21_CTRL

value: RAD21 AID


title: RNA-seq_Tby cells, lung, cGVHD, Rep2

value: Lung

value: Ly108-CD69- CD4+Tby


title: Ind1_VEH_0.5_3

description: Library name: iPSC-CM_Ind1_VEH_0.5_3


title: HG_S15

description: Library name: Sample 15


title: RNA-seq_Trm cells, lung, cGVHD, Rep1

value: Ly108-CD69+ CD4+Trm


title: HG+ORG_S18

description: Library name: Sample 18


title: HG_S12

description: Library name: Sample 12


title: HG+ORG_S20

description: Library name: Sample 20


title: RNA-seq_Tsm cells, lung, cGVHD, Rep1

value: Ly108+CD69- CD4+Tsm


title: PBS_S8

description: Library name: Sample 8


title: RNA-seq_Trmp cells, lung, cGVHD, Rep2

value: Ly108+CD69+ CD4+Trmp


title: ATAC-seq_Tby cells, lung, cGVHD, Rep1

data_processing:
Basecalls were performed using CASAVA.
Reads were trimmed for adaptor sequence, then mapped to UCSC mm10 using bwa with default settings.
Peaks were called using using Genrich v0.5.
Assembly: mm10
Supplementary files format and content: Peak files are in ENCODE narrowPeak format, which includes the following columns: chromosome, start, end, name, score (1000), strand, signalValue, -log10(pvalue), -log10(qvalue), peak.

extract_protocol:
Cells were counted using Chamber Slide and about 2 million cells were prcessed.
Sequencing libraries were constrcuted using the Illumina Nextera DNA Sample prep kit.


title: RNA-seq_Tsm cells, lung, cGVHD, Rep2


title: Ind1_DOX_0.1_3

description: Library name: iPSC-CM_Ind1_DOX_0.1_3


title: HiC_ESC

description: Library name: HiC_ESC

growth_protocol: Cells were maintained in Serum+Lif (S/L) medium (KnockOut DMEM supplemented with 15% ES cell qualified FBS, 1% GlutaMAX, 1% MEM non-essential amino acids, 1% penicillin-streptomycin, 0.1 mM 2-mercaptoethanol, 10 ng/mL Lif (Miltenyi Biotec, Cat #130-099-895) on gelatine-coated plates in a humidified incubator (37°C, 5% CO2). ES R1 cell line was maintained under the same conditions. To sort MERVL Tomato-positive and Tomato-negative cells, mouse ESCs were seeded in 150mm culture dishes at 5 million cells per plate. In case of treatments, the compounds were supplemented in the media while seeding. After 48h (or 24h post siRNA transfection), cells were trypsinized and resuspended in PBS.  Prior to sorting using The BD FACSAria™ III Cell Sorter, cells were incubated with DRAQ7 (Invitrogen, Cat#D15106) for 10 mins in the dark at room temperature to exclude non-viable cells.

treatment_protocol: All the drug treatments were carried out for 48hrs in S/L media unless mentioned otherwise. Curaxin (CBl0137) treatment: 0.5mM; Polyamine inhibition: 0.25mM of DFMO and 15mM of AMXT-1501. PladienolideB (PlaB) treatment: 2.5nM; Mouse ESCs were plated in Serum/Lif medium in 6-well plates or in 150mm culture plates at 0.2 x 10^6 cells per well or 4 x 10^6 cells per plate. On the following day, the cells were transfected with a combination of two siRNAs against Zscan4; Ambion: Cat#4390771, ID: s233512 and Horizon discovery: J-162176-02-0050) or ON-TARGETplus Non-targeting Control siRNAs using Lipofectamine RNAiMAX at 50pM each per well for a 6-well plate and 1nM for 150mm culture plates. The transfection was repeated the following day and cells were harvested 24h post-transfection.

value: ESC (Mervl -)


title: ATAC-seq_Trm cells, lung, cGVHD, Rep2


title: Ind1_VEH_0.1_24

description: Library name: iPSC-CM_Ind1_VEH_0.1_24


title: PBS_S11

description: Library name: Sample 11


title: ATAC-seq_Tby cells, lung, cGVHD, Rep2


title: Ind1_DOX_0.1_24

description: Library name: iPSC-CM_Ind1_DOX_0.1_24


title: SHAM_S6

description: Library name: Sample 6


title: HiC_CTCF_CTRL

description: Library name: HiC_CTCF_CTRL

value: ESC (unsorted)

value: CTCF-AID


title: HiC_RAD21_AUXIN-CURAXIN

description: Library name: HiC_RAD21_AUXIN-CURAXIN

value: Auxin-curaxin


title: RNA-seq_Trmp cells, lung, cGVHD, Rep1


title: Ind1_DOX_0.5_48

description: Library name: iPSC-CM_Ind1_DOX_0.5_48

value: induced pluripotent stem cell-derived cardiomyocytes


title: ATAC-seq_Trm cells, lung, cGVHD, Rep1


title: Ind1_VEH_0.1_3

description: Library name: iPSC-CM_Ind1_VEH_0.1_3


title: HG_S13

description: Library name: Sample 13

value: endometrium

value: tissue

value: endometrial tissue


title: Ind1_DOX_0.1_48

description: Library name: iPSC-CM_Ind1_DOX_0.1_48


title: ATAC-seq_Trmp cells, lung, cGVHD, Rep2


title: HiC_CTCF_AUXIN_CURAXIN

description: Library name: HiC_CTCF_AUXIN_CURAXIN


title: Ind1_DOX_0.5_24

description: Library name: iPSC-CM_Ind1_DOX_0.5_24


title: HiC_2CLC_PlaB

description: Library name: HiC_2CLC_PlaB

value: 2CLC (Mervl +)

value: PlaB


title: PBS_S7

description: Library name: Sample 7


title: ATAC-seq_Trmp cells, lung, cGVHD, Rep1


title: HiC_2CLC_Si_Zscan4

description: Library name: HiC_2CLC_Si_Zscan4

value: Si Zscan4


title: SHAM_S3

description: Library name: Sample 3


title: HiC_RAD21_CURAXIN

description: Library name: HiC_RAD21_CURAXIN

value: RAD21 AID

value: curaxin


title: Ind1_CX_0.5_48

description: Library name: iPSC-CM_Ind1_CX_0.5_48

value: female


title: ATAC-seq_Tsm cells, lung, cGVHD, Rep1

value: Lung


title: HiC_2CLC_DFMO_AMXT_24h

description: Library name: HiC_2CLC_DFMO_AMXT_24h

value: DFMO AMXT 24h


title: ATAC-seq_Tsm cells, lung, cGVHD, Rep2

value: Ly108+CD69- CD4+Tsm


title: Ind1_CX_0.1_24

description: Library name: iPSC-CM_Ind1_CX_0.1_24


title: Ind1_CX_0.1_3

description: Library name: iPSC-CM_Ind1_CX_0.1_3


title: Mu_Mervl_to

description: Library name: Mu_Mervl_to

library_source: transcriptomic single cell

data_processing:
The ParseBioscience processing pipeline (v1.1.2) was used with default settings to align sequencing reads to the mm10 mouse genome and hg38 human genome
The count matrixes were analyzed with the Seurat R package in order to cluster the data and generate UMAPs.
for Hu_iPSCs dataset Hu_iPSCs_ctrl A1-A4, Lib_not_used A5-A8, Hu_iPSCs_Curaxin A9-A12
for Mu_Mervl_to not_used A1-A9, Mu_Mervl_to_Curaxin A12, Mu_Mervl_to_ctrl A10-A11
Assembly: mm10 or hg38
Supplementary files format and content: csv file and matrix files that are output of the ParseBioscience pipeline

growth_protocol: Mouse : Cells were maintained in Serum+Lif (S/L) medium (KnockOut DMEM supplemented with 15% ES cell qualified FBS, 1% GlutaMAX, 1% MEM non-essential amino acids, 1% penicillin-streptomycin, 0.1 mM 2-mercaptoethanol, 10 ng/mL Lif (Miltenyi Biotec, Cat #130-099-895) on gelatine-coated plates in a humidified incubator (37°C, 5% CO2). ES R1 cell line was maintained under the same conditions. Human : HuIPSCs were maintained on feeders in PXGL culture medium: N2B27 (1:1 DMEM/F12:Neurobasal, 0.5X N2 supplement, 0.5X B27 supplement, 1X nonessential amino acids, 2mM L-Glutamine, 1X penicillin-streptomycin, 0.1mM 2-mercaptoethanol, supplemented with 1mM PD0325901 (Stemcell Technologies, #72184), 2mM Gö6983 (Stemcell Technologies, #72462), 2mM XAV939 (Stemcell Technologies, #72674) and 10ng/ml human LIF (Stemcell Technologies, #78055). Medium was refreshed every day for all the cell lines.

extract_protocol:
Mouse ESCs and human iPSCs (untreated and treated with curaxin) were subjected to a split-pool combinatorial barcoding method of scRNA-sequencing using single-cell whole-transcriptome kits (Evercode WT Mini v2) from Parse Biosciences according to the manufacturer’s instructions.
(Evercode WT Mini v2) from Parse Biosciences according to the manufacturer’s instructions.

treatment_protocol: Curaxin (CBl0137) treatment: 0.5mM for 48h

value: Mouse ESCs

value: none/Curaxin


title: PmDay4

city: Providence

first: Nathalie

last: Oulhen

state: RI

address: 185 meeting street

institute: Brown university

description:
Library name: PmDay4
10X Genomics

data_processing:
Single cell encapsulation was performed using the Chromium Single Cell kit on the 10x Genomics Chromium Controller. Single cell cDNA and libraries were prepared using the Chromium Single Cell 3′ Reagent kit v3.1 Chemistry. Libraries were sequenced by Genewiz/Azenta on the Illumina NovaSeq. Single-cell unique molecular identifier (Fujii et al., 2009) counting (counting of unique barcodes given to individual transcript molecules) was performed using Cell Ranger from 10x Genomics. The reference files were generated using CellRanger mkref (Pm v3 assembly available on echinobase). Cellranger gene expression matrices were further analyzed using the R package Seurat (Stuart et al., 2019). Cell numbers were forced to 12000 for each time point. tSNE analysis for PmDay3 was performed with the following parameters: dimension 15 and resolution 0.5. UMAP analysis for the integration of the four time points was performed with Harmony and with the following parameters: dimension 20 and resolution 1. Marker genes for single cell RNA sequencing datasets were extracted using the FindMarkers function in Seurat (using R) and were then sorted based on the pct1/pct2 ratio.
Assembly: Pmv3 available on Echinobase
Supplementary files format and content: PmDay3_Dim15_res0.5.rds
Supplementary files format and content: PmDays_harmony_umap_Dim20_res1.rds

organism: Patiria miniata

source_name: Late Larva

extract_protocol:
The embryos were collected and washed twice with calcium-free sea water, and then suspended in hyalin-extraction media (HEM) for 10-15 min, depending on the stage of dissociation. When cells were beginning to dissociate, the embryos were collected and washed in 0.5 M NaCl, gently sheared with a pipette, run through a 40 μm Nitex mesh, counted on a hemocytometer and diluted to reach the appropriate concentration for the scRNA-seq protocol.
Single cell encapsulation was performed using the Chromium Single Cell kit on the 10x Genomics Chromium Controller. Single cell cDNA and libraries were prepared using the Chromium Single Cell 3’ Reagent kit v3.1 Chemistry. Libraries were sequenced by Genewiz on the Illumina Novaseq.

value: Late Larva


title: HiC_2CLC_Si_Ctrl

description: Library name: HiC_2CLC_Si_Ctrl

value: Si Ctrl


title: Ind1_CX_0.5_3

description: Library name: iPSC-CM_Ind1_CX_0.5_3

value: induced pluripotent stem cell-derived cardiomyocytes


title: SHAM_S5

description: Library name: Sample 5

value: endometrium


title: PmDay3

description:
Library name: PmDay3
10X Genomics

source_name: Early Larva

value: Early Larva


title: SHAM_S1

description: Library name: Sample 1

value: tissue

value: endometrial tissue


title: HiC_2CLC_DFMO_AMXT_48h

description: Library name: HiC_2CLC_DFMO_AMXT_48h

value: 2CLC (Mervl +)

value: DFMO AMXT 48h


title: SHAM_S2

description: Library name: Sample 2


title: Ind1_CX_0.1_48

description: Library name: iPSC-CM_Ind1_CX_0.1_48


title: HiC_2CLC

description: Library name: HiC_2CLC


title: C8_3, vehicle, IgG

city: Tianjin

first: Mengfan

last: Li

address: 154 Anshan Road, Heping District, Tianjin

institute: Tianjin Medical University General Hospital

data_processing:
DNA sequencing. The size distribution of libraries was determined by Agilent 4200 TapeStation analysis, and libraries were mixed  to achieve equal representation as desired aiming for a final concentration as recommended by the manufacturer.  Sequencing was performed in the Illumina Novaseq 6000 using 150bp paired-end following the manufacturer’s  instructions.
Quality control.  Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data  (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads  from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream  analyses were based on the clean data with high quality.
Reads mapping to the reference genome. Mapping of pair-end reads. Before read mapping, clean reads were obtained from the raw reads by removing the  adaptor sequences. The clean reads were then aligned to reference genome sequences using the bwa program.
Call peak. The bam file generated by the unique mapped reads as an input file, using macs2 software for callpeak with cutoff  qvalue < 0.05
Assembly: mm10
Supplementary files format and content: bigwig, narrow peak
Library strategy: CUT&Tag

source_name: colon

extract_protocol:
Briefly, about 500000 native nuclei were purified from frozen colon samples and were incubated with Concanavalin A coated magnetic beads. Then, the unbound supernatant was removed and the resuspended bead-bound cells were incubated with a primary antibody(AHR antibody, 83200, CST）or IgG control antibody(normal mouse IgG：Millipore cat.no. 12-371) overnight. After incubation with the secondary antibody（Rabbit Anti Mouse IgG H&L：abcam，ab611709 ) for 1h next day, the cells were washed and incubated with pA-Tn5 adapter complex for 1h and then were resuspended in tagmentation buffer (10mM MgCl2 in Dig-med Buffer) and incubated for 1 h. Next, DNA was purified and amplified to prepare libraries for sequencing. Finally, the sequencing was performed in the Illumina Novaseq 6000 using 150bp paired-end following the manufacturer’s instructions.
The size distribution of libraries was determined by Agilent 4200 TapeStation analysis, and libraries were mixed  to achieve equal representation as desired aiming for a final concentration as recommended by the manufacturer.  Sequencing was performed in the Illumina Novaseq 6000 using 150bp paired-end following the manufacturer’s  instructions.

value: colon

tag: strain

value: wild type

tag: cut&tag antibody

value: mouse IgG (Millipore cat.no. 12-371)

value: vehicle


title: SHAM_S4

description: Library name: Sample 4


title: C2_2, IAA, IgG

value: IAA


title: Ribo_kidney

city: Ithaca

first: Saori

last: Uematsu

state: New York

address: 526 Campus Road, Cornell University

institute: Cornell University

library_source: other

data_processing:
The sequencing results were demultiplexed and converted to FASTQ format using Illumina bcl2fastq (v2.20.0.422) software.
The 5’ and 3’ adapters of the reads were trimmed by Cutadapt (version 2.8) using the following parameters:  -a “A{10}” -m 15 –max-n=0.1. The trimmed reads with length shorter than 15 nucleotides were excluded from the analysis.
The trimmed reads were first aligned to rRNAs using Bowtie (version 1.2.3) with the following parameters: -v 0 –norc.
The reads unaligned to rRNAs were then mapped to the custom mouse transcriptome using STAR (version 2.7.10a) with default parameters. To avoid ambiguity, reads mapped to multiple positions or with >2 mismatches were disregarded for further analysis.
Normalized read density was calculated by custom python scripts.
Assembly: GRCm39.106
Supplementary files format and content: comma-delimited text files including normalized read density around start codons for each sample.

molecule: other

source_name: kidney

extract_protocol:
RNA was extracted using Trizol LS reagent (Invitrogen) followed by ethanol precipitation. The ribosome-protected mRNA fragments (RPFs) were separated on a 15% polyacrylamide TBE-urea gel (Invitrogen) and visualized using SYBR Gold (Invitrogen). Selected regions in the gel corresponding to 25-35 nt were excised and dissolved by soaking in 400 μl RNA elution buffer (300 mM NaOAc pH 5.2, 1 mM EDTA, 0.1 U/μl SUPERase·In) for 10 min at 70 °C. The gel debris was removed using a Spin-X column (Corning), followed by ethanol precipitation.
14 μl RNAs (10~200 ng) were mixed with 1 μl T4 PNK (NEB), 20 U SUPERase·In in 1 × T4 PNK buffer and incubated at 37 °C for 30 min followed by 65 °C for 20 min. After ethanol precipitation, 10 μl dissolved RNA were mixed with 1 μl homemade Ezra enzyme, 1 μl Poly(A) Polymerase (NEB) and 20 U SUPERase·In in 7 μl Ezra buffer. After incubation at 37 °C for 30 min followed by 65 °C for 20 min, 1 μl of 1 μM 5’ end adaptor, 1 μl of 1 μM biotinylated reverse transcription primer, 20 U SUPERase·In were added and incubated at 70 °C for 3 min followed by slowly cooling down (3 °C/min) to 25 °C. The hybridized RNA sample was mixed with 10 μl of pre-washed streptavidin beads and incubated at room temperature for 10 min. Beads were washed and re-suspended in 10 μl nuclease-free water. Ligation was performed for 60 min at 25 °C by mixing beads with a 10 μl reaction mixture (1 × T4 Rnl2 reaction buffer, 20 U SUPERase·In, 15% PEG8000 and 200 U T4 RNA ligase 2 truncated KQ (NEB)). After washing once with 2 × SSC, beads were re-suspended in 12 μl nuclease-free water and mixed with 8 μl cDNA synthesis mixture (5 × first strand buffer, 0.1 M DTT, 10 mM dNTP, RNaseOUT and SuperScript III) followed by incubation at 50 °C for 30 min. After washing once with 2 × SSC, beads were resuspended in 10 μl nuclease-free water and incubated at 95 °C for 2 min, then immediately placed on the ice for 1 min. After placing on magnet stand for 1 min, the supernatant cDNA was amplified by PCR using barcoded sequencing primers. PCR was performed by mixing 1 × HF buffer, 0.5 mM dNTP, 0.25 μM PCR 5primers and 0.025 U Phusion polymerase. PCR was carried out under the following conditions: 98 °C, 30 s; (98 °C, 5 s; 68 °C, 15 s; 72 °C, 10 s) for 12 cycles; 72 °C, 3 min. PCR products were separated on a 8% polyacrylamide TBE gel (Invitrogen). DNA products with the expected size 180 bp were excised and recovered from DNA elution buffer (300 mM NaCl, 1 mM EDTA).

value: kidney

value: WT


title: HiC_2CLC_Curaxin

description: Library name: HiC_2CLC_Curaxin

value: Curaxin


title: Ribo_heart

source_name: heart

value: heart


title: Ind1_CX_0.5_24

description: Library name: iPSC-CM_Ind1_CX_0.5_24

value: female


title: Ribo_brain

value: brain


title: C8_3, vehicle, AHR


title: Ribo_testis

source_name: testis

value: testis


title: Rat lung CD31+ cells, Glenn surgery Vit A excess diet 3 weeks post-surgery, rep5

city: Milwaukee

first: Andrew

middle: D

last: Spearman

state: Wisconsin

address: 8701 Watertown Plank Rd

institute: Medical College of Wisconsin

description: Library name: R2025-604

data_processing:
Raw FASTQ files were assessed using FastQC, trimmed with Trim Galore, duplicate reads were marked using Picard MarkDuplicates, reads were aligned to the reference genome with STAR, and raw counts were generated by Salmon
Assembly: Norway rat genome; mRatBN7.2/rn7
Supplementary files format and content: salmon.merged.gene_counts.tsv contains merged gene-level raw counts generated by Salmon quantification for all samples

organism: Rattus norvegicus

source_name: Lung CD31+ cells

extract_protocol:
RNA was harvested using PureLink RNA mini kit (ThermoFisher)
RNA libraries for RNA-seq were prepared using the SMART-Seq Ultra Low v4 Kit (Takara)

value: Lung CD31+ cells

value: Wild-type

value: Glenn surgery, Vit A excess diet


title: PmDay1

description:
Library name: PmDay1
10X Genomics

source_name: Blastula

value: Blastula


title: C2_2, IAA, AHR


title: Ribo_liver

source_name: liver

value: liver


title: Rat lung CD31+ cells, Glenn surgery Vit A excess diet 3 weeks post-surgery, rep3

description: Library name: R2025-600


title: PmDay2

description:
Library name: PmDay2
10X Genomics

source_name: Late Gastrula

value: Late Gastrula


title: Rat lung CD31+ cells, Glenn surgery Vit A excess diet 3 weeks post-surgery, rep4

description: Library name: R2025-603


title: Md4A_MethylC-Seq

city: West Lafayette

first: Jian-Kang

last: Zhu

state: IN

address: 625 Agriculture Mall Dr.

department: Department of Horticulture and Landscape Architecture

institute: Purdue University

data_processing:
For data analysis, adapters were trimmed using Cutadapt with parameter “--minimum-length 50”, and trimmed reads were mapped to the reference genome using BSMAP. The reference genome is GDDH13 Version 1.1.
Genome_build: GddH13 Version 1.1
Supplementary_files_format_and_content: The bigWig files give methylation level for all Cs(three contexts) with depth >= 4 in all the samples. Methylation level of each cytosine base was calculated according to number of converted and unconverted C mapped at that position ( unconverted_C / ( converted_C+ unconverted_C ) ).

organism: Malus domestica

source_name: fruit

extract_protocol: Fruits of "Golden Delicious" (non-red cultivar) (Malus × domestica Borkh.) were harvested from an apple experimental station of Northwest A&F University (Yangling, China). Apple fruit samples were stored after picking immediately in liquid nitrogen and then at −80°C until DNA extraction. Genomic DNA was extracted from fruits using a DNeasy Plant Maxi Kit (Qiagen) and then was used for library construction using Illumina’s standard DNA methylation analysis protocol and the NEB Ultra II DNA Library Prep Kit. The samples were sequenced at the Genomics Core Facility of the Shanghai Centre for Plant Stress Biology, Chinese Academy of Sciences using Illumina HiSeq2500.

value: fruit

tag: days after bloom


title: Md4B_MethylC-Seq


title: Rat lung CD31+ cells, Glenn surgery Vit A excess diet 3 weeks post-surgery, rep1

description: Library name: R2025-372


title: Rat lung CD31+ cells, Glenn surgery Vit A excess diet 3 weeks post-surgery, rep2

description: Library name: R2025-374


title: Md3B_MethylC-Seq


title: Md3A_MethylC-Seq


title: Case57_lymphoma_FFPE

type: RNA

city: Isehara

first: Shunsuke

last: Nagase

address: 143 Shimokasuya

country: Japan

institute: Tokai University

description: IFNG-H group

hyb_protocol: Following fragmentation, 5.5 ug of ds-cDNA were hybridized for 16 hr at 45C on GeneChip Clariom S 400-format  Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Gene Chip Scanner GCS30007G.

data_processing: Data were processed with Transcriptome Analysis Console (version 4.0) using the SST-RMA analysis algorithm

label: biotin

source_name: lymphoma sample, 10% neutral-buffered formalin fixed, paraffin embedded

label_protocol: Biotinylated ds-cDNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (GeneChip 3'IVT Pico Kit  Manual Workflow user guide, 2020 ThermoFisherScientific).

extract_protocol: Allprep DNA/RNA FFPE extraction of total RNA was performed according to the manufacturer's instructions.

tag: diagnosis

value: EBV+ CHL

value: male


title: Rat lung CD31+ cells, sham surgery Vit A excess diet 3 weeks post-surgery, rep5

description: Library name: R2025-359

value: Sham surgery, Vit A excess diet


title: Case56_lymphoma_FFPE

description: IS group

value: EBV+ mDLBCL


title: Md2B_MethylC-Seq


title: Case55_lymphoma_FFPE

description: IS group


title: Rat lung CD31+ cells, sham surgery Vit A excess diet 3 weeks post-surgery, rep2

description: Library name: R2025-356


title: Case53_lymphoma_FFPE

description: IS group


title: Case52_lymphoma_FFPE

description: 9p24.1-H group


title: Md2A_MethylC-Seq


title: Rat lung CD31+ cells, sham surgery Vit A excess diet 3 weeks post-surgery, rep4

description: Library name: R2025-358


title: Case51_lymphoma_FFPE

description: IFNG-L group


title: Rat lung CD31+ cells, sham surgery Vit A excess diet 3 weeks post-surgery, rep3

description: Library name: R2025-357


title: Md1A_MethylC-Seq


title: Case50_lymphoma_FFPE

description: IFNG-L group


title: P844

type: genomic

city: Montreal

first: Jacquetta

last: Trasler

state: Quebec

address: 1001 Decarie Boul, Block E, ES1.4380

department: Pharmacology & Therapeutics; Human Genetics

country: Canada

institute: McGill University

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: The R package minfi (v1.42.0) was used for preprocessing of IDAT files, quality control, and normalization in RStudio. Normalization was performed with noob using the preprocessNoob function in the minfi package. Two samples failed quality control due to elevated detection p-values (>0.01) and were excluded from further analyses, leaving a remaining total of 62 placenta samples.   A total of 865859 probes were detected on the Illumina 850K array. Unreliable probes (probes with elevated detection p-values >0.01, probes located on sex chromosomes, probes containing single nucleotide polymorphisms (SNPs) of minor allele frequency >1% within 5bp of the CpG site, and cross-reactive probes) were removed, leaving a total of 773321 filtered probes for downstream analyses. Additional normalization was performed with beta-mixture quantile normalization (BMIQ) using the ChAMP package (v2.26.0) in RStudio. Batch correction was also performed using the ChAMP package.

label: Cy5 and Cy3

source_name: Placenta

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted using the QIAamp DNA Mini Kit (Qiagen cat. #51304) as per the manufacturer’s protocol.

treatment_protocol: The current study includes 64 placenta samples from the 3D Study, which were split evenly based on paternal age at conception: younger (n=21), middle (n=22) and older (n=21).

tag: paternal age group

value: Old


title: Case46_lymphoma_FFPE

description: IFNG-H group

value: EBV+ pDLBCL


title: Rat lung CD31+ cells, Glenn surgery Vit A deficient diet 3 weeks post-surgery, rep5

description: Library name: R2025-602

tag: tissue

value: Glenn surgery, Vit A deficient diet


title: HCT116, 5aza-treat, RNA-seq 3

city: Guangzhou

first: Huichuan

last: Yu

state: Guangdong

address: 26 Yuancun Erheng Road

institute: Sun Yat-sen University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using STAR and paired-end clean reads were aligned to the reference genome using STAR (v2.5.1b). STAR used the method of Maximal Mappable Prefix(MMP) which can generate a precise mapping result for junction reads.
HTSeq v0.6.0 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.10.1). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed.
Alternative Splicing is an important mechanism for regulate the expression of genes and the variable of protein. rMATS(3.2.1) software was used to analysis the ASevent.
Genome_build: GRCh38 for HCT116 and Rnor_6.0 for NP
Supplementary_files_format_and_content: xls files include FPKM values for each Sample

source_name: HCT116 cells

growth_protocol: All cell lines were either purchased from ATCC or provided by Shanghai Institutes for Biological Sciences, which had their identity confirmed by DNA genotyping and cultured according to manufacturer’s protocol.

extract_protocol:
RNA was isolated from cells of each group using RNeasy mini kit (Qiagen) according to manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The cells were treated by 5 uM 5aza for 48 hours and cultured in fresh medium for additional 48 hours.

tag: passages


title: Case44_lymphoma_FFPE

description: IFNG-H group


title: P864


title: Case49_lymphoma_FFPE

description: IFNG-H group


title: HCT116, 5aza-treat, RNA-seq 1

tag: treatment


title: Rat lung CD31+ cells, Glenn surgery Vit A deficient diet 3 weeks post-surgery, rep2

description: Library name: R2025-379


title: Rat lung CD31+ cells, sham surgery Vit A excess diet 3 weeks post-surgery, rep1

description: Library name: R2025-355


title: Rat lung CD31+ cells, Glenn surgery Vit A deficient diet 3 weeks post-surgery, rep3

description: Library name: R2025-380


title: Rat lung CD31+ cells, Glenn surgery Vit A deficient diet 3 weeks post-surgery, rep4

description: Library name: R2025-601


title: Rat lung CD31+ cells, Glenn surgery Vit A deficient diet 3 weeks post-surgery, rep1

description: Library name: R2025-378


title: P863

value: Middle


title: P874


title: Case45_lymphoma_FFPE

description: IFNG-L group


title: Case42_lymphoma_FFPE

description: IFNG-H group

value: female


title: P861


title: P860


title: Rat lung CD31+ cells, sham surgery Vit A deficient diet 3 weeks post-surgery, rep5

description: Library name: R2025-606

value: Sham surgery, Vit A deficient diet


title: P872


title: Rat lung CD31+ cells, sham surgery Vit A deficient diet 3 weeks post-surgery, rep3

description: Library name: R2025-598

value: Lung CD31+ cells


title: HCT116, control, RNA-seq 3

value: control

tag: cell line


title: Case43_lymphoma_FFPE

description: IFNG-L group


title: P875

value: Young


title: Md1B_MethylC-Seq


title: P853


title: HCT116, control, RNA-seq 2


title: P847


title: Rat lung CD31+ cells, sham surgery Vit A deficient diet 3 weeks post-surgery, rep2

description: Library name: R2025-361

tag: genotype

value: Wild-type


title: Case41_lymphoma_FFPE

description: IFNG-L group


title: GBM28_OncoD-0J1 4

city: Augusta

first: Balveen

last: Kaur

state: GA

address: CN-3205, 1410 Laney-Walker Blvd

department: Pathology

institute: Augusta University

description: Library name: 28J5

data_processing:
Quality control of raw reads was performed using FastQC
Adapter trimming was performed using Cutadapt
Cleaned reads were aligned to the human (GRCh38) and mouse (GRCm39) genomes using STAR aligner
XenofilteR (R v4.4.1) was used to perform species-specific read separation between human and mouse reads.
Normalization, quality control, and differential gene expression analysis were performed in R using DESeq2.
Assembly: GRCh38, GRCm39
Supplementary files format and content: Count matrix in CSV format with rows as genes and columns as samples, values represent raw read counts.

organism:
Homo sapiens
Mus musculus

source_name: cell line

growth_protocol: Primary GBM cells GBM12 and GBM28 were maintained in 150 mm TC-treated Culture Dishes with 2%FBS DMEM. RAW 264.7 murine macrophages were maintained in petri dishes with 10% FBS RMPI 1640. For infection, tumor cells were infected in 2% FBS DMEM for 1 hour but media was changed to 0.5% FBS DMEM after the 1-hour incubation. RAW 264.7 macrophages were depleted of serum (0.5% FBS RPMI 1640) overnight before overlaying them on infected tumor cells.

extract_protocol:
Total RNA was isolated using the Rneasy Plus kit from Qiagen and samples were submitted for bulk RNA sequencing
Library preparation was performed with the SMARTer® Stranded Total RNA Sample Prep Kit (Takara Bio USA, Inc., cat# 634878). This process incorporated RiboGone™ and SMART® (Switching Mechanism at the 5' end of RNA Template) technologies, along with PCR amplification, to generate Illumina-compatible libraries without adapter ligation. RiboGone efficiently depleted rRNA from total RNA before library construction. Library quality was assessed using the TapeStation 2000 (Agilent Technologies), and concentrations were measured with Qubit (Thermo Fisher Scientific) before sequencing. Dual-indexed i5/i7 paired-end libraries were sequenced on the NovaSeq 6000 system (Illumina) with a minimum coverage of 50-60 million reads per sample.

tag: cell type

value: glioblastoma and macrophage


title: GBM28_OncoD-0J1 1

description: Library name: 28J2


title: P866


title: Rat lung CD31+ cells, sham surgery Vit A deficient diet 3 weeks post-surgery, rep4

description: Library name: R2025-605


title: GBM28_OncoD 4

description: Library name: 28U6


title: P851


title: GBM28_OncoD-0J1 3

description: Library name: 28J4


title: Rat lung CD31+ cells, Glenn surgery control diet 3 weeks post-surgery, rep4

description: Library name: R2025-385

value: Glenn surgery, control diet


title: GBM28_OncoD-0J1 2

description: Library name: 28J3


title: HCT116, 5aza-treat, RNA-seq 2


title: Case36_lymphoma_FFPE


title: P865


title: Rat lung CD31+ cells, sham surgery Vit A deficient diet 3 weeks post-surgery, rep1

description: Library name: R2025-360


title: Rat lung CD31+ cells, Glenn surgery control diet 3 weeks post-surgery, rep5

description: Library name: R2025-387


title: Case38_lymphoma_FFPE

description: IFNG-L group


title: P878


title: Case37_lymphoma_FFPE

description: IS group


title: Case39_lymphoma_FFPE

description: IFNG-H group


title: Case35_lymphoma_FFPE

description: IS group


title: Case40_lymphoma_FFPE

description: 9p24.1-H group


title: Rat lung CD31+ cells, Glenn surgery control diet 3 weeks post-surgery, rep2

description: Library name: R2025-383


title: GBM28_OncoD 1

description: Library name: 28U1


title: Rat lung CD31+ cells, Glenn surgery control diet 3 weeks post-surgery, rep1

description: Library name: R2025-381


title: Case32_lymphoma_FFPE

description: 9p24.1-H group


title: GBM28_PBS 4

description: Library name: 28P6


title: HCT116, control, RNA-seq 1


title: P876


title: GBM28_OncoD 2

description: Library name: 28U2


title: P873


title: GBM28_OncoD 3

description: Library name: 28U5


title: GBM28_PBS 3

description: Library name: 28P4


title: Rat lung CD31+ cells, Glenn surgery control diet 3 weeks post-surgery, rep3

description: Library name: R2025-384


title: Case30_lymphoma_FFPE

description: 9p24.1-H group


title: P848


title: Rat lung CD31+ cells, sham surgery control diet 3 weeks post-surgery, rep4

description: Library name: R2025-370

value: Sham surgery, control diet


title: Case29_lymphoma_FFPE

description: IFNG-H group


title: Rat lung CD31+ cells, sham surgery control diet 3 weeks post-surgery, rep5

description: Library name: R2025-371


title: Case31_lymphoma_FFPE

description: IFNG-L group

value: EBV+ CHL


title: P857


title: Rat lung CD31+ cells, sham surgery control diet 3 weeks post-surgery, rep1

description: Library name: R2025-365


title: Case34_lymphoma_FFPE

description: 9p24.1-H group

value: male


title: GBM28_PBS 1

description: Library name: 28P1


title: GBM28_PBS 2

description: Library name: 28P2


title: Case26_lymphoma_FFPE

description: IS group


title: Rat lung CD31+ cells, sham surgery control diet 3 weeks post-surgery, rep3

description: Library name: R2025-369


title: P849


title: GBM12_OncoD-0J1 4

description: Library name: 12J6


title: P869


title: Rat lung CD31+ cells, sham surgery control diet 3 weeks post-surgery, rep2

description: Library name: R2025-367


title: GBM12_OncoD-0J1 3

description: Library name: 12J3


title: P846


title: DF1 chicken cells, human catalytically inactive KHNYN mutant, PR8 infected- Rep 2

city: Minneapolis

first: Frances

last: Shepherd

state: MN

address: 689 23rd Ave SE

institute: University of Minnesota

description: Library name: D468_WT_B

data_processing:
Reads were trimmed of adapter sequences and low-quality bases with Trimmomatic (version 0.39) and mapped to the chicken reference genome from Ensembl (GRCg6a release 105) with STAR (version 2.7.8a).
Reads per gene were counted with HTSeq (version 1.99.2). Differential expression testing was performed with DESeq2 (version 1.42).
Assembly: GRCg6a release 105
Supplementary files format and content: Tab-separated gene count files from HTSeq

organism: Gallus gallus

growth_protocol: Chicken DF-1 cells (ATCC UMNSAH/DF-1, CRL-3586) were grown in DMEM supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin at 37 degrees 5% CO2 50% humidity.

extract_protocol:
Cells were harvested at 24-hours post-infection and total RNA extracted using Qiagen RNeasy Plus Mini Kit following the standard manufacturer's protocol.
Library preparation was performed using the TruSeq stranded mRNA LP kit (Illumina).

treatment_protocol: Cells were seeded into 6-well tissue-culture plates and infected in duplicate with influenza A virus (A/Puerto Rico/9/1934/(H1N1)) or a CpG-enriched version (PMID:26878752) at an multiplicity of infection equal to 0.05 plaque-forming units per cell.

value: cell line

value: embryonic fibroblasts

value: PR8 infected

tag: cell treatment

value: inactive KHNYN transduced


title: GBM12_OncoD-0J1 2

description: Library name: 12J2


title: DF1 chicken cells, human catalytically inactive KHNYN mutant, CG-elevated PR8 infected- Rep 2

description: Library name: D468_CG_B

value: CG elevated PR8 infected


title: Case24_lymphoma_FFPE

description: IS group

value: EBV+ mDLBCL

tag: Sex


title: GBM12_OncoD-0J1 1

description: Library name: 12J1


title: Case23_lymphoma_FFPE

description: IS group


title: Case27_lymphoma_FFPE

description: IFNG-L group


title: GBM12_OncoD 4

description: Library name: 12U5


title: GBM12_OncoD 3

description: Library name: 12U4


title: Case21_lymphoma_FFPE

description: IFNG-L group

value: EBV+ pDLBCL

value: female


title: DF1 chicken cells, human catalytically inactive KHNYN mutant, CG-elevated PR8 infected- Rep 1

description: Library name: D468_CG_A


title: Case22_lymphoma_FFPE

description: IFNG-L group


title: P852


title: Case25_lymphoma_FFPE

description: IS group


title: P868


title: Case20_lymphoma_FFPE

description: IFNG-L group


title: DF1 chicken cells, human catalytically inactive KHNYN mutant, uninfected- Rep 1

description: Library name: D468_Mock_A

value: uninfected


title: DF1 chicken cells, human catalytically inactive KHNYN mutant, PR8 infected- Rep 1

description: Library name: D468_WT_A


title: DF1 chicken cells, human catalytically inactive KHNYN mutant, uninfected- Rep 2

description: Library name: D468_Mock_B


title: GBM12_OncoD 1

description: Library name: 12U2


title: GBM12_OncoD 2

description: Library name: 12U3


title: Case19_lymphoma_FFPE

description: IFNG-L group


title: P858

value: Middle


title: GBM12_PBS 4

description: Library name: 12P6


title: DF1 chicken cells, human KHNYN, PR8 infected- Rep 2

description: Library name: D455_WT_B

value: KHNYN transduced


title: DF1 chicken cells, human KHNYN, CG-elevated PR8 infected- Rep 2

description: Library name: D455_CG_B


title: GBM12_PBS 3

description: Library name: 12P5


title: Case15_lymphoma_FFPE

description: 9p24.1-H group


title: DF1 chicken cells, human KHNYN, uninfected- Rep 2

description: Library name: D455_Mock_B


title: P862

value: Old


title: DF1 chicken cells, human KHNYN, CG-elevated PR8 infected- Rep 1

description: Library name: D455_CG_A


title: GBM12_PBS 1

description: Library name: 12P1

value: glioblastoma and macrophage


title: P871

value: Young


title: P819


title: Case16_lymphoma_FFPE

description: IFNG-L group


title: DF1 chicken cells, human KHNYN, PR8 infected- Rep 1

description: Library name: D455_WT_A


title: Case14_lymphoma_FFPE

description: 9p24.1-H group


title: MAC-T cells, heat stress differentiated and recovered 6hr, rep3

first: Guangsheng

state: NY

address: 507 Tower Rd.

department: Animal Science

institute: Cornell

data_processing:
FeatureCounts (v2.0.3) was used to extract raw read counts of genes (Liao et al., 2014). Gene expression level normalization was performed using the DEseq2 R package (Love et al., 2014). The principal component analysis (PCA) was performed using the top variable 300 genes identified by DEseq2 (Love et al., 2014) and the batch effect was removed by limma R package (Ritchie et al., 2015). To identify differentially expressed genes (DEGs), the raw read count matrix was imported into DEseq2 R package (Love et al., 2014) with differentiation treatment, HS treatment, and cell passage information used as experiment factors. The pair-wise comparison was performed and DEGs were selected among six groups. The selecting criteria of DEGs was: |Fold Change (FC)| > 1.5 and adjusted p-value < 0.1. Next, k-means clustering of top DEGs, heatmaps, and gene ontology (GO) enrichment analysis were performed using ClusterGVis R package (Zhang, 2022). Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment of DEGs under different treatments were performed using clusterProfiler (v4.0.5) (Wu et al., 2021). Promoter TF analysis was performed using ShinyGo (v0.77) (Ge et al., 2020). The promoter regions were defined as 300bp upstream   of transcription start site (TSS).
Assembly: ARS-UCD 1.3
Supplementary files format and content: tab-delimited text files include raw read count for each Sample

organism: Bos taurus

source_name: MAC-T cells

growth_protocol: MAC-T were revived and cultured in a basal medium consisting of Dulbecco’s Modified Eagle’s Medium (DMEM, high glucose) (Corning, NY), 10% fetal bovine serum (FBS), 1% penicillin-streptomycin, 1% L-glutamine, 5 μg/ml insulin, and 1 μg/ml hydrocortisone. MAC-T were grown in T75 flasks at 37°C with 5% CO2. When 80% confluent, cells were transferred to three PureCoatTM 6-well plates (Corning) and divided into six groups (2 x 105 cell/well). Plate I was seeded with non-HS undifferentiated (NHSUD) group and non-HS differentiated (NHSD) group. Plate II was seeded with HS undifferentiated (HSUD) group and HS differentiated (HSD) group. Plate III was seeded with HS differentiated with 2 hr recovery (D2R) group and HS differentiated with 6 hr recovery (D6R) group. All six groups had three technical replicates on their corresponding plates, and the whole experiment was repeated three times

extract_protocol:
Total RNA was isolated from cell pellets with TRIzol reagent (Invitrogen), Phasemaker tubes (Invitrogen), and RNeasy Mini Kit (Qiagen, Germany) according to the manufacturer’s instructions with minor modifications. Cell pellets were homogenized in 1 mL TRIzol reagent using a pellet mixer (VWR International, PA) for 30s, and lysates were transferred to Phasemaker tubes with chloroform for 20 min centrifugation at 4°C. The aqueous phase was then transferred to the gDNA elimination column for 1 min centrifugation at room temperature. The eluted RNA was washed with cold 50% ethanol, transferred to the RNeasy mini spin column, and washed with buffer RPE and RW1 (RNeasy Mini Kit). Finally, RNAs were eluted in RNase-free water. Concentrations of RNA samples were determined by a NanoDrop 1000 spectrophotometer (Thermo Fisher Scientific), and samples with 260/280 and 260/230 ratios around 2 were considered as pure RNA. Qualities of RNA samples were determined by an Agilent 2100 Bioanalyzer (Agilent Technology, CA), and all samples has high RNA integrity number (RIN) larger than 9. Two technical replicates of each group with high concentration and quality were pooled for RNA sequencing.
The quality control, library construction, and RNA sequencing of RNA samples were conducted by Novogene Inc. (Sacramento, CA). Briefly, messenger RNA (mRNA) was purified from total RNA using poly-T selection. mRNA was then fragmented and reverse transcribed. Following end-repairing and A-tailing, cDNA was ligated with adapters and selected based on fragment sizes. Finally, PCR amplification was performed, and quantified libraries were pooled and sequenced on Illumina platforms to generate paired-end raw reads. From the raw sequencing data, adaptors were removed, and quality control was conducted using fastp (v0.23.2) (Chen et al., 2018). Reference genome of bus taurus (ARS-UCD 1.3) was downloaded from the UCSC database, and alignment was conducted using STAR (v2.7.9a) (Dobin et al., 2013).

treatment_protocol: Undifferentiated groups were cultured in the basal medium. Differentiated groups were cultured in the lactogenic medium as previously described with modifications (Lee et al., 2013), consisting of the basal medium supplemented with 5% FBS, 5 μg/ml ovine prolactin (Protein Laboratories Rehovot Ltd., Israel), and 10 μg/ml dexamethasone (Sigma-Aldrich, MO). All groups were cultured for four days and media were changed daily. Non-HS groups were incubated at 37°C until collection. HS groups were incubated at 42°C for 1 hr before collection on the fourth day. The recovery groups were continue cultured at 37°C for 2 hr or 6 hr after the HS treatment. Cells were collected by digesting with 0.25% trypsin/EDTA solution (Thermo Fisher Scientific, MA).

value: MAC-T cells

value: Bovine mammary epithelium


title: Case13_lymphoma_FFPE

description: 9p24.1-H group

value: EBV+ CHL

value: male


title: Case17_lymphoma_FFPE

description: IS group


title: P867


title: GBM12_PBS 2

description: Library name: 12P4


title: MAC-T cells, heat stress differentiated and recovered 6hr, rep2


title: P463


title: DF1 chicken cells, human KHNYN, uninfected- Rep 1

description: Library name: D455_Mock_A

value: cell line

value: embryonic fibroblasts


title: DF1 chicken cells, human ZAP-S, CG-elevated PR8 infected- Rep 2

description: Library name: D454_CG_B

value: ZAP-S transduced


title: Case11_lymphoma_FFPE

description: IFNG-L group


title: DF1 chicken cells, human ZAP-S, PR8 infected- Rep 2

description: Library name: D454_WT_B

value: PR8 infected


title: Case12_lymphoma_FFPE

description: IFNG-L group


title: DF1 chicken cells, human ZAP-S, uninfected- Rep 2

description: Library name: D454_Mock_B


title: P409


title: MAC-T cells, heat stress differentiated and recovered 2hr, rep2


title: Case10_lymphoma_FFPE

description: 9p24.1-H group

value: EBV+ mDLBCL


title: MAC-T cells, heat stress differentiated and recovered 6hr, rep1


title: Case08_lymphoma_FFPE

description: IFNG-L group


title: Case09_lymphoma_FFPE

description: IFNG-L group


title: P854


title: DF1 chicken cells, human ZAP-S, CG-elevated PR8 infected- Rep 1

description: Library name: D454_CG_A

value: CG elevated PR8 infected


title: MAC-T cells, heat stress differentiated and recovered 2hr, rep1


title: P850


title: P461


title: Case06_lymphoma_FFPE

description: IFNG-H group

value: EBV+ pDLBCL


title: P413


title: MAC-T cells, heat stress differentiated and recovered 2hr, rep3


title: MAC-T cells, heat stress differentiated, rep3

value: heat stress differentiated


title: P438


title: DF1 chicken cells, human ZAP-S, PR8 infected- Rep 1

description: Library name: D454_WT_A


title: DF1 chicken cells, human ZAP-S, uninfected- Rep 1

description: Library name: D454_Mock_A

value: uninfected


title: P476

value: Middle


title: Case03_lymphoma_FFPE

description: IFNG-L group


title: P403

value: Old


title: Thrap3 KO C2C12 with T3 treatment_3

city: Nagakute

first: Taku

last: Fukushima

state: Aichi

institute: Aichi Medical University

description: Library name: KO_T3

data_processing:
MGI DNB seq (strand-specific).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers.
Second strand cDNA was synthesized using dUTP, instead of dTTP. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification.
Assembly: mm10
Supplementary files format and content: TPM values for each Sample

source_name: C2C12  myotubes

growth_protocol: DMEM, +2% horse serum, 1% PS

extract_protocol:
Media were removed, and after 1 wash by PBS, RNA was harvested using RNAiso reagent.
NEBNext® Ultra™II Directional RNA Library Prep Kit

value: C2C12  myotubes

value: Thrap3 KO


title: DF1 chicken cells, human ZAP-L, CG-elevated PR8 infected- Rep 2

description: Library name: D453_CG_B

value: ZAP-L transduced


title: MAC-T cells, heat stress differentiated, rep1

value: MAC-T cells

value: Bovine mammary epithelium


title: P411


title: Case02_lymphoma_FFPE

description: IFNG-H group

value: male


title: Thrap3 KO C2C12 with T3 treatment_2

description: Library name: KO_T2


title: DF1 chicken cells, human ZAP-L, PR8 infected- Rep 2

description: Library name: D453_WT_B

value: cell line


title: MAC-T cells, heat stress undifferentiated, rep3

value: heat stress undifferentiated


title: Thrap3 KO C2C12 with T3 treatment_1

description: Library name: KO_T1


title: MAC-T cells, heat stress undifferentiated, rep2


title: Thrap3 KO C2C12_3

description: Library name: KO_3


title: MAC-T cells, heat stress undifferentiated, rep1


title: DF1 chicken cells, human ZAP-L, CG-elevated PR8 infected- Rep 1

description: Library name: D453_CG_A

value: embryonic fibroblasts


title: DF1 chicken cells, human ZAP-L, PR8 infected- Rep 1

description: Library name: D453_WT_A

value: PR8 infected


title: MAC-T cells, non-heat stress differentiated, rep3

value: non-heat stress differentiated


title: Thrap3 KO C2C12_1

description: Library name: KO_1


title: P422


title: DF1 chicken cells, human ZAP-L, uninfected- Rep 1

description: Library name: D453_Mock_A


title: P483


title: Thrap3 KO C2C12_2

description: Library name: KO_2


title: DF1 chicken cells, empty vector, CG-elevated PR8 infected- Rep 2

description: Library name: D305_CG_B

value: CG elevated PR8 infected

value: untransduced


title: MAC-T cells, non-heat stress differentiated, rep2


title: P494


title: P424

value: Young


title: P499


title: wild type C2C12 with T3 treatment_3

description: Library name: Ctrl_T3

value: wild type


title: P478


title: wild type C2C12 with T3 treatment_2

description: Library name: Ctrl_T2


title: P418

value: Middle


title: MAC-T cells, non-heat stress undifferentiated, rep3

value: non-heat stress undifferentiated


title: wild type C2C12 with T3 treatment_1

description: Library name: Ctrl_T1

value: C2C12  myotubes


title: DF1 chicken cells, empty vector, uninfected- Rep 2

description: Library name: D305_Mock_B

value: uninfected


title: MAC-T cells, heat stress differentiated, rep2

value: heat stress differentiated


title: DF1 chicken cells, empty vector, PR8 infected- Rep 2

description: Library name: D305_WT_B


title: P467


title: P456

value: Old


title: MAC-T cells, non-heat stress undifferentiated, rep2

value: MAC-T cells

value: Bovine mammary epithelium


title: wild type C2C12_3

description: Library name: Ctrl_3


title: P415


title: DF1 chicken cells, empty vector, CG-elevated PR8 infected- Rep 1

description: Library name: D305_CG_A

value: cell line


title: wild type C2C12_2

description: Library name: Ctrl_2


title: MAC-T cells, non-heat stress undifferentiated, rep1


title: DF1 chicken cells, human ZAP-L, uninfected- Rep 2

description: Library name: D453_Mock_B

value: ZAP-L transduced


title: DF1 chicken cells, empty vector, PR8 infected- Rep 1

description: Library name: D305_WT_A

value: embryonic fibroblasts


title: P436


title: P482


title: wild type C2C12_1

description: Library name: Ctrl_1


title: Mature adult hindguts

city: Durham

first: Jessica

middle: K

last: Sawyer

state: NC

address: PO Box 3813

institute: Duke University

description:
Library name: Sample 1
Mature tab in Young vs. Mature Log Fold Change.csv. Young vs Mature Raw Counts compares young vs mature for differential expression.

data_processing:
TrimGalore!
HISAT2 was used to align and mapped to the DM.BDGP6.32.105 genome downloaded from Ensembl
The feature counts function was used to count the reads per feature, then followed by DESeq2 to determine differential gene expression.
Assembly: DM.BDGP6.32.105
Supplementary files format and content: xlsx files contains logfold change young vs mature
Supplementary files format and content: xlsx files contains counts and logfold change young vs mature

organism: Drosophila melanogaster

source_name: adult hindgut

growth_protocol: bynGal4 animals were raised at 25. Adult hindguts were dissected at two different developmental time points.

extract_protocol:
Trizol extraction
NovaSeq PE150

treatment_protocol: Young animals were dissected immediately after eclosing. Mature animals were dissected after 4 days at 18C after eclosion. 100-150 guts were dissected for each condition, with 3 replicates each. Young (Y1,Y2,Y3). Mature (A1,A2,A3)

value: adult hindgut

value: adult ileal cells

value: mature


title: P448


title: Young adult hindguts

description:
Library name: Sample 2
Young tab in Young vs. Mature Log Fold Change.csv. Young vs Mature Raw Counts compares young vs mature for differential expression.

value: young


title: bone marrow_monocyte_untreated_rep3

status: Public on Dec 10 2025

city: BETHESDA

first: Beatriz

last: León

state: MD

address: 10 CENTER DR

department: Division of Intramural Research (DIR)

institute: National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH)

description: Library name: AH-3

data_processing:
TrimGalore 0.4.4 (phred33, Nextera adapters, paired)
STAR 2.5.2 (default settings)
HTSeq-Count 0.6.1p1 (stranded=no, GCF_000001635.27_GRCm39_genomic.gtf)
EdgeR 4.4.1 for DEG analysis
Assembly: GRCm39
Supplementary files format and content: htSeq-Count text files

source_name: bone marrow

extract_protocol:
total RNA isolation
Genewiz (Azenta Life Sciences)

value: bone marrow

value: monocyte

value: untreated


title: bone marrow_monocyte_untreated_rep2

description: Library name: AH-2


title: bone marrow_monocyte_untreated_rep1

description: Library name: AH-1


title: lung_macrophage_untreated_rep3

description: Library name: naive-3

source_name: lung

value: lung

value: perivascular macrophage


title: MAC-T cells, non-heat stress differentiated, rep1

value: non-heat stress differentiated


title: lung_macrophage_untreated_rep2

description: Library name: naive-2


title: lung_macrophage_papain_rep4

description: Library name: WT-4

value: papain, in vivo, 24h prior to isolation


title: lung_macrophage_papain_rep2

description: Library name: WT-2


title: lung_macrophage_papain_rep3

description: Library name: WT-3


title: lung_macrophage_papain_rep1

description: Library name: WT-1


title: P449

value: Middle


title: lung_macrophage_untreated_rep1

description: Library name: naive-1


title: P425

value: Young


title: DF1 chicken cells, empty vector, uninfected- Rep 1

description: Library name: D305_Mock_A

value: uninfected

value: untransduced


title: LLC tumor, KO-PAK2EC, 3

first: Jean-Philippe

last: Gratton

address: 2900 Bd Edouard-Montpetit

institute: Université de Montréal

description:
Library name: KO-PAK2EC 3
Column name in counts_normalized_relative_to_library_size.xlsx: ko_ecpak2_3

data_processing:
Tumors: Quality control of raw reads was assessed with FASTQC (v0.11.8), combined with MultiQC version 1.3. Reads were aligned to the GRCm38 genome using STAR (v2.5.1b), and raw counts were calculated with featureCounts (v1.6). DESeq2 (v1.24.0) was used to normalize gene readcounts.
HUVEC: Raw read quality was assessed with MultiQC (v1.11). Sequences were trimmed for sequencing adapters and low quality 3' bases using Trimmomatic (v0.35) and aligned to the reference human genome version GRCh38 (gene annotation from Gencode v37, based on Ensembl 103) using STAR (v2.7.1a). Gene expressions were obtained from STAR both as readcounts and TPM values as well as computed using RSEM in order to obtain normalized gene and transcript level expression, in FPKM and TPM values. DESeq2 (v1.30.1) was then used to normalize gene readcounts.
Assembly: GRCm38 and GRCh38
Supplementary files format and content: Excel file includes Deseq readcounts normalized to library for each Sample

source_name: tumor

growth_protocol:
Lewis lung carcinoma (LLC) were cultured in Dulbecco modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 2 mM L-glutamine, 100 U/ml penicillin, and 100 ug/ml streptomycin. 1.5 x10^6 LLC cells were injected subcutaneously into the flank of 6- to 8-weeks old mice. The tumors grew for 18 days, after which tumors were harvested.
Human umbilical vein ECs (HUVECs) were cultured in M199 media supplemented with 20% FBS, 2 mM L-glutamine, 100 U/ml penicillin, 100 µg/ml streptomycin and 0.05 mg/mL ECGS.

extract_protocol:
Total mRNA from tumors and HUVEC experiments was extracted using TRIzol Reagent, according to the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: 5 mg/21 days Tamoxifen slow-release pellets

value: tumor

value: LL/2 (LLC1)

value: Lewis lung carcinoma

value: PAK2 endothelial knockdown

value: Tamoxifen

tag: batch

value: RNAseq tumor


title: LLC tumor, CT-PAK2EC, 3

description:
Library name: CT-PAK2EC 3
Column name in counts_normalized_relative_to_library_size.xlsx: ct_ecpak2_3

value: CT


title: LLC tumor, CT-PAK2EC, 1

description:
Library name: CT-PAK2EC 1
Column name in counts_normalized_relative_to_library_size.xlsx: ct_ecpak2_1