title: Left lung_Niave_Wild type_Male_3


title: B16

status: Public on Mar 03 2025

type: SRA

city: Beijing

first: Xuejiao

last: Ren

address: Beijing

country: China

institute: Nanjing Medical university

description:
Library name: Sample 2
BD Rhapsody

library_source: transcriptomic single cell

data_processing:
All samples were merged in Seurat and high-quality cells were kept with a detection threshold of 500 - 5,000 genes and a proportion of expressed mitochondrial genes less than 10%.  After quality control, a total of 9,693 cells from 3 groups of HCC samples (sgCtrl, sgNcor1-1 and sgNcor1-2), and 4,910 cells from 3 groups of melanoma samples (sgCtrl, sgNcor1-1 and sgNcor1-2) were retained for downstream analyses.
Data of different samples were integrated utilizing Harmony (Korsunsky et al., 2019) to identify anchors.
Data were log-normalized (divided by the total expression and amplified scaling factor 10,000) using the “NormalizeData” function in Seurat.
For clustering, we implemented the “FindVariableFeatures” function in Seurat to select the top 2,000 highly variable genes (HVGs).
A principal component analysis (PCA) matrix was calculated to reduce noise using the “RunPCA” function in Seurat with default parameters.
Assembly: mm10
Supplementary files format and content: matrix file

molecule: polyA RNA

organism: Mus musculus

source_name: Tumor

extract_protocol:
Subcutaneous xenografts derived from Hepa1-6 and B16 cells were generated in immunocompetent C57BL/6J mice. Subcutaneous xenografts were dissociated and the single-cell suspensions were obtained using the MACS Miltenyi Mouse Tumor Dissociation kit (130-096-730, Miltenyi Biotec, Germany) on gentleMACs dissociator with Octo Heaters (130-096-427, Miltenyi Biotec, Germany) according to manufacturer’s instructions. Cell suspensions were passed through a 70-µm filter twice. CD45+ immune cells were then sorted from the cell suspension using flow cytometry (Cat# 35-0451-U100, TONBO Biosciences, USA), and then subjected to the BD Rhapsody Single-Cell Analysis System (BD Biosciences, USA) following the manufacturer’s guidelines.
The scRNA-seq libraries were constructed using BD Rhapsody WTA Amplification Kit (BD Biosciences, USA). WTA libraries and LMO libraries were pooled and sequenced on NovaSeq 6000 (Illumina, USA), and the data was processed using the BD Rhapsody WTA analysis pipeline (v1.9.1; BD Biosciences, USA). WTA reads were aligned to the mm10 reference mouse genome, allowing a maximum of 1 mismatch.

tag: tissue

value: Tumor


title: Left lung_Niave_Wild type_Male_1

city: Chapel Hill

first: Matthew

last: McPeek

state: NC

address: 125 Mason Farm Rd. CB:7248

country: USA

institute: University of North Carolina

library_source: transcriptomic

data_processing:
Paired-end sequencing output were processed by Illumina bcl2fastq used for basecalling.
Sequence reads in FASTQ files were mapped to GRCm39 reference genome with GENCODE vM29 gene annotation by STAR, to generate BAM files.
Gene expression estimates were made as counts, and TPMs, by StringTie from BAM files and GENCODE vM27 annotation.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file with gene information, counts, and columns as samples
Supplementary files format and content: tab-delimited text file with gene information, TPMs, and columns as samples

molecule: total RNA

source_name: Left lung

extract_protocol: miRNeasy Mini Kit (Qiagen)

treatment_protocol:
Naïve left lung: Naïve mice were euthanized by isoflurane overdose immediently prior to tissue collection. The left lung was collected and immediently flash frozen in liquid nitrogen and stored at -80°C prior to RNA isolation.
Pneumonic left lung: Mice were inoculated with Streptococcus pneumoniae (1.74 ± 0.14 x 10^6 bacterium) by intratracheal instillation into the left lung. 24 hours post inoculation, mice were euthanized by isoflurane overdose and the left lung was collected and flash frozen in liquid nitrogen. Tissue was stored at -80°C prior to RNA isolation.

value: Left lung

tag: genotype

value: Wild type

tag: Sex

value: Male

tag: treatment

value: Naïve


title: BLaER, CaptureC_set1_promoter, 96h, biological replicate 2

city: Goettingen

first: Yi

last: Zhu

address: Am Fassberg 11

country: Germany

institute: Max Planck Insitute for Multidisciplinary Sciences

description: each biological replicate has 4 technical replicates

library_source: genomic

data_processing:
*library strategy: Capture-C
Capture-C data were analyzed using the CapCruncher pipeline (Downes, D. J. et al., 2022)  (v.0.2.3) in capture mode.
Assembly: hg38
Supplementary files format and content: normalized bigWig files

molecule: genomic DNA

organism: Homo sapiens

source_name: BLaER

extract_protocol: Capture-C experiments were performed in 2 biological replicates per condition following the published protocol (Downes, D. J. et al., 2022).

tag: cell line

value: BLaER

tag: cell type

value: Leukemia cell line

value: 96h, biological rep2, promoter viewpoints set 1


title: Hepa1-6

description:
Library name: Sample 1
BD Rhapsody


title: BLaER, CaptureC_set1_promoter, 0h, biological replicate 2

value: 0h, biological rep2, promoter viewpoints set 1


title: Left lung_Naive_Mertk-/-_Male_5

value: Mertk -/-


title: Set1_RA002, Mouse, LratCre negatie Rspo3 floxed

city: New York

first: Atsushi

last: Sugimoto

state: NY

address: 1130 Saint Nicholas Avenue

institute: Columbia University

description: Library name: Set1_RA002

data_processing:
Cellranger software (v2.0.0) for human samples and cell ranger (v8.0.1) for mice sample was used to process the data.
BCL files were demultiplexed with 10x Cell Ranger's mkfastq command and analysis and alignment were performed using Cell Ranger's count command with Cell Ranger's reference mm10 (mouse).
Assembly: GRCh38
Supplementary files format and content: h5 format raw counts

molecule: nuclear RNA

source_name: liver

growth_protocol: None (human and mice samples)

extract_protocol:
Nuclear isolation as described (Filliol et, Nature 2022 Oct;610(7931):356-365). In brief, frozen liver tissue was minced with scissors in 1 ml TST buffer in the well of a 6-well plate for 10 min on ice. The homogenised solution was then passed through a 40 μm cell strainer. An additional 1 mL of TST buffer and 3 ml of 1xST buffer were used to wash the well and passed through a 40 μm cell strainer. The resulting 5 ml of nuclei suspension was centrifuged for 5 min at 500 g at 4°C. The supernatant was discarded, and the pellet resuspended in 1 ml of 1xST buffer. The nuclei suspension was then passed through a 35 μm filter.
Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 5′ v2 Reagent Kit (10x Genomics) according to manufacturer’s instructions, 12 cycles of cDNA amplification and 12 cycles of library amplification were performed, and samples were sequenced on an Illumina NovaSeq 6000 sequencing system instrument at the JP Sulzberger Columbia Genome Center.

treatment_protocol: Human samples are from healthy liver, liver with metabolic dysfunction-associated liver disease (MASLD) and alcohol-associated liver disease (ALD). Mouse samples are from untreated liver.

value: liver

value: LratCre- Rspo3 floxed (8 weeks old male)


title: Set1_RA001, Mouse, LratCre positive Rspo3 floxed

description: Library name: Set1_RA001

value: LratCre+ Rspo3 floxed (9 weeks old male)


title: Aorta, WT

city: New Haven

first: Carlos

last: Fernandez-Hernando

address: 10 Amistad St

institute: Yale University

description: 10x Genomics

data_processing:
The demultiplexing, barcod processing, gene counting and aggregation were made using the CellRanger software (version 7.1.0, 10x Genomics)
Assembly: custom reference mouse genome mm10 that include eGFP and tdTomato marker sequences
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Aorta

extract_protocol:
Aortas were harvested from WT and LXRiSMC mice and digested in 1.5mg/ml collagenase A (10103578001, Roche) + 0.5 mg/ml elastase (6365, Worthington) buffer at 37oC for 45 minutes with gentle shaking.
eGFP+ and tdTomato+ cells were encapsulated into droplets and processed following manufacturer’s specifications using 10X Genomics GemCode technology. Equal numbers of cells per sample were loaded on a 10x Genomics Chromium controller instrument to generate single-cell Gel Beads in emulsion (GEMs) at the Yale Center for Genome Analysis. Lysis and barcoded reverse transcription of polyadenylated mRNA from single cells were performed inside each GEM followed by complementary DNA (cDNA) generation using the Single-Cell 3′ Reagent Kits version 2 (10X Genomics).

value: Aorta

value: immune and vascular cells

value: 16 weeks of Western diet feeding


title: 20-week-old mouse patellar tendon cell replicate 1, scRNA-seq

city: Houston

first: Dongsu

last: Park

state: TX

address: One Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

description:
Library name: PT1_20week
10x genomics

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were made using the Cell Ranger software v 6.1.2. (https://www.10xgenomics.com/support/software/cell-ranger/latest/analysis/running-pipelines/cr-choosing-a-pipeline)
Assembly: mm10
Supplementary files format and content: tab-separated values files and matrix files

source_name: Patellar tendon

extract_protocol:
To isolate patellar tendon cells, skin around the hindlimb joint was exposed and washed with PBS to minimize contamination. The patellar tendon was elevated and secured a space for micro dissecting scissor to enter underneath. The patellar tendon was cut under the apex of patellar bone and above the tibial tuberosity. The collected patellar tendon was washed with PBS and incubated in 1X PBS, 10% FBS, and 0.2% type I collagenase (100mg/ml) at 37C for 30-60 minutes. After digestion, solution was filtered through 40um strainer to remove any remaining debris and cetrifuged at 350x g for 5 minute.
Libraries were constructed using the Chromium Single Cell 3' v3.1 (10x genomics, PN-11000121) Reagent Kit, according to the manufacturer's protocol. Amplified cDNA and final libraries were evaluated on an Agilent BioAnalyzer using a High Sensitivity DNA Kit (Agilent Technologies).

value: Patellar tendon

value: Patellar tendon cells

value: WT

tag: age


title: 20-week-old mouse patellar tendon cell replicate 2, scRNA-seq

description:
Library name: PT2_20week
10x genomics


title: Left lung_Naive_Mertk-/-_Male_4

value: Left lung


title: BLaER subclone CTCF-AID, MED26_ChIP _96h_depl_rep2

description: Library name: Sample 8

data_processing:
ChIPmentation data were analyzed with the NGseqBasic pipeline (Jelena Telenius et al., 2018).
For MED26 and SMC1A ChIPmentation, BigWig files were generated using deeptools (v.3.3.0) bamCoverage funtion with RPKM normalization and a binning size of 10bp.
For CTCF ChIPmentation, BigWig files were normalized with spike-in.
Covarege tracks of replicates were merged using UCSC bigWigMerge.
Assembly: hg38
Supplementary files format and content: bigWig files: reads coverage

extract_protocol:
Aliquots of 1.5 M cells were crosslinked in a single fixation reaction with 1% formaldehyde for 10 min at room temperature, quenched with ice-cold glycine at a final concentration of 125 mM, and washed 2 times with ice-cold PBS. Fixed cells were first gently lysed with Farnham lysis buffer (5 mM PIPES pH 8, 85 mM KCl, 0.5% NP-40) to isolate nuclei, which was followed by nuclear lysis with 0.5% SDS buffer (10 mM Tris-HCl pH 8, 1 mM EDTA, 0.5% SDS). Then, chromatin was fragmented, using an optimized procedure for each target. In the CTCF ChIPmentation experiments, chromatin was fragmented by sonication (time: 7 min, duty factor: 5 %, peak incident power: 140 W, cycles per burst: 200). In MED26 and SMC1A ChIPmentation experiments, chromatin was first fragmented by a titrated amount of MNase (2.5 Kunitz) and then gently sonicated (time: 1 min, duty factor: 2 %, peak incident power: 105 W, cycles per burst: 200). To perform immunoprecipitation, a mixture of Protein A (10008D, Invitrogen) and Protein G Dynabeads (10003D, Invitrogen) in 1:1 ratio was blocked with 0.5 % BSA, washed and pre-incubated with 2 µg of primary antibody (CTCF: Diagenode, C15410210-50; SMC1A: Abcam, ab9262; MED26: Bethyl Laboratories, A302-370) and 1 µg of spike-in antibody (Biozol, 61686) for 6 h, at 4 °C. Sheared chromatin was diluted in IP buffer , and added along with 50 ng Drosophila spike-in chromatin to the bead-bound antibodies. The samples were incubated overnight on a rotator at 4 °C, and washed with stringent buffers the next morning.
Sequencing adapters were added to the bead-bound DNA by Tagmentation with the Illumina Tagment DNA Enzyme and Buffer Kit (Illumina, 20034197). After washes, the bead-bound samples were de-crosslinked overnight at 65 °C in the presence of proteinase K (0.2 mg/mL, final) and cleaned with 1.8x volume of Mag-Bind TotalPure NGS beads (Omega Bio-Tek, M1378-01). The tagmented DNA was used for library preparation with the NEBNext High-Fidelity 2X PCR Master Mix (NEB, M0541).

value: BLaER subclone CTCF-AID (Auxin Inducible Degron)

value: 96h, auxin, rep2


title: 2-week-old mouse patellar tendon cell, scRNA-seq

description:
Library name: PT_2week
10x genomics


title: Left lung_Naive_Mertk-/-_Male_3

value: Male

value: Naïve


title: BLaER subclone CTCF-AID, MED26_ChIP _96h_depl_rep1

description: Library name: Sample 7

value: BLaER

value: Leukemia cell line

value: 96h, auxin, rep1


title: STAT3-M7

city: shenzhen

first: zhiguang

last: chang

address: No. 1068, Xueyuan Avenue, Shenzhen University Town, Xili, Nanshan District

department: Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology

institute: Chinese Academy of Sciences

description:
Library name: STAT3-M7
STAT3 group,replicable biosample 1

data_processing:
Raw fastq files were processed with fastp (version 0.23.2) to remove adapter sequences and low-quality reads. The quality, adapter content, and duplication rates were assessed using FastQC (version 0.11.9). Cleaned reads were aligned to the mouse reference genome (NCBI build 37, mm9) using Bowtie2 (version 2.4.4), and duplicate alignments were removed using the MarkDuplicates tool in Picard (version 2.25.0). Genome-wide coverage files for H3K27ac, STAT3, H3K4me3, and immunoglobulin G (IgG) were generated using the bamCoverage tool from deepTools (version 3.5.0) (Ramírez et al., 2014). Peaks were called using MACS2 and annotated with the annotatePeaks.pl script from the Homer software suite. Genome region visualizations were created using the Integrative Genomics Viewer (IGV).
Assembly: mm9
Supplementary files format and content: tab-delimited text file includes the PEAK information for each sample
Library strategy: CUT&Tag

source_name: spleen-derived CD8+T cell

extract_protocol:
Processed samples were incubated with 10 μl of Concanavalin A-coated magnetic beads (NovoNGS® Concanavalin A-coated Magnetic Beads, N251). Bead-bound cells were suspended in Dig Wash Buffer and incubated with antibodies targeting STAT3 (Proteintech, 10253-2-ap), H3K27ac (Abcam, ab4729), or H3K4me3 (Abcam, ab8580) at 4 °C overnight. Subsequently, cells were incubated with secondary antibodies for 60 minutes, followed by incubation with pA-Tn5 adapter complexes for 1 hour.
The samples were then resuspended in fragmentation buffer and incubated at 37 °C for 1 hour. DNA was purified using phenol-chloroform-isoamyl alcohol extraction and ethanol precipitation. The sequencing was performed on the Illumina Novaseq6000 platform using 150 bp paired-end reads.

value: spleen-derived CD8+T cell

value: The time-matched control group for the M4 group


title: BLaER, CaptureC_set2_promoter, 0h, biological replicate 1

value: 0h, biological rep1, promoter viewpoints set 2


title: BLaER subclone CTCF-AID,MED26_ChIP _96h_control_rep2

description: Library name: Sample 6

value: 96h, no treatment control, rep2


title: Left lung_Naive_Mertk-/-_Male_2

value: Mertk -/-


title: STAT3-M6

description:
Library name: STAT3-M6
STAT3 group,replicable biosample 1

value: The time-matched control group for the M3 group


title: Left lung_Naive_Mertk-/-_Male_1


title: BLaER subclone CTCF-AID, MED26_ChIP _96h_control_rep1

description: Library name: Sample 5

value: 96h, no treatment control, rep1


title: STAT3-M5

description:
Library name: STAT3-M5
STAT3 group,replicable biosample 1

value: The time-matched control group for the M2 group


title: Left lung_Pneumonic_Wild type_Male_8

value: Wild type

value: 24 hour, S. pneumoniae induced pneumoniae


title: Left lung_Pneumonic_Wild type_Male_7

value: Left lung


title: BLaER, CaptureC_set1_promoter, 96h, biological replicate 1

value: 96h, biological rep1, promoter viewpoints set 1


title: BLaER subclone CTCF-AID, SMC1A_ChIP _96h_depl_rep2

description: Library name: Sample 4

value: BLaER subclone CTCF-AID (Auxin Inducible Degron)

value: 96h, auxin, rep2


title: Left lung_Pneumonic_Wild type_Male_6

value: Male


title: BLaER subclone CTCF-AID, SMC1A_ChIP _96h_depl_rep1

description: Library name: Sample 3

value: BLaER

value: Leukemia cell line


title: STAT3-M4-2

description:
Library name: STAT3-M4-2
STAT3 group,replicable biosample 2

value: spleen-derived CD8+T cell

value: Subsequent exposure (same as Rest, with an additional 6-h stimulation with 10 ng/ml IL-10)


title: BLaER subclone CTCF-AID, SMC1A_ChIP _96h_control_rep2

description: Library name: Sample 2


title: STAT3-M4-1

description:
Library name: STAT3-M4-1
STAT3 group,replicable biosample 1


title: BLaER subclone CTCF-AID, SMC1A_ChIP _96h_control_rep1

description: Library name: Sample 1


title: Left lung_Pneumonic_Wild type_Male_5


title: Left lung_Pneumonic_Wild type_Male_4


title: STAT3-M2-2

description:
Library name: STAT3-M2-2
STAT3 group,replicable biosample 2

value: Initial exposure (stimulated with 10 ng/ml IL-10 for 6 h)


title: STAT3-M3-1

description:
Library name: STAT3-M3-1
STAT3 group,replicable biosample 1

value: Rest (stimulated with 10 ng/ml IL-10 for 6 h, washed, and cultured for 48 h in 0.5 ng/ml IL-10 with medium changes every 12 h)


title: Left lung_Pneumonic_Wild type_Male_3


title: STAT3-M2-1

description:
Library name: STAT3-M2-1
STAT3 group,replicable biosample 1


title: Left lung_Pneumonic_Wild type_Male_2


title: hiPSC-CMs expanded in bioreactor in normoxia for 11 days rep3

city: Pamplona

first: Asier

last: Ullate-Agote

state: Navarra

address: Av. de Pío XII, 55

department: Hemato-Oncology

country: Spain

institute: CIMA

data_processing:
bcl2fastq v2.20 was used to demultiplex and FASTQ files were aligned to the human genome (hg38) using STAR (v2.7.0d). Gene expression quantification was performed using the featureCounts function implemented in the R package Rsubread (v2.4.3) counting uniquely mapped paired-end reads with reverse strandness. The Ensembl v103 gene annotation was considered as the reference.
Normalization, processing and differential expression analyses were performed using DEseq2
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

extract_protocol:
Cells were harvested, then stored in TRIzol at -80C. RNA was extracted as recommended by the manufacturer.
RNA-seq libraries were prepared using Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus according to the manufacturer’s instructions

value: hiPSC-derived cardiomyocytes

value: XX


title: hiPSC-CMs cultured for two weeks after expansion in bioreactor in mild hypoxia rep3


title: STAT3-M1-2

description:
Library name: STAT3-M1-2
STAT3 group, replicable biosample 2

value: Pre-exposure (direct sample collection)


title: hiPSC-CMs expanded in bioreactor in mild hypoxia for 11 days rep3


title: hiPSC-CMs expanded in T-flasks for 11 days rep3


title: STAT3-M3-2

description:
Library name: STAT3-M3-2
STAT3 group,replicable biosample 2


title: STAT3-M1-1

description:
Library name: STAT3-M1-1
STAT3 group, replicable biosample 1


title: hiPSC-CMs 11 days after differentiation rep3

value: hiPSC-CMs 11 days after differentiation


title: BLaER, CaptureC_set1_promoter, 0h, biological replicate 1

value: 0h, biological rep1, promoter viewpoints set 1


title: Left lung_Pneumonic_Wild type_Male_1

value: Wild type

value: 24 hour, S. pneumoniae induced pneumoniae


title: Left lung_Pneumonic_Mertk-/-_Male_8

value: Left lung

value: Mertk -/-


title: H3K27ac-M7

description:
Library name: H3K27ac-M7
H3K27ac group,replicable biosample 1

value: The time-matched control group for the M4 group


title: hiPSC-CMs cultured for two weeks after expansion in bioreactor in mild hypoxia rep2


title: H3K27ac-M4-2

description:
Library name: H3K27ac-M4-2
H3K27ac group,replicable biosample 2


title: hiPSC-CMs expanded in bioreactor in normoxia for 11 days rep2


title: Left lung_Pneumonic_Mertk-/-_Male_4

value: Male


title: Left lung_Pneumonic_Mertk-/-_Male_6


title: hiPSC-CMs expanded in bioreactor in mild hypoxia for 11 days rep2


title: H3K27ac-M5

description:
Library name: H3K27ac-M5
H3K27ac group,replicable biosample 1

value: The time-matched control group for the M2 group


title: Left lung_Pneumonic_Mertk-/-_Male_5


title: hiPSC-CMs 11 days after differentiation rep2


title: Left lung_Pneumonic_Mertk-/-_Male_3


title: H3K27ac-M4-1

description:
Library name: H3K27ac-M4-1
H3K27ac group,replicable biosample 1


title: Left lung_Pneumonic_Mertk-/-_Male_1


title: hiPSC-CMs expanded in bioreactor in normoxia for 11 days rep1


title: H3K27ac-M3-2

description:
Library name: H3K27ac-M3-2
H3K27ac group,replicable biosample 2


title: hiPSC-CMs cultured for two weeks after expansion in bioreactor in mild hypoxia rep1


title: Left lung_Pneumonic_Mertk-/-_Male_2


title: Brain-enriched, mtmr5-knockout, biol rep4

city: Toronto

first: Jordan

last: Lindzon

state: Ontario

address: 686 Bay St.

department: Genetics & Genome Biology

country: Canada

institute: Peter Gilgan Centre for Research and Learning

description:
Library name: brain-enriched_mtmr5-KO4
KO4

data_processing:
Adaptors trimmed using Trim Galore! (Galaxy Version 0.6.7+galaxy0)
Raw trimmed reads aligned to reference genome using RNA STAR (Galaxy Version 2.7.11a+galaxy1)
Filtered STAR alignments processed to extract raw read counts for genes using htseq-count (Galaxy Version 2.0.5+galaxy0) (mode: intersection - nonempty)
Normalized count matrix was generated using DESeq2 v3.2 in R v4.4.0. Minimum expression cut-off: 10 read counts in at least 3 samples.
Assembly: GRCz11/Ensembl release 113 (primary assembly), downloaded on October 21, 2024.
Supplementary files format and content: raw-counts_allSamples.csv includes raw counts for every gene for all samples
Supplementary files format and content: normalized-counts_allSamples.csv includes normalized counts for genes above minimum expression cutoff for all samples

organism: Danio rerio

source_name: head

growth_protocol: Zebrafish (AB strain) were raised and maintained at 28.5°C at the Zebrafish Facility at the Hospital for Sick Children, Toronto, ON, Canada. Zebrafish embryos were grown in blue water (0.3 g/L Instant Ocean, 1 mg/L methylene blue, pH 7.0) from the one-cell stage up to 7 dpf. All zebrafish procedures were performed in strict accordance with the Animals for Research Act of Ontario and the Guidelines of the Canadian Council on Animal Care.

extract_protocol:
Zebrafish larvae were fin clipped and genotyped at 4-6 dpf. At 7 dpf, n=11-17 zebrafish heads were dissected per genotype, and immediately frozen at -80C. RNA extraction was performed for all samples (4x WT, and 4x mtmr5-KO) using the RNeasy kit (Qiagen).
Quality control, RNA library preparation, cDNA synthesis, and library validation were performed by The Centre for Applied Genomics—Next-Generation Sequencing Facility (PGCRL, The Hospital for Sick Children, Toronto).

value: head


title: hiPSC-CMs expanded in bioreactor in mild hypoxia for 11 days rep1


title: H3K27ac-M2-2

description:
Library name: H3K27ac-M2-2
H3K27ac group,replicable biosample 2

value: spleen-derived CD8+T cell


title: Brain-enriched, mtmr5-knockout, biol rep3

description:
Library name: brain-enriched_mtmr5-KO3
KO3


title: Left lung_Pneumonic_Mertk-/-_Male_7


title: H3K27ac-M2-1

description:
Library name: H3K27ac-M2-1
H3K27ac group,replicable biosample 1


title: H3K27ac-M6

description:
Library name: H3K27ac-M6
H3K27ac group,replicable biosample 1

value: The time-matched control group for the M3 group


title: hiPSC-CMs expanded in T-flasks for 11 days rep1


title: hiPSC-CMs expanded in T-flasks for 11 days rep2


title: H3K27ac-M3-1

description:
Library name: H3K27ac-M3-1
H3K27ac group,replicable biosample 1


title: Brain-enriched, mtmr5-knockout, biol rep2

description:
Library name: brain-enriched_mtmr5-KO2
KO2


title: H3K27ac-M1-2

description:
Library name: H3K27ac-M1-2
H3K27ac group, replicable biosample 2


title: H3K27ac-M1-1

description:
Library name: H3K27ac-M1-1
H3K27ac group, replicable biosample 1


title: hiPSC-CMs 11 days after differentiation rep1


title: Brain-enriched, mtmr5-knockout, biol rep1

description:
Library name: brain-enriched_mtmr5-KO1
KO1


title: BLaER subclone CTCF-AID, TriC enhancer, 96h-depl, rep3

description: viewpoint: enhancer; each biological replicate has 3 technical replicates

data_processing:
*library strategy: Tri-C
Tri-C data were analyzed using the CapCruncher pipeline (Downes, D. J. et al., 2022)  (v.0.2.3) in capture mode.
A custom script was used to extract reads with two or more cis reporters. These reads were used to calculate multi-way interaction counts between reporter fragments for each viewpoint.
The interaction counts were binned in 1500, 2000, or 2500 bp bins and corrected for the number of restriction fragments present in each bin. The matrices were normalized for the total multi-way interaction counts within a 2 Mb region (which was corrected for the number of restriction fragments present in the region) surrounding the viewpoint.
Assembly: hg38
Supplementary files format and content: txt file: the coordinates and the read counts of restriction fragments pairs interacting with the viewpoint.

extract_protocol: Tri-C experiments were performed in 3 biological replicates per condition following the published protocol (Downes, D. J. et al., 2022).

value: BLaER

value: Leukemia cell line

value: BLaER subclone CTCF-AID (Auxin Inducible Degron)

value: 96h, auxin, biological rep3


title: Brain-enriched, wild-type, biol rep3

description:
Library name: brain-enriched_mtmr5-WT3
WT3

value: wild-type


title: H3K4me3-M5

description:
Library name: H3K4me3-M5
H3K4me3 group,replicable biosample 1


title: BLaER subclone CTCF-AID, TriC enhancer, 96h-depl, rep2

value: 96h, auxin, biological rep2


title: Brain-enriched, wild-type, biol rep2

description:
Library name: brain-enriched_mtmr5-WT2
WT2


title: BLaER subclone CTCF-AID, 96h_CTCF_depl_rep1

data_processing:
RNA-seq data were processed using the nf-core/rnaseq pipeline (v.3.12.0). After sequence alignment with STAR (v.2.6.1d), the expression of protein-coding exons was quantified with featureCounts (v.2.0.6).
Assembly: hg38
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample
Supplementary files format and content: bigWig

growth_protocol: RPMI 1640 medium, 10% fetal bovine serum, 25mM HEPES, 2% Glutamax. Cells were cultured at 37C and 5% CO2.

extract_protocol:
Cells were collected, centrifuged at 200g, 5 min, then lysed with Qiazol. RNA extraction was performed using standard chroroform-isopropanol extraction method.
150ug of RNA for each condition was diluted to 130 uL, sonicated using Covaris (100W intensity, 1% duty cycel, 10s). For each sample 2 uL of sonicated RNAs is used for RNA clean up with miRNeasy micro kit (Qiagen), followed by DnaseI digestion. Library prep is used with Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus kit, and indexed with Illumina UD Indexes, then sequenced with Nextseq 2000.

treatment_protocol: Cells were treated as described in the Methods section of the paper.

value: 96h, auxin, rep1


title: H3K4me3-M7

description:
Library name: H3K4me3-M7
H3K4me3 group,replicable biosample 1


title: Brain-enriched, wild-type, biol rep4

description:
Library name: brain-enriched_mtmr5-WT4
WT4


title: H3K4me3-M6

description:
Library name: H3K4me3-M6
H3K4me3 group,replicable biosample 1


title: BLaER subclone CTCF-AID, 96h_control_rep2

value: 96h, no treatment control, rep2


title: H3K4me3-M4-1

description:
Library name: H3K4me3-M4-1
H3K4me3 group,replicable biosample 1

value: Subsequent exposure (same as Rest, with an additional 6-h stimulation with 10 ng/ml IL-10)


title: BLaER subclone CTCF-AID, 96h_CTCF_depl_rep2

value: 96h, auxin, rep2


title: BLaER subclone CTCF-AID, 0h_control_rep2

value: 0h, no treatment control, rep2


title: H3K4me3-M4-2

description:
Library name: H3K4me3-M4-2
H3K4me3 group,replicable biosample 2


title: Brain-enriched, wild-type, biol rep1

description:
Library name: brain-enriched_mtmr5-WT1
WT1


title: SHP77 circRMST shRNA 2 rep 1

first: Housheng

middle: Hansen

last: He

address: 101 College Street

institute: Princess Margaret Cancer Centre

description:
Sample 5
shjunction2_1
Pair-end 150bp

data_processing:
Adapters were trimmed with cutadapt (v.2.5). Raw reads were mapped to human genome hg38 GENCODE vM25 annotation with STAR (v2.5.2b). Gene counts were performed with STAR.
Assembly: hg38
Supplementary files format and content: SHP77_shRNA_normalized_counts.csv: Comma-separated-value file containing normalized counts of shRNA samples as generated by DESeq2. In brief, raw counts were normalized by a normalization factor for each sample based on sequencing depth and RNA composition. This allows for comparison between samples. It is not normalized for transcript length.
Supplementary files format and content: SHP77_siRNA_normalized_counts.csv: Comma-separated-value file containing normalized counts of siRNA samples as generated by DESeq2. In brief, raw counts were normalized by a normalization factor for each sample based on sequencing depth and RNA composition. This allows for comparison between samples. It is not normalized for transcript length.

growth_protocol: SHP77 cells were grown in RPMI with 10% FBS and 1% penicillin-streptomycin. Cells were infected by lentivirus containing appropriate shRNAs and selected with 3 ug/mL puromycin for at least 3 days before harvesting.

extract_protocol:
Cells were collected and lysed with Trizol. Total RNA was extracted with RNeasy Mini Kit (QIAGEN, cat. #74106). Genomic DNA was removed with RNase-Free DNase Set (QIAGEN, cat. #79254).
1ug of RNA was used for library construction with the TruSeq stranded total RNA library prep kit (Illumina, cat. #20020597) following manufacturer’s protocol.

value: Small cell lung cancer cell line

value: circRMST knockdown


title: BLaER subclone CTCF-AID, 96h_control_rep1

value: 96h, no treatment control, rep1


title: SHP77 circRMST shRNA 1 rep 2

description:
Sample 4
shjunction1_2
Pair-end 150bp


title: SHP77 circRMST shRNA 1 rep 1

description:
Sample 3
shjunction1_1
Pair-end 150bp


title: BLaER subclone CTCF-AID, 0h_control_rep1

value: 0h, no treatment control, rep1


title: H3K4me3-M3-1

description:
Library name: H3K4me3-M3-1
H3K4me3 group,replicable biosample 1

value: spleen-derived CD8+T cell

value: Rest (stimulated with 10 ng/ml IL-10 for 6 h, washed, and cultured for 48 h in 0.5 ng/ml IL-10 with medium changes every 12 h)


title: H3K4me3-M2-1

description:
Library name: H3K4me3-M2-1
H3K4me3 group,replicable biosample 1

value: Initial exposure (stimulated with 10 ng/ml IL-10 for 6 h)


title: SHP77 circRMST shRNA 2 rep 2

description:
Sample 6
shjunction2_2
Pair-end 150bp


title: SHP77 shGFP rep 2

description:
Sample 2
shGFPV2_2
Pair-end 150bp

value: Negative control


title: H3K4me3-M3-2

description:
Library name: H3K4me3-M3-2
H3K4me3 group,replicable biosample 2


title: BLaER subclone CTCF-AID, TriC enhancer, 96h-depl, rep1

value: BLaER

value: Leukemia cell line

value: BLaER subclone CTCF-AID (Auxin Inducible Degron)

value: 96h, auxin, biological rep1


title: BLaER subclone CTCF-AID, MCC promoter, 96h-depl, rep6

description: viewpoint: promoter

data_processing:
*library strategy: Micro-Capture-C (MCC)
MCC pipeline (https://github.com/jojdavies/Micro-Capture-C)
Assembly: hg38
Supplementary files format and content: Normalized bigWig files

extract_protocol:
Multiple aliquots of 15 M cells were crosslinked in 10 mL of culture medium with 2% formaldehyde (ThermoFischer, 28908). Next, the cells were permeabilized by digitonin (0.0025%; Sigma-Aldrich, D141). Digestion was performed with MNase (NEB, M0247) in low Ca2+ MNase buffer (10 mM Tris-HCl pH 7.5, 10 mM CaCl2) for 1 h at 37 °C. After confirming efficient digestion, samples were ligated and de-crosslinked. DNA was extracted using the DNeasy Blood and Tissue Kit (Qiagen, 69504).
Before sonication, samples were size-selected to remove fragments corresponding to mono-nucleosomes using Mag-Bind TotalPure NGS beads (Omega Bio-Tek, M1378-01). MCC libraries were sheared using a Covaris S220 Focused-Ultrasonicator to a mean size of 200 bp (time: 280 s, duty factor: 10%, peak incident power: 175 W, cycles per burst: 200). Afterwards, the sonicated DNA fragments were indexed using 2 µg of DNA per indexing reaction. To increase library complexity, each reaction was indexed in duplicate in 7 PCR cycles using Herculase II polymerase (Agilent, 600677). The duplicate reactions were pooled and the libraires were enriched for viewpoints of interest in a double capture procedure, using ssDNA 5’-biotinylated 120 nt oligonucleotides. Briefly, 2 separate hybridization reactions were performed for each condition, using 2 µg of each sample as input. Captured DNA was pulled down using M-270 Streptavidin Dynabeads (Invitrogen, 65305), and amplified in 12 PCR cycles. After library quality assessment with a fragment analyzer, the libraries were sequenced on the Illumina sequencing platform with 300 cycles paired-end reads.

value: 96h, auxin, rep6


title: H3K4me3-M1-1

description:
Library name: H3K4me3-M1-1
H3K4me3 group, replicable biosample 2

value: Pre-exposure (direct sample collection)


title: H3K4me3-M2-2

description:
Library name: H3K4me3-M2-2
H3K4me3 group,replicable biosample 2


title: SHP77 shGFP rep 1

description:
Sample 1
shGFPV2_1
Pair-end 150bp


title: Gene expression of the 182 Danish ash accessions [ERR977776]

city: Heslington, York

first: Sara

last: Franco Ortega

address: Wentworth Way

department: Department of Biology

country: United Kingdom

institute: Centre for Novel Agricultural Products, University of York

data_processing:
Trimmomatic
Salmon 0.8
tximport in R
Assembly: Fraxinus excelsior 2451S ONT; PRJNA865134
Supplementary files format and content: tximport_182.txt

organism: Fraxinus excelsior

source_name: Leaves

extract_protocol:
Harper et al., 2016, https://doi.org/10.1038/srep19335
100 bp Illumina HiSeq reads

value: Leaves

tag: accession


title: BLaER subclone CTCF-AID, MCC promoter, 96h-depl, rep4

description: viewpoint: promoter

value: 96h, auxin, rep4


title: BLaER subclone CTCF-AID, MCC promoter, 96h-depl, rep5

description: viewpoint: promoter

value: 96h, auxin, rep5


title: ATAC-M7

description:
Library name: ATAC-M7
replicable biosample 1

data_processing:
Raw fastq files were processed using fastp (version 0.23.2)  (Chen et al., 2018) to remove adapter sequences and low-quality reads. Quality, adapter content, and duplication rates were evaluated using FastQC (version 0.11.9). Cleaned reads were aligned to the mouse reference genome (NCBI build 37, mm9) using Bowtie2 (version 2.4.4) (Langmead et al., 2009), and duplicate alignments were removed using the MarkDuplicates tool in Picard (version 2.25.0). Accessible chromatin regions were identified by peak calling with MACS2 (Model-based analysis of ChIP-seq) (version 2.2.7.1)(Zhang et al., 2008). Differential accessibility analysis was performed using the DiffBind package (version 3.6.2). Peaks with log2(fold change) > 0.5 and FDR < 0.05 were considered significantly differentially accessible. Peak annotation was conducted using the annotatePeaks.pl script from the Homer suite. ATAC signal tracks were visualized using the Integrative Genomics Viewer(Robinson et al., 2011).
Assembly: mm9
Supplementary files format and content: tab-delimited text file includes the PEAK information for each sample

extract_protocol:
Processed primary cells were subjected to transposition reactions using the TruePrep DNA Library Prep Kit V2 for Illumina (TD501) and TruePrep Index Kit V2 for Illumina (TD202) according to the manufacturer’s instructions.
Nuclei from 5 × 10⁴ cells were pelleted and incubated with Tn5 transposase at 37 °C for 30 minutes. The resulting transposed DNA fragments were purified using the MolPure® PCR Purification Kit. Purified DNA fragments were amplified using 1× NEBNext High-Fidelity PCR Master Mix (New England Biolabs). The resulting library was further purified with the MolPure® PCR Purification Kit, quantified using a Qubit Fluorometer, and analyzed on an Agilent 2100 Bioanalyzer. Sequencing was performed on the Illumina Novaseq6000 platform using a paired-end 150 bp (PE150) strategy.

value: The time-matched control group for the M4 group


title: Gene expression of the 182 Danish ash accessions [ERR977775]


title: BLaER subclone CTCF-AID, MCC promoter, 96h-depl, rep3

description: viewpoint: promoter

value: 96h, auxin, rep3


title: Gene expression of the 182 Danish ash accessions [ERR977774]


title: ATAC-M6

description:
Library name: ATAC-M6
replicable biosample 1

value: The time-matched control group for the M3 group


title: BLaER subclone CTCF-AID, MCC promoter, 96h-depl, rep2

description: viewpoint: promoter

value: 96h, auxin, rep2


title: Gene expression of the 182 Danish ash accessions [ERR977773]


title: Kidney organoids cultured with human dECM rep1

data_processing:
bcl2fastq v2.20 was used to demultiplex and FASTQ files were aligned to the human genome (hg38) using STAR (v2.7.0d). Gene expression quantification was performed using the featureCounts function implemented in the R package Rsubread (v2.4.3) counting uniquely mapped paired-end reads with reverse strandness. The Ensembl v93 gene annotation was considered as the reference.
Normalization, processing and differential expression analyses were performed using DEseq2
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for human dECM samples

source_name: kidney organoid

extract_protocol:
Cells were collected by scraping and RNA was extracted using Trizol reagent
RNA-seq libraries were prepared using Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus according to the manufacturer’s instructions

value: kidney organoid

value: human induced pluripotent stem cell

value: XX

value: kidney organoid protocol with human dECM


title: ATAC-M3-2

description:
Library name: ATAC-M3-2
replicable biosample 2

value: spleen-derived CD8+T cell

value: Rest (stimulated with 10 ng/ml IL-10 for 6 h, washed, and cultured for 48 h in 0.5 ng/ml IL-10 with medium changes every 12 h)


title: Kidney organoids cultured with human dECM rep2


title: ATAC-M4-1

description:
Library name: ATAC-M4-1
replicable biosample 1

value: Subsequent exposure (same as Rest, with an additional 6-h stimulation with 10 ng/ml IL-10)


title: Gene expression of the 182 Danish ash accessions [ERR977769]


title: Kidney organoids cultured with pig dECM rep2

data_processing:
bcl2fastq v2.20 was used to demultiplex and FASTQ files were aligned to the human genome (hg38) using STAR (v2.7.0d). Gene expression quantification was performed using the featureCounts function implemented in the R package Rsubread (v2.4.3) counting uniquely mapped paired-end reads with reverse strandness. The Ensembl v93 gene annotation was considered as the reference.
Normalization, processing and differential expression analyses were performed using DEseq2
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

value: human embryonic stem cell

value: male

value: kidney organoid protocol with pig dECM


title: Gene expression of the 182 Danish ash accessions [ERR977770]

value: Leaves


title: Gene expression of the 182 Danish ash accessions [ERR977768]


title: H3K4me3-M1-2

description:
Library name: H3K4me3-M1-2
H3K4me3 group, replicable biosample 1

value: Pre-exposure (direct sample collection)


title: ATAC-M2-2

description:
Library name: ATAC-M2-2
replicable biosample 2

value: Initial exposure (stimulated with 10 ng/ml IL-10 for 6 h)


title: Kidney organoids cultured with pig dECM rep1


title: Kidney organoids in control conditions rep2

value: kidney organoid protocol


title: ATAC-M5

description:
Library name: ATAC-M5
replicable biosample 1

value: The time-matched control group for the M2 group


title: Gene expression of the 182 Danish ash accessions [ERR977772]


title: ATAC-M4-2

description:
Library name: ATAC-M4-2
replicable biosample 2


title: Gene expression of the 182 Danish ash accessions [ERR977771]


title: Gene expression of the 182 Danish ash accessions [ERR977767]


title: ATAC-M3-1

description:
Library name: ATAC-M3-1
replicable biosample 1


title: BLaER subclone CTCF-AID, MCC promoter, 96h-depl, rep1

description: viewpoint: promoter

value: BLaER

value: Leukemia cell line

value: BLaER subclone CTCF-AID (Auxin Inducible Degron)

value: 96h, auxin, rep1


title: Gene expression of the 182 Danish ash accessions [ERR977766]


title: ATAC-M1-2

description:
Library name: ATAC-M1-2
replicable biosample 2


title: Kidney organoids in control conditions rep1

value: kidney organoid


title: Gene expression of the 182 Danish ash accessions [ERR977765]


title: ATAC-M1-1

description:
Library name: ATAC-M1-1
replicable biosample 1


title: Gene expression of the 182 Danish ash accessions [ERR977764]


title: Gene expression of the 182 Danish ash accessions [ERR977763]


title: AR010, Rspo3 KO HSC_5

data_processing:
For each sample, a minimum of 20 million 100-bp single-end reads were sequenced on an Illumina NovaSeq 6000.
RTA (Illumina) was used for base calling and bcl2fastq2 (v.2.19 and v.2.20) for converting BCL to fastq format, coupled with adaptor trimming.
A pseudoalignment to a kallisto index was created from transcriptomes (human, GRCh38; mouse, GRCm38) using kallisto (0.44.0).
To explore similarities and dissimilarities between samples, count data were normalized using the variance stabilizing transformation function from the DESeq2 package.
Assembly: GRCm38
Supplementary files format and content: h5 format raw counts

extract_protocol:
Liver tissue was homogenized in a Tissuelyser in Trizol and purified using chloroform, followed by isolation of total RNA using RNA isolation kits (QIAGEN, Roche or Sigma-Aldrich). Total RNA from cells was isolated directly using RNA isolation kits.
Libraries were constructed using Illumina TruSeq RNA Preparation Kit according to the manufacturer’s instructions.

treatment_protocol: For genetic HSC depletion, LratCre+TdTomhetiDTRhet or LratCre+TdTomhomoiDTRwt controls were intraperitonially injected with DT (0.25 ng g−1) once per week as indicated.

value: liver

value: LratCre+, Rspo3 floxed

value: 8 weeks old


title: ATAC-M2-1

description:
Library name: ATAC-M2-1
replicable biosample 1

value: spleen-derived CD8+T cell


title: AR009, Control for Rspo3 KO HSC_5

value: LratCre-, Rspo3 floxed


title: Gene expression of the 182 Danish ash accessions [ERR977762]


title: AR006, Control for Rspo3 KO HSC_3

value: male


title: Gene expression of the 182 Danish ash accessions [ERR977761]


title: AR007, Control for Rspo3 KO HSC_4


title: Gene expression of the 182 Danish ash accessions [ERR977760]


title: Susceptible Prunus inoculated with RKN Rep3

city: Sophia Antipolis

first: cyril

last: van ghelder

address: 400 route des Chappes

country: France

institute: INRAE

data_processing:
Quality Control and filtering were performed on raw reads using SOAPnuke v1.5.2
filtered clean reads were aligned on the reference Prunus persica v2.0 from NCBI (GCF_000346465.2_Prunus_persica_NCBIv2) using HISAT2 v2.0.4
Reads were aligned to the reference P. persica genes with Bowtie2 v2.2.5 and then used RSEM (v1.2.8) to calculate the gene expression level of each sample
analyses for differential gene expression were performed using the analysis method DESeq2 with |log2FC| >=0 and Qvalue <= 0.05
According to the results of differential gene detection, the R package pheatmap (with default parameters) was used to perform hierarchical clustering analysis on the union set differential genes.
Assembly: version 2 of Prunus persica reference genome GCF_000346465.2_Prunus_persica_NCBIv2
Supplementary files format and content: table excel file include, the raw counts for each sample
Supplementary files format and content: table excel file include, the log2Ratio (B / A)  values for each sample using DESeq2

organism: Prunus cerasifera

source_name: roots

growth_protocol: in vitro Prunus cerasifera plantlets were acclimatized in perlite during 3 weeks at 24 degrees (light 16/8) then transferred for 1 week in 50ml pierced falcon tubes containing pure sandy soil

extract_protocol:
total RNA form root systems was isolated using the protocol described in Van Ghelder et al. 2018 - Frontiers in plant science
libraries were prepared using the DNBSEQ Eucaryotic Stranded PE 150. mRNA  enrichment was performed using oligodT beads Fragment the RNA and first-strand cDNA was generated using random N6-primed reverse transcription, followed by a second-strand cDNA synthesis with dUTP instead of dTTP.

treatment_protocol: both Prunus accessions were either let untreated (control) or inoculated with approx. 15000 Meloidogyne incognita juvenile stage 2 for 48 h.

tag: background strain

value: P. 2032 (Myrabi)

value: ma/ma susceptible to RKN

value: inoculated with Meloidogyne incognita for 48h


title: Resistant Prunus inoculated with RKN Rep 1

value: Ma/ma resistant to RKN


title: Resistant Prunus untreated Rep3

value: untreated


title: Resistant Prunus inoculated with RKN Rep 2


title: Susceptible Prunus inoculated with RKN Rep2


title: Susceptible Prunus inoculated with RKN Rep1


title: Resistant Prunus inoculated with RKN Rep 3


title: Gene expression of the 182 Danish ash accessions [ERR977759]

value: Leaves


title: Resistant Prunus untreated Rep2


title: AR004, Control for Rspo3 KO HSC_1


title: Gene expression of the 182 Danish ash accessions [ERR977758]


title: Susceptible Prunus untreated Rep3


title: AR008, Rspo3 KO HSC_4

value: 9 weeks old


title: Gene expression of the 182 Danish ash accessions [ERR977757]


title: AR003, Rspo3 KO HSC_3


title: Gene expression of the 182 Danish ash accessions [ERR977756]


title: Resistant Prunus untreated Rep1


title: Susceptible Prunus untreated Rep1


title: Gene expression of the 182 Danish ash accessions [ERR977754]


title: Susceptible Prunus untreated Rep2


title: Gene expression of the 182 Danish ash accessions [ERR977755]


title: AR002, Rspo3 KO HSC_2


title: AR001, Rspo3 KO HSC_1

value: female


title: AS_Endo_R_4, Rspo3 KO EC_4

description:
AS_Endo_R_4
RSPO3_Age_Endo_est_counts.txt

data_processing:
For each sample, a minimum of 20 million 100-bp single-end reads were sequenced on an Illumina NovaSeq 6000.
RTA (Illumina) was used for base calling and bcl2fastq2 (v.2.19 and v.2.20) for converting BCL to fastq format, coupled with adaptor trimming.
A pseudoalignment to a kallisto index was created from transcriptomes (human, GRCh38; mouse, GRCm38) using kallisto (0.44.0).
To explore similarities and dissimilarities between samples, count data were normalized using the variance stabilizing transformation function from the DESeq2 package.
Assembly: GRCm38
Supplementary files format and content: RSPO3_Age_Endo_est_counts.txt

growth_protocol: None (mouse samples)

value: Lyve1Cre+, Rspo3 floxed


title: AR005, Control for Rspo3 KO HSC_2


title: Aerobic Exercise Training #3

city: Madison

middle: D

last: Bruss

state: WI

address: 201 West Lakeside Street

department: Medicine

institute: UW-Madison

description: Library name: AK_11N

data_processing:
Sequencing reads were adapter-trimmed using Skewer (v0.2.2b) (Jiang et al., 2014) and aligned to the Mus musculus GRCm38 genome assembly using STAR (v2.5.3a) (Dobin et al., 2013), a splice-junction-aware aligner.
Gene-level quantification of expected read counts was achieved using RSEM (v1.3.0; Li and Dewey, 2011) with annotation from Ensembl release 104.
Differential gene expression (DGE) analysis was conducted using edgeR (v3.34.0; Robinson et al., 2010). Prior to analysis, read counts were normalized using the trimmed mean of M-values (TMM) method to account for differences in library sizes (Robinson and Oshlack, 2010). Lowly expressed genes were filtered using edgeR’s filterByExpr function, requiring a minimum count-per-million (CPM) threshold of 10 in at least the smallest group of biological replicates.
Assembly: Mus musculus GRCm38 genome assembly
Supplementary files format and content: tab-delimited text file with raw counts for each sample

source_name: Gastrocnemius

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Mice allocated to AET (or AET + MET) were exercised on a 6-lane motorized treadmill (Columbus Instruments Exer 3/6 treadmill) 5 days/week, 60min/day for 8 weeks. For the AET + MET group, Metformin (Cayman chemical 13118) was provided in the drinking water at 2mg/mL and replaced weekly.

value: Gastrocnemius


title: Aerobic Exercise Training + Metformin #2

description: Library name: AK_12R


title: AS_Endo_R_1, Rspo3 KO EC_1

description:
AS_Endo_R_1
RSPO3_Age_Endo_est_counts.txt


title: AS_Endo_R_2, Rspo3 KO EC_2

description:
AS_Endo_R_2
RSPO3_Age_Endo_est_counts.txt


title: Gene expression of the 182 Danish ash accessions [ERR977751]


title: Gene expression of the 182 Danish ash accessions [ERR977750]


title: Tumor organoid with MRTX1133 treatment

city: Seongnam

first: Ji-Won

last: Kim

state: Gyeonggi-do

address: 82 Gumi-ro-173-beon-gil

department: Internal Medicine

country: South Korea

institute: Seoul National University Bundang Hospital

description: Library name: Resistant

data_processing:
The .fastq files were preprocessed using Cell Ranger version 7.0.1. Reads were aligned to the GRCh38 reference genome, including intronic regions. Subsequent analyses were performed using Scanpy verion 1.10.1. Quality control filtering exclude cells with (1) fewer than 200 detected genes, (2) less than 10,000 counts, and (3) mitochondrial content exceeding 20%. Doublets were removed using Scrublet implemented within Scanpy. 2,000 highly variable genes were indentified using the Pearson residual method. For clustering analysis, experession values were normalized using Pearson residuals. Log-transformed counts per million (logCPM) were used for expression visualization and Gene Set Variation Analysis (GSVA). Clustering was performed using the top 40 principal components, followed by neighborhood graph construction with default parameters and cluster identification via the Leiden algorithm at a resolutionof 0.4
Assembly: GRCh38
Supplementary files format and content: tab-separated files and matrix files

extract_protocol:
To generate MRTX1133-resistant patient-derived organoids, SNU-4646S1-TO cells were treated with MRTX1133. The half-maximal inhibitory concentration (IC50) of MRTX1133 for each model was calculated using the CellTiter-Glo assay (Promega, Madison, WI, USA). After MRTX1133 treatment, surviving cells were cultured in drug-free medium for 3 days before further treatment. The dosages used in this procedure were gradually increased from IC6.25 to IC50. After 6 months, the IC50 values of MRTX1133 in the resistant cell lines exceeded 1 mM. For the parental organoids, SNU-4646S1-TO cells were cultured for 6 months without MRTX1133 treatment. Normal organoids, SNU-4646S1-NO, were directly used for library extraction.
Library was constructed using Chromium Next GEM Single Cell 3' Reagent Kits version3.1 (10x Genomics)

value: epithelial cell


title: Tumor organoid without treatment

description: Library name: Parental

value: No


title: Gene expression of the 182 Danish ash accessions [ERR977749]


title: AS_Endo_C_3, Control for Rspo3 KO EC_3

description:
AS_Endo_C_3
RSPO3_Age_Endo_est_counts.txt

value: liver

value: Lyve1Cre-, Rspo3 floxed


title: Gene expression of the 182 Danish ash accessions [ERR977753]


title: AS_Endo_C_1, Control for Rspo3 KO EC_1

description:
AS_Endo_C_1
RSPO3_Age_Endo_est_counts.txt

value: 8 weeks old


title: AS_Endo_C_2, Control for Rspo3 KO EC_2

description:
AS_Endo_C_2
RSPO3_Age_Endo_est_counts.txt


title: Gene expression of the 182 Danish ash accessions [ERR977752]


title: RIBOMT

city: shanghai

first: Dengfeng

last: Huang

address: 301 Yanchang Middle Road

institute: Shanghai Tenth People's Hospital

data_processing:
The RNA-seq count data is converted by dividing the counts per kilobase by the total read counts (in millions).The Ribo-seq count data is calculated using TPM = counts per kilobase divided by total read counts (in millions)
Assembly: hg18
Supplementary files format and content: FPKM matrix
Library strategy: Ribo-seq

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen) following the manufacturer's instructions. In the processing of Ribo-seq, to block translational elongation, 100 µg/ml of cycloheximide was added to the cell culture medium, and the cell extracts were collected after treatment. Subsequently, ribosome-protected fragments (RFs) were generated by adding RNase I and DNase I, and rRNA was removed using an RNA purification kit and antisense DNA probes, ultimately constructing the Ribo-seq library.
Ribo-seq library was created using the NEBNext® Small RNA Library Prep Set for Illumina, RNA-seq cDNA using the NEBNext Ultra RNA Library Prep Kit for Illumina

value: ccRCC

value: overexpressing PHYHD1 (MT)


title: AS_Age_R_5, Aged Rspo3 KO HSC_5

description:
AS_Age_R_5
RSPO3_Age_Endo_est_counts.txt

value: LratCre+, Rspo3 floxed

value: 32 weeks old

value: male


title: AS_Age_R_4, Aged Rspo3 KO HSC_4

description:
AS_Age_R_4
RSPO3_Age_Endo_est_counts.txt


title: F_cmCis1

city: Kyoto

first: Tetsuro

last: Kusaba

state: Kyoto

address: 465 Kajii-cho, Kamigyo-ku

department: Department of Nephrology

country: Japan

institute: Graduate School of Medical Science, Kyoto Prefectural University of Medicine

data_processing:
Sequenced reads were mapped to the rat reference genome sequences (Rnor6) using STAR v 2.7.10a (https://github.com/alexdobin/STAR/) and uniquely mapped reads were counted by featureCounts function in the Subread package (https://subread.sourceforge.net).
Assembly: Rnor6
Supplementary files format and content: tab-delimited text files include  gene counts for each Sample

organism: Rattus norvegicus

growth_protocol: NRK52E and NRK49F were cultured in DMEM (Wako, Osaka, Japan) containing 1% penicillin and streptomycin (Invitrogen, Carlsbad, CA) and 5% FBS (Invitrogen) at 37°C in a humidified 5% CO2 and 95% air atmosphere.

extract_protocol:
Total RNA was extracted from NRK-52E and NRK-49F cells using TRIzol (Life Technologies, Carlsbad, CA) and Direct-zol RNA MiniPrep (Zymo Research, Irvine, CA)
Library preparation was performed using a TruSeq stranded mRNA sample prep kit (Illumina, San Diego, CA) according to the manufacturer’s instructions.

treatment_protocol: We administered cisplatin or vehicle to NRK52E when the culture reaches 50% confluence. After 6 hours, cells were rinsed two times in sterile PBS and the growth medium was replaced with DMEM containing 1% penicillin and streptomycin (Invitrogen) and 5% FBS (Invitrogen). The culture was then maintained for 24 hours to condition the medium.

value: Kidney fibroblast

value: Cis 40 CM


title: Gene expression of the 182 Danish ash accessions [ERR977747]

value: Leaves


title: Normal organoid

description: Library name: Normal


title: Gene expression of the 182 Danish ash accessions [ERR977746]


title: F_cmU3

value: Untreated CM


title: F_cmCis3


title: F_cmCis2


title: F_cmU2


title: Gene expression of the 182 Danish ash accessions [ERR977748]


title: Gene expression of the 182 Danish ash accessions [ERR977745]


title: Control sample 8

first: Ye-guang

last: Chen

address: Tsinghua Road, Medical Building

department: School of life science

institute: Tsinghua University

description: 10x Genomics

data_processing:
The initial demultiplexing of raw sequencing reads involved the utilization of Illumina bcl2fastq software, resulting in the generation of 150-bp paired-end read files in FASTQ format.
Subsequently, alignment of these reads to the GRCh38 human reference genome was executed using the Cell Ranger (v7.2.0) tool provided by 10X Genomics
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Colon

extract_protocol:
The fresh biopsy intestinal fragments from 2-3 volunteers were mixed into one tube, incubated with EDTA buffer, suspended and washed in cold PBS to obtain the crypt fractions as described above. Followed by shaking-incubated with digestive solution containing 1TrypLE Express (Gbico, 12604021) and 0.2 mg/ml DNase I (Thermo, EN0523) at 37℃ for 3-6 minutes, the single cells were centrifuged at 4℃ with 350g for 5 minutes. Then the cell pellets were resuspended and filtered through a 40 m cell strainer (BD). After centrifugating and discarding the supernatant, the cell sediments were stained with Zombie Dyes (Biolegend, 423105; 1:100 dilution) in the dark at the room temperature for 10 minutes. Zombie-negative cells were then sorted and collected by FACS analysis (BD, melody)
Single cells were captured in the 10X Genomics Chromium Single Cell 3′ Solution, and RNA-seq libraries were prepared according to the manufacturer’s protocol (10X Genomics). Then the libraries were sequenced on an Illumina Hiseq X Ten PE150 platform.

value: Colon


title: RIBOEV

value: empty vector


title: AS_Age_R_3, Aged Rspo3 KO HSC_3

description:
AS_Age_R_3
RSPO3_Age_Endo_est_counts.txt


title: Gene expression of the 182 Danish ash accessions [ERR977744]


title: Skyfall_no_earthworms_water

description: Column NW_Sky in gene counts matrix

data_processing:
Fastq reads were processed by Novogene (UK) in house perl scripts, to cleand the reads by removing the adapter, and remove low quality reads (Quality value) of over 50% bases of the read is <= 5). Reads containing N > 10% (N represents base that could not be determined) were also removed
Clean reads were mapped against the IWGSC V1.1 reference (https://wheat-urgi.versailles.inra.fr/Seq-Repository/Assemblies). Index of the genome was built with Hisat2 v2.0.5m and paired-end clean reads were aligned with the same programme.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene and FPKM were calculated based on the length of the gene and reads count mapped to this gene
Assembly: IWGSC V1.1 reference (https://wheat-urgi.versailles.inra.fr/Seq-Repository/Assemblies)
Supplementary files format and content: Gene reads count obtained with Featurecounts

organism: Triticum aestivum

growth_protocol: A commercially available wheat Skyfall (RAGT) and four landraces, YoGI_178, YoGI_203, YoGI_287 and YoGI_349, from the AE Watkins collection (Accession identifiers 1190336, 1190451, 1190779, respectively) and accession Shamrock from the Gediflux collection (all supplied by the John Innes Centre) were grown on soil collected from BSSE field, Leeds experimental farm which was hand-cleaned to remove earthworms, large stones and roots. The plants were germinated in wet tissue at room temperature for 6 days. Germinated seeds were transferred to the soil after this time, keeping two seedlings per pot. Four plants per treatment were used for a total of 80 plants. The plants were grown in a glasshouse 20°C±5°C daytime and 16°C±5°C night-time with a 16-hour photoperiod. High-pressure sodium lamps (Philips 400W), were used to supplement ambient sunlight conditions when  these fell below 150W m-2

extract_protocol:
RNA was extracted from two leaves (one leaf from each plant of the pot (two plants/pot)). The leaves were flash frozen in liquid nitrogen and stored at -80 °C until further processing. Plant material was ground whilst frozen using a Retsch MM200 ball mill and extracted for RNA using Omega Bio-Tek EZNA plant RNA kits according to manufacturer’s instructions. After extraction the four biological replicates were pooled into one at equal amounts of RNA.
The library was obtained using TruSeq Stranded mRNA (Illumina). The mRNA was purified using poly-T oligo attached magnetic beads, fragmented and the first strand cDNA synthesized using random hexamer primers, whilst the second strand cDNA using dUTP for directional library. End-repair, A-tailing, adapter ligation, size selection,USER enzyme digestion to remove the UTP-containing second strand cDNA, PCR amplification and purification
TruSeq stranded mRNA

treatment_protocol: The plants were watered for the first 38 days. drought plants were then no longer watered until the end of the experiment (53 days)/ Samples were collected on day 53 from the beginning of the experiment. Earthworms were collected from Warren paddock, a pasture field at Leeds experimental farm and earthworms treated plants had three earthworms in each pot to give an earthworm biomass of 0.59 ± 0.07 g per pot.

value: Skyfall (RAGT)


title: F_cmU1


title: AS_Age_R_2, Aged Rspo3 KO HSC_2

description:
AS_Age_R_2
RSPO3_Age_Endo_est_counts.txt


title: YoGI_349_no_earthworms_water

description: Column NW_349 in gene counts matrix

value: YoGI_349=Shamrock from the Gediflux collection


title: Gene expression of the 182 Danish ash accessions [ERR977743]


title: E_Cis3

value: Kidney epithelial cell

value: Cis 40


title: E_Cis2


title: Control sample 7

description: 10x Genomics


title: Gene expression of the 182 Danish ash accessions [ERR977742]


title: AS_Age_R_1, Aged Rspo3 KO HSC_1

description:
AS_Age_R_1
RSPO3_Age_Endo_est_counts.txt

value: liver


title: E_Cis1


title: Gene expression of the 182 Danish ash accessions [ERR977741]


title: AS_Age_C_4, Aged control_4

description:
AS_Age_C_4
RSPO3_Age_Endo_est_counts.txt

value: LratCre-, Rspo3 floxed


title: YoGI_287_no_earthworms_water

description: Column NW_287 in gene counts matrix

value: YoGI_287=Watkins collection accession identifier 1190779


title: AS_Age_C_5, Aged control_5

description:
AS_Age_C_5
RSPO3_Age_Endo_est_counts.txt


title: AS_Endo_R_3, Rspo3 KO EC_3

description:
AS_Endo_R_3
RSPO3_Age_Endo_est_counts.txt

value: Lyve1Cre+, Rspo3 floxed

value: 8 weeks old


title: Gene expression of the 182 Danish ash accessions [ERR977740]


title: E_Ctrl3

value: Control


title: YoGI_178_no_earthworms_water

description: Column NW_178 in gene counts matrix

value: YoGI_178=Watkins collection accession identifier 1190336


title: AS_Age_C_3, Aged control_3

description:
AS_Age_C_3
RSPO3_Age_Endo_est_counts.txt

value: 32 weeks old

value: male


title: Gene expression of the 182 Danish ash accessions [ERR977739]

value: Leaves


title: RIBOWT

value: ccRCC

value: WT


title: YoGI_203_no_earthworms_water

description: Column NW_203 in gene counts matrix

value: YoGI_203=Watkins collection accession identifier 1190451


title: Gene expression of the 182 Danish ash accessions [ERR977738]


title: AS_Age_C_2, Aged control_2

description:
AS_Age_C_2
RSPO3_Age_Endo_est_counts.txt


title: E_Ctrl1


title: YoGI_349_no_earthworms_drought

description: Column ND_349 in gene counts matrix


title: AS_Age_C_1, Aged control_1

description:
AS_Age_C_1
RSPO3_Age_Endo_est_counts.txt

value: 34 weeks old


title: Gene expression of the 182 Danish ash accessions [ERR977737]


title: YoGI_287_no_earthworms_drought

description: Column ND_287 in gene counts matrix


title: mouse_Mac_CCL3_3

city: changsha

first: Muqi

last: Liu

state: Hunan

address: No.138 Tongzipo Road, Yuelu District, Changsha

department: Institute for Cell Transplantation and Gene Therapy

institute: the 3rd Xiangya Hospital of Central South University

data_processing:
CLC Genomics Workbench v 11.0.1
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Mouse bone marrow-derived macrophages

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug oftotal RNA was used for the construction ofsequencing libraries
RNA libraries for RNA-seg were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Mouse bone marrow-derived macrophages


title: E_Ctrl2

value: Kidney epithelial cell


title: YoGI_178_no_earthworms_drought

description: Column ND_178 in gene counts matrix


title: mouse_Mac_CTRL3


title: mouse_Mac_CCL3_2


title: YoGI_203_no_earthworms_drought

description: Column ND_203 in gene counts matrix


title: Gene expression of the 182 Danish ash accessions [ERR977736]


title: Skyfall_earthworms_water

description: Column EW_Sky in gene counts matrix

value: Skyfall (RAGT)

value: Earthworm/Water


title: YoGI_349_earthworms_water

description: Column EW_349 in gene counts matrix

value: YoGI_349=Shamrock from the Gediflux collection


title: mouse_Mac_CCL3_1


title: Skyfall_no_earthworms_drought

description: Column ND_Sky in gene counts matrix


title: SB2

city: Hat Yai

first: Raphatphorn

last: Navakanitworakul

state: Songkhla

address: Department of Biomedical Sciences and Biomedical Engineering, Faculty Of Medicine, Prince of Songkla University

country: Thailand

institute: Prince of Songkla University

description:
Library name: sample 2
column name in raw count: SB2

data_processing:
The small RNA tags were mapped to reference sequence by Bowtie (Langmead et al., 2009) without mismatch or with only one mismatch to analyze their expression and distribution on the reference.
Assembly: Mapped small RNA tags were used to looking for known miRNA. miRBase22.0 was used as reference, modified software mirdeep2 (Friedlander et al., 2011) and srna-tools-cli were used to obtain the potential miRNA and draw the secondary structures. Custom scripts were used to obtain the miRNA counts as well as base bias on the first position of identified miRNA with certain length and on each position of all identified miRNA respectively
Supplementary files format and content: tab txt file includes raw count for each sample
Supplementary files format and content: csv file includes TPM for each sample

source_name: Blood plasma exosome form Imatinib sensitive

extract_protocol:
Total RNA was extracted using the miRNeasy Micro kit
3’ and 5’ adaptors were ligated to 3’ and 5’ end of small RNA, respectively. Then the first strand cDNA was synthesized after hybridazition with reverse transcription primer. The double-stranded cDNA library was generated through PCR enrichment. After purification and size selection, libraries with insertions between 18~40 bp were ready for sequencing. At least one of the samples has empty library name

value: Sensitive to Immatinib


title: Gene expression of the 182 Danish ash accessions [ERR977734]


title: Gene expression of the 182 Danish ash accessions [ERR977733]


title: Gene expression of the 182 Danish ash accessions [ERR977732]


title: SB1

description:
Library name: sample 1
column name in raw count: SB1

value: Blood plasma exosome form Imatinib sensitive


title: RB1

description:
Library name: sample 4
column name in raw count: RB1

source_name: Blood plasma exosome form Imatinib resistant

value: Resistant to Immatinib


title: RB2

description:
Library name: sample 5
column name in raw count: RB2

value: Blood plasma exosome form Imatinib resistant


title: SB3

description:
Library name: sample 3
column name in raw count: SB3


title: RB3

description:
Library name: sample 6
column name in raw count: RB3


title: YoGI_287_earthworms_water

description: Column EW_287 in gene counts matrix

value: YoGI_287=Watkins collection accession identifier 1190779


title: mouse_Mac_CTRL1


title: Gene expression of the 182 Danish ash accessions [ERR977731]


title: 2HREC, PBS, 24h

first: wenyi

last: wu

state: hunan

address: 87 xiangya road

department: ophthalmology

institute: xiangya hospital central south university

description:
Library name: Sample 5
PBS_treat_group_2

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: vascular

growth_protocol: human retina endothelial cells were maintained in Endothelial growth media  (EGM, Lonza, cat 1001) composed of 3% Fetal Bovine Serum (FBS) andEndothelial Cell Growth Supplements and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was isolated using TRIzol according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.

treatment_protocol: Normal vitreous and PBS was treat of 24 hours post confluent cells

value: vascular

value: human retina endothelial cells

value: primary cell

value: PBS treat


title: 1HREC, PBS, 24h

description:
Library name: Sample 4
PBS_treat_group_1


title: RSCY-8, HSC depleted_3

last: Sugimoto

address: 1130 Saint Nicholas Avenue

institute: Columbia University

data_processing:
For each sample, a minimum of 20 million 100-bp single-end reads were sequenced on an Illumina NovaSeq 6000.
RTA (Illumina) was used for base calling and bcl2fastq.gz2 (v.2.19 and v.2.20) for converting BCL to fastq.gz format, coupled with adaptor trimming.
A pseudoalignment to a kallisto index was created from transcriptomes (human, GRCh38; mouse, GRCm38) using kallisto (0.44.0).
To explore similarities and dissimilarities between samples, count data were normalized using the variance stabilizing transformation function from the DESeq2 package.
Assembly: GRCm38
Supplementary files format and content: h5 format raw counts

value: liver

value: LratCre+, iDTR het

value: 8 weeks old

value: male


title: Gene expression of the 182 Danish ash accessions [ERR977730]

data_processing:
Trimmomatic
Salmon 0.8
tximport in R
Assembly: Fraxinus excelsior 2451S ONT; PRJNA865134
Supplementary files format and content: tximport_182.txt

value: Leaves


title: YoGI_203_earthworms_water

description: Column EW_203 in gene counts matrix

value: YoGI_203=Watkins collection accession identifier 1190451


title: YoGI_178_earthworms_water

description: Column EW_178 in gene counts matrix

value: YoGI_178=Watkins collection accession identifier 1190336

value: Earthworm/Water


title: AS_Endo_C_4, Control for Rspo3 KO EC_4

description:
AS_Endo_C_4
RSPO3_Age_Endo_est_counts.txt

value: Lyve1Cre-, Rspo3 floxed


title: RSCY-6, HSC depleted_1


title: Skyfall_earthworms_drought

description: Column ED_Sky in gene counts matrix

value: Skyfall (RAGT)

value: Earthworm/drought


title: YoGI_349_earthworms_drought

description: Column ED_349 in gene counts matrix

value: YoGI_349=Shamrock from the Gediflux collection


title: Gene expression of the 182 Danish ash accessions [ERR977728]


title: 3HREC, Normal vitreous, 24h

description:
Library name: Sample 3
Normal_vitreous_3

value: normal vitreous treat


title: RSCY-5, Control for HSC depleted_3

value: LratCre+, iDTR wt


title: RSCY-7, HSC depleted_2


title: 1HREC, Normal vitreous, 24h

description:
Library name: Sample 1
Normal_vitreous_1

value: vascular

value: human retina endothelial cells


title: YoGI_287_earthworms_drought

description: Column ED_287 in gene counts matrix

value: YoGI_287=Watkins collection accession identifier 1190779


title: Gene expression of the 182 Danish ash accessions [ERR977727]


title: 2HREC, Normal vitreous, 24h

description:
Library name: Sample 2
Normal_vitreous_2

value: primary cell


title: mouse_Mac_CTRL2

value: Mouse bone marrow-derived macrophages


title: Gene expression of the 182 Danish ash accessions [ERR977729]


title: Gene expression of the 182 Danish ash accessions [ERR977726]


title: RSCY-3, Control for HSC depleted_1

value: liver

value: 8 weeks old


title: 2HUVEC Cells, Normal vitreous, 24h

description:
Library name: Sample 2
HUNorVit_2

data_processing:
Illumina Casava 1.8 software used for basecalling
Raw data (raw reads) of fastp 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 Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes gene count for all Sample

growth_protocol: human umbilical vein endothelial cells were maintained in Endothelial culture medium (ECM, ScienCell, cat 1001) composed of 5% Fetal Bovine Serum (FBS)  and endothelial cell growth supplements (ECGS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

value: human umbilical vein endothelial cells


title: 1HUVEC Cells, PBS, 24h

description:
Library name: Sample 3
HUPBSTreat

value: PBS treat


title: Gene expression of the 182 Danish ash accessions [ERR977725]

value: Leaves


title: Gene expression of the 182 Danish ash accessions [ERR977735]


title: YoGI_203_earthworms_drought

description: Column ED_203 in gene counts matrix

value: YoGI_203=Watkins collection accession identifier 1190451


title: RSCY-4, Control for HSC depleted_2

value: male


title: YoGI_178_earthworms_drought

description: Column ED_178 in gene counts matrix

value: YoGI_178=Watkins collection accession identifier 1190336


title: mouse eye, 3PD, rep 1

city: Canberra

first: Ulrike

last: Schumann

state: ACT

address: 131 Garran Road

country: Australia

institute: The Australian National University

description: fresh-frozen Visium spatial transcriptomics

data_processing:
*library strategy: Visium spatial transcriptomics
sequencing data and images were processed using the 10X Genomics Space Ranger software and reads aligned to the mm10 genome.
Assembly: mm10
Supplementary files format and content: aligned_fiducials.jpg: image of the alignment of tissue with fiducial frame
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: detected_tissue_image.jpg:  image of spots overlapped with tissue
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in matrix market file format
Supplementary files format and content: scalefactors_json.json: scalefactors in Java Script Object Notation file format
Supplementary files format and content: tissue_hires_image.png: high resolution image file of tissue
Supplementary files format and content: tissue_lowres_image.png: low resolution image file of tissue
Supplementary files format and content: tissue_positions_list.list.csv: List of spatial barcodes and corresponding spot position coordinates

source_name: 6-week old mouse eye

growth_protocol: 6-week old WT C57BL6/J mice were utilised for this experiment

extract_protocol:
Mice were culled by cervical dislocation. The superior of the eye was marked and eyes enucleated and briefly washed in PBS. Eye were immediately fresh frozen in optimal cutting medium in a liquid N2/Isopentane cooling bath. Embedded eyes were stored at -80C until processing. 10um parasaggital eye sections were subjected to the 10X Genomics Visium spatial gene expression protocol according to manufacturer's instructions.
According to the 10c Genomics Visium spatial gene expression protocol.

treatment_protocol: Mice were exposed to 100K lux white LED light continuously for 1, 3 or 5 days. Dim-reared mice were used as controls. Two biological replicates were performed

value: 6-week old mouse eye

value: 3-day photo-oxidative damage


title: 1HUVEC Cells, Normal vitreous, 24h

description:
Library name: Sample 1
HUNorVit_1

value: normal vitreous treat


title: mouse eye, 5PD, rep 1

value: 5-day photo-oxidative damage


title: Crossbred (SxHF) PBMC infected with M. tuberculosis H37Rv,rep3

city: Hyderabad

first: Bappaditya

last: Dey

state: Telangana

address: Survey No. 37, Extended Q City Road, Gachibowli

country: India

institute: National Institute of Animal Biotechnology

data_processing:
The raw fastq reads were preprocessed using Fastp v.0.20.1 using default parameters.
The processed reads were aligned to the STAR indexed Bos taurus ARS-UCD1.2.107 genome using STAR aligner v 2.7.9a (parameters:’--outSAMtype’ BAM SortedByCoordinate, ‘--outSAMunmapped’ Within, ‘--quantMode’, TranscriptomeSAM, '--outSAMattributes' Standard--outFilterScoreMinOverLread 0.33 --outFilterMatchNminOverlread 0.33)
The alignment file (sorted BAM) from individual samples were quantified using featureCounts v. 0.46.1 based on the rRNA filtered GTF file to obtain gene counts
Gene counts were used as inputs to DESeq2  for differential expression estimation (parameters: threshold of statistical significance --alpha 0.05; p-value adjustment method: BH). The DESeq2 result files were filtered based on adjusted p-value <= 0.05 and Log2FoldChange ∓ 1.
Assembly: Bos taurus ARS-UCD1.2.107
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

organism: Bos taurus

source_name: PBMC

extract_protocol:
RNA was isolated from bovine PBMC using the RNeasy Plus Mini Kit (QIAGEN) in accordance with the manufacturer’s instructions.
The library preparation was carried out using TrueSeq stranded Total RNA kit following manufacturing protocol.

value: PBMC

value: Infected with M. tuberculosis H37Rv


title: Gene expression of the 182 Danish ash accessions [ERR977722]


title: Crossbred (SxHF) PBMC infected with M. tuberculosis H37Rv,rep2


title: RPE-1_100ng/ml TNFa_3day_4

city: Tarrytown

first: Kun

last: Xiong

address: 777 Old Saw Mill River Road

department: Molecular Profiling and Data Science

institute: Regeneron Pharmaceuticals

description: Library name: X1707906

data_processing:
Sequencing reads were processed with ArrayStudio RNA-seq pipeline to quantify gene expression levels. For reference, we used b37 genome reference.
Assembly: B37.3
Supplementary files format and content: tab-delimited text files include raw counts for each sample

source_name: RPE-1 hTERT

extract_protocol:
RNA was extracted from cell pallets preserved in TRIzol reagent (Thermo Fisher) using MagMax-96 total RNA isolation kit (Thermo Fisher). RNA concentration was quantified using NanoDrop Spectrophotometer (NanoDrop Technologies), and the integrity was assessed using Fragment Analyzer (Agilent).
Strand-specific total RNA-seq libraries were prepared using Kapa RNA HyperPrep kit (Roche) with Fastselect rRNA HMR ribosome RNA removal kit (Qiagen).

value: RPE-1 hTERT

value: retinal pigment epithelial cell

value: WT

value: TNFa


title: mouse eye, 1PD, rep 1

value: 1-day photo-oxidative damage


title: RPE-1_100ng/ml TNFa_3day_3

description: Library name: X1707905


title: RPE-1_100ng/ml TNFa_3day_5

description: Library name: X1707907


title: Crossbred (SxHF) PBMC infected with M. tuberculosis H37Rv,rep1


title: mouse eye, DR, rep 1

value: dim-reared control


title: Gene expression of the 182 Danish ash accessions [ERR977721]

extract_protocol:
Harper et al., 2016, https://doi.org/10.1038/srep19335
100 bp Illumina HiSeq reads


title: Gene expression of the 182 Danish ash accessions [ERR977720]


title: Sahiwal PBMC infected with M. tuberculosis H37Rv,rep3


title: RPE-1_100ng/ml TNFa_3day_2

description: Library name: X1707904


title: Sahiwal PBMC infected with M. tuberculosis H37Rv,rep2


title: mouse eye, 5PD, rep 2


title: Gene expression of the 182 Danish ash accessions [ERR977724]


title: Gene expression of the 182 Danish ash accessions [ERR977723]


title: Gene expression of the 182 Danish ash accessions [ERR977719]


title: mouse eye, 3PD, rep 2


title: RPE-1_100ng/ml TNFa_3day_1

description: Library name: X1707903


title: Sahiwal PBMC infected with M. tuberculosis H37Rv,rep1


title: RPE-1_100ng/ml IL6/sIL6R_3day_5

description: Library name: X1707897


title: Crossbred (SxHF) PBMC infected with M. bovis BCG,rep2

value: PBMC infected with M. bovis BCG

value: Infected with M. bovis BCG


title: RNA-seq, Beige Ad. Diff. 8d, rep3

city: Gwangju

first: Daehwa

last: Youn

address: 123 Cheomdangwagi-ro, Buk-gu

department: Department of Biomedical Science & Engineering

institute: Gwangju Institute of Science and Technology (GIST)

data_processing:
RNA-seq reads were mapped to the contaminant sequences, including rRNA, tRNA, and srpRNA, using hisat2. Mapped readswere filtered out.
RNA-seq reads were aligned to genome by hisat2.
RNA-seq reads mapped within the repeat regions (repeatmasker) were filtered out.
The read count table of RNA-seq dataset were generated by featureCounts.
Assembly: Mouse (GRCm39)
Supplementary files format and content: A tab-delimited text file include RNA-seq read counts for each sample

source_name: iWAT preadipocyte

extract_protocol:
Cultured cells were washed two times with 1X Phosphate-base buffer (PBS) and then incubated for 30 min on ice with the lysis buffer (10 mM/mL Tris-HCl, pH 7.4 (AM9850G, AM9855G, Invitrogen); 5 mM/mL MgCl2 (#AM9530G, Invitrogen); 100 mM/mL KCl (#AM9640G, Invitrogen); 2 mM/mL dithiothreitol (DTT, #707265ML, Thermo Fisher); 100 μg/mL cycloheximide (CHX, #C1988, Sigma‒Aldrich); 1% Triton X-100 (#T8787, Sigma‒Aldrich); 1X protease inhibitor (#539134, Sigma-Aldrich); 2 μL/mL SUPERase inhibitor (#AM2696, Invitrogen); and 2 μL/mL RNase inhibitor (#AM2694, Invitrogen). After centrifuging the lysates at 20000 g for 15 min at 4 °C, the supernatant was separated into three portions for RNA-seq, Ribo-Seq, and Mass Spectrometry. For RNA-seq, the supernatant was treated with TRIzol LS (#10296028, Invitrogen) to isolate RNA.
After the purification of total RNA, libraries were constructed with TruSeq Stranded Total RNA Library Prep Gold (#20020599 Illumina) as per the manufacturer’s protocol, followed with sequencing via NovaSeq 6000 system.

treatment_protocol: Adipocyte precursors were exposed to a differentiation induction media containing 2 μg/mL dexamethasone, 0.5 mmol/L 3-isobutyl-1-methylxanthine, 125 μmol/L indomethacin, 5 μg/mL insulin, 1 μmol/L 3,3′,5-triiodo-L-thyronine, and 0.5 μmol/L rosiglitazone. After a two-day induction period, the cells were cultured in maintenance media without 3-isobutyl-1-methylxanthine, indomethacin, and dexamethasone, with media changes every two days.

value: iWAT preadipocyte

value: Beige adipocyte differentiation induction media

tag: time

value: 8 days differentiation

tag: library type

value: RNA-seq


title: Gene expression of the 182 Danish ash accessions [ERR977718]

value: Leaves


title: Gene expression of the 182 Danish ash accessions [ERR977717]


title: RPE-1_100ng/ml IL6/sIL6R_3day_4

description: Library name: X1707896


title: RNA-seq, Beige Ad. Diff. 8d, rep2


title: mouse eye, DR, rep 2

value: 6-week old mouse eye


title: Crossbred (SxHF) PBMC infected with M. bovis BCG,rep3


title: mouse eye, 1PD, rep 2


title: RNA-seq, Beige Ad. Diff. 8d, rep1


title: Sahiwal PBMC infected with M. bovis BCG,rep3


title: RNA-seq, Beige Ad. Diff. 4d, rep3

value: 4 days differentiation


title: Crossbred (SxHF) PBMC infected with M. bovis BCG,rep1

value: PBMC


title: Sahiwal PBMC infected with M. bovis BCG,rep2


title: Sahiwal PBMC infected with M. bovis BCG,rep1


title: RNA-seq, Beige Ad. Diff. 4d, rep2


title: Crossbred (SxHF) PBMC control,rep3

value: PBMC control

value: Uninfected


title: RNA-seq, Beige Ad. Diff. 4d, rep1


title: Gene expression of the 182 Danish ash accessions [ERR977711]


title: Gene expression of the 182 Danish ash accessions [ERR977714]


title: Gene expression of the 182 Danish ash accessions [ERR977713]


title: Gene expression of the 182 Danish ash accessions [ERR977712]


title: Gene expression of the 182 Danish ash accessions [ERR977716]


title: RNA-seq, Beige Ad. Diff. 0d, rep3


title: Crossbred (SxHF) PBMC control,rep2


title: RNA-seq, Beige Ad. Diff. 0d, rep2


title: Gene expression of the 182 Danish ash accessions [ERR977715]


title: Gene expression of the 182 Danish ash accessions [ERR977710]


title: Crossbred (SxHF) PBMC control,rep1


title: Sahiwal PBMC control,rep3


title: Gene expression of the 182 Danish ash accessions [ERR977778]


title: Gene expression of the 182 Danish ash accessions [ERR977709]


title: RNA-seq, Beige Ad. Diff. 0d, rep1


title: STAT3-control-2

first: zhiguang

last: chang

address: No. 1068, Xueyuan Avenue, Shenzhen University Town, Xili, Nanshan District

institute: Chinese Academy of Sciences

description:
Library name: STAT3-control-2
replicable biosample 2

data_processing:
Raw fastq files were processed with fastp (version 0.23.2) to remove adapter sequences and low-quality reads. The quality, adapter content, and duplication rates were assessed using FastQC (version 0.11.9). Cleaned reads were aligned to the mouse reference genome (NCBI build 37, mm9) using Bowtie2 (version 2.4.4), and duplicate alignments were removed using the MarkDuplicates tool in Picard (version 2.25.0). Genome-wide coverage files for H3K27ac, STAT3, H3K4me3, and immunoglobulin G (IgG) were generated using the bamCoverage tool from deepTools (version 3.5.0) (Ramírez et al., 2014). Peaks were called using MACS2 and annotated with the annotatePeaks.pl script from the Homer software suite. Genome region visualizations were created using the Integrative Genomics Viewer (IGV).
Supplementary files format and content: tab-delimited text file includes the PEAK information for each sample
Library strategy: CUT&Tag

source_name: Jurkat

extract_protocol:
Processed samples were incubated with 10 μl of Concanavalin A-coated magnetic beads (NovoNGS® Concanavalin A-coated Magnetic Beads, N251). Bead-bound cells were suspended in Dig Wash Buffer and incubated with antibodies targeting STAT3 (Proteintech, 10253-2-ap), H3K27ac (Abcam, ab4729), or H3K4me3 (Abcam, ab8580) at 4 °C overnight. Subsequently, cells were incubated with secondary antibodies for 60 minutes, followed by incubation with pA-Tn5 adapter complexes for 1 hour.
The samples were then resuspended in fragmentation buffer and incubated at 37 °C for 1 hour. DNA was purified using phenol-chloroform-isoamyl alcohol extraction and ethanol precipitation. The sequencing was performed on the Illumina Novaseq6000 platform using 150 bp paired-end reads.

value: Jurkat

value: Pre-exposure (direct sample collection)


title: Sahiwal PBMC control,rep2


title: Ribo-seq, Beige Ad. Diff. 8d, rep3

data_processing:
Adaptor sequences were trimmed by the cutadapt tool.
Ribo-seq reads were mapped to the contaminant sequences, including rRNA, tRNA, and srpRNA, using hisat2. Mapped readswere filtered out.
Ribo-seq reads were aligned to genome by hisat2.
Ribo-seq reads mapped within the repeat regions (repeatmasker) were filtered out.
The read count table of Ribo-seq dataset were generated by featureCounts.
Assembly: Mouse (GRCm39)
Supplementary files format and content: A tab-delimited text file include Ribo-seq read counts for each sample
Library strategy: Ribo-seq

extract_protocol:
Cultured cells were washed two times with 1X Phosphate-base buffer (PBS) and then incubated for 30 min on ice with the lysis buffer (10 mM/mL Tris-HCl, pH 7.4 (AM9850G, AM9855G, Invitrogen); 5 mM/mL MgCl2 (#AM9530G, Invitrogen); 100 mM/mL KCl (#AM9640G, Invitrogen); 2 mM/mL dithiothreitol (DTT, #707265ML, Thermo Fisher); 100 μg/mL cycloheximide (CHX, #C1988, Sigma‒Aldrich); 1% Triton X-100 (#T8787, Sigma‒Aldrich); 1X protease inhibitor (#539134, Sigma-Aldrich); 2 μL/mL SUPERase inhibitor (#AM2696, Invitrogen); and 2 μL/mL RNase inhibitor (#AM2694, Invitrogen). After centrifuging the lysates at 20000 g for 15 min at 4 °C, the supernatant was separated into three portions for RNA-seq, Ribo-Seq, and Mass Spectrometry. For Ribo-seq, the supernatant was treated with 3 U/mL RNase I (#EN0601, Thermo Fisher) for 30 min at 25 °C to digest mRNA regions not associated with ribosomes. The samples were passed through MicroSpin S400 HR Columns (#27-5140-01, Cytiva), and prewashed with a polysome buffer (20 mM HEPES-KOH, pH 7.4 (#H0887, Sigma‒Aldrich); 5 mM MgCl2; 100 mM KCl; 2 mM DTT; and 100 μg/mL CHX). The filtered samples of ribosome-protected mRNA-containing lysate excluding the digested mRNA fragments were treated with TRIzol LS to isolate RNA. Ribosomal RNAs were removed using a Ribo-Zero Gold Kit of the TruSeq Stranded Total RNA Library Prep Gold protocol (#20020599 Illumina). The RNA samples were then precipitated in 100% ethanol (#A995-1, Thermo Fisher) at -20 °C and labeled with the radioisotope γ-P32 ATP (#NEG-502H-1 PerkinElmer) using T4 Polynucleotide kinase (T4 PNK, #M0201L New England Biolabs) and separated on a 10% denaturing Urea-PAGE (#U5128, Sigma‒Aldrich) gel. The signals were visualized using an Amersham Typhoon Biomolecular imager (v2.0.0.6 GE Healthcare). Following the analysis of radioisotope signals with MultiGauge (v3.0) software, the gel was excised to isolate RNA samples of approximately 30 nucleotides. The extracted RNA from a gel with RNA elution buffer (0.3M NaOAc, #AM9740, Invitrogen; 2% sodium dodecyl sulfate) was then dephosphorylated using Antarctic Phosphatase (#M0289S New England Biolabs) and relabeled with γ-P32 ATP using the T4 PNK reaction. The labeled samples were separated on a 10% denaturing Urea-PAGE gel to remove free ATPs, followed by gel excision and RNA extraction.
Adapter ligation and PCR amplification were performed using a RealSeq®-AC miRNA Library Kit (#500-00048, RealSeq Biosciences). The adapter-ligated PCR products were purified with SPRIselect magnetic beads and then subjected to sequencing in the NovaSeq 6000 system.


title: Gene expression of the 182 Danish ash accessions [ERR977708]


title: STAT3-control-1

description:
Library name: STAT3-control-1
replicable biosample 1

value: WT


title: Sahiwal PBMC control,rep1


title: Gene expression of the 182 Danish ash accessions [ERR977707]


title: Gene expression of the 182 Danish ash accessions [ERR977706]


title: STAT3-re_stimu_2

description:
Library name: STAT3-re_stimu_2
replicable biosample 2

value: Subsequent exposure (same as Rest, with an additional 6-h stimulation with 10 ng/ml IL-10)


title: Pulmosphere,M.tb,24hrs,rep1

data_processing:
The raw fastq reads were preprocessed using Fastp v.0.20.1 (parameters: --trim_front1 9 --trim_front2 9 --length_required 50 --correction--trim_poly_g --qualified_quality_phred 30)
The processed reads were aligned to the STAR indexed Bos taurus ARS-UCD1.2 genome using STAR aligner v 2.7.9a (parameters:’--outSAMtype’ BAM SortedByCoordinate, ‘--outSAMunmapped’ Within, ‘--quantMode’, TranscriptomeSAM, '--outSAMattributes' Standard)
The alignment file (sorted BAM) from individual samples were quantified using featureCounts v. 0.46.1 based on the rRNA filtered GTF file to obtain gene counts
Gene counts were used as inputs to DESeq2  for differential expression estimation (parameters: threshold of statistical significance --alpha 0.05; p-value adjustment method: BH). The DESeq2 result files were filtered based on adjusted p-value <= 0.05 and Log2FoldChange ∓ 1.
Assembly: Bos taurus ARS-UCD1.2
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

source_name: Lung

extract_protocol:
RNA was isolated from pulmospheres using the RNeasy Plus Mini Kit (QIAGEN) in accordance with the manufacturer’s instructions.
The library preparation was carried out using TrueSeq stranded Total RNA kit following manufacturing protocol.

value: Lung

value: Primary cell

value: Lung mixed cells


title: Gene expression of the 182 Danish ash accessions [ERR977705]


title: STAT3-re_stimu_1

description:
Library name: STAT3-re_stimu_1
replicable biosample 1


title: Pulmosphere,M.tb,24hrs,rep2


title: STAT3-interval_2

description:
Library name: STAT3-interval_2
replicable biosample 2

value: Rest (stimulated with 10 ng/ml IL-10 for 6 h, washed, and cultured for 48 h in 0.5 ng/ml IL-10 with medium changes every 12 h)


title: Pulmosphere,BCG,24hrs,rep3

value: BCG-infected


title: STAT3-interval_1

description:
Library name: STAT3-interval_1
replicable biosample 1


title: Ribo-seq, Beige Ad. Diff. 4d, rep1

value: iWAT preadipocyte

value: Beige adipocyte differentiation induction media


title: Ribo-seq, Beige Ad. Diff. 8d, rep1

value: 8 days differentiation


title: Ribo-seq, Beige Ad. Diff. 8d, rep2


title: Pulmosphere,M.tb,24hrs,rep3


title: Gene expression of the 182 Danish ash accessions [ERR977703]

value: Leaves


title: Ribo-seq, Beige Ad. Diff. 4d, rep3

value: 4 days differentiation


title: Ribo-seq, Beige Ad. Diff. 4d, rep2


title: Gene expression of the 182 Danish ash accessions [ERR977704]


title: Pulmosphere,BCG,24hrs,rep2


title: STAT3-stimu_2

description:
Library name: STAT3-stimu_2
replicable biosample 2

value: Initial exposure (stimulated with 10 ng/ml IL-10 for 6 h)


title: Gene expression of the 182 Danish ash accessions [ERR977702]


title: STAT3-stimu_1

description:
Library name: STAT3-stimu_1
replicable biosample 1


title: H3K27ac-control-2

description:
Library name: H3K27ac-control-2
replicable biosample 2


title: Ribo-seq, Beige Ad. Diff. 0d, rep2


title: Pulmosphere,BCG,24hrs,rep1


title: Gene expression of the 182 Danish ash accessions [ERR977701]


title: Ribo-seq, Beige Ad. Diff. 0d, rep3


title: H3K27ac-control-1

description:
Library name: H3K27ac-control-1
replicable biosample 1


title: Ribo-seq, Beige Ad. Diff. 0d, rep1


title: Gene expression of the 182 Danish ash accessions [ERR977700]


title: Gene expression of the 182 Danish ash accessions [ERR977699]