title: H3K27ac ChIP-seq, fly adult, day45, replicate 3

description: Library name: day45-rep3-ip

value: whole body


title: w1_HS1hr37C_1hRec_antiIgG_rep2

status: Public on Feb 24 2026

type: SRA

city: Worcester

first: Samantha

last: Ho

state: MA

address: 373 Plantation St.

department: Department of Molecular Medicine

country: USA

institute: University of Massachusetts Chan Medical School

library_source: genomic

data_processing:
Cut and Run analysis was performed using piSet_chipseq pipeline on GitHub. Briefly, Bowtie2 (Version 2.2.5) was used to map sequencing reads to the Drosophila genome (dm6) and transposon consensus sequence, signal mapping to transposons were normalized to total number of genome mapping Cut and Run reads.
Assembly: dm6
Supplementary files format and content: bigWig files
Library strategy: CUT and RUN

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: Ovary

extract_protocol:
Ovaries were dissected from 2-4 day flies and bound to ConA beads, incubated with primary antibody, DNA digested with pAMA and DNA was recovered.
Recovered DNA undergone library construction with the following steps: end repair, A-tailing, adaptor ligation, and PCR amplification.

treatment_protocol: Heat shock was carried on 2-4 day old flies with yeast for 1 hour in a water bath kept at 37oC. Flies were allowed to recover at room temp for designated times before proceeding with extraction and library construction.  No Shock control flies were kept at room temp as controls.

tag: tissue

value: Ovary

tag: genotype

tag: age

value: 2-4 day old

tag: treatment

value: Heat Shock for 1 hour at 37oC

tag: recovory time_after_heat_stress

value: 1 hour recovoery after heat stress

tag: cut-and-run antibody

value: guinea pig IgG


title: H3K27ac ChIP-seq, fly adult, day33, replicate 1

city: Bad Nauheim

first: Lei

last: Gu

state: Hessen

address: Parkstraße 1

department: Epigenetics

country: Germany

institute: Max Planck Institute for Heart and Lung Research

description: Library name: day33-rep1-ip

data_processing:
Raw reads were trimmed to remove adapter sequences and low-quality bases using Trim Galore v0.6.7 (--stringency 4, --length 35, --quality 25). The quality of the filtered reads was assessed using FastQC v0.11.8 and summarized with MultiQC v1.11. Trimmed reads were aligned to the human hg19 reference genome using HISAT2 v2.2.1 (--dta). Gene-level read counts and expression levels were quantified and normalized using StringTie v2.2.1 with default parameters.
Raw reads were trimmed to remove adapter sequences using Trim Galore v0.6.7 (--stringency 4, --length 35, --quality 20). The trimmed reads were aligned to the Drosophila dm6 reference genome using Bowtie2 v2.4.5 with default parameters. Peaks were identified using MACS2 v2.2.7.1. bigWig files were generated with deepTools bamCoverage v3.5.1, with scores representing normalized fragment coverage at 1 bp resolution.
Assembly: hg19 for RNA-seq; dm6 for ChIP-seq
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: bigWig

source_name: whole body

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (Qiagen). RNA quality (RIN > 9) was assessed using the TapeStation 4200 system (Agilent Technologies). Approximately 1 μg of RNA was used for sequencing library preparation.
Adult fruit flies were homogenized using a Dounce tissue grinder. Cells were fixed with 1% formaldehyde for 10 minutes, followed by quenching and cell lysis. Chromatin was then digested with micrococcal nuclease (MNase) at 37 °C for 15 minutes.
Preparation of RNA library and transcriptome sequencing was conducted by Biomarker Technologies (BMK) GmbH (Münster, Germany).
Preparation of ChIP library and sequencing was conducted by Biomarker Technologies (BMK) GmbH (Münster, Germany).


title: RNAPolIIempty rep2

city: Tianjin

first: Xueyang

last: Pang

state: Tianjin

address: 22 Meteorological Observatory Road, Heping District, Tianjin

country: China

institute: TMU

description: Library name: SAMPLES4

data_processing:
The CUT&Tag reads were checked for quality and trimmed using Fastp. Reads were aligned to the Ensembl hg38 human reference genome using Bowtie2 (version 2.4.4) with the options “--very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700 -p 12”. Duplicate reads were removed using Picard tools for downstream analyses. Samtools was used to convert the read format and sort the reads. To visualize the genomic occupancy from the transcription start site (TSS) to the transcription end site (TES), bam files were converted into BigWig files using the bamCoverage function from deepTools, with the parameter set to 'normalizeUsing RPKM'. Subsequently, computeMatrix and plotHeatmap from deeptools were used with the options “--beforeRegionStartLength 3000 --regionBodyLength 5000 --afterRegionStartLength 3000 --skipZeros -o”. Then MACS2 was employed for peak scanning across the entire genome with the option of “q 0.05”. ChIPseeker was used to annotate the positions of peaks within genomic features.
Assembly: hg38
Supplementary files format and content: BigWig

organism: Homo sapiens

growth_protocol: HEK293T was cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% FBS and 1% penicillin-streptomycin. All cells were maintained at 37℃ and 5% CO2.

extract_protocol:
The CUT&Tag assay was conducted using Hyperactive Universal the CUT&Tag Assay Kit for Illumina (Vazyme, Cat No. TD903) according to the manufacturer’s instructions.
80,000 cells were harvested and washed twice in wash buffer. Concanavalin A beads were then added to the cell suspension and incubated at room temperature for 10 mins. Bead-bound cells were separated from the supernatant and were resuspended in antibody buffer. Antibodies against RNA Pol II (Cell Signaling Technology, Cat No.14958, at 1:50 dilution), H3K4Me3 (Abcam, Cat No. ab12209, 1 μg), S9.6 (Absoluteantibody, Cat No. AB01137, with 1 μg), or IgG control (Cell Signaling Technology, Cat No.2729s, with 1 μg) were added to the cells, and incubated at 4°C overnight. For S9.6 CUT & Tag, 10 μg/μl of RNase A was supplemented as negative control. The following day, the secondary antibody diluted in dig-wash buffer was added to the beads and incubated at room temperature for 1 h. After incubation, beads were washed three times with dig-wash buffer. pA/G-Tnp transposomes diluted in dig-300 buffer were incubated with beads at room temperature for 1 h. After three washes with dig-300 buffer, samples were then tagmented with TTBL from the kit. After 1 h of tagmentation, proteinase K and spike-in were added. Fragmented DNA was purified using DNA Extract Beads. The eluted DNA was amplified using Illumina i7/i5 indexed primers. After that, VAHTS DNA Clean Beads (Vazyme #N411) were employed for the purification of the libraries, which were then subjected to quality control and Illumina sequencing.

treatment_protocol: HEK293 cells were transfected with pcDNA3.1 or pcDNA3.1-sigma3 (either WT or K287T mutant). At 48 h post-transfection, cells were treated with TNFa at 10 ng/ μl for 3 h

tag: cell line

tag: cell type

value: Human embryonic kidney 293

value: WT

value: TNF


title: H3K27ac ChIP-seq, fly adult, day33, replicate 3

description: Library name: day33-rep3-ip


title: RAM_BAL_KO_naive_rep1

city: Aurora

first: Qihua

last: Ye

state: CO

address: Research Complex II  12700 East 19th Avenue

department: Pulmonary

institute: University of Colorado Anschutz Medical Campus

description: Library name: RAM_BAL_KO_naive_rep1

library_source: transcriptomic

data_processing:
Raw fastq files were trimmed using cutadapt (4.2)
Aligned to reference genome GRCm38/mm10 using STAR (2.7.10b).
Picardtool (2.27.5) was used to collect strandedness information for each sample.
Raw gene-level counts were filtered to remove genes with low expression, retaining only those with >10 raw counts in at least 10 of the 27 total samples. This strategy removes genes with limited and inconsistent expression across the dataset while preserving those robustly detected across multiple samples.
Normalized counts were acquired using DESeq2 (1.38.2) in R (4.2.2).
The log fold change shrunk gene set enrichment analysis (GSEA) was performed using fgsea (1.24.0) in R (4.2.2).
Assembly: GRCm38/mm10
Supplementary files format and content: .csv file for raw counts, normalized counts

molecule: total RNA

organism: Mus musculus

source_name: lung lavage

extract_protocol:
RNA was isolated from freshly sorted cells using micro RNA kit (Qiagen, Germantown, MD), following manufacturer's protocols.
RNA purity, quantity, and integrity were determined by NanoDrop (ThermoFisher Scientific, Waltham, MA) and TapeStation 4200 (Agilent, Santa Clara, CA) analyses prior to RNA-seq library preparation. MGIEasy RNA Library Prep Set (3.1, cat. 1000006384) was used to generate libraries with an input of 100 ng of total RNA.

value: lung lavage

value: RAMs

value: KO

value: naïve

tag: timepoint (day)


title: w1_HS1hr37C_1hRec_antiIgG_rep1


title: RNAPolIIK287T rep1

description: Library name: SAMPLES3

value: SIGMA3K287T OVEREXPRESSION


title: w1_noHS_control_antiRhi_rep3

value: No heat shock

value: Rhino


title: RAM_BAL_WT_naive_rep3

description: Library name: RAM_BAL_WT_naive_rep3


title: RAM_BAL_WT_naive_rep2

description: Library name: RAM_BAL_WT_naive_rep2


title: RNAPolIIWT rep1

description: Library name: SAMPLES2

value: SIGMA3 OVEREXPRESSION


title: H3K27ac ChIP-seq, fly adult, day20, replicate 3

description: Library name: day20-rep3-ip

value: whole body


title: w1_noHS_control_antiRhi_rep2

value: Ovary


title: H3K27ac ChIP-seq, fly adult, day20, replicate 1

description: Library name: day20-rep1-ip


title: H3K27ac ChIP-seq, fly adult, day33, replicate 2

description: Library name: day33-rep2-ip


title: H3K27ac ChIP-seq, fly adult, day20, replicate 2

description: Library name: day20-rep2-ip


title: RNAPolIIempty rep1

description: Library name: SAMPLES1


title: RAM_BAL_WT_naive_rep1

description: Library name: RAM_BAL_WT_naive_rep1


title: diplod  EE2 group rep3

city: Liběchov

first: Tomáš

last: Tichopád

address: Rumburská 89

country: Czech Republic

institute: ÚŽFG

description: Library name: D22

data_processing:
bbduk.sh \ in1="$i"R1_001.fastq.gz \ in2="$i"R2_001.fastq.gz \ out1="$i"_sequenceclean1.fastq.gz \ out2="$i"_sequenceclean2.fastq.gz \ ktrim=r \ k=23 \ mink=11 \ hdist=1 \ ftm=5 \ tpe \ tbo \ ref=/bbmap/resources/adapters.fa \ qtrim=rl \ trimq=10 \ maq=10 \ minlen=40 done
for i in $(find -type f -name "*.fastq.gz" | while read F; do basename "$F" | rev | cut -c 34- | rev; done | sort | uniq) do     /home/tichopad/bbmap/bbduk.sh \         in1="${i}_ME_L001__sequenceclean1.fastq.gz" \         in2="${i}_ME_L001__sequenceclean2.fastq.gz" \         k=25 \         ref=smr_v4.3_default_db.fasta \         out1="${i}_rRNAsequclean1.fastq" \         out2="${i}_rRNAsequclean2.fastq" \ done
STAR --runMode genomeGenerate --runThreadN 18 --genomeDir index_zebra --genomeFastaFiles Danio_rerio.GRCz11.dna.toplevel.fa --sjdbGTFfile Danio_rerio.GRCz11.113.gtf --sjdbOverhang 79
for sample in $(ls *_rRNAsequclean1.fastq | sed 's/_rRNAsequclean1.fastq//') do     STAR --genomeDir index_zebra \          --runThreadN 8 \          --outSAMtype BAM SortedByCoordinate \          --outSAMstrandField intronMotif \          --readFilesIn "${sample}_rRNAsequclean1.fastq" "${sample}_rRNAsequclean2.fastq" \          --outFileNamePrefix /zebra/bam_results_102_2/"$sample" done
featureCounts -p --countReadPairs -T 18 -s 2 -t exon -a Danio_rerio.GRCz11.113.gtf -o counts_zebra.txt *.bam
Assembly: Danio_rerio.GRCz11.dna.toplevel.fa
Supplementary files format and content: counts_zebra.txt

organism: Danio rerio

source_name: testis

extract_protocol:
Male gonads were collected into 2 ml tubes and stored at − 80 °C freezer. Samples were homogenized using TissueLyser LT (Qiagen) for 10 min at 50 Hz. Total RNA was isolated using 1 ml of TRI Reagent (Sigma-Aldrich, T9424) following the manufacturer’s manual. The RNA pellet was then dissolved in 40 μl DNAse solution (32 μl Nuclease-free water, 4 μl 10x reaction buffer, 4 μl DNAse I, Sigma-Aldrich, AMPD I), and incubated at 37 °C for 30 min. Afterwards, 40 μl of 8 M LiCl (Sigma-Aldrich, L7026) were added for RNA precipitation. This solution was incubated overnight in − 20 °C freezer and then centrifuged for 30 min at 16,000 g. The supernatant was removed, and the RNA was then washed twice with 1 ml of 80% ethanol followed by centrifugation for 30 min. The final total RNA was diluted in 20 μl of 1xTE buffer (Invitrogen, 12,090–015). The concentration of RNA was measured using Nanodrop 8000 (Thermo Scientific), and the quality of RNA was analysed using Fragment Analyzer (AATI, Standard Sensitivity RNA analysis kit, DNF-471). Only samples with RQN higher than 6.9 were used for the following analysis.
SureSelect Strand-Specific mRNA library protocol was used for library preparation with 360 ng mRNA as input. All steps were according to the manufactory manual with one exception; RiBO cop Select and Deplete rRNA Depletion Kit V1.2 (Lexogen) was used for rRNA depletion instead of poly-A method. Final libraries were pooled and controlled with DNF-474-0500 HS NGS Fragment kit (1-6000bp) using Fragment Analyzer (AATI) according to the manual.

treatment_protocol: exposure to 17α-ethinyl estradiol (EE2) in 2n  and 3n zebrafish

value: testis

value: AB strain

value: Ethinylestradiol


title: w1_noHS_control_antiIgG_rep3

value: 2-4 day old

value: guinea pig IgG


title: H3K27ac ChIP-seq, fly adult, day13, replicate 2

description: Library name: day13-rep2-ip


title: FgSj-b

city: Debrecen

first: Laszlo Attila

last: Papp

state: Hajdú-Bihar Vármegye

address: Egyetem tér 1.

department: Department of Genetics and Applied Microbiology

country: Hungary

institute: University of Debrecen

data_processing:
Alignment with HISAT2 aligner
Generation of BAM files
FeatureCount values were generated using Liao Y, Smyth GK and Shi W (2014). featureCounts software.
Quantification and normalization using StrandNGS with DeSeq algorithm
Assembly: In case of S. japonicus yFS275 was used.
Supplementary files format and content: Fgsj_SJG_all_genes.txt file contains the tab delimited raw count values of S. japonicus control (SJG) vs S. japonicus co-cultured (FgSj).
Supplementary files format and content: FgSj_SJG_medT-test_with_BH-FDR.xlsx file contains the normalized data with statistics (moderated T-test, BH-FDR).

organism:
Fusarium graminearum
Schizosaccharomyces japonicus yFS275

source_name: Co-cultured S. japonicus with F. graminearum (FgSj - S. japonicus co-cultured)

growth_protocol: Control S. japonicus cells were grown on YEA (yeast-extract agar) media. Control F. graminearum cells were grown on MXGB media. Both strains were cultured at 25°C.

extract_protocol:
RNA were extracted from cells using the method described by Lyne et al. (2003).RNA quality was checked with Agilent BioAnalyzer.
RNA libraries for RNA-seq were prepared using NEBNext Ultra II RNA Library Prep kit for Illumina

treatment_protocol: In case of co-culturing conditions: 100 µl.of overnight S. japonicus cells were inoculated into 150ml MXGB. We excised 5x5 mm of F. graminearum hyphaes were transferred from another pre-cultured F. graminearum flask. S. japonicus and F. graminearum were co-cultured for 2 days at 25°C without shaking. Then the cells were separated and S. japonicus cells were submitted to RNA extraction.

value: WT

value: co-culture


title: H3K27ac ChIP-seq, fly adult, day13, replicate 3

description: Library name: day13-rep3-ip


title: diplod EE2 group rep4

description: Library name: D26


title: FgSj-c


title: H3K27ac ChIP-seq, fly adult, day13, replicate 1

description: Library name: day13-rep1-ip


title: w1_noHS_control_antiIgG_rep2


title: diplod EE2 group rep2

description: Library name: D21


title: FgSj-a


title: 42ABDfxw1-F1s_antiRhi_rep1


title: H3K27ac ChIP-seq, fly adult, day5, replicate 2

description: Library name: day5-rep2-ip


title: w1_noHS_control_antiRhi_rep1


title: 42ABDfxw1-F1s_antiIgG_rep1


title: Treatment 1: Z. tritici, Treatment 2: P. graminis, biol rep 2

city: Uppsala

first: Salim

last: Bourras

address: Almas Alle 5

department: Plant Biology

country: Sweden

institute: Swedish University of Agricultural Sciences

description: Library name: P29206_511_S11_L003

data_processing:
Raw sequencing data quality was assessed using FastQC v0.11.9 (Andrews 2010) to evaluate read quality metrics, sequence duplication levels, and potential adapter contamination. Adapter sequences and low-quality bases were removed using Trimmomatic v0.39 (Bolger et al. 2014) with the following parameters: ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:4:15 MINLEN:36.
Transcript abundance was quantified using Salmon v1.4.0 (Patro et al. 2017) in quasi-mapping mode with the following key parameters: --validateMappings --gcBias –seqBias. The Triticum turgidum subsp. durum cultivar Svevo transcriptome was used as a reference. Salmon indexing was performed using the salmon index command with default k-mer length (k=31). Quantification was executed using the salmon quant command in paired-end mode (-l A for automatic library type detection), which employed Salmon’s dual-phase parallel inference algorithm with selective alignment validation (--validateMappings) to improve mapping accuracy. Bias correction models were applied for fragment GC content (--gcBias) and positional sequence biases (--seqBias).
Assembly: GCA_900231445.1
Supplementary files format and content: .sf files: Salmon generates transcript per million (TPM) values and estimated counts for all transcripts across all libraries using its expectation-maximization algorithm.

molecule: polyA RNA

organism: Triticum turgidum subsp. dicoccum

source_name: Leaf

extract_protocol:
Leaf tissue samples were collected at 12 days post-inoculation with Z. tritici. Total RNA was extracted using the miRNeasy kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol.
Total RNA (1–2 µg per sample) was used as input for library construction with the TruSeq Stranded mRNA Library Preparation Kit (Illumina, San Diego, CA, USA; RS-122-2101) according to the manufacturer’s protocol.

treatment_protocol:
Nine-day-old wheat seedlings were placed in a closed humidity chamber. A composite Z. tritici inoculum was applied using a spray gun (0.33 ml per seedling). Mock control plants were inoculated with 0.01% Tween-20 using the same application method. Following inoculation, plants were maintained in the humidity chamber at >70% relative humidity in complete darkness for 24 hours. Plants were then returned to standard day-night cycle (photoperiod of 18 hours light and 6 hours darkness with a light intensity of 300 μmol m−2 s−1) and maintained at high relative humidity through daily misting with distilled water using a low-pressure spray gun.
At three days post-inoculation with Z. tritici or mock treatment, plants designated for P. graminis infection were inoculated by applying the urediniospore suspension (250 spores/μl) directly to all leaf surfaces using sterile brushes until complete coverage was achieved. Control plants received 0.01% Tween-20 applied in the same manner. All plants were maintained under the standard photoperiod and high relative humidity conditions until sampling.

value: Leaf

value: Zymoseptoria tritici, Puccinia graminis

tag: time

value: 12 days post-inoculation (dpi)


title: H3K27ac ChIP-seq, fly adult, day5, replicate 1

description: Library name: day5-rep1-ip


title: H3K27ac ChIP-seq, fly adult, day5, replicate 3

description: Library name: day5-rep3-ip


title: w1_noHS_control_antiIgG_rep1


title: triploid EE2 group rep4

description: Library name: C9


title: Treatment 1: Z. tritici, Treatment 2: P. graminis, biol rep 1

description: Library name: P29206_510_S10_L003


title: triploid EE2 group rep2_outlier

description: Library name: C2


title: H3K27ac ChIP-seq, fly adult, day3, replicate 3

description: Library name: day3-rep3-ip


title: Treatment 1: mock, Treatment 2: P. graminis, biol rep 3

description: Library name: P29206_509_S9_L003

value: Mock, Puccinia graminis


title: w1x42ABDf-F1s_antiIgG_rep1


title: triploid EE2 group rep1

description: Library name: C1


title: H3K27ac ChIP-seq, fly adult, day3, replicate 2

description: Library name: day3-rep2-ip


title: triploid EE2 group rep3

description: Library name: C8


title: Treatment 1: Z. tritici, Treatment 2: P. graminis, biol rep 3

description: Library name: P29206_512_S12_L003


title: Treatment 1: mock, Treatment 2: P. graminis, biol rep 2

description: Library name: P29206_508_S8_L003


title: 42ABDfxOreR-F1s_antiRhi_rep1


title: H3K27ac ChIP-seq, fly adult, day3, replicate 1

description: Library name: day3-rep1-ip


title: diplod EE2 group rep1

description: Library name: D7


title: Treatment 1: mock, Treatment 2: P. graminis, biol rep 1

description: Library name: P29206_507_S7_L003


title: w1x42ABDf-F1s_antiRhi_rep1


title: OreRx42ABDf-F1s_antiRhi_rep1


title: Treatment 1: Z. tritici, Treatment 2: mock, biol rep 3

description: Library name: P29206_506_S6_L003

value: Zymoseptoria tritici, Mock


title: 42ABDfxOreR-F1s_antiIgG_rep1

value: No heat shock


title: diplod  control group rep2

description: Library name: B3

value: control


title: H3K27ac ChIP-seq, fly adult, day1, replicate 2

description: Library name: day1-rep2-ip


title: Treatment 1: Z. tritici, Treatment 2: mock, biol rep 2

description: Library name: P29206_505_S5_L003


title: H3K27ac ChIP-seq, fly adult, day1, replicate 3

description: Library name: day1-rep3-ip


title: diplod control group rep1

description: Library name: B2


title: OreRx42ABDf-F1s_antiIgG_rep1


title: H3K27ac ChIP-seq, fly adult, day1, replicate 1

description: Library name: day1-rep1-ip


title: diplod  control group rep3

description: Library name: B4


title: Treatment 1: mock, Treatment 2: mock, biol rep 3

description: Library name: P29206_503_S3_L003

value: Mock, Mock


title: Treatment 1: Z. tritici, Treatment 2: mock, biol rep 1

description: Library name: P29206_504_S4_L003


title: triploid control group rep4

description: Library name: A4


title: SJG-c

organism: Schizosaccharomyces japonicus yFS275

source_name: S. japonicus was grown in MXGB media


title: Circular RNA_siRNASEK_biological rep2

type: RNA

city: Daejeon

first: Seung-Jae

middle: V

last: Lee

address: 291 Daehak-ro

department: Biological Sciences

country: South Korea

institute: KAIST

description: Circular RNA_siRNASEK_biological rep2

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.

scan_protocol: The signals were scanned using the Agilent Scanner G2505C

data_processing: Quantification was processed and normalized based on quantiles by using Agilent Feature Extraction software (v.11.0.1.1). Because of high variability between replicates with HeLa cells, average values of two biological replicates were used.

source_name: HeLa

label_protocol: The enriched circular RNAs were amplified and transcribed into Cy3 labeled cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (QIAGEN)

growth_protocol: HeLa cells were grown with Dulbecco’s Modified Eagles Medium (Sigma-aldrich) supplemented with 10% (vol/vol) fetal bovine serum (Sigma-aldrich) and 1% (vol/vol) penicillin/streptomycin (Sigma-aldrich)

extract_protocol: Total cell RNAs were purified TRIzol by manufacturer's recommendations.

treatment_protocol: HeLa cells were transfected with a siRNA targeting RNASEK.

tag: Sex

value: Female


title: SJG-b


title: triploid control group rep3

description: Library name: A3


title: triploid control group rep2

description: Library name: A2


title: Treatment 1: mock, Treatment 2: mock, biol rep 2

description: Library name: P29206_502_S2_L003


title: Treatment 1: mock, Treatment 2: mock, biol rep 1

description: Library name: P29206_501_S1_L003


title: SJG-a


title: Circular RNA_siRNASEK_biological rep1

description: Circular RNA_siRNASEK_biological rep1


title: CLIP_INPUT

status: Public on Feb 23 2026

city: Vienna

first: Dominik

last: Handler

address: Dr. Bohr-Gasse 3

country: Austria

institute: IMBA-Institute of Molecular Biotechnology of Austrian Academy of Sciences

description: Library name: CLIP_INPUT

library_source: other

data_processing:
Illumina reads were processed by removing adapters using cutadapt and filtered for low-complexity sequences using bbduk (entropy = 0.35, entropy window = 18, k = 4). Reads were trimmed of 4 random nucleotides from both ends and filtered for length (>18 nt and ≤35 nt). Reads were first aligned to Drosophila rRNA precursor sequences and the mitochondrial genome using Bowtie. Remaining unmapped reads were mapped to the OSC_r1.01 genome using STAR.
Assembly: OSC_r1.01
Supplementary files format and content: All mapping and unique mapping bigwig files for sense and antisense

molecule: other

source_name: OSC

growth_protocol: Ovarian somatic cells (OSCs) were maintained at 27 °C in a humidified incubator with 2.5% CO₂, as previously described (Niki, Yamaguchi et al. 2006, Saito, Inagaki et al. 2009) Cells were cultured in M3 basal medium supplemented with 10% fetal bovine serum (FBS), insulin, glutathione, and fly extract.

extract_protocol:
Harvested cell pellets were lysed in lysis buffer (30 mM HEPES-KOH pH 7.4, 150 mM NaCl, 2 mM MgCl₂, 0.5% Triton X-100, 0.2 mM DTT, 0.2 mM Pefabloc) and clarified by centrifugation. Lysates were treated with RNase I (0.08 U per 100 µl cell pellet; Thermo Fisher) for 30 min at room temperature, followed by inhibition with SUPERase In (Thermo Fisher). Immunoprecipitation was performed using monoclonal anti-Yb antibodies coupled to Dynabeads M-280 sheep anti-mouse in TBS-Tx. Beads were incubated with lysates for 4 h at 4 °C and washed four times with high-salt wash buffer (30 mM HEPES-KOH pH 7.4, 1 M NaCl, 2 mM MgCl₂, 1% Empigen).
On-bead RNA end repair was performed using T4 polynucleotide kinase (T4 PNK) without ATP to open 2′,3′-cyclic phosphates, followed by 5′-OH radiolabeling with [γ-³²P]-ATP and final phosphorylation with 10 mM cold ATP. Protein–RNA complexes were eluted in SDS buffer, resolved by 8% SDS-PAGE, and transferred to a 0.45 µm nitrocellulose membrane. Complexes were visualized by autoradiography, and corresponding membrane regions were excised and digested with proteinase K (1 mg/ml). RNA was extracted via acid phenol–chloroform, precipitated, and used for small RNA library preparation. Libraries were generated following standard gel based small RNA cloning and sequenced on an Illumina platform (single-end 50 bp).

value: OSC

value: ovarian somatic cells

value: wildtype

value: Cells were washed with PBS and UV-crosslinked on ice (254 nm, 200 mJ/cm² twice at 90° rotation) using a UV Stratalinker.


title: triploid control group rep1

description: Library name: A1

value: testis

value: AB strain


title: Circular RNA_siContorl_biological rep1

description: Circular RNA_siContorl_biological rep1


title: CLIP_YB_Rep1

description: Library name: CLIP_YB_Rep1


title: diplod  control group rep4

description: Library name: B6


title: Seamcell_L3_HDA-1_TaDa_HDA-1-DAM_Rep2

city: London

first: Mar

last: Ferrando Marco

address: Imperial College Road

country: United Kingdom

institute: Imperial College London

description:
Library name: Seam4
amplicons of GATC-6mA-methylated genomic DNA fragments

data_processing:
Sequencing data were fully processed using the automated pipeline defined by the perl script damidseq_pipeline v1.4.5 (Marshall and Brand, 2015) (available at https://github.com/owenjm/damidseq_pipeline). The pipeline  was used calling Bowtie 2 v2.3.4 (Langmead and Salzberg, 2012) for alignment to C. elegans bowtie indices from genome assembly WBcel235 (available from illumina® iGenomes page), Samtools v1.9 (Li et al., 2009) for alignment manipulations and generation of BAM files. Using a GATC fragment file with the coordinates of all GATC fragments across the C. elegans genome in gff format, built from a WBcel235 FASTA file (available at https://www.ensembl.org/Caenorhabditis_elegans/Info/Index) using the gatc.track.marker.pl script (available at https://github.com/owenjm/damidseq_pipeline), the pipeline calculated genome-wide log2(Dam-fusion/Dam-control) signal enrichment scores per GATC fragment of the genome as gff files from pairs of BAM files from HDA-1-Dam and Dam-only samples.
Using damidseq_pipeline v1.4.5 all pairwise calculations of log2(HDA-1:DAM/DAM-only) scores between pairs of HDA-1:DAM and Dam-only sample replicates were performed producing 4 independet bedgraph signal files.
The 4 bedgraph signal files were averaged arithmetically per GATC fragment of the genome to genarate a single averaged signal bedgraph.
Statistically significant enrichment peaks with an FDR<0.05 were identified from the averaged profiles using the the perl script find_peaks (available at https://github.com/owenjm/find_peaks) which generated peak interval gff files.
Assembly: WBcel235
Supplementary files format and content: BEDGRAPH interval files representing coordinates of GATC fragments of the genome with a log2(HDA-1:Dam/Dam-only) score each.
Supplementary files format and content: BED files representing statistically singificant peaks (FDR<0.05).
Library strategy: DamID-Seq

organism: Caenorhabditis elegans

source_name: Epidermis - srf-3i expression domain

growth_protocol: For each replicate of each strain used for TaDa nine 55 mm NGM plates seeded with dam-/dcm- bacterial lawns and fully populated by gravid adults were used for large-scale egg preparation with isolated embryos seeded in new dam-/dcm- plates that were incubated at 20 °C. The resulting synchronised populations were collected in a 15 ml centrifuge tube after 35 hours, at the L3 stage. All collected populations pellets (~100 μl) underwent extensive washing with 10 ml M9 at least 5 times and were frozen at -20C.

extract_protocol:
gDNA for each sample was extracted by lysing animal pellets with Cell Lysis Solution (QIAGEN) containing Proteinase K. RNA was removed by treating with RNase A  and DNA was isolated after treatment with Protein precipitation solution (QIAGEN) by percipitating in isopropanol and washing with 70% ethanol. gDNA was redissolved in water. For isolation and amplification of the GATC methylated gDNA fragments the protocol followed was an adapted version of the one presented in (Marshall et al., 2016).
Amplicon sonication and library preparation was outsourced to GENEWIZ which used illumina protocols for sequencing on the Illumina HiSeq 2x150 platform.

value: Epidermis - srf-3i expression domain

tag: strain

tag: developmental stage

value: icbSi164[pMFM10 (srf-3i1::pes-10::wcherry::hda-1::Dam-myc::unc-543UTR::unc119 3UTR::unc-119::punc119::ttTi5605_left]II; unc119(ed3) III

tag: biological replicate

value: Replicate 2


title: Seamcell_L3_HDA-1_TaDa_HDA-1-DAM_Rep1

description:
Library name: Seam3
amplicons of GATC-6mA-methylated genomic DNA fragments

value: Replicate 1


title: Seamcell_L3_HDA-1_TaDa_dam-only_Rep2

description:
Library name: Dam2SC
amplicons of GATC-6mA-methylated genomic DNA fragments

value: icbSi263[pMFM8 (srf-3i1::pes-10::wcherry::NLS::GFP::Dam-myc::unc-54 3UTR::unc119 3UTR::unc-119::punc119) II;119(ed3) III


title: Circular RNA_siContorl_biological rep2

description: Circular RNA_siContorl_biological rep2


title: CLIP_YB_Rep2

description: Library name: CLIP_YB_Rep2


title: Seamcell_L3_HDA-1_TaDa_dam-only_Rep1

description:
Library name: Dam1SC
amplicons of GATC-6mA-methylated genomic DNA fragments

value: icbSi263[pMFM8(srf-3i1::pes-10::wcherry::NLS::GFP::Dam-myc::unc-54 3UTR::unc119 3UTR::unc-119::punc119) II;119(ed3) III


title: MDA-MB-231 cells, RN1_1

city: Houston

first: Thai Quynh Anh

last: Nguyen

state: TX

address: 6565 MD Anderson Blvd

department: Systems Biology

institute: The University of Texas MD Anderson Cancer Center

description:
Library name: Sample 4
Colume_name_in_raw_counts_All_samples.txt: RN1_1

data_processing:
Raw sequencing reads (FASTQ files) were assessed for quality using FastQC. Adapter sequences and low-quality bases were trimmed as needed prior to alignment.
Clean reads were aligned to the human reference genome GRCh38 (hg38) using the STAR aligner (v2.x) with default parameters. Gene-level read counts were generated directly from STAR using the --quantMode GeneCounts option, producing the count matrix file (STAR.ReadsPerGene). Raw read counts were used for downstream differential expression analysis.
Assembly: Homo sapiens GRCh38 (hg38)
Supplementary files format and content: csv file includes raw count for all samples
Supplementary files format and content: csv file includes LogCPM for all samples

source_name: Breast

growth_protocol: Human TNBC cell line MDA-MB-231 were cultured in RPMI-1640 supplemented with 10% fetal bovine serum (FBS). Cells were maintained at 37°C in 5% CO₂.

extract_protocol:
Total RNA from control and RNASEH2A-deficient MDA-MB-231 cells were extracted using a Total RNA Kit I (RNeasy Kit, Qiagen). RNA from three different passages per group was extracted according to the kit manufacturer’s instructions. RNA purity and concentration were assessed using a NanoDrop spectrophotometer (Thermo Scientific), and RNA integrity was evaluated using the Agilent 2100 Bioanalyzer system (Agilent Technologies). Samples with RNA integrity number (RIN) ≥ 7.0 and A260/A280 ratio between 1.8–2.1 were used for library preparation.
Strand-specific mRNA library constructed using the poly-A enrichment method.

value: Breast

value: MDA-MB-231 cells

value: Breast cancer cell line

value: RNASEH2A KO

tag: batch


title: MDA-MB-231 cells, CTRV2_1

description:
Library name: Sample 1
Colume_name_in_raw_counts_All_samples.txt: CTRV2_1

value: CTRV2 control


title: 231_N2_R1.fastq.gz

city: Gandhinagar

first: Amit Kumar

last: Pandey

state: Gujarat

address: NIPER-Ahmedabad, Palaj

department: Biotechnology

country: India

institute: National Institute of Pharmaceutical Education and Research

description:
Library name: Sample 2
raw_counts for all sample.txt

data_processing:
RNAseq
Read count data were normalized using DESeq2.
For the RNA-Seq analysis, we begin by removing the unwanted sequences, especially non-polyA tailed RNAs from the sample (assuming that poly-A tailed RNAs are sequenced). The unwanted sequences include - mitochondrial genome sequences, ribosomal RNAs, transfer RNAs, adapter sequences and others. Contamination removal was performed using Bowtie2
The paired-end reads are aligned to the reference human genome (hg19). Alignment was performed using HISAT2
The aligned reads are used for estimating expression of the genes. The raw read counts were estimated using FeatureCoun
Assembly: The raw read counts were normalized using DESeq2.The ratio of normalized read counts for treated over control was taken as the fold change. Genes were first filtered based on the p-adj value (<= 0.05). A distribution of these log2 (foldchange) values were found to be normally distributed. Those genes which were found to have -1 <= log2(foldchange) >= 1 were considered as statistically significant.
Supplementary files format and content: hg19 platform
Supplementary files format and content: tab-delimited text file includes raw counts for each samples
Supplementary files format and content: tab-delimited text file includes RPKM values for each samples

growth_protocol: MDA-MB-2317TGP-POS and MDA-MB-2317TGP-NEG cells  were propagated in DMEM supplemented with 10% FBS under standard cell culture conditions, maintained at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol:
RNA was harvested using RNAeasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA library was prepared for RNAseq by using Ultra2 NEB (Ultra™ II RNA Library Prep Kit for Illumina® (NEB #E7775)) as per manufactures protocol.

treatment_protocol: WNT activity TNBC reporter cell lines were generated by lipofectamine transfection of the 7TGP reporter plasmid. followed by stable selection with puromycin (3μg/mL) for a minimum of five passages. The 7TGP reporter vector has 7 copies of TCF-binding sites as a bimodal WNT responsive element promoter. Upon nuclear translocation of β-catenin and subsequent binding to the TCF/LEF1 factors, eGFP is expressed. 7TGP/eGFP status is analyzed by flow cytometry and microscopy under optimal growth conditions. FACS sorting was carried out on the MDA-MB-231-7TGP stable cell line to enrich for either 7TGP negative or 7TGP positive subpopulations,

value: Mesenchymal Cell line

value: Wnt-negative cell line

value: Control MDA-MB-2317TGP-NEG


title: 231_P1_R1.fastq.gz

description:
Library name: Sample 3
raw_counts for all sample.txt

value: Wnt-positive cell Line

value: 7TGP vector transfected MDA-MB-2317TGP-POS


title: MDA-MB-231 cells, RN1_2

description:
Library name: Sample 5
Colume_name_in_raw_counts_All_samples.txt: RN1_2


title: MDA-MB-231 cells, RN1_3

description:
Library name: Sample 6
Colume_name_in_raw_counts_All_samples.txt: RN1_3


title: SNB19 TEAD1 Cut&Tag (anti-HA), biological replicate 3

city: Milan

first: Michal

last: Kubacki

address: Via Olgettina 58

country: Italy

institute: San Raffaele Scientific Institute

description:
Library name: TEAD1-3
Cut&Tag for overexpressed TEAD1 using anti-HA antibody in SNB19 glioblastoma cells, replicate 3

data_processing:
Raw reads assessed with FastQC. Adapters and low-quality bases removed using Trim Galore in paired-end mode (--paired) with quality threshold Phred 20, adapter detection stringency 5 bp, minimum read length 20 bp, gzip-compressed output (--gzip). FastQC run on trimmed reads (--fastqc).
Trimmed reads aligned to GRCh38 using Bowtie2 with Cut&Tag-optimized parameters: very-sensitive mode (--very-sensitive), proper pairs only (--no-mixed --no-discordant), insert size range 10-700 bp (-I 10 -X 700), Phred33 quality encoding.
Read groups added using Picard AddOrReplaceReadGroups. PCR duplicates removed using Picard MarkDuplicates (REMOVE_DUPLICATES=true). Filtered with SAMtools for properly paired reads (flag 2), MAPQ >= 30, excluding unmapped/mate-unmapped/secondary/failed-QC/duplicates (-F 1804). Restricted to canonical chromosomes (1-22, X, Y).
Narrow peaks called using MACS2 in BAMPE mode (-f BAMPE), effective genome size 2913022398 (-g 2913022398), q-value 0.05 (-q 0.05), --keep-dup all. Mouse IgG as control for TES, rabbit IgG for TEAD1. Peaks filtered for fold enrichment >= 2. ENCODE blacklist regions (hg38-blacklist.v2.bed) removed using bedtools intersect (-v). Consensus and per-replicate peaks called.
Normalized coverage tracks (BigWig) generated using deepTools bamCoverage at 10 bp resolution (--binSize 10) with read extension (--extendReads). CPM normalization and RPGC normalization (--effectiveGenomeSize 2913022398) applied.
Assembly: hg38
Supplementary files format and content: bigWig files: CPM-normalized coverage tracks for genome browser visualization
Supplementary files format and content: narrowPeak files: MACS2 narrow peak calls in BED6+4 format (chrom, start, end, name, score, strand, signalValue, pValue, qValue, peak)
Library strategy: CUT&Tag

source_name: brain

growth_protocol: SNB19 human glioma cells were cultured in plastic-adherence condition in DMEM medium (Dulbecco Modified Eagle Medium - high glucose, Sigma-Aldrich) containing 10% fetal bovine serum (FBS, Sigma-Aldrich), 1% penicillin/streptomycin (Sigma-Aldrich), 2 mM Glutamine (Sigma-Aldrich), 1% non-essential amino acids (MEM NEAA, ThermoFisher Scientific), 1% sodium pyruvate solution (Sigma-Aldrich). Cells were maintained in humidified atmosphere of 5% CO2 at 37C under atmospheric oxygen conditions.

extract_protocol:
CUT&Tag was performed according to the CUTANA CUT&Tag Protocol (EpiCypher). Briefly, cells were harvested to obtain single-cell suspension, nuclei were extracted, and 100,000 nuclei were used for each replicate. Nuclei were bound to activated Concanavalin A-Conjugated Paramagnetic Beads (EpiCypher) and incubated overnight at 4C with primary antibodies: anti-V5 (mouse, Thermo Fisher Scientific R96025) for TES samples, anti-HA (rabbit, Cell Signaling Technology 3724S) for TEAD1 samples, mouse IgG (Diagenode C15400001) and rabbit IgG (Diagenode C15410206) as controls.
Following overnight primary antibody incubation, nuclei suspensions were incubated with secondary antibodies (Goat Anti-Mouse IgG, Vector Laboratories I-9200-1.5; Goat Anti-Rabbit IgG, Vector Laboratories AI-1000-1.5), washed, and chromatin tagmentation was performed using pA-Tn5 Transposase (Diagenode C01070001). DNA was released from nuclei, and sequencing libraries were amplified using single-index barcodes, cleaned up, and paired-end sequenced on an Illumina NovaSeq platform.

treatment_protocol: SNB19 cells were transduced with lentiviral constructs expressing TES (V5-tagged KRAB-hTEAD1(1-166)-DNMT3A/3L, driven by EF1aL promoter) or wild-type TEAD1 (V5-tagged, HA-tagged). Cut&Tag was performed on transduced cells using anti-V5 antibody for TES detection, anti-HA antibody for TEAD1 detection, and mouse/rabbit IgG isotype controls.

value: brain

value: glioblastoma

tag: antibody


title: MDA-MB-231 cells, CTRV2_2

description:
Library name: Sample 2
Colume_name_in_raw_counts_All_samples.txt: CTRV2_2


title: SNB19 TES Cut&Tag (anti-V5), biological replicate 3

description:
Library name: TES-3
Cut&Tag for TES (V5-tagged KRAB-hTEAD1(1-166)-DNMT3A/3L) using anti-V5 antibody in SNB19 glioblastoma cells, replicate 3

value: anti-V5 (mouse, Thermo Fisher Scientific R96025)


title: SNB19 TEAD1 Cut&Tag (anti-HA), biological replicate 2

description:
Library name: TEAD1-2
Cut&Tag for overexpressed TEAD1 using anti-HA antibody in SNB19 glioblastoma cells, replicate 2

value: anti-HA (rabbit, Cell Signaling Technology 3724S)


title: 231_N1_R1.fastq.gz

description:
Library name: Sample 1
raw_counts for all sample.txt


title: SNB19 TES Cut&Tag (anti-V5), biological replicate 2

description:
Library name: TES-2
Cut&Tag for TES (V5-tagged KRAB-hTEAD1(1-166)-DNMT3A/3L) using anti-V5 antibody in SNB19 glioblastoma cells, replicate 2


title: SNB19 TEAD1 Cut&Tag (anti-HA), biological replicate 1

description:
Library name: TEAD1-1
Cut&Tag for overexpressed TEAD1 using anti-HA antibody in SNB19 glioblastoma cells, replicate 1


title: SNB19 TES Cut&Tag (anti-V5), biological replicate 1

description:
Library name: TES-1
Cut&Tag for TES (V5-tagged KRAB-hTEAD1(1-166)-DNMT3A/3L) using anti-V5 antibody in SNB19 glioblastoma cells, replicate 1


title: SNB19 mouse IgG control (Cut&Tag)

description:
Library name: IggMs
Cut&Tag negative control using mouse IgG isotype antibody (Diagenode) in SNB19 cells, control for TES (anti-V5) samples

value: mouse IgG (Diagenode C15400001)


title: SNB19 rabbit IgG control (Cut&Tag)

description:
Library name: IggRb
Cut&Tag negative control using rabbit IgG isotype antibody (Diagenode) in SNB19 cells, control for TEAD1 (anti-HA) samples

value: rabbit IgG (Diagenode C15410206)


title: Asp14, control, total RNA, replicate 3

city: Wien

first: Christoph

middle: P

last: Dotter

address: Zimmermannplatz 10

institute: St. Anna Children’s Cancer Research Institute (St. Anna CCRI)

description:
Library name: NT3_R
Asp14 Clone of Ewing sarcoma A-673 cell line with doxycycline inducible EWS-FLI1 knockdown construct; Column name in featureCounts_NTDOX.tsv: NT3_R

data_processing:
First, UMI sequences were transferred from the RX tag to read names using a custom python script before adapter sequence trimming with fastp (v0.23.4).
Reads were aligned to a ribosomal DNA (rDNA) reference using bowtie2 (v2.5.1) to remove rDNA reads before alignment to the human genome (GRCh38, gencode v41) with STAR (v2.7.8a) and parameters --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000.
Aligned reads were deduplicated using umi_tools dedup (v1.1.4) with parameters –paired --unmapped-reads discard --unpaired-reads discard --chimeric-pairs discard --spliced-is-unique.
Read count matrices were generated using featureCounts (v1.6.3) with parameters -p -T 20 -s 2 -B -C
Assembly: GRCh38, gencode v41
Supplementary files format and content: tab-delimited text file includes raw counts with one column per sample

extract_protocol:
Cells were cultured for 48h and harvested in cycloheximide-containing lysis buffer. Following mechanical lysis and flash-freezing, samples were fractionated along a 10-50% sucrose-gradient prepared with the BioComp Gradient Station (“LONG, Sucr, 10-50%, w/v” program) through ultracentrifugation (38.000 rpm, 2.30h, 4°C – TH-641 swinging bucket rotor). Samples were then scanned for the absorbance at 260 nm with the BioComp Gradient Station, and all the fractions were manually retrieved, flashed-frozen and subsequently stored at -80°C until use. For each sample, all the fractions corresponding to each polysome peak were pulled together, followed by RNA extraction and library preparation for RNA seq. Total RNA seq was isolated from the matched lysate that did not underwent fractionation.
NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® was employed for RNA-seq library preparation.

value: Ewing sarcoma

value: doxycycline


title: Asp14, control, polysome-bound, replicate 3

description:
Library name: NT3_P
Asp14 Clone of Ewing sarcoma A-673 cell line with doxycycline inducible EWS-FLI1 knockdown construct; Column name in featureCounts_NTDOX.tsv: NT3_P


title: Asp14, control, total RNA, replicate 2

description:
Library name: NT2_R
Asp14 Clone of Ewing sarcoma A-673 cell line with doxycycline inducible EWS-FLI1 knockdown construct; Column name in featureCounts_NTDOX.tsv: NT2_R


title: Asp14, EWSR1::FLI1 knockdown, total RNA, replicate 3

description:
Library name: D3_R
Asp14 Clone of Ewing sarcoma A-673 cell line with doxycycline inducible EWS-FLI1 knockdown construct; Column name in featureCounts_NTDOX.tsv: D3_R

value: control


title: Asp14, control, polysome-bound, replicate 1

description:
Library name: NT1_P
Asp14 Clone of Ewing sarcoma A-673 cell line with doxycycline inducible EWS-FLI1 knockdown construct; Column name in featureCounts_NTDOX.tsv: NT1_P


title: Asp14, control, polysome-bound, replicate 2

description:
Library name: NT2_P
Asp14 Clone of Ewing sarcoma A-673 cell line with doxycycline inducible EWS-FLI1 knockdown construct; Column name in featureCounts_NTDOX.tsv: NT2_P


title: Asp14, EWSR1::FLI1 knockdown, polysome-bound, replicate 2

description:
Library name: D2_P
Asp14 Clone of Ewing sarcoma A-673 cell line with doxycycline inducible EWS-FLI1 knockdown construct; Column name in featureCounts_NTDOX.tsv: D2_P


title: Asp14, EWSR1::FLI1 knockdown, total RNA, replicate 1

description:
Library name: D1_R
Asp14 Clone of Ewing sarcoma A-673 cell line with doxycycline inducible EWS-FLI1 knockdown construct; Column name in featureCounts_NTDOX.tsv: D1_R


title: Asp14, control, total RNA, replicate 1

description:
Library name: NT1_R
Asp14 Clone of Ewing sarcoma A-673 cell line with doxycycline inducible EWS-FLI1 knockdown construct; Column name in featureCounts_NTDOX.tsv: NT1_R


title: Asp14, EWSR1::FLI1 knockdown, total RNA, replicate 2

description:
Library name: D2_R
Asp14 Clone of Ewing sarcoma A-673 cell line with doxycycline inducible EWS-FLI1 knockdown construct; Column name in featureCounts_NTDOX.tsv: D2_R


title: U2OS, total RNA, replicate 3

description:
Library name: U3_R
Column name in featureCounts_CellLines.tsv: U3_R

value: osteosarcoma


title: Asp14, EWSR1::FLI1 knockdown, polysome-bound, replicate 1

description:
Library name: D1_P
Asp14 Clone of Ewing sarcoma A-673 cell line with doxycycline inducible EWS-FLI1 knockdown construct; Column name in featureCounts_NTDOX.tsv: D1_P


title: Asp14, EWSR1::FLI1 knockdown, polysome-bound, replicate 3

description:
Library name: D3_P
Asp14 Clone of Ewing sarcoma A-673 cell line with doxycycline inducible EWS-FLI1 knockdown construct; Column name in featureCounts_NTDOX.tsv: D3_P


title: U2OS, polysome-bound, replicate 2

description:
Library name: U2_P
Column name in featureCounts_CellLines.tsv: U2_P


title: U2OS, total RNA, replicate 1

description:
Library name: U1_R
Column name in featureCounts_CellLines.tsv: U1_R


title: U2OS, total RNA, replicate 2

description:
Library name: U2_R
Column name in featureCounts_CellLines.tsv: U2_R


title: TC-32, polysome-bound, replicate 3

description:
Library name: T3_P
Column name in featureCounts_CellLines.tsv: T3_P


title: U2OS, polysome-bound, replicate 3

description:
Library name: U3_P
Column name in featureCounts_CellLines.tsv: U3_P


title: TC-32, total RNA, replicate 2

description:
Library name: T2_R
Column name in featureCounts_CellLines.tsv: T2_R


title: U2OS, polysome-bound, replicate 1

description:
Library name: U1_P
Column name in featureCounts_CellLines.tsv: U1_P


title: TC-32, total RNA, replicate 3

description:
Library name: T3_R
Column name in featureCounts_CellLines.tsv: T3_R


title: TC-32, polysome-bound, replicate 2

description:
Library name: T2_P
Column name in featureCounts_CellLines.tsv: T2_P


title: TC-32, total RNA, replicate 1

description:
Library name: T1_R
Column name in featureCounts_CellLines.tsv: T1_R


title: SK-N-MC, total RNA, replicate 2

description:
Library name: S2_R
Column name in featureCounts_CellLines.tsv: S2_R

source_name: SK-N-MC

value: SK-N-MC


title: SK-N-MC, polysome-bound, replicate 3

description:
Library name: S3_P
Column name in featureCounts_CellLines.tsv: S3_P


title: SK-N-MC, polysome-bound, replicate 1

description:
Library name: S1_P
Column name in featureCounts_CellLines.tsv: S1_P


title: TC-32, polysome-bound, replicate 1

description:
Library name: T1_P
Column name in featureCounts_CellLines.tsv: T1_P


title: RD, polysome-bound, replicate 3

description:
Library name: R3_P
Column name in featureCounts_CellLines.tsv: R3_P

source_name: RD

value: RD

value: rhabdomyosarcoma


title: SK-N-MC, total RNA, replicate 1

description:
Library name: S1_R
Column name in featureCounts_CellLines.tsv: S1_R


title: SK-N-MC, polysome-bound, replicate 2

description:
Library name: S2_P
Column name in featureCounts_CellLines.tsv: S2_P


title: RD, total RNA, replicate 1

description:
Library name: R1_R
Column name in featureCounts_CellLines.tsv: R1_R


title: RD, polysome-bound, replicate 2

description:
Library name: R2_P
Column name in featureCounts_CellLines.tsv: R2_P


title: RD, polysome-bound, replicate 1

description:
Library name: R1_P
Column name in featureCounts_CellLines.tsv: R1_P


title: SK-N-MC, total RNA, replicate 3

description:
Library name: S3_R
Column name in featureCounts_CellLines.tsv: S3_R


title: RH-30, polysome-bound, replicate 3

description:
Library name: RH3_P
Column name in featureCounts_CellLines.tsv: RH3_P


title: RD, total RNA, replicate 3

description:
Library name: R3_R
Column name in featureCounts_CellLines.tsv: R3_R


title: RH-30, total RNA, replicate 3

description:
Library name: RH3_R
Column name in featureCounts_CellLines.tsv: RH3_R


title: RH-30, polysome-bound, replicate 2

description:
Library name: RH2_P
Column name in featureCounts_CellLines.tsv: RH2_P


title: RD, total RNA, replicate 2

description:
Library name: R2_R
Column name in featureCounts_CellLines.tsv: R2_R


title: RH-30, total RNA, replicate 1

description:
Library name: RH1_R
Column name in featureCounts_CellLines.tsv: RH1_R


title: hMSC, total RNA, replicate 3

description:
Library name: M3_R
Column name in featureCounts_CellLines.tsv: M3_R

source_name: hMSC

value: hMSC

value: human mesenschymal stem cells


title: hMSC, polysome-bound, replicate 3

description:
Library name: M3_P
Column name in featureCounts_CellLines.tsv: M3_P


title: 231_P2_R1.fastq.gz

description:
Library name: Sample 4
raw_counts for all sample.txt

value: Mesenchymal Cell line

value: Wnt-postitve cell line


title: RH-30, polysome-bound, replicate 1

description:
Library name: RH1_P
Column name in featureCounts_CellLines.tsv: RH1_P


title: hMSC, polysome-bound, replicate 2

description:
Library name: M2_P
Column name in featureCounts_CellLines.tsv: M2_P


title: hMSC, total RNA, replicate 2

description:
Library name: M2_R
Column name in featureCounts_CellLines.tsv: M2_R


title: RH-30, total RNA, replicate 2

description:
Library name: RH2_R
Column name in featureCounts_CellLines.tsv: RH2_R


title: IMR90, total RNA, replicate 3

description:
Library name: I3_R
Column name in featureCounts_CellLines.tsv: I3_R

value: fibroblast


title: hMSC, total RNA, replicate 1

description:
Library name: M1_R
Column name in featureCounts_CellLines.tsv: M1_R


title: IMR90, polysome-bound, replicate 3

description:
Library name: I3_P
Column name in featureCounts_CellLines.tsv: I3_P


title: IMR90, polysome-bound, replicate 2

description:
Library name: I2_P
Column name in featureCounts_CellLines.tsv: I2_P


title: hMSC, polysome-bound, replicate 1

description:
Library name: M1_P
Column name in featureCounts_CellLines.tsv: M1_P


title: CHLA-9, total RNA, replicate 2

description:
Library name: C2_R
Column name in featureCounts_CellLines.tsv: C2_R


title: A-673, total RNA, replicate 3

description:
Library name: A3_R
Column name in featureCounts_CellLines.tsv: A3_R


title: CHLA-9, polysome-bound, replicate 1

description:
Library name: C1_P
Column name in featureCounts_CellLines.tsv: C1_P


title: IMR90, polysome-bound, replicate 1

description:
Library name: I1_P
Column name in featureCounts_CellLines.tsv: I1_P


title: A-673, total RNA, replicate 1

description:
Library name: A1_R
Column name in featureCounts_CellLines.tsv: A1_R


title: A-673, polysome-bound, replicate 3

description:
Library name: A3_P
Column name in featureCounts_CellLines.tsv: A3_P


title: IMR90, total RNA, replicate 1

description:
Library name: I1_R
Column name in featureCounts_CellLines.tsv: I1_R


title: CHLA-9, polysome-bound, replicate 2

description:
Library name: C2_P
Column name in featureCounts_CellLines.tsv: C2_P


title: CHLA-9, total RNA, replicate 3

description:
Library name: C3_R
Column name in featureCounts_CellLines.tsv: C3_R


title: CHLA-9, polysome-bound, replicate 3

description:
Library name: C3_P
Column name in featureCounts_CellLines.tsv: C3_P


title: IMR90, total RNA, replicate 2

description:
Library name: I2_R
Column name in featureCounts_CellLines.tsv: I2_R


title: A-673, polysome-bound, replicate 1

description:
Library name: A1_P
Column name in featureCounts_CellLines.tsv: A1_P


title: CHLA-9, total RNA, replicate 1

description:
Library name: C1_R
Column name in featureCounts_CellLines.tsv: C1_R


title: MDA-MB-231 cells, CTRV2_3

description:
Library name: Sample 3
Colume_name_in_raw_counts_All_samples.txt: CTRV2_3

value: Breast

value: MDA-MB-231 cells

value: Breast cancer cell line

value: CTRV2 control


title: GC Primary tumor, patient GC26

city: Seongnam-si

first: Clementine

last: Charton

state: Gyeonggi-do

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

institute: Seoul National University Bundang Hospital

description: Library name: GC26_GCPT

data_processing:
Raw reads were trimmed using cutadapt (v1.15) 38 with options -q 15 and --minimum-length 36 to remove adapter sequences and low-quality bases.
Processed reads were analyzed using the Nextflow (v23.04.3) nf-core/rnaseq pipeline (v3.12.0) 39, employing the STAR-RSEM aligner 40,41 with assembly GRCh37 and default parameters. The pipeline performed quality control, alignment, and generated a matrix of gene-level TPM values across all samples, which was subsequently used for downstream analyses.
Assembly: GRCh37
Supplementary files format and content: Tab delimited tsv file includes raw counts for each sample

source_name: GC Primary tumor

extract_protocol:
RNA was extracted from FFPE blocks or FF tissues using the ReliaPrep FFPE Total RNA Miniprep System (Promega) and RNeasy Mini Kit (Qiagen) for FFPE and FF specimens, respectively, according to the manufacturer’s protocol. Nucleic acid yield and purity were assessed using a NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies, Thermo-Fisher Scientific, MA, USA).
RNA libraries were constructed using a TruSeq RNA Access library prep kit (Illumina, San Diego, CA, USA) or Exome capture kit according to the manufacturer’s protocols. Briefly, ribosomal RNA (rRNA) was depleted, followed by fragmentation and conversion of RNA molecule to complementary DNA (cDNA) using reverse transcriptase. The single-stranded cDNAs were then converted to double-stranded cDNAs, end-repaired, adenosine-tailed, and adaptor-ligated. The constructed libraries were amplified using polymerase chain reaction (PCR). Subsequently, cDNA libraries were submitted to an Illumina NovaSeq6000 (Illumina, Inc.), and paired-end (2×100 bp) sequencing was performed by Macrogen Incorporated.

value: GC Primary tumor

value: Male

tag: preservation method

value: fresh-frozen


title: GC Peritoneal metastatic tumor, patient GC26

description: Library name: GC26_GCPM

source_name: GC Peritoneal metastatic tumor

tag: tissue

value: GC Peritoneal metastatic tumor


title: GC Peritoneal metastatic tumor, patient GC23

description: Library name: GC23_GCPM

value: Female


title: GC Lymph node metastatic tumor, patient GC26

description: Library name: GC26_GCLN

source_name: GC Lymph node metastatic tumor

value: GC Lymph node metastatic tumor


title: GC Primary tumor, patient GC22

description: Library name: GC22_GCPT

value: FFPE


title: GC Omentum metastatic tumor, patient GC21

description: Library name: GC21_GCOM

source_name: GC Omentum metastatic tumor

value: GC Omentum metastatic tumor


title: GC Peritoneal metastatic tumor, patient GC25

description: Library name: GC25_GCPM


title: A-673, polysome-bound, replicate 2

description:
Library name: A2_P
Column name in featureCounts_CellLines.tsv: A2_P

value: Ewing sarcoma


title: GC Primary tumor, patient GC21

description: Library name: GC21_GCPT


title: A-673, total RNA, replicate 2

description:
Library name: A2_R
Column name in featureCounts_CellLines.tsv: A2_R


title: GC Peritoneal metastatic tumor, patient GC24

description: Library name: GC24_GCPM


title: GC Peritoneal metastatic tumor, patient GC20

description: Library name: GC20_GCPM


title: GC Primary tumor, patient GC20

description: Library name: GC20_GCPT


title: GC Peritoneal metastatic tumor, patient GC19

description: Library name: GC19_GCPM


title: GC Peritoneal metastatic tumor, patient GC21

description: Library name: GC21_GCPM


title: GC Primary tumor, patient GC19

description: Library name: GC19_GCPT


title: GC Peritoneal metastatic tumor, patient GC22

description: Library name: GC22_GCPM


title: GC Peritoneal metastatic tumor, patient GC18

description: Library name: GC18_GCPM


title: NAT, patient GC18

description: Library name: GC18_NAT

source_name: NAT

value: NAT


title: GC Primary tumor, patient GC17

description: Library name: GC17_GCPT


title: GC Peritoneal metastatic tumor, patient GC17

description: Library name: GC17_GCPM


title: GC Primary tumor, patient GC18

description: Library name: GC18_GCPT


title: GC Primary tumor, patient GC16

description: Library name: GC16_GCPT


title: NAT, patient GC21

description: Library name: GC21_NAT


title: GC Peritoneal metastatic tumor, patient GC14

description: Library name: GC14_GCPM


title: GC Peritoneal metastatic tumor, patient GC16

description: Library name: GC16_GCPM


title: NAT, patient GC15

description: Library name: GC15_NAT


title: GC Peritoneal metastatic tumor, patient GC15

description: Library name: GC15_GCPM


title: GC Peritoneal metastatic tumor, patient GC12

description: Library name: GC12_GCPM


title: GC Primary tumor, patient GC15

description: Library name: GC15_GCPT


title: GC Peritoneal metastatic tumor, patient GC10

description: Library name: GC10_GCPM


title: GC Peritoneal metastatic tumor, patient GC13

description: Library name: GC13_GCPM


title: NAT, patient GC10

description: Library name: GC10_NAT


title: GC Peritoneal metastatic tumor, patient GC11

description: Library name: GC11_GCPM


title: GC Primary tumor, patient GC10

description: Library name: GC10_GCPT


title: NAT, patient GC09

description: Library name: GC09_NAT


title: GC Primary tumor, patient GC09

description: Library name: GC09_GCPT


title: GC Lymph node metastatic tumor, patient GC08

description: Library name: GC08_GCLN


title: GC Primary tumor, patient GC08

description: Library name: GC08_GCPT


title: GC Omentum metastatic tumor, patient GC07

description: Library name: GC07_GCOM


title: NAT, patient GC08

description: Library name: GC08_NAT


title: GC Peritoneal metastatic tumor, patient GC07

description: Library name: GC07_GCPM


title: GC Primary tumor, patient GC11

description: Library name: GC11_GCPT


title: GC Peritoneal metastatic tumor, patient GC05b

description: Library name: GC05b_GCPM


title: GC Primary tumor, patient GC06

description: Library name: GC06_GCPT


title: GC Peritoneal metastatic tumor, patient GC09

description: Library name: GC09_GCPM


title: GC Primary tumor, patient GC05b

description: Library name: GC05b_GCPT


title: GC Peritoneal metastatic tumor, patient GC05a

description: Library name: GC05a_GCPM


title: GC Peritoneal metastatic tumor, patient GC03

description: Library name: GC03_GCPM


title: GC Peritoneal metastatic tumor, patient GC04

description: Library name: GC04_GCPM


title: GC Primary tumor, patient GC05a

description: Library name: GC05a_GCPT


title: GC Peritoneal metastatic tumor, patient GC02

description: Library name: GC02_GCPM


title: K562 LDB1 antibody ChIP-seq

city: Charlottesville

first: Francine

middle: E.

last: Garrett-Bakelman

state: VA

address: 1340 Jefferson park Ave.

department: Medicine and BMG

institute: University of Virginia

description: Library name: K562 LDB1

data_processing:
Reads aligned to hg38 using BWA (default) algorithm. Duplicates were removed. Reads were extended at the 3'-end by 200 bp and stored in bigWig files. Peaks were determined by MACSv2 and ENCODE blacklist peaks were removed.
Assembly: hg38
Supplementary files format and content: bigWig files for K562 LDB1 antibody binding annotated to the hg38 genome.

extract_protocol:
Performed by active motif
Illumina sequencing libraries were prepared from the ChIP and Input DNAs with NEBNext Ultra™ II DNA Library Prep Kit for Illumina (NEB catalog # E7645). After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina’s NovaSeq 6000 (PE50 reads).

tag: chip antibody


title: GC Peritoneal metastatic tumor, patient GC01

description: Library name: GC01_GCPM

tag: age


title: GC Primary tumor, patient GC02

description: Library name: GC02_GCPT


title: K562 IgG input

description: Library name: K562 Input

value: IgG


title: GC Peritoneal metastatic tumor, patient GC06

description: Library name: GC06_GCPM


title: Mock_scRNA_1

city: Wuhan

first: Harris

last: Han

state: Hubei

address: No. 115, East Lake Road, Wuchang District

department: Medical Research Institute

institute: Wuhan University

description: Library name: Sample1

library_source: transcriptomic single cell

data_processing:
10xGenomics chromium single cell software Cell Ranger version 7.1.0 analysis pipelines performed sample demultiplexing, barcode processing, and single cell 3' gene counting. Single cell gene expression raw data were processed using the single cell R software Seurat 4.
Assembly: hg38
Supplementary files format and content: RDS files including processed Seurat V4 object of intergrated all sequenced cells and DCs.

source_name: Spleen

extract_protocol:
The tissue was cut into as small blocks as possible by scissors, and digested with 2 mg/ml. collagenase IV (2091GR001, BioFRoXX, Guangzhou, China) in the presence of 0.1 mg/ml DNase (Roche, Basel, Switzerland) for 20 min and ground by gentleMACS Dissociatir (Miltenyi Biotec, Germany) to obtain a single-cell suspension. Afterward, the cells were filtered with a 70-um cell strainer (Corning). Mononuclear cells were isolated from Ficoll-Paque Plus (17-1440-03; GE Healthcare) density gradient (lymphoprep; axis shield).
Sorted single-cell suspension, 10x 3’ barcoded gel beads, and oil was loaded into Chromium Single Cell B Chip to capture single cells in nanoliter-scale oil droplets by Chromium Controller and to generate Gel Bead-In-EMulsions (GEMs). Full-length cDNA libraries were prepared by incubation of GEMs in a thermocycler machine. GEMs containing cDNAs were broken and all single-cell cDNA libraries were pooled together, cleaned using DynaBeads MyOne Silane beads (PN 37002D; Fisher), and preampliﬁed by PCR to generate sufﬁcient mass for sequencing library construction. Sequencing libraries were constructed by following the steps cDNA fragmentation, end repair and A-tailing, size selection by SPRIselect beads (PN B23318; Beckman Coulter), adaptor ligation, sample index PCR ampliﬁcation, and repeat SPRIselect beads size selection.

value: Spleen


title: Mock_scRNA_2

description: Library name: Sample2


title: GC Primary tumor, patient GC01

description: Library name: GC01_GCPT


title: TSLP_scRNA_1

description: Library name: Sample3


title: Sorted cDCs, Dnr12_IL7R+CCR7+

description: Library name: Sample18

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed. Clean Reads were further treated with in-house scripts to eliminate duplication bias introduced in library preparation and sequencing. In brief, clean reads were first clustered according to the UMI sequences, in which reads with the same UMI sequence were grouped into the same cluster. Reads in the same cluster were compared to each other by pairwise alignment, and then reads with sequence identity over 95% were extracted to a new sub-cluster. After all sub-clusters were generated, multiple sequence alignment was performed to get one consensus sequence for each sub-cluster. After these steps, any errors and biases introduced by PCR amplification or sequencing were eliminated.  The de-duplicated consensus sequences were used for standard RNA-seq analysis. They were mapped to the human reference genome using STAR software (version 2.5.3a) with default parameters. Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor). Data generated from each individual donor were transformed to TPM for visualization. For the integrated analysis of 4 donors, batch effect were adjusted using ComBat-seq and the adjusted matrix were transformed to TPM and visualized. DE analysis were performed using limma-voom method. Genome_build: hg38
Assembly: hg38
Supplementary files format and content: .csv files contain counts matrices and TPMs, a TPM of batch-corrected, combined , matrix is also provided in the supplemental file

extract_protocol:
Total RNAs were extracted from each sample using TRIzol Reagent (Invitrogen, cat. NO 15596026).
RNA-seq libraries were prepared by KC-DigitalTM Stranded mRNA-seq Library Prep Kit for Illumina® (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction. The library products corresponding to 200-500 bps were enriched, quantified, and finally sequenced on a Novaseq 6000 sequencer (Illumina) with a PE150 mode.

tag: treatment

value: polyA RNA


title: Sorted cDCs, Dnr12_IL7R-CCR7+

description: Library name: Sample19


title: Sorted cDCs, Dnr12_cDC2

description: Library name: Sample16


title: TSLP_scRNA_2

description: Library name: Sample4


title: GC Primary tumor, patient GC03

description: Library name: GC03_GCPT


title: Sorted cDCs, Dnr12_IL7R+CCR7-

description: Library name: Sample17


title: Sorted cDCs, Dnr6_IL7R+CCR7+

description: Library name: Sample13


title: Sorted cDCs, Dnr6_cDC2

description: Library name: Sample11


title: Sorted cDCs, Dnr2_IL7R-CCR7+

description: Library name: Sample9


title: Sorted cDCs, Dnr6_cDC1

description: Library name: Sample10


title: Sorted cDCs, Dnr12_cDC1

description: Library name: Sample15


title: Sorted cDCs, Dnr2_IL7R+CCR7+

description: Library name: Sample8


title: Sorted cDCs, Dnr2_IL7R+CCR7-

description: Library name: Sample7


title: Sorted cDCs, Dnr2_cDC1

description: Library name: Sample5


title: Sorted cDCs, Dnr1_cDC2

description: Library name: Sample2


title: Sorted cDCs, Dnr1_IL7R+CCR7+

description: Library name: Sample4


title: Sorted cDCs, Dnr1_cDC1

description: Library name: Sample1


title: Sorted cDCs, Dnr2_cDC2

description: Library name: Sample6


title: Spleen, PAMP_LPS+IFNG_ctr_2

description: Library name: Sample13

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed. Clean Reads were further treated with in-house scripts to eliminate duplication bias introduced in library preparation and sequencing. In brief, clean reads were first clustered according to the UMI sequences, in which reads with the same UMI sequence were grouped into the same cluster. Reads in the same cluster were compared to each other by pairwise alignment, and then reads with sequence identity over 95% were extracted to a new sub-cluster. After all sub-clusters were generated, multiple sequence alignment was performed to get one consensus sequence for each sub-cluster. After these steps, any errors and biases introduced by PCR amplification or sequencing were eliminated.  The de-duplicated consensus sequences were used for standard RNA-seq analysis. They were mapped to the human reference genome using STAR software (version 2.5.3a) with default parameters. Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor). Data generated from each individual donor were transformed to TPM for visualization. For the integrated analysis of 4 donors, batch effect were adjusted using ComBat-seq and the adjusted matrix were transformed to TPM and visualized. DE analysis were performed using limma-voom method. Genome_build: hg38
Assembly: hg38
Supplementary files format and content: .csv files contain counts matrices, for TLR-agonist cocktail (PAMPs) experiments including data from 2 different batches, the batch effect-corrected counts are provided as well.


title: Sorted cDCs, Dnr6_IL7R+CCR7-

description: Library name: Sample12


title: Spleen, PAMP_LPS+IFNG_ctr_3

description: Library name: Sample14


title: Sorted cDCs, Dnr1_IL7R+CCR7-

description: Library name: Sample3


title: Spleen, LPS_IFNG_sti_3

description: Library name: Sample11


title: Spleen, PAMP_sti_5

description: Library name: Sample7


title: Spleen, PAMP_sti_4

description: Library name: Sample6


title: Spleen, PAMP_sti_6

description: Library name: Sample8


title: Spleen, PAMP_ctr_1

description: Library name: Sample1


title: Spleen, LPS_IFNG_sti_2

description: Library name: Sample10


title: TSLP_SI_2

description:
Library name: Sample5
TSLP_SI_2

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed. Clean Reads were further treated with in-house scripts to eliminate duplication bias introduced in library preparation and sequencing. In brief, clean reads were first clustered according to the UMI sequences, in which reads with the same UMI sequence were grouped into the same cluster. Reads in the same cluster were compared to each other by pairwise alignment, and then reads with sequence identity over 95% were extracted to a new sub-cluster. After all sub-clusters were generated, multiple sequence alignment was performed to get one consensus sequence for each sub-cluster. After these steps, any errors and biases introduced by PCR amplification or sequencing were eliminated.  The de-duplicated consensus sequences were used for standard RNA-seq analysis. They were mapped to the human reference genome using STAR software (version 2.5.3a) with default parameters. Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor). The limma-voom method was utilized to perform differential expression analysis. Genome_build: hg38
Assembly: hg38
Supplementary files format and content: .csv files of count matrix


title: TSLP_SI_3

description:
Library name: Sample6
TSLP_SI_3


title: TSLP_SI_1

description:
Library name: Sample4
TSLP_SI_1


title: Spleen, LPS_IFNG_sti_1

description: Library name: Sample9


title: Spleen, PAMP_sti_2

description: Library name: Sample4


title: Spleen, PAMP_LPS+IFNG_ctr_1

description: Library name: Sample12


title: Med-cDC2_3

description: Library name: Sample9


title: TSLP_woSI_3

description:
Library name: Sample3
TSLP_3


title: Spleen, PAMP_sti_1

description: Library name: Sample3


title: TSLP_woSI_1

description:
Library name: Sample1
TSLP_1


title: Spleen, PAMP_sti_3

description: Library name: Sample5


title: Med-cDC2_1

description: Library name: Sample7


title: Spleen, PAMP_ctr_2

description: Library name: Sample2


title: Med-cDC2_2

description: Library name: Sample8


title: TSLP_woSI_2

description:
Library name: Sample2
TSLP_2


title: TSLP-cDC2_2

description: Library name: Sample5


title: cDC2_2

description: Library name: Sample2


title: TSLP-cDC2_3

description: Library name: Sample6


title: cDC2_3

description: Library name: Sample3


title: cDC2_1

description: Library name: Sample1


title: Donor_6_snRNA-seq

data_processing:
10xGenomics chromium single cell software Cell Ranger arc version 2.0.2 analysis pipelines performed sample demultiplexing, barcode processing, and single cell 3' gene counting. Single cell gene expression raw data were processed using the single cell R software Seurat 4 and Signac. Genome_build: hg38
Assembly: hg38
Supplementary files format and content: RDS files composing processed  Seurat V4/Signac object inlcuding multiomic data of all sorted cells and cDCs.

extract_protocol:
The tissue was cut into as small blocks as possible by scissors, and digested with 2 mg/ml. collagenase IV (2091GR001, BioFRoXX, Guangzhou, China) in the presence of 0.1 mg/ml DNase (Roche, Basel, Switzerland) for 20 min and ground by gentleMACS Dissociatir (Miltenyi Biotec, Germany) to obtain a single-cell suspension. Afterward, the cells were filtered with a 70-um cell strainer (Corning). Mononuclear cells were isolated from Ficoll-Paque Plus (17-1440-03; GE Healthcare) density gradient (lymphoprep; axis shield).
Cells were lysed and nuclei were isolated according to the manufacturers’ instructions: Nuclei Isolation for Single Cell Multiome ATAC + Gene Expression Sequencing protocol (CG000365 Rev A), and genomic DNA and RNA were processed with a Chromium Single Cell Multiome ATAC + Gene Expression kit refer to the following protocol: Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide (CG000338 Rev E). Single-cell RNA-seq and ATAC seq libraries were prepared in the Wuhan Biobank using the following reagents: Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent bundle (PN-1000283), Chromium Next GEM Chip J Single Cell Kit (PN-1000234). Nuclei were transposed in bulk solution in a Veriti 96-Well Thermal Cycler. The transposed nuclei suspensions were then loaded into a microfluidic chip and run in the Chromium Controller to generate Gel Beads-in-emulsion (GEMs) containing single nuclei. All steps to produce single-cell ATAC and gene expression libraries were performed according to the manufacturer’s instructions. cDNA, ATAC library, and gene expression library quantity and quality were assessed using the Agilent 2100 Bioanalyzer (High Sensitivity DNA chip). Libraries were sequenced on a NovaSeq6000 instrument.
Chromium Single Cell Multiome ATAC + Gene Expression

tag: library type

value: mRNA


title: Donor_6_scATAC-seq

value: ATAC


title: Donor_6_scRNA-seq

data_processing:
10xGenomics chromium single cell software Cell Ranger version 7.1.0 analysis pipelines performed sample demultiplexing, barcode processing, and single cell 3' gene counting. Single cell gene expression raw data were processed using the single cell R software Seurat 4. Software velocyto was utilized to quantify spliced and unspliced mRNA UMIs and further RNA velocity analysis was performed using Python package scvelo. Genome_build: hg38
Assembly: hg38
Supplementary files format and content: RDS files composing preprocessed Seurat V4 object for all sorted cells and cDCs in individual samples, and an object intergrating cDCs from all 3 samples


title: Donor_10_scRNA-seq


title: Donor_12_scRNA-seq


title: WN cells, hypoxia, rep3

city: Chicago

first: Mark

last: Applebaum

state: IL

address: 900 E 57th St

department: Pediatrics, Section of Hematology/Oncology

institute: University of Chicago

data_processing:
Trimmomatic (version 0.36) was used to process raw reads
reads were aligned to GRCh38 using STAR-aligner (version 2.6.1d)
Aligned reads were counted using featureCounts of subread (version 1.5.3), with the -exon flag
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw counts for each sample

source_name: NBL-W-N

growth_protocol: Cells were grown in RPMI1640 medium (Life Technologies) supplemented with 10% heat-inactivated FBS, 2 mmol/L l-glutamine, and 1% penicillin/streptomycin

extract_protocol:
RNA was isolated using TRIzol® reagent (Life Technologies) according to the manufacture’s protocol
Strand-specific RNA-SEQ libraries were prepared using an oligo-dT based RNA-SEQ library protocol (Illumina/NEB/Kapa provided).

treatment_protocol: Cells were grown at 1% O2 for 48 hours prior to RNA collection.

value: NBL-W-N

value: neuroblastoma cell line, MYCN-amplified

tag: genotype

value: WT

value: hypoxia

value: Day 2


title: WS cells, hypoxia, rep2

source_name: NBL-W-S

tag: cell line

value: NBL-W-S


title: WS cells, hypoxia, rep1

tag: cell type


title: WN cells, hypoxia, rep2


title: WN cells, hypoxia, rep1


title: SY5Y cells, hypoxia, rep1

value: neuroblastoma cell line, MYCN-non-amplified


title: SY5Y cells, hypoxia, rep2


title: SHEP cells, hypoxia, rep2

source_name: SHEP

value: SHEP


title: SY5Y cells, hypoxia, rep3


title: NBLS cells, hypoxia, rep2

source_name: NBL-S

value: NBL-S

value: neuroblastoma celll line, MYCN-overexpressing


title: WS cells, hypoxia, rep3


title: BE2 cells, hypoxia, rep3


title: NBLS cells, hypoxia, rep1


title: BE2 cells, hypoxia, rep2


title: SHEP cells, hypoxia, rep3


title: 5S cells, hypoxia, rep3


title: 5S cells, hypoxia, rep2


title: 55N cells, hypoxia, rep2


title: BE2 cells, hypoxia, rep1


title: 5S cells, hypoxia, rep1


title: Whole-blood RNA-seq from pre-ACLF(S99)

city: Barcelona

first: Ferran

last: Aguilar Parera

state: BARCELONA

address: Avinguda Diagonal 477, 11th floor, EF CLIF

country: Spain

institute: EF-CLIF

data_processing:
The reads were aligned to the hg38 genome assembly and the transcriptome using STAR v2.5.3a and GENCODE 26 annotation
Gene expression was quantified using STAR (–quantMode GeneCounts) and VSN-transformed (variance stabilizing normalization)
Then a quantile normalization method was applied to normalize the nonbiological variability.
Using the HUGO Genome Nomenclature Committee (HGNC), which is a resource for approved human gene nomenclature, we included protein-coding genes, and among other gene locus types, immunoglobulin genes, and T cell receptor genes. Genes brought by sexual chromosomes and mitochondrial DNA were not included in the analysis.
Assembly: hg38
Supplementary files format and content: tab-delimited file with expected counts (RSEM) for each sample

source_name: Whole blood

extract_protocol:
RNA was isolated from blood stored in Tempus tubes using the Tempus™ Spin RNA Isolation Kit (reference 4380204, Applied Biosystems). RNA quality was assessed using Agilent RNA 6000 Nano and Pico Chips (Agilent Technologies, Cat.# 5067-1511 and Cat.# 5067-151, respectively) and concentration via Qubit RNA HS Assay Kit (Thermo Fisher Scientific, Cat.# Q32855).
Sequencing libraries were prepared using the TruSeq Stranded Total RNA with Ribo-Zero Globin kit (Illumina Inc., Cat.# 20020612) and TruSeq RNA CD Index Plate (Illumina Inc., Cat.# 20019792) following TruSeq Stranded Total RNA Sample Prep-guide (Part # 15031048 Rev. E). Briefly, starting from 500 ng of total RNA, rRNA and globin mRNA were depleted and remaining RNA was purified, fragmented and primed for cDNA synthesis. cDNA first strand was synthesized with SuperScript-II Reverse Transcriptase (Thermo Fisher Scientific, Cat.#18064-014) for 10 min at 25°C, 15 min at 42°C, 15 min at 70°C and pause at 4°C. cDNA second strand was synthesized with Illumina reagents at 16°C for 1 hour. Then, A-tailing and adaptor ligation were performed. Finally, enrichment of libraries was achieved by PCR (30 sec at 98°C; 15 cycles of 10 sec at 98°C, 30 sec at 60°C, 30 sec at 72°C; 5min at 72°C and pause at 4°C). Afterwards, libraries were visualized on an Agilent 2100 Bioanalyzer using Agilent High Sensitivity DNA kit (Agilent Technologies, Cat. # 5067-4626), quantified using Qubit dsDNA HS DNA Kit (Thermo Fisher Scientific, Cat. # Q32854) and sequenced in a NovaSeq-6000 (Illumina Inc.) by at least 100 million paired-end 100nt reads.

value: Whole blood

value: pre-ACLF


title: Whole-blood RNA-seq from pre-ACLF(S94)


title: Whole-blood RNA-seq from pre-ACLF(S92)


title: Whole-blood RNA-seq from pre-ACLF(S97)


title: 55N cells, hypoxia, rep3


title: Whole-blood RNA-seq from pre-ACLF(S89)


title: Whole-blood RNA-seq from AD(S90)

value: AD


title: Whole-blood RNA-seq from pre-ACLF(S88)


title: 55N cells, hypoxia, rep1


title: Whole-blood RNA-seq from pre-ACLF(S85)


title: Whole-blood RNA-seq from pre-ACLF(S86)


title: Whole-blood RNA-seq from pre-ACLF(S84)


title: Whole-blood RNA-seq from pre-ACLF(S93)


title: Whole-blood RNA-seq from pre-ACLF(S81)


title: Whole-blood RNA-seq from AD(S79)


title: Whole-blood RNA-seq from pre-ACLF(S71)


title: Whole-blood RNA-seq from pre-ACLF(S72)


title: Whole-blood RNA-seq from pre-ACLF(S65)


title: Whole-blood RNA-seq from pre-ACLF(S87)


title: Whole-blood RNA-seq from pre-ACLF(S68)


title: Whole-blood RNA-seq from pre-ACLF(S63)


title: Whole-blood RNA-seq from pre-ACLF(S69)


title: Whole-blood RNA-seq from pre-ACLF(S59)


title: Whole-blood RNA-seq from pre-ACLF(S61)


title: Whole-blood RNA-seq from AD(S55)


title: Whole-blood RNA-seq from pre-ACLF(S50)


title: Whole-blood RNA-seq from pre-ACLF(S77)


title: Whole-blood RNA-seq from pre-ACLF(S45)


title: Whole-blood RNA-seq from pre-ACLF(S52)


title: Whole-blood RNA-seq from pre-ACLF(S66)


title: Whole-blood RNA-seq from AD(S46)


title: Whole-blood RNA-seq from pre-ACLF(S62)


title: Whole-blood RNA-seq from pre-ACLF(S40)


title: Whole-blood RNA-seq from pre-ACLF(S41)


title: Whole-blood RNA-seq from AD(S43)


title: Whole-blood RNA-seq from AD(S38)


title: Whole-blood RNA-seq from pre-ACLF(S42)


title: Whole-blood RNA-seq from AD(S35)


title: Whole-blood RNA-seq from pre-ACLF(S37)


title: Whole-blood RNA-seq from pre-ACLF(S31)


title: Whole-blood RNA-seq from AD(S33)


title: Whole-blood RNA-seq from pre-ACLF(S26)


title: Whole-blood RNA-seq from pre-ACLF(S28)


title: Whole-blood RNA-seq from AD(S25)


title: Whole-blood RNA-seq from AD(S20)


title: Whole-blood RNA-seq from pre-ACLF(S22)


title: Whole-blood RNA-seq from pre-ACLF(S16)


title: Whole-blood RNA-seq from AD(S102)


title: Whole-blood RNA-seq from pre-ACLF(S14)


title: Whole-blood RNA-seq from AD(S11)


title: Whole-blood RNA-seq from pre-ACLF(S27)


title: Whole-blood RNA-seq from AD(S18)


title: Whole-blood RNA-seq from pre-ACLF(S07)


title: Whole-blood RNA-seq from AD(S100)


title: Whole-blood RNA-seq from pre-ACLF(S02)


title: Whole-blood RNA-seq from AD(S03)


title: Whole-blood RNA-seq from AD(S01)


title: Whole-blood RNA-seq from pre-ACLF(S04)


title: Whole-blood RNA-seq from pre-ACLF(pS75)


title: Whole-blood RNA-seq from pre-ACLF(pS73)


title: Whole-blood RNA-seq from pre-ACLF(pS71)


title: Whole-blood RNA-seq from AD(pS70)


title: Whole-blood RNA-seq from AD(S17)


title: Whole-blood RNA-seq from pre-ACLF(pS74)


title: Whole-blood RNA-seq from AD(S104)


title: Whole-blood RNA-seq from AD(pS69)


title: Whole-blood RNA-seq from pre-ACLF(pS72)


title: Whole-blood RNA-seq from pre-ACLF(pS68)


title: Whole-blood RNA-seq from pre-ACLF(pS63)


title: Whole-blood RNA-seq from pre-ACLF(pS67)


title: Whole-blood RNA-seq from AD(pS65)


title: Whole-blood RNA-seq from AD(pS66)


title: Whole-blood RNA-seq from pre-ACLF(pS53)


title: Whole-blood RNA-seq from pre-ACLF(pS52)


title: Whole-blood RNA-seq from pre-ACLF(pS51)


title: Whole-blood RNA-seq from pre-ACLF(pS50)


title: Whole-blood RNA-seq from pre-ACLF(pS48)


title: Whole-blood RNA-seq from pre-ACLF(pS64)


title: Whole-blood RNA-seq from AD(pS62)


title: Whole-blood RNA-seq from pre-ACLF(pS46)


title: Whole-blood RNA-seq from pre-ACLF(pS60)


title: Whole-blood RNA-seq from AD(pS43)


title: Whole-blood RNA-seq from AD(pS29)


title: Whole-blood RNA-seq from pre-ACLF(pS47)


title: Whole-blood RNA-seq from AD(pS39)


title: Whole-blood RNA-seq from pre-ACLF(pS49)


title: Whole-blood RNA-seq from pre-ACLF(pS24)


title: Whole-blood RNA-seq from pre-ACLF(pS33)


title: Whole-blood RNA-seq from pre-ACLF(pS26)


title: Whole-blood RNA-seq from AD(pS56)


title: Whole-blood RNA-seq from pre-ACLF(pS22)


title: Whole-blood RNA-seq from pre-ACLF(pS32)


title: Whole-blood RNA-seq from pre-ACLF(pS18)


title: Whole-blood RNA-seq from pre-ACLF(pS17)


title: Whole-blood RNA-seq from pre-ACLF(pS30)


title: Whole-blood RNA-seq from pre-ACLF(pS27)


title: Whole-blood RNA-seq from pre-ACLF(pS25)


title: Whole-blood RNA-seq from AD(pS16)


title: Whole-blood RNA-seq from pre-ACLF(pS15)


title: Whole-blood RNA-seq from pre-ACLF(pS21)


title: Whole-blood RNA-seq from pre-ACLF(pS23)


title: Whole-blood RNA-seq from pre-ACLF(pS34)


title: Whole-blood RNA-seq from pre-ACLF(pS14)


title: Whole-blood RNA-seq from AD(pS09)


title: Whole-blood RNA-seq from pre-ACLF(pS12)


title: Whole-blood RNA-seq from pre-ACLF(pS13)


title: Whole-blood RNA-seq from pre-ACLF(pS05)


title: Whole-blood RNA-seq from pre-ACLF(pS11)


title: Whole-blood RNA-seq from pre-ACLF(pS10)


title: Whole-blood RNA-seq from pre-ACLF(pS06)


title: Whole-blood RNA-seq from pre-ACLF(pS07)


title: Whole-blood RNA-seq from AD(58_009_S02_08)


title: Whole-blood RNA-seq from pre-ACLF(pS08)


title: Whole-blood RNA-seq from AD(58_008_S01_08)


title: Whole-blood RNA-seq from ACLF(53_002_S00_08)

value: ACLF


title: Whole-blood RNA-seq from pre-ACLF(pS03)


title: Whole-blood RNA-seq from AD(58_009_S00_08)


title: Whole-blood RNA-seq from pre-ACLF(pS02)


title: Whole-blood RNA-seq from pre-ACLF(58_003_S00_08)


title: Whole-blood RNA-seq from AD(51_022_S00_08)


title: Whole-blood RNA-seq from AD(51_021_S02_08)


title: Whole-blood RNA-seq from AD(51_017_S00_08)


title: Whole-blood RNA-seq from AD(51_026_S00_08)


title: Whole-blood RNA-seq from AD(51_022_S01_08)


title: Whole-blood RNA-seq from AD(51_026_S01_08)


title: Whole-blood RNA-seq from AD(51_026_S02_08)


title: Whole-blood RNA-seq from AD(51_021_S00_08)


title: Whole-blood RNA-seq from AD(51_011_S01_08)


title: Whole-blood RNA-seq from AD(51_015_S02_08)


title: Whole-blood RNA-seq from ACLF(51_008_S00_08)


title: Whole-blood RNA-seq from AD(51_009_S00_08)


title: Whole-blood RNA-seq from ACLF(53_002_A01_08)


title: Whole-blood RNA-seq from AD(51_009_S02_08)


title: Whole-blood RNA-seq from AD(51_002_S00_08)


title: Whole-blood RNA-seq from AD(51_015_S00_08)


title: Whole-blood RNA-seq from AD(51_013_S00_08)


title: Whole-blood RNA-seq from ACLF(50_023_A01_08)


title: Whole-blood RNA-seq from AD(51_011_S00_08)


title: Whole-blood RNA-seq from AD(51_022_S02_08)


title: Whole-blood RNA-seq from AD(50_013_S00_08)


title: Whole-blood RNA-seq from ACLF(50_023_S00_08)


title: Whole-blood RNA-seq from AD(50_013_S01_08)


title: Whole-blood RNA-seq from AD(50_013_S02_08)


title: Whole-blood RNA-seq from AD(51_002_S02_08)


title: Whole-blood RNA-seq from AD(50_025_S00_08)


title: Whole-blood RNA-seq from AD(49_033_S00_08)


title: Whole-blood RNA-seq from AD(49_027_S02_08)


title: Whole-blood RNA-seq from AD(49_023_S02_08)


title: Whole-blood RNA-seq from AD(49_021_S02_08)


title: Whole-blood RNA-seq from AD(49_026_S02_08)


title: Whole-blood RNA-seq from AD(49_023_S00_08)


title: Whole-blood RNA-seq from AD(49_021_S00_08)


title: Whole-blood RNA-seq from AD(49_027_S00_08)


title: Whole-blood RNA-seq from AD(49_012_S01_08)


title: Whole-blood RNA-seq from AD(49_016_S00_08)


title: Whole-blood RNA-seq from AD(49_012_S00_08)


title: Whole-blood RNA-seq from AD(49_012_S02_08)


title: Whole-blood RNA-seq from AD(49_004_S02_08)


title: Whole-blood RNA-seq from AD(49_004_S00_08)


title: Whole-blood RNA-seq from AD(49_007_S00_08)


title: Whole-blood RNA-seq from AD(49_026_S00_08)


title: Whole-blood RNA-seq from ACLF(46_010_S00_08)


title: Whole-blood RNA-seq from AD(49_016_S02_08)


title: Whole-blood RNA-seq from AD(46_011_S02_08)


title: Whole-blood RNA-seq from ACLF(45_030_S00_08)


title: Whole-blood RNA-seq from AD(45_029_S00_08)


title: Whole-blood RNA-seq from ACLF(46_010_A02_08)


title: Whole-blood RNA-seq from AD(46_009_S02_08)


title: Whole-blood RNA-seq from ACLF(45_030_A01_08)


title: Whole-blood RNA-seq from AD(45_027_S02_08)


title: Whole-blood RNA-seq from AD(45_027_S00_08)


title: Whole-blood RNA-seq from AD(46_011_S00_08)


title: Whole-blood RNA-seq from AD(45_024_S02_08)


title: Whole-blood RNA-seq from AD(45_024_S00_08)


title: Whole-blood RNA-seq from AD(45_011_S02_08)


title: Whole-blood RNA-seq from AD(46_009_S00_08)


title: Whole-blood RNA-seq from AD(45_006_S00_08)


title: Whole-blood RNA-seq from AD(45_014_S00_08)


title: Whole-blood RNA-seq from AD(45_011_S00_08)


title: Whole-blood RNA-seq from AD(45_014_S02_08)


title: Whole-blood RNA-seq from AD(45_009_S02_08)


title: Whole-blood RNA-seq from AD(45_005_S00_08)


title: Whole-blood RNA-seq from AD(45_003_S02_08)


title: Whole-blood RNA-seq from ACLF(45_001_A02_08)


title: Whole-blood RNA-seq from ACLF(45_001_S00_08)


title: Whole-blood RNA-seq from AD(44_I_004_S00_09)


title: Whole-blood RNA-seq from ACLF(432001_S01)


title: Whole-blood RNA-seq from AD(44_I_008_S00_09)


title: Whole-blood RNA-seq from AD(45_003_S00_08)


title: Whole-blood RNA-seq from AD(44_I_010_S00_09)


title: Whole-blood RNA-seq from AD(44_I_005_S00_09)


title: Whole-blood RNA-seq from AD(44_I_007_S00_09)


title: Whole-blood RNA-seq from AD(45_009_S00_08)


title: Whole-blood RNA-seq from ACLF(43045_S00)


title: Whole-blood RNA-seq from ACLF(43045_A02)


title: Whole-blood RNA-seq from pre-ACLF(43025_500)


title: Whole-blood RNA-seq from pre-ACLF(43038_A00)


title: Whole-blood RNA-seq from pre-ACLF(43025_S01)


title: Whole-blood RNA-seq from ACLF(43_060_A01_08)


title: Whole-blood RNA-seq from ACLF(43_060_S00_08)


title: Whole-blood RNA-seq from ACLF(432001_S00)


title: Whole-blood RNA-seq from pre-ACLF(43038_S00)


title: Whole-blood RNA-seq from AD(43_056_S01_08)


title: Whole-blood RNA-seq from ACLF(43_057_A01_08)


title: Whole-blood RNA-seq from AD(43_056_S02_08)


title: Whole-blood RNA-seq from AD(43_056_S00_08)


title: Whole-blood RNA-seq from AD(43_050_S02_08)


title: Whole-blood RNA-seq from AD(43_052_S02_08)


title: Whole-blood RNA-seq from AD(43_052_S00_08)


title: Whole-blood RNA-seq from AD(43_047_S01_08)


title: Whole-blood RNA-seq from AD(43_047_S02_08)


title: Whole-blood RNA-seq from ACLF(43_057_S00_08)


title: Whole-blood RNA-seq from AD(43_047_S00_08)


title: Whole-blood RNA-seq from ACLF(43_046_S00_08)


title: Whole-blood RNA-seq from ACLF(43_042_S00_08)


title: Whole-blood RNA-seq from ACLF(43_027_A01_08)


title: Whole-blood RNA-seq from ACLF(43_046_A02_08)


title: Whole-blood RNA-seq from ACLF(43_018_A01_08)


title: Whole-blood RNA-seq from ACLF(43_013_S00_08)


title: Whole-blood RNA-seq from ACLF(43_013_A01_08)


title: Whole-blood RNA-seq from ACLF(43_007_S00_08)


title: Whole-blood RNA-seq from ACLF(43_007_A01_08)


title: Whole-blood RNA-seq from ACLF(43_018_S00_08)


title: Whole-blood RNA-seq from pre-ACLF(43_004_S00_08)


title: Whole-blood RNA-seq from AD(43_050_S00_08)


title: Whole-blood RNA-seq from ACLF(43_027_S00_08)


title: Whole-blood RNA-seq from AD(421011_S01)


title: Whole-blood RNA-seq from ACLF(43_003_S00_08)


title: Whole-blood RNA-seq from ACLF(43_003_A01_08)


title: Whole-blood RNA-seq from AD(421008_S01)


title: Whole-blood RNA-seq from AD(421008_S00)


title: Whole-blood RNA-seq from AD(421005_S01)


title: Whole-blood RNA-seq from AD(421003_S01)


title: Whole-blood RNA-seq from AD(49_033_S02_08)


title: Whole-blood RNA-seq from ACLF(42027_S00)


title: Whole-blood RNA-seq from ACLF(42027_A02)


title: Whole-blood RNA-seq from ACLF(42024_S00)


title: Whole-blood RNA-seq from AD(421003_S00)


title: Whole-blood RNA-seq from AD(421011_S00)


title: Whole-blood RNA-seq from ACLF(42024_A02)


title: Whole-blood RNA-seq from pre-ACLF(42001_A00)


title: Whole-blood RNA-seq from pre-ACLF(42001_S00)


title: Whole-blood RNA-seq from AD(42_I_005_S00_09)


title: Whole-blood RNA-seq from AD(42_I_002_S00_09)


title: Whole-blood RNA-seq from pre-ACLF(42_I_012_S00_09)


title: Whole-blood RNA-seq from AD(42_026_S00_08)


title: Whole-blood RNA-seq from AD(42_021_S00_08)


title: Whole-blood RNA-seq from AD(42_023_S02_08)


title: Whole-blood RNA-seq from pre-ACLF(42_038_S00_08)


title: Whole-blood RNA-seq from AD(42_026_S02_08)


title: Whole-blood RNA-seq from AD(42_019_S02_08)


title: Whole-blood RNA-seq from AD(42_021_S02_08)


title: Whole-blood RNA-seq from AD(42_011_S02_08)


title: Whole-blood RNA-seq from AD(42_019_S00_08)


title: Whole-blood RNA-seq from AD(42_023_S00_08)


title: Whole-blood RNA-seq from AD(42_011_S00_08)


title: Whole-blood RNA-seq from ACLF(42_005_S00_08)


title: Whole-blood RNA-seq from AD(42_003_S02_08)


title: Whole-blood RNA-seq from AD(42_003_S00_08)


title: Whole-blood RNA-seq from ACLF(42_005_A02_08)


title: Whole-blood RNA-seq from AD(411003_S01)


title: Whole-blood RNA-seq from AD(411003_S00)


title: Whole-blood RNA-seq from AD(42_002_S00_08)


title: Whole-blood RNA-seq from ACLF(41004_S00)


title: Whole-blood RNA-seq from ACLF(41004_A01)


title: Whole-blood RNA-seq from ACLF(41001_S00)


title: Whole-blood RNA-seq from AD(41_I_010_S00_09)


title: Whole-blood RNA-seq from ACLF(41_023_A02_08)


title: Whole-blood RNA-seq from ACLF(41_023_S00_08)


title: Whole-blood RNA-seq from ACLF(41_019_S00_08)


title: Whole-blood RNA-seq from ACLF(412002_S00)


title: Whole-blood RNA-seq from ACLF(41_019_A02_08)


title: Whole-blood RNA-seq from ACLF(41_011_S00_08)


title: Whole-blood RNA-seq from ACLF(41_003_A01_08)


title: Whole-blood RNA-seq from ACLF(41_002_S00_08)


title: Whole-blood RNA-seq from ACLF(41_002_A01_08)


title: Whole-blood RNA-seq from ACLF(41001_A02)


title: Whole-blood RNA-seq from ACLF(402001_S00)


title: Whole-blood RNA-seq from AD(40_I_022_S00_09)


title: Whole-blood RNA-seq from ACLF(41_003_S00_08)


title: Whole-blood RNA-seq from ACLF(402002_S01)


title: Whole-blood RNA-seq from ACLF(402002_S00)


title: Whole-blood RNA-seq from pre-ACLF(40_I_019_S00_09)


title: Whole-blood RNA-seq from AD(40_I_005_S00_09)


title: Whole-blood RNA-seq from AD(40_I_003_S00_09)


title: Whole-blood RNA-seq from ACLF(382014_S01)


title: Whole-blood RNA-seq from ACLF(382014_S00)


title: Whole-blood RNA-seq from AD(39_I_010_S00_09)


title: Whole-blood RNA-seq from ACLF(382009_S01)


title: Whole-blood RNA-seq from ACLF(382003_S01)


title: Whole-blood RNA-seq from ACLF(382004_S01)


title: Whole-blood RNA-seq from ACLF(382009_S00)


title: Whole-blood RNA-seq from AD(40_I_015_S00_09)


title: Whole-blood RNA-seq from ACLF(382003_S00)


title: Whole-blood RNA-seq from ACLF(382012_S00)


title: Whole-blood RNA-seq from ACLF(382015_S00)


title: Whole-blood RNA-seq from ACLF(382004_S00)


title: Whole-blood RNA-seq from ACLF(382012_S01)


title: Whole-blood RNA-seq from ACLF(382006_S00)


title: Whole-blood RNA-seq from ACLF(382001_S00)


title: Whole-blood RNA-seq from pre-ACLF(38011_A00)


title: Whole-blood RNA-seq from ACLF(38004_S00)


title: Whole-blood RNA-seq from ACLF(38004_S02)


title: Whole-blood RNA-seq from ACLF(38003_S00)


title: Whole-blood RNA-seq from ACLF(38_009_A01_08)


title: Whole-blood RNA-seq from ACLF(38_009_S00_08)


title: Whole-blood RNA-seq from pre-ACLF(38011_A02)


title: Whole-blood RNA-seq from ACLF(372001_S00)


title: Whole-blood RNA-seq from ACLF(372003_S00)


title: Whole-blood RNA-seq from AD(371020_S00)


title: Whole-blood RNA-seq from AD(371018_S00)


title: Whole-blood RNA-seq from ACLF(38003_S02)


title: Whole-blood RNA-seq from AD(37_I_008_S00_09)


title: Whole-blood RNA-seq from AD(37_I_012_S00_09)


title: Whole-blood RNA-seq from AD(36_I_024_S00_09)


title: Whole-blood RNA-seq from AD(37_I_014_S00_09)


title: Whole-blood RNA-seq from AD(36_I_011_S00_09)


title: Whole-blood RNA-seq from AD(36_I_014_S00_09)


title: Whole-blood RNA-seq from AD(36_I_021_S00_09)


title: Whole-blood RNA-seq from AD(37_I_016_S00_09)


title: Whole-blood RNA-seq from AD(36_I_001_S00_09)


title: Whole-blood RNA-seq from AD(36_I_016_S00_09)


title: Whole-blood RNA-seq from AD(36_I_010_S00_09)


title: Whole-blood RNA-seq from pre-ACLF(33035_S00)


title: Whole-blood RNA-seq from ACLF(332007_S00)


title: Whole-blood RNA-seq from AD(36_I_003_S00_09)


title: Whole-blood RNA-seq from ACLF(332007_S01)


title: Whole-blood RNA-seq from ACLF(332016_S00)


title: Whole-blood RNA-seq from pre-ACLF(33029_A00)


title: Whole-blood RNA-seq from AD(37_I_002_S00_09)


title: Whole-blood RNA-seq from ACLF(33020_S00)


title: Whole-blood RNA-seq from pre-ACLF(33022_S00)


title: Whole-blood RNA-seq from ACLF(33020_A01)


title: Whole-blood RNA-seq from pre-ACLF(33019_S00)


title: Whole-blood RNA-seq from AD(42_002_S02_08)


title: Whole-blood RNA-seq from pre-ACLF(33035_A01)


title: Whole-blood RNA-seq from pre-ACLF(33019_A00)


title: Whole-blood RNA-seq from pre-ACLF(33022_A00)


title: Whole-blood RNA-seq from pre-ACLF(33017_S00)


title: Whole-blood RNA-seq from ACLF(33001_S00)