title: HT-F2

description:
Library name: sample14
14_FPKM


title: early_OE_lncPRESS1DATG_b

status: Public on Feb 20 2026

type: SRA

city: Redwood City

first: Jin

last: Chen

state: CA

address: 2800 Bridge Parkway

country: USA

institute: Altos Labs

description:
Sample_104
rna_seq_gene_counts_length_scaled.tsv

library_source: transcriptomic

data_processing:
RNA-seq FASTQ files were trimmed, aligned to the human reference genome (GRCh38, v108), and quantified using the nf-core/rnaseq pipeline with the star_salmon option (v3.12.0).
Assembly: GRCh38, v108
Supplementary files format and content: text file includes length scaled quantification for each sample.

molecule: polyA RNA

organism: Homo sapiens

source_name: H1 ESC

growth_protocol: H1-hESCs WA01 (WiCell) and iPSC (derived from BJ fibroblasts cells from ATCC CRL-2522 using the Thermo CytoTune-iPS Sendai Reprogramming #A16517) confirmed via STR Profiling were cultured on Corning™ Matrigel™ hESC-Qualified Matrix (Fisher Scientific #08-774-552) or Geltrex™ LDEV-Free (Thermo Scientific #A1413202) coated cell culture dishes using mTeSR™ Plus media (STEMCELL Technologies #5825) with daily media changes.

extract_protocol:
The WT, KO, and ΔATG hESCs and trilineage differentiated cells were collected and RNA was extracted in accordance with Qiagen RNeasy Mini (Qiagen #74106) protocol with 650 uL lysis buffer.
Libraries were prepared in accordance with Illumina Stranded mRNA Prep, Ligation (Illumina #20040534) protocol using 100 ng RNA input.

treatment_protocol:
Neural progenitor cells (NPCs): The differentiation of stem cells into NPCs was performed by using the STEMdiff™ SMADi Neural Induction Kit (STEMCELL Technologies #8581), following the manufacturer's protocol. Briefly, dissociated single cells were seeded on Geltrex™ coated 6-well plates at a density of 2 x 106 cells per well with 10 µM Y-27632 ROCK inhibitor on day 0. Cells were maintained in 2 mL of STEMdiff™ Neural Induction Medium + SMADi per well with daily media changes.
Definitive Endoderm: The differentiation of stem cells into definitive endoderm was performed by using the STEMdiff™ Definitive Endoderm Kit (STEMCELL Technologies #5110), following the manufacturer's protocol. Briefly, cells were first dissociated into single cells and then seeded on Matrigel™ coated 6-well plates at a density of 2 x 106 cells per well with 10 µM Y-27632 ROCK inhibitor on day 0. On day 1, the media was changed to 2 mL of medium 1 (diluted STEMdiff™ Definitive Endoderm Supplement MR and STEMdiff™ Definitive Endoderm Supplement CJ 1 in 100 in STEMdiff™ Endoderm Basal Medium). From day 2 to day 5, the media was changed daily to 2 mL medium 2 (diluted STEMdiff™ Definitive Endoderm Supplement CJ 1 in 100 in STEMdiff™ Endoderm Basal Medium).
Mesoderm: The differentiation of stem cells into mesoderm was performed by using the STEMdiff™ Mesoderm Induction Medium (STEMCELL Technologies #05221), following the manufacturer's protocol. The cells were first dissociated into single cells and then seeded on Matrigel™ coated 15 cm2 plates at a density of 7.5 x 106 cells in 20 mL mTesR medium with 10 µM Y-27632 ROCK inhibitor on day 0. On day 1, the media was changed to 45 mL STEMdiff™ Mesoderm Induction Medium. From day 2 to day 5, the media was changed daily.
H1-hESCs were differentiated into mesoderm germ layers using bone morphogenetic protein 4 (BMP4, Sigma-Aldrich #H4916). The hESCs were seeded at 0.5 x 106 cells per well in a Matrigel™ coated 6-well plate with mTeSR media on day 0 and changed to mTeSR + 50 ng/mL BMP4 on day 1 to day 5.
The spontaneous differentiation experiments were conducted according to  reference (18): hESCs were seeded at a density of 0.5 x 106 cells per well in a Matrigel™ coated 6-well plate with mTesR medium and changed to spontaneous differentiation medium (DMEM/F12, 15% knockout serum replacement, MEM non-essential amino acid solution, and 0.1 mM β-mercaptoethanol) on day 1 to day 5.

tag: cell line

value: H1 ESC

tag: cell type

value: Human Embryonic Stem Cells


title: HT-F3

city: haikou

first: yue

last: chen

address: No. 58 Renmin Avenue, Meilan District

country: China

institute: Hainan University

description:
Library name: sample15
15_FPKM

data_processing:
Total RNA was extracted from tissue samples. The concentration and purity of the extracted RNA were measured using Nanodrop 2000, while RNA integrity was assessed by agarose gel electrophoresis. The RQN value was determined using the Agilent 5300 system. For library construction, the RNA sample must meet the following criteria: a total amount of ≥1 μg, a concentration of ≥30 ng/μL, an RQN > 6.5, and an OD260/280 ratio between 1.8 and 2.2.
The 3' end of eukaryotic mRNA has a poly(A) tail. Magnetic beads with oligo(dT) sequences can hybridize with the poly(A) tail through A-T base pairing, allowing the isolation of mRNA from total RNA for transcriptome analysis.
Second-generation high-throughput sequencing platforms are designed for sequencing short DNA fragments. The enriched mRNA consists of full-length RNA sequences with an average length of several kilobases. Therefore, random fragmentation is required. By adding fragmentation buffer and optimizing the conditions, mRNA can be randomly fragmented into small fragments of approximately 300 bp.
Under the action of reverse transcriptase and using random primers, first-strand cDNA is synthesized from the mRNA template. Subsequently, the second strand is synthesized, forming a stable double-stranded structure.
The double-stranded cDNA has sticky ends. End Repair Mix is added to convert them into blunt ends. Subsequently, an A-base is added to the 3' end to facilitate the ligation of adapter sequences in the next step.The adapter-ligated products are purified and size-selected. The selected fragments are then subjected to PCR amplification, followed by purification to obtain the final library.
Assembly: GCF_014851395.1
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample.（processed data.xlsx）

molecule: total RNA

organism: Micropterus salmoides

source_name: gonad

extract_protocol:
RNA was harvested using Trizol reagent. 0.4 ug of total RNA was used for the construction of sequencing libraries；
RNA libraries were prepared for sequencing using standard Illumina protocols；

tag: tissue

value: gonad


title: Breast cancer serum sample 270

type: RNA

city: Santander

first: Inés

last: Gómez-Acebo

state: CANTABRIA

address: Avda. Cardenal Herrera Oria S/N

country: Spain

institute: Division of Epidemiology and Computational Biology, School of Medicine, University of Cantabria,  IDIVAL, Santander, Spain

data_processing: Cq values were determined using the second derivative method in Roche LightCycler software. Quality control included melting curve analysis, exclusion of reactions with more than one melting temperature, deviation from reference melting temperatures, and low amplification efficiency. Endogenous miRNAs let-7d-5p and let-7i-5p were used as internal reference controls. Expression data were normalized and subsequently log2-transformed for statistical analysis. Batch information is provided in the sample annotations.

label: SYBR Green

source_name: Serum

label_protocol: Not applicable. Quantification was performed using SYBR Green chemistry.

growth_protocol: Not applicable. Human serum samples collected from participants in the MCC-Spain study.

extract_protocol: Total RNA was extracted from 200 µL of serum using the miRNeasy Serum/Plasma Advanced Kit (QIAGEN). Serum samples were thawed on ice and centrifuged at 3,000×g for 5 minutes at 4 °C. Buffer RPL containing carrier RNA and spike-in template mix was added, followed by Buffer RPP. RNA was eluted in 50 µL according to the manufacturer’s protocol.

treatment_protocol: Blood samples were collected prior to any oncological treatment (surgery, chemotherapy, or radiotherapy).

value: Serum

value: case

value: Luminal A

tag: age


title: Breast cancer serum sample 275

value: Basal-like


title: Single cell CD4+CD44hiTomato+ isolated from PR8 infected mice 9 d.p.i, lung, medLN and spleen, exp 4

city: New York

first: Tiago

last: Castro

state: New York

address: 1230 York Avenue

institute: The Rockefeller University

description: Library name: RP121523_d9

library_source: transcriptomic single cell

data_processing:
Raw scRNA-seq FASTQ files were processed using Cell Ranger v7.0.1 for alignment, gene expression quantification, and feature barcode counting.
Gene expression and antibody-derived tag (ADT) matrices were imported into R and analyzed using Seurat v5.3. ADT counts were normalized using the centered log-ratio (CLR) method, and sample demultiplexing was performed using HTODemux. Cells with multiple hashtag assignments were classified as doublets and removed.
Cells with >5% mitochondrial gene expression were excluded. Expression data were normalized using SCTransform. Dimensionality reduction was performed by PCA, followed by UMAP for visualization. Differential gene expression analysis was conducted using the Wilcoxon rank-sum test with Bonferroni correction.
Plate-based TCR sequencing reads were demultiplexed, merged using PANDASEQ, collapsed, and aligned using IMGT/HighV-QUEST. Clonotypes were defined based on identical TCRβ CDR3 nucleotide sequences.
TCR repertoire analyses from scRNA-seq were performed using Cell Ranger filtered_contig_annotations files. Clonal relationships were assigned based on shared V/J genes, CDR3 length, and paired TRA/TRB sequences. Diversity and overlap metrics were calculated using custom R scripts and the divo package.
Assembly: Mouse reference genome mm10 (GRCm38).
Supplementary files format and content: Processed data include gene expression count matrices, feature barcode (ADT/hashtag) matrices, cell metadata tables, dimensionality reduction coordinates, and clonotype annotations. TCR sequencing outputs include FASTA files, IMGT alignment results, and clonotype assignment tables. All processed files are provided in tab-delimited text or Matrix Market formats suitable for downstream analysis in R.

organism: Mus musculus

source_name: Lung, medLN, Spleen

growth_protocol: Genetically engineered Cd69-CreERT2, Sell-DreERT2, and TRACK mice were maintained on a C57BL/6J background. Adult male and female mice (6–13 weeks old) were housed under specific pathogen-free conditions at 22.2 °C and 30–70% humidity on a 12 h light/dark cycle with ad libitum access to food and water. All animal procedures were approved by the Rockefeller University Institutional Animal Care and Use Committee (protocol 22071-H).

extract_protocol:
Single-cell suspensions were prepared from spleen, lung, lymph node, or intestinal tissues by mechanical dissociation or enzymatic digestion using collagenase and DNase I, followed by Percoll gradient centrifugation where applicable. CD4⁺ T cells were enriched by negative magnetic selection. Fate-mapped CD44⁺Tomato⁺ T cells were isolated by fluorescence-activated cell sorting (FACS). For scRNA-seq, sorted cells were immediately processed for droplet encapsulation. For plate-based TCR sequencing, single cells were index-sorted into lysis buffer and stored at −80 °C prior to reverse transcription.
Single-cell RNA-seq libraries were generated using the 10x Genomics Chromium Single Cell 3′ platform according to the manufacturer’s instructions. Feature barcode (TotalSeq-C hashtag) libraries were prepared in parallel. Plate-based single-cell TCRβ libraries were generated by RT-PCR amplification from sorted single cells, followed by multiplexed barcoding and Illumina TruSeq Nano library preparation. Libraries were sequenced on Illumina NextSeq 500 (scRNA-seq) or MiSeq (TCR sequencing) instruments.

value: Lung, medLN, Spleen

value: T cells

tag: treatment

value: Influenza PR8 infection


title: Single cell CD4+CD44hiTomato+ isolated from PR8 infected mice 9 d.p.i, lung, medLN and spleen, exp 5

description: Library name: RP230221_d9


title: NC-M3

description:
Library name: sample12
12_FPKM


title: Breast cancer serum sample 271


title: HT-F1

description:
Library name: sample13
13_FPKM


title: Breast cancer serum sample 268


title: Single cell CD4+CD44hiTomato+ isolated from PR8 infected mice 56 d.p.i, lung, medLN and spleen, exp 5

description: Library name: RP230324_d56


title: Single cell CD4+CD44hiTomato+ isolated from PR8 infected mice 120 d.p.i, lung, medLN and spleen, exp 2

description: Library name: RP110223_d120


title: Breast cancer serum sample 272


title: early_OE_lncPRESS1DATG_a

description:
Sample_100_Redo
rna_seq_gene_counts_length_scaled.tsv


title: Breast cancer serum sample 269

value: Luminal B


title: Single cell CD4+CD44hiTomato+ isolated from PR8 infected mice 9 d.p.i, lung, medLN and spleen, exp 3

description: Library name: RP112623_d9


title: NC-M1

description:
Library name: sample10
10_FPKM


title: early_OE-lncSIRP_a

description:
Sample_99
rna_seq_gene_counts_length_scaled.tsv


title: early_OE_lncPRESS1_b

description:
Sample_102
rna_seq_gene_counts_length_scaled.tsv


title: early_OE_lncPRESS1_a

description:
Sample_101
rna_seq_gene_counts_length_scaled.tsv


title: Breast cancer serum sample 266


title: early_OE-lncSIRP_b

description:
Sample_103
rna_seq_gene_counts_length_scaled.tsv


title: NC-F3

description:
Library name: sample9
9_FPKM


title: Single cell CD4+CD44hiTomato+ isolated from PR8 infected mice 56 d.p.i, lung, medLN and spleen, exp 4

description: Library name: RP080423_d56


title: Breast cancer serum sample 267


title: NC-M2

description:
Library name: sample11
11_FPKM


title: NC-F2

description:
Library name: sample8
8_FPKM


title: early_OE-vector_b

description:
Sample_98
rna_seq_gene_counts_length_scaled.tsv


title: Single cell CD4+CD44hiTomato+ isolated from PR8 infected mice 56 d.p.i, lung, medLN and spleen, exp 3

description: Library name: RP071824_d56


title: Single cell CD4+CD44hiTomato+ isolated from PR8 infected mice 9 d.p.i, lung, medLN and spleen, exp 2

description: Library name: RP070323_d9


title: early_OE-vector_a

description:
Sample_97
rna_seq_gene_counts_length_scaled.tsv


title: IC-M3

description:
Library name: sample6
6_FPKM


title: DATG_D5_Endo_b

description:
Sample_96
rna_seq_gene_counts_length_scaled.tsv


title: Breast cancer serum sample 263

value: Control


title: IC-M2

description:
Library name: sample5
5_FPKM


title: DATG_D5_Endo_a

description:
Sample_95
rna_seq_gene_counts_length_scaled.tsv


title: Single cell CD4+CD44hiTomato+ isolated from PR8 infected mice 56 d.p.i, lung, medLN and spleen, exp 2

description: Library name: RP062124_d56


title: Breast cancer serum sample 264


title: Breast cancer serum sample 265


title: Single cell CD4+CD44hiTomato+ isolated from PR8 infected mice 9 and 120 d.p.i, lung, medLN and spleen, exp 1

description: Library name: RP030724_d120_d9


title: KO_D5_Endo_b

description:
Sample_94
rna_seq_gene_counts_length_scaled.tsv


title: NC-F1

description:
Library name: sample7
7_FPKM


title: IC-F3

description:
Library name: sample3
3_FPKM


title: Single cell CD4+CD44hiTomato+ isolated from PR8 infected mice 56 d.p.i, lung, medLN and spleen, exp 1

description: Library name: RP010424_d56


title: KO_D5_Endo_a

description:
Sample_93
rna_seq_gene_counts_length_scaled.tsv


title: Breast cancer serum sample 259


title: Breast cancer serum sample 262


title: Breast cancer serum sample 260


title: IC-F2

description:
Library name: sample2
2_FPKM


title: Breast cancer serum sample 20664-039, case

description: Library name: 20664-039

data_processing:
Data integrity was maintained through a multi-step bioinformatic pipeline. We implemented stringent quality control measures, which included UMI collapsing to ensure unique sequence identification and the application of Phred score thresholds for sequencing accuracy. Short reads under 15 nucleotides were discarded, and the remaining sequences were aligned to the GRCh37 reference genome. To further refine the data, background filtering was performed to eliminate low-abundance reads; any samples failing to meet these rigorous benchmarks were excluded from subsequent analysis.
Assembly: GRCh37 human reference genome
Supplementary files format and content: Processed data is provided in individual TSV files for each sample, including: miRNA name, representative sequence, raw read counts, unique sequence counts, and normalized expression values as TPM.

growth_protocol: Human serum samples collected from women recruited in a population-based case-control study.

extract_protocol:
Total RNA was extracted from 200 µL of serum using the miRNeasy Serum/Plasma Kit (Qiagen) according to the manufacturer's instructions.
Raw FASTQ files were generated for each sample. Reads were processed using Cutadapt for UMI correction, Bowtie2 for alignment to Homo sapiens miRNA sequences from miRBase v22.1, and edgeR (Bioconductor) for differential expression analysis. Counts were normalized using the Trimmed Mean of M-values (TMM) method and log₂-transformed to obtain ΔCq values. Sequence annotation was performed against the GRCh37 human reference genome and miRBase v22.1.

treatment_protocol: No experimental treatment was applied

value: Blood sample

tag: screening group

value: C

tag: disease status


title: IC-M1

description:
Library name: sample4
4_FPKM


title: Breast cancer serum sample 261


title: WT_D5_Endo_b

description:
Sample_92
rna_seq_gene_counts_length_scaled.tsv


title: WT_D5_Endo_a

description:
Sample_91
rna_seq_gene_counts_length_scaled.tsv


title: Breast cancer serum sample 20664-038, control

description: Library name: 20664-038

value: A

value: control


title: Breast cancer serum sample 258


title: IC-F1

description:
Library name: sample1
1_FPKM


title: Breast cancer serum sample 20664-040, case

description: Library name: 20664-040


title: DATG_D4_Endo_b

description:
Sample_90
rna_seq_gene_counts_length_scaled.tsv


title: DATG_D4_Endo_a

description:
Sample_89
rna_seq_gene_counts_length_scaled.tsv


title: bEnd.3, WT, infected,  repeat 3

city: Baltimore

first: Amir

last: Rattner

state: MD - Maryland

address: 725 North Wolfe St.

institute: Johns Hopkins University

description:
Library name: 9-WT
bEnd3_counts_matrix.csv

data_processing:
snRNA-seq: Reads were aligned with the PIPseeker program (Fluent BioSiences, version 3.3.0). The CellBender program was used to detect empty droplets and remove background (version 0.3.2; Fleming et al., 2023). The SOLO program was used to remove doublets (scVI-tools 1.2.2-post2; Bernstein et al., 2020). Manual curation was used to further remove potentially mixed (doublet) nuclei. The data were normalized using a regularized negative binomial regression algorithm implemented with the SCTransform function (Hafemeister and Satija, 2019). Batch effects were corrected using the Seurat RPCAIntegration function. UMAP dimensional reduction was performed using the R uwot package (https://github.com/jlmelville/uwot) integrated into the Seurat R package (Melville, 2022).  RNA-seq on WT and Tlr4KO bEnd.3 cells: RNA-seq processing and normalization Gene-level count matrices from bEnd.3 cells were analyzed in R (v4.5) with Bioconductor (v3.21).
Assembly: Mouse mm10, mm39
Supplementary files format and content: Tab-separated values files, comma-separated values files, and matrix files.

extract_protocol:
For single-nucleus RNA sequencing, leptomeninges were collected as previously described (Wang et al., 2023). In brief, P6 mice were euthanized 24 hours after infection, brains were rapidly removed, and the leptomeninges were dissected into ice-cold Hibernate-A medium. The leptomeninges were frozen at -80 °C. Single nucleus (sn)RNA-seq libraries were preparedusing the PIPseq T20 3’ Single Cell RNA Kit v4.0 PLUS (Fluent BioSiences; Clark et al., 2023). Frozen tissue was suspended in homogenization buffer (0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM Tricine-KOH,pH 7.8) supplemented with 1 mM DTT, 0.15 mM spermine, 0.5 mM spermidine, EDTA free protease inhibitor (Roche 11836 170 001), 0.5% IGEPAL-630, and 40 U/mL Protector RNase Inhibitor (Sigma, 03335402001). Samples were homogenized in a 2 mL Dounce homogenizer,  sing 15 strokes with a loose-fitting pestle followed by 30 strokes with a tight-fitting pestle. The sample was filtered through a 10 μm filter (CellTrix, Sysmex, 04-004-2324), and nuclei were pelleted in Low Retention 1.5 mL microcentrifuge tubes (Thermo Scientific, 3451) for 5 min at 500 x g at 4 °C. Nuclei were washed twice with Nuclei Suspension Buffer (supplied in the Fluent BioSciences kit) supplemented with 1% BSA and 40 U/mL Protector RNase Inhibitor. Nuclei were counted, and ~40,000 nuclei (for the T20 kit) or ~20,000 nuclei (for the T10 kit) were used for library production following the Fluent BioSiences protocol.  RNA-seq on WT and Tlr4KO bEnd.3 cells: libraries and sequencing bEnd.3 mouse brain endothelial cells were cultured in 10-cm tissue culture dishes and grown to confluency under standard conditions (37 C, 5% CO₂). Total RNA was isolated using the Zymo Research RNA purification kit according to the manufacturer’s instructions. Briefly, culture medium was aspirated, cells were rinsed once with ice-cold PBS, and 600 μL of the provided lysis buffer with β-mercaptoethanol was added directly to the dish. The lysate was collected by scraping and transferred to a microcentrifuge tube, briefly mixed, and applied to the Zymo spin column. After binding, the column was washed with the supplied wash buffers, including an on-column DNase I treatment step to remove contaminating genomic DNA, and RNA was eluted in 50 μL of DNase/RNase-free water.
RNA-seq library construction was performed with the Illumina mRNA stranded kit following the manufacturer's protocol, and sequencing was performed on an Illumina NovaSeqX

value: cell culture

tag: genotype

value: WT

value: E.coli K1


title: Breast cancer serum sample 20664-037, case

description: Library name: 20664-037

value: D


title: Breast cancer serum sample 20664-035, control

description: Library name: 20664-035

value: Serum


title: KO_D4_Endo_b

description:
Sample_88
rna_seq_gene_counts_length_scaled.tsv

value: H1 ESC

value: Human Embryonic Stem Cells


title: bEnd.3, WT, infected,  repeat 2

description:
Library name: 8-WT
bEnd3_counts_matrix.csv


title: Breast cancer serum sample 255

value: case

value: Basal-like


title: Breast cancer serum sample 257


title: Breast cancer serum sample 20664-034, case

description: Library name: 20664-034


title: bEnd.3, WT, infected,  repeat 1

description:
Library name: 7-WT
bEnd3_counts_matrix.csv


title: KO_D4_Endo_a

description:
Sample_87
rna_seq_gene_counts_length_scaled.tsv


title: Breast cancer serum sample 20664-036, case

description: Library name: 20664-036

value: B


title: Breast cancer serum sample 254

value: Luminal A


title: WT_D4_Endo_b

description:
Sample_86
rna_seq_gene_counts_length_scaled.tsv


title: Breast cancer serum sample 20664-033, case

description: Library name: 20664-033


title: bEnd.3, Tlr4-KO, control, repeat 2

description:
Library name: 5-TLR4KO
bEnd3_counts_matrix.csv

value: PBS


title: bEnd.3, Tlr4-KO, control, repeat 1

description:
Library name: 4-TLR4KO
bEnd3_counts_matrix.csv


title: Breast cancer serum sample 20664-032, case

description: Library name: 20664-032


title: bEnd.3, Tlr4-KO, control, repeat 3

description:
Library name: 6-TLR4KO
bEnd3_counts_matrix.csv


title: Breast cancer serum sample 253


title: Breast cancer serum sample 20664-031, case

description: Library name: 20664-031


title: WT_D4_Endo_a

description:
Sample_85
rna_seq_gene_counts_length_scaled.tsv


title: Breast cancer serum sample 252


title: bEnd.3, WT, control,  repeat 3

description:
Library name: 3-WT
bEnd3_counts_matrix.csv


title: Breast cancer serum sample 256


title: Breast cancer serum sample 251


title: DATG_D3_Endo_a

description:
Sample_83
rna_seq_gene_counts_length_scaled.tsv


title: KO_D3_Endo_b

description:
Sample_82
rna_seq_gene_counts_length_scaled.tsv


title: Breast cancer serum sample 20664-030, case

description: Library name: 20664-030


title: Breast cancer serum sample 250


title: bEnd.3, WT, control,  repeat 2

description:
Library name: 2-WT
bEnd3_counts_matrix.csv


title: DATG_D3_Endo_b

description:
Sample_84
rna_seq_gene_counts_length_scaled.tsv


title: Breast cancer serum sample 20664-029, case

description: Library name: 20664-029


title: Breast cancer serum sample 249


title: bEnd.3, Tlr4-KO, infected, repeat 4

description:
Library name: 14-TLR4KO
bEnd3_counts_matrix.csv


title: KO_D3_Endo_a

description:
Sample_81
rna_seq_gene_counts_length_scaled.tsv


title: WT_D3_Endo_b

description:
Sample_80
rna_seq_gene_counts_length_scaled.tsv


title: Breast cancer serum sample 20664-028, case

description: Library name: 20664-028


title: Breast cancer serum sample 247


title: Breast cancer serum sample 20664-027, control

description: Library name: 20664-027


title: Breast cancer serum sample 248


title: bEnd.3, Tlr4-KO, infected, repeat 2

description:
Library name: 12-TLR4KO
bEnd3_counts_matrix.csv


title: bEnd.3, Tlr4-KO, infected, repeat 1

description:
Library name: 11-TLR4KO
bEnd3_counts_matrix.csv


title: Breast cancer serum sample 20664-026, control

description: Library name: 20664-026


title: WT_D3_Endo_a

description:
Sample_79
rna_seq_gene_counts_length_scaled.tsv


title: Breast cancer serum sample 20664-025, control

description: Library name: 20664-025


title: bEnd.3, WT, infected,  repeat 4

description:
Library name: 10-WT
bEnd3_counts_matrix.csv


title: DATG_D2_Endo_a

description:
Sample_77
rna_seq_gene_counts_length_scaled.tsv


title: bEnd.3, Tlr4-KO, infected, repeat 3

description:
Library name: 13-TLR4KO
bEnd3_counts_matrix.csv


title: Breast cancer serum sample 246


title: Breast cancer serum sample 244


title: Breast cancer serum sample 245


title: Breast cancer serum sample 20664-024, case

description: Library name: 20664-024


title: Breast cancer serum sample 20664-023, case

description: Library name: 20664-023


title: DATG_D2_Endo_b

description:
Sample_78
rna_seq_gene_counts_length_scaled.tsv


title: leptomeninges, Tlr4-CKO/-; WT, control, repeat  2

description:
Library name: PS8
PIPseq 4PLUS
PS_meninges_metadata.csv
PS_meninges_clusters.csv
PS_meninges_umap.csv
PS_meninges_barcodes.tsv.gz
PS_meninges_features.tsv.gz
PS_meninges_matrix.mtx.gz

molecule: nuclear RNA

source_name: leptomeninges

value: leptomeninges


title: KO_D2_Endo_a

description:
Sample_75
rna_seq_gene_counts_length_scaled.tsv


title: Breast cancer serum sample 20664-022, case

description: Library name: 20664-022

value: Blood sample


title: Breast cancer serum sample 243


title: leptomeninges, Tlr4-CKO/-; WT, control, repeat  1

description:
Library name: PS4
PIPseq 4PLUS
PS_meninges_metadata.csv
PS_meninges_clusters.csv
PS_meninges_umap.csv
PS_meninges_barcodes.tsv.gz
PS_meninges_features.tsv.gz
PS_meninges_matrix.mtx.gz


title: bEnd.3, WT, control,  repeat 1

description:
Library name: 1-WT
bEnd3_counts_matrix.csv


title: WT_D2_Endo_b

description:
Sample_74
rna_seq_gene_counts_length_scaled.tsv


title: Breast cancer serum sample 242


title: Breast cancer serum sample 241


title: KO_D2_Endo_b

description:
Sample_76
rna_seq_gene_counts_length_scaled.tsv


title: Breast cancer serum sample 20664-021, case

description: Library name: 20664-021


title: leptomeninges, Tlr4-CKO/-; WT, infected, repeat 3

description:
Library name: PS13
PIPseq 4PLUS
PS_meninges_metadata.csv
PS_meninges_clusters.csv
PS_meninges_umap.csv
PS_meninges_barcodes.tsv.gz
PS_meninges_features.tsv.gz
PS_meninges_matrix.mtx.gz


title: WT_D2_Endo_a

description:
Sample_73
rna_seq_gene_counts_length_scaled.tsv


title: leptomeninges, Tlr4-CKO/-; WT, infected, repeat 2

description:
Library name: PS6
PIPseq 4PLUS
PS_meninges_metadata.csv
PS_meninges_clusters.csv
PS_meninges_umap.csv
PS_meninges_barcodes.tsv.gz
PS_meninges_features.tsv.gz
PS_meninges_matrix.mtx.gz


title: DATG_D1_Endo_b

description:
Sample_72
rna_seq_gene_counts_length_scaled.tsv


title: Breast cancer serum sample 20664-020, case

description: Library name: 20664-020

value: C


title: Breast cancer serum sample 239


title: DATG_D1_Endo_a

description:
Sample_71
rna_seq_gene_counts_length_scaled.tsv


title: Breast cancer serum sample 20664-019, case

description: Library name: 20664-019


title: leptomeninges, Tlr4-CKO/-; Vecad-Cre,control, repeat 2

description:
Library name: PS10
PIPseq 4PLUS
PS_meninges_metadata.csv
PS_meninges_clusters.csv
PS_meninges_umap.csv
PS_meninges_barcodes.tsv.gz
PS_meninges_features.tsv.gz
PS_meninges_matrix.mtx.gz

value: Tlr4-CKO/-; Vecad-Cre


title: Breast cancer serum sample 240

value: Luminal B


title: Breast cancer serum sample 20664-017, case

description: Library name: 20664-017


title: leptomeninges, Tlr4-CKO/-; WT, infected, repeat 1

description:
Library name: PS2
PIPseq 4PLUS
PS_meninges_metadata.csv
PS_meninges_clusters.csv
PS_meninges_umap.csv
PS_meninges_barcodes.tsv.gz
PS_meninges_features.tsv.gz
PS_meninges_matrix.mtx.gz


title: Breast cancer serum sample 238


title: Breast cancer serum sample 20664-016, case

description: Library name: 20664-016


title: leptomeninges, Tlr4-CKO/-; Vecad-Cre, infected, repeat 3

description:
Library name: PS15
PIPseq 4PLUS
PS_meninges_metadata.csv
PS_meninges_clusters.csv
PS_meninges_umap.csv
PS_meninges_barcodes.tsv.gz
PS_meninges_features.tsv.gz
PS_meninges_matrix.mtx.gz


title: Breast cancer serum sample 237


title: Breast cancer serum sample 20664-018, control

description: Library name: 20664-018

value: A

value: control


title: leptomeninges, Tlr4-CKO/-; Vecad-Cre,control, repeat 1

description:
Library name: PS9
PIPseq 4PLUS
PS_meninges_metadata.csv
PS_meninges_clusters.csv
PS_meninges_umap.csv
PS_meninges_barcodes.tsv.gz
PS_meninges_features.tsv.gz
PS_meninges_matrix.mtx.gz


title: WT_D1_Endo_b

description:
Sample_68
rna_seq_gene_counts_length_scaled.tsv


title: Breast cancer serum sample 20664-015, control

description: Library name: 20664-015


title: KO_D1_Endo_b

description:
Sample_70
rna_seq_gene_counts_length_scaled.tsv


title: leptomeninges, Tlr4-CKO/-; Vecad-Cre, infected, repeat 2

description:
Library name: PS11
PIPseq 4PLUS
PS_meninges_metadata.csv
PS_meninges_clusters.csv
PS_meninges_umap.csv
PS_meninges_barcodes.tsv.gz
PS_meninges_features.tsv.gz
PS_meninges_matrix.mtx.gz


title: Breast cancer serum sample 235


title: KO_D1_Endo_a

description:
Sample_69
rna_seq_gene_counts_length_scaled.tsv


title: Breast cancer serum sample 236


title: Breast cancer serum sample 20664-014, case

description: Library name: 20664-014


title: WT_D1_Endo_a

description:
Sample_67
rna_seq_gene_counts_length_scaled.tsv


title: Breast cancer serum sample 234


title: Breast cancer serum sample 233


title: Breast cancer serum sample 20664-013, control

description: Library name: 20664-013


title: DATG_D5_SMADi_b

description:
Sample_150
rna_seq_gene_counts_length_scaled.tsv


title: DATG_D5_SMADi_a

description:
Sample_149
rna_seq_gene_counts_length_scaled.tsv


title: leptomeninges, Tlr4-CKO/-; Vecad-Cre, infected, repeat 1

description:
Library name: PS1
PIPseq 4PLUS
PS_meninges_metadata.csv
PS_meninges_clusters.csv
PS_meninges_umap.csv
PS_meninges_barcodes.tsv.gz
PS_meninges_features.tsv.gz
PS_meninges_matrix.mtx.gz


title: leptomeninges, Tlr4-CKO/-; Lys2-Cre, control, repeat 2

description:
Library name: PS18
PIPseq 4PLUS
PS_meninges_metadata.csv
PS_meninges_clusters.csv
PS_meninges_umap.csv
PS_meninges_barcodes.tsv.gz
PS_meninges_features.tsv.gz
PS_meninges_matrix.mtx.gz

value: Tlr4-CKO/-; Lys2-Cre


title: leptomeninges, Tlr4-CKO/-; Lys2-Cre, control, repeat 1

description:
Library name: PS14
PIPseq 4PLUS
PS_meninges_metadata.csv
PS_meninges_clusters.csv
PS_meninges_umap.csv
PS_meninges_barcodes.tsv.gz
PS_meninges_features.tsv.gz
PS_meninges_matrix.mtx.gz


title: Breast cancer serum sample 20664-012, case

description: Library name: 20664-012

value: D


title: Breast cancer serum sample 20664-011, case

description: Library name: 20664-011

value: Serum


title: leptomeninges, Tlr4-CKO/-; Lys2-Cre, infected, repeat 3

description:
Library name: PS17
PIPseq 4PLUS
PS_meninges_metadata.csv
PS_meninges_clusters.csv
PS_meninges_umap.csv
PS_meninges_barcodes.tsv.gz
PS_meninges_features.tsv.gz
PS_meninges_matrix.mtx.gz


title: Breast cancer serum sample 231


title: Breast cancer serum sample 20664-010, control

description: Library name: 20664-010


title: KO_D5_SMADi_a

description:
Sample_147
rna_seq_gene_counts_length_scaled.tsv

value: H1 ESC


title: leptomeninges, Tlr4-CKO/-; Lys2-Cre, infected, repeat 2

description:
Library name: PS12
PIPseq 4PLUS
PS_meninges_metadata.csv
PS_meninges_clusters.csv
PS_meninges_umap.csv
PS_meninges_barcodes.tsv.gz
PS_meninges_features.tsv.gz
PS_meninges_matrix.mtx.gz


title: Breast cancer serum sample 232


title: Breast cancer serum sample 20664-009, case

description: Library name: 20664-009


title: KO_D5_SMADi_b

description:
Sample_148
rna_seq_gene_counts_length_scaled.tsv

value: Human Embryonic Stem Cells


title: Breast cancer serum sample 229

value: case


title: BMDC Cells, MSA2 Treated, replicate2

city: Ann Arbor

first: Chengyi

last: Li

state: Michigan

address: B520, 1600 Huron Pkwy

institute: University of Michigan

description:
11430-CL-10
gene_expected_count.annot_BMDC.txt

data_processing:
This pool was subjected to 151bp paired-end sequencing according to the manufacturer’s protocol (Illumina NovaSeqXPlus). BCL Convert Conversion Software v4.0 (Illumina) was used to generate de-multiplexed Fastq files.
The reads were trimmed using Cutadapt v4.8(Martin, 2011). The reads were evaluated with FastQC(Andrews, 2010)(v0.11.8) to determine quality of the data. Reads were mapped to the reference genome GRCm38 (ENSEMBL 102), using STAR v2.7.8a(Dobinet al., 2013)and assigned count estimates to genes with RSEM v1.3.3(Li and Dewey, 2011). Alignment options followed ENCODE standards for RNA-seq(Dobin). QC metrics from several different steps in the pipeline were aggregated by multiQC v1.20(Ewelset al., 2016).
Assembly: mm10
Supplementary files format and content: tab-delimited text file included gene expected count for each sample

source_name: bone marrow

extract_protocol:
RNA was harvested using Rnaeasy mini plus kit (Qiagen)
RNA libraries for RNA-seq were prepared using Illumina Library Prepparaion kit following manufacturer's protocols.

value: bone marrow

value: dendritic cells

value: BMDC cells

value: WT

value: Control


title: leptomeninges, Tlr4-CKO/-; Lys2-Cre, infected, repeat 1

description:
Library name: PS3
PIPseq 4PLUS
PS_meninges_metadata.csv
PS_meninges_clusters.csv
PS_meninges_umap.csv
PS_meninges_barcodes.tsv.gz
PS_meninges_features.tsv.gz
PS_meninges_matrix.mtx.gz

value: leptomeninges


title: Breast cancer serum sample 20664-007, case

description: Library name: 20664-007

value: Blood sample

value: B


title: Breast cancer serum sample 228


title: Breast cancer serum sample 20664-008, case

description: Library name: 20664-008

value: C


title: Breast cancer serum sample 20664-006, control

description: Library name: 20664-006

value: A


title: DATG_D4_SMADi_a

description:
Sample_143
rna_seq_gene_counts_length_scaled.tsv


title: Breast cancer serum sample 230

value: Luminal A


title: BMDC Cells, MSA2 Treated

description:
11430-CL-3
gene_expected_count.annot_BMDC.txt


title: WT_D5_SMADi_b

description:
Sample_146
rna_seq_gene_counts_length_scaled.tsv


title: KO_D4_SMADi_b

description:
Sample_142
rna_seq_gene_counts_length_scaled.tsv


title: DATG_D4_SMADi_b

description:
Sample_144
rna_seq_gene_counts_length_scaled.tsv


title: WT_D5_SMADi_a

description:
Sample_145
rna_seq_gene_counts_length_scaled.tsv


title: Breast cancer serum sample 225


title: BMDC Cells, MSA2 Treated, replicate

description:
11430-CL-8
gene_expected_count.annot_BMDC.txt


title: Breast cancer serum sample 20664-004, case

description: Library name: 20664-004


title: BMDC Cells, MSA2+IPI-549 Treated

description:
11430-CL-4
gene_expected_count.annot_BMDC.txt


title: Breast cancer serum sample 224


title: Breast cancer serum sample 227


title: WT_D4_SMADi_b

description:
Sample_140
rna_seq_gene_counts_length_scaled.tsv


title: Breast cancer serum sample 20664-003, case

description: Library name: 20664-003


title: Breast cancer serum sample 226


title: Breast cancer serum sample 223


title: Breast cancer serum sample 20664-005, case

description: Library name: 20664-005


title: BMDC Cells, MSA2+IPI-549 Treated, replicate

description:
11430-CL-6
gene_expected_count.annot_BMDC.txt


title: BMDC Cells, Control, replicate2

description:
11430-CL-7
gene_expected_count.annot_BMDC.txt


title: WT_D4_SMADi_a

description:
Sample_139
rna_seq_gene_counts_length_scaled.tsv


title: Breast cancer serum sample 20664-002, case

description: Library name: 20664-002


title: KO_D4_SMADi_a

description:
Sample_141
rna_seq_gene_counts_length_scaled.tsv


title: BMDC Cells, Control, replicate

description:
11430-CL-5
gene_expected_count.annot_BMDC.txt


title: Breast cancer serum sample 222


title: DATG_D3_SMADi_b

description:
Sample_138
rna_seq_gene_counts_length_scaled.tsv


title: Breast cancer serum sample 20664-001, case

description: Library name: 20664-001


title: DATG_D3_SMADi_a

description:
Sample_137
rna_seq_gene_counts_length_scaled.tsv


title: Breast cancer serum sample 220


title: B Cells, MSA2 Treated, replicate2

description:
11360-CL-12
gene_expected_count.annot_B.txt

source_name: spleen

value: spleen

value: lymphocytes

value: B cells


title: Skin punch biopsy, hld7 patient, rep 3

city: Milan

first: Letizia

last: Messa

address: Piazza Leonardo Da Vinci 32

department: Electronics, Informatics and Bioengineering

country: Italy

institute: Politecnico di Milano

description:
Library name: POLR3A_PED1_3
POLR3A

data_processing:
Quality control of the raw data output were examined on FastQC software
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt software. UMI were detected and extracted with UMI tools
Trimmed sequence reads were mapped to GRCh38.p13 using STAR
Read count extraction was performed using FeatureCounts
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text files for each Sample

source_name: Skin

growth_protocol: Skin punch biopsies (5mm diameter) were obtained from the volar forearms of one pediatric patient with POLR3A-HLD, her unaffected parents, and healthy controls matched for age and sex. Tissue fragments were cut into smaller fragments, plated overnight in 6 well plates with fetal bovine serum (FBS, Sigma-Aldrich) at 37°C and 5% CO2 and then transferred in fibroblast medium composed by Dulbecco’s Modified Eagle Medium (DMEM) High Glucose (Sigma-Aldrich) with 20% FBS (Sigma-Aldrich), 1% L-Glutamine (Sigma-Aldrich), 1% Penicillin-Streptomycin (Sigma-Aldrich) and 1% Non-Essential Amino Acids (Sigma-Aldrich). Fibroblasts migrating from tissue fragments were expanded until confluency.

extract_protocol:
Total RNA from fibroblast cells was extracted using TRIZOL® reagent (Thermo Fisher Scientific) following manufacturer’s instructions, quantified on a Multiskan GO spectrophotometer, and quality-assessed using the TapeStation 4200 (Agilent). Three cellular replicates per patients were processed.
Ribosomal RNA was removed using the RiboCop kit (Lexogen), and RNA-seq libraries were prepared with the CORALL Total RNA-Seq Library Prep Kit (Lexogen) using 500 ng total RNA. The quality and quantity of the prepared libraries was assessed with D1000 ScreenTape Assay using the 4200 TapeStation System (Agilent). Libraries were sequenced using 75 bp paired-end reads on the Illumina NextSeq 500 platform (Illumina).

value: Skin

value: fibroblasts


title: Breast cancer serum sample 221

value: Serum

value: case


title: Skin punch biopsy, hld7 patient, rep 2

description:
Library name: POLR3A_PED1_2
POLR3A


title: KO_D3_SMADi_b

description:
Sample_136
rna_seq_gene_counts_length_scaled.tsv

value: H1 ESC

value: Human Embryonic Stem Cells


title: B Cells, MSA2 Treated, replicate

description:
11360-CL-11
gene_expected_count.annot_B.txt

value: WT


title: Breast cancer serum sample 219


title: KO_D3_SMADi_a

description:
Sample_135
rna_seq_gene_counts_length_scaled.tsv


title: Skin punch biopsy, hld7 patient, rep 1

description:
Library name: POLR3A_PED1_1
POLR3A


title: BMDC Cells, Control

description:
11430-CL-2
gene_expected_count.annot_BMDC.txt

value: bone marrow

value: dendritic cells

value: BMDC cells

value: Control


title: B Cells, MSA2 Treated

description:
11360-CL-8
gene_expected_count.annot_B.txt


title: WT_D3_SMADi_a

description:
Sample_133
rna_seq_gene_counts_length_scaled.tsv


title: Skin punch biopsy, carrier dad, rep 2

description:
Library name: CARRIER DAD 2
CARRIER DAD


title: Breast cancer serum sample 217

value: Luminal B


title: Breast cancer serum sample 218

value: Basal-like


title: B Cells, MSA2+IPI-549 Treated, replicate

description:
11360-CL-5
gene_expected_count.annot_B.txt


title: B Cells, MSA2+IPI-549 Treated, replicate2

description:
11360-CL-6
gene_expected_count.annot_B.txt


title: Skin punch biopsy, carrier dad, rep 1

description:
Library name: CARRIER DAD 1
CARRIER DAD


title: Breast cancer serum sample 215


title: DATG_D2_SMADi_b

description:
Sample_132
rna_seq_gene_counts_length_scaled.tsv


title: DATG_D2_SMADi_a

description:
Sample_131
rna_seq_gene_counts_length_scaled.tsv


title: Skin punch biopsy, carrier mum, rep 2

description:
Library name: CARRIER MUM 2
CARRIER MUM


title: WT_D3_SMADi_b

description:
Sample_134
rna_seq_gene_counts_length_scaled.tsv


title: Breast cancer serum sample 216

value: Luminal A


title: Skin punch biopsy, carrier mum, rep 1

description:
Library name: CARRIER MUM 1
CARRIER MUM


title: B Cells, Control, replicate2

description:
11360-CL-4
gene_expected_count.annot_B.txt

value: spleen


title: Breast cancer serum sample 214


title: Skin punch biopsy, Ctr ped, rep 3

description:
Library name: CTR_PED3_3
CTR


title: KO_D2_SMADi_b

description:
Sample_130
rna_seq_gene_counts_length_scaled.tsv


title: Breast cancer serum sample 213


title: B Cells, MSA2+IPI-549 Treated

description:
11360-CL-2
gene_expected_count.annot_B.txt

value: lymphocytes


title: B Cells, Control, replicate

description:
11360-CL-3
gene_expected_count.annot_B.txt

value: B cells


title: KO_D2_SMADi_a

description:
Sample_129
rna_seq_gene_counts_length_scaled.tsv


title: B Cells, Control

description:
11360-CL-1
gene_expected_count.annot_B.txt


title: Skin punch biopsy, Ctr ped, rep 2

description:
Library name: CTR_PED3_2
CTR

value: Skin


title: Skin punch biopsy, Ctr ped, rep 1

description:
Library name: CTR_PED3_1
CTR

value: fibroblasts


title: WT_D2_SMADi_b

description:
Sample_128
rna_seq_gene_counts_length_scaled.tsv


title: CUT&Tag of G4-DNA in 293T rep2

city: hefei

first: sun

last: xuedan

address: daoxiangcun

institute: ustc

description: Library name: Early_S_NELFA_2

library_source: genomic

data_processing:
(CUT-tag)The data analysis workflow first involved adapter trimming and removal of low-quality bases from paired-end reads were conducted using Trim Galore software. Clean reads were then aligned to the hg38 reference genome using Bowtie2, followed by the removal of PCR duplicates with Picard. Genome browser tracks in bigWig format were produced from merged replicates using samtools, and peak calling was performed with MACS2 using the parameters -f BAMPE --broad -nomodel. The resulting bigWig data were visualized using the Integrative Genomics Viewer (IGV) software from the Broad Institute, while peak visualizations were prepared using Deeptools.
Assembly: hg38
Supplementary files format and content: bigwig for CUT&Tag
Library strategy: CUT&Tag

molecule: genomic DNA

source_name: liver

extract_protocol:
CUT&Tag experiments, cell capture was achieved using ConA-coated magnetic beads for cell enrichment.
CUT&Tag libraries were prepared according to the protocol established by Steven Henikoff's laboratory.

value: liver

value: normal cells

value: Ctrl


title: Breast cancer serum sample 212

value: Serum

value: case


title: Breast cancer serum sample 211


title: CUT&Tag of G4-DNA in 293T rep1

description: Library name: Early_S_NELFA_1


title: DATG_D1_SMADi_b

description:
Sample_126
rna_seq_gene_counts_length_scaled.tsv

value: H1 ESC

value: Human Embryonic Stem Cells


title: Breast cancer serum sample 210


title: siDDX24_1_RNAseq_rep2

city: Zhuhai

first: Simeng

last: He

address: 52 Meihuadong Road, Xiangzhou

institute: Sun Yat-sen University

description: Library name: siDDX24_1_RNAseq_rep2

data_processing:
For Ribo-seq data analysis, cutadapt (v2.0.dev0) [3] was used to trim adapter sequences, remove low-quality reads, and filter reads outside the 24-35 nucleotide range. Ribosomal RNA reads were removed using bowtie (v1.1.2) [4] with default parameters. The remaining reads were mapped to the GRCh38 reference genome using STAR (v2.4.2a)[5] with default options except for the following: --outFilterMismatchNmax 2, --outFilterMultimapNmax 5, --outFilterMatchNmin 16, --alignEndsType EndToEnd. The changes in translation efficiency were calculated using deltaTE [6]. Only protein coding genes with baseMean at less 100 were selected for further analysis.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes the changes in translation efficiency

source_name: cell line

extract_protocol:
HUVEC cells were transfected with DDX24-specific siRNA or negative control siRNA for 48 hours. For cell lysis preparation, the culture medium was removed, and cells were washed with ice-cold PBS containing cycloheximide (CHX, 100 µg/mL; MP Biomedicals 0219452701). The ribosome profiling assay was conducted following previously described protocols with modifications. Cells were lysed in ice-cold mammalian polysome buffer containing 20 mM Tris-HCl (pH 7.5), 150 mM NaCl, 5 mM MgCl₂, supplemented with 1 mM DTT, 1% Triton X-100, 0.1% NP-40, 500 U/mL RNase Inhibitor, 1× EDTA-free Complete protease inhibitors, 1 U/µL DNase I, and 100 µg/mL cycloheximide. The lysate was homogenized by passing through a 26-gauge needle ten times and clarified by centrifugation (20,000×g, 5 minutes, 4°C). Ten percent of the cell lysate was reserved as an input control for RNA sequencing after mRNA enrichment. The supernatant (120 µL) was treated with RNase I (3 µL; Life Technologies, AM2294) for 45 minutes at room temperature. The reaction was terminated by adding SUPERase•In RNase Inhibitor (Life Technologies, AM2694). Monosomes were purified using MicroSpin S-400 HR columns (GE Healthcare, 27-5140-01), and RNA was isolated from the flow-through (approximately 125 µL) using RNAzol (1 mL). Ribosome footprints (RFPs) were enriched by depleting ribosomal RNA fragments using biotin-labeled probes specific for rRNA sequences. The remaining RNA was separated on a 17% 7.5M Urea-PAGE gel, and fragments between 26-30 nucleotides were excised using a 14-30 ssRNA Ladder Marker (Takara, #3416) as reference. For the input control, RNA was isolated using RNAzol, treated with DNase I, and enriched for mRNA using Oligo-dT beads (NEB, E7490). The polyA mRNA was then fragmented, and 30-50 nucleotide fragments were recovered from the Urea-PAGE gel.
Before library construction, both ribosome-protected fragments (RPFs) and input fragments were subjected to T4 polynucleotide kinase treatment for end repair. The libraries were prepared following the protocol previously described in Nature Methods and were sequenced on the HiSeq X Ten platform at Annoroad.

value: cell line

value: HUVEC

value: Human umbilical vein endothelial cells

value: DDX24 knockdown


title: CUT&Tag of HA in 293T rep2

description: Library name: Early_S_DHX_2


title: DATG_D1_SMADi_a

description:
Sample_125
rna_seq_gene_counts_length_scaled.tsv


title: WT_D2_SMADi_a

description:
Sample_127
rna_seq_gene_counts_length_scaled.tsv


title: CUT&Tag of HA in 293T rep1

description: Library name: Early_S_DHX_1


title: siDDX24_1_RNAseq_rep1

description: Library name: siDDX24_1_RNAseq_rep1


title: CUT&Tag of G4-DNA in S cells rep1

description: Library name: Early_S_BRIP1_2

value: tumor cells

value: S Phase-Synchronized


title: siNC_RNAseq_rep3

description: Library name: siNC_RNAseq_rep3

value: WT


title: Breast cancer serum sample 209

value: Luminal A


title: KO_D1_SMADi_a

description:
Sample_123
rna_seq_gene_counts_length_scaled.tsv


title: CUT&Tag of G4-DNA in S cells rep2

description: Library name: Early_S_BRIP1_1


title: siDDX24_1_RNAseq_rep3

description: Library name: siDDX24_1_RNAseq_rep3


title: siNC_RNAseq_rep2

description: Library name: siNC_RNAseq_rep2


title: Breast cancer serum sample 207


title: WT_D1_SMADi_b

description:
Sample_122
rna_seq_gene_counts_length_scaled.tsv


title: Breast cancer serum sample 208


title: Breast cancer serum sample 205


title: siNC_RNAseq_rep1

description: Library name: siNC_RNAseq_rep1


title: Breast cancer serum sample 206


title: CUT&Tag of G4-DNA in G1 cells rep1

description: Library name: Early_S_BG4_2

value: G1 Phase-Synchronized


title: WT_D1_SMADi_a

description:
Sample_121
rna_seq_gene_counts_length_scaled.tsv


title: DATG_D5_BMP4_b

description:
Sample_66
rna_seq_gene_counts_length_scaled.tsv


title: siDDX24_1_RiboSeq_rep3

description: Library name: siDDX24_1_RiboSeq_rep3

library_source: other

data_processing:
For Ribo-seq data analysis, cutadapt (v2.0.dev0) [3] was used to trim adapter sequences, remove low-quality reads, and filter reads outside the 24-35 nucleotide range. Ribosomal RNA reads were removed using bowtie (v1.1.2) [4] with default parameters. The remaining reads were mapped to the GRCh38 reference genome using STAR (v2.4.2a)[5] with default options except for the following: --outFilterMismatchNmax 2, --outFilterMultimapNmax 5, --outFilterMatchNmin 16, --alignEndsType EndToEnd. The changes in translation efficiency were calculated using deltaTE [6]. Only protein coding genes with baseMean at less 100 were selected for further analysis.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes the changes in translation efficiency
Library strategy: Ribo-Seq

molecule: other


title: CUT&Tag of G4-DNA in G1 cells rep2

description: Library name: Early_S_BG4_1


title: siDDX24_1_RiboSeq_rep2

description: Library name: siDDX24_1_RiboSeq_rep2


title: GRDIM_tumor_rep3

city: Göttingen

first: Sybille

middle: Dorothee

last: Reichardt

address: Humboldtallee 34

department: Institute for Cellular and Molecular Immunology

country: Germany

institute: University Medical Center Göttingen

description: Library name: 18_DIM

data_processing:
Base calling and demultiplexing of NovaSeq BCL files with Illumina bcl2fastq v2.20.0.422
Adapter and quality trimming of paired-end reads with Trim Galore (paired-end mode, --nextseq 20), QC with FastQC, summary with MultiQC.
Alignment of trimmed reads to Mus musculus GRCm39 (Ensembl release 112) with STAR v2.7.8a
Gene-level read counting from BAM files with featureCounts (Subread v1.5.0; paired-end mode, minimum fragment length 40 bp) using Ensembl Mus musculus GRCm39.112 gene annotation.
Assembly: Mus musculus GRCm39 (Ensembl release 112).
Supplementary files format and content: Tab-delimited per-sample files with raw gene-level counts (Ensembl gene ID and fragment count) generated by featureCounts.
Supplementary files format and content: Gene-by-sample count matrix and DESeq2 v1.40.2 differential expression result tables (log2 fold change, p value, adjusted p value) for each comparison

source_name: colonic tumor

extract_protocol:
RNA was pepared using RNeasy Mini Kit (Qiagen) and mRNA was prepared with the Dynabeads mRNA DIRECT KIT (Thermofischer scientific)
Library preparation for RNA-Seq analysis was performed on the STAR Hamilton NGS automation platform by using the Illumina Stranded mRNA Prep Kit (Cat. No. 20040534) in combination with the Illumina RNA UD Indexes Set A, Ligation with 96 Indexes (Cat. No. 20091646).

value: colonic tumor

value: GRdim

value: AOM/DSS


title: Breast cancer serum sample 204


title: siDDX24_1_RiboSeq_rep1

description: Library name: siDDX24_1_RiboSeq_rep1


title: DATG_D5_BMP4_a

description:
Sample_65
rna_seq_gene_counts_length_scaled.tsv


title: GRDIM_tumor_rep2

description: Library name: 73_DIM


title: KO_D5_BMP4_b

description:
Sample_64
rna_seq_gene_counts_length_scaled.tsv


title: KO_D1_SMADi_b

description:
Sample_124
rna_seq_gene_counts_length_scaled.tsv


title: siNC_RiboSeq_rep3

description: Library name: siNC_RiboSeq_rep3


title: GRWT_tumor_rep3

description: Library name: 19T-WT

value: GRwt


title: siNC_RiboSeq_rep2

description: Library name: siNC_RiboSeq_rep2


title: KO_D5_BMP4_a

description:
Sample_63
rna_seq_gene_counts_length_scaled.tsv


title: Breast cancer serum sample 200

value: Serum


title: Breast cancer serum sample 201

value: case


title: Breast cancer serum sample 202


title: GRDIM_tumor_rep1

description: Library name: 18T_DIM


title: siNC_RiboSeq_rep1

description: Library name: siNC_RiboSeq_rep1


title: GRWT-tumor_rep2

description: Library name: 81_WT


title: Breast cancer serum sample 203


title: GRWT_tumor_rep1

description: Library name: 02_WT


title: DATG_D4_BMP4_b

description:
Sample_54
rna_seq_gene_counts_length_scaled.tsv

value: H1 ESC


title: Breast cancer serum sample 199


title: HUVEC,siDDX24,8h,rep3

data_processing:
Raw reads underwent initial processing, involving trimming for adaptor removal and elimination of low-quality reads, achieved through cutadapt (v2.0.dev0). Subsequently, alignment to the human genome (hg38) was executed using STAR (v2.4.2a), employing ENCODE standard options tailored for the long RNA-seq pipeline. The gencode transcriptome (gencode v39) served as the reference during this alignment. Read counts were quantified using featureCounts (v1.6.4) with default settings and was converted to RPKM by a custom script. RKPM were converted to attomole by linear-fitting of the RNA spike-in. half-life was calculated by using custom script.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values and mRNA half-life

source_name: HUVEC

growth_protocol: HUVEC was maintained in ECM medium (Sciencell) supplemented with 5% FBS, 1% Endothelial growth factor and 1% penicillin-streptomycin.

extract_protocol:
Total RNA was extracted using RNAzol. mRNA was further purified using Oligo dT-based Poly(A) mRNA Magnetic Isolation Module (NEB).
RNA libraries for RNA-seq were prepared using Ultra II Directional RNA Library Prep Kit for Illumina (NEB).

treatment_protocol: HUVECs were transfected with siNC or siDDX24-1 at 50nM.

value: vasuclar endothelial cell

tag: time


title: WT_D5_BMP4_a

description:
Sample_61
rna_seq_gene_counts_length_scaled.tsv

value: Human Embryonic Stem Cells


title: Breast cancer serum sample 198

value: Basal-like


title: Islets Ctnna1_KO_MUT6

city: Duarte

first: Hung-Ping

last: Shih

address: 1500 E. Duarte Road

department: Translational Research and Cellular Therapeutics

institute: City of Hope

description: Library name: Ctnna1_KO_467

data_processing:
Sequencing was performed on an Illumina NovaSeq 6000 with a single read mode of 151 cycles. HiSeq Real-Time Analysis (RTA) 2.2.38 software was used to process the image analysis.
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Islets

growth_protocol: 8 week old mice

extract_protocol:
RNA was extracted using the Rneasey Mini Kit (QIAGEN, 74104)
RNA sequencing libraries were prepared with the Kapa mRNA HyperPrep Kit (Kapa Biosystems, KR1352) according to the manufacturer's protocol, and the final libraries were validated using the Agilent Bioanalyzer DNA High Sensitivity Kit (Agilent, 5067-4626) and quantified with a Qubit Fluorometer (Thermo Fisher)

value: Islets

value: Ngn3-Cre; Ctnna1 flox/flox

value: 8 weeks old


title: Breast cancer serum sample 197


title: WT_D5_BMP4_b

description:
Sample_62
rna_seq_gene_counts_length_scaled.tsv


title: HUVEC,siNC,8h,rep3

value: HUVEC

value: siNC


title: DATG_D4_BMP4_a

description:
Sample_53
rna_seq_gene_counts_length_scaled.tsv


title: HUVEC,siDDX24,4h,rep3

value: WT


title: KO_D4_BMP4_b

description:
Sample_52
rna_seq_gene_counts_length_scaled.tsv


title: Breast cancer serum sample 196


title: Islets Ctnna1_KO_MUT3

description: Library name: Ctnna1_KO_457


title: Islets Ctnna1_KO_MUT4

description: Library name: Ctnna1_KO_460


title: KO_D4_BMP4_a

description:
Sample_51
rna_seq_gene_counts_length_scaled.tsv


title: WT_D4_BMP4_b

description:
Sample_50
rna_seq_gene_counts_length_scaled.tsv


title: HUVEC,siNC,0h,rep3


title: Breast cancer serum sample 194

value: Luminal B


title: HUVEC,siNC,4h,rep3


title: Breast cancer serum sample 195


title: Islets Ctnna1_KO_MUT5

description: Library name: Ctnna1_KO_466


title: Islets Ctnna1_KO_MUT1

description: Library name: Ctnna1_KO_445


title: HUVEC,siDDX24,8h,rep2


title: WT_D4_BMP4_a

description:
Sample_49
rna_seq_gene_counts_length_scaled.tsv


title: DATG_D3_BMP4_b

description:
Sample_42
rna_seq_gene_counts_length_scaled.tsv


title: Islets Ctnna1_KO_MUT2

description: Library name: Ctnna1_KO_448


title: DATG_D3_BMP4_a

description:
Sample_41
rna_seq_gene_counts_length_scaled.tsv


title: Breast cancer serum sample 191


title: HUVEC,siNC,8h,rep2


title: Islets Ctnna1_CTRL_WT6

description: Library name: Ctnna1_CTRL_459

value: Wild type


title: HUVEC,siDDX24,0h,rep3


title: HUVEC,siDDX24,4h,rep2


title: Islets Ctnna1_CTRL_WT5

description: Library name: Ctnna1_CTRL_458


title: Breast cancer serum sample 193

value: Luminal A


title: Breast cancer serum sample 192


title: Islets Ctnna1_CTRL_WT4

description: Library name: Ctnna1_CTRL_453


title: KO_D3_BMP4_b

description:
Sample_40
rna_seq_gene_counts_length_scaled.tsv


title: HUVEC,siNC,4h,rep2


title: Breast cancer serum sample 190


title: Islets Ctnna1_CTRL_WT3

description: Library name: Ctnna1_CTRL_447


title: Breast cancer serum sample 189


title: KO_D3_BMP4_a

description:
Sample_39
rna_seq_gene_counts_length_scaled.tsv


title: HUVEC,siDDX24,0h,rep2


title: Breast cancer serum sample 187


title: HUVEC,siNC,0h,rep2


title: Islets Ctnna1_CTRL_WT2

description: Library name: Ctnna1_CTRL_446


title: WT_D3_BMP4_b

description:
Sample_38
rna_seq_gene_counts_length_scaled.tsv


title: Islets Ctnna1_CTRL_WT1

description: Library name: Ctnna1_CTRL_444


title: HUVEC,siDDX24,8h,rep1


title: Breast cancer serum sample 186


title: Islets MUT4

description: Library name: MUT8

growth_protocol: 8 weeks old

value: Ngn3-Cre; Srebf2 flox/flox


title: DATG_D2_BMP4_a

description:
Sample_29
rna_seq_gene_counts_length_scaled.tsv


title: Breast cancer serum sample 188


title: HUVEC,siNC,8h,rep1


title: DATG_D2_BMP4_b

description:
Sample_30
rna_seq_gene_counts_length_scaled.tsv


title: HUVEC,siDDX24,4h,rep1


title: Islets MUT3

description: Library name: MUT7


title: KO_D2_BMP4_b

description:
Sample_28
rna_seq_gene_counts_length_scaled.tsv


title: HUVEC,siNC,4h,rep1


title: Breast cancer serum sample 184


title: Breast cancer serum sample 183


title: KO_D2_BMP4_a

description:
Sample_27
rna_seq_gene_counts_length_scaled.tsv


title: Islets MUT2

description: Library name: MUT6


title: WT_D3_BMP4_a

description:
Sample_37
rna_seq_gene_counts_length_scaled.tsv


title: HUVEC,siDDX24,0h,rep1


title: WT_D2_BMP4_b

description:
Sample_26
rna_seq_gene_counts_length_scaled.tsv


title: Breast cancer serum sample 185


title: Islets MUT1

description: Library name: MUT5


title: Breast cancer serum sample 182


title: Islets WT4

description: Library name: WT4


title: Breast cancer serum sample 181


title: WT_D2_BMP4_a

description:
Sample_25
rna_seq_gene_counts_length_scaled.tsv


title: HUVEC,siNC,0h,rep1


title: DATG_D1_BMP4_b

description:
Sample_18
rna_seq_gene_counts_length_scaled.tsv


title: HUVEC,DDX24-FLAG,CLIP,rep4

data_processing:
After obtaining the irCLIP-seq raw datasets, we first applied fastp with the default parameter, filtering the adaptor sequence, removing PCR duplicates and degenerate barcode to acquire the clean data. Identical sequences with the same 4 nt random barcode on both 3’ and 5’ ends were regarded as one tag to exclude PCR duplication. We then implemented the STAR alignment algorithm to map reads to the genome (hg38) and gene annotation (gencode v39) with the parameters: --outFilterMultimapNmax 1 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --sjdbScore 1 --alignEndsType EndToEnd. Further analysis utilized rbsSeeker (https://github.com/kerenzhou062/rbsSeeker), a tool previously employed for CLIP-seq dataset analysis in starBase43. This step aimed to identify target mRNAs for the DDX24 protein, employing the following parameters: -p 0.05, -q 0.05, --rm, -S 0.99, -d 5, -N, -L 2, --skip, –rnafold.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include DDX24-binding peaks information and p value.

extract_protocol:
DDX24 bound RNAs were enriched by magnetic beads, and digested by S1 Nuclease on beads. Then irRA3-adaptor was ligated, and RNAs were visualized in SDS page. DDX24 protein-RNA fragment complexes in 115 to 185 kDa position were collected, and RNA-fragment were extracted using RNAzol.
RNA libraries for irCLIP-seq were prepared using small RNA library preperation, including reverse transcription, DNA-adaptor ligation, PCR and agarose-gel size control.

treatment_protocol: HUVECs were transfected with DDX24-FLAG plasmids and applied puromycin selection to be stable overexpression.

tag: irclip antibody


title: Islets WT3

description: Library name: WT3


title: HUVEC,DDX24-FLAG,CLIP,rep2


title: HUVEC,DDX24-FLAG,CLIP,rep3


title: Islets WT1

description: Library name: WT1


title: Breast cancer serum sample 180


title: Islets WT2

description: Library name: WT2


title: HUVEC,DDX24-FLAG,CLIP,rep1


title: DATG_D1_BMP4_a

description:
Sample_17
rna_seq_gene_counts_length_scaled.tsv


title: Breast cancer serum sample 179


title: KO_D1_BMP4_b

description:
Sample_16
rna_seq_gene_counts_length_scaled.tsv


title: high-fat diet with MICT intervention6

city: Quanzhou

first: Weihao

last: Hong

address: Donghai

institute: Quanzhou Normal University

description: Library name: HM6

data_processing:
Paired-end reads underwent quality assessment and trimming using Trim-galore (v.0.6.0).
Alignment of the reads to the mouse genome reference sourced from GENCODE was executed using STAR (v.2.7.3a).
FeatureCounts (v.1.6.3) was employed to quantify the reads mapped to exon sites of genes listed in GTF files obtained from GENCODE.
Assembly: GRCm38.p6
Supplementary files format and content: excel file includes raw counts for each sample

source_name: gastrocnemius muscle

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1μg of total RNA was used for the construction of sequencing libraries.
mRNA sequencing libraries were constructed using the Hieff NGS Ultima Dual-mode mRNA Library Prep Kit for Illumina (Yeasen Biotechnology, Shanghai, China) in accordance with the manufacturer’s protocol.

treatment_protocol: After 1 week of acclimation, 3-week-old male C57BL/6J mice were randomly allocated to four groups: standard chow diet (C), standard chow diet plus MICT (CM), HFD (H), and HFD plus MICT (HM). The dietary intervention was maintained throughout the entire experiment (weeks 1–21). Starting at week 13, mice assigned to the exercise groups completed a 1-week treadmill acclimation phase (10 m/min for 10 min/day, 5 days/week), followed by an 8-week MICT intervention (weeks 14–21). Each session lasted 45 min and was performed 5 days per week, preceded by a 10-min warm-up at 10 m/min. Treadmill speed was progressively increased from 13 m/min (weeks 14–15) to 15 m/min (weeks 16–17), and then to 17 m/min (weeks 18–21). Gastrocnemius muscles were collected for RNA-seq at the endpoint.

value: gastrocnemius muscle

tag: Sex

value: male

tag: time point

tag: strain


title: Single cell CD4+CD44hiTomato+ isolated from PR8 infected TRACK parabiotic mice d9 d.p.i, TCR library

description: Library name: 080223_PB_CSA_d9_TCR

value: Lung, medLN, Spleen

value: T cells

value: Influenza PR8 infection


title: Breast cancer serum sample 178

value: Serum

value: Control


title: Breast cancer serum sample 177


title: WT_D1_BMP4_b

description:
Sample_14
rna_seq_gene_counts_length_scaled.tsv

value: H1 ESC

value: Human Embryonic Stem Cells


title: Single cell CD4+CD44hiTomato+ isolated from PR8 infected TRACK parabiotic mice d9 d.p.i, TotalSeq-C library

description: Library name: 080223_PB_CSA_d9_HTO


title: high-fat diet with MICT intervention5

description: Library name: HM5


title: high-fat diet with MICT intervention4

description: Library name: HM4


title: WT_D1_BMP4_a

description:
Sample_13
rna_seq_gene_counts_length_scaled.tsv


title: KO_D1_BMP4_a

description:
Sample_15
rna_seq_gene_counts_length_scaled.tsv


title: Breast cancer serum sample 175


title: high-fat diet with MICT intervention3

description: Library name: HM3


title: Breast cancer serum sample 174


title: DATG_D0_b

description:
Sample_6
rna_seq_gene_counts_length_scaled.tsv


title: high-fat diet with MICT intervention2

description: Library name: HM2


title: Single cell CD4+CD44hiTomato+ isolated from PR8 infected TRACK parabiotic mice d9 d.p.i, Gene expression library

description: Library name: 080223_PB_CSA_d9_GEX


title: Breast cancer serum sample 173


title: Breast cancer serum sample 176


title: Single cell CD4+CD44hiTomato+ isolated from PR8 infected TRACK parabiotic mice d56 d.p.i, TotalSeq-C library

description: Library name: 100323_PB_CSA_d59_HTO


title: DATG_D0_a

description:
Sample_5
rna_seq_gene_counts_length_scaled.tsv


title: high-fat diet with MICT intervention1

description: Library name: HM1


title: KO_D0_b

description:
Sample_4
rna_seq_gene_counts_length_scaled.tsv


title: Single cell CD4+CD44hiTomato+ isolated from PR8 infected TRACK parabiotic mice d56 d.p.i, Gene expression library

description: Library name: 080223_PB_CSA_d56_GEX


title: high-fat diet6

description: Library name: H6


title: Single cell CD4+CD44hiTomato+ isolated from PR8 infected TRACK parabiotic mice d56 d.p.i, TCR library

description: Library name: 100323_PB_CSA_d59_TCR


title: Breast cancer serum sample 171

value: case


title: Single cell CD4+CD44hiTomato+ isolated from PR8 infected TRACK mice d9 d.p.i (droplet, 10x), TCR library

description: Library name: 020524_CSA_d9_VDJ


title: KO_D0_a

description:
Sample_3
rna_seq_gene_counts_length_scaled.tsv


title: Single cell CD4+CD44hiTomato+ isolated from PR8 infected TRACK mice d9 d.p.i (droplet, 10x), TotalSeq-C library

description: Library name: 020524_CSA_d9_HTO


title: WT_D0_b

description:
Sample_2
rna_seq_gene_counts_length_scaled.tsv


title: high-fat diet5

description: Library name: H5


title: Breast cancer serum sample 169

value: Basal-like


title: Breast cancer serum sample 170


title: high-fat diet4

description: Library name: H4


title: high-fat diet3

description: Library name: H3


title: Breast cancer serum sample 168


title: Breast cancer serum sample 172


title: WT_D0_a

description:
Sample_1
rna_seq_gene_counts_length_scaled.tsv


title: Single cell CD4+CD44hiTomato+ isolated from PR8 infected TRACK mice d9 d.p.i (droplet, 10x), gene expression library

description: Library name: 020524_CSA_9_GEX


title: Single cell CD4+CD44hiTomato+ isolated from PR8 infected TRACK mice d56 d.p.i (droplet, 10x), TCR library

description: Library name: 020524_CSA_d56_VDJ


title: RNA-seq of MXP5 IK1 rep2

city: Burlington

first: Seth

last: Frietze

state: VT

address: 149 Beaumont Avenue

department: Biomedical and Health Sciences

institute: University of Vermont

description:
Library name: MXP5_IK1_rep2
MXP5 IK1 (IKAROS), replicate 2
MXP5_PDX2_raw_counts.tsv

data_processing:
Raw reads were quality-checked with FastQC.
Reads were aligned to the human genome (hg38) using STAR v2.7.11b with GENCODE v36 annotation.
Gene-level read counts were obtained using STAR with --quantMode GeneCounts.
Raw counts were used directly as processed data for GEO submission; no normalization or filtering was applied.
Assembly: hg38 / GENCODE v36
Supplementary files format and content: Two tab-delimited .tsv files with raw gene counts: MXP5_PDX2_raw_counts.tsv (IK1 induction RNA-seq, 8 samples: MXP5 and PDX2, with PDX2 from GSE90659) and bulk_panel_raw_counts.tsv (bulk B-ALL panel, 9 samples).

growth_protocol: Cells were cultured at 37°C in a humidified incubator with 5% CO₂ in MEMα GlutaMAX (Gibco) supplemented with 20% FBS.

extract_protocol:
Total RNA was extracted using the Direct-zol RNA Miniprep Kit (Zymo Research) according to the manufacturer’s instructions.
Ribosomal RNA was depleted using NEBNext rRNA Depletion Kit (Illumina). Libraries were prepared with NEBNext Ultra II Directional RNA Library Prep Kit (NEB) using 1000 ng of total RNA.

treatment_protocol: For inducible expression samples, wild-type IK1 or control (GFP) was induced with 1 μg/mL doxycycline for 24 hours. Bulk RNA-seq panel samples were not treated and reflect endogenous gene expression profiles.


title: RNA-seq of MXP5 IK1 rep1

description:
Library name: MXP5_IK1_rep1
MXP5 IK1 (IKAROS), replicate 1
MXP5_PDX2_raw_counts.tsv


title: Breast cancer serum sample 167


title: Single cell CD4+CD44hiTomato+ isolated from PR8 infected TRACK mice d56 d.p.i (droplet, 10x), TotalSeq-C library

description: Library name: 020524_CSA_d56_HTO


title: Breast cancer serum sample 166


title: high-fat diet1

description: Library name: H1


title: high-fat diet2

description: Library name: H2


title: RNA-seq of MXP5 GFP rep2

description:
Library name: MXP5_GFP_rep2
MXP5 GFP (control), replicate 2
MXP5_PDX2_raw_counts.tsv

value: GFP


title: control6

description: Library name: C6


title: Breast cancer serum sample 165


title: Single cell CD4+CD44hiTomato+ isolated from PR8 infected TRACK mice d56 d.p.i (droplet, 10x), gene expression library

description: Library name: 020524_CSA_d56_GEX


title: Breast cancer serum sample 164


title: control4

description: Library name: C4


title: RNA-seq of JFK10R bulk sample

description:
Library name: JFK10R_bulk
JFK10R bulk RNA-seq
bulk_RNAseq_raw_counts.tsv

value: bulk


title: RNA-seq of MXP5 GFP rep1

description:
Library name: MXP5_GFP_rep1
MXP5 GFP (control), replicate 1
MXP5_PDX2_raw_counts.tsv


title: Breast cancer serum sample 162


title: LacZ_TNFa_Replicate2

city: Louisville

first: Richa

last: Singhal

state: KY

address: 580 S Preston Street, Baxter II Building, Office 321B

department: Medicine

institute: University of Louisville

description: Library name: 803-63re-x_S18

data_processing:
Raw sequences were checked for quality values using fastQC v0.10.1.  Quality trimming was not deemed necessary.
The sequences were directly aligned to the Mus musculus reference genome assembly (mm10) using Star version 2.6.
Read counts for gene regions were obtained with HTSeq v.0.10.0 using Ensembl annotations (GRCm38.93).
Assembly: mm10/GRCm38.93
Supplementary files format and content: tab-delimited file includes raw counts for each sample

source_name: cardiac fibroblast

growth_protocol: Isolated cardiac fibroblasts from TAK1fl/fl mice were maintained in DMEM/F12 + 10% fetal bovine serum + 1% insulin transferrin selenium + 20 ng/ml human bFGF + 1% penicillin/streptomycin/amphotericin B. All cells were used for treatment at passage 1

extract_protocol:
Total RNA was isolated using the Qiagen RNeasy Micro Kit (74004)
NEBNext Ultra II RNA Library Prep Kit for Illumina was used for library prep

treatment_protocol: Isolated cardiac fibrobalsts from TAK1fl/fl mice were treated with either LacZ or iCre to induce TAK1 knockdown. Then, cells were treated under serum-starved conditions with bFGF (20 ng/ml), TGFb (10ng/ml), TNFa (10ng/ml), or IL-1b (15ng/ml) for 24 h prior to RNA isolation

value: cardiac fibroblast


title: RNA-seq of IAH8R bulk sample

description:
Library name: IAH8R_bulk
IAH8R bulk RNA-seq
bulk_RNAseq_raw_counts.tsv


title: LacZ_TNFa_Replicate4

description: Library name: 803-65re-x_S20


title: RNA-seq of ICN1 bulk sample

description:
Library name: ICN1_bulk
ICN1 bulk RNA-seq
bulk_RNAseq_raw_counts.tsv


title: control5

description: Library name: C5


title: control3

description: Library name: C3


title: control2

description: Library name: C2


title: Breast cancer serum sample 161

value: Luminal B


title: LacZ_TGF_Replicate4

description: Library name: 803-59re-x_S12


title: Breast cancer serum sample 163


title: LacZ_TGF_Replicate3

description: Library name: 803-58re-x_S11


title: 72h post-LPS Rep2

city: Chicago

first: Jalees

last: Rehman

state: IL

address: 900 S. Ashland Ave. MBRB 2072, Mailcode 669

department: Biochemistry and Molecular Genetics

institute: UIC

description: Library name: S7

data_processing:
Adapters were trimmed by TrimGalore.
Trimmed reads were aligned to the mm10 reference genome using Bowtie2.
Unique reads with a quality score equal or more than 30 were kept. Tn5 offset was asjusted.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01
Irreproducibility Discovery Rate framework was applied to get peaks that were consistent among biological replicates.
Assembly: Count tables were generated using Rsubread R package.
Supplementary files format and content: Assembly: mm10
Supplementary files format and content: narrowPeak, csv

source_name: Lung

extract_protocol:
The flow sorted alveolar macrophages were collected. 200,000 cells were then further used for ATACseq using Active Motif Kit Cat # 53150 by following the manufraturer protocol
Library were contructed with 10 cycles of PCR using the Active motif Kit Cat # 53150, index promer according to the manufracturer protocol

value: Lung

value: lung macrophage

value: LPS inhalation


title: LacZ_TNFa_Replicate3

description: Library name: 803-64re-x_S19


title: Breast cancer serum sample 160

data_processing: Cq values were determined using the second derivative method in Roche LightCycler software. Quality control included melting curve analysis, exclusion of reactions with more than one melting temperature, deviation from reference melting temperatures, and low amplification efficiency. Endogenous miRNAs let-7d-5p and let-7i-5p were used as internal reference controls. Expression data were normalized and subsequently log2-transformed for statistical analysis. Batch information is provided in the sample annotations.

value: Luminal A


title: RNA-seq of SF05 bulk sample

description:
Library name: SF05_bulk
SF05 bulk RNA-seq
bulk_RNAseq_raw_counts.tsv


title: control1

description: Library name: C1

value: gastrocnemius muscle

value: male


title: RNA-seq of MXP2 bulk sample

description:
Library name: MXP2_bulk
MXP2 bulk RNA-seq
bulk_RNAseq_raw_counts.tsv


title: Breast cancer serum sample 158


title: Breast cancer serum sample 159


title: LacZ_TNFa_Replicate1

description: Library name: 803-35re-x_S17


title: 72h post-LPS Rep1

description: Library name: S3


title: RNA-seq of LAX7 bulk sample

description:
Library name: LAX7_bulk
LAX7 bulk RNA-seq
bulk_RNAseq_raw_counts.tsv


title: ageing Muscle Satellite Cells, hMG53, Rep3

city: Columbus

first: Jethro

middle: WANG

last: Zih-Shuo

state: Ohio

address: 460 W 12th Ave.

department: Department of Surgery

institute: Ohio State University

description:
Library name: MusSCs_hMG53_6
Column name in MG53_ageing_Mus_SCs_gene_counts_matrix: S6.sorted.bam

data_processing:
The libraries were sequenced on an Illumina platform (Next-Generation Sequencing) to generate 2×150 bp paired-end reads, with a depth of approximately 40 million reads per sample (20M in each direction).
Raw reads were aligned to the mouse reference genome (mm10) using STAR
Gene expression counts were quantified using featureCounts
Differential expression analysis was performed using EdgeR in R software. Gene expression levels were normalized using the TMM method.
Assembly: mm10
Supplementary files format and content: MG53_ageing_Mus_SCs_gene_counts_matrix.csv

source_name: ageing Muscle Satellite Cells

growth_protocol: Primary satellite cells were isolated from the hindlimb muscles of C57BL/6 mice. Cells were cultured in DMEM supplemented with 20% FBS and bFGF. Cells were maintained in a humidified incubator at 37°C with 5% CO2.

extract_protocol:
Total RNA was extracted from the collected cells using TRIzol reagent following the manufacturer's instructions. RNA quality and integrity were assessed using an Agilent Bioanalyzer 2100.
RNA-seq libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit with Poly(A) mRNA Magnetic Isolation Module, following the "Low Input" protocol according to the manufacturer's instructions.

treatment_protocol: Cells were cultured to appropriate confluency and then treated with either recombinant human MG53 protein (rhMG53) or Bovine Serum Albumin (BSA) as a vehicle control for 72 hours.

value: ageing Muscle Satellite Cells

value: WT

tag: batch

value: Day 3


title: LacZ_TGF_Replicate1

description: Library name: 803-33re-x_S9


title: LacZ_TGF_Replicate2

description: Library name: 803-57re-x_S10


title: ageing Muscle Satellite Cells, hMG53, Rep2

description:
Library name: MusSCs_hMG53_5
Column name in MG53_ageing_Mus_SCs_gene_counts_matrix: S5.sorted.bam


title: RNA-seq of LAX7R bulk sample

description:
Library name: LAX7R_bulk
LAX7R bulk RNA-seq
bulk_RNAseq_raw_counts.tsv


title: ageing Muscle Satellite Cells, hMG53, Rep1

description:
Library name: MusSCs_hMG53_4
Column name in MG53_ageing_Mus_SCs_gene_counts_matrix: S4.sorted.bam


title: RNA-seq of PDX2 bulk sample

description:
Library name: PDX2_bulk
PDX2 bulk RNA-seq
bulk_RNAseq_raw_counts.tsv


title: RNA-seq of MXP5 bulk sample

description:
Library name: MXP5_bulk
MXP5 bulk RNA-seq
bulk_RNAseq_raw_counts.tsv


title: LacZ_IL1b_Replicate2

description: Library name: 803-60re-x_S14


title: Breast cancer serum sample 156

extract_protocol: Total RNA was extracted from 200 µL of serum using the miRNeasy Serum/Plasma Advanced Kit (QIAGEN). Serum samples were thawed on ice and centrifuged at 3,000×g for 5 minutes at 4 °C. Buffer RPL containing carrier RNA and spike-in template mix was added, followed by Buffer RPP. RNA was eluted in 50 µL according to the manufacturer’s protocol.

value: Serum

value: Control


title: Breast cancer serum sample 155


title: LacZ_IL1b_Replicate3

description: Library name: 803-61re-x_S15


title: ChIP-seq of H3K4me1 in MXP5 IK1 rep2

description:
Library name: MXP5_H3K4me1_IK_rep2
H3K4me1 ChIP-seq in MXP5 IK1 rep2

data_processing:
ChIP-seq reads were quality-checked with FastQC, and adapter sequences were trimmed. Reads were aligned to the human genome (hg38) using STAR (v2.7.11b) with intron-spanning alignments disabled. Duplicates and low-quality reads were removed using samtools. Peaks were called with MACS2 (v2.2.9) using matched input controls and a q-value cutoff of 0.01. Replicate reproducibility was assessed using IDR (IDR < 0.01) to define high-confidence peaks. Signal tracks were generated using bedGraphToBigWig. QC metrics including FRiP scores and peak counts were computed using seqsetvis and deepTools. Peaks were annotated using ChIPseeker and GENCODE v36 gene models.
Assembly: hg38
Supplementary files format and content: Each file is a .narrowPeak file generated by MACS2, containing peak calls for individual ChIP-seq experiments

extract_protocol:
Cells were fixed in 1% formaldehyde for 10 minutes at room temperature and quenched with 125 mM glycine. After washing with cold PBS, cell pellets were snap-frozen and stored at −80°C. Nuclei were lysed in SDS lysis buffer (50 mM Tris-Cl pH 8.1, 10 mM EDTA pH 8.0, 1% SDS, plus protease inhibitors) for 30 minutes, followed by one freeze–thaw cycle. Chromatin was sheared to 200–500 bp using a Covaris S220 sonicator. Immunoprecipitation was performed with 50 µg of chromatin and primary antibodies overnight, followed by capture with protein A/G magnetic beads (Pierce #88803). Input chromatin (500 ng) was processed in parallel. After sequential washes and elution, cross-links were reversed and DNA purified using the PureLink PCR Purification Kit (Invitrogen #K310001). Libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit (NEB #E7645) and sequenced as 50 bp single-end reads on an Illumina HiSeq 1500 platform.
Libraries were constructed using NEBNext Ultra II Kit according to manufacterer's intstructions.

treatment_protocol: MXP5 stably expressing wild-type IK1 or control were induced with 1 μg/mL doxycycline for 24 hours.

tag: antibody


title: Breast cancer serum sample 157


title: Breast cancer serum sample 153


title: ageing Muscle Satellite Cells, BSA, Rep3

description:
Library name: MusSCs_BSA_3
Column name in MG53_ageing_Mus_SCs_gene_counts_matrix: S3.sorted.bam

value: BSA


title: Breast cancer serum sample 152


title: LacZ_bFGF_Replicate4

description: Library name: 803-56re-x_S8


title: ChIP-seq of H3K4me1 in MXP5 control rep2

description:
Library name: MXP5_H3K4me1_GFP_rep2
H3K4me1 ChIP-seq in MXP5 GFP rep2

value: control


title: LacZ_IL1b_Replicate1

description: Library name: 803-34re-x_S13


title: LacZ_IL1b_Replicate4

description: Library name: 803-62re-x_S16


title: ageing Muscle Satellite Cells, BSA, Rep1

description:
Library name: MusSCs_BSA_1
Column name in MG53_ageing_Mus_SCs_gene_counts_matrix: S1.sorted.bam


title: ageing Muscle Satellite Cells, BSA, Rep2

description:
Library name: MusSCs_BSA_2
Column name in MG53_ageing_Mus_SCs_gene_counts_matrix: S2.sorted.bam


title: Breast cancer serum sample 154


title: Input for MXP5 ChIP-seq control rep1

description:
Library name: MXP5_input_GFP_rep1
Input control for MXP5 ChIP-seq

value: input


title: Breast cancer serum sample 151

value: case

value: Basal-like


title: LacZ_bFGF_Replicate3

description: Library name: 803-55re-x_S7

value: cardiac fibroblast


title: ChIP-seq of H3K4me1 in MXP5 IK1 rep1

description:
Library name: MXP5_H3K4me1_IK_rep1
H3K4me1 ChIP-seq in MXP5 IK1 rep1


title: hypSugeneT5224

city: Pittsburgh

first: Alyxzandria

last: Gaydosik

state: PA

address: 200 Lothrop St

institute: University of Pittsburgh

description: Library name: BC016

data_processing:
Raw data was demultiplexed using CellRanger 9.0 "multi" function and aligned with Transcriptome Probe Set_v1.0.1_mm10-2020-A. Seurat 5.0 was used for downstream analysis.
Assembly: Chromium_Mouse_Transcriptome_Probe_Set_v1.0.1_mm10-2020-A
Supplementary files format and content: h5 file

source_name: lung

extract_protocol:
Formalin fixed, paraffin embedded tissue was dissociated and single nuclei were isolated using the standard 10x Genomics FLEX assay protocol. Each sample was pooled with additional samples following barcoding.
The 10x Genomics Single Cell Gene Expression FLEX protocol was used for probe hybiridization and library construction according to the manufacter's instructions.

value: lung


title: ChIP-seq of H3K4me1 in MXP5 control rep1

description:
Library name: MXP5_H3K4me1_GFP_rep1
H3K4me1 ChIP-seq in MXP5 GFP rep1


title: hypSugenePVP2

description: Library name: BC015

value: HxSuPVP


title: LacZ_bFGF_Replicate2

description: Library name: 803-54re-x_S6


title: ChIP-seq of H3K36me3 in MXP5 IK1 rep2

description:
Library name: MXP5_H3K36me3_IK_rep2
H3K36me3 ChIP-seq in MXP5 IK1 rep2


title: LacZ_bFGF_Replicate1

description: Library name: 803-32re-x_S5


title: Breast cancer serum sample 149


title: ChIP-seq of H3K36me3 in MXP5 IK1 rep1

description:
Library name: MXP5_H3K36me3_IK_rep1
H3K36me3 ChIP-seq in MXP5 IK1 rep1


title: LacZ_Con_Replicate3

description: Library name: 803-52re-x_S3


title: ChIP-seq of H3K36me3 in MXP5 control rep2

description:
Library name: MXP5_H3K36me3_GFP_rep2
H3K36me3 ChIP-seq in MXP5 GFP rep2


title: Breast cancer serum sample 150


title: hypT5224

description: Library name: BC013


title: hypSugenePVP1

description: Library name: BC014


title: Breast cancer serum sample 148


title: Breast cancer serum sample 146


title: ChIP-seq of H3K36me3 in MXP5 control rep1

description:
Library name: MXP5_H3K36me3_GFP_rep1
H3K36me3 ChIP-seq in MXP5 GFP rep1


title: LacZ_Con_Replicate2

description: Library name: 803-51re-x_S2


title: WT_3

description: Library name: BC011

value: untreated


title: ChIP-seq of H3K27ac in MXP5 IK1 rep2

description:
Library name: MXP5_H3K27ac_IK_rep2
H3K27ac ChIP-seq in MXP5 IK1 rep2


title: FRA_RAGko2

description: Library name: BC010


title: iCre_TNFa_Replicate4

description: Library name: 803-80re-x_S40


title: Breast cancer serum sample 145

value: Luminal B


title: LacZ_Con_Replicate4

description: Library name: 803-53re-x_S4


title: ChIP-seq of H3K27ac in MXP5 IK1 rep1

description:
Library name: MXP5_H3K27ac_IK_rep1
H3K27ac ChIP-seq in MXP5 IK1 rep1


title: FRA_RAGko1

description: Library name: BC009


title: hypPVP

description: Library name: BC012

value: HxPVP


title: Breast cancer serum sample 144


title: Breast cancer serum sample 147


title: RAGko

description: Library name: BC008


title: ChIP-seq of H3K27ac in MXP5 control rep2

description:
Library name: MXP5_H3K27ac_GFP_rep2
H3K27ac ChIP-seq in MXP5 GFP rep2


title: Breast cancer serum sample 143


title: iCre_TNFa_Replicate2

description: Library name: 803-78re-x_S38


title: iCre_TNFa_Replicate3

description: Library name: 803-79re-x_S39


title: ChIP-seq of H3K27ac in MXP5 control rep1

description:
Library name: MXP5_H3K27ac_GFP_rep1
H3K27ac ChIP-seq in MXP5 GFP rep1


title: FRA2_2

description: Library name: BC007


title: FRA2_1

description: Library name: BC006


title: Breast cancer serum sample 141


title: LacZ_Con_Replicate1

description: Library name: 803-31re-x_S1


title: Breast cancer serum sample 140


title: WT_2

description: Library name: BC005


title: iCre_TGF_Replicate4

description: Library name: 803-74re-x_S32


title: ChIP-seq of CTCF in MXP5 IK1 rep2

description:
Library name: MXP5_CTCF_IK_rep2
CTCF ChIP-seq in MXP5 IK1 rep2

value: CTCF


title: iCre_TNFa_Replicate1

description: Library name: 803-40re-x_S37


title: ChIP-seq of CTCF in MXP5 control rep2

description:
Library name: MXP5_CTCF_GFP_rep2
CTCF ChIP-seq in MXP5 GFP rep2


title: iCre_TGF_Replicate3

description: Library name: 803-73re-x_S31


title: Breast cancer serum sample 142


title: ChIP-seq of CTCF in MXP5 IK1 rep1

description:
Library name: MXP5_CTCF_IK_rep1
CTCF ChIP-seq in MXP5 IK1 rep1


title: ChIP-seq of CTCF in MXP5 control rep1

description:
Library name: MXP5_CTCF_GFP_rep1
CTCF ChIP-seq in MXP5 GFP rep1


title: iCre_TGF_Replicate2

description: Library name: 803-72re-x_S30


title: iCre_TGF_Replicate1

description: Library name: 803-38re-x_S29


title: Breast cancer serum sample 138


title: TG_nKO, snRNA-seq

city: San Antonio

first: Chu

last: Chen

state: Texas

address: 7703 Floyd Curl Dr

department: Cellular and Integrative Physiology

institute: UT Health San Antonio

description:
Library name: TG_nKO_GEX
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were using Cellranger-arc-2.0.0.
SnATAC sequence data were deleted due to low quality.
Ambient RNA was removed using Cellbender
Differentially expressed genes were calculated by Seurat packages
Plots were generated by OriginPro 2024.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Hippocampus

extract_protocol:
Tissue samples were subjected to lysis in 1 ml of lysis buffer (10 mM Tris-HCl, 5% Nonidet P40, 3 mM MgCl2, and 10 mM NaCl) along with 1 U/μl RNasin Plus RNase Inhibitor (Promega) for 15 minutes in a douncing tube placed on ice. The tissue was then homogenized using a loose pestle with ten dounces. The resulting suspension was filtered through a 70 μm mesh and centrifuged at 500 g for 5 minutes at 4°C. Post-lysis, the sample was treated with 2 ml of ice-cold nucleus wash buffer (5% wt/vol BSA, 0.25% wt/vol glycerol, 40 U/mL Protector RNAse inhibitor, 0.5X PBS), passed through a 20 μm mesh twice, and re-centrifuged under the same conditions. The supernatant was discarded, and the nuclear pellet was resuspended in 500 μl of wash buffer. An additional 500 μl of 50% (wt/vol) iodixanol (Optiprep) working solution was added to aid in further cleaning. This suspension was then layered over 1 mL of 29% (wt/vol) iodixanol solution in a 2 mL centrifuge tube and centrifuged at 10,000g for 30 minutes at 4°C. Finally, the nuclei were resuspended in a suitable volume of nuclei buffer to achieve a concentration of 500-1,000 nuclei/μl for subsequent capture.
Library was constructed according to manufacter's instructions (https://cdn.10xgenomics.com/image/upload/v1666737555/support-documents/CG000338_ChromiumNextGEM_Multiome_ATAC_GEX_User_Guide_RevF.pdf).

value: Hippocampus

value: Brain cells

value: 5xFAD_neuron specific MAGL-KO


title: Breast cancer serum sample 137

source_name: Serum

value: Serum


title: ChIP-seq of ERG in MXP5 IK1 rep2

description:
Library name: MXP5_ERG_IK_rep2
ERG ChIP-seq in MXP5 IK1 rep2

value: ERG


title: Breast cancer serum sample 136

value: Control


title: TG_aKO, snRNA-seq

description:
Library name: TG_aKO_GEX
10x Genomics

value: 5xFAD_astrocyte specific MAGL-KO


title: Breast cancer serum sample 139


title: TG_tKO, snRNA-seq

description:
Library name: TG_tKO_GEX
10x Genomics

value: 5xFAD_global MAGL-KO


title: TG, snRNA-seq

description:
Library name: TG_GEX
10x Genomics

value: 5xFAD mice


title: ChIP-seq of ERG in MXP5 IK1 rep1

description:
Library name: MXP5_ERG_IK_rep1
ERG ChIP-seq in MXP5 IK1 rep1


title: WT, snRNA-seq

description:
Library name: WT_GEX
10x Genomics

value: Wild type


title: ChIP-seq of ERG in MXP5 control rep2

description:
Library name: MXP5_ERG_GFP_rep2
ERG ChIP-seq in MXP5 GFP rep2

value: control


title: iCre_IL1B_Replicate4

description: Library name: 803-77re-x_S36

value: cardiac fibroblast


title: iCre_IL1b_Replicate2

description: Library name: 803-75re-x_S34


title: ChIP-seq of ERG in MXP5 control rep1

description:
Library name: MXP5_ERG_GFP_rep1
ERG ChIP-seq in MXP5 GFP rep1


title: Breast cancer serum sample 135


title: Breast cancer serum sample 134

value: case


title: iCre_IL1b_Replicate3

description: Library name: 803-76re-x_S35


title: iCre_IL1b_Replicate1

description: Library name: 803-39re-x_S33


title: Breast cancer serum sample 133


title: iCre_bFGF_Replicate4

description: Library name: 803-71re-x_S28


title: Mouse, beta cells, Control. Replicate 5

city: Indianapolis

first: Jason

last: Spaeth

state: IN

address: 1210 Waterway Blvd

department: Pediatrics

institute: Indiana University

description: Library name: Control_5

data_processing:
The generated FASTQ files were processed and interpreted using the Genialis visual informatics platform (https://www.genialis.com). Sequence quality checks were performed on raw and trimmed reads with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc), and Trimmomatic was used to trim adapters and filter out poor quality reads. Trimmed reads were then mapped to the mm10 UCSC reference genome using the HISAT2 aligner. Gene expression levels were quantified with HTSeq-count, and differential gene expression analyses performed with DESeq2. Poorly expressed genes, which have expression count summed over all samples below 10, were filtered out from the differential expression analysis input matrix.
Assembly: GRCm39
Supplementary files format and content: TPM all paired files included in 1 table

source_name: Pancreatic beta cells

extract_protocol:
RNA was isolated from FACS-purified β cells using the RNAqueous-Micro Total RNA Isolation Kit (Thermo Fisher). The DNAse treated RNA was analyzed on an Agilent 2100 Bioanalyzer. Only samples with an RNA Integrity Number above 7.5 were used for cDNA synthesis and library preparation.
cDNA was first synthesized using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Clontech Laboratories, Inc.). A dual indexed cDNA library was then prepared using Nextera XT DNA Library Prep Kit (Illumina, Inc.). Each library was quantified, and its quality accessed by Qubit and Agilent Bioanalyzer, and multiple libraries were pooled in equal molarity. The average size of the library insert was approximately 300-400 bp

value: Pancreatic beta cells

value: beta cell


title: Mouse, beta cells, Control. Replicate 3

description: Library name: Control_3


title: ChIP-seq of IKAROS in MXP5 IK1 rep1

description:
Library name: MXP5_IKAROS_IK_rep1
IKAROS ChIP-seq in MXP5 IK1 rep1

value: IKAROS


title: ChIP-seq of IKAROS in MXP5 IK1 rep2

description:
Library name: MXP5_IKAROS_IK_rep2
IKAROS ChIP-seq in MXP5 IK1 rep2


title: Breast cancer serum sample 132

city: Santander

first: Inés

last: Gómez-Acebo

address: Avda. Cardenal Herrera Oria S/N

institute: Division of Epidemiology and Computational Biology, School of Medicine, University of Cantabria,  IDIVAL, Santander, Spain

value: Basal-like


title: Breast cancer serum sample 131

value: Luminal A


title: Mouse, beta cells, Control. Replicate 2

description: Library name: Control_2


title: ChIP-seq of IKAROS in MXP5 control rep1

description:
Library name: MXP5_IKAROS_GFP_rep1
IKAROS ChIP-seq in MXP5 GFP rep1


title: Mouse, beta cells, Control. Replicate 1

description: Library name: Control_1


title: Mouse, beta cells, Control. Replicate 4

description: Library name: Control_4


title: iCre_bFGF_Replicate1

description: Library name: 803-37re-x_S25


title: ChIP-seq of IKAROS in MXP5 control rep2

description:
Library name: MXP5_IKAROS_GFP_rep2
IKAROS ChIP-seq in MXP5 GFP rep2


title: iCre_bFGF_Replicate3

description: Library name: 803-70re-x_S27


title: Breast cancer serum sample 130


title: iCre_bFGF_Replicate2

description: Library name: 803-69re-x_S26


title: Breast cancer serum sample 129


title: shCBL_mock_2

city: Davis

first: Tina

last: Truong

state: California

address: One Shields Ave

institute: UC Davis

description:
Library name: Sample 11
Column name in Supplemental Data_File_1_RNA_Seq_Raw_Counts.txt:   shCBL_mock_2

data_processing:
R was used for limma-voom pipeline on R with multiple testing correction using Benjamini-Hochberg procedure.
Assembly: GRCh38.p13 human genome
Supplementary files format and content: Tab-delineated text file includes normalized counts for each sample.

growth_protocol: purchased from ATCC. THP-1 cells were cultured in RPMI media containing 10% fetal bovine serum (FBS), 10mM HEPES, 1mM sodium pyruvate, 4500 mg/L glucose, and 0.05 mM 2-mercaptoethanol.

extract_protocol:
Macrophages were lysed in Trizol and lysates were purified with silica spin columns (Purelink) per manufacturer instructions.
RNA was purified and barcoded 3'Tag-Seq libraries prepared using the QuantSeq FWD kit (Lexogen, Vienna, Austria) for multiplexed sequencing according to the recommendations of the manufacturer by the UC Davis DNA Sequencing core.

treatment_protocol: Differentiated THP-1 cells were infected at MOI=10 for 6 h with lpqN Mtb in three independent experiments on different days.

value: Macrophage

value: CBL knockdown

value: Uninfected


title: Mouse, beta cells, Chd3/4Db. Replicate 2

description: Library name: Chd3-4Db_2


title: iCre_Con_Replicate4

description: Library name: 803-68re-x_S24


title: shCBL_mock_3

description:
Library name: Sample 12
Column name in Supplemental Data_File_1_RNA_Seq_Raw_Counts.txt:   shCBL_mock_3


title: Breast cancer serum sample 128

value: Serum


title: shCBL_mock_1

description:
Library name: Sample 10
Column name in Supplemental Data_File_1_RNA_Seq_Raw_Counts.txt:   shCBL_mock_1


title: iCre_Con_Replicate3

description: Library name: 803-67re-x_S23


title: Mouse, beta cells, Chd3/4Db. Replicate 1

description: Library name: Chd3-4Db_1


title: shCBL_TB_3

description:
Library name: Sample 9
Column name in Supplemental Data_File_1_RNA_Seq_Raw_Counts.txt:   shCBL_TB_3

value: Mtb infected


title: Mouse, beta cells, Chd3/4Db. Replicate 3

description: Library name: Chd3-4Db_3


title: iCre_Con_Replicate2

description: Library name: 803-66re-x_S22


title: Breast cancer serum sample 126


title: Mouse, beta cells, Chd3Db. Replicate 3

description: Library name: Chd3Db_3


title: shCBL_TB_2

description:
Library name: Sample 8
Column name in Supplemental Data_File_1_RNA_Seq_Raw_Counts.txt:   shCBL_TB_2


title: iCre_Con_Replicate1

description: Library name: 803-36re-x_S21


title: Breast cancer serum sample 127


title: shCBL_TB_1

description:
Library name: Sample 7
Column name in Supplemental Data_File_1_RNA_Seq_Raw_Counts.txt:   shCBL_TB_1


title: Mouse, beta cells, Chd3Db. Replicate 2

description: Library name: Chd3Db_2


title: Con_mock_3

description:
Library name: Sample 6
Column name in Supplemental Data_File_1_RNA_Seq_Raw_Counts.txt:   Con_mock_3

value: WT


title: Mouse, beta cells, Chd3-4Db. Replicate 3

description: Library name: Chd3-4Db_3

data_processing:
The pooled libraries were then denatured and neutralized before loading to NovaSeq 6000 sequencer at 300 pM final concentration for 100b paired-end sequencing (Illumina, Inc.). Approximately 100 x 106 reads per library were generated. A Phred quality score (Q score) was used to measure the quality of sequencing. More than 90% of the sequencing reads reached Q30 (99.9% base call accuracy).
Assembly: GRCm39
Supplementary files format and content: TPM all paired files included in 1 table

extract_protocol:
Tomato+ mature β-cells were collected for ATAC-Sequencing. Cells were first lysed to collect nuclei by incubating with 100 μL lysis buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 0.10% Tween-20, 0.10% Nonidet P40 Substitute, 0.01% Digitonin, 1% BSA, 1 mM DTT, 40 U/uL RNase Inhibitor) for 3 minutes, centrifuging at 300 rcf for 5 minutes at 4°C, and discarding the supernatant. The resulting nuclei were then washed with 1 mL wash buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 0.10% Tween-20, 1% BSA, 1 mM DTT, 40 U/μl RNase Inhibitor) and centrifuged at 200 rcf for 5 minutes at 4°C for 2-3 times. The final nuclei were used for tagmentation and library preparation
Nuclei were immediately suspended in 50 μL tagmentation reaction using 2xTD buffer (Illumina, FC-121-1030) and Nextera Tn5 Transposase enzyme (Illumina, FC-121-1030). Fragments greater than 600 bp were excluded in library preparation. Each resulting indexed library was quantified and its quality assessed by Qubit and Agilent Bioanalyzer, and multiple libraries pooled in equal molarity