title: Thymus, CD45+, 14-weeks-old male mice, Castration at 10th week, rep1

description: 10x Genomics

value: Pb-cre+;PtenLoxP/LoxP

value: Castration at 10th week


title: sample99: Patient 41, Visit V4

status: Public on Jun 18 2025

type: SRA

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

library_source: transcriptomic

data_processing:
Read quality was assessed with the FastQC tool (version 0.11.8)
Reads were mapped to the human genome hg38 with STAR (version 2.7.9a) with default parameters, except filtering out multimapping reads with more than 10 alignment locations (outFilterMultimapNmax=10) and filtering reads without evidence in the spliced junction table (outFilterType=“BySJout”).
The featureCounts() function from the Bioconductor Rsubread package (version 2.0.1) was used to count the number of reads (5' ends) overlapping with the exons of each gene (Ensembl release 102) assuming an exon union model. All subsequent analyses were performed using the R software (version 4.3.1) and Bioconductor 3.18 packages.
Assembly: hg38
Supplementary files format and content: Counts_Table.tsv: TSV file (tab separated values) including read counts for each sample and gene (ENSEMBL ID release 102). Column headers indicate the sample number.
Supplementary files format and content: Gene_Info.tsv: TSV file (tab separated values) including information about each gene used in the file Counts_Table.tsv (ENSEMBL release 102).
Supplementary files format and content: Sample_Info.tsv: TSV file (tab separated values) including information about each sample. Row sample number correspond to columns of the file Counts_Table.tsv.

molecule: total RNA

organism: Homo sapiens

source_name: Whole blood

extract_protocol:
Blood samples were collected on PAXtubes, and RNA extraction was performed on samples from visit 1, visit 1b, visit 2, visit 3 and visit 4. After quality control the resulting RNA was stored at -80°C for RNA-seq library preparation.
Illumina library preparation and sequencing were performed at the Oxford High-Throughput Genomics Hub. Sequencing was performed for 91 RNA-seq samples across 51 patients on an Illumina Hiseq 2000 instrument to produce paired-end 92 bp-long reads.

tag: donor

tag: tissue

value: Whole blood

tag: visit

tag: patient subgroup

value: Unknown

tag: surgery type

value: gastric sleeve

tag: Sex

value: female


title: Spleen, CD45+, 14-weeks-old male mice, Castration at 10th week, rep1

city: Beijing

first: Zhenpeng

last: Wu

address: No.5 Yiheyuan Road Haidian District

country: China

institute: Peking University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Cell Ranger software (version 4.0.0) were used to process reads, barcode and generate count expression matrices.
Assembly: mm10
Supplementary files format and content: cellranger generated barcode, genes and counts matrix files

organism: Mus musculus

source_name: spleen

extract_protocol:
tissues were dissociated to single cell  suspension, then stained with fluorescence-labed antibodies. Cells used for library construction were sorted using FACS strategy.
Single cell libraries were prepared using 10x Gemonics 3' or V(D)J kits following manufacturers' protocols.

value: spleen

tag: cell type

tag: genotype

tag: treatment


title: Primordial Follicles at T0, Replicate 2

city: Lodi

first: Alberto Maria

last: Luciano

state: LO

address: Via dell'Università 6

department: Department of Veterinary Medicine and Animal Sciences

country: Italy

institute: University of Milan

description: Library name: 23PM00

data_processing:
Trimming of the reads was performed to remove artificial constructs like adapters, primers, and overcalled polyG sequences with TrimGalore and Fastp.
Trimmed reads were mapped to the bovine transcriptome assembly, ARS UCD 1.3 using Salmon.
Mapped reads were quantified in TPM (transcripts per million) with Salmon.
Assembly: Bos taurus ARS UCD 1.3
Supplementary files format and content: Tab delimited files contains raw counts and TPM values generated with Salmon

organism: Bos taurus

source_name: Ovarian Follicles (oocyte and pre-granulosa cells)

extract_protocol:
Total RNA was extracted using the miRNeasy Tissue/Cells Advanced Micro Kit (Qiagen) and eluted in RNAse-free water following the manufacturer instructions.
cDNA was generated using SMART-Seq v4 Ultra Low Input RNA kit (Clontech). From the cDNA obtained, libraries were prepared using NEBNext® Ultra DNA Library Prep for Illumina® kit according to the manufacturer's protocol.

value: Isolated primordial follicles retrieved after collection (T0)


title: sample98: Patient 44, Visit V4

value: Insulin dependent T2D / No remission

value: gastric bypass


title: PBMC_OLD_RM215-15_female_Tp 3

type: genomic

city: Pittsburgh

first: Anna

middle: J

last: Jasinska

state: PA

address: 3550 Terrace Street

department: School of Medicine

country: USA

institute: University of Pittsburgh

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to the the Beadchip HorvathMammalMethylChip40 using standard Illumina protocol

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

data_processing: SeSaMe normalization as described in W. Zhou et al 2018. PMID: 30085201

label: Cy3 and Cy5

molecule: genomic DNA

organism: Macaca mulatta

source_name: PBMC

label_protocol: Standard Illumina Protocol, Cy3 and Cy5

extract_protocol: AllPrep DNA/RNA (Qiagen)

tag: gender

tag: dpi

tag: age day


title: PBMC_YOUNG_RM244-15_female_Tp 2


title: Prostate, CD45-, 14-weeks-old male mice, Castration at 10th week, rep1

description: 10x Genomics

source_name: prostate

value: prostate


title: Prostate, CD45+Gr1-, 14-weeks-old male mice, Castration at 10th week, rep1

description: 10x Genomics


title: Primordial Follicles at T0, Replicate 1

description: Library name: 22PM00

value: Ovarian Follicles (oocyte and pre-granulosa cells)


title: sample97: Patient 12, Visit V3


title: PBMC_OLD_RM215-15_female_Tp 2


title: sample96: Patient 7, Visit V1

value: T2D / No remission

value: revision

value: male


title: land_96h_young_stem_r3

city: shanghai

first: Qian

middle: qian

last: Hu

address: Xinjiangwancheng

department: School of Life Sciences

institute: Fudan University

description: Library name: Ap_land_96h_young_stem_r3

data_processing:
The 3'-adapters from all sequenced reads were clipped and the resulting small RNA reads were obtained, the reads shorter than 18nt were discarded, the redundant reads were removed to obtain unique reads with counts.
In order to identify homologs of conserved miRNAs in Alternanthera philoxeroides, mature miRNAs sequences of other plants were downloaded from the miRBase (v22) and the unique mature miRNAs sequences were obtained. These unique miRNAs were aligned to the genome using NCBI BLASTN (v 2.2.26) with the options of “-m 8 -e 0.01".
The frequencies of mature miRNAs in different small RNA sequencing profiles were calculated by aligning the small RNA reads to mature miRNAs using NCBI BLASTN (v2.2.26) with the options of “-S 1 -m 8 -e 0.01", and normalized to Reads Per Ten Million (RPTM) sequencing tags.
Assembly: Alternanthera philoxeroides
Supplementary files format and content: Excel

organism: Alternanthera philoxeroides

source_name: young stem

extract_protocol:
Young(1-2 internodes) and old (3-4 internodes) stems were collected at different time points on land or after waterlogged treatment, total RNA of stems were extracted using TRIzol reagent (Invitrogen, USA), the concentration  of RNA were assessed using Qubit (Thermo, USA) and quality of RNA were assessed using a Qsep100 and R1 RNA Cartridge Kit (BiOptic Inc., China).
Small RNA-Seq libraries were prepared using the VAHTS Small RNA Library Prep Kit for Illumina V2 (Vazyme, NR811-01) following the manufacturer’s instructions, samples were prepared from three independent biological replicates.

value: young stem


title: Prostate, CD45+CD11b+Gr1+, 14-weeks-old male mice, Castration at 10th week, rep1

description: 10x Genomics


title: sample95: Patient 33, Visit V1

value: No diabetes

value: unknown


title: land_96h_young_stem_r1

description: Library name: Ap_land_96h_young_stem_r1


title: land_96h_young_stem_r2

description: Library name: Ap_land_96h_young_stem_r2


title: PBMC_YOUNG_RM244-15_female_Tp 1


title: Blood, CD45+, 14-weeks-old male mice, Castration at 10th week, rep1

description: 10x Genomics

source_name: blood

value: blood

value: Pb-cre+;PtenLoxP/LoxP

value: Castration at 10th week


title: land_72h_young_stem_r3

description: Library name: Ap_land_72h_young_stem_r3


title: sample92: Patient 48, Visit V4

value: Whole blood

value: gastric sleeve


title: Prostate, CD45-, 14-weeks-old male mice, Control, rep4

description: 10x Genomics

value: Control


title: Bone marrow, CD45+, 14-weeks-old male mice, Castration at 10th week, rep1

description: 10x Genomics

source_name: bone marrow

value: bone marrow


title: land_72h_young_stem_r2

description: Library name: Ap_land_72h_young_stem_r2


title: sample93: Patient 31, Visit V4

value: female


title: Prostate, CD45-, 14-weeks-old male mice, Control, rep3

description: 10x Genomics


title: sample91: Patient 49, Visit V1

value: Unknown

value: gastric bypass


title: PBMC_OLD_RM215-15_female_Tp 1


title: Comb-2

city: Guangzhou

first: Xin

last: Guo

address: No. 106 Zhongshan Second Road, Yuexiu District, Guangzhou

institute: Guangdong Provincial People's Hospital

description:
Library name: Sample 8
VSVΔ51+GSK8612

data_processing:
Doublets were identified by the R package DoubletFinder (version 2.0.3) and filtered from the count matrix. After quality control, R package Seurat (version 4.0.4) was applied for downstream analysis. Gene expression was normalized, and highly variable genes were identified by the SCTransform function with default parameters. Based on highly variable genes, principal component analysis was performed by RunPCA function. Function RunHarmony from R package harmony (version 0.1.0) was applied to remove the potential batch effects between batches or samples.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files (barcodes.tsv, features.tsv, matrix.mtx).

molecule: polyA RNA

extract_protocol:
Centrifuge the cell suspension after homogenization (approximately 300g for 5 minutes), discard the supernatant, and then resuspend the cells in PBS. Count the live cells using Trypan Blue exclusion method or other staining methods to confirm cell viability. Take an appropriate amount of cell suspension and, according to the instructions of the magnetic bead sorting kit, add anti-CD45 antibody-coated magnetic beads, mix gently, and incubate at room temperature for 30 minutes to ensure binding. After incubation, wash the cells once with PBS to remove unbound magnetic beads. Count the collected CD45+cells and conduct further analyses as needed.
The single-cell 3’ cDNA libraries were constructed using the DNBelab C Series Single-Cell Library Prep Set (MGI, 940-001924-00) and sequenced on a sequenced DNBSEQ-T7 sequencer (MGI, 940-001924-00).

tag: cell line

value: Colorectal cancer cells

tag: strain


title: land_72h_young_stem_r1

description: Library name: Ap_land_72h_young_stem_r1


title: PBMC_YOUNG_RM243-15_female_Tp 4


title: sample90: Patient 5, Visit V1

value: T2D / Remission


title: PBMC_OLD_RM211-15_male_Tp 4


title: VSV51-2

description:
Library name: Sample 6
VSVΔ51


title: land_48h_young_stem_r3

description: Library name: Ap_land_48h_young_stem_r3


title: Spleen, CD45+, 14-weeks-old male mice, Control, rep2

description: 10x Genomics

value: spleen


title: Thymus, CD45+, 14-weeks-old male mice, Control, rep2

description: 10x Genomics

source_name: thymus

value: thymus


title: Spleen_YOUNG_RM241-15_male_Nx

source_name: Spleen

extract_protocol: Tri Reagent (Sigma-Aldrich) with column purification (Zymo)

value: male


title: VSV51-1

description:
Library name: Sample 5
VSVΔ51


title: sample89: Patient 35, Visit V1

value: Insulin dependent T2D / No remission


title: land_48h_young_stem_r2

description: Library name: Ap_land_48h_young_stem_r2

value: young stem


title: GSK-2

description: Library name: Sample 4


title: Prostate, CD45-, 14-weeks-old male mice, Control, rep2

description: 10x Genomics

value: prostate


title: sample88: Patient 20, Visit V1


title: land_48h_young_stem_r1

description: Library name: Ap_land_48h_young_stem_r1


title: Prostate, CD45+Gr1-, 14-weeks-old male mice, Control, rep2

description: 10x Genomics

value: Pb-cre+;PtenLoxP/LoxP


title: GSK-1

description: Library name: Sample 3


title: Comb-1

description:
Library name: Sample 7
VSVΔ51+GSK8612


title: land_24h_young_stem_r3

description: Library name: Ap_land_24h_young_stem_r3


title: sample87: Patient 36, Visit V1B

value: No diabetes


title: sample86: Patient 24, Visit V1

value: Whole blood


title: Control-2

description: Library name: Sample 2

value: DMSO


title: Prostate, CD45+CD11b+Gr1+, 14-weeks-old male mice, Control, rep2

description: 10x Genomics

value: Control


title: land_24h_young_stem_r2

description: Library name: Ap_land_24h_young_stem_r2


title: sample85: Patient 6, Visit V1

value: T2D / No remission


title: Blood, CD45+, 14-weeks-old male mice, Control, rep2

description: 10x Genomics

value: blood


title: SN_ROT_9_LANE2

city: London

first: Maria

last: Tsalenchuk

address: Maurice Wohl Clinical Neuroscience Institute, 5 Cutcombe Road

country: United Kingdom

institute: King's College London

library_source: genomic

data_processing:
Initial screening for sample anomalies was performed with FastQC (version 0.11.9). Adapter sequences were trimmed using Trim Galore! (version 0.6.7). For ChIP-seq, the trimmed FASTQ files were then mapped to the rat reference genome (mRatBN7.2) using Bowtie2 (version 2.4.4), followed by the removal of duplicate reads with Picard (version 2.6.0). Peak calling was conducted using MACS2 (version 2.2.7.1) on merged samples. For normalisation, we used merged control inputs pooled from multiple animals. Specifically, reads from individual replicates were combined into a single dataset prior to peak calling, allowing us to detect regions consistently enriched across samples. The pooled input control ensured accurate background normalisation across the merged data. The parameters for calling peaks were set for paired-end BAM files, using a genome size of 2.7 billion, a shift size of 50, and all duplicate reads were retained. Finally, FeatureCounts (version 2.0.5) quantified the alignment of reads to these identified peak regions.
Assembly: Rn7
Supplementary files format and content: narrowPeak, merged across brain regions

organism: Rattus norvegicus

source_name: ventral midbrain

extract_protocol:
Nuclei isolation from rat midbrain and cortical tissue was performed following a previously published protocol with slight modifications DOI: 10.1038/s41596-020-00472-3
For library preparation, the NEBNext Ultra II DNA Library Prep kit (New England BioLabs, E7645) was used for End Prep and Adapter Ligation, following the manufacturer’s instructions. Unique barcoded adapters (NextFlex, Bioo Scientific) were added. To decrosslink, libraries were incubated with RNase A (Thermo Scientific, EN0531) and Proteinase K (New England BioLabs, P8107) at 55°C for 1 hour and 65°C overnight. Libraries were then PCR amplified for 14 cycles with NEBNext Ultra II Q5® Master Mix (New England BioLabs, M0544).

treatment_protocol: Male Lewis rats aged 8-10 months received either rotenone at a dose of 2.8 mg/kg or a vehicle solution (Miglyol) administered intraperitoneally once daily for 21 days.24 hours after the final rotenone injection, rats were perfused using a saline-buffered solution. The cortex and SN were microdissected and immediately placed on dry ice

value: ventral midbrain

value: Rotenone


title: sample84: Patient 34, Visit V1

value: gastric sleeve

value: female


title: land_24h_young_stem_r1

description: Library name: Ap_land_24h_young_stem_r1


title: land_3h_young_stem_r3

description: Library name: Ap_land_3h_young_stem_r3


title: Bone marrow, CD45+, 14-weeks-old male mice, Control, rep2

description: 10x Genomics

value: bone marrow


title: sample83: Patient 2, Visit V1

value: gastric bypass


title: SN_ROT_8_LANE2


title: SN_ROT_7_LANE2


title: Thymus, CD45+, 14-weeks-old male mice, Control, rep1

description: 10x Genomics

value: thymus


title: sample82: Patient 9, Visit V1


title: land_3h_young_stem_r1

description: Library name: Ap_land_3h_young_stem_r1


title: Spleen, CD45+, 14-weeks-old male mice, Control, rep1

description: 10x Genomics

value: spleen


title: Prostate, CD45-, 14-weeks-old male mice, Control, rep1

description: 10x Genomics


title: sample81: Patient 19, Visit V1

value: Unknown

value: male


title: land_0h_young_stem_r3

description: Library name: Ap_land_0h_young_stem_r3

value: young stem


title: sample80: Patient 28, Visit V4

value: No diabetes


title: SN_ROT_5_LANE2


title: land_0h_young_stem_r2

description: Library name: Ap_land_0h_young_stem_r2


title: SN_VEH_4_LANE2

value: PBS


title: Prostate, CD45+Gr1-, 14-weeks-old male mice, Control, rep1

description: 10x Genomics

value: prostate

value: Pb-cre+;PtenLoxP/LoxP


title: Prostate, CD45+CD11b+Gr1+, 14-weeks-old male mice, Control, rep1

description: 10x Genomics

value: Control


title: sample79: Patient 5, Visit V4

value: Whole blood

value: T2D / Remission


title: sample78: Patient 24, Visit V4


title: SN_VEH_3_LANE2

value: ventral midbrain


title: land_96h_old_stem_r3

description: Library name: Ap_land_96h_old_stem_r3

source_name: old stem

value: old stem


title: Blood, CD45+, 14-weeks-old male mice, Control, rep1

description: 10x Genomics

value: blood


title: Bone marrow, CD45+, 14-weeks-old male mice, Control, rep1

description: 10x Genomics

value: bone marrow


title: SN_ROT_6_LANE2

value: Rotenone


title: SN_VEH_2_LANE2


title: land_3h_young_stem_r2

description: Library name: Ap_land_3h_young_stem_r2


title: SN_VEH_1_LANE2


title: sample74: Patient 7, Visit V4

value: T2D / No remission

value: revision


title: land_96h_old_stem_r1

description: Library name: Ap_land_96h_old_stem_r1


title: sample76: Patient 29, Visit V1

value: gastric sleeve

value: female


title: CORTEX_ROT_9_LANE2

source_name: cortex

value: cortex


title: Control-1

description: Library name: Sample 1

value: Colorectal cancer cells

value: DMSO


title: sample73: Patient 20, Visit V4

value: gastric bypass

value: male


title: Ntrk2 mutant H3N2 14dpi scRNA

city: Cincinnati

first: Jichao

last: Chen

state: OH

address: 3333 Burnet Avenue

institute: Cincinnati Children's Hospital

description: Constitutive deletion of Ntrk2 from adult endothelial cells

data_processing:
Raw sequencing files (fastq) were demultiplexed and analyzed using 10X Genomics Cell Ranger software
Assembly: mm10
Supplementary files format and content: Tsv and mtx files can be opened with Seurat (R package) for analysis.
Supplementary files format and content: filtered_feature_bc_matrix.h5 can be opened with Seurat (R package)

molecule: nuclear RNA

source_name: lung

extract_protocol:
Mouse lungs were collected and processed for dissociation and FACS according to our published protocol with modifications. Briefly, after removal of connective tissue and trachea, lungs were minced finely with forceps. Next, lungs were digested in 1.35ml Leibovitz media (Gibco, 21083-027) consisting of 2mg/ml collagenase type I (Worthington, CLS-1, LS004197), 0.5mg/ml DNase I (Worthington, D, LS002007), and 2mg/ml elastase (Worthington, ESL, LS002294) at 37°C for 45 minutes. To stop the enzymatic digestion, 300ul of fetal bovine serum (FBS, Invitrogen, 10092-139) was added for a final concentration of 20%. The digested tissue was filtered through a 70μm cell strainer (Falcon, 352350) on ice, in 4°C cold room, transferred into a 2ml microcentrifuge tube and pelleted at 1537 rcf for 1 min. The supernatant was removed and 1ml of red blood cell lysis buffer (15mM NH4Cl, 12mM NaHCO3 0.1mM EDTA, pH 8.0) was added to resuspend the pellet and incubated on ice for 3 min. Cells were centrifuged at 1537 rcf for 1 min, washed with Leibovitz + 10% FBS, resuspended in Leibovitz + 10% FBS, and filtered through a 35μm cell strainer into a 5ml glass tube. Samples for scRNA- and scATAC-seq were stained with CD45-PE/Cy7, ECAD-PE, and ICAM2-AF647 antibodies, as well as SYTOX Blue for 30 min on ice, in 4°C cold room. Samples were pelleted, washed again in Leibovitz + 10% FBS, filtered through a 35μm cell strainer into a 5ml glass tube and sorted using Aria II Cell sorter with a 70μm nozzle.
FACS-purified lung epithelial, endothelial, mesenchymal, and immue cells were processed through the CG000315 Chromium Single Cell 3' Reagent Kits User Guide & CG000331 Chromium Single Cell 5' Reagent Kits User Guide
Library was performed using the CG000315 Chromium Single Cell 3' Reagent Kits User Guide & CG000331 Chromium Single Cell 5' Reagent Kits User Guide (28 cycles read 1, 90 cycles read 2, 10 cycles Index 1, and 10 cycles Index 2)

value: lung

value: epithelial, endothelial, mesenchymal, immune

value: Ntrk2CKO/CKO; Sun1GFP; Tek-Cre

tag: age

value: pooled male and female


title: Control H3N2 14dpi scRNA

value: Ntrk2CKO/+; Sun1GFP; Tek-Cre


title: sample71: Patient 29, Visit V4

value: Whole blood

value: No diabetes


title: Ntrk2 mutant Sendai 14dpi scRNA

description: Conditional deletion of Ntrk2 from adult endothelial cells

value: Ntrk2CKO/CKO; Cdh5-CreER

value: 3 doses of Tamoxifen each at 3mg


title: CORTEX_ROT_8_LANE2

value: Rotenone


title: land_72h_old_stem_r2

description: Library name: Ap_land_72h_old_stem_r2

value: old stem


title: sample70: Patient 12, Visit V1

value: Insulin dependent T2D / No remission

value: gastric sleeve

value: female


title: land_0h_young_stem_r1

description: Library name: Ap_land_0h_young_stem_r1

value: young stem


title: land_72h_old_stem_r1

description: Library name: Ap_land_72h_old_stem_r1


title: Control Sendai 14dpi scRNA

value: Ntrk2CKO/+; Cdh5-CreER


title: Control Sendai 14dpi scATAC

description: 2-wk post Sendai virus injury

data_processing:
Raw sequencing data (fastq file) was demultiplexed and analyzed using 10X Genomics Cell Ranger software
Further analysis can be achieved using the Cell Ranger atac-derived analysis files on R
Assembly: mm10
Supplementary files format and content: Cell Ranger-atac processed files can be opened with Signac (R package) and analyzed.

extract_protocol:
Mouse lungs were collected and processed for dissociation and FACS according to our published protocol with modifications. Briefly, after removal of connective tissue and trachea, lungs were minced finely with forceps. Next, lungs were digested in 1.35ml Leibovitz media (Gibco, 21083-027) consisting of 2mg/ml collagenase type I (Worthington, CLS-1, LS004197), 0.5mg/ml DNase I (Worthington, D, LS002007), and 2mg/ml elastase (Worthington, ESL, LS002294) at 37°C for 45 minutes. To stop the enzymatic digestion, 300ul of fetal bovine serum (FBS, Invitrogen, 10092-139) was added for a final concentration of 20%. The digested tissue was filtered through a 70μm cell strainer (Falcon, 352350) on ice, in 4°C cold room, transferred into a 2ml microcentrifuge tube and pelleted at 1537 rcf for 1 min. The supernatant was removed and 1ml of red blood cell lysis buffer (15mM NH4Cl, 12mM NaHCO3 0.1mM EDTA, pH 8.0) was added to resuspend the pellet and incubated on ice for 3 min. Cells were centrifuged at 1537 rcf for 1 min, washed with Leibovitz + 10% FBS, resuspended in Leibovitz + 10% FBS, and filtered through a 35μm cell strainer into a 5ml glass tube. Samples for scRNA- and scATAC-seq were stained with CD45-PE/Cy7, ECAD-PE, and ICAM2-AF647 antibodies, as well as SYTOX Blue for 30 min on ice, in 4°C cold room. Samples were pelleted, washed again in Leibovitz + 10% FBS, filtered through a 35μm cell strainer into a 5ml glass tube and sorted using Aria II Cell sorter with a 70μm nozzle.
FACS-purified lung endothelial and mesenchymal cells were purified through the CG000496 Chromium Single Cell ATAC Reagent Kits User Guide
50 cycles for Read 1, 50 cycles for Read 2, 8 cycles for Index 1, 16 cycles for Index 2

value: endothelial, mesenchymal

value: BdnfCKO/CKO; Ntf5CKO/+ (male) & Ntf5CKO/CKO (female)

value: Sendai virus treatment at 8-wk, lung harvest at 10wk


title: sample69: Patient 14, Visit V1

value: T2D / No remission


title: CORTEX_ROT_INPUT_LANE2

value: cortex


title: land_96h_old_stem_r2

description: Library name: Ap_land_96h_old_stem_r2


title: land_48h_old_stem_r3

description: Library name: Ap_land_48h_old_stem_r3


title: land_48h_old_stem_r2

description: Library name: Ap_land_48h_old_stem_r2


title: CORTEX_VEH_3_LANE2

value: PBS


title: CORTEX_VEH_2_LANE2


title: land_48h_old_stem_r1

description: Library name: Ap_land_48h_old_stem_r1


title: sample67: Patient 11, Visit V1

value: Whole blood

value: T2D / Remission


title: land_72h_old_stem_r3

description: Library name: Ap_land_72h_old_stem_r3


title: RT_TMZ_MET glioma, replicate 1

city: Milano

first: Stefano

last: de Pretis

address: Via Olgettina, 58

department: Center for Omics Sciences

institute: IRCCS San Raffaele Institute

description: 10X Genomics

data_processing:
CellRanger v6.0.2 software (10X Genomics) was used to perform the preliminary steps of the analysis, including demultiplexing of the input FASTQ files, alignment to the mm10 mouse reference genome (Ensembl 98), UMI quantification and assignment to the GENCODE (v32) gene annotation.
Assembly: mm10
Supplementary files format and content: Tab separated files and matrix files

source_name: GBM tumor samples

growth_protocol: Seven to eight weeks old female C57BL/6 mice (Envigo RMS, San Pietro al Natisone, Italy), were housed at constant temperature (23°C) and relative humidity (40%) under a regular light/dark schedule. Food and water were available ad libitum. The orthotopic tumor model was obtained by the stereotactic injection of 1x105  murine GBM GL261 cells (ACC 802, Leibniz Institute DSMZ, Germany) in 2 µl of plain DMEM with a 10 µl Hamilton syringe as previously described (Valtorta 2021). After cell injection, mice were monitored every day for body weight and clinical signs of disease (fur, eye, motor impairment) and sacrificed at the appearance of evident signs of illness or loss of more than 25% of the initial body weight.

extract_protocol:
Immediately after sacrifice, GBM tumor samples of mice treated with vehicle, RT, RT plus TMZ, RT plus TMZ and MET were collected and dissociated enzymatically to obtain a single-cell suspension with the Tumor Dissociation Kit – mouse (130-096-730, Miltenyi Biotech, Bergisch Gladbach, Germany) and GentleMACS Octo Dissociator (Miltenyi Biotec), according to the manufacturer’s protocol. Directly after tissue dissociation, cell concentration and viability were assessed.
Single cells were processed for transcriptome analyses using the Chromium Controller (10x Genomics) and the Chromium Single Cell 3' Reagent Kits User Guide (v3.1 Chemistry) (10x Genomics) with a cell recovery target of 4000 single cells. Libraries were prepared following manufacturer’s directions. After quality controls, libraries were sequenced on Novaseq platform (Illumina) aiming at 50’000 reads/cell.

treatment_protocol: In a first group of mice, the effect of vehicle, MET (D150959, Merck), TMZ (T2577, Merck) or TMZ plus MET on tumor growth was evaluated. Tumor bearing mice were randomly assigned to 4 groups of treatment, according to the following scheme: Group A received daily oral administration of TMZ (70 mg/kg) in 10% DMSO, 5 days for a 28 days cycle and repeated with this scheme (5/28) until sacrifice of animal; group B received intra peritoneal (i.p.) administration of MET (250 mg/kg) in saline for 5d/wk for the entire treatment period; group C received the combination of daily oral administration of TMZ (70 mg/kg) 5 days for a 28 days cycle and i.p. daily administration of MET (250 mg/kg); group D, as vehicle group, received vehicle (10% DMSO in saline by oral gavage and 100% saline i.p.). The treatment schedule was decided on the basis of previous studies (Valtorta 2021) and of the dose regimen used in clinical practice adapted to mice body surface (Valtorta 2021).

value: GBM tumor samples

tag: orthotopic tumor_cell_line

value: murine GBM GL261 cells

value: RT+TMZ+MET


title: PBS scATAC

description: 2-wk post Sendai virus injury

value: lung

value: PBS treatment at 8-wk, lung harvest at 10-wk

value: pooled male and female


title: CORTEX_VEH_4_LANE2


title: RT_TMZ_MET glioma, replicate 2

description: 10X Genomics


title: RT_TMZ glioma, replicate 2

description: 10X Genomics

value: RT+TMZ


title: land_24h_old_stem_r3

description: Library name: Ap_land_24h_old_stem_r3

value: old stem


title: sample65: Patient 28, Visit V1

value: No diabetes

value: gastric bypass

value: female


title: CORTEX_VEH_1_LANE2


title: land_24h_old_stem_r2

description: Library name: Ap_land_24h_old_stem_r2


title: CORTEX_VEH_INPUT_LANE2


title: CORTEX_ROT_7_LANE2

value: Rotenone


title: RT_TMZ glioma, replicate 1

description: 10X Genomics


title: sample63: Patient 8, Visit V1

value: revision


title: RT glioma, replicate 2

description: 10X Genomics

value: RT


title: SN_ROT_8

value: ventral midbrain


title: land_3h_old_stem_r3

description: Library name: Ap_land_3h_old_stem_r3


title: SN_ROT_9


title: sample66: Patient 22, Visit V1

value: Whole blood

value: male


title: RT glioma, replicate 1

description: 10X Genomics

value: GBM tumor samples


title: land_24h_old_stem_r1

description: Library name: Ap_land_24h_old_stem_r1


title: sample68: Patient 15, Visit V1

value: Insulin dependent T2D / No remission


title: sample61: Patient 47, Visit V4


title: sample62: Patient 28, Visit V2


title: SN_ROT_7


title: SN_ROT_6


title: untreated glioma, replicate 1

description: 10X Genomics

value: murine GBM GL261 cells

value: untreated


title: untreated glioma, replicate 2

description: 10X Genomics


title: land_3h_old_stem_r2

description: Library name: Ap_land_3h_old_stem_r2


title: land_0h_old_stem_r3

description: Library name: Ap_land_0h_old_stem_r3


title: sample59: Patient 1, Visit V2

value: gastric sleeve


title: SN_ROT_5


title: Il10KO_hh

city: New York

first: Jordan

last: Zhou

state: NY

address: 413 E 69th St

institute: Weill Cornell Medical College

description: 10x Genomics

data_processing:
The barcoding , gene counts, and alignment were generated using the Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab seperated values files and matrix files

source_name: Large Intestine

extract_protocol:
Large intestine from Stingfl/fl and Stingfl/fl RORγtcre mice were dissected and fat tissues were removed. Intestines were opened longitudinally, extensively cleaned with cold Dulbecco's PBS (Corning) and cut approximately into 0.5-cm sections. Cut tissues were incubated in Hanks' balanced salt solution) containing 5 mM EDTA (Thermo Fisher Scientific), 1 mM dithiothreitol (Sigma-Aldrich) and 2% fetal bovine serum twice at 37 °C for 20 min to dissociate epithelial cells. Tissues were vortexed, transferred to digestion buffer containing collagenase III (1 mg mL-1; Worthington), dispase (0.4 U mL-1; Thermo Fisher Scientific), DNase I (20 μg mL-1 ;Sigma-Aldrich) and 10% FBS in RPMI 1640 (Corning), and incubated in a shaker at 200 rpm for 1 hour at 37°C. Leukocytes were enriched by 40/80% Percoll gradient (GE Healthcare).
Library construction was performed by epigenomics core at Weill Cornell Medicine.

value: Large Intestine

value: APCs

value: H. hepaticus


title: sample60: Patient 45, Visit V4

value: T2D / Remission


title: SN_VEH_4

value: PBS


title: sample58: Patient 30, Visit V2

value: T2D / No remission


title: land_0h_old_stem_r2

description: Library name: Ap_land_0h_old_stem_r2

value: old stem


title: sample64: Patient 3, Visit V1

value: gastric bypass


title: B6_hh

description: 10x Genomics


title: SN_VEH_3


title: sample57: Patient 32, Visit V4

value: unknown

value: female


title: B6_Control

description: 10x Genomics

value: Control


title: sample56: Patient 23, Visit V1

value: Whole blood

value: male


title: water_96h_young_stem_r3

description: Library name: Ap_water_96h_young_stem_r3

value: young stem


title: SN_VEH_2

value: ventral midbrain


title: Heart, MacroD1_knockout_LPS, rep2

city: Shang hai

first: chen

middle: xiao

last: qiang

state: China

address: 650 New Songjiang Road

department: Department of Cardiology

institute: Shanghai General Hospital, Shanghai Jiaotong University School of Medicine

data_processing:
After the sample is sequenced on the computer, the image file is obtained, which is converted by the built-in software of the sequencing platform to generate the Raw Data of FASTQ, that is, the data off the computer. The Raw Data for each sample were counted separately, including sample name, Q30, percentage of fuzzy bases, and Q20(%) and Q30(%).
The sequencing data contained some low-quality Reads with junctions, which would greatly interfere with the subsequent information analysis, so further filtering of the sequencing data was required. The data filtering criteria mainly include: 1) Cutadapt is used to remove the 3' end junction, and the removed part has at least 10 bp Overlap (AGATCGGAAG) with the known junction, allowing 20% base mismatch; 2) Reads with average mass fraction lower than Q20 were removed.
The filtered Reads were compared to the reference genome using an updated version of TopHat2's HISAT2 software.
HTSeq was used to statistically compare the Read Count value of each gene as the original expression of the gene.
Assembly: mm39
Supplementary files format and content: Tab-delimited text files include raw counts for each sample.

source_name: Heart left ventricular tissues

growth_protocol: The mice utilized in this study were bred and maintained on a C57BL/6J background. They were housed in conditions of standard temperature (24°C) and humidity (40-60%), with a 12-hour light/dark cycle (from 6 AM to 6 PM). The mice were provided with unrestricted access to water and were nourished with a standard rodent chow diet.

extract_protocol:
Total RNA was extracted from tissues according to standard protocols using TRIzol reagent (Invitrogen, CA, USA).
An Agilent Bioanalyzer was employed to evaluate the quality of RNA. Sequencing libraries were generated using the TruSeq RNA Sample Preparation Kit (Illumina, San Diego, CA, USA).

treatment_protocol: The 8-week-old cardiac-specific conditional MacroD1 knockout mice (Mac_ko) and control mice (WT) were injected intraperitoneally with LPS (10mg/kg) or saline for 18 hours.

value: Heart left ventricular tissues

value: Male

value: MacroD1 knockout

value: 8 weeks

value: LPS for 18h


title: land_3h_old_stem_r1

description: Library name: Ap_land_3h_old_stem_r1


title: water_96h_young_stem_r2

description: Library name: Ap_water_96h_young_stem_r2


title: Heart, MacroD1_knockout_LPS, rep1


title: sample55: Patient 34, Visit V4

source_name: Whole blood

value: No diabetes

value: gastric sleeve


title: SN_VEH_1

value: PBS


title: CORTEX_ROT_9

value: cortex

value: Rotenone


title: Heart, WT_LPS, rep2

value: WT


title: water_96h_young_stem_r1

description: Library name: Ap_water_96h_young_stem_r1


title: water_72h_young_stem_r3

description: Library name: Ap_water_72h_young_stem_r3


title: sample51: Patient 40, Visit V4

value: Insulin dependent T2D / No remission

value: gastric bypass


title: Heart, WT_LPS, rep1


title: sample53: Patient 43, Visit V4

value: Whole blood

value: T2D / No remission


title: water_72h_young_stem_r2

description: Library name: Ap_water_72h_young_stem_r2

value: young stem


title: CORTEX_VEH_4


title: CORTEX_ROT_8


title: sample50: Patient 1, Visit V1

value: male


title: Heart, MacroD1 knockout, rep2

value: Heart left ventricular tissues

value: saline for 18h


title: Heart, MacroD1 knockout, rep1

value: Male

value: MacroD1 knockout


title: land_0h_old_stem_r1

description: Library name: Ap_land_0h_old_stem_r1

value: old stem


title: water_72h_young_stem_r1

description: Library name: Ap_water_72h_young_stem_r1


title: sample49: Patient 23, Visit V2

value: T2D / Remission


title: CORTEX_ROT_INPUT


title: Heart, WT, rep2

value: 8 weeks


title: water_48h_young_stem_r2

description: Library name: Ap_water_48h_young_stem_r2


title: CORTEX_VEH_3

value: PBS


title: sample48: Patient 12, Visit V4

value: gastric sleeve

value: female


title: Heart, WT, rep1

value: WT


title: sample52: Patient 3, Visit V4

value: Insulin dependent T2D / No remission


title: sample47: Patient 17, Visit V4

value: gastric bypass


title: CORTEX_VEH_2

value: cortex


title: water_48h_young_stem_r1

description: Library name: Ap_water_48h_young_stem_r1


title: IL21 HTO

city: Boston

first: Stephanie

last: Dougan

address: 450 Brookline Ave

institute: Dana Farber Cancer Institute

description:
TotalSeq-C0301 anti mouse hashtag 1, TotalSeq-C0302 anti mouse hashtag 2, TotalSeq-C0303 anti mouse hashtag 3, TotalSeq-C0304 anti mouse hashtag 4, TotalSeq-C0305 anti mouse hashtag 5
IL21_raw_feature_bc_matrix.h5

library_source: other

data_processing:
A custom reference was built using Cellranger (v7.0.0) with GTF/fasta files for Mus musculus (Ensembl 108) and TRP1 high/low TCR sequences (PMID: 24459675). Cellranger was used to align and count FASTQ reads
The count matrices were imported for downstream analysis into R using the Seurat (v4.3.0) package. Cells were called from barcodes using the Seurat R package
Hashtag demultiplexing (HTODemux), count normalization, clustering, and differential expression analysis was done in Seurat
Assembly: Custom: Mus musculus Ensembl release 108 + appended TRP1 high/low TCR chain sequences. Built with 'cellranger mkref'
Supplementary files format and content: Tar file of HDF5 (.h5) stored count/feature matrices output from Cellranger

molecule: protein

source_name: Tumor

extract_protocol:
Tumors were excised, digested with Miltenyi tumor digest kit, washed and magnetically sorted for CD45+ cells. Each different tumor sample within a treatment group was incubated with a unique hashing antibody. Samples within each treatment group were then pooled and loaded onto a 10x controller to generate single cell GEMs
Library preparation was performed with the 10x Genomics Chromium Single Cell 5’ v2 library kit with Feature Barcode Kit Library

value: Tumor

value: Melanoma

value: Wild-type


title: 21h10 rep 2 HTO

description:
TotalSeq-C0301 anti mouse hashtag 1, TotalSeq-C0302 anti mouse hashtag 2, TotalSeq-C0303 anti mouse hashtag 3, TotalSeq-C0304 anti mouse hashtag 4, TotalSeq-C0305 anti mouse hashtag 5
21h10_2_raw_feature_bc_matrix.h5


title: CORTEX_ROT_7

value: Rotenone


title: water_24h_young_stem_r2

description: Library name: Ap_water_24h_young_stem_r2

value: young stem


title: CORTEX_VEH_1


title: PBS rep 2 HTO

description:
TotalSeq-C0301 anti mouse hashtag 1, TotalSeq-C0302 anti mouse hashtag 2, TotalSeq-C0303 anti mouse hashtag 3, TotalSeq-C0304 anti mouse hashtag 4, TotalSeq-C0305 anti mouse hashtag 5
PBS_2_raw_feature_bc_matrix.h5


title: CORTEX_VEH_INPUT


title: sample46: Patient 37, Visit V4

value: Whole blood

value: male


title: CORTEX_ROT_6


title: IL21 GEX


title: water_3h_young_stem_r3

description: Library name: Ap_water_3h_young_stem_r3


title: water_24h_young_stem_r1

description: Library name: Ap_water_24h_young_stem_r1


title: water_3h_young_stem_r2

description: Library name: Ap_water_3h_young_stem_r2


title: CORTEX_ROT_5


title: PBS rep 2 GEX


title: water_48h_young_stem_r3

description: Library name: Ap_water_48h_young_stem_r3


title: sample42: Patient 23, Visit V4


title: water_3h_young_stem_r1

description: Library name: Ap_water_3h_young_stem_r1


title: water_24h_young_stem_r3

description: Library name: Ap_water_24h_young_stem_r3


title: 21h10 rep 1 HTO

description:
TotalSeq-C0301 anti mouse hashtag 1, TotalSeq-C0302 anti mouse hashtag 2, TotalSeq-C0303 anti mouse hashtag 3, TotalSeq-C0304 anti mouse hashtag 4, TotalSeq-C0305 anti mouse hashtag 5
21h10_raw_feature_bc_matrix.h5


title: water_96h_old_stem_r3

description: Library name: Ap_water_96h_old_stem_r3

value: old stem


title: sample40: Patient 17, Visit V1

value: T2D / Remission


title: sample45: Patient 18, Visit V1

value: T2D / No remission


title: sample41: Patient 16, Visit V1

value: No diabetes

value: gastric band


title: 21h10 rep 2 GEX


title: Neo2 HTO

description:
TotalSeq-C0301 anti mouse hashtag 1, TotalSeq-C0302 anti mouse hashtag 2, TotalSeq-C0303 anti mouse hashtag 3, TotalSeq-C0304 anti mouse hashtag 4, TotalSeq-C0305 anti mouse hashtag 5
Neo2_raw_feature_bc_matrix.h5


title: sample39: Patient 42, Visit V4

value: gastric sleeve


title: sample43: Patient 4, Visit V4

value: female


title: water_96h_old_stem_r1

description: Library name: Ap_water_96h_old_stem_r1


title: PBS rep 1 HTO

description:
TotalSeq-C0301 anti mouse hashtag 1, TotalSeq-C0302 anti mouse hashtag 2, TotalSeq-C0303 anti mouse hashtag 3, TotalSeq-C0304 anti mouse hashtag 4, TotalSeq-C0305 anti mouse hashtag 5
PBS_raw_feature_bc_matrix.h5

value: PBS


title: 21h10 rep 1 GEX


title: water_72h_old_stem_r3

description: Library name: Ap_water_72h_old_stem_r3


title: sample44: Patient 22, Visit V4

value: gastric bypass


title: sample37: Patient 1, Visit V4


title: Neo2 GEX


title: ASCs treated with DMSO rep3

type: RNA

city: Linköping

first: Mouna

last: Tababi

state: Östergötland

country: Sweden

institute: Linköping University

description: RMA expression value derived from Transcriptome Analysis Console Software (Affymetrix)

hyb_protocol: Samples were hybridized with GeneChip Clariom S Human Arrays (Affymetrix)

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G  according to the manufacturer's instruction (Affymetrix)

data_processing: Raw data were processed with the Transcriptome Analysis Console Software (Affymetrix) for background correction, quality control, normalization and the calculation of log2 fold-changes between sample expression values. DEGs (differentially expressed genes ) were defined based on a log2 fold change value |FC| of ≥ 1.5 and an adjusted false discovery rate (FDR) p-value < 0.05.

label: biotin

source_name: ASCs treated with DMSO

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: The adipose-derived mesenchymal stem cell (ASCs) line, ASC52telo (SCRC-4000, ATCC) immortalized with human telomerase reverse transcriptase, were expanded in DMEM (Thermo Fisher, Cat. 31885049) supplemented with 10% fetal bovine serum (FBS, Thermo Fisher, Cat. 10500064) and 1% penicillin/streptomycin, in a humidified incubator at 37°C with 5% CO₂, according to the provider recommendations.

extract_protocol: Total cellular RNA was extracted using the RNeasy Plus Mini kit (Qiagen , Cat. 74134), according to the manufacturer’s instructions

treatment_protocol: The cells were divided into three experimental groups: a control group with cells cultured in DM alone, a vehicle control group with cells treated with DM and 0.1%  DMSO, and a treatment group that received  DM and the Rab7 inhibitor, CID-1067700 at 40 μM (SigmaAldrich, Cat. SML0545 ). Cells were maintained at 37°C with 5% CO₂, and the differentiation media, along with the respective additives, was refreshed every 2-3 days. Cells were harvested for downstream analyses after ten days


title: water_72h_old_stem_r2

description: Library name: Ap_water_72h_old_stem_r2


title: sample36: Patient 21, Visit V2

value: revision


title: PBS rep 1 GEX

value: Tumor


title: ASCs treated with DMSO rep1

value: The adipose-derived mesenchymal stem cell (ASCs) line, ASC52telo


title: ASCs treated with CID rep3

source_name: ASCs treated with CID


title: water_72h_old_stem_r1

description: Library name: Ap_water_72h_old_stem_r1


title: sample35: Patient 18, Visit V2


title: ASCs treated with CID rep2


title: sample34: Patient 8, Visit V4


title: water_96h_old_stem_r2

description: Library name: Ap_water_96h_old_stem_r2


title: water_48h_old_stem_r3

description: Library name: Ap_water_48h_old_stem_r3


title: H_M_2

city: Shanghai

first: Junjie

last: Gao

address: 600 Yishan Road

institute: Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/ , version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/ , version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/ , version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software (http://ccb.jhu.edu/software/stringtie/gffcompare.shtml , version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: GRCm38
Supplementary files format and content: 1_genes_fpkm_expression.xlsx: Excel file includes counts and FPKM values for each Sample.

growth_protocol: bEnd.3 endothelial cells were maintained in high-glucose DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
RNA was harvested using RNeasy Mini kit ( Qiagen, Germany). RNA quality was examined by gel electrophoresis and with Qubit (Thermo, Waltham, MA, USA).
RNA libraries for RNA-seq were prepared using Stranded mRNA-seq Library Prep Kit (Vazyme)following manufacturer's protocols.

treatment_protocol: Sample H_M_1-3 were co-incubated with isolated mitochondria reconstituted by 100ul of culture medium; Sample H_1-3 were treated with equal amount of culture medium alone.

value: endothelial cells

value: WT

value: Mitochondrial transplantation


title: water_48h_old_stem_r2

description: Library name: Ap_water_48h_old_stem_r2


title: ASCs treated with Differentiation media rep3

source_name: ASCs treated with Differentiation media


title: ASCs treated with DMSO rep2


title: ASCs treated with CID rep1


title: H_M_1


title: sample33: Patient 10, Visit V3

value: Whole blood

value: Unknown


title: N

city: Yantai

first: Mengqi

last: Jiang

address: 346 Guanhai Road, Laishan District, Yantai City, Shandong Province, China

institute: Binzhou Medical University

description: Library name: Sample 2

data_processing:
Basecalls performed using SOAPnuke (v1.5.6).    Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome using bowtie HISAT2.    Each sample peaks and differentially enriched peaks were analyzed by DESeq2 (v1.4.5).
Assembly: GCF_000001405.39_GRCh38.p13
Supplementary files format and content: tab-delimited text fole includes raw counts for each sample

extract_protocol:
The whole RNA of two group of hiPSC-CMs  using Trizol reagent.Total RNA of the sample was subjected to test the RNA integrity using agarose gel.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample(KitKAPA Stranded mRNA-seq Kit). Including cDNA synthesis, add A in 3’end,

value: Cardiac myocytes differentiated from human multipotential stem cells

value: Cardiomyocytes differentiated


title: sample38: Patient 16, Visit V2

extract_protocol:
Blood samples were collected on PAXtubes, and RNA extraction was performed on samples from visit 1, visit 1b, visit 2, visit 3 and visit 4. After quality control the resulting RNA was stored at -80°C for RNA-seq library preparation.
Illumina library preparation and sequencing were performed at the Oxford High-Throughput Genomics Hub. Sequencing was performed for 91 RNA-seq samples across 51 patients on an Illumina Hiseq 2000 instrument to produce paired-end 92 bp-long reads.


title: water_48h_old_stem_r1

description: Library name: Ap_water_48h_old_stem_r1

value: old stem


title: H_3

value: Control


title: ASCs treated with Differentiation media rep2


title: sample31: Patient 27, Visit V1

value: No diabetes


title: WT

description: Library name: Sample 1


title: sample30: Patient 26, Visit V1

value: min gastric bypass


title: ASCs treated with Differentiation media rep1


title: H_2


title: water_24h_old_stem_r2

description: Library name: Ap_water_24h_old_stem_r2


title: sample29: Patient 27, Visit V1B

value: gastric sleeve

value: female


title: water_24h_old_stem_r1

description: Library name: Ap_water_24h_old_stem_r1


title: sample28: Patient 32, Visit V2

value: Insulin dependent T2D / No remission

value: unknown


title: vimR deletion in MM  biol rep 1

city: Hong Kong

last: DENG

address: 1/F, Block 1, To Yuen Building, City University of Hong Kong, 31 To Yuen Street, Kowloon Tong

department: Department of Biomedical Sciences

country: Hong Kong

institute: City University of Hong Kong

description: Library name: sample 7

data_processing:
the raw reads were mapped to the Psph genome (NC_005777.3) or PAO1 genome(NC_002516.2) using hisat2 (version 2.1.0)
Differentially expressed genes (DEGs) were identified by DESeq2 (p-value < 0.05 and |log2 Fold Change| > 1 of Psph strains in KB and P. aeruginosa strains in LB, and p-value < 0.05 and -1<log2 Fold Change > log2(1.5) of Psph strains in MM
Assembly: 1448A/PAO1
Supplementary files format and content: csv file includes log2FC, padj and gene information for each sample(compare with corresponding WT)

organism: Pseudomonas savastanoi pv. phaseolicola 1448A

source_name: Pseudomonas savastanoi

growth_protocol: P. savastanoi  bacteria were routinely cultured at 28°C in King’ B broth with shaking at 220 rpm . And P. aeruginosa  bacteria were routinely cultured at 37°C in LB (Luria-Bertani) broth with shaking at 220 rpm.

extract_protocol:
1mL of stationary phase (OD600= 2-2.5) bacterial culture, 3mL of mid-log-phase culture (WT and ∆vimR strains) cultured in MM for 6 hours, and 1mL of PAO1-WT and PA3565 overexpressing strains in logarithmic phase(OD600=0.6-1.0) were collected and centrifuged (12,000rpm, 4℃). Subsequent RNA extraction and purification were performed using RNeasy mini kit (Qiagen) and treated with DNaseI (NEB).
After removing rRNA using the MICROBExpress kit (Ambion), cDNA Libraries were constructed using mRNA according to NEBNext® UltraTM II RNA Library Prep Kit protocol (Illumina). It was then sequenced using the HiSeq 2000 system (Illumina) platform. All RNA-seq experiments were performed for two biological replicates.

treatment_protocol: P. savastanoi  bacteria were cultured until they reached an optical density at 600 nm (OD600) of 2.0 to 2.5. P. aeruginosa  bacteria were culturerd until they reached an optical density at 600 nm (OD600) of 0.6 to 1.0.

value: Pseudomonas savastanoi

value: Gram-negative bacteria

value: induced in MM

tag: time


title: Psph-WT in MM biol rep 2

description: Library name: sample 6


title: H_1

value: endothelial cells

value: WT


title: E16.5 brains, Knockout

city: Aachen

first: Geraldine

last: Zimmer-Bensch

address: Worringerweg 3

department: Biology 2

country: Germany

institute: RWTH Aachen University

description:
SDT-GH8-417-PW_VMSC05801CP_region_0_cell_boundaries
SDT-GH8-417-PW_VMSC05801CP_region_0_cell_by_gene
SDT-GH8-417-PW_VMSC05801CP_region_0_cell_metadata
SDT-GH8-417-PW_VMSC05801CP_region_0_detected_transcripts

hyb_protocol: Hybridization with the Pan Neuro panel, gel embedding, clearing and DAPI/polyT staining were performed according to the Manufacturers Guide for fresh frozen tissue

scan_protocol: The Merscope platform was used to scan the brainsections and localize transcripts.

data_processing: Multichanel fluorescence images were analysed directly on the Merscope. The measurement output consists of (1) DAPI and PolyT images (2) coordinates for all detected transcripts (3) cell coundaries identified through segmentation

label: Vizgen Pan Neuro panel

source_name: Mouse Brain E16.5, Sst-Cre/tdTomato/Dnmt1 loxp2

label_protocol: 10 µm cryosections were fixed and permeabilized according to the Manufacturers guide for fresh frozen tissue (Vizgen)

extract_protocol: pregnant females were anesthetized by intraperitoneal administration of ketamine/xylazine (200/25 mg/kg living weight per injection up to a maximum application of 600/75 mg ketamine/xylazine per kg living weight in total). Upon reaching surgical tolerance, the abdominal cavity was opened to expose the uterine horns that were removed. Embryos were isolated from the uteri and decapitated. Whole heads were immediately flash-frozen in liquid nitrogen.

value: coronal

value: Ssttm2.l(cre)Zjh/J x B6.CgGt(ROSA)26Sortm14(CAG-tdTomato)Hze x B6; 129S-Dnmt1tm2Jae/J (Sst-Cre+/-/tdTomato/Dnmt1 loxP2

value: Knockout


title: H_M_3

value: Mitochondrial transplantation


title: E16.5 brains, Control

description:
ST-GH4-481-PW_VMSC05801_region_0_boundaries
ST-GH4-481-PW_VMSC05801_region_0_cell_by_gene
ST-GH4-481-PW_VMSC05801_region_0_cell_metadata
ST-GH4-481-PW_VMSC05801_region_0_detect_transcripts

source_name: Mouse Brain E16.5, Sst-Cre/tdTomato

value: Ssttm2.l(cre)Zjh/J x B6.CgGt(ROSA)26Sortml 4( CAG-tdTomato )Hze (Sst+/--Cre/tdTomato)


title: water_3h_old_stem_r3

description: Library name: Ap_water_3h_old_stem_r3

value: old stem


title: sample27: Patient 10, Visit V2

city: Basel

last: Core Facility

institute: University of Basel

data_processing:
Read quality was assessed with the FastQC tool (version 0.11.8)
Reads were mapped to the human genome hg38 with STAR (version 2.7.9a) with default parameters, except filtering out multimapping reads with more than 10 alignment locations (outFilterMultimapNmax=10) and filtering reads without evidence in the spliced junction table (outFilterType=“BySJout”).
The featureCounts() function from the Bioconductor Rsubread package (version 2.0.1) was used to count the number of reads (5' ends) overlapping with the exons of each gene (Ensembl release 102) assuming an exon union model. All subsequent analyses were performed using the R software (version 4.3.1) and Bioconductor 3.18 packages.
Assembly: hg38
Supplementary files format and content: Counts_Table.tsv: TSV file (tab separated values) including read counts for each sample and gene (ENSEMBL ID release 102). Column headers indicate the sample number.
Supplementary files format and content: Gene_Info.tsv: TSV file (tab separated values) including information about each gene used in the file Counts_Table.tsv (ENSEMBL release 102).
Supplementary files format and content: Sample_Info.tsv: TSV file (tab separated values) including information about each sample. Row sample number correspond to columns of the file Counts_Table.tsv.

tag: donor

value: Whole blood

value: Unknown

value: male


title: vimR deletion in KB biol rep 2

description: Library name: sample 4

tag: tissue

value: cultured in KB


title: sample26: Patient 25, Visit V1B

tag: visit

value: No diabetes

value: gastric band

value: female


title: sample24: Patient 25, Visit V2

tag: patient subgroup


title: vimR deletion in KB  biol rep 1

description: Library name: sample 3

value: Pseudomonas savastanoi

value: Gram-negative bacteria


title: water_3h_old_stem_r2

description: Library name: Ap_water_3h_old_stem_r2


title: HuCCT1 cell line transfected with human THY1-CMV-GFP_replicate 2

city: Castellana Grotte (BA)

first: Grazia

last: Serino

address: Via Turi, 27

institute: National Institute of Gastroenterology “S. de Bellis”, Research Hospital

description: Library name: HuCCT1 CD90+_2

data_processing:
Basecalling (Ion Torrent S5)
Alignment (Torrent mapping alignment program)
Quantification (Ion Torrent Ampliseq RNA plugin, unique mapping mode)
Count Normalizition (Transcriptome Analysis Console)
Assembly: hg19_Ampliseq transcriptome
Supplementary files format and content: Count Normalized in reads per million

growth_protocol: HuCCT1 were cultured in RPMI supplemented with Sodium Pyruvate, Antibiotic–Antimycotic, Hepes, and 10% Fetal Bovine Serum

extract_protocol:
Total RNA from HuCCT1 was extracted with miRNeasy® Mini kit (QIAGEN, Hilden, Germany)
Libraries were templated with the Ion Chef and sequenced using a 540 chip on the Ion GeneStudio S5 Prime system (Thermo Fisher Scientific,Waltham, MA, USA).

treatment_protocol: HuCCT1 were  transfected with human THY1-CMV-GFP and Lenti-CMV-GFP-2A-Puro-Blank Lentivirus (Aurogene, Italy) at MOI 40

value: Transfection with human THY1-CMV-GFP


title: HuCCT1 cell line transfected with human THY1-CMV-GFP_replicate 3

description: Library name: HuCCT1 CD90+_3


title: HuCCT1 cell line transfected with human THY1-CMV-GFP_replicate 1

description: Library name: HuCCT1 CD90+_1


title: Psph-WT in KB  biol rep 2

description: Library name: sample 2


title: water_24h_old_stem_r3

description: Library name: Ap_water_24h_old_stem_r3

extract_protocol:
Young(1-2 internodes) and old (3-4 internodes) stems were collected at different time points on land or after waterlogged treatment, total RNA of stems were extracted using TRIzol reagent (Invitrogen, USA), the concentration  of RNA were assessed using Qubit (Thermo, USA) and quality of RNA were assessed using a Qsep100 and R1 RNA Cartridge Kit (BiOptic Inc., China).
Small RNA-Seq libraries were prepared using the VAHTS Small RNA Library Prep Kit for Illumina V2 (Vazyme, NR811-01) following the manufacturer’s instructions, samples were prepared from three independent biological replicates.


title: vimR deletion in MM biol rep 2

description: Library name: sample 8

value: induced in MM


title: RNA-Seq, epithelium, siPRMT1, rep 3

city: HeFei

first: Liu

last: Shixian

address: No. 81 Meishan Road

institute: Anhui Medical University

data_processing:
Cutadapt was used to filter out unqualified sequences (sequencing adapters, low-quality sequences, etc.) from the raw data
Assembly: hg18
Supplementary files format and content: tab-delimited text fle includes raw counts for each Sample

organism: Homo

source_name: epithelium

extract_protocol:
RNA was extracted and purified using TRIzol (Thermo Fisher, 15596018). A concentration>50ng/µL, RIN value>7.0, and total RNA>1µg are sufficient for downstream experiments. Use oligo (dT) magnetic beads (Dynabeads Oligo (dT), cat. 25-61005, Thermo Fisher, USA) to specifically capture mRNA containing PolyA (polyadenylation) through two rounds of purification. The captured mRNA was fragmented using the NEBNextR Magnesium RNA Fragmentation Module (cat. E6150S, USA) under high temperature conditions at 94 ℃ for 5-7 minutes.
cDNA was synthesized using Invitrogen SuperScriptTM II Reverse Transcriptase (cat. 1896649, CA, USA), and E Escherichia coli DNA polymerase I (NEB, cat. m0209, USA) and RNase H (NEB, cat. m0297, USA) were subjected to double stranded synthesis. The double stranded DNA was digested using UDG enzyme (NEB, cat. m0280, MA, US), and a library with fragment size of 300bp ± 50bp was formed by PCR (chain specific library)

value: epithelium

value: FaDu

value: head and neck squamous cell carcinoma cells


title: RNA-Seq, epithelium, siPRMT1, rep 2


title: sample22: Patient 35, Visit V3

first: DBM Bioinformatics

address: Hebelstrasse 20

value: Insulin dependent T2D / No remission

tag: surgery type

value: gastric bypass


title: Psph-WT in KB biol rep 1

description: Library name: sample 1


title: HuCCT1 cell line transfected with Lenti-CMV-GFP-2A-Puro-Blank Lentivirus_replicate 3

description: Library name: HuCCT1 CD90-_3

value: Transfection with Lenti-CMV-GFP-2A-Puro-Blank Lentivirus


title: RNA-Seq, epithelium, siPRMT1, rep 1


title: Psph-WT in MM  biol rep 1

description: Library name: sample 5


title: HuCCT1 cell line transfected with Lenti-CMV-GFP-2A-Puro-Blank Lentivirus_replicate 2

description: Library name: HuCCT1 CD90-_2


title: sample21: Patient 21, Visit V1

value: Whole blood

value: revision

tag: Sex


title: RNA-Seq, epithelium, control, rep 3

tag: cell type


title: sample20: Patient 21, Visit V4


title: Lost Hills cracked hull tissue, 133 days post anthesis, biorep 2

city: Davis

first: Shuxiao

last: Zhang

state: CA

address: One Shields Ave

department: Plant Sciences

institute: UC Davis

description:
Library name: N19
column name in gene_fpkm.xls: LH2c_133

data_processing:
Raw reads was cleaned using in-house perl scripts by Novogene Co and data quality calculated. Reads were mapped to reference genome using Hisat2 v2.0.5. Mapped reads were assembled using StringTie v1.3.3b. FeatureCounts v1.5.0-p3 was used to count reads.
Assembly: An early, pre-publication of the Pistacia vera 'Kerman' genome published by Adaskaveg et al 2025 was used for mapping. Index of reference genome was built using Hisat2 v2.0.5.
Supplementary files format and content: Excel spreadsheet .xls file containing FPKM count for each sample.

organism: Pistacia vera

source_name: exo-mesocarp

growth_protocol: Commercially grown in orchard.

extract_protocol:
RNA was extracted using an Rneasy kit (Qiagen), snap frozen, and 600ng per sample was sent to Novogene Co for RNAseq.
Library was constructed by Novogene Co. mRNA was enriched using poly-T oligo-attached magnetic beads before fragmentation. First strand cDNA was synthesized with random hexamer primers. Second strand was synthesized using dUTP. End repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification was then performed.

value: exo-mesocarp

tag: genotype

value: Lost Hills

value: 133 days post anthesis


title: RNA-Seq, epithelium, control, rep 2


title: CN_115

city: Berlin

first: Leonille

last: Schweizer

address: Charitépl. 1

institute: Charité - Universitätsmedizin

hyb_protocol: Methylation analysis was performed with the Illumina Infinium Methylation EPIC BeadChip (n = 129 tumor samples), Illumina Infinium Methylation EPICv2 BeadChip (n = 1) or the Illumina Infinium Human Methylation 450k array (n = 14)

scan_protocol: not applicable

data_processing:
Data was analyzed using the R minfi package v1.30.0 and NOOB preprocessing [Fortin, J.P., T.J. Triche, Jr., and K.D. Hansen, Preprocessing, normalization and integration of the Illumina HumanMethylationEPIC array with minfi. Bioinformatics, 2017. 33(4): p. 558-560]. Probes with p-values ≥ 0.01 in 90% of the samples, probes located on sex chromosomes, and cross-reactive probes [Chen, Y.A., et al., Discovery of cross-reactive probes and polymorphic CpGs in the Illumina Infinium HumanMethylation450 microarray. Epigenetics, 2013. 8(2): p. 203-9.] were removed before beta-value calculation. Furthermore, probes with poor correlation between both array types and absolute differences ≥ 0.1 in beta-values [Fernandez-Jimenez, N., et al., Comparison of Illumina 450K and EPIC arrays in placental DNA methylation. Epigenetics, 2019. 14(12): p. 1177-1182.] were discarded. The filtering resulted in 339,381 sites for the n = 111 primary tumors and 339,394 sites for the n = 133 primary and recurrent tumors.
Processed value definition:  beta values for the n = 133 primary and recurrent central neurocytoma samples.

label: Cy3, Cy5

source_name: central neurocytoma (FFPE)

label_protocol: not applicable

growth_protocol: not applicable

extract_protocol: DNA was isolated from FFPE material using the Maxwell® RSC FFPE Plus DNA Kit (Promega).

treatment_protocol: not applicable

value: central neurocytoma (FFPE)

tag: diagnosis

tag: case


title: Lost Hills cracked hull tissue, 133 days post anthesis, biorep 1

description:
Library name: N18
column name in gene_fpkm.xls: LH1c_133


title: water_3h_old_stem_r1

city: shanghai

first: Qian

last: Hu

address: Xinjiangwancheng

institute: Fudan University

description: Library name: Ap_water_3h_old_stem_r1

data_processing:
The 3'-adapters from all sequenced reads were clipped and the resulting small RNA reads were obtained, the reads shorter than 18nt were discarded, the redundant reads were removed to obtain unique reads with counts.
In order to identify homologs of conserved miRNAs in Alternanthera philoxeroides, mature miRNAs sequences of other plants were downloaded from the miRBase (v22) and the unique mature miRNAs sequences were obtained. These unique miRNAs were aligned to the genome using NCBI BLASTN (v 2.2.26) with the options of “-m 8 -e 0.01".
The frequencies of mature miRNAs in different small RNA sequencing profiles were calculated by aligning the small RNA reads to mature miRNAs using NCBI BLASTN (v2.2.26) with the options of “-S 1 -m 8 -e 0.01", and normalized to Reads Per Ten Million (RPTM) sequencing tags.
Assembly: Alternanthera philoxeroides
Supplementary files format and content: Excel

source_name: old stem

value: old stem


title: sample19: Patient 13, Visit V2

value: female


title: RNA-Seq, epithelium, control, rep 1


title: Lost Hills intact hull tissue, 133 days post anthesis, biorep 3

description:
Library name: N17
column name in gene_fpkm.xls: LH3i_133


title: sample23: Patient 35, Visit V4


title: Lost Hills intact hull tissue, 133 days post anthesis, biorep 2

description:
Library name: N16
column name in gene_fpkm.xls: LH2i_133


title: ATAC-Seq, epithelium, PRMT1 knockdown, rep 2

extract_protocol:
Firstly, cell nuclei were isolated. The specific procedures were as follows: initially, a complete and uniform cell suspension was obtained. Subsequently, 50,000 cells were counted and centrifuged at 500 ×g for 5 minutes at 4°C centrifuge. The pellet was washed with 50 μl cold 1*PBS buffer and centrifuged again at 500 ×g for 5 minutes at 4°C. After discarding the supernatant, 50 μl of pre-chilled nuclear lysis buffer was added, followed by slow pipetting to resuspend the pellet. The mixture was then centrifuged at 500 ×g for 5 minutes at 4°C.
The denatured and diluted libraries were loaded onto the FlowCell at a specific concentration based on the expected sequencing data volume. The libraries were hybridized with adapters on the FlowCell and underwent bridge PCR amplification on the cBot cluster generation platform, followed by sequencing on the sequencer.


title: sample17: Patient 39, Visit V4

value: Unknown

value: gastric sleeve

value: male


title: CN_110


title: sample18: Patient 38, Visit V4

value: T2D / Remission


title: Spinal cord, distal region,10 days after injury

first: Fangbing

state: shanghai

address: Children’s Hospital of Fudan University Wanyuan Ro

institute: Fudan university

description: Library name: Distal region

data_processing:
Mapping to GRCh38 human genome, quality control and read counting of Ensembl genes was performed by cellranger software with default parameter (v7.1.0). Nuclei with more than or equal 200 genes and less than or equal 10% percentage of mitochondrial genes detected were retained for subsequent analyses. Normalization, dimensionality reduction and clustering of single cells were also performed by cellranger. Using top 30 principal components, we reduced the dimensionality by t-Distributed Stochastic Neighbor Embedding (tSNE). Cell clustering were performed using the graph-based clustering algorithm which consists of building a sparse nearest-neighbor graph (where cells are linked if they among the k nearest Euclidean neighbors of one another), followed by Louvain Modularity Optimization (Blondel, Guillaume, Lambiotte, & Lefebvre, 2008). Seurat-FindAllMarkers was used to find differentially expressed genes between clusters . Gene ontology enrichment analysis for these significant differetially expressed genes was performed by TopGO R package and the KEGG pathway enrichment analysis was performed using the Hypergeometric test in R. Significantly enriched GO terms and KEGG pathways were selected by a threshold FDR (adjusted P-value) ≤ 0.05.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: spinal cord tissue

extract_protocol:
Single nucleus isolation and sequencing Spinal cords were rapidly extruded from iNeuroD1GFP mice (n=3) after anesthesia. Each cord was separated into lesion core and peri-injury regions.
Single cell nuclei suspension of frozen tissues were prepared using the Nuclei PURE Prep kit (Sigma, NUC201). The nuclei that have passed the test are washed and resuspended to prepare a suitable cell concentration of 700~1200 nuclei/ul for 10x Genomics ChromiumTM. The system is operated on the machine. GEMs (Gel Bead in Emulsion) were constructed for single nuclei separation according to the number of nuclei to be harvested. After GEMs were normally formed, GEMs were collected for reverse transcription in a PCR machine for labeling. The GEMs were oil-treated, and the amplified cDNA was purified by magnetic beads, and then subjected to cDNA amplification and quality inspection. The 3ʹ Gene Expression Library was constructed with the quality-qualified cDNA. After fragmentation, adaptor ligation, sample index PCR, etc., the library is finally quantitatively examined.

value: spinal cord tissue

value: spinal cord cells


title: Spinal cord,injury core,10 days after injury

description: Library name: Injury core

value: 8 weeks


title: Lost Hills intact hull tissue, 133 days post anthesis, biorep 1

description:
Library name: N15
column name in gene_fpkm.xls: LH1i_133


title: sample16: Patient 27, Visit V2

value: No diabetes


title: Golden Hills tattered hull tissue, 133 days post anthesis, biorep 3

description:
Library name: N14
column name in gene_fpkm.xls: GH3t_133

value: Golden Hills


title: ATAC-Seq, epithelium, PRMT1 knockdown, rep 1

value: epithelium

value: head and neck squamous cell carcinoma cells


title: ATAC-Seq, epithelium, control, rep 2


title: CN_109


title: Lost Hills cracked hull tissue, 133 days post anthesis, biorep 3

description:
Library name: N20
column name in gene_fpkm.xls: LH3c_133

value: exo-mesocarp


title: sample15: Patient 13, Visit V4

value: Whole blood

value: Insulin dependent T2D / No remission

value: gastric bypass


title: HuCCT1 cell line transfected with Lenti-CMV-GFP-2A-Puro-Blank Lentivirus_replicate 1

description: Library name: HuCCT1 CD90-_1

tag: treatment

value: Transfection with Lenti-CMV-GFP-2A-Puro-Blank Lentivirus


title: ATAC-Seq, epithelium, control, rep 1


title: sample14: Patient 19, Visit V4


title: CN_108

value: central neurocytoma (FFPE)


title: Golden Hills tattered hull tissue, 133 days post anthesis, biorep 2

description:
Library name: N13
column name in gene_fpkm.xls: GH2t_133

value: 133 days post anthesis


title: NECA-treated_MI_mouse_4

city: Gwangju

first: Yunju

last: Jo

address: 123, Cheomdangwagi-ro

country: South Korea

institute: Gwangju Institute of Science and Technology

data_processing:
The integrity of the sequencing data was assessed using FastQC v0.11.9. Alignment of FASTQ files to the mouse reference genome (GRCm39, release 109, December 2022) was performed utilizing the Spliced Transcripts Alignment to a Reference (STAR) software v2.7.10a. Gene abundance was quantified employing the RNA-Seq by Expectation-Maximization (RSEM) tool v1.3.1.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: myocardial tissue

extract_protocol:
Total RNAs were extracted using EasyBlue RNA extraction Solution according to the manufacture's instruction.
3’UTR RNA-seq was performed using the CEL-Seq2 protocol except that Second Strand Synthesis Module (NEB) was used for double-stranded cDNA synthesis and library was amplified by 9 cycles of PCR without any sample pooling.

value: myocardial tissue

value: Wild type

value: NECA local deliery into infarcted myocardium


title: Golden Hills tattered hull tissue, 133 days post anthesis, biorep 1

description:
Library name: N12
column name in gene_fpkm.xls: GH1t_133


title: CN_107


title: sample13: Patient 27, Visit V4

value: gastric sleeve

value: female


title: CN_106


title: Golden Hills intact hull tissue, 133 days post anthesis, biorep 3

description:
Library name: N11
column name in gene_fpkm.xls: GH3i_133


title: sample12: Patient 25, Visit V4

value: gastric band


title: NECA-treated_MI_mouse_3


title: CN_105


title: NECA-treated_MI_mouse_2


title: Golden Hills intact hull tissue, 133 days post anthesis, biorep 2

description:
Library name: N10
column name in gene_fpkm.xls: GH2i_133


title: sample10: Patient 15, Visit V4


title: Golden Hills intact hull tissue, 133 days post anthesis, biorep 1

description:
Library name: N9
column name in gene_fpkm.xls: GH1i_133


title: NECA-treated_MI_mouse_1


title: sample11: Patient 11, Visit V4

value: T2D / Remission


title: CN_104


title: sample9: Patient 6, Visit V4

value: T2D / No remission

value: male


title: Lost Hills intact hull tissue, 91 days post anthesis, biorep 4

description:
Library name: N8
column name in gene_fpkm.xls: LH4_91

value: Lost Hills

value: 91 days post anthesis


title: CN_103


title: CN_102


title: MI_modeling_mouse_3_2nd

value: Left coronary ligation


title: sample8: Patient 14, Visit V4

value: Whole blood


title: MI_modeling_mouse_3_1st


title: Lost Hills intact hull tissue, 91 days post anthesis, biorep 3

description:
Library name: N7
column name in gene_fpkm.xls: LH3_91

value: exo-mesocarp


title: CN_101


title: Lost Hills intact hull tissue, 91 days post anthesis, biorep 2

description:
Library name: N6
column name in gene_fpkm.xls: LH2_91


title: sample7: Patient 9, Visit V4

value: gastric bypass


title: MI_modeling_mouse_2_1st


title: MI_modeling_mouse_2_2nd


title: Lost Hills intact hull tissue, 91 days post anthesis, biorep 1

description:
Library name: N5
column name in gene_fpkm.xls: LH1_91


title: sample6: Patient 50, Visit V4


title: CN_100_recurrence

value: central neurocytoma (FFPE)


title: MI_modeling_mouse_1


title: CN_99


title: sample5: Patient 51, Visit V4


title: Golden Hills intact hull tissue, 91 days post anthesis, biorep 4

description:
Library name: N4
column name in gene_fpkm.xls: GH4_91

value: Golden Hills


title: Vehicle-treated_mouse_3

value: myocardial tissue

value: Vihecle


title: Golden Hills intact hull tissue, 91 days post anthesis, biorep 3

description:
Library name: N3
column name in gene_fpkm.xls: GH3_91


title: sample4: Patient 25, Visit V1

value: No diabetes


title: Vehicle-treated_mouse_2

value: Wild type


title: Golden Hills intact hull tissue, 91 days post anthesis, biorep 2

description:
Library name: N2
column name in gene_fpkm.xls: GH2_91


title: CN_98


title: CN_97


title: sample2: Patient 3, Visit V3

value: Insulin dependent T2D / No remission


title: Vehicle-treated_mouse_1


title: Corticosterone and PBS treated neonate-2

status: Public on Jun 17 2025

first: Dr. Shruti

last: Naik

address: 1425 Madison Ave

department: Immunology and Immunotherapy

institute: Icahn School of Medicine at Mount Sinai

description: Library name: P4.C.P.2

data_processing:
Sequencing results were demultiplexed and converted to FASTQ format using Illumina bcl2fastq software
The fastq files were trimmed for adaptor sequences using trimmomatic version 0.36 in paried end mode with parameters - minimal read length option set to 35 base pairs, trailing set to 5 and sliding window set to 4:15.
After trimming, the data was aligned to the mouse genome (mm10/GRCm38) using STAR.
The featureCounts program was used to generate raw counts for each gene.
Normalized gene counts were generated using DESeq2 package in an R environment.
Assembly: (mm10/GRCm38)
Supplementary files format and content: The raw counts are stored in .tsv format.
Supplementary files format and content: DESeq2 median of ratios normalized counts are also stored in .csv format

source_name: skin dendritic cells

extract_protocol:
Dendritic cell RNA were extracted with Rneasy micro plus kit (Qiagen) as per manufacturer’s instructions
Dendritic cell derived libraries were generated with Revelo™ RNA-Seq High Sensitivity library preparation kit per manufacturer’s instructions.

treatment_protocol: Neonate an adult mice were intradermally injected with house dust mite extract (HDM) and PBS controls, for some samples corticosterone or DMSO vehicle were intraperitoneally injected 30 minutes prior HDM or PBS. 9 hours after HDM or PBS injection, skin CD301b+cDC2 were enriched by flow cytometry sorting, and RNA were isolated for bulk sequencing.

value: skin dendritic cells

value: wild type

value: Corticosterone 30minutes and PBS treated 9hrs


title: Corticosterone and PBS treated neonate-1

description: Library name: P4.C.P.1


title: Corticosterone and PBS treated neonate-3

description: Library name: P4.C.P.3


title: DMSO and PBS treated neonate-4

description: Library name: P4.D.P.4

value: DMSO 30minutes and PBS treated 9hrs


title: DMSO and PBS treated neonate-3

description: Library name: P4.D.P.3


title: DMSO and PBS treated neonate-2

description: Library name: P4.D.P.2


title: DMSO and PBS treated neonate-1

description: Library name: P4.D.P.1


title: HDM treated adult-4

description: Library name: P60.H.4

value: HDM treated 9 hours


title: Corticosterone and PBS treated neonate-4

description: Library name: P4.C.P.4


title: HDM treated adult-1

description: Library name: P60.H.1


title: PBS treated adult-4

description: Library name: P60.P.4

value: PBS treated 9 hours


title: HDM treated adult-2

description: Library name: P60.H.2


title: PBS treated adult-1

description: Library name: P60.P.1


title: PBS treated adult-3

description: Library name: P60.P.3


title: Corticosterone and HDM treated neonate-4

description: Library name: P4.C.H.4

value: Corticosterone 30minutes and HDM treated 9hrs


title: Corticosterone and HDM treated neonate-3

description: Library name: P4.C.H.3


title: Corticosterone and HDM treated neonate-1

description: Library name: P4.C.H.1


title: HDM treated adult-3

description: Library name: P60.H.3


title: Corticosterone and HDM treated neonate-2

description: Library name: P4.C.H.2


title: Golden Hills intact hull tissue, 91 days post anthesis, biorep 1

description:
Library name: N1
column name in gene_fpkm.xls: GH1_91

value: 91 days post anthesis


title: DMSO and HDM treated neonate-2

description: Library name: P4.D.H.2

value: DMSO 30minutes and HDM treated 9hrs


title: PBS treated adult-2

description: Library name: P60.P.2


title: DMSO and HDM treated P14 mouse - male

data_processing:
Sequencing results were demultiplexed and converted to FASTQ format using Illumina bcl2fastq software
The fastq files were trimmed for adaptor sequences using trimmomatic version 0.36 in paried end mode with parameters - minimal read length option set to 35 base pairs, trailing set to 5 and sliding window set to 4:15.
After trimming, the data was aligned to the mouse genome (mm10/GRCm38) using STAR.
The featureCounts program was used to generate raw counts for each gene.
Assembly: (mm10/GRCm38)
Supplementary files format and content: The raw counts are stored in .csv format.
Supplementary files format and content: DESEQ2 median of ratios normalized counts are also stored in .csv format

source_name: dendritic cells

extract_protocol:
Skin tissue total RNA were extracted with RNeasy Mini Kit and Dendritic cell RNA were extracted with Rneasy micro plus kit (Qiagen) as per manufacturer’s instructions
Whole skin tissue derived libraries were generated with NEXTFLEX® Rapid Directional RNA-Seq Kit 2.0 and Dendritic cell derived libraries were generated with Revelo™ RNA-Seq High Sensitivity library preparation kit per manufacturer’s instructions.

treatment_protocol: Neonate an adult mice were intradermally injected with house dust mite extract (HDM), Alternaria alternata Extract (ALT)and PBS controls. Full thickness skin biopsy were isolated 6 days after allergens inoculation. For Dendritic cell sorting, neoante mice were intraperitonealy injected with Corticosterone or DMSO for 30 minutes, and then were intradermally injected with HDM or PBS for 9 hours.

value: dendritic cells


title: DMSO and PBS treated P14 mouse - female


title: Corticosterone and HDM treated neonate-s3


title: DMSO and HDM treated neonate-1

description: Library name: P4.D.H.1


title: DMSO and HDM treated neonate-4

description: Library name: P4.D.H.4


title: DMSO and HDM treated P14 mouse - female


title: DMSO and PBS treated P14 mouse - male


title: DMSO and HDM treated neonate-3

description: Library name: P4.D.H.3


title: DMSO and HDM treated neonate-s3


title: Corticosterone and PBS treated neonate-s1


title: Corticosterone and PBS treated neonate-s2


title: DMSO and HDM treated neonate-s2


title: No_IP-control

city: La Jolla

first: Sam

last: Van de Velde

address: 10010 North Torrey Pines Road

department: PBL

institute: Salk Institute

description: Library name: Sample21

data_processing:
ChIPseq reads were aligned to the rn6 reference genome with Star. Tag directories, peak calling, motif enrichment analysis were performed with Homer.
Assembly: rn6
Supplementary files format and content: BigWig

source_name: pancreatic beta cell

growth_protocol: INS-1 cells were maintained in RPMI-1640 with 10% FBS and 2 mM glutamate/1mM Na-pyruvate, penicillin/streptomycin, beta-mercaptoethanol

extract_protocol:
Cells were fixed for 10 min with 0.75% formaldehyde, quenched with 150 mM glycine for 5 min. Chromatin was sonicated for 100 seconds with tip sonicator.
ChIP-seq libraries were constructed with NEBNext Ultra II DNA Library Prep Kit for Illumina according to manufacturer's instructions.

treatment_protocol: Cells were treated with 10 uM FSK for 4 hours

value: pancreatic beta cell

value: insulinoma

value: WT


title: Med14S983A_FLAG-Med19_FSK

description: Library name: Sample20

value: FSK


title: Med14S983A_FLAG-Med19_CON

description: Library name: Sample19


title: Med14S983A_PolIIpS2_CON

description: Library name: Sample15


title: Med14S983A_PolIIpS2_FSK

description: Library name: Sample16


title: WT_FLAG-Med19_CON

description: Library name: Sample17


title: Med14S983A_H3K27Ac_FSK

description: Library name: Sample14


title: WT_FLAG-Med19_FSK

description: Library name: Sample18


title: Med14S983A_H3K27Ac_CON

description: Library name: Sample13


title: Med14S983A_CRTC2_FSK

description: Library name: Sample12


title: DMSO and PBS treated neonate-s3


title: Med14S983A_CRTC2_CON

description: Library name: Sample11


title: Med14S983A_CREB_CON

description: Library name: Sample9


title: WT_PolIIpS2_CON

description: Library name: Sample7


title: Med14S983A_CREB_FSK

description: Library name: Sample10


title: WT_H3K27Ac_CON

description: Library name: Sample5


title: Corticosterone and HDM treated neonate-s2


title: WT_CRTC2_CON

description: Library name: Sample3


title: WT_CRTC2_FSK

description: Library name: Sample4


title: WT_CREB_FSK

description: Library name: Sample2


title: DMSO and PBS treated neonate-s2


title: Med14S983A_CON

description: Library name: Sample4

data_processing:
Reads were trimmed with TrimGalore, aligned to rn6 reference genome with bwa mem.
Mitochondrial, low quality and duplicate reads were filtered out with Samtools
Peaks were called with macs2
Assembly: rn6
Supplementary files format and content: Normalized counts in all peaks across conditions (.txt)

extract_protocol:
Nuclei were extracted with hypotonic cell lysis.
Tagmentation was performed on 50,000 nuclei for 30 min at 37C using Illumina Tagment DNA enzyme. DNA was isolated using Qiagen MinElute Reaction Cleanup Kit and amplified with Illumina/Nextera i5 common and i7 index adapters.

treatment_protocol: Cells were washed and exposed to serum-free media prior to treatment wit Exendin-4 (10nM) or forskolin (10uM)


title: WT_Ex-4

description: Library name: Sample3


title: Med14S983A_FSK

description: Library name: Sample5


title: WT_FSK

description: Library name: Sample2


title: WT_CON

description: Library name: Sample1


title: Med14S983A_16hFSK_2

description: Library name: Sample28

data_processing:
Raw sequencing reads, including ERCC spike-in controls, were mapped to a combined reference genome comprising the rn6 rat genome and ERCC sequences using STAR (v2.5.3a) with default parameters. Following alignment, quality control and gene quantification were conducted using the ‘QoRTs.jar QC’ function from the QoRTs (Quality of RNA-Seq ToolSet) software package (v1.3.6). This process generated raw expression counts for both ERCC spike-ins and rat genes. Gene expression levels were also quantified in transcripts per kilobase million (TPM) across all exons of RefSeq genes using analyzeRepeats.pl in HOMER (v4.11.1), with the top-expressed isoform used as a proxy for gene expression. Differential gene expression analysis was performed using DESeq2 (v1.24.0) [7] based on raw gene counts, incorporating biological replicates to estimate within-group dispersion. ERCC spike-in abundances were used as quality controls to calculate size factors for normalization in DESeq2. Genes were considered differentially expressed with a false discovery rate (FDR) threshold of <0.05 and an absolute fold-change (FC) >1.5 between experimental conditions.
Assembly: rn6
Supplementary files format and content: Spike-in normalized raw counts for each sample (txt)
Supplementary files format and content: Spike-in normalized TPM for each sample (txt)

extract_protocol:
RNA was extracted with Tri reagent and chloroform, precipitated with isopropanol, washed with 70% ethanol and cleaned up using Direct-zol RNA mini cleanup kit (Zymo research). ERCC mix was spiked in prior to library construction.
RNA-seq libraries were constructed with NEBNext Ultra II Directional RNA Library Prep Kit for Illumina according to manufacturer's instructions

value: Forskolin


title: Med14S983A_8hFSK_1

description: Library name: Sample25


title: Med14S983A_8hEx-4_2

description: Library name: Sample20


title: Med14S983A_16hFSK_1

description: Library name: Sample27


title: Med14S983A_8hFSK_2

description: Library name: Sample26


title: Med14S983A_1hEx-4_2

description: Library name: Sample18


title: Med14S983A_16hEx-4_1

description: Library name: Sample21


title: Med14S983A_16hEx-4_2

description: Library name: Sample22


title: Med14S983A_1hFSK_2

description: Library name: Sample24


title: Med14S983A_8hEx-4_1

description: Library name: Sample19


title: Med14S983A_1hEx-4_1

description: Library name: Sample17


title: WT_PolIIpS2_FSK

description: Library name: Sample8


title: WT_H3K27Ac_FSK

description: Library name: Sample6


title: Med14S983A_CON_1

description: Library name: Sample15


title: WT_16hFSK_2

description: Library name: Sample14


title: Med14S983A_Ex-4

description: Library name: Sample6


title: Med14S983A_CON_2

description: Library name: Sample16


title: WT_CREB_CON

description: Library name: Sample1


title: WT_8hFSK_1

description: Library name: Sample11


title: WT_16hFSK_1

description: Library name: Sample13


title: WT_16hEx-4_2

description: Library name: Sample8


title: WT_16hEx-4_1

description: Library name: Sample7


title: WT_8hEx-4_2

description: Library name: Sample6


title: WT_1hFSK_2

description: Library name: Sample10


title: WT_8hFSK_2

description: Library name: Sample12


title: WT_1hFSK_1

description: Library name: Sample9


title: WT_8hEx-4_1

description: Library name: Sample5


title: Med14S983A_1hFSK_1

description: Library name: Sample23


title: WT_1hEx-4_1

description: Library name: Sample3


title: PAB Pig 2

city: Minneapolis

first: Kurt

last: Prins

state: MN

address: 2231 6th St Se

institute: University of Minnesota

description:
Library name: Sample 6
10x Genomics

data_processing:
cellranger-7.2.0
Assembly: Sscrofa10.2
Supplementary files format and content: Matrix files for analysis

organism: Sus scrofa domesticus

source_name: Right atrium

extract_protocol:
Nuclei were isolated from frozen RA samples and then subjected to flow cytometry to isolate pure nuclei fractions
RNA libraries from RNA-seq were prepared by the University of Minnesota Genomics center.

value: RV tissue

value: Right atrium

value: 10 weeks

value: male


title: WT_CON_1

description: Library name: Sample1


title: Control Pig 3

description:
Library name: Sample 3
10x Genomics


title: Control Pig 2

description:
Library name: Sample 2
10x Genomics


title: NELF siRNA #1 flu infection cap sequencing #2

city: San Diego

first: Alistair

middle: Brian

last: Russell

address: 9500 Gilman Dr,

department: Biological Sciences

institute: University of California, San Diego

description:
Library name: Sample 21
viral genome RNA sequenced by 5' RACE

data_processing:
Data were processed with a custom pipeline described in the associated manuscript.
Assembly: Gecko V2
Supplementary files format and content: Individual counts of guide sequences and associated gene targets

molecule: other

organism: Influenza A virus

growth_protocol: Samples were from infections of A549-Cas9 cells bearing a CRITR-seq library with a type III interferon reporter with guides cloned from the GECKO library. Cells were allowed to undergo editing or silencing for 10 days, after which they were infected by A/WSN/1933 bearing segment 8 from A/PR/8 with stop codons interrupting the NS1 reading frame at an MOI of 2 in influenza growth media. RNA and DNA harvested at 8 hours post infection. RNA more samples represent increased input of RNA, which we found to greatly improve the quality of the dataset. Silenced samples were processed for flu cap lengths using 5' RACE.

extract_protocol:
RNA was extracted using Monarch Total RNA Miniprep Kit from New England Biolabs (NEB #T2010), DNA by the Monarch spin gDNA extraction kit (NEB #T3010).
Custom amplicon sequencing

treatment_protocol: Infection at MOI 2 by A/WSN/1933 with segment 8 from A/PR/8 bearing stop codons in the NS1 reading frame for 8 hours.

value: Silencing followed by infection by flu lacking NS1


title: PAB Pig 3

description:
Library name: Sample 7
10x Genomics


title: WT_CON_2

description: Library name: Sample2


title: PAB Pig 1

description:
Library name: Sample 5
10x Genomics


title: Non-targeting control flu infection cap sequencing #2

description:
Library name: Sample 19
viral genome RNA sequenced by 5' RACE


title: Untreated flu infection cap sequencing #2

description:
Library name: Sample 17
viral genome RNA sequenced by 5' RACE


title: Untreated flu infection cap sequencing #1

description:
Library name: Sample 16
viral genome RNA sequenced by 5' RACE


title: PAB Pig 4

description:
Library name: Sample 8
10x Genomics


title: NELF siRNA #2 flu infection cap sequencing #2

description:
Library name: Sample 23
viral genome RNA sequenced by 5' RACE


title: Non-targeting control flu infection cap sequencing #1

description:
Library name: Sample 18
viral genome RNA sequenced by 5' RACE


title: shAB2

city: Hefei

first: Xu

last: Junchao

state: Anhui

address: No. 443, Mount Huangshan Road, Daoxiangcun Street

institute: University of Science and Technology of China

description: Library name: Sample 8

data_processing:
Use Solexa pipeline version 1.8 (Off Line Base Caller software, version 1.8) for image processing and base recognition. FastQC software is used to evaluate the sequencing quality of reads, and then cutadapt is used to remove the 3 'and 5' adapters. Align to the reference genome using Hisat2 software. Use StringTie software to estimate transcription abundance by referencing official database annotation information. Use R software Ballgown - to perform FPKM calculations at the gene and transcript levels, and calculate the expression differences at both the gene and transcript levels to screen for differentially expressed genes between samples or groups. The prediction of new genes/transcripts was assembled and merged separately for each sample using StringTie, and compared with official annotation information. The results were obtained through Ballgown calculations, and the coding ability of the new transcripts was predicted using CPAT. Use rMATS for alternative splicing event detection, differential calculation, and mapping. PCA analysis and correlation analysis based on gene expression levels, clustering of differentially expressed genes, GO functional significance enrichment analysis, pathway significance enrichment analysis, and other further data mining analyses were completed through our company's custom program (Python/R/shell, etc.).
Assembly: hg38, GCF_000001405.39_GRCh38.p13
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

growth_protocol: MCF-7 cells were cultured in RPMI-1640 (31800022, Gibco, Carlsbad, USA) supplemented with 10% FBS (ExCell Bio, Shanghai, China) at 37℃ and 5% CO2. All medium contained 1% Pen-Strep solution (C0222, Beyotime, Shanghai, China).

extract_protocol:
The RNA was harvested using TRIzol reagent (GK20008, GlpBio, California, USA). Total RNA sample was extracted and quantified with OD 260/280 ratio > 1.8 and OD 230/260 ratio > 2 were sent to BGI Genomics (Shenzhen, China) for sequencing.
RNA libraries for RNA-seq were prepared using KAPA Stranded RNA-Seq Library Prep Kit (Roche) following manufacturer's protocols.

treatment_protocol: MCF-7 cells were infected circESR1 or HNRNPAB shRNAs with lentivirus.

value: Human breast cancer cells

value: HNRNPAB knockdown


title: WT_1hEx-4_2

description: Library name: Sample4


title: shAB1

description: Library name: Sample 7


title: sh72

description: Library name: Sample 5

value: circESR1 knockdown


title: sh71

description: Library name: Sample 4


title: plko2

description: Library name: Sample 2


title: plko3

description: Library name: Sample 3


title: shAB3

description: Library name: Sample 9


title: plko1

description: Library name: Sample 1


title: CF RNA 60

city: Heidelberg

first: Thomas

middle: Georg Philipp

last: Grunewald

address: Im Neuenheimer Feld 280

department: Division of Translational Pediatric Sarcoma Research

institute: German Cancer Research Center (DKFZ)

hyb_protocol: Affymetrix Clariom D Array one-color based hybridization protocol, cDNA samples were hybridized at 45°C for 16 h on separate Affymetrix Human Clariom D™ Arrays

scan_protocol: Affymetrix GeneChip 3000 Scanner

data_processing:
Raw data (.CEL files) were processed using the RMA (Robust Multi-array Average) normalization method implemented in the `oligo` package in R (version 4.0.3). Background correction and probe summarization were performed as described in the Affymetrix Clariom D Human array documentation. ProbeIDs were matched to Gene Symbols using the R package clariomdhumantranscriptcluster.db.
Values in the normalized data matrix represent log2-transformed expression intensities of genes obtained from Affymetrix Clariom D Human array experiments.

source_name: Ewing Sarcoma cell line

label_protocol: Affymetrix GeneChip WT PLUS Reagent Kit, according to the manufacturer's protocol.

growth_protocol: To assess local tumor growth of subcutaneous xenografts cells containing either a Dox-inducible negative control shRNA or specific shRNAs were injected subcutaneously with a 1:1 mix of PBS and Geltrex n the right flanks of 4–8 week old NSG mice.

extract_protocol: For RNA extraction, the NucleoSpin RNA kit from Macherey-Nagel (Duren, Germany) was used following the manufacturer’s protocol.

treatment_protocol: When tumors were first palpable, mice were randomized to the control group (17.5 mg/ml sucrose (Sigma-Aldrich) in drinking water) or the treatment group (2 mg/ml Dox Beladox, bela-pharm) and 50mg/ml sucrose (Sigma-Aldrich) in drinking water.

tag: shRNA

value: control shRNA

value: Plus Dox


title: Control Pig 1

description:
Library name: Sample 1
10x Genomics


title: CF RNA 59

tag: cell line

value: Minus Dox


title: NELF siRNA #1 flu infection cap sequencing #1

description:
Library name: Sample 20
viral genome RNA sequenced by 5' RACE


title: CF RNA 51

value: EIF4EBP1-targeting specific shRNA


title: Control Pig 4

description:
Library name: Sample 4
10x Genomics


title: CF RNA 43


title: CF RNA 47


title: CF RNA 36


title: CF RNA 53


title: CF RNA 50


title: CF RNA 56


title: sh73

description: Library name: Sample 6


title: NELF siRNA #2 flu infection cap sequencing #1

description:
Library name: Sample 22
viral genome RNA sequenced by 5' RACE


title: CF RNA 44


title: CF RNA 28


title: CF RNA 26


title: CF RNA 34


title: CF RNA 13


title: CF RNA 27


title: CF RNA 11


title: CF RNA 12


title: CF RNA 20


title: CF RNA 42


title: CF RNA 06


title: CF RNA 04


title: CF RNA 18


title: CF RNA 17


title: CF RNA 02


title: CF RNA 54


title: CF RNA 55