title: daf-2; aak(0) post-dauer larvae, biological replicate 3

city: Montreal

first: Elena

last: Jurczak

state: QC

address: 845 Sherbrooke St W

country: Canada

institute: McGill University

data_processing:
3′ Adapter, reads below 18 nt length and reads with a length above 32 were removed using Cutadapt.
Remaining reads were aligned using STAR against the C. elegans genome WS235 allowing multimapping reads
Assembly: C. elegans genome WS235
Supplementary files format and content: Tab-separated files include read counts for each sample
Supplementary files format and content: FB306_read_alg34_heatmap.xlsx is an Excel file containing read counts for each Sample
Supplementary files format and content: FB306_read_mirna_heatmap.xlsx is an Excel file containing read counts for each Sample
Supplementary files format and content: FB306_read_csr1_heatmap.xlsx is an Excel file containing read counts for each Sample
Supplementary files format and content: FB306_read_ergo1_heatmap.xlsx is an Excel file containing read counts for each Sample
Supplementary files format and content: FB306_read_geneid_heatmap.xlsx is an Excel file containing read counts for each Sample
Supplementary files format and content: FB306_read_germline_heatmap.xlsx is an Excel file containing read counts for each Sample
Supplementary files format and content: FB306_read_hrde1_heatmap.xlsx is an Excel file containing read counts for each Sample
Supplementary files format and content: FB306_read_pirna_heatmap.xlsx is an Excel file containing read counts for each Sample
Supplementary files format and content: FB306_read_soma_heatmap.xlsx is an Excel file containing read counts for each Sample
Supplementary files format and content: FB306_read_wago_heatmap.xlsx is an Excel file containing read counts for each Sample

organism: Caenorhabditis elegans

source_name: Whole animal

extract_protocol:
RNA was isolated from wild-type, aak(0), and aak(0); Ex[sur-5p::mir-51] dauer larvae via TRIzol extraction and resuspended in nuclease-free H2O.
Library generation was obtained using TruSeq Small RNA Library Preparation kits

treatment_protocol: C. elegans adults were synchronized using alkaline hypochlorite bleaching solution, as previously described (Porta-de-la-Riva et al., 2012). Worms were washed with distilled water and centrifuged for 40 seconds at 1.9 rpm. The supernatant was discarded, 1-2 mL of alkaline hypochlorite solution were added and the tube was vortexed for six minutes. The worm pellet was washed twice with distilled water and then resuspended before the embryos were plated on NGM or RNAi plates with a Pasteur pipette. Animals were incubated at 25ºC for 96 hours to induce dauer, and switched at 15ºC for seven days to allow exit and recovery from dauer.

value: Whole animal

value: Dauer was induced by growing the larvae at 25C. Animals were switched to 15C to exit and recover from dauer.


title: hMSC_donor2_sham_24h_exp2_rep1

status: Public on Jul 01 2026

type: RNA

city: Warsaw

first: Alicja

last: Trebinska-Stryjewska

address: gen. S. Kaliskiego 2

department: Institute of Optoelectronics

country: Poland

institute: Military University of Technology

description:
257236328897_2_3
hMCS donor2, sham, 24h, experiment 2, replicate 1

hyb_protocol: 600 ng of Cy3-labeled cRNA was fragmented following the manufacturer's protocol at 60°C for 30 min; fragmentation reaction was stopped by adding 2 × Hi-RPM Hybridization buffer. Fragmented Cy3-labeled cRNA was hybridized to Agilent-072363 SurePrint G3 Human Gene Expression v3 8x60K microarrays for 17 h at 65°C in a rotating hybridization oven. After hybridization, microarrays were washed following manufacturer's instructions with GE Wash Buffer 1 and 2 (Agilent).

scan_protocol: Microarray slides were scanned immediately after washing with the SureScan Microarray Scanner (Agilent) using the Agilent Microarray Scan Control program version 9.1 with the following settings: resolution of 3 µm; dye channel green; green PMT sensitivity of 100%.

data_processing: Data from scanned images were extracted with the Feature Extraction Software 12.0 using default parameters (protocol: GE1_1200_Jun14, grid: 072363_D_F_20190214) to obtain the background-subtracted and detrended processed signal intensities. Obtained results were further processed with GeneSpring version 14.9, and log2-transformed normalized signal intensities were obtained after normalization by a percentile shift (75th percentile). The baseline was set to the median of all samples.

molecule: total RNA

organism: Homo sapiens

source_name: hMCS donor2, sham, 24h

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng of Total RNA using the Low Input Quick Amp Labeling Kit, One Color (Agilent) according to manufacturer's instructions, followed by RNAeasy column purification (Qiagen). Addition of RNA Spike-In, One color (Agilent) served as an internal control. Cy3-labeled cRNA quality and quantity were assessed using 2100 Agilent Bioanalyzer (Agilent) and Agilent RNA 6000 Nano Reagent (Agilent).

growth_protocol: Poietics Normal Human Bone Marrow Derived Mesenchymal Stem Cells (hMSC) (Lonza) from two different donors were propagated in MSCGM Mesenchymal Stem Cell Growth Medium BulletKit (Lonza), and antibiotic/antimycotic in 5% carbon dioxide at 37ºC until semi-confluent.

extract_protocol: Immediately, 4 h or 24 h after treatment, cells were trypsinized, harvested, washed twice in ice-cold PBS and centrifuged at 150xg (hMSC donor 1) or 300xg (hMSC donor 2) for 5 min at 4ºC; cell pellets were frozen at -80ºC. Total RNA was isolated from the frozen pellets using the RNeasy Mini Kit (QIAGEN) according to manufacturer's instructions (including on-column DNaseI treatment). RNA was quantified using the QuantiFluor RNA System and Quantus Fluorometer (Promega). RNA quality was assessed with 2100 Agilent Bioanalyzer and Agilent RNA 6000 Nano Reagent. RIN ranged from 9.2 to 10.0.

treatment_protocol: Human MSC were used for experiments at the fourth or fifth passage, at 80% confluence. Before the exposure, standard hMSC medium in 175 cm2 cell culture flask was replaced with 10 ml of new, warm medium. Cells were exposed to a single high-peak power electromagnetic pulse (peak field: 1 Mv/m, rise time: 3 ns, pulse width: 30 ns, center frequency: 50 MHz). Cells were either harvested immediately after treatment or cultured for another 4 h or 24 h after adding 40 ml of standard hMSC medium. Sham-treated cells were prepared as above, except during exposure they were placed in a Faraday cage (80 dB attenuation for frequencies ranging from 100 kHz to 1 GHz). Control cells were kept in an incubator in standard cell culture conditions before harvesting.

tag: cell line

tag: age of the donor

value: 24 years

tag: sex of the donor

value: Female

tag: race/ethnicity of the donor

value: Black

tag: treatment

value: Sham-exposed

tag: time


title: daf-2; aak(0) post-dauer larvae, biological replicate 2

type: SRA

middle: M

library_source: transcriptomic

tag: tissue

tag: genotype


title: hMSC_donor2_sham_24h_exp1_rep3

description:
257236328909_1_3
hMCS donor2, sham, 24h, experiment 1, replicate 3

value: Normal Human Bone Marrow Derived Mesenchymal Stem Cells (hMSC)


title: Group3_PND10_125, GEX

city: New York

first: Chrysothemis

last: Brown

state: New York

department: Immuno-Oncology Program

country: USA

institute: Memorial Sloan Kettering Cancer Center

description:
Library name: Group3_PND10_125_mRNA
GEX (3' mRNA) library from lung and medLN of neonatal mice

data_processing:
Single-cell RNA-seq FASTQ files were aligned to mm10 (Cell Ranger mouse reference genome mm10-2020-A) and counted by Cell Ranger v8.0.1 with default parameters. HTO sequencing data were aligned to the HTO barcodes, and UMIs were counted for each cell using CITE-seq-Count. Samples were then demultiplexed using the SHARP v0.1.3 pipeline. The singlet barcodes were further filtered based on the number of RNA-seq transcripts (>400 and <22,000), the number of detected genes (>400 and <8,000), and the fraction of mitochondrial transcripts (<8%). Following quality control filtering, raw counts were library-size normalized and log-transformed (‘log-normalized’ expression values) using Scanpy v1.10.3. A nearest-neighbor graph was constructed using the top 50 principal components (PCs) with 30 nearest neighbors. Clustering was performed using PhenoGraph (k = 30, clustering_algo = ‘louvain’). Cell clustering was visualized using UMAP, computed from the nearest neighbor graph built by PhenoGraph.
Assembly: mm10-2020-A
Supplementary files format and content: CellRanger processed output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: Output files for hashtag: Group1_124_PND10_HTO_barcodes.tsv.gz, Group1_124_PND10_HTO_features.tsv.gz, Group1_124_PND10_HTO_matrix.mtx.gz Group2_124_PND10_HTO_barcodes.tsv.gz, Group2_124_PND10_HTO_features.tsv.gz, Group2_124_PND10_HTO_matrix.mtx.gz Group3_124_PND10_HTO_barcodes.tsv.gz, Group3_124_PND10_HTO_features.tsv.gz, Group3_124_PND10_HTO_matrix.mtx.gz Group4_124_PND10_HTO_barcodes.tsv.gz, Group4_124_PND10_HTO_features.tsv.gz, Group4_124_PND10_HTO_matrix.mtx.gz Group1_125_PND10_HTO_barcodes.tsv.gz, Group1_125_PND10_HTO_features.tsv.gz, Group1_125_PND10_HTO_matrix.mtx.gz Group2_125_PND10_HTO_barcodes.tsv.gz, Group2_125_PND10_HTO_features.tsv.gz, Group2_125_PND10_HTO_matrix.mtx.gz Group3_125_PND10_HTO_barcodes.tsv.gz, Group3_125_PND10_HTO_features.tsv.gz, Group3_125_PND10_HTO_matrix.mtx.gz Group4_125_PND10_HTO_barcodes.tsv.gz, Group4_125_PND10_HTO_features.tsv.gz, Group4_125_PND10_HTO_matrix.mtx.gz, Group1_124_5DPI_HTO_barcodes.tsv.gz, Group1_124_5DPI_HTO_features.tsv.gz, Group1_124_5DPI_HTO_matrix.mtx.gz Group2_124_5DPI_HTO_barcodes.tsv.gz, Group2_124_5DPI_HTO_features.tsv.gz, Group2_124_5DPI_HTO_matrix.mtx.gz Group3_124_5DPI_HTO_barcodes.tsv.gz, Group3_124_5DPI_HTO_features.tsv.gz, Group3_124_5DPI_HTO_matrix.mtx.gz Group4_124_5DPI_HTO_barcodes.tsv.gz, Group4_124_5DPI_HTO_features.tsv.gz, Group4_124_5DPI_HTO_matrix.mtx.gz Group1_125_5DPI_HTO_barcodes.tsv.gz, Group1_125_5DPI_HTO_features.tsv.gz, Group1_125_5DPI_HTO_matrix.mtx.gz Group2_125_5DPI_HTO_barcodes.tsv.gz, Group2_125_5DPI_HTO_features.tsv.gz, Group2_125_5DPI_HTO_matrix.mtx.gz Group3_125_5DPI_HTO_barcodes.tsv.gz, Group3_125_5DPI_HTO_features.tsv.gz, Group3_125_5DPI_HTO_matrix.mtx.gz Group4_125_5DPI_HTO_barcodes.tsv.gz, Group4_125_5DPI_HTO_features.tsv.gz, Group4_125_5DPI_HTO_matrix.mtx.gz
Supplementary files format and content: Analysis results from Scanpy including pheno louvain clusters, celltype annotations, treatment groups and UMAP
Library strategy: CITE-seq

molecule: polyA RNA

organism: Mus musculus

source_name: Lung and medLN

extract_protocol:
For single cell RNA seq of stem-like progenitors, pre-DCs and differentiated-DCs, lung and mediastinal lymph nodes from OPN+/+ or OPN-/- reared neonates treated with D-PLA were pooled from six biological replicates. Cells were incubated with 𝛼-CD16/32-BV605 in PBS-2% FBS for 20 min at 4°C to block binding to Fc receptors. Cell surface antigens were then stained for 30 mins at 4°C in PBS-2% FBS. Cells from distinct tissues were ‘stained’ with BioLegend TotalSeq B oligo-conjugated antibodies consisting of a pool of antibodies directed against CD45 (BioLegend; Clone 30-F11) and H2 MHC Class I alloantigens (BioLegend; clone M1/42). Immediately prior to fluorescent-assisted cell sorting (FACS), cells were resuspended in sorting buffer with SYTOX blue (Invitrogen; Cat# S34857) for dead cell exclusion. Live, lineage (CD3, CD19, NK1.1, Siglec-F, TCRβ, TCR𝛾𝛿)- singlets were then sort purified into six distinct populations: cDCs (CD11chi MHCII+ B220-), pDCs (CD11clo/int B220+ SiglecH+), pre-cDCs (CD11chi MHCII- CD135+ CD172a-), MDP/CDPs (CD11c- MHCII- cKIT+ SCA1- CD135+), LMPP/CMPs (CD34+ cKIT+ CD127- SCA1+/- CD16/32-) and CLPs (CD34- cKIT+ CD127+ Flt3+). Cells were sorted into cRPMI (Gibco; Cat# 11875093), each of the sort populations were counted and then pooled together to a final concentration of ~1600 cells per µL according to 10X Genomics guidelines for optimal cell recovery.
Single Cell Gene Expression was performed on a Chromium X (10X Genomics) following the user guide manual for Chromium GEM-X Single Cell 3’ Reagent Kit V4 (CG000732; Rev B). Briefly, cell viability was confirmed >90% with 0.5% (v/v) Trypan Blue (Sigma-Aldrich; Cat# T8154) staining and hemocytometer quantification. Cells were then captured in gel bead emulsions (GEMs). Following reverse transcription and cell barcoding, the GEMs were broken and cDNA purified using Dynabeads MyOne SILANE (Invitrogen; Cat# 37002D) followed by PCR amplifications as instructed by the manual. ~240,000 cells were targeted in total. Cells from different tissues and replicates were multiplexed together on one lane of 10X Chromium X using Hash Tag Oligonucleotides - HTO following a previously described protocol (Stoeckius et al., 2018). The final 3’ Gene Expression and cell surface protein libraries were loaded in a ratio of 9:1 and sequenced on an Illumina NextSeq 2000 (2 x P3 Flow Cell 1200mil reads) platform (Read 1 – 28 cycles, i7 index – 10 cycles, i5 index – 10 cycles, Read 2 – 90 cycles).

value: Lung and medLN

tag: cell type

value: Lymphocytes

tag: age

value: post-natal day 10

tag: host strain

tag: foster mother_strain

value: Osteopontin-/-

value: OPN

tag: infection

value: uninfected

tag: library type

value: mRNA


title: daf-2; aak(0) post-dauer larvae, biological replicate 1


title: T26_0215

type: genomic

city: Tübingen

first: Daniel

middle: J.

last: Merk

address: Otfried-Müller-Str. 27

country: Germany

institute: Hertie-Institute for Clinical Brain Research

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hypridized to human Infinium MethylationEPIC version 2 array using standard Illumina protocols

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

data_processing:
SeSAMe pipline (v1.24.0)
Average Beta values

label: Cy3 and Cy5

molecule: genomic DNA

source_name: meningioma

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA from human meningiomas was extracted using QIAamp DNA Blood Mini Kit

value: meningioma


title: hMSC_donor2_sham_24h_exp1_rep2

description:
257236328898_1_3
hMCS donor2, sham, 24h, experiment 1, replicate 2


title: Group2_PND10_125, GEX

description:
Library name: Group2_PND10_125_mRNA
GEX (3' mRNA) library from lung and medLN of neonatal mice

value: PBS


title: T26_0166


title: Group4_PND10_124, GEX

description:
Library name: Group4_PND10_124_mRNA
GEX (3' mRNA) library from lung and medLN of neonatal mice

value: PLA


title: daf-2; aak(0) dauer larvae, biological replicate 1

value: Whole animal

value: Dauer was induced by growing the larvae at 25C


title: hMSC_donor1_sham_24h_exp2_rep2

description:
257236328901_2_3
hMSC donor1, sham, 24h, experiment 2, replicate 2

source_name: hMSC donor1, sham, 24h

value: 22 years

value: Male

value: Hispanic/Latino


title: hMSC_donor1_sham_24h_exp2_rep3

description:
257236328902_2_3
hMSC donor1, sham, 24h, experiment 2, replicate 3

value: Sham-exposed


title: Group3_PND10_124, GEX

description:
Library name: Group3_PND10_124_mRNA
GEX (3' mRNA) library from lung and medLN of neonatal mice


title: hMSC_donor1_sham_24h_exp2_rep1

description:
257236328900_2_3
hMSC donor1, sham, 24h, experiment 2, replicate 1

value: Normal Human Bone Marrow Derived Mesenchymal Stem Cells (hMSC)


title: T26_0070


title: hMSC_donor1_HPEM_24h_exp1_rep3

description:
257236328902_1_4
hMSC donor1, HPEM, 24h, experiment 1, replicate 3

source_name: hMSC donor1, HPEM, 24h

value: Exposed to a high power electromagnetic pulse (HPEM), 1 MV/m


title: Group2_PND10_124, GEX

description:
Library name: Group2_PND10_124_mRNA
GEX (3' mRNA) library from lung and medLN of neonatal mice

value: Lung and medLN

value: Lymphocytes


title: T26_0205


title: hMSC_donor1_sham_24h_exp1_rep3

description:
257236328902_1_3
hMSC donor1, sham, 24h, experiment 1, replicate 3


title: Group1_PND10_124, GEX

description:
Library name: Group1_PND10_124_mRNA
GEX (3' mRNA) library from lung and medLN of neonatal mice

value: post-natal day 10


title: daf-2 post-dauer larvae, biological replicate 2

value: Dauer was induced by growing the larvae at 25C. Animals were switched to 15C to exit and recover from dauer.


title: daf-2 post-dauer larvae, biological replicate 1


title: mouse brain Mockulum infection

city: Lebanon

first: David

last: Leib

state: NH

address: 1 Medical Center Drive

department: Dept. of Microbiology and Immunology

institute: Geisel School of Medicine at Dartmouth

description: Library name: F2-14AD

data_processing:
Spatial transcriptomics were aligned and quantified using spaceranger with default parameters
Assembly: GRCm39
Supplementary files format and content: Hi-res and lo-res tissue image (png)
Supplementary files format and content: Scale factors (json)
Supplementary files format and content: aligned fiducials (jpeg), count and feature matrices (.csv, .tsv)
Library strategy: Spatial Transcriptomics

source_name: whole brain

growth_protocol: All procedures were performed in accordance with federal and university policies and according to Dartmouth IACUC protocol #2151. C57BL/6 (B6) mice were purchased from the Jackson Laboratory (Bar Harbor, ME) and bred in a barrier facility in the Center for Comparative Medicine and Research at the Geisel School of Medicine at Dartmouth.

extract_protocol:
10X visium protocol according to manufacturerers instructions
10X visium protocol according to manufacturerers instructions

treatment_protocol: HSV-1 strain 17syn+ stocks were prepared as previously described by K.A. Radar et al. Vero cells were cultured in Dulbecco's modified Eagle's medium and supplemented with 5% fetal bovine, 250 U/ml penicillin, and 250 ug/ml streptomycin. Neonatal subclinical infections were performed as described by C.D. Patel et al. Briefly, neonatal mide postpartum days 1 to 2 were infected intranassaly (i.n.) with 10^2 PFU of HSV-1 strain 17 or mockulum (cell debris in DMEM) in a volume of 5 ul under isoflurane anesthesia.

value: whole brain

value: Infection with mockulum

tag: batch


title: T26_0222

value: meningioma


title: daf-2 dauer larvae, biological replicate 3


title: hMSC_donor1_sham_24h_exp1_rep1

description:
257236328900_1_3
hMSC donor1, sham, 24h, experiment 1, replicate 1


title: hMSC_donor2_HPEM_4h_exp2_rep3

description:
257236328909_2_2
hMCS donor2, HPEM, 4h, experiment 2, replicate 3

source_name: hMCS donor2, HPEM, 4h

value: 24 years

value: Female

value: Black

value: 4 h


title: mouse brain 100 pfu HSV-1 infection

description: Library name: 100pfu

value: Infection with 100PFU HSV-1


title: T26_0058


title: daf-2 dauer larvae, biological replicate 2

value: Whole animal

value: Dauer was induced by growing the larvae at 25C


title: scRNA-seqVV(2e6)+OXP: oxaliplatin ip, hIL-7/mIL-12-VV 2E6 pfu it

city: Ibaraki

first: Kentaro

last: Ikegami

address: 21 Miyukigaoka, Tsukuba

country: Japan

institute: Astellas Pharma Inc.

description: Library name: sample_4

library_source: transcriptomic single cell

data_processing:
The sequencing reads were aligned onto an mm10 genome sequence and reads were counted for each gene for each cell using the Cell Ranger “multi” command.
Assembly: mm10
Supplementary files format and content: cellranger output (sample_filtered_feature_bc_matrix directory compressed into a ZIP file)

source_name: LLC1 tumor

extract_protocol:
Harvested tumor tissues were dissociated and single cell suspensions were prepared with a commercial kit (Chromium Next GEM Single Cell Fixed RNA Sample Preparation Kit).
Library preparation was conducted with Chromium Fixed RNA Kit, Mouse Transcriptome using Chromium iX according to the manufacturer's protocol.

value: LLC1 tumor


title: T26_0100


title: hMSC_donor2_HPEM_4h_exp2_rep2

description:
257236328898_2_2
hMCS donor2, HPEM, 4h, experiment 2, replicate 2

value: Normal Human Bone Marrow Derived Mesenchymal Stem Cells (hMSC)


title: Patient 402

city: Istanbul

first: Elif

last: ÖNEL

address: Buyukdere Street

country: Turkey

institute: Istanbul Technicial University

description: DNA is isolated from peripheral blood samples via salting-out procedure is genotyped using HumanOmniExpress-24-v1-0-B.

hyb_protocol: Allele-specific staining was performed for chips.

scan_protocol: BeadArray Reader (Illumina) is used after bead chips are stained.

data_processing:
GenomeStudio v2.0 is used for deriving genotypes.
value definition: Genotype:  AA,AB,BB,or 00 (no call)

label: biotin

source_name: Blood

label_protocol: DNA fragmentation is applied.

extract_protocol: DNA is isolated from peripheral blood samples via salting-out procedure.

value: Blood

tag: Sex

value: Male


title: T26_0143


title: daf-2 dauer larvae, biological replicate 1


title: T26_0235


title: hMSC_donor2_HPEM_4h_exp2_rep1

description:
257236328897_2_2
hMCS donor2, HPEM, 4h, experiment 2, replicate 1

value: Exposed to a high power electromagnetic pulse (HPEM), 1 MV/m


title: hMSC_donor2_sham_24h_exp2_rep2

description:
257236328898_2_3
hMCS donor2, sham, 24h, experiment 2, replicate 2

value: Sham-exposed


title: scRNA-seqOXP: oxaliplatin ip, PBS it

description: Library name: sample_2


title: CAF12

city: guangzhong

first: yurui

last: liu

address: No. 1023-1063, Shatai South Road, Baiyun District, Guangzhou City, Guangdong Province

country: China

institute: Southern Medical University

description: SAMPLE 24

hyb_protocol: Genomic DNA was bisulfite conversed, amplified, incubated, fragmented, precipitated, resuspended, and hybridized to a BeadChip from the Infinium MethylationEPIC Kit

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

data_processing:
BeadStudio software
MatrixProcessed.txt represents Average Beta values.

source_name: Colorectal cancer tissue

extract_protocol: Genomic DNA was extracted using the TIANamp Genomic DNA Kit(TIANGEN), and the quality was verified by spectrometry.

value: Colorectal cancer tissue

value: fibroblast

value: WT


title: T26_0069

value: meningioma


title: hMSC_donor2_HPEM_0h_exp1_rep3

description:
257236328909_1_2
hMCS donor2, HPEM, 0h, experiment 1, replicate 3

source_name: hMCS donor2, HPEM, 0h

value: 24 years

value: 0 h


title: CAF11

description: SAMPLE 23


title: scRNA-seq vehicle: 5%glucose ip, PBS it

description: Library name: sample_1


title: T26_0168


title: CAF10

description: SAMPLE 22


title: whole mouse brain 7 DPI Mock sample 5

description:
Library name: 177059_12
column name in raw counts X177059_12

data_processing:
Single-end reads were trimmed using cutadapt v4.6
Reads were aligned to the mouse genome reference GRCm39 using STAR v 2.7.10a
Genes were quantified using FeatureCounts v 2.0.1 with GENCODE vM34 as the gene annotation reference
Alignment and quantification metrics were calculated using Samtools v1.15.1 and Picard v 2.27.1
Assembly: GRCm39
Supplementary files format and content: Combined_RNASeq_Counts.csv: Contains the raw counts as output by FeatureCounts with gene names specified as ENSEMBL_ID - Symbol
Supplementary files format and content: TPM counts: contains TPM values

extract_protocol:
Quantseq FWD workflow
100 ng of RNA was used as input into the Quantseq FWD workflow (Lexogen) for library preparation following manufacturer's instructions. Libraries were pooled for sequencing on an Illumina NextSeq 2000 instrument targetting 10M single-end 100bp reads per sample

value: whole brain

value: Mockulum 7 DPI


title: T26_0013


title: daf-2; aak(0) dauer larvae, biological replicate 2


title: daf-2; aak(0) dauer larvae, biological replicate 3


title: whole mouse brain 7 DPI Mock sample 4

description:
Library name: 177059_11
column name in raw counts X177059_11


title: T26_0002


title: hMSC_donor1_HPEM_0h_exp2_rep3

description:
257236328902_2_2
hMSC donor1, HPEM, 0h, experiment 2, replicate 3

source_name: hMSC donor1, HPEM, 0h

value: 22 years

value: Hispanic/Latino


title: CAF8

description: SAMPLE 20


title: hMSC_donor1_HPEM_0h_exp2_rep2

description:
257236328901_2_2
hMSC donor1, HPEM, 0h, experiment 2, replicate 2


title: whole mouse brain 7 DPI Mock sample 3

description:
Library name: 177059_10
column name in raw counts X177059_10


title: T26_0162


title: CAF7

description: SAMPLE 19


title: T26_0023


title: whole mouse brain 7 DPI Mock sample 2

description:
Library name: 177059_09
column name in raw counts X177059_09


title: hMSC_donor1_HPEM_0h_exp2_rep1

description:
257236328900_2_2
hMSC donor1, HPEM, 0h, experiment 2, replicate 1


title: CAF6

description: SAMPLE 18


title: hMSC_donor1_HPEM_0h_exp1_rep3

description:
257236328902_1_2
hMSC donor1, HPEM, 0h, experiment 1, replicate 3


title: whole mouse brain 7 DPI Mock sample 1

description:
Library name: 177059_08
column name in raw counts X177059_08


title: T26_0049


title: whole mouse brain 7 DPI 100 PFU HSV-1 sample 7

description:
Library name: 177059_07
column name in raw counts X177059_07

value: 100 PFU HSV-1 7 DPI


title: T26_0087


title: hMSC_donor1_HPEM_0h_exp1_rep2

description:
257236328901_1_2
hMSC donor1, HPEM, 0h, experiment 1, replicate 2


title: CAF4

description: SAMPLE 16


title: T26_0017


title: whole mouse brain 7 DPI 100 PFU HSV-1 sample 6

description:
Library name: 177059_06
column name in raw counts X177059_06


title: CAF3

description: SAMPLE 15


title: hMSC_donor2_sham_4h_exp2_rep3

description:
257236328909_2_1
hMCS donor2, sham, 4h, experiment 2, replicate 3

source_name: hMCS donor2, sham, 4h

value: Female

value: Black

value: 4 h


title: T26_0200


title: hMSC_donor2_sham_4h_exp2_rep2

description:
257236328898_2_1
hMCS donor2, sham, 4h, experiment 2, replicate 2

value: Normal Human Bone Marrow Derived Mesenchymal Stem Cells (hMSC)


title: scRNA-seqVV(2e6)-mono: 5%glucose ip, hIL-7/mIL-12-VV 2E6 pfu it

description: Library name: sample_3

value: LLC1 tumor


title: CAF2

description: SAMPLE 14


title: T26_0233


title: hMSC_donor2_sham_0h_exp1_rep3

description:
257236328909_1_1
hMCS donor2, sham, 0h, experiment 1, replicate 3

source_name: hMCS donor2, sham, 0h

value: Sham-exposed


title: NF12

description: SAMPLE 12

source_name: para-carcinoma tissue

value: para-carcinoma tissue


title: T26_0050


title: hMSC_donor2_sham_0h_exp1_rep2

description:
257236328898_1_1
hMCS donor2, sham, 0h, experiment 1, replicate 2


title: T26_0231


title: whole mouse brain 7 DPI 100 PFU HSV-1 sample 1

description:
Library name: 177059_01
column name in raw counts X177059_01


title: T26_0072


title: CAF9

description: SAMPLE 21

value: Colorectal cancer tissue

value: fibroblast


title: NF10

description: SAMPLE 10

value: WT


title: CAF5

description: SAMPLE 17


title: whole mouse brain 5 WPI Mock sample 1

description:
Library name: M-1 Mock
column name in raw counts M.1_Mock

value: Mockulum 5 WPI


title: hMSC_donor1_HPEM_0h_exp1_rep1

description:
257236328900_1_2
hMSC donor1, HPEM, 0h, experiment 1, replicate 1

value: Male

value: Exposed to a high power electromagnetic pulse (HPEM), 1 MV/m

value: 0 h


title: hMSC_donor2_sham_0h_exp1_rep1

description:
257236328897_1_1
hMCS donor2, sham, 0h, experiment 1, replicate 1

value: 24 years


title: T26_0140

value: meningioma


title: whole mouse brain 7 DPI 100 PFU HSV-1 sample 5

description:
Library name: 177059_05
column name in raw counts X177059_05

value: whole brain

value: 100 PFU HSV-1 7 DPI


title: hMSC_donor1_sham_0h_exp2_rep3

description:
257236328902_2_1
hMSC donor1, sham, 0h, experiment 2, replicate 3

source_name: hMSC donor1, sham, 0h

value: 22 years

value: Hispanic/Latino


title: whole mouse brain 7 DPI 100 PFU HSV-1 sample 4

description:
Library name: 177059_04
column name in raw counts X177059_04


title: T26_0113


title: NF9

description: SAMPLE 9


title: whole mouse brain 5 WPI Mock sample 2

description:
Library name: M-2 Mock
column name in raw counts M.2_Mock


title: hMSC_donor1_sham_0h_exp2_rep2

description:
257236328901_2_1
hMSC donor1, sham, 0h, experiment 2, replicate 2

value: Normal Human Bone Marrow Derived Mesenchymal Stem Cells (hMSC)


title: CAF1

description: SAMPLE 13


title: NF8

description: SAMPLE 8


title: hMSC_donor2_sham_4h_exp2_rep1

description:
257236328897_2_1
hMCS donor2, sham, 4h, experiment 2, replicate 1

value: Female

value: Black

value: 4 h


title: whole mouse brain 7 DPI 100 PFU HSV-1 sample 3

description:
Library name: 177059_03
column name in raw counts 177059_03


title: whole mouse brain 5 WPI Mock sample 3

description:
Library name: M-3 Mock
column name in raw counts M.3_Mock


title: T26_0095


title: NF7

description: SAMPLE 7

value: para-carcinoma tissue


title: T26_0088


title: whole mouse brain 5 WPI Mock sample 4

description:
Library name: M-4 Mock
column name in raw counts M.4_Mock


title: hMSC_donor1_sham_0h_exp2_rep1

description:
257236328900_2_1
hMSC donor1, sham, 0h, experiment 2, replicate 1

value: Sham-exposed


title: NF6

description: SAMPLE 6

value: fibroblast

value: WT


title: T26_0188


title: whole mouse brain 5 WPI 100 PFU HSV-1 sample 1

description:
Library name: 100-1 100 PFU HSV-1
column name in raw counts X100.1_100_PFU_HSV.1

value: 100 PFU HSV-1 5 WPI


title: hMSC_donor1_sham_0h_exp1_rep3

description:
257236328902_1_1
hMSC donor1, sham, 0h, experiment 1, replicate 3

value: Male


title: NF5

description: SAMPLE 5


title: hMSC_donor1_sham_0h_exp1_rep2

description:
257236328901_1_1
hMSC donor1, sham, 0h, experiment 1, replicate 2

value: 0 h


title: T26_0173


title: whole mouse brain 5 WPI 100 PFU HSV-1 sample 2

description:
Library name: 100-2 100 PFU HSV-1
column name in raw counts X100.2 _100_PFU_HSV.1


title: NF4

description: SAMPLE 4


title: hMSC_donor1_sham_0h_exp1_rep1

description:
257236328900_1_1
hMSC donor1, sham, 0h, experiment 1, replicate 1


title: whole mouse brain 5 WPI 100 PFU HSV-1 sample 3

description:
Library name: 100-3 100 PFU HSV-1
column name in raw counts X100.3_100_PFU_HSV.1


title: T26_0120


title: ECRT patient tumor, RNA029_16_201

city: Paris

first: Franck

last: Bourdeaut

address: 26 rue d'ulm

country: France

institute: Institut Curie

description:
Library name: RNA029_16_201
Column name in raw counts and TPM matrixes : RNA029_16_201
raw_counts_RT_MAM_RNAseq.txt
TPM_RT_MAM_RNAseq.txt

data_processing:
Raw data were processed using an in-house pipeline developed at the Institut Curie Bioinformatics Core Facility, following standard analysis in the field and available at https://github.com/bioinfo-pf-curie/RNA-seq.
Sequencing adaptors were trimmed using TrimGalore!
read QC were performed using fastqc
read mapping on GRCh39/hg19 reference genome were performed using STAR (version 2.5.3a) and the refFlat gene annotation downloaded from UCSC
duplicated reads were marked with picard and then removed
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: a single tab-delimited text file includes matrix of TPM values with sample in columns and genes on rows

source_name: tumor

growth_protocol: I2A cells were maintained in RPMI containing 10% fetal bovine serum (FBS) and supplemented with 50 ng/mL doxycycline, 50 μg/mL hygromycin B and 300 μg/mL geneticin. G401-i cells were maintained in RPMI containing 10% FBS and supplemented with 50 ng/mL doxycycline. For both inducible cell lines, medium was changed every 3-4 days to renew drugs and cells were washed three times in Phosphate Buffer Saline (PBS) to completely remove doxycycline in order to induce SMARCB1 expression.

extract_protocol:
Total RNAs from cell line samples were extracted using the Nucleospin II kit (Macherey-Nagel). Total RNAs from frozen human tumors were extracted using the QIAamp RNAeasy kit (Qiagen)
Barcoded Illumina compatible libraries were generated from 750 ng of total RNA for each sample using TruSeq Stranded mRNA Library Preparation Kit (Illumina, San Diego, California, U.S.,).

treatment_protocol: For low-dose decitabine (DAC) experiments, I2A cells were treated with DAC at 100 nM or DMSO as a control for 21 days.

value: tumor

value: Rhabdoid tumor

tag: patient id


title: whole mouse brain 7 DPI 100 PFU HSV-1 sample 2

description:
Library name: 177059_02
column name in raw counts X177059_02

value: whole brain


title: NF3

description: SAMPLE 3


title: whole mouse brain 5 WPI 100 PFU HSV-1 sample 4

description:
Library name: 100-4 100 PFU HSV-1
column name in raw counts X100.4_100_PFU_HSV.1


title: T26_0227

value: meningioma


title: ECRT patient tumor, INI-180

description:
Library name: INI-180
Column name in raw counts and TPM matrixes : INI-180
raw_counts_RT_MAM_RNAseq.txt
TPM_RT_MAM_RNAseq.txt


title: NF2

description: SAMPLE 2


title: 8mM Pyruvate 3

city: kyoto

first: takehiro

last: miyazaki

state: kyoto

address: 53 Kawahara-cho, Shogoin, Sakyo

institute: Kyoto University

data_processing:
Sequencing was performed on an Illumina NextSeq 2000 platform with the paired-end mode.
Illumina RTA version 3.10.30 and  bcl2fastq version 2.20 were used for basecalling and fastq generation, respectively.
Adapter sequences and low-quality bases were trimmed from the raw reads by cutadapt v4.6. The trimmed reads were mapped to the mouse reference genome sequences (mm10) using STAR v2.7.11a with the GENCODE vM32 gtf file.
The uniquely and properly mapped reads were used for further analysis. Raw read counts were calculated using htseq-count v2.0.5 with the GENCODE gtf file. Gene expression levels were determined as transcripts per million (TPM).
Assembly: mm10
Supplementary files format and content: raw count matrix data

source_name: cell

extract_protocol:
RNA was extracted from GS cells using the TRIzol Reagent (Invitrogen) and purified using the RNeasy Plus mini kit (QIAGEN).
The library preparation was performed using an Illumina Stranded mRNA Prep Kit (Illumina) according to the manufacturer’s instructions.

value: cell

tag: cell line

value: DBA-GFP GS cell

value: germline stem cell

value: 8mM Pyruvate mediume culture


title: ATRT patient tumor, INI-177

description:
Library name: INI-177
Column name in raw counts and TPM matrixes : INI-177
raw_counts_RT_MAM_RNAseq.txt
TPM_RT_MAM_RNAseq.txt


title: 8mM Pyruvate 2


title: T26_0057


title: NF1

description: SAMPLE 1


title: T26_0134


title: ECRT patient tumor, INI53

description:
Library name: INI53
Column name in raw counts and TPM matrixes : INI53
raw_counts_RT_MAM_RNAseq.txt
TPM_RT_MAM_RNAseq.txt


title: HCC patient 87

city: Rome

first: Stefano

last: Scalera

address: Via Elio Chianesi 53

country: Italy

institute: IRCCS Regina Elena National Cancer Institute

library_source: other

data_processing:
data was analyzed with The BaseSpace® TruSeq® Targeted RNA v1.0.1 app
Assembly: hg19
Supplementary files format and content: tab-delimited text file include normalized counts value for each Sample
Supplementary files format and content: tab-delimited text file include raw counts value for each Sample

molecule: other

source_name: hepatocellular carcinoma tissue

extract_protocol:
Genomic DNA and RNA were extracted from 5 μm FFPE tissue sections using the AllPrep DNA/RNA FFPE kit (Qiagen, Valencia, CA, USA). The concentration and integrity of purified DNA/RNA samples were assessed by Qubit fluorometer (Thermo Fisher Scientific, Hampton, NH, USA) and 2200 TapeStatio (Agilent Technologies, Santa Clara, CA, USA), respectively.
RNA-Sequencing library were prepared using AmpliSeq for Illumina RNA WNT panel (the panel include 169 genes involved in the regulation of WNT signaling pathway) by following the manufacturer’s. Pooled sequencing libraries were sequencing in 150-bp paired-end reads on Illumina MiSeq sequencer (Illumina).

value: hepatocellular carcinoma tissue

value: liver cancer

value: liver


title: 8mM Pyruvate 1


title: T26_0175

source_name: meningioma


title: ECRT patient tumor, INI19b

description:
Library name: INI19b
Column name in raw counts and TPM matrixes : INI19b
raw_counts_RT_MAM_RNAseq.txt
TPM_RT_MAM_RNAseq.txt


title: HCC patient 86


title: control 3

value: complete mediume culture


title: ECRT patient tumor, SARC_T26

description:
Library name: SARC_T26
Column name in raw counts and TPM matrixes : SARC_T26
raw_counts_RT_MAM_RNAseq.txt
TPM_RT_MAM_RNAseq.txt


title: HCC patient 85


title: T26_0167


title: control 2


title: NF11

description: SAMPLE 11

value: para-carcinoma tissue

value: fibroblast


title: T26_0209


title: RD cells, siBAZ1A, UV-exposed, replicate 3

city: Augusta

middle: S

last: Kim

state: GA

department: Vascular Biology Center

institute: Augusta University

description:
Library name: RD_siBAZ1A_UV_rep3
Column in normalized_counts_all_samples.txt: RD_siBAZ1A_UV_3

data_processing:
Raw reads were trimmed using Cutadapt version 4.1
Trimmed reads were aligned to the GRCh38/hg38 human genome assembly using STAR version 2.7.0
Normalized read counts and differential gene expression analysis were performed using DESeq2 version 1.22 with a false discovery rate (FDR) threshold < 0.05
Analysis was performed using RStudio version 494 and the public server of usegalaxy.org
Hallmark gene set enrichment analysis (GSEA) was performed using the fgsea package with gene sets from MSigDB Hallmark collection
Assembly: GRCh38/hg38
Supplementary files format and content: Tab-delimited text files containing DESeq2 normalized counts for each sample
Supplementary files format and content: Tab-delimited text files containing annotated DESeq2 differential expression results (log2 fold change, p-value, adjusted p-value) for each comparison

source_name: RD (rhabdomyoblast)

growth_protocol: Human saphenous vein smooth muscle cells (HSVSMCs) were cultured in DMEM or SmGM-2 (Lonza) supplemented with 10% FBS and 1% penicillin-streptomycin at 37°C in a 5% CO2 humidified incubator. Rhabdomyoblast (RD) cells were cultured in DMEM supplemented with 10% FBS and 1% penicillin-streptomycin at 37°C in a 5% CO2 humidified incubator. Cells were seeded in 6-well plates and grown to 60-70% confluence before overnight starvation with 0.2% FBS.

extract_protocol:
Total RNA was extracted using QIAzol Lysis Reagent and purified with miRNeasy Mini Kit (Qiagen) according to the manufacturer's protocol. RNA integrity was assessed using an Agilent Bioanalyzer; only samples with RNA integrity number (RIN) > 8 were used for library preparation.
RNA-seq libraries were prepared from polyadenylated or ribosome-depleted RNA at Genewiz or the Genomics Core at Augusta University. Libraries were sequenced at a depth of 20 million reads per replicate using the Illumina HiSeq 2500 system with a 150 bp paired-end protocol.

treatment_protocol: For BAZ1A-AS1 knockdown, HSVSMCs were transfected with 25 nM locked nucleic acid (LNA) gapmeR antisense oligonucleotides targeting BAZ1A-AS1 (AS1-ASO; Qiagen) or negative control ASO (NC-ASO) using Lipofectamine RNAiMAX (Invitrogen). For BAZ1A knockdown, RD cells were transfected with 25 nM siRNA targeting BAZ1A (siBAZ1A; Qiagen) or scrambled siRNA (siScram) using Lipofectamine RNAiMAX (Invitrogen). RD cells were exposed to UVC irradiation (254 nm, 15 seconds) using the germicidal lamp of a biological safety cabinet 24 hours post-transfection. Cells were harvested 6 hours after UV exposure for RNA extraction.

value: RD (rhabdomyoblast)

value: rhabdomyoblast

value: wild type

value: BAZ1A siRNA (25 nM) + UV exposure (15 sec, 254 nm)


title: HCC patient 84


title: control 1

value: WT


title: T26_0093


title: RD cells, siBAZ1A, UV-exposed, replicate 2

description:
Library name: RD_siBAZ1A_UV_rep2
Column in normalized_counts_all_samples.txt: RD_siBAZ1A_UV_2


title: T26_0090


title: CKH08, biological replicate 4

city: Gdansk

first: Adam

last: Iwanicki

address: Debinki 1

department: Department of Medical Biotechnlogy

institute: Intercollegiate Faculty of Biotechnology University of Gdansk and Medical University of Gdansk

description:
Library name: Sample 8
Column name in All_samples_raw_counts.csv: CKH08_4_htseq

data_processing:
Adapters removed with Cutadapt (v. 4.9) with quality parameter q 25 and minimal reads length m 20
Reads mapped against C. difficile R20291 reference genome GCF_000027105.1 with Hisat2 (v. 2.2.1) run with -rna-strandness RF and -novel-splicesite-outfile options
Pairs of reads counted with HTseq (v. 0.10.0)
Assembly: GCF_000027105.1
Supplementary files format and content: csv files include raw counts for each sample

organism: Clostridioides difficile

source_name: bacterial cell

growth_protocol: C. difficile strains 500/12 and CKH08 were inoculated into 40 ml of pre‑reduced BHI broth and cultured under the anaerobic growth conditions until the late logarithmic phase

extract_protocol:
RNA was extracted usin RNeasy Mini Kit (QIAGEN)
QIAseq FastSelect RNA Lib Bac. Kit (QIAGEN) following manufacturer's protocol

value: bacterial cell


title: HCC patient 83


title: HCC patient 82


title: CKH08, biological replicate 3

description:
Library name: Sample 7
Column name in All_samples_raw_counts.csv: CKH08_3_htseq


title: RD cells, siScram, UV-exposed, replicate 3

description:
Library name: RD_siScram_UV_rep3
Column in normalized_counts_all_samples.txt: RD_siScram_UV_3

value: scrambled siRNA + UV exposure (15 sec, 254 nm)


title: HCC patient 81


title: CKH08, biological replicate 2

description:
Library name: Sample 6
Column name in All_samples_raw_counts.csv: CKH08_2_htseq


title: T26_0195

value: meningioma


title: RD cells, siBAZ1A, UV-exposed, replicate 1

description:
Library name: RD_siBAZ1A_UV_rep1
Column in normalized_counts_all_samples.txt: RD_siBAZ1A_UV_1


title: HCC patient 80


title: T26_0060


title: CKH08, biological replicate 1

description:
Library name: Sample 5
Column name in All_samples_raw_counts.csv: CKH08_1_htseq


title: T26_0031


title: RD cells, siScram, UV-exposed, replicate 2

description:
Library name: RD_siScram_UV_rep2
Column in normalized_counts_all_samples.txt: RD_siScram_UV_2


title: RD cells, siScram, UV-exposed, replicate 1

description:
Library name: RD_siScram_UV_rep1
Column in normalized_counts_all_samples.txt: RD_siScram_UV_1


title: HCC patient 79


title: 500/12, biological replicate 4

description:
Library name: Sample 4
Column name in All_samples_raw_counts.csv: A_500_4_htseq


title: T26_0139


title: HSVSMC, BAZ1A-AS1 ASO, replicate 3

description:
Library name: HSVSMC_AS1_ASO_rep3
Column in normalized_counts_all_samples.txt: HSVSMC_AS1_ASO_3

source_name: HSVSMCs

value: HSVSMCs

value: human saphenous vein smooth muscle cells

value: BAZ1A-AS1 LNA gapmeR ASO (25 nM)


title: 500/12, biological replicate 3

description:
Library name: Sample 3
Column name in All_samples_raw_counts.csv: A_500_3_htseq


title: HCC patient 78

value: hepatocellular carcinoma tissue


title: T26_0082


title: HSVSMC, BAZ1A-AS1 ASO, replicate 2

description:
Library name: HSVSMC_AS1_ASO_rep2
Column in normalized_counts_all_samples.txt: HSVSMC_AS1_ASO_2


title: T26_0202


title: 500/12, biological replicate 2

description:
Library name: Sample 2
Column name in All_samples_raw_counts.csv: A_500_2_htseq


title: HCC patient 77

value: liver cancer


title: HSVSMC, BAZ1A-AS1 ASO, replicate 1

description:
Library name: HSVSMC_AS1_ASO_rep1
Column in normalized_counts_all_samples.txt: HSVSMC_AS1_ASO_1


title: HCC patient 76

value: liver


title: 500/12, biological replicate 1

description:
Library name: Sample 1
Column name in All_samples_raw_counts.csv: A_500_1_htseq


title: T26_0076


title: HSVSMC, NC-ASO, replicate 3

description:
Library name: HSVSMC_NC_ASO_rep3
Column in normalized_counts_all_samples.txt: HSVSMC_NC_ASO_3

value: NC-ASO (negative control antisense oligonucleotide)


title: HCC patient 75


title: T26_0152


title: HCC patient 74


title: HSVSMC, NC-ASO, replicate 2

description:
Library name: HSVSMC_NC_ASO_rep2
Column in normalized_counts_all_samples.txt: HSVSMC_NC_ASO_2


title: VPA-adult-TE-3

city: Kodaira

first: Satoshi

last: Watanabe

state: Tokyo

address: 4-1-1 Ogawa Higashi

institute: National Center of Neurology and Psychiatry

description:
299-9
Gene expression in TE from adult VPA marmoset

hyb_protocol: The arrays were hybridized and washed using the GeneChip Hybridization, Wash, and Stain Kit (Affymetrix) according to the manufacturer's instructions.

scan_protocol: The arrays were scanned using the GeneChip Scanner 3000 (Affymetrix).

data_processing: The data were normalized by GCRMA.

organism: Callithrix jacchus

source_name: TE from adult VPA marmoset

label_protocol: Biotin-labeled cRNA was generated using the GeneChip 3'IVT Express Kit (Affymetrix) according to the manufacturer's instructions.

growth_protocol: For production of VPA marmoset, pregnant marmoset was administered with VPA at post-conception days 60-66, and the offspring were used.

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Marmosets were anesthesized with ketamine followed by pentobarbital. Phosphate-buffered saline was transcardially perfused. Cortical tissues were isolated and immersed in RNAlater (Thermo Fisher).

tag: animal id

value: Female

value: VPA

tag: age (days)

value: Cortical TE


title: HSVSMC, NC-ASO, replicate 1

description:
Library name: HSVSMC_NC_ASO_rep1
Column in normalized_counts_all_samples.txt: HSVSMC_NC_ASO_1


title: T26_0075


title: HCC patient 73


title: VPA-adult-Area12-3

description:
299-8
Gene expression in Area12 from adult VPA marmoset

source_name: Area12 from adult VPA marmoset

value: Cortical Area12


title: T26_0234


title: IR-Snc-siC3-4

city: Kuning

first: Runzi

last: Zheng

state: Yunnan

address: No. 727, Jingming South Road, Chenggong District

institute: Kunming University of Science and Technology

description: Library name: samples14

data_processing:
Samples are sequenced on the platform to getimage files, which are transformed by thesoftware of the sequencing platform, and theoriginal data in FASTQ format (Raw Data) isgenerated. Sequencing data contains a numberof connectors, low-quality Reads, so we usefastp(0.22.0) software to filter the sequencingdata to get high quality sequence (Clean Data)for further analysis
Assembly: GRCh38
Supplementary files format and content: CSV file including Reads count for each sample

source_name: skin

extract_protocol:
total RNA was extracted by the chloroform method
RNA-seq library was cunstruscted by using NEBnext ultra II RNA library Prep Kit for illumina

value: skin

value: HDF

value: human neonatal foreskin

value: senecense WT c3 knockdown


title: VPA-adult-TE-2

description:
299-2
Gene expression in TE from adult VPA marmoset


title: HCC patient 72


title: T26_0165


title: IR-Snc-siC3-3

description: Library name: samples13


title: HCC patient 71


title: VPA-adult-TE-1

description:
299-16
Gene expression in TE from adult VPA marmoset

value: Male


title: T26_0032

value: meningioma


title: VPA-adult-Area12-2

description:
299-15
Gene expression in Area12 from adult VPA marmoset


title: IR-Snc-siC3-2

description: Library name: samples12


title: HCC patient 70


title: T26_0174


title: daf-2 post-dauer larvae, biological replicate 3

source_name: Whole animal

value: Whole animal

value: Dauer was induced by growing the larvae at 25C. Animals were switched to 15C to exit and recover from dauer.


title: IR-Snc-siC3-1

description: Library name: samples11


title: VPA-adult-Area12-1

description:
299-1
Gene expression in Area12 from adult VPA marmoset


title: HCC patient 69


title: T26_0067


title: HCC patient 68


title: VPA-90d-TE-2

description:
286-09
Gene expression in TE from 90d VPA marmoset

source_name: TE from 90d VPA marmoset


title: T26_0208


title: IR-Snc-4

description: Library name: samples10

value: senecense WT


title: IR-Snc-3

description: Library name: samples9


title: HCC patient 67

value: hepatocellular carcinoma tissue


title: T26_0062


title: T26_0190


title: HCC patient 66

value: liver cancer


title: IR-Snc-2

description: Library name: samples8


title: VPA-90d-Area12-2

description:
286-08
Gene expression in Area12 from 90d VPA marmoset

source_name: Area12 from 90d VPA marmoset


title: VPA-90d-TE-1

description:
286-02
Gene expression in TE from 90d VPA marmoset


title: T26_0155


title: VPA-90d-Area12-1

description:
286-01
Gene expression in Area12 from 90d VPA marmoset


title: HCC patient 65

value: liver


title: IR-Snc-1

description: Library name: samples7


title: T26_0123


title: HCC patient 64


title: Non-Snc-siC3-3

description: Library name: samples6

value: WT c3 knockdown


title: VPA-180d-TE-2

description:
274B-09
Gene expression in TE from 180d VPA marmoset

source_name: TE from 180d VPA marmoset

value: Female


title: T26_0196


title: Non-Snc-siC3-2

description: Library name: samples5


title: VPA-180d-Area12-2

description:
274B-08
Gene expression in Area12 from 180d VPA marmoset

source_name: Area12 from 180d VPA marmoset

value: VPA


title: T26_0132


title: HCC patient 63


title: Non-Snc-siC3-1

description: Library name: samples4


title: HCC patient 62


title: T26_0019


title: Non-Snc-3

description: Library name: samples3

value: WT


title: HCC patient 61


title: T26_0071


title: VPA-180d-Area12-1

description:
274B-01
Gene expression in Area12 from 180d VPA marmoset

value: Cortical Area12


title: VPA-180d-TE-1

description:
274B-02
Gene expression in TE from 180d VPA marmoset

value: Cortical TE


title: Non-Snc-2

description: Library name: samples2

value: skin

value: HDF


title: HCC patient 60


title: T26_0191


title: VPA-60d-TE-2

description:
264-04
Gene expression in TE from 60d VPA marmoset

source_name: TE from 60d VPA marmoset


title: VPA-60d-TE-1

description:
264-03
Gene expression in TE from 60d VPA marmoset


title: Non-Snc-1

description: Library name: samples1

value: human neonatal foreskin


title: T26_0015


title: 143B cells, shZDHHC8, Cisplatin, bio rep 2

city: Shanghai

first: Yangbai

last: Sun

address: No.270 Dongan Road

department: Department of Musculoskeletal Oncology

institute: Fudan University

description:
Library name: Sample 8
Column names in processed data.xls: 143B-C4-2

data_processing:
Raw sequencing reads were subjected to quality control to remove adapter sequences and low-quality reads. Clean reads were aligned to the human reference genome (hg38) using a standard splice-aware aligner. Gene-level read counts were generated based on annotated gene models. Differential gene expression analysis was performed using a statistical framework designed for RNA-seq count data. Genes with statistically significant changes in expression were identified based on adjusted p-values and fold-change thresholds. Downstream analyses, including overlap analysis and pathway enrichment, were conducted using differentially expressed gene sets.
Assembly: hg38
Supplementary files format and content: xls files include FPKM values for each sample

source_name: Bone

growth_protocol: 143B cells stably expressing control or ZDHHC8 shRNA were maintained in DMEM supplemented with 10% FBS, 1% penicillin–streptomycin and cultured at 37 °C with 5% CO₂.

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen) following the manufacturer’s protocol. Residual genomic DNA was removed by DNase I treatment. RNA quantity and purity were measured spectrophotometrically, and RNA integrity was assessed using an Agilent Bioanalyzer prior to RNA-seq library construction.
RNA-seq libraries were prepared from total RNA using a standard Illumina-compatible library construction protocol. Briefly, mRNA was enriched from total RNA by poly(A) selection using oligo(dT) magnetic beads. The purified mRNA was fragmented and reverse-transcribed to generate first- and second-strand cDNA. The resulting cDNA fragments were end-repaired, A-tailed, and ligated to indexed sequencing adapters. Adapter-ligated fragments were amplified by PCR to generate the final sequencing libraries. Library quality and size distribution were assessed prior to sequencing.

treatment_protocol: Cells were treated with cisplatin or vehicle for 48 hours prior to RNA isolation.

value: Bone

value: Osteosarcoma  cells

value: ZDHHC8 knockdown

value: Cisplatin


title: HCC patient 59


title: VPA-60d-Area12-2

description:
264-02
Gene expression in Area12 from 60d VPA marmoset

source_name: Area12 from 60d VPA marmoset


title: T26_0028

value: meningioma


title: HCC patient 58

value: hepatocellular carcinoma tissue


title: 143B cells, shZDHHC8, Cisplatin, bio rep 1

description:
Library name: Sample 7
Column names in processed data.xls: 143B-C4-1


title: HCC patient 57

value: liver cancer


title: T26_0119


title: VPA-60d-Area12-1

description:
264-01
Gene expression in Area12 from 60d VPA marmoset


title: 143B cells, shControl, Cisplatin, bio rep 2

description:
Library name: Sample 6
Column names in processed data.xls: 143B-C3-2


title: VPA-0d-TE-4

description:
260-09
Gene expression in TE from 0d VPA marmoset

source_name: TE from 0d VPA marmoset


title: HCC patient 56

source_name: hepatocellular carcinoma tissue

value: liver


title: T26_0193

source_name: meningioma


title: 143B cells, shControl, Cisplatin, bio rep 1

description:
Library name: Sample 5
Column names in processed data.xls: 143B-C3-1


title: HCC patient 55


title: VPA-0d-Area12-4

description:
260-08
Gene expression in Area12 from 0d VPA marmoset

source_name: Area12 from 0d VPA marmoset


title: T26_0144


title: HCC patient 54


title: 143B cells, shZDHHC8, Vehicle, bio rep 2

description:
Library name: Sample 4
Column names in processed data.xls: 143B-2-2

value: PBS


title: VPA-0d-TE-3

description:
260-02
Gene expression in TE from 0d VPA marmoset

value: Female


title: T26_0137


title: HCC patient 53


title: 143B cells, shZDHHC8, Vehicle, bio rep 1

description:
Library name: Sample 3
Column names in processed data.xls: 143B-2-1


title: T26_0053


title: VPA-0d-Area12-2

description:
239-9Re
Gene expression in Area12 from 0d VPA marmoset

value: VPA


title: VPA-0d-Area12-3

description:
260-01
Gene expression in Area12 from 0d VPA marmoset


title: HCC patient 52


title: 143B cells, shControl, Vehicle, bio rep 2

description:
Library name: Sample 2
Column names in processed data.xls: 143B-1-2

value: WT


title: NCH93_REP_B

source_name: malignant meningioma

growth_protocol: IOMM-Lee, KT1-MG1, and NCH93 cells were grown in DMEM media supplemented with 10% FCS and 0.1% gentamycin. BEN-MNE-1 cells were grown in DMEM media supplemented with 20% FCS and 0.1% gentamycin. HBL-52 cells were grown in DMEM/F12 media  supplemented with 1x ITS, 10% FCS and 0.1% gentamycin.

value: malignant meningioma


title: 143B cells, shControl, Vehicle, bio rep 1

description:
Library name: Sample 1
Column names in processed data.xls: 143B-1-1


title: HCC patient 51


title: UE-0d-TE-4

description:
239-6
Gene expression in TE from 0d unexposed marmoset

source_name: TE from 0d unexposed marmoset

value: Male

value: UE

value: Cortical TE


title: NCH93_REP_A


title: HCC patient 50


title: Grade 2R ACR Rep12

city: Valencia

first: Estefanía

last: Tarazón

address: Avenida Fernando Abril Martorell 106

country: Spain

institute: Instituto de investigación Sanitaria La Fe

description: Library name: B41_2

data_processing:
Quality control of the raw sequence data was performed using FastQC software. Bias was prevented through adapter identification and elimination using Trim Galore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). Following this, the raw paired-end reads were mapped against the human hg38 genome using the bowtie algorithm. Insufficient quality reads, with a phred score ≤20, were eliminated using the SAMtools method. RNA quantification was then estimated using HTSeq software (version 0.6.0). Lastly, differential expression analysis between conditions were assessed using the DESeq2 method (version 3.4). The FDR method adjusts the original p value using the number of tests. An interpretation of this method is implemented in DESeq2 in which the genes are rank in function of the p value and then are multiply by a correction rank value, similar to original FDR method. Differentially expressed RNAs with fold change (FC) values ±1.5, and with false discovery rate (FDR) adjusted p ≤ .05 were included to avoid identification of false positives across the differential expression data.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts  for each sample

source_name: Serum

extract_protocol:
RNA extraction was carried out using NucleoSpin® miRNA Plasma of Macherey Nagel, following the protocol and instructions provided by the manufacturer. RNA quantification was performed using a NanoDrop 1000 spectrophotometer and the Qubit 3.0 fluorometer (Thermo Fisher Scientific). The purity and integrity of RNA samples were determined using the RNA 6000 Nano Kit and Small RNA Kit with 0.8% agarose gel and the Agilent 2100 Bioanalyzer (Agilent Technologies).
cDNA libraries were obtained following Illumina’s recommendations. Briefly, 3′ and 5′ adapters were sequentially ligated to RNA prior to reverse transcription and cDNA synthesis. Size selection was performed using a 6% polyacrylamide gel. The quality and quantity of cDNA libraries were analyzed using the High-Sensitivity D1000 ScreenTape Assay and the 4200 TapeStation System (Agilent Technologies). cDNA libraries were then pooled and sequenced by two lanes of 100 bp paired-end sequencing using an Illumina HiSeq 2500 sequencer.

value: Serum

value: female

tag: disease state

value: Post-trasplant rejection


title: Grade 2R ACR Rep11

description: Library name: B41_1


title: UE-0d-Area12-4

description:
239-5
Gene expression in Area12 from 0d unexposed marmoset

source_name: Area12 from 0d unexposed marmoset

tag: treatment

value: Cortical Area12


title: KT21-MG1_REP_B


title: HCC patient 49


title: Grade 2R ACR Rep10

description: Library name: B40_1

value: male


title: UE-0d-TE-3

description:
239-2
Gene expression in TE from 0d unexposed marmoset


title: KT21-MG1_REP_A


title: HCC patient 48


title: Grade 2R ACR Rep9

description: Library name: B37_1


title: HBL-52_REP_B

source_name: benign meningioma

value: benign meningioma


title: VPA-0d-TE-2

description:
239-14
Gene expression in TE from 0d VPA marmoset


title: VPA-0d-Area12-1

description:
239-13
Gene expression in Area12 from 0d VPA marmoset


title: HCC patient 47

value: hepatocellular carcinoma tissue


title: HBL-52_REP_A


title: Grade 2R ACR Rep8

description: Library name: B35_2


title: HCC patient 46

value: liver cancer


title: VPA-0d-TE-1

description:
239-10
Gene expression in TE from 0d VPA marmoset


title: Grade 2R ACR Rep7

description: Library name: B34_3


title: BEN-MEN-1_REP_B


title: UE-0d-Area12-3

description:
239-1
Gene expression in Area12 from 0d unexposed marmoset


title: BEN-MEN-1_REP_A


title: UE-0d-TE-2

description:
218-6
Gene expression in TE from 0d unexposed marmoset


title: Grade 2R ACR Rep5

description: Library name: B26_5


title: HCC patient 45

value: liver


title: Grade 2R ACR Rep4

description: Library name: B25_3


title: HCC patient 42


title: IOMM_Lee_REP_B

value: IOMM-Lee


title: Grade 2R ACR Rep6

description: Library name: B32_1


title: UE-0d-Area12-1

description:
218-3
Gene expression in Area12 from 0d unexposed marmoset


title: HCC patient 44


title: IOMM_Lee_REP_A


title: HCC patient 43


title: UE-0d-Area12-2

description:
218-7
Gene expression in Area12 from 0d unexposed marmoset

value: Female


title: F3

city: Ya, an

first: Qin

last: Wang

state: Sichuan

address: xinkang road No.46

department: College of Life Sciences

institute: Sichuan Agricultural University

description: Library name: F3

data_processing:
1. Raw data quality control: Raw sequencing reads were filtered using Trimmomatic v0.39 to remove adapter sequences, low-quality reads (Q < 20), and short reads (<50 bp). 2. Alignment: Clean reads were aligned to the Bombyx mori reference genome (SilkDB 3.0) using HISAT2 v2.2.1 with default parameters. 3. Quantification: Gene expression levels were quantified as raw counts using StringTie v2.2.1. 4. Normalization: Counts were normalized to FPKM/TPM using StringTie, and differential expression analysis was performed using DESeq2 v1.38.3.
Assembly: https://ftp.ncbi.nlm.nih.gov/genomes/refseq/invertebrate/Bombyx_mori/latest_assembly_versions/GCF_014905235.1_Bmori_2016v1.0/GCF_014905235.1_Bmori_2016v1.0_genomic.fna.gz
Supplementary files format and content: File 1: silkworm_molt_all_sample_count.txt  The first column contains the gene IDs of *Bombyx mori*, followed by columns representing all experimental samples (A1, A2, A3, TA1, TA2, TA3, T1, T2, T3, F1, F2, F3). Values are raw read counts for each gene in different samples, with 0 filled for genes without expression signals in corresponding samples.  File 2: silkworm_molt_all_sample_fpkm.txt. The format is consistent with the count matrix, and values are FPKM-normalized expression levels of each gene in all samples.

organism: Bombyx mori

source_name: head and thoracic tissues

extract_protocol:
Total RNA was extracted from head and thoracic tissues using the RNAiso™ Plus RNA Kit (TaKaRa) according to the manufacturer’s instructions. The quantity and quality of the extracted RNA were assessed using a NanoDrop 2000™ spectrophotometer and the Agilent 5400 system (Agilent Technologies, USA). RNA integrity was verified by agarose gel electrophoresis. Subsequently, mRNA with poly(A) tails was enriched using Oligo(dT) magnetic beads, and fragmented into small pieces via ion interruption. Using these mRNA fragments as templates, cDNA fragments of 250–300 bp in length were synthesized. The library construction was completed by PCR amplification and purification of the cDNA fragments.
Dual-end sequencing was performed on the Illumina NovaSeq 6000 platform built by Novogene Bioinformatics Technology Co., Ltd. (Beijing, China). Paired-end sequencing was then aligned to the reference genome using HISAT2 (v2.0.5) to generate high-quality base calls.

value: head and thoracic tissues

value: Gurangri 3

value: Tetra-molting

value: Batch 2


title: F1

description: Library name: F1


title: Grade 2R ACR Rep3

description: Library name: B26_4


title: HCC patient 40


title: HCC patient 41


title: UE-0d-TE-1

description:
218-2
Gene expression in TE from 0d unexposed marmoset

value: Male

value: UE


title: Grade 2R ACR Rep2

description: Library name: B21_7

value: Serum


title: UE-60d-Area12-3

description:
216-7
Gene expression in Area12 from 60d unexposed marmoset

source_name: Area12 from 60d unexposed marmoset


title: F2

description: Library name: F2


title: UE-60d-TE-3

description:
216-6
Gene expression in TE from 60d unexposed marmoset

source_name: TE from 60d unexposed marmoset

value: Cortical TE


title: Grade 2R ACR Rep1

description: Library name: B21_6

value: Post-trasplant rejection


title: HCC patient 39


title: UE-60d-Area12-2

description:
216-3
Gene expression in Area12 from 60d unexposed marmoset

value: Cortical Area12


title: T3

description: Library name: T3

value: Tri-molting


title: Grade 1R ACR Rep16

description: Library name: B39_1

value: male


title: HCC patient 38

value: hepatocellular carcinoma tissue


title: T1

description: Library name: T1


title: T2

description: Library name: T2


title: Grade 1R ACR Rep15

description: Library name: B37_4


title: HCC patient 37

value: liver cancer


title: Grade 1R ACR Rep14

description: Library name: B35_4


title: HCC patient 36

value: liver


title: UE-180d-Area12-3

description:
216-23
Gene expression in Area12 from 180d unexposed marmoset

source_name: Area12 from 180d unexposed marmoset


title: UE-180d-TE-3

description:
216-22
Gene expression in TE from 180d unexposed marmoset

source_name: TE from 180d unexposed marmoset


title: TA3

description: Library name: TA3

value: Batch 1


title: UE-60d-TE-2

description:
216-2
Gene expression in TE from 60d unexposed marmoset


title: Grade 1R ACR Rep13

description: Library name: B33_3


title: HCC patient 35


title: UE-180d-Area12-2

description:
216-19
Gene expression in Area12 from 180d unexposed marmoset


title: TA2

description: Library name: TA2


title: Grade 1R ACR Rep12

description: Library name: B30_3


title: TA1

description: Library name: TA1


title: HCC patient 34


title: Grade 1R ACR Rep11

description: Library name: B28_3


title: HCC patient 33


title: UE-180d-TE-2

description:
216-18
Gene expression in TE from 180d unexposed marmoset


title: UE-90d-Area12-3

description:
216-15
Gene expression in Area12 from 90d unexposed marmoset

source_name: Area12 from 90d unexposed marmoset

value: Female


title: A3

description: Library name: A3

value: head and thoracic tissues


title: Grade 1R ACR Rep10

description: Library name: B27_6


title: A2

description: Library name: A2

value: Gurangri 3


title: Grade 1R ACR Rep9

description: Library name: B27_4


title: HCC patient 31


title: HCC patient 32


title: UE-90d-TE-3

description:
216-14
Gene expression in TE from 90d unexposed marmoset

source_name: TE from 90d unexposed marmoset


title: Grade 1R ACR Rep8

description: Library name: B27_3


title: A1

description: Library name: A1


title: HCC patient 30


title: UE-90d-Area12-2

description:
216-11
Gene expression in Area12 from 90d unexposed marmoset


title: HCC patient 29


title: scRNA-seq for wild type of the four mixed cell lines (HEK293, A549, 143B, WAL2A)

city: Philadelphia

first: Ting

last: Peng

state: PA

address: CTRB 6200

department: Pathology and Laboratory Medicine

institute: Children's hospital of Philadelphia

description:
Library name: WT
10X Genomics

data_processing:
scRNA-seq was analyzed by using scMOCHA; PacBio long-read DNA-seq data analysis: Reads were aligned with pbmm2 to the GRCh38 reference genome, in which the mitochondrial contig (chrM) was duplicated head-to-tail (33,138 bp) to accommodate mitochondrial genome circularity; mitochondrial positions were folded to canonical 16,569 bp rCRS coordinates. Reads with mapping quality (MAPQ)≥40 and PacBio predicted read quality (rq)≥0.998 were retained. Reads in the following categories were excluded: putative NUMT-derived reads identified from supplementary alignments (≥500 bp, MAPQ≥20), reads outside the expected long-range PCR amplicon boundaries (±100 bp from primer positions), and reads<10 kb. Variant AF was calculated as the number of reads carrying the variant allele divided by the total number of reads spanning that position. Homopolymer-associated indels were excluded based on the systematic error pattern characterized in a 2.5 kb mtDNA plasmid control, with position-level assessment against the control applied within the region it covered. Variants with AF≥5% were reported.
Assembly: GRCh38, rCRS
Supplementary files format and content: RDS, sc_azimuth.rds

source_name: mixture of 4 cell lines(HEK293, A549, 143B, WAL2A)

extract_protocol:
All cell lines were maintained at 37°C in a humidified incubator with 5% CO2. The human osteosarcoma thymidine kinase-deficient cell line 143B(TK−) (ATCC CRL-8303) and human embryonic kidney HEK293 cells were maintained in Dulbecco’s Modified Eagle Medium GlutaMAX (DMEM; Thermo Fisher Scientific, 10569044) containing high glucose (4.5 g/L) and sodium pyruvate (110 mg/L), supplemented with 1% non-essential amino acids (NEAA) and 10% fetal bovine serum (FBS). The human lung adenocarcinoma cell line A549 and the WAl2A WAL2A lymphoblastoid49 cell line were cultured in RPMI 1640 medium with ATCC modifications (Thermo Fisher Scientific, A1049101), supplemented with 1% NEAA and 10% FBS. Corresponding mitochondrial DNA-depleted (ρ⁰ or Rho0) derivatives were maintained in the same medium supplemented with 50 μg/mL uridine (Sigma-Aldrich, U3750-100G). Adherent cell lines were passaged at 70-95% confluence by washing with PBS (Thermo Fisher Scientific, 14190250) and dissociating with 0.25% trypsin-EDTA (Thermo Fisher Scientific, 25200114). Cells used for comparative experiments were harvested at the same passage number.
Single-cell RNA-seq Library Preparation
For the WT and Rho0 samples, an equal mixture of four cell lines (143B, WAL2A, HEK293, A549) was processed using the Chromium Single Cell 3′ Reagent Kit v3.1 (10x Genomics). Cell barcoding, reverse transcription, cDNA amplification, and 3′ gene expression library preparation were performed according to the manufacturer's protocol.
PacBio Library Preparation
Genomic DNA was extracted from cell pellets and quantified using the Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific, Q33231). Full-length mitochondrial genomes were amplified by long-range PCR using using PrimeSTAR GXL DNA Premix (Takara, R051B) with custom primers and reaction conditions as previously described50. PCR products were purified with SMRTbell Cleanup Beads (PacBio, 102-158-300), and assessed for fragment size distribution using the Femto Pulse system (Agilent, FP-1002-0275). PacBio libraries were prepared using the SMRTbell Prep Kit 3.0 (PacBio, 102-182-700) according to their standard protocol. Following adapter ligation and nuclease treatment, libraries were size-selected using AMPure PB beads (PacBio, 100-265-900). Libraries were annealed to sequencing primers using the Sequel II Binding Kit 3.2 (PacBio, 102-333-300), bound to Sequel II Polymerase 2.2, loaded onto SMRT Cell 8M (PacBio, 102-281-700).

value: osteosarcoma cell line, lung adenocarcinoma cell line,  embryonic kidney cell line, lymphoblastoid cell line


title: UE-90d-TE-2

description:
216-10
Gene expression in TE from 90d unexposed marmoset


title: Grade 1R ACR Rep7

description: Library name: B25_4

value: female


title: Grade 1R ACR Rep6

description: Library name: B24_4


title: Grade 1R ACR Rep5

description: Library name: B22_6


title: HCC patient 27


title: HCC patient 28


title: PPCM LV rep2

city: Torrance

first: Michelle

middle: L

last: Matter

state: CA

address: 1124 West Carson Street

department: Genomics

institute: The lundquist Institute

description:
Library name: PPCM Sample 2
PPCM_190682

data_processing:
Raw data contained reads of low quality, reads with adaptor sequence and reads with high level of N base. Those reads were filtered and cleaned by cutadapt (version 1.9) and paired end were produced. Bowtie2 was used to align clean reads to reference genes and HISAT was used to align clean reads to reference genome.
Assembly: Human:GCF_000001405.39_GRCh38.p13
Supplementary files format and content: csv files include FPKMs for all human data and csv files include TPMs for all mouse data

source_name: Human LV heart

extract_protocol:
Total RNA (human) was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure.
Human: RNA libraries for RNAseq were prepared with MGIEasy RNA library Prep Set (Proprietary for DNBSEQ platforms).

value: Human LV heart

value: Knockout


title: PPCM LV rep3

description:
Library name: PPCM Sample 3
PPCM_190716


title: UE-180d-Area12-1

description:
210-8
Gene expression in Area12 from 180d unexposed marmoset

value: UE


title: UE-180d-TE-1

description:
210-7
Gene expression in TE from 180d unexposed marmoset

value: Cortical TE


title: UE-90d-Area12-1

description:
210-4
Gene expression in Area12 from 90d unexposed marmoset

value: Male


title: Grade 1R ACR Rep4

description: Library name: B22_5

value: Serum

value: Post-trasplant rejection


title: HCC patient 26

source_name: hepatocellular carcinoma tissue


title: Donor LV rep1

description:
Library name: NORMAL Sample 1
NORMAL_1803

value: wildtype


title: Grade 1R ACR Rep3

description: Library name: B19_6

value: male


title: UE-90d-TE-1

description:
210-3
Gene expression in TE from 90d unexposed marmoset


title: 3% O2 wo Doxy replicate 3

city: Natori

first: Nobuhiro

last: Tanuma

address: 47-1 Noda-yama, Medeshima-shiode

institute: Miyagi Cancer Center Research Institute

description: Library name: D3

data_processing:
Raw reads were quality filtered to remove adaptor sequences and low-quality reads. Clean reads were aligned to the human reference genome (GRCh38) using STAR. Gene-level read counts were generated using featureCounts. Downstream normalization and differential expression analysis were performed using DESeq2. For samples A1 and A2, one of the paired-end FASTQ files (R1) was lost during data transfer; therefore only R2 FASTQ files are available in the repository.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file containing gene-level raw read counts generated by featureCounts. For samples A1 and A2, only R2 FASTQ files are available due to loss of the corresponding R1 files during data transfer.

extract_protocol:
Total RNAs were prepared from FDX2-iKO ES2 cells cultured 6 days with or without Doxy at 20% O2 using Maxwell RSC simplyRNA Kits (Promega). Alternatively, cells were cultured for an additional 3 days at 3% O2 after a 4-days of preculture at 20% O2.
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. 5'-ends of each library were phosphorylated and cyclized. Subsequently, loop amplification was performed to generate DNA nanoballs.


title: HCC patient 25

value: hepatocellular carcinoma tissue

value: liver cancer


title: Grade 1R ACR Rep2

description: Library name: B18_7


title: HCC patient 24

value: liver


title: UE-60d-Area12-1

description:
209-4
Gene expression in Area12 from 60d unexposed marmoset

value: Female

value: Cortical Area12


title: Grade 1R ACR Rep1

description: Library name: B18_6


title: 3% O2 wo Doxy replicate 2

description: Library name: D2


title: UE-60d-TE-1

description:
209-3
Gene expression in TE from 60d unexposed marmoset


title: HCC patient 23


title: 3% O2 wo Doxy replicate 1

description: Library name: D1


title: 3% O2 + Doxy replicate 3

description: Library name: C3


title: UE-adult-Area12-3

description:
205-3
Gene expression in Area12 from adult unexposed marmoset

source_name: Area12 from adult unexposed marmoset


title: HCC patient 22


title: Grade 0R ACR Rep12

description: Library name: B29_3

value: No post-trasplant rejection


title: Grade 0R ACR Rep11

description: Library name: B22_7


title: UE-adult-TE-3

description:
205-2
Gene expression in TE from adult unexposed marmoset

source_name: TE from adult unexposed marmoset


title: HCC patient 21


title: 3% O2 + Doxy replicate 2

description: Library name: C2


title: UE-adult-Area12-2

description:
201-6
Gene expression in Area12 from adult unexposed marmoset


title: Grade 0R ACR Rep10

description: Library name: B38_1


title: HCC patient 20


title: Donor LV rep2

description:
Library name: NORMAL Sample 2
NORMAL_367


title: HCC patient 19


title: 3% O2 + Doxy replicate 1

description: Library name: C1


title: Grade 0R ACR Rep9

description: Library name: B36_1


title: UE-adult-TE-2

description:
201-4
Gene expression in TE from adult unexposed marmoset


title: Grade 0R ACR Rep8

description: Library name: B30_4


title: HCC patient 18


title: 20% O2 wo Doxy replicate 3

description: Library name: B3


title: UE-adult-Area12-1

description:
200-6
Gene expression in Area12 from adult unexposed marmoset


title: 20% O2 wo Doxy replicate 2

description: Library name: B2


title: Grade 0R ACR Rep7

description: Library name: B29_4


title: HCC patient 17


title: UE-adult-TE-1

description:
200-4
Gene expression in TE from adult unexposed marmoset


title: 20% O2 + Doxy replicate 3

description: Library name: A3


title: Grade 0R ACR Rep5

description: Library name: B23_4


title: HCC patient 16


title: HCC patient 15


title: 20% O2 wo Doxy replicate 1

description: Library name: B1


title: Grade 0R ACR Rep6

description: Library name: B23_5


title: Embryos treated with DMSO vehicle Replicate 2

city: Lexington

first: Jeramiah

middle: James

last: Smith

state: KY

address: 101 Morgan Building

department: Biology

institute: University of Kentucky

description: Library name: DMSO_2

data_processing:
RNA-seq reads were aligned to the reference genome using HISAT2 v2.2.1 (Kim et al. 2019).
Gene expression estimates were obtained from these alignments using StringTie v2.2.3 (Pertea et al. 2015)
Assembly: GCA_040938575.1
Supplementary files format and content: Gene Count matrix from StringTie V2.2.3 in .csv format

organism: Ambystoma mexicanum

source_name: St42 embryo

extract_protocol:
RNA was isolated using TRIzol (Invitrogen) and syringe needles for initial tissue disruption, and then following instructions included with a Monarch Total RNA Isolation Kit (NEB).
RNA samples were submitted to a commercial vendor (Novogene) to generate approximately 25-30 million raw reads per sample on an Illumina sequencer.

value: St42 embryo

value: DMSO vehicle


title: Embryos treated with A-485 Replicate 3

description: Library name: A485_3


title: HCC patient 14


title: 20% O2 + Doxy replicate 2

description: Library name: A2


title: Grade 0R ACR Rep4

description: Library name: B21_5


title: 20% O2 + Doxy replicate 1

description: Library name: A1


title: Grade 0R ACR Rep3

description: Library name: B20_6


title: HCC patient 13


title: Embryos treated with A-485 Replicate 2

description: Library name: A485_2


title: Grade 0R ACR Rep2

description: Library name: B19_7


title: HCC patient 12


title: CAGE TSS mapping - green/symbiotic H. viridissima clone 2

city: Baltimore

first: Alex

last: Bortvin

state: MD

address: 3520 San Martin Dr

department: Embryology

institute: Carnegie Institution

description:
Library name: CAGE_Green
CAGE (Cap Analysis of Gene Expression), green/symbiotic

data_processing:
Trimmed with fastp 1.1.0 (adapter removal, quality filtering).
Aligned to Carnegie v1 with STAR 2.7.11b (2-pass mode).
CTSS extracted from 5' end of uniquely mapped R1 reads.
TSS clusters called by merging CTSS within 20 bp (min 5 supporting reads).
Strand-specific BigWig tracks generated with bedGraphToBigWig (UCSC kent utils 482).
Assembly: Carnegie v1 (JBWVZK010000000), 111 scaffolds, 315.1 Mb
Supplementary files format and content: CTSS BED: chrom, start, end, name, score (tag count), strand. One row per CAGE transcription start site.
Supplementary files format and content: TSS cluster BED: merged clusters with min 5 reads. Columns: chrom, start, end, cluster_id, total_tags, strand.
Supplementary files format and content: BigWig: combined (both strands) signal tracks of CAGE tag density.

organism: Hydra viridissima

source_name: whole organism

growth_protocol: Hydra viridissima clone 2 cultured at room temperature (+24C) in hydra medium, fed freshly hatched brine shrimp 3-4 times per week. Large polyps harvested 2-3 days after last feeding.

extract_protocol:
Total RNA extracted from ~200 large animals using TRIzol LS. After phase separation, aqueous phase purified with Direct-zol RNA miniprep kit (Zymo Research). DNase-treated (Baseline Zero DNase I), then cleaned with Monarch RNA Cleanup Kit (NEB). RIN = 10.
Custom CAGE protocol: RNA dephosphorylation and 3' terminus blocking with inverted T, Decapping enzyme (NEB) treatment, ligation of 5'-Biotin-ApG (Jena Bioscience) to 5' end of decapped RNA. Reverse transcription with random primers, RNase If (NEB) treatment, capture of biotinylated RNA/cDNA hybrids with magnetic Streptavidin beads (NEB), release of cDNA by alkali treatment. Adapter ligation and library amplification used reagents from Zymo-Seq RiboFree Total RNA library kit (Sections 3 and 4). R2 reads contain extra 0-3 nt + [AG] signature for 5'-capped RNA filtering.

value: whole organism

tag: strain

value: green/symbiotic clone 2

tag: condition

value: green/symbiotic


title: Embryos treated with A-485 Replicate 1

description: Library name: A485_1

tag: tissue


title: CAGE TSS mapping - aposymbiotic H. viridissima clone 2

description:
Library name: CAGE_Apo2
CAGE (Cap Analysis of Gene Expression), aposymbiotic

value: aposymbiotic clone 2

value: aposymbiotic


title: Grade 0R ACR Rep1

description: Library name: B17_8

source_name: Serum

value: Serum


title: Ovis aries, plasma, OBESE, week 14, replicate 3

city: Krakow

first: Tomasz

last: Szmatoła

state: Małopolskie

address: Mickiewicza 21

department: OMEI

institute: University of Agriculture in Krakow

description:
Library name: OBESE_C3
Sequencing internal ID: 31621-018

data_processing:
Raw reads (76 nt single-end, AVITI) were demultiplexed by the sequencing provider; UMI barcodes (12 nt) and 3' Illumina P7 adapter were removed using cutadapt v4.9, retaining inserts ≥17 nt.
UMI-aware deduplication was performed by collapsing reads with identical (sequence, UMI) pairs.
Trimmed reads were aligned to extended ovine miRNA hairpin sequences (miRBase v22, Ovis aries) using bowtie v1.3.1; per-miRNA counts (raw and normalized) were obtained with a custom Python counter handling multi-mappers with fractional counting.
Novel miRNA candidate discovery was performed using miRDeep2 v0.1.3 against the Ovis aries reference genome ARS-UI_Ramb_v3.0 (Ensembl).
Differential expression analysis was performed in R using DESeq2 v1.42 with a paired design accounting for repeated measures within individuals (~ group + group:individual + timepoint + group:timepoint).
Assembly: Ovis aries ARS-UI_Ramb_v3.0 (Ensembl release 113); miRBase release 22.1
Supplementary files format and content: GEO_raw_counts_matrix.tsv: tab-delimited matrix of raw read counts per miRNA (rows) per sample (columns); 364 miRNAs (known + novel) x 18 samples.
Supplementary files format and content: Per-sample raw count files (31621-001_counts.tsv to 31621-018_counts.tsv): tab-delimited two-column files (miRNA, count) for each individual sample.

organism: Ovis aries

source_name: plasma

growth_protocol: Twelve Polish Longwool ewes (ovariectomized, with estradiol implants) were housed under standard conditions and randomly assigned to CTRL (n=6, standard diet) or OBESE (n=6, high-fat diet) groups.

extract_protocol:
Total RNA including small RNA was extracted from 200 µL plasma using the QIAseq miRNA Library Kit (QIAGEN). RNA quality and quantity were assessed by Qubit fluorometry and TapeStation analysis.
Small RNA libraries were prepared using QIAseq miRNA Library Kit (QIAGEN) with UMI-based deduplication. Libraries were sequenced on the AVITI platform (Element Biosciences) using 1x76 single-end reads.

treatment_protocol: OBESE animals received a high-fat diet for 14 weeks. Blood samples were collected at week 7 (T1), week 10 (T2) and week 14 (T3). Plasma was isolated by centrifugation and stored at -80°C until use.

tag: animal breed

value: Polish Longwool

value: plasma

tag: group

value: OBESE

tag: timepoint

value: week 14

value: female

value: high-fat diet


title: ATAC-seq - green/symbiotic H. viridissima clone 2, rep 2

description:
Library name: ATAC_Green_R2
ATAC-seq, green/symbiotic, biological replicate 2

library_source: genomic

data_processing:
Trimmed with Trim Galore 0.6.10 (Nextera adapter sequences).
Aligned to Carnegie v1 with Bowtie2 2.5.4 (--very-sensitive --no-mixed --no-discordant -X 2000).
Filtered MAPQ >= 30 and deduplicated with sambamba 1.0.1 markdup.
Tn5-shifted with deepTools alignmentSieve (--ATACshift).
Peaks called with MACS3 3.0.4 (narrow: -q 0.05 --nomodel --shift -75 --extsize 150; effective genome size 232 Mb).
Assembly: Carnegie v1 (JBWVZK010000000), 111 scaffolds, 315.1 Mb
Supplementary files format and content: narrowPeak: ENCODE narrowPeak format (BED6+4): chrom, start, end, name, score, strand, signalValue, pValue, qValue, peak.
Supplementary files format and content: BigWig: RPGC-normalized (reads per genomic content) signal tracks.

growth_protocol: Hydra viridissima clone 2 cultured at room temperature (+24C) in hydra medium, fed freshly hatched brine shrimp 3-4 times per week. 50 large animals (without buds/gonads, last fed 2 days prior) maintained in filter-sterilized HM with Pen/Strep.

extract_protocol:
Animals washed in cold filter-sterilized Hydra dissociation medium (HDM), dissociated with disposable blue pestle (~60-70 rotations) in 400 ul HDM, brief spin, upper phase cells collected (~0.3-0.5M cells per reaction).
Zymo-Seq ATAC Library kit with modifications: doubled lysis/nuclear isolation reagent volumes (5-10x more cells than standard protocol, justified by hydra genome size). Tn5 transposase enzyme and buffer from Zymo kit.

tag: replicate


title: HCC patient 11

value: hepatocellular carcinoma tissue

value: liver cancer

tag: cell type

value: liver


title: ARP-1 cells, Carfilzomib Resistance, Replicate_2

city: houston

first: chuanchao

last: zhang

address: 6550 fanin st

institute: houston methodist

description: Library name: ARP1-Carfilzomib Resistance-Replicate-2

data_processing:
After adapter trimming and removal of low-quality reads, the clean data were aligned to the reference genome using STAR. Gene expression levels (FPKM) and differential gene expression were calculated using the Cufflinks package.
Assembly: MG38
Supplementary files format and content: including gene expression levels (FPKM) in each sample

extract_protocol:
RNA was extracted using the TRIzol method, and 1 μg of total RNA was used as the starting material for library preparation.
RNA-seq libraries were prepared using a standard mRNA-seq protocol with the RNA Library Prep Kit , following the manufacturer’s instructions.

value: Multiple myeloma cancer cell


title: Ovis aries, plasma, OBESE, week 14, replicate 2

description:
Library name: OBESE_C2
Sequencing internal ID: 31621-017


title: HCC patient 10


title: ATAC-seq - aposymbiotic H. viridissima clone 2, rep 2

description:
Library name: ATAC_Apo2_R2
ATAC-seq, aposymbiotic, biological replicate 2


title: HCC patient 9


title: Ovis aries, plasma, OBESE, week 14, replicate 1

description:
Library name: OBESE_C1
Sequencing internal ID: 31621-016


title: ARP-1 cells, Carfilzomib Resistance, Replicate_1

description: Library name: ARP1-Carfilzomib Resistance-Replicate-1


title: ARP-1 cells，WT，Replicate_2

description: Library name: ARP1-WT-Replicate-2


title: ATAC-seq - green/symbiotic H. viridissima clone 2, rep 1

description:
Library name: ATAC_Green_R1
ATAC-seq, green/symbiotic, biological replicate 1


title: HCC patient 8


title: Ovis aries, plasma, CTRL, week 14, replicate 3

description:
Library name: CTRL_C3
Sequencing internal ID: 31621-015

value: CTRL

value: control diet


title: ATAC-seq - aposymbiotic H. viridissima clone 2, rep 1

description:
Library name: ATAC_Apo2_R1
ATAC-seq, aposymbiotic, biological replicate 1

value: whole organism


title: ARP-1 cells，WT，Replicate_1

description: Library name: ARP1-WT-Replicate-1


title: HCC patient 7


title: Ovis aries, plasma, CTRL, week 14, replicate 2

description:
Library name: CTRL_C2
Sequencing internal ID: 31621-014


title: Total RNA-seq - green/symbiotic H. viridissima clone 2

description:
Library name: TotalRNA_Green
Total RNA-seq, green/symbiotic, Zymo-Seq RiboFree library

data_processing:
Trimmed with fastp 1.1.0 (default adapter detection, quality filtering Q15, minimum length 36 bp).
Aligned to Carnegie v1 with STAR 2.7.11b (2-pass mode). Genome index built with --sjdbGTFfile BRAKER3 conservative GTF, --sjdbOverhang 149.
Gene-level counts with featureCounts (subread 2.1.1) using BRAKER3 conservative GTF (-p --countReadPairs -t exon -g gene_id).
BigWig tracks with deepTools bamCoverage 3.5.6 (CPM and RPKM normalizations).
Assembly: Carnegie v1 (JBWVZK010000000), 111 scaffolds, 315.1 Mb
Supplementary files format and content: gene_counts.tsv: tab-delimited gene-level raw read counts matrix, rows = genes, columns = samples.
Supplementary files format and content: BigWig files: CPM (.cpm.bw) and RPKM (.rpkm.bw) normalized signal tracks.

extract_protocol:
Total RNA extracted from ~200 large animals using TRIzol LS. After phase separation, aqueous phase purified with Direct-zol RNA miniprep kit (Zymo Research). DNase-treated (Baseline Zero DNase I), then cleaned with Monarch RNA Cleanup Kit (NEB). RIN = 10.
Zymo-Seq RiboFree Total RNA Library kit with enzymatic rRNA depletion (Section 2 of kit protocol).

value: green/symbiotic clone 2

value: green/symbiotic


title: B6

city: Shenzhen

first: Wen

middle: Ting

last: Li

address: No,1120,LianHua Road,FuTian District

institute: Shenzhen PKU-HKUST Medical Center

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5). We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: hg38
Supplementary files format and content: gene_counts.txt
Supplementary files format and content: gene_fpkm.txt

source_name: HaCaT

growth_protocol: HaCat cells were cultured in DMEM (Gibco, Carlsbad, CA) supplemented with 10% fetal bovine serum (Gibco), 100 U/mL penicillin and 100 µg/mL streptomycin (Gibco). Cells were incubated at 37 °C in a humidified condition supplemented with 5% CO2.

extract_protocol:
Total RNA was extracted from si-PAXBP1/si-CTL transfected HaCaT cells using TRIzol reagent. Purified RNA was quantified using a NanoDrop 2000 (Thermo Scientific) and the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).CA, USA).
RNA libraries were prepared for sequencing using standard illumina protocols

treatment_protocol: HaCaT cells were cultured to 70% confluent and then transfected with PAXBP1 siRNAs and controls using Lipofectamine™ RNAiMAX Transfection Reagent (#13778150, Thermo Scientific) according to the manufacturer’s instruction.

value: HaCaT

value: Keratinocyte

tag: genotype

value: PAXBP1 knockdown


title: HCC patient 6

data_processing:
data was analyzed with The BaseSpace® TruSeq® Targeted RNA v1.0.1 app
Assembly: hg19
Supplementary files format and content: tab-delimited text file include normalized counts value for each Sample
Supplementary files format and content: tab-delimited text file include raw counts value for each Sample

extract_protocol:
Genomic DNA and RNA were extracted from 5 μm FFPE tissue sections using the AllPrep DNA/RNA FFPE kit (Qiagen, Valencia, CA, USA). The concentration and integrity of purified DNA/RNA samples were assessed by Qubit fluorometer (Thermo Fisher Scientific, Hampton, NH, USA) and 2200 TapeStatio (Agilent Technologies, Santa Clara, CA, USA), respectively.
RNA-Sequencing library were prepared using AmpliSeq for Illumina RNA WNT panel (the panel include 169 genes involved in the regulation of WNT signaling pathway) by following the manufacturer’s. Pooled sequencing libraries were sequencing in 150-bp paired-end reads on Illumina MiSeq sequencer (Illumina).


title: Ovis aries, plasma, CTRL, week 14, replicate 1

description:
Library name: CTRL_C1
Sequencing internal ID: 31621-013

value: Polish Longwool

value: plasma


title: B5


title: Total RNA-seq - aposymbiotic H. viridissima clone 2

description:
Library name: TotalRNA_Apo2
Total RNA-seq, aposymbiotic, Zymo-Seq RiboFree library

value: aposymbiotic clone 2

value: aposymbiotic


title: HCC patient 5


title: Zhongpu No. 18 ovule,day 61 rep2

city: Zhengzhou

first: Yongzhou

address: No. 28, Gangwan Road, Guancheng District

institute: Chinese Academy of Agricultural Sciences Zhengzhou Fruit Research Institute

description:
Library name: SAMPLE 16
ZP61-2

data_processing:
sequence reads were obtained by filtering out reads containing adapters, poly-N sequences, and low-quality reads. Transcriptome analysis involved mapping the clean reads to a reference genome (https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_030704535.1/)
Gene expression levels were calculated by fragments per kilobase of transcript per million mapped reads (FPKM) values
Assembly: genome assemblies:69
Supplementary files format and content: Excel file includes FPKM values for each saple

organism: Vitis vinifera

source_name: grape  ovule

extract_protocol:
Store to -80 °C with skin retained.RNA extraction and subsequent sequencing were done by metware Biology (Wuhan, China).
RNA library were prepared for sequence using stabdard  illumina nova seq X plus protocol

value: grape  ovule

tag: variety

value: Zhongpu No. 18

tag: time

value: day 61


title: Ovis aries, plasma, OBESE, week 10, replicate 3

description:
Library name: OBESE_B3
Sequencing internal ID: 31621-012

value: OBESE

value: week 10

tag: Sex

value: female

value: high-fat diet


title: B4

tag: cell line


title: HCC patient 4

city: Rome

institute: IRCCS Regina Elena National Cancer Institute

value: hepatocellular carcinoma tissue

value: liver cancer

value: liver


title: Zhongpu No. 18 ovule,day 61 rep1

description:
Library name: SAMPLE 15
ZP61-1


title: HCC patient 3


title: A3

value: HaCaT

value: CTL


title: Zhongpu No. 18 ovule,day 55 rep2

description:
Library name: SAMPLE 14
ZP55-2

value: day 55


title: Ovis aries, plasma, OBESE, week 10, replicate 1

description:
Library name: OBESE_B1
Sequencing internal ID: 31621-010

value: Polish Longwool


title: Ovis aries, plasma, OBESE, week 10, replicate 2

description:
Library name: OBESE_B2
Sequencing internal ID: 31621-011

value: plasma


title: A2

value: Keratinocyte


title: Ovis aries, plasma, CTRL, week 10, replicate 3

description:
Library name: CTRL_B3
Sequencing internal ID: 31621-009

value: CTRL

value: control diet


title: Zhongpu No. 18 ovule,day 55 rep1

description:
Library name: SAMPLE 13
ZP55-1

value: grape  ovule

value: Zhongpu No. 18


title: HCC patient 2


title: A1


title: Ovis aries, plasma, CTRL, week 10, replicate 2

description:
Library name: CTRL_B2
Sequencing internal ID: 31621-008


title: HCC patient 1


title: Zhongpu No. 18 ovule,day 45 rep2

description:
Library name: SAMPLE 12
ZP45-2

value: day 45


title: Ovis aries, plasma, CTRL, week 10, replicate 1

description:
Library name: CTRL_B1
Sequencing internal ID: 31621-007

value: week 10


title: MCF10DCIS_rep2

city: Burlington

first: Seth

last: Frietze

state: VT

address: 149 Beaumont Avenue

department: Biomedical and Health Sciences

institute: University of Vermont

data_processing:
RNA-seq reads were aligned to the hg38 genome using STAR version v2.7.9a using  default parameters.
Raw RNA-seq count data were processed and normalized using edgeR to generate a table of Transcripts Per Million (TPM) values.
Assembly: hg38
Supplementary files format and content: tab-delimited text file including TPM values for each sample

growth_protocol: Cells were grown in DMEM: F12 with 5%  horse serum supplmented with 10mg/ml human insulin + 20ng/ml recombinant hEGF + 100 ng/ml cholera toxin + 0.5 mg/ml hydrocortisone + penicillin/streptomycin and 2 mM glutamine. Cells were cultured at 37C at 5% CO2.

extract_protocol:
RNA was harvested using Directzol  kit (Zymo). 1ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEB Ultra2 stranded RNA-seq library Prep Kit following manufacturer's protocols.
Stranded RNA-seq libraries

value: cell line


title: MCF10DCIS_rep3


title: Zhongpu No. 18 ovule,day 45 rep1

description:
Library name: SAMPLE 11
ZP45-1


title: Ovis aries, plasma, OBESE, week 7, replicate 3

description:
Library name: OBESE_A3
Sequencing internal ID: 31621-006

value: OBESE

value: week 7

value: female

value: high-fat diet


title: Zhongpu No. 18 ovule,day 35 rep2

description:
Library name: SAMPLE 10
ZP35-2

value: day 35


title: HL60-DIMATE-004

city: Lyon

first: Céline

last: BAIER

address: 655 Allée des Parcs

institute: Advanced Biodesign

description: Gene expression after 6hr DIMATE

hyb_protocol: SurePrint G3 human GE 8x60K V2 chips

scan_protocol: Microarrays were  scanned through standard Agilent protocol

data_processing: Data were processed using Feature Extraction software. A multiple test correction was performed a false discovery rate (FDR) of 5% and a fold change of 1,5 were fixed

label_protocol: One hundred nanogram of total RNA was labelled using One-Color Microarray-Based Gene Expression Analysis: Low Input Quick Amp (LIQA) labelling protocol

growth_protocol: HL60 grew in 6well plates

extract_protocol: RNA was extracted with Qiagen Protocol, RNeasy Mini kit (Qiagen, France)

treatment_protocol: DIMATE 10µM during 6h

value: DIMATE


title: HL60-DIMATE-003

description: Gene expression after 6hr DIMATE


title: MCF10DCIS_rep1


title: Ovis aries, plasma, OBESE, week 7, replicate 2

description:
Library name: OBESE_A2
Sequencing internal ID: 31621-005


title: Zhongpu No. 18 ovule,day 35 rep1

description:
Library name: SAMPLE 9
ZP35-1


title: MCF10CA1a_rep3


title: Muscat Hamburg ovule,day 61 rep2

description:
Library name: SAMPLE 8
MH61-2

value: Muscat Hamburg

value: day 61


title: Ovis aries, plasma, OBESE, week 7, replicate 1

description:
Library name: OBESE_A1
Sequencing internal ID: 31621-004

value: Polish Longwool

value: plasma