title: EMD, not treated with CAR T cells, with custom probes

city: Cologne

first: Till

last: Braun

address: Kerpener Strasse 62

department: Clinic I for Internal Medicine

country: Germany

institute: University Hospital of Cologne

description:
Library name: H21088-21_Sonden_SpikeIn
Visium spatial gene expression workflow for FFPE (10x Genomics)

data_processing:
Space Ranger count pipeline applied with the custom reference and custom probe set to quantify spatial feature counts
Space Ranger output processed using the R package Semla
Raw gene expression data normalized in logarithmic space with a pseudocount of 1
Assembly: Custom reference created by adding CAR nucleotide sequence (patent WO2022116086A1) to the human reference genome (GRCh38, Ensembl release 98) and GENCODE v32 annotation using the mkref function from Space Ranger v3.0.1
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: filtered_feature_bc_matrix.h5: Contains only detected cell-associated barcodes in MEX format. Each element of the matrix is the number of UMIs associated with a feature (row) and a barcode (column), as described in the feature-barcode matrix page in HDF5 format.
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: raw_feature_bc_matrix.h5: Contains all detected barcodes in MEX format. Each element of the matrix is the number of UMIs associated with a feature (row) and a barcode (column), as described in the feature-barcode matrix page in HDF5 format.
Supplementary files format and content: scalefactors_json.json: scalefactors in JSON format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions.csv: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

source_name: extramedullary disease (lumbar vertebral body)

extract_protocol:
Sample placed on Visium Spatial Gene Expression Slides
Three custom probe sets were added to the Visium Human Transcriptome Probe Set v1 during probe hybridization according to the specifications of 10x Genomics

value: no CAR T cell


title: pDC from WT mice, biological rep 1

status: Public on Jan 05 2025

type: RNA

city: La Jolla

first: Trever

last: Greene

state: CA

address: 9500 Gilman Dr,

country: USA

institute: University of California San Diego

hyb_protocol: Affymetrix GeneChip WT Terminal Labeling and Hybridization Manual

scan_protocol: Array scanning was performed according to manufacturer (Affymetrix) instructions

data_processing: Bioconductor Oligo package (Carvalho & Irizarry et al 2010) was used for preprocessing data (RMA normalization). Expression sets were then filtered using genefilter (Gentleman et al 2018) to exclude values with low expression or variance, as well as probes that did not correspond to an ENTREZ entry.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: pDC

label_protocol: Extracted RNA was labeled and hybridized to Affymetrix Mouse Transcriptome Array 1.0 (MTA-1.0; one array per subject) according to the manufacturer’s instructions. WT cDNA Synthesis and Amplification kit and WT Sense Target Labelling and Control Reagents (Affymetrix) were used

extract_protocol: Qiagen Rneasy Micro Kit

treatment_protocol: Mixed bone marrow chimeras were infected with LCMV Cl13, and WT or TLR7ko pDC were isolated from the spleens of these mice at day 8 post infection prior to RNA extraction.

tag: tissue

value: spleen


title: Fresh sorted gd T cells from Donor 938 PBMC

type: SRA

city: Blainville

first: Adam-Nicolas

last: Pelletier

state: Quebec

address: 97, Montcalm

country: Canada

institute: RPM Bioinfo Solutions

description: Library name: gd-R200-938

library_source: transcriptomic

data_processing:
FASTQ files were trimmed for sequencing adapters and low-quality 30 bases using Trimmomatic version 0.38 and aligned to the reference human genome version GRCh38 (from Ensembl build 106) using STAR version 2.7.6a.
Aligned reads were deduplicated using UMI-Tools version 1.01.
HTSeq version 0.12.3 was used to estimate transcript abundance from unique mapped reads
Raw reads were normalized using DESeq2 v1.26.0
Assembly: GRCh38
Supplementary files format and content: raw counts
Supplementary files format and content: normalized counts

molecule: polyA RNA

organism: Homo sapiens

source_name: PBMC

growth_protocol: Isolated PBMCs from three healthy donors were stained with antibodies against the following markers: CD4, CD8a, CD56, TCRab, and TCRgd (all from BioLegend). Cell populations were sorted using an Aria III cytometer (BD Biosciences) as follows: CD4+ T cells (CD56-TCRab+TCRgd-CD4+CD8a-), CD8+ T cells (CD56-TCRab+TCRgd-CD4-CD8a+), TCRgd cells (CD56-TCRab-TCRgd+), and DN T cells (CD56-TCRab+TCRgd-CD4-CD8a-). Cells were stained in PBS containing 2% fetal bovine serum (FBS) (Thermo Fisher Scientific) and 1mMEDTA. A total of 10^5 cells were resuspended immediately in TRIzol (Thermo Fisher Scientific) and are referred to as ex vivo samples. The remaining sorted cells were resuspended in ImmunoCult-XF T cell expansion medium (STEMCELL Technologies) (0.5x10^6 cells/mL) with 1% penicillin-streptomycin (50 U/mL–50 mg/mL) (Wisent) and added to plates coated with anti-CD3 (1 mg/mL) and anti-CD28 (5 mg/mL) antibodies (both BioLegend). After 24 h, the following human cytokines were added: IL-1b (560 U/mL), IL-2 (30 U/mL), IL-7 (200 U/mL), and IL-15 (125 U/mL) (from Miltenyi Biotec). Cells were cultured for 14 days, with fresh medium containing cytokines being added every 2–3 days. At the end of the culture, cells were washed twice with PBS, resuspended at 5x10^5 cells/mL in TRIzol (Thermo Fisher Scientific) and stored at -80°C prior to sequencing.

extract_protocol:
RNA was extracted from samples in TRIzol using chloroform separation and precipitation with isopropanol 100%. Following washes with ethanol 75%, the RNA was diluted in RNAse-free water. DNAse and EDTA were added.
Libraries were prepared using the KAPA RNA HyperPrep PolyA Single-End Read Kit.

value: PBMC

tag: cell type

value: gd T cells

tag: donor

tag: condition

value: Ex vivo

tag: culture status

value: Fresh


title: Skin, treated with CAR T cells, with custom probes

description:
Library name: C24_13076_Sonden_SpikeIn
Visium spatial gene expression workflow for FFPE (10x Genomics)

source_name: FFPE skin sample of left dorsal region

value: FFPE skin sample of left dorsal region

tag: treatment

value: CAR T cell (cilta-cel)


title: Culture sorted gd T cells from Donor 924 PBMC

description: Library name: gd-R200-924-C

value: Activated in vitro with anti-CD3 (1mg/mL) and anti-CD28 (5mg/mL). After 24 hours, IL-1B (560 U/mL) , IL-2 (30U/mL), IL-7 (200U/mL) and IL-15 (125U/mL) were added every 2-3 days for 14 days.

value: Culture


title: siControl H3K4me3 Replicate 3

city: Boston

first: Tovah

middle: A.

last: Day

state: MA

address: 330 Huntington Avenue, Northeastern University Mugar Life Science Building, Room 134

department: Biology

institute: Northeastern University

description:
Library name: siControl H3K4me3 Replicate 3
Peaks present in at least two replicates are included in the high quality peak file. Bedtools intersect was used with the biggest peak file as -a option.

library_source: genomic

data_processing:
FASTQ reads were aligned to the hg19 and the dm6 reference genomes (downloaded from the UCSC database) using Bowtie2 (v.2.4.5), the mosaic adapter sequences were trimmed during this step using the -5 19 parameters.
The SAM files were deduplicated using Picard MarkDuplicates (v.2.27.4) followed by conversion to BAM format using samtools (v.1.15.1) and blacklist removal from the BAM files with bedtools intersect (v.2.30.0) using the ENCODE blacklist bed file for hg19.
Peaks were called using MACS2 (v.2.1.4) and high quality peaks were identified as peaks present in two or more replicates generated with bedtools intersect.
Assembly: hg19 and dm6
Supplementary files format and content: narrowPeak files (containing the high quality peaks as defined above)
Library strategy: CUT&Tag

molecule: genomic DNA

source_name: lung

growth_protocol: A549 cells (ATCC, CCL-185) were cultured in DMEM (Corning, 10-013-CV) supplemented with 10% fetal bovine serum (FBS; Gibco, 10437028), 100 U/mL penicillin and 100 μg/mL streptomycin (Gibco, 15140163). All cells were cultured in a humidified incubator with  5% CO2 at 37°C.

extract_protocol:
Briefly, 5 x 105 (G4 CUT&Tag) or 1 x 106 (HA CUT&Tag) cells were harvested per condition, washed with PBS and resuspended in NP40-digitonin buffer (20 mM HEPES, pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 0.05% digitonin, 0.01% NP40 and Roche cOmplete Protease Inhibitor EDTA-free). The cells were then centrifuged at 600 x g for 3 min, resuspended in 200 mL antibody buffer (NP40-digitonin buffer with 1% BSA, for the BG4 step only, 2 mM EDTA is added) containing 2 mg of BG4 (purified from E. coli), anti-H3K4me3 Ab (G4 CUT&Tag: EDM Millipore, MC315; HA CUT&Tag: EpiCypher, 13-0060) or anti-HA Ab (EpiCypher, 13-2010) and 35 ng Drosophila Spike-in Chromatin (Active Motif, 53083) and incubated overnight at 4°C. Nuclei were washed once with NP40-digitonin buffer followed by centrifugation at 600 x g for 4 min, whereafter the nuclei were resuspended in 200 mL antibody buffer containing 1:50 anti-Flag Ab (Sigma-Aldrich, F1804-200UG) for the BG4 samples or 2 ug anti-Rabbit Ab (G4 CUT&Tag: Antibodies Online, ABIN101961; HA CUT&Tag: EpiCypher, 13-0047) and incubated for 1 hr at room temperature with end-over-end rotation. For the BG4 samples an additional antibody incubation followed three washes by resuspending the nuclei in 200 mL antibody buffer with 1:50 anti-mouse Ab (Sigma-Aldrich, M7023) and incubating for 1 hr at room temperature. The nuclei were then washed three times and resuspended in 200 mL dig-300 wash buffer (20 mM HEPES, pH 7.5, 300 mM NaCl, 0.5 mM Spermidine, 0.01% digitonin, 0.01% NP40 and Roche cOmplete Protease Inhibitor EDTA-free) with 2.5 μL pA-Tn5 (EpiCypher, 15-1017) and incubated at room. After three washes with dig-300 wash buffer with centrifugation at 300 x g for 6 min, the nuclei were resuspended in 200 mL tagmentation buffer (dig-300 wash buffer containing 10 mM MgCl2) and incubated at 37°C for 1 hr. The reaction was then stopped by adding 6.7 mL of 0.5 M EDTA, 2 mL of 10% SDS and 5 mL of 20 mg/mL proteinase K and incubating at 63°C for 1 hr. Genomic DNA was purified using a DNA Clean & Concentrator-5 kit (Zymo Research, D4014), eluted in 20 mL, and RNA was digested by adding 1 mL RNase cocktail (Fisher Scientific, AM2288) with incubation for 20 min at 37°C.
For the library prep, 2 uL of 10 uM uniquely barcoded universal i5 and i7 primers as well as 25 uL NEBNext Ultra II Q5 2x PCR Master mix (NEB, M0544L) were added to the 21 uL DNA and a short PCR was performed (72°C for 5 min, 98°C for 30 sec, 13 x (98°C for 10 sec, 63°C for 30 sec), 72°C for 1 min). The library PCR products were cleaned up with Agencourt AMPure XP beads (Beckman Coulter, A63881)

treatment_protocol: A549 cells were transfected with 71 nM siRNA using lipofectamine 3,000 transfection reagent (Fisher Scientific, L3000015) for 48 hours.

value: lung

tag: cell line

value: epithelial cell

value: siControl

tag: antibody


title: Fresh sorted gd T cells from Donor 924 PBMC

description: Library name: gd-R200-924


title: siControl H3K4me3 Replicate 4

description:
Library name: siControl H3K4me3 Replicate 4
Peaks present in at least two replicates are included in the high quality peak file. Bedtools intersect was used with the biggest peak file as -a option.


title: siControl H3K4me3 Replicate 1

description:
Library name: siControl H3K4me3 Replicate 1
Peaks present in at least two replicates are included in the high quality peak file. Bedtools intersect was used with the biggest peak file as -a option.


title: Culture sorted DN T cells from Donor 938 PBMC

description: Library name: DNT-R200-938-C

value: DN T cells


title: Fresh sorted DN T cells from Donor 938 PBMC

description: Library name: DNT-R200-938


title: Culture sorted gd T cells from Donor 937 PBMC

description: Library name: gd-R200-937-C


title: Fresh sorted gd T cells from Donor 937 PBMC

description: Library name: gd-R200-937


title: Culture sorted DN T cells from Donor 924 PBMC

description: Library name: DNT-R200-924-C


title: siBAZ2B Replicate 3

description:
Library name: siBAZ2B BG4 Replicate 3
Peaks present in at least two replicates are included in the high quality peak file. Bedtools intersect was used with the biggest peak file as -a option.


title: siControl H3K4me3 Replicate 2

description:
Library name: siControl H3K4me3 Replicate 2
Peaks present in at least two replicates are included in the high quality peak file. Bedtools intersect was used with the biggest peak file as -a option.


title: WT SMARCA4 high salt rep 1

city: London

first: Jessica

middle: A

last: Downs

address: 237 Fulham Road

country: United Kingdom

institute: The Institute of Cancer Research

description:
WT_SMARCA4_LH_r1.bw
SMARCA4_vs_IgG_enriched_kmers.bw

data_processing:
Fastq reads were trimmed using TrimGalore (v0.6.6) using the options--trim-n--paired.
The human CHM13-T2Tv1.1 (GenBank GCA_009914755.3) and S. cerevisiae S288C (GenBank GCA_000146045.2) assemblies were combined into one FASTA file, then trimmed reads were mapped using Bowtie2 (v2.4.2) using the parameters --local --very-sensitive-local --no-unal --no-mixed --no-discordant --dovetail --soft-clipped-unmapped-tlen --non-deterministic --phred33 -I 50 -X 1500.
Reads with more than 3 mismatches were removed with Sambamba (v0.5.0), and their corresponding mates were removed with Picard tools (v2.23.8).
Sam files were converted to bam with SAMtools (v1.11). Reads mapped to the CHM13-T2Tv1.1 assembly were extracted using BAMtools (v2.5.1) split. Low and high salt BAM files from each sample were merged, sorted, and indexed using SAMtools.Uniquely mapped reads were extracted using sambamba (v0.5.0).
Bigwig files were made using Deeptools (v3.1.3) bamCoverage --extendReads --maxFragmentLength 1500 --binSize 10 –outFileFormat bigwig and normalised by total number of mapped reads.
Briefly, for k-mer analysis, reads that mapped to the peri/centromere in the CHM13-T2Tv1.1 assembly were extracted, deduplicated, trimmed and interleaved (L+H salt separately) using bedtools (v2.29.2), BBmap (v38.84) and trimmomatic (v0.39) packages. 51-mers that occur at least twice in each replicate were counted and dumped using kmc (v3.2.1). K-mers not counted in specific replicates were given an arbitrary count of 1, to allow average and fold change calculations. k-mer counts were normalised by dividing by the total base count (in reads that map to the whole genome), before average and fold change calculation. Adjusted p-values were calculated between groups using the genefilter (v1.80.0) package, with a BH-adjustment. Enriched k-mers were defined as those with at least 3 replicates having a normalised k-mer count > 2e-09, and an adjusted p-value < 0.1.
Bowtie2 (v2.4.2) was used to map these enriched k-mers back to the CHM13-T2Tv1.1 genome, using the specific parameters -f -k 5000 --score-min C,0,0
Bigwig files were generated from enriched k-mer bam files using deepTools (v3.5.1) bamCoverage tool using the following parameters --binSize 1 --scaleFactor 1
Assembly: T2T-CHM13v1.1
Supplementary files format and content: Bigwig files showing CUT&RUN read coverage for reads mapped uniquely (no multimapping) to the T2T-CHM13v1.1 reference genome.
Supplementary files format and content: Bigwig files showing mapping locations of k-mers (up to 5000 exact matches per k-mer) after being mapped to the T2T-CHM13v1.1 reference genome.
Library strategy: CUT&RUN

growth_protocol: hTERT-RPE1 cells were cultured in Dulbecco Modified Minimal Essential Medium (DMEM)/F-12 (Sigma) supplemented with 10% FBS (Gibco), 200µM glutamax (Gibco), 0.26% sodium bicarbonate (Gibco), and 1% penicillin/streptomycin (P/S)(Sigma). Cells were maintained at 37oC in a humified incubator with 5% CO2

extract_protocol:
CUT&RUN was performed according to the CUT&RUN Assay Kit protocol (Cell Signaling Technology) with the following modifications. Cells were detached with Accutase (Sigma). 200,000 cells were collected per experiment and pelleted by centrifugation for 5 minutes at 600 x g. Beads were incubated in primary antibody on a nutator overnight at 4°C. MNase digestion was carried out at 0°C in an ice water bath for 30 minutes. Salt fractionation and DNA purification were carried out according to the CUT&RUN.salt protocol (PMID: 29386331). Briefly, after STOP buffer addition, samples were incubated at 4°C for 1 hour to release low-salt fragments. Beads were resuspended in low salt buffer (175mM NaCl, 10mM EDTA, 2mM EGTA, 0.1% TritonX-100, 20μg/mL glycogen), rocked at 4°C for 1 hour, centrifuged for 5 minutes at 16,000 x g, and the supernatant containing the low salt fraction was collected. High salt buffer (825mM NaCl, 10mM EDTA, 2mM EGTA, 0.1% TritonX-100, 20μg/mL glycogen) was added to beads dropwise with gentle vortexing. Samples were again rocked at 4°C for 1 hour, centrifuged for 5 minutes at 16,000 x g, and the supernatant containing the high salt fraction was collected. Low salt fractions were adjusted to 500mM NaCl. RNAse A (Thermo Fisher Scientific) was added to all fractions and samples were incubated at 37°C for 20 minutes. SDS (sodium dodecyl sulfate) and Proteinase K (Cell Signaling Technology) were added and samples were incubated at 50°C for 1 hour. DNA was extracted using phenol/chloroform and precipitated in 100% ethanol as described.
CUT&RUN libraries were constructed using the NEB Ultra II DNA library prep kit for Illumina with at least 12 cycles of PCR amplification. Libraries were profiled using the Agilent TapeStation D1000 high sensitivity ScreenTape on the Agilent 4150 TapeStation System

value: Retinal pigment epithelial

tag: genotype

value: WT

tag: cut&run antibody

value: SMARCA4 (Abcam ab110641)


title: Fresh sorted CD8 T cells from Donor 938 PBMC

description: Library name: CD8-R200-938

value: CD8 T cells


title: Fresh sorted CD8 T cells from Donor 937 PBMC

description: Library name: CD8-R200-937


title: Culture sorted DN T cells from Donor 937 PBMC

description: Library name: DNT-R200-937-C


title: Fresh sorted DN T cells from Donor 924 PBMC

description: Library name: DNT-R200-924


title: Culture sorted CD8 T cells from Donor 938 PBMC

description: Library name: CD8-R200-938-C_


title: siBAZ2A Replicate 2

description:
Library name: siBAZ2A BG4 Replicate 2
Peaks present in at least two replicates are included in the high quality peak file. Bedtools intersect was used with the biggest peak file as -a option.


title: medial meniscus, white zone

city: Poznań

first: Monika

last: Mankowska

address: Uniwersytetu Poznańskiego

department: Centre for Applied Technology

country: Poland

institute: Adam Mickiewicz University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Output fastq files were uploaded to 10x Genomics Cell Ranger Software (cellranger-6.1.2). Data were demultiplexed, pre-analyzed and mapped to the custom-built pig reference genome (Sscrofa11.1) with a provided by 10x Genomics cellranger mkref pipeline.
Assembly: Sscrofa11.1
Supplementary files format and content: tab separated values files
Supplementary files format and content: matrix files

organism: Sus scrofa

source_name: Meniscus

extract_protocol:
Tissues were rinsed in 5% Betadine in PBS solution followed by two rinsing in PBS, transported in MACS® Tissue Storage Solution on ice for up to 1 hour and processed immediately after arrival. The tissue was dissected away from the synovium, segmented into white and red zones, then cut into small pieces followed by enzymatic digestion, and disaggregation steps. In particular first incubation was carried out with 4mg/ml Pronase enzyme blend at 37oC for one hour followed by second in 3 mg/ml Collagenase P 37oC for another two hours. Mixture was filtered through 70 µm pluriStrainer® and centrifuged. Cell pellet was resuspended in 0,1% BSA in PBS and centrifuged for better removal of dead cells. Finally cells were filtered through 30 µm pluriStrainer® and resuspended in 1% BSA in PBS to prevent re-aggregation of cells.
Cells isolated from meniscal zones were subjected to library construction with the use of Chromium Next GEM Single Cell 3’ Reagent Kit v3.1 (10x Genomics, #PN-1000269). Samples were processed according to the manufacturer's protocol. Firstly cell suspensions were divided into the single-cell format with a Chromium X Series controller (10x Genomics) that encapsulates single cells within nanoliter-scale Gel Beads-in-emulsion (GEMs), where all generated cDNA share a common barcode. Incubation of the GEMs produced barcoded full-length cDNA from polyadenylated mRNA. After incubation, the GEMs were ruptured and the pooled fractions were recovered. Silane magnetic beads were used to purify the first-strand cDNA from the reaction mixture. Barcoded, full-length cDNA was amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the size of the cDNA amplicons. Samples` indexes and TruSeq Read 2 were added via End Repair, A-tailing, Adaptor Ligation, and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification.

value: Meniscus


title: siBAZ2A Replicate 3

description:
Library name: siBAZ2A BG4 Replicate 3
Peaks present in at least two replicates are included in the high quality peak file. Bedtools intersect was used with the biggest peak file as -a option.


title: siBAZ2B Replicate 4

description:
Library name: siBAZ2B BG4 Replicate 4
Peaks present in at least two replicates are included in the high quality peak file. Bedtools intersect was used with the biggest peak file as -a option.


title: Skin, treated with CAR T cells, without custom probes

description:
Library name: C24_13076
Visium spatial gene expression workflow for FFPE (10x Genomics)


title: siBAZ2B Replicate 1

description:
Library name: siBAZ2B BG4 Replicate 1
Peaks present in at least two replicates are included in the high quality peak file. Bedtools intersect was used with the biggest peak file as -a option.


title: Fresh sorted DN T cells from Donor 937 PBMC

description: Library name: DNT-R200-937

value: PBMC


title: siBAZ2A Replicate 4

description:
Library name: siBAZ2A BG4 Replicate 4
Peaks present in at least two replicates are included in the high quality peak file. Bedtools intersect was used with the biggest peak file as -a option.


title: Culture sorted CD8 T cells from Donor 937 PBMC

description: Library name: CD8-R200-937-C_


title: Culture sorted gd T cells from Donor 938 PBMC

description: Library name: gd-R200-938-C

value: gd T cells


title: Fresh sorted CD4 T cells from Donor 937 PBMC

description: Library name: CD4-R200-937

value: CD4 T cells

value: Ex vivo


title: Culture sorted CD4 T cells from Donor 937 PBMC

description: Library name: CD4-R200-937-C


title: siBAZ2B Replicate 2

description:
Library name: siBAZ2B BG4 Replicate 2
Peaks present in at least two replicates are included in the high quality peak file. Bedtools intersect was used with the biggest peak file as -a option.


title: Cd10_3

city: Harbin

first: Yu

last: Zhang

address: Huanghe Street No.73

country: China

institute: Harbin Institute of Technology

data_processing:
Illumina Casava1.8 software used for basecalling.
Raw data (raw reads) of fastq format were processed through in-house perl scripts. Adaptor sequences, poly-N, and low-quality sequences were removed from raw data to obtain clean data (clean reads) in this step.
Transcriptome assembly was performed using Trinity (v2.4.0) software
The gene functions were annotated according to the following databases: Nr, Nt, Pfam (protein family), Swiss-Prot, KOG, KO (KEGG Ortholog database), and GO (gene ontology).
Genome_build: de novo assembly. FASTA of transcript sequences is available on the series record.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

organism: Procambarus clarkii

source_name: Hepatopancreas_10 mg/L Cd

extract_protocol:
Hepatopancreas were removed and flash frozen in liquid nitrogen. Total RNA was extracted from the collected hepatopancreas samples using the Tri Reagent based on the manufacturer's protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Four groups: Control (0 mg/L Cd); Cd2 (2 mg/L Cd); Cd5 (5 mg/L Cd); Cd10 (10 mg/L Cd). Time: 72 h.

value: Hepatopancreas

tag: gender

value: Male


title: Culture sorted CD8 T cells from Donor 924 PBMC

description: Library name: CD8-R200-924-C_

value: Activated in vitro with anti-CD3 (1mg/mL) and anti-CD28 (5mg/mL). After 24 hours, IL-1B (560 U/mL) , IL-2 (30U/mL), IL-7 (200U/mL) and IL-15 (125U/mL) were added every 2-3 days for 14 days.


title: Culture sorted CD4 T cells from Donor 924 PBMC

description: Library name: CD4-R200-924-C

value: Culture


title: Fresh sorted CD8 T cells from Donor 924 PBMC

description: Library name: CD8-R200-924

value: Fresh


title: siBAZ2A Replicate 1

description:
Library name: siBAZ2A BG4 Replicate 1
Peaks present in at least two replicates are included in the high quality peak file. Bedtools intersect was used with the biggest peak file as -a option.

value: lung

value: epithelial cell


title: Culture sorted CD4 T cells from Donor 938 PBMC

description: Library name: CD4-R200-938-C


title: medial meniscus, red zone

description: 10x Genomics


title: Cd10_2


title: lateral meniscus, white zone

description: 10x Genomics


title: lateral meniscus, red zone

description: 10x Genomics


title: Fresh sorted CD4 T cells from Donor 924 PBMC

description: Library name: CD4-R200-924


title: siControl Replicate 1

description:
Library name: siControl BG4 Replicate 1
Peaks present in at least two replicates are included in the high quality peak file. Bedtools intersect was used with the biggest peak file as -a option.

value: siControl


title: siControl Replicate 3

description:
Library name: siControl BG4 Replicate 3
Peaks present in at least two replicates are included in the high quality peak file. Bedtools intersect was used with the biggest peak file as -a option.


title: HA-BAZ2B H3K4me3 Replicate 3

description:
Library name: A549 HA-BAZ2B H3K4me3 Replicate 3
Peaks present in at least two replicates are included in the high quality peak file. Bedtools intersect was used with the biggest peak file as -a option.

value: endogenously tagged BAZ2B with 5' HA insertion.


title: pDC, LCMV Cl13, 30 days post infection Rep3

description: Library name: pDC_d30_Rep3

data_processing:
Illumina Casava1.8.2 software used for basecalling
Raw sequencing data were aligned to mouse genome (mm10) using STAR aligner
Assembly: Mm10 (GRCm38)
Supplementary files format and content: csv file includes raw counts values for each sample

source_name: spleen

extract_protocol:
Qiagen Rneasy Micro Kit
Illumina TruSeq RNA Library Prep Kit v2

treatment_protocol: Mice were infected with LCMV Clone 13 for the indicated times (24 hours, 8 days, 30 days).

value: spleen

value: primary isolated

value: plasmacytoid DC

tag: strain

tag: batch


title: A_48_3_biol rep 3

city: Nottingham

first: Meshach

last: Maina

address: University Of Nottingham, Sutton Bonington Campus

department: One Virology, Wolfson Center for Global Virus Research, Vet. School

institute: University of Nottingham

data_processing:
Deseq2 pipeline
Reads were trimed on TrimGalore and read quality control completed by runing FastQC
Trimmed reads were mapped to Bos_taurus.ARS-UCD1.2.107 using STAR
Gene expression was then quantified and normalised using Rsubread’s FeatureCounts version 2.0.0.
Deseq2
Assembly: Bos_taurus.ARS-UCD1.2.107
Supplementary files format and content: tab-delimited text files for each sample
Supplementary files format and content: xlsx file

organism: Bos taurus

source_name: Turbinate cells

growth_protocol: Bovine turbinate cells (BT-cells) were maintained in IMDM supplemented with 2 mM L-glutamine, 1% penicillin (100 units/ml) - streptomycin (100 μg/ml) and 10% (FBS) at 37°C in humidified air enriched with 5% CO2.

extract_protocol:
Total RNA from uninfected control and infected cells was extracted using RNeasy kit (Qiagen Ltd, Hilden, Germany).
cDNA libraries were prepared according to standard Illumina protocol

treatment_protocol: In a 3 biological replicate experiment, BT-cells non-infected and infected with IDV at an MOI of 0.1 were collected at 3 time points 0 (non-infected control),  24 and 48 hours post infection

value: Turbinate cells

value: Infected 48h


title: siControl Replicate 2

description:
Library name: siControl BG4 Replicate 2
Peaks present in at least two replicates are included in the high quality peak file. Bedtools intersect was used with the biggest peak file as -a option.


title: A_48_1_biol rep 1


title: pDC, LCMV Cl13, 30 days post infection Rep1

description: Library name: pDC_d30_Rep1


title: siControl Replicate 4

description:
Library name: siControl BG4 Replicate 4
Peaks present in at least two replicates are included in the high quality peak file. Bedtools intersect was used with the biggest peak file as -a option.


title: Cd10_1


title: pDC, LCMV Cl13, 30 days post infection Rep2

description: Library name: pDC_d30_Rep2


title: Fresh sorted CD4 T cells from Donor 938 PBMC

description: Library name: CD4-R200-938

value: PBMC


title: pDC, LCMV Cl13, 8 days post infection Rep3

description: Library name: pDC_d8_Rep3


title: Cd5_3

source_name: Hepatopancreas_5 mg/L Cd


title: A_24_3_biol rep 3

value: Infected 24h


title: HA-BAZ2B H3K4me3 Replicate 2

description:
Library name: A549 HA-BAZ2B H3K4me3 Replicate 2
Peaks present in at least two replicates are included in the high quality peak file. Bedtools intersect was used with the biggest peak file as -a option.


title: pDC, LCMV Cl13, 8 days post infection Rep2

description: Library name: pDC_d8_Rep2


title: A_24_2_biol rep 2


title: WT Replicate 2

description:
Library name: A549 WT HA Replicate 2
Peaks present in at least two replicates are included in the high quality peak file. Bedtools intersect was used with the biggest peak file as -a option.

value: Wild type A549 cells

value: HA


title: pDC, LCMV Cl13, 24hr Rep2

description: Library name: pDC_24hr_Rep2


title: pDC, LCMV Cl13, 8 days post infection Rep1

description: Library name: pDC_d8_Rep1


title: pDC, LCMV Cl13, 24hr Rep1

description: Library name: pDC_24hr_Rep1


title: HA-BAZ2B H3K4me3 Replicate 1

description:
Library name: A549 HA-BAZ2B H3K4me3 Replicate 1
Peaks present in at least two replicates are included in the high quality peak file. Bedtools intersect was used with the biggest peak file as -a option.


title: Cd5_2

value: Hepatopancreas

value: Male


title: Cd5_1


title: WT Replicate 3

description:
Library name: A549 WT HA Replicate 3
Peaks present in at least two replicates are included in the high quality peak file. Bedtools intersect was used with the biggest peak file as -a option.


title: Cd2_1

source_name: Hepatopancreas_2 mg/L Cd


title: HA-BAZ2B Replicate 3

description:
Library name: A549 HA-BAZ2B HA Replicate 3
Peaks present in at least two replicates are included in the high quality peak file. Bedtools intersect was used with the biggest peak file as -a option.


title: pDC, LCMV Cl13, 24hr Rep3

description: Library name: pDC_24hr_Rep3


title: pDC, Uninfected, Rep3

description: Library name: pDC_NI_Rep_3


title: Control3


title: A_0_2_biol rep 2

value: Mock


title: Cd2_3


title: A_0_1_biol rep 1


title: HA-BAZ2B Replicate 1

description:
Library name: A549 HA-BAZ2B HA Replicate 1
Peaks present in at least two replicates are included in the high quality peak file. Bedtools intersect was used with the biggest peak file as -a option.


title: Control1


title: pDC, Uninfected, Rep1

description: Library name: pDC_NI_Rep_1


title: Cd2_2


title: A_24_1_biol rep 1


title: WT Replicate 1

description:
Library name: A549 WT HA Replicate 1
Peaks present in at least two replicates are included in the high quality peak file. Bedtools intersect was used with the biggest peak file as -a option.


title: DK9699b

status: Public on Jan 04 2025

city: Bloomington

first: Ayushi

last: Mishra

state: Indiana

address: Biology Building, BB432, 1001 E 3rd St

institute: Indiana University

description: Library name: DK9699b

data_processing:
CLC Genomics Workbench v 11.0.1.
Paired end min 50 max 2000 and failed reads were removed.
Sequences were mapped to NZ_CP020102.1 CLC genomic benchwork (parameters- match score:1 mismath cost:2 insertion cost:3 deletion cost:3 length fraction: 0.5 similarity fraction: 0.8).
rRN sites were removed and the TPM values for each gene was calculated using CLC genome browser.
Assembly: Bacillus subtilis 3610 (NZ_CP020102.1) was used as reference.
Supplementary files format and content: csv files include TPM values for each gene in a sample.

organism: Bacillus subtilis subsp. subtilis NCIB 3610 = ATCC 6051 = DSM 10

source_name: Bacterial

extract_protocol:
Cells grown in LB at 37C were collected at OD600=1. RNA was extracted once with the hot phenol chloroform method and then further extracted with Trizol.
rRNA depletion and library preparation was performed by Indiana University Center for genomics and bioinformatics.

treatment_protocol: Cells were grown in LB, flash frozen in methanol and RNA was extracted by hot phenol and Trizol method.

value: Bacterial

value: DepsE


title: A_48_2_biol rep 2


title: DK9699a

description: Library name: DK9699a


title: A_0_3_biol rep 3


title: DB1438b

description: Library name: DB1438b

value: DepsE site1* amyE::PslrA-slrA


title: DB141b

description: Library name: DB141b

value: DepsE DslrR amyE::PslrA-slrA


title: HA-BAZ2B Replicate 2

description:
Library name: A549 HA-BAZ2B HA Replicate 2
Peaks present in at least two replicates are included in the high quality peak file. Bedtools intersect was used with the biggest peak file as -a option.

value: lung

value: epithelial cell

value: endogenously tagged BAZ2B with 5' HA insertion.


title: WGS_DK9314_DslrR_DsinR_rep1

description: Library name: WGS_DK9314_DslrR_DsinR_rep1

data_processing:
Reads from each end of a DNA fragment were represented in each of the two FASTQ files generated by Illumina paired-end sequencing.
CLC Genomics Workbench v 11.0.1.
Paired end min 50 max 2000 and failed reads were removed.
Sequences were mapped to NZ_CP020102.1 CLC genomic benchwork (parameters- match score:1 mismath cost:2 insertion cost:3 deletion cost:3 length fraction: 0.5 similarity fraction: 0.8).
rRN sites were removed and the TPM values for each gene was calculated using CLC genome browser.
Assembly: Bacillus subtilis 3610 (NZ_CP020102.1) was used as reference.
Supplementary files format and content: Files ending with .csv files are comma-separated values files of ChIP-seq/WGS results.

growth_protocol: Wild type and mutant cells of Bacillus subtilis 3610 growing in LB were crosslinked using 3% formaldehyde.

extract_protocol:
Cells were lysed with lysozyme and 1% SDS and the DNA bound to the antibody was extracted using magnetic beads.
Standard library construction protocol was used for Nextseq550 sequencing platforms. Illumina TruSeq indexes were used.

treatment_protocol: Cells were grown in LB, fixed by 3% formaldehyde for 30min at room temperature.

value: DslrR DsinR


title: pDC, Uninfected, Rep2

description: Library name: pDC_NI_Rep_2

value: spleen

value: primary isolated

value: plasmacytoid DC


title: ChIP_SinR_DK9314_DslrR_DsinR_rep1

description: Library name: ChIP_SinR_DK9314_DslrR_DsinR_rep1

value: anti-SinR


title: Control2


title: DB154b

description: Library name: DB154b

value: DepsE amyE::PslrA-slrA


title: WGS_DS6776_DepsH

description: Library name: WGS_DS6776_DepsH

value: DepsH


title: WGS_DK9093_DepsHPslrA_slrA

description: Library name: WGS_DK9093_DepsHPslrA_slrA

value: DepsH amyE::PslrA-slrA


title: DB1522b

description: Library name: DB1522b

value: DepsE site(12)* amyE::PslrA-slrA


title: WGS_DB154

description: Library name: WGS_DB154


title: WGS_DB1705

description: Library name: WGS_DB1705

value: DepsE site(12345)* amyE::PslrA-slrA


title: DB154a

description: Library name: DB154a

value: Bacterial


title: DB141a

description: Library name: DB141a


title: DB1438a

description: Library name: DB1438a


title: ChIP_SinR_DS6776_DepsH_rep2

description: Library name: ChIP_SinR_DS6776_DepsH_rep2


title: DB1522a

description: Library name: DB1522a


title: ChIP_SinR_DK9314_DslrR_DsinR_rep2

description: Library name: ChIP_SinR_DK9314_DslrR_DsinR_rep2


description: Library name: ChIP_SinR_DK9332_DepsHslrR_PslrA_slrA_rep2

value: DepsH DslrR amyE::PslrA-slrA


title: ChIP_SinR_DK9314_DslrR_DsinR_rep3

description: Library name: ChIP_SinR_DK9314_DslrR_DsinR_rep3


title: WGS_DK9090_DepsHsinR

description: Library name: WGS_DK9090_DepsHsinR

value: DepsH DsinR


title: ChIP_SinR_DK9093_DepsHPslrA_slrA_rep3

description: Library name: ChIP_SinR_DK9093_DepsHPslrA_slrA_rep3


title: WGS_DB225

description: Library name: WGS_DB225

value: DepsH DsinR DslrR DygzD


title: ChIP_SinR_DS6776_DepsH_rep3

description: Library name: ChIP_SinR_DS6776_DepsH_rep3


description: Library name: ChIP_SinR_DK9332_DepsHslrR_PslrA_slrA_rep3


title: ChIP_SinR_DK9090_DepsHsinR_rep1

description: Library name: ChIP_SinR_DK9090_DepsHsinR_rep1


title: ChIP_SinR_DB225_rep2_R1

description: Library name: ChIP_SinR_DB225_rep2_R1


description: Library name: ChIP_SinR_DK9332_DepsHslrR_PslrA_slrA_rep1


title: ChIP_SinR_DB225_rep1_R1

description: Library name: ChIP_SinR_DB225_rep1_R1


title: ChIP_SinR_DK9093_DepsHPslrA_slrA_rep1

description: Library name: ChIP_SinR_DK9093_DepsHPslrA_slrA_rep1


title: ChIP_SinR_DK9313_DepsHslrR_rep3

description: Library name: ChIP_SinR_DK9313_DepsHslrR_rep3

value: DepsH DslrR


title: ChIP_SinR_DK9313_DepsHslrR_rep1

description: Library name: ChIP_SinR_DK9313_DepsHslrR_rep1


title: ChIP_SinR_DK9093_DepsHPslrA_slrA_rep2

description: Library name: ChIP_SinR_DK9093_DepsHPslrA_slrA_rep2


title: ChIP_SinR_DS6776_DepsH_rep1

description: Library name: ChIP_SinR_DS6776_DepsH_rep1


title: WGS_DK9332_DepsHslrR_PslrA_slrA

description: Library name: WGS_DK9332_DepsHslrR_PslrA_slrA


title: 24 h biofilms grown at 37 ºC, BR2

city: Oviedo

first: Lucia

last: Fernandez

address: C/ Francisco Pintado Fe 26

country: Spain

institute: Instituto de Productos Lacteos de Asturias (IPLA-CSIC)

data_processing:
Quality of the sequences was verified with FastQC 0.11.2
EDGE-pro 1.3.1 workflow was employed for read processing. The pipeline as described by T.Magoc, et al., Evolutionary Bioinformatics, 2013, employs Bowtie2 (v2.2.3) to map reads to the reference genome (IPLA16), filters multimapped reads based on scoring alignments and determines read coverage for each genomic position and gene.
EDGE-pro output files were formated using the edgeToDeseq script provided in the EDGE-pro package and used as input for DESeq2 (v1.12.4) to calculate RPKMs per gene and quantify differential expression between conditions.
Assembly: S. aureus IPLA16 genome (CP134617)
Supplementary files format and content: test_DESeq2results_normalized.csv: plain text file with comma-separated values. The file includes RPKM values for IPLA16 genes in 25 ºC and 37 ºC replicates as well as differential expression estimations, expressed as a log2 fold change between conditions.

organism: Staphylococcus aureus

source_name: bacterial cell

growth_protocol: Biofilms were grown in TSB supplemented with 0.25% glucose for 24 hours at 25 ºC or 37 ºC in a static incubator. The planktonic phase was removed and the adhered cells were washed and harvested for RNA purification.

extract_protocol:
Bacterial cells were harvested, treated with RNA protect (Qiagen) and kept at -80ºC until RNA purification. RNA was obtained by mechanical disruption in the presence of acid phenol and subsequent purification was carried out with illustra RNA spin minikit (GE Healthcare)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: bacterial cell

value: 37 ºC


title: ChIP_SinR_DB154_rep1

description: Library name: ChIP_SinR_DB154_rep1


title: ChIP_SinR_DB1705_rep1

description: Library name: ChIP_SinR_DB1705_rep1


title: WGS_DK9313_DepsHslrR

description: Library name: WGS_DK9313_DepsHslrR


title: 24 h biofilms grown at 25 ºC, BR3

value: 25 ºC


title: 24 h biofilms grown at 25 ºC, BR1


title: ChIP_SinR_DB1705_rep2

description: Library name: ChIP_SinR_DB1705_rep2


title: ChIP_SinR_DK9090_DepsHsinR_rep2

description: Library name: ChIP_SinR_DK9090_DepsHsinR_rep2


title: ChIP_SinR_DK9090_DepsHsinR_rep3

description: Library name: ChIP_SinR_DK9090_DepsHsinR_rep3


title: ChIP_SinR_DB154_rep2

description: Library name: ChIP_SinR_DB154_rep2


title: 24 h biofilms grown at 37 ºC, BR3


title: Tumor implants from TrkA^WT;NOD-Scid, pooled triplicates, sc-RNAseq

city: Baltimore

first: Aaron

last: James

state: Maryland

address: 720 Rutland Avenue, Ross Bldg., Room 529

department: Pathology

institute: Johns Hopkins University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Raw sequencing data were processed using the 10x Genomics Cell Ranger pipeline to generate FASTAQ files
Sequences were aligned to mm10 and hg38 genome to gene expression count using Cell Ranger's default settings
Gene expression level of Reseq coding genes were quantified using Cell Ranger's default settings
Seurat v4.4.0 was used for further analysis.
Assembly: mm10 and hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Xenograft OS tumor

growth_protocol: Xenograft tumors were microdissected 12 days after human 143B OS cell inoculation and digested with collagenase type I/II (1 mg/ml) digestion.

extract_protocol:
After collagenase digestion, enzyme activity was diluted by adding PBS. Cell fractions were collected and resuspended in red blood cell lysis buffer (37°C for 5 min). Digestions were sequentially filtered through 100-μm and 40-μm sterile strainers. Cells were then washed in PBS and resuspended in HBSS at a concentration of ~1000 cells/μl. Cell viability was assessed with Trypan blue exclusion on a Countess II (Thermo Fisher Scientific) automated counter and showed a >85% viability.
Cells were sent to JHMI Transcriptomics and Deep Sequencing Core. The library was generated using the 10x Genomics Chromium controller following the manufacturer’s protocol. Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

treatment_protocol: For 143B OS cell implantation, 8–10-wk-old, male and female, TrkAWT;NOD-Scid or TrkAF592A;NOD-Scid mice were used. A total of 1 × 106 human 143B cells in 50 μl PBS were injected subperiosteally within the left proximal tibia metaphysis under 1.0-1.5% isoflurane in 100% O2.

value: Xenograft OS tumor

value: 143B human OS

value: human osteosarcoma cells + mouse tumor cells

value: TrkA^WT; NOD-Scid

value: 10 weeks old


title: 24 h biofilms grown at 37 ºC, BR1


title: Tumor implants TrkA^F592A;NOD-Scid + 1NMPP1, pooled triplicates, sc-RNAseq

description: 10x Genomics

value: human osteosarcoma cells + mouse tumor niche cells

value: TrkA^F592A; NOD-Scid


title: 24 h biofilms grown at 25 ºC, BR2


title: Input.WT.BM.9.5Gy.1

city: WEST HOLLYWOOD

first: Moray

last: Campbell

address: 8687 Melrose Avenue, Office B227.5G

institute: Cedars-Sinai Medical Center

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using FASTQC and Trimmomatic.
Supplementary files format and content: Cistromes were analyzed with Rsubread/csaw along with TF motif analyses (MotifDb) all in R.
Assembly: mm10
Supplementary files format and content: bedgraph files

source_name: bone marrow

extract_protocol:
Briefly, approximately 20x10^6 cells were crosslinked with 1% formaldehyde solution, quenched with glycine (0.125 M) and harvested in cold PBS. Sonication of crosslinked chromatin was performed using a Bioruptor® UCD-200TM Sonicator (Diagenode) with optimized cycles for each cell type. Immunoprecipitation of sonicated material was performed with antibodies against VDR (D2K6W) – Cell Signaling) or IgG (Rabbit IgG sc2729 – Santa Cruz) for 16 hours, and antibody/bead complexes isolated with Magna ChIPTM Protein A+G magnetic beads (Millipore). Complexes were washed, reverse crosslinked, and treated sequentially with RNase and proteinase K prior to DNA isolation.
Sequencing libraries prepared from immunoprecipitated DNA.
ChIP-Seq libraries were prepared using Illumina’s TruSeq Stranded protocol.

value: bone marrow

value: Xray 9.5Gy 3h

value: IgG


title: Input.SJ.BM.9.5Gy.1


title: Input.WT.BM.9.5Gy.2


title: ChIP_SinR_DK9313_DepsHslrR_rep2

description: Library name: ChIP_SinR_DK9313_DepsHslrR_rep2

value: Bacterial

value: anti-SinR


title: Input.M.null.BM.9.5Gy.2


title: Input.M.plus.BM.9.5Gy.1


title: ChIP.WT.BM.9.5Gy.2


title: ChIP.SJ.BM.9.5Gy.2


title: ChIP.SJ.BM.9.5Gy.1


title: ChIP.M.plus.BM.9.5Gy.1


title: Input.M.null.BM.9.5Gy.1


title: Input.SJ.BM.9.5Gy.2


title: ChIP.WT.BM.9.5Gy.1


title: BM_delta19.R2

data_processing:
Transcript abundance estimates were normalized and differentially expressed genes (DEGs) identified using a standard edgeR pipeline, and gene set enrichment analysis (GSEA) performed.
Assembly: mm10
Supplementary files format and content: Comma-separated text file includes RPKM values for each Sample

extract_protocol:
Total RNA was extracted E.Z.N.A.® Total RNA Kit I, Omega Bio-tek®) and subjected to DNase treatment and purification by the RNA Clean & Concentrator kit (Zymo Research) to yield high-quality RNA for library preparation. RNA-seq libraries were prepared using Illumina’s TruSeq Stranded protocol. ~70 million paired-end 150 bp sequence reads were generated for each library on the HiSeq 2500 platform.
RNA-seq libraries were prepared using Illumina’s TruSeq Stranded protocol.

value: control


title: ChIP.M.null.BM.9.5Gy.2


title: ChIP.M.plus.BM.9.5Gy.2


title: ChIP.M.null.BM.9.5Gy.1


title: BM_delta19.R3


title: BM_delta19.R1


title: BM_WT_IR_6_GY_3h.2.R2

value: Xray 6Gy 3h


title: BM_WT_IR_6_GY_3h.1.R1


title: BM_delta19.IR_6_GY_3h.R1


title: BM_R172H.plus.8w.R3


title: BM_R172H.plus.8w.R2


title: BM_R172H_minus_8w.R3


title: BM_R172H.plus.8w.R1


title: Input.M.plus.BM.9.5Gy.2


title: BM_Mdm2_Tg.8w.R1


title: BM_Mdm2_Tg.8w.R3


title: BM_Mdm2_Tg.8w.R2


title: BM_WT_p53.8w.R3


title: BM_WT_p53.8w.R2


title: M_plus_9_5_Gy.R2


title: M_9_5_Gy.R1


title: M_plus_9_5_Gy.R4


title: Null_9_5_Gy.R2


title: BM_delta19.IR_6_GY_3h.R2


title: Null_9_5_Gy.R3


title: Null_9_5_Gy.R1


title: SJ_9_5_Gy.R3


title: SJ_9_5_Gy.R2


title: SJ_9_5_Gy.R4


title: WT_9_5_Gy.R4


title: BM_WT_IR_6_GY_3h.3.R3


title: BM_R172H_minus_8w.R2


title: BM_R172H_minus_8w.R1


title: WT_9_5_Gy.R1


title: WT_9_5_Gy.R2


title: miRNA profile subject 314

city: Orbassano

first: Giulio

last: Ferrero

state: TO

address: Regione Gonzole, 10

department: Dept. Clinical and Biological Sciences

country: Italy

institute: University of Turin

description: Library name: 314

data_processing:
Reads were trimmed from the adapter sequences using Cutadapt v1.10 by imposing a maximum error rate in terms of mismatches, insertions, and deletions equal to 0.15. Reads shorter than 14 nt were removed.
Trimmed reads were mapped against a miRNA reference based on miRBase v22 annotations using the small RNA-Seq module of Docker4Seq. The alignment was performed using BWA algorithm v0.7.127 with the default settings.
The human miRNAs were annotated and quantified using two methods called the "knowledge-based" and "position-based". miRNAs whose assigned arms were derived from the "position-based" methodology were indicated in italics.
The results generated by the annotation and quantification methods were merged into a unique mature miRNA count matrix. In the case of mature miRNAs processed from different precursors but characterized by the same mature sequence, the read counts were summed.
Assembly: hg38
Supplementary files format and content: Matrix table with the raw mature miRNA read counts for each sample

source_name: Saliva

extract_protocol:
Total RNA from saliva samples was extracted using the Maxwell® RSC miRNA Tissue (Promega, Milan, Italy) following the manufacturer’s instructions. Initially, 400 µL of saliva samples were added to chilled 200 μl of 1-Thioglycerol per ml of Homogenization Solution and following the instructions of manufacturer. At the end of the automated extraction, RNA samples were eluted in 60 µL of water. RNA concentration was measured with a Qubit fluorometer using Qubit microRNA assay (Thermofisher, Milan, Italy).
NEBNext Multiplex Small RNA Library Prep for Illumina kit (New England Biolabs, Inc) was used to convert small RNA transcripts into barcoded complementary DNA (cDNA) libraries. For each library, 100 ng of RNA was processed as starting material. Each library was prepared with a unique indexed primer. Multiplex adapter ligations, RT primer hybridization, RT reaction, and PCR amplification were performed according to the manufacturer’s protocol. After PCR amplification, the cDNA constructs were purified with the Monarch PCR & DNA cleanup kit (New England Biolabs, Inc), following the modifications suggested by the NEBNext Multiplex Small RNA Library Prep for Illumina protocol. Final libraries were loaded on the Bioanalyzer 2100 (Agilent Technologies) using the DNA High Sensitivity Kit (Agilent Technologies) according to the manufacturer’s protocol. Libraries were pooled together (in 35-plex or 40-plex) and further purified with a gel size selection. A final Bioanalyzer 2100 run with the High Sensitivity DNA Kit (Agilent Technologies) allowed to assess DNA library quality regarding size, purity, and concentration.

value: Saliva


title: miRNA profile subject 315

description: Library name: 315


title: BM_WT_p53.8w.R1


title: miRNA profile subject 312

description: Library name: 312


title: miRNA profile subject 320

description: Library name: 320


title: miRNA profile subject 306

description: Library name: 306


title: M_9_5_Gy.R9


title: M_9_5_Gy.R8


title: miRNA profile subject 301

description: Library name: 301


title: miRNA profile subject 290

description: Library name: 290


title: miRNA profile subject 298

description: Library name: 298


title: M_plus_9_5_Gy.R3


title: miRNA profile subject 291

description: Library name: 291


title: miRNA profile subject 276

description: Library name: 276


title: miRNA profile subject 283

description: Library name: 283


title: miRNA profile subject 265

description: Library name: 265


title: miRNA profile subject 264

description: Library name: 264


title: miRNA profile subject 270

description: Library name: 270


title: miRNA profile subject 263

description: Library name: 263


title: WT, YPD cultivated, rep2

city: Seoul

first: Seo Hyeon

last: Shin

state: Seoul

address: Seoul 동작구 흑석로 84

country: South Korea

institute: Chung-ang University

data_processing:
We check total RNA integrity using Agilent 2100 BioAnalyzer with RNA Integrity Number (RIN) value greater than 6.
RNA stranded library construction process was followed by 2015, Illumina , Inc.
The sequencing method was followed by Annual Review of Genomics and Human Genetics Vol. 9:387-402.
Assembly: PO1f
Supplementary files format and content: The files include readcount, RPKM and TPM values for each samples.
Supplementary files format and content: The files include annotations from GO, InterPro, Pfam, and NCBI DB.

organism: Yarrowia lipolytica

growth_protocol: Y. lipolytica PO1f strains were grown to an OD600 of 0.8 in YPD medium at 28°C.

extract_protocol:
Total RNA was isolated according to the liquid nitrogen method, and harvested using Rneasy mini kit (Qiagen). About 3~5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA Sample Prep Kit following manufacturer's protocols.

value: cell pellet


title: WT, YPD cultivated, rep1


title: miRNA profile subject 262

description: Library name: 262


title: miRNA profile subject 258

description: Library name: 258


title: COV434, Triptolide, 6h, rep4

city: Madison

middle: Diane

last: Lang

state: Wisconsin

address: 1111 HIGHLAND AVE WIMR 2766

department: Pathology and Laboratory Medicine

institute: University of Wisconsin-Madison

data_processing:
Alignment: STAR (v2.7.7a)
Abundance measurement: Salmon (v1.4.0)
Assembly: GRCh38

growth_protocol: SCCOHT cell lines BIN67 and SCCOHT-1 were maintained in RPMI 1640 (Thermo Fisher Scientific) supplemented with 10% Fetal Bovine Serum (FBS; Thermo Fisher Scientific) and 1% Penicillin/Streptomycin (Thermo Fisher Scientific). COV434 cells were cultured in DMEM (Thermo Fisher Scientific) supplemented with 10% FBS and 1% Penicillin/Streptomycin. All cells were maintained at 37°C in a humidified incubator containing 5% CO2 and were routinely monitored for mycoplasma testing and STR profiled for cell line verification.

extract_protocol:
RNA was extracted using Quick-DNA/RNA Miniprep Plus Kit (Zymo Research Cat#D7003), per manufacturer's instructions, with on-column DNase digestion.
500ng of total RNA was used to generate mRNA libraries using KAPA mRNA HyperPrep Kit library prep kit (Roche, cat#08098123702) per manufacturer's instructions. Final libraries were evaluated by TapeStation, quantitated using the Life Technologies/Invitrogen Qubit, and equimolarly pooled. Paired-end sequencing was performed on a NovaSeq6000 using a NovaSeq S4 300 cycle kit (cat#20028312) (151x11x11x151).

treatment_protocol: 100nM triptolide for 6 hours, or equivalent vehicle for matched time

value: SCCOHT, ovarian

value: triptolide


title: sur2Δ mutant, YPD cultivated, rep2

source_name: ku70∆::tc sur2∆::LEU2

value: ku70{delta}::tc sur2{delta}::LEU2


title: sur2Δ mutant, YPD cultivated, rep1


title: COV434, Triptolide, 6h, rep3


title: miRNA profile subject 255

description: Library name: 255


title: miRNA profile subject 303

description: Library name: 303


title: COV434, Triptolide, 6h, rep2


title: miRNA profile subject 251

description: Library name: 251


title: miRNA profile subject 246

description: Library name: 246


title: COV434, Triptolide, 6h, rep1


title: miRNA profile subject 252

description: Library name: 252


title: miRNA profile subject 256

description: Library name: 256


title: COV434, Vehicle, 6h, rep3

value: vehicle


title: miRNA profile subject 242

description: Library name: 242


title: miRNA profile subject 236

description: Library name: 236


title: COV434, Vehicle, 6h, rep1


title: miRNA profile subject 231

description: Library name: 231


title: BIN67, Triptolide, 6h, rep4


title: COV434, Vehicle, 6h, rep4


title: miRNA profile subject 260

description: Library name: 260


title: BIN67, Triptolide, 6h, rep3


title: BIN67, Triptolide, 6h, rep2


title: miRNA profile subject 227

description: Library name: 227


title: BIN67, Triptolide, 6h, rep1


title: miRNA profile subject 226

description: Library name: 226


title: BIN67, Vehicle, 6h, rep4


title: BIN67, Vehicle, 6h, rep3


title: miRNA profile subject 222

description: Library name: 222


title: miRNA profile subject 224

description: Library name: 224


title: miRNA profile subject 225

description: Library name: 225


title: BIN67, Vehicle, 6h, rep2


title: miRNA profile subject 211

description: Library name: 211


title: miRNA profile subject 209

description: Library name: 209


title: BIN67, Vehicle, 6h, rep1


title: COV434, Vehicle, 6h, rep2


title: miRNA profile subject 199

description: Library name: 199


title: COV434, Triptolide, 16h, IgG, rep2

data_processing:
Alignment with bowtie2 v2.4.2 arguments: --local --very-sensitive-local --no-unal -- no-mixed --no-discordant --phred33 --minins 10 --maxins 700 -q
QC: FastQC (v0.11.8) samtools stats (v1.11) and deepTools (v3.3.1)
Peak calling with MACS2 callpeak (v2.2.6) with the following arguments: -f BAMPE -B -q 0.01 --keep-dup all
Assembly: GRCh38
Supplementary files format and content: bw: bigwig files of tracks of signal across genome
Supplementary files format and content: narrowPeak: bed files of peaks called by MACS2
Library strategy: CUT&RUN

extract_protocol:
DNA enriched in binding to K27-acetylated histone H3 (H3K27ac) was determined using CUT&RUN and sequencing. Cell lines were harvested at greater than 70% confluency with 0.05% trypsin. 10cm plates were seeded with 2-3x106 cells and allowed to adhere overnight. The next day, fresh media was added with either 50nM (SCCOHT-1) or 100nM (BIN67 and COV434) triptolide with total DMSO concentration of less than 0.3%. After 6 or 16 hours of drug treatment, cells were harvested with 0.05% trypsin and total cell amount determined with cell count with dead cell exclusion with trypan blue staining using a Countess II. For tissues, we used 10-20mg frozen tissues and disassociated by pipetting in the first buffer in the protocol. EpiCypher CUTANA CUT&RUN protocol v1.5.2 was followed with 1x106 cells used for input of each cell line for both the H3K27ac and control (IgG) sample. H3K27ac antibody (Active Motif, cat#39133) was used at a 1:50 dilution (1ug/sample) in the antibody buffer and incubated overnight at 4°C. A normal rabbit IgG antibody (CST, cat#2729) was similarly used at a 1:50 dilution (1ug/sample). For targeted DNA cleavage, 2µL of EpiCypher CUTANA pAG-MNase (cat#15-1016) was added to each reaction. After completion of the CUT&RUN protocol, each sample was purified using the ChIP DNA Clean & Concentrator kit (ZYMO Research, cat#D5205). Samples were eluted in 30-50µL.
Material was QC using an Agilent 4200 TapeStation with High Sensitivity D1000 ScreenTape (cat#5067-5584, reagents cat#5067-5585) and Qubit dsDNA HS Assay Kit (ThermoFisher, cat#Q32854). Typical yields were single digit nanograms with the main DNA fragment detected at ~150bp. KAPA HyperPrep Kit (Roche, cat#07962363001) was used to generate DNA libraries for sequencing. Protocol v6.17 was followed with following modifications: (a) 1ng of input DNA from the CUT&RUN experiments, (b) 0.5µL of 1.5µM KAPA UDI Adapter (Roche, cat#08861919702) adapter stock was used during adapter ligation step, (c) final KAPA bead purification used a first cut of 0.65x beads followed by 0.25x bead purification. Samples were QC as above using TapeStation and Qubit. Typical library yields were ~500ng. An equimolar pooling of libraries was performed for a final 1500pmols in 150µL with Tris pH8.5 buffer as final fill volume. Pooled libraries were loaded onto a NovaSeq6000 using a NovaSeq SP 100 cycle kit (cat#20027464) (51x9x9x51).

treatment_protocol: 100nM triptolide for 6 or 16 hours, or equivalent vehicle for matched time

tag: time


title: COV434, Triptolide, 16h, IgG, rep1


title: miRNA profile subject 233

description: Library name: 233


title: COV434, Triptolide, 16h, IgG, rep3


title: miRNA profile subject 201

description: Library name: 201


title: COV434, Vehicle, 16h, IgG, rep3


title: miRNA profile subject 193

description: Library name: 193


title: miRNA profile subject 192

description: Library name: 192


title: COV434, Triptolide, 6h, IgG, rep4


title: miRNA profile subject 198

description: Library name: 198


title: COV434, Vehicle, 16h, IgG, rep2


title: miRNA profile subject 191

description: Library name: 191


title: miRNA profile subject 180

description: Library name: 180


title: COV434, Triptolide, 6h, IgG, rep2


title: miRNA profile subject 178

description: Library name: 178


title: COV434, Triptolide, 6h, IgG, rep3


title: miRNA profile subject 174

description: Library name: 174


title: miRNA profile subject 173

description: Library name: 173


title: COV434, Triptolide, 6h, IgG, rep1


title: COV434, Vehicle, 6h, IgG, rep4


title: COV434, Vehicle, 6h, IgG, rep3


title: miRNA profile subject 170

description: Library name: 170


title: COV434, Vehicle, 6h, IgG, rep2


title: miRNA profile subject 200

description: Library name: 200


title: miRNA profile subject 166

description: Library name: 166


title: COV434, Vehicle, 6h, IgG, rep1


title: miRNA profile subject 163

description: Library name: 163


title: COV434, Triptolide, 16h, H3K27ac, rep3


title: miRNA profile subject 156

description: Library name: 156


title: COV434, Triptolide, 16h, H3K27ac, rep2


title: miRNA profile subject 155

description: Library name: 155


title: COV434, Triptolide, 16h, H3K27ac, rep1


title: COV434, Vehicle, 16h, IgG, rep1


title: miRNA profile subject 154

description: Library name: 154


title: miRNA profile subject 153

description: Library name: 153


title: COV434, Vehicle, 16h, H3K27ac, rep2


title: miRNA profile subject 150

description: Library name: 150


title: COV434, Vehicle, 16h, H3K27ac, rep1


title: COV434, Triptolide, 6h, H3K27ac, rep3


title: miRNA profile subject 145

description: Library name: 145


title: COV434, Triptolide, 6h, H3K27ac, rep4


title: COV434, Triptolide, 6h, H3K27ac, rep2


title: miRNA profile subject 140

description: Library name: 140


title: COV434, Vehicle, 6h, H3K27ac, rep3


title: COV434, Vehicle, 6h, H3K27ac, rep4


title: miRNA profile subject 143

description: Library name: 143


title: COV434, Triptolide, 6h, H3K27ac, rep1


title: miRNA profile subject 147

description: Library name: 147


title: miRNA profile subject 139

description: Library name: 139


title: COV434, Vehicle, 6h, H3K27ac, rep2


title: miRNA profile subject 136

description: Library name: 136


title: miRNA profile subject 135

description: Library name: 135


title: miRNA profile subject 169

description: Library name: 169


title: miRNA profile subject 133

description: Library name: 133


title: COV434, Vehicle, 16h, H3K27ac, rep3


title: miRNA profile subject 132

description: Library name: 132


title: BIN67, Triptolide, 16h, IgG, rep2


title: COV434, Vehicle, 6h, H3K27ac, rep1


title: BIN67, Triptolide, 16h, IgG, rep1


title: BIN67, Triptolide, 16h, IgG, rep3


title: BIN67, Vehicle, 16h, IgG, rep2


title: BIN67, Vehicle, 16h, IgG, rep3


title: miRNA profile subject 130

description: Library name: 130


title: miRNA profile subject 125

description: Library name: 125


title: miRNA profile subject 126

description: Library name: 126


title: BIN67, Vehicle, 16h, IgG, rep1


title: miRNA profile subject 129

description: Library name: 129


title: miRNA profile subject 142

description: Library name: 142


title: miRNA profile subject 123

description: Library name: 123


title: miRNA profile subject 118

description: Library name: 118


title: BIN67, Triptolide, 6h, IgG, rep3


title: miRNA profile subject 116

description: Library name: 116


title: BIN67, Triptolide, 6h, IgG, rep2


title: miRNA profile subject 111

description: Library name: 111


title: BIN67, Vehicle, 6h, IgG, rep4


title: BIN67, Triptolide, 6h, IgG, rep1


title: BIN67, Vehicle, 6h, IgG, rep3


title: miRNA profile subject 110

description: Library name: 110


title: BIN67, Vehicle, 6h, IgG, rep2


title: miRNA profile subject 103

description: Library name: 103


title: BIN67, Vehicle, 6h, IgG, rep1


title: miRNA profile subject 93

description: Library name: 93


title: miRNA profile subject 97

description: Library name: 97


title: BIN67, Triptolide, 16h, H3K27ac, rep2


title: BIN67, Triptolide, 16h, H3K27ac, rep3


title: miRNA profile subject 91

description: Library name: 91


title: miRNA profile subject 84

description: Library name: 84


title: miRNA profile subject 90

description: Library name: 90


title: miRNA profile subject 85

description: Library name: 85


title: BIN67, Vehicle, 16h, H3K27ac, rep2


title: BIN67, Vehicle, 16h, H3K27ac, rep1


title: BIN67, Vehicle, 16h, H3K27ac, rep3


title: BIN67, Triptolide, 6h, IgG, rep4


title: BIN67, Triptolide, 6h, H3K27ac, rep4


title: miRNA profile subject 112

description: Library name: 112


title: miRNA profile subject 82

description: Library name: 82


title: BIN67, Triptolide, 6h, H3K27ac, rep3


title: miRNA profile subject 79

description: Library name: 79


title: BIN67, Triptolide, 6h, H3K27ac, rep1


title: BIN67, Triptolide, 6h, H3K27ac, rep2


title: miRNA profile subject 73

description: Library name: 73


title: miRNA profile subject 66

description: Library name: 66


title: miRNA profile subject 75

description: Library name: 75


title: BIN67, Vehicle, 6h, H3K27ac, rep4


title: miRNA profile subject 63

description: Library name: 63


title: BIN67, Vehicle, 6h, H3K27ac, rep2


title: BIN67, Triptolide, 16h, H3K27ac, rep1


title: miRNA profile subject 92

description: Library name: 92


title: miRNA profile subject 62

description: Library name: 62


title: BIN67, Vehicle, 6h, H3K27ac, rep1


title: COV434, IgG, rep3

data_processing:
Alignment with bowtie2 v2.4.2 arguments: --local --very-sensitive-local --no-unal -- no-mixed --no-discordant --phred33 --minins 10 --maxins 700 -q
QC: FastQC (v0.11.8) samtools stats (v1.11) and deepTools (v3.3.1)
Peak calling with MACS2 callpeak (v2.2.6) with the following arguments: -f BAMPE -B -q 0.01 --keep-dup all
Assembly: GRCh38
Supplementary files format and content: bw: bigwig file of tracks of signal across genome
Supplementary files format and content: narrowPeak: bed file of peaks called by MACS2
Library strategy: CUT&RUN

treatment_protocol: No treatment


title: COV434, IgG, rep2


title: miRNA profile subject 59

description: Library name: 59


title: miRNA profile subject 60

description: Library name: 60


title: COV434, IgG, rep1


title: miRNA profile subject 57

description: Library name: 57


title: miRNA profile subject 51

description: Library name: 51


title: SCCOHT1, IgG, rep2


title: miRNA profile subject 50

description: Library name: 50


title: SCCOHT1, IgG, rep1


title: SCCOHT1, IgG, rep3


title: miRNA profile subject 46

description: Library name: 46


title: miRNA profile subject 52

description: Library name: 52


title: miRNA profile subject 42

description: Library name: 42


title: BIN67, IgG, rep1


title: BIN67, IgG, rep3


title: BIN67, IgG, rep2


title: miRNA profile subject 38

description: Library name: 38


title: COV434, H3K27ac, rep3


title: BIN67, Vehicle, 6h, H3K27ac, rep3


title: COV434, H3K27ac, rep2


title: COV434, H3K27ac, rep1


title: miRNA profile subject 32

description: Library name: 32


title: miRNA profile subject 58

description: Library name: 58


title: SCCOHT1, H3K27ac, rep3


title: SCCOHT1, H3K27ac, rep2


title: miRNA profile subject 27

description: Library name: 27


title: miRNA profile subject 25

description: Library name: 25


title: miRNA profile subject 19

description: Library name: 19


title: SCCOHT1, H3K27ac, rep1


title: BIN67, H3K27ac, rep3


title: Dtx2-/- MEF cells-Rep2

city: Tianjin

first: Zexing

last: Li

address: No.92 Weijin road

department: School of Life Sciences

institute: Tianjin University

description:
Library name: Sample 4
Dtx2-/- MEF cells-Rep2
V350010326_L04_WHMOUihlqTAAFRAA-646

data_processing:
In RNA-seq analysis, the raw fastq files were analyzed using FastQC (v0.11.9).
Sequencing adaptors and low quality (base quality score<20) reads were trimmed by trim galore (v0.6.6).
Reads shorter than 20nt were discarded. The trimmed reads were aligned to the Moue GRCm39 by Hisat2 (v2.2.1) and the aligned data was further proceeded by Samtools (v1.3.1).
The transcript was quantified by String Tie (v2.1.7).
The gene counts were next analyzed by DESeq2 and the significant different genes were defined as absolute(log2FoldChange) >1.5 and pvalue < 0.05.
Assembly: GRCm39
Supplementary files format and content: NO

source_name: MEF cells

growth_protocol: MEFs from wild-type and knockout mice were generated from 13.5-day-old embryos and cultured in complete DMEM containing 1 mM sodium pyruvate (Invitrogen, Cat# 11360070), 10mM L-glutamine (Invitrogen, Cat# 25030081), 10mM β-mercaptoethanol (Invitrogen, Cat# 21985-023), and 1% nonessential amino acids (Gibco, Cat# 11140).

extract_protocol:
Cells were subjected to total RNA extraction using TRIZOL reagent (Invitrogen)
Library preparation and sequencing were finished by LC-Bio Technology CO., Ltd., Hangzhou, China. The protocol is as follows: 1) RNA fragment and reverse transcription; 2) End repair, add A and adaptor ligation; 3) PCR; 4)Single strand separation and cyclization; 5) DNA nanoball synthesis; 7) Sequencing.

treatment_protocol: MEF cells were isolated and infected with 100HA Sendai virus for 8h

value: MEF cells

value: Sendai virus infection


title: BIN67, H3K27ac, rep2


title: BIN67, H3K27ac, rep1


title: TGEN-I

data_processing:
TopHat 1.2 was used to align fastq to genome assembly GRCh37.62. Parameters: th_paired_end="yes"; th_mate_inner_dist=35; th_mate_std_dev=40; convertBAM2SAM="no".
Cufflinks 1.3 was used to assemble alignments and estimate relative abundances (FPKM). Default parameters used.
Assembly: GRCh37.62
Supplementary files format and content: *.csv: Comma-separated text files include gene list and FPKM values.

source_name: SCCOHT tumor tissue

extract_protocol:
FFPE tissues were sectioned into scrolls, and RNA was harvested using Qiagen RNeasy FFPE Kit.
200ng of total RNA was heat fragmented on an ABI 9700 to a target peak of 150bp and libraries were generated using the Agilent SureSelect XT RNA capture following the manufacturer’s protocol.

value: Tumor

tag: tumor type

value: Small cell carcinoma of the ovary-hypercalcemic type (SCCOHT)

tag: sample site

value: Primary

tag: tissue storage

value: FFPE


title: miRNA profile subject 16

description: Library name: 16

tag: tissue


title: miRNA profile subject 18

description: Library name: 18


title: TGEN-J

value: Unknown (primary or metastasis)


title: Dtx2-/- MEF cells-Rep1

description:
Library name: Sample 3
Dtx2-/- MEF cells-Rep1
V350010326_L04_WHMOUihlqTAAERAA-644

tag: cell type


title: miRNA profile subject 34

description: Library name: 34


title: TGEN-H

value: Metastatic


title: miRNA profile subject 41

description: Library name: 41


title: Dtx2+/+ MEF cells-Rep1

description:
Library name: Sample 1
Dtx2+/+ MEF cells-Rep1
V350010326_L03_WHMOUihlqTAACRAA-639


title: TGEN-F


title: miRNA profile subject 11

description: Library name: 11


title: Dtx2+/+ MEF cells-Rep2

description:
Library name: Sample 2
Dtx2+/+ MEF cells-Rep2
V350010326_L04_WHMOUihlqTAADRAA-643


title: 3D-VSMCs rep3

city: Guangzhou

first: Jiang

last: Liu

address: 106 Zhongshan 2nd Road, Guangzhou City, Guangdong Province

institute: Guangdong Provincial People's Hospital ,Guangdong Academic of Medical Sciences

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM and count values for each Sample

source_name: vascular smooth muscle

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase, which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP Solution. An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: vascular

value: primary vascular smooth muscle cells

value: cultuerd in 3D conditions


title: TGEN-G


title: miRNA profile subject 15

description: Library name: 15

value: Saliva


title: TGEN-E


title: miRNA profile subject 8

description: Library name: 8


title: 3D-VSMCs rep1


title: 2D-VSMCs rep3

value: cultuerd in 2D conditions


title: miRNA profile subject 5

description: Library name: 5


title: 2D-VSMCs rep2


title: 2D-VSMCs rep1


title: miRNA profile subject 7

description: Library name: 7


title: Δcrp, LB +5mM Sodium Nitrate, rep 5

status: Public on Jan 03 2025

city: boston

first: jamaurie

last: james

state: ma

address: 300 longwood ave

institute: Boston Childrens Hospital

data_processing:
llumina cDNA libraries were generated using a modified version of the RNAtag-seq protocol [1,2]. Briefly, 500ng-1 μg of total RNA was fragmented, depleted of genomic DNA, dephosphorylated, and ligated to DNA adapters carrying 5’-AN8-3’ barcodes of known sequence with a 5’ phosphate and a 3’ blocking group. Barcoded RNAs were pooled and depleted of rRNA using the RiboZero rRNA depletion kit (Illumina).
Pools of barcoded RNAs were converted to Illumina cDNA libraries in 2 main steps: (i) reverse transcription of the RNA using a primer designed to the constant region of the barcoded adaptor with addition of an adapter to the 3’ end of the cDNA by template switching using SMARTScribe (Clontech) as described [3]; (ii) PCR amplification using primers whose 5’ ends target the constant regions of the 3’ or 5’ adaptors and whose 3’ ends contain the full Illumina P5 or P7 sequences. cDNA libraries were sequenced to generate paired end reads.
Sequencing reads from each sample in a pool were demultiplexed based on their associated barcode sequence using custom scripts (https://github.com/broadinstitute/split_merge_pl). Up to 1 mismatch in the barcode was allowed provided it did not make assignment of the read to a different barcode possible. Barcode sequences were removed from the first read as were terminal G’s from the second read that may have been added by SMARTScribe during template switching.
Assembly: Vibrio cholerae N16961
Supplementary files format and content: tab deliited TSV file which includes raw counts for each sample
Supplementary files format and content: tab deliited TSV file which includes raw counts for each sample

organism: Vibrio cholerae C6706

growth_protocol: From an overnight culture, bacterial cells were diluted 1:100 in 3mL and grown in their respective media statically for 8 hours at 27°C

extract_protocol:
RNA was extracted and purified using Zymo Research "Direct-zol RNA Miniprep Plus Kit". 500ng of RNA was used for the construction of sequencing libraries
RNA libraries for RNA-Seq were prepped and prepared using the RIboPOOLs kit from siTOOLs and a modified version of the RNAtag-Seq protocol to generate illuminastrand specific cDNA libraries.

value: {delta}crp

value: LB Media +5mM Sodium Nitrate


title: Δcrp, LB +5mM Sodium Nitrate, rep 6


title: WT, LB +5mM Sodium Nitrate, rep 6

value: WT


title: 3D-VSMCs rep2


title: Δcrp, LB +5mM Sodium Nitrate, rep 4


title: WT, LB +5mM Sodium Nitrate, rep 5


title: A375-S cells, 10 Nm

city: Bursa

first: Ceyda

last: Colakoglu Bergel

address: Görükle Kampüsü, Nilüfer

country: Turkey

institute: Bursa Uludag University

description:
Library name: Sample 4
A375-S-10_mRNA_count.txt for mRNA count, A375-S-10_miRNA_count.txt for miRNA count

data_processing:
RPKM (reads per kilobase of exon per million reads mapped)-normalized count data from total RNA sequencing were used for analysis to identify differentially expressed genes and mature miRNAs via the R Bioconductor package “NOISeq”
Assembly: hg19
Supplementary files format and content: text files

growth_protocol: The MM cell A375 (CRL-1619TM)  were maintained in DMEM  high glucose +%10 FBS

extract_protocol:
Total RNA extraction was carried out using the RNeasy Mini Kit (Hilden, Germany) from resist and sensitive cells. To perform RNA sequencing, mRNA and small RNA libraries were generated using the NGS sequencing Illumina NextSeq 500 platform with the SMARTer smRNA-Seq Kit (Illumina, Takara Bio, Shiga, Japan) according to the manufacturer’s instructions. The libraries were gel-purified and assessed using the D1000 ScreenTape System (Agilent Technologies, Waldbronn, Germany).
To perform RNA sequencing, mRNA and small RNA libraries were generated using the NGS sequencing Illumina NextSeq 500 platform with the SMARTer smRNA-Seq Kit (Illumina, Takara Bio, Shiga, Japan) according to the manufacturer’s instructions. The libraries were gel-purified and assessed using the D1000 ScreenTape System (Agilent Technologies, Waldbronn, Germany).

treatment_protocol: 10 nM Enco for 48h

value: Malign melanoma cells

value: BRAF- mutated

value: 10 nM


title: WT, LB, rep 9

value: LB Media


title: WT, LB, rep 8


title: WT, LB, rep 6


title: A375-S cells, Control

description:
Library name: Sample 3
A375-S-K_mRNA_count.txt for mRNA count, A375-S-K_miRNA_count.txt for miRNA count

value: No treatment


title: A375-R cells, Control

description:
Library name: Sample 1
A375-RK_mRNA_count.txt for mRNA count, A375-RK_miRNA_count.txt for miRNA count


title: WT, LB, rep 7


title: A375-R cells, 10 nM

description:
Library name: Sample 2
A375-R-10_mRNA_count.txt for mRNA count, A375-R-10_miRNA_count.txt for miRNA count


title: WT, LB, rep 5


title: CR705, AHRKO, Rep5

city: Oslo

first: Jason

last: Matthews

address: Sognsvannsveien 9

department: Nutrition

country: Norway

institute: University of Oslo

data_processing:
The raw RNA seq paired end fastq files were  aligned using Hisat2 tool to mm10 transcriptome index files obtained from the Hisat2 server. The resulting sequencing alignment format (SAM) file was converted to a binary alignment format (BAM) file using Samtools and subsequent sorted and indexed using the same. HT-seq count was used to obtain raw counts of aligned reads to the exonic regions of the genes using the mm10 version of the gene text format (GTF) file with the flags –“q -m union -s no -r pos -t exon -i gene_id”
For all comparisons, WT tumor samples were considered as the control and the AHRKO as treated.
Significant genes were considered as those with absolute log fold change greater than 1 and Benjamin Hochberg false discovery rate value of differential expression less than 0.01 and tested using the Wald Test implemented in DESeq2.
Assembly: mm10
Supplementary files format and content: tab delimited text file containing raw count for all samples

source_name: Pancreas

growth_protocol: CR705 cells were plated at a density of 1 × 105 cells/well in a 6-well plate and treated with test compounds the following day. After 24 h incubation, cells were lysed and harvested using 10 mM Tris-Cl buffer containing 1 mM EDTA and 1% SDS, with pH of 8.0, and sonicated 2 × 30 seconds on/off with Bioruptor (Diagenode, Denville, NJ, USA). Pierce™ BCA Protein Assay Kit (Thermo Fischer Scientific, Waltham, MA, USA) was used to determine protein concentration.

extract_protocol:
Total RNA from isolated from approximately 100 mg of tumors from CR705 WT or AhrKO cells using the Aurum™ Total RNA isolation kit (BioRad) according to the manufacturer’s protocol.
Messenger RNA 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. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

treatment_protocol: Cells were plated in a 24-well plate at a density of 5 × 104 cells/well. Test compounds were added the following day. RNA was isolated using Aurum™ Total RNA isolation kit (BioRad, Hercules, CA, USA) according to manufacturer’s instructions. Subsequently, High-Capacity cDNA Reverse Transcription kit (Applied Biosystems, Waltham, MA, USA) was used to generate cDNA.

value: Pancreas

value: Pancreatic cancer

value: AHRKO


title: CR705, AHRKO, Rep6


title: CR705, AHRKO, Rep3


title: Δcrp/hapR, LB +5mM Sodium Nitrate, rep 3

value: {delta}crp/hapR


title: Δcrp/hapR, LB +5mM Sodium Nitrate, rep 1


title: CR705, AHRKO, Rep4


title: ΔhapR, LB +5mM Sodium Nitrate, rep 3

value: {delta}hapR


title: CR705, AHRKO, Rep2


title: ΔhapR, LB +5mM Sodium Nitrate, rep 2


title: ΔhapR, LB +5mM Sodium Nitrate, rep 1


title: CR705, WT, Rep6


title: CR705, WT, Rep5


title: Δcrp, LB +5mM Sodium Nitrate, rep 3


title: CR705, AHRKO, Rep1


title: CR705, WT, Rep3


title: Δcrp, LB +5mM Sodium Nitrate, rep 2


title: WT, LB +5mM Sodium Nitrate, rep 4


title: CR705, WT, Rep4


title: CR705, WT, Rep2


title: WT, LB +5mM Sodium Nitrate, rep 3


title: CR705, WT, Rep1


title: WT, LB, rep 4


title: WT, LB +5mM Sodium Nitrate, rep 1


title: THK-5-3

city: Lan zhou

first: Pan

middle: Yu

last: Cai

state: Gansu

address: Yin Tan Road Street, An Ning District

department: College of Animal Science and Technology

institute: Gansu Agricultural University

description: Library name: Sample 36

data_processing:
Reads obtained from the sequencing machines included raw reads containing adapters or low quality bases which would affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered according to the following rules: 1) Removing reads containing adapters; 2) Removing reads consisting of all A bases; 3) Removing reads containing more than 10% of unknown nucleotides (N); 4) Removing low quality reads containing more than 50% of low quality (Q-value≤20) bases
Short reads alignment tool Bowtie2 (2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads were then removed. The remaining reads were further used in assembly and analysis of transcriptome.
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2. 2.4 and other parameters set as a default.
After aligned with reference genome, unmapped reads (or mapped very poorly) were then re-aligned with Bowtie2, the enriched unmapped reads were split into smaller segments which were then used to find potential splice sites. The section and the section position of these short segments were predicted as well. A set of splice sites was built with initial unmapped reads  without relying on the known genes annotation. Not only be used for identifying expressed genes and their quantitative expression, the sequence alignment will also be helpful to find alternative splicing and new transcripts.
Assembly: Oncorhynchus mykiss USDA_OmykA_1.1
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Oncorhynchus mykiss

source_name: head kidney tissues

growth_protocol: Healthy rainbow trout (85 ± 0.5 g) used in this study were obtained from a fish farm in Gansu Province, and acclimatized for two weeks. These fish are six-month old road style rainbow trout and are full siblings. The fish were cultivated in 1000 L tanks at water temperatures of 12 ± 1℃. During the fish experiments, the pH ranged from 7.6 to 7.8 and the dissolved oxygen was about 8.5 mg/L. Feeding with commercial dry feed pellets (Shandong Hanye Biotechnology Co., Ltd, China) was performed twice daily, a rate of 2% of their body weight.

extract_protocol:
The total RNA was extracted using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Two weeks after rainbow trout were suspended, healthy rainbow trout were randomly divided into three groups, including normoxia, moderate hypoxia, and severe hypoxia groups, the oxygen levels were maintained at 8.5 ± 0.1, 4.5 ± 0.1, and 3.0 ± 0.1 mg/L, respectively, and the low oxygen environment was created by mixing oxygen and nitrogen.

value: head kidney tissues

value: control group_IHNV challenged


title: WT, LB +5mM Sodium Nitrate, rep 2


title: Δcrp/hapR, LB +5mM Sodium Nitrate, rep 2


title: Δcrp/hapR, LB, rep 3


title: THK-5-1

description: Library name: Sample 34


title: THK-4-3

description: Library name: Sample 33

value: P-APS+vaccine group_IHNV challenged


title: THK-5-2

description: Library name: Sample 35


title: Δcrp/hapR, LB, rep 1


title: ΔhapR, LB, rep 3


title: THK-4-2

description: Library name: Sample 32


title: THK-4-1

description: Library name: Sample 31


title: Δcrp/hapR, LB, rep 2


title: ΔhapR, LB, rep 2


title: ΔhapR, LB, rep 1


title: THK-3-3

description: Library name: Sample 30

value: vaccine group_IHNV challenged


title: THK-3-2

description: Library name: Sample 29


title: Δcrp, LB, rep 3

value: {delta}crp


title: Δcrp, LB +5mM Sodium Nitrate, rep 1

value: LB Media +5mM Sodium Nitrate


title: THK-3-1

description: Library name: Sample 28


title: Δcrp, LB, rep 2


title: THK-2-3

description: Library name: Sample 27

value: P-APS+vaccine

value: 7 d


title: THK-2-2

description: Library name: Sample 26


title: Δcrp, LB, rep 1


title: WT, LB, rep 3

value: WT


title: THK-2-1

description: Library name: Sample 25


title: WT, LB, rep 2


title: WT, LB, rep 1


title: THK-1-1

description: Library name: Sample 22

value: vaccine


title: CHK-3

description: Library name: Sample 21

value: control


title: CHK-1

description: Library name: Sample 19


title: TSP-5-3

description: Library name: Sample 18

source_name: spleen tissues

value: spleen tissues


title: THK-1-2

description: Library name: Sample 23


title: TSP-5-2

description: Library name: Sample 17


title: CHK-2

description: Library name: Sample 20


title: TSP-4-3

description: Library name: Sample 15


title: TSP-4-2

description: Library name: Sample 14


title: TSP-3-3

description: Library name: Sample 12


title: TSP-2-3

description: Library name: Sample 9


title: TSP-3-1

description: Library name: Sample 10


title: TSP-2-2

description: Library name: Sample 8


title: TSP-2-1

description: Library name: Sample 7


title: TSP-1-3

description: Library name: Sample 6


title: CSP-3

description: Library name: Sample 3


title: TSP-1-1

description: Library name: Sample 4


title: CSP-2

description: Library name: Sample 2


title: TSP-1-2

description: Library name: Sample 5


title: CSP-1

description: Library name: Sample 1


title: THK-1-3

description: Library name: Sample 24


title: ovcar3_velip_5-2-19

city: New York City

first: Alireza

last: Khodadadi-Jamayran

state: NY

address: 550 1st Ave, MSB 304

department: Division of Advanced Research Technologies (DART)

institute: New York University, NYU Langone Medical Center

description: Library name: sample 16

data_processing:
Basecalls performed using CASAVA
RNA-Seq reads were mapped to mm10 using STAR guided by GTF
Calculating insert size and standard deviation performed using Picard tools
RNA-Seq read counting performed using HT-seq
Normalization and Deferential expression analyses performed using DEseq2
Assembly: hg19
Supplementary files format and content: read counts (*.txt)

growth_protocol: HEK-293T, CAOV3 and COV362 cell lines were maintained in Dulbecco's Modified Eagle's Medium (DMEM) with L-Glutamine, 4.5g/L glucose, sodium pyruvate supplemented with 10% fetal bovine serum (FBS) and penicillin/streptomycin (P/S). OVCAR3, OVCAR4, and OVCAR8 cells were cultured in Roswell Park Memorial Institute (RPMI) 1640 medium supplemented with 10% FBS and P/S.

extract_protocol:
Total RNA was isolated using the RNeasy mini kit (Qiagen; catalog # 74124). Two mg of RNA was reverse transcribed to generate cDNA using the High-Capacity CDNA Reverse Transcription Kit (Applied Biosystems; catalog # 4368813) as per manufacturer’s instructions.
The NYU Genome Technology Center constructed the libraries followed their standard protocol

treatment_protocol: Ovarian cancer cells were treated with a vehicle control (DMSO), 10mM of veliparib (non-PARP trapper), or 2mM of talazoparib (most potent PARP trapper) for 48 hours.

value: Ovarian carcinoma cell line

value: Veliparib


title: ovcar3_talap_7-8-19

description: Library name: sample 14

value: Talazoparib


title: ovcar3_talap_5-2-19

description: Library name: sample 13


title: TSP-5-1

description: Library name: Sample 16


title: ovcar3_dmso_5-2-19

description: Library name: sample 10

value: DMSO


title: ovcar3_dmso_8-25-19

description: Library name: sample 12


title: TSP-4-1

description: Library name: Sample 13


title: caov3_velip_7-12-19

description: Library name: sample 7


title: TSP-3-2

description: Library name: Sample 11


title: caov3_velip_8-25-19

description: Library name: sample 9


title: caov3_velip_7-8-19

description: Library name: sample 8


title: caov3_talap_8-25-19

description: Library name: sample 6


title: caov3_dmso_8-25-19

description: Library name: sample 3


title: caov3_dmso_7-12-19

description: Library name: sample 1


title: ovcar3_velip_8-25-19

description: Library name: sample 18


title: ovcar3_velip_7-8-19

description: Library name: sample 17


title: Sample_2_AIT

city: New York

first: Michael

last: Gildea

state: New York

address: 550 1st avenue

institute: NYU Langone Health

description:
Library name: Sample_2_AIT
10x Genomics

data_processing:
Cell Ranger (10x Genomics, v7.1.0) was used to perform alignment (GRCh38, Ensembl 93), filtering, barcode counting and UMI counting of sequencing reads from fastq files.
Assembly: GRCh38
Supplementary files format and content: Tab -separated values files and matrix files

source_name: coronary plaque

extract_protocol:
Left and right anterior descending arteries were washed, minced, and digested then filtered using cell strainers. Following a dead cell removal step, single-cell suspensions were counted and loaded onto a Chromium Controller (10x Genomics).
Libraries were prepared using the Chromium Single Cell 3’ Library v3 reagent, Gel Bead and Multiplex Kit and Chip Kit (10X Genomics; 1000268, 1000215 and 100127, respectively)

value: coronary plaque


title: caov3_talap_7-12-19

description: Library name: sample 4


title: caov3_dmso_7-8-19

description: Library name: sample 2


title: Sample_3_plaque

description:
Library name: Sample_3_plaque
10x Genomics


title: Patient 25, end of treatment

city: Houston

first: Zheng

last: Yin

state: TX

address: 6565 Fannin St, MC: F6-300

department: Systems Medicine and Bioengineering

institute: Houston Methodist Cancer Center

description:
Library name: P25_EOT
S1 flow cell
Puri_Yn_Chang_Counts_Jan02_2025.xlsx, Column AK

data_processing:
confirming the quality of the data using FastQC
using STAR 2.7.9a to map the raw data to reference human genome version GRCH38 and generated BAM files
using SubRead.featurecounts V2.0.3 was applied to the BAM files to estimate the abundance of genes within each sample
Using R package DESeq to identify differentially expressed genes in EOT vs. BL conditions
Using ConsensusPathDB v050621 to carry out overrepresentation analysis and identify canonical pathways enriched with EOT up- and down-regulated genes, respectively
Assembly: human genome version GRCH38
Supplementary files format and content: Excel workbook containing raw counts for 44,759 transcripts in 32 samples

source_name: breast

extract_protocol:
Total RNA was extracted from frozen biopsies according to the manufacturer's protocol using the RNeasy® Lipid Tissue Mini Kit (Qiagen, #74804). Briefly, up to 100 mg of frozen tissue sections were homogenized in 1ml QIAzol Lysis reagent using the TissueLyzer II (Qiagen). The homogenate was placed on the benchtop at room temperature (15–25°C) for 5 min to allow nucleoprotein complexes dissociation. RNA was eluted with 40 µl of RNase-free water and quantified using a Qubit 4 Fluorometer (Invitrogen).
Total RNA sequencing library was prepared following Illumina’s TruSeq-stranded-mRNA sample preparation protocol.

treatment_protocol: 25mg/day oral dose of HT were given for 12 months in pre- and post-menopausal women at increased risk of breast cancer.

value: breast

value: 25mg/day oral dose of hydroxytyrosol (HT) for 12 months


title: ovcar3_talap_8-25-19

description: Library name: sample 15


title: Sample_1_AIT

description:
Library name: Sample_1_AIT
10x Genomics


title: Patient 26, end of treatment

description:
Library name: P26_EOT
S1 flow cell
Puri_Yn_Chang_Counts_Jan02_2025.xlsx, Column AL


title: Patient 23, end of treatment

description:
Library name: P23_EOT
S1 flow cell
Puri_Yn_Chang_Counts_Jan02_2025.xlsx, Column AI


title: Patient 24, end of treatment

description:
Library name: P24_EOT
S1 flow cell
Puri_Yn_Chang_Counts_Jan02_2025.xlsx, Column AJ


title: Patient 22, end of treatment

description:
Library name: P22_EOT
S1 flow cell
Puri_Yn_Chang_Counts_Jan02_2025.xlsx, Column AH


title: MEF, KO2

city: 武汉

first: zixuan

last: wang

state: 湖北省

address: 湖北省武汉市东湖南路7号

institute: 中国科学院水生生物研究所

description: Library name: sample 5

data_processing:
Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.
Fastp (version 0.19.7) was used to perform basic statistics on the quality of the raw reads.
The clean reads were then mapped to the mouse genome using HISAT.
Assembly: GRCm39
Supplementary files format and content: file folder includes raw counts for each Sample
Supplementary files format and content: excel files included differentially expressed genes for each sample

source_name: MEF

growth_protocol: cells were cultured in Dulbeccos’ modified Eagle's medium (DMEM) (VivaCell) supplemented with 10% fetal bovine serum (FBS) (VivaCell).

extract_protocol:
Whole RNA of mef cells were purified using RNeasy Mini Kit (QIAGEN NO. 74104).
Sequencing libraries were generated using the NEB Next Ultra RNA Library Prep Kit for Illumina (NEB, USA, #E7530L) accordingly to the manufacturer’s protocol, and index codes were added to assign sequences to each sample.

value: MEF

value: Mouse Embryonic Fibroblast

value: SMYD3 KO


title: ovcar3_dmso_7-8-19

description: Library name: sample 11


title: Patient 21, end of treatment

description:
Library name: P21_EOT
S1 flow cell
Puri_Yn_Chang_Counts_Jan02_2025.xlsx, Column AG


title: MEF, KO3

address: 湖北省武汉市东湖南路7号

institute: 中国科学院水生生物研究所

description: Library name: sample 6


title: MEF, KO1

address: 湖北省武汉市东湖南路7号

institute: 中国科学院水生生物研究所

description: Library name: sample 4


title: caov3_talap_7-8-19

description: Library name: sample 5


title: MEF, WT3

address: 湖北省武汉市东湖南路7号

institute: 中国科学院水生生物研究所

description: Library name: sample 3


title: MEF, WT2

address: 湖北省武汉市东湖南路7号

institute: 中国科学院水生生物研究所

description: Library name: sample 2


title: Patient 18, end of treatment

description:
Library name: P18_EOT
S1 flow cell
Puri_Yn_Chang_Counts_Jan02_2025.xlsx, Column AD


title: MEF, WT1

address: 湖北省武汉市东湖南路7号

institute: 中国科学院水生生物研究所

description: Library name: sample 1


title: Patient 20, end of treatment

description:
Library name: P20_EOT
S1 flow cell
Puri_Yn_Chang_Counts_Jan02_2025.xlsx, Column AF